Annual Report 2014 - SV by EPFL School of Life Sciences

EPFL School of Life Sciences

EPFL School of Life Sciences - 2014 Annual Report

Front Cover: Simone Allazetta, PhD, (Laboratory of Stem Cell Bioengineering - Prof. Matthias Lutolf) Cell Planet: The image shows C2C12 myoblasts cultured on the surface of a hydrogel microcarrier with engineered biomechanical and biochemical properties. The cellâ&#x20AC;&#x2122;s nuclei are stained in blue, cell actin filaments in green with phalloidin and the expression of tropomyosin, responsible for muscle contraction, in red. Last Page: Christopher Tremblay, (Laboratory of Lymphatic and Cancer Bioengineering - Prof. Melody Swartz) Holographic representations of Fibroblastic Reticulum Cells (FRCs) and Lymphatic Endothelial Cells (LECs) from Lymph node stroma, digitally stained based on the refractive index of the cell components.

EPFL School of Life Sciences - 2014 Annual Report

Welcome to SV

The School of Life Sciences has set itself the goal to teach students at the interfaces between biology, engineering, mathematics, physics and chemistry leading to quantitative, analytical and design-oriented life scientists through the acquisition of a Bachelor of Science in Life Sciences and Technology, a Master of Science in Life Sciences and Technology or Bioengineering, or a Doctor of Philosophy in Molecular Life Sciences, Neurosciences, or Biotechnology and Bioengineering. The School’s professors reflect its aims, coming from diverse backgrounds in biology, chemistry, physics, engineering and medicine. They share their passion for developing new fundamental understanding of critical questions in the life sciences and translating that understanding towards impacting human health through engineering solutions. Since its launching in the early 2000’s, the Faculty of Life Sciences is continuing its ascendance, as illustrated by the numerous ERC awards at all levels (Starter, Consolidator and Advanced), the increase of our position in the various rankings of the world academic institutions and the frequent prize awards received by the various Life Science professors and other members. The School of Life Sciences also greatly benefits from the dynamism of the Lemanic region, the so-called Health Valley, leading or participating in various projects bringing together the Universities of Lausanne and Geneva, the University Hospitals of the two cities and EPFL. These include the Campus Biotech in Geneva which hosts the Wyss Center for neuro-engineering and the EPFL Center for Neuroprosthetics and the Swiss Cancer Center Lausanne.

Introduction

Gisou Van der Goot - Dean of the School of Life Sciences

EPFL School of Life Sciences - 2014 Annual Report

Table Of Contents

Welcome to SV .............................................................................................................................................. 3 Honors & Awards........................................................................................................................................... 5 Undergraduate Studies................................................................................................................................... 6 Doctoral Programs ......................................................................................................................................... 7 SV Doctoral Graduates .................................................................................................................................. 8 SV Master’s Graduates ................................................................................................................................. 10 School of Life Sciences at a Glance ............................................................................................................. 11 Blue Brain Project ........................................................................................................................................ 12 Center for Biomedical Imaging Research ..................................................................................................... 14 Center for Neuroprosthetics ......................................................................................................................... 16

BMI - Brain Mind Institute .......................................................................................................... 19 Aebischer Lab .............................................................................................................................................. 20 Blanke Lab................................................................................................................................................... 22 Courtine Lab ................................................................................................................................................ 24 Fraering Lab ................................................................................................................................................. 26 Gerstner Lab ................................................................................................................................................ 28 Gräff Lab ..................................................................................................................................................... 30 Herzog Lab .................................................................................................................................................. 32 Lashuel Lab ................................................................................................................................................. 34 Magistretti Lab ............................................................................................................................................. 36 Markram Lab ............................................................................................................................................... 38 Petersen Lab ................................................................................................................................................ 40 Sandi Lab..................................................................................................................................................... 42 Schneggenburger Lab .................................................................................................................................. 44 Hill Lab ....................................................................................................................................................... 46 Schürmann Lab............................................................................................................................................ 47

IBI - Institute of Bioengineering .................................................................................................. 49 Auwerx Lab ................................................................................................................................................. 50 Baekkeskov Lab ........................................................................................................................................... 52 Barrandon Lab ............................................................................................................................................. 54 Dal Peraro Lab ............................................................................................................................................. 56 Deplancke Lab ............................................................................................................................................ 58 Hubbell Lab................................................................................................................................................. 60 Jensen Lab ................................................................................................................................................... 62 Lutolf Lab .................................................................................................................................................... 64 Naef Lab ...................................................................................................................................................... 66 Naveiras Lab ................................................................................................................................................ 68 Schoonjans Lab ........................................................................................................................................... 70 Suter Lab ..................................................................................................................................................... 72 Swartz Lab ................................................................................................................................................... 74 Aminian Lab ................................................................................................................................................ 76 Fantner Lab .................................................................................................................................................. 77 Guiducci Lab ............................................................................................................................................... 78 Hatzimanikatis Lab ...................................................................................................................................... 79 Ijspeert Lab .................................................................................................................................................. 80 Johnsson Lab ............................................................................................................................................... 81 Jolles-Haeberli Lab ...................................................................................................................................... 82 Lacour Lab................................................................................................................................................... 83 Lasser Lab .................................................................................................................................................... 84 Maerkl Lab .................................................................................................................................................. 85 Mermod Lab ................................................................................................................................................ 86 Micera Lab .................................................................................................................................................. 87 Millán Lab ................................................................................................................................................... 88 Pioletti Lab .................................................................................................................................................. 89

Psaltis Lab.................................................................................................................................................... 90 Radenovic Lab ............................................................................................................................................. 91 Renaud Lab ................................................................................................................................................. 92 Roke Lab ..................................................................................................................................................... 93 Stellacci Lab ................................................................................................................................................ 94 Stergiopulos Lab .......................................................................................................................................... 95 Van de Ville Lab........................................................................................................................................... 96

GHI - Global Health Institute ..................................................................................................... 99 Ablasser Lab .............................................................................................................................................. 100 Blokesch Lab ............................................................................................................................................. 102 Cole Lab .................................................................................................................................................... 104 Fellay Lab .................................................................................................................................................. 106 Harris Lab .................................................................................................................................................. 108 Lemaitre Lab .............................................................................................................................................. 110 McKinney Lab ........................................................................................................................................... 112 Trono Lab .................................................................................................................................................. 114 Van der Goot Lab ...................................................................................................................................... 116

ISREC - Swiss Institute for Experimental Cancer Research ........................................................ 119 Aguet Lab .................................................................................................................................................. 120 Brisken Lab ................................................................................................................................................ 122 Constam Lab.............................................................................................................................................. 124 De Palma Lab ............................................................................................................................................ 126 Duboule Lab.............................................................................................................................................. 128 Gönczy Lab ............................................................................................................................................... 130 Hanahan Lab ............................................................................................................................................. 132 Hantschel Lab............................................................................................................................................ 134 Huelsken Lab............................................................................................................................................. 136 Lingner Lab................................................................................................................................................ 138 Meylan Lab................................................................................................................................................ 140 Oricchio Lab ............................................................................................................................................. 142 Radtke Lab................................................................................................................................................. 144 Simanis Lab ............................................................................................................................................... 146 Bucher Group ............................................................................................................................................ 148 Frey Group ................................................................................................................................................ 150 Molinari Group.......................................................................................................................................... 152 Rainer Group ............................................................................................................................................. 154 Schorderet Group ...................................................................................................................................... 156 Tanner - Swiss TPH .................................................................................................................................... 158

Core Facilities & Technology Platforms ..................................................................................... 159 Bioelectron Microscopy - BioEM ............................................................................................................... 160 BioImaging & Optics - BIOP ...................................................................................................................... 161 Bioinformatics & Biostatisitcs - BBCF ......................................................................................................... 162 Biomolecular Screening - BSF .................................................................................................................... 163 Flow Cytometry - FCCF.............................................................................................................................. 164 Histology - HCF & Comparative Pathology ................................................................................................ 165 Proteomics - PCF ....................................................................................................................................... 166 Protein Crystallography - PCRYCF.............................................................................................................. 167 Protein Expression - PECF .......................................................................................................................... 168 Centre of PhenoGenomics - Transgenic - CPG-TCF .................................................................................... 169 Center of PhenoGenomics – Phenotyping Unit - CPG-UDP ....................................................................... 170

EPFL School of Life Sciences - 2014 Annual Report

Honors & Awards

Hello Tomorrow Challenge, European Startup contest

Received the Pfizer Research Award

Leanne Li

Pierre Magistretti

Johan Auwerx

Carmen Sandi

2014 iGEM EPFL

Mattias Lutolf

Stewart Cole

Melody

ERC Advanced Grants

Johan Auwerx

Johannes Gräff

Anokion listed in Nature Biotech among top 10 innovative startups

Carl Petersen G. Van der Goot Bruno Lemaitre Jeffrey Hubbell Pierre Gönczy

Douglas Hanahan

Carmen Sandi

Andrea Ablasser

Leiden Ranking EPFL’s

Elected to Board of 3R Research Foundation and Board of the Gen Suisse Foundation

Carmen Sandi

Distinguished Visiting Scientist Fellow, Hungarian Academy of Sciences

Received the Emil von Behring Prize

Jeffrey Hubbell

Elected to National Academy of Inventors (USA)

Honorary member of the Chinese Association for Physiological Sciences.

Swartz & Jeffrey Hubbell

Fellow & received Lifetime Achievement Award from AACR (USA).

Mitokine listed in Nature Biotech among top 10 innovative startups of 2014

Scientific Advisory Board, BRAIN LabEX, Bordeaux Neuroscience

Behavioral Brain Research Prize, EBBS-Elsevier

One of 400 most influential bioscientists, European Journal of Clinical Investigation

Awarded the SNSF Starting Grant

SV student team awarded gold medal for their innovative Biopad design, MIT.

Young Investigator Award, Swiss Society for Biological Psychiatry

School of Life Sciences ranked as #3 in Europe

Introduction

Grégoire Courtine

EPFL School of Life Sciences - 2014 Annual Report

Undergraduate Studies The Life Sciences curriculum

aims to educate a new generation of engineers who can master the technical and scientific skills needed for studying life processes and developing the biomedical technologies of tomorrow. This educational program, is unique in Switzerland and Europe.

Bachelor’s Program (3 years)

The first two years provide basic courses followed throughout the EPFL, such as analysis, linear algebra, physics, chemistry (general and organic), statistics and numerical methods. Specific courses in Life Sciences begin with biochemistry, cellular, molecular biology, biophysics, computer sciences, and biothermodynamics. In the first two years, life sciences courses make up less than 20% of the total academic load. In the third year, engineering courses (signals and systems, electronic and electrical systems) and typical life sciences courses such as genetics and genomics, immunology, developmental biology, biocomputing, systems biology via the study of human physiology are integrated. Physiology also gives the opportunity to integrate the engineering and biological knowledge acquired up to this point. During this year, the students also fine tune their training by choosing some specific credits to better prepare themselves for one of the orientations offered in our masters’ programs. This includes a bachelor project either in bioengineering, in bio-computing, in biomedical technologies, in neurosciences, or in molecular medicine. 2014 iGEM team received a gold medal for their innovative Biopad design at the MIT competion, USA. Photo: Bruno Liardon

Master’s Programs (2 years)

The Master’s in Life Science and Technology includes several specializations. Among these are Neurosciences and Neuroengineering, Molecular Medicine and System Biology. Each specialization is made up of a coherent group of optional courses providing basic as well as advanced knowledge in the chosen field. Students aiming to focus their training on interdisciplinary subjects will have the possibilities to choose different minors such as Biocomputing and Computational Neurosciences. The Master’s in Bioengineering is organized in collaboration with STI, and provides classical courses in bioengineering; in addition students can chose different possible orientations through the choice of a minor such as Biomedical Technologies (STI), Biocomputing (I&C) or Neuroprosthetics. Each minor requires taking 30 specific credits chosen under the guidance of a mentor. The minors, as indicated, are organized within the different schools at EPFL. Both degree programs share some common basic curriculum that aims to provide students with the knowledge of the modern technologies used in the life sciences such as imaging, bio-computing and optical systems applied to biology, etc.... In addition, courses in management, economics, applied laws and ethics for the life sciences are offered. A large portion of the master’s program (60 credits) can be dedicated to laboratory work and projects. http://ssv.epfl.ch/

Bertrand Rey - photographer

EPFL School of Life Sciences - 2014 Annual Report

Doctoral Programs All three graduate programs combine coursework, laboratory-based research, in-house seminars, and national or international conferences. Highly qualified applicants worldwide are chosen during our Hiring Days which occur twice a year, the end of January and the end of June. Hiring Days last two and a half days: one-half day of general information followed by two days of lab immersion and evaluation.

Molecular Life Sciences (EDMS)

aims at providing doctoral students with the education necessary to become leaders in biological research, implementing the latest state of the art. The combination of laboratory based research with access to modern technological platforms, coursework, in-house seminars, national and international conferences, etc., forms the basis of this education. The program’s themes include cell biology, developmental biology, biochemistry & biophysics, molecular genetics, cancer research, microbiology, host-pathogen interactions, immunology, systems biology, computational biology, human genetics, stem cells and metabolism. The EDMS PhD program offers exciting PhD positions to talented and ambitious young researchers. http://phd.epfl.ch/edms

Biotechnology and Bioengineering (EDBB)

prepares doctoral students to become leaders in the fast-growing academic and industrial biotechnology and bioengineering sectors by providing a depth of knowledge and competence in their specific research areas as well as a breadth of knowledge in biology, bioengineering, and biotechnology. Focus areas include: biomolecular engineering and biomaterials; cell, tissue, and process engineering; biomechanics and mechanobiology; molecular and cellular biophysics; stem cell biotechnology; advanced biomedical imaging and image processing; microtechnology and nanotechnology; orthopaedic engineering; biomimetic robotics; computational biology; ‘omics’ technologies (genomics, transcriptomics, proteomics, metabolomics).

Neuroscience (EDNE) provides its students with training from the genetic to the behavioural level including molecular, cellular, cognitive, and computational neuroscience. Students enroll in the highly dynamic and interdisciplinary environment of the BMI-EPFL of the SV. The program is further strengthened by research and training opportunities in collaboration with the Universities of Lausanne and Geneva. http://phd.epfl.ch/edne

Introduction

http://phd.epfl.ch/edbb

EPFL School of Life Sciences - 2014 Annual Report

SV Doctoral Graduates

Introduction

EPFL School of Life Sciences - 2014 Annual Report

SV Master’s Graduates

Master’s in Life Sciences & Technology Graduates 2014

Master’s in Bioengineering Graduates 2014

EPFL School of Life Sciences - 2014 Annual Report

Introduction

School of Life Sciences at a Glance

EPFL School of Life Sciences - 2014 Annual Report

Blue Brain Project http://bluebrain.epfl.ch/

Director: Prof. Henry Markram Mission

The ultimate goal of the Blue Brain Project (BBP) is to build and simulate biologically detailed models of the mammalian brain that integrate information about the brain’s multiple levels of organization, from molecules to largescale circuits, and that act as a scaffold for future iterative refinement. BBP software tools and workflows make it possible to build models from sparse data, and to perform in silico experiments, simulating the spontaneous activity of the model brain and the activity evoked by different forms of stimulation. We have used these facilities to integrate an unprecedented collection of anatomical and physiological data in a cellular level model of a neural microcircuit in rat somatosensory cortex. We are now using the same tools to probe the operation of the cortex, and to build meso-scale and whole brain models.

Keywords

Brain simulation, neocortical microcircuit, Human Brain Project, rat, mouse, high performance computing, neuroinformatics.

Description of BBP Activities & Results 2014

In January 2013, the European Commission, announced the selection of the Human Brain Project (HBP) as one of its two FET Flagship Projects. In 2013 and 2014, the BBP worked to transform BBP tools into components of the HBP Neuroinformatics and Brain Simulation Platforms and contributed to the development of the HBP’s High Performance Computing Platform, mouse brain atlas and to HBP models of the mouse brain. The BBP also contributed to the organization of the HBP summit, held in Lausanne in October 2013, and to the preparation of the HBP proposal for the next phase of the project. Simultaneously, the project expanded its infrastructure.

June 2013 saw the delivery of an IBM Blue Gene/Q supercomputer, at the Swiss Super Computing Centre (CSCS) in Lugano, in the context of a three-way BBP-CSCS-IBM collaboration on data-intensive computing. The dedicated system supports all the BBP’s development and simulation activities and is being integrated in the HBP’s High Performance Computing Platform. In a separate development, the BBP headquarters moved from the main EPFL campus to the new Biotech Campus in Geneva. Meanwhile, the BBP intensified its efforts in techniques for model building. An important achievement was the development of a technique for synthesizing arbitrary numbers of biologically accurate neuronal morphologies - making it possible to make the best possible use of available neuronal reconstructions. Two papers, in Cerebral Cortex and in Nature Reviews of Neuroscience, focused on the classification of neuron types, another critical issue for brain modelling. The project also expanded its efforts in in silico experimentation. In 2013, members of the BBP published a major Neuron paper in which they used simulation to investigate the biophysics linking local and cross-layer processing to Local Field Potentials (LFPs). These and other aspects of the HBP were presented in numerous posters at SfN 2013 in San Diego and SfN 2014 in Washington.

on the JuQueen supercomputer at Jülich Supercomputing Centre, demonstrated the possibility of simulating up to 155 million morphologically detailed neurons. The BBP continued to collaborate on data management with the EPFL DIAS laboratory and with groups in Spain, Germany and Switzerland on scientific visualization. The project also maintained close relations with the Allen Brain Institute, which contributed valuable data to the HBP’s mouse brain atlas, and which began to use an optimized version of the Neuron simulator developed at BBP. Egidio D’Angelo’s group at University of Pavia began to use BBP tools to develop simulations of the cerebellum. Idan Segev’s group at Hebrew University, Israel, is now using the tools to develop human cell models. A new collaboration with the Britton Chance Centre for Biomedical Photonics in Wuhan, China, has given the project access to large numbers of high quality, high-resolution images of rodent brains.

The BBP continued its work to integrate the vasculatureglia system into BBP models - work conducted in collaboration with the King Abdullah University in Saudi Arabia (KAUST) - and to build the first point neuron models on the scale of the whole mouse brain. The BBP neurorobotics group used these models to build exploratory closed loop systems coupling brain models to virtual robots. Meanwhile BBP engineering teams made major progress on optimizing the NEST and Neuron simulators, the latter work conducted in close collaboration with Michael Hines. Other work focused on the project’s visualization capabilities, and on scaling up BBP modelling and software tools to support larger-scale models. Experiments

EPFL School of Life Sciences - 2014 Annual Report

A visualization of a group of neurons. © BBP/EPFL 2014

Selected Publications

Centers

» S. Druckmann, S. Hill, F. Schürmann, H. Markram, and I. Segev, A Hierarchical Structure of Cortical Interneuron Electrical Diversity Revealed by Automated Statistical Analysis. Cerebral Cortex 23 (2013) 2994-3006. » J. DeFelipe, P.L. López-Cruz, R. Benavides-Piccione, C. Bielza, P. Larrañaga, S. Anderson, A. Burkhalter, B. Cauli, A. Fairén, D. Feldmeyer, G. Fishell, D. Fitzpatrick, T.F. Freund, G. González-Burgos, S. Hestrin, S. Hill, P.R. Hof, J. Huang, E.G. Jones, Y. Kawaguchi, Z. Kisvárday, Y. Kubota, D.A. Lewis, O. Marín, H. Markram, C.J. McBain, H.S. Meyer, H. Monyer, S.B. Nelson, K. Rockland, J. Rossier, J.L.R. Rubenstein, B. Rudy, M. Scanziani, G.M. Shepherd, C.C. Sherwood, J.F. Staiger, G. Tamás, A. Thomson, Y. Wang, R. Yuste, and G.A. Ascoli, New insights into the classification and nomenclature of cortical GABAergic interneurons. Nature Reviews Neuroscience 14 (2013) 202-216. » E. Hay, F. Schurmann, H.Markram, , & I. Segev, (2013). Preserving axosomatic spiking features despite diverse dendritic morphology. J Neurophysiol, 109(12), 2972-2981. doi: 10.1152/jn.00048.2013. » E.R. Kandel, H. Markram, P.M. Matthews, R. Yuste, and C. Koch, Neuroscience thinks big (and collaboratively). Nature Reviews Neuroscience 14 (2013) 659-664. » A. Loebel, J.-V.L. Bé, M.J.E. Richardson, H. Markram, and A.V.M. Herz, Matched Pre- and Post-Synaptic Changes Underlie Synaptic Plasticity over Long Time Scales. The Journal of Neuroscience 33 (2013) 6257-6266. » R. Perin, M. Telefont, & H. Markram (2013). Computing the size and number of neuronal clusters in local circuits. Front Neuroanat, 7, 1. doi: 10.3389/fnana.2013.00001. » Michael W. Reimann, Costas A. Anastassiou, R. Perin, S.L. Hill, H. Markram, and C. Koch, A Biophysically Detailed Model of Neocortical Local Field Potentials Predicts the Critical Role of Active Membrane Currents. Neuron 79 (2013) 375-390. » J. DeFelipe, E. Garrido, and H. Markram, The death of Cajal and the end of scientific romanticism and individualism. Trends in Neurosciences 37 (2014) 525-527. » F. Schürmann, F.Delalondre, P.S.Kumbhar, J.Biddiscombe, M.Gila, D.Tacchella, A.Curioni, B.Metzler, P.Morjan, J.Fenkes, M.M.Franceschini, R.S.Germain, L.Schneidenbach, T.J.C.Ward, B.G.Fitch: Rebasing I/O for Scientific Computing: Leveraging Storage Class Memory in an IBM BlueGene/Q Supercomputer. In J.M. Kunkel, T. Ludwig, and H.W. Meuer (Eds.): ISC 2014, LNCS 8488, pp. 331--347. Springer International Publishing Switzerland (2014). » F. Tauheed, T. Heinis, F. Schurmann, H. Markram, and A. Ailamaki, OCTOPUS: Efficient query execution on dynamic mesh datasets, Data Engineering (ICDE), 2014 IEEE 30th International Conference on, IEEE, 2014, pp. 1000-1011.

EPFL School of Life Sciences - 2014 Annual Report

Center for Biomedical Imaging Research http://www.cibm.ch/

Director: Prof. Rolf Gruetter Mission

The CIBM aims to advance our understanding of biomedical processes in health and disease, focusing on mechanisms of normal functioning, pathogenic mechanisms, characterization of disease onset prior to structural damage, metabolic and functional consequences of gene expression, and non-invasive insights into disease processes under treatment. The research will use model systems ranging from transgenic animals to human patients (“from mouse to man”) and foster multi-disciplinary collaboration between basic science, biomedical science and clinical applications. The overall goal of the CIBM is to foster state-of-the-art applications of biomedical imaging and in the context of biomedical applications to further advance the technological development and vice-versa. The CIBM aims to enhance biomedical research capabilities of the founding institutions and beyond, as well as within the CIBM. Its main aim to develop novel imaging capabilities in the context of questions of biomedical importance. It further aims to bring together basic scientists, engineers and biomedical researchers through research collaborations, which distinguishes it from a traditional service facility.

• EEG Brain Mapping • Signal Processing and Image Analysis * • Phase Contrast Radiology * • Positron Emission Tomography * • Clinical Research (3Tesla MRI) • Animal Imaging and Technology (9.4, 14 and 7 Tesla human MRI) * * effort present at EPFL campus At the EPFL, the CIBM offers access to unique MRI instrumentation, namely a dedicated 7T scanner for human brain MRI and a 14T scanner for rodent MRI investigations. Techniques that are available include, but are not limited to:

cer, among others. Investigators have access to an animal PET scanner adjacent to a 9.4 Tesla MRI system. All rodent investigations are supported by two physiology suites and an on-site small animal house. In addition, we provide support for cutting edge x-ray imaging at um resolution at the Swiss Light Source (PSI). The CIBM supports undergraduate education of the SSV, through bachelor projects, lab immersions and master projects. For establishing a project, feel free to contact the CIBM staff or info@cibm.ch.

• whole head fMRI with 2mm resolution in 400ms • phase imaging • anatomical imaging, and • MR spectroscopy of multiple nuclei.

Keywords

Magnetic resonance imaging, fMRI, ASL, DTI, PET, phase contrast tomography, multinuclear MR spectroscopy.

CIBM’s Research Activities

Overall, research projects cover a range of disciplines, such as transgenic mouse models, neuroscience and can-

The CIBM is organized on 3 sites with 7 research cores. Please see www.cibm.ch for details.

EPFL School of Life Sciences - 2014 Annual Report

Copper promotes tumor growth. (A and B) RIP1– Tag2 mice were subjected to 20 µM copper in drinking water or regular water from the time of weaning (4 wk of age). (A) Dissected tumors from 15-wk-old RIP1–Tag2 mice are dissociated and displayed adjacent to the pancreas (whitish tissue), where spleen (dark red, oblong tissue) is shown in the upper right corner. (B) Quantification of angiogenic islets and tumors are shown. Results are means and SEM (n = 15). *P < 0.05. (C) Schematic diagram of stepwise tumorigenesis phases in RIP1–Tag2 mice and pharmacological trial regimens involving the copper chelator TM. (D) RIP1–Tag2 mice were given 1 mg of TM daily from 6 to 9 wk (n = 17) (Left), 9 to 12 wk (n = 8) (Center), or 12 to 15 wk (n = 12) (Right) as diagramed in C and assessed by the same parameters as in B. Mice were euthanized at the end of each treatment period for analyses of angiogenic islets and tumors. Results are means and SEM. *P < 0.05. n.a., not applicable.

Selected Publications

Centers

» Seyer P, Vallois D, Poitry-Yamate C, Schütz F, Metref S, Tarussio D, Maechler P, Staels B, Lanz B, Gruetter R, Decaris J, Turner S, da Costa A, Preitner F, Minehira K, Foretz M, Thorens B. Hepatic glucose sensing is required to preserve β cell glucose competence. The Journal of Clinical Investigation 2013;123(4):1662-1676. » C. Granziera, A. Daducci, D. Romascano, A. Roche and G. Helms et al. Structural abnormalities in the thalamus of migraineurs with aura: a multiparametric study at 3T, in Human Brain Mapping, vol. 35, num. 4, p. 1461-1468, 2013. » Eichhorn TR, Takado Y, Salameh N, Capozzi A, Cheng T, Hyacinthe J-N, Mishkovsky M, Roussel C, Comment A. Hyperpolarization without persistent radicals for in vivo real-time metabolic imaging. Proceedings of the National Academy of Sciences 2013; 110: 18064-18069. » S. Ishida, P. Andreux, C. Poitry-Yamate, J. Auwerx and D. Hanahan. Bioavailable copper modulates oxidative phosphorylation and growth of tumors, in Proceedings Of The National Academy Of Sciences Of The United States Of America, vol. 110, num. 48, p. 19507-12, 2013. » Hara M, Salomon R, van der Zwaag W, Kober T, Rognini G, Nabae H, Yamamoto A, Blanke O, Higuchi T. A novel manipulation method of human body ownership using an fMRI-compatible master-slave system. J Neurosci Methods. 2014 Sep 30;235:25-34. » Martuzzi R, van der Zwaag W, Farthouat J, Gruetter R, Blanke O. Human finger somatotopy in areas 3b, 1, and 2: A 7T fMRI study using a natural stimulus. Hum Brain Mapp 2014; 35: 213–226.

EPFL School of Life Sciences - 2014 Annual Report

Center for Neuroprosthetics http://cnp.epfl.ch/

Director: Prof. Olaf Blanke / Deputy Director: Dr Bruno Herbelin Mission

Engineering the nervous system to improve sensation, cognition, and mobility, we strive to create major breakthroughs in bioengineering and neuroscience and efficiently translate them to viable clinic applications.

Research Activities & Main Results Obtained

The Center for Neuroprosthetics (CNP) capitalizes on its unique access to the advanced technologies and state of the art brain research present at EPFL. We strive to develop new technologies that support, repair and replace functions of the nervous system. The development of such technologies or devices, called neuroprostheses, requires a fundamental understanding of the neurobiological mechanisms of the functions that should be replaced or repaired, for example sensory perception, cognitive operations or movement. It also requires technological capabilities to design novel devices, to record and process signals and to translate them into outputs that can commend artificial limbs, bodies and robots, for motor function, or produce signals to activate the brain, in the case of sensory and cognitive prostheses. The impact of neuroprosthetics for the treatment of sensory loss and impaired mobility has already been demonstrated. Over 200,000 people with impaired hearing have received cochlear implants and over 80,000 patients suffering from Parkinson’s disease and other neurological movement disorders have been treated with deep brain stimulation. With approximately a third of the population in Europe and the US afflicted by brain disorders, major advances in neuroprosthetics are necessary, also including breakthroughs in cognitive neuroprosthetics for treating patients suffering from cognitive deficits such as those caused by Alzheimer’s disease and vascular stroke. The Center for Neuroprosthetics is part of the School of Life Sciences and the School of Engineering. It draws upon EPFL’s expertise in biology, neuroscience, brain imaging,

and genetics as well as biomedical, electrical, mechanical engineering, micro- and nanotechnology. The Center will also draw upon EPFL’s cutting edge research in signal analysis, theoretical and computational neuroscience, the European Flagship Human Brain Project and the Swiss National Center of Competence in Research in Robotics and in Psychiatric diseases. In addition, through support from the Bertarelli foundation, a research collaboration dedicated to translational neuroscience and neuroengineering has been created between Harvard Medical School, EPFL’s Institutes of Bioengineering and Neuroscience, and the Center for Neuroprosthetics. The Center has strategic partnerships with Geneva University Hospital (Hôpitaux Universitaires de Genève, HUG), Lausanne University Hospital (Centre Hospitalier Universitaire Vaudois, CHUV), and the Swiss Rehabilitation Clinic in Sion (Clinique Romande de Réadaptation, CRR), as well as with the regional biomedical industry.

Center Laboratories Prof Olaf Blanke p. 22

Bertarelli Foundation Chair in Cognitive Neuroprosthetics http://lnco.epfl.ch

Prof Grégoire Courtine p. 24

International Paraplegic Foundation (IRP) Chair in Spinal Cord Repair http://courtine-lab.epfl.ch/

Prof Diego Ghezzi

Medtronic Chair in Neuroengineering http://cnp.epfl.ch/Ghezzilab

Prof Stéphanie P. Lacour - p. 83

Bertarelli Foundation Chair in Neuroprosthetic Technology http://lsbi.epfl.ch

Prof Silvestro Micera - p. 87

Bertarelli Foundation Chair in Translational Neuroengineering http://tne.epfl.ch/

Prof José del R. Millán - p. 88

Défitech Foundation Chair in Non-Invasive Brain-Machine Interface http://cnbi.epfl.ch

EPFL School of Life Sciences - 2014 Annual Report

Electronic dura mater (e-dura). The soft elastomeric implant is prepared with silicone rubber, stretchable thin-gold film interconnects, platinum-silicone composite electrode coating, and hosts a silicone microfluidic channel for in situ drug delivery. This surface electrode implant can be inserted below the natural dura mater to conform the very surface of the brain or the spinal cord (Minev et al., Science 2015).

Selected Publications

Centers

» Minev, I.R., Musienko, P., Hirsch, A., Barraud, Q., Wenger, N., Moraud, E. M., Gandar, J., Capogrosso, M., Milekovic, T., Asboth, L., Torres, R. F., Vachicouras, N., Liu, Q., Pavlova, N., Duis, S., Larmagnac, A., Vörös, J., Micera, S., Suo, Z., Courtine, G. and Lacour, S. P. (2015). Biomaterials. Electronic dura mater for long-term multimodal neural interfaces. Science, 347(6218). » Blanke, O., Pozeg, P., Hara, M., Heydrich, L., Serino, A., Yamamoto, A., Higuchi, T., Salomon, R., Seeck, M., Landis, T., Arzy, S., Herbelin, B., Bleuler, H., Rognini, G. (2014). Neurological and Robot-Controlled Induction of an Apparition. Current Biology, 24(22). » Perdikis, S., Leeb, R., Williamson, J., Ramsey, A., Tavella, M., Desideri, L., Hoogerwerf, E.J., Al-Khodairy, A., Murray-Smith, R., Millán, J.del R. (2014). Clinical evaluation of BrainTree, a motor imagery hybrid BCI speller. Journal of Neural Engineering, 11(3). » Raspopovic, S., Capogrosso, M., Petrini, F. M., Bonizzato, M., Rigosa, J., Di Pino, G., Carpaneto, J., Controzzi, M., Boretius, T., Fernandez, E., Granata, G., Oddo, C.M., Citi, L., Ciancio, A.L., Cipriani, C., Carrozza, M.C., Jensen, W., Guglienmelli, E., Stieglitz, T., Rossini, P.M., Micera, S. (2014). Restoring Natural Sensory Feedback in Real-Time Bidirectional Hand Prostheses. Science Translational Medicine, 6(222). » Wenger, N., Martin Moraud, E., Raspopovic, S., Bonizzato, M., DiGiovanna, J., Musienko, P., Morari, M., Micera S. and Courtine, G. (2014). Closed-loop neuromodulation of spinal sensorimotor circuits controls refined locomotion after complete spinal cord injury. Science Translational Medicine, 6(255).

EPFL School of Life Sciences - 2014 Annual Report

BMI

Brain Mind Institute

The mission of the Brain Mind Institute (BMI) is to understand the fundamental principles of brain function in health and disease, by using and developing unique experimental, theoretical, technological and computational approaches. The scientific challenge addressed by the BMI consists of connecting different levels of analysis of brain activity, such that cognitive functions can be understood as a manifestation of specific brain processes; specific brain processes as emerging from the collective activity of thousands of cells and synapses; synaptic and neuronal activity in turn as emerging properties of the biophysical and molecular mechanisms of cellular compartments. Research at the BMI focuses on four main areas: • Mechanisms of brain function and dysfunction, with a particular focus on neurodegeneration and stress-related psychopathologies. • Molecular and cellular mechanisms of synapse and microcircuit function up to the behavioral level and including metabolic aspects. • Sensory and body perception and cognition in humans.

Sandi Carmen - Director

In all areas, the BMI strives to integrate knowledge gained by multidisciplinary approaches and across different disciplines and research laboratories. An important second mission of the BMI is to bridge scientific approaches and questions with research carried out in the EPFL campus, as well as in related institutions and companies in the area, specifically with the fields of nano- and micro-technology, computer sciences, physics, neuroprosthetics, robotics, signal and medical imaging processing, genetics, metabolism, neuroeconomics, psychiatry and neurology. Major goals of the BMI are to bridge basic science approaches with clinical applications and to merge areas of experimental work with theory and modeling. Finally, the BMI is fully engaged in the teaching mission of the School of Life Sciences at the Bachelor and Master levels –with a full Neuroscience track at the Master level– and organizes the PhD program in Neurosciences. http://sv.epfl.ch/

BMI - Brain Mind Institute

• Designing innovative interventions to restore sensorimotor functions after neural disorders.

EPFL School of Life Sciences - 2014 Annual Report

Aebischer Lab t c

eb sche

Full Professor - President of EPFL

http://len.epfl.ch/

Introduction

Patrick Aebischer was trained as an MD (1980) and a Neuroscientist (1983) at the Universities of Geneva and Fribourg in Switzerland. Until 1992, he worked as Faculty member at Brown University in Providence (USA), where he became Chairman of the Section of Artificial Organs, Biomaterials and Cellular Technology in 1991. He returned to Switzerland in 1992, as Professor and Director of the Surgical Research Division and Gene Therapy Center at the Centre Hospitalier Universitaire Vaudois in Lausanne. Since 2000, Patrick Aebischer has been President of the EPFL. He is the founder of 3 biotech companies.

Understanding the cause of neurodegeneration and translating these findings into effective treatments is a daunting task. A number of findings suggest that protein misfolding during brain aging is a key mechanism in several neurodegenerative diseases, providing novel targets for therapeutic intervention. However, it remains uncertain how these pathologies could be cured or prevented. Our lab explores the causes and possible treatments for neurodegenerative diseases using state-of-the-art techniques to manipulate gene expression in the central nervous system (CNS). In particular, we develop viral vector technologies, mainly based on adeno-associated and lentiviral vectors, to target in the rodent CNS the cell types that contribute to pathogenic changes in amyotrophic lateral sclerosis and Parkinson’s disease. In parallel, we explore the possibility to use genetically modified cells to deliver therapeutic molecules in the brain, such as recombinant antibodies for passive immunization against misfolded protein species. Furthermore, our lab develops relevant animal and cellular models of neurodegenerative pathologies, including Alzheimer’s and Parkinson’s diseases, with the objective to test and validate therapies. In particular, we develop gene transfer technologies to replicate pathologies linked to the accumulation and misfolding of molecules such as Tau and alphasynuclein in the rodent brain. Our aim is to use these animal models to validate the efficacy of specific compounds and gene therapies, and explore the mechanisms that lead to neuronal dysfunction and death. In this context, one line of research is to understand how the protein pathology observed in several diseases propagates throughout the CNS, which may open new avenues for therapeutic intervention.

Keywords

Gene therapy, animal models of disease, Parkinson’s disease, Amyotrophic lateral sclerosis, Alzheimer’s disease, viral vectors, adeno-associated virus, cell encapsulation, passive immunization.

Results Obtained in 2014

During the past two years, our lab has mainly focused its research on three research axes. In order to design a gene therapy approach against amyotrophic lateral sclerosis (ALS), we have explored the possibility to target motoneurons and astrocytes throughout the spinal cord using adeno-associated viral vectors (AA ). Specific combinations of AA capsids and promoters have been found that allow for widespread gene delivery in the mutated SOD1 mouse model of ALS (Dirren et al., 2014). This technology has been used to express artificial microRNAs in order to reduce SOD1 levels. We have obtained significant improvements in the motor function of the treated mice, providing preclinical proof-of-principle evidence for the therapeutic efficacy of this approach (Dirren et al, 2015). We are currently addressing the possibility to evaluate gene therapy in SOD1 ALS patients. A second line of research has explored the delivery of anti-amyloid β antibodies using encapsulated cellular implants (see Figure). A novel encapsulation technology has been developed to support the long-term implantation of muscle cells genetically engineered to secrete recombinant antibodies in the subcutaneous tissue (Lathuilière et al, 2014). Peripheral delivery of anti-amyloid β antibodies prevents the deposition of amyloid plaques in the brain of a mouse model of Alzheimer’s disease. Finally, using an animal of Parkinson’s disease based on AAV-induced overexpression of human -synuclein in nigral dopaminergic neurons (Gaugler et al, 2012), we have explored possible interaction of the pathology with genetic determinants of the aging process. We have found that the activity of the transcription factor FoxO3a has a strong effect on -synuclein toxicity, and controls accumulation of the protein via changes in autophagic activity (Pino et al, 2014). This study adds to our work on the role of the FoxO3a/PGC-1 axis in the -synuclein pathology, highlighting the critical importance of the transcriptional control of autophagic and mitochondrial activities in Parkinson’s disease.

EPFL School of Life Sciences - 2014 Annual Report

Team Members Senior Scientist Bernard Schneider Postdoctoral Fellows Julianne Aebischer Nathalie Bernard-Marissal Maria Gabriela Mercado Guerra Pamela Valdès

PhD Students Wojciech Bobela Vanessa Laversenne Sameer Nazeeruddin Cylia Rochat Lu Zheng

Technicians Aline Aebi Philippe Colin Geneviève Dayer Fabienne Pidoux Vivianne Padrun Christel Sadeghi

Visiting Students Patrick Chirdon (Fullbright) Abhishek Verma (Fullbright) Giorgio Ulrich Duygu Deniz Bas Caitriona Mae Callan Hena Sara Ahmed Veselina Petrova Marco Edoardo Schukraft

Administrative Assistants Marie Künzle Ursula Zwahlen

BMI - Brain Mind Institute

(a) mplantation of geneticall modified cells within a permeable de ice to produce antibodies targeting the am loid patholog in the brain. ncapsulating de ice (b) and implanted cells (c). (d) he sur i al of cells geneticall modified to e press luciferase can be monitored b light emission.

Selected Publications » Dirren E., Towne C.L., Setola ., Redmond D.E. Jr, Schneider B.L., Aebischer P. 2014. Intracerebroventricular injection of adeno-associated virus 6 and vectors for cell type-specific transgene expression in the spinal cord. Hum Gene Ther. 25(2):10 -20. » Lathuilière A., Cosson S., Lutolf M.P., Schneider B.L., Aebischer P. 2014. A high-capacity cell macroencapsulation system supporting the long-term survival of genetically engineered allogeneic cells. Biomaterials. 35(2):77 - 1. » Lathuilière A., Bohrmann B., Kopetzki E., Schweitzer C., Jacobson H., Moniatte M., Aebischer P., Schneider B.L. 2014. Genetic engineering of cell lines using lentiviral vectors achieves high-level antibody secretion following encapsulated implantation. Biomaterials. 35(2): 7 2- 02. » Kaplan A, Spiller KJ, Towne C, Kanning KC, Choe GT, Geber A, Akay T, Aebischer P, Henderson CE. 2014. Neuronal matrix metalloproteinase-9 is a determinant of selective neurodegeneration. Neuron. 81(2):333-48. » Pino E., Amamoto R., Zheng L., Cacquevel M., Sarria J.C., Knott G.W., Schneider B.L. 2014. FO O3 determines the accumulation of -synuclein and controls the fate of dopaminergic neurons in the substantia nigra. Hum Mol Genet. 23(6):1435-52. » Valdés P., Mercado G., Vidal R.L., Molina C., Parsons G., Court F.A., Martinez A., Galleguillos D., Armentano D., Schneider B.L., Hetz C. 2014. Control of dopaminergic neuron survival by the unfolded protein response transcription factor XBP1. Proc Natl Acad Sci U S A. 111(18):6804-9. » Oueslati A., Schneider B.L., Aebischer P., Lashuel H.A. 2013. Phosphorylation by PLK2 enhances -synuclein turnover and protects against its toxicity . coli. Proc Natl Acad Sci U S A. 110(41): E3 45-54. » Löw K., Aebischer P., Schneider B.L. 2013. Direct and retrograde transduction of nigral neurons with AAV6, 8 and 9, and intraneuronal persistence of viral particles, Hum Gene Ther. 24(6):613-29.

EPFL School of Life Sciences - 2014 Annual Report

Blanke Lab n e

Full Professor - Director of the Center for Neuroprosthetics

http://lnc .epfl.ch

Introduction

Olaf Blanke is the founding director of the Center for Neuroprosthetics and Bertarelli Foundation Chair in Cognitive Neuroprosthetics at the Ecole Polytechnique Fédérale de Lausanne (EPFL). He also directs the Laboratory of Cognitive Neuroscience at EPFL and is Professor of Neurology at the Department of Neurology at the University Hospital of Geneva. Blanke’s human neuroscience research is dedicated to the understanding of how the brain represents our body and the neuroscientific study of consciousness using human neuroimaging and cognitive psychology. In clinical neuroscience he pursues intracranial neurosurgical investigations as well as neuroprosthetics and neurorehabilitation in neurological, orthopaedic, and psychiatric patients. He pioneered cognitive neuroprosthetics by using engineering techniques such as robotics, haptics, virtual reality to develop novel treatments for cognition and consciousness disorders.

The Laboratory of Cognitive Neuroscience (Bertarelli Chair in Cognitive Neuroprosthetics) is part of the Brain Mind Institute and the Center for Neuroprosthetics. Research in the Blanke Lab targets the brain mechanisms of multisensory body perception and consciousness. Projects rely on the investigation of healthy subjects, neurological, psychiatric, and orthopedic patients by combining psychophysical and cognitive paradigms, neuroimaging techniques (high resolution fMRI, EEG, and intracranial human recordings) with several engineering-based approaches (robotics, brain-computer interfaces, virtual reality, augmented reality). Our work over the last 10 years has been fundamental to describe a neuroscientific theory of self-consciousness. For this we used technology to induce complex altered states in humans under controlled-conditions (virtual and augmented reality, robotics) and were able to describe the detailed mechanisms of bottom-up sensory signals and their integration in a brain network consisting of posterior parietal cortex, insula and frontal cortex. Finally, we are dedicated to applying our neuroscience and technology findings in the fields of neuroprosthetics, sensory substitution, and neurorehabilitation with our clinical partners at the Sion Rehabilitation Hospital, as well as the Geneva and Lausanne University Hospitals, where we continue to develop the fields of robotic psychiatry and cogniceuticals.

Keywords

Multisensory perception, bodily awareness, consciousness, neuroprosthetics, neurorehabilitation, intracranial human electrophysiology, neuroimaging, EEG, neuropsychology, cognitive neurology, epileptology, virtual reality, robotics, haptics.

Results Obtained in 2014

In robotic psychiatry, a major achievement was the design and application of a master-slave robotic system (Hara et al., Journal of Neuroscience Methods, 2014) that manipulates sensorimotor signals to induce altered bodily experience and psychosis-like states in healthy participants (Blanke et al., Current Biology 2014). We also studied the same mental states and the involved brain circuits in a large group of neurological patients (Blanke et al., Current Biology 2014). Most recently, we have started to investigate the involved brain circuits in healthy participants by using a new robotic system that is fully compatible with modern brain imaging (MRI). In cogniceuticals, we have launched a major effort in treating patients with chronic pain, of neurological and orthopedic origin. These studies on chronic pain are directly motivated by our neuroscience research on multisensory brain mechanisms (including interoceptive signals) of bodily experience and consciousness. In neuroscience we showed that bodily experience and consciousness arise from the integration of visual and tactile signals with interoceptive signals (Aspell et al., Psychological Science 2013) and that such integration occurs in bilateral insular and temporo-parietal cortex (Heydrich & Blanke, Brain 2013; Ionta et al., Social Cognitive and Affective Neuroscience 2014). We also showed that manipulating multisensory bodily inputs impact physiological states of the body, leading to a decrease in physical body temperature (Salomon et al., Frontiers in Neuroscience 2013) and to analgesia (Romano et al., Beh Brain Res 2014). To translate our cogniceutical approach to patients with chronic pain, we have setup a new integrated virtual reality platform with our clinical partners in the Rehabilitation clinics in Sion and Geneva (ongoing research). Finally, a new line of our research in neuroscience focuses on how these low-level multisensory mechanisms affect cognitive functions, such as social cognition (Teneggi et al., Current Biology, 2013), processing of bodily sounds (Van Elk et al., Biological Psychology, 2014a, 2014b) and visual consciousness (Faivre et al., Current Opinion in Neurology, 2015).

EPFL School of Life Sciences - 2014 Annual Report

Team Members PhD Students Akselrod Michel Brechet Lucie Gale Steven Grivaz Petr Kaliuzhna Mariia Marchesotti Silvia Pfeiffer Christian Pozeg Polona Rognini Giulio Solcà Marco

Master’s Students Blondiaux Eva Dönz Jonathan Muhech Amira Lukowska, Marta Vuillaume Laurène Visiting PhD Students Muret Dollyane Noël Jean-Paul

Laboratory Engineers Bello Ruiz Javier Mange Robin

Administrative Assistant Neffati-Laifi Sonia

Physician/MDs Pierre Prognin Solcà Marco

BMI - Brain Mind Institute

Postdoctoral Fellows Bernasconi Fosco Blefari Maria Laura Canzoneri Elisa Faivre Nathan Martuzzi Roberto Ronchi Roberta Salomon Roy Schurger Aaron Serino Andrea Kanayama Noriaki

obot-controlled feeling of a presence. articipants performed hand mo ements in the front, while recei ing altered sensor feedbac on their bac . f the spatio-temporal congruenc between mo ements and feedbac was manipulated b the robot, participants illusoril felt as another person was standing behind them.

Selected Publications » Blanke, O., Pozeg, P., Hara, M., Heydrich, L., Serino, A., Yamamoto, A., Higuchi, T., Salomon, R., Seeck, M., Landis, T., Arzy, S., Herbelin, B., Bleuler, H., Rognini, G. (2014). Neurological- and robot-controlled induction of an apartition. Cell Current Biology 24(22):2681-6. » Hara, M., Salomon, R., van der Zwaag, W., Kober, T., Rognini, G., Nabae, H., Yamamoto, A., Blanke, O., Higuchi, T. (2014). A novel manipulation method of human body ownership using an fMRI-compatible master-slave system. J Neuroscience Methods. 235:25-34. » Romano, D., Pfeiffer, C., Maravita, A., Blanke, O. (2014). Illusory self-identification with an avatar reduces arousal responses to painful stimuli. Behavioral Brain Research 261:275- 1. » Heydrich, L., Blanke, O. (2013). Distinct illusory own-body perceptions caused by damage to posterior insula and extrastriate cortex. Brain 136: 7 0- 03. » Aspell, J.E., Heydrich, L., Blanke, O. (2013). Turning body and self inside out: isualized heartbeats alter bodily self-consciousness and tactile perception. Psychological Science 24: 2445-2453. » Teneggi, C., Canzoneri, E., di Pellegrino, G., Serino, A. (2013). Social modulation of peripersonal space boundaries. Cell Current Biology 23(5):406-11. » Ionta, S., Martuzzi, R., Salomon, R., Blanke, O. (2013). The brain network reflecting bodily self-consciousness: a functional connectivity study. Social Cognitive Affective Neuroscience. (12):1 04-13.

EPFL School of Life Sciences - 2014 Annual Report

Courtine Lab e

t ne

Associate Professor - IRP Chair in Spinal Cord Repair

http://c urtine lab.epfl.ch/

Introduction

Grégoire Courtine was trained in Mathematics, Physics, and Neurosciences in France and Italy. After a Postdoc in Los Angeles (UCLA), he established his laboratory at the University of Zurich. In 2012, he was appointed the International Paraplegic Foundation Chair in Spinal Cord Repair at the Center for Neuroprosthetics at EPFL. His research program aims to develop neuroprosthetic treatments to improve recovery after spinal cord injury—an endeavor that has been reported in high-profile publications, and has extensively been covered in the media. His start-up, G-Therapeutics SA, aims to translate these medical and technological breakthroughs into treatments.

The World Health Organization (WHO) estimates that as many as 500’000 people suffer from a spinal cord injury each year. Over the past decade, we implemented an unconventional research program with the aim to develop radically new treatment paradigms to improve functional recovery after spinal cord injury. We have progressively conceived a treatment that integrates a serotonergic replacement therapy (Nature Neuroscience, 2009), electrical spinal cord stimulation (Science Translational Medicine, 2014; Science, 2015), next-generation weight-supporting robotic systems (Nature Medicine, 2012) and novel will-powered training regimes (Science, 2012). We have shown that this combinatorial treatment restored and refined locomotion after severe spinal cord injury in rodent models. Recovery occurs through the extensive and ubiquitous remodeling of residual neuronal connections in the brain and spinal cord. The goal of the laboratory is to translate this treatment into a medical practice for improving functional recovery after spinal cord injury in humans. To this aim, we have structured a translational, neuroprosthetic program that combines work in mice, rats, non-human primates, and humans. Specifically, our objective is to (i) identify the mechanisms underlying the immediate and long-term effects of our treatment in genetically modified mice using virus-mediated experimental manipulations, calcium imaging and optogenetics; (ii) refine all our methods and procedures in rat models of spinal cord injury; (iii) optimize and validate our new neurotechnologies and therapeutic concepts in non-human primate models; and (iv) deploy clinical studies that progressively integrate the different components of our interventions.

Keywords

Spinal cord injury, neural repair, neurorehabilitation, neuroprosthetics, brain-machine interface, robotics, neuronal recordings, optogenetics, EMG, kinematics, locomotion, neuromorphology, mice, rats, monkeys, humans.

Results Obtained in 2014

Mechanisms of recovery after spinal cord injury (Cell 2014): We had previously demonstrated that recovery after spinal cord injury relies on novel detour connections that bypass the injury. However, the circuit-level mechanism behind this process was not elucidated. We found that muscle spindles and associated circuits promote the establishment of these detour connections. These findings may contribute to improving our treatment strategies. Neuromodulation therapies (Science Translational Medicine, 2014; Science 2015): We have identified the mechanisms underlying the facilitation of locomotion with electrical spinal cord stimulation. This conceptual framework guided the development of innovative hardware and software to improve our neuromodulation therapies. We designed the first entirely stretchable, multimodal implants that exhibit unprecedented bio-integration in the central nervous system. This implant, developed in collaboration with Prof. Lacour, can deliver both electrical and chemical stimulations over the brain and spinal cord. In parallel, we collaborated with Prof. Micera to develop a control platform through which neuromodulation parameters can be adjusted in real-time, based on movement feedback. Using this hardware and software, we designed control algorithms that achieve precise adjustment of leg movements in animal models of neurological disorders. Wireless neurosensor (Neuron, 2014): Neuroscience research has been constrained by cables required to connect brain sensors to computers. In collaboration with Brown University, we developed and validated a wireless brain-sensing system that allows recordings of high-fidelity neural data during unconstrained behavior in primates. Gait rehabilitation platform: In collaboration with the CHUV, the SUVA and the Canton of Valais, we established a new Gait Platform that brings together innovative monitoring and rehabilitation technology. We will exploit this Gait Platform to evaluate the ability of our electrical stimulation protocols and robot-assisted training procedures to improve motor function after spinal cord injury.

EPFL School of Life Sciences - 2014 Annual Report

Team Members PhD Students Anderson Mark Asboth Leonie Bartholdi Kay Beauparlant Janine Friedli Wittler Lucia Gander Jérôme Pidpruzhnykova Galyna Vollenweider Isabel Wenger Nikolaus Le Goff Camille Anil Selin

Technicians /Research Assistants Baud Laetitia Duis Simone Kreider Julie

Scientiﬁc Coordinator Van den Brand Rubia

Administrative Assistant Nguyen Kim-Yen

BMI - Brain Mind Institute

Postdoctoral Fellows Barraud Quentin Borton David Laurens Jean Martinez Gonzalez Cristina Mignardot Jean-Baptiste Milekovic Tomislav Musienko Pavel Pavlova Natalia Von Zitzewitz Joachim Wagner Fabien

completel paral ed rat can be made to wal o er obstacles and upstairs b electricall stimulating the se ered part of the spinal cord. scientists disco ered how to control in real-time how the rat mo es forward and how high it lifts its limbs.

Selected Publications » » » » » » » » » »

Courtine G, Bloch J. (2015) Defining ecological strategies in neuroprosthetics. Neuron. 2015 April. Minev I.R., et al. (2015) Electronic dura mater for long-term multimodal neural interfaces, Science 347, 621 , 15 -163. ollenweider I et al. (2014) Muscle spindle feedback directs locomotor recovery and circuit reorganization after spinal cord injury, Cell, 15 (7):1626-3 . Yin M et al. (2014) Wireless Neurosensor for Full-Spectrum Electrophysiology Recordings during Free Behavior. Neuron. 2014 Dec 17; 4(6):1170- 2. Wenger N et al. (2014) Closed-loop neuromodulation of spinal sensorimotor circuits controls refined locomotion after complete spinal cord injury. Science Translational Medicine. 2014 Sep 24;6(255):255ra133. Borton D et al. Personalized neuroprosthetics Science Translational Medicine. 2013 Nov 6;5(210):210rv2. Capogrosso M et al. (2013) A computational model for epidural electrical stimulation of spinal sensorimotor circuits. Journal of Neuroscience 33: 19326-40. Beauparlant J et al. (2013) Undirected compensatory plasticity contributes to neuronal dysfunction after severe spinal cord injury. Brain. 2013 Nov;136(Pt 11):3347-61. an den Brand R et al. (2012) Restoring voluntary control of locomotion after paralyzing spinal cord injury. Science. 336(60 5): 11 2-11 5. Dominici N et al. (2012) Novel robotic interface to evaluate, enable, and train locomotion and balance after neuromotor disorders. Nature Medicine. (1 ) 1142–1147.

EPFL School of Life Sciences - 2014 Annual Report

Fraering Lab t c

e n

Tenure-track Assistant Professor

http:// raerin

Introduction

Patrick Fraering studied biology at the University Louis Pasteur of Strasbourg, where he earned a master’s degree in biochemistry (1 5) and pre-doctoral research degree in molecular and cellular biology at the CNRS (1996). In 2001, he received his PhD at the University of Fribourg. In 2002, he joined the lab of Prof. D. Selkoe at Harvard Medical School where he studied the molecular basis of Alzheimer’s disease. In 2007, he has been appointed assistant professor at the EPFL’s School of Life Sciences.

Our main interest is the understanding of the molecular and biological mechanisms implicated in the pathological process that leads to Alzheimer’s disease, the most frequent age related neurological disorder. More specifically, we focus our research on -secretase, an intramembranecleaving protease that is directly implicated in the generation of the amyloid-beta peptides (Aβ), the accumulation of which causes AD. Toward advancing the biochemistry and neurobiological functions of -secretase, with attendant therapeutic applications, our long-term goals are: • To get new insight into the structure and function of the secretase protease complex, including a better understanding of its regulatory mechanisms, • To understand how mutations in Presenilin and APP causing early onset familial Alzheimer’s disease affect the biochemical properties of secretase and the processing of APP, • To shed new light on the neurobiological functions of -secretase, and understand how, through the cleavage of Neurexins and Neuroligins, it regulates the activity and the plasticity of neuronal synapses, • To identify endogenous -secretase modulators of APP processing and Aβ production, and • To elucidate the precise mode of action, at the molecular level, of chemical secretase modulators (GSMs) currently tested in clinical trials. Our vision is to provide new molecular targets and strategies for rational drug design to safely treat or prevent Alzheimer’s disease.

Keywords

Molecular and cellular biology of Alzheimer’s disease, -secretase, amyloid-beta peptides (Aβ), intramembrane-cleaving proteases, synaptic activity and plasticity, therapeutic targets, translational research.

lab.epfl.ch/

Results Obtained in 2014

The adipocyte differentiation protein APMAP is an endogenous modulator of -secretase and Aβ production. The deposition of amyloid-beta (Aβ) aggregates in the brain is a major pathological hallmark of Alzheimer’s disease (AD) and the endogenous modulation of -secretase may be implicated in the sporadic, age-dependent form of this disorder. In this study, we report the identification of the adipocyte differentiation protein APMAP as a novel endogenous modulator of Aβ generation. We found that APMAP interacts physically with -secretase and its substrate APP. In cells, the partial depletion of APMAP drastically increased the levels of APP-CTFs, with the consequence being increased secretion of Aβ. In wild-type and APPPS1 transgenic mice, partial adeno-associated virus-mediated APMAP knockdown in the hippocampus increased Aβ production by 20% and 55%, respectively. Together, our data demonstrate that APMAP is a negative regulator of Aβ production through its interaction with -secretase and APP. Early-onset Alzheimer’s disease mutations in APP, but not -secretase modulators, affect epsilon-cleavage-dependent AICD production. Pathological amino acid substitutions in the amyloid precursor protein (APP) and chemical -secretase modulators (GSMs) affect the processing of APP by the -secretase complex, and the production of Aβ42, the accumulation of which is considered causative of Alzheimer’s disease (AD). We demonstrate in this study that mutations in the transmembrane domain of APP causing aggressive early-onset familial AD (FAD) affect both - and -cleavage sites, by raising the Aβ42/40 ratio and inhibiting the production of AICD50- , one of the two physiological APP intracellular domains (ICDs). Our findings suggest that it is the combination of higher Aβ42 to Aβ40 ratio and the loss of AICD50- that explains the extreme aggressiveness of APP mutations with regard to the onset of the disease. We further show that GSMs, which shift Aβ42 production towards the shorter Aβ38, unequivocally spare the -site and APP- and Notch-ICDs production and conserve their Aβ42-lowering and Aβ38-raising properties on all tested FAD substrates. GSMs can thus be used for the treatment of patients with both sporadic and genetic forms of AD.

EPFL School of Life Sciences - 2014 Annual Report

Team Members Postdoctoral Fellows Jean-René Al Attia Eugenio Barone Erika Borcel

PhD Students Mitko Dimitrov Sébastien Mosser Magda Palczynska

Master’s Students/Internships Juliette Ezpeleta Jeremy Fraering Claudia Freymond Hermeto Gerber Andres Lopez Alexandre Matz Risa Suzuki Giorgio Ulrich

Administrative Assistants Monica Navarro Francine Sallin

BMI - Brain Mind Institute

he adipoc te differentiation protein (green), b colocalizing in primary cortical neurons with secretase comthe ple (red), regulates the production of the am loid-beta peptides implicated in l heimer s disease.

Selected Publications » S. Mosser, J.R. Alattia, M. Dimitrov, A. Matz, J. Pascual, B. Schneider, and P.C. Fraering* (2014). The adipocyte differentiation protein APMAP is an endogenous suppressor of Aβ production in the brain. Hum. Mol. Genet. 2015 Jan 15;24(2):371- 2. » A. Matz, B. Halamoda-Kenzaoui, R. Hamelin, S. Mosser, J.R. Alattia, M. Dimitrov, M. Moniatte, and P.C. Fraering (2014). Identification of new Presenilin-1 phosphosites: implications in the activity of secretase and Aβ production. J Neurochem. 2014 Dec 2. doi: 10.1111/jnc.12996. » E. Barone, S. Mosser, and P.C. Fraering (2014). Cofilin-1 activity is modulated by age, Alzheimer’s disease pathology and secretase. BBA Molecular Basis of Disease, 2014 Oct 11. pii: S0 25-443 (14)00310- . doi: 10.1016/j.bbadis.2014.10.004. » M. Dimitrov, J.R. Alattia, T. Lemmin, L. Rajwinder, A. Fligier, J. Houacine, I. Hussain, F. Radtke, M. Dal Peraro, D. Beher, and P.C. Fraering* (2013). Alzheimer’s disease mutations in APP but not -secretase modulators affect epsilon-cleavage-dependent AICD production. Nature Commun., 2013 Aug 2;4:2246 » J.R. Alattia, M. Matasci, M. Dimitrov, L. Aeschbach, D.L. Hacker, F.M. Wurm, and P.C. Fraering (2013). Highly efficient production of the Alzheimer’s -secretase integral membrane protease complex by a multi-gene stable integration approach. Biotechnol Bioeng. 2013 Jul;110(7):1 5-2005. » I. Hussain, J. Fabrègue, L. Anderes, S. Ousson, F. Borlat, V. Eligert, S. Berger, M. Dimitrov, J.R. Alattia, P.C. Fraering, and D. Beher. (2013). The role of -secretase activating protein (GSAP) and imatinib in the regulation of -secretase activity and amyloid-β generation. J Biol Chem. 2013 Jan 25;2 (4):2521-31.

EPFL School of Life Sciences - 2014 Annual Report

Gerstner Lab m

e stne

Full Professor - Director of the Teaching Section

http://lcn .epfl.ch/

Introduction

At the Laboratory of Computational Neuroscience, we use neural modeling in order to understand the role of dynamics for computation in brainlike structures. Dynamics and temporal aspects play a role on all levels of information processing in the brain. Wulfram Gerstner is Director of the Laboratory of Computational Neuroscience LCN at the EPFL. He studied physics at the universities of Tubingen and Munich and received a PhD from the Technical University of Munich. His research in computational neuroscience concentrates on models of spiking neurons and spike-timing dependent plasticity, on the problem of neuronal coding in single neurons and populations, as well as on the role of spatial representation for navigation of rat-like autonomous agents. He currently has a joint appointment at the School of Life Sciences and the School of Computer and Communications Sciences at the EPFL. He teaches courses for Physicists, Computer Scientists, Mathematicians, and Life Scientists.

We have three different lines of work: Neurons, Learning rules, and functional networks. On the neuronal level, we study aspects of temporal coding by `spikesâ&#x20AC;&#x2122;, i.e., the short electrical pulses (action potentials) that neurons use for signal transmission. The lab is well known for its work on the adaptive exponential integrate-and-fire neuron as well as for generalized integrate-andfire models that can be fitted to experimental data during somatic current injections. In particular, the time course of the subthreshold membrane potential and spike times are predicted by the model for arbitrary timedependent currents. On the level of synaptic learning rules, the lab has a long tradition in modeling synaptic plasticity, in particular spike-timing dependent plasticity. We have described synaptic plasticity as a function of postsynaptic voltage in combination with spike-timing, and have also developed models of synaptic consolidation across multiple time scales. We are also interested in developing a framework of learning under neuromodulatory control. On the behavioral level, we focus on the dynamics of visual processing or memory retrieval in large model networks. Via modeling we aim to link the dynamics of synaptic plasticity to learning of new behaviors. We put particular emphasis on the potential role of Spike Timing Dependent Plasticity (STDP) under the influence of neuromodulators. This concept can be applied to reward-based learning of novel motor task; long-term storage and consolidation of memory, or learning by surprise.

Keywords

Computational neuroscience, models of spiking neurons, models of synaptic plasticity and STDP, models of learning.

Results Obtained in 2014

Models of brain dynamics: Experimentalists have recently shown that during an arm movement, neurons in the motor cortex show characteristic activity patterns. In a paper in Neuron (Hennequin et al. 2014), we have now shown that many of these features can be explained by a model of interacting neurons where the activity of excitatory neurons is stabilized through smartly tuned inhibition. Most of the work reported in the paper was performed as part of the PhD thesis of Guillaume Hennequin here at EPFL, undertaken in the frame of the PhD Program in Neuroscience. Temporal Coding in single neurons: Neurons have to transmit information about time-dependent stimuli they receive, but they should not spend too much energy and therefore minimize the number of output spikes. In a paper in Nature Neuroscience (Pozzorini et al., 2013), we demonstrate that neurons achieve close-tooptimal information transmission by using adaptation on many different time scales ranging from tens of milliseconds to tens of seconds. These results have been possible thanks to a novel mathematical method of extracting parameters of neuron models directly from experimental data of neurons during patch-clamp recordings while stimulated with a timedependent input. Synaptic Plasticity and Learning: Hebbian learning is a candidate rule for synaptic plasticity, and can be formulated as models of rate-based or spike-timing dependent plasticity. Whatever the exact formulation, Hebbian learning needs to be complemented by a weight control mechanism to avoid instabilities. Previously, theoreticians often applied ad-hoc rescaling of synaptic weights with the argument that homeostasis would be the analogous biological mechanism. In a paper in PLOS Computational Biology (Zenke et al. 2013), we now show that plasticity with homeostasis needs an ultra-fast rate detector and control loop. Indeed, the control loop has to be as fast as plasticity itself. The conclusion is that the biologically found homeostatic mechanisms are excluded as candidates for weight normalization.

EPFL School of Life Sciences - 2014 Annual Report

Team Members PhD Students Dane Corneil Mohammadjavad Faraji Felipe Gerhard Olivia Gozel Marco Lehmann Laureline Logiaco Skander Mensi

PhD Students con’t Samuel Muscinelli Christian Pozzorini Alex Seeholzer Hesam Setareh Carlos Stein Friedemann Zenke Lorric Ziegler

Master’s Students Parima Ahmadipour Alexander Aivazidis Florian Colombo Vasiliki Liakoni Claire Meissner Ivan Slijep evi Tomas van Pottelbergh

Administrative Assistant Chantal Mellier

BMI - Brain Mind Institute

Postdoctoral Fellows Moritz Deger David Kastner Kerstin Preuschoff Tilo Schwalger

hat is a good neuron model f the same stimulus is in ected in both the model and a real neuron, the model should be able to predict the spi e times as well as the subthreshold oltage of the real neuron.

Selected Publications » » » » » » »

Gerstner W., Kistler W. M., Naud R. and Paninski L. euronal namics rom ingle eurons to etwor s and odels of ognition. Cambridge University Press, 7 -1-107-060 3- , 2014. Book. Deger M., Schwalger T., Naud R. and Gerstner W (2014). Fluctuations and information filtering in coupled populations of spiking neurons with adaptation, Physical Review E, vol. 0, num. 6, p. 062704. Zenke F. and Gerstner W. (2014). Limits to high-speed simulations of spiking neural networks using general-purpose computers, Frontiers in Neuroinformatics, vol. , num. 76. Hennequin G., Vogels T. and Gerstner W. (2014). Optimal Control of Transient Dynamics Balanced Networks Supports Generation of Complex Movements, Neuron, vol. 82, p. 1394–1406 Zenke F., Hennequin G. and Gerstner W. (2013). Synaptic Plasticity, in Neural Networks Needs Homeostasis with a Fast Rate Detector, Plos Computational Biology, vol. 9, num. 11. Pozzorini C. A., Naud R., Mensi S. and Gerstner W. (2013). Temporal whitening by power-law adaptation in neocortical neurons, Nature Neuroscience, vol. 16, num. 7, p. 42-U216. Rüter J., Sprekeler H., Gerstner W. and Herzog M. H. (2013). The Silent Period of Evidence Integration in Fast Decision Making, PLoS ONE, vol. , num. 1, p. e46525.

EPFL School of Life Sciences - 2014 Annual Report

Gräff Lab h nnes

Tenure-track Assistant Professor

http:// rae flab.epfl.ch

Introduction

Our lab is interested in three main questions. How and where are longterm memories stored in the brain? Why are memories lost during neurodegeneration such as in Alzheimer’s Disease? How can traumatic memories from the past be overcome? Intrigued by how genes can influence behavior – and vice versa – Johannes Gräff conducted his PhD in the lab of Isabelle Mansuy at the ETH Zürich to specialize in neuroepigenetic processes that regulate learning and memory. Then as a postdoc at MIT with Li-Huei Tsai, he showed that epigenetic mechanisms are causally involved in neurodegeneration-associated memory loss, as well as with updating traumatic memories from the distant past. Since 2013, Dr. Gräff has been a tenure-track assistant professor at the Brain Mind Institute of the Faculty of Life Sciences, and the Nestle Chair for Neurosciences at EPFL.

To answer these questions, our lab focuses on the emerging field of neuroepigenetics. Epi-genetic mechanisms, i.e., modifications to the chromatin that regulate gene expression without changing the DNA sequence, have not only been shown to react to fluctuating environmental contingencies, but also to encode the fate of neurons and other cell types during development. With this Janus-faced property of being at once dynamic and stable, we hypothesize that epigenetic mechanisms might underlie the processes that converge newly learned information into a persisting memory. In particular, we focus on the following research topics: We speculate that epigenetic modifications might provide molecular memory marks on the chromatin to facilitate both the processing and storage of memories. We are deciphering how this molecular mnemonic can best be installed and subsequently read. We could show that malfunctioning epigenetic mechanisms contribute to the neurodegeneration-associated cognitive decline. Using a combination of genetic and environmental tools in mice, we are now addressing what triggers such malfunctioning, and how can we counteract it? Just as epigenetic mechanisms contribute to cognitive decline, they also contribute to engrave memories from the past. Using an animal model of PTSD in combination with cognitive behavioral therapy-like approaches, pharmacological interventions and molecular biology, we are aiming at elucidating the molecular basis for resilient traumatic memories and new approaches to overcome them.

Keywords

Neuroepigenetics, long-term memories, neurodegeneration, Alzheimer’s disease, traumatic memories, memory loss, memory trace.

Results Obtained in 2014

The lab opened in the fall of 2013 and we have since installed all necessary equipment and techniques so that we hope that the years to come will yield valuable results. In our current project, we propose to identify the neuronal subpopulations and the molecular mechanisms underlying remote fear memory extinction. To this end, we will use an innovative combination of transgenic mouse models with direct in situ manipulations of neuronal subpopulations and cell type-specific transcriptomic and epigenetic analyses. Specifically, we will address the following groundbreaking questions: What are the neuronal subpopulations that are causally implicated in the successful extinction of remote fear memories? The answer to this question will allow to determine whether the original traumatic memory trace has been permanently modified, or whether a new memory trace of safety has been superimposed over the original one – an important unanswered question in the field of memory research. What are the epigenetic mechanisms that underlie successful memory extinction? Answering this question reaches beyond the state-of-the-art in the field of neuroepigenetics, as it pledges to analyze memory-related epigenetic modifications in a cell population-specific manner, a hitherto unachievable level of specificity. Is there a common molecular denominator that defines successfully extinguished memories By defining a molecular signature of the neuronal subpopulations that subserve successful memory extinction, this approach will provide an easy-to-use and reliable tool for the future efficacy comparison of intervention strategies against traumatic memories, which is a significant improvement over currently employed methods with that purpose. This proposed tool will further help to better understand remote memory extinction, which is not only worth achieving in the context of traumatic memories, but also for other dysfunctions such as addictive behaviors, where associative memories form a physiologically harmful fundament.

EPFL School of Life Sciences - 2014 Annual Report

Team Members Postdoctoral Fellows Jose Sanchez-Mut

PhD Students Ossama Khalaf Leonhard von Meyenn

Technician Liliane Glauser

Administrative Assistant Soledad Andany

BMI - Brain Mind Institute

mmunohistochemical labeling of the mouse hippocampus showing cells that are acti ated when recalling traumatic memories (green) and those acti ated after successful memor e tinction (red).

Selected Publications » Tsai, L.-H., and J. Gr ff, 2014 On the resilience of remote traumatic memories against exposure-therapy-mediated attenuation . EMBO Reports, 15, 53- 61. » Gräff J.*, Joseph N.F.*, Horn M.E., Meng J., Samiei A., Meng J., Seo J., Rei D., Bero A.W., Phan T.X., Wagner F., Holson E., Xu J., Sun J., Neve R.L., Mach R.H., Haggarty S.J., and L.-H. Tsai, 2014 “Epigenetic priming of memory updating during reconsolidation to attenuate remote fear memories”. » Gräff J., Kahn M., Samiei A., Gao J., Ota K.T., Rei D., and L.-H. Tsai, 2013 “A Dietary Regimen of Caloric Restriction or Pharmacological Activation of SIRT1 to Delay the Onset of Neurodegeneration”. Journal of Neuroscience, 33, 51-60. » Gr ff J., and L.-H.Tsai, 2013 Histone acetylation: Molecular mnemonics on the chromatin . Nature Reviews Neuroscience, 14, 7-111. » Gr ff J., and L.-H.Tsai, 2013 The potential of HDAC inhibitors as cognitive enhancers . Annual Reviews of Pharmacology and Toxicology, 53, 311-330.

EPFL School of Life Sciences - 2014 Annual Report

Herzog Lab ch e

Associate Professor - Director of the Doctoral Program in Neuroscience (EDNE)

http://lp

Introduction

Michael Herzog studied Mathematics, Biology, and Philosophy. In 1996, he earned a PhD in biology under the supervision of Prof. Fahle (Tübingen) and Prof. Poggio (MIT). Then, he joined Prof. Koch’s lab at Caltech as a post-doctoral fellow. From 1999-2004, Dr. Herzog was a senior researcher at the University of Bremen and then he held a professorship for neurobiopsychology at the University of Osnabrück for one year. Since 2004, Dr. Herzog has been a professor of psychophysics at the Brain Mind Institute at the EPFL where he has established his laboratory.

In humans, vision is the most important sense. Surprisingly, the neural and computational mechanisms of even the simplest forms of visual processing, such as spotting a pen on a cluttered desk, are largely unknown. For this reason, robots are still “object blind”. Our research aims to understand how and why humans can cope with visual tasks so remarkably well. In addition, we investigate vision in healthy aging and have established an endophenotype of schizophrenia based on visual masking.

Keywords

Spatio-temporal vision (crowding, non-retinotopic processing, visual masking), perceptual and reinforcement learning, ageing & schizophrenia research.

.epfl.ch/

Results Obtained in 2014

Crowding & Masking. In crowding, the perception of a target strongly deteriorates when flanked by neighboring elements. Crowding is usually explained by pooling models, which are well in the spirit of the hierarchical, feedforward model of object recognition. Neurons in higher visual areas, with larger receptive fields, pool information from lower level neurons. Because of pooling, features of the target and flanking elements are jumbled and so feature identification is lost at the earliest stages of processing. A prediction of these models is that crowding increases when flankers are added. We showed that, to the contrary, adding flankers can improve performance (Manassi et al., 2013) and that neural processing occurs in later, rather than early, visual areas (Chicherov, et al., 2014). Perceptual learning & individual differences. Perceptual learning is learning to perceive. Features that we have not learned to detect, will be blind to us. For example, only wine experts can differentiate between different types of grapes, an ability that usually needs years of training. One prediction of perceptual learning is that we all should see the world differently depending on what we have learned during our life time. However, we found no correlation in the performance of basic visual stimuli. The same person can be good in Gabor detection and inferior with Vernier acuity (Cappe et al., 2014). Decision Making. It is usually assumed that stimulus evidence drives a drift process towards one of two decision variables. We found that there is a silent evidence integration stage, which was overlooked previously. In collaboration with Wulfram Gerstner, we characterized these processes mathematically (Rüter et al., 2013).

EPFL School of Life Sciences - 2014 Annual Report

Team Members Postdoctoral Fellows Céline Cappe Aaron Clarke Daniela Herzig Aire Raidvee Albulena Shaqiri

PhD Students Vitaly Chicherov Ophélie Favrod Lukasz Grzeczkowski Marc Lauffs Mauro Manassi Izabela Szumska Evelina Thunell

Master’s Student Adrien Doerig

Invited Professor Gregory Francis

Administrative Assistant Laure Dayer

Engineer Marc Repnow

BMI - Brain Mind Institute

n crowding, flan ers deteriorate performance. suall , target-flan er interactions are thought to occur earl on. sing and in erse solution techni ues, we found that crowding is best reflected b processes in higher cortical areas including the lateral occipital corte (with parietal and temporal o erlap) and a smaller area on the medial surface (precuneus). rom hichero et al., .

Selected Publications » Bakanidze G., Roinishvili M., Chkonia E., Kitzrow W., Richter S., Neumann K., Herzog M.H., Brand A., Puls I. (2013). Association of the nicotinic receptor backward masking. Front. Psychiatry, 4:133. doi: 10.3389/fpsyt.2013.00133. » Cappe, C., Clarke, A., Mohr, C., Herzog M. H. (2014). Is there a common factor for vision? Journal of Vision. 14(8): 1—11. » Chicherov, V., Plomp, G., Herzog, M.H., (2014). Neural correlates of visual crowding. NeuroImage, 93, 23–31. » Manassi M., Sayim B., Herzog M.H. (2013). When crowding of crowding leads to uncrowding. Journal of ision, 13(13):10. doi: 10.1167/13.13.10. » Rüter J., Sprekeler H., Gerstner W., Herzog M.H. (2013). The silent period of evidence integration in fast decision making. PLOS ONE, (1):e46525

7 subunit gene (CHRNA7) with schizophrenia and visual

EPFL School of Life Sciences - 2014 Annual Report

Lashuel Lab .

sh e

Associate Professor

http://la huel lab.epfl.ch

Introduction

Hilal A. Lashuel received his B.Sc. degree in chemistry from the City University of New York in 1994 and his PhD in bioorganic chemistry from Texas A&M University in 2000. In 2001, he moved to Harvard Medical School and the Brigham and Women’s Hospital as a research fellow in the Center for Neurologic Diseases where he was later promoted to an instructor in neurology. In 2005, Dr. Lashuel joined the Brain Mind Institute as a tenure track assistant professor and was promoted in 2011 to an associate professor. Currently, Dr. Lashuel is on sabbatical leave from EPFL, and serves as the executive director of the Qatar Biomedical Research Institute (QBRI) in Doha, Qatar.

Research in the Lashuel laboratory focuses on applying integrated chemical, biophysical, and molecular/cellular biology approaches to elucidate the molecular and structural basis of protein misfolding and aggregation and the mechanisms by which these processes contribute to the pathogenesis of neurodegenerative diseases including Parkinson’s disease (PD), Alzheimer’s disease (AD) and Huntington’s disease (HD). Current research efforts cover the following topics: • Elucidating the sequence, molecular and cellular determinants underlying protein aggregation, propagation and toxicity; • developing innovative chemical approaches and novel tools to monitor and control protein folding, self-assembly and post-translation in itro and in i o with spatial and temporal resolution; • developing novel cellular and animal models of neurodegenerative diseases to validate novel therapeutic targets, and assess disease modifying strategies based on modulating protein aggregation and clearance.

Keywords

Chemical biology, protein folding, protein aggregation, post-translational modifications, protein synthesis, amyloid, phosphorylation, neurodegeneration, Alzheimer’s disease, Parkinson’s disease, Huntington’s disease.

Results Obtained in 2014

Developing chemical and semisynthetic approaches to enable site-specific introduction of single and multiple post-translational modifications into -syn. -synuclein -syn) is subjected to several post-translational modifications (PTMs), including acetylation, nitration, phosphorylation and ubiquitylation. Towards understanding the mechanisms by which these modifications regulate -syn function, aggregation, cellular properties and toxicity, our group has developed a combination of total chemical and semisynthetic strategies that enable for the first time the site-specific introduction of simple (phosphorylation and acetylation) and complex (mono-, di- and tetra-ubiquitin chains) PTMs into -syn and the generation of these proteins in sufficient (mgs) quantities. In addition, our group has played important roles in identifying novel enzymes that regulate -syn phosphorylation, including c-Abl and PLK2, thus providing important tools for assessing the roles of these modifications in cellular and animal models of Parkinson’s disease (PD). In fact, we found that whereas phosphorylation at S129 by PLK2 targets syn for degradation and attenuates toxicity,Y39 phosphorylation by c-Abl decreases -syn degradation. These findings highlight the potential role of PTMs in regulating -syn clearance, and suggest that these enzymes may constitute viable therapeutic targets for the treatment of PD. Elucidating the effect of post-translational modifications and polyQ-length on the structure, aggregation, localization and toxicity of Huntingtin. Increasing evidence suggests that the expanded poly ( 37 ) within the first exon of Huntingtin (Httex1) plays a central role in the pathogenesis of Huntington’s disease (HD). PTMs within the N-terminal residues of the Htt protein have been also shown to play critical roles in modulating the structure, aggregation, subcellular localization and toxicity of N-terminal fragments and full-length Htt protein. Our laboratory has developed and optimized for the first time several efficient strategies that enable the production of all known PTM Httex1 species site-specifically (semi-synthetic), or unmodified proteins with unexpanded and expanded polyQ-lengths. We are now working on determining the structure, conformation, aggregation properties, toxicity and subcellular localization of these proteins to better understand how Httex1 contributes to the molecular pathogenesis of HD.

EPFL School of Life Sciences - 2014 Annual Report

Team Members Postdoctoral Fellows Ritwik Burai Jean-Christoph Copin Sean Deguire Bruno Fauvet Mahmood Haj-Yahya Bohumil Maco Anne-Laure Mahul-Mellier Juan Reyes John Warner

PhD Students Nadine Ait-Bouziad Mohamed Bilal Fares Sophie Vieweg

Technical Staff Anass Chiki Nathalie Jordan Céline Vocat

Administrative Assistant Dorothée Demeester

BMI - Brain Mind Institute

hemical protein s nthesis for elucidating the role of -s nuclein post-translational modifications (nitration, ubi uitination and phosphor lation) in regulating -s nuclein function (neurotransmission) and its role in ew bod formation and the pathogenesis of ar inson s disease.

Selected Publications » Ansaloni, A., Wang, ZM., Jeong, JS., Ruggeri, FS., Dietler, G., Lashuel, HA. (2014). One-pot semisynthesis of exon 1 of the Huntingtin protein: new tools for elucidating the role of posttranslational modifications in the pathogenesis of Huntington’s disease. Angew Chem Int Ed Engl. 53(7):1 2 -33. » Mahul-Mellier, AL., Fauvet, B., Gysbers, A., Dikiy, I., Oueslati, A., Georgeon, S., Lamontanara, AJ., Bisquertt, A., Eliezer, D., Masliah, E., Halliday, G., Hantschel, O., Lashuel, HA. (2013). c-Abl phosphorylates -synuclein and regulates its degradation: implication for -synuclein clearance and contribution to the pathogenesis of Parkinson’s disease. Hum Mol Genet. 23(11):2 5 -7 . » Fauvet, B., Butterfield, SM., Fuks, J., Brik, A., Lashuel HA. (2013). One-pot total chemical synthesis of human -synuclein. Chem Commun. 4 ( 1): 254-6. » Oueslati, A., Schneider, BL., Aebischer, P., Lashuel, HA. (2013). Polo-like kinase 2 regulates selective autophagic -synuclein clearance and suppresses its toxicity in i o. Proc Natl Acad Sci. 110(41):E3 45-54. » Schmid, AW., Fauvet, B., Moniatte, M., Lashuel, HA. Alpha-synuclein post-translational modifications as potential biomarkers for Parkinson disease and other synucleinopathies. Mol Cell Proteomics. 12(12):3543-5 . » Haj-Yahya, M., Fauvet, B., Herman-Bachinsky, Y., Hejjaoui, M., Bavikar, S.N., Karthikeyan, S.V., Ciechanover, A., Lashuel, H.A., and Brik, A. (2013). Synthetic polyubiquitinated alpha-Synuclein reveals important insights into the roles of the ubiquitin chain in regulating its pathophysiology. Proc Natl Acad Sci U S A 110, 17726-17731.

EPFL School of Life Sciences - 2014 Annual Report

Magistretti Lab e e

st ett

Full Professor

http://ln c.epfl.ch/

Pierre Magistretti is a professor at the Brain Mind Institute at EPFL and at the Center for Psychiatric Neuroscience of the University of Lausanne/ CHUV and an internationally recognized leader in the field of brain energy metabolism and glia biology. His group has discovered some of the mechanisms that underlie the coupling between neuronal activity and energy consumption by the brain. Professor Magistretti received the Theodore-Ott Prize (1 7), was the international Chair (20072008) at the Collège de France, Paris, was President of FENS (2002 – 2004) and IBRO Secretary General (2009-2012). Since October 2010, Dr. Magistretti is the director of NCCR SYNAPSY “The synaptic bases of mental diseases”.

Introduction

Results Obtained in 2014

The laboratory is also interested in imaging microscopic techniques that allow the visualization of dynamic cellular processes, including those involved in plasticity and neurodegeneration. We collaborate with the Advanced Photonics Laboratory at the STI Faculty, in the application of digital holographic microscopy (DHM) combined with fluorescence microscopy and other coherent imaging approaches.

We next explored the role of lactate in another form of synaptic plasticity, namely addiction. Disruption of astrocyte-derived lactate release in the basolateral amygdala of rats not only transiently impaired the acquisition of a cocaine-induced conditioned place preference, but also persistently disrupted an established conditioning. These findings reveal a novel amygdala-dependent reconsolidation process, whose disruption may offer a novel therapeutic target to reduce drug seeking.

Research in the LNDC is centered on the study of the cellular and molecular mechanisms of brain energy metabolism. The key question addressed is how the energy is delivered to neurons in register with synaptic activity. We have identified a set of mechanisms demonstrating the role of astrocytes in coupling synaptic signals mediated by glutamate to the entry of glucose into the brain parenchyma and the provision of energy substrates to restore the energy budget of neurons. We have also shown that energy can be delivered to neurons in register to neuronal activity from glycogen selectively stored in astrocytes. These results are relevant to functional brain imaging as they have provided understanding of the signals detected by these imaging techniques activation of specific neuronal pathways. Another dimension the metabolic coupling between astrocytes and neurons that our group has unveiled is related to synaptic plasticity and the processes of learning and memory. We have shown that lactate transfer from astrocytes to neurons is required for these processes. We have also demonstrated the existence of “metabolic plasticity” through which transcriptionally-regulated adaptations of certain genes of brain energy metabolism occur in relation to synaptic plasticity as observed during learning, the sleep-wake cycle and addiction.

Keywords

Neuroenergetics, neuro-glia interaction, brain metabolism, neuronal and glial plasticity, high-resolution optical imaging, digital holographic microscopy, cell dynamics, neurodegeneration, sleep, psychiatric disorders.

The main focus of our work during the last two years has been to better understand the role of signaling mediated by lactate produced by astrocytes on neuronal function. In addition to its role as an energy substrate for neurons, we have discovered that lactate plays a role in learning and memory. In collaboration with the group of Christina Alberini at NYU, we found that astrocyte-derived lactate was necessary for the establishment of long term memory as well as for the maintenance of long-term potentiation in i o in rat (Suzuki et al, 2011). By further addressing its mechanism of action on neurons, we found that lactate has a direct stimulatory effect on the expression of plasticity-related genes (e.g. Arc, Zif268, BDNF), both in primary cortical neurons and in i o (Yang et al. 2014). Biochemical and electrophysiological results showed that this effect is due to the potentiation by lactate of ionotropic NMDA receptor activity and the downstream Erk1/2 signaling cascade. These results provide insights for the understanding of the molecular mechanisms underlying the critical role of astrocyte-derived lactate in long-term memory and reveal a previously unidentified action of L-lactate as a signaling molecule for neuronal plasticity (see Figure).

Finally, we characterized the neuro-protective properties of lactate using Digital Holographic Microscopy, a new imaging technique able to detect early signs of cell death in culture. Indeed, lactate was shown to efficiently protect neurons from an excitotoxic insult through a mechanism involving ATP signaling on purinergic receptors.

EPFL School of Life Sciences - 2014 Annual Report

Team Members

Scientists Igor Allaman Pascal Jourdain Sylvain Lengacher (CTI) Jean-Marie Petit

Postdoctoral Fellows Maha Elsayed Charles Finsterwald (CTI) PhD Students Benjamin Boury-Jamot Monika Tadi Manuel Zenger

Technicians Cendrine Barrière Elena Gasparotto Evelyne Ruchti Trainee Nathalie Bigler Administrative Assistant Monica Navarro Suarez

Group Digital Holographic* Microscopy* Pierre Marquet

PhD Students* Keven Bourgeaux Kaspar Rothenfusser

Professor Emeritus* Christian Depeursinge

Technician* Sandra Borel

Scientist* Stéphane Chamot

BMI - Brain Mind Institute

Senior Scientist Gabriele Grenningloh

stroc tic gl cogen-deri ed lactate in s naptic plasticit processes. ollowing learning-dependent tas s, astroc tic gl cogen is mobili ed, leading to lactate transfer to neurons. actate potentiates receptor acti it promoting e pression of s naptic plasticit -related genes in neurons ( -noradrenaline).

Selected Publications » » » »

Cotte Y, Toy F, Jourdain P, Pavillon N, Boss D, Magistretti P, Marquet P, Depeursinge C. Marker-free phase nanoscopy. Nat. Photonics. 2013; 7(2): 113-117. Magistretti PJ. Synaptic plasticity and the Warburg effect. Cell Metab. 2014;1 (1):4-5. Marquet P, Depeursinge C, Magistretti PJ. Exploring neural cell dynamics with digital holographic microscopy. Annu Rev Biomed Eng. 2013;15:407-31. Perreten Lambert, H., Zenger, M., Azarias, G., Chatton, J.Y., Magistretti, P.J., Lengacher, S. Control of Mitochondrial pH by Uncoupling Protein 4 in Astrocytes Promotes Neuronal Survival. J Biol Chem. 2014;2 (45):3101428. » Petit JM, Gyger J, Burlet-Godinot S, Fiumelli H, Martin JL, Magistretti PJ. Genes involved in the astrocyte-neuron lactate shuttle (ANLS) are specifically regulated in cortical astrocytes following sleep deprivation in mice. Sleep. 2013 ;36(10):1445-5 . » Yang, J., Ruchti, E., Petit, J.M., Jourdain, P., Grenningloh, G., Allaman, I., Magistretti, P.J. Lactate promotes plasticity gene expression by potentiating NMDA signaling in neurons. Proc Natl Acad Sci U S A. 2014 Aug 1 ; 111(33):12228-33.

EPFL School of Life Sciences - 2014 Annual Report

Markram Lab en

Full Professor - Director of the Blue Brain Project - BBP

http://mar ram lab.epfl.ch

Introduction

Henry Markram is the Principal Investigator of the LNMC, Director of the Blue Brain Project and Co-Director of the FET flagship Human Brain Project. He began his research career in South Africa in the 1980s, moved to Israel and then to the EPFL, where he founded the BMI in 2002. He has focused on neural microcircuitry pioneering the multi-neuron patch-clamp approach. His discoveries include Spike Timing Dependent Plasticity, Redistribution of Synaptic Efficacy, and Long-Term Microcircuit Plasticity. He has also been active in autism research and co-developed the Intense World Theory of Autism.

The Laboratory of Neural Microcircuitry (LNMC) is dedicated to understanding the structure, function and plasticity of the microcircitry of the neocortex. To investigate these neocortical microcircuits, LNMC makes use of state-of-the-art technologies including: multineuron and automated patchclamp, multielectrode arrays, 2-photon and ultramicroscopy, 3D reconstruction, high throughput, single neuron gene expression profiling (mRNAseq) and multiplex RTPCR, microfluidics and supercomputers. Transcriptomics of neuron populations and single cells - The aim of this research project is to correlate the electrical and structural properties of individual neurons with the genes they express. The Channelome project aims to characterize the biophysics of these ion channels in a controlled and consistent environment with an automated patch clamp setup. Neuroanatomy - Using 3D reconstructions of neurons in slices combined with immunohistochemistry and whole mount imaging of brains, our goal is to map the complete set of cortical neuron morphologies and the relative composition of cortical neuron subtypes. Electrophysiology & Microcircuits - We use up to 12 multipatch setups to study the individual neuronal properties and quantify the principles of local connectivity in these microcircuits. Plasticity - LNMC studies short and long term plasticity, occurring under different time scales ranging from few milliseconds to hours. Neuromodulation - the LNMC has engaged in a consortium (DDPDGENES) that aims to characterize the properties of dopaminergic (DA) cells across development and aging in both mouse and human tissue. Autism - The aim of our group is to address if neural microcircuitry hyperfunctioning is at the heart of the neuropathology of autism, as predicted by the Intense World Theory.

Keywords

Results Obtained in 2014

Recent results obtained by the Laboratory of Neural Microcircuitry were multiple and diversified. Our neuroanatomy team completed the reconstruction over 1000 neuron morphologies from the somatosensory cortex and we are expanding to other areas and also acquiring human neuronal morphologies. In the Channelome project we now have more than 120 stable cell lines expressing individual ion channels, which are ready for biophysical and/ or drug screening. Channelpedia (www.channelpedia.net), has been developed to systematically store and share the data generated by the Channelome project as an online resource. In the transcriptomics project, we have introduced a high-throughput protocol that enables us to obtain ~100 single cell transcriptional (SCT) profiles in one experiment. With this protocol we are currently generating SCT profiles from dopaminergic cells of the brain stem and cortical neurons in the mouse. With this data we can unravel the neuronal diversity in these two brain regions based on the gene expression of individual cells. To correlate this with the electrophysiological properties, we are adjusting our SCT protocol to work with cells harvested with patch clamp setups, such that the gene expression profile can be obtained from single cells after electrophysiological characterization. With this data we aim to build neuron models that reproduce the measured electrophysiological properties based on their expressions of relevant channels and receptors. The microcircuitry of Layer I of the somatosensory cortex was extensively described at the level of neurons, synapses and cellular morphologies. We have also published our study on the effects of extracellular electric activity and how neuronal activity gives rise to such extracellular signals, an example of successful collaboration between theoreticians and experimentalists of leading institutions, using numerous experimentally obtained measurements and morphological reconstructions and the power of novel supercomputers.

Neurons, synaptic plasticity, neural microcircuits, neuronal coding, patch clamp, signal integration, electrophysiology, single cell gene expression, ion channels, neuron morphology, modeling, autism. 38

EPFL School of Life Sciences - 2014 Annual Report

Team Members PhD Students Ayah Khubieh Jean-Pierre Ghobril Monica Favre Technical Staff Deborah La Mendola Julie Meystre Mirjia Herzog

Trainees Dejan Jovandic Dimitri Christodoulou Karim Achouri Nittin Khanna Oh Hyeon Choung Quentin Herzig Valérie Tâche

Visiting Professor Giogio Innocenti

Administrative Assistant Christiane Debono

External Employee Michele Gigliano

BMI - Brain Mind Institute

Postdoctoral Fellows Emmanuelle Logette Jesper Ryge Kamila Markram Maurizio Pezzoli Ferdinando Michela Marani Olivier Hagens Rajnish Ranjan Rodrigo Perin Sara Gonzalez Andino Séverine Petitprez

ntra- and e tracellular bioph sics of indi idual neurons. ( op row) reconstructed and connected (red) and (green) p ramids and bas et cells (blue). ( econd row) onnection probabilit as a function of distance. (Bottom) tracellular action potentials for the three neural t pes considered.

Selected Publications » Camacho S, Michlig S, de Senarclens-Bezen on C, Meylan J, Meystre J, Pezzoli M, Markram H, le Coutre J. (2015) Anti-Obesity and Anti-Hyperglycemic Effects of Cinnamaldehyde via altered Ghrelin Secretion and Functional impact on Food Intake and Gastric Emptying. Sci Rep. 2015 Jan 21;5:7 1 . » Pezzoli M, Elhamdani A, Camacho S, Meystre J, González SM, le Coutre J, Markram H. (2014) Dampened neural activity and abolition of epileptic-like activity in cortical slices by active ingredients of spices. Sci Rep. 4:6 25. » Toledo-Rodriguez M, Markram H. (2014) Single-cell RT-PCR, a technique to decipher the electrical, anatomical, and genetic determinants of neuronal diversity. Methods Mol Biol. 11 3:143-5 . » Muralidhar S, Wang Y, Markram H. (2014) Synaptic and cellular organization of layer 1 of the developing rat somatosensory cortex. Front Neuroanat 7:52. » Perin R, Markram H. (2013) A computer-assisted multi-electrode patch-clamp system. J is Exp. ( 0):e50630. » Delattre V, La Mendola D, Meystre J, Markram H, Markram K. (2013) Nlgn4 knockout induces network hypo-excitability in juvenile mouse somatosensory cortex in itro. Sci Rep. 3:2 7. » Favre MR, Barkat TR, Lamendola D, Khazen G, Markram H, Markram K. General developmental health in the PA-rat model of autism. (2013) Front Behav Neurosci. 7: . » Reimann MW, Anastassiou CA, Perin R, Hill SL, Markram H, Koch C. (2013) A biophysically detailed model of neocortical local field potentials predicts the critical role of active membrane currents. Neuron. 7 (2):375- 0. » Loebel A, Le B J , Richardson MJ, Markram H, Herz A . (2013) Matched pre- and post-synaptic changes underlie synaptic plasticity over long time scales. J Neurosci. 33(15):6257-66.

EPFL School of Life Sciences - 2014 Annual Report

Petersen Lab ete sen

Full Professor

http://l en .epfl.ch/

Introduction

Carl Petersen studied physics as a bachelor student in Oxford (1989-1992). During his PhD supervised by Prof. Sir Michael Berridge in Cambridge (1992-1996) he investigated cellular and molecular mechanisms of calcium signalling. As a postdoc he joined the laboratory of Prof. Roger Nicoll at the University of California San Francisco (1996-1998) to investigate synaptic transmission and plasticity in the hippocampus. Moving to the Max Planck Institute for Medical Research in Heidelberg in the laboratory of Prof. Bert Sakmann (1999-2003), he began working on primary somatosensory cortex. Dr. Petersen opened his Laboratory of Sensory Processing in the Brain Mind Institute in the School of Life Sciences in the EPFL in 2003 as an Assistant Professor. In 2010 he was promoted to Associate Professor and again in 2014 to Full Professor.

Carl Petersen joined the Brain Mind Institute of the Faculty of Life Science at the Ecole Polytechnique Federale de Lausanne (EPFL) in 2003, setting up the Laboratory of Sensory Processing to investigate the functional operation of neural circuits in mice during quantified behavior. The goal is to obtain a causal and mechanistic understanding of sensory perception and associative learning at the level of individual neurons and their synaptic interactions within the complex neural circuits of the mammalian brain. Our experiments focus primarily on tactile sensory perception in the mouse whisker sensorimotor system. To understand sensory processing at the level of individual neurons and their synaptic connections, we make electrophysiological recordings combined with imaging techniques and molecular interventions. These studies are carried out both in itro and in i o. We want to know how specific neuronal networks contribute to learning and processing of sensory information ultimately leading to behavioural decisions. We are currently working on several complementary areas of research: - Measurement and perturbation of neuronal activity correlated with quantified behavior in mice, focusing on the analysis of sensory percepts informed by the C2 whisker and reported through the execution of learned motor output. - Basic operating principles and wiring diagrams of neocortical microcircuits, focusing on the mouse C2 barrel column. - Genetic analysis of the determinants of sensory perception and associative learning, through combination of viral manipulations and genetargeted mice.

Keywords

Sensory perception, motor control, sensorimotor integration, learning, neocortex, neural circuits, synaptic transmission, whole-cell membrane potential recording, optogenetics, two-photon microscopy.

Results Obtained in 2014

Research in the Laboratory of Sensory Processing during 2013-2014 contributed to three important areas of neuroscience: Neuromodulation of cortical function (Eggermann et al., 2014): Mice actively move their tactile whiskers to explore their immediate environment. During such periods of active sensing, there is a profound change in brain state. The pattern of neocortical activity changes from the slow, large-amplitude fluctuations observed during quiet wakefulness to a desynchronised state during whisking. Part of this state change is driven by the thalamus. Here, in addition, we report that acetylcholine (ACh) is released in the somatosensory neocortex during active whisker sensing and that the released acetylcholine hyperpolarises cortical membrane potential (Vm), thus contributing to blocking the slow cortical activity. Target-specific function of cortical projection neurons (Yamashita et al., 2013): Excitatory pyramidal neurons in the superficial layers of primary somatosensory can project to motor cortex or secondary somatosensory cortex. Yamashita et al. (2013) describe functional differences between these two types of projection neurons, finding that neurons projecting to motor cortex rapidly signal the onset of tactile sensory stimulation, whereas neurons projecting to secondary somatosensory cortex have slower but sustained activity during repetitive touch. Membrane potential correlates of sensory perception (Sachidhanandam et al., 2013): In this study we investigated cortical function in mice performing a simple goal-directed sensorimotor task. Mice had to lick a spout to obtain a reward in response to a detected whisker stimulus. Membrane potential recordings in primary somatosensory cortex revealed two components to the sensory response, an early initial response invariant to behavioural outcome and a later secondary depolarisation which was enhanced on hit trials.

EPFL School of Life Sciences - 2014 Annual Report

Team Members Senior Scientist Sylvain Crochet PhD Students Matthieu Auffret Pierre Le Merre Semihcan Sermet Varun Sreenivasan Angeliki Vavladeli

Master’s Students Lucie Eberhard Achille Othenin-Girard Yifei Zhang

Technicians Eloïse Charrière Katia Galan

Administrative Assistant Severine Janot

BMI - Brain Mind Institute

Postdoctoral Fellows Emmanuel Eggermann Célia Gasselin Taro Kiritani Natalya Korogod Yves Kremer Alexandros Kyriakatos Damien Lapray Johannes Mayrhofer Aurélie Pala Shankar Sachidhanandam Tanya Sippy Takayuki Yamashita

ice acti el mo e their tactile whis ers to e plore their en ironment. ggermann et al. ( ) find that acet lcholine ( h) is released in the somatosensor neocorte during acti e whis er sensing and that the released acet lcholine bloc s slow cortical membrane potential ( m) fluctuations.

Selected Publications » » » » » »

Eggermann, E., Kremer, Y., Crochet, S. and Petersen, C.C.H. (2014). Cholinergic signals in mouse barrel cortex during active whisker sensing. Cell Reports : 1654-1660. Petersen, C.C.H. (2014). Cortical control of whisker movement. Annu. Rev. Neurosci. 37: 1 3-203. Tomm, C., Avermann, M., Petersen, C.C.H., Gerstner, W. and ogels, T.P. (2014). Connection-type specific biases make random network models consistent with cortical recordings. J. Neurophysiol. 112: 1 01-1 14. Yamashita, T., Pala, A., Pedrido, L., Kremer, Y., Welker, E. and Petersen, C.C.H. (2013). Membrane potential dynamics of neocortical projection neurons driving target-specific signals. Neuron 0: 1477-14 0. Sachidhanandam, S., Sreenivasan, ., Kyriakatos, A., Kremer, Y. and Petersen, C.C.H. (2013). Membrane potential correlates of sensory perception in mouse barrel cortex. Nat. Neurosci. 16: 1671-1677. Petersen, C.C.H. and Crochet, S. (2013). Synaptic computation and sensory processing in neocortical layer 2/3. Neuron 7 : 2 -4 .

EPFL School of Life Sciences - 2014 Annual Report

Sandi Lab men

Full Professor - Director of Brain Mind Institute - BMI

http://l c.epfl.ch

Introduction

The Laboratory of Behavioral Genetics investigates the impact and mechanisms whereby stress and personality affect brain function and behavior, with a focus on the social domain and, particularly, on aggression and social hierarchies. Specifically, we investigate: Carmen Sandi was trained in Psychology and carried out her Ph.D. studies in Behavioral Neuroscience at the Cajal Institute, Madrid, in Spain. After postdoctoral appointments at the University of Bordeaux and the Open University, UK, she was recruited by UNED in Madrid, where she headed the Stress and Memory Lab. After a sabbatical year in the University of Bern, she joined the EPFL in 2003. Her goal is to understand how stress affects brain function and behavior. She has presided the European Brain and Behavior Society and is Editor-in-Chief of the journal Frontiers in Behavioral Neuroscience.

• he neurobiological mechanisms in ol ed in the formation of social hierarchies, and their modulation b stress and an iet . Our current work focuses in the mesolimbic system and the role of mitochondrial function in motivation and social competition. • he mechanisms whereb earl life stress enhances ris to deelop ps chopatholog , with a main focus on the emergence of pathological aggression. We investigate the role of glucocorticoids in determining different neurodevelopmental trajectories following exposure to early life adversity. • he mechanisms lin ing altered neuroplasticit during de elopment and pathological aggression. We focus on genes involved in the polysialylation of the neural cell adhesion molecule NCAM and investigate alterations in gene expression and brain connectivity linked to dysfunctional behaviors. Experimental approaches in the lab include a combination of behavioral, neurobiological, neuroimaging, neurochemical, pharmacological, metabolic, genetic and optogenetic methods. Although traditionally, the core of our work is carried out in rodents, we are currently translating our findings to humans using behavioral economics, experimental psychology (eye-tracking, computer-based tests) and neuroimaging approaches.

Keywords

Stress, glucocorticoids, aggression, social hierarchy, psychopathology, anxiety, personality, neural cell adhesion molecules, mitochondrial function, psychopharmacology, optogenetics, neuroeconomics.

Results Obtained in 2014

Stress is a risk factor for the development of psychopathologies characterized by cognitive dysfunction and deregulated social behaviors. We have investigated mechanisms linked to the immediate impact of chronic stress and to the programming effects of exposure to early life adversity. We have identified two cell adhesion molecules, neuroligin-2 (NLGN-2) and nectin-3, in the hippocampus as critically implicated in behavioral and functional alterations induced by exposure to chronic stress. NLGN-2 is reduced by stress throughout the hippocampus; and viral-induced gene expression and pharmacological treatments targeting NLGN-2 confirm its role in sociability and aggression. Nectin-3 is reduced in the perisynaptic CA1, but not in the CA3, compartment and was found to be implicated in the effects of stress in social exploration, social recognition and a CA1-dependent cognitive task. We further identified NMDA-induced proteolytic processing of nectin-3 by matrix metalloproteinase-9 (MMP9) involved in nectin-3 cleavage and chronic stress-induced social and cognitive alterations. Early life stress is investigated in our laboratory through a rodent model of peripubertal stress-induced psychopathology that leads to increased emotionality, decreased sociability and pathological aggression. While the orbitofrontal cortex shows hypoactivation in social confrontations, the amygdala, particularly its central nucleus, is hyperactivated in this model, consistent with evidence implicating this nucleus in the regulation of social and aggressive behaviors. We have identified alterations in both brain areas in the gene expression of molecular markers of excitatory and inhibitory neurotransmission, as well as NLGN-2. Our findings highlight peripuberty as a period in which stress can lead to long-term programming of the genes involved in excitatory and inhibitory neurotransmission in brain regions that play a key role in the regulation of social, emotional and cognitive behaviors.

EPFL School of Life Sciences - 2014 Annual Report

Team Members Postdoctoral Fellows Alexandre Bacq Samuel Bendahan Fiona Hollis Thomas Larrieu Orbicia Riccio Wicht John Thoresen Michael van der Kooij Ioannis Zalachoras

PhD Students Damien Huzard Leyla Loued-Khenissi Laura Lozano Montes Aurélie Papilloud Alina Strasser Sophie Walker

Technicians Jocelyn Grosse Marie-Isabelle Guillot de Suduiraut Olivia Zanoletti

Master’s Students Victoire Gorden Jennifer Mackay Kévin Meng

Administrative Assistant Barbara Goumaz

Trainee Biology Lab Assistants Timothée Naegeli Elodie Schranz

BMI - Brain Mind Institute

ocial e ploration in two rats unfamiliar to each other. posure to earl life stress or to chronic stress in adulthood reduces animals sociabilit , as e idenced b reduced interest in e ploring conspecifics.

Selected Publications » van der Kooij, M.A., Fantin, M., Rejmak, E., Grosse, J., Zanoletti, O., Fournier, C., Ganguly, K., Kalita, K., Kaczmarek, L. and Sandi, C. (2014) Role for MMP-9 in stress-induced downregulation of nectin-3 in hippocampal CA1 and associated behavioural alterations. Nat. Commun. 5:4 5. » Tzanoulinou, S., Riccio, O., de Boer, M. and Sandi, C. (2014) Peripubertal stress-induced behavioral changes are associated with altered expression of genes involved in excitation and inhibition in the amygdala. Transl. Psychiatry, 4, e410. » van der Kooij, M.A., Fantin, M., Kraev, I., Korshunova, I., Grosse, J., Zanoletti, O., Guirado, R., Garcia-Mompó, C., Nacher, J., Stewart, M.G., Berezin, V. and Sandi, C. (2014) Impaired hippocampal neuroligin-2 function by chronic stress or synthetic peptide treatment is linked to social deficits and increased aggression. Neuropsychopharmacology 3 (5):114 -115 . » Márquez, C., Poirier, G.L., Cordero, M.I., Larsen, M.H., Groner, A., Marquis, J., Magistretti, P.J., Trono, D. and Sandi, C. (2013) Peripuberty stress leads to abnormal aggression, altered amygdala and orbitofrontal reactivity and increased prefrontal MAOA gene expression. Transl. Psychiatry 3:e216. » Poirier, G.L., Imamura, N., Zanoletti, O. and Sandi, C. (2014) Social deficits induced by peripubertal stress in rats are reversed by resveratrol. J. Psychiatr. Res. 57:157-164. » eenit, ., Riccio, O. and Sandi, C. (2014) CRHR1 links peripuberty stress with deficits in social and stress-coping behaviors. J. Psychiatr. Res. 53:1-7. » Cordero, M.I., Ansermet, F. and Sandi, C. (2013) Long-term programming of enhanced aggression by peripuberty stress in female rats. Psychoneuroendocrinology, 3 (11):275 -276 .

EPFL School of Life Sciences - 2014 Annual Report

Schneggenburger Lab chne

enb

Full Professor

http://l

Introduction

Ralf Schneggenburger obtained a PhD in Natural Sciences at the University of Göttingen in 1993, and was a post-doctoral fellow at the University of Saarland (1994) and at the Ecole Normale Supérieure (1994 - 1996). During further postdoctoral work and as a Research Group Leader at the MaxPlanck Institute for biophysical Chemistry (Göttingen, 1 6- 2005), he developed a research program in transmitter release mechanisms and presynaptic plasticity. In 2005, he was appointed as a Professor at EPFL and has since then been leading the Laboratory for Synaptic Mechanisms at the Brain Mind Institute.

The main interest of the lab lies in understanding the cellular and molecular mechanisms of neuronal communication at synapses. We investigate basic mechanisms of transmitter release and its short- and long-term plasticity, and we study signaling mechanisms which determine synapse connectivity and synapse function in neuronal circuits. This research aims to gain insight into neuronal network function, and it might help to understand the pathophysiology of neuropsychiatric and neurodevelopmental disorders, many of which represent diseases of the synapse.

Keywords

Synaptic transmission, nerve terminal, neurotransmitter, exocytosis, shortterm plasticity, synapse development, synapse connectivity.

m.epfl.ch/

Results Obtained in 2014

In 2013 and 2014, the lab has made important contributions to the understanding of molecular mechanisms underlying presynaptic plasticity, and the specific development of synapses in the brain. Post-tetanic potentiation (PTP) is a presynaptic plasticity caused by an increased transmitter release with a duration of about one minute. We could show that PTP is mediated by an activity-dependent phosphorylation of the presynaptic protein Munc18 by protein kinase-C (Genc et al., 2014). This discovery was made possible by developing a novel virus-mediated gene replacement strategy, which allowed us to replace the endogenous Munc18 protein with a phosphorylation-deficient mutant in i o. Furthermore, we could show that de-phosphorylation of Munc18 leads to the termination of enhanced transmitter release. In the lower auditory system of the brain, large excitatory synapses like the calyx of Held form at specific points to mediate ultrafast synaptic transmission. The mechanisms guaranteeing the specific development of calyx synapses has however remained enigmatic. Using methods of cDNA-array analyses of gene expression, we first identified that BMPs were differentially expressed in the target area of calyces of Held, the medial nucleus of the trapezoid body (MNTB). Since BMPs were previously shown to play a role in neuromuscular synapse development in the fruit fly, we then used Cre-lox mediated conditional gene deletion in the auditory circuits, and found that in the absence of BMP-receptor genes, calyces of Held fail to undergo the characteristic mono-innervation of their target neurons. Instead, several smaller pre-calyceal nerve terminals innervate a given MNTB neuron (see Figure). This shows that BMP signaling is necessary for establishing correct synapse connectivity, and correct nerve terminal size in the mammalian brain. The cellular mechanisms of how BMPs act to instruct large synapse growth and the elimination of supernumerary synapses is currently under investigation.

EPFL School of Life Sciences - 2014 Annual Report

Team Members PhD Students Ozgür Genç Enida Gjoni Elin Kronander Wei Tang

Technicians Jessica Dupasquier Heather Murray

Master’s Student Aiste Baleisyte

Administrative Assistant Laure Dayer

BMI - Brain Mind Institute

Postdoctoral Fellows Norbert Babai Brice Bouhours Christopher Clark Michael Kintscher Olexiy Kochubey Evan Vickers

ltrastructural reconstruction of single cal of eld s napses in wild-t pe control mice (top green structure represents the pres naptic ner e terminal), and in conditional B -receptor a b doublemice (bottom). ote the presence of se eral s naptic terminals in the mice, indicating that B signaling is both important for s napse elimination, and s napse growth. a en, with permission, from iao et al., .

Selected Publications » Babai N., Kochubey O., Keller D., Schneggenburger R. (2014). An alien divalent ion reveals a major role for Ca2 buffering in controlling slow transmitter release. J Neurosci. 34:12622-12635. » Gen , O., Kochubey, O., Toonen, R.F., erhage, M., and Schneggenburger, R. (2014) Munc1 -1 is a dynamically regulated PKC target during short-term enhancement of transmitter release. Elife 2014 Feb 11;3: e01715. doi: 10.7554/eLife.01715. » iao L., Michalski N., Kronander E., Gjoni E., Genoud C., Knott G., Schneggenburger R. (2013) BMP-signaling specifies the development of a large and fast CNS synapse. Nat Neurosci.16: 56- 64. » Michalski N., Babai N., Renier N., Perkel D.J., Ch dotal A., Schneggenburger R. (2013) Robo3-Driven Axon Midline Crossing Conditions Functional Maturation of a Large Commissural Synapse. Neuron 7 : 55- 6 .

EPFL School of Life Sciences - 2014 Annual Report

Hill Lab e n

Adjunct Professor

http://hill lab.epfl.ch

Research Interests

Sean Hill is co-Director of the Blue Brain Project and co-Director of Neuroinformatics in the European Union funded Human Brain Project (HBP). He also serves as the Scientific Director of the International Neuroinformatics Coordinating Facility (INCF) at the Karolinska Institutet in Stockholm, Sweden. After completing his Ph.D. in computational neuroscience at the Université de Lausanne, Switzerland, Dr. Hill held postdoctoral positions at The Neurosciences Institute in La Jolla, California and the University of Wisconsin, Madison, then joined the IBM T.J. Watson Research Center and served as the Project Manager for Computational Neuroscience in the Blue Brain Project until his appointment at the EPFL.

The Hill Laboratory focuses on research in neural systems and neuroinformatics. Key research interests include the use of biologically-realistic models to study the role of emergent phenomena in information processing, as well as network connectivity and synaptic plasticity in the central nervous system, from the neocortical column to the whole brain, and across different arousal conditions including wakefulness and sleep. Other interests include computational approaches to neural tissue interfaces including simulated local field potentials (LFP), electroencephalography (EEG) and transcranial magnetic stimulation (TMS). Prof. Hill leads work on the Human Brain Project’s Neuroinformatics Platform: a collaborative platform for organizing, analysing and predicting neuroscience data including multi-scale brain atlases, machine learning, machine vision, data and text mining, cluster analysis and data-driven ontologies.

Keywords

Large-scale simulation, neuroinformatics, microcircuitry, neocortex, thalamus, connectome, sleep, wakefulness, integrated information, brain atlases, TMS, EEG.

Team Members In the hiring stage

Selected Publications » Richardet, R., Chappelier, J. C., Telefont, M., & Hill, S. (2015). Large-scale extraction of brain connectivity from the neuroscientific literature. Bioinformatics, btv025. » Reimann, M. W., Anastassiou, C. A., Perin, R., Hill, S. L., Markram, H., & Koch, C. (2013). A biophysically detailed model of neocortical local field potentials predicts the critical role of active membrane currents. Neuron. 7 (2), 375-3 0. doi: 10.1016/j.neuron.2013.05.023 » S. Druckmann, S. Hill, F. Schürmann, H. Markram, and I. Segev, A Hierarchical Structure of Cortical Interneuron Electrical Diversity Revealed by Automated Statistical Analysis. Cerebral Cortex 23 (2013) 2994-3006. » J. DeFelipe, P.L. López-Cruz, R. Benavides-Piccione, C. Bielza, P. Larrañaga, S. Anderson, A. Burkhalter, B. Cauli, A. Fairén, D. Feldmeyer, G. Fishell, D. Fitzpatrick, T.F. Freund, G. González-Burgos, S. Hestrin, S. Hill, P.R. Hof, J. Huang, E.G. Jones, Y. Kawaguchi, Z. Kisvárday, Y. Kubota, D.A. Lewis, O. Marín, H. Markram, C.J. McBain, H.S. Meyer, H. Monyer, S.B. Nelson, K. Rockland, J. Rossier, J.L.R. Rubenstein, B. Rudy, M. Scanziani, G.M. Shepherd, C.C. Sherwood, » J.F. Staiger, G. Tamás, A. Thomson, Y. Wang, R. Yuste, and G.A. Ascoli, New insights into the classification and nomenclature of cortical GABAergic interneurons. Nature Reviews Neuroscience 14 (2013) 202-216. » Hill, S. L., Wang, Y., Riachi, I., Schurmann, F., & Markram, H. (2012). Statistical connectivity provides a sufficient foundation for specific functional connectivity in neocortical neural microcircuits. Proc Natl Acad Sci U S A, 10 (42), E2 5-2 4. doi: 10.1073/pnas.120212 10

EPFL School of Life Sciences - 2014 Annual Report

Schürmann Lab e

m nn

Adjunct Professor

http:// chuermann lab.epfl.ch

Research Interests

The Schürmann Laboratory focuses on research at the interface between in silico neuroscience and computer architectures to guide novel computing substrates.

n silico neuroscience, neurosimulation, high performance computing.

Team Members In the hiring stage

Modern in silico neuroscience can leverage the computational capabilities of some of the largest computers available to science. However, it also has its own special characteristics and requirements and will remain a computational grand challenge for many years to come. Against this background, the Schürmann group focuses on the interface between in silico neuroscience and computer architectures. Key areas of research include techniques enabling faster and more detailed simulations of brain tissue, the development of novel techniques for model building and visualization, and new ideas for brain-inspired computing substrates.

Selected Publications » F.Schürmann, F.Delalondre, P.S.Kumbhar, J.Biddiscombe, M.Gila, D.Tacchella, A.Curioni, B.Metzler, P.Morjan, J.Fenkes, M.M.Franceschini, R.S.Germain, L.Schneidenbach, T.J.C.Ward, B.G.Fitch: Rebasing I/O for Scientific Computing: Leveraging Storage Class Memory in an IBM BlueGene/ Supercomputer. In J.M. Kunkel, T. Ludwig, and H.W. Meuer (Eds.): ISC 2014, LNCS 4 , pp. 331--347. Springer International Publishing Switzerland (2014). » E. Hay, F. Schürmann, H.Markram, , & I. Segev, (2013). Preserving axosomatic spiking features despite diverse dendritic morphology. J Neurophysiol, 10 (12), 2 72-2 1. doi: 10.1152/jn.0004 .2013. » S. Druckmann, S. Hill, F. Schürmann, H. Markram, and I. Segev, A Hierarchical Structure of Cortical Interneuron Electrical Diversity Revealed by Automated Statistical Analysis. Cerebral Cortex 23 (2013) 2994-3006. » Hill, S. L., Wang, Y., Riachi, I., Schürmann, F., & Markram, H. (2012). Statistical connectivity provides a sufficient foundation for specific functional connectivity in neocortical neural microcircuits. Proc Natl Acad Sci U S A, 10 (42), E2 5-2 4. doi: 10.1073/pnas.120212 10 .

BMI - Brain Mind Institute

Felix Schürmann is co-director of the Blue Brain Project and involved in several research challenges of the European Human Brain Project. He studied physics at the University of Heidelberg, Germany, supported by the German National Academic Foundation. Later, as a Fulbright Scholar, he obtained his Master’s degree (M.S.) in Physics from the State University of New York, Buffalo, USA, under the supervision of Richard Gonsalves. During these studies, he became curious about the role of different computing substrates and dedicated his master thesis to the simulation of quantum computing. He studied for his Ph.D. at the University of Heidelberg, Germany, under the supervision of Karlheinz Meier. For his thesis he co-designed an efficient implementation of a neural network in hardware.

Keywords

EPFL School of Life Sciences - 2014 Annual Report

IBI

Institute of Bioengineering The Mission of the Institute of Bioengineering (IBI) is to perform world-class quantitative, systems- and design-oriented research in and for the life sciences. By breaking down the boundaries between engineering, physics, chemistry, computer science and the life sciences, IBI labs strive to better understand basic biological principles and transform this knowledge into innovative technology platforms and clinical applications.

The IBI’s research agenda has evolved into six main themes: biomechanics and neuroengineering, bio-optics and bio-imaging, nano- and micro-bioengineering, molecular, cell and tissue engineering, systems and computational biology, systems physiology and immunoengineering.

Mattias Lutolf - Director

2014 has witnessed a change in leadership at the IBI’s helm, with Melody Swartz passing the Director’s baton to Matthias Lutolf on April 1st. Other notable events in 2014 include: Olaia Naveira’s arrival as new (junior) member of the Institute (appointment shared with the Lausanne University Hospital CHUV) and Theo Lasser’s courtesy appointment in IBI, alongside his principal affiliation to the Institute of Microengineering; tenures obtained by Matteo Dal Peraro, Bart Deplancke and Matthias Lutolf (all three promoted to Associate Professor); the annual Bioengineering Day held for the first time at the new on-campus SwissTech Convention Center; the launch of an annual IBI-sponsored ‘Future Leader in Bioengineering Award’, the first recipient of which is Rudolf Griss, postdoc in Kai Johnsson’s lab; a faculty retreat held at nearby beautiful “Les Bois Chamblards” estate as well as the second meeting of the IBI’s Scientific Advisory Board. In addition, several IBI faculty were honored in 2014; they are highlighted in the introduction of this Annual Report (p. 5). http://b en nee n .epfl.ch

IBI - Institute of Bioengineering

The IBI sits at the interface of the life sciences and of engineering, being situated in both the School of Life Sciences and the School of Engineering. This dual affiliation allows great diversity in hiring faculty from different backgrounds and with different research perspectives. It also provides a rich educational environment, both at the Bachelor/Master’s and at the Doctoral levels. This partnership is especially demonstrated by IBI’s joint Master’s program in Bioengineering which is shared by the two Schools. In 2013, this joint program awarded 47 MSc diplomas to graduates, up from 35 in 2013. IBI-affiliated labs also awarded 35 doctoral diplomas in 2014 as opposed to 32 in 2013.

EPFL School of Life Sciences - 2014 Annual Report

Auwerx Lab Johan Auwerx

Full Professor - NestlĂŠ Chair in Energy Metabolism

http://auwer

Introduction

Johan Auwerx received an M.D. and Ph.D. from the Katholieke Universiteit Leuven, Belgium. He performed post-doctoral training in Medical Genetics at the University of Washington, Seattle. He is certified in Endocrinology, Metabolism and Nutrition. He was elected as a member of EMBO in 2003 and received a dozen of international scientific prizes, including the Danone Nutrition Award, the Minkowski Prize, and the Morgagni Gold Medal. Prof. Auwerx is an editorial board member of Cell Metabolism, Molecular Systems Biology, EMBO Journal, Cell, and Science and he co-founded a handful of biotech companies (most recently Mitokyne) and serves on several scientific advisory boards.

The laboratory of Dr. Auwerx has been using molecular physiology and systems genetics to understand mitochondrial function and metabolism in health, aging and disease. Mitochondria are derived from endo-symbiotic -proteobacteria that contain multiple copies of their own circular DNA (mtDNA), vestiges of bacterial DNA. The large majority of mitochondrial proteins, however, are encoded in the nuclear DNA (nDNA) and these proteins are after their translation in the cytoplasm, imported, processed, and assembled with the proteins encoded by mtDNA. Assembly of the complexes of the mitochondrial electron transport chain, responsible for energy harvesting, hence relies on a perfect synchrony between proteins encoded by nDNA and mtDNA through the convergence and coordinated expression of these two genomes. Much of the initial work of his team focused on understanding how mitochondrial function and metabolism is controlled by altering the activity of transcription factors and their associated cofactors. His work was instrumental for the development of agonists of nuclear receptors - a particular class of transcription factors - into drugs, which now are used to treat high blood lipid levels, fatty liver, and diabetes. Dr. Auwerx was also amongst the first to recognize that transcriptional cofactors, which fine-tune the activity of transcription factors, act as energy sensors/effectors that influence mitochondrial function. His research validated these cofactors as targets to treat metabolic diseases, and spurred the clinical use of natural compounds, such as resveratrol and NAD+ precursors, as modulators of these cofactor pathways.

Results Obtained in 2014

Whereas the initial work of Johan Auwerx (see lab introduction) was instrumental to elucidate how transcription factors and their associated transcriptional cofactors are involved in the antegrade control of mitochondrial activity, more recently, he elucidated a novel retrograde signaling pathway that emanates from the mitochondria to influence nuclear function, i.e. mitochondria nucleus. Interference with mitochondrial translation either through genetic (mutations and variation in expression of the mitochondrial ribosomal proteins) or pharmacological strategies (doxycycline and chloramphenicol) reduces the production of mtDNA encoded ETC components, resulting into a mitonuclear imbalance between mtDNA and nDNA encoded ETC proteins, which subsequently activates the mitochondrial unfolded protein response (UPRmt). UPRmt is an adaptive response that restores mitochondrial function, which in the worm is linked with the extension of lifespan. He furthermore discovered that exposing mice, worms and cells to compounds, which activate mitochondrial biogenesis, such as well-known longevity compounds rapamycin and resveratrol, as well as compounds that boost NAD levels, also induce UPRmt. This work indicates that UPRmt is triggered both during mitochondrial biogenesis and mitonuclear proteostatic imbalance, and in each case has beneficial effects on mitochondrial function and organismal health.

The work of the laboratory has been trend-setting in the field and is highly cited by his peers (h-factor > 105).

Keywords

Aging, atherosclerosis, C. elegans, diabetes, genetics, mitochondria, metabolism, mouse genetic reference populations, obesity, phenogenomics, transcription, transcription factors.

lab.epfl.ch/

EPFL School of Life Sciences - 2014 Annual Report

Team Members Visiting Professor Eduardo Rochete-Ropelle

Postdoctoral Fellows Taoufiq Harach Seiko Ishida Pooja Jha Jo Young Suk Giuseppe Lo Sasso Olli Matilainen Keir Menzies Pedro Moral Quiros Laurent Mouchiroud Eija Pirinen Dongryeol Ryu Vincenzo Sorrentino

PhD Students Pénélope Andreux Virginija Jovaisaite Elena Katsyuba Adrienne Mottis Evan Williams Hongbo Zhang

Technicians Sabrina Bichet Norman Moullan

Administrative Assistant Valérie Stengel

Internships Student Tiffany Amariuta Bachelor project Student Tarik Ouhmad

IBI - Institute of Bioengineering

C.elegans expressing a GFP reporter gene under the control of the hsp-60 promotor lights up in the presence of mitochondrial stress.

Selected Publications » Houtkooper, R.H., Mouchiroud, L., Ryu, D., Moullan, N., Katsyuba, E., Knott, G., Williams, R.W., and Auwerx, J. (2013). Mitonuclear protein inbalance as a conserved longevity mechanism. Nature 4 7:451-457. » Mouchiroud, L., Houtkooper, R.H., Moullan, N., Katsyuba, E., Ryu, D., Canto, C., Mottis, A., Jo, Y.-S., iswanathan, M., Schoonjans, K., Guarente, L., and Auwerx, J. (2013). The NAD /sirtuin pathway modulates longevity through activation of mitochondrial UPR and FO O signaling. Cell 154:430-441. » Pirinen, E., Canto, C., Jo, Y.-S., Morato, L., Zhang, H., Menzies, K., Williams, E., Mouchiroud, L., Moullan, N., Hagberg, C., Li, W., Timmers, S., Imhof, R., erbeek, J., Pujol, A., van Loon, B., iscomi, C., Zeviani, M., Schrauwen, P., Sauve, A., Schoonjans, K., and Auwerx, J. (2014). Pharmacological Inhibition of Poly(ADP-Ribose) Polymerases Improves Fitness and Mitochondrial Function in Skeletal Muscle. Cell Metabolism 1 :1034-1041. » Williams, E.G., Mouchiroud, L., Frochaux, M., Pandey, A., Andreux, P.A., Deplancke, B., and Auwerx, J. (2014). An evolutionary conserved role for the aryl hydrocarbon receptor in the regulation of movement. Plos Genetics 10:e1004673. » Ryu, D., Jo, Y.-S., Lo Sasso, G., Stein, S., Zhang, H., Perino, A., Lee, J.U., Zeviani, M., Romand, R., Hottiger, M.O., Schoonjans, K., and Auwerx, J. (2014). A Sirt7-dependent acetylation switch of GABPbeta1 controls mitochondrial function. Cell Metabolism 20:856-869. » Wu, Y., Williams, E.G., Dubuis, S., Mottis, A., Jovaisaite, ., Houten, S.M., Argmann, C.A., Faridi, P., Wolski, W., Kutalik, Z., Zamboni, N., Auwerx, J. , and Aebersold, R. ( co-last and co-corresponding authors) (2014). Multilayered genetic and omics dissection of mitochondrial activity in a mouse genetic reference population. Cell 158:1415-1430.

EPFL School of Life Sciences - 2014 Annual Report

Baekkeskov Lab Steinunn Baekkeskov

Visiting Professor

Introduction

Steinunn Baekkeskov received her PhD in Biochemistry from the University of Copenhagen in 1984 identifying and characterizing target antigens of the autoimmune response involved in pancreatic beta cell destruction and development of type 1 diabetes. She held positions of Research Scientist and Senior Research Scientist and group leader at the Hagedorn Research Laboratory in Copenhagen until 1989 when she was appointed Assistant Professor in the Departments of Medicine and Microbiology/Immunology, University of California San Francisco (UCSF). She was a full professor at UCSF 1998-2014. In 2012 she became a part time Visiting Professor in the School of Life Sciences at EPFL.

Type 1 Diabetes (T1D) in humans develops following an autoimmune destruction of pancreatic beta-cells in the islets of Langerhans. In earlier work, we and others identified three intracellular human beta cell membrane proteins which are targeted by the autoimmunity associated with beta cell destruction. These include GAD65, the smaller isoform of the GABA synthesizing enzyme glutamic acid decarboxylase (GAD), a tyrosine phosphatase, IA-2, and a zinc transporter, ZnT8. Autoantibodies to those proteins can be detected in the blood several years before clinical onset of T1D and identify individuals at risk. However, although T1D can be prevented in animal models, no safe methods are currently available in humans. GAD65, IA-2, and ZnT are also expressed in CNS neurons, which are protected behind the blood brain barrier. However, GAD65 is also a target antigen in a rare neurological disorder, stiff-man syndrome that affects GABAergic neurons. In contrast, the highly homologous isoform, GAD67, is not a target antigen in either disease. The two isoforms differ mainly in the N-terminal region that controls membrane targeting and trafficking of the proteins. Pancreatic beta cells have a well developed, extensive, and highly active ER, reflecting their role in synthesizing and secreting large amounts of insulin. Beta cells are unusually sensitive to ER stress. There is evidence to suggest that induction of ER-stress and apoptosis by cytokines secreted by inflammatory cells plays a role in the loss of beta cells that precedes clinical onset of Type 1 diabetes. Current research in the Baekkeskov Lab, aims at elucidating the mechanisms of early events leading to autoimmunity towards the beta cell. We focus on i) understanding why the GAD65 isoform of GAD is so susceptible to become a target of autoimmunity in contrast to GAD67; and ii) testing the hypothesis that ER stress is an important factor in inducing autoimmunity to GAD65, IA2, and ZnT8.

Keywords

Type 1 diabetes, autoimmunity, beta cell autoantigens, intracellular membrane proteins, protein targeting, protein trafficking, endoplasmic reticulum stress, GAD65, GAD67, GABA.

Results Obtained in 2014

unction and Membrane Traffic ing of D and D . GABA is a paracrine and autocrine signaling molecule regulating the function of islet endocrine cells. The localization of GAD65 and GAD67 to vesicular membranes is important for rapid delivery and accumulation of GABA for regulated secretion. While the membrane anchoring and trafficking of GAD65 is mediated by intrinsic hydrophobic modifications, GAD67 remains hydrophilic, and yet is targeted to vesicular membrane pathways and synaptic clusters in neurons by both a GAD65-dependent and a distinct GAD65-independent mechanism. We investigated the trafficking of the GAD isoforms in beta cells. While GAD65 membrane trafficking is similar to neurons, beta cells lack the neuronal mechanism for GAD65-independent membrane anchoring of GAD67. Thus, only GAD65:GAD65 homodimers and GAD67:GAD65 heterodimers, but not GAD67:GAD67 homodimers gain access to vesicular compartments in beta cells to facilitate rapid accumulation of newly synthesized GABA for regulated secretion and fine tuning of GABA-signaling in islets of Langerhans. Effect of E stress on membrane traffic ing of D . ER stress is implicated in loss of beta cells during the pathogenesis of T1D. ER-stress may facilitate the formation and release of immunogenic forms of intracellular proteins into an inflammatory environment contributing to antigen presentation and induction of autoimmunity. Cytokine induced ER stress in primary beta cells results in accumulation of GAD65 in trans-Golgi membranes and a diversion from its postGolgi trafficking route. We are testing the hypothesis that such accumulated forms are highly immunogenic. ippocampal neurons and islet endocrine cells can form synapses. Islet endocrine cells have developed a system of expression of neurotransmitters and their receptors for paracrine and autocrine regulation of hormone secretion and maintenance of glucose homeostasis. An additional level of regulation may be provided by both sympathetic and parasympathetic fibers innervating the pancreas. A complete picture integrating neuronal and endocrine regulation is lacking. We developed a protocol for co-culturing primary rat pancreatic islet cells and hippocampal neurons, which revealed that several types of neurons make synaptic contacts with the subtypes of endocrine cells (Figure). The co-cultures of primary neurons and islet cells provide a system to investigate mechanisms of signaling between these cells.

EPFL School of Life Sciences - 2014 Annual Report

Team Members Postdoctoral Fellow Edward Phelps

PhD Student Chiara Cianciaruso

Administrative Assistants Doris Sapin Miriella Pasquier

IBI - Institute of Bioengineering

Lab Manager Miriella Pasquier

Co-culture of hippocampal neurons and pancreatic islet cells forming synaptic contacts. Cells are immunostained for insulin (magenta, islet beta cells), glucagon (dark-blue, islet alpha cells), MAP2 (light-blue, neuronal dendrites), and the GABA synthesizing enzyme GAD65 (green), expressed in beta cells and in the soma and presynaptic clusters of GABA-ergic neurons.

Selected Publications Âť Kanaani, J., Ciaciaruso, C., Phelps, E. A., Pasquier, M., Brioudes, E., Billestrup, N. and Baekkeskov S. (2015). Compartmentalization of GABA synthesis by GAD67 differs between pancreatic beta cells and neurons. PLoS One 10(2) : e0117130.

EPFL School of Life Sciences - 2014 Annual Report

Barrandon Lab Yann Barrandon

Full Professor Joint Chair EPFL – Unil – CHUV, Head of Laboratory of Stem Cell Dynamics EPFL & Experimental Surgery, CHUV

http://l c .epfl.ch/

Introduction

Yann Barrandon, MD PhD graduated in Dermatology in Paris and obtained his PhD on the long-term cultivation of human hematopoietic stem cells. Prof. Barrandon was a post-doctoral fellow at Stanford Medical School (1982-1983) and Harvard Medical School (1983-1990) where he worked with Pr. Howard Green, a pioneer in Regenerative Medicine of Skin using cultured human epidermal stem cells. He moved to Paris in 1990 as Director of Research at the INSERM and Head of Laboratory at the Ecole Normale Supérieure (Paris-Ulm). Dr. Barrandon is a member of the EMBO, of the EPFL Research Commission, Initiative Director of the Joint Doctoral Program between EPFL and Singapore-A Star, and a visiting professor, Department of Ophthalmology, Kyoto Prefectural University of Medicine.

Adult (tissue) stem cells are instrumental for renewal, repair and regeneration and hold great potential for disease modeling, drug discovery and regenerative medicine. Skin is privileged because several skin stem cells (epidermal, mesenchymal and melanocyte) can be expanded in culture, manipulated and transplanted. Epidermis, the skin’s outer layer is a stratified epithelium that is constantly renewing. Its basal layer contains adult stem cells and progenitor/transient amplifying cells whose multiplication balances the loss of squames that are continuously sloughed off in the environment. The Barrandon laboratory has three main objectives: 1- to understand the relationship between stem/progenitors cells of stratified epithelia, 2- to understand the impact of the environment on stem cell behavior and 3- to comprehend stem cell engraftment. All projects ultimately aim at improving cell and gene therapy. A major project is to understand how stratified epithelia respond to environmental cues since chronic exposure to environmental hazards can result in metaplasia, a situation in which an epithelium adopts another phenotype and that is linked to carcinogenesis. The laboratory has demonstrated that clonogenic epithelial cells of the ocular surface, the oral cavity, the oesophagus, the vagina and the bladder can increase their lineage capabilities and behave like bona fide multipotent hair follicle stem cells. Most importantly, this capacity is maintained in serial transplantations and is intrinsic because cells that have never been exposed to cell culture behave in a similar fashion. These observations together with the finding that clonogenic thymic epithelial cells can also function as bona fide multipotent hair follicle stem cells (Bonfanti et al., Nature 2010) indicates that the microenvironment can impact the potency of epithelial stem/progenitor cells.

Results Obtained in 2014

Safety is critical when it comes to ex vivo autologous gene therapy but current stem cell technology makes it difficult to thoroughly investigate the properties of human recombinant stem cells before cells are transplanted. Because of the remarkable property of epidermal stem cells to be massively expanded ex vivo, it is theoretically possible to completely reconstruct the epidermis of an adult human from the progeny of a single autologous epidermal stem cell. We have explored the feasibility of a single cell approach for ex vivo gene therapy of skin using recessive dystrophic epidermolysis bullosa (RDEB), a horrendous blistering genodermatosis, as a model system. This approach allows for a full characterization of the recombinant clone(s) both for stem cell capabilities (long term production of the medicinal protein, long term regeneration of a cured human epidermis onto immunodeficient mice) and for safety criteria (determination of proviral insertions, absence of tumorogenicity and dissemination). The combination of a clonal approach with high throughput technologies should permit to thoroughly evaluate the properties of the genetically corrected stem cells before the patient is transplanted and bringing safety to a level that otherwise is difficult to achieve (Droz-Georget Lathion et al., EMBO Mol Med 2015).

Keywords

Stem cell, microenvironment, epithelia, skin, cornea, thymus, cell and gene therapy.

EPFL School of Life Sciences - 2014 Annual Report

Team Members Senior Scientists Stéphanie Claudinot Ariane Rochat Postdoctoral Fellows Michiko Kanemitsu Melissa Maggioni

PhD Students Tiphaine Arlabosse Marine de Lageneste Diane Hemon Pierluigi Manti Georges Muller Marie-Noëlle Perseguers Matteo Pluchinotta Lilia Salimova Andrea Zaffalon

Master’s Students Amélie Borghini Bérénice Charrez Sara de Meyer

Research Assistants Marco Burki Olga de Souza Silva Dorinne Savoy

Administrative Assistant Guex Nathalie

IBI - Institute of Bioengineering

Confocal image of a 12 days old colony of clonogenic epithelial cells isolated from a human thymus and immunostained against KERATIN 5 (red) and KERATIN 8 (green). K8/K5 double positive cells appear yellow.

Selected Publications » Nanba, D., Toki, F., Tate, S., Imai, M., Matsushita, N., Shiraishi, K., Sayama, K., Toki H., Higashiyama, S., Barrandon, Y. (2015). Cell motion predicts human epidermal stemness. J Cell Biol. In press » Droz-Georget Lathion, S., Rochat, A., Knott, G., Recchia, A., Martinet, D., Benmohammed S., Grasset, N, Zaffalon, A., Besuchet Schmutz N., Savioz-Dayer, E., Beckmann, J.S., Rougemont J., Mavilio, F., Barrandon, Y. (2015). A Single Epidermal Stem Cell Strategy for Safe Ex vivo Gene Therapy. EMBO Mol. Med. 7:3 0- 3. » Nakamura T, Hamuro J, Takaishi M, Simmons S, Maruyama K, Zaffalon A, Bentley AJ, Kawasaki S, Tagata-Takaoka M, Fullwood NJ, Itami S, Sano S, Ishii M, Barrandon Y, Kinoshita S (2014). LRIG1 inhibits STAT3-dependent inflammation to maintain cornea homeostasis. J Clin Invest 124:3 5-3 7. » Hirata-Tominaga, K., Nakamura, T., Okumura, N., Kawasaki, S., Kay, E.P., Barrandon, Y., Koizumi, N, Kinoshita, S. (2013). Corneal endothelial cell fate is maintained by LGR5 via the regulation of hedgehog and Wnt pathway. Stem Cells. 31:1396-1407. » Nanba, D., Toki, F., Matsushita, N., Matsushita, S., Higashiyama, S. Barrandon, Y. (2013). Actin filament dynamics impacts keratinocyte stem cell maintenance EMBO Mol. Med. 5:640-653. » Barrandon, Y., Grasset, N., Zaffalon, A., Gorostidi, F., Claudinot, S., Droz-Georget, S.L., Nanba, D., Rochat, A. (2012). Capturing epidermal stemness for regenerative medicine. Semin. Cell Dev. Biol. 23: 37- 44. » Shakhova, O., Zingg, D., Schaefer, S.M., Hari, L., Civenni, G., Blunschi, J., Claudinot, S., Okoniewski, M., Beermann, F., Mihic-Probst, D., Moch, H., Wegner, M., Dummer, R., Barrandon, Y., Cinelli, P., Sommer, L. (2012). Sox10 promotes the formation and maintenance of giant congenital naevi and melanoma. Nat Cell Biol. 14:882-90. » Bonfanti, P., Claudinot, S., Amici, A.W., Farley, A., Blackburn, C.C, Barrandon, Y. (2010). Microenvironmental reprogramming of thymic epithelial cells to skin multipotent stem cells. Nature 466: 978-82. (Press release) Commentary in Bilousova and Roop Cell Stem Cell (2010) 7:41 -420.

EPFL School of Life Sciences - 2014 Annual Report

Dal Peraro Lab Matteo Dal Peraro

Associate Professor

lbm.epfl.ch

Introduction

Matteo Dal Peraro graduated in Physics at the University of Padova in 2000 and obtained his Ph.D. in Biophysics at the International School for Advanced Studies (SISSA, Trieste) in 2004. After a postdoctoral training at the University of Pennsylvania (Philadelphia, USA), he was nominated Tenure Track Assistant Professor at the School of Life Sciences in 2007, and became Associate in 2014. Prof. Dal Peraro’s research at the Laboratory for Biomolecular Modeling, within the Institute of Bioengineering (IBI), focuses on the multiscale modeling of large macromolecular systems.

The Laboratory for Molecular Modeling (LBM) carries out research to understand the physical and chemical properties of complex biological systems, in particular their function emerging from their atomistic structure. To this end, the laboratory uses and develops a broad array of methods for multiscale molecular simulation and modeling, which have nowadays the ability to mimic the conditions found in the cellular environment. By blending theory, computation supported by high-performance computing (HPC) resources and integration with actual experimental data allows for the close description of the composition and evolution of biological systems. The current research program at the LBM is mainly focused in three major axes: • to understand the architecture of large molecular assemblies by integrating a variety of experimental inputs at different resolution; • to accurately study large portions of biological membrane compartments and their interaction with surrounding proteins; and • to capture the effects of cellular crowding on the dynamic determinants of proteins and their molecular interactions.

Keywords

Integrative modeling, molecular simulation, structure-based drug discovery, structural biology, computational biology, biophysics, high-performance computing.

Results Obtained in 2014

Macromolecular assembly - Proteins often assemble in large macromolecular complexes to achieve a specific biological task. Unfortunately, owing to their size and complexity, these structures are difficult to determine at atomistic resolution, preventing thus a complete understanding of their mechanism of action. To approach this problem, the laboratory developed novel ways to predict the structure and function of large biological assemblies. To this end, we established a new approach (that we called POWER: parallel optimization workbench to enhance resolution) that uses heuristic optimization strategies guided by experimental-based restraints to characterize quaternary protein structure accounting for native dynamics. Using this integrative strategy, we were able for instance to reveal the assembly mechanism of aerolysin, a bacterial pore-forming toxin that produces heptameric pores at the target membrane by a concerted swirling motion of its components. Moreover, we determined the basal body structure of Yersinia type III secretion system, and discovered how its flexibility is critical for adapting to thickness variations at the periplasmic space. The native dynamics of individual components emerges, in these studies, as the key determinant to define the architecture, and understand the function of large multi-protein complexes. Therefore, the ability of our approach to integrate protein dynamics with sparse experimental data is a promising step towards the molecular characterization of large pathogenic systems. Towards realistic molecular modeling of subcellular organization - To enhance the general capabilities and accuracy of molecular simulations, the laboratory also worked on a new generation of methods, where an electrostatic-consistent coarse-grained representation of proteins was developed to extend the time- and size-scale accessible to current molecular simulations. Also, novel molecular models of key components of the biological membrane were developed, such for instance as cardiolipins that are fundamental anionic lipids constituting the inner membrane of mitochondria and Gramnegative bacteria. Along with these models, we developed also a framework, currently implemented in the web-server LipidBuilder (at http://lipidbuilder. epfl.ch) that is able to construct bilayers of any given lipid composition in order to mimic as precisely as possible the biological membrane.

EPFL School of Life Sciences - 2014 Annual Report

Team Members Postdoctoral Fellows Luciano Abriata Anna Lindeløv Vestergaard Maria Josefina Marcaida-Lopez

PhD Students Deniz Aydin Martina Audagnotto Christophe Bovigny Alexandra Kalantzi

PhD Students Michele Larocca Thomas Lemmin Enrico Spiga Hassan Pezeshgi Modarres Giorgio Tamo

Administrative Assistant Marie-France Radigois

IBI - Institute of Bioengineering

Near-atomistic models of the prepore and membrane-inserted pore conformations derived from a combination of crystallography, cryo-EM, single-particle analysis, molecular simulation and modeling reveal a swirling mechanism of membrane insertion and pore formation by aerolysin.

Selected Publications » Lemmin, T., Dimitrov, M., Fraering, P.C., Dal Peraro, M. (2014). Perturbations of the straight transmembrane -helical structure of the amyloid precursor protein affect its processing by -secretase. J. Biol. Chem. 289(10): 6763-6774. » Spiga, E., Abriata, L.A., Piazza, F., Dal Peraro, M. (2014). Dissecting the Effects of Concentrated Carbohydrate Solutions on Protein Diffusion, Hydration, and Internal Dynamics. J. Phys. Chem. B 118(20): 5310-5321. » estergaard, A.L., Coleman, J.A., Lemmin, T., Mikkelsen, S.A., Molday, L.L., ilsen, B., Molday, R.S., Dal Peraro, M., Andersen, J.P. (2014). Critical roles of isoleucine-364 and adjacent residues in a hydrophobic gate control of phospholipid transport by the mammalian P4-ATPase ATP8A2. Proc. Natl. Acad. Sci. USA 111(14): E1334-E1343. » Degiacomi M., Dal Peraro M. (2013). Macromolecular Symmetric Assembly Prediction Using Swarm Intelligence Dynamic Modeling. Structure 21(7): 1097-1104. » Degiacomi, M., Iacovache, I. Pernot, L., Chami, M., Kudryashev, M., Stahlberg, H., an Der Goot, F.G., Dal Peraro, M. (2013). Molecular assembly of the aerolysin pore reveals a swirling membrane-insertion mechanism. Nat. Chem. Biol. 9(10): 623–629. » Kudryashev, M., Stenta M., Schmelz, S., Amstutz, M., Wiesand, U., Casta o-D ez, D., Degiacomi, M.T., Münnich, S., Bleck, S.E.K., Kowal, J., Diepold, A., Heinz, D.W., Dal Peraro, M., Cornelis, G.R., Stahlberg, H. (2013). In situ structural analysis of the Yersinia enterocolitica injectisome. eLife 2: e00792. » E Spiga, D Alemani, MT Degiacomi, M Cascella, MD Peraro, M. (2013). Electrostatic-consistent coarse-grained potentials for molecular simulations of proteins. J. Chem. Theory Comput. 9(8): 3515-3526. » Abriata, L.A., Spiga, E., Dal Peraro, M. (2013). All-atom simulations of crowding effects on ubiquitin dynamics. Phys. Biol. 10(4): 045006. » Lemmin, T., Soto, C.S., Clinthorne, G., DeGrado, W.L., Dal Peraro, M. (2013). Assembly of the transmembrane domain of E. coli PhoQ histidine kinase: implications for signal transduction from molecular simulations. PLoS Comp. Biol. 9(1): e1002878.

EPFL School of Life Sciences - 2014 Annual Report

Deplancke Lab t

nc e

Associate Professor

http:// eplanc elab.epfl.ch/

Introduction

Bart Deplancke received his M.Sc. in bio-engineering from Ghent University (Belgium), and his Ph.D. from the University of Illinois (Urbana-Champaign, USA). After a postdoc at Harvard Medical School and then the University of Massachusetts Medical School, he moved to the EPFL at the end of 2007. His group develops and uses integrative and population genomics approaches to study the gene regulatory properties of the metazoan genome. He is currently also guest professor at Ghent University and co-founded the BioTech-IT company Genohm SA.

Gene regulatory networks play a vital role in metazoan development and function, and deregulation of these networks is often implicated in disease. The interactions between genes and their respective regulatory transcription factors (TFs) that form the basis of gene regulatory networks have however been poorly characterized. This is because the transcriptional function of most metazoan TFs, which denotes the regulatory elements they bind to, the genes they regulate, the transcriptional consequence of their DNA interactions, and the transcriptional complexes in which they function, remains unknown. Our main focus is to unravel the metazoan gene regulatory code and to examine how variations in this code affect molecular and organismal diversity. Our systems of interest are: • Drosophila melanogaster: the impact of genomic and molecular variation on gut immunity and aging (e.g. Massouras et al., Nat Methods, 2010; PLoS Genetics, 2012; Huang, Massouras et al., Genome Research, 2014) • Mouse: mesenchymal stem cell function and differentiation with a specific focus on understanding the regulatory mechanisms mediating white and brown fat cell differentiation (e.g. Raghav et al. Mol Cell, 2012; Simicevic et al., Nature Methods, 2013, Gubelmann et al., eLife, 2014). • Human: linking genomic to regulatory variation (e.g. Kilpinen et al. Science, 2013). Next to these research interests, we are also actively pursuing the development of new research tools or pipelines that enable a better characterization of gene regulatory networks (e.g. microfluidics and yeast-based screening platforms, Hens et al. Nature Methods, 2011 & Gubelmann et al., Mol Syst Biol, 2013; targeted proteomics of TFs, Simicevic et al., Nature Methods, 2013)

Keywords

Gene regulatory network, integrative genomics, transcription, quantitative genetics, mouse, Drosophila, yeast, genetic engineering, adipogenesis, genomic variation.

Results Obtained in 2014

- A comprehensive understanding of adipogenesis is of high biomedical and societal value, given the current burden of obesity and its associated range of diseases. In a study published in eLife (2014), we presented the results of a large-scale transcription factor (TF) overexpression screen in mouse preadipocytes that led to the identification of 23 novel adipogenic regulators. Going beyond the resource value of this target list, we extensively examined the adipogenic function of our top candidate ZEB1, previously known for its role in epithelial-to-mesenchymal transition and tumor metastasis. Using genome-wide, high-throughput sequencing-based approaches, in vitro and in vivo differentiation assays in both mice and humans, as well as integrative computational analyses, we demonstrate here for the first time ZEB1’s key regulatory importance for adipogenesis, constituting a major conceptual advance in our understanding of the transcriptional mechanisms controlling this important process. - We published in Genome Reserarch (2014) a consortium-driven effort to comprehensively characterize naturally occurring genetic variation in the Drosophila melanogaster Genetic Reference Panel (DGRP) consisting of 205 sequenced inbred lines. Specifically, we employed an integrated genotyping strategy to identify almost 5 million single nucleotide polymorphisms (SNPs) and 1.3 million non-SNPs at high resolution. This level of naturally occurring genetic variation is about 10-fold larger than that found in humans, thus constituting a powerful resource to molecularly dissect quantitative trait loci down to the nucleotide level.

EPFL School of Life Sciences - 2014 Annual Report

Team Members PhD Students Roel Bevers Riccardo Dainese Michael Frochaux Rachana Pradhan

Technician Julie Russeil

Administrative Assistant Marie-France Radigois

IBI - Institute of Bioengineering

Postdoctoral Fellows Alina Isakova Antonio Meireles-Filho Petra Schwalie

Graphical summary of the paper by Gubelmann et al., eLife, 2014.

Selected Publications » Gubelmann, C., Schwalie, P.C., Raghav, S.K., Roder, E., Delessa, T., Kiehlmann, E., Waszak, S.M., Corsinotti, A., Udin, G., Holcombe, W., et al. (2014). Identification of the transcription factor ZEB1 as a central component of the adipogenic gene regulatory network. Elife 3, e03346. » Huang, W., Massouras, A., Inoue, Y., Peiffer, J., R mia, M., Tarone, A.M., Turlapati, L., Zichner, T., Zhu, D., Lyman, R.F., et al. (2014). Natural variation in genome architecture among 205 Drosophila melanogaster Genetic Reference Panel lines. Genome Research 24, 11 3-120 . » Waszak, S.M., Kilpinen, H., Gschwind, A.R., Orioli, A., Raghav, S.K., Witwicki, R.M., Migliavacca, E., Yurovsky, A., Lappalainen, T., Hernandez, N., et al. (2014). Identification and removal of low-complexity sites in allelespecific analysis of ChIP-seq data. Bioinformatics 30, 165-171. » Kilpinen, H., Waszak, S.M., Gschwind, A.R., Raghav, S.K., Witwicki, R.M., Orioli, A., Migliavacca, E., Wiederkehr, M., Gutierrez-Arcelus, M., Panousis, N.I., et al. (2013). Coordinated Effects of Sequence ariation on DNA Binding, Chromatin Structure, and Transcription. Science 342, 744-747. » Gubelmann, C., Waszak, S.M., Isakova, A., Holcombe, W., Hens, K., Iagovitina, A., Feuz, J.D., Raghav, S.K., Simicevic, J., and Deplancke, B. (2013). A yeast one-hybrid and microfluidics-based pipeline to map mammalian gene regulatory networks. Molecular Systems Biology 9, 682. » Waszak, Sebastian M., and Deplancke, B. (2013). Rounding Up Natural Gene Expression ariation during Development. Developmental Cell 27, 601-603.

EPFL School of Life Sciences - 2014 Annual Report

Hubbell Lab Jeffrey A. Hubbell

Full Professor - Merck-Serono Chair in Drug Delivery

http://lmrp.epfl.ch

Introduction

We design novel materials for applications in medicine such as regenerative medicine, vaccination and tolerogenic vaccination. We focus on examples where novel materials or biomolecules are necessary to solve the problem, thus working at the interface between molecular science and life sciences. Jeffrey Hubbell was trained as a chemical engineer from Kansas State University (B.S.) and Rice University (Ph.D.) in the United States. Previous to moving to Lausanne, he was on the faculty at the Swiss Federal Institute of Technology Zurich, at the California Institute of Technology, and at the University of Texas in Austin. He is author of more than 250 papers in peer-reviewed journals and inventor on more than 100 patents. He is a member of the National Academy of Engineering, USA. and the National Academy of Inventors, USA.

Regenerative medicine - We study the interaction of protein growth factors, which induce tissue morphogenesis, with proteins of the extracellular matrix, seeking to understand the complex interplay between these two classes of signaling molecules in vivo. Based on this interaction, we design and develop novel biomaterial and growth factor designs, to present these molecules in vivo in a molecular context that resembles their natural biological function. Vaccines and immunotherapeutics - In collaboration with the Laboratory for Lymphatic and Cancer Bioengineering (Prof. M.A. Swartz), we develop approaches to target vaccine antigen and adjuvant formulations to the lymph nodes that drain an injection site. We are particularly interested in situations where one must induce a CD8+ T cell response, for example generating cancer-fighting cytotoxic T lymphocytes for anti-cancer therapeutic vaccination. Tolerogenic vaccination - In addition to effector immune responses, we are also keenly interested in protein engineering approaches to tolerize versus cellular immunity, harnessing the tolerogenic antigen presentation that occurs with antigen from apoptotic cells yet using simple engineered antigen forms that are clinically tractable. We explore ways to deliver antigens to induce these aspects of peripheral tolerance, with a focus on preventing immune responses to protein drugs and on preventing and reversing immune responses in autoimmunity, most notably type-1 diabetes antigens.

Keywords

Immunoengineering, tissue engineering, protein engineering, biomaterials.

Results Obtained in 2014

Regenerative medicine: We have determined that a broad collection of extracellular matrix proteins comprise high affinity binding sites for a broad collection of growth factors. We have also identified certain growth factors that comprise binding sites for matrix proteins that are very high affinity and promiscuous. This has allowed us to develop an engineering concept for cytokines and chemokines, including morphogenetic growth factors, creating molecular variants that display superaffinity for extracellular matrix proteins. We have shown substantial enhancement of efficacy of these candidate drugs in models of chronic skin wounds in diabetics and in bone defects. Vaccines and immunotherapeutics: In collaboration with the laboratory of Prof. M.A. Swartz, we have developed novel nanomaterials as vaccines that comprise conjugated antigen proteins and adjuvant biomolecules, and we have explored the efficacy of these nanomaterials in cancer models in the mouse, for example in lymphoma and melanoma models. We have demonstrated that the nanomaterials can beneficially targeted to the lymph nodes that drain the tumor, which are already primed by having experienced tumor antigens draining to that site. We showed that vaccination of the tumor-draining lymph node was much more effective than vaccinating an uninvolved lymph node. Tolerogenic vaccination: We have shown that antigens can be engineered to bind in situ to erythrocytes, and that this leads to antigen deposition in antigen presenting cells in the liver and spleen very efficiently, the antigen circulating on the erythrocyte until it is cleared in the liver and spleen as it ages. We are exploring this technology in inducing tolerance to protein drugs, for example in protein replacement therapies in rare diseases, and to autoimmune antigens, most notably type-1 diabetes antigens. We have spun out a company, located in the EPFL Science Park, to carry this work forward in clinical development.

EPFL School of Life Sciences - 2014 Annual Report

Team Members Postdoctoral Fellows Balet, Eva-Maria Bonner Daniel Borcard Françoise Brubaker Carrie Gai, Shunning Ishihara, Jun Larsson, Mattias Hans Phelps, Edward Allen Sancho, Nuria Oltra Tortelli, Federico Wilson, David Scott

PhD Students Briquez, Priscilla Brünggel, Kym Cianciarus, Chiara Damo, Martina De Titta, Alexandre Grimm, Aliz e Julier, Ziad Panagiotou, Vasiliki Vardar, Elif Kivell , Anna-Sofia (external) Nagpal, Medhavi (external)

Master’s Students Dellacherie, Maxence Jahnsen, Ann-Lena Mottart, avier Vincentelli, Helena Specialized Technicians Diaceri, Giacomo uaglia-Thermes, avier

Internships Buck, Emily Calderon, Gisele

Administrative Assistant Carol Bonzon

t er Scientiﬁc er onne Dr. Wandrey, Christine - Maître d’enseignement et de recherche Prof. Frey, Peter - Adjunct professor Dr. Simeoni, Eleonora – Scientist Gaudry, Jean-Philippe – Bio-engineer

IBI - Institute of Bioengineering

Repair of bone defects in the skull of the rat. On the right, repair is done using growth factors with their wild-type natural form. On the left, repair is enhanced by applying our engineering concept to design the same growth factors, at the same dose, but in a second-generation molecular design.

Selected Publications » Zakrzewski, J.L., van den Brink, M.R. & Hubbell, J.A. (2014) Overcoming immunological barriers in regenerative medicine. Nat Biotechnol 32:7 6-7 4. » Martino, M.M., Briquez, P.S., Guc, E., Tortelli, F., Kilarski, W.W., Metzger, S., Rice, J.J., Kuhn, G.A., Muller, R., Swartz, M.A. & Hubbell, J.A. (2014) Growth factors engineered for super-affinity to the extracellular matrix enhance tissue healing. Science 343:885-888. » Jeanbart, L., Ballester, M., de Titta, A., Corthesy, P., Romero, P., Hubbell, J.A. & Swartz, M.A. (2014) Enhancing efficacy of anti-cancer vaccines by targeted delivery to tumor-draining lymph nodes. Cancer Immunology Research 2:436-447. » Martino, M.M., Briquez, P.S., Ranga, A., Lutolf, M.P. & Hubbell, J.A. (2013) Heparin-binding domain of fibrin(ogen) binds growth factors and promotes tissue repair when incorporated within a synthetic matrix. Proc Natl Acad Sci U S A 110:4563-4568. » Kontos, S., Kourtis, I.C., Dane, K.Y. & Hubbell, J.A. (2013) Engineering antigens for in situ erythrocyte binding induces T-cell deletion. Proc Natl Acad Sci U S A 110:E60-68. » de Titta, A., Ballester, M., Julier, Z., Nembrini, C., Jeanbart, L., van der lies, A.J., Swartz, M.A. & Hubbell, J.A. (2013) Nanoparticle conjugation of CpG enhances adjuvancy for cellular immunity and memory recall at low dose. Proc Natl Acad Sci U S A 110:19902-19907.

EPFL School of Life Sciences - 2014 Annual Report

Jensen Lab Jeffrey D. Jensen

Tenure-track Assistant Professor

http:// en enlab.epfl.ch

Introduction

Jeff Jensen is a population geneticist, broadly interested in the study of adaptation in natural populations. He received a BS / BA from the University of Arizona in 2002 in Ecology & Evolutionary Biology and Biological Anthropology, respectively. Jeff earned his PhD in Molecular Biology & Genetics at Cornell University in 2006, and did his postdoc work as an NSF Biological Informatics Fellow at UCSD and UC Berkeley. He founded the Jensen Lab at the University of Massachusetts Medical School in the Program for Bioinformatics & Integrative Biology in 2009, and re-located the lab to EPFL in the Fall of 2011.

The primary research theme of our group is centered around drawing statistical inference from DNA polymorphism data - specifically, describing the processes that determine the amount and distribution of genetic variation within and between populations, and between species. Lab members work on both applied and theoretical problems in fields ranging from population genomics to medical genetics.

Keywords

Population genetics, adaptation.

Results Obtained in 2014

Over the past year we have thought primarily about how populations adapt to challenging environments. Within this theme, we have developed novel population genetic theory to describe expectations, as well as novel statistical machinery to quantify the distribution of fitness effects under these models and to identify adaptively important mutations in the genome â&#x20AC;&#x201C; generally within a Bayesian framework. Applying these theoretical and statistical approaches, we have primarily focused upon the following empirical data: Ecological - how wild populations of deer mice evolve crypsis in order to adapt to the selective pressure of avian predation on novel substrates. Experimental - how populations of yeast evolve tolerance for high temperature and salinity under controlled laboratory conditions. Clinical - how influenza virus adapts to drug treatment in order to become resistant, and how human cytomegalovirus (HCMV) adapts in the face of the immune response of a newly infected patient. This line of research offers both novel insight in to the mode and tempo of adaptation as an evolutionary process, as well as demonstrates the power of evolutionary analysis to provide insights to related research communities ranging from ecology to virology.

EPFL School of Life Sciences - 2014 Annual Report

Team Members Postdoctoral Fellows Claudia Bank Greg Ewing Anna Ferrer-Admetlla Matthieu Foll Stefan Laurent Lisha Mathew Cornelia Pokalyuk Nicholas Renzette

PhD Students Adamandia Kapopoulou Louise Ormond Hyunjin Shim Alfred Simkin

Staff Kristen Irwin

Administrative Assistant Sophie Barret

IBI - Institute of Bioengineering

Figure from Foll et al. (2014), utilizing our developed statistical software (termed WFABC). In panel A, we plot 10,000 simulated mutational frequency trajectories (where Fs’d indicates the extent to which a mutant frequency decreases through time, and Fs’i the extent to which a mutant frequency increases through time). In the legend, the color-coding indicates the simulated selection coefficient (s). hus, mutations that are strongl positi el selected (shown in red) have a high value of Fs’i and low value of Fs’d (i.e., they almost exclusively increase in frequency), whereas deleterious mutations (shown in green) generally decrease in frequency, and neutral mutations (in yellow) have an equal probability of increasing or decreasing owing to the effects of genetic drift. Thus, comparing an experimentally observed mutational frequency trajectory (shown by the black dot) with the simulated data allows for an estimation of s (an approach known as Approximate Bayesian Computation (ABC)). In panel B the corresponding example is shown as a heat plot, where an estimate of the effecti e population si e ( e) of the influen a irus, and the selection coefficient (s) of an identified oseltami ir resistance mutation, are shown. hus, using this approach, resistance mutations can not onl be identified from whole genome data, but their selective effect on the population can also be measured.

Selected Publications » Jensen, J.D., 2014. On the unfounded enthusiasm for soft selective sweeps. Nature Communications 5: 5281 selective sweeps. Nature Communications 5: 5281. » Simkin, A., J. Bailey, B. Theurkauf, F.-B. Gao, and J.D. Jensen, 2014. Inferring the evolutionary history of primate miRNA binding sites: overcoming motif counting biases. Molecular Biology & Evolution 31: 1 4- 01. » Bank, C., R.T. Hietpas, A. Wong, D.N. Bolon, and J.D. Jensen, 2014. A Bayesian MCMC approach to assess the complete distribution of fitness effects of new mutations: uncovering the potential for adaptive walks in challenging environments. Genetics 1 6: 41-52. » Foll, M., Y.-P. Poh, N. Renzette, A. Ferrer-Admetlla, C. Bank, H. Shim, A.-S. Malaspinas, G. Ewing, P. Liu, D. Wegmann, D.R. Caffrey, K.B. Zeldovich, D.N. Bolon, J.P. Wang, T.F. Kowalik, C.A. Schiffer, R.W. Finberg, and J.D. Jensen, 2014. Influenza virus drug resistance: a time-sampled population genetics perspective. PLoS Genetics 10(2):e10041 5. » Simkin, A., A. Wong, Y.-P. Poh, B. Theurkauf, and J.D. Jensen, 2013. Recurrent and recent selective sweeps in the piRNA pathway. Evolution 67: 10 1- 0. » Linnen, C.R., Y.-P. Poh, B. Peterson, R. Barrett, J. Larson, J.D. Jensen, and H.E. Hoekstra, 2013. Adaptive evolution of multiple traits through multiple mutations at a single gene. Science 33 : 1312-1316.

EPFL School of Life Sciences - 2014 Annual Report

Lutolf Lab Matthias Lutolf

Associate Professor - Director of the Institute of Bioengineering - IBI

http://l cb.epfl.ch/

Introduction

Matthias Lutolf was trained as a Materials Scientist at ETH Zurich where he also carried out his Ph.D. studies (awarded with the ETH medal in 2004). Lutolf carried out postdoctoral studies at the Baxter Laboratory in Stem Cell Biology at the Stanford University. He started up his independent research group at EPFL in 2007 with a European Young Investigator (EURYI) award. Lutolf serves as an editorial board member of four international journals and he is founder of the biotech company Gel SA.

By interfacing advanced biomaterials engineering, microtechnology and stem cell biology, the overarching goal of the Lutolf Laboratory is to uncover mechanisms of stem cell fate regulation; knowledge that will contribute to better ways to grow stem cells in culture and use them for various applications. A major recent goal in his lab aims at inducing organogenesis in 3D stem cell culture.

Keywords

Stem cells, self-renewal, differentiation, niche, single cell analysis, hydrogel engineering, microfluidics, stem cell-based organogenesis.

Results Obtained in 2014

The behaviour of cells in tissues is governed by the 3D microenvironment, which involves a dynamic interplay between biochemical and mechanical signals. The complexity of microenvironments and the context-dependent cell responses that arise from these interactions have posed a major challenge to understanding the underlying regulatory mechanisms. To systematically dissect the role of the various factors that can determine cell fate in 3D, we have developed novel experimental paradigms to simultaneously generate thousands of unique microenvironments and probe their effects on (single) cell fate in vitro (e.g. Ranga et al., Nature Communications, 2014). We have applied this unique approach to discover minimal artificial niches for hematopoietic stem cells (Roch et al., in revision), as well as chemically defined 3D microenvironments that promote neuroepithelial differentiation of pluripotent stem cells and their self-organization into neural tube-like morphogenetic structures (Meinhardt et al., Stem Cell Reports, 2014 and Ranga et al., in revision).

EPFL School of Life Sciences - 2014 Annual Report

Team Members Postdoctoral Fellows Simone Allazetta Massimiliano Caiazzo Nikolce Gjorevski Adrian Ranga Aline Roch

PhD Students Nathalie Brandenberg Sonja Giger Mehmet Girgin Mukul Girotra Laura Kolb Gennady Nikitin Lilia Salimova Yoji Tabata Vincent Trachsel

Master’s Students Thibaud Cherbuin Michael Snyder

Administrative Assistant Maria Fernandes Coelho

IBI - Institute of Bioengineering

3D combinatorial screening from a modular materials library: a, Enzymatically mediated cross-linking scheme, where represents specific peptide se uence. b, omponents of the combinatorial toolbo are assembled from biologically relevant factors in categorized form. Stiffness and MMP sensitivity of the matrix are set within the experimentally measured ranges shown. c, Experimental process consists of combining the components library with reporter cells using robotic mixing and dispensing technology into 1536 well plates. d, Automated microscopy and image processing to determine colony size and GFP intensity. Average cell density per well is set by the initial cell concentration used in the experiment, and exact initial cell density for each well is determined retrospectively by imaging. Examples of a set of images tracking colony growth in a single well over the course of a 5-day experiment, three-dimensional confocal reconstruction and image segmentation are shown.

Selected Publications » » » » » » » »

A Meinhardt, D Eberle, A Tazaki, A Ranga, M Niesche, A Stec, G Schackert, MP Lutolf, EM Tanaka (2014). 3D Reconstitution of the Patterned Neural Tube from Embryonic Stem Cells, Stem cell reports 3 (6), 7Gjorevski N, Ranga A, Lutolf MP, (2014). Bioengineering approaches to guide stem cell-based organogenesis, Development 141 ( ), 17 4-1 04 Ranga A, Gobaa S, Mosiewicz KA, Okawa Y, Negro A, Lutolf MP (2014). Systems biology of cell-matrix interactions: Discovery of cell fate regulators via arrays of 3D microenvironments, Nature Communications, 5, 4324 A Ranga, N Gjorevski, MP Lutolf (2014). Drug discovery through stem cell-based organoid models, Advanced drug delivery reviews 6 , 1 -2 Mosiewicz KA, Kolb L, van der lies AJ, Martino MM, Lienemann PS, Hubbell JA, Ehrbar M, Lutolf MP (2014). In situ cell manipulation through enzymatic hydrogel photopatterning, Nature Materials, 12 (11), 1072-1078 Cosson S, Lutolf MP (2014) Hydrogel microfluidics for the patterning of pluripotent stem cells, Scientific Reports, Mar 25;4:4462 Roccio M, Schmitter D, Knobloch M, Okawa Y, Sage D, Lutolf MP (2013). Predicting stem cell fate changes by differential cell cycle progression patterns, Development, 140(2):45 -70 M Knobloch, SMG Braun, L Zurkirchen, C on Schoultz, N Zamboni, MJ Ara zo-Bravo, WJ Kovacs, Karalay, U Suter, RAC Machado, M Roccio, MP Lutolf, CF Semenkovich, S Jessberger (2013). Metabolic control of adult neural stem cell activity by Fasn-dependent lipogenesis, Nature 493 (7431), 226-230 » Woodruff K, Fidalgo LM, Gobaa S, Lutolf MP, Maerkl SJ, (2013). Live mammalian cell arrays, Nature Methods, Jun;10(6):550-2 » Allazetta S, Hausherr TC, Lutolf MP (2014). Microfluidic synthesis of cell-type-specific artificial extracellular matrix hydrogels, Biomacromolecules, Apr ;14(4):1122-31 » Cosson S, Allazetta S, Lutolf MP (2013). Patterning of cell-instructive hydrogels by hydrodynamic flow focusing, Lab on a Chip. 2013 Jun 7;13(11):20

-105

EPFL School of Life Sciences - 2014 Annual Report

Naef Lab Felix Naef

Associate Professor

http://nae

Introduction

Our lab is interested in computational, quantitative and systems biology. We work on various problems including circadian rhythms, developmental patterning, gene expression networks, and stochastic transcription in single cells. To study these systems we combine theoretical, computational and experimental approaches. Felix Naef studied theoretical physics at the ETHZ and obtained his PhD from the EPFL in 2000. He then received postdoctoral training at the Center for Studies in Physics and Biology at the Rockefeller University (NYC) under the guidance of Prof. Magnasco. His research at the interface of physics and biology focuses on the gene regulation, transcription, circadian rhythms and single cell analysis. He joined EPFL in 2006 where he is currently Associate Professor in the Institute of Bioengineering (IBI).

Diurnal oscillations of gene expression controlled by the circadian clock underlie rhythmic physiology across most living organisms. In this context our lab is highly interested in combining functional genomics (RNA-seq, ChIPseq, DNAse1-seq, mass spectrometry), bioinformatics and mathematical modeling to understand how the circadian clock impinges on many of the regulatory layers underlying rhythmic gene expression. The ultimate goal is to better understand rhythms in physiology, notably in the mouse liver, but also in other tissues. We are also very keen on using microscopy to study cellular rhythms in individual mammalian cells. Notably, we have been intrigued by the interactions of the circadian and cell cycles, since previously work has argued that the clock might control cell division timing. Better understanding of how the two systems mutually interact is currently of great interest, notably with regards to the role of circadian clocks in proliferating tissues, such as the epidermis, immune or stem cells. Another main focus of our group is on transcriptional kinetics in single mammalian cells. Mammalian genes are often transcribed discontinuously as short bursts of RNA synthesis followed by longer silent periods. However, how these “on” and “off” transitions, together with the burst sizes, are controlled in single cells is still poorly characterized. To address this problem, we combine single-cell time-lapse luminescence imaging with stochastic modeling of the time.

Results Obtained in 2014

ircadian cloc -dependent and -independent rhythmic proteomes implement distinct diurnal functions in mouse liver , Mauvoisin et al., S 201 . We quantified temporal profiles in the murine hepatic proteome under physiological light–dark conditions using quantitative MS. Our analysis identified over 5,000 proteins, of which several hundred showed robust diurnal oscillations with peak phases enriched in the morning and during the night. Combined mathematical modeling of temporal protein and mRNA profiles indicated that proteins accumulate with reduced amplitudes and significant delays, consistent with protein half-life data. Moreover, some rhythmic proteins showed no corresponding rhythmic mRNAs. Such rhythms were highly enriched in secreted proteins accumulating tightly during the night and persisted in clock-deficient animals, suggesting that food-related entrainment signals influence rhythms in circulating plasma factors. “Robust synchronization of coupled circadian and cell cycle oscillators in single mammalian cells , ieler et al., MS 201 . Circadian and cell cycles are two periodic cell-autonomous processes with a period of about one day. Consequently, when these cycles run in parallel in the same cell, their coupling may lead to resonances or even synchronization. Observations of circadian variations in mitotic indices and on the daytime-dependence of cell divisions led to the hypothesis that the circadian cycle might gate cell-cycle progression. We completed a quantitative time-lapse imaging study of circadian cycles in dividing mammalian NIH3T3 cells clearly indicated that both oscillators tick in a tightly synchronized state. Moreover, contrary to our expectations, we unambiguously showed that in NIH3T3 cells the cell cycle progression exerts a unilateral influence on the circadian clock, and not the opposite.

Keywords

Gene regulation, circadian rhythms, chronobiology, single cell analysis, transcriptional bursting.

lab.epfl.ch

EPFL School of Life Sciences - 2014 Annual Report

Team Members Postdoctoral Fellows Paola Gilardoni Saeed Omidi Jingkui Wang Kyle Gustafson

PhD Students Johannes Becker Jonathan Bieler Simon Blanchoud Rosamaria Cannavo Damien Nicolas Jonathan Sobel Laura Symul Onur Tidin Jake Yeung

Master’s Students C dric Gobet Matthieu Quinodoz Nicolas Villa

Administrative Assistant Sophie Barret

IBI - Institute of Bioengineering

Circadian cycles resonate to the cell cycle. Model underlying the synchronization of circadian and cell cycle oscillators in individual mammalian cells. Time runs clockwise as indicated, key circadian event are indicated. Cell division at the different times can either phase advance or phase delay the circadian cycle, as indicated by the red and green arrows. This phase shifting by cell division induces a resonance of the circadian clock, such that the two cycles are synchronized (1:1 mode locking) with division occurring typically just after the night-day transition.

Selected Publications » Bieler, J., Cannavo, R., Gustafson, K., Gobet, C., Gatfield, D., Naef, F,. Robust synchronization of coupled circadian and cell cycle oscillators in single mammalian cells. Mol Syst Biol. 2014 Jul 15. 10:73 . doi: 10.15252/ msb.20145218. PubMed PMID: 25028488; PubMed Central PMCID: PMC4299496. » Mauvoisin, D., Wang, J., Jouffe, C., Martin, E., Atger, F., Waridel, P., uadroni, M., Gachon, F., Naef, F. Circadian clock-dependent and -independent rhythmic proteomes implement distinct diurnal functions in mouse liver. Proc. Natl. Acad. Sci. U S A. 2014 Jan 7;111(1):167-72. doi: 10.1073/pnas.1314066111. Epub 2013 Dec 16. PubMed PMID: 24344304; PubMed Central PMCID: PMC3890886. » Molina, N., Suter, D.M., Cannavo, R., Zoller, B., Gotic, I., Naef, F. Stimulus-induced modulation of transcriptional bursting in a single mammalian gene. Proc. Natl. Acad. Sci. U S A. 2013 Dec 17;110(51):20563- . doi: 10.1073/pnas.1312310110. Epub. 2013 Dec 2. PubMed PMID: 24297917; PubMed Central PMCID: PMC3870742. » d’Eysmond, T., De Simone, A., Naef, F. Analysis of precision in chemical oscillators: implications for circadian clocks. Phys. Biol. 2013 Oct;10(5):056005. doi: 10.1088/1478-3975/10/5/056005. Epub. 2013 Sep 16. PubMed PMID: 24043227. » Jouffe, C., Cretenet, G., Symul, L., Martin, E., Atger, F., Naef, F., Gachon, F. The circadian clock coordinates ribosome biogenesis. PLoS Biol. 2013;11(1):e1001455. doi: 10.1371/journal.pbio.1001455. Epub 2013 Jan 3. PubMed PMID: 23300384; PubMed Central PMCID: PMC3536797. » Simicevic, J., Schmid, A.W., Gilardoni, P.A., Zoller, B., Raghav, S.K., Krier, I., Gubelmann, C., Lisacek, F., Naef, F., Moniatte, M., Deplancke, B. Absolute quantification of transcription factors during cellular differentiation using multiplexed targeted proteomics. Nat Methods. 2013 Jun;10(6):570-6. doi: 10.1038/nmeth.2441. Epub 2013. Apr 14. PubMed PMID: 23584187.

EPFL School of Life Sciences - 2014 Annual Report

Naveiras Lab Olaia Naveiras

SNSF Professor, IBI (50%), Haematology Service, CHUV (50%)

http://na eira

Introduction

Olaia Naveiras obtained a Medical Degree from Universidad Aut贸noma de Madrid (Spain), studied Immunology at the Pasteur Institute (Paris, France) and pursued her PhD in Experimental Haematology with George Q. Daley in Harvard Medical School (Boston, USA). She moved to Switzerland to gain medical training in Internal Medicine and Haematology, while being a parttime postdoctoral fellow with Prof. Matthias Lutolf at EPFL. In 2014, she founded the Laboratory of Regenerative Haematopoiesis. She shares her research time at EPFL with clinical responsibilities at the local CHUV Haematology Service.

We are interested in understanding the regulation of the reversible transition between mammalian yellow (adipocyitic) and red bone marrow (hematopoietic). This naturally occurring process can be enhanced to increase safety and efficacy of hematopoietic stem cell (HSC) transplantation, and, possibly, to slow the progression of myelodysplasia or even aplastic anemia into overt leukemia. Currently, all clinical approaches to increase HSC engraftment and to enhance hematopoiesis target the HSC itself. Alternatively, we focus on studying how manipulations of the HSC niche can enhance hematopoiesis and, in particular, how inhibiting adipocytic differentiation within failing marrow accelerates hematopoietic recovery. Specifically, we are developing several strategies to induce metabolic changes in the HSC niche and to regulate the function of mesenchymal stem cells (MSCs), the main precursor to stromal supportive cells within the hematopoietic marrow, and to dissect the differential fates of MSCs within the adipocytic and hematopoietic marrow. The relevance of this research relies on the early mortality associated to HSC transplantation. Reducing the toxicity of the preparative regimen and accelerating the time to engraftment is critical to improving the safety of hematopoietic stem cell transplantation and making this most successful stem cell therapy available to a wider subset of patients.

Keywords

Hematopoietic stem cell (HSC), bone marrow transplantation, adipocyte, preadipocyte, mesenchymal Stem Cell (MSC), HSC niche, regenerative hematopoiesis.

lab.epfl.ch/

Results Obtained in 2014

Our laboratory was established in January 2014. Since then, we have optimized complex models of hematopoietic stem cell (HSC) transplantation extending to, thanks to our collaborators, single cell transplants and NSG human-into-mouse xenotransplantation. We have established a high-throughput screening platform for mesenchymal stem cell differentiation based on digital holographic microscopy (DHM), adapted for the study of bone marrow adipogenesis, and have developed quantitative methods to assess the red-to-yellow and yellow-to-red bone marrow transitions upon bone marrow transplantation. Aside from method-development, following up on the work initiated by our group at the Laboratory of Stem Cell Bioengineering, we have demonstrated the capacity of specific mitochondrial modulators within the NAD pathway to accelerate the yellow-to-red bone marrow transition upon HSC transplant in mice, opening the possibility of translating these findings to reduce the mortality associated to HSC transplant in patients suffering from leukemia or lymphoma. Future work will concentrate on characterizing the mesenchymal stem cell (MSC) and preadipocyte populations in relationship to the expanding hematopoietic compartment, as well as identifying small molecule inhibitors of the yellow-to-red bone marrow transition that may be used in the context of HSC transplantation and aplastic anemia. A special emphasis will be placed on developing in vivo screening tissue-based bioassays for the creation of microenvironments capable of mediating hematopoietic progenitor expansion.

EPFL School of Life Sciences - 2014 Annual Report

Team Members Postdoctoral Fellows Shanti Rojas-Sutterlin Nicola Vannini

PhD Students Vasco Campos Josefine Tratwal

Bachelor Students Chiheb Boussema Yannick Yersin

Research Assistant Evangelos Panopoulos

Administrative Assistant Laura Bischoff

IBI - Institute of Bioengineering

Master’s Students Cédric Jules-Etienne Jasmina Rubattelol

Mixed yellow (adipocytic) and red (hematopoietic) marrow in the mouse tail vertebra. Bone marrow adipocytes are seen as white, empty ovals surrounded by hematopoietic cells in classic H&E stains (left). Right: adipocyte uantification ia the dipoQ tool de eloped in the lab.

Selected Publications » annini N, Roch A, Naveiras O, Griffa A, Kobel S, Lutolf MP, Identification of in vitro HSC fate regulators by differential lipid raft clustering, Cell Cycle. 2012 Apr 15;11( ):1535-43. » Naveiras O, Nardi , Wenzel PL, Hauschka P , Fahey F, Daley G , Bone-marrow adipocytes as negative regulators of the haematopoietic microenvironment, Nature. 200 Jul ;460(7252):25 -63. » Adamo L, Naveiras O, Wenzel PL, McKinney-Freeman S, Mack PJ, Gracia-Sancho J, Suchy-Dicey A, Yoshimoto M, Lensch MW, Yoder MC, Garc a-Carde a G, Daley G , Biomechanical forces promote embryonic haematopoiesis, Nature. 2009 Jun 25;459(7250):1131-5. doi: 10.1038/nature08073. Epub 2009 May 13. » Wang Y, Yates F, Naveiras O, Ernst P, Daley G , Embryonic stem cell-derived hematopoietic stem cells. Proc Natl Acad Sci U S A. 2005 Dec 27;102(52):1 0 1-6. Epub 2005 Dec 15.

EPFL School of Life Sciences - 2014 Annual Report

Schoonjans Lab st n

Adjunct Professor

http:// ch

Introduction

Kristina Schoonjans obtained her Ph.D in Molecular Biology and Pharmacology from the University of Lille, France in 1995. After her postdoctoral training at the Pasteur Institute in Lille in 1999, she moved to the IGBMC in Strasbourg and was appointed Research Director with INSERM in 2007. In 200 , Kristina Schoonjans joined the EPFL, where she is currently pursuing her research on bile acid and metabolite signaling to identify novel mechanisms and strategies to target metabolic disorders.

The liver-gut axis is a physiological system specialized in the sensing and processing of nutrients. Our laboratory focuses on this system in order to gain insight into the mechanisms by which nutrient-derived metabolites in general and bile acids in particular coordinate metabolism, immune function and cancer. A major part of our research involves the study of a subset of nuclear receptors that are directly or indirectly affecting metabolite and bile acid signaling, including LRH-1 (NR5A2), SHP (NROB2) and F R (NR1H4). The other main research axis focuses on the non-genomic effects of bile acids by investigating the role of the bile acid-responsive GPCR, TGR5. We are using state-of-the-art approaches in biochemistry, metabolomics, molecular and cellular biology, pharmacology and mouse genetics to investigate these different research topics. An integrative approach combining functional studies and metabolic phenotyping in genetically engineered mouse models together with in-depth molecular profiling in cellular models is used to reconstruct the networks that are modified by metabolite signaling. By investigating the molecular basis by which metabolites signal to convey adaptive responses in metabolic organs, our laboratory aims to identify novel mechanisms and strategies to prevent and treat metabolic disorders.

Keywords

Liver-gut axis, macrophages, bile acids, nutrient sensing, intermediary metabolism, immuno-metabolism, nuclear receptors, TGR5, type 2 diabetes, atherosclerosis.

n an

lab.epfl.ch

Results Obtained in 2014

In the past we established the metabolic role of several enterohepatic nuclear receptors and causally linked their functions to immune regulation and cancer. An example is the enterohepatic orphan nuclear receptor, LRH-1, which we identified as a critical regulator of hepatic glucose sensing, steroid hormone production and of bile acid homeostasis. We showed that some of these actions, if perturbed by inappropriate activity of LRH-1, have farreaching effects on multiple intestinal diseases, including IBD and colorectal cancer. More recently, we identified SUMOylation as a prime mode of LRH-1 regulation. We discovered that SUMOylation of LRH-1 promotes its interaction with the co-repressor, PRO 1, and selectively inhibits gene programs linked to reverse cholesterol transport. By generating an LRH-1 K2 R knockin mouse model, we showed that SUMOylation-defective LRH-1 mice display enhanced cholesterol and bile acid fluxes in the liver and are protected against the development of atherosclerosis, highlighting the physiological and pathophysiological importance of this post-translational modification of LRH-1. Earlier studies in our lab also identified bile acids as endocrine regulators of energy expenditure and glucose homeostasis, through the activation of the GPCR, TGR5. More recently, we have highlighted the role of macrophage TGR5 in the context of inflammation-driven metabolic disorders, such as atherosclerosis. In a follow-up study, we provided evidence that the anti-inflammatory response of TGR5 also directly contributes to the insulin sensitizing effects of bile acids. More specifically, we showed that TGR5 activation reduces chemokine expression in macrophages via mTOR-dependent stimulation of translation of the dominant-negative C/EBPÎ˛-LIP isoform, thereby ameliorating obesity-induced insulin resistance

EPFL School of Life Sciences - 2014 Annual Report

Team Members PhD Students Vera Lemos Pan u

Project Student Silas Kieser

Technicians Thibaud Clerc Soline Odouard

Administrative Assistant Soledad Andany

IBI - Institute of Bioengineering

Postdoctoral Fellows Alessia Perino Ning Shen Matthias Stein

Hepatoma cell line AML-12 as an in vitro model to study metabolite signaling.

Selected Publications » Alemi F, Kwon E, Poole DP, Lieu T, Lyo , Cattaruzza F, Cevikbas F, Steinhoff M, Nassini R, Materazzi S, Guerrero-Alba R, aldez-Morales E, Cottrell GS, Schoonjans K, Geppetti P, anner SJ, Bunnett NW, Corvera CU. The TGR5 receptor mediates bile acid-induced itch and analgesia. J Clin Invest. 2013, 123, 1513-30. » Zhang C, Large MJ, Duggavathi R, DeMayo FJ, Lydon JP, Schoonjans K, Kovanci E, Murphy BD. Liver receptor homolog-1 is essential for pregnancy. Nat Med. 2013, 1 , 1061-6. » Oosterveer M.H. and K. Schoonjans. Hepatic glucose sensing and integrative pathways in the liver. Cell Mol. Life Sci. 2014, 71, 1453-67. » Perino A. and K. Schoonjans. Another Shp on the horizon for bile acids. Cell Metab. 2014, 20, 203-5. » Macchiarulo A., A. Gioiello A, C. Thomas, T.W. Pols, R. Nuti, C. Ferrari, N. Giacch , F. De Franco, M. Pruzanski, J. Auwerx, K. Schoonjans and R. Pellicciari. Probing the binding site of bile acids in TGR5. ACS Med Chem Lett. 2013, 4, 1158-62. » Stein S., M.H. Oosterveer, C. Mataki, P. u, . Lemos, R. Havinga, C. Dittner, D. Ryu, K.J. Menzies, . Wang, A. Perino, S.M. Houten, F. Melchior and K. Schoonjans. SUMOylation-dependent LRH-1/PRO 1 interaction promotes atherosclerosis. Cell Metab. 2014, 20, 603-13. » Ryu D., Y.S. Jo, G. Lo Sasso, S. Stein, H. Zhang, A. Perino, J.U. Lee, M. Zeviani, R. Romand, M.O. Hottiger, K. Schoonjans and J. Auwerx. A SIRT7-dependent acetylation switch of GABPβ1 controls mitochondrial function. Cell Metab. 2014, 20, 856-69. » Perino A., T.W.H. Pols, M. Nomura, R. Pellicciari and K. Schoonjans. TGR5 reduces macrophage migration through mTOR-induced C/EBP differential translation. J Clin Invest. 2014, 124, 5424-36.

EPFL School of Life Sciences - 2014 Annual Report

Suter Lab David Suter

Tenure-track Assistant Professor and SNSF Professor - Sponsored Stem Cell Research Chair

http:// uter lab.epfl.ch/

Introduction

David Suter obtained his MD/PhD at the University of Geneva on stem cell biology. He then worked on single cell monitoring of transcription in Geneva before joining Harvard University where he developed a new method for single molecule live imaging of transcription factors in mammalian cells. Since 2013, he is a Swiss National Science Foundation Professor and tenure track Assistant Professor at the Bioengineering Institute of the EPFL School of Life Sciences. His research focuses on mechanisms of cell fate choices using single cell and single molecule approaches.

We are interested in understanding how cell fate choices are made during early embryogenesis, and use embryonic stem (ES) cells as a model system. ES cells are derived from the inner cell mass of the embryo at the blastocyst stage. They can be maintained in culture and instructed to differentiate towards virtually any cell type of the body, thereby providing a powerful tool to study developmental processes in vitro. In addition, they are a promising source for future cell therapy applications, which aim at replacing cells lost in pathological conditions such as Parkinson’s disease, myocardial infarction, diabetes, and other major human diseases. Our aim is to decipher the molecular mechanisms underlying cell fate choices made at early developmental stages. To address this question, we are using new single-cell and single-molecule approaches to investigate the dynamics of gene expression during embryonic stem (ES) cell differentiation and their relationship to cell fate choices. We are particularly interested in the following questions: • How does gene expression fluctuate in ES cells, and to what extent do these fluctuations influence cell fate decisions • What are the gene regulatory networks active at different stages of differentiation • What are the dynamics of DNA-binding proteins in ES cells and differentiated cells

Keywords

Embryonic stem cells, gene expression dynamics, single cell analysis, single molecule imaging, cell fate choices, high throughput screening.

Results Obtained in 2014

Over the past year we have been working on the development of molecular and cellular tools to monitor gene expression at different levels. First, we improved and adapted our previously developed approach to monitor transcription at high temporal resolution in single embryonic stem (ES) cells. Briefly, this method is based on gene trap of a short-lived luciferase under the control of various endogenous genes. The oscillations of the luminescence signal can then be deconvolved to obtain time traces of transcriptional oscillations. Second, we developed a CRIPSR-Cas knock-in approach to tag endogenous transcription factors with luciferase. We successfully generated a heterozygous knock-in ES cell line allowing to monitor absolute levels of Sox2 in single living cells. We are currently engineering a homozygous Sox2-luciferase knock-in cell line that will be used to correlate Sox2 fluctuations to cell fate choices. Third, we developed a new method to analyze the contribution of protein synthesis and degradation to protein level fluctuations in single living cells. Briefly, we generated over 100 ES cell lines in which different endogenous proteins are tagged with a fluorescent timer, allowing to disentangle changes in protein synthesis from changes in protein degradation. Our ultimate goal is to analyze the contribution of protein synthesis and degradation to changes in protein level both in undifferentiated ES cells and during differentiation. Finally, at the end of 2014 we started a parallel line of research focused on the development of a new functional high throughput screening strategy to discover novel mediators of cell fate choices. We plan to use this new method to discover novel regulators of the first specification events occurring in the embryo proper, using in vitro differentiation of ES cells as a model system.

EPFL School of Life Sciences - 2014 Annual Report

Team Members PhD Students Andrea Alber Elias Friman Aleksandra Mandic Mah Raccaud Daniel Strebinger Onur Tidin

Technician Cédric Deluz

Administrative Assistant Laura Bischoff

IBI - Institute of Bioengineering

Single frame of a gene trap mouse embryonic stem cell line taken with our luminescence microscope. Monitoring luminescence intensity over time allows to follow the expression of endogenous genes in single living cells, with a time resolution of 5 minutes over several days of recording.

Selected Publications » Zhao ZW , Roy R , Gebhardt JC , Suter DM , Chapman AR, ie S. Equal contribution (2014). Spatial organization of RNA polymerase II inside a mammalian cell nucleus revealed by reflected light-sheet superresolution microscopy. Proc. Natl.Acad.Sci U S A. 111(2):681-6. » Molina N , Suter DM , Cannavo R, Zoller B, Gotic I, Naef F . Equal contribution. Corresponding authors (2014) Stimulus-induced modulation of transcriptional bursting in a single mammalian gene. Proc. Natl.Acad.Sci U S A. 110(51):20563-8. » Gebhardt JCM Suter DM , Roy R, Zhao ZW, Chapman A, Basu S, Maniatis T, ie S. Equal contribution (2013). Probing Transcription Factor DNA Binding at the Single Molecule Level in Live Mammalian Cells. Nature Methods 10(5):421-6.

EPFL School of Life Sciences - 2014 Annual Report

Swartz Lab Melody Swartz

Full Professor

http:// wart

Introduction

Melody Swartz is a Professor in the Institutes of Bioengineering (IBI) and Experimental Cancer Research (ISREC). She received her BS from Johns Hopkins and PhD from M.I.T., both in Chemical Engineering. After a postdoc at Harvard, she moved to Northwestern University as an Assistant Professor of Biomedical Engineering, and then relocated to the EPFL in 2003. Throughout her career, she has focused her research on the lymphatic system, integrating physiology, bioengineering, tissue mechanics, and cell biology to elucidate its functionalbiological regulation and more recently on how immune cells and cancer cells gain access to the lymphatics. Her lab has helped to define new paradigms in the field of lymphangiogenesis and cancer metastasis.

The human body has roughly 1000 lymph nodes (LN) that act as subsidiary immune centers where adaptive immune responses are launched and local tolerance is maintained. Lymphatic vessels are the conduits that communicate local conditions to these LNs by transporting immune cells as well as the cytokines, growth factors, and antigens present in the periphery. Once considered simply a passive ‘sewer drain’, a major focus of our lab is the active roles that lymphatics play in regulating immunity. By uncovering its complex roles in immunity and tolerance, we hope to understand – and ultimately manipulate – the immunomodulatory roles of lymphatic vessels in cancer progression and metastasis.

Keywords

Lymphatics, cancer, immunomodulation, lymphangiogenesis, immunology, in vitro models, microfluidics, intravital imaging, nanoparticles, immunotherapy, antigen presentation.

lab.epfl.ch/

Results Obtained in 2014

In 2014, we furthered our understanding of how tumor-associated lymphangiogenesis promotes immune tolerance and directly demonstrated that lymphatic endothelial cells (LECs) can scavenge and process exogenous antigen for MHCI presentation, leading to dysfunctional activation of CD8+ T cells (Hirosue et al, 2014). In collaboration with Stephanie Hugues’s lab at the University of Geneva, we found that LEC expression of MHCII could dysfunctionally activate CD4+ T cells (Dubrot et al, 2014). Furthermore, although LECs express endogenous, IFN-g-inducible MHCII, they could also acquire peptide-MHC II complexes from dendritic cells via exosomes. In both of these studies, LECs expressed higher levels of PD-L1 compared to other LN stromal cells, leading to early PD-1 expression by T cells. In collaboration with the Hubbell lab (EPFL), we explored targeting strategies for nanoparticle cancer vaccines. Although tumor-draining (td) LNs are immune suppressed, they were also more antigen-primed and ultimately more sensitive to immune activation compared to non-tdLN, suggesting that specific targeting of tdLN could be interesting for immunotherapy. Our lab continued to develop new tools for exploring lymphatic immunophysiology. Our intravital imaging method allows real-time investigation of tumor cell migration and interactions with the extracellular matrix (Gu et al., 2014 and Kilarski et al., 2013). Stromal cell, including LECs, and immune cell interactions can be observed using this method. We have also developed microfluidic chambers to study both interstitial and transmural flow, the two types of flow that the LECs experience, especially in the initial lymphatics (Pisano et al, in revision). In summary, our research accomplishments in 2014 bring us closer to our overall goals of elucidating the immunological roles of LECs and lymph angiogenesis in cancer and more generally in regulating immunity and tolerance, so that we can develop novel therapeutic strategies to exploit and target lymphatics for immunomodulation.

EPFL School of Life Sciences - 2014 Annual Report

Team Members Postdoctoral Fellows Marie Ballester Maria Broggi Cara Buchanan Catherine Card Sachiko Hirosue Jeanbart Laura Witold Kilarski Oliver Scott Shann Yu

PhD Students Manuel Fankhauser Gabriele Galliverti Esra Gü Sylvie Hauert Marco Pisano Lambert Potin Marcela Rincon Valentina Triacca Ingrid Van Mier Efthymia Vocali

Vistiting Scientists Prof. Sanjay Kumar Dr. Renata Mecyk Kopec

Technicians Patricia Corthésy Henrioud Yassin Ben Saida

Administrative Assistants Ingrid Margot Stéphanie Bouchet

Master’s /Internship Students Christopher Tremblay Thomas Vetterli

IBI - Institute of Bioengineering

Live imaging of the tumor microenvironment using multi-photon microscopy. Shown is the tumor margin of an implanted B16-F10 melanoma (cyan) with total fibrillar collagen detected by second harmonic generation (SHG, green) and the extracellular matrix protein tenascin C (red), detected using intravital immunofluorescence. Scale 100 µm.

Selected Publications » » » » » » » » »

S Hirosue, et al. (2014). Steady-state antigen scavenging, cross-presentation and CD8+ T cell priming: a new role for lymphatic endothelial cells. J. Immunol. 192(11):5002-11. L Jeanbart, M Ballester, A de Titta, P Corth sy, P Romero, JA Hubbell, MA Swartz (2014). Enhancing efficacy of anticancer vaccines by targeted delivery to tumor-draining lymph nodes. Cancer Immunol Res. 2(5):436-47. J Dubrot, et al. (2014). Lymph node stromal cells acquire peptide-MHCII complexes from dendritic cells and induce antigen-specific CD4 T cell tolerance. J Exp. Med. 221(6):1153-66. C.M. Card, S.S. Yu, M.A. Swartz (2014). Emerging roles of lymphatic endothelium in regulating adaptive immunity. J. Clin. Invest. 124(3):943-52. SN Thomas, E Vokali, AW Lund, JA Hubbell, and MA Swartz (2014). Targeting the tumor-draining lymph node with adjuvanted nanoparticles reshapes the anti-tumor immune response. Biomaterials, 35(2):814-24. A de Titta, et al. (2013). Nanoparticle conjugation of CpG enhances adjuvancy for cellular immunity and memory recall at low dose. Proc Natl Acad Sci USA. 110(4 ):1 02-7 JM Rutkowski, et al. (2013). EGFR-3 neutralization inhibits ovarian lymphangiogenesis, follicle maturation, and murine pregnancy. Am. J. Pathol. 1 3(5):15 6-607. IC Kourtis, S Hirosue, A deTitta, J Stegmann, JA Hubbell, and MA Swartz (2013). Peripherally administered nanoparticles target monocytic myeloid cells, secondary lymphoid organs and tumors in mice. PLoS One (4):e61646. WW Kilarski, E Gü , JCM Teo, SR Oliver, AW Lund, MA Swartz (2013). Intravital immunofluorescence for visualizing the microcirculatory and immune microenvironments in the mouse ear dermis. PLoS One (2):e57135.

» JM Munson, R Bellamkonda, and MA Swartz (2013). Interstitial flow in a 3D microenvironment increases glioma invasion by a C CR4-dependent mechanism. Cancer Res. 73(5):1536-46.

EPFL School of Life Sciences - 2014 Annual Report

Aminian Lab Kamiar Aminian

Adjunct Professor - School of Engineering (STI)

http://lmam.epfl.ch

Research Interests

LMAM has three major focus: • 1) Design of measuring and analysing systems using wearable technology for biomechanics of movement; Kamiar Aminian received his PhD degree in biomedical engineering in 1989 from EPFL. He is currently Professor of medical instrumentation and the director of the Laboratory of Movement Analysis and Measurement of EPFL. His research interests include methodologies for human movement monitoring and analysis in real world conditions mainly based on wearable technologies and inertial sensors with emphasis on gait, physical activity and sport. He is author or co-author of more than 450 scientific papers published in reviewed journals and presented at international conferences and holds 8 patents related to medical devices.

• 2) Monitoring patients activity behaviour outside the laboratory and in various clinical settings to gather clinically significant data and objective information on mobility impairment and movement disorders; • 3) Designing assistive devices and original rehabilitation approaches using new technologies and based on adapted physical activity, exercises and interventions that involve cognitive and sensorimotor capacities. Four PhD theses have been finalized in 2013 and 2014 in the field of orthopaedic and sport. Based on these projects a new instrumented knee implant for in vivo 3D kinematics and prediction of implant loosening has been designed and soft tissue artefact has been quantified. Daily upper limb mobility in patients with the cervical and shoulder disease was quantified using inertial sensor. In

swimming, coordination, performance and energy expenditure were measured accurately with the use of sensors worn on the swimming suit. LMAM was involved in the large Cohorte 65+ of the city of Lausanne where for the first time the inter-relation between gait speed and foot clearance were analysed on 1400 elderly adults using inertial sensors. Moreover in the framework of EU project (FARSEEING) LMAM designed a new type of smart home for active aging and analysis of the complexity of physical activity (fractal behaviour and entropy). Member of the LMAM obtained three awards including the Prix de la ville de Lausanne.

Keywords

Human movement, biomechanics, sport performance, rehabilitation, clinimetry, wearable systems, daily activity, gait analysis, data mining, pain treatment, fall prevention, parkinson disease, orthopaedics, stroke.

Team Members Postdoctoral Fellows Anisoara Inoescu Alan Bourke Nan Wang Arash Arami

PhD Students Arnaud Barré Cyntia Duc Farzin Dadashi Fabien Massé Christopher Moufawad El Achkar Matteo Mancuso Master’s Students Natacha Vida Martins Sylvain Hirth Rebekka Anker Serge Métrailler Techniciens Jean Gramiger Pascal Morel Exchange PhD Students Nora Millor Lai Kuan Tham Administrative Assistants Francine Eglez Danielle Alvarez

Selected Publications » Dadashi, F., Millet, G. P. and Aminian K. (2014) Estimation of Front-Crawl Energy Expenditure UsingWearable Inertial Measurement Units, IEEE Sensors Journal, 14 (4), 1020-1027 » Arami, A., Rechenmann, J.D. and Aminian, K. (2014) Reference-Free Calibration of Magnetic Sensors for Angle Estimation in Smart Knee Prostheses, IEEE Sensors, 14 (6), 17 -17 6 » Duc, C., Pichonnaz, C., Bassin, JP., Farron, A., Jolles, B., Aminian, K. (2014) Evaluation of the muscular activity duration in shoulders with rotator cuff tear using inertial sensors and electromyography accepted in Physiological Measurement, 35, 2389-2400. » Chardonnens, J., Favre, J., B., Cuendet, F., Gremion, G., Aminian, K. (2014) Measurement of the dynamics in ski jumping using a wearable inertial sensor-based system. Journal of Sports Sciences, 32:6, 5 1-600 » Paraschiv-Ionescu, A., Buchser E., Aminian K. (2013) Unraveling dynamics of human physical activity patterns in chronic pain conditions, Scientific Reports, 3, 201 , DOI: 10.103 /srep0201 » Barr , A., Thiran, JP., Jolles, BM, Theumann, N., Aminian, K. (2013) Soft tissue artifact assessment during treadmill walking in subjects with total knee arthroplasty, IEEE TBME, 60(11), 3131-314

EPFL School of Life Sciences - 2014 Annual Report

Fantner Lab Georg Ernest Fantner

Tenure-track Assistant Professor - School of Engineering (STI)

http://lbni.epfl.ch nism”, which protects bone against the formation of micro fractures. Currently we are studying which factors (such as age and disease) can influence the sacrificial bonds, and if this mechanism is a potential target for therapeutic approaches against osteoporosis.

Keywords

High speed atomic force microscopy, lipid membranes, MEMS, NEMS, superresolution microscopy/AFM, microfluidics, bone, single molecule force spectroscopy, live cell imaging, mycobacteria.

Team Members

Postdoctoral Fellows Jonathan D. Adams Soma Biswas Haig-Alexander Eskandarian PhD Students Maja Dukic Nahid Hosseini Adrian Pascal Nievergelt Pascal Damian Odermatt Oliver Peric Joëlle Ven Chen Yang Master’s Student Santiago Andany Administrative Assistant Tamina Sissoko

Selected Publications » » » »

A. B duer, T. Braschler, O. Peric, G. E. Fantner and S. Mosser et al. (2015) A Compressible Scaffold for Minimally Invasive Delivery of Large Intact Neuronal Networks, Advanced Healthcare Materials, vol. 4, num. 2, p. 301-312 A. P. Nievergelt, J. D. Adams, P. D. Odermatt and G. E. Fantner. (2014)High-frequency multimodal atomic force microscopy. Beilstein Journal of Nanotechnology, vol. 5, p. 245 -2467, 2014. J. D. Adams, A. Nievergelt, B. W. Erickson, C. Yang and M. Dukic et al. (2015) High-speed imaging upgrade for a standard sample scanning atomic force microscope using small cantilevers. Rev.Sci.Instrum., 5( ) Erickson, B. W., Coquoz, S., Adams, J. D., Burns, D. J., & Fantner, G. E. (2012). Large-scale analysis of high-speed atomic force microscopy data sets using adaptive image processing. Beilstein journal of nanotechnology, 3, 747–5 . doi:10.3762/bjnano.3.84. » Huth, M., Porrati, F., Schwalb, C., Winhold, M., Sachser, R., Dukic, M., Adams, J., et al. (2012). Focused electron beam induced deposition: A perspective. Beilstein journal of nanotechnology, 3, 5 7–61 . doi:10.3762/bjnano.3.70

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Georg Fantner is a TenureTrack Assistant Professor for bio- and nano-instrumentation in the Interfaculty Institute of Bioengineering, with an affiliation in the department of science and engineering (STI). His research focuses on answering fundamental biological questions using novel nanoscale characterization methods. These research questions include understanding the mechanical properties of bacterial membranes and protein-membrane interactions, as well as the molecular scale mechanisms that determine the mechanical properties of biomaterials such as bone. Prof. Fantner has a strong background in atomic force microscopy, biomaterials and microfabrication. He received his MS from the Technical University of Graz, his PhD from UC Santa Barbara and did his post-doc in the biomolecular materials lab at MIT.

Our research aims to advance nanoscale measurement technology for life-science applications, with a special focus on time-resolved atomic force microscopy (AFM). Towards this end, we work on the integration of high-speed AFM with super-resolution optical microscopy, microand nano-fluidics for high throughput AFM sample handling and NEMS cantilever design. Using these new technologies we study the structure of cell membranes and lipid model-membranes with nanometer resolution, and can observe changes two orders of magnitude faster than previously possible with AFM. Recently we have also developed long-term AFM imaging to characterize bacterial cell division with nanometer resolution. The high spatial resolution images recorded over multiple cell generations yield unprecedented insights into the cell division process. Other research interests include molecular interactions in organic/inorganic composites such as bone, and their contribution to bone fracture toughness. In bone, we have found a molecular level energy dissipation mechanism called the sacrificial-bond, hidden-length mecha-

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Research Interests

EPFL School of Life Sciences - 2014 Annual Report

Guiducci Lab tt

d cc

Tenure-track Assistant Professor - Swiss Up Engineering Chair - School of Engineering (STI)

http://cl e.epfl.ch

Research Interests

The achievement of individualized medicine relies on breakthrough innovations in analytical systems for sample analysis in clinical laboratories and at the patient’s bedside. Carlotta Guiducci received her Ph.D. degree in Electrical Engineering from University of Bologna. She has been visiting scientist at Minatech, Grenoble and ParisTech (ESPCI). She joined EPFL in 2009 as a tenure track assistant professor with IBI and IEL. She holds the Swiss Up Chair on Engineering and she is the recipient of the Intel Early Career Faculty Award. Her work and interview on the role of Silicon in personalized medicine have been featured in “IET Electronics Letters” in 2012. In 2013, she has been invited by Nature Methods to comment on the novel pH-based electronic solutions for quantitative PCR.

In the clinical research and practice, the need to dramatically increase the number of analyzed samples and push towards companion diagnostics can only be fulfilled by highly automatized devices integrating both processing and analytical functions that are entirely or partially disposable. More-than-Moore electronics holds the promise to play a fundamental role in providing analytical systems with high-throughput capabilities, high sensitivity and packaged in USB-sized systems. Prof. Guiducci’s research team is committed to: • innovate the therapeutic drug monitoring practice by DNA aptamer-based assays for in vitro drug quantification;

• push the scalability of solid-state nanosensors to enable high-throughput digital DNA quantification; • provide innovative 3D integration solutions for BioMEMS; • contribute to develop clinically compliant approaches for T cell-based therapeutics by label-free microsystems for cell characterization. The research activity is carried on in close collaboration with clinical institutes and with private companies working in the biomedical, electronic and pharmaceutical fields.

Keywords

Micro-nano sensors, bioanalytics, lab-on-a-chip, 3D sensors, drug monitoring, aptamers, DNA quantification, trigate FET nanosensors, electrochemical impedance, circulating biomarkers.

Team Members Postdoctoral Fellows Enrico Accastelli Giulia Cappi Marco Letizia Enrico Tenaglia

PhD Students Elena-Diana Burghelea Anna Ferretti Samuel Kilchenmann Enrica Rollo Master’s Students Andrea De Micheli Edna Luz Sanchez Vera Administrative Assistant Homeira Salimi

Selected Publications » Cappi, G., Spiga, F., Moncada, Y., Ferretti, A., Beyeler, M., Bianchessi, M. Decosterd, L., Buclin, T., Guiducci, C. (2015) Label-free detection of Tobramycin in Serum by Transmission-LSPR. to appear in Analytical Chemsitry. » Spiga, F., Maietta, P., Guiducci, C., (2015). More DNA aptamers for small drugs: a capture SELE coupled with Surface Plasmon Resonance and High Throughput Sequencing. To appear in ACS Combinatorial Science. » Spiga, F.M., Bonyár, A., Ring, B., Onofri, M., inelli, A., Sántha, H., Guiducci, C., Zuccheri, G. (2014) Hybridization chain reaction performed on a metal surface as a means of signal amplification in SPR and electrochemical biosensors. Biosensors and Bioelectronics, 54:102-108. » Guiducci, C., Spiga, F.M. (2013). Another transistor-based revolution: On-chip qPCR . Nature Methods, 10 (7): pp. 617-61 . » Kilchenmann, S.C., Rollo, E., Bianchi, E., Guiducci, C. (2013). Metal-coated silicon micropillars for freestanding 3D-electrode arrays in microchannels. Sensors and Actuators, B: Chemical. 1 5 : 713-71 . » Cappi, G., Accastelli, E., Cantale, ., Rampi, M.A., Benini, L., Guiducci, C. (2013). Peak shift measurement of localized surface plasmon resonance by a portable electronic system. Sensors and Actuators, B: Chemical, 176: 225-231. » Temiz, Y., Guiducci, C., Leblebici, Y. (2013). Post-CMOS processing and 3-D integration based on dry-film lithography. IEEE Transactions on Components, Packaging and Manufacturing Technology, 3( ) :145 -1466.

EPFL School of Life Sciences - 2014 Annual Report

Hatzimanikatis Lab Vassily Hatzimanikatis

Associate Professor - School of Basic Sciences (SB)

http://lc b.epfl.ch

Vassily Hatzimanikatis received his PhD (1996) and MS (1994) in Chemical Engineering from the California Institute of Technology and his Diploma (1991) in Chemical Engineering from the Uni Patras. Over the years, he has held positions such as Group leader (ETH Zurich); Senior research Scientist (DuPont and Cargill) and Assistant Professor (Northwestern University). Prof. Hatzimanikatis has authored over 70 technical publications and has three patents and patent applications. He has given over 100 invited lectures. He is the associate editor of the journals Biotechnology & Bioengineering , Biotechnology Journal, Integrative Biology and Metabolic Engineering and on the editorial advisory board of four biotechnology journals.

LCSB develops expertise in the formulation of mathematical models of cellular processes, in process systems engineering methods for the integration, and in the analysis of experimental information from different levels. As most of this information in biological systems is partial and it is subject to uncertainty, researchers in LCSB develop methods that can account quantitatively for the uncertainty in the available information and can provide guidance on solving problems in biotechnology and medicine.

LCSB is one of the leading laboratories in the study of energetics and thermodynamics of complex cellular processes. Research in LCSB has also pioneered the development of computational methods for the discovery of novel metabolic pathways for metabolic engineering and synthetic biology. The applications areas of research in LCSB are: metabolic engineering and metabolic diseases, bioenergetics, protein synthesis, lipidomics, and drug discovery for infectious diseases.

Keywords

Metabolism, metabolic engineering, systems biology, computational biology, chemical biology.

Team Members

Postdoctoral Fellows Anirikh Chakrabarti Georgios Fengos Alexandros Kiparissides Georgios Savoglidis Katerina Zisaki PhD Students Stefano Andreozzi Meric Ataman Yves Berset Anush Chiappino Pepe Tiziano Dallavilla Noushin Hadadi Tuure Hameri Daniel Hernadez Gardiol Joana Piento Vieira Julien Racle Milenko Tokic Stepan Tymoshenko Research Associate Ljubisa Miskovic Administrative Assistant Christine Kupper

Selected Publications » » » »

Hadadi, N., Soh, K. C., Seijo, M., Zisaki, A., Guan, ., Wenk, M.R., and Hatzimanikatis . (2014). A computational framework for integration of lipidomics data into metabolic pathways. Metab Eng. 23:1- . Racle, J., Picard, F., Girbal, L., Cocaign-Bousquet, M., Hatzimanikatis, . (2013). A genome-scale integration and analysis of Lactococcus lactis translation data. PLoS Comput Biol. (10):e1003240. Tymoshenko, S., Oppenheim, R. D., Soldati-Favre, D., and Hatzimanikatis, . (2013). Functional genomics of Plasmodium falciparum using metabolic modelling and analysis. Brief Funct Genomics. 12(4):316-327. Fierro-Monti, I., Racle, J., Hernandez, C., Waridel, P., Hatzimanikatis, ., and uadroni, M. (2013). A novel pulse-chase SILAC strategy measures changes in protein decay and synthesis rates induced by perturbation of proteostasis with an Hsp90 inhibitor. PLoS One. 8(11):e80423. » Chakrabarti, A., Miskovic, L., Soh, K. C., and Hatzimanikatis, . (2013). Towards kinetic modeling of genome-scale metabolic networks without sacrificing stoichiometric, thermodynamic and physiological constraints. Biotechnol J. ( ):10431057.

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The Laboratory of Computational Systems Biotechnology (LCSB) focuses on the development of mathematical models and systems engineering frameworks for accelerating the design and purposeful manipulation of complex cellular processes.

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Research Interests

EPFL School of Life Sciences - 2014 Annual Report

Ijspeert Lab e

spee t

Associate Professor - School of Engineering (STI)

http://bi r b.epfl.ch/

Research Interests

Auke Ijspeert is an associate professor at the EPFL in the Institute of Bioengineering, and head of the Biorobotics Laboratory. He is also an Adjunct faculty at the Department of Computer Science at the University of Southern California. He has a “diplôme d’ingénieur” in physics from the EPFL, and a PhD in artificial intelligence from the University of Edinburgh. With his colleagues, he has received the Best Paper Award at ICRA2002, the Industrial Robot Highly Commended Award at CLAWAR2005, and the Best Paper Award at the IEEE-RAS Humanoids 2007 conference. He is an associate editor for the IEEE Transactions on Robotics. For more information see: http://biorob.epfl.ch.

Our research is at the intersection of robotics and computational neuroscience. It addresses the topics of movement control, sensorimotor coordination, and learning in autonomous robots with multiple degrees of freedom (from snake robots to quadruped robots to humanoid robots). Our ambition is two-fold: • to program and design robots that exhibit motor skills with the same efficiency, adaptivity, and robustness as animals, and • to get a better understanding of the functioning of animals using numerical simulation and robots as scientific tools. Together with neurobiologists (Jean-Marie Cabelguen and Sten Grillner), we have developed mathematical models of the neural circuits controlling locomotion in lower vertebrates. We have demonstrated how a primitive neural circuit for swimming like the one found in the lamprey can be extended by phylogenetically more recent limb oscillatory centers to explain the ability of salamanders to switch between swimming and walking. These models have been tested in an innovative salamander-like robot capable of swimming and walking.

We also develop a dynamical systems approach for controlling movements in robots. For instance, we designed the concept of dynamical movement primitives: nonlinear dynamical systems with well-defined attractor properties that can learn demonstrated discrete or rhythmic movements. Our methods are applied to various robots (quadruped, humanoid and reconfigurable modular robots) and more recently to lower limb exoskeletons for patients with locomotor deficiencies.

Keywords

Biorobotics, computational neuroscience, locomotion control, modeling of spinal cord circuits, central pattern generators.

Team Members Postdoctoral Fellows Bonardi Stéphane Colasanto Luca Crespi Alessandro Estier Thomas Melo Kamilo Müllhaupt Philippe Renjewski Daniel

PhD Students Ajallooeian Mostafa Eckert Peter Faraji Salman Horvat Tomislav Mutlu Mehmet Thiandackal Robin Tuleu Alexandre Van der Noot Nicolas Vespignani Massimo Administrative Assistant Fiaux Sylvie

Selected Publications » » » » » » »

A. Ijspeert. Biorobotics: Using robots to emulate and investigate agile animal locomotion, Science, vol. 346, num. 6206, p. 196-203, 2014. D. Floreano, A. Ijspeert and S. Schaal. Robotics and Neuroscience, Current Biology, vol. 24, p. R 10-R 20, 2014. F. Dzeladini, J. an Den Kieboom and A. Ijspeert. The contribution of a central pattern generator in a reflex-based neuromuscular model, Frontiers In Human Neuroscience, vol. , 2014. M. D. Mcdonnell, K. Boahen, A. Ijspeert and T. J. Sejnowski. Engineering Intelligent Electronic Systems Based on Computational Neuroscience, in Proceedings Of The IEEE, vol. 102, num. 5, p. 646-651, 2014. A. J. Ijspeert, J. Nakanishi, H. Hoffmann, P. Pastor and S. Schaal. Dynamical Movement Primitives: Learning Attractor Models for Motor Behaviors, Neural Computation, vol. 25, num. 2, p. 328-373, 2013. Crespi, A.; Karakasiliotis, K.; Guignard, A.; Ijspeert, A. J., Salamandra Robotica II: An Amphibious Robot to Study Salamander-Like Swimming and Walking Gaits, IEEE Transactions on Robotics, vol. 2 (2), p. 30 – 320, 2013. A. Sproewitz, A. Tuleu, M. espignani, M. Ajallooeian and E. Badri et al. Towards Dynamic Trot Gait Locomotion---Design, Control and Experiments with Cheetah-cub, a Compliant uadruped Robot, in International Journal of Robotics Research, vol. 32, num. , p. 32 - 50, 2013.

EPFL School of Life Sciences - 2014 Annual Report

Johnsson Lab Kai Johnsson

Full Professor - School of Basic Science (SB)

http://lip.epfl.ch

Research Interests

The primary research interests of the Johnsson group are in the field of chemical biology and its major scientific achievements were in the following three areas:

Keywords

Chemical biology, protein engineering, fluorescent probes.

Postdoctoral Fellows Rudolf Griss Julien Hiblot Grazvydas Lukinavicius Luc Reymond Alberto Schena Lin ue PhD Students Hellen Farrants Nioclas Goeldel Olvier Sallin Silvia Scarabelli Administrative Assistant Claudia Gasparini

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e uorescent probes One of the key strengths of the Johnsson group is its expertise in synthetic chemistry. This has allowed the group to design and synthesize various novel fluorescent probes to visualize biochemical activities.

Team Members

Selected Publications » Lukinavicius, G., Reymond, L., D’Este, E., Masharina, A., Gottfert, F., Ta, H., Guther, A., Fournier, M., Rizzo, S., Waldmann, H., Blaukopf, C., Sommer, C., Gerlich, D. W., Arndt, H. D., Hell, S. W., Johnsson, K. (2014). Fluorogenic probes for live-cell imaging of the cytoskeleton. Nature Methods. 11, 731. » Griss, R., Schena, A., Reymond, L., Patiny, L., Werner, D., Tinberg, C. E., Baker, D., Johnsson, K. (2014). Bioluminescent sensor proteins for point-of-care therapeutic drug monitoring. Nature Chem Biol. 10, 5 . » Haruki, H., Pedersen, M. G., Gorska, K. I., Pojer, F., Johnsson, K. (2013). Tetrahydrobiopterin biosynthesis as an off-target of sulfa drugs. Science. 340, 7. » Lukinavicius, G., Lavogina, D., Orpinell, M., Umezawa, K., Reymond, L., Garin, N., Gonczy, P., Johnsson, K. (2013). Selective Chemical Crosslinking Reveals a Cep57-Cep63-Cep152 Centrosomal Complex. Curr Biol. 23, 265. » Lukinavicius, G., Umezawa, K., Olivier, N., Honigmann, A., Yang, G., Plass, T., Mueller, ., Reymond, L., Correa, I. R. Jr., Luo, Z. G., Schultz, C., Lemke, E. A., Heppenstall, P., Eggeling, C., Manley, S., Johnsson, K. (2013). A near-infrared fluorophore for live-cell super-resolution microscopy of cellular proteins. Nature Chemistry. 5, 132.

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Kai Johnsson obtained his PhD at ETHZ in Organic Chemistry. After a postdoctoral stay at UC Berkeley he took a position as a tenuretrack assistant professor at EPFL in 1999. Continuing at the EPFL, Prof. Johnsson then became an Associate Professor (2005) and finally a Full Professor (2009). He has received several awards for his ground breaking work in protein engineering and chemical biology.

Protein-based tools for research in biology and medicine One of the main achievements of the lab is the development of a new class of protein tags, i.e. SNAP-tag, CLIP-tag and ACP-tag, which can be labeled with synthetic probes in living cells. These tags have become popular research tools as they enable scientists to approach problems that cannot be resolved with conventional techniques.

Drug mechanism of action The Johnsson group has a long-standing interest in studying the mechanism of action of clinically used drugs or drug candidates. For example, the group was able to identify the target of the important anti-inflammatory drug sulfasalazine, whose mechanism of action has remained obscure since its introduction in 1942! The Johnsson group furthermore identified an off-target for anti-bacterial sulfa drugs that provides a rational for the CNS side effects of this important class of drugs. This work should also translate into an improved medical use of sulfa drugs.

EPFL School of Life Sciences - 2014 Annual Report

Jolles-Haeberli Lab Brigitte Jolles-Haeberli

Adjunct Professor - School of Enginerring (STI) - Director of Center of Translational Biomechanics

http://cbt.epfl.ch/

Research Interests

We promote and support the transfer of findings from the basic science laboratory to clinical application with a strong relationship between clinicians and engineers for each specific project. Brigette Haeberli-Jolles graduated from EPFL with a MSc Diploma of Professional Engineer in Microtechnology in 1990. In 1995, she obtained her MD. She then received the Diploma in Clinical Epidemiology in 2002 and completed a Clinical Fellowship in Arthritis Surgery at the University of Toronto and obtained the FMH Specialist title in Orthopaedic the same year. In 2008 she was nominated Adjunct Professor (EPFL) where she heads the Interinstitutional Center of Translational Biomechanics (CBT). She was nominated Associate Professor (UNIL) in 2010 and is the director of the Swiss BioMotion Lab.

Our groups develop medical devices and wearable systems to characterize human mobility and locomotion in daily conditions. Based on these instruments, we provide objective clinical metrics for diagnosis and outcome evaluation of treatments as well as useful parameters to increase sport performances.

analyses, original solutions are developed such as fetal cell therapy, scaffolds with high mechanical properties or orthopaedic implants used as drug delivery systems.

Team Members

Keywords

PhD Student Adeliya Latypova

Orthopaedic engineering, translational research, numerical modelling, biomechanical analysis, surgery outcome evaluation, sport performance evaluation, regenerative therapy.

We also carry out work in tissue engineering of musculoskeletal tissues, implant and joints biomechanics, drug delivery systems and mechanobiology. A combination of biomechanical and biological approaches is used to describe and understand different clinical problems of interest such as bone loss following total joint arthroplasty, arthritis or intervertebral disc degeneration. Based on these

Postdoctoral Fellow Julien Favre

Master’s Students Alessandro Cavinato Pritish Chakravarty Laura Dalang Administrative Assistants Aline Inamahoro Center Groups

• LBO Lab • LMAM Lab for orthopaedic and sport medicine activities • Regenerative Therapy Unit (CHUV) • Swiss BioMotion Lab (CHUV)

Selected Publications » Grzesiak A, Aminian K, L cureux E, Jobin F, Jolles BM. Total hip replacement with a collarless polished cemented anatomic stem: clinical and gait analysis results at ten years follow-up. Int Orthop. 2014 Apr;3 (4):717-24. doi: 10.1007/ s00264-013-2186-9. » Hasenkamp W, illard J, Delaloye JR, Arami A, Bertsch A, Jolles BM, Aminian K, Renaud P. Smart instrumentation for determination of ligament stiffness and ligament balance in total knee arthroplasty. Med Eng Phys. 2014 Jun 36(6): 721-5. doi: 10.1016/j.medengphy.2013.12.001. PMID: 24405737. » Favre J, Erhart-Hledik JC, Andriacchi TP. Age-related differences in sagittal-plane knee function at heel-strike of walking are increased in osteoarthritic patients. Osteoarthritis Cartilage. 2014 Mar; 22(3):464-71. doi: 10.1016/j. joca.2013.12.014. PMID: 24445065. » Roshan-Ghias A, Terrier A, Jolles BM, Pioletti DP. Translation of biomechanical concepts in bone tissue engineering: from animal study to revision knee arthroplasty. Comput Methods Biomech Biomed Engin. vol. 17, num. , p. 45- 52, 2014. » Pichonnaz C, Bassin JP, Currat D, Martin E, Jolles BM. Bioimpedance for Oedema Evaluation after Total Knee Arthroplasty. Physiother Res Int 2013 Sep;1 (3):140-7. doi: 10.1002/pri.1540. » Nicodeme JD, L cherbach C, Jolles BM. Tibial tunnel placement in posterior cruciate ligament reconstruction: a systematic review. Knee Surg Sports Traumatol Arthros 2014 Jul;22(7):1556-62; DOI 10.1007/s00167-013-2563-3.

EPFL School of Life Sciences - 2014 Annual Report

Lacour Lab t ph n e

Tenure-track Assistant Professor - Bertarelli Foundation Chair in Neuroprosthetic Technology - Center for Neuroprosthetics - School of Engineering (STI)

http://l bi.epfl.ch We develop novel characterization tools adapted to mechanically compliant bioelectronic circuits. Moving soft bioelectronics forward requires innovation in the fields of materials science, fabrication, engineering and biocompatibility, and a multidisciplinary mindset.

Keywords

Microfabrication, soft bioelectronics, implantable electrodes, elastomer, electronic skin.

Team Members Postdoctoral Fellows De Luca Alba Gerratt Aaron Gupta Swati Kulmala Tero Minev Ivan Musick Kate PhD Students Gribi Sandra Guex Am lie Hirsch Arthur Michaud Hadrien Michoud Frédéric Paulou Cédric Romeo Alessia Wu Yi-Li

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Stéphanie P. Lacour holds the Bertarelli Foundation Chair in Neuroprosthetic Technology at the School of Engineering at the Ecole Polytechnique Fédérale de Lausanne. She received her PhD in Electrical Engineering from INSA de Lyon, France, and completed postdoctoral research at Princeton University (USA) and the University of Cambridge (UK). She is the recipient of the 2006 MIT TR35, a University Research Fellowship from the Royal Society (UK), a European Research Council ERC Starting Grant, the 2011 Zonta award and the 2014 World Economic Forum Young Scientist award.

Bioelectronics integrates principles of electrical engineering to biology, medicine and ultimately health. The Laboratory for Soft Bioelectronics Interfaces (LSBI) challenges and seeks to advance our fundamental concepts in man-made electronic interfaces applied to biological systems. Specifically, the focus is on designing and manufacturing electronic devices with mechanical properties close to that of the host biological tissues so that long-term reliability and minimal perturbation are induced in vivo and/or truly wearable systems become possible. Applications include assistive technologies for patients with impaired neurological functions in the form of soft implantable electrodes, and wearable interfaces in skin-like formats for prosthetic tactile skins. We use fabrication methods borrowed from the MEMS industry and adapt them to soft substrates like elastomers.

Master’s Students Pas Jolien Young Jolien Administrative Assistants Daidié Christel Weissenberger Carole

Selected Publications » Minev IR , Musienko P , Hirsch A, Barraud , Wenger N, Moraud EM, Gandar J, Capogrosso M, Milekovic T, Asboth L, Torres RF, achicouras N, Liu SP (2015). Electronic dura mater for long-term multimodal neural interfaces. Science, 347(621 ): 15 -63.

, Pavlova N, Duis S, Larmagnac A, oros J, Micera S, Z. Suo, Courtine G , and Lacour

» Gerratt AP, Sommer N, Lacour SP and Billard A (2014), Stretchable capacitive tactile skin on humanoid robot fingers - first experiments and results, 2014 IEEE-RAS International Conference on Humanoid Robots, Madrid, Spain, paper 202617. » Robinson A, Aziz A, Liu , Suo Z, and Lacour SP (2014). Hybrid stretchable circuits on silicone substrate, Journal of Applied Physics, 115(14): 143511. » D. J. Chew DJ, Zhu L, Delivopoulos E, Minev IR, Musick KM, Mosse CA, Craggs M, Donaldson N, Lacour SP, McMahon SB, and Fawcett JW (2013), A microchannel neuroprosthesis for bladder control after spinal cord injury in rat Science Translational Medicine, 5(210), 210ra155. » andeparre H, Liu , Minev IR, Suo Z, and Lacour SP (2013), Localization of folds and cracks in thin metal films coated on flexible elastomer foams, Advanced Materials, 25(22), 3117-21. » A. Romeo, . H. Liu, Z. G. Suo, and S.P. Lacour, Elastomeric substrates with embedded stiff platforms for stretchable electronics, Applied Physics Letters, 2013, 102(13), 131 04.

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Research Interests

EPFL School of Life Sciences - 2014 Annual Report

Lasser Lab Theo Lasser

Full Professor - School of Engineering (STI)

l b.epfl.ch

Research Interests

The Laboratoire d’Optique Biomédicale (LOB) pursues research on optical functional imaging for life sciences and medicine.

Theo Lasser is heading the Laboratoire d’Optique Biomédicale (LOB). He and his coworkers are focusing their research on functional imaging for biological and medical applications. The main research topics are coherent microscopy for small animal imaging applied to diabetes research, functional brain imaging related to neurodegenerative disease and super-resolution fluorescence microscopy for advanced cell imaging. Before joining EPFL he pursued an industry career at Carl Zeiss as R&D manager for ophthalmic instruments and in his last assignment as director of Carl Zeiss Research, Jena.

We pioneered Optical Coherence Microscopy (OCM) as a label-free 3D imaging modality. OCM has been successfully applied for high resolution imaging of islets of Langerhans in the pancreas of living mice. The latest achievement has been “diabetes imaging” where we succeeded in imaging transplanted islets (in the anterior eye chamber) during several weeks from the pre-diabetic to the final diabetic state in NOD mice. This animal model and imaging modality is an ideal platform for diabetes research and drug testing.

Our recent research on super-resolved cell imaging, based on SOFI, allows 3D living cell imaging with a spatial resolution < 80 nm. The fast 3D acquisition is an additional feature for functional cell monitoring. More images related to our research can be seen on www. voirestsavoir.ch .

Keywords

Optical microscopy, tomography, super-resolution, diabetes, Alzheimer disease, mitochondria.

Brain Imaging in rodents revealed the extra cellular plaque formation and its progression during several weeks. Recently we extended this OCM imaging towards functional brain imaging trying to “see” the brain response upon electrical stimuli with high spatial and temporal resolution.

Team Members Postdoctoral Fellows Jerome Extermann Taoufiq Harach Amir Nahas Marcin Sylwestrzak Daniel Szlag Tristan Bolmont PhD Students Corinne Berclaz Severine Coquoz Tomas Lukes Paul Marchand David Nguyen Azat Sharipov Miguel Sison Master’s Students Adrien Descloux Moritz Schmidlin Arik Girsault Technical Employee Antonio Lopez Engineer Antonio Lopez Administrative Assistant Noelia Simone

Selected Publications » » » » »

Geissbuehler, Stefan; Sharipov, Azat; Godinat, Aurelien; et al.. (2014) Live-cell multiplane three-dimensional super-resolution optical fluctuation imaging. Nature Communications 5, Article Number: 5 30 . Broillet, Stephane; Szlag, Daniel; Bouwens, Arno; et al. (2014)Visible light optical coherence correlation spectroscopy. Optics Express 22(18) : 21944-21957. Bouwens, Arno; Bolmont, Tristan; Szlag, Daniel; et al. (2014) uantitative cerebral blood flow imaging with extended-focus optical coherence microscopy. Optics Letters 3 (1) : 37-40. Geissbuehler, Matthias; Lasser, Theo. (2013). How to display data by color schemes compatible with red-green color perception deficiencies. Optics Express ,21( ): 62- 74. Bolmont, Tristan; Bouwens, Arno; Pache, Christophe; et al., Label-Free Imaging of Cerebral beta-Amyloidosis with Extended-Focus Optical Coherence Microscopy. (2012)Journal Of Neuroscience, 32 (42) :14548-14556 .

EPFL School of Life Sciences - 2014 Annual Report

Maerkl Lab Sebastian Maerkl

Associate Professor - School of Engineering (STI)

http://lbnc.epfl.ch Progress in biological engineering is also heavily dependent on technological and methodological innovation. To address these needs we are developing novel, state-ofthe-art microfluidic technologies and molecular methods to address current limitations in biological engineering and other fields.

Keywords

Microfluidics, systems biology, synthetic biology, diagnostics

Team Members Postdoctoral Fellow Francesco Piraino

PhD Students Matthew Blackburn Henrike Niederholtmeyer Francesca Volpetti Kristina Woodruff Ekaterina Petrova Master’s Students Zuzana Tatarova Amanda Verpoorte Administrative Assistant Helen Chong

Our specific biological interests lie primarily in reverse engineering gene regulatory networks, transcriptional regulation, transcription factor biophysics, cell-free synthetic biology, protein engineering, and in developing next-generation molecular diagnostic devices.

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Sebastian Maerkl received a B.S. degree in Biology and a B.S. degree with honors in Chemistry from FairleighDickinson University. He then joined the Biophysics and Biochemistry Option at Caltech as a graduate student and contributed to the early development of microfluidic technology. Prof. Maerkl was awarded the Demetriades-Tasfka-Kokalis prize for the best Caltech PhD thesis in the field of Biotechnology in 2008. He was awarded the 1st place at the Innovator’s Challenge, a competition amongst Stanford, UC Berkeley, and Caltech. Since 2008 Prof. Maerkl holds a position as an Assistant Professor at the EPFL in the Institute of Bioengineering and the School of Engineering and in 2012 received the EPFL Prix SSVAmbition.

The Maerkl lab conducts research at the interface of engineering and biology and we are active in the areas of systems biology, synthetic biology and molecular diagnostics. We are driven by a desire to learn how to rationally design and engineer biological systems. Unfortunately, despite a vast foundation of fundamental biological knowledge accumulated over the last century, it remains difficult to engineer biological systems, indicating that basic biological research alone is not sufficient to enable biological engineering. We propose that injecting engineering concepts into biology such as reverse engineering, quantitative analysis, and computational/biophysical modeling will enable biological engineering and fundamentally change how the scientific community and the general public applies biological systems in the 21st century.

Selected Publications » Knight B., Kubik S., Ghosh B., Bruzzone M.J., Geertz M., Martin ., Denervaud N., Jacquet P., Ozkan B., Rougemont J., Maerkl S.J., Naef F., and Shore D. (2014). Two distinct promoter architectures centered on dynamic nucleosomes control ribosomal protein gene transcription. Genes & Development. DOI: 10.1101/gad.244434.114 » Acimovic S.S., Ortega M.A., Sanz ., Berthelot J., Garcia-Cordero J.L., Renger J., Maerkl S.J., Kreuzer M., and uidant R. (2014). LSPR Chip for Parallel, Rapid, and Sensitive Detection of Cancer Markers in Serum. Nano Letters. DOI: 10.1021/ nl500574n. » Nobs J.B. and Maerkl S.J. (2014). Long-term single cell analysis of S. pombe on a microfluidic chemostat. PLoS One. DOI: 10.1371/journal.pone.00 3466. » Garcia-Cordero J.L. and Maerkl S.J. (2013). A 1,024-sample serum analyzer chip for cancer diagnostics. Lab on a Chip. DOI: 10.103 /C3LC51153G. » Niederholtmeyer H., Stepanova V. and Maerkl S.J. (2013). Implementation of cell-free genetic networks at steady-state. PNAS. DOI: 10.1073/pnas.1311166110. » Denervaud N., Becker J., Delgado-Gonzalo R., Damay P., Rajkumar A.S., Unser M., Shore D., Naef F. and Maerkl S.J. (2013). A chemostat array enables the spatio-temoral analysis of the yeast proteome. PNAS. DOI:10.1073/ pnas.1308265110. » Rajkumar A., Denervaud N. and Maerkl S.J. (2013). Mapping the fine-structure of a eukaryotic promoter input-output function. Nature Genetics. DOI:10.103 /ng.272 . » Woodruff K., Fidalgo L.M., Gobaa S., Lutolf M.P. and Maerkl S.J. (2013). Live Mammalian Cell Arrays. Nature Methods. DOI:10.103 /nmeth.2473.

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Research Interests

EPFL School of Life Sciences - 2014 Annual Report

Mermod Lab c

e m d

Full Professor - IBI- UNIL

http://www.unil.ch/bi tech/en/h me.html

Research Interests

Nic Mermod did a PhD on environmental biotechnology with Ken Timmis at the University of Geneva. As a postdoc with Bob Tjian at the University of California at Berkeley, he identified and characterized some of the first mammalian transcription factors. He then joined the University of Lausanne as an assistant Professor of the Swiss National Science Foundation, to become full professor and director of the Institute of Biotechnology. Nic’s laboratory is located at the Center for Biotechnology of UNIL and EPFL. He is also co-founder of Selexis SA, a biotechnology company developing therapeuticproducing cell lines, and he has authored a number of scientific publications and patents.

One of our project aims at identifying epigenetic regulatory sequences and/or DNA recombination pathways that mediate more predictable, higher and/or more stable expression of transgenes in mammalian cells, and to identify more effective gene transfer techniques. This work has led to the development of new methods that were successfully applied to the synthesis of therapeutic proteins, and which may improve the development of new approaches to treat muscular dystrophies by cell therapy. Stable and efficient production of heterologous proteins in mammalian cells and transgenic organisms is limited by technological bottlenecks. For instance, the establishment of stable cell lines requires the production and analysis of numerous clonal cell lines in order to detect the most efficient producer cells. Our work indicates that potent epigenetic insulator elements and microhomology mediated DNA recombination pathways act synergistically to mediate and stabilize very high expression of therapeutic proteins by cultured cells. These discoveries led to the creation of biotechnology companies, such Selexis SA in Switzerland and Selexis Inc. in the U.S., which have become world leaders in the manufacture of cells producing

recombinant therapeutic proteins. These genetic elements and transposable vectors also allow efficient expression of therapeutic genes in animal models of incurable human diseases. Our work has shown an improvement in the expression of therapeutic proteins, and therefore of the therapeutic efficacy in the treatment of animal models for Duchenne muscular dystrophy by gene therapy. Favorable results were also obtained from the use of adult stem cells that may be transplanted in cell therapies after gene transfer. By this work, which has been supported by the European Network of Excellence in Gene Therapy, the Swiss Telethon and the Swiss Foundation for Research on Muscle diseases, we hope to reach safe and effective therapies for these diseases.

Keywords

Molecular biotechnology, epigenetics, genomics, cell biology, gene expression.

Postdoctoral Fellows Niko Niederländer St phanie Renaud Niamh Harraghy Elena Aritonovska Solenne Bire uan Luo Lucille Pourcell PhD Students Ruthger van Zwieten Deborah Ley Simone Edelmann Kaja Kostyrko Yaroslav Shcherba Matthias Contie Pavithra Iyer Sandra Bosshardt

Engineers, Informaticians and Bioinformaticians Thomas Junier Etienne Lançon Daniel Peter Technicians Yves Dusserre Jacqueline Masternak Armindo Texeira Ione Gutscher

Selected Publications » » » » » » » » »

Team Members

Ley D, Puttini S, van Zwieten R, Iyer P, and Mermod N. (2014). A PiggyBac-mediated approach for muscle gene transfer or cell therapy. Stem Cell Res. 13:3 0-403 Administrative Assistant Majocchi S, Aritonovska E and Mermod N. (2014). Epigenetic regulatory elements associate with specific histone modifications to prevent silencing of telomeric genes. Nucl. Acids Res., 42:1 3-204 Nassim Berberat Le Fourn , Girod PA, Buceta M, Regamey A, and Mermod N. (2014). CHO cell engineering to prevent polypeptide aggregation and improve therapeutic protein secretion. Metab. Eng., 21: 1-102 Bire S, Casteret S, Ley D, Mermod N, Bigot Y, and Rouleux-Bonnin F. (2013). Optimization of PiggyBac gene delivery tool using mRNA and insulators. PloS ONE, :e 255 Arope S, Harraghy N, and Mermod N. (2013). Molecular characterization of a human matrix attachment region epigenetic regulator. PLoS ONE, 8:e79262 Pjanic M, Schmid CD, Gaussin A, Ambrosini G, Adamcik J, Pjanic P, Plasari G, Kerschgens J, Dietler G, Bucher P and Mermod N. (2013). Nuclear Factor I genomic binding associates with chromatin boundaries. BMC Genomics, 14: Ley D, Harraghy N, Le Fourn , Bire S, Girod P-A, Regamey A, Rouleux-Bonnin F, Bigot Y and Mermod N. (2013). MAR Elements and Transposons for Improved Transgene Integration and Expression. PLoS ONE, :e627 4 Puttini S, van Zwieten R, Saugy D, Lekka M, Hogger F, Ley D, Kulik AJ and Mermod N. (2013). MAR-mediated integration of plasmid vectors for in vivo gene transfer and regulation. BMC Molec. Biol., 14:26 van Zwieten RW, Puttini S, Lekka M, Witz G, Gicquel-Zouida E, Richard I, Lobrinus JA, Chevalley F, Brune H, Dietler G, Kulik A, Kuntzer T and Mermod N. (2014). Assessing dystrophies and other muscle diseases at nanometer scale by atomic force microscopy. NanoMedicine, 9:393-406

EPFL School of Life Sciences - 2014 Annual Report

Micera Lab vest

Associate Professor - Bertarelli chair in Translational Neurotechnology - Center for Neuroprosthetics -School of Engineering (STI)

http://tne.epfl.ch

Keywords

Implantable neuroprostheses, rehabilitation robotics, wearable devices, neuro-controlled artificial limbs, reaching and grasping, locomotion, functional electrical stimulation.

In 2014, we published the first example of a biodirectional arm neuroprosthesis in humans. We showed, for the first time, the possibility to develop a real-time bidirectional control of hand prostheses using intraneural peripheral electrodes. We were also deeply involved in the activities led by Professor Courtine’s team to develop a novel neuroprosthesis to restore locomotion using epidural electrical stimulation (EES). Finally, we developed

Selected Publications » Minev IR, Musienko P, Hirsch A, Barraud , Wenger N, Moraud EM, Gandar J, Capogrosso M, Milekovic T, Asboth L, Torres RF, achicouras N, Liu , Pavlova N, Duis S, Larmagnac A, r s J, Micera S, Suo Z, Courtine G, Lacour SP., Biomaterials. Electronic dura mater for long-term multimodal neural interfaces. Science. 2015 Jan ;347(621 ):15 -63. doi: 10.1126/science.1260318. » Wenger N, Moraud EM, Raspopovic S, Bonizzato M, DiGiovanna J, Musienko P, Morari M, Micera S, Courtine G., Closed-loop neuromodulation of spinal sensorimotor circuits controls refined locomotion after complete spinal cord injury., Science Translational Medicine. 2014 Sep 24;6(255):255ra133. doi: 10.1126/scitranslmed.300 325. » Nguyen TA, Ranieri M, DiGiovanna J, Peter O, Genovese , Perez Fornos A, Micera S.,A real-time research platform to study vestibular implants with gyroscopic inputs in vestibular deficient subjects.. IEEE Transaction on Biomedical Circuits and Systems 2014 Aug; (4):474- 4. doi: 10.110 /TBCAS.2013.22 00 . » Raspopovic S, Capogrosso M, Petrini FM, Bonizzato M, Rigosa J, Di Pino G, Carpaneto J, Controzzi M, Boretius T, Fernandez E, Granata G, Oddo CM, Citi L, Ciancio AL, Cipriani C, Carrozza MC, Jensen W, Guglielmelli E, Stieglitz T, Rossini PM, Micera S., Restoring natural sensory feedback in real-time bidirectional hand prostheses. , Science Translational Medicine 2014 Feb 5;6(222):222ra19. doi: 10.1126/scitranslmed.3006820. » Capogrosso M, Wenger N, Raspopovic S, Musienko P, Beauparlant J, Bassi Luciani L, Courtine G, Micera S. A computational model for epidural electrical stimulation of spinal sensorimotor circuits. Journal of Neuroscience 2013 Dec 4;33(4 ):1 326-40. doi: 10.1523/JNEUROSCI.16 -13.2013.

Team Members Scientists Jack DiGiovanna Stanisa Raspopovic Jacopo Rigosa

Postdoctoral Fellows Marco Capogrosso Martina Coscia Eduardo Martin-Moraud PhD Students Marco Bonizzato Andrea Crema Edoardo D’Anna Emanuele Formento Beryl Jehenne (visiting) Jenifer Miehlbradt T. Khoa Nguyen Francesco M. Petrini (visiting) Elvira Pirondini Sophie Wurth Master’s Students Yann Amoural Laura Dalong Drissi Daoudi Nicolas Duthilleul Philippe Fabrice Gabrielle Federici Ivan Furfaro Manasi Kane Nawal Noelle Kinani Antoine Philippides Isabelle Pitteloud Flavio Raschella’ Georgia Sousouri Aurelie Staphan

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Silvestro Micera is Associate Professor and Head of the Translational Neural Engineering Laboratory and Bertarelli Chair in Translational Neuroengineering at the Center for Neuroprosthetics and the Institute of Bioengineering. He received the Laurea degree in Electrical Engineering from the University of Pisa and the PhD in Biomedical Engineering from the Scuola Superiore Sant’Anna. In 2009 he was the recipient of the “Early Career Achievement Award” of the IEEE Engineering in Medicine and Biology Society. Dr. Micera’s research interests include the development of hybrid neuroprosthetic systems (interfacing the nervous system with artificial systems) and of mechatronic and robotic systems for function and assessment restoration in disabled and elderly persons.

The goal of the Translational Neural Engineering (TNE) Laboratory is to develop implantable neural interfaces and robotic systems to restore sensorimotor function in people with different kinds of disabilities (spinal cord injury, stroke, amputation, etc.). In particular, the TNE lab’s aim is to be a technological bridge between basic science and the clinical environment. Therefore, TNE’s novel technologies and approaches are designed and developed, starting from basic scientific knowledge in the fields of neuroscience, neurology and geriatrics. The idea being that the better we understand these fields, the better will be the development of clinical solutions.

a wearable system for functional electrical stimulation to restore grasping in highly disabled subjects. The system is currently in clinical testing in Italy.

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Research Interests

Administrative Assistant Anouk Hein

EPFL School of Life Sciences - 2014 Annual Report

Millán Lab José del R. Millán

Associate Professor - Defitech Foundation Chair in Non-Invasive Brain-Machine Interface - Center for Neuroprosthetics - School of Engineering (STI)

http://cnbi.epfl.ch

Research Interests

Jos del R. Millán holds the Defitech Chair at the cole Polytechnique Fédérale de Lausanne (EPFL). His research on brain-computer interfaces was nominated finalist of the European Descartes Prize 2001 and he has been named Research Leader 2004 by the journal Scientific American for his work on brain-controlled robots. He is the recipient of the IEEE Nobert Wiener Award 2011 for his seminal and pioneering contributions to non-invasive braincomputer interfaces. Dr. Millán is an IEEE SMC Distinguished Lecturer.

The Chair in Non-Invasive Brain-Machine Interface laboratory (CNBI) carries out research on the direct use of human brain signals to control devices and interact with our environment. In this multidisciplinary research, we are bringing together our pioneering work on the two fields of brain-machine interfaces and adaptive intelligent robotics. Our approach to design intelligent neuroprostheses balances the development of prototypes‚ where robust real-time operation is critical‚ and the exploration of new interaction principles and their associated brain correlates. A key element at each stage is the design of efficient machine learning algorithms for real-time analysis of brain activity that allow users to convey their intents rapidly, on the order of hundred milliseconds. Our neuroprostheses are explored in cooperation with clinical partners and disabled volunteers for the main purposes of motor restoration and rehabilitation.

BCI applications extend beyond disabled users, as it has the potential to augment the interaction experience by providing information associated to brain correlates of volitional cognitive processes. We are interested in decoding some of these processes during both covert behavior (no observable action) and while the user is undertaking natural actions such as eye movements to scan a scene or body movements to drive a car.

Team Members

Keywords

PhD Students Andrea Biasiucci Pierluca Borsó Lucian Gheorghe Zahra Khaliliardali Stéphanie Martin Michael Pereira Luca Randazzo Sareh Saeedi Christoph Schneider Huaijian Zhang

Brain-computer interfaces, neuroprosthetics, statistical machine learning, neuroscience, translational medicine, EEG, local field potentials, human-robot interaction.

We have continued to design and test brain-computer interface (BCI) principles for replacing lost motor functions and for enhancing interaction experiences. Users with motor disabilities have demonstrated the effectiveness of our brain-controlled devices, which are based on the voluntary, spontaneous modulation of EEG rhythms.

Postdoctoral Fellows Ricardo Chavarriaga Robert Leeb Aleksander Sobolewski Maria Laura Blefari I aki Iturrate Kyuhwa Lee Serafeim Perdikis

Master’s Student Laetitia Perroud Research Engineers avier Dubas Hadrien Renold Administrative Assistants Beatriz Descloux Najate G choul

Selected Publications » Chavarriaga, R., Sobolewski, A., and Millán, J.d.R. (2014). Errare Machinale Est: The Use of Error-related Potentials in Brain-Machine Interfaces. Front. Neurosci. :20 . doi:10.33 /fnins.2014.0020 . » Perdikis, S., Leeb, R., Williamson, J., Ramsey, A., Tavella, M., Desideri, L., Hoogerwerf, E.-J., Al-Khodairy, A., Murray-Smith, R., and Millán, J.d.R. (2014). Clinical Evaluation of BrainTree, a Motor Imagery Hybrid BCI Speller. J. Neural Eng. 11(3):036003. » Iturrate, I., Chavarriaga, R., Montesano, L., Minguez, J., and Millán, J.d.R. (2014). Latency Correction of Event-Related Potentials between Different Experimental Protocols. J. Neural Eng. 11(3):036005. » Carlson, T.E. and Millán, J.d.R. (2013). Brain-Controlled Wheelchairs: A Robotic Architecture. IEEE Robot. Automat. Mag. 20(1):65–73. » Leeb, R., Perdikis, S., Tonin, L., Biasiucci, A., Tavella, M., Molina, A., Al-Khodairy, A., Carlson, T., and Millán, J.d.R. (2013). Transferring Brain-Computer Interfaces beyond the Laboratory: Successful Application Control for Motor-Disabled Users. Artif. Intell. Med. 59(2):121–132. » Borton, D., Micera, S. Millán, J.d.R., and Courtine, G. (2013). Personalized Neuroprosthetics. Sci. Transl. Med. 5(210):210rv2.

EPFL School of Life Sciences - 2014 Annual Report

Pioletti Lab Dominique Pioletti

Associate Professor- Center of Translational Biomechanics - School of Engineering (STI)

http://lb .epfl.ch

Keywords

Biomechanics, orthopaedics, mechanobiology, implant, tissue engineering, translational research.

Team Members Group Leader Alexandre Terrier

Postdoctoral Fellow Philippe Abdel-Sayed PhD Students Ulrike Kettenberger Mohamadreza Nassajian Christoph Engelhardt Adeliya Latypova Tanja Hausherr Valérie Malfroy Camine Naser Nasrollahzadeh Mamaghani Jérôme Hollenstein Master’s Students Jules Bourgnon Nicolas Chatel Patrick Schwizer Sandra Gribi Stefania Rissone Raphael Obrist Anouk Grandegeorge Marco Ammann Annick Baur Arthur Hirsch Lab Assistant Sandra Jaccoud Administrative Assistant irginie Kokocinski

Selected Publications » » » » »

Kettenberger, U., Ston, J., Thein, E., Procter, P., Pioletti, D.P. (2014). Does locally delivered Zoledronate influence peri-implant bone formation – Spatio-temporal monitoring of bone remodeling in vivo. Biomaterials. 35:9995-10006. Nassajian Moghadam, M., Kolesov, ., ogel, A., Klok, H.A., Pioletti, D.P. (2014). Controlled release from a mechanically-stimulated thermosensitive self-heating composite hydrogel. Biomaterials. 35:450-456. Abdel-Sayed, P., Darwiche, S., Kettenberger, U., Pioletti, D.P. (2014). The role of energy dissipation of polymeric scaffolds in the mechanobiological modulation of chondrogenic expression. Biomaterials. 35:1 0-1 7. Gortchacow, M., Terrier, A., Pioletti, D.P. (2013). A flow sensing model for mesenchymal stromal cells using morphogen dynamics. Biophysical J. 104:2132-2136. Terrier, A., Larrea, ., Malroy-Camine, ., Pioletti, D.P., Farron, A. (2013). Importance of the subscapularis muscle after total shoulder arthroplasty. Clinical Biomechanics. 2 :146-150.

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Dominique Pioletti received his Master in Physics from the Swiss Federal Institute of Technology Lausanne (known as EPFL) in 1992. He pursued his education in the same Institution and obtained his PhD in biomechanics in 1997. Then he spent two years at UCSD as a post-doc fellow where he evaluated the reaction of bone cells in contact to orthopedic implant. From 2006 to 2013, he was an Assistant Professor at EPFL and since August 2013, was appointed Associate Professor of Biomechancis at EPFL.

The research topics of the laboratory include biomechanics and tissue engineering of musculo-skeletal tissues; mechano-transduction in bone, and development of orthopedic implant as drug delivery system. The Pioletti lab is a pioneer in the development of orthopedic implants used as drug delivery systems. The drug is delivered either passively from implant surface or through a smart delivery system using dissipative phenomena to trigger spatially and temporally the release of a drug. These approaches offer versatile solutions to the release of a drug for cartilage or nucleus pulposus tissues. Projects in tissue engineering combine biomechanical analysis for scaffold development, use of biomechanical stimulation to control and enhance tissue formation in scaffold and cell therapy for bone and cartilage tissues.

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Research Interests

EPFL School of Life Sciences - 2014 Annual Report

Psaltis Lab Demetri Psaltis

Full professor - Dean of the School of Engineering (STI)

http://l .epfl.ch

Research Interests

Demetri Psaltis was educated at Carnegie-Mellon University where he received his Bachelor of Science in Electrical Engineering and Economics degree in 1974, his Master’s degree in 1975, and his PhD in Electrical Engineering in 1977. In 1980, he joined the faculty of the California Institute of Technology (Caltech). He served as Executive Officer of the Computation and Neural Systems department at Caltech from 1992-1996. From 1996 until 1999 he was Director of the National Science Foundation research center on Neuromorphic Systems Engineering at Caltech and also director of the Center for Optofluidic Integration at Caltech. In 2007 he moved to EPFL where he is a professor and director of the Optics Laboratory, as well as the Dean of the School of Engineering.

The Optics Laboratory focuses on biological imaging and optofluidics. Biological imaging deals with phase conjugation through multimode fibers and biological tissues, imaging through biological media and nonlinear optics for bioparticle characterization. Optofluidics focuses on developing technologies for energy harvesting purposes by leveraging the advantages of microfluidic systems. Biological imaging We utilize imaging techniques to improve detection of the types of cochlear damage. In preliminary studies, two-photon fluorescence microscopy is used to detect the damage on individual hair cells located in the inner ear. We study second harmonic generation (SHG) from nanoparticles for new types of imaging applications. The coherent nature of SHG allows us to capture the complex radiated field information, thus allowing for many novel imaging applications.

We develop and research novel applications of ultrafast ablation for microsurgery. Specifically we are developing a catheter device to remove atheroscerotic plaque and a method to remove bone from the cochlea to allow for advanced imaging of the organ of corti. pto uidics By combining optical elements into microfluidic devices, optofluidic chips hold promise in the portable devices for applications such as environment monitoring, medical diagnosis and point of care testing.

Keywords

Optofluidics, nanoparticles, holography, nonlinear optics, phase conjugation, endoscopy, Solar energy, digital confocal microscope, laser ablation, optical microsurgery.

Team Members Scientists Donald Conkey Laurent Descloux Salma Farahi Miguel Modestino Ye Pu Marcin Zielinski

Postdoctoral Fellow Morteza Hasani Shoreh PhD Students Marilisa Romito Gr goire Laporte Mohammad Hashemi Nicolino Stasio Thomas Lanvin Administrative Assistant Carole Loeffen Berthet

Selected Publications » » » » » » » » »

Gr goire P. J. Laporte, Nicolino Stasio, Colin J. R. Sheppard, and Demetri Psaltis (2014), Resolution enhancement in nonlinear scanning microscopy through post-detection digital computation. Optica. 1 (6): 455-460. Claudia Rodriguez, Miguel A. Modestino, Christopher Moser and Demetri Psaltis (2014), Design and cost considerations for practical solar-hydrogen generators. Energy & Environmental science. 7: 3 2 . Choi JW, Hosseini Hashemi SM, Erickson D, Psaltis D (2014), A micropillar array for sample concentration via in-plane evaporation. Biomicrofluidics. (4): 04410 . Hosseini Hashemi SM, Choi JW, Psaltis D (2014), Solar thermal harvesting for enhanced photocatalytic reactions. Physical Chemistry Chemical Physics. 16 (11): 5137-5141. Yang , Pu Y, Psaltis D (2014), Imaging blood cells through scattering biological tissue using speckle scanning microscopy. Optics Express. 22 (3): 3405-3413. Laporte GPJ, Conkey DB, asdekis A, Piestun R, Psaltis D (2013), Double-helix enhanced axial localization in STED nanoscopy. Optics Express. 21 (25): 30 4-30 2. Goy A, Psaltis D (2013), Imaging in focusing Kerr media using reverse propagation. Photonics Research. 1 (2): 6-101. Yang, ., Pu, Y., Hsieh, C.L., Ong, C.A., Psaltis, D., Stankovich, K. (2013), Two photon microscopy of the mouse cochlea in situ for cellular diagnosis. Journal of Biomedical Optics. 18 (3): 031104. Papadopoulos, I.N., Farahi, S., Moser, C., Psaltis, D. (2013), High-resolution, lensless endoscope based on digital scanning through a multimode optical fiber. Biomedical Optics Express. 4 (2): 260-270.

EPFL School of Life Sciences - 2014 Annual Report

Radenovic Lab e s nd

den v c

Tenure-track Assistant Professor - School of Engineering (STI)

http://lben.epfl.ch/

Our current research is focused on three major directions: • Developing and using nanopores as a platform for molecular sensing and manipulation. In particular, we focus on solid-state nanopores realized either in glass nanocapillaries, or on suspended 2d-material membranes and standard silicon-nitride membranes.

• Developing super-resolution optical microscopy, based on single molecule localizations (SMLM) in cells with molecular-scale resolution, with an aim to extract quantitative information.

Keywords

Nanopores, 2d materials, nanocapillaries, biosensing, optical tweezers Anti-Brownian Electrokinetic (ABEL) trap, single molecule localization microscopy (SMLM) DNA, proteins, DNA-protein interaction.

• Studying how biomolecules function, especially how proteins and nucleic acids interact, using force-based manipulation single-molecule techniques, in particular optical tweezers, optical wrench system, Anti-Brownian Electrokinetic (ABEL) trap and combination of nanopore/nanocapillaries with OT.

Team Members Postdoctoral Fellows Ke Liu Hendrik Deschout Lorenz Steinbock Flavio Mor

PhD Students Roman Bulushev Jiandong Feng Michael Graf Martina Lihter Metin Kayci Arun Shivanandan Alexander Timin (visiting) Lab Assistant Lely Feletti Administrative Assistant Helen Chong

Selected Publications » R. D. Bulushev, L. J. Steinbock, S. Khlybov J. F. Steinbock and A. Radenovic, Measurement the position-dependent electrophoretic force on DNA in a glass nanocapillary, Nano Letters 2014. » H.-C. Chang and A. Radenovic, Electron spin resonance of nitrogen-vacancy defects embedded in single nanodiamonds in an ABEL trap M. Kayci, Nano Letters 14 ( ), pp 5335–5341 2014. » C. Macias-Romero, M.E. P. Didier, .Zubkovs, L. Delannoy, F. Dutto A. Radenovic, and S.Roke, Probing rotational and translational diffusion of nanodoublers in living cells on microsecond time scales Nano Letters 14 (5), pp 2552–2557 2014. » O. Lopez-Sanchez, . Koman, E. A. Llado, A. Fontcuberta i Morral, A. Radenovic, and A. Kis, Light Generation and Harvesting in a an der Waals Heterostructures, ACS Nano, (3), pp 3042–304 2014. » K. Liu, J. D. Feng, A. Kis and A. Radenovic, Atomically thin molybdenum disulfide nanopores with high sensitivity for DNA translocation, ACS Nano (3), pp 2504–2511 2014. » A.Fanget, F. Traversi, S. Khlybov, P. Granjon, A. Magrez, L. Forr and A. Radenovic, Nanopore integrated nanogaps for DNA detection, Nano Letters 14 (1), pp 244–24 2014. » L. J. Steinbock, R. Bulushev, S. Krishnan and A. Radenovic, DNA translocation through low noise glass nanopores, ACS Nano 7 (12), pp 11255–11262 2013. » F. Dutto, H. Martin, A. M. Fontcuberta and A. Radenovic, Enhancement of Second Harmonic Signal in Nanofabricated Cones, Nano Letters 13 (12), pp 604 –6054 2013 . » F. Traversi, C. Raillon, S. M. Benameur, K. Liu, S. Khlybov, M. Tosun, D. Krasnozhon, A.Kis and A. Radenovic, Detecting the translocation of DNA through a nanopore using graphene nanoribbons, Nature Nanotechnology , 3 – 45 2013. » O. L pez Sánchez, D.S. Lembke, M. Kayci, A. Radenovic and A. Kis, Ultrasensitive photodetectors based on monolayer MoS2, Nature Nanotechnology , 4 7–501 2013. » L.J. Steinbock, J.F. Steinbock and A. Radenovic, Controllable shrinking and shaping of glass nanocapilaries under electron irradiation, Nano Letters, 13 (4), pp 1717–1723 2013.

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Aleksandra Radenovic received her master’s degree in physics from the University of Zagreb in 1999 before joining Professor Giovanni Dietler’s Laboratory of Physics of Living Matter in 2000 at University of Lausanne. There she earned her Doctor of Sciences degree in 2003. In 2003 she was also awarded a research scholarship for young researchers from the Swiss Foundation for Scientific Research which allowed her to spend 3 years as postdoctoral fellow at the University of California, Berkeley (2004 2007). Before joining EPFL as Assistant Professor in 2008, she spent 6 months at NIH and Janelia Farm. In 2010 she received the ERC starting grant, and in 2015 SNF Consolidator Grant. Her group is interested in using novel nanomaterials and single molecule experimental techniques to study fundamental questions in molecular and cell biology.

LBEN works in the research field that can be termed single molecule biophysics. We develop techniques and methodologies based on optical imaging, biosensing and single molecule manipulation with the aim to monitor the behaviour of individual biological molecules and complexes in vitro and in live cells.

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Research Interests

EPFL School of Life Sciences - 2014 Annual Report

Renaud Lab Philippe Renaud

Full Professor - School of Engineering (STI)

http://lmi

Research Interests

Philippe Renaud joined EPFL in 1993 as an assistant Professor in Microengineering. He was appointed full Professor in 1997. He is Scientific Director of the EPFL Centre of Microtechnology (CMI). Prior to joining EPFL, Professor Philippe Renaud worked in the Sensors and Actuators group at the Swiss Centre for Electronics and Microtechnology (CSEM) in Neuchâtel, Switzerland. He received a Ph.D. in Physics from the University of Lausanne, Switzerland. He conducted his post-doctoral research at the University of California, Berkeley, USA, and then at the IBM Zürich Research Laboratory in Switzerland.

The research of the Microsystems Laboratory 4 (LMIS4) is related to micro and nanotechnologies in biomedical applications (BioMEMS), with emphasis on cell-chips, nanofluidics and bioelectronics. We use the microfabrication technologies available in the cleanrooms of the EPFL Center of MicroNanoTechnology (CMI) for the realization of our devices. We developed new methods in flow cytometry and cell sorting based on the dielectric properties of cells. We also study micro-bioreactors for on-chip co-culture of cells in drug screening and toxicology applications in such areas as breast cancer and Alzheimer’s disease. In parallel we work on a variety of other biomedical applications such as capillary driven blood plasma separation, bioelectronic implants for neural recordings and stimulation, biosensors for environmental monitoring, 3D cell printing and biomechanical sensors for eye pressure or articular implants.

Research on basic nanofluidic phenomena is used to increase our understanding of molecular transport and electrical conductance in nanochannels. Our group has been involved in the valorisation of our research by means of the creation of several start-up companies.

Keywords

Nanotechnology, microfabrication, BioMEMS, cell chip nanofluidics, flow-cytometry, dielectric cell sorting, micro-bioreactor, drug screening, toxicology, implant, neural recording , biosensor, molecular transport.

.epfl.ch

Team Members Postdoctoral Fellows & Engineers Amélie Beduer Arnaud Bertsch Thomas Braschler Harald van Lintel Robert Meissner Niccolo Piacentini

PhD Students David Bonzon Jonathan Cottet Carolin Drieschner David Forchelet Guillaume Petitpierre Yufei Ren Ludovic Serex Mojtaba Taghipoor Stefano Varricchio Master’s Students Stéphanie Becker Niklas van Neyghem Gaelle Thurre Administrative Assistant Sylvie Clavel

Selected Publications » » » » »

A. B duer, T. Braschler, O. Peric, G. E. Fantner and S. Mosser et al. A Compressible Scaffold for Minimally Invasive Delivery of Large Intact Neuronal Networks, Advanced Healthcare Materials,.4, 2, 301, 2015. J. J. andersarl, A. Mercanzini and P. Renaud. Integration of 2D and 3D Thin Film Glassy Carbon Electrode Arrays for Electrochemical Dopamine Sensing in Flexible Neuroelectronic Implants, Advanced Functional Materials,25,1, p. 7 , 2015. M. Shaker, L. Colella, F. Caselli, P. Bisegna and P. Renaud. An impedance-based flow microcytometer for single cell morphology discrimination, Lab on a Chip,14,14, 254 , 2014. A. Kunze, S. Lengacher, E. Dirren, P. Aebischer and P. J. Magistretti et al. Astrocyte–neuron co-culture on microchips based on the model of SOD mutation to mimic ALS, in Integrative Biology, 5, 7, 64, 2013. B. Eker, R. Meissner, A. Bertsch, K. Mehta and P. Renaud. Label-Free Recognition of Drug Resistance via Impedimetric Screening of Breast Cancer Cells, PLoS ONE, , 3, e5742, 2013.

EPFL School of Life Sciences - 2014 Annual Report

Roke Lab Sylvie Roke

Associate Professor - Julia Jacobi Chair in Photomedicine - School of Engineering (STI)

http://lbp.epfl.ch/ Topics: • The unexplained charging of hydrophobic/ aqueous interfaces, • The formation and stabilization of amphiphilic aqueous interfaces • The formation and molecular properties of the electric double layer and the role that charge plays in biology.

Sum frequency scattering: Probes molecular composition, orientation, interactions and dynamics on nanoscopic 3D interfaces (e.g. nanodroplets, lipid vesicles).

• Theoretical models that can link our optical readouts to interfacial electrostatic potentials and chirality.

Second harmonic scattering: Probes correlations between water molecules in aqueous systems.

• The role water plays in cellular dynamics, such as the electrical, metabolic and mechanical activity of neurons.

Multiphoton / second harmonic microscopy: based on our scattering technology a high throughput microscope that allows for a 3-4 orders of magnitude improvement in acquisition time was constructed, which can be used for probing cell dynamics, label-free.

Keywords

Team Members

Postdoctoral Fellows Carlos Macias-Romero Gabriele Tocci Chungwen Liang PhD Students Yixing Chen Marie Didier Yvonne Hu Filip Kovacik Cornelis Lütgebaucks Orly Tarun Nikolay Smolentsev Evangelia Zdrali Vitalijs Zubkovs Administrative Assistant Rebecca eselinov

Water, aqueous interfaces, nonlinear optics / light scattering / imaging, biological imaging, nanodroplets & particles, membranes.

Selected Publications » C. Macias-Romero, M. E. P. Didier, P. Jourdain, P. Marquet, P. Magistretti, O. B. Tarun, . Zubkovs, A. Radenovic, and S. Roke. (2014). High throughput second harmonic imaging for label-free biological applications. Opt. Express. 22 (25), 31102-31112 » C. Macias-Romero, M. E. P. Didier, L. Delannoy, F. Dutto, A. Radenovic, S. Roke. Probing rotational and translational diffusion of nanodoublers in living cells on microsecond time scales. (2014). Nano Lett. 14, 2552–2557 » R. Scheu, B. M. Rankin, Y. Chen, K. C Jena, D. Ben-Amotz, S. Roke. Charge Asymmetry at Aqueous Hydrophobic Interfaces and Hydration-Shells. (2014). Angew. Chem. Int. Ed.. 53, 560- 563 » R. Scheu, Y. Chen, H. B. de Aguiar, B. M. Rankin, D. Ben-Amotz, S. Roke. Specific ion effects in surfactant hydration and nanodroplet stabilization. (2014). J. Am. Chem. Soc.. 136, 2040 – 2047 » J-S. Samson, R. Scheu, N. Smolentsev, S. W. Rick, S. Roke. Sum Frequency Spectroscopy of the Hydrophobic Nanodroplet/Water Interface: Absence of Hydroxyl Ion and Dangling OH Bond Signatures. (2014). Chem. Phys. Lett. Frontiers. 615, 124-130 » R. Scheu, Y. Chen, M. Subinya, S. Roke. Stern layer formation induced by hydrophobic interactions, a molecular level study. (2013). J. Am. Chem. Soc..135, 1 330 – 1 335

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Sylvie Roke studied chemistry and physics at Utrecht University (highest honors) and graduated from Leiden University (PhD, highest honors, nonlinear optics). In 2005 she became MaxPlanck Group Leader position (Stuttgart). She moved to EPFL in 2011. She was awarded the LJ Oosterhoff prize (NL, 2003), an Alexander von Humboldt Fellowship (De, 2005), the Minerva Prize (NL, 2006), the Hertha Sponer prize (De, 2006), an ERC starting grant (EU, 2009), membership to the German Young Academy (De, 2010), the Julia Jacobi chair in photomedicine (EPFL, 2011), and an ERC consolidator grant (EU, 2014).

Water is the liquid of life. Its quantum, molecular, and microscopic properties are essential in understanding the complexity of life. The active role that water plays in biology can be understood better by developing and using label-free and non-invasive optical methods that report on multiple length scales, from quantum effects to millisecond/micrometer time and length scales. Examples include:

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Research Interests

EPFL School of Life Sciences - 2014 Annual Report

Stellacci Lab ncesc

Full Professor - Constellium Chair - School of Engineering (STI) - Director of Integrative Food and Nutrition Center

http:// unmil.epfl.ch

Research Interests

Francesco Stellacci graduated in Materials Engineering at the Politecnico di Milano in 1998 with a thesis on photochromic polymers with Prof. Giuseppe Zerbi and Mariacarla Gallazzi. In 1999 he moved to the Chemistry Department of the University of Arizona for as a post-doc in the group of Joe Perry in close collaboration with the group of Seth Marder. In 2002 he moved to the Department of Materials Science and Engineering at the Massachusetts Institute of Technology as an assistant professor. He was then promoted to associate without (2006) and with tenure (2009). In 2010 he moved to the Institute of Materials at EPFL as a full Professor. He holds the Constellium Chair. Francesco was one of the recipients of the Technology Review TR35 35 Innovator under 35” award in 2005, and the Popular Science Magazine “Brilliant 10” award in 2007. He has been a Packard Fellow starting 2005.

The Supramolecular Nano-Materials and Interfaces Laboratory (SuNMIL) research focuses on interfacing supramolecular chemistry to nanoscale materials and surface engineering. One of the overarching goals of the group stems from a simple observation. A bird’s eye view of any folded protein shows a complex surface composed of hydrophobic and hydrophilic patches closely packed. To date, little is known on the fundamental properties that such packing determines. SuNMIL aims at finding these properties. They can be basic physical chemistry ones (i.e. interfacial energy, PNAS ‘08, Nature Materials ‘09) as well as biological interactions (interactions with cell membranes, Nature Materials ‘08, Nature Communications ‘14).

The Laboratory spans many fields, from synthesis and characterization to property measurements, with a multidisciplinary approach and many active collaborations. All forms of diversity are welcomed and fostered.

Keywords

Nanoparticles, nanoclusters, supramolecules, mixed selfassembled monolayers, biological interactions.

Team Members Postdoctoral Fellows Guldin Stefan Quy Ong

Le Ouay Benjamin Timothée Nicolas

Jones Samuel Thomas

PhD Students Allegri Sergio

Athanasopoulou Evangelia Nefeli

Bekdemir Ahmet Ertem Bekdemir Elif Güven Zekiye Pelin Jacob Silva Paulo Henrique Kocabiyik zgün Luo Zhi Müller Marie Nianias Nikolaos Ricci Maria goto Zhao Shun

Administrative Assistant Chiara Donini

Selected Publications » R. C. an Lehn, M. Ricci, P. H. J. Silva, P. Andreozzi and J. Reguera et al. Lipid tail protrusions mediate the insertion of nanoparticles into model cell membranes, in Nature Communications, vol. 5, 2014. » Y.-S. Yang, R. Carney, y P., F. Stellacci and D. J. Irvine, Enhancing Radiotherapy by Lipid Nanocapsule-Mediated Delivery of Amphiphilic Gold Nanoparticles to Intracellular Membranes, Acs Nano, vol. , num. , p. 2- 002, 2014. » R. Huang, R. R. Carney, K. Ikuma, F. Stellacci and B. L. T. Lau, Effects of Surface Compositional and Structural Heterogeneity on Nanoparticle-Protein Interactions: Different Protein Configurations, Acs Nano, vol. , num. 6, p. 5402-5412, 2014. » S. Sabella, R. P. Carney, . Brunetti, M. A. Malvindi, N. Al-Juffali, G. ecchio, S. M. Janes, O. M. Bakr, R. Cingolani, F. Stellacci and P. P. Pompa, A general mechanism for intracellular toxicity of metal-containing nanoparticles, Nanoscale, vol. 6, num. 12, p. 7052-7061, 2014. » . Lehn, C. Reid, P. U. Atukorale, R. P. Carney, Y.-S. Yang, F. Stellacci, D. J. Irvine and A. Alexander-Katz, Effect of Particle Diameter and Surface Composition on the Spontaneous Fusion of Monolayer-Protected Gold Nanoparticles with Lipid Bilayers, Nano Letters, vol. 13, num. 9, p. 4060-4067, 2013. » . L. S. Lapointe, A. T. Fernandes, N. C. Bell, F. Stellacci and M. M. Stevens, Nanoscale Topography and Chemistry Affect Embryonic Stem Cell Self-Renewal and Early Differentiation, Advanced Healthcare Materials, vol. 2, num. 12, p. 16441650, 2013.

EPFL School of Life Sciences - 2014 Annual Report

Stergiopulos Lab Nikos Stergiopulos

Full Professor - School of Engineering (STI)

http://lhtc.epfl.ch

Keywords

Cardiovascular mechanics, hemodynamics, atherosclerosis, hypertension, ocular mechanics and glaucoma filtration surgery, erectile dysfunction, implantable devices.

Team Members

Postdoctoral Fellows Rodrigo Araujo Fraga da Silva Bram Trachet PhD Students Thiresia Gialourou Orestis Vardoulis Adan Villamarin Lydia Aslanidou Research & Technical Staff Michel Bachmann Stéphane Bigler Fabiana Fraga Sylvain Roy Administrative Assistants Tamina Sissoko Sylvia Widmer

Selected Publications » illamarin A, Stergiopulos N, Bigler S, Mermoud A, Moulin A, Roy S. (2014) In vivo testing of a novel adjustable glaucoma drainage device. Investigative ophthalmology & visual science, 55:7520-4. » Papaioannou TG, Protogerou AD, Stergiopulos N, ardoulis O, Stefanadis C, Safar M, Blacher J. (2014) Total arterial compliance estimated by a novel method and all-cause mortality in the elderly: the PROTEGER study. Age, 36: 661. » Fraga-Silva RA, Costa-Fraga FP, Faye Y, Sturny M, Santos RA, da Silva RF and Stergiopulos N. (2014) An increased arginase activity is associated with corpus cavernosum impairment induced by hypercholesterolemia. The journal of sexual medicine, 11:1173-81. » illamarin A, Roy S, Bigler S, Stergiopulos N. (2014) A new adjustable glaucoma drainage device. Investigative ophthalmology & visual science, 55:1 4 -52. » Papaioannou TG, ardoulis O, Stergiopulos N. (2014) alidation of algorithms for the estimation of pulse transit time: where do we stand today Annals of biomedical engineering, 42:1143-4.

roups

Nikos Stergiopulos studied Mechanical Engineering at the National Technical University of Athens, Greece and obtained his Ph.D. in Biomedical Engineering from Iowa State University in 1990. His research interests are Hemodynamics, Cardiovascular Mechanics and Medical Implant Technology. He has authored more than 150 publications and holds more than 15 patents in medical technology. He co-founded EndoArt, world leader in telemetric implants for the treatment of congenital heart disease and morbid obesity, Antlia SA, developer of implantable drug delivery pumps and Rheon Medical, developer of the implantable shunt for the surgical treatment of glaucoma.

The Laboratory of Hemodynamics and Cardiovascular Technology (LHTC) focuses is on the relation between blood flow and the development, progression and regression of cardiovascular disease. We also study the interaction between the heart and arterial system and the resulting wave propagation phenomena, with the goal of understanding hypertension and aging as well to improve diagnostic and blood flow monitoring techniques. Development of implants and non-invasive or mini-invasive technologies for the diagnosis and treatment of disease is also a major objective.

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Research Interests

EPFL School of Life Sciences - 2014 Annual Report

Van de Ville Lab Dimitri Van de Ville

Tenure-track Assistant Professor - SNSF Professor - School of Engineering (STI)

http://miplab.epfl.ch

Research Interests

Dimitri Van De Ville holds an SNSF Professorship with Tenure-Track at the School of Engineering at the EPFL. He has a joint affiliation with the Department of Radiology and Medical Informatics at the University of Geneva. He received his M.S. and Ph.D. in Computer Sciences from Ghent University, Belgium. He has been the Chair of the Biomedical Imaging & Signal Processing (BISP) Technical Committee of the IEEE Signal Processing Society. In 2012, he received the Pfizer Research Award in the category ‘Neurosciences and Diseases of the Nervous System’ for the work on fractal organization of the rapid switching between scalp topographies in spontaneous EEG, which was published in the Proceedings of the National Academy of Sciences. In 2014, he was the recipient of a NARSAD Independent Investigator Award.

MIPLab’s mission is to advance our understanding of human brain function in health and disorder using non-invasive imaging techniques. To that aim, we pursue the development and integration of innovative data-processing tools at various stages of the acquisition, analysis, and interpretation pipeline of neuroimaging data. The first highlight is on modelling of functional brain networks at the systems level; i.e., based on whole-brain functional magnetic resonance imaging (fMRI). Using graph theory, multiscale techniques, and pattern recognition we are able to identify and characterise brain networks in a meaningful way during cognitive tasks, as well as alterations by neurological conditions, which opens the potential for new imaging-based biomarkers that might for instance complement neuropsychological testing in prodromal stage of Alzheimer’s Disease. The second highlight is on temporal dynamics of these networks during spontaneous activity. We have pioneered subspace discovery methods for dynamic functional connectivity, which reveal meaningful interactions between large-scale distributed networks in terms of ongoing fluctuations. These techniques bring us closer to capturing the global brain state, which is essential for future development of invasive and non-invasive neuroprosthetics, such as neurofeedback based on real-

time fMRI. Finally, we can also relate the slow dynamics of fMRI back to fast millisecond-scale EEG signals.

Keywords

Signal processing, neuroimaging, pattern recognition, network modeling, neurofeedback, fMRI, EEG, cognitive & clinical applications.

Team Members Postdoctoral Fellows Isik Karahanoglu Yury Koush Djalel Meskaldji Elena Migacheva Maria Giulia Preti Gwladys Rey Frank Scharnowski PhD Students Zafer Dogan Kirsten Emmert Jeffrey Kasten Rotem Kopel Nora Leonardi Naghmeh Ghazaleh David Nguyen Master’s Students Alessandro Cavinato Marta Comino Jeremy Hofmeister Chiara Musimeci Giorgio Policella Davide Zanchi Administrative Assistant Ruth Fiaux

Selected Publications » » » » »

J. A. Kasten, T. etterli, F. Lazeyras, D. an De ille, 3D-printed Shepp-Logan phantom as a real-world benchmark for MRI, Magnetic Resonance in Medicine, in press. N. Leonardi, W. Shirer, M. Greicius, D. an De ille, Disentangling dynamic networks: separated and joint expressions of functional connectivity patterns in time, Human Brain Mapping, vol. 35, pp. 5 4-5 5, 2014. J. Richiardi, S. Achard, H. Bunke, D. an De ille, Machine learning with brain graphs, IEEE Signal Processing Magazine, vol. 30, pp. 5 -70, 2013. I. Karahanoglu, C. Caballero Gaudes, F. Lazeyras, D. an De ille, Total activation: fMRI deconvolution through spatio-temporal regularization , NeuroImage, vol. 73, pp.121-134, 2013. N. Leonardi, J. Richiardi, M. Gschwind, S. Simoni, J.-M. Annoni, M. Schluep, P. uilleumier, D. an De ille, Principal components of functional connectivity: a new approach to study dynamic brain connectivity during rest, NeuroImage, vol. 83, pp. 937-950, 2013.

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EPFL School of Life Sciences - 2014 Annual Report

GHI

Global Health Institute

The research portfolio at the GHI includes a balanced mixture of basic and translational work. Mechanisms of host-pathogen interactions and innate and acquired immunity against disease are being studied using multidisciplinary approaches. A unique feature of the GHI is its ability to tackle crucial world health issues by harnessing cutting edge technologies developed elsewhere at EPFL to underpin research on diagnostics, drugs and vaccines as well as disease mechanisms. Prominent amongst these are the nanotechnologies, micro-engineering and bioinformatics. Aware of the impact of the microbiota on human health, the GHI is actively developing new programs in this area. http://sv.epfl.ch/

Stewart Cole - Director

GHI - Global Health Institute

Since its foundation in 2006, the Global Health Institute (GHI) has contributed to the understanding, diagnosis, prevention and treatment of infectious diseases, which account for half of the deaths in the developing world and claim 18 million human lives every year. The GHI is comprised of nine groups, all engaged in different facets of research linked to human health but with strong emphasis on diseases of truly global importance such as HIV/AIDS and tuberculosis. The current workforce comprises ~120 students, postdoctoral-fellows, technicians and scientists, representing more than 25 different nations.

EPFL School of Life Sciences - 2014 Annual Report

Ablasser Lab Andrea Ablasser

Tenure-track Assistant Professor

http://abla

Introduction

After graduating in medicine at the University of Munich, Germany in 2008, Andrea Ablasser moved to the University of Bonn to do her post-doctoral research which focused on understanding innate nucleic acid sensing mechanism that lead to an antiviral immune response. In 2014, the Ablasser lab was opened as part of the Global Health Institute in the School of Life Sciences of the EPFL.

The innate immune system is the first line of defense against pathogen infection. Central to this task are so called pattern recognition receptors, which allow the cells of the immune system to sense the presence of microbes and to respond accordingly. Our research focus is centered on delineating intracellular nucleic acid sensing pathways, which constitute one major innate sensing strategy during viral and bacterial infection. During infection viral or bacterial DNA or RNA is detected in the cytosol of host cells by distinct nucleic acid sensors, which upon activation lead to the induction of antiviral and pro-inflammatory gene expression. Recently, it was shown that the cytosolic nucleotidyltransferase cyclic GMP AMP synthase (cGAS) is the major receptor for intracellular DNA, which upon activation leads to the synthesis of a second messenger cyclic dinucleotide, cyclic GMP-AMP (cGAMP). This second messenger molecule in turn stimulates the endoplasmic reticulum protein Stimulator of Interferon Genes (STING) to trigger downstream signaling. In our previous work we characterized the nature of the second messenger cGAMP, which represents an unorthodox molecule that is composed of a 2`-5` and a 3`-5`phosphodiester linkage. Intriguingly, we have recently described that this second messenger system takes advantage of gap junction mediated cGAMP transfer to propagate an antiviral immune response rapidly towards neighboring cells. Of note, the two-receptor system of cGAS and STING not only plays a pivotal role during pathogen infection, but it also seems to be key in mediating stress responses by sensing endogenous DNA species that arise during tissue damage and cell death.

Focus for 2015

One major focus of our current work is centered on the pathogen Mycobacterium tuberculosis (Mtb), the causative agent of Tuberculosis. As such it is known that intracellular detection of mycobacterium-derived products is key for the initiation of an innate immune response. But while the receptors responsible for the inflammatory part of the innate immune response had been identified, the sensor system responsible for activation of the type I interferon pathway after infection with Mtb remained elusive. Ongoing work from our laboratory in collaboration with the laboratory of Stewart Cole now demonstrates that the cGAS-STING pathway is essential for mounting type I interferon production upon infection with Mtb. For the future we now aim to understand the precise molecular mechanism that underlies the activation of intracellular DNA sensing mechanism in the setting of Mtb infection in more detail. Another focus of our current research is to delineate the cause of the rare, congenital autoimmune disease Aicardi-GoutiĂ¨res Syndrome (AGS). Previously we had demonstrated that DNA sensing through cGAS plays a key role in the initiation of this complex autoimmune disorder. We are now trying to understand the molecular mechanism of cGAS activation and we are aiming at identifying agents that block the cGAS-STING pathway, which could serve as a novel therapeutic opportunity for AGS patients.

Keywords

Innate immunology, antiviral immunity, Type I Interferons, nucleic acid sensing.

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EPFL School of Life Sciences - 2014 Annual Report

Team Members Postdoctoral Fellows Muhammet Fatih Gülen Michael Heymann

PhD Student Simone Haag

Technician Sonia Garcia

Administrative Assistant Marisa Marciano Wynn

GHI - Global Health Institute

Schematic representation of the activation of the innate immune system through virus sensing mechanisms that activate IFN and ISG production in the infected as well as neighboring cells. The secreted IFNs, in turn induce the production of the full set of ISGs as well as other genes.

Selected Publications » » » » »

Ablasser A, Hemmerling I, Schmid-Burgk JL, Behrendt R, Roers A, Hornung . TRE 1-deficiency triggers cell-autonomous immunity in a cGAS-dependent manner.Journal of Immunology. 2014 Jun 15;1 2(12):5 3-7. Ablasser A, Schmid-Burgk JL , Hemmerling I, Horvath G, Schmidt T, Latz E, Hornung . Cell intrinsic immunity spreads to bystander cells via the intercellular transfer of cGAMP.Nature. 2013 Nov 2 ;503(7477):530-4. Ablasser A, Goldeck M, Cavlar T, Deimling T, Witte G, R hl I, Hopfner K-P, Ludwig J, Hornung . cGAS produces a 2 -5 -linked cyclic dinucleotide second messenger that activates STING.Nature 2013 Jun 20;4 (7454):3 0-4. Civril F, Deimling T, de Oliveira Mann C. C, Ablasser A, Moldt M, Witte G, Hornung , Hopfner K-P. Structural mechanism of cytosolic DNA sensing by cGAS.Nature 2013 Jun 20;4 (7454):332-7. Hornung , Hartmann R, Ablasser A, Hopfner K.-P. OAS and cGAS: unifying concepts in the sensing and signaling in response to cytosolic RNA and DNA.Nature Reviews Immunology. 2014 Aug;14( ):521- .

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EPFL School of Life Sciences - 2014 Annual Report

Blokesch Lab e

esch

Tenure-track Assistant Professor

http://bl

Introduction and Lab Description

Melanie Blokesch studied biology at Ludwig-MaximiliansUniversity (LMU) in Munich, Germany. In 2004 she obtained her PhD degree with highest honor from the LMU Munich based on her work on bacterial hydrogen production and metalloenzyme maturation. Her thesis was honored by the German Academy of Sciences Leopoldina and the German Association for General and Applied Microbiology. From 2005 to 2009 she worked as a postdoctoral fellow at Stanford University (USA) before being appointed as tenure-track assistant professor within the School of Life Sciences of EPFL.

The research of our group focuses on the question “How and why do bacteria evolve to become facultative human pathogens ?” Our model organism is Vibrio cholerae, the causative agent of cholera. Cholera is still widespread around the globe with up to 5 million cases every year. As the infection is linked to contaminated water, cholera is primarily a disease of developing countries. The goal of our research is to link the ecology of the organism with the epidemiology of the disease in order to learn more about the pathogen’s evolution. V. cholerae is a normal member of aquatic habitats and is often found associated with small crustaceans as part of the zooplankton. Under these conditions V. cholerae is able to induce a developmental program known as natural competence for genetic transformation, which allows the bacterium to take up free DNA from the surroundings and to recombine the DNA into its own genome. Natural competence for transformation is one out of three modes of horizontal gene transfer and therefore contributes to the spread of antibiotic resistance cassettes, virulence genes, and pathogenicity islands. During the last years we have focused on the regulatory circuits driving natural competence in V. cholerae in order to understand the environmental factors governing this process. More recently, we also started investigating the DNA uptake process itself. DNA uptake involves a macromolecular complex, which we are studying using cell biology-based approaches. Apart from these topics we are also interested in the interaction of V. cholerae with free-living amoebae and the role that virulence factors play in this context.

Keywords

Horizontal gene transfer, evolution of human pathogens, bacterial regulatory networks, cholera, environmental hosts.

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Results Obtained in 2014

Localization and visualization of the DNA uptake machinery DNA uptake machineries are generally not well understood. We therefore investigated the mechanistic aspects of the DNA uptake process. To do so, we genetically engineered V. cholerae to enable visualization of the subcellular localization of the essential competence protein ComEA. We showed that upon the addition of external DNA to competent cells, ComEA re-localized and formed discrete foci, which co-localized with the incoming DNA. Next, we used bacterial genetic approaches to better understand the shuffling role of ComEA between the outside of the cells and the inner membrane of the bacterium. Finally, we used timelapse microscopy imaging to visualize DNA uptake in real time. Our data strongly suggest that DNA uptake is promoted through ratcheting and entropic forces associated with ComEA binding. Killing for DNA: The type VI secretion system of Vibrio cholerae fosters horizontal gene transfer V. cholerae is considered an important model organism for elucidating virulence regulation. In this context, the involvement of quorum sensing (QS) and a predatory killing device (the type VI secretion system, T6SS) have been extensively studied even though the T6SS is considered to be “silent” (under laboratory conditions) in pandemic V. cholerae isolates. Much less is known about the bacterium’s environmental lifestyle, where it often associates with the chitinous surfaces of small crustaceans. We recently showed that the chitin and QS-dependent competence regulon includes the T6SS-encoding gene cluster and that the T6SS contributes to enhanced horizontal gene transfer by means of natural transformation. Moreover, we used live-cell imaging to visualize the T6SS-mediated killing of prey cells and the subsequent uptake of their DNA by predator cells. Our results indicate that the chitin-dependent induction of the T6SS enhances horizontal gene transfer by deliberate killing of neighboring non-immune cells and absorption up of their DNA (see Figure).

EPFL School of Life Sciences - 2014 Annual Report

Team Members Postdoctoral Fellows David Adams Milena Jaskolska Lisa Metzger Charles Van der Henst

PhD Student Noémie Matthey

Technicians Sandrine Borgeaud Tiziana Scrignari

Administrative Assistant Marisa Marciano Wynn

GHI - Global Health Institute

Horizontal gene transfer is achieved through deliberate killing of prey cells. Competence-induced V. cholerae (predator; red) were mixed with prey cells (green) and imaged. The appearance of rounded and lysed prey is followed by absorption of the released DNA by the predator (indicated by the arrows).

Selected Publications » Borgeaud S., Metzger L.C., Scrignari T., and Blokesch M. (2015) The type VI secretion system of Vibrio cholerae fosters horizontal gene transfer. Science, 347:63-67. » Lo Scrudato M., Borgeaud S., Blokesch M. (2014) Regulatory elements involved in the expression of competence genes in naturally transformable Vibrio cholerae. BMC Microbiol., 14: 327. » Kühn J., Finger F., Bertuzzo E., Borgeaud S., Gatto M., Rinaldo A., Blokesch M. (2014) Glucose- but not rice-based oral rehydration therapy enhances the production of virulence determinants in the human pathogen Vibrio cholerae. PLoS Negl. Trop. Dis., : e3347. » Seitz P., Blokesch M. (2014) DNA transport across the outer and inner membrane of naturally transformable Vibrio cholerae is spatially but not temporally coupled. mBio, 5:e0140 -14. » Metzger L.C., Blokesch M. (2014) Composition of the DNA-uptake complex of Vibrio cholerae. Mob. Genet. Element., 4: e2 142. » Seitz P., Pezeshgi Modarres H., Borgeaud S., Bulushev R.D., Steinbock L.J., Radenovic A., Dal Peraro M., Blokesch M. (2014) ComEA Is Essential for the Transfer of External DNA into the Periplasm in Naturally Transformable Vibrio cholerae Cells. PLoS Genet., 10: e1004066. » Venkova-Canova T., Baek J.H., FitzGerald P.C., Blokesch M., Chattoraj D.K. (2013) Evidence for two Different Regulatory Mechanisms Linking Replication and Segregation of Vibrio cholerae Chromosome II. PLoS Genet., : e100357 . » Seitz P., Blokesch M. (2013) DNA-uptake machinery of naturally competent Vibrio cholerae. Proc. Natl. Acad. Sci. USA, 110:17 7- 2. » Lo Scrudato M., Blokesch M. (2013) A transcriptional regulator linking quorum sensing and chitin induction to render Vibrio cholerae naturally transformable. Nucleic Acids Res., 41: 3644-5 .

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EPFL School of Life Sciences - 2014 Annual Report

Cole Lab

Stewart T. Cole

Full Professor - Director of the Global Health Institute - GHI

http://c le lab.epfl.ch/

Introduction

Professor Stewart Cole is an internationally acclaimed authority on the pathogenicity, drug resistance, evolution and genomics of the tubercle and leprosy bacilli. His laboratory is currently focused on discovering new drugs to treat tuberculosis. The findings of his research are of direct relevance to public health and disease-control in both the developing world and the industrialized nations. He has published over 300 scientific articles and been honored by many professional prizes, decorations and awards.

The Cole laboratory, UPCOL, is using a multidisciplinary approach to tackle major public health problems such as tuberculosis (TB), Buruli ulcer and leprosy. The laboratory is home to experts in genomics, functional genomics, bioinformatics, biochemistry, chemistry, chemical biology, molecular microbiology, cellular microbiology and structural biology. Using genome biology as a platform we are actively involved in discovering new drugs to treat TB and believe that knowledge gained through discovery must be broadly and swiftly disseminated. Given the global importance of the TB problem, we are trying to strike the correct balance between competition and collaboration. As part of a major, international collaboration UPCOL is leading the More Medicines for Tuberculosis (MM4TB) integrated project from the European Commissionâ&#x20AC;&#x2122;s Seventh Framework Program. The goal of MM4TB is to validate pharmacologically five new TB drug targets and to discover at least one family of compounds for development as a drug candidate. In this context, we have discovered many interesting leads for development including the natural product, pyridomycin, the thienopyrimidines, the carboxyquinoxalines and, above all, the benzothiazinone (BTZ) series. The latter gave rise to PBTZ169, a highly potent drug candidate that irreversibly inhibits an essential enzyme called DprE1, which plays a critical role in the biogenesis of the mycobacterial cell wall. The preclinical development of PBTZ16 is being undertaken by the not-for-profit foundation Innovative Medicines for Tuberculosis (iM4TB), an EPFL spin-off.

Keywords

Tuberculosis, leprosy, drug discovery, pathogenesis.

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Results Obtained in 2014

TB Drug Discovery Among our most notable achievements was solving the crystal structure of the flavoenzyme DprE1 in complex with BTZ043 and PBTZ16 . This explains how these inhibitors act and provides a template for further rational drug design. We have also shown that PBTZ169 is compatible with all leading TB drugs and drug candidates and thus has the potential for inclusion in a new combination therapy. Protein secretion and pathogenicity The ESX-1 secretion system, the major virulence determinant of M. tuberculosis, is required for the export of small helical-hairpin proteins from the ESAT-6 family as well as other effector proteins of unknown function. We are using an integrated approach to elucidate the organization, architecture, structure and function of this ATP-driven secretory apparatus. The EspB protein has been shown to bind bioactive phospholipids with prominent roles in eukaryotic cell signaling and to act independently of ESAT-6. A regulatory map of the M. tuberculosis genome We are studying gene regulation by using chromatin-immunoprecipitation of DNA-binding proteins in conjunction with high-throughput sequencing to localize the various binding sites along the genome. We mapped all the RNA polymerase, NusA and EspR binding sites in two different strains in the log and stationary phases of growth. Regulatory information is displayed in TubercuList, http://tuberculist.epfl.ch/. Phylogeography of leprosy Despite the successful implementation of multidrug therapy, leprosy remains a serious public health problem in several countries. We have developed an epidemiological tool that employs SNP (single nucleotide polymorphism) analysis of M. leprae, to monitor transmission of the disease. We retraced the spread of leprosy in the Middle Ages from skeletal remains (Figure). Together with the WHO, we are also monitoring the emergence of drug resistance worldwide.

EPFL School of Life Sciences - 2014 Annual Report

Team Members Postdoctoral Fellows Andrej Benjak Jeffrey Chen Ruben Hartkoorn Raju Mukherjee Florence Pojer Jan Rybniker Claudia Sala Pushpendra Singh

PhD Students Charlotte Avanzi Benjamin Blasco Gaëlle Kolly Benoit Lechartier Lou Ye Zhang Ming Nina Odermatt

Master’s Student Stéphanie Cherbuin

Technicians Stefanie Boy-Röttger Philippe Busso Anthony Vocat

Administrative Assistants Suzanne Dubsky Cécile Prébandier

GHI - Global Health Institute

Skull of leprosy victim SK2 from Winchester, UK, circa 1270 used as source of ancient M. leprae DNA for genome sequence analysis (Schuenemann et al. 2013. Science 341: 179-183.)

Selected Publications » Chen, J.M., Zhang, M., Rybniker, J., Boy-Rottger, S., Dhar, N., Pojer, F., and Cole, S.T., 2013. Mycobacterium tuberculosis EspB binds phospholipids and mediates EsxA-independent virulence. Molecular Microbiology : 11541166. » Chen, J.M., Zhang, M., Rybniker, J., Basterra, L., Dhar, N., Tischler, A.D., Pojer, F., and Cole, S.T., 2013. Phenotypic profiling of Mycobacterium tuberculosis EspA point mutants reveals that blockage of ESAT-6 and CFP-10 secretion in vitro does not always correlate with attenuation of virulence. Journal of Bacteriology 1 5: 5421-5430. » Hartkoorn, R.C., Pojer, F., Read, J.A., Gingell, H., Neres, J., Horlacher, O.P., Altmann, K.H., and Cole, S.T., 2014. Pyridomycin bridges the NADH- and substrate-binding pockets of the enoyl reductase InhA. Nature Chemical Biology 10: 6- . » Schuenemann, V.J., Singh, P., Mendum, T.A., Krause-Kyora, B., Jager, G., Bos, K.I., Herbig, A., Economou, C., Benjak, A., Busso, P., Nebel, A., Boldsen, J.L., Kjellstrom, A., Wu, H., Stewart, G.R., Taylor, G.M., Bauer, P., Lee, O.Y., Wu, H.H., Minnikin, D.E., Besra, G.S., Tucker, K., Roffey, S., Sow, S.O., Cole, S.T., Nieselt, K., and Krause, J., 2013. Genome-wide comparison of medieval and modern Mycobacterium leprae. Science 341: 17 -1 3. » Uplekar, S., Rougemont, J., Cole, S.T., and Sala, C., 2013. High-resolution transcriptome and genome-wide dynamics of RNA polymerase and NusA in Mycobacterium tuberculosis. Nucleic Acids Research 41: 6177. » Zumla, A., Nahid, P., and Cole, S.T., 2013. Advances in the development of new tuberculosis drugs and treatment regimens. Nature Reviews Drug Discovery 12: 3 -404.

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EPFL School of Life Sciences - 2014 Annual Report

Fellay Lab c

es e

SNSF Professor

http:// ella

Introduction

Jacques Fellay is a medical scientist with expertise in infectious diseases and human genomics. He obtained an MD from the University of Lausanne and a PhD from the University of Utrecht. Jacques Fellay joined the EPFL in April 2011 as an SNSF Professor; he is also a Group Leader at the Swiss Institute of Bioinformatics and a Visiting Physician at the Service of Infectious Diseases of the CHUV in Lausanne. In 2012, he was awarded the National Latsis Prize for his work on HIV and HCV host genomics.

Research in the Fellay lab focuses on human genomics of infection. Using a range of contemporary DNA and RNA analysis strategies, we explore the genetic roots of inter-individual differences in response to infectious agents. The work in the lab includes both classical genetics of infection susceptibility that measures clinical outcome, and a novel approach investigating the imprint of human polymorphisms on pathogen genetic diversity. In an effort to identify rare genetic variants conferring extreme susceptibility to specific infections, we use a combination of exome and RNA sequencing in patients with unusually severe clinical presentations upon infection with HIV, hepatitis B virus and respiratory viruses, as well as in children with bacterial sepsis. Candidate genes and variants are then genetically validated and functionally characterized. Our group is leading a large international project that aims at understanding how human genetic variation impacts HIV control. In collaboration with >25 cohorts or centers, we have collected genome-wide genotyping data on ~11,000 HIV infected individuals with clinical follow-up, allowing an unprecedented description of the impact of common genetic variants on HIV disease. To improve understanding of human-virus interactions at the genomic level, we also developed an innovative strategy to simultaneously analyze host and pathogen genetic variation. We are currently applying it to HIV, hepatitis C virus, cytomegalovirus and Epstein Barr virus infections. Finally, we collaborate with colleagues from the EPFL I&C Faculty to develop innovative solutions for genomic privacy, an essential trust-building component on the road toward genomic-based medicine.

Results Obtained in 2014

The past 2 years have seen important progress in our work on HIV host genomics. We coordinate the International Collaboration for the Genomics of HIV (ICGH), which has three main goals 1) To identify common genetic markers (>1% frequency) associating with HIV disease progression 2) To identify likely causal variants underlying associated regions through fine-mapping and 3) To quantify the proportion of variation in HI disease progression that can be attributed to host genetics (heritability). Meta-analyses of HIV acquisition and HIV control phenotypes have been completed. In addition, we are investigating the influence of rare polymorphisms that occur within genes. This project uses exome sequencing to identify mutations that alter protein sequence (missense, frameshift and nonsense) and test them for an impact on HIV viral load individually (i.e. a single variant), in combination within a gene (i.e. burden of variation) and across relevant gene sets (i.e. gene networks). Currently we have obtained and analyzed exome sequence data on ~1,000 HIV infected patients. We also developed an online compendium of host genomic data in HIV biology and disease (www.guavah.org). This intuitive web interface allows queries and supports validation of the rapidly growing body of host genomic information pertinent to HIV research. After the publication of our joint analysis of human and viral genomes (Bartha et al, 2013), we further developed the genome-to-genome strategy, notably by using it for other chronic viral diseases. This pioneering work also allowed us to start new academic and industrial collaborations. We have been working on different aspects of genomic privacy in strong collaboration with the group of Prof JP Hubaux (EPFL IC). In particular, studies aiming at protecting and evaluating genomic privacy in medical tests and personalized medicine have resulted in a number of conference papers and patents.

Keywords

Human genomics, infectious diseases, host-pathogen interactions, deep-sequencing, translational genomics, genomic privacy, personalized medicine.

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EPFL School of Life Sciences - 2014 Annual Report

Team Members Postdoctoral Fellows Paul McLaren Istvan Bartha Christian Hammer Nimisha Chaturvedi Thomas Junier

PhD Students Samira Asgari Ana Bittencourt Petar Scepanovic Christian Thorball

Master’s Student Caroline Perraudin

Administrative Assistant Marisa Marciano Wynn

GHI - Global Health Institute

Results of human-HIV “genometo-genome” association analyses (from Bartha et al, 2013). Associations between (A) human SNPs and HIV viral load (B) human SNPs and HIV amino acids; (C) HLA class I genes and associated SNPs in the region (D) Associations projected on the HIV proteome.

Selected Publications » » » » »

Regoes RR, McLaren PJ, Battegay M, Bernasconi E, Calmy A, Günthard HF, Hoffmann M, Rauch A, Telenti A and Fellay J. (2014). Disentangling human tolerance and resistance against HI . PLoS Biology. 12( ):e1001 51. Rausell A, Mohammadi P, McLaren PJ, enarios I, Fellay J and Telenti A. (2014) Analysis of stop-gain and frameshift variants in human innate immunity genes. PLoS Computational Biology. 10(7):e1003757. Bartha I, McLaren PJ, Ciuffi A, Fellay J and Telenti A. (2014). GuavaH: A compendium of host genomic data in HI biology and disease. Retrovirology. 11(1):6. Bartha I, Carlson JM, Brumme CJ, McLaren PJ, Brumme ZL, et al. (2013) A Genome-to-Genome Analysis of Associations between Human Genetic ariation, HI -1 Sequence Diversity, and iral Control. eLife. 2:e01123. McLaren PJ, Coulonges C, Ripke S, van den Berg L, Buchbinder S, et al. (2013) Association Study of Common Genetic ariants and HI -1 Acquisition in 6,300 Infected Cases and 7,200 Controls. PLoS Pathogens. (7): e1003515. » Lane J, McLaren PJ, Dorrell L, Shianna KV, Stemke A, et al. (2013) A genome-wide association study of resistance to HIV infection in highly exposed uninfected individuals with hemophilia A. Human Molecular Genetics. 22( ):1 03-1 10. » Apps R, i Y, Carlson JM, Chen H, Gao , et al. (2013) Opposing effects of HLA-C expression level in viral versus inflammatory disease. Science. 340(612 ): 7- 1.

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EPFL School of Life Sciences - 2014 Annual Report

Harris Lab c

Associate Professor

http://harri

Introduction

Nicola Harris was born in New Zealand where she completed her undergraduate studies and PhD thesis. In 2002 she moved to Switzerland as a postdoctoral fellow where she worked with Hans Hengartner and the Nobel Laureate Rolf Zinkernagel at the Institute for Experimental Immunology, University of Zurich. In July 2005 she joined the ETH Zurich as an Assistant Professor and in August 2009 she moved to the Global Health Institute, Department of Life Sciences, EPFL where she was recently promoted to the position of Associate Professor.

The intestinal mucosa represents an extensive interface between the body and the external environment that is constantly exposed to environmental micro-organisms. Amongst these commensal bacteria are present in vast numbers (1012 per gram of intestinal contents) in all individuals at all times. Worms (helminths) can also establish chronic infections within our intestines and were present in a near ubiquitous manner throughout mammalian evolution. Today intestinal helminths still infect approximately 1/3 of the world’s population, with the heaviest infections found in children living in poor communities within developing countries. Our work aims to investigate: • how the immune system can provide protection against heavy burdens of intestinal helminths, and • how intestinal helminths and/or commensal bacteria can modulate the responsiveness of our immune system. In regard to the latter aim we would like to understand why and how reduced exposure to specific intestinal bacteria species and/or intestinal helminths can predispose towards increased autoimmune and allergic diseases.

Keywords

Mucosal immunology, intestinal helminths, intestinal microbiota, allergy.

lab.epfl.ch/

Results Obtained in 2014

As part of our earlier work we uncovered an essential role for antibodies in providing effective immunity against helminth parasites. In 2013-2014 we expanded on these findings to show that these antibodies function by activated macrophages to attach to and paralyze these large multicellular parasites. We also identified the antibody isotype and host receptors involved in this response and found a very surprisingly role for antibodies normally associated with bacterial but not helminth infection. We are now investigating the regulation of protective antibody production following helminth infection with the hope of building better strategies for vaccine development in the future. We also noted a novel role for antibody-cellular interactions in regulating wound healing following helminth infection. Wound healing forms an integral arm of the host response to helminths as these large multicellular organisms migrate through various tissues causing widespread damage. Our findings indicate that the immune response functions not just to attack these larvae but also to promote tissue repair. This latter work in on-going and we hope to publish our findings in early 2015. In a separate project we investigated how mammals regulate the extent and type of immune responses occurring in the gut and identified two important innate cytokines, TSLP and IL-1 as key factors in the decision as to whether to raise a pro or anti-inflammatory response against intestinal bacteria and helminths respectively. This work is now complete and we are currently focusing our efforts on understanding how responses in the lymphoid organs, particularly those of non-immune stromal cells, regulate the extent of immune activation. 2013-4 also saw continuation of a project aimed at investigating the interactions between intestinal helminths and commensal bacteria. This project has revealed an ability of helminths to regulate inflammatory diseases such as allergy indirectly through alterations to intestinal bacteria and we expect to publish these novel findings in the upcoming year.

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EPFL School of Life Sciences - 2014 Annual Report

Team Members PhD Students Luc Lebon Ilaria Mosconi Alexis Rapin Beatrice Volpe

Master’s Students Marion Chassouant Jade Sternberg Morgan Study

Administrative Assistant Caroline Rheiner

GHI - Global Health Institute

Postdoctoral Fellows Julia Esser-von Bieren Lalit Kumar Dubey Duncan Sutherland Mario Zaiss

Cover Image for the Journal of Immunology Feb 1st 2015: Motility of the infective larval stage of the intestinal helminth Heligmosomoides polygyrus bakeri shown in temporal color code (120 frames, 60 seconds).

Selected Publications » Esser-von Bieren J, Volpe B, Kulagin M, Sutherland DB, Guiet R, Seitz A, Marsland BJ, Verbeek JS, Harris NL. (2015). Antibody-Mediated Trapping of Helminth Larvae Requires CD11b and Fc Receptor I. J Immunol. 1;1 4(3):1154-63 » Zaph C, Cooper PJ, Harris NL. (2014). Mucosal immune responses following intestinal nematode infection. Parasite Immunol. 36( ):43 -52. Review. » Trompette A, Gollwitzer ES, Yadava K, Sichelstiel AK, Sprenger N, Ngom-Bru C, Blanchard C, Junt T, Nicod LP, Harris NL, Marsland BJ. (2014). Gut microbiota metabolism of dietary fiber influences allergic airway disease and hematopoiesis. Nat Med. 20(2):15 -66. » Esser-von Bieren, Julia; Mosconi, Ilaria; Guiet, Romain; Piersigilli, Alessandra; olpe, Beatrice; Chen, Fei; Gause, William C.; Seitz, Arne; erbeek, J. Sjef; Harris, Nicola. (2013). Antibodies Trap Tissue Migrating Helminth Larvae and Prevent Tissue Damage by Driving IL-4R -Independent Alternative Differentiation of Macrophages. Plos Pathogens. (11) e1003771. » Zaiss, Mario M.; Maslowski, Kendle M.; Mosconi, Ilaria; Guenat, Nadine; Marsland, Benjamin J.; Harris, Nicola L. (2013). IL-1β Suppresses Innate IL-25 and IL-33 Production and Maintains Helminth Chronicity. PLoS pathogens. 9(8) e1003531 » Mosconi, I.; Geuking, M. B.; Zaiss, M. M.; Massacand, J. C.; Aschwanden, C.; Kwong Chung, C. K. C.; Mccoy, K. D.; Harris, N. L. (2013). Intestinal bacteria induce TSLP to promote mutualistic T-cell responses. Mucosal Immunol. (6)6: 157-67 » Yadava K, Sichelstiel A, Luescher IF, Nicod LP, Harris NL, Marsland BJ. (2013). TSLP promotes influenza-specific CD T-cell responses by augmenting local inflammatory dendritic cell function. Mucosal Immunol. 6(1): 3- 2

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EPFL School of Life Sciences - 2014 Annual Report

Lemaitre Lab n

t e

Full Professor - Director of the Doctoral Program in Molecular Life Sciences (EDMS)

http://lemaitrelab.epfl.ch/

Introduction

Our group uses Drosophila and its powerful genetics as a model to analyze integrated physiological questions at the organismal level. We currently have three main axes of researches focusing on:

Bruno Lemaitre obtained his PhD in 1992 with Dario Coen at the University Pierre and Marie Curie (Paris) on the P element transposition in Drosophila. Next, he joined the laboratory of Jules Hoffmann (Strasbourg, France) as a research associate where he began a genetic dissection of the Drosophila antimicrobial response. In 1998, Dr Lemaitre started his own laboratory on Drosophila immunity at the Centre Génétique Moléculaire (Gif-sur-Yvette, France). In 2007, he was appointed professor at EPFL.

Drosophila innate immunity Our research focuses on understanding mechanisms of microbial infection and corresponding host defense responses in Drosophila. Our current project is to delete systematically all genes belonging to large immune gene families both individually and collectively. We are especially interested in the molecular mechanisms underlying phagocytosis and encapsulation, two poorly characterized insect immune defenses. The Drosophila-Spiroplasma interaction: a model for insect endosymbiont Virtually every species of insect harbors facultative bacterial endosymbionts (ex. Wolbachia,) that are transmitted from females to their offspring. These symbionts play crucial roles in the biology of their hosts manipulating reproduction and protecting from pathogens. In spite of growing interest in endosymbionts, very little is known about the molecular mechanisms underlying most endosymbiont-insect interactions. Our laboratory analyses the interaction between Drosophila and its endosymbiont Spiroplasma poulsonii. We believe that the knowledge generated on the Drosophila-Spiroplasma interaction will serve as a paradigm for other endosymbiont-insect interactions that are less amenable to genetic studies. The digestive tract: an interactive barrier Aside from its central role in digesting and absorbing nutrients, the inner lining of the digestive tract must also serve as the first line of defense against a wide variety of pathogens. The gut is also a major source of neuronal and endocrine signals able to modulate nutrient storage or food intake by regulating the activity of other organs. Using an integrated approach, we are studying the mechanisms that make the gut an efficient and interactive barrier despite its constant interactions with microbes.

Keywords

Innate immunity, gut homeostasis, host-pathogen interactions, Drosophila, symbiosis.

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Results Obtained in 2014

Drosophila innate immunity The melanization reaction is a major immune response in Arthropods and involves the rapid synthesis of a black pigment, melanin, at the site of infection and injury. In a recent study, we have generated flies carrying deletions in the prophenoloxidases 1 and 2 genes and by analyzing these mutations alone and in combination, we have demonstrated the importance of melanization in combating microbial infection (Bingelli et al., 2014). We have also analyzed the impact of the gut microbiota on the intestinal epithelium. Our study shows that the microbiota affects gut morphology through their impacts on epithelial renewal rate, cellular spacing, and the composition of different cell types in the epithelium. Thus, the influence of the microbiota at large has far reaching effects on host physiology (Broderick et al., 2014; Buchon et al., 2014). The Drosophila-Spiroplasma interaction: a model for insect endosymbiont We have recently shown that the proliferation of the Drosophila endosymbiont Spiroplasma is limited by the availability of hemolymph lipids. This feature limits endosymbiont over-proliferation under conditions of host nutrient limitation (Herren et al., 2014). We have also deciphered the mechanism of vertical transmission by showing that Spiroplasma coopts the yolk transport and uptake machinery to colonize the germ line and ensure efficient vertical transmission (Herren et al., 2013). The uptake of yolk is a female germ line-specific feature and therefore an attractive target for co-option by endosymbionts that need to maintain high fidelity maternal transmission. The digestive tract: an interactive barrier We recently provided an atlas of the Drosophila adult midgut uncovering a fine-grained compartmentalization. We also revealed the role of intestinal stem cell in gut repair during bacterial infection (Buchon et al., 2013; 2014). Our laboratory is now working on the gene regulatory networks that govern gut regional identity and how regionalization affects various gut function such as immunity and digestive enzyme regulation. In this line we have recently demonstrated that the TGF-ß/Activin pathway functions as a carbohydrate- sensing mechanism in the adult Drosophila midgut to regulate digestive enzyme expression (Chng et al., 2014).

EPFL School of Life Sciences - 2014 Annual Report

Team Members Postdoctoral Fellows Anna Dostalova Igor Iatsenko Dani Osman Elodie Ramond Samuel Rommelaere Zongzhao Zhai

PhD Students Maroun Bou Sleiman Wen Bin (Alfred) Chng Jan Dudzic Mario Gonzalo Garcia Arraez Juan Paredes

Masters Student Laurent Alter

Technicial Support Jean-Philippe Boquete Christophe Rémondeulaz Fanny Schüpfer Tiffany Thébault

Administrative Assistant Véronique Dijkstra

GHI - Global Health Institute

Shown are wild-type (left) and eater deficient (right) transgenic Drosophila larvae expression GFP in hemocytes. Many hemocytes are sessile attached to inner parts of the cuticle (left). We have recently shown that formation of the sessile hematopoietic niche is disrupted in the eater mutant that affects a gene of the EGF repeat Nimrod family (right). Credit photo: Andrew Brestcher.

Selected Publications » » » » » » » » »

Binggeli, O., Neyen, C., Poidevin, M., and Lemaitre, B. (2014). Prophenoloxidase activation is required for survival to microbial infections in Drosophila. PLoS pathogens 10, e1004067. Broderick, N.A., Buchon, N., and Lemaitre, B. (2014). Microbiota-induced changes in Drosophila melanogaster host gene expression and gut morphology. mBio 5, e01117-01114. Chakrabarti, S., Poidevin, M., and Lemaitre, B. (2014). The Drosophila MAPK p38c regulates oxidative stress and lipid homeostasis in the intestine. PLoS genetics 10, e1004659. Chng, W.B., Bou Sleiman, M.S., Schupfer, F., and Lemaitre, B. (2014). Transforming growth factor beta/activin signaling functions as a sugar-sensing feedback loop to regulate digestive enzyme expression. Cell reports 9, 336-348. Herren, J.K., Paredes, J.C., Schupfer, F., Arafah, K., Bulet, P., and Lemaitre, B. (2014). Insect endosymbiont proliferation is limited by lipid availability. eLife 3, e02964. Buchon, N., Osman, D., David, F.P., Fang, H.Y., Boquete, J.P., Deplancke, B., and Lemaitre, B. (2013b). Morphological and molecular characterization of adult midgut compartmentalization in Drosophila. Cell reports 3, 1725-173 . Herren, J.K., Paredes, J.C., Schupfer, F., and Lemaitre, B. (2013). Vertical transmission of a Drosophila endosymbiont via cooption of the yolk transport and internalization machinery. mBio 4. Lemaitre, B., and Girardin, S.E. (2013). Translation inhibition and metabolic stress pathways in the host response to bacterial pathogens. Nature reviews. Microbiology 11, 365-369. Lemaitre, B., and Miguel-Aliaga, I. (2013). The digestive tract of Drosophila melanogaster. Annual review of genetics 47, 377-404.

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EPFL School of Life Sciences - 2014 Annual Report

McKinney Lab hn

nne

Full Professor - Director of the Doctoral Program in Biotechnology & Bioengineering (EDBB)

http://mc inne

Introduction

John McKinney received his PhD from The Rockefeller University in 1994 for studies on eukaryotic cell cycle regulation. His postdoctoral studies at the Albert Einstein College of Medicine were focused on tuberculosis (1995-1998). Prof. McKinney headed the Laboratory of Infection Biology at Rockefeller University from 1 -2007. Since 2007, Prof. McKinney heads the Laboratory of Microbiology and Microsystems at EPFL. He is the director of EPFLâ&#x20AC;&#x2122;s Doctoral Program in Biotechnology and Bioengineering (EDBB) and is affiliated also with the Institute of Biotechnology (IBI).

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Research in the McKinney lab is focused on understanding the mechanistic basis of microbial individuality, defined as cell-to-cell phenotypic variation that is not attributable to genetic or environmental differences. A deeper understanding of this phenomenon will lead to new strategies to eliminate subpopulations of bacteria that are refractory to antimicrobial therapy and host immunity. Our interdisciplinary research program comprises equal parts microbiology and microengineering. In particular, we seek to design, develop, and apply new microfabricated tools for singlecell microbiology, combined with advanced imaging techniques based on optical and atomic force microscopy.

Keywords

Microbiology, microengineering, microbial individuality, single-cell biology, time-lapse microscopy, atomic force microscopy, microelectromechanical systems, microfluidics, mycobacteria, persistence, antibiotics.

Results Obtained in 2014

lab.epfl.ch/

Bacterial cells behave as individuals. Mutation and horizontal DNA transfer are important drivers of bacterial individuation, but these genetic changes are relatively rare. At much higher frequencies, genetically identical cells display metastable variation in growth rates, response kinetics, stress resistance, and other quantitative phenotypes. These cell-to-cell differences arise from non-genetic sources, such as stochastic fluctuations in gene expression and asymmetric partitioning of components during cell division. Temporal variation at the single-cell level generates phenotypic diversity at the population level. This diversity is critical for bacterial persistence in changing environments because it ensures that some individuals will survive potentially lethal stresses that would otherwise extinguish the population. Our research focuses on the pathogenic species Mycobacterium tuberculosis. We use time-lapse optical and atomic force microscopy and custom-made microfabricated devices (microfluidics and MEMS) to study the real-time dynamics of bacterial behavior at the single-cell level.

EPFL School of Life Sciences - 2014 Annual Report

Team Members Senior Staff Scientist Neeraj Dhar

Postdoctoral Fellows Alex Eskandarian Giulia Manina Paul Murima

PhD Students Matthieu Delincé Oleg Mikhajlov Katrin Schneider Joëlle Ven Amanda Verpoorte

Masters Students Laurent Alter Coralie Boulet Kunal Sharma Thomas Simonet Gaëlle Thurre

Information Technologist: Olivia Mariana Research Technician François Signorino-Gelo Administrative Assistant Cécile Prébandier

GHI - Global Health Institute

Mycobacterium tuberculosis bacilli e pressing a fluorescent reporter of single-cell ribosomal RNA production rates (green is high, red is low), which correlate with single-cell growth rates. See: Manina G, Dhar N, McKinney JD (2015) Cell Host Microbe 17(1): 32-46.

Selected Publications » Manina G, Dhar N, McKinney JD (2015) Stress and host immunity amplify Mycobacterium tuberculosis heterogeneity and induce non-growing metabolically active forms. Cell Host Microbe 17(1): 32-46. » Vaubourgeix J, Lin G, Dhar N, Chenouard N, Jiang X, Botella H, Lupoli T, Mariani O, Yang G, Ouerfelli O, Unser M, Schnappinger D, McKinney JD, Nathan C (2015) Stressed mycobacteria use the chaperone ClpB to sequester irreversibly oxidized proteins asymmetrically within and between cells. Cell Host Microbe PMID: 2562054 . » Dhar N, Dubee V, Ballell L, Cuinet G, Hugonnet JE, Signorino-Gelo F, Barros D, Arthur M, McKinney JD (2015) Rapid cytolysis of Mycobacterium tuberculosis by faropenem, an orally available beta-lactam antibiotic. Antimicrob Agents Chemother 5 (2): 130 -131 . » Chopra T, Hamelin R, Armand F, Chiappe D, Moniatte M, McKinney JD (2014) uantitative mass spectrometry reveals plasticity of metabolic networks in Mycobacterium smegmatis. Mol Cell Proteomics 13(11): 3014-3028. » Elitas M, Martinez-Duarte R, Dhar N, McKinney JD, Renaud P (2014) Dielectrophoresis-based purification of antibiotic-treated bacterial subpopulations. Lab Chip 14(11): 1 50-1 57. » Santi I, Dhar N, Bousbaine D, Wakamoto Y, McKinney JD (2013) Single-cell dynamics of the chromosome replication and cell division cycles in mycobacteria. Nature Commun 4: 2470. » Wakamoto Y, Dhar N, Chait R, Schneider K, Signorino-Gelo F, Leibler S, McKinney JD (2013) Dynamic persistence of antibiotic-stressed mycobacteria. Science 33 (6115): 1- 5. » Tischler AD, Leistikow RL, Kirksey MA, Voskuil MI, McKinney JD (2013) Mycobacterium tuberculosis requires phosphate-responsive gene regulation to resist host immunity. Infect Immun 1(1): 317-32 .

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EPFL School of Life Sciences - 2014 Annual Report

Trono Lab Didier Trono

Full Professor

http://tr n lab.epfl.ch/

Introduction

After obtaining an M.D. from the University of Geneva and completing clinical training in pathology, internal medicine and infectious diseases in Geneva and at Massachusetts General Hospital, Didier Trono started a scientific career at the Whitehead Institute of MIT. In 1990, he joined the Salk Institute in San Diego to launch a center for AIDS research. Prof. Trono moved back to Europe seven years later, before taking the reins of the newly created EPFL School of Life Sciences, which he directed from 2004 to 2012. His research has long gravitated around interactions between viruses and their hosts and the development of tools for gene therapy. This led him to epigenetics, the current focus of his labâ&#x20AC;&#x2122;s investigation.

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More than half of the human genome is derived from transposable elements (TEs), most of them retrotransposons that spread by the copy-andpaste mechanism used by retroviruses. These endogenous retroelements (EREs) are essential motors of evolution, which can disrupt, activate or repress genes, move pieces of chromosomes around, and serve as hot spots for genetic recombination. The resulting mutations can either be evolutionarily advantageous or deleterious, and whether for their inactivation or their exaptation, transposable elements are under tight epigenetic control established from the earliest stages of embryogenesis. Our research explores this delicate equilibrium between transposable elements and their hosts, and investigates how these genetic invaders and their controlling mechanisms impact on the development, the physiology and the evolution of higher organisms, and how their deregulation can affect human health.

Keywords

Transposable elements, retroviruses, epigenetics, gene expression, stem cells, evolution.

Results Obtained in 2014

A few years ago, we discovered that the early embryonic control of endogenous retroviruses is mediated by KRAB-containing zinc finger proteins (KRABZFPs), a large family of tetrapod-restricted transcriptional repressors that act by recruiting inducers of heterochromatin and DNA methylation via their cofactor KAP1 (KRAB-associated protein 1). More recently, we found that KRAB-ZFPs are collectively responsible for silencing in an evolutionally dynamic fashion, a much broader range of TEs than previously thought, and that they exert as a consequence a marked influence on the transcriptional networks of human embryonic stem cells. We also demonstrated that, whereas the early embryonic silencing of EREs is a highly orderly process, their transcriptional control is profoundly altered during the reprogramming of somatic cells to induced pluripotent stem cells (iPSCs). This deregulation of EREs may be partly necessary for achieving pluripotency, but owing to its stochastic nature it likely decreases the overall efficiency of reprogramming. Furthermore it confers iPSCs with a great degree of epigenetic heterogeneity, and is a potential source of phenotypic anomalies for these cells. We also pursued our exploration of the functions and mechanisms of action of the KRAB/KAP1 system in somatic tissues. Adding to our previous results indicating that it is an essential regulator of the homeostasis of higher vertebrates, we unveiled that this system influences events as crucial as muscle differentiation and multiple steps of hematopoiesis. Through these experiments, we discovered that KAP1 can switch from a co-repressor to a co-activator state through phosphorylation, and that it can partake in multilayered transcription regulatory cascades, where protein- and RNA-based repressors are super-imposed in combinatorial fashion to govern the timely triggering of important physiological processes.

EPFL School of Life Sciences - 2014 Annual Report

Team Members Senior Scientist Priscilla Turelli

Postdoctoral Fellows Isabelle Barde Marco Cassano Marc Friedli Michael Imbeault Suk Min Jang Benjamin Rauwel Carmen Unzu

PhD Students Natali Castro Diaz Gabriella Ecco Pierre-Yves Helleboid Alexandra Iouranova Annamaria Kauzlaric Flavia Marzetta Andrea Coluccio

Master Student Marcelle Arrigo Bioinformaticians Julien Duc Evarist Planet

Technicians Sandra Offner Charlène Raclot Sonia Verp Administrative Assistant Séverine Reynard

GHI - Global Health Institute

Evolutionally dynamic control and co-option of transposable elements. New elements are partially controlled by RNA interference or cytidine deamination by APOBEC proteins, leaving room for some retrotransposition. Transcriptional repressors of the KRABZFP family eventually emerge that block the spread of these elements and partake in their domestication. Many EREs completely decay through genetic drift.

Selected Publications » Singh, K., Cassano, M., Planet, E., Soji, S., Jang, S.M., Sohi, G., Faralli, H., Choi, J., Youn, H.-D., Dillworth, J.D & Trono, D. (2015). A KAP1 phosphorylation switch controls MyoD function during skeletal muscle differentiation. Genes & Dev, in press. » Friedli, M. & Trono, D. (2015). The developmental control of transposable elements and the evolution of higher species. Ann Rev Cell Dev Bio, in press. Castro-Diaz, N., Friedli, M. & Trono, D. (2015). Drawing a fine line on endogenous retroelement activity. Mob Genet Elements, online Feb. 3. » Turelli, P., Castro-Diaz, N., Marzetta, F., Kapopoulou, A., Raclot, C., Duc, J., Tieng, V., Quenneville, S. & Trono, D. (2014). Interplay of TRIM28 and DNA methylation in controlling human endogenous retroelements. Genome Res 24, 1260-70. » Imbeault, M. & Trono, D. (2014). As Time Goes by: KRABs Evolve to KAP Endogenous Retroelements. Dev Cell 31, 257- . » Friedli, M., Turelli, P., Kapopoulou, A., Rauwel, B., Castro-Diaz, N., Rowe, H.M., Ecco, G., Unzu, C., Planet, E., Lombardo, A., Mangeat, B., Wildhaber, B.E., Naldini, L. & Trono, D. (2014). Loss of transcriptional control over endogenous retroelements during reprogramming to pluripotency. Genome Res 24, 1251-9. » Castro-Diaz, N., Ecco, G., Coluccio, A., Kapopoulou, A., Yazdanpanah, B., Friedli, M., Duc, J., Jang, S.M., Turelli, P. & Trono, D. (2014). Evolutionally dynamic L1 regulation in embryonic stem cells. Genes Dev 28, 13 7-40 . » Rowe, H.M., Kapopoulou, A., Corsinotti, A., Fasching, L., Macfarlan, T.S., Tarabay, Y., Viville, S., Jakobsson, J., Pfaff, S.L. & Trono, D. (2013). TRIM28 repression of retrotransposon-based enhancers is necessary to preserve transcriptional dynamics in embryonic stem cells. Genome Res 23, 452-61. » Rowe, H.M., Friedli, M., Offner, S., Verp, S., Mesnard, D., Marquis, J., Aktas, T. & Trono, D. (2013). De novo DNA methylation of endogenous retroviruses is shaped by KRAB-ZFPs/KAP1 and ESET. Development 140, 519-29. » Barde, I., Rauwel, B., Marin-Florez, R.M., Corsinotti, A., Laurenti, E., Verp, S., Offner, S., Marquis, J., Kapopoulou, A., Vanicek, J. & Trono, D. (2013). A KRAB/KAP1-miRNA cascade regulates erythropoiesis through stage-specific control of mitophagy. Science 340, 350-3.

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EPFL School of Life Sciences - 2014 Annual Report

Van der Goot Lab .

v n de

Full Professor - Dean of the School of Life Sciences

http://

Introduction

The general interest of our laboratory is to understand how biological membranes compartmentalize space, in 3D but also 2D; how shape is used to specify function; how transmission of information across membranes can be mediated. These over arching questions are addressed through the following main focuses: Gisou van der Goot studied engineering at the Ecole Centrale de Paris, then did a PhD in Molecular Biophysics at the Nuclear Energy Research Center, Saclay, France, followed by a postdoc at the European Molecular Biology Laboratory (EMBL) in Heidelberg. She started her own group in 1994 in the department of Biochemistry, University of Geneva, became Associate professor at the Faculty of Medicine (Univ. Geneva) in 2001 and Full Professor at the EPFL in 2006, where she cofounded the Global Health Institute. In 2014, she was appointed Dean of the School of Life Sciences.

• To understand how mammalian cell are compartmentali ed, ho compartmentali ation of specific membranes is achieved and how this is related to function. We are particularly interested in the architecture of the endoplasmic reticulum and how palmitoylation, a uniquely reversible lipidation of proteins, regulates organelle structure and function by targeting key proteins. • To understand the physiological and pathological roles of the anthrax toxin receptors, TEM8 and CMG2. These two single spanning membrane proteins are well known to enable intoxication by anthrax but are poorly understood with respect to their role in communicating with the extracellular matrix. They are also palmitoylated and represent a useful model system to study this post-translationnal modification. • To unravel the molecular mechanisms responsible for Hyaline Fibromatosis and GAPO syndromes. These two rare genetic diseases are the result of mutations in the anthrax toxin receptor.

Keywords

Anthrax toxin, systemic hyalinosis, hyaline fibromatosis, TEM , CMG2, endoplasmic reticulum, calnexin, DHHC, palmitoylation.

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.epfl.ch/

Results Obtained in 2014

Over the last few years, the laboratory has undergone a major change in focus, shifting the efforts from the study of bacterial toxins to studying how protein palmitoylation affects protein structure and functions and how cells make use of this reversible lipidation mechanism to organize the endomembrane system and generate compartments/domains with specific function. Major effort has been devoted to implementing high through putanalysis methods to study palmitoyl proteomes under various conditions and to establish a knowledge based database for palmitoylated proteins: SwissPalm. Since little is known about the regulations and dynamics of protein palmitoylation, we have chosen a set of key ER proteins as model proteins. In particular the ER chaperone calnexin, a type I membrane proteins harbouring a large lectin chaperone domain in the ER lumen and a 90 residue cytosolic tail that mediates unexpected functions such as association with the ribosome translocon complex and as well as signalling. We have combined experiment analysis with mathematical modelling (Coll. V. Hatzimanikatis, EPFL, Basic Sciences), to understand the dynamics and regulation of the calnexin palmitoylation cycle and how if affects function. This has also led us to study the enzyme that we have found palmitoylate scalnexin, DHHC6. We could also establish that DHHC6 is itself palmitoylated, providing the first evidence for palmitoylation cascades, reminiscent of phosphorylation cascades. On-going efforts are devoted to complexify the model, to evolve towards a complete model of the ER palmitoylation network. We have also pursued our studies to understand the physiological functions of the anthrax toxin receptors and the consequences of Hyaline Fibromatosis Syndrome mutations (HFS). Over the last 2 years, our focus has been to determine whether anthrax toxin receptors are actually receptors for a specific extracellular matrix component. We are particularly interested in determining how, mechanistically, the proteins are capable of transmitting information regarding the extracellular matrix to the interior of the cell and for what purpose. In these studies we combine analysis of CMG2 WT and mutants in tissue culture cells, the study of patient derived cells as well as the study of cmg2 KO mice.

EPFL School of Life Sciences - 2014 Annual Report

Team Members Scientist Collaborator Laurence Abrami

Postdoctoral Fellows Nicole Andenmatten Mathieu Blanc Sanja Blaskovic Elsa Perrody Oksana Sergeeva Maria Eugenia Zaballa

PhD Students Jérôme Bürgi Tiziano Dallavilla Mustafa Demir Sarah Friebe Patrick Sandoz Shixu Yan

Laboratory Assistants Sylvia Ho Béatrice Kunz

Administrative Assistant Geneviève Rossier

GHI - Global Health Institute

Schematic Representation of the Long-Term and Long-Distance LF Delivery Modes Anthrax LT is internalized via a dynamin-dependent pathway and delivered to early endosomes. There, the toxin-receptor complex is sorted into nascent ILVs. Anthrax PA forms a channel into the membrane of the ILV and translocates LF into the lumen. LF, encapsulated in the ILVs, is transported in a microtubule-dependent manner to later stages of the endocytic pathway. There, two fates are observed: LF is either delivered to the cytosol, presumably by back fusion, over periods of days, or LF-containing ILVs are released into the extracellular medium as exosomes. These exosomes can be taken up by naïve recipient cells via an ATR-independent dynamin-dependent mechanism. LF is subsequently released into the cytosol of the recipient cell in a Tgs101- and Alix-dependent manner (inspired by Raposo and Stoorvogel, 2013).

Selected publications » Abrami, L., Brandi, L., Moayeri, M., Brown, M. J., and Krantz, B. A. et al. (2013). Hijacking Multivesicular Bodies Enables Long-Term and Exosome-Mediated Long-Distance Action of Anthrax Toxin. Cell Reports. vol. 5, num. 4, p. 986-996. » Lakkaraju, A. K. and van der Goot, F.G. (2013). Calnexin Controls the STAT3-Mediated Transcriptional Response to EGF. Molecular Cell. vol. 51, num. 3, p. 386-396. » Yan, S. E., Lemmin, T., Salvi, S., Lausch, E. and Superti-Furga, A. D. Rokicki, M.D. Peraro, and F.G. van der Goot (2013). In-depth analysis of hyaline fibromatosis syndrome frameshift mutations at the same site reveal the necessity of personalized therapy. Human mutation. vol. 34, num. 7, p. 1005-17. » Castanon, I., Abrami, L., Holtzer, L., Heisenberg, C. P. van der Goot F. G. and M. González–Gaitán . (2013). Anthrax toxin receptor 2a controls mitotic spindle positioning. Nature Cell Biology. (15): 2 -3 . Co-senior corresponding author » Degiacomi M.T. #, Iacovache I.#, Pernot L., Chami M., Kudryashev M., Stahlberg H., van der Goot F.G.* and Dal Peraro M. * (2013) The molecular assembly of the aerolysin pore reveals a unique swirling membraneinsertion mechanism. Nature Chemical Biology :623- . doi: 10.103 /nchembio.1312 Co-senior corresponding author » Blaskovic, S., Blanc, M. and van der Goot, F. G. (2013). What does S-palmitoylation do to membrane proteins The FEBS journal. vol. 2 0, num. 12, p. 2766-74.

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EPFL School of Life Sciences - 2014 Annual Report

ISREC

The Swiss Institute for Experimental Cancer Research (ISREC) has continued its contributions to the School of Life Sciences at EPFL, via cutting-edge research, mentoring young scientists, and classroom teaching. In addition, ISREC is playing a key role in the new Swiss Cancer Center Lausanne (SCCL), a joint venture with the University of Lausanne and its Hospital and Medical Center (CHUV). This new cancer center, announced in January 2013, has a mission statement to become the first comprehensive cancer center in Switzerland, as defined by depth and breadth in basic and translational cancer research, in clinical research and clinical trials of new therapies, and excellent care of cancer patients. ISREC, with 15 faculty research groups focused on cancer research or fundamental cell and developmental biology, brings exceptional strength and talent to this new cancer center. ISREC also has been centrally involved in community-building initiatives for the SCCL, including a series of annual faculty-only and faculty + staff retreats, held in the Spring and Fall, respectively. Both retreats - initiated in 2013 - have been successful at building bridges across the multiple sites in Lausanne that house cancer-related faculty.

Douglas Hanahan - Director

In addition to the retreats, The Lola and John Grace Distinguished Lectures in Cancer Research – sponsored by the Grace family – bring in eminent cancer scientists for a once-monthly lecture at EPFL that is televised to the CHUV and Biopole/Epalinges sites of the SCCL. Furthermore, ISREC sponsors a monthly faculty-only research presentation, and a weekly informal seminar series for ISREC students and postdocs. Finally, ISREC had a very successful bi-annual symposium in January 2014, held in Crans Montana, on Metastatic Colonization. There were two notable faculty transitions in 2013-2014: Lukas Kühn retired after 25 years studying molecular biology as a member of ISREC, and Elisa Oricchio joined ISREC as an assistant professor; Elisa is developing a research program investigating mechanisms of and innovative therapeutic strategies for follicular lymphoma, an understudied cancer type in need of new insights. http://sv.epfl.ch/

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ISREC - Swiss Institute for Experimental Cancer Research

Swiss Institute for Experimental Cancer Research

EPFL School of Life Sciences - 2014 Annual Report

Aguet Lab che

Full Professor

http://a uet lab.epfl.ch/

Introduction

Michel Aguet, MD, held positions in academia and industry (associate professor, Institute of Molecular Biology, University of Zürich; director Molecular Oncology, Genentech, San Francisco) before he was appointed director of ISREC (1996-2009). He joined EPFL when ISREC became integrated into the school and led the National Center of Competence in Research (NCCR) in Molecular Oncology from 2001-2013. In the past, his research focused on interferon signaling, more recently on the role of the Wnt pathway in cancer cell differentiation. His laboratory will close in 2015 due to retirement.

Mutational activation of Wnt signaling is a key oncogenic event in most colorectal cancers (CRCs), but approaches targeting the Wnt pathway downstream of driving mutations prove challenging. Bcl9/9l proteins are components of the Wnt- β-catenin transcriptional activation complex, which is situated downstream of driver mutations in CRC. Our work focuses on exploring the role of the β-catenin-Bcl9/9l complex in mouse models of CRC. We have previously shown that in adult mice Bcl9/9l proteins are dispensable for normal homeostasis of the gastrointestinal epithelium. These results contrasted with the severe phenotypes observed upon ablation of other Wnt pathway components, which elicited strong proliferative defects resulting in crypt loss. Thus, in adult mammals, Bcl9/9l proteins seem to play a less critical role in Wnt signaling. Our previous work indicated that despite the only partial contribution of β-catenin-Bcl9/9l to Wnt transcriptional output, this complex might play a critical regulatory role in the maintenance of intestinal stem cells (ISC). While there were no overt anomalies in intestinal homeostasis, mice lacking Bcl9/9l proteins were deficient in epithelial regeneration as shown in an ulcerative colitis model, pointing to a possible deficiency in ISC expansion and/or maintenance. The role of Bcl9/9l in regulating stemness properties became overtly apparent in a mouse chemical carcinogenesis model of CRC, in which ablation of Bcl9/9l proteins resulted in virtual loss of ISC markers concomitantly with vastly down-regulated expression of Wnt targets and genes related to epithelial-mesenchymal transition (EMT).

Results Obtained in 2014

We made use of chemically or genetically induced mouse CRC models and RNA sequencing to establish a robust Bcl9/9l dependent gene expression signature, which showed a positive correlation of Bcl9/9l induced effects across the models. Importantly, this overlapping gene expression signature, which corroborated the striking Bcl9/9l dependence of stemness and EMT traits, correlated strongly with outcome in human CRC patients. The prognostic capacity of this Bcl9/9l core signature was independent of known clinical and molecular parameters as revealed by multivariate analyses. Therefore, the involvement of Bcl9/9l-β-catenin signaling in human CRC outcome is likely to depend on other prognostic tumor properties, such as tumor dissemination and/or chemoresistance. Even though underlying mechanisms remain elusive, our findings corroborate that the Bcl9/9l β-catenin arm of Wnt-β catenin signaling is critical for stemness maintenance, possibly through maximally enhancing the Wnt-β-catenin transcriptional output. This is in accordance with the notion that a gradient of Wnt-β-catenin signaling along the crypt villus axis regulates cellular hierarchy and continuous renewal, whereby strongest Wnt signaling is required for stem cell maintenance at the crypt bottom. Collectively, the rather subtle role of Bcl9/9l-β catenin signaling that is critical for wound healing but not homeostasis in the normal intestine, yet strongly affects tumor traits associated with patient outcome, renders it attractive as a potential therapeutic target.

Keywords

WNT pathway, Bcl9/9l, cancer stem cells, epithelial-mesenchymal transition, cancer cell differentiation, drug target validation.

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EPFL School of Life Sciences - 2014 Annual Report

Team Members MD/PhD Student Andreas Moor

Bioinformatician Pascale Anderle

Administrative Assistant NCCR Christine Skaletzka

ISREC - Swiss Institute for Experimental Cancer Research

Postdoctoral Fellows Frédérique Baruthio Patrick Rodriguez

mmunofluorescence staining of chemically induced mouse colon adenocarcinomas. Wildtype tumors, which strongly express stemness and EMT-related genes, stain positively for the mesench mal intermediate filament vimentin (green) and show a discontinuous basement membrane (laminin; red). Bcl9/Bcl9lko tumors virtually lost stemness and EMT gene expression, which is paralleled by the loss of vimentin staining and the restoration of a continuous basement membrane, indicative of a more differentiated tumor phenotype.

Selected Publications » Cantu, C., Valenta, T., Hausmann, G., Vilain, N., Aguet, M., and Basler, K. (2013). The Pygo2-H3K4me2/3 interaction is dispensable for mouse development and Wnt signaling-dependent transcription. Development 140, 2377-2386. » Cantu, C., Zimmerli, D., Hausmann, G., Valenta, T., Moor, A., Aguet, M., and Basler, K. (2014). Pax6-dependent, but beta-catenin-independent, function of Bcl9 proteins in mouse lens development. Genes & Dev. 28, 1879-1884. » Christensen, J., Bentz, S., Sengstag, T., Shastri, V. P., and Anderle, P. (2013). FOXQ1, a novel target of the Wnt pathway and a new marker for activation of Wnt signaling in solid tumors. PloS One 8, e60051. » Pisco, A. O., Brock, A., Zhou, J., Moor, A., Mojtahedi, M., Jackson, D., and Huang, S. (2013). Non-Darwinian dynamics in therapy-induced cancer drug resistance. Nat. Commun. 4, 2467.

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EPFL School of Life Sciences - 2014 Annual Report

Brisken Lab th n

s en

Associate Professor

http://bri

Introduction

Cathrin Brisken received an MD and a Doctorate in Biophysics from the University of Göttingen in 1993. She worked as a postdoc and research scientist at the Whitehead Institute, MIT, Cambridge, USA. She was assistant professor at the MGH Cancer Center, Harvard University before joining the NCCR Molecular Oncology at ISREC in 2002. In 2012 she was appointed Associate Professor and Dean of EPFL Doctoral School. Cathrin Brisken is a member of various scientific advisory boards and the International Breast Cancer Study Group (IBCSG) and of the “Hinterzartener Kreis”, the cancer think tank of the German Science Foundation (DFG).

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Breast cancer is a complex disease that is under hormonal control. We are interested in understanding why breast cancer incidence continues to increase and how we can prevent it. Our research focusses on the cellular and molecular mechanisms by which reproductive hormones control cell proliferation, cell-cell communication and morphogenesis in the breast in vivo and how deregulation of the response of various breast cell populations to hormones contributes to human breast carcinogenesis. We characterized the role of the reproductive hormones estrogens, progesterone, and prolactin in mammary gland development using the mouse as a model and identified key downstream mediators. Contrary to the widely held view that estrogens are tightly related to breast carcinogenesis, we have provided evidence that in adulthood, a key to breast cancer development is repeated exposure to progesterone. We are using side branching in the mouse mammary gland as a model of progesterone-induced changes in the human breast and determine the cellular and molecular events that are elicited by progesterone in vivo in the mouse mammary gland. The work in mice is complemented by studies with fresh human breast tissue specimens, that we obtain in collaboration with groups at the CHUV and that we process in the laboratory to assess the relevance of the findings in mice to the human breast.

Keywords

Hormones, mammary gland development, breast carcinogenesis, paracrine signaling, estrogen, progesterone, RANKL, Wnt-4, stem cells, preclinical xenograft models.

Results Obtained in 2014

en lab.epfl.ch/

The ovarian hormones, estrogens and progesterone, increase breast cancer risk by poorly understood mechanisms. We have assessed the role of progesterone in mammary epithelial stem cell function. We have done so by serially transplanting mouse mammary epithelia that are either WT or lack specific genes. We found that in the absence of progesterone receptor signaling, the regeneration capacity of the mammary epithelium was severely impaired. Receptor activator of NF-kB ligand (RANKL), a progesterone receptor target gene, previously linked to stem cell function, was not required for the regenerative potential of the mammary epithelium. However, deletion of Wnt4, another factor we had identified as a downstream mediator of progesterone receptor signaling reduced the mammary regeneration capacity even more than ablation of progesterone receptor signaling. We used a novel sensitive reporter to reveal so far undetected perinatal expression of Wnt4 and showed that, at this developmental stage, Wnt4 expression is independent of hormone signaling. This early, previously unappreciated, Wnt4 expression was found to be functionally important. Later, during puberty and adulthood the central stem cell control factor, Wnt4 is exquisitely controlled by PR signaling. We provided genetic evidence that canonical Wnt signaling in the myoepithelium requires progesterone receptor signaling and Wnt4 expression, whereas the canonical Wnt signaling activities observed in the embryonic mammary bud and in the stroma around terminal end buds were independent of Wnt4. Thus, progesterone and Wnt4 control stem cell function through a luminal–myoepithelial crosstalk with Wnt4 acting independent of progesterone receptor signaling perinatally.

EPFL School of Life Sciences - 2014 Annual Report

Team Members Postdoctoral Fellows Valerian Dormoy Georgios Sflomos Stéphanie Cagnet

PhD Student Dalya Ataca Duje Buric Rachel Jeitziner Valentina Scabia Marie Shamseddin

Master’s Student Caroline Contat Lab Manager Ayyakkannu Ayyanan

Technicians Mélanie Wirth Laura Battista Administrative Assistant Valérie Pahud

ISREC - Swiss Institute for Experimental Cancer Research

Senior Scientist Cécile Lebrand

Model of Wnt4 action in the mammary epithelium. Progesterone stimulation results in Wnt4 induction in the progesterone receptor+ luminal cells (LC), the ‘sensor cells.’ The secreted Wnt4 acts on adjacent basal/myoepithelial cells (MC). In the myoepithelial cells, Wnt4 activates canonical Wnt signaling which induces changes in gene expression. This results in the secretion of factors and changes in the ECM (light blue arrows) that in turn impinge on stem cells (SC), luminal-restricted stem cells (L-RSC), and basal-restricted stem cells (B-RSC). Wnt4 may also act directly on stem cells that are found within the basal layer. Repeated activation of this intercellular signaling cascade downstream of progesterone receptor signaling may promote tumorigenesis by expanding luminal progenitor cells with oncogenic mutations and by expanding the stem/progenitor cell compartment.

Selected Publications » Tanos, T.,Sflomos, G., Echeverria, P. C., Ayyanan, A., Gutierrez, M., Delaloye, J.-F., Raffoul, W., Fiche, M., Dougall, W., Schneider, P., Yalcin-Ozuysal,O., Brisken C (2013) Progesterone/ RANKL is a major regulatory axis in the human breastSci Transl Med 5 (182) » Cimino, D., C. De Pittà, F. Orso, S. Casara, M. Zampini, C. Romualdi, E. Penna, E. Quaglino, M. Forni, C. Damasco, E. Pinatel, P. Provero, R. Ponzone, C. Brisken, M. De Bortoli, N. Biglia, G. Lanfranchi and D. Taverna.(2013) miR148b is a major coordinator of breast cancer progression in a relapse-associated microRNA signature by targeting ITGA5, ROCK1, PIK3CA, NRAS and CSF1FASEB J; 27(3):1233-35. » Hickman JA, Graeser R, de Hoogt R, Vidic S, Brito C, Gutekunst M, van der Kuip H; IMI PREDECT Consortium. (2014) Three-dimensional models of cancer for pharmacology and cancer cell biology; capturing tumor complexity in vitro/ex vivo Biotechnol J. (9):1115-28. » Brisken C., Sflomos, G., Tanos, T.(2013) Reply to Is progesterone a neutral or protective factor for breast cancer Nat Rev Cancer.14(6):146. » Sflomos, G., Brisken C. (2013) A new Achilles Heel in breast cancer Oncotarget Aug;4( ):1126-7. » Brisken C. (2013) Progesterone signalling in breast cancer: a neglected hormone coming into the limelight. Nat Rev Cancer.13(6):385-96. » Soto AM, Brisken C, Schaeberle C, Sonnenschein C. (2013) Does Cancer Start in the Womb Altered Mammary Gland Development and Predisposition to Breast Cancer due to in Utero Exposure to Endocrine Disruptors.J Mammary Gland Biol Neoplasia.18(2):199-208. doi: 10.1007/s10911-013-9293-5.

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EPFL School of Life Sciences - 2014 Annual Report

Constam Lab ne

nst m

Associate Professor

http://c n tam lab.epfl.ch/

Introduction

Daniel Constam obtained his doctoral degree from ETH Zürich for studies on TGF isoforms in the central nervous system. He conducted postdoctoral studies as an EMBO fellow at Harvard University to investigate the regulation of TGF signaling by proprotein convertases. He joined ISREC as a group leader in 2000 and EPFL in 2005. He has been associate professor at the School of Life Sciences since 2007. He is interested in the molecular interactions between stem cells and their microenvironments that govern morphogenesis and tissue homeostasis.

We investigate novel molecular mechanisms that govern the differentiation and self-renewal of pluripotent stem cells in the mammalian embryo. Genetic and biochemical approaches are used to decipher specific interactions with the microenvironment, and how certain cancers may co-opt such developmental programs to promote tumor progression. Identifying cues that guide the maturation of progenitor cells into functional tissues during development is important because impaired differentiation increases the aggressiveness of tumor cells and limits the use of stem cell-derived transplants in regenerative medicine. A current focus is to image proprotein convertases in cells and transgenic mice using new reporter substrates as biosensors, and on elucidating the role of these secreted enzymes in the processing of specific growth factors and cell-cell adhesion molecules. Of particular interest to us are TGFβ related factors and how dimerization and cleavage of their prodomains regulates ligand stability and signaling range. Proprotein convertases also activate other oncogenic factors as well as neurotrophic signals, but the regulation of these proteases at the level of subcellular compartmentalization and their potential as drug targets remain to be investigated. We also study gene silencing by the RNA-binding protein Bicc1 and its role in regulating cAMP/PKA and Wnt signaling. We have shown that mutations in Bicc1 randomize visceral left-right asymmetry and instigate cystic growth in the kidney and pancreas. Identifying relevant interacting proteins and target RNAs should shed important new light on the etiology of polycystic kidney diseases and pave a way for improved therapy of renal cysts.

Keywords

Imaging, proprotein convertases, TGFβ signaling, stem cells and cancer, cell adhesion, mRNA silencing, polycystic kidney diseases, ciliopathies.

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Results Obtained in 2014

Development of placental mammals until the blastocyst stage segregates a pluripotent inner cell mass (ICM) from trophectoderm that enables survival in the uterus. Proliferating stem cells in the ICM give rise to pluripotent epiblast cells that form endoderm, mesoderm or ectoderm during gastrulation. Epiblast stem cells and their germ layer allocation are specified by distinct signaling thresholds of the TGFβ family member Nodal. Potentiation of Nodal signaling in the epiblast requires cleavage of the Nodal precursor by cell non-autonomous forms of the proprotein convertases (PC) Pace4 and Furin that are secreted by the extra-embryonic microenvironment. However, cleavage mutant Nodal precursor can still induce mesoderm, raising the question “how”. To address this, we compared mature and uncleaved forms of Nodal for their potential to synergize with the co-ligands Gdf1 or Gdf3. Biochemical analysis revealed that Nodal heterodimerizes with Gdf1 and remains associated with cleaved prodomains, and that cleavage of the Gdf1 subunit was sufficient to significantly synergize even with uncleaved Nodal. To our surprise, soluble mature Nodal was unable to signal in the absence of serum except as a heterodimer with full-length Gdf1. Our results suggest that paracrine Nodal signaling requires heterodimerization with Gdf1 or Gdf3 and binding to their cleaved prodomains. Recent live imaging revealed Furin and Pace4 activities already in the blastocyst, together with an unidentified convertase. Analysis of compound mutant embryos showed that this activity involves PC7 and mediates morula compaction (manuscript submitted). Analysis of PC7 single mutants in addition led to the identification of BDNF as the first validated in vivo substrate. Impaired BDNF processing may accelerate the onset of Alzheimer’s disease. However, this hypothesis awaits further investigation since a mouse model that we used to test this prediction failed to develop AD-like disease under pathogen-free conditions.

EPFL School of Life Sciences - 2014 Annual Report

Team Members PhD Students Florian Bernet Teresa Didonna Lucia Leal-Esteban Pierpaolo Ginefra

Master’s Student Mariela Castelblanco

Laboratory Assistants St phane Baflast Séverine Urfer

Administrative Assistant Virginie Kokocinski

ISREC - Swiss Institute for Experimental Cancer Research

Postdoctoral Fellows Sylvain Bessonnard Prudence Donovan Christophe Fuerer Benjamin Rothé

Characterization of Nodal.Gdf1. A) Nodal expression and B) signal transduction. C) urification of odal. df heterodimer. ) cti it of odal. df in ep reporter cells. Gdf1 alone is inactive (not shown). E) Nodal.Gdf1 is serum (FBS)-independent. F) Active Nodal.Gdf1 is bound to its prodomains.

Selected Publications » Constam, D. B. (2014). Regulation of TGFβ and related signals by precursor processing. Semin. Cell Dev. Biol. 32, 85-97. » Fuerer, C., Nostro, M. C. and Constam, D. B. (2014). Nodal·Gdf1 heterodimers with bound prodomains enable serum-independent Nodal signaling and endoderm differentiation. J. Biol. Chem. 289, 17854-17871. » Tzanoulinou, S., Brandi, R., Arisi, I., D’Onofrio, M., Urfer, S. M., Sandi, C., Constam, D. and Capsoni, S. (2014). Pathogen-Free Husbandry Conditions Alleviate Behavioral Deficits and Neurodegeneration in AD10 Anti-NGF Mice. Journal of Alzheimer’s Disease 38, 951-964. » Wetsel, W. C., Rodriguiz, R. M., Guillemot, J., Rousselet, E., Essalmani, R., Kim, I. H., Bryant, J. C., Marcinkiewicz, J., Desjardins, R., Day, R., et al. (2013). Disruption of the expression of the proprotein convertase PC7 reduces BDNF production and affects learning and memory in mice. Proc. Natl. Acad. Sci. U. S. A. 110, 17362-17367. » Essalmani, R., Susan-Resiga, D., Chamberland, A., Asselin, M. C., Canuel, M., Constam, D., Creemers, J. W., Day, R., Gauthier, D., Prat, A., et al. (2013). Furin is the primary in vivo convertase of angiopoietin-like 3 and endothelial lipase in hepatocytes. J. Biol. Chem. 288, 26410-26418.

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EPFL School of Life Sciences - 2014 Annual Report

De Palma Lab che e

Tenure-track Assistant Professor

http:// epalma lab.epfl.ch

Introduction

Miki De Palma graduated in Biology (1999) and obtained a PhD degree in cell biotechnologies (2004) from the University of Torino Medical School, Italy, with a thesis on the regulation of tumor angiogenesis by bone-marrowderived cells. He performed post-doctoral training (20052008) at the Telethon Institute for Gene Therapy in Milan, where he developed strategies for engineering monocytes and reprogramming them into antitumoral immune cells. He was appointed group leader at the San Raffaele Institute, Milan, in 2008 (tenured in 2011), and joined ISREC/EPFL in 2012. He serves on the advisory boards of several international journals, including Science Translational Medicine and Cell Reports.

Early works of De Palma and colleagues have illustrated the important contribution of monocytes/macrophages to tumor angiogenesis and progression, and their functional heterogeneity in mouse and human cancer. By employing genetically engineered mouse models (GEMMs) of cancer, our laboratory investigates the interplay among macrophages, blood vessels and T-cells in tumors. By pharmacologically or genetically targeting these tumor-associated cells and their reciprocal cross talk, we aim to reprogram the immunosuppressive tumor microenvironment and rationally design combination treatments that may enhance the efficacy of conventional anticancer drugs and achieve more effective and enduring responses in cancer patients. Current research topics include: • The analysis of the molecular and functional heterogeneity of macrophages in mouse and human tumors; • The engineering and reprogramming of monocytes for adoptive cell therapy of cancer; • The role of macrophages in tumor responses to antiangiogenic (anti-VEGFA/angiopoietin-2) and immunostimulatory (immune check-point blockade) therapies; • The influence of macrophages on tumor evolution and response to therapies targeting pro-proliferative signaling (RTK inhibitors); • The mechanisms of tumor resistance to antiangiogenic therapy, including compensatory proangiogenic pathways (angiopoietin-2/TIE2) and the role of the extra-cellular matrix; • microRNA regulation of the macrophage phenotype in tumors; • The molecular determinants of microRNA sorting to exosomes and their transfer to acceptor cells (macrophage-endothelial cross talk).

Keywords

Macrophages, tumor angiogenesis, antiangiogenic therapy, immunotherapy, angiopoietin-2, microRNAs, exosomes, GEMMs of cancer, gene modification of hematopoietic cells, lentiviral vectors.

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Results Obtained in 2014

During the past two years we have mainly focused on the following projects: 1) Tumor resistance to anti-VEGFA therapy. Angiopoietin-2 (ANG2/ANGPT2) is a pro-angiogenic factor that promotes tumor angiogenesis in concert with vascular-endothelial growth factor-A (VEGFA). We previously showed that blocking ANG2 in mouse models of cancer inhibits tumor angiogenesis and metastasis. However, it was unclear whether blocking ANG2 could induce long-lasting antitumor responses, and/or overcome tumor resistance to VEGFA-targeted drugs. We have now shown that ANG2 plays an important role in driving tumor resistance to anti-VEGFA therapy, but only in selected cancer types. Specifically in these tumors, targeting VEGFA induced a compensatory response involving increased ANG2 levels, which promoted tumor resistance to anti-VEGFA therapy. Co-targeting VEGFA and ANG2 signaling in these tumors effectively blocked angiogenesis, halted cancer progression, and reversed tumor resistance to anti-VEGFA therapy (Rigamonti, Kadioglu, et al., 2014). 2) Role of microRNAs in exosome-mediated macrophage-to-endothelial communication. Our unpublished data show that microRNAs operate to sustain the protumoral functions of macrophages while limiting their immunostimulatory and antitumoral potential. We also found that macrophages secrete microRNAs via small microvesicles, called exosomes, which can fuse with and deliver their RNA cargo to neighboring cells. Interestingly, we noted that the microRNA composition of exosomes differed from that of the producer macrophages, suggesting an active mechanism of exosomal sorting. By employing cellular assays, RNA sequencing and bioinformatics tools, we determined that the sorting of microRNAs to macrophage-derived exosomes is partly regulated by the cellular levels of their targeted gene transcripts, which fluctuate in response to cell activation (see Figure). These findings have revealed a general (motif-independent) mechanism of microRNA sorting to exosomes, which may have implications for macrophage-to-endothelial cell communication in the tumor microenvironment (Squadrito, Baer, et al., 2014).

EPFL School of Life Sciences - 2014 Annual Report

Team Members PhD Students Caroline Baer Ece Kadioglu Shodai Takahashi (visiting)

Master’s Students Daniela Pais Ferreira Lucie Giesbrecht Luisa Spisak Fabien Jammes

Lab Manager Celine Rmili Wyser Bachelor’s Students Ka Ho Nicholas Cheung Yannick Francioli

Technicians Claudio Maderna; Axel Bellotti Administrative Assistant Soledad Andany

ISREC - Swiss Institute for Experimental Cancer Research

Postdoctoral Fellows Mario Leonardo Squadrito Nicolo’ Rigamonti Daniela Biziato Ioanna Keklikoglou

Mechanism of microRNA sorting to macrophage-derived exosomes. profiling of macrophages and their exosomes shows that microRNA sorting to exosomes is modulated by cell-activationdependent changes of microRNA target levels in the producer cells. Genetically perturbing the expression of individual microRNAs or their targeted transcripts promotes bidirectional microRNA relocation from the cell cytoplasm/P bodies (sites of microRNA activity) to multivesicular bodies (sites of exosome biogenesis) and controls microRNA sorting to exosomes. For details, see uadrito et al. ( ).

Selected Publications » Squadrito, M.L. , Baer, C. , Burdet, F., Maderna, C., Gilfillan, G.D. Lyle, R., Ibberson, M., & De Palma, M. (2014). Endogenous RNAs modulate microRNA sorting to exosomes and transfer to acceptor cells. Cell Rep. 11;8(5):1432-1446. » Keklikoglou I. & De Palma, M. (2014). Vascular modulatory functions of macrophages. In Macrophages: Biology and Role in the Pathology of Diseases. Edited by S. Biswas and A. Mantovani. 2014 Springer Science, New York, NY USA, pp 131-16 . » Rigamonti, N.*, Kadioglu, E.*, Keklikoglou, I., Wyser Rmili, C., Leow, C.C., & De Palma, M. (2014). Role of angiopoietin-2 in adaptive tumor resistance to VEGF signalling blockade. Cell Rep. 7;8(3):696-706. » Escobar, G., Moi, D., Ranghetti, A., Ozkal-Baydin, P., Squadrito, M.L., Kajaste-Rudnitski, A., Bondanza, A., Gentner, B., De Palma, M., Mazzieri, R., & Naldini, L. (2014). Genetic engineering of hematopoiesis for targeted IFN- delivery inhibits breast cancer progression. Sci Transl Med. 6(217):217ra3. » Squadrito, M.L., Etzodt, M., De Palma, M.*, & Pittet, J.M.* (2013). MicroRNA-mediated control of macrophages and its implications for cancer. Trends Immunol. 34(7):350-9. » Patel, A.S., Smith, A., Nucera, S., Biziato, D., Saha P, Attia RQ, Humphries J, Mattock K, Grover SP, Lyons OT, Guidotti LG, Siow R, Ivetic A, Egginton S, Waltham M, Naldini L, De Palma, M.*, & Modarai, B.* (2013). TIE2-expressing monocytes/macrophages regulate revascularization of the ischemic limb. EMBO Mol Med. 5(6):858-69. » De Palma, M. & Lewis, C.E. (2013). Macrophage regulation of tumor responses to anticancer therapies. Cancer Cell 18; 23(3):277-286.

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EPFL School of Life Sciences - 2014 Annual Report

Duboule Lab en s

Full Professor - EPFL & University of Geneva

http:// ub ule lab.epfl.ch/

Introduction

Denis Duboule earned his PhD in Biology in 1984. He is currently Professor of Developmental genetics and genomics at the EPFL and at the department of Genetics and Evolution of the University of Geneva. Duboule has a longstanding interest in the function and regulation of Hox genes, a family of genes responsible for the organization and evolution of animal body plans. More generally, he is interested in transcriptional regulation during development and evolution. He is an elected member of several academies and societies and has received many national and international awards.

Our laboratory opened at EPFL in 2007. Its major aim is to study some of the principles of mammalian embryological developmental genetics by using the recent tools of functional genomics. A special focus is given to those similarities and differences that exist between the embryological development of vertebrates (to whom mammals belong) and those of other animals (invertebrates), from whom vertebrates derive. To achieve this task, we use the developing mouse embryo in vivo as an experimental system, and try and apply the methodology developed following the sequencing of complex genomes. Our major aim is the understanding of the regulation of a critical family of transcription factors during the construction of the animal body plan, referred to as architect genes (the Hox gene family). These genes have a special interest in the study of both our ontogeny (our development as individuals) and our phylogeny (our origin as a group of individuals) and the detailed understanding of their regulations and functions will be an important step in the deciphering of our evolutionary and developmental trajectories.

Keywords

Embryos, development, evolution, transcription, epigenetic regulation, Hox gene clusters, enhancers.

Results Obtained in 2014

Over the past two years, progress has been made along several lines of research. By using biochemical, genetic and epigenetic approaches, we have finally managed to obtained a fair understanding of the collinear mechanism at work during limb development, a project that started in 1989 with the discovery of this intriguing phenomenon, whereby the order of Hox genes along the chromosomal locus does reflect the place and the time where these genes will be transcribed during development. To understand the molecular mechanisms underlying this process, we first had to localize and characterize the enhancer sequences driving Hox gene expression during limb development. We observed that such sequences are found within large gene deserts flanking the HoxD cluster. We next deciphered the chromatin structure around the HoxA and HoxD clusters, precisely in those places where such numerous long-range acting enhancers are located. We observed that the two gene deserts flanking the HoxD cluster perfectly match the extent of Topologically Associating Domains (TADs), as defined by the HiC technology (data from the Bing Ren laboratory). These large structural and regulatory domains are specifically acting during the development of different structures, with Hox genes contacting alternatively either the telomeric, or the centromeric TAD. We also observed that both the HoxA and HoxD clusters evolved similar regulatory structures and hence we speculate that such a large integrated regulatory landscapes were already present in an ancestor animal, which only had one gene cluster, before the emergence of present days vertebrate animals. We also speculate that these TADs may have been instrumental in the emergence of long-range acting enhancer sequences, by providing chromatin niches where to evolve regulatory sequences. Likewise, these structures may have helped develop pleiotropic regulation, i.e. to recruit an entire regulatory machinery from one tissue to the other, in the course of evolution. We provided a possible example of such a process by showing how similar Hox gene regulations are between the development of digits and the external genital organs. In parallel, we imported and developed in the laboratory optical tools allowing for the direct visualization of these regulatory structures (figure 1). In this context, we have used either classical DNA FISH methodologies or super-resolution (STORM) approaches in collaboration with the laboratory of Sulyana Manley (School Basic Science - EPFL).

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EPFL School of Life Sciences - 2014 Annual Report

Team Members PhD Students Fabrice Darbellay Nicolas Lonfat Rita Lhopitallier

Master’s Students Cécile Fruchard Olivier Selmoni Alexandra Iouranova

SNF Ambizione Fellow Anouk Necsulea

Technician Elisabeth Joye

Visiting Fulbright Student Ben Mormann

Administrative Assistant Doris Sapin

ISREC - Swiss Institute for Experimental Cancer Research

Postdoctoral Fellows Pierre Fabre Daan Noordermeer Nayuta Yakushiji-Kaminatsui

Super-resolution (STORM) microscopy is used to resolve the various levels of decompaction of the HoxD cluster, using DNA probes (A) scanning the locus (B,C,D : coll. with the laborartory of Sulyana Manley (EPFL). E, F. 3D DNA-FISH to assess the relative conformations of Topologically Associating Domains (TADs) in the developing forelimb.

Selected Publications » » » » »

N. Lonfat, T. Montavon, F. Darbellay, S. Gitto and D. Duboule (2014). Convergent evolution of complex regulatory landscapes and pleiotropy at Hox loci. Science, 346, 1004-1006, 2014. J. Lopez-Rios, A. Duchesne, D. Speziale, G. Andrey and K. A. Peterson et al. (2014) Attenuated sensing of SHH by Ptch1 underlies evolution of bovine limbs. Nature, 511, 548-553. G. Andrey and D. Duboule. SnapShot: Hox Gene Regulation (2014). Cell, 4. De Laat, W. and Duboule, D. (2013) Topology of mammalian developmental enhancers and their regulatory landscapes. Nature, 502, 499-506. Andrey, G., Montavon, T., Mascrez, B., Gonzalez, F., Noordermeer, D., Leleu, M., Trono, D., Spitz, F. and Duboule, D. A switch between topological domains underlies collinearity in mouse limbs. (2013) Science, 340(6137):1234167

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EPFL School of Life Sciences - 2014 Annual Report

GĂśnczy Lab e e

Full Professor

http://

Introduction

Pierre GĂśncyz obtained his PhD from The Rockefeller University (New York City, USA) in 1995. Thereafter, he conducted postdoctoral work at the EMBL (Heidelberg, Germany), before starting his laboratory in Lausanne in 2000 at ISREC, joining EPFL in 2005.

We are interested in understanding fundamental cell division processes and focus on two that are crucial for genome integrity: centriole formation and asymmetric cell division. To uncover the underlying mechanisms, we use a combination of genetic, functional genomic, biochemical, proteomic and cell biological approaches, primarily in the nematode C. elegans and human cells in culture. Centriole formation - Centrioles are evolutionarily conserved organelles essential for the assembly of cilia, flagella, and centrosomes, and which are characterized by a striking 9-fold radial symmetry of microtubules. Despite their importance, the mechanisms governing centriole formation have remained elusive until recently. We and others identified five proteins required for centriole formation in C. elegans, the relatives of which are likewise crucial in other organisms. In collaboration with the Steinmetz laboratory, we discovered that one of these protein families (SAS-6 proteins) can form 9-fold symmetric rings, leading us to propose that their self-assembly dictates the 9-fold symmetry of centrioles. Asymmetric cell division - Asymmetric division is crucial for generating diversity during development and stem cell lineages. For successful asymmetric division, the mitotic spindle must be positioned in a manner that ensures proper segregation of cytoplasmic constituents to daughter cells. Work performed in many laboratories, including ours, indicates that spindle positioning requires an evolutionary conserved ternary complex, which anchors the minus end directed motor protein complex dynein at the cell cortex. Dynein is thought to generate pulling forces on astral microtubules that emanate from the spindle poles, thus positioning the mitotic spindle.

Keywords

lab.epfl.ch/

Results Obtained in 2014

Centriole formation - We have pursued an innovative multidisciplinary research program to gain novel insight into the mechanisms governing centriole formation. Thus, we elucidated the complete architecture of the centriole proximal part using cryo-tomography (Guichard et al., 2013; Figure 1). Moreover, we conducted an siRNA-based functional genomic screen that enabled us to identify novel genes that regulate centriole number in human cells (Balestra et al., 2013). In C. elegans, we reported that SAS-1 encodes a C2 domain protein that is critical for centriole integrity and whose homologue is mutated in a human ciliopathy syndrome (von Tobel et al., 2014). Overall, these and other findings have led to a better understanding of the mechanisms governing centriole formation. Asymmetric cell division - We have continued our work on spindle positioning in both C. elegans and human cells to better understand the mechanisms governing asymmetric cell division. In human cells, we uncovered that levels of cortical dynein increase during anaphase in a manner that depends on dephosphorylation of the ternary component NuMA at a specific threonine residue (Kotak et al., 2013). Further work established that NuMA directly associates with PtdInsP (PIP) and PtdInsP2 (PIP2) phosphoinositides in vitro, and that depletion of PIP/PIP2 prevents NuMA cortical localization in vivo. These findings uncover a novel function for plasma membrane phospholipids in governing cortical dynein distribution (Kotak et al., 2014). In C. elegans, we have shown notably that clathrin negatively regulates pulling forces acting on centrosomes during interphase and on spindle poles during asymmetric division. Our work, which includes computational modeling, reveals that clathrin plays a critical role in this instance by promoting acto-myosin cortical tension (Spiro et al., 2014). The above experiments have contributed to enhance understanding of the mechanisms governing metazoan spindle positioning.

Cell biology, developmental biology, cell division, centriole formation, spindle positioning, C. elegans, human cells.

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EPFL School of Life Sciences - 2014 Annual Report

Team Members PhD Students Alessandro De Simone Melina Scholze Veronika Villimova

Technicians Coralie Busso Isabelle Fluckiger

Administrative Assistant Nicole De Montmollin

ISREC - Swiss Institute for Experimental Cancer Research

Postdoctoral Fellows Nicola Brown Paul Guichard Virginie Hamel Sachin Kotak Jian Quiu Lukas von Tobel Benita Wolf

Schematic (left), super-resolution image (SIM, center) and interpretation thereof (right) of centriole pair isolated from the green alga Chlamydomonas reinhardtii stained with antibodies against acet lated-tubulin (green) and the - protein Bld p (purple). ee amel et al. for details.

Selected Publications » von Tobel L, Mikeladze-Dvali T, Delattre M, Balestra FR, Blanchoud S, Finger S, Knott G, Müller-Reichert T, Gönczy P. (2014) SAS-1 is a C2 Domain Protein Critical for Centriole Integrity in C. elegans. PLoS Genet. Nov 20;10(11):e1004777. doi: 10.1371/journal.pgen.1004777. » Kotak S., Busso C. and Gönczy P. (2014) NuMA interacts with phosphoinositides and links the mitotic spindle with the plasma membrane EMBO J. 33:1815-1830. » Spiró Z., Thyagarajan K., De Simone A., Träger S., Afshar, K. and Gönczy P. (2014) Clathrin regulates centrosome positioning by promoting acto-myosin cortical tension in C. elegans embryos Development 141:27122123. » Keller D., Orpinell M., Olivier N., Wachsmuth M., Mahen R., Wyss R., Hachet V., Ellenberg J., Manley S. and Gönczy P. (2014) Mechanisms of HsSAS-6 assembly during centriole formation in human cells. J. Cell Biol. 204:697-712. » Guichard P., Hachet ., Majubu N., Neves A. , Demurtas D., Olieric N., Fluckiger I., Yamada A., Kihara K., Nishida Y., Moriya S., Steinmetz M.O., Hongoh Y. and G nczy, P. (2013) Native architecture of the centriole proximal region reveals novel features underlying their 9-fold radial symmetry Curr. Biol. 23:1620-1628. » Balestra F.R., Strnad P., Flückiger I. and Gönczy P. (2013) Discovering Regulators of Centriole Biogenesis through siRNA-Based Functional Genomics in Human Cells. Dev Cell. 25:555-571.

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EPFL School of Life Sciences - 2014 Annual Report

Hanahan Lab s

n h n

Full Professor - Director of Swiss Institute of Experimental Cancer Research - ISREC - Merck-Serono Professor of Molecular Oncology

http://hanahan lab.epfl.ch/

Introduction

Douglas Hanahan, born in Seattle, Washington, USA, received a bachelorâ&#x20AC;&#x2122;s degree in Physics from MIT (1976), and a Ph.D. in Biophysics from Harvard (1983). He worked at Cold Spring Harbor Laboratory in New York (1 7 - ) initially as a graduate student and then as a group leader. From 1988-2010 he was on the faculty of the Department of Biochemistry & Biophysics at UCSF in San Francisco. He has been elected to the American Academy of Arts & Sciences (2007), the Institute of Medicine (USA) (2008), the US National Academy of Science (2009), and EMBO (2010). In 2011, Hanahan received an honorary degree from the University of Dundee (UK).

The Hanahan group investigates tumor development and progression using genetically engineered mouse models of cancer that recapitulate important characteristics of human cancers, with strategic goals to elucidate pathogenic mechanisms underlying multi-step tumorigenesis and malignant progression, and to develop new therapeutic strategies based on knowledge of mechanism for translation to clinical trials aiming to improve the treatment of human cancers. Currently the lab focuses on melanoma, glioblastoma, pancreatic cancer and squamous carcinomas elicited by human papillomaviruses. Topics include mechanistic studies on acquired capabilities â&#x20AC;&#x201C; hallmarks of cancer - including resistance to programmed cell death, tumor angiogenesis, and invasion and metastasis. A crosscutting theme is the role of the heterotypic tumor microenvironment and the accessory cells that collaborate with cancer cells to manifest malignant disease. In addition, the lab is studying mechanisms of adaptive resistance to therapies targeting these and other hallmark capabilities, which present fascinating perturbations into the regulatory systems, and offer potential avenues to circumvent such drug resistance with combinatorial therapies.

Keywords

Cancer, translational oncology, genetically engineered mouse models of human cancer, transgenic mice, tumor microenvironment, angiogenesis, invasion, metastasis, metabolism, pre-clinical trials.

Results Obtained in 2014

The Hanahan laboratory continues to study the RIP-Tag mouse model of multi-step pancreatic neuroendocrine cancer (PanNET), which is still proving instructive about mechanisms of cancer 30 years after its inception (Hanahan, Nature, 1985). Recent results include the discovery that this ostensibly homogeneous oncogene-driven mouse tumor model is actually heterogeneous, being defined by two molecular subtypes identified by transcriptome profiling, that recapitulate similar subtypes in the cognate human pancreatic neuroendocrine cancer (Sadanandam et al, 2015). The tumors are fueled by both aerobic glycolysis and oxidative phosphorylation, the latter of which is restricted in productivity by limited bioavailable copper in the tumor microenvironment (Ishida et al, PNAS, 2014). New insights have also been gained into the invasive growth state, which is facilitated by activation of an autocrine signalling circuit involving glutamate ligand and NMDA receptor (Li and Hanahan, Cell, 2013). Additionally, impairment of tumor angiogenesis heightens invasiveness as an alternative route to vascularization via normal vessel co-option, most recently exemplified by genetic knockout of the gene encoding the proangiogenic protease MMP-9 (Shchors, et al Oncogene, 2013). Another study (Sadanandam, Nature Medicine, 2013) reported on distinctive molecular subtypes that differentiate human colorectal carcinomas, reflecting different physiological phenotypes and likely cell-of-origin. Another project area has focussed on a mouse model of the lethal brain cancer glioblastoma, assessing new therapeutic strategies targeting the p53 tumor suppressor or the autophagic cellular recycling system (Shchors, et al, PNAS, 2013; Shchors, et al Cancer Cell, 2015).

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EPFL School of Life Sciences - 2014 Annual Report

Team Members PhD Students Gabriele Galliverti Leanne Li Julie Scotton

Bachelor Students Agata Mlynska Sadegh Saghafina Ismael Wafy

Lab Manager Ehud Drori Sabbatical Professors Luisa Arispe (UCLA) David Helfman (KAIST)

Technical Staff Sylvie André Balfast Pasqualina Magliano Aristea Massaras Mei-Wen Peng Bruno Torchia Administrative Assistant Annissa Bayer

ISREC - Swiss Institute for Experimental Cancer Research

Postdoctoral Fellows Elizabeth Allen Krisztian Homiscko Iacovos Michael Ksenya Shchors Courtney Thomas Stephan Wullschleger Qian (Sophia) Zeng

A new mode of invasive growth regulation has been discovered, involving activation of glutamate-stimulated NMDA Receptor signaling (LI & Hanahan, ). nterstitial fluid pressure flow in solid tumors induces autocrine glutamate secretion and NMDAR activity, leading to heightened invasiveness.

Selected Publications » Sadanandam, A., Wullschleger, S., Lyssiotis, C., Gr tzinger, C., Barbi, S., Bersani, S., K rner, J., Wafy, I., Mafficini, A., Lawlor, R.T., Asara, J., Bl ker, H., Cantley, L.C., Wiedenmann, B., Scarpa, A., & Hanahan, D. (2014). Pancreatic neuroendocrine tumors: cross-species analysis reveals molecular subtypes with distinctive metastatic, developmental, and metabolic characteristics. Manuscript submitted. » Shchors, K. Massaras, A. & Hanahan, D. (2015). Dual targeting of the autophagic regulatory circuitry in gliomas with repurposed drugs elicits cell-lethal rates of autophagy and therapeutic benefit. Manuscript in revision, Cancer Cell. » Hanahan, D. (2014). Rethinking the war on cancer. Lancet 383: 558-563. » Ishida, S., Andreux, P., Poitry-Yamate, C., Auwerx, J., and Hanahan, D. (2013). Bioavailable copper modulates oxidative phosphorylation and growth of tumors. PNAS. 110: 1 507-1 512. » Shchors, K., Persson, A.I., Rostker, F., Tihan, T., Lyubynska, N., Li, N., Swigart, L.B., Berger, M.S., Hanahan ,D., Weiss, W.A., & Evan, G.I. (2013). Using a preclinical mouse model of high-grade astrocytoma to optimize p53 restoration therapy. Proc Natl Acad Sci U S A. 110: E1480-9. » Shchors, K., Nozawa, H., u, J., Rostker, F., Swigart-Brown, L., Evan, G., & Hanahan, D. (2013). Increased invasiveness of MMP- -deficient tumors in two mouse models of neuroendocrine tumorigenesis. Oncogene 32: 502-513. » Sadanandam, A., Lyssiotis, C.A., Homicsko, K., Collisson, E.A., Gibb, W.J., Wullschleger, S., Ostos, L.C., Lannon, W.A., Grotzinger, C., Del Rio, M., Lhermitte, B., Olshen, A.B., Wiedenmann, B., Cantley, L.C., Gray, J.W., & Hanahan, D. (2013). A colorectal cancer classification system that associates cellular phenotype and responses to therapy. Nat Med. 1 : 61 -625. » Li, L., & Hanahan, D. (2013). Hijacking the neuronal NMDAR signaling circuit to promote tumor growth and invasion. Cell. 153: 86-100.

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EPFL School of Life Sciences - 2014 Annual Report

Hantschel Lab ve

ntsche

Tenure-track Assistant Professor - ISREC Foundation Chair for Translational Oncology

http://hant chel lab.epfl.ch/

Introduction

Oliver Hantschel studied biochemistry at the University of Regensburg and at Rockefeller University in New York City. He received his PhD in 2004 from the European Molecular Biology Laboratory in Heidelberg and did postdoctoral work at the Research Center for Molecular Medicine of the Austrian Academy of Sciences in Vienna. In 2010, he obtained his Venia Docendi (Habilitation) in Experimental Haematology from the Medical University of Vienna and joined the EPFL School of Life Sciences as a Tenure Track Assistant Professor in 2011.

Protein kinases are involved in almost all aspects of oncogenesis. The inhibition of particular aberrantly activated kinases is considered to be beneficial for cancer treatment for numerous tumor types. Over the past ten years, 25 different inhibitors of a few oncogenic driver kinases in haematological and solid tumor types have received regulatory approval and entered clinical practice. Despite remarkable clinical responses that could be achieved in selected diseases, it is now well-established that most kinase inhibitors merely improve progression-free survival, but not overall survival. The main reasons is the development of drug resistance, often caused by point mutations in the targeted kinase that prevents or inhibits drug binding. Moreover, it is difficult to develop highly selective kinase inhibitors, as there are more than 500 kinases in humans with a conserved sequence and structure. Therefore, side effects caused by the inhibition of off-target kinases may also limit its clinical utility. The Hantschel lab studies oncogenic kinase signaling pathways by using interdisciplinary approaches at the interface of biochemistry, proteomics, chemical biology and protein engineering with the aim to identify innovative and novel ways for therapeutic intervention. Main research avenues include: • Structure-function analysis of protein kinases • Analysis of oncogenic signaling networks using interactionand phospho-proteomics. • Targeting of intracellular protein-protein interactions and posttranslational modifications with engineered high-affinity protein antagonists • Mechanism-of-action and specificity studies of kinase inhibitors.

Results Obtained in 2014

Chronic myelogenous leukemia (CML) is caused by BCR-ABL, which is a constitutively active form of the Abelson tyrosine kinase. While treatment with the different kinase inhibitors leads to durable remissions in the majority CML patients, drug resistance remains a clinical problem. Targeting additional sites in BCR-ABL may be an alternative strategy to restrict drug resistance. Our recent work has shown that an intramolecular interaction of the BCR-ABL SH2 domain with its kinase domain is critical for leukemogenesis and can be targeted with an engineered high-affinity binding protein. In the past two years, we have elucidated the molecular mechanisms responsible for the regulation of BCR-ABL by its SH2 domain: Using an efficient E. coli expression system for the BCR-ABL SH2-kinase domain unit allowed us to quantitatively study regulation of BCR-ABL with purified recombinant proteins in vitro. Unexpectedly, we found that the interaction of the SH2 domain with the kinase domain is the critical switch that shifts the BCR-ABL activation loop from an otherwise closed to a fully open conformation and enables its autophosphorylation. The activation loop is a central control element that regulates the activity of protein kinases. We show that the SH2-kinase interaction enables autophosphorylation of the activation loop in trans by rendering a key phosphorylation site (Tyr-412) highly accessible. In summary, our study demonstrates a novel mechanism by which a protein-protein interaction domain may allosterically mediate the transition of an inactive to an active kinase conformation in a key oncoprotein. This work may serve as an archetype to identify further allosteric regulatory mechanisms in other tyrosine kinases that are activated in haematological malignancies and facilitate the development of new allosteric inhibitors targeting oncogenic tyrosine kinases.

Keywords

Leukemia, oncoproteins, tyrosine kinases, kinase inhibitors, protein engineering, protein structures, protein phosphorylation, proteomics, proteinprotein interaction domains.

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EPFL School of Life Sciences - 2014 Annual Report

Team Members PhD Students Emel Gencer Barbara Gerig Allan Lamontanara Nadine Schmit

Master’s Students Delphine Harduin

Technician Sandrine Georgeon

Administrative Assistant Christine Skaletzka

ISREC - Swiss Institute for Experimental Cancer Research

Postdoctoral Fellows Tim Kükenshöner Sina Reckel

The Abl kinase domain has a predominantly inactive activation loop conformation that is similar to the conformation once imatinib or other t pe inase inhibitors are bound (upper panel). pon formation of the - inase interface, the e uilibrium is shifted to a predominantly open activation loop similar to the conformation once dasatinib or other type 1 inhibitors bind to the kinase domain (lower panel).

Selected Publications » Lamontanara, A.J., Georgeon, S., Tria, G., Svergun, D.I. and Hantschel, O. (2014). The SH2 domain of ABL kinases regulates kinase autophosphorylation by controlling activation loop accessibility, Nat. Commun. 5, 5470. » Mahul-Mellier, A.-L., Fauvet, B., Gysbers, A., Dikiy, I., Oueslati, A., Georgeon, S., Lamontanara, A.J., Bisquertt, A., Eliezer, D., Masliah, E., Halliday, G., Hantschel, O. and Lashuel, H.A. (2014). c-Abl phosphorylates -syn and regulates its degradation, implication for -syn clearance and contribution to the pathogenesis of Parkinson’s Disease. Hum. Mol. Genet. 23(11), 2858-2879. » Zhou, T., Georgeon, S., Moser, R., Moore, D.J., Caflisch, A., Hantschel, O. (2014). Specificity and mechanism-of-action of the JAK2 tyrosine kinase inhibitors ruxolitinib and SAR302503 (TG10134 ) Leukemia. 2 , 404–407. » De Keersmaecker, K., Porcu, M., Cox, L., Girardi, T., Vandepoel, R., Girardi, T., Gielen, G., Mentens, N., Bennett, K.L. and Hantschel, O. (2014). NUP214-ABL1 mediated cell proliferation in T-cell acute lymphoblastic leukemia is dependent on the LCK kinase and various interacting proteins. Haematologica, 99(1), 85-93. » Sha, F., Gencer, E.B., Georgeon, S., Koide, A., Yasui, N., Koide, S. and Hantschel, O. (2013). Dissection of the BCR-ABL signaling network using highly specific monobody inhibitors to the SHP2 SH2 domains. Proc. Natl. Acad. Sci. USA, 110(37), 14924-14929.

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EPFL School of Life Sciences - 2014 Annual Report

Huelsken Lab e

e s en

Associate Professor - Debiopharm Chair in Signal Transduction in Oncogenesis

http://huel

Introduction

Joerg Huelsken received his PhD in 1998 at the Humboldt University, Berlin, and did postdoctoral research at the Max-DelbrĂźck Center for Molecular Medicine, Berlin. He joined ISREC as an associate scientist and an NCCR project leader in January 2003 and was nominated Associate Professor at the EPFL School of Life Sciences in 2011. He holds the Chair in Signal Transduction in Oncogenesis sponsored by Debiopharm, Lausanne.

The last years of cancer research have established the concept of cancer stem cells (CSC) as sub-population of cells within a tumor responsible for tumor initiation and long-term tumor growth. We are interested in understanding the biology of these cells, studying their interaction with other tumor cells and the tumor stroma and to revealing how targeting this population could be achieved and whether this would improve overall survival. We have explored several therapeutic options to interfere with these cells at the root of disease and have identified a number of successful strategies which can cure breast and colon cancer by eliminating cancer stem cells in pre-clinical models. We further provided evidence that these cancer stem cells are also essential for the initiation of metastatic disease and characterized the interaction between stem cells and their environment as an essential factor for metastatic growth. Understanding in detail the communication between cancer cells and surrounding stroma will help to define new therapeutic options to block spreading of cancer to secondary sites. The process of metastasis is rather inefficient and requires formation of local support structures, so called metastatic niches, which exploit wound repair mechanisms of the normal tissue to drive tumor progression. Since this support relies on activated, but otherwise normal, non-mutated cells, we are optimistic that it should be possible to interfere with these support signals and thereby prevent metastasis formation in the future.

Keywords

Cancer stem cells, metastatic colonization, differentiation therapy, immunotherapy.

136

en lab.epfl.ch

Results Obtained in 2014

Using an experimental system to study the process of hepatic metastasis formation, we characterized in detail factors which are altered in response to metastatic seeding using RNA expression profiling. We identified key components which determine metastatic success, and in particular the family of Hedgehog (Hh) ligands was found to play a major role in enabling tumor cells to initiate metastasis. These results are supported by analysis of human pancreatic cancer samples which revealed increased expression of Hh ligands in pancreatic liver metastases. Liver stromal cell respond to this Hh signal and support tumor cell survival by blocking resident innate immune cells which would otherwise attack and eliminate invading tumor cells. Interestingly, tumor cells of human colon cancers appear to have adapted this mechanism in an alternative, more direct way enabling them to block innate immune reactions in the liver. Overcoming this novel, immune suppressive activity should help to prevent metastatic spread to the liver, one of the major complications of abdominal cancers. Most cancers, even in an advanced stage, resemble their tissue of origin indicating that tumor cells maintain parts of the normal differentiation program of their non-transformed ancestors. We now have identified the homeobox transcription factor HoxA5 as an important inducer of intestinal epithelial differentiation. In colon cancer, HoxA5 is down-regulated during cancer progression, but when re-activated can induce loss of the cancer stem cell phenotype and can strikingly overcome tumor growth and metastasis in vivo. HoxA5 is interconnected with the Wnt pathway in a negative feedback loop which ensures definitive bimodal fate decisions enforcing cells to halt cell cycling and exit the stem cell pool. Since HoxA5 expression can be triggered by certain drugs, this may allow to treat colon cancer patients by Hox-mediated elimination of cancer stem cells.

EPFL School of Life Sciences - 2014 Annual Report

Team Members PhD Students Zuzana Tartarova Nicolas Desbaillets

Master’s Student Raphael Sommer

Technicians Fanny Cavat Pierre Dessen Nancy Thompson

Administrative Assistant Ursula Winter

ISREC - Swiss Institute for Experimental Cancer Research

Postdoctoral Fellows Jean-Paul Abbuehl Caroline Dafflon Anja Irmisch Stefania Mejetta Paloma Ordóñez Morán Albert Santamaria Martínez Patrick Schmidt

ntestinal organoids reflect the differentiation potential of intestinal stem cells (marked by Lgr5-GFP). Loss of the tumor suppressor gene APC expands the stem cell pool and blocks terminal differentiation. The homeobox gene HoxA5 overcomes this transformation by depleting Lgr5+ cancer stem cells.

Selected Publications » Dafflon, C., S. Mejetta, P. Ordonez-Moran, A. Santamaria-Martinez, T. Hussenet, F. Naef, J. Huelsken (2015). Stromal cross-talk prevents anti-tumor immunity and facilitates liver metastasis. in preparation » Ordóñez-Morán, P., C. Urech, J. Huelsken (2015). HoxA5 counteracts stem cell traits by inhibiting Wnt signalling in colorectal cancer. Cancer Cell, in revision » Ord ez-Morán, P., A. Irmisch, A. Barbachano, I. Chicote,S. Tenbaum, S. Landolfi, J. Tabernero, J. Huelsken, A. Mu oz, H.G. Pálmer (2013). SPROUTY2 is a β-catenin and FOXO3a target gene indicative of poor prognosis in colon cancer. Oncogene, 33, 1975-85. » Ord ez-Morán, P., J. Huelsken (2014). Complex metastatic niches: already a target for therapy Curr. Opin. Cell Biol., 31, 2 -3 . » Irmisch, A. and J. Huelsken (2013). Metastasis: New insights into organ-specific extravasation and metastatic niches. Exp. Cell Res., 31 ,1604-10. » Petherick, K.J., A.C. Williams, J.D. Lane, P. Ordóñez-Morán, J. Huelsken, T.J. Collard, H.J.M. Smartt, J. Batson, K. Malik, C. Paraskeva and A. Greenhough (2013). Autolysosomal β-catenin degradation regulates Wntautophagy-p62 crosstalk. EMBO J. 32,1903-16.

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EPFL School of Life Sciences - 2014 Annual Report

Lingner Lab ch m

n ne

Full Professor

http://lin ner lab.epfl.ch

Introduction

Joachim Lingner received his PhD in 1989 from the Biocenter, University of Basel under the supervision of Walter Keller. He then pursued a Postdoc working with Thomas Cech at the Howard Hughes Medical Institute in Boulder, Colorado. In 1997, he became a group leader at ISREC and then was promoted to Senior group leader in 2002. Prof. Lingner became an Associate Professor at EPFL in 2005 and then a Full Professor in 2009. He has received many honors including the STARTfellowship from the Swiss National Science Foundation in 1997; Friedrich Miescher Prize from the Swiss Society of Biochemistry in 2002; EMBO member in 2005; ERC advanced investigator grant in 2008.

The physical ends of chromosomes, known as telomeres, play critical roles in cancer development, other age-related disorders and short telomere syndromes. Telomeres protect chromosomes from degradation and rearrangements that are typically seen in cancer. Telomeres also serve as cellular clocks. They shorten in most normal, human, somatic cells with every round of DNA replication due to the DNA end replication problem and the absence of telomerase. Short telomeres elicit a DNA damage response triggering a permanent cell cycle arrest termed cellular senescence. Thus, the replicative potential of primary cells is limited, restraining the growth of pre-cancerous lesions that have lost normal growth control. During progression towards malignancy, senescence is overcome by mutations in cell cycle regulators such as p53 and pRB. Further telomere shortening, however, will lead to loss of telomere protection from the DNA end fusion machinery, which is repressed at intact telomeres. When telomeres are fused, cells enter a crisis state at which fused chromosomes that contain multiple centromeres become missegregated or become torn apart during mitosis due to pulling of centromeres towards opposite poles by the spindle apparatus. Cells can escape crisis by re-gaining telomerase expression. Through the expression of telomerase, human cancer cells acquire an immortal phenotype. Our laboratory combines telomeric chromatin analysis by mass spectrometry, biochemistry and molecular genetics to study the dynamics of telomere structure, function and replication in human cells under normal and pathological situations. Our work may allow manipulation of telomere functions in tumors and other diseased tissues in the future.

Keywords

Telomeres, TERRA, chromatin, long noncoding RNA, cellular senescence and immortality, genome stability, DNA replication, telomeropathies, cancer development.

138

Results Obtained in 2014

Our labâ&#x20AC;&#x2122;s work concentrated on the analysis of telomerase structure, the telomeric long noncoding (lnc) RNA TERRA and telomeric chromatin. In collaboration with Daniela Rhodes (Cambridge-UK), we determined the first three-dimensional structure of active human telomerase by single particle electron microscopy (Sauerwald et al., 2013). Human telomerase has a bilobal dimeric structure and it can bind two DNA substrates. We functionally characterized the single strand telomeric DNA binding complex CST. We identified the molecular defects in the CST complex that cause a telomere syndrome known as dyskeratosis congenita/Coats Plus. Our data indicate that telomere DNA replication defects in mutant CST are the primary cause of the disease (Chen et al., 2013). Our lab also discovered novel roles of the lnc RNA TERRA at telomeres when they become uncapped or critically short. TERRA is upregulated upon telomere uncapping (Porro et al., 2014a) promoting the recruitment of the LSD1 lysine demethylase to MRE11 at the damaged telomeres. LSD1 stimulates the nuclease activity of MRE11 and the nucleolytic processing of uncapped telomeres (Porro et al., 2014b). In addition, TERRA associates with SUV39H1 H3K9 histone methyltransferase, which promotes accumulation of H3K9me3 at damaged telomeres and sustains telomere endto-end fusions that occur upon loss of the telomeric shelterin component TRF2 during cell crisis. Finally, we established a quantitative telomeric chromatin isolation protocol (QTIP), to biochemically isolate the entity of proteins and nucleic acids present at telomeres and compare different telomeric states by mass spectrometry (Grolimund et al., 2013). We uncovered several new telomeric factors (Pfeiffer et al., 2013), which are under study. QTIP will provide the basis to tackle one of the biggest challenges in the telomere field, which is to identify the molecular changes at telomeres that occur during normal development, in cancer and in telomere syndromes.

EPFL School of Life Sciences - 2014 Annual Report

Team Members PhD Students Alix Christen Larissa Grolimund Jana Majerska Patricia Renck-Nunes Anna-Sophia Reis Aleksandra Vancevska

Technician Thomas Lunardi

Administrative Assistant Nicole de Montmollin

ISREC - Swiss Institute for Experimental Cancer Research

Postdoctoral Fellows Eric Aeby Reyes Babiano Marianna Feretzaki Verena Pfeiffer Sophie Redon Ivo Zemp

Quantitative telomeric chromatin isolation protocol (QTIP). (a) or flow of Q . (b) ffects of depletion at telomeres. (c) Comparison of telomeric protein composition at long versus short telomeres. ee rolimund, eb et al., ature ommunications ( ) for details.

Selected Publications » » » » » » »

Grolimund, L., Aeby, E., Hamelin, R., Armand, F., Chiappe, D., Moniatte, M., and Lingner, J. (2013). A quantitative telomeric chromatin isolation protocol identifies different telomeric states. Nat Commun 4:2 4 . Chen, L.Y., Majerska, J., and Lingner, J. (2013). Molecular basis of telomere syndrome caused by CTC1 mutations. Genes Dev 27:20 -210 . Pfeiffer, V., Crittin, J., Grolimund, L., and Lingner, J. (2013). The THO complex component Thp2 counteracts telomeric R-loops and telomere shortening. Embo J 32:2861-2871. **Sauerwald, A., **Sandin, S., Cristofari, G., Scheres, S.H., *Lingner, J., and *Rhodes, D. (2013). Structure of active dimeric human telomerase. Nat struct & mol biol 20:454-460. Porro A, Feuerhahn S, Delafontaine J, Riethman H, Rougemont J, Lingner J. (2014). Functional characterization of the TERRA transcriptome at damaged telomeres. Nat Commun 5:5379. Porro, A., Feuerhahn, S., and Lingner, J. (2014). TERRA-reinforced association of LSD1 with MRE11 promotes processing of uncapped telomeres. Cell Reports 6:765-776. Zemp I, Lingner J. (2014). The shelterin component TPP1 is a binding partner and substrate for the deubiquitinating enzyme USP7. J Biol Chem. 289:28595-28606.

» Redon S, Zemp I, Lingner J. (2013). A three-state model for the regulation of telomerase by TERRA and hnRNPA1. Nucleic Acids Res. 41(19):9117-9128.

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EPFL School of Life Sciences - 2014 Annual Report

Meylan Lab t enne

Tenure-track Assistant Professor - SNSF Professor

http://me lan lab.epfl.ch/

Introduction

In our research laboratory, we are studying the mechanisms that govern the development of non-small cell lung cancer (NSCLC). To this end, we use a combination of bioinformatics analyses, cancer-derived mouse and human cell lines, tumor tissue material and genetically-engineered mouse models of human NSCLC. Our research focuses on two main areas: Etienne Meylan received a PhD in Life Sciences from the University of Lausanne in 2006, for his work on innate immunity performed in the laboratory of Jürg Tschopp. From 2007 to 2010, he worked as postdoctoral fellow in the laboratory of Tyler Jacks, at the Koch Institute for Integrative Cancer Research, MIT, Cambridge USA. In 2011, he established his research laboratory at ISREC, as a Swiss National Science Foundation Professor and later as tenure-track Assistant Professor. His laboratory focuses on the molecular mechanisms that contribute to the development of non-small cell lung cancer.

Alterations in glucose metabolism - Since the pioneering work of Otto Warburg almost a century ago, it is recognized that tumors are at increased need for glucose compared to normal cells. We aim to address the mechanisms of derailed glucose utilization during the development of NSCLC – and increasingly other tumor types –, and the consequences on tumor progression. Specifically, we focus on the first and rate-limiting step of glucose usage: its entry that is mediated by glucose transporters of the GLUT family. Hopefully, our findings will lead to possible developments of therapies aimed to inhibit tumor-specific characteristics of glucose utilization. nnate immune and in ammatory path ays - Building upon our previous studies where we identified the NF-kB signaling pathway being critical for lung tumor development, we are currently investigating the role of several proteins and pathways – known to regulate innate immunity and/ or inflammatory processes – in the development of lung cancer. Specifically, we use genetic approaches to perturb these pathways directly in the lung tumor epithelial cells in vivo, to obtain a clear picture of their role and impact on tumor growth control. Collectively, we hope our research will help to understand better how lung cancer grows and progresses, in order to develop knowledge-based strategies to combat this devastating disease.

Results Obtained in 2014

Because it is known that tumor cells consume increased quantities of glucose to build their biomass required for proliferation, it is important to understand the biological consequences of increased glucose utilization, and to identify the limiting factors for glucose entry into tumor cells. To this end, we began to analyze the regulation of various glucose transporters, and to explore their contribution to lung tumor progression. We initially focused on GLUT3, a glucose transporter best characterized as a neuronal transporter with high affinity for glucose. We observed that, although GLUT3 is not expressed in normal lungs, it is induced in tumors from genetically-engineered mouse models of human lung cancer. In human cell lines derived from non-small cell lung cancer, we made the intriguing observation that GLUT3 was expressed to high mRNA and protein levels, specifically in some cell lines but not others. We elucidated this dichotomy in GLUT3 expression, unraveling a strong induction during an epithelial-mesenchymal transition (EMT, an important developmental pathway reactivated in cancer to promote tumor progression). Specifically, we found that, during EMT, GLUT3 transcription is induced by ZEB1, a crucial transcription factor of the EMT program, which directly binds to the second intron of the GLUT3 gene to activate its transcription (Figure). Currently, we are focusing on the regulation and importance of this and other glucose transporters in tumor progression, in lung tumors and other cancer types. In other important projects of the laboratory, we are developing methods for genetic perturbation and monitoring of the activity of innate immune or inflammatory pathways directly in lung tumors in vivo, to better understand their impact on tumor growth, the tumor microenvironment and the response to chemotherapy.

Keywords

Lung cancer; glucose metabolism; glucose transporters; innate immunity; mouse models of cancer; NF-kappaB.

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EPFL School of Life Sciences - 2014 Annual Report

Team Members PhD Students Caroline Contat Svenja Groeneveld Jawahar Kopparam Mark Masin

Master’s Student Bernard Moret

Technician Jessica Vazquez

Administrative Assistant Christine Skaletzka

ISREC - Swiss Institute for Experimental Cancer Research

Postdoctoral Fellows Stefania Crippa Julien Faget

GLUT3 regulation during EMT - During EMT, GLUT3 expression increases dramatically, due to B binding to the intron of gene. ells with mesench mal characteristics express GLUT3 to high levels, and need it for sustained proliferation. See also Masin et al., ancer etabolism, .

Selected Publications » Masin, M., Vazquez, J., Rossi, S., Groeneveld, S., Samson, N., Schwalie, P.C., Deplancke, B., Frawley, L.E., Gouttenoire, J., Moradpour, D., Oliver, T.G. and Meylan, E. (2014). GLUT3 is induced during epithelialmesenchymal transition and promotes tumor cell proliferation in non-small cell lung cancer. Cancer & Metabolism. 2:11. » Peters, S. and Meylan, E. (2013). Targeting receptor activator of nuclear factor-kappa B as a new therapy for bone metastasis in non-small cell lung cancer. Current Opinion in Oncology. 25(2):137-144.

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EPFL School of Life Sciences - 2014 Annual Report

Oricchio Lab s

cch

Tenure-track Assistant Professor - ISREC Foundation Chair for Translational Oncology

http:// ricchi lab.epfl.ch

Introduction and Research Interests

In November 2014, Elisa Oricchio was appointed as tenure track Assistant Professor at ISREC/EPFL. Prof. Oricchio graduated in Genetics with highest honor in 2004 and obtained a PhD in 2008 at the National Italian Institute of Health in Rome Italy. In Sept 2008, she joined the group of Dr. HG Wendel at Memorial Sloan Kettering (NY, USA) as a post-doc. Her research work focused on the genetics of Lymphoma exploring innovative therapeutic approaches.

Research in the Oricchio laboratory focuses on the genetics of lymphoma and its translation into new therapies. Lymphoma is a heterogeneous disease characterized by multiple genomic alterations. Our goal is to define the functional role of recurrent genetic lesions in the lymphomagenesis. We combine genomic analyses of human tumors with functional in vivo studies and we use mosaic models of lymphomas to functionally annotate genes of interest identified by genomic analyses and to perform preclinical treatment studies. Project Description Initially, we analyze lymphoma patient samples by RNA sequencing to quantitatively measure cancer associated variations in gene expression and specific isoform levels, as well as to identify potential novel gene fusions. We integrate these data with mutations and chromosomal aberrations to provide unprecedented insights into the genomics of lymphoma. We complement the genomic analyses with functional screenings to define the phenotypical contribution of these alterations to lymphomagenesis. This step is critical to the design of in vivo functional studies.

Our ultimate goal is to use our genetic and biological studies to design new therapeutic strategies. Frequent genomic alterations can influence therapeutic response, determine mechanisms of resistance and potentially targeted by using selective inhibitors. To test our hypotheses, we use highly controlled experimental systems that resemble the design of clinical trials in a physiological context. We test combination therapies in genetically defined tumors, we directly compare the impact of different genetic lesions on therapy and we measure the effect of tumor intrinsic heterogeneity to the treatment. The Oricchio laboratory opened at ISREC-EPFL in November 2014. A senior technician and a junior post-doc with experience in cancer biology have been recruited to start our research activity.

Next, we use genetically engineered mouse models of lymphoma to study the genetics and pathology of the disease. These murine models retain key human features and we will exploit these murine models to dissect the impact of recurrent genomic alterations on lymphoma initiation and transformation in vivo.

Keywords

Cancer genetics, mouse models, therapy.

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Team Members Technician Katanayeva Natalya

Administrative Assistant Demeester Dorothée

ISREC - Swiss Institute for Experimental Cancer Research

Postdoctoral Fellow Roli Misra

Functional in vivo studies using murine model of lymphoma. A) Schematic of adoptive transfer strateg that enable to uic l define the role of genetic lesions in l mphomagenesis and progression in vivo B) Representative data indicating how distinct genetic lesions affect tumor latency in vivo.

Selected Publications » Oricchio E. Papapetrou EP, Lafaille F, Ganat YM, Kriks S, Mark WH, Teruya-Feldstein J, Huse JT, Reuter , Sadelain M, Studer L, Wendel HG (2014) A cell engineering strategy to enhance the safety of stem cell therapies”. Cell Rep. Sep 25;8(6):1677-85. » Oricchio E., Ciriello G, Schatz JH, Jiang M, Heguy A, Viale A, de Stanchina E, Teruya-Feldstein J, Sander C, Wayne T, Seshan VE, Chaganti RSK Wendel HG. (2014) Frequent disruption of the RB pathway in indolent follicular lymphoma suggests a new combination therapy. J Exp. Med. Jun 30;211(7):1379-91.

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EPFL School of Life Sciences - 2014 Annual Report

Radtke Lab edd

dt e

Full Professor

ra t e lab.epfl.ch

Introduction

Freddy Radtke graduated from the University of ZĂźrich in molecular biology 1994, a postdoctoral fellowship at Genentech Inc. USA 19951996 was followed by a postdoctoral position at ISREC Switzerland 1997-1999; Assistant Member of the Ludwig Institute for Cancer Research 1999-2004 promoted to Associate Member in 2004; joined ISREC as Senior Scientist in 2006, before joining EPFL in August 2006 as associate professor; promoted to full professor in 2012.

Our group is interested in the molecular mechanisms controlling stem cell maintenance, lineage commitment and differentiation in self-renewing systems (such as the hematopoietic system, the skin and the gut) and cancer. The basic principle of self-renewing tissues is that they continuously produce cells from a stem cell reservoir that gives rise to proliferating transient amplifying cells, which subsequently differentiate and migrate to the correct compartment. These processes have to be tightly regulated to ensure life-long homeostasis. In recent years a substantial body of evidence has accumulated to support the notion that signaling pathways known to be important during embryonic development (such as e.g. Wnt and Notch) play important roles in regulating self-renewing tissues. Moreover, these pathways are often deregulated during tumorigenesis due to mutations in key elements involved in these pathways. Using mouse genetics we study the role of evolutionarily conserved signaling pathways under physiological and pathological situations to gain a better understanding of their role in cancer. In addition, the lab optimizes and validates potential drug development candidates that target developmental signaling pathways to assess their mode of action and their efficacy in pre-clinical cancer models and in primary human tumor samples.The laboratory also studies how inflammation can either promote or inhibit tumor progression.

Keywords

Cancer, leukemia, stem cells, differentiation, immunity, notch, Wnt, preclinical drug development and trials.

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Results Obtained in 2014

Specific fibroblastic niches in secondary lymphoid organs orchestrate Notch-regulated immune responses : Primary and secondary lymphoid organs provide specialized microenvironments that support the development and maturation of immune cells as well as the induction and control of immune responses. Until recently the primary function of fibroblasts within secondary lymphoid organs (SLO) was thought to be mainly structural. However, fibroblasts of SLO are now known to consist of several subsets fulfilling distinct and important physiological functions through their cross talk with immune cells. These fibroblasts are distinct from endothelial cells, which control cell entry/exit from SLO. In addition, Notch signalling has been shown to play critical roles in multiple aspects of immune cell differentiation and function within SLO, although the cellular interactions that regulate these events have remained elusive. We identified and characterized specific fibroblast subsets within SLO that control and specify Notch mediated immune regulation for marginal zone B cells, and certain dendritic cell subsets in the spleen as well as T follicular helper cells in the lymph node. Notch signaling in the pigmented epithelium of the anterior eye segment promotes ciliary body development at the expense of iris formation: The iris and ciliary body are pigmented structures of the anterior eye segment and are each essential for normal ocular function. Perturbed development and/or function of either structure results in detrimental pathological conditions such as glaucoma and Phtisis bulbi. We showed that canonical Notch signaling promotes ciliary body development and opposes iris formation. In addition, we demonstrate that genetic manipulation of Notch signaling in ocular pigment cells facilitates robust modeling of human pathologies such as glaucoma and Phthisis bulbi.

EPFL School of Life Sciences - 2014 Annual Report

Team Members PhD Students Marzia Amaro Monique Coersmeyer Chhavi Jain Delphine Harduin Annaise Jauch Fabian Junker Viktoria Reinmüller Bhushan Sarrode Silvia Wirth

Technicians Laure Bardouillet Christelle Dubey Marianne Nkosi

o-staining of and the otch ligand (red) in acti ated cl re mice re eals o erlapping e pression in specific fibroblastic known as follicular dendritic cells (FDCs, in blue).

Administrative Assistant Catherine Pache

ISREC - Swiss Institute for Experimental Cancer Research

Postdoctoral Fellows & Scientists Ute Koch Markus Germann Craig Nowell

of cells also

Selected Publications » Fasnacht N., Huang HY., Koch U., Favre, S., Auderset F., Cai, ., Onder L., Kallert S., Pinschewer D., MacDonald HR., Tacchini-Cottier F., Ludewig B., Luther SA. Radtke, F. Specififc fibroblastic niches in secondary lymphoid organs orchestrate distinct Notch-regulated immune responses. J Ex Med. (2014) Oct 20;211(11):2265-79. » Maes H., Kuchnio A., Peric A., Moens S., Nys K., De Bock K., Quaegebeur A., Schoors S., Georgiadou M., Wouters J., Vinckier S., Vankelecom H., Garmyn M., Vion AC., Radtke F., Boulanger C., Gerhardt H., Dejana E., Dewerchin M., Ghesquière B., Annaert W., Agostinis P and Carmeliet P. Tumor vessel normalization by chloroquine independent of autophagy Cancer Cell (2014) Aug 11;26(2):190-206. » Sarrode B., Nowell CS.,Ihm J., Kostic C., Arsenijevic Y., Moulin AP., Schorderet DF., Beermann F., Radtke F. Notch signaling in the pigmented epithelium of the anterior eye segment promotes ciliary body development at the expense of iris formation. Pigment Cell Melanoma Res. (2014) jul 27 (4):580-9. » Auderset F, Schuster S, Fasnacht N, Coutaz M, Charmoy M, Koch U, Favre S, Wilson A, Trottein F, Alexander J, Luther SA, MacDonald HR, Radtke F, Tacchini-Cottier F. Notch signaling regulates follicular helpoer T cell differentiation. J Immunol. (2013) Sep 1; 191 (5):2344-50. » Radtke F., MacDonald HR., and Tacchini-Cottier F. Regulation of Innate and Adaptive Immunity by Notch. (2013) Nature Reviews Immunology ,13(6):427-37. » Licciulli S. Aviala JL, Hanlon L, Troutman S, Cesaroni M, Kota S, Keith B, Simon MC, Pure E, Radtke F, Capobianco AJ, Kissil JL. Notch1 is required for Kras-induced lung adenocarcinoma and controls tumor cell survival via p53. Cancer Res. (2013) Oct 1;73(19):5974-84

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EPFL School of Life Sciences - 2014 Annual Report

Simanis Lab est

m ns

Associate Professor

http:// imani

Introduction

Viesturs Simanis studied Biochemistry at Imperial College, graduating with a First Class Honours Degree in 1980. He did his Ph.D. studies with Professor Sir David Lane, at Imperial College London (awarded 1984). He did his postdoctoral studies with Professor Sir Paul Nurse, at ICRF in London, and the Department of Microbiology in Oxford (1984 to 1988). He then moved to the Swiss Institute for Experimental Cancer Research in Lausanne (Switzerland), as a junior, then senior group leader (1988 to 2006). He was appointed Associate Professor at EPFL in 2006.

Cell division is essential for the propagation of all organisms. If the fidelity of the processes involved in cell division is reduced, there is an increased risk that errors will occur in the transmission of genetic information from a cell to its daughters; this can result in cell death, or alter the cell’s behaviour, which can contribute to the development of diseases such as cancer. We study cytokinesis, the final event of the cell cycle, using the S. pombe model system. If a cell divides without segregating its DNA, the outcome is a dead cell devoid of chromosomal DNA and a cell with increased ploidy, which is genetically less stable than a normal cell. Alternatively, if cytokinesis is triggered before chromosome segregation has been completed, then the nucleus may be “cut”; resulting in cell death, or aneuploidy. Our goal is to understand how cytokinesis is regulated and coordinated with other events in the cell cycle. In S. pombe a GTPase-regulated NDR-kinase signalling network known as the SIN (septation initiation network) acts at multiple points during cytokinesis. Failure of SIN signalling results in the production of multinucleated cells that die, while inappropriate activation of the SIN promotes cytokinesis from any cell cycle stage. The SIN is considered to be the functional counterpart of the mammalian “Hippo” signalling pathway, which regulates growth and proliferation. The SIN also plays a role in meiosis, where it is essential for generating the spores/gametes following completion of the two meiotic divisions. Our primary tools are forward and reverse genetics using the S. pombe model, coupled to cell biology and biochemical analysis. Our goal is to identify regulators and targets of the SIN in mitosis and meiosis.

Keywords

Schizosaccharomyces pombe, cytokinesis, signal transduction, cell cycle, meiosis, protein kinase, protein phosphatase.

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lab.epfl.ch

Results Obtained in 2014

Semi-automated image analysis reveals new facets of SIN regulation Localisation of SIN proteins at the spindle pole bodies (SPBs) is important for SIN regulation. Quantitative analysis of SIN protein localisation was performed using a semi-automated image analysis plug-in developed for the Image J platform in collaboration with the Unser lab (EPFL); (Schmitter et al., 2013). We used this to analyse large numbers of mutant and wild-type cells, which revealed several novel facets of SIN regulation; (Wachowicz et al., 2014). First, the SIN exists in two states; in early mitosis the SPB localisation of SIN proteins is positionally unstable, and depends upon the conserved POLO-family kinase Plo1p. This corresponds to the time when the SIN plays its role in contractile ring assembly. In late mitosis, when the SIN signals the onset of cytokinesis, SIN protein localisation now becomes dependent upon the signalling GTPase Spg1p and its regulator Etd1p. The transition between these states is tightly coupled to other events in mitosis, and regulators that promote and delay it, were identified. This provides the basis for further studies of the nature of these two states and how the transition between them is regulated. Regulation of the SIN in meiosis We studied the regulation of the SIN in meiosis, and found that the regulatory hierarchy of the signalling is different from that seen in mitosis. We discovered that stage-specific protein degradation is important for the regulation of SIN signalling, with the conserved ubiquitin ligase Dma1p playing a central role (Krapp and Simanis, 2014). Future studies will examine the basis for these differences. Others We contributed to a study of mitotic and morphogenetic control in S. pombe (Grallert et al., 2013). We also collaborated to studies that optimised the analogue-sensitive cdc2 mutant (Aoi et al., 2014) and described new vectors for S. pombe (Fennessey et al., 2014).

EPFL School of Life Sciences - 2014 Annual Report

Team Members PhD Students Manuela Moraru

Administrative Assistant Catherine Pache

ISREC - Swiss Institute for Experimental Cancer Research

Postdoctoral Fellows Andrea Krapp Paulina Wachowicz

The SPB association of Cdc7p early mitotic requires full Plo1p function. Cells were mixed, synchronised, incubated at 36°C and imaged. Note the presence of a Cdc7p-GFP signal on the SPBs of the plo1+ cell (blue nuclear signal) and its absence from the plo1ts cell ( achowic et al., ).

Selected Publications » Wachowicz, P., Chasapi, A., Krapp, A., Cano Del Rosario, E., Schmitter, D., Sage, D., Unser, M., Xenarios, I., Rougemont, J. and Simanis, V. (2014). Analysis of S. pombe SIN protein SPB-association reveals two genetically separable states of the SIN. J Cell Sci in press. » Krapp, A. and Simanis, V. (2014). Dma1-dependent degradation of SIN proteins during meiosis in Schizosaccharomyces pombe. J Cell Sci 127, 3149-61. » Aoi, Y., Kawashima, S. A., Simanis, ., Yamamoto, M. and Sato, M. (2014). Optimization of the analogue-sensitive Cdc2/Cdk1 mutant by in vivo selection eliminates physiological limitations to its use in cell cycle analysis. Open Biol 4. 140063 » Fennessy, D., Grallert, A., Krapp, A., Cokoja, A., Bridge, A. J., Petersen, J., Patel, A., Tallada, V. A., Boke, E., Hodgson, B. et al. (2014). Extending the Schizosaccharomyces pombe molecular genetic toolbox. PLoS One 9, e97683. » Schmitter, D., Wachowicz, P., Sage, D., Chasapi, A., enarios, I., Simanis, . and Unser, M. (2013). A 2D/3D image analysis system to track fluorescently labeled structures in rod-shaped cells: application to measure spindle pole asymmetry during mitosis. Cell Div 8, 6. » Grallert, A., Patel, A., Tallada, . A., Chan, K. Y., Bagley, S., Krapp, A., Simanis, . and Hagan, I. M. (2013). Centrosomal MPF triggers the mitotic and morphogenetic switches of fission yeast. Nat Cell Biol 15, - 5.

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Bucher Group h

che

Group leader

http://bucher lab.epfl.ch/

Introduction

New technologies allow for comprehensive characterization of the molecular changes that cause a healthy cell to become cancerous. These technologies produce vast amounts of data. We develop computational methods that will help to extract insights and knowledge from such data. Philipp Bucher was first trained as a molecular biologist at the University of Zürich, and subsequently received his PhD in computational biology at the Weizmann Institute of Science in Israel. He then worked as a postdoctoral fellow with Sam Karlin at Stanford University before he moved to ISREC where he was promoted senior scientist in 2001.

Our main focus is on gene regulation. Transcription factors are key elements of regulatory circuits that control the expression of genes. By binding to specific sites in the genome, they turn on and off the expression of neighboring genes. We are interested in the molecular processes that guide transcription factors to their target sites, in a developmental stage-, tissue- and environmental condition-specific manner, and we are studying these processes by analyzing high-throughput functional genomics data produced by technologies such as ChIP-Seq, DNase-seq or CAGE. We are also developing novel computer algorithms for this purpose. We are further interested in the use of molecular profiling data for medical diagnosis. To this end we develop and test machine learning methods in the framework of open prediction challenges organized by the DREAM and sbv IMPROVER consortia. Besides research, our group develops and maintains bioinformatics databases and web servers. Our best known resource is the Eukaryotic Promoter Database EPD, created in 1986 and regularly updated since then. The ChIP-seq server features web-based programs to access and analyze a large collection of public functional genomics data sets. The Signal Search Analysis (SSA) server offers DNA motif discovery and search tools. These three resources are tightly interlinked and together form a comprehensive web-based system for gene regulatory regions analysis.

Keywords

Gene regulation, epigenetics, ChIP-Seq data analysis, bioinformatics algorithms, computational molecular diagnostics.

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Results Obtained in 2014

Novel bioinformatics methods for epigenome analysis Together with Bernard Moret’s group from computer science, we are developing new computational methods to study epigenetic phenomena with Next-Generation Sequencing (NGS) data. We recently published a probabilistic partitioning algorithm which serves for the detection of subclasses and extraction of chromatin signatures from selected genomic regions. Moreover, we have applied phylogenetic inference methods to reconstruct cell differentiation trees from ChIP-seq data. sing molecular profiling data for clinical diagnosis We carried out a proof-of-concept study to evaluate the usefulness of ChIP-Seq data from surgically removed breast tumor tissues as prognostic and predictive signatures. In addition, we participated in the Acute Myeloid Leukemia Outcome challenge organized by the DREAM consortium (http://dreamchallenges.org/). The goal of this challenge was to predict drug-response, remission duration, and overall survival time from patient data composed of clinical correlates and phosphoprotein expression levels. EPDNew now covers 5 model organisms EPDnew is a recently introduced, automatically compiled section of EPD. Its goal is to provide comprehensive, single-base resolution annotation of transcription start sites (TSS) for important model organisms. The massive release of new TSS mapping data over the last two years has enabled us to substantially expand the contents of EPDnew. By the end of 2014, we reached nearly complete gene coverage for human, mouse, and Drosophila, and about 50% coverage for zebrafish and C. elegans. PWMscan: a fast tool for scanning genomes for DNA motifs. Responding to needs created by NGS data, we created a new web-server, PWMscan, for scanning whole genomes for transcription factor binding site motifs defined by a position weight matrix. High speed is achieved by the use of pre-computed indexed genomes together with fast string matching software. Searching the human genome for a PWM-defined motif usually takes less than 30 seconds.

EPFL School of Life Sciences - 2014 Annual Report

Team Members Administrative Assistant Sophie Barret

ISREC - Swiss Institute for Experimental Cancer Research

Postdoctoral Fellows Giovanna Ambrosini Rouayda Cavin Périer René Dreos Sunil Kumar

Input form and results page of the PWMScan server. Upper right: Input form. Center left: sequence logo of the position weight matrix entered. Bottom: results page with action buttons for saving the match list, for extracting surrounding DNA sequences or sending the results to another web application.

Selected Publications » Nair, N.U., Lin, Y., Manasovska, A., Antic, J., Grnarova, P., Sahu, A.D., Bucher, P. and Moret, B.M. (2014). Study of cell differentiation by phylogenetic analysis using histone modification data. BMC Bioinformatics 15:269. » Nair, N.U., Kumar, S., Moret, B.M. and Bucher, P. (2014). Probabilistic partitioning methods to find significant patterns in ChIP-Seq data. Bioinformatics 30(17), 2406-2413. » Aghaeepour, N., Finak, G., FlowCAP Consortium, DREAM Consortium, Hoos, H., Mosmann, T.R., Brinkman, R., Gottardo, R. and Scheuermann, R.H. (2013). Critical assessment of automated flow cytometry data analysis techniques. Nat. Method 10(3), 228-238. » Weirauch, M.T., Cote, A., Norel, R., Annala, M., Zhao, Y. et al. (2013). Evaluation of methods for modeling transcription factor sequence specificity. Nat. Biotechnol. 31(2), 126-134. » Dreos, R., Ambrosini, G., Cavin Périer, R. and Bucher. P. (2013). EPD and EPDnew, high-quality promoter resources in the next-generation sequencing era. Nucleic Acids Res. 41(Database issue), D157-164. » Dimitrieva, S. and Bucher, P. (2013). UCNEbase--a database of ultraconserved non-coding elements and genomic regulatory blocks. Nucleic Acids Res. 41(Database issue), D101-109.

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Frey Group ete

External Adjunct Professor EPFL, Honorary Professor UNIL

http://lmrp.epfl.ch

Introduction

The main research area of the lab is tissue engineering and regenerative medicine for urological applications in particular for the treatment of congenital malformations.

Peter Frey received his master’s in Medical Zoology from the University of Basel in 1973 and then his Swiss Medical Degree in 1980. He received a Fellowship in Pediatric Surgery for the Swiss Academy of Medicine in 1988 and later became a Senior Lecturer in Basel (1990) and in Lausanne (2000). Dr. Frey then became an Associate Professor and head of Pediatric Urology at the CHUV in 2003, Visiting Professor at the EPFL in 2004 and then an Adjunct Professor in 2008. Prof. Frey was also a Visiting Professor at the University of Malaya, Kuala Lumpur (2012). He is a Member of the Swiss Commission of Technology and Innovation (CTI) and of the European Research Council. Over the years, Prof. Frey has received several grants from the EC, SNF and from CTI.

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The lab is involved in investigating the biology of human urothelial and smooth muscle cells, and in molecular and stem cell biology with particular interest in urothelial precursor cells. Further it evaluates smart, morphogen/growth factor loaded collagen and collagen fibrin hybrid matrices for tissue engineering purposes and develops flow bioreactors, imitating physiological conditions. In addition the lab is involved in the development of smart injectable bulking biomaterials for the treatment of vesico-ureteral reflux and urinary incontinence.

Results Obtained in 2014

Mechanically compressed tubular collagen and IGF1 loaded smart collagen matrices as well as collagen-fibrin hybrid matrices were developed and further, “humanized” tubular cell-engineered matrices were created. These matrices were successfully investigated in a preclinical rabbit urethral model.

Keywords

Tissue engineering, urology, pediatrics, urothelial cells, smooth muscle cells, stem cells, collagen, fibrin, growth factors, bioreactors.

EPFL School of Life Sciences - 2014 Annual Report

Team Members PhD Students Elif Vardar

Master’s Students Xavier Mottart Ann-Lena Jahnsen

Administrative Assistant Carol Bonzon

External Adjunct Professors

Postdoctoral Fellows Eva Maria Balet Mattias Larsson Kalitha Pinnagoda

Cross section of urethral tubular collagen graft 3 months after replacement of excised urethra in the rabbit. Note urethral lining and smooth muscle regeneration.

Selected Publications » Arenas da Silva, LF., Micol, LA., Tiemessen, D., Kuppevelt, TH., Frey, P., Oosterwijk, E., Geutjes, PJ. and Feitz, WFJ. (2013) Is there a need for smooth muscle cell transplantation in urethral reconstruction Tissue Engineering Part A 12/2013; DOI:10.1089/ten.TEA.2013.0185. » Larsson, HM., Gorostidi, F., Hubbell, JA. and Frey, P. (2014) Clonal, Self-Renewing and Differentiating Human and Porcine Urothelial Cells, a Novel Stem Cell Population PlosOne February 26, 2014 DOI:10.1371/ journal.pone.0090006.

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EPFL School of Life Sciences - 2014 Annual Report

Molinari Group n

External Adjunct Professor - Institute for Reseasrch in Biomedicine - Bellinzona

http://www.irb.u i.ch/pr tein

Introduction

The aim of the research performed in our group is to understand how mammalian cells insure expression of the cellular proteome and how they respond to variations in ER load with folding-defective or foldingcompetent polypeptides. Maurizio Molinari earned a PhD in Biochemistry at the ETH-Zurich in 1995. After post-docs in the laboratory of Cesare Montecucco (Padua) and Ari Helenius (Zurich), in 2000 he accepted the position of group leader at the IRB, Bellinzona. Maurizio Molinari received the Science Award 2002 from the Foundation for the study of neurodegenerative diseases, the Kiwanis Club Award 2002, the Friedrich-Miescher Award 2006 and the Research Award Aetas 2007. Since 2008, he is Adjunct Professor at the EPFL. Since 2013 he is member of the Research Committee at the Università della Svizzera italiana.

The endoplasmic reticulum (ER) contains high concentrations of molecular chaperones and enzymes that assist maturation of newly synthesized polypeptides destined to the extracellular space, the plasma membrane and the organelles of the endocytic and secretory pathways. It also contains quality control factors that select folding-defective proteins for ER retention and/or ER-associated degradation (ERAD). Mutations, deletions and truncations in the polypeptide sequences may cause protein-misfolding diseases characterized by a “loss-of-function” upon degradation of the mutant protein or by a “gain-of-toxic-function” upon its aggregation/ deposition. Pathogens hijack the machineries regulating protein biogenesis, quality control and transport for host invasion, genome replication and progeny production. Our long-standing interest is to understand the molecular mechanisms regulating chaperone-assisted protein folding and the quality control processes determining whether a polypeptide can be secreted, should be retained in the ER, or should be transported across the ER membrane for degradation. A thorough knowledge of these processes will be instrumental to design therapies or to identify drug targets for diseases caused by inefficient functioning of the cellular protein factory, resulting from expression of defective gene products, or elicited by pathogens.

ualit

c ntr l

Results Obtained in 2014

We have pursued our studies to better characterize the mechanisms regulating protein folding and quality control, with particular emphasis on the role of the UDP-glucose:glycoprotein glucosyltransferase (UGGT1). In a collaboration with the group of Randy Kaufman we revealed the importance of UGGT1-mediated protein re-glucosylation in maintaining the solubility of folding-competent and folding-defective polypeptides expressed in the ER lumen. We are also interested in the characterization of novel and druggable quality control mechanisms operating in the secretory compartment. In a collaboration with the group of Paolo Paganetti, transgenic mice were prepared that express a single open reading frame encoding the heavy and light chain of the specific antibody to the N-terminus of the Aβ peptide linked by the mouth and foot virus peptide 2A (to promote equimolar expression of light and heavy chains that are efficiently processed and assembled in the ER of transgenic cells). The in situ production of the antibody substantially reduced Aβ formation and aggregation compared to age-matched, mock-treated APP23 micecombinant proteins to be employed in the clinics and in the industry.

Keywords

Endoplasmic reticulum (ER), proteostasis, molecular chaperones and folding enzymes, protein quality control, autophagy, ER-associated degradation (ERAD), conformational diseases, UPR.

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l in

EPFL School of Life Sciences - 2014 Annual Report

Team Members PhD Students Giorgia Brambilla Pisoni Fiorenza Fumagalli Timothy Bergmann Ilaria Fregno

Visiting Scientists Tim Beltraminelli (UNIL) Ivan Hang (ETH-ZH) Ilaria Fegno (Erasmus)

External Adjunct Professors

Senior Scientists Carmela Galli Tatiana Soldà Elisa Fasana

Schematic representation of the proteostasis network

Selected Publications » » » »

Noack, J. and Molinari, M. (2014) RESETting proteostasis. Nature Chem. Biol. 10, 881-882. Noack, J., Brambilla-Pisoni, G. and Molinari, M. (2014) Proteostasis: Bad News and Good News From the Endoplasmic Reticulum. Swiss Medical Weekly 144:w14001, 1-13. Noack, J., Bernasconi, R. and Molinari, M. (2014) How Viruses Hijack the ERAD Tuning Machinery. J. Virology 88, 10272-10275. Paganetti, P., Reichwald, J., Bleckmann, D., Abramowski, D., Ammaturo, D., Barske, C., Danner, S., Molinari, M., Müller, M., Papin, S., Rabe, S., Schmid, P. and Staufenbiel, M (2013) , Transgenic Expression of β1 Antibody in Brain Neurons Impairs Age-Dependent Amyloid Deposition in APP23 Mice. Neurobiology of Aging 34, 2866-2874. » Ferris, S.P., Jaber, N.S., Molinari, M., Arvan, P. and Kaufman R.J. (2013) UDP-glucose: Glycoprotein Glucosyltransferase (UGGT1) Promotes Substrate Solubility in the Endoplasmic Reticulum. Mol. Biol. Cell 24, 25972608. » Merulla, J., Fasana, E., Sold , T. and Molinari, M. (2013) Specificity and Regulation of the Endoplasmic Reticulum-Associated Degradation Machinery. Traffic 14, 767-777.

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EPFL School of Life Sciences - 2014 Annual Report

Rainer Group e

External Adjunct Professor - University of Fribourg

http://www.uni r.ch/inph/ clab/

Introduction

Gregor Rainer is an ESF EURYI young investigator, Associate Professor at the University of Fribourg and adjunct Professor at EPFL. Previously he was a group leader at the Max-Planck Institute for biological cybernetics in T端bingen. He received his MSc in Physics from the Univ. of Vienna in 1994, a PhD in Systems Neuroscience from the Massachusetts Institute of Technology in 1999 and a Habilitation in Neurobiology from Univ. of T端bingen in 2003. He was awarded an APART scholarship, a DFG Heisenberg award, a teaching prize from the T端bingen graduate school and an Otto Hahn Medal.

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In the visual cognition laboratory, we perform research on various aspects of visual neurophysiology, including sensory representations of visual information, visual decision making and integration of sensory signals with reward-, motivation- and basal forebrain activation - related signals. We study both cortical and relevant subcortical components of the visual processing brain network. We complement this work with behavioural studies of visually guided behaviour, including exploratory behaviours as well as task performance after appropriate operant conditioning training. We are particularly interested in comparative aspects of visual cognition and the underlying neural mechanisms, and thus study these processes in several species including rodents, tree shrews and macaques. This approach allows us to distinguish species-specific adaptations from more general principles of neural processing related to visual cognition. Large scales electrophysiological recordings from multichannel arrays, iontophoretic drug application, deep brain stimulation, eye tracking and mass spectrometry based quantification of neuroactive biomolecules are among the techniques currently employed in the laboratory. .

Keywords

Primary visual cortex, basal forebrain, acetylcholine, psychopharmacology, pulvinar, lateral geniculate nucleus, eye tracking, mass spectrometry, liquid chromatography.

Results Obtained in 2014

In the period 2013/14, we have published several studies on neural activity in the tree shrew primary visual cortex (V1). For example, in one study we were able to show that tree shrew V1 contains virtually no simple cells, as estimated by the parameter of overlap between white and black visual receptive subfields. This is of interest because the visual cortex of the cat, the classical animal model for V1 function, contains many simple cells, and these simple cells are thought to represent and obligatory step in the cortical transformation of thalamic inputs. Our findings show that this is not the case in general, since the tree shrew V1 contains in fact almost exclusively complex cells. Although tree shrew V1 neurons are temporally modulated by drifting gratings, this is in fact not a result of separate subfields but rather due to a striking neural responses dominance for responses to black stimuli (i.e. luminance decrements) over white stimuli. Additional work in the lab has focused on how deep brain stimulation of the basal forebrain increases contrast sensitivity of 1 neurons, a finding that underscores the importance of ascending cholinergic projections in modulating cortical activation. These neurophysiological results are complemented by reports on behavioural findings during object exploration in tree shrews, and a detailed description of a hard- and software solution for eye tracking without the need for rigid fixation. In parallel, we have further developed mass spectrometry based neurochemical analysis methods for small molecule quantitation, and applied these methods to study neuropeptide regulation by chronic nicotine administration.

EPFL School of Life Sciences - 2014 Annual Report

Team Members PhD Students Paolo de Luna Mohammed Faiz Jordan Poirot Jayakrishnan Nair Wenxue Li

External Adjunct Professors

Postdoctoral Fellows Xiaozhe Zhang Abbas Khani

isual recepti e field of a single neuron recorded in the supragranular la er of ree Shrew V1 for white (left) and black (right) sparse noise stimuli. The colorbar to the right of each panel denotes mean firing rate in ert . riented two dimensional , as well aussian functions were fit to the acti ation maps to obtain its slant as the e act spread of the recepti e field ( l and s). ecepti e fields tend to be elliptical and horizontally slanted.

Selected Publications » » » » »

eit J., Bhattacharyya A., Kretz R., Rainer G. (2014) On the relation between receptive field structure and stimulus selectivity in the tree shrew primary visual cortex. Cerebral Cortex 24(10):2761-71. De Luna P., Faiz M., Rainer G. (2014) A MATLAB-based eye tracking control system using non-invasive helmet head restraint in the macaque J Neurosci Methods 235: 41–50. Falasca S., Ranc V., Petruzziello F., Khani A., Kretz R., Zhang X., Rainer G (2014) Altered neurochemical levels in the rat brain following chronic nicotine treatment J Chem Neu: 59-60:29-35. Nair J., Topka M., Khani A., Isenschmid M., Rainer G. (2014) Tree shrews (Tupaia belangeri) exhibit novelty preference in the novel location memory task with 24-h retention periods. Frontiers in Psychology 5:303. Bhattacharyya A., Veit J., Bondar I., Kretz R., Rainer G. (2013) Basal forebrain activation controls contrast sensitivity in primary visual cortex BMC Neuroscience 14:55.

» Petruzziello F., Falasca S., Andren P., Rainer G., Zhang X. (2013) Chronic nicotine treatment impacts the regulation of opioid and non-opioid peptides in the rat dorsal striatum. Mol Cell Prot 12(6):1553-62.

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EPFL School of Life Sciences - 2014 Annual Report

Schorderet Group ne

de et

External Adjunct Professor - Institute for Research in Ophthalmology (IRO) - Sion- Director

www.ir

Introduction

Born in Fribourg, Daniel Schorderet studied Pediatrics in Geneva and did a post-doctoral fellowship at the University of Washington in Seattle with Arno Motulsky (medical Genetics) and Stanley Gartler (genetics). He was appointed research assistant professor in 1988. On his return, he became associate professor of Molecular Genetics and head of the Unit of Molecular Genetics at the Division autonome de Génétique médicale of the CHUV. He took over the direction of that division in 1 7. He is board certified in Pediatrics, Medical Genetics and in genetic analyses. In 2003, he became director of IRO in Sion, an institute founded among others by EPFL and UNIL. In 2005, he became adjunct professor of Genetics at EPFL and in 2013 full professor at UNIL.

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The Institute for Research in Ophthalmology (IRO) is dedicated to study vision. Since 2003, we run a translational program called “Genes & Vision”, that takes advantage of the patients seen at the genetics clinics of the Jules-Gonin Eye Hospital as well as at other places through national and international collaborations. Genes & Vision has 6 research avenues: gene identification, study of retinal degeneration induced by these genes, investigate ophthalmic malignancies, and develop new animal models specifically in the zebrafish. These animal models are then used to develop new molecular therapies based on small peptides and patent-free drugs. Currently, we are developing a new program called ZebEye that aims at generating zebrafish models for all retinal degeneration diseases in order to use them for new drug screening. The gene identification program is based on next-generation sequencing of patients mostly affected with recessive disorders. More than 20 genes have been identified recently. We also focused on the role of HMX1, a transcription factor responsible for the oculoauricular syndrome of Schorderet-Munier-Franceschetti.

Results Obtained in 2014

i i n.ch

Our investigation of numerous families with anophthalmia/ microphthalmia (M/A) allowed us to identify a major role for ALDH1A3 in the development of the eye and to show that mutations in this gene represent an important factor in recessively inherited M/A. We also determined that MCT12 was implicated in cataract and glucosuria and acted as a creatine transporter and participated in the discovery of LRIT3, a new gene responsible for congenital stationary night blindness. A major part of our research is devoted to understand the role of HMX1, a gene that we discovered 5 years ago. We showed that it needs dimerization to be active, characterized the domain of dimerization, developed a predictive model to identify its targets and validated EPHA6 as its first target. Using a yeast two-hybrid approach, we characterized several proteins as member of the HMX1 inhibitory complex. We also evaluated several molecules and showed that a small peptide based on a BH3 domain is able to kill retinoblastoma cells.

Keywords

Oculogenetics, gene identification, HM 1, RPE65, NR2E3, retinal ischemia, hypoglycemia, age-related retinal degeneration, zebrafish.

EPFL School of Life Sciences - 2014 Annual Report

Team Members PhD Students Antille Mélanie Von Alpen Désirée Linda Wicht

Administrative Assistant Evéquoz Pascale

External Adjunct Professors

Postdoctoral Fellows Allaman-Pillet Nathalie Boulling Arnaud Marcelli Fabienne Renner Nicole

Family with anophthalmia. A. Pedigree showing 4 affected children in one generation. B. artial electropherogram of e on with homozygous and heterozygous (*) mutation. C. Picture of affected individuals including brain MRI of IV.1 showing absence of globe and hypoplastic optic nerves. (From Abouzeid et al. Human utation )

Selected Publications » Marcelli F, Boisset G, Schorderet DF(2014). A Dimerized HM 1 Inhibits EPHA6/epha4b in Mouse and Zebrafish Retinas. PLoS One (6):e1000 6. » Abouzeid H, Favez T, Schmid A, Agosti C, Youssef M, Marzouk I, El Shakankiry N, Bayoumi N, Munier FL, Schorderet DF (2014). Mutations in ALDH1A3 represent a frequent cause of microphthalmia /anophthalmia in consanguineous families. Hum Mutation, 35(8):949-53. » Boulling A, Wicht L, Schorderet DF (2013). Identification of HM 1 target genes: a predictive promoter model approach. Molecular ision 1 :177 -17 4. » Yahyavi M , Abouzeid H , Gawdat G, de Preux A-S, iao T, Bardakjian T, Schneider A, Choi A, Jorgenson E, Baier H, El Sada M, Schorderet DF , Slavotinek AM (2013). ALDH1A3 Loss of Function Causes Bilateral Anophthalmia/Microphthalmia and Hypoplasia of the Optic Nerve and Optic Chiasm. Hum Molec Genet, 22(16):3250-3258 (*contributed equally) » Abplanalp J, Laczko E, Philip NJ, Neidhardt J, Zuercher J, Braun P, Schorderet DF, Munier FL, Verrey F, Berger W, Camargo SMR, Kleockener-Gruissem B (2013). The cataract and glucosuria associated monocarboxylate transporter MCT12 is a new creatine transporter. Hum Molec Genet, 22(16):3218-3226. » Zeitz et al. (2013). Whole exome sequencing identifies mutations in LRIT3 as a cause for autosomal recessive complete congenital stationary night blindness. Am J Hum Genet 2:67-75.

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EPFL School of Life Sciences - 2014 Annual Report

Tanner - Swiss TPH ce

nne

External Adjunct Professor - Swiss TPH Institute - Basel - Director

www.ir

Research Interests

Marcel Tanner holds a PhD in medical biology from the University of Basel and a MPH from the University of London. He is Director of the Swiss Tropical & Public Health Institute and Professor (chair) of Epidemiology and Medical Parasitology, University of Basel. The research ranges from basic research in cell biology and immunology on malaria, schistosomiasis, trypanosomiasis and filariasis to epidemiological and public health research. Research, teaching and health planning are based on long term work in Africa and Asia. He is a member of various national and international bodies and boards.

158

i i n.ch

Swiss TPH (Swiss Tropical and Public Health Institute) and the EPFL School of Life Sciences are collaborating with the goal to bring together complementary expertise of the two institutions in research on hostpathogen interaction in infectious and chronic diseases and the development of new diagnostics, drugs and vaccines. Besides the collaboration in research, exchanges of teaching faculty and students within the MSc courses is continuing. Furthermore, a collaboration with the EPFL School of Computer and Communication Sciences on the development of Massive Open Access Online Courses (MOOCs) is initiated.

and the preclinical profiling of vaccine candidates. These activities rely heavily on the BSL3 animal facilities at the GHI. A mouse model for Buruli ulcer has been successfully established and is used to evaluate the protective efficacy of candidate vaccines. The model is also used for studies towards the re-purposing of tuberculosis drug candidates.

The two mycobacterial pathogens, Mycobacterium tuberculosis and M. ulcerans, the causative agents of the human diseases tuberculosis and Buruli ulcer, are being investigated as part of the GHI-Swiss TPH collaboration. Collaborative activities towards the clinical testing of a tuberculosis drug candidate developed by GHI in Tanzania are one major focus. Work in vaccinology is concentrated on the emerging disease Buruli ulcer and involves studying the immune responses to infection with M. ulcerans

Keywords

The biannual report of Swiss TPH: http:// b

sstph.ch/ es

ces/p b c t

ns/b enn

.htm

Epidemiology, public health, vaccines, drugs and diagnostics.

ts/

EPFL School of Life Sciences - 2013 Annual Report

Core Facilities & Technology Platforms

In addition, scientists from our School of Life Sciences closely collaborate with other services in the Lemanic region, including the Center for Biomedical Imaging’ (http://www.cibm.ch) and the Lausanne Genomics Technologies Facility’ (http://www.unil.ch/gtf/en/home.html) The following pages describe the Life Sciences-related core facilities and technology platforms currently available at the EPFL School of Life Sciences.

159

Core Facilities & Technology Platforms

In its goal to offer maximal support to its students and scientists in their training and research capabilities, EPFL and its School of Life Sciences have made a significant investment over the past years to establish stateof-the-art technology platforms and core facilities. These facilities are directed and managed by dedicated teams of highly trained and experienced staff and are run on a fee-for-service basis. They offer training, access to technology, assistance with experimental design and high level data analysis, and collaborations. The platforms are also involved in the School’s undergraduate and graduate teaching programs.

EPFL School of Life Sciences - 2014 Annual Report

Bioelectron Microscopy - BioEM http:// i

Introduction

The BioEM Facility provides life scientists at the EPFL and the lemanic area with the equipment and expertise for imaging biological samples with electron microscopy. This platform has a wide range of techniques available with both transmission and scanning electron microscopy using preparation techniques at either cryo or ambient temperatures.

Services and Technologies

The facility offers training and services in the following methods: • Transmission electron microscopy • Cryo transmission electron microscopy • Scanning electron microscopy • Focussed ion beam scanning electron microscopy • Correlated light and electron microscopy • Pre-embedding immunolabelling • Post-embedding immuno labelling • Single particle imaging and analysis • Cryo fixation with high pressure freezing • Standard chemical fixation methods including microwave

Image: Transmission electron microscograph showing mitochondria and the endoplasmic reticulum in an heptocyte of a young rat.

Selected Publications » Guichard, P., Desfosses, A., Maheshwari, A., Hachet, ., Dietrich, C., Brune, A., Ishikawa, T., Sachse, C., and G nczy, P. (2012). Cartwheel architecture of Trichonympha basal body. Science. 337(60 4):553. » Pino, E., Amamoto, R., Zheng, L., Cacquevel, M., Sarria, J.C., Knott, G.W., Schneider, B.L. (2013) FO O3 determines the accumulation of -synuclein and controls the fate of dopaminergic neurons in the substantia nigra. Hum Mol Genet. 23(6):1435-52. » von Tobel L, Mikeladze-Dvali T, Delattre M, Balestra FR, Blanchoud S, Finger S, Knott G, Müller-Reichert T, G nczy P. (2014). SAS-1 is a C2 domain protein critical for centriole integrity in C. elegans. PLoS Genet. 10(11). » Maco, B., Cantoni, M., Holtmaat, A., Kreshuk, A., Hamprecht, F.A., Knott, G.W. (2014). Semiautomated correlative 3D electron microscopy of E. coli-imaged axons and dendrites. Nat Protoc. 2014; (6):1354-66

160

.epfl.ch

Team Members Facility Head Graham Knott

Senior Scientist Davide Demurtas Scientiﬁc i tant Catherine Maclachlan Technicians St phanie Clerc-Rosset, Mary-Claude Croisier-Coeytaux d in trati e i tant Annick Evequoz Contact n or ation Graham Knott EPFL S PTBIOEM AI 0143 Station 19 CH-1015 Lausanne Tel: 41 (0) 21 6 3 1 62 graham.knott epfl.ch

EPFL School of Life Sciences - 2014 Annual Report

a in

tic http://bi p.epfl.ch/

The Bioimaging and Optics platform (BIOP) located in the faculty of Life Science (S ) provides access to state of the art light microscopes and important expertise to solve challenging (biological) questions with modern light-microscopy. A broad range of instruments ranging from simple wide-field imaging systems over standard point-scanning confocal microscopes up to a high-end 2-Photon-excitation microscope and microscopes which allow imaging below the diffraction limit (high/ super resolution microscopes) are currently available. Scientists who want to make use of the available equipment are trained so that they can use the instruments either independently or under the supervision of the BIOP team. The competence in sample preparation and image acquisition is complemented with strong image processing skills and necessary computer power to perform image processing. The idea is to link the image analysis with the image acquisition as early as possible in order to guarantee optimal scientific results.

Services and Technologies • Wide-field transmission and fluorescent microscopes • Life cell imaging microscopes • Single and multiple-beam confocal microscopes • 2P microscope • Fluorescence Lifetime Microscopy (FLIM) • High resolution and super resolution microscopes • (SIM, STROM, STED) • Image Processing tools (commercially available and/or custom built)

Team Members Facility Head Arne Seitz

Microscopy Jose Artacho Luigi Bozzo Thierry Laroche a e roce in Olivier Burri Romain Guiet d ini trati e i tant Maureen Hersperger Contact n or ation Arne Seitz EPFL S PTBIOP AI-0241 Station 15, CH-1015 Lausanne Tel: 41 (0) 21 6 3 6 1 Fax: 41 (0) 21 6 3 5 5 arne.seitz epfl.ch

Selected Publications » Esser-von Bieren J, Mosconi I, Guiet R, Piersgilli A, olpe B, Chen F, Gause WC, Seitz A, erbeek JS, Harris NL. (2013) Antibodies trap tissue migrating helminth larvae and prevent tissue damage by driving IL-4R independent alternative differentiation of macrophages. PLoS Pathog. (11): e1003771. » Lukinavi ius G, Reymond L, D’Este E, Masharina A, G ttfert F, Ta H, Güther A, Fournier M, Rizzo S, Waldmann H, Blaukopf C, Sommer C, Gerlich DW, Arndt HD, Hell SW, Johnsson K. (2014) Fluorogenic probes for livecell imaging of the cytoskeleton. Nat Methods. 11(7):731-3. » irginie Hamel, Paul Guichard, Mathias Fournier, Romain Guiet, Isabelle Flückiger, Arne Seitz, and Pierre G nczy (2014) Correlative multicolor 3D SIM and STORM microscopy. Biomedical Optics Express 5(10): 3326-3336. » Burri O., Guiet R., Seitz A. (2014) Development of freely available software tools from the perspective of a multi user core facility. Microscopy: advances in scientific research and education 2 (13): 7 - 4.

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Core Facilities & Technology Platforms

Introduction

EPFL School of Life Sciences - 2014 Annual Report

ioin or atic

io tati itc

C http://bbc .epfl.ch

Introduction

The Bioinformatics and Biostatistics Core Facility (BBCF) provides the EPFL and Lemanic institutions with extensive support in bioinformatics and biostatistics, from designing experiments to interpreting and visualizing complex data. Its main competences are in management and analysis of genomic data, mathematical modeling and statistical analysis of quantitative biological data. The facility works in close relationship with the Geneva and Lausanne Genomics platforms and complements their respective bioinformatics team with additional support for the analysis of large or complex data sets, for the implementation of data processing pipelines for new highthroughput technologies, and for the statistical planning in complex experimental designs. It also helps researchers with mining public databases, designing and setting up local databases, inferring mathematical models from experimental data and running simulations to validate a model. The facility acts as a point of contact between the experimental biologists and the research groups in bioinformatics and in basic sciences. It also makes the junction between the EPFL Life Science community and the various resources maintained by the Swiss Institute of Bioinformatics, in particular the ital-IT high performance computing center.

Services and Technologies • Analysis of high-throughput sequencing data: http://htsstation.epfl.ch • Management of genomics data http://biorepo.epfl.ch • Software development for genomics and bioinformatics: https://github.com/bbcf and http://bbcftools.epfl.ch • Building blocks for online genomic data manipulations: http://gdv.epfl.ch/bs • Databases and tools for lipidomics: http://lipidomes.org • Atlas of the Drosophila midgut: http://flygut.epfl.ch • Database of PCR primers http://bbcftools.epfl.ch/primerviz • Database of palmitoylated proteins: http://swisspalm.epfl.ch

Selected Publications » » » » »

David, F. P. A. et al. (2014). HTSstation: A Web Application and Open-Access Libraries for High-Throughput Sequencing Data Analysis. PLoS ONE :e 5 7 . Porro, A. et al. (2014). Functional characterization of the TERRA transcriptome at damaged telomeres. Nat Commun 5:537 . Steijger, T. et al. (2013). Assessment of transcript reconstruction methods for RNA-seq. Nat Methods 10:1177–11 4. Andrey, G. et al. (2013). A switch between topological domains underlies HoxD genes collinearity in mouse limbs. Science 340:1234167. Buchon, N. et al. (2013). Morphological and molecular characterization of adult midgut compartmentalization in Drosophila. Cell Rep 3:1725–173 .

162

Team Members Facility Head Jacques Rougemont

o tdoctora e earc er Fabrice David Philippe Jacquet Marion Leleu Scientiﬁc i tant Sara Benmohammed Julien Delafontaine Yohan Jarosz Yoann Mouscaz d in trati e Lisa Cessy

i tant

Contact n or ation Dr. Jacques Rougemont EPFL S PTBB AAB 025, Station 15 CH-1015 Lausanne 41 (0) 21 6 3 573 jacques.rougemont epfl.ch

EPFL School of Life Sciences - 2014 Annual Report

S http://b

Introduction

The Biomolecular Screening Facility is a multidisciplinary platform created in 2006 at the EPFL for performing screens in life sciences-related projects. In the frame of the NCCR-Chemical Biology, the BSF is hosting ACCESS, Academic Chemical Screening Platform for Switzerland, that provides chemical diversity, screening facilities and know-how in chemical genetics for academics countrywide.

Services and Technologies • Access to instrumentation dedicated to microplates and cell culture facilities • Chemical libraries of about 100’000 small molecules (BSF-ACCESS)

• Pilot screenings & Primary screening campaigns • Hits confirmation, Dose response assays & Secondary screens

• Genome–wide siRNA collections

• High Content Screening. Phenotypic assays by Digital Holographic Imaging (label free) and Fluorescence Microscopy

• Compound storage and management

• Image processing for high content screening read-outs

• Compounds delivery to partners • Assay development and validation for HTS

• Data management using in house developed Laboratory Implementation Management System (LIMS).

• Assay automation and statistical validations

• Cheminformatics

.epfl.ch/

Team Members Facility Head Gerardo Turcatti Scientists Damiano Banfi Marc Chambon Fabien Kuttler o tdoctora e earc er Benjamin Rappaz Marianne Seijo i tant Nathalie Ballanfat Julien Bortoli G rald Cruciani Antoine Gibelin d ini trati e i tant Maureen Hersperger Contact n or ation Gerardo Turcatti, PhD, MER EPFL S PTCB AAB 003, Station 15 CH-1015 Lausanne Tel: 41(0) 21 6 3 666 gerardo.turcatti epfl.ch

Selected Publications » Turcatti, G. (2014) Developing the Biomolecular Screening Facility at the EPFL into the Chemical Biology Screening Platform for Switzerland, Comb Chem High T Scr 17: 36 -376. » R hrig, U. F., Majjigapu, S. R., Chambon, M., Bron, S., Pilotte, L., Colau, D., an den Eynde, B. J., Turcatti, G., ogel, P., Zoete, ., and Michielin, O. (2014) Detailed analysis and follow-up studies of a high-throughput screening for indoleamine 2,3-dioxygenase 1 (IDO1) inhibitors, European Journal of Medicinal Chemistry 4: 2 4-301. » Rappaz, B., Breton, B., Shaffer, E., and Turcatti, G. (2014) Digital Holographic Microscopy: A uantitative Label-Free Microscopy Technique for Phenotypic Screening, Comb Chem High T Scr 17: 0- . » Makhlouf Brahmi, M., Portmann, C., D’Ambrosio, D., Woods, T. M., Banfi, D., Reichenbach, P., Da Silva, L., Baudat, E., Turcatti, G., Lingner, J., and Gademann, K. (2013) Telomerase Inhibitors from Cyanobacteria: Isolation and Synthesis of Sulfoquinovosyl Diacylglycerols from Microcystis aeruguinosa PCC 7 06, Chemistry – A European Journal 1 : 45 6-4601. » Kuhn, J., Shaffer, E., Mena, J., Breton, B., Parent, J., Rappaz, B., Chambon, M., Emery, Y., Magistretti, P., Depeursinge, C., Marquet, P., and Turcatti, G. (2013) Label-Free Cytotoxicity Screening Assay by Digital Holographic Microscopy, ASSAY and Drug Development Technologies 11: 101-107.

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Core Facilities & Technology Platforms

io o ec ar Screenin

EPFL School of Life Sciences - 2014 Annual Report

C to etr

CC http:// cc .epfl.ch/

Introduction

Flow cytometry is a technology that simultaneously measures and then analyzes multiple physical characteristics of single particles, usually cells, as they flow in a fluid stream through a beam of light. The properties measured include a particle’s relative size, relative granularity or internal complexity, and relative fluorescence intensity. Sorting allows us to capture and collect theses particles of interest for further analysis. The Flow Cytometry Core Facility (FCCF) is located in the School of Life Sciences (S ) at the Ecole Polytechnique F d rale de Lausanne (EPFL) and is part of a network of the core facilities at the school. FCCF’s mission is to provide to all investigators at EPFL and outside, comprehensive flow cytometric analysis and sorting including instrumentation, technical and professional assistance, training and consultation. The FCCF facility aims to keep on the cutting edge of cytometric technology by constantly updating hardware. New techniques are introduced according to the user’s needs. All the facility staff are members of the ISAC society. Currently the Flow Cytometry Core Facility is equipped with seven state of the art self-service bench top analyzers as well as two high-speed BLS2 cell sorters. The Core Facility also operates an automated immunomagnetic bead cell separator from Miltenyi Biotec MACS Technology. Researchers have the option, once trained, of performing their own acquisition/analysis or utilizing the expertise of the facility’s staff to run their samples with them.

Equipment • 1 - LSRII (Becton Dickinson) 5 lasers bench top analyser with 20 parameters. • 1 - LSRII (Becton Dickinson) 4 lasers bench top analyser with 15 parameters. • 3 - Cyan ADP (Beckman Coulter) 3 laser bench top analyser with 11 parameters. • 1 - Galios (Beckman Coulter) is a 3 laser bench top analyser with 12 parameters. • 1 - Accuri C6 is a 2 laser bench top analyser with 6 parameters and a plate reader • 1 - AutoMACS Pro is a fully automated bench-top magnetic bead sorter that can be used to perform sterile bulk sorts. • 1 - FACSAria (Becton Dickinson) 4-ways high-speed BLS-2 cell sorter, 5 lasers with 20 parameters and ACDU. • 1 - MoFlo Astrios (Beckman Coulter) 6-ways high-speed BLS-2 cell sorter, 4-laser with 1 parameters.

Services • Cell sorting • User training (machines and software) • Flow Cytometry teaching • Advice on experimental design • Setup and optimization of flow cytometry protocols • Expertise and advice include consultation on flow cytometry acquisition and data analysis • Support, in reporting flow cytometry data for manuscript and grant applications

164

Team Members Facility Head Miguel Garcia

C to etr erator al rie Glutz Lo c Tauzin d in trati e i tant Maureen Hersperger Contact n or ation Miguel Garcia EPFL S PTCF AI 0147, Station 15 CH – 1015 Lausanne Tel: 41 (0) 21 6 3 0 01 miguel.garcia epfl.ch https://twitter.com/Cytometry_ EPFL

EPFL School of Life Sciences - 2014 Annual Report

i to o

arati e at o o http://hc .epfl.ch

Histology involves the use of a set of techniques to examine the morphology, architecture and composition of tissues. The tissue samples are processed for the study of structures seen under the microscope, also called microscopic anatomy, as opposed to gross anatomy which involves structures that can be observed with the naked eye. The histology core facility is a competence pole which provides expertise in those analyses as well as routine work for researchers. All the techniques would be worthless without the expertise of a specialist in veterinarian pathology helping researchers to analyze their slides.

Services and Technologies

The facility assists researchers in the setting up and optimizing of histological approaches specific for each scientific project. Members of the S faculty can be trained on the available instruments like microtomes or cryostats and have then access to them for their own experiments. Also facility technicians are available to perform work for researchers: • Tissue processing to frozen, paraffin or resin sections • Histological stains like the standard Hematoxyline and eosin and special stains like Sirius red among others both manually or automated (Prisma from Sakura) • Setup and optimization of immunohistochemistry and immunofluorescence protocols manually as well as automated ( entana Discovery xT)

• Tests of newly available techniques (RNAscope from ACDbio) or useful published methods (double immunofluorescence for two primary antibodies of the same species using TSA technology). Pathology service Pathology support is provided by a specialist who has formal postgraduate training in veterinary anatomic pathology officially acknowledged by board certification of specialty. The pathologist is trained to diagnose, describe and interpret morphologic macro- and microscopic lesions within organs and tissues. Appropriate interpretation implies proper recognition of tissue abnormalities and sound knowledge of pathologic processes of diseases that manifest as morphologic changes as well as of the experimental design and settings. The service provides the following activities: • Consulting - at the study design level for issues related to pathology investigation • Morphologic phenotyping - whole body or organ targeted for genetically engineered animals • Analysis of histological specimens • Support - in reporting pathology data for manuscript submission and grant application • Diagnostics - Post mortem examination of diseased animals within the colony.

Team Members

Facility Head Jessica Sordet-Dessimoz Collaborators Gian-Filippo Mancini Nathalie Müller Agn s Hautier anessa Mack Co arati e at o o i t Alessandra Piersigilli d ini trati e i tant Maureen Hersperger Contact n or ation Jessica Sordet-Dessimoz EPFL S PTH AI0342, Station1 CH-1015 Lausanne 41 (0) 21 6 30 62 info.hcf epfl.ch

• Detection of mRNA and miRNA using cold probes on the Discovery xT from Roche- entana Selected Publications » Lo Sasso G, Menzies KJ, Mottis A, Piersigilli A, Perino A, Yamamoto H, Schoonjans K, Auwerx J. (2014). SIRT2 deficiency modulates macrophage polarization and susceptibility to experimental colitis. PLoS One. (7):e103573. » Lo Sasso G, Ryu D, Mouchiroud L, Fernando SC, Anderson CL, Katsyuba E, Piersigilli A, Hottiger MO, Schoonjans K, Auwerx J. (2014). Loss of Sirt1 function improves intestinal anti-bacterial defense and protects from colitisinduced colorectal cancer. PLoS One. (7):e1024 5. » Esser-von Bieren J, Mosconi I, Guiet R, Piersigilli A, olpe B, Chen F, Gause WC, Seitz A, erbeek JS, Harris NL. (2013). Antibodies trap tissue migrating helminth larvae and prevent tissue damage by driving IL-4R -independent alternative differentiation of macrophages. PLoS Pathog. (11):e1003771.

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Core Facilities & Technology Platforms

Introduction

EPFL School of Life Sciences - 2014 Annual Report

roteo ic

C http://pc

Introduction

In the last 10 years mass spectrometry based protein analysis has become an invaluable tool in the arsenal of techniques offered to the biologist to study the proteome, the expressed and active part of the genome. The rapid evolution of the technique has been tightly bound to the continuous increase in performance of mass spectrometers. Nowadays it is possible to get quantitative information about thousands of proteins in one experiment. Researchers can begin to think more globally. But there is still room for very detailed studies on single proteins especially those modified by post-translational modifications. The EPFL Proteomics Core Facility is a technological platform that has been created to address these needs and help researchers in using these techniques.

Services and Technologies

Instrumentation The PCF-PTP laboratory is currently equipped with sample preparation and fractionation devices (HPLC, FPLC, pI) and several mass spectrometers coupled to liquid chromatography: 3 Orbitraps, 2 LC-ESIMS/MS and 1 MALDI-TOF/TOF instruments. A mass cytometry instrument (CyTOF 2) jointly operated with the Flow Cytometry platform (PTCF) will soon complete the instrument base. The bioinformatics analysis pipeline includes Mascot, tandem SEUEST and Peaks servers for matching MS data with protein sequence databases and data post-treatment tools like Maxquant, Perseus, Pro-

teome Discoverer, PinPoint and Scaffold for protein identification, validation and pipelining of quantitative studies. Services The PCF-PTP has implemented several complementary workflows for protein analysis and offers an increasing palette of services... • Protein/Peptide Molecular Weight Measurements by Mass Spectrometry. • Mass Spectrometry based Protein/Peptide Identification from Gel or Solution. • Protein Relative uantification by SILAC or Label-free uantitative Analysis on collaborative basis. • Protein separation by FPLC and HPLC.

• Accurate protein quantification by SRM-MRM. • Localization and quantification of PTM’s other than phosphorylation. mixtures

profiling

and

targeted

quantification

... entertains tight collaboration with other proteomics facilities (UNILPAF, UNIGE-PCF, UNIBE) and with computer science and bioinformatics research centers ( ital-IT, SIB, etc..).

Selected Publications » Chopra, T., Hamelin, R., Armand, F., Chiappe, D., Moniatte, M., and McKinney, J.D. (2014). uantitative Mass Spectrometry Reveals Plasticity of Metabolic Networks in Mycobacterium smegmatis. Mol. Cell. Proteomics 13, 3014–302 . » Grolimund, L., Aeby, E., Hamelin, R., Armand, F., Chiappe, D., Moniatte, M., and Lingner, J. (2013). A quantitative telomeric chromatin isolation protocol identifies different telomeric states. Nat. Commun. 4, 2 4 » Schmid, A.W., Fauvet, B., Moniatte, M., and Lashuel, H.A. (2013). Alpha-synuclein Post-translational Modifications as Potential Biomarkers for Parkinson Disease and Other Synucleinopathies. Mol. Cell. Proteomics 12, 3543–355 . » Simicevic, J., Schmid, A.W., Gilardoni, P.A., Zoller, B., Raghav, S.K., Krier, I., Gubelmann, C., Lisacek, F., Naef, F., Moniatte, M., and Deplancke B. (2013). Absolute quantification of transcription factors during cellular differentiation using multiplexed targeted proteomics. Nat. Meth. 10, 570–576.

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Team Members Facility Head Marc Moniatte

Scientiﬁc Co a orator Diego Chiappe Florence Armand Adrian Schmid e earc i tant Romain Hamelin Jonathan Paz-Montoya Lisa Pilet d in trati e i tant Maureen Hersperger

... contributes also to collaborative based services requiring heavy involvement of both parties such as:

• Lipid

ptp.epfl.ch/

Contact n or ation Dr. Marc Moniatte AI 014 , Station 15 CH-1015, Lausanne 41 (0)21 6 3 17 53 marc.moniatte epfl.ch

EPFL School of Life Sciences - 2014 Annual Report

rotein Cr ta o ra

C http://pcr c .epfl.ch

The Protein Crystallography Core Facility provides instrumentation and expertise at every stage of the structure determination process for noncrystallography groups who are interested in solving the structures of their favorite macromolecule. Expertise and advice include consultation on protein purification, crystallization, and crystal optimization, as well as assistance with -ray crystal screening, data collection, data processing and structure determination and analysis. -ray crystallography is the primary method for determining three-dimensional structures of biological macromolecules, and is therefore an essential tool, which should be available to a broad range of researchers. Nowadays, it is possible for a noncrystallographer to access this technology thanks to automation and a variety of commercially available kits as well as to the friendlier and more intuitive programs that have been developed in recent years. With personalized advice, training, and follow-up, users are in the optimal environment to manage their crystallization screens, and to solve, refine and analyze the structures of their favorite proteins.

Services and Technologies • Advice on larger-scale protein expression and purification, if required. • Set-up of crystallization screens using commercial and facility-made conditions. • Optimization of crystals. • Data collection of quality crystals at facility x-ray source and synchrotrons. • Data processing using popular packages such as DS and Mosflm. • Structure determination using molecular replacement and MAD techniques. • Structure refinement, fitting and analysis using ccp4i and Phenix software.

Team Members Facility Head Florence Pojer

Technician Aline Reynaud d ini trati e Manuelle Mary

i tant

Contact n or ation Florence Pojer EPFL S PTCRYP S 3 27 Station 19 CH-1015 Lausanne Tel: 41 (0) 21 6 3 143 pcrycf-platform epfl.ch

• Deposition of structures in the protein database. • Preparation of images for publication using PyMol software.

Selected Publications » » » »

Neres J et al. (2014). 2-Carboxyquinoxalines Kill Mycobacterium tuberculosis through Noncovalent Inhibition of DprE1. ACS Chem Biol. Dec Chen S et al. (2014). Peptide Ligands Stabilized by Small Molecules. Angew Chem Int Ed Engl. 53(6):1602-6 Hartkoorn RC et al. (2014) Pyridomycin bridges the NADH- and substrate-binding pockets of the enoyl reductase InhA. Nat Chem Biol. 10(2): 6Haruki H et al. (2013). Tetrahydrobiopterin biosynthesis as an off target of sulfa drugs. Science. 340(6135): 7- 1

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Introduction

EPFL School of Life Sciences - 2014 Annual Report

rotein

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C http://pec .epfl.ch

Introduction

The objective of the PECF is to provide recombinant proteins, rapidly and at low cost, to EPFL researchers. Both cultivated mammalian cells and E. coli are used as production hosts. One of our main activities is recombinant protein production by transient transfection of Chinese hamster ovary (CHO) or human embryo kidney (HEK2 3) cells in suspension at volumetric scales from 5 mL to 10 L. We also produce proteins from existing recombinant cell lines developed by our clients. This may involve adapting the cell line to serum-free suspension culture. In this case, cultures at volumetric scales up to 10 L are used. For protein production in mammalian cells, we have a number of expression vectors available. We produce monoclonal antibodies by scale-up of existing hybridoma cell lines. When using E. coli as a host for protein production, the scales of operation range up to 20 L. For all the types of production mentioned, the PECF has non-instrumented bioreactors available for use. After production, we also provide services in protein recovery, mainly by affinity chromatography of proteins secreted from mammalian cells (antibodies and Fc- and his-tagged proteins) and GSTand his-tagged proteins produced in E. coli. For protein production in mammalian cells, we have a number of expression vectors available.

Services and Technologies • Large-scale transient transfection for recombinant protein in mammalian cells • Scale-up of existing cell lines for recombinant protein production • Scale-up of existing hybridoma cell lines for monoclonal antibody production • Recombinant protein production in E. coli • Affinity protein purification • Provision of vectors for protein production in mammalian cells

Selected Publications » Shen, ., Hacker, D.L., Baldi, L., and Wurm, F.M. (2014). irus-free transient protein production in Sf cells. J. Biotechnol. 171:61-70. » Kilpinen, H., Waszak, S.M., Gschwind, A.R., Raghav, S.K., Witwicki, R.M., Orioli, A., Migliavacca, E., Wiederkehr, M., Gutierrez-Arcelus, M., Panousis, N.I., Yurovsky, A., Lappalainen, T., Romano-Palumbo, L., Planchon, A., Bielser, D., Bryois, J., Padioleau, I., Udin, G., Thurnheer, S., Hacker, D., Core, L.J., Lis, J.T., Hernandez, N., Reymond, A., Deplancke, B., and Dermitzakis, E.T. (2013). Coordinated effects of sequence variation on DNA binding, chromatin structure, and transcription. Science 342(615 ):744-747. » Hacker, D.L., Kiseljak, D., Rajendra, Y., Thurnheer, S., Baldi, L., Wurm, F.M. (2013). Polyethyleneimine-based transient gene expression processes for suspension-adapted HEK-2 3E and CHO-DG44 cells. Protein Expr. Purif. 2(1):67-76. » Alattia, J.R., Matasci, M., Dimitrov, M., Aeschbach, L., Balasubramanian, S., Hacker, D.L., Wurm, F.M., Fraering, P.C. 2013. Highly efficient production of the Alzheimer’s -secretase integral membrane protease complex by a multi-gene stable integration approach. Biotechnol. Bioeng. 110(7):1 5-2005.

Team Members Facility Head David Hacker

Technicians Laurence Durrer Soraya uinche Contact n or ation David Hacker EPFL S PECF Station 6, CH J2 506 CH-1015 Lausanne Tel: 41 (0)21 63 6142 david.hacker epfl.ch

EPFL School of Life Sciences - 2014 Annual Report

Centre o

eno eno ic

ran enic C

C http://tc .epfl.ch/

Genetic manipulation of rodents through the generation of transgenic animals is a procedure of primary importance for biomedical research, either to address fundamental questions or to develop preclinical models of human diseases. We offer a centralized resource with various technologies for the generation of transgenic animals including pronuclear injection of DNA, lentiviral vector injection in the mouse oocyte and embryonic stem cells injection into the blastocyst. We are also a general support in both vector design and lentiviral vector production and titration, as our expertise in lentiviral vectors has become of general interest for many other applications than transgenesis. An important variable that affects the results of mouse studies is the sanitary status of the animals. Taking advantage of our expertise in embryo manipulation we also propose the sanitary cleaning of mouse transgenic lines by embryo transfer as a routine service. This procedure allows cleaning and hosting of a wide range of mouse lines in the SPF (Specific Pathogen Free) area of the EPFL animal facility.

Services and Technologies • Pronuclear injection: plasmids and BACs. • Lentiviral vector mediated transgenesis. • ES cells microinjection into blastocysts. • Lentiviral vectors production/titration. • ectorology. • Cleaning of established mouse lines by embryo transfer. • Cryopreservation of mouse lines by sperm freezing. • In vitro fertilization assay (I F).

Team Members Facility Head Isabelle Barde

Collaborators Dalil Ait-Bara Michelle Blom Sandra Offner Sonia erp Contact n or ation Isabelle Barde EPFL S CPG-GE S 1 36, Station 1 CH-1015 Lausanne 41 (0)21 6 3 17 02 isabelle.barde epfl.ch

For long-term preservation of mouse line of particular interest, we now propose cryopreservation by sperm freezing and recovery by in vitro fertilization (I F).

Selected Publications » Lonfat, N., Montavon, T., Darbellay, F., Gitto, S., Duboule, D. (2014) Convergent evolution of complex regulatory landscapes and pleiotropy at Hox loci. Science;346(6212):1004-6. » Delpretti, S., Montavon, T., Leleu, M., Joye, E., Tzika, A., Milinkovitch, M., Duboule, D. (2013) Multiple enhancers regulate Hoxd genes and the Hotdog LncRNA during cecum budding. Cell Rep.;5(1):137-50. » Andrey, G., Montavon, T., Mascrez, B., Gonzalez, F., Noordermeer, D., Leleu, M., Trono, D., Spitz, F., Duboule, D. (2013) A switch between topological domains underlies HoxD genes collinearity in mouse limbs. Science.;340(6137):1234167. » Gubelmann, C., Waszak, S.M., Isakova, A., Holcombe, W., Hens, K., Iagovitina, A., Feuz, J.D., Raghav, S.K., Simicevic, J., Deplancke, B. (2013) A yeast one-hybrid and microfluidics-based pipeline to map mammalian gene regulatory networks. Mol Syst Biol.; :6 2.

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Core Facilities & Technology Platforms

Introduction

EPFL School of Life Sciences - 2014 Annual Report

Center o

eno eno ic

Introduction

The development of genetic tools for the manipulation of the mouse genome has led to the creation of numerous and sophisticated mouse models. The in-depth characterization of the phenotype of these mouse lines is crucial to decipher the roles of the genes of interest. The Phenotyping Unit of the CPG is composed of highly interactive service platforms including clinical chemistry laboratory, metabolic and functional exploration platform, behavior and cognition exploration platform. The UDP provides a range of state-of-the-art equipment to enable cardio-metabolic, biochemical, oncologic and behavioural exploration of mouse models. We offer different types of support to the users of the platform, going from general support and training in protocols establishment to full completion of tests and analysis. We benefit from the scientific expertise of professors of the School of Life Sciences, such as Prof. Johan Auwerx and Prof. Carmen Sandi, both experts in their respective fields, namely cardio-metabolism and neurobiology.

enot

nit C

Services and Technologies

Team Members

A series of tests can be combined in a pipeline in order to answer questions related to a given topic such as neurodegenerative diseases or obesity or diabetes.

C ana er Roy Combe Rapha l Doenlen

The in-vivo imaging platform allows monitoring of disease progress in oncology by the assessment of tumor development, progression, metastasis, and response to therapy in models of cancer. Imaging modalities include high resolution CT scan, ultrasound and optical imaging (invivo bioluminescence or fluorescence). They improve cancer research by allowing longitudinal and non-invasive assessment.

Collaborators Arnaud Bichat Cristina Cartoni S bastien Lamy Adeline Langla Elodie Schneider C line Waldvogel Camille Aebischer Sybil Bron Cindy Bula Christine Pehm

We offer tests in the different scientific fields mentioned in the opposite figure.

The UDP is part of the animal facility barrier unit, and encompasses a working area constituted of housing, testing and analysis rooms. The mouse models are housed in individual ventilated cages and maintained at a conventional sanitary status. The UDP equipment has been chosen to ensure a high level of flexibility for the tests that can be performed. Additionally, most of experiments can be run by fully programmable and automated interfaces and thus the impact of experimental interventions by the researcher over the experimental period is reduced. Selected Publications » Trachet, B., Fraga-Silva, R.A., Piersigilli, A., Tedgui, A., Sordet-Dessimoz, J., Astolfo, A., an der Donckt, C., Modregger, P., Stampanoni, M.F., Segers, P. and Stergiopulos, N. (2015). Dissecting abdominal aortic aneurysm in Ang II-infused mice: suprarenal branch ruptures and apparent luminal dilatation. Cardiovasc Res. 105(2):213-22. » Boutant, M., Joffraud, M., Kulkarni, S.S., Garc a-Casarrubios, E., Garc a-Roves, P.M., Ratajczak, J., Fernández-Marcos, P.J., alverde A.M., Serrano M., and Cant C. (2014). SIRT1 enhances glucose tolerance by potentiating brown adipose tissue function. Mol. Metab. 4(2):11 -31. » Doenlen, R., Cettour-Rose, P., Bichat, A., Cartoni, C., Lamy, S., Langla, A., aret, M. and Warot, ., (2013). Impact of Fenbendazole on neurobiological and metabolic functions in mice. FELASA meeting. June 10-13. » Cant , C., Houtkooper, R.H., Pirinen, E., Youn, D.Y., Oosterveer, M.H., Cen, Y., Fernandez-Marcos, P.J., Yamamoto, H., Andreux, P.A., Cettour-Rose, P., Gademann, K., Rinsch, C., Schoonjans, K,. Sauve, A.A. and Auwerx, J. (2012). The NAD( ) precursor nicotinamide riboside enhances oxidative metabolism and protects against high-fat diet-induced obesity. Cell Metabolism. 15(6): 3 - 47.

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Facility Head avier Warot

Contact n or ation avier Warot CPG head Tel: 41 (0) 21 6 3 1 6 xavier.warot epfl.ch Rapha l Doenlen UDP manager Tel: 41 (0) 21 6 3 0 53 raphael.doenlen epfl.ch

Core Facilities & Technology Platforms

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EPFL School of Life Sciences - 2014 Annual Report

11th edition 2014/2015 Produced and edited by the EPFL School of Life Sciences Printed at the EPFL “Atelier de Reprographie” Image - Christopher Tremblay (Prof. Melody Swartz Lab) see p.2

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Editor: Alice Emery-Goodman With many thanks to Bruno Liardon (photographs & cover design), Roland Chabloz (Reprographie), and Harald Hirling for their help and support!