Epfl School of Life Sciences AR2012 by EPFL School of Life Sciences

SV 2 0 12 ANNUAL REPORT

EPFL School of Life Sciences - 2012 Annual Report

Table Of Contents

Preamble.....................................................................................................................................3 Highlights of 2012.......................................................................................................................6 Honors-Awards-Announcements.................................................................................................7 Undergraduate Studies.................................................................................................................8 Doctoral Programs.......................................................................................................................9 SV Doctoral Graduates..............................................................................................................10 SV Masters Graduates................................................................................................................12 School of Life Sciences at a Glance...........................................................................................13

Centers.............................................................................................................................14

Blue Brain Project......................................................................................................................14 Center for Biomedical Imaging Research....................................................................................16 Center for Neuroprosthetics ......................................................................................................18

BMI..................................................................................................................................21

Aebischer Lab............................................................................................................................22 Blanke Lab.................................................................................................................................24 Courtine Lab..............................................................................................................................26 Fraering Lab...............................................................................................................................28 Gerstner Lab..............................................................................................................................30 Herzog Lab................................................................................................................................32 Lashuel Lab...............................................................................................................................34 Magistretti Lab...........................................................................................................................36 Markram Lab.............................................................................................................................38 Moore Lab.................................................................................................................................40 Petersen Lab..............................................................................................................................42 Sandi Lab...................................................................................................................................44 Schneggenburger Lab................................................................................................................46

IBI....................................................................................................................................49

Auwerx - Schoonjans 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 Swartz Lab.................................................................................................................................68 Wurm Lab.................................................................................................................................70

Co-affiliated Research Groups.........................................................................................72

Aminian Lab..............................................................................................................................72 Fantner Lab ...............................................................................................................................73 Guiducci Lab.............................................................................................................................74 Hatzimanikatis Lab....................................................................................................................75 Ijspeert Lab................................................................................................................................76 Johnsson Lab.............................................................................................................................77 Jolles-Haeberli Lab ...................................................................................................................78 Lacour Lab ................................................................................................................................79 Maerkl Lab ...............................................................................................................................80 Mermod Lab..............................................................................................................................81 Micera Lab ...............................................................................................................................82 Millán Lab ................................................................................................................................83 Pioletti Lab ...............................................................................................................................84

EPFL School of Life Sciences - 2012 Annual Report

Psaltis Lab .................................................................................................................................85 Radenovic Lab ..........................................................................................................................86 Renaud Lab ..............................................................................................................................87 Roke Lab ..................................................................................................................................88 Stergiopulos Lab .......................................................................................................................89 Van de Ville Lab ........................................................................................................................90 Van den Bergh Lab ...................................................................................................................91

GHI..................................................................................................................................93

Blokesch Lab.............................................................................................................................94 Cole Lab....................................................................................................................................96 Fellay Lab..................................................................................................................................98 Harris Lab................................................................................................................................100 Lemaitre Lab............................................................................................................................102 McKinney Lab.........................................................................................................................104 Trono Lab................................................................................................................................106 Van der Goot Lab....................................................................................................................108

ISREC.............................................................................................................................111

Aguet Lab................................................................................................................................112 Brisken Lab..............................................................................................................................114 Constam Lab............................................................................................................................116 De Palma Lab..........................................................................................................................118 Duboule Lab............................................................................................................................120 Gönczy Lab.............................................................................................................................122 Hanahan Lab...........................................................................................................................124 Hantschel Lab..........................................................................................................................126 Huelsken Lab ..........................................................................................................................128 Kühn Lab.................................................................................................................................130 Lingner Lab..............................................................................................................................132 Meylan Lab..............................................................................................................................134 Radtke Lab...............................................................................................................................136 Simanis Lab.............................................................................................................................138 Bucher Group..........................................................................................................................140

Other Professors............................................................................................................142

Knowles...................................................................................................................................142 Tanner - Swiss TPH..................................................................................................................143 Molinari Group........................................................................................................................144 Rainer Group...........................................................................................................................146 Schorderet Group....................................................................................................................148 Core Facilities & Technology Platforms.....................................................................................151 Bioelectron Microscopy...........................................................................................................152 BioImaging & Optics...............................................................................................................153 Bioinformatics & Biostatistics...................................................................................................154 Biomolecular Screening...........................................................................................................155 Flow Cytometry ......................................................................................................................156 Histology ................................................................................................................................157 Proteomics...............................................................................................................................158 Protein Crystallography............................................................................................................159 Protein Expression...................................................................................................................160 Transgenic ..............................................................................................................................161 Phenotyping Unit.....................................................................................................................162

Introduction

Core Facilities & Technology Platforms..........................................................................151

EPFL School of Life Sciences - 2012 Annual Report

Preamble The School of Life Sciences is organized to teach students at the interface of biology and engineering - indeed quantitative, analytical and design-oriented life scientists, whether pursuing 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 come from diverse backgrounds in biology, chemistry, physics, engineering and medicine to bring their passion for developing new fundamental understanding of critical questions in the life sciences and translating that understanding toward impacting human health through engineering solutions. The School’s span from the fundamental to the translational incorporating both basic scientists and engineers positions it in a unique position for profound impact.

Jeffrey A. Hubbell - Dean of Life Sciences

Introduction

The situation within the School in 2012 is exciting. Our professors have been awarded a total of 18 ERC grants, reflecting the broad enthusiasm of the scientific community for our scientific performance. The Center for Neuroprosthetics, a collaboration with the School of Engineering, has been launched and is fully up to speed, including ongoing human clinical investigations. The Human Brain Project, led by professors in the Brain Mind Institute, is having broad impact in neuroscience in Europe and worldwide. The Swiss Institute for Experimental Cancer Research has launched a collaboration with the University of Lausanne and the Centre Hospitalier Universitaire Vaudoise to create the Swiss Cancer Center Lausanne, bringing together basic and translational scientists and engineers to solve fundamental problems in cancer biology and therapy. These and other strategic activities are exciting expressions of the enthusiasm and leadership roles of the professors of the School of Life Sciences.

EPFL School of Life Sciences - 2012 Annual Report

Highlights of 2012 February: Marc Moniatte, EPFL Proteomics Core Facility and INSERM-EPFL joint laboratory led by Christian Doerig joined forces with a team at Institut Pasteur (Paris) on an Antivalarial joint research project. http://actu.epfl.ch/news/ antimalarial-successful-joint-research/

March: The SV labs welcomed 17 enthusiastic high school students from all corners of Switzerland under the framework of La Science Appelle les Jeunes! (Schweizer Jugend forscht!) These students experienced lab work first-hand while completing and presenting a mini-project. http:// fr.sjf.ch/index.cfm

March : As a part of “Science, qui tourne.” , Denis Duboule (ISREC) and Jacques Neirynck, a national councilor, held a joint interview at the Rolex Learning Center on the subject of the future effect on society caused by low cost human DNA sequencing. http://actu.epfl.ch/news/low-cost-genome-decoding-for-better-or-for-worse-2/

EPFL Announces the Next Phase for its Center for Neuroprosthetics, (CNP) defining and establishing a truly interdisciplinary field of study merging neuroscience with engineering and medicine, and efficiently translating major breakthroughs from bioengineering and neuroscience into clinical settings. http://cnp.epfl.ch/

March: EPFL Prospective Students Days: The Life Sciences Teaching Section welcomed more than 200 high school and “Lycées” students from the French speaking areas of Switzerland and France. The same event took place for Swiss Italian and Swiss German speaking high school students in December. More information : http://sv.epfl.ch/ prospective-students/march2012

Summer: The 2012 International Summer Research Program for undergraduate students hosted 25 high potential future researchers from all over the world. They joined the SV labs and learned cutting edge research techniques while investigating scientific questions relevant to today’s world. http://sv.epfl.ch/summer-research

August: The annual Life Sciences Symposium was hosted by GHI, on the theme “Global Health meets Infection Biology” with a topnotch roster of speakers. The symposium as usual was a resounding success. During the symposium, the 2012 Debiopharm Life Sciences Award was given to Professor Daniel D. Pinschewer (University of Geneva) and Doctors Daan Noordermeer (EPFL) and Kelly Tan (University of Geneva) each received a Junior Debiopharm Group™ Life Sciences Award. http://actu.epfl.ch/news/three-scientiﬁc-prizes-awarded-by-debiopharm/

For more information and up-to-date SV news:

http://actu.epfl.ch/search/sv/

EPFL School of Life Sciences - 2012 Annual Report

Honors-Awards-Announcements Dimitri Van De Ville (IBI - STI) - Pfizer Award

Olaia Naveiras (IBI) - Jose Carreras Junior Investigator

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Career Fellowship

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Denis Duboule (ISREC) - New member of the British Royal Society.

Nicola Harris (GHI) and Felix Naef (IBI) - 2012 Leenaards

Swiss Final, Zurich.

Hilal Lashuel (BMI) - World Economic Forum Honoree

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Switzerland participants, CERN, Geneva. Muralidhar -

Shruti Muralidhar (BMI) & Adrian Ranga (IBI) - FameLab

Foundation Scientific Prize

QGel (start-up) - IBI co-founders: Matthias Lutolf and Jeff

Kai Johnsson (IBI-SB) – new member of the EMBO-

Hubbell - PERL Prizes

European Molecular Biology Organization.

Denis Duboule (ISREC) - US National Academy election.

QGel (start-up) - IBI co-founders: Matthias Lutolf and Jeff

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Hubbell - Vigier Prizes

Daan

Noordermeer

(ISREC)

Junior

Douglas Hanahan (ISREC) - 2012 Award for Cancer

Debiopharm

Research from the Fondazione San Salvatore, Lugano, CH

Group™ Prize

Melanie Blokesch (GHI), Nicola Harris (GHI), Jeffrey Melody Swartz (GHI)

Jensen (IBI), and Matthias Lutolf (IBI) European Research

- 2012 MacArthur Foundation

Council (ERC) Starting Grants

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Fellow

Bart Deplancke (IBI) Prix SSV- Ambition Wulfram Gerstner (BMI) Prix SSV – Education

Jacques Fellay (GHI) - National Latsis Prize

Gisou van der Goot (GHI) - Prix Polysphère d-Or

Melanie Blokesch (GHI) - Best Teaching Evaluation prize

Olaf Blanke (BMI) - Cloëtta Foundation Prize

Introduction

Friedemann Zenken (BMI) - Teaching Assistant IC Award

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Swiss League Against Cancer

Joerg Huelsken (ISREC) - Robert Wenner Prize by the

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Ambition prize

Bart Deplancke (IBI) and Sebastian Maerkl (IBI - STI) -

EPFL School of Life Sciences - 2012 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, established under the direction of Prof. William F. Pralong, M. D., 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, bio-computing, 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.

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 19 credits of optional courses selected under the supervision of a mentor. 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. Bertrand Rey - photographer

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/

EPFL School of Life Sciences - 2012 Annual Report

Doctoral Programs All three graduate programs comprise a combination of coursework, laboratory-based research, in-house seminars, and national or international conferences. Highly qualified applicants worldwide are chosen during our Hiring Days which occurs 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.

Neuroscience (EDNE) provides its stu-

dents 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

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; stem cell biotechnology; orthopaedic engineering; microtechnology and nanotechnology; biomechanics and mechanobiology; molecular and cellular biophysics; computational biology; genomics and proteomics; advanced biomedical imaging and image processing. http:// phd.epfl.ch/edbb

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 programâ&#x20AC;&#x2122;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.

Introduction

http://phd.epfl.ch/edmshttp://phd.epfl.ch/edms

EPFL School of Life Sciences - 2012 Annual Report

SV Doctoral Graduates

Introduction

EPFL School of Life Sciences - 2012 Annual Report

SV Masters Graduates Master Bioengineering Graduates 2012

Master Life Sciences & Technology Graduates 2012

EPFL School of Life Sciences - 2012 Annual Report

Introduction

School of Life Sciences at a Glance

Centers

EPFL School of Life Sciences - 2012 Annual Report

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

Director: Prof. Henry Markram Introduction

The ultimate goal of the Blue Brain Project is to reverse engineer the mammalian brain by iteratively reconstructing models using biological data and principles and building on predictions generated. To achieve this goal the project has set itself four key objectives: • Create a generic Brain Simulation Facility with the ability to reconstruct brain models of the healthy and diseased brain, at different scales, with different levels of detail for different species. • Demonstrate the feasibility and value of this strategy by creating and validating a biologically detailed model of the neocortical column in the somatosensory cortex of young rats. • Use this model to refine the basic strategy to reconstruct brain models using biological data and principles and determine the extent to which new design insights can be predicted. • Exploit these validated and predicted principles to create larger more detailed brain models, and to develop strategies to eventually reconstruct the complete human brain using.

Keywords

Neocortex, simulation-based research, reverse engineering, high performance computing, unifying models, cortical column, mesocircuits, human brain project.

Description of BBP activities & results 2012

The combination of experiment and theory has long formed the basis of the scientific method. As computers become faster, computer simulations – combining experimental measurements and theoretical models – are beginning to capture the biological complexity of the brain. This is the goal of the Blue Brain Project, now in its eighth year. Over this time the project has constructed a prototype brain simulation facility with the software tools, the knowhow and the supercomputing infrastructure to build unifying models of the detailed structure of neuronal circuits and to simulate the way they function. The first version of the unifying model of the neocortical column was completed in 2008 and presented at the FENS meeting by the Blue Brain Project. The BBP integrated (and continually integrates) vast amounts of biological data on the rat neocortex and uses this reservoir of reconciled data to generate a continuously updated model, which is then simulated on Blue Brain Simulation Platform. The results were showcased during a presidential lecture at the Forum for European Neuroscience (FENS, Barcelona) and discussed with the scientific community at the largest annual convention of neuroscientists (Neuroscience, New Orleans), where 20 coordinated scientific posters were presented to detail the development and refinement of the cortical column unifying model.

Several insights from this first unifying model have been published in high impact journal publications and the full publication and release of the model are foreseen for 2013. Technical advances to the platform have been published at competitive conferences and a keynote lecture at the major supercomputing conference (Supercomputing, Salt Lake City) have been given. A notable insight from the model (published in PNAS 2012) is that the locations of synapses (the local connectome) between neurons can be accurately predicted using the reconstruction algorithms developed. Through the reconstruction the column, the BBP was able to identify key principles that determine synapse-scale connectivity by comparing the reconstructed circuit to a mammalian sample. Using these principles, it has become possible to accurately predict synapse location with 75-95% accuracy . Additionally, a systemic simplification strategy for the detailed model of the neocortical column was developed, which allows BBP to develop progressively abstract (simpler) models such that it is possible to focus on a particular aspect or function. Another scientific focus of the BBP in 2012 was to drive and coordinate the preparation of the Human Brain Project (HBP) proposal, selected as a FET Flagship initiative of the European Commission in 2013. This enormous effort involved numerous BBP scientists and managers as well as 150 scientific groups in various parts of the world. The preparatory phase project HBP-PS was successfully completed in April 2012 and a publically available report was created and disseminated. The HBP, involving initially 87 partner institutions, will be coordinated by EPFL and have a budget of one billion euros to deliver 10 years of world-beating science at the crossroads of science and technology. This success, essentially the largest research grant in EU funding history, represents a huge success for the EPFL and the ETH Board, who have backed the project during its preparation, and Swiss science in general. Following the mandate of the ETH Board, substantial efforts also went into the preparation of Blue Brain in the form of a national research infrastructure from 2013 onwards. Most notably, this includes the technical and infrastructural preparation for a future opening of certain Blue Brain assets to a larger group of scientists. This work will intensify in 2013 and lead to the release of a first web-based portal allowing scientists to use the Blue Brain Simulation Platform. Lastly, the Blue Brain Project succeeded in securing important international collaborations such as a strategic alliance between the King Abdullah University of Science and Technology (KAUST) and EPFL/BBP on neuro-inspired high performance computing and a participation in the Helmholtz Portfolio Grant allowing future collaboration with important computing centers in Germany.

EPFL School of Life Sciences - 2012 Annual Report

Team Members

Selected Publications

S.L.Hill, Y.Wang, I.Riachi, F.Schürmann, H.Markram: Statistical connectivity provides a sufficient foundation for specific functional connectivity in neocortical neural microcircuits, PNAS, 2012 Oct 16;109(42):E2885-94. doi: 10.1073/ pnas.1202128109. Epub 2012 Sep 18. S.Druckmann, S.Hill, F.Schürmann, H.Markram, I.Segev: A Hierarchical Structure of Cortical Interneuron Electrical Diversity Revealed by Automated Statistical Analysis, Cerebral Cortex, Cereb. Cortex (2012), doi: 10.1093/cercor/bhs290. A.Gidon and I.Segev: Principles governing the operation of synaptic inhibition in dendrites, Neuron, 2012 Jul 26;75(2):330-41. G.Khazen, S.L.Hill, F.Schürmann, and H.Markram: Combinatorial Expression Rules of Ion Channel Genes in Juvenile Rat (Rattus norvegicus) Neocortical Neurons, PLoS One, 7(4): e34786. doi:10.1371/journal.pone.0034786. S.Lasserre, J.Hernando, S.Hill, F.Schürmann, P. de Miguel Anasagasti, G.Abou Jaoudé, H.Markram: A Neuron Mesh Representation for Visualization of Electrophysiological Simulations, IEEE Transactions on Visualization and Computer Graphics, 18 (2): p. 214-217. S.Ramaswamy, S.L.Hill, J.G.King, F.Schürmann, Y.Wang, and H.Markram: Intrinsic Morphological Diversity of Thick-tufted Layer 5 Pyramidal Neurons Ensures Robust and Invariant Properties of in silico Synaptic Connections. J Physiol. 2012 Feb 15;590(Pt 4):737-52. Epub 2011 Nov 14. F.Tauheed, T.Heinis, F.Schürmann, H.Markram, A.Ailamaki: SCOUT: Prefetching of Latent Structure Following Queries, VLDB 2012 S.Eilemann, A.Bilgili, M.Abdellah, J.Hernando, M.Makhinya, R.Pajarola, and F.Schürmann: Parallel Rendering on Hybrid Multi-GPU Clusters, EGPGV 2012 J. Hernando, F.Schürmann, L.Pastor (2012), Towards real-time visualization of detailed neural tissue models: view frustum culling for parallel rendering, BioVis 2012 1Tauheed F, Biveinis L, Heinis T, Schürmann F, Markram H, Ailamaki A. Accelerating range queries for brain simulations, Proceedings of the 28th International Conference on Data Engineering (2012), pp. 941-952

General Project Manager Felix Schürmann Project Managers Buncic Nenad Fabien Delalondre Marc-Oliver Gewaltig Sean Hill Eilif Muller Julian Shillcock Stefan Eilemann Senior Science Writer Richard Walker Operations Alejandro Schiliuk Postdoctoral Fellows Guy Antoine Atenekeng Ahmet Bilgili Joe Graham Juan Hernando Daniel Keller Srikanth Ramaswamy Rajnish Ranjan Martin Telefont Benjamin Torben-Nielsen Werner Van Geit Thomas Heinis Research Assistant Melissa Cochrane

Engineers Carlos Aguado Sanchez Athanassia Chalimoudra Jean-Denis Courcol Valentin Haenel James Gonzalo King Bruno Ricardo Magalhaes Daniel Nachbaur Jeff Muller Stefano Zaninetta Sandro Wenzel PhD Students Marwan Abd Ellah Guiseppe Chindemi Lida Kanari Michael Reimann Renaud Richardet Farhan Tauheed Anirudh Vij Rahul Valiya Veettil Willem Wybo Interns Jafet Villafranca Diaz Ronny Hatteland Dan Ibanez Amine Achkar Kay G Hartmann Drew P Minnear Sarah Strauss Berat Denizdurduran Bidur Bohara Visiting Researcher Yun Wang Visiting Professors Karlheinz Wilhelm Meier Michael Hines Administration Christian Fauteux Catherine Hanriot Amanda Pingree Daphne Rondelli

of selected touch between neurons.

locations

Centers

Illustration

EPFL School of Life Sciences - 2012 Annual Report

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

Director: Prof. Rolf Gruetter

From Mouse to Patient History of the Center

The CIBM is the result of a major research and teaching initiative of the partners in the Science-Vie-Societe (SVS) project, i.e. Ecole Polytechnique Federale de Lausanne (EPFL), Universite de Lausanne (UNIL), Universite de Geneve (UNIGE), Hopitaux Universitaire Geneve (HUG), Centre Hospitalier Universitaire Vaudois Lausanne (CHUV), founded with generous support from the Fondations Jeantet and Leenaards. The CIBM was designed an imaging research center, committed to conducting biomedical imaging research in the context of biomedical research questions of importance, with the overall aim to bring together as equals imaging scientists and biomedical researchers. The Center is comprised of seven Research Cores focused on specialized research support and technology development and is active on three main sites at the EPFL, CHUV and HUG.

2012 Highlights • 115 publications • 1 starting ERC grant

Mission and Aim

The CIBMseeks 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 uses model systems ranging from transgenic animals to human subjects (“from mouse to man”) and fosters multi-disciplinary collaboration between basic science, biomedical science and clinical applications. The goal is to advance biomedical imaging, i.e. functional and metabolic imaging, while addressing biomedical questions of importance at the same time. This is accomplished by establishing a research network in imaging science to enhance biomedical research capabilities of the founding institutions and beyond, as well as within the CIBM.

Contact

To establish research projects, feel free to contact the Core director concerned (see below or www.cibm.ch) or info@ cibm.ch and we will be delighted to assist you.

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EPFL School of Life Sciences - 2012 Annual Report

Structure and Scope CIBM: 1 Center, 3 Sites, 5 Institutions, 7 Research Cores

Signal Processing and Image analysis core (M. Unser): The infrastructure includes multiple servers for data storage and processing. The aim is to perform high-level research in medical image analysis and develop theoretical foundations for new algorithms and mathematical tools for imaging addressing the need for advanced signal processing with large datasets being acquired, and complex questions to be answered. Phase Contrast Radiology core (G. Margaritondo): Ultra-high spatial and temporal resolution using using the TOMCAT beamline of the high quality swiss light source at the PSI in Villigen. The aim is to reach isotropic resolutions at the submicron scale within milliseconds and to develop novel approaches for phase-contrast radiology using conventional, laboratory-based sources. PET core (O. Ratib): A micro PET scanner linked to advanced radiochemistry research at the HUG, as well as a scanner at EPFL. The aim is to provide “conventional” imaging capabilities for the immediate evaluation of novel radiotracers, another is to focus on the synergies provided with combined studies on MR, including innovative mechanism for image registration.

Clinical Research Satellite at the HUG (F. Lazeyras): Clinical 3 Tesla TIM Trio scanner, 50% dedicated to clinical research and 50% to clinical service, with a complete accessary of functional-MRI equipment up to simultaneous EEG and MRI acquisition. A minimally invasive abdominal tumor ablation HiFU platform is operational. The aim is to develop and maintain state of the art MRI capabilities relevant for clinical research focusing on cognitive (dys)function and recovery in humans, as well as brain development. Clinical Research Satellite at the CHUV (M. Stuber): Clinical 3 Tesla TIM Trio scanner, 50% dedicated to clinical research and 50% to clinical service. A 32-channel cardiac coil and a 4-element carotid coil are available for cardiovascular research together with numerous high-end coils for neuro applications. The aim is to advance research and discovery through a better fundamental understanding of biological processes through advanced methods development enabling a direct translation from the bench to the bedside. Animal Imaging and Technology core (R. Gruetter): Ultra-high field MR equipment (100% research) • human 7 Tesla (1st actively shielded) • rodent 14 Tesla (world’s first) • rodent 9.4 Tesla The short bore of the 7 Tesla magnet makes it particularly suited for clinical studies and novel interventions, supported by a room for accommodating patients/volunteers. To minimize stress due to transport from the collaborating labs, a small on-site animal holding facility is present. Complemented with an RF laboratory and physiology support laboratories. The aim is to develop magnetic resonance imaging and spectroscopy capabilities in the context of specific biomedical research questions for animal imaging in rodents (primarily rats and mice) and for human brain imaging at very high magnetic fields. For more information see http://www.cibm.ch/page-60484-en.html.

A selection of images from all seven research cores.

Centers

EEG Brain Mapping core (C. Michel): State-of-the-art high density (MRI-compatible) EEG in- stallations at the university hospital in Geneva (HUG), the university medical school in Geneva (CMU), and at the university hospital in Lausanne (CHUV). The aim is to provide recording and analysis tools that allow studying the spatiotemporal dynamics of large-scale networks.

EPFL School of Life Sciences - 2012 Annual Report

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

Director: Prof. Olaf Blanke

Introduction

The Center for Neuroprosthetics (CNP) capitalizes on its unique access to advanced technologies and state of the art brain research present on the EPFL campus. Its aim is to develop new technologies that could 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 the generation of motor commands. It also requires technological capabilities to design novel devices, to record and process signals and to translate them into control signals that can commend artificial limbs, bodies and robots, for motor function, or produce signals to activate the brain, in the case of sensory 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, breakthroughs in cognitive neuroprosthetics will be necessary for treating patients suffering from cognitive deficits such as those caused by Alzheimer’s disease and vascular stroke.

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The Center for Neuroprosthetics is part of both the School of Engineering and the School of Life Sciences. It draws upon the EPFL’s expertise in biology, neuroscience, brain imaging, and genetics as well as biomedical, electrical, mechanical engineering, and nanotechnology. The Center will also draw upon EPFL’s cutting edge research in signal analysis, theoretical and computational neuroscience, the recently launched European Flagship “Human Brain Project” and the Swiss National Center of Competence in Research in “Robotics”. In addition, through support from the Bertarelli foundation, a new research collaboration - dedicated to translational neuroscience and neuroengineering - has been created between Harvard Medical School, EPFL’s Institute of Bio-engineering, and the Center for Neuroprosthetics. The Center for Neuroprosthetics is currently developing strategic partnerships with Geneva University Hospital (Hôpitaux Universitaires de Genève, HUG), Lausanne University Hospital (Centre Hospitalier Universitaire Vaudois, CHUV), and a major Swiss Rehabilitation Clinic (Clinique Romande de Réadaptation, CRR in Sion), as well as with the regional biomedical industry.

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EPFL School of Life Sciences - 2012 Annual Report

Four key projects define the core activities of the center: Walk again Restoring sensorimotor functions after spinal cord injury Intentions of a paralyzed rodent with spinal cord injury are decoded from real-time recording of brain activity. Decoded information is directly fed into a brain-spinal interface that computes optimal spinal cord stimulation patterns to execute the desired movement. As a result the animal is capable of locomotion and obstacle avoidance, even though the spinal cord motoneurons are physically separated from the brain. Bionic hand Restoring sensory and motor functions after arm or hand amputation Biocompatible flexible electrodes are implanted into different peripheral arm nerves of amputee patients. Movement commands of the amputee patient are decoded from signals in the implanted electrodes and transmitted to the prosthetic hand, where they are translated into movements of the prosthetic hand and fingers. Signals from different sensors in the prosthetic hand can also be transmitted via the implanted electrodes to the peripheral nerve to enable sensory functions such as the sense of touch and of finger position.

Rehabilitation of upper limb sensorimotor loss Providing neuro-technological tools for vascular stroke rehabilitation Merging insights from robotics and neuroengineering, our devices enable novel neurorehabilitation training for patients suffering from sensorimotor loss of the upper extremity. These tools are complemented by techniques from brain computer interfaces and virtual reality to further enhance rehabilitation outcomes for patients with sensorimotor loss, but also for patients suffering from chronic pain or cognitive deficits. Human-Computer confluence Decoding brain activity for feeling and moving artificial bodies and robots With robust real-time movement control of wearable devices and robots and with pioneering work in brain-machine interface and cognitive neuroscience, novel interaction paradigms are provided for mobility restoration, communication, neuroscience research, and entertainment.

Selected Publications:

Courtine G, Micera S, DiGiovanna J and MillĂĄn JdR (2013). Brain-machine interface: closer to therapeutic reality? The Lancet 381:515-7. Van den Brand R, Heutschi J, Barraud Q, DiGiovanna J, Bartholdi K, Huerlimann M, Friedli L, Vollenweider I, Moraud EM, Duis S, Dominici N, Micera S, Musienko P, Courtine G (2012). Restoring voluntary control of locomotion after paralyzing spinal cord injury. Science 336(6085):1182-5. Blanke O Multisensory brain mechanisms of bodily self-consciousness (2012). Nat Rev Neurosci 13(8):556-571. Dominici N, Keller U, Vallery H, Friedli L, van den Brand R, Starkey ML, Musienko P, Riener R, Courtine G (2012). Novel robotic interface to evaluate, enable, and train locomotion and balance after neuromotor disorders. Nature Medicine 18:1142-7. Panarese A, Colombo R, Sterpi I, Pisano F, Micera S (2012). Tracking motor improvement at the subtask level during robot-aided neurorehabilitation of stroke patients. Neurorehabil Neural Repair 26(7):822-33. Tombini M, Rigosa J, Zappasodi F, Porcaro C, Citi L, Carpaneto J, Rossini PM, Micera S (2012). Combined analysis of cortical (EEG) and nerve stump signals improves robotic hand control. Neurorehabil Neural Repair 26(3):275-81. Delivopoulos E, Chew D, Minev IR, Fawcett JW, Lacour SP (2012). Concurrent recordings of bladder afferents from multiple nerves using a microfabricated PDMS microchannel electrode array. Lab on Chip 12:2540-2551. Huang YY, Terentjev E, Oppenheim T, Lacour SP, Welland ME (2012). Fabrication and electromechanical characterization of near-field electrospun composite fibers. Nanotechnology 23:105305. Tzovara A, Murray M, Bourdaud N, Chavarriaga R, MillĂĄn JdR and De Lucia M (2012). The timing of exploratory decision-making revealed by single-trial topographic EEG analyses. Neuroimage 4:1959-69.

Centers

Ionta S, Heydrich L, Lenggenhager B, Mouthon M, Fornari E, Chapuis D, Gassert R, Blanke O (2011). Multisensory mechanisms in temporo-parietal cortex support self-location and first-person perspective. Neuron 70(2):363-74.

EPFL School of Life Sciences - 2012 Annual Report

BMI

Brain Mind Institute

Sandi Carmen - Director

The mission of the Brain Mind Institute is to understand the fundamental principles of brain function in health and disease, by 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: • Molecular neurobiology and 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. • Designing innovative interventions to restore sensorimotor functions after neural disorders.

BMI - Brain Mind Institute

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, 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.

EPFL School of Life Sciences - 2012 Annual Report

Aebischer Lab http://len.epfl.ch/

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 is President of EPFL. He is the founder of 3 biotech companies.

Patrick Aebischer Full Professor President of EPFL

Introduction

Our laboratory is involved in understanding the cause of neurodegenerative diseases of the central nervous system including Parkinson’s disease, Amyotrophic Lateral Sclerosis and Alzheimer’s disease, as well as in designing innovative treatments to slow down the progression of neuronal degeneration. We develop new technologies for animal modeling of these devastating pathologies and comprehensive analysis of the degenerative process. Preclinical studies in animal models are designed to investigate gene therapies as a novel approach to treat neurodegenerative disorders.

Keywords

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

Results Obtained in 2012

With the recent discovery of genes implicated in familial forms of neurodegenerative diseases, our understanding of the pathogenesis has vastly improved. However, it is critical to design effective animal models to investigate how the disease process affects neuronal survival and, most importantly, brain functions. In the context of Parkinson’s disease, our lab has been involved in designing an animal model based on the expression of pathogenic proteins including α-synuclein in the basal ganglia. We found that α-synuclein accumulation leads to deficient dopamine neurotransmission in the striatum, preceding overt neurodegeneration. Defects in dopamine neurotransmission contribute to the apparition of motor symptoms in these animals (Gaugler et al., 2012). In addition, these functional defects are linked to impairments in the secretory pathway of the diseased neurons (Coune et al., 2011). We are currently investigating how genetic determinants of aging, the main risk factor for Parkinson’s disease, modify α-synuclein pathology. In particular, we found that PGC-1alpha, a transcriptional co-regulator implicated in the control of the mitochondrial function, has a major role in the survival of nigral dopaminergic neurons, a population of neurons which

is selectively vulnerable to Parkinson’s disease (Ciron et al., 2012). Along these lines, our lab has pursued the development of animal models of the Alzheimer’s pathology using the viral vector technology. In particular, we have developed AAV vectors expressing tau and the amyloid precursor protein, which proved effective at replicating cardinal features of the disease, such as amyloid plaques and hyperphosphorylated tau tangles in neurons of the mouse frontal cortex. We found that the tau pathology led to prominent neurodegeneration and brain dysfunction as demonstrated by behavioural tests. In the past two years, we have explored advanced imaging approaches to assess the changes in the abundance of metabolites in animal by NMR spectroscopy (in collaboration with R. Gruetter; Mlynarik et al., 2012, Coune P et al, 2013), as well as the deposition of amyloid plaques in whole brain by X-ray coherent tomography (in collaboration with the Paul Scherrer Institute; Pinzer et al., 2012). These studies highlight state-of-the-art techniques to quantitatively assess early pathological signatures of neurodegeneration, in representative animal models of Parkinson’s and Alzheimer’s disease. Our laboratory is dedicated to the development of gene therapy systems for the treatment of motor neuron diseases including amyotrophic lateral sclerosis and spinal muscular atrophy. We focus on adeno-associated vectors, which are currently considered as the most effective vector to target post-mitotic cells inside the CNS. Our goal is to tackle the identified cause of disease, such as the gain of toxic function for mutated human SOD1, or the loss of SMN function that lead to motor neuron degeneration. Using relevant animal models of disease, we work on establishing the proof-of-principle of gene therapy based on stringent criteria for systemic efficacy, and explore how to up-scale these techniques from rodent to primate species (Towne et al., 2011).

EPFL School of Life Sciences - 2012 Annual Report

Selected publications

Pinzer BR, Cacquevel M, Modregger P, McDonald SA, Bensadoun JC, Thuering T, Aebischer P, Stampanoni M. (2012) Imaging brain amyloid deposition using grating-based differential phase contrast tomography. Neuroimage, 16;61(4):1336-46. Gaugler MN, Genc O, Bobela W, Mohanna S, Ardah MT, El-Agnaf OM, Cantoni M, Bensadoun JC, Schneggenburger R, Knott GW, Aebischer P, Schneider BL. (2012) Nigrostriatal overabundance of α-synuclein leads to decreased vesicle density and deficits in dopamine release that correlate with reduced motor activity. Acta Neuropathol.,123(5):653-69 Aebischer P. (2012) Philanthropy: The price of charity. Nature, 481:260 Ciron C., Lengacher S., Dusonchet J., Aebischer P., Schneider B.L. (2012) Sustained expression of PGC-1α in the rat nigrostriatal system selectively impairs dopaminergic function, Hum Mol Genet., 21:1861-76 Coune P.G., Bensadoun J.C., Aebischer P., Schneider B.L. (2011) Rab1A OverExpression Prevents Golgi Apparatus Fragmentation and Partially Corrects Motor Deficits in an Alpha-Synuclein Based Rat Model of Parkinson’s Disease. Journal Parkinsons Dis., 1:373-387 Marroquin Belaunzaran O., Campana C., Cordero M.I., Setola V., Bianchi S., Galli C., Bouche N., Mlynarik V., Gruetter R., Sandi C., Bensadoun J.C., Molinari M., Aebischer P. (2011) Chronic Delivery of Antibody Fragments Using Immunoisolated Cell Implants as a Passive Vaccination Tool. Plos One, 6:e18268, Dusonchet J., Kochubey O., Stafa K., Young S.M. Jr., Zufferey R., Moore D.J., Schneider B.L., Aebischer P. (2011) A rat model of progressive nigral neurodegeneration induced by the Parkinson’s disease-associated G2019S mutation in LRRK2. J Neurosci., 31:907-12

Team Members Research Associate Bernard Schneider

Postdoctoral Fellows Julianne Aebischer Matthias Cacquevel Carine Ciron David Genoux Karin Löw PhD students Wojciech Bobela Elisabeth Dirren Aurélien Lathuilière Cylia Rochat Lu Zheng Technicians Aline Aebi Philippe Colin Fabienne Pidoux Vivianne Padrun Christel Sadeghi Julien Barroche Sandrine Faustino Pinheiro Visiting Students Nathalie Bossanne Patrick Chirdon (Fulbright) Smitha Sarma Maria Zamfir Administrative Assistant Ursula Zwahlen

BMI - Brain Mind Institute

Towne C., Setola V., Schneider B.L., Aebischer P. (2011) Neuroprotection by Gene Therapy Targeting Mutant SOD1 in Individual Pools of Motor Neurons Does not Translate into Therapeutic Benefit in fALS Mice. Mol Ther., 19:274-83

AAV vectors injected in the lateral ventricle of mouse neonates transduce motoneurons (stained for ChAT) and astrocytes (stained for GFAP) in the lumbar spinal cord. We compare GFP expression induced by AAV6-cmv (in motoneurons, left panel) with AAV9-gfaABC1D (in astrocytes, right panel).

EPFL School of Life Sciences - 2012 Annual Report

Blanke Lab http://lnco.epfl.ch/ Olaf Blanke is director of the Center for Neuroprosthetics at the Ecole Polytechnique FĂŠdĂŠrale de Lausanne (EPFL), holds the Bertarelli Foundation Chair in Cognitive Neuroprosthetics, and is Professor of Neurology at the Department of Clinical Neurosciences at Geneva University Hospital. In his research, he applies paradigms from cognitive science, neuroscience, neuroimaging, robotics, and virtual reality in healthy subjects and neurological patients to understand and control neural-own-body-representations, to develop a neurobiological model of self-consciousness, and to apply these findings in the emerging field of cognitive neuroprosthetics and neurorehabilitation.

Olaf Blanke Full Professor

Introduction

The Laboratory of Cognitive Neuroscience targets the brain mechanisms of body perception, body awareness and selfconsciousness. Projects rely on the investigation of healthy subjects and neurological patients by combining psychophysical and cognitive paradigms, state of the art neuroimaging techniques (fMRI, intracranial and surface EEG), and engineering-based approaches (virtual reality, vestibular stimulation, and robotic devices). Next to studying the brain mechanisms of body perception, cognition, and selfconsciousness, we actively pursue research in neuroprosthetics, neurorehabilitation and in interdisciplinary fields of virtual reality, neuroscience robotics, presence research, and brain-computer interfaces.

Keywords

Multisensory integration, sensorimotor, neuroscience robotics, perception, neuroprosthetics, temporo-parietal cortex, bodily awareness, self-consciousness, self-location, first-person perspective, neuroimaging, fMRI, EEG, neuropsychology, cognitive neuroscience, neurology, virtual reality, vestibular system, mental imagery.

Zwaag et al., 2012). This method allowed us to define several distinct representations of each individual finger in the cortex and the cerebellum. Ongoing work extends these findings to the understanding of how these representations are altered in cases of phantom limb pain in amputee patients and patients suffering from paraplegia due to spinal cord injury. In 2012 we also developed a novel system that integrates the technologies of virtual reality (VR) and brain computer interfaces (BCI) with cognitive neuroscience. Using automatize stimulation we induced ownership for virtual hands at unprecedented levels and described the electrophysiological brain mechanisms (Evans & Blanke, 2013). Additionally, the study showed that the experimentallyinduced extension of ownership to virtual hands recruits highly similar brain mechanisms in fronto-parietal cortex as does motor imagery based BCI. We currently extend this knowledge to VR- and BCI-based neuroprosthetics translating these insights to patients with limb amputation and limb paralysis following vascular stroke.

Results Obtained in 2012

One of the major developments and results achieved in 2012 was the description of a method for mapping individual finger representation in the somatosensory cortex of the brain and of the cerebellum, using ultra-high field magnetic resonance imaging (Martuzzi et al., 2012; van der

EPFL School of Life Sciences - 2012 Annual Report

Selected Publications

Blanke O. Multisensory brain mechanisms of bodily self-consciousness (2012). Nat Rev Neurosci. 13(8):556-571. Aspell JE, Palluel E, Blanke O (2012b). Early and late activity in somatosensory cortex reflects changes in bodily self-consciousness: an evoked potential study. Neuroscience. 216:110-122. Evans N, Blanke O (2013). Shared electrophysiology mechanisms of body ownership and motor imagery. Neuroimage. 64:216-228. Ionta S, Sforza A, Funato M, Blanke O (2013). Anatomically plausible illusory posture affects mental rotation of body parts. Cogn Affect Behav Neurosci. 13(1):197-209. Kannape OA, Blanke O (2012). Agency, gait and self-consciousness. Int J Psychophysiol. 83(2):191-199. Lopez C, Blanke O, Mast FW (2012). The human vestibular cortex revealed by coordinate-based activation likelihood estimation meta-analysis. Neuroscience. 212:159-179. Martuzzi R, van der Zwaag W, Farthouat J, Gruetter R, Blanke O (2012). Human finger somatotopy in areas 3b, 1, and 2: A 7T fMRI study using a natural stimulus. Hum Brain Mapp. doi: 10.1002/hbm.22172. Prsa M, Gale S, Blanke O (2012). Self-motion leads to mandatory cue fusion across sensory modalities. J Neurophysiol. 108(8):2282-2291.

Team Members Postdoctoral Fellows Kanayama Noriaki Llobera Mahy Joan Martuzzi Roberto Salomon Roy Prsa Mario Palluel Estelle Herbelin Bruno Ionta Silvio Serino Andrea Van Elk Michiel Brooks Anna

PhD students Akselrod Michel Berger Steve Michel Evans Nathan Forget Joachim Gale Steven Jimenez Rezende Danilo Marchesotti Silvia Pasqualini Isabella Pfeiffer Christian Kaliuzhna Mariia Pozeg Polona Rognini Giulio Sengul Ali Romano Daniele Peer Michael

Sengül A, van Elk M, Rognini G, Aspell JE, Bleuler H, Blanke O (2012). Extending the body to virtual tools using a robotic surgical interface: evidence from the crossmodal congruency task. PLoS One. 7(12):e49473.

Master students Macku Petr Noel Jean-Paul Visciòla Ludovica Tsimpanouli Maria-Efstratia

van der Zwaag W, Kusters R, Magill A, Gruetter R, Martuzzi R, Blanke O, Marques JP (2012). Digit somatotopy in the human cerebellum: A 7T fMRI study. Neuroimage, 67(C):354-62.

Administrative Assistant Gordana Kokorus

van Elk M, Blanke O (2012). Balancing bistable perception during self-motion. Exp. Brain. Res., 222(3):219-228. Ionta S., Heydrich L., Lenggenhager B., Mouthon M., Fornari E, Chapuis D., Gassert R., Blanke O. (2011). Multisensory mechanisms in temporo-parietal cortex support self-location and first-person perspective. Neuron, 70(2):363-74. Lopez C., Mercier M. R., Halje P. and Blanke O. (2011). Spatiotemporal dynamics of visual vertical judgments: early and late brain mechanisms as revealed by high-density electrical neuroimaging. Neuroscience, 181:134-49.

BMI - Brain Mind Institute

Lenggenhager B., Halje P. and Blanke O. (2011). Alpha band oscillations correlate with illusory self-location induced by virtual reality. European Journal of Neuroscience, 33(10):1935-43.

Schematic representation of the finger maps within the primary somatosensory area, as obtained using ultra-high field fMRI.

EPFL School of Life Sciences - 2012 Annual Report

Courtine Lab

http://courtine-lab.epfl.ch/

Even though Grégoire Courtine was trained in Mathematics and Physics, he received his PhD in Experimental Medicine from the Inserm Plasticity and Repair, France, in 2003. After a Post-doctoral training at Los Angeles (UCLA), he established his own laboratory at the University of Zurich in 2008. In Dec 2011, he accepted the International paraplegic foundation (IRP) chair in spinal cord repair in the center for neuroprosthetics at the EPFL. He has received numerous honors such as the UCLA Chancellor’s award, the Schellenberg Prize for his advances in spinal cord repair, and a fellowship from the European Research Council (ERC). Several of his works received substantial coverage in the national and international media.

Grégoire Courtine Associate Professor

Introduction

There are over 3,000 persons living with a spinal cord injury (SCI) in Switzerland, and several million worldwide. SCI leads to a range of disabilities that seriously diminish the patient’s quality of life. Over the past 15 years, we implemented an unconventional research program with the aim to develop radically new treatment paradigms to restore sensorimotor functions in severely paralyzed people. Our therapeutic interventions are developed in rodents and optimized in non-human primates, and clinical trials are in the implementation phase.

Keywords

Spinal cord injury, neural repair, neurorehabilitation, neuroprosthetics, brain-machine interface, robotic, neuronal recordings, optogenetic, EMG, kinematic, locomotion, neuromorphology, mice, rats, monkeys, humans.

Results Obtained in 2012

Over the past 10 years, we have developed, methodically, a series of neuroprosthetic technologies to enable motor control after neuromotor disorders. This includes an electrochemical spinal neuroprosthesis to transform lumbosacral circuits from non-functional to highly functional networks, and a robotic postural neuroprosthesis to establish optimal conditions of balance and support during rehabilitative training. In 2012, we introduced a treatment paradigm that combined all these neuroprosthetic technolo-

gies. We showed that rats with a spinal cord injury, leading to complete and permanent paralysis, regained supraspinal control over complex locomotor movements. Anatomical evaluations revealed that training encouraged the brain to elaborate a multiplicity of alternative pathways to regain access to the denervated spinal locomotor circuits. No previous interventions restored voluntary locomotor movements after a paralyzing SCI. Our objective is to translate these discoveries from rodents to a viable intervention for humans. To achieve this, we have gathered a highly multidisciplinary and synergistic team of advanced basic and clinical investigators at the EPFL and the CHUV. Through this network, we have developed an electrochemical spinal neuroprosthesis uniquely fitted to the human spinal cord, and robotic systems for rehabilitation of subjects with impaired gait. Upon validation by the ethical boards, these new technologies will be tested in spinal cord injured individuals. In parallel, we have established an advanced non-human primate model that will allow us to demonstrate the efficacy and safety of our interventions. Our aim is to prepare the second phase of clinical trials with refined neuroprosthetic technologies. We anticipate that 2013 will be a year full of new, exciting discoveries.

EPFL School of Life Sciences - 2012 Annual Report

Courtine G, Micera S, Digiovanna J, Del R Millán J. (2012) Brain-machine interface: closer to therapeutic reality? Lancet 2012 Dec 13. Van den Brand R, Heutschi J, barraud Q, Digiovanna J, Bartholdi K, Huerlimann M, Friedli L, Vollenweider I, Martin Moraud E, Duis S, Dominici N, Micera S, Musienko PE, Courtine G (2012) Restoring voluntary control of locomotion after paralyzing spinal cord injury. Science 336(6085): 1182-1185 Dominici N, Keller U, Vallery H, Friedli L, van den Brand R, Starkey ML, Musienko P, Riener R, Courtine G (2012) Novel robotic interface to evaluate, enable, and train locomotion and balance after neuromotor disorders. Nature Medicine 18(7):1142-7. Horst M, Heutschi J, den Brand RV, Andersson KE, Gobet R, Sulser T, Courtine G, Eberli D. (2012) Multisystem Neuroprosthetic Training Improves Bladder Function After Severe Spinal Cord Injury. J Urol. 2012 Oct 8. Musienko P, Courtine G, Tibbs JE, Kilimnik V, Savochin A, Garfinkel A, Roy RR, Edgerton VR, Gerasimenko Y (2012) Somatosensory control of balance during locomotion in decerebrated cat. Journal of neurophysiology 107:2072-2082. Musienko P, Heutschi J, Friedli L, den Brand R, Courtine G (2012) Multi-system neurorehabilitative strategies to restore motor functions following severe spinal cord injury. Experimental neurology 235:100-109. Nout YS, Ferguson AR, Strand SC, Moseanko R, Hawbecker S, Zdunowski S, Nielson JL, Roy RR, Zhong H, Rosenzweig ES, Brock JH, Courtine G, Edgerton VR, Tuszynski MH, Beattie MS, Bresnahan JC (2012) Methods for Functional Assessment After C7 Spinal Cord Hemisection in the Rhesus Monkey. Neurorehabilitation and neural repair 26(6):556-69. Nout YS, Rosenzweig ES, Brock JH, Strand SC, Moseanko R, Hawbecker S, Zdunowski S, Nielson JL, Roy RR, Courtine G, Ferguson AR, Edgerton VR, Beattie MS, Bresnahan JC, Tuszynski MH (2012) Animal models of neurologic disorders: a nonhuman primate model of spinal cord injury. Neurotherapeutics : 9:380-392. Courtine G, van den Brand R, Musienko P (2011) Spinal cord injury: time to move. Lancet 377:1896-1898. Musienko P, van den Brand R, Marzendorfer O, Roy RR, Gerasimenko Y, Edgerton VR, Courtine G (2011) Controlling specific locomotor behaviors through multidimensional monoaminergic modulation of spinal circuitries. J Neuroscience 31:9264-9278.

Team Members Postdoctoral Fellows Quentin Barraud David Borton Nadia Dominici Jean Laurens Cristina Martinez Gonzales Pavel Musienko Natalia Pavlova Rubia van den Brand Joachim von Zitzewitz PhD students Léonie Asboth Janine Beauparlant Lucia Friedli Wittler Isabel Vollenweider Fang Wang Nikolaus Wenger Marco Bonizzato Martin Moraud Eduardo Master’s Students Sélin Anil Steve Blachut Leonardo Caranzano Jérome Gandar Sam Ghazanfari Paul Giroud Nili Hamili Pierre-Yves Helleboid Hugo Hoedemaker Alexander Kuck Julie Kreider Bastien Martin Frédéric Michoud Audrey Nguyen JuneSeung Lee Solange Richter Livio Ruzzante Giorgio Ulrich Charles Vila Ambroise Vuaridel Numa Perez Technicians Kay Bartholdi Simone Duis Administrative Assistant Anne-Marie Rodel Stéphanie Bouchet

BMI - Brain Mind Institute

Selected Publications

A rat received a spinal cord injury leading to permanent paralysis. A robot-assisted training paradigm enabled by an electrochemical spinal neuroprosthesis restored supraspinal control over refined locomotion through the extensive and ubiquitous remodeling of neuronal pathways.

EPFL School of Life Sciences - 2012 Annual Report

Fraering Lab

http://fraering-lab.epfl.ch/

Patrick Fraering

Patrick Fraering studied biology at the University Louis Pasteur of Strasbourg, where he earned a master’s degree in biochemistry (1995) and pre-doctoral research degree in molecular and cellular biology at the CNRS (1996). In 2001, he received his PhD, conducting biochemical studies on the GPI-transamidase complex and on the process of protein secretion at the University of Fribourg. In 2002, he joined the lab of Prof. D. Selkoe at Harvard Medical School where he focused on the structure and function relationships of γ-secretase, an intra-membrane-cleaving protease responsible for the production of the Alzheimer’s disease amyloid-β peptides. In 2007, he was appointed assistant professor at the EPFL’s School of Life Sciences.

Tenure Track Assistant Professor Merck-Sorono Chair in Neuroscience

Introduction

The Laboratory of Molecular and Cellular Biology of Alzheimer’s Disease has a clear focus on the biochemistry, pharmacology and neurobiology of γ-secretase, an intramembrane-cleaving protease that is directly implicated in the generation of the amyloid-beta peptides (Aβ), which are central players in the pathogenesis of Alzheimer’s disease (AD). Our long-term goals are i) To get new insight into the structure-function relationships of γ-secretase, ii) To shed new light on the neurobiological functions of γ-secretase, and iii) To develop new therapeutic strategies to selectively reduce Aβ production by modulating γ-secretase activity.

Keywords

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

Results Obtained in 2012

Highly efficient production of γ-secretase and Fabs for use in structural studies. Although γ-secretase represents a prime target for structure-based design of therapeutic compounds to safely treat AD, the scarcity of its supply has been a major hurdle for determining its high-resolution structure. We applied a transposon-mediated multigene stable integration technology to produce active γ-secretase in mammalian cells in amounts adequate for crystallization studies and drug screening. The amounts of γ-secretase were sufficient for immunization of mice and generation of Fab fragments binding exposed regions of native γ-secretase, and therefore useful as specific tools to facilitate crystal formation. Our strategy is expected to contribute to the crystallization of γ-secretase and to be widely used for the production of other multiprotein complexes for applications in structural biology and drug development. Alzheimer’s disease-linked mutations in Presenilin-1 result in a drastic loss of activity in purified γ-secretase complexes. Mutations linked to familial AD are found most frequently in PSEN1, the gene encoding PS1, the

catalytic subunit of γ-secretase. We took advantage of a mouse embryonic fibroblast cell line lacking PS1 and PS2 to purify human γ-secretase complexes with the pathogenic PS1 mutants L166P, ΔE9, or P436Q. The functional characterization of these complexes revealed that all PS1 FAD-linked mutations caused a drastic reduction of Aβ and APP intracellular domain productions in vitro. Our findings support the view that PS1 mutations lead to a strong γ-secretase loss-of-function phenotype associated with an increased Aβ1-42 to Aβ1-40 ratio, two mechanisms that are likely involved in the pathogenesis of AD. Selective neutralization of APP-C99 with monoclonal antibodies reduces the production of Alzheimer’s Aβ peptides. Recent phase 3 clinical trials testing γ-secretase inhibitors revealed unwanted side effects likely attributed to impaired Notch cleavage, critically involved in cell fate regulation. We developed a new therapeutic approach to reduce Aβ production with monoclonal antibodies selectively targeting the Amyloid-β Precursor Protein C-terminal fragment, without affecting other γ-secretase functions. These antibodies, generated by immunizing mice with human APPC99 adopting a native conformation, bound accessible Nor C-terminal epitopes of this substrate and led to reduced Aβ levels in vitro and in vivo. Label-free imaging of cerebral β-Amyloidosis with extended-focus optical coherence microscopy (xfOCM). We demonstrated label-free imaging of cerebral β-amyloidosis ex vivo and in a living mouse model of AD using xfOCM. This technique offers advantages in terms of high-resolution and deep imaging of Aβ deposits, in a minimally invasive way and without the administration of contrast agents, thereby precluding variations in data collection due to interindividual and intraindividual variability in the uptake of amyloid dyes/radioactive tracers. It may support translational applications to evaluate the efficacy of new Aβ-targeting therapeutic strategies.

EPFL School of Life Sciences - 2012 Annual Report

Selected Publications

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 γ-secretase integral membrane protease complex by a multi-gene stable integration approach. Biotechnol Bioeng. 2013 Jan 28. In press. I. Hussain, J. Fabrègue, S. Ousson, L. Anderes, F. Borlat, V. Eligert, S. Berger, M. Dimitrov, J.R. Alattia, P.C. Fraering, and D. Beher. (2013). Gamma Secretase Activating Protein, GSAP is not a major regulator of γ-secretase activity and amyloid-β generation. J Biol Chem. 2013 Jan 25;288(4):2521-31. T. Bolmont, A. Bouwens, C. Pache, M. Dimitrov, C. Berclaz, M. Villiger, B.M. Wegenast-Braun, T. Lasser, P.C. Fraering. (2012). Label-Free Imaging of Cerebral β-Amyloidosis with Extended-Focus Optical Coherence Microscopy. J Neurosci. 2012 Oct 17;32(42):14548-14556. J.R. Alattia, C. Schweizer, M. Cacquevel, M. Dimitrov, L. Aeschbach, M. OuladAbdelghani, P.C. Fraering. (2012). Generation of Monoclonal Antibody Fragments Binding the Native γ-Secretase Complex for Use in Structural Studies. Biochemistry. 2012 Nov 6;51(44):8779-90.

Team Members Postdoctoral Fellows Jean-René Alattia Eugenio Barone PhD students Jemila Houacine Mitko Dimitrov Sebastien Mosser Magda Palcynska Master’s Students Andrzej Fligier Alexandre Matz Technicians Lorene Aeschbach Justine Pascual Administrative Assistant Monica Navarro Suarez

M. Cacquevel, L. Aeschbach, J. Houacine, P.C. Fraering. (2012). Alzheimer’s disease-linked mutations in presenilin-1 result in a drastic loss of activity in purified γ-secretase complexes. PLoS One. 2012;7(4):e35133. Epub 2012 Apr 18. J. Houacine, T. Bolmont, L. Aeschbach, M. Oulad-Abdelghani, and PC. Fraering. (2012). Selective neutralization of APP-C99 with monoclonal antibodies reduce the production of Alzheimer’s Aβ peptides. Neurobiol Aging. 2012 Nov;33(11):2704-14. JR Alattia, T. Kuraishi, I. Chang, B. Lemaître, and PC. Fraering. (2011). Methylmercury is a direct and potent γ-secretase inhibitor affecting Notch processing and embryonic development. FASEB J. 2011 Jul;25(7):2287-95.

BMI - Brain Mind Institute

Bot N, Schweizer C, Ben Halima S, and Fraering PC. (2011). Processing of the synaptic cell-adhesion molecule neurexin-3β by Alzheimer’s disease α- and γ-secretases. J Biol Chem. 2011 Jan 28;286(4):2762-73.

In vivo longitudinal xfOCM imaging of cerebral Aβ amyloidosis (green) in a transgenic mouse model of Alzheimer’s disease.

EPFL School of Life Sciences - 2012 Annual Report

Gerstner Lab http://lcn1.epfl.ch/

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.

Wulfram Gerstner

Full Professor Life Sciences and Computer & Communication Sciences

Introduction

The Laboratory of Computational Neuroscience uses theoretical methods from mathematics, computer science, and physics to understand brain function. Questions addressed are: what is the code used by neurons in the brain? How can changes of synapses lead to learning?

Keywords

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

Results Obtained in 2012

We have been active in three different, but connected areas: Single-Neuron Modeling: We have shown that the electrical behaviour of neurons under somatic current or conductance injection can be well described by simplified neuron models with only one or two equations. The parameters of these neuron models can be directly extracted from experimental data. We found that the best simplified neuron model is an exponential integrate-and fire model combined with adaptation and/or refractoriness. The work on single-neuron modeling involves collaborations with the labs of Henry Markram and Carl Petersen. A review paper on these topics has appeared in Science. A scientific paper together with Carl Petersen was published in the Journal of Neurophysiology.

Modeling synaptic plasticity: We have developed a model that combines induction of synaptic plasticity with consolidation of synapses. The model of induction accounts for induction of Long-Term Potentiation under protocols of voltage-dependent and Spike-Timing Dependent Plasticity and leads to the tagging of the synapse. We studied consequences of plasticity in a recurrent network (Nature Neuroscience 2010). We also studied the role of plasticity of inhibitory synapses and showed that a generic class of inhibitory learning rules leads to a stabilization of network dynamics, since inhibition automatically balances excitation (Science 2011). Network Simulation: In two collaborations with the labs of Michael Herzog and Carl Petersen, we simulate properties of networks of neurons. Christian Tomm, who works with data from the Petersen lab, obtained interesting results on network topology which has been published in 2012. A model of perceptual learning in vision has appeared in a paper with Michael Herzog.

EPFL School of Life Sciences - 2012 Annual Report

Selected Publications

W. Gerstner, H. Sprekeler and G. Deco, (2012) Theory and Simulation in Neuroscience. Science, vol. 338, p. 60-65. R. Naud and W. Gerstner, (2012) Coding and Decoding with Adapting Neurons: A Population Approach to the Peri-Stimulus Time Histogram. Plos Computational Biology, vol. 8, num. 10, p. e1002711, 2012. M. Avermann, C. Tomm, C. Mateo, W. Gerstner and C. C. H. Petersen, (2012) Microcircuits of excitatory and inhibitory neurons in layer 2/3 of mouse barrel cortex. Journal of Neurophysiology, vol. 107, num. 11, p. 3116-3134. M. H. Herzog, K. C. Aberg, N. Frémaux, W. Gerstner and H. Sprekeler, (2012) Perceptual learning, roving and the unsupervised bias. Vision Research, vol. 61, p. 95-99. S. Mensi, R. Naud, C. Pozzorini, M. Avermann and C. C. H. Petersen et al. Parameter extraction and classification of three cortical neuron types reveals two distinct adaptation mechanisms, Journal Of Neurophysiology, vol. 107, num. 6, p. 1756-1775, 2012. T. Vogels, H. Sprekeler, F. Zenke, C. Clopath and W. Gerstner, (2011) Inhibitory Plasticity Balances Excitation and Inhibition in Sensory Pathways and Memory Networks, Science, Vol. 334, Nr. 6062, pp. 1569-1573 R. Naud, F. Gerhard, S. Mensi and W. Gerstner, (2011) Improved Similarity Measures for Small Sets of Spike Trains, Neural Computation, Vol. 23, Nr. 12, pp. 3016-3069.

Team Members Postdoctoral Fellows Moritz Deger Kerstin Preuschoff Tim Vogels

PhD students Dane Corneil Andrea De Antoni Mohammadjavad Faraji Nicolas Frémaux Felipe Gerhard Skander Mensi Christian Pozzorini Alex Seeholzer Hesam Setareh Carlos Stein Friedemann Zenke Lorric Ziegler Master’s Students Julien Duc Everton João Agnes William Podlaski Guillaume Riesen Varun Sharma Administrative Assistant Chantal Mellier

H. Markram, W. Gerstner and P.J. Sjöström, (2011) A history of spike-timing-dependent plasticity, Frontiers in Synaptic Neuroscience, Vol. 3, Nr. 4, pp. 1-24.

BMI - Brain Mind Institute

Inhibitory synaptic plasticity restores asynchronous irregular activity in recurrent network models. (A) Epileptic activity. (Top) heat map of the network firing where cells are arranged on a 2D grid. (Bottom) spike raster of different subpopulations of cells. (B) Activity after one hour of network activity in the presence of inhibitory synaptic plasticity. Network activity is stable and de-correlated at low activities. (C) Activity after two cell memories have been introduced in the excitatory weight matrix. (D) Activity after another hour. Memories have been masked by “anti memories”, but can be recalled by an external cue (E,F,G).

EPFL School of Life Sciences - 2012 Annual Report

Herzog Lab http://lpsy.epfl.ch/

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 lab.

Michael Herzog Associate Professor

Introduction

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.

Results Obtained in 2012

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. A prediction of these models is that crowding increases when adding flankers. We showed that to the contrary that adding flanks improves performance. (Manassi et al., 2012).

Perceptual learning & the power of the mind. Usually, it is believed that learning is driven by the repeated presentations of stimuli which change synaptic weights. No stimulus, no learning. We found that perceptual learning can occur even if there are no stimuli presented at all when observers imagine the stimuli- showing the power of the mind (Tartaglia et al. 2012; Mast et al., 2012). In collaboration with Wulfram Gerstner, we have identified a very general mathematical mechanism that explains why perceptual learning does not occur under roving conditions (Herzog et al., 2012). In collaboration with Carmen Sandi, we showed how stress influences perceptual learning (Aberg et al., 2012). In 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., 2012).

EPFL School of Life Sciences - 2012 Annual Report

Selected Publications

Rüter J, Marcille N, Sprekeler H, Gerstner W, Herzog MH (2012). Paradoxical Evidence Integration in Rapid Decision Processes. PLoS Computational Biology, 8(2), e1002382. Herzog MH, Aberg KC, Frémaux N, Gerstner W, Sprekeler H (2012). Perceptual learning, roving and the unsupervised bias. Vision Research, 61, p95-99. Plomp G, Kunchulia M, Herzog MH (2012). Age-related changes in visually evoked electrical brain activity. Human Brain Mapping, 33(5), p1124-1136. Manassi M, Sayim B, Herzog MH (2012). Grouping, pooling, and when bigger is better in visual crowding. Journal of Vision, 12(10), p1-14. Aberg K, Clarke A, Sandi C, Herzog MH (2012). Trait anxiety and post-learning stress do not affect perceptual learning. Neurobiology of Learning and Memory, 98(3), p246-53. Cappe C, Herzog MH, Herzig DA, Brand A, Mohr C (2012). Cognitive disorganisation in schizotypy is associated with deterioration in visual backward masking. Psychiatry Research, 200, p652-659. Plomp G, Michel CM, Herzog MH (2011). Electrical source dynamics in three functional localizer paradigms. Neuroimage, 54, p1763.

Team Members Postdoctoral Fellows Céline Cappe Aaron Clarke Daniela Herzig Karin Pilz Marcus Vergeer

PhD Students Vitaly Chicherov Lukasz Grzeczkowski Mauro Manassi Izabela Szumska Evelina Thunell Master Student Sophie Lonchampt SHS Student Ophélie Favrod Engineer Marc Repnow Administrative Assistant Laure Dayer

Boi M, Vergeer M, Öğmen H, Herzog MH (2011). Nonretinotopic Exogenous Attention. Current Biology, 21(20), p1732-1737.

BMI - Brain Mind Institute

Healthy elderly (ELD) and younger controls (CON) performed a visual discrimination task in four conditions (vernier, long SOA, short SOA, mask only). We recorded high density EEG. On the left, global field power is shown in the four conditions for ELD and CON separately. Global field power (GFP) is an overall measure of brain activity. It is obvious, that brain activity of elderly is strongly diminished. For example, at 200ms after stimulus onset, a strong GFP peak occurs in the controls but not in the elderly. On the right, maps are shown that correspond to single electrode activity. Obviously, elderly show, particularly at around 200ms, clearly different maps than controls (compare maps 3 and 5). In most conditions, it seems that elderly use very different brain areas to solve the visual tasks than younger controls. From: Plomp G, Kunchulia M, Herzog MH (2012) Age-related changes in visually evoked electrical brain activity. Hum Brain Mapp. 2012 May;33(5):1124-36. doi: 10.1002/hbm.21273. Epub 2011 Apr 29.

EPFL School of Life Sciences - 2012 Annual Report

Lashuel Lab

http://lashuel-lab.epfl.ch/

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.

Hilal Lashuel

Associate Professor

Introduction

Research in the Lashuel laboratory focuses on applying chemical, biophysical, and molecular 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. Current research efforts cover the following topics: (1) Elucidating the sequence, molecular and cellular determinants underlying protein aggregation, propagation and toxicity. (2) Developing innovative chemical approaches and novel tools to monitor and control protein folding, self-assembly and post-translation in vitro and in vivo with spatial and temporal resolution; and (3) developing novel therapeutic strategies to treat Parkinson’s disease 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 2012

Chemical and semisynthetic strategies for Site-specific modification of proteins - Protein Post-translational modifications (PTMs) play important roles in regulating protein function and many biological processes and are increasingly implicated in the pathogenesis of several neurodegenerative diseases including Alzheimer’s, Parkinson’s and Huntington’s disease. Therefore a better understanding of how individual modifications and cross-talk between different modifications influence protein structure and function is essential to understanding the role of PTMs in health and disease. Our laboratory has developed and optimized for the first time multiple efficient synthetic and semisynthetic strategies that enable site-specific introduction of single or multiple PTMs into α-syn and exon1 of the Huntingtin protein (Httex1), two proteins that are linked to the pathogenesis of Parkinson’s and Huntington’s disease, respectively.

Using these semisynthetic proteins we were able to provide novel insight into the potential roles of diseases-associated α-syn on the native structure, aggregation, membrane binding, subcellular localization and protein-protein interactions of α-syn in vitro. Our results show that some of these modifications (phosphorylation at S87 and S129 and Uiquitination at K6) inhibit α-syn aggregation and protect against α-syn induced toxicity (pS87 and pS129). In addition, in collaboration with Dr. Ashraf Brik and Dr. Aaron Ciechanover group, we showed that mono-ubiquitination is sufficient to target α-syn for degradation by the proteasome, whereas phosphorylation at S129 by the Polo Like Kinase 2 (PLK2) targets α-syn for degradation by lysosomal-autophagic pathways. These findings highlight the potential role of PTMs in regulating α-syn degradation and suggest that the enzymes that regulate these modifications may constitute a viable therapeutic target for the treatment of PD and related synucleinopathies. Discovery of a novel aggregation and functional domain in the Huntingtin protein - Increasing evidence suggests that although the expanded polyQ in Htt and other proteins plays a central role in the pathogenesis of HD, it is not the sole determinant of Htt aggregation and toxicity. Through a systematic analysis of the N-terminal sequence of Htt, we discovered a novel amyloidogenic domain outside of exon1. A systematic analysis of peptides spanning different regions within this domain led to the identification of two distinct sequence motifs (106-116 and 128-135) that are responsible for the aggregation of this domain. Preliminary results using cellular models of Htt aggregation and toxicity suggest that the aggregation propensity of this novel amyloidogenic domain influence the rate and aggregation pathway of the NtHtt fragments and their toxicity. Further studies are currently underway in our laboratory to investigate potential cross-talk between the novel domains identified in this work and the polyQ repeat region and to elucidate their potential roles in regulating the physiological and pathogenic properties of the full-length protein and disease-associated N-terminal fragments in cell culture and animal models of HD.

EPFL School of Life Sciences - 2012 Annual Report

Selected Publications

Lashuel HA, Overk C, Ouelati A, and Masliah E (2012) “α-synuclein oliogmerizatoin in health and disease”, Nature Rev. Neuroscience. 14(1):38-48. Shabek N, Herman-Bachinsky Y, Buchsbaum S, Lewinson O, Haj-Yahya M, Hejjaoui M, Lashuel HA, Sommer T, Brik A, Ceichanover A. (2012) The size of the proteasomal substrate determines whether its degradation will be mediated by Mono- or Polyubiquitination. Mol. Cell. 12;48(1):87-97 Hejjaoui M, Butterfield S, Fauvet B, Vercryusse F, Cun J, Dikiy I, Prudent M, Olschewski D, Zhang Y, Eliezer D., Lashuel HA*. Chemical Biology of α-synuclein: Elucidating the role of C-terminal post-translational modifications using protein semisynthetic strategies: Phosphorylation at Tyrosine 125”, J. Amer. Chem. Soc. 21;134(11):5196-210. Oueslati A, Paleologou KE, Schneider BL, Aebischer P., Lashuel HA*. (2012) Mimicking phosphorylation at Serin87 inhibits the aggregation of human alphasynuclein and protects against its toxicity in a rat model of Parkinson’s disease, J. Neuroscience, 2012, 1;32(5):1536-44. Fauvet B., Mebfo MK, Fares BM, Desobry C, Michael S, Ardah MT, Tsika E, Coune P, Eliezer D, Moore DJ, Schneider B, Aebischer P., El-agnaf OM, Masliah E, and Lashuel HA*. (2012) Alpha-synuclein in the central nervous system, in mammalian cells, and produced by E. coli exists predominantly as a disorderd monomer. J. Biol. Chem, 287, 15345-15364

Team Members Postdoctoral Fellows Baillie Mark Burai Ritwik Mahul Mellier Anne-Laure Oueslati Abid Wang Zheming PhD Students Ansaloni Annalisa Ait Bouziad Nadine Desobry Carole Fares Mohamed-Bilal Fauvet Bruno Khalaf Ossama Mbefo Kamdem Martial Vercruysse Filip Master’s Student Chiki Anass Technical Staff Jordan Nathalie Perrin John Vocat Céline Administrative Assistants Favre Sandrine

Fauvet B, Fares BM, Samuel F, Kikiy I, Tandon A, Eliezer D, Lashuel HA*. (2012) Characterization of semisynthetic and natural N-terminal acetylated α-synuclein in vitro and in intact cells: Iimplications for α-synuclein aggregation and cellular properties” J. Biol. Chem. 17;287(34):28243-62. Butterfield S, Hejjaoui M, Fauvet B, and Lashuel HA*. (2012) Chemical approaches to elucidate the mechanisms of amyloid formation and toxicity. J. Mol. Biol. 421, 204-236 Hejjaoui H, Haj-Yahya M, Kumar KS, Brik A* and Lashuel HA. (2011) Towards elucidating the role of ubiquitination in the pathogenesis of Parkinson’s disease using semisynthetic ubquitinated α-synuclein”. Angew Chem Int Ed.10;50(2):405-9.

BMI - Brain Mind Institute

Schematic depictions illustrating the different semisynthetic and chemical strategies developed by our group to allow controlled and site-specific introduction of single or multiple modifications in different regions of α-synuclein.

EPFL School of Life Sciences - 2012 Annual Report

Magistretti Lab http://lndc.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. He was a recipient of the Theodore-Ott Prize (1997), was the international Chair (20072008) at the Collège de France, Paris, 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”. Currently on sabbatical.

Pierre Magistretti

Full Professor Joint Chair EPFL/UNIL-CHUV

Introduction

two other related energy substrates, glucose and pyruvate, revealing a novel role of lactate as a signaling molecule. We will now extend the molecular characterization of this thus far unknown action of lactate. In particular we will explore the signaling mechanisms triggered by lactate on NMDA receptor activity.

Keywords

We have continued to explore the role of metabolic coupling between astrocytes and neurons in synaptic plasticity and in neuroprotection. In this context, we have promoted three very fruitful collaborations with groups that have provided us with access to well established in vivo models of learning and memory, neurodegeneration and stroke (Suzuki et al, 2011; Lee et al, 2012; Berthet et al, 2012). These studies have demonstrated in vivo a fundamental role of astrocyte-derived lactate, as predicted by the Astrocyte Neuron Lactate Shuttle (ANLS) model that we have proposed several years ago, in learning and memory and in neuroprotection (Pellerin and Magistretti, 2012).

We will continue the analysis of the plasticity in the expression of genes related to neuron-glia metabolic coupling during learning paradigms. Using (14C) 2-Deoxyglucose (2-DG) technique we have identified the brain areas that are engaged in context-dependent avoidance behavior in mice using the step-through inhibitory avoidance paradigm (IA). Regional brain metabolic activity, as measured by the 2DG uptake, was quantified in several brain regions. This metabolic mapping revealed increased glucose utilization in hippocampus, amygdala, anterior cingulate cortex and mammillary bodies. Microdissection of the dorsal hippocampus followed by qRT-PCR analysis has indicated that genes expressed by astrocytes such MCT 1, MCT 4, alpha2 subunit of the Na K-ATPase, Glut 1 and all genes coding for enzymes of glycogen metabolism are upregulated 3 and 24 hours after IA learning. We will now extend this analysis to longer time-points and to other brain areas that are engaged in the learning process as demonstrated by the 2-DG technique.

With Cristina Alberini’s group at NYU we have shown that astrocyte-derived lactate is necessary for the establishment of long term memory (LTM) as well as for the maintenance of long-term potentiation (LTP) in vivo in mice. Following up on these results we have demonstrated that lactate stimulates expression of genes related to synaptic plasticity such as Arc, Zif268 and BDNF in primary cultures of cortical neurons as well as in vivo. Biochemical and electrophysiological initial results show that this effect results from the modulation by lactate of ionotropic NMDA receptor activity. The effects of lactate on plasticity gene expression are blocked by the NMDA receptor antagonist MK 801. Furthermore the generation by lactate of a transient MK 801-sensitive inward current is necessary for gene expression induction. These effects are not observed with

We are continuing the application of Digital Holographic Microscopy (DHM) to the study of neuronal and glial dynamics. Thus we have been able to monitor the transmembrane water fluxes resulting from the activation of glutamate ionotropic receptors and of the co-transporters KCC2 and NKCC1 (Jourdain et al, 2011). In addition, this optical monitoring of transmembrane water movements has also been efficiently used to simultaneously record in multiple cells chloride current associated to activation of the ligand-gated chloride channel GABAA receptor (Jourdain et al, in press). The quantitative phase signal monitored with DHM followed by appropriate numerical analysis has allowed us to detect optical signs of early cell death (Pavillon et al, 2012) with which we can test the potential neurprotective effects of a variety of compounds, including lactate (see above).

We investigate the cellular and molecular mechanisms of brain energy metabolism, in particular the interactions between neurons and astrocytes and the role of this interaction in normal brain function (e.g. learning and memory) as well as dysfunction (neurodegenerative diseases). Neuroenergetics, neuro-glia interaction, brain metabolism, neuronal and glial plasticity, high-resolution optical imaging, digital holographic microscopy, cell dynamics, neurodegeneration, sleep, psychiatric disorders.

Results Obtained in 2012

EPFL School of Life Sciences - 2012 Annual Report

Team Members

Selected Publications

Jourdain P., Boss D., Rappaz B., Moratal C., Hernandez M.C., Depeursinge C., Magistretti P.J. and Marquet P. (2012). Simultaneous optical recording in multiple cells by digital holographic microscopy of chloride current associated to activation of the ligand-gated chloride channel GABA(A) receptor. PLoS One. 7(12):e51041. Berthet C., Castillo X., Magistretti P.J. and Hirt L. (2012). New evidence of neuroprotection by lactate after transient focal cerebral ischaemia: extended benefit after intracerebroventricular injection and efficacy of intravenous administration. Cerebrovasc Dis. 34(5-6):329-35.

Senior Scientist Gabriele Grenningloh Scientists Igor Allaman Nicolas Aznavour Stéphane Chamot Pascal Jourdain Sylvain Lengacher Jean-Marie Petit Jiangyan Yang

Lee Y., Morrison B.M., Li Y, Lengacher S., Farah M.H., Hoffman P.N., Liu Y., Tsingalia A., Jin L., Zhang P.W., Pellerin L., Magistretti P.J. and Rothstein J.D. (2012). Oligodendroglia metabolically support axons and contribute to neurodegeneration. Nature. 487(7408):443-8.

PhD Students Daniel Boss Benjamin Boury-Jamot Elena Migacheva Monika Saxena Manuel Zenger

Pavillon N., Kühn J. Moratal C., Jourdain P., Depeursinge C., Magistretti P.J. and Marquet P. (2012). Early cell death detection with digital holographic microscopy. PLoS One. 7(1):e30912.

Master’s Students Johannes Kacerovsky Anna Mikhaleva

Bélanger M., Yang J., Petit J.M., Laroche T., Magistretti P.J.* and Allaman I.* (2011). Role of the glyoxalase system in astrocyte-mediated neuroprotection. J Neurosci. 31(50):18338-52. * Co-last authors.

Technicians Cendrine Barrière Elena Gasparotto Joel Gyger Evelyne Ruchti

Jourdain P., Pavillon N., Moratal C., Boss D., Rappaz B., Depeursinge C., Marquet P. and Magistretti P.J. (2011). Determination of Transmembrane Water Fluxes in Neurons Elicited by Glutamate Ionotropic Receptors and by the Cotransporters KCC2 and NKCC1: A Digital Holographic Microscopy Study. J Neurosci. 31(33):11846-54. Lavoie S., Allaman I., Petit J.M., Do K.Q. and Magistretti P.J. (2011). Altered glycogen metabolism in cultured astrocytes from mice with chronic glutathione deficit; relevance for neuroenergetics in schizophrenia. PLoS One. 6(7):e22875.

Trainee Biology Laboratory Assistant Nathalie Bigler Administrative Assistant Monica Navarro Suarez

Wyss M.T., Jolivet R., Buck A., Magistretti P.J. and Weber B. (2011). In vivo evidence for lactate as a neuronal energy source. J Neurosci. 31(20):7477-85.

BMI - Brain Mind Institute

Suzuki A., Stern S.A., Bozdagi O., Huntley G.W., Walker R.H., Magistretti P.J.* and Alberini C.M.* (2011). Astrocyte-neuron lactate transport is required for long-term memory formation. Cell. 144(5):810-23 *Corresponding authors.

High expression of Glo-1 in astrocytes of the mouse cerebral cortex, This enzyme is important for the detoxification of methylglyoxal, a cytotoxic by product of glycolysis. Coronal sections of mouse brain were immunostained with Glo-1 and with the astrocytic marker GFAP. Glo-1 immunoreactivity is located in the cell body and processes along the GFAP+ filaments.

EPFL School of Life Sciences - 2012 Annual Report

Markram Lab http://bmi.epfl.ch/

Henry Markram Full Professor

Henry Markram is the Principal Investigator of the Laboratory of Neural and Microcircuitry, the Director of the Blue Brain Project, and the Co-Director of the recently awarded FET flagship, the Human Brain Project. (p. 14) He began his research career in South Africa in the early 1980s, later moving to Israel and then to the EPFL, where he founded the Brain Mind Institute in 2002. Since the start of his career, he has focused on neural microcircuitry, applying a broad range of anatomical, physiological, biophysical and molecular techniques, and pioneering the multi-neuron patch-clamp approach. His best-known discoveries are the principles of Spike Timing Dependent Plasticity (STDP), Redistribution of Synaptic Efficacy (RSE), and Long-Term Microcircuit Plasticity (LTMP). He has worked with theoreticians to develop the concept of “liquid computing”, a novel technique for handling real time continuous input to recurrent neural networks. He has also been active in autism research, a field in which he has co-developed the Intense World Theory of Autism.

Introduction

The Laboratory of Neural Microcircuitry (LNMC) is dedicated to understanding the structure, function and plasticity of the microcircuitry of the neocortex. To investigate these neocortical microcircuits, LNMC makes use of state of art technologies including: multi-neuron patch-clamp technologies, automated patch clamp, multi-electrode arrays (MEAs), photo-activation, a variety of imaging systems including fast CCD imaging, 2 photon and ultramicroscopy, 3D reconstruction, high throughput, single neuron gene expression profiling (mRNA-seq) and multiplex RT-PCR, microfluidics, informatics tools, and supercomputers.

Keywords

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

Results Obtained in 2012

The Research in the lab is organized into a number of projects, namely: 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. Expression profiles have been obtained from as little as 100 FACS sorted cells, serving as proof of principle for the novel method developed in LNMC to extract and sort fluoresenctly tagged cells from tissue. Channelome - The aim of the Channelome project is to characterize biophysics of these ion channels in a controlled and consistent environment with an automated patch clamp setup. Currently, we have more than 50 stable cell lines expressing individual ion channels, which are ready for analysis. Channelpedia has been developed to systematically store all the data generated by the Channelome project.

Neuroanatomy - Using 3D reconstructions of neurons in slices combined with immunohistochemistry and whole mount imaging of brains, our goal is to map: 1) the complete set of cortical neuron morphologies, 2) the relative composition of cortical neuron subtypes, and 3) the long range projections between cortical microcircuits and other brain structures. We currently have close to 1000 reconstructed neuron morphologies from the somatosensory cortex, and we are expanding this to other cortical areas as well. Electrophysiology & Microcircuits - We use up to 12 multi-patch clamp setups to study the individual neuronal properties and quantify the principles of local connectivity between these neurons (microcircuits). Plasticity - LNMC studies short and long-term plasticity, occurring under different time scales ranging from few milliseconds to hours. We are currently focusing on the role of STDP in the context of network activity using MEA stimulation in combination with patch clamp recordings. Neuromodulation - To start mapping the intricate relationship between the cortex and subcortical nuclei containing the neuromodulatory neurons, 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 hyper-functioning is at the heart of the neuropathology of autism, as predicted by the Intense World Theory. In our current investigations we try to address if autism is characterized by disproportionately stronger emotional responses to stimulation, due to limbic hyper-functionality.

EPFL School of Life Sciences - 2012 Annual Report

Selected Publications

Team Members

Postdoctoral Fellows/ Research Staff Christodoulou Dimitri Marco Hagens Olivier Logette Emmanuelle Markram Kamila Perin Rodrigo de Campos Petitprez Séverine Pezzoli Maurizio Ferdinando Rajnish Ranjan Ryge Jesper Svensson Erik Anders PhD Students Delattre Vincent Favre Mônica Ghobril Jean Pierre Muralidhar Shruti

Khazen G, Hill SL, Schürmann F, Markram H (2012) Combinatorial Expression Rules of Ion Channel Genes in Juvenile Rat (Rattus norvegicus) Neocortical Neurons. PLoS ONE 7(4): e34786. doi:10.1371/journal.pone.0034786.

Trainees Achouri Karim Perrenoud Matthieu Ludovic Rakonjac Marija

Eilemann S, Bilgili A, Abdellah M, Hernando J, Makhinya M, Pajarola R, and Schürmann F (2012). Parallel Rendering on Hybrid Multi-GPU Clusters, EGPGV 2012.

Technical Staff Herzog Mirjia La Mendola Deborah Meystre Julie

Lasserre S., Hernando J., Hill S., Schuermann F., Anasagasti P.M., Jaoudé, G.A., Markram H. (2012), A Neuron Membrane Mesh Representation for Visualization of Electrophysiological Simulations, IEEE Transactions on Visualization and Computer Graphics, 18 (2): p. 214-217.

External Employee Giugliano Michele Administrative Assistant Christiane Debono

F.Tauheed, T.Heinis, F.Schürmann, H.Markram, A.Ailamaki: SCOUT: Prefetching of Latent Structure Following Queries, VLDB 2012 Ranjan R, Khazen G, Gambazzi L, Ramaswamy S, Hill SL, Schürmann F, and Markram H (2011). Channelpedia: an integrative and interactive database for ion channels, Front. Neuroinform. 5:36. doi: 10.3389/fninf.2011.00036

BMI - Brain Mind Institute

Hay E., Hill S., Schürmann F., Markram H, Segev I (2011). Models of Neocortical Layer 5b Pyramidal Cells Capturing a Wide Range of Dendritic and Perisomatic Active Properties. PLoS Computational Biology 7(7): e1002107. doi:10.1371/journal.pcbi.1002107

Neurons in brain slices are patched via multi neuron patch-clamp setups and then stained with biocytin before they can be computationally reconstructed in 3D.

EPFL School of Life Sciences - 2012 Annual Report

Moore Lab

http://moorelab.epfl.ch/

Darren Moore conducted his PhD in molecular neuroscience at the University of Cambridge (1998-2002) and post-doctoral research on familial Parkinson’s disease (2002-05) in the Department of Neurology at the Johns Hopkins University School of Medicine, Baltimore. He spent 3 years on the Neurology faculty at Johns Hopkins as an Instructor (2005-06) and later as Assistant Professor (2006-08). Prof. Moore established the Laboratory of Molecular Neurodegenerative Research at EPFL in 2008 to focus on understanding the molecular basis of Parkinson’s disease and related neurodegenerative disorders.

Darren Moore Tenure Track Assistant Professor

Introduction

The Laboratory of Molecular Neurodegenerative Research investigates the pathophysiology of Parkinson’s disease, a chronic neurodegenerative movement disorder. Our laboratory investigates the normal biological function and pathophysiology of various proteins, that when genetically mutated, cause an inherited (familial) form of Parkinson’s disease. Our mission is to understand the molecular mechanisms and pathways through which disease-associated mutations in these proteins cause neurodegeneration. We aim to use this information in to develop novel strategies to delay or prevent this devastating disease.

Keywords

Parkinson’s disease, parkinsonism, neurodegeneration, genetic mutations, disease models, neuronal cell death, leucine-rich repeat kinase 2 (LRRK2), α-synuclein, ATP13A2, VPS35, therapeutic targets.

Results Obtained in 2012

The Moore laboratory focuses its investigations on a number of gene products that when mutated cause familial Parkinson’s disease (PD), including leucine-rich repeat kinase 2 (LRRK2), α-synuclein, ATP13A2 and VPS35. Mutations in the LRRK2, α-synuclein and VPS35 genes cause autosomal dominant forms of PD, whereas ATP13A2 mutations cause autosomal recessive PD. Mutations in the LRRK2 gene were first discovered in 2004 and we have focused over the years to understand and model the pathogenic effects of these dominant mutations in simple model organisms such as the baker’s yeast, Saccharomyces cerevisiae, cultured neurons, and rodent models. In 2012, we extended our observations from a simple yeast model of LRRK2-dependent cytotoxicity where we previously identified a number of novel genetic modifiers of toxicity. We recently demonstrated that the mammalian ortholog of one of these yeast genes, ADP-ribosylation factor GTPase-activating protein 1 (ArfGAP1), acts as a novel regulator of LRRK2 enzymatic activity and neuronal toxicity, and also serves as a kinase substrate of LRRK2. Importantly, inhibition of ArfGAP1 provided neuroprotection

against LRRK2 in cultured neurons and we are currently validating these effects in animal models of PD and dissecting the underlying mechanism involved. In other work, we have explored the relationship between the two dominant PD gene products, LRRK2 and α-synuclein, in animal models. We have been able to demonstrate that PD-related neurodegenerative phenotypes that develop in α-synuclein transgenic mice occur independent of LRRK2 expression suggesting that LRRK2 does not mediate α-synucleindependent neuronal damage in vivo. We are currently evaluating whether α-synuclein expression is oppositely required for LRRK2-dependent neurodegeneration in animal models in order to define common pathological pathways leading to PD. In 2012, we have also continued to develop a novel adenoviral-mediated gene transfer model for delivering disease-associated human LRRK2 variants to the nigrostriatal dopaminergic pathway of rodents, the neuronal circuit that selectively degenerates in PD. This new rodent model of LRRK2-associated PD will prove essential for understanding the molecular basis of familial LRRK2 mutations in precipitating neurodegeneration. Finally, our research is attempting to clarify the mechanisms underlying neuronal cell death induced by mutated LRRK2 and here we continue to explore the role of novel proteins or protein complexes that functionally interact with or are phosphorylated by LRRK2. In 2012 we continued to investigate the function and pathological dysfunction of the ATP13A2 protein. ATP13A2 is a novel P5-type ATPase protein that is thought to actively transport an unknown substrate across lysosomal membranes. We are attempting to understand the normal function of ATP13A2 in neurons and the pathogenic effects of familial mutations. Furthermore, we are creating rodent models based upon viral-mediated gene silencing to understand the effects of recessive “loss-of-function” mutations. We have also continued with a relatively new project to understand the contribution of VPS35 to PD. Our work is exploring the pathogenic effects of VPS35 mutations in yeast, neuronal and rodent models.

EPFL School of Life Sciences - 2012 Annual Report

Selected Publications

Team Members

Podhajska, A., Musso, A., Trancikova, A., Stafa, K., Moser, R., Glauser, L., Sonnay, S., Moore, D.J. (2012). Common pathogenic effects of missense mutations in the P-type ATPase ATP13A2 (PARK9) associated with early-onset parkinsonism. PLoS One 7(6): e39942.

PhD Students Alice Biosa Alessandra Musso Agata Podhajska Klodjan Stafa

Biosa, A., Trancikova, A., Civiero, L., Glauser, L., Bubacco, L., Greggio, E., Moore, D.J. (2013). GTPase activity regulates kinase activity and cellular phenotypes of Parkinson’s disease-associated LRRK2. Hum. Mol. Genet. 22(6): 1140-56.

Daher, J.P.L., Pletnikova, O., Biskup, S., Musso, A., Gellhaar, S., Galter, D., Troncoso, J.C., Lee, M.K., Dawson, T.M., Dawson, V.L., Moore, D.J. (2012). Neurodegenerative phenotypes in an A53T α-synuclein transgenic mouse model are independent of LRRK2. Hum. Mol. Genet. 21(11): 2420-31. Stafa, K., Trancikova, A., Webber, P.J., Glauser, L., West, A.B., Moore, D.J. (2012). GTPase activity and neuronal toxicity of Parkinson’s disease-associated LRRK2 is regulated by ArfGAP1. PLoS Genet. 8(2): e1002526. Ramonet, D., Podhajska, A., Stafa, K., Sonnay, S., Trancikova, A., Tsika, E., Pletnikova, O., Troncoso, J.C., Glauser, L., Moore, D.J. (2012). PARK9-associated ATP13A2 localizes to intracellular acidic vesicles and regulates cation homeostasis and neuronal integrity. Hum. Mol. Genet. 21(8): 1725-43.

Postdoctoral Fellows Guillaume Daniel Roger Moser Alzbeta Trancikova Elpida Tsika

Master’s Students Duygu Bas Aris Fiser Caroline Foo Meghna Kannan Laboratory technician Liliane Glauser Administrative Assistant Caroline Rheiner

Ramonet, D., Daher, J.P.L., Lin, B.M., Stafa, K., Kim, J., Banerjee, R., Westerlund, M., Pletnikova, O., Glauser, L., Yang, L., Liu, Y., Swing, D.A., Beal, M.F., Troncoso, J.C., McCaffery, J.M., Jenkins, N.A., Copeland, N.G., Galter, D., Thomas, B., Lee, M.K., Dawson, T.M., Dawson, V.L., Moore, D.J. (2011). Dopaminergic neuronal loss, reduced neurite complexity and autophagic abnormalities in transgenic mice expressing G2019S mutant LRRK2. PLoS One 6(4): e18568. Dusonchet, J., Kochubey, O., Stafa, K., Young, S.M., Zufferey, R., Moore, D.J., Schneider, B.L., Aebischer, P. (2011). A rat model of progressive nigral neurodegeneration induced by the Parkinson’s disease-associated G2019S mutation in LRRK2. J. Neurosci. 31(3): 907-12.

BMI - Brain Mind Institute

Xiong, Y., Coombes, C.E., Kilaru, A., Li, X., Gitler, A.D., Bowers, W.J., Dawson, V.L., Dawson, T.M., Moore, D.J. (2010). GTPase activity plays a key role in the pathobiology of LRRK2. PLoS Genet. 6(4): e1000902.

Models of familial Parkinson’s disease: LRRK2. (A) 2D phospho-proteome profiling of brain tissue from LRRK2 transgenic mice. (B) Degeneration of dopaminergic neurons in the substantia nigra of LRRK2 transgenic mice. (C) Accumulation of autophagosomes in the brain of G2019S LRRK2 mice. (D) Adenoviral (rAd)-mediated expression of human LRRK2 in midbrain dopaminergic (TH) neurons. Lower panel: protein architecture and familial mutations of LRRK2.

EPFL School of Life Sciences - 2012 Annual Report

Petersen Lab http://lsens.epfl.ch/

Carl Petersen studied physics as a bachelor student in Oxford (1989-1992). During his PhD studies under the supervision of Prof. Michael Berridge in Cambridge (1992-1996), he investigated cellular and molecular mechanisms of calcium signalling. In his first postdoctoral period (1996-1998), he joined the laboratory of Prof. Roger Nicoll to investigate synaptic transmission and plasticity in the hippocampus. During a second postdoctoral period with Prof. Bert Sakmann (1999-2003), he began working on the primary somatosensory barrel cortex, investigating cortical circuits and sensory processing.

Carl Petersen

Associate Professor

Introduction

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 complex neural circuits. Our experiments focus primarily on tactile sensory perception in the mouse whisker sensorimotor system.

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 2012

Research in the Laboratory of Sensory Processing during 2012 contributed to three important areas of neuroscience in which we advanced towards our goal of a causal and mechanistic description of neural circuit function in sensory perception: Synaptic Connectivity of Neocortical Microcircuits (Avermann et al., 2012) Synaptic interactions between nearby excitatory and inhibitory neurons in the neocortex are thought to play fundamental roles in sensory processing. Here, we combine optogenetic stimulation and multiple simultaneous wholecell recordings in vitro to define key functional microcircuits within layer 2/3 of mouse primary somatosensory barrel cortex. A simple computational model based on the experimentally determined electrophysiological properties of the different classes of layer 2/3 neurons and their unitary synaptic connectivity accounted for key aspects of the network activity evoked by optogenetic stimulation, including the strong recruitment of fast-spiking GABAergic

neurons acting to suppress firing of excitatory neurons. We conclude that fast-spiking GABAergic neurons play an important role in neocortical microcircuit function through their strong local synaptic connectivity, which might contribute to driving sparse coding in excitatory layer 2/3 neurons of mouse barrel cortex in vivo. Cell-type Specific Function of Neocortical Microcircuits (Gentet et al., 2012) Neocortical GABAergic neurons have diverse molecular, structural and electrophysiological features, but the functional correlates of this diversity are largely unknown. Here, in this study, we reported unique membrane potential dynamics of somatostatin-expressing neurons in layer 2/3 of the primary somatosensory barrel cortex of awake behaving mice. Somatostatin-expressing neurons were spontaneously active during periods of quiet wakefulness. However, somatostatin-expressing cells hyperpolarized and reduced action potential firing in response to both passive and active whisker sensing, in contrast to all other recorded types of nearby neurons, which were excited by sensory input. Optogenetic inhibition of somatostatin-expressing neurons increased burst-firing in nearby excitatory neurons. We hypothesize that the spontaneous activity of somatostatin-expressing neurons during quiet wakefulness provides a tonic inhibition to the distal dendrites of excitatory pyramidal neurons. Conversely, the inhibition of somatostatin-expressing cells during active cortical processing likely enhances distal dendritic excitability, which may be of critical importance for top-down computations and sensorimotor integration. Thalamic control of cortical states (Poulet et al., 2012) In thus study, we investigated the impact of thalamus on ongoing cortical activity in the awake, behaving mouse. We demonstrated that the desynchronised cortical state during active behavior is driven by a centrally generated increase in thalamic action potential firing, which can also be mimicked by optogenetic stimulation of the thalamus. The thalamus therefore plays a key role in controlling cortical states.

EPFL School of Life Sciences - 2012 Annual Report

Selected Publications

Avermann, M., Tomm, C., Mateo, C., Gerstner, W. and Petersen, C.C.H. (2012). Microcircuits of excitatory and inhibitory neurons in layer 2/3 of mouse barrel cortex. J. Neurophysiol. 107: 3116-3134. Gentet, L.J., Kremer, Y., Taniguchi, H., Huang, Z.J., Staiger, J.F., Petersen, C.C.H. (2012). Unique functional properties of somatostatin-expressing GABAergic neurons in mouse barrel cortex. Nat. Neurosci. 15: 607-612. Mensi, S., Naud, R., Pozzorini, C., Avermann, M., Petersen, C.C.H. and Gerstner, W. (2012). Parameter extraction and classification of three cortical neuron types reveals two distinct adaptation mechanisms. J. Neurophysiol. 107: 17561775.

Team Members Postdoctoral Fellows Sylvain Crochet Emmanuel Eggermann Taro Kiritani Natalya Korogod Yves Kremer Alexandros Kyriakatos Damien Lapray Szabolcs Olah Shankar Sachidhanandam Tanya Sippy Nadia Urbain Takayuki Yamashita

Poulet, J.F.A., Fernandez, L.M., Crochet, S. and Petersen, C.C.H. (2012). Thalamic control of cortical states. Nat. Neurosci. 15: 370-372.

PhD Students Aurelie Pala Varun Sreenivasan

Mateo, C., Avermann, M., Gentet, L.J., Zhang, F., Deisseroth, K. and Petersen, C.C.H. (2011). In vivo optogenetic stimulation of neocortical excitatory neurons drives brain-state-dependent inhibition. Curr. Biol. 21: 1593-1602.

Administrative Assistant SĂŠverine Janot

Crochet, S., Poulet, J.F.A., Kremer, Y. and Petersen, C.C.H. (2011). Synaptic mechanisms underlying sparse coding of active touch. Neuron 69: 1160-1175.

BMI - Brain Mind Institute

Whole-cell recording electrodes (red fluorescence) were targeted using a two-photon microscope to two excitatory pyramidal neurons (Cell 1 and Cell 2) and one GFP-labelled (green) fast-spiking inhibitory GABAergic neuron (Cell 3) in a brain slice from a GAD67-GFP mouse (Avermann et al., 2012).

EPFL School of Life Sciences - 2012 Annual Report

Sandi Lab

http://lgc.epfl.ch/

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-inChief of the journal Frontiers in Behavioral Neuroscience.

Carmen Sandi Full Professor Director of BMI

Introduction

The Laboratory of Behavioral Genetics investigates the impact and mechanisms whereby stress affects brain function and behavior, with a focus on the social domain. We are particularly interested in understanding the link between stress, personality traits and pathological aggression and social hierarchies both, under normal conditions and in the framework of psychopathology. Our work has highlighted glucocorticoid pathways as critical mediators of stress effects. Our goal is to uncover key neurobiological mechanisms and to develop opportunities for intervention on stress-related disorders.

Keywords

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

Results Obtained in 2012

Exposure to adverse experiences during childhood and adolescence has been associated with the development of psychiatric disorders, including increased aggression. We have developed an animal model based on exposure of outbred rats to fearful experiences during the peripuberty period that recapitulates the key features of a â&#x20AC;&#x2DC;cycle of violenceâ&#x20AC;&#x2122;: peripuberty stressed males become abnormally aggressive against both other males and females. The females that cohabitate with them develop behavioral, endocrine and neurobiological alterations. Their male offspring (despite not having been in contact with their fathers or exposed themselves to any experimental stress) show, as well, increased aggressive behaviors. Peripuberty stress induces as well other important behavioral alterations. This animal model allows us to investigate the effector pathways from stress to pathological aggression. We have found that peripuberty stressed rats exhibit alterations in the activation of the amygdala and the medial orbitofrontal cortex, as well as in their connectivity patterns. We have identified changes in the expression and epigenetic control

of genes from the serotonergic pathway in the prefrontal cortex, and verified that their pharmacological blockade (i.e., administration of a MAOA inhibitor) reversed the peripuberty stress-induced antisocial behaviors. As potential molecular mechanisms linking stress and asocial and aggressive behaviors, we have recently investigated on the role of synapse-specific cell adhesion molecules (this work relates to the FP7 EU project MemStick that we have coordinated). We have focused on the involvement of molecules of the nectin and neuroligin families in the social and cognitive abnormalities induced by stress. While information regarding nectins involvement in brain function and behavior is scarce, the neurexin-neuroligin transsynaptic adhesion complexes (neuroligin-1 associated with excitatory, while neuroligin-2 with inhibitory synapses) have revealed highly important for cognitive function, particularly social behaviors. Stress leads to profound structural and molecular changes in several brain regions, notably including the hippocampus. We have identified specific alterations in neuroligin-2 and nectin-3 in the hippocampus of rats submitted to stress protocols that result in alterations in cognitive and social (reduced social exploration and increased aggression). Importantly, we found evidence that the specific reduction of nectin-3 in the perisynaptic CA1 compartment after chronic stress is causally linked with stress-induced deficits in a CA1-dependent cognitive task and in social behaviors in experiments involving AAV-induced overexpression of nectin-3. We also found increased gelatinase activity in chronically stressed animals, which along with cell culture and pharmacological experiments implicated a role for matrix metalloproteinase (MMP) activity in the cleavage of nectin-3 in an NMDA-receptor-dependent mechanism. Our results are pioneer in indicating that stress impairs social behaviors by regulating mechanisms implicated in neurodevelopmental disorders that course with alterations in the social domain (e.g., autism, schizophrenia).

EPFL School of Life Sciences - 2012 Annual Report

Selected Publications

Cordero, M.I., Poirier, G.L., Marquez, C., Veenit, V., Fontana, X., Salehi, B., Ansermet, F. and Sandi, C. (2012) Evidence for biological roots in the transgenerational transmission of intimate partner violence. Transl. Psychiatry 2:e106. Knafo, S., Venero, C., Sanchez-Puelles, C., Pereda-Perez, I., Franco, A., Sandi, C., et al. DeFelipe, J. and Esteban, J.A. (2012) Facilitation of AMPA receptor synaptic delivery as a molecular mechanism for cognitive enhancement. PLoS Biol. 10:e1001262. Castro, J.E., Diessler, S., Varea, E., Márquez, C. and Larsen, M.H., Cordero, M.I. and Sandi, C. (2012) Personality traits in rats predict vulnerability and resilience to developing stress-induced depression-like behaviors, HPA axis hyperreactivity and brain changes in pERK1/2 activity. Psychoneuroendocrinology 37:1209-1223. Conboy, L., Varea, E., Castro, J.E., Sakouhi-Ouertatani, H., Calandra, T., Lashuel, H. and Sandi, C. (2011) Macrophage migration inhibitory factor (MIF) is critically involved in basal and fluoxetine-stimulated adult hippocampal cell proliferation and in anxiety, depression and memory related behaviours. Mol. Psychiatry 16:533-547. Timmer, M., Cordero, M.I., Sevelinge, Y. and Sandi, C. (2011) Evidence for a role of oxytocin receptors in the long-term establishment of dominance hierarchies. Neuropsychopharmacology 36:2349-2356. Sandi C. (2011) Glucocorticoids act on glutamatergic pathways to affect memory processes. Trends Neurosci. 34:165-176. Bisaz, R., Schachner, M. and Sandi, C. (2011) Causal evidence for the involvement of the neural cell adhesion molecule, NCAM, in chronic stress-induced cognitive impairments. Hippocampus 21(1):56-71. Sandi C. (2011) Healing anxiety disorders with glucocorticoids. Proc. Natl. Acad. Sci. USA 108:6343-6344.

Team Members

Postdoctoral Fellows Alexandre Claude Gustave Bacq Samuel Bendahan Martina Fantin Fiona Hollis Guillaume Poirier Ricardo Ramires Orbicia Riccio Wicht John Christian Thoresen Michael van der Kooij External Employee Maria Isabel Cordero Campana PhD Students Laura Lozano Montes Stamatina Tzanoulinou Vandana Veenit Sophie Elisabeth Walker Scientific Assistant Christine Kohl Lab Technicians Céline Fournier Jocelyn Grosse Olivia Zanoletti Trainees Shishir Balyian Eleni Batzianouli Lejla Colic Matthijs de Boer Clara Garcia Mompo Leyla Loued-Khenissi Aurélie Papilloud Julia Simon Alina Strasser Agnieszka Szpakowska Ipshita Zutshi Students Damien Huzard Aya Imam Natsuko Imamura Alain Jacot-Guillarmod Doris Li Martin Vogel Academic Guest Lorenz Goette

BMI - Brain Mind Institute

Administrative Assistant Barbara Goumaz

Early life experiences are critical for determining neurodevelopmental trajectories linked to mental health or psychopathology. In the image, a pubertal rat is exposed to a harmless novel environment.

EPFL School of Life Sciences - 2012 Annual Report

Schneggenburger Lab http://www.lsym.epfl.ch/

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 Max-Planck Institute for biophysical Chemistry (Göttingen, 1996- 2005), he developed a research program in transmitter release mechanisms, and presynaptic plasticity. In 2005, he was appointed at EPFL and has since then been leading the Laboratory for Synaptic Mechanisms at the Brain Mind Institute.

Ralf Schneggenburger Full Professor

Introduction

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 also study activity dependent and -independent signaling mechanisms which determine synapse connectivity and synapse function at specific points in neuronal circuits. This research aims to gain insight into neuronal network function, and it forms the basis for understanding the pathophysiology of neuropsychiatric and neurodegenerative disorders, many of which represent diseases of the synapse.

Keywords

Synaptic transmission, nerve terminal, neurotransmitter, exocytosis, short-term plasticity, synapse development, synapse specificity, synapse connectivity, axonal signaling.

Results Obtained in 2012

We use an exceptionally large synapse located in the auditory pathway, the calyx of Held, at which we can gain access to the physiology of the presynaptic nerve terminal (see Figure 1). In 2012, we could show a relation between axon midline crossing, and the later functional maturation of the calyx of Held synapse (Michalski et al. 2013). At the calyx of Held projection, synapses usually strictly form on the opposite, “contralateral” brain side. In conditional Robo3 KO mice which lack Robo3 specifically in the lower auditory system, essentially all calyces of Held formed on the wrong, ipsilateral side of the brain. Ipsilateral calyces of Held were nearly normal in morphological terms, except for a slight deficit in the elimination of competing synaptic inputs. The functional maturation of ipsilateral calyces of Held was, however, strongly impaired. Thus, the excitatory postsynaptic currents (EPSCs) were smaller and had irregularities in their rising phase, indicating fewer released vesicles and more asynchronous release. Presyn-

aptic plasticity like post-tetanic potentiation (PTP), which normally disappears during development due to more effective Ca2+ ion handling in the nerve terminal, persisted with development in the Robo3 cKO mice. Some of the functional changes in synaptic transmission persisted up to adulthood in Robo3 cKO mice. These data indicate an apparent coupling between the development of synapse function, and the location of an output synapse in terms of the “correct” side of the brain. This coupling might serve to limit the influence of mis-localized synapses on the computations performed in a neuronal circuit. Further work needs to decipher the molecular mechanisms leading to the apparent coupling between functional synapse development and axon localization; perturbed axonal protein translation and related signaling deficiencies in Robo3 cKO mice might be involved. In a collaborative study with the laboratory of Prof. P. Aebischer (Gaugler et al., 2012), we elucidated the role of the presynaptic protein α-Synuclein in the pathogenesis of Parkinson’s Disease (PD). Some familial forms of PD are associated with multiplications of the α-Synuclein gene locus. To model the disease initiation in the dopaminergic nigrostriatal projection which is most relevant for PD, we moderately overexpressed the protein in the substantia nigra of rats, using adeno-associated viral vectors (AAV). Rats with unilateral overexpression of α-Synuclein in the substantia nigra showed significant asymmetries in spontaneous and drug-induced rotational motor behaviors as a sign of hemiparkinsonian impairments. The behavioral changes were associated with functional deficits in striatal dopamine release and ultrastructural changes in dopaminergic fibers, like a decreased density of dopaminergic vesicles and contact sites. Importantly, these axonal and presynaptic changes exceeded dopaminergic neuron- or fiber loss, indicating that an impaired function at dopaminergic synapses is an early component in this form of PD.

EPFL School of Life Sciences - 2012 Annual Report

Selected Publications

Michalski, N., Babai, N., Renier, N., Perkel, D.J., Chedotal, A., and Schneggenburger, R. (2013). Robo3-driven axon midline crossing conditions functional maturation of a large commissural synapse. Neuron 78, in press. Schneggenburger, R., Han, Y., Kochubey, O. (2012). Ca2+ channels and transmitter release at the active zone. Cell Calcium 52: 199 - 207. Gaugler M.N., Genç O., Bobela W., Mohanna S., Ardah M.T., El-Agnaf O.M., Cantoni M., Bensadoun J.C., Schneggenburger R., Knott G.W., Aebischer P., Schneider B.L. (2012) Nigrostriatal overabundance of α-synuclein leads to decreased vesicle density and deficits in dopamine release that correlate with reduced motor activity. Acta Neuropathologica, 123:653-69. Kochubey, O., Lou, X., and Schneggenburger, R. (2011). Regulation of transmitter release by Ca2+ and synaptotagmin: insights from a large CNS synapse. Trends in Neurosciences 34: 237-246. Han, Y., Kaeser, P. S., Südhof, T. C., and Schneggenburger, R. (2011). RIM determines Ca2+ channel density and vesicle docking at the presynaptic active zone. Neuron 69, 304-316.

Team Members Postdoctoral Fellows Norbert Babai Naila Ben Fredj Brice Bouhours Olexiy Kochubey Evan Vickers PhDStudents Ozgür Genc Enida Gjoni Elin Kronander Wei Tang Technicians Jessica Dupasquier Heather Murray Administrative Assistant Laure Dayer

BMI - Brain Mind Institute

Kochubey, O., and Schneggenburger, R. (2011). Synaptotagmin increases the dynamic range of synapses by driving Ca2+ - evoked release and by clamping a near-linear remaining Ca2+ sensor. Neuron 69: 736 - 748.

A, The calyx of Held as a multi- active zone synapse. B, C reconstruction of all vesicles (B, bottom) and of the x-y location of membrane-docked vesicles at individual active zones (C). Taken from Schneggenburger et al. 2012 with permission; see also Han et al. 2011.

EPFL School of Life Sciences - 2012 Annual Report

IBI

Institute of Bioengineering

Melody Swartz - Director The Institute of Bioengineering (IBI) brings together discovery in fundamental biology with engineering design principles. Its labs pursue quantitative, systems- and design-oriented research in and for the life sciences, both to better understand complex biological and physiological networks as well as through the development of (bio)molecules, techniques, or devices that in many cases translate into novel therapeutics and diagnostics. The IBI is situated in both the School Life Science (SV) and the School of Engineering (STI). This dual affiliation allows great diversity in hiring faculty from different backgrounds and with different research perspectives. The dual affiliation also provides a rich educational environment, both at the BS/MS and PhD levels, especially since a joint MS program in Bioengineering has come into effect in the fall of 2010, shared between the two Schools. After 10 years under the founding leadership of Jeffrey Hubbell, Melody Swartz became the new Institute Director in 2012 when Prof. Hubbell became the Dean of the School of Life Sciences. Among other notable events were the promotion of Prof. Felix Naef to Associate Professor, the success of our annual “IBI Day” (this year’s theme was Systems/Computational Bioengineering), and the launch and first meeting of a Scientific Advisory Board, which will convene regularly in the future. In addition, several IBI faculty were honored in 2012 and are highlighted in the introduction of this SV Annual Report (p. 7).

IBI - Institute of Bioengineering

On the educational side, 20 new PhDs were awarded in IBI-affiliated labs, and 35 graduates received their MSc in Bioengineering. This includes the first 4 Bertarelli Fellows, whose thesis work done partially at Harvard Medical School was featured at the 2nd Symposium of the Bertarelli Program on Translational Neuroscience and Neuroengineering (http://ptnn.epfl.ch), which is hosted by IBI. The Symposium was held at EPFL on Oct. 11-12. IBI’s continuing success is reflected in the Quantitative Ranking of Engineering Disciplines (http://sti.epfl.ch/ page-84929.html), a strictly bibliometric ranking which finds it in 3rd place worldwide and number 1 in Europe, as already in 2011. http://sv.epfl.ch/page-37989.html

EPFL School of Life Sciences - 2012 Annual Report

Auwerx - Schoonjans Lab http://auwerx-lab.epfl.ch/

Johan Auwerx Full Professor Nestlé Chair in Energy Metabolism

Kristina Schoonjans Adjunct Professor Co-group Leader

Introduction

Johan Auwerx and Kristina Schoonjans use a systems physiology approach to understand metabolic homeostasis and the pathogenesis of common metabolic diseases. Their research aims to understand how regulatory proteins, including nuclear receptors, membrane receptors and transcriptional cofactors, act as sensors for molecules of nutritional, metabolic or pharmacological origin, and translate this into altered gene expression and protein patterns affecting metabolic function.

Keywords

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

Results Obtained in 2012

Johan Auwerx received an M.D. (1982) and Ph.D. (Molecular Endocrinology; 1989) degree from the Katholieke Universiteit Leuven, Belgium. He performed post-doctoral training in Medicine and Genetics at the University of Washington, Seattle. He is certified in Endocrinology, Metabolism and Nutrition. 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 (Lille) in 1999, she moved to the IGBMC in Strasbourg and was appointed Research Director with INSERM in 2007. They both codirect the LISP lab at the EPFL since 2008.

Membrane and nuclear receptors in bile acid signaling and metabolism - Earlier studies in our lab established how the enterohepatic nuclear receptors - farnesoid X receptor (FXR), liver receptor homolog-1 (LRH-1) and short heterodimer partner (SHP) - govern hepatic lipid and bile acid metabolism, and regulate cell proliferation. We furthermore identified bile acids as endocrine regulators of energy expenditure and glucose homeostasis, through the activation of a novel GPCR, TGR5. This work on bile acid signaling revealed a protective role for bile acids against the development of diabetes and sparked a paradigm shift that transformed bile acids, known to be lipid solubilizers in the gut, to versatile endocrine signals that impact various aspects of physiology. More recently, we have highlighted the role of macrophage TGR5 in the context of inflammationdriven metabolic diseases, such as atherosclerosis. TGR5 activation in macrophages by bile acid mimetics inhibits pro-inflammatory cytokine production and reduces atherosclerosis via cAMP-dependent interference of p65 nuclear translocation.

Cofactors and fine-tuning of energy homeostasis - The role of transcriptional cofactors in the control of metabolic homeostasis, in general, and of mitochondrial function, in particular, is still poorly understood. We have established that a yin-yang between corepressors - NCoR1 and the sirtuin family of deacetylases - and co-activators - PGC1α, SRC-2 and -3 and GCN5 - fine-tunes transcriptional networks that control oxidative metabolism. We showed that increased cellular NAD+ levels during energy stress, activate SIRT1 to deacetylate and induce the activity of PGC-1α, the master controller of mitochondrial function. This process, together with reduced activity of NCoR1 favors oxidative metabolism, thereby enhancing the use of stored energy during caloric restriction. These processes are reversed by excessive energy intake, when the activity of AMPK and SIRT1 is attenuated due to high intracellular ATP and low NAD+ levels. A high fat diet, furthermore induces the expression of the acetyltransferases, SRC-3 and GCN5, while concomitantly reducing SIRT1 levels. This work has established that complex transcriptional networks convert signals associated with caloric intake and cellular energy status into changes of chromatin state and transcription. The BXD Genetic Reference Population as a resource to study metabolism - A cohort of 42 strains of BXDs has recently been pushed through an extensive metabolic phenotyping program. This study focused on differential effects of diet as well as exercise, weight gain, fat deposition, gene expression, and many classic metabolic traits. More than 400 metabolic phenotypes related to mitochondrial function were measured. This program is an expansion of an earlier pilot study that focused on sex differences in 140 metabolic traits on BXD cohorts. We have observed striking variation in the response of body weight to diet and exercise among BXD strains. These ongoing experiments further validate the BXD family as an excellent resource for the genetic dissection of metabolic networks.

EPFL School of Life Sciences - 2012 Annual Report

Selected Publications

C. Canto, R.H. Houtkooper, E. Pirinen, D.Y. Youn, M.H. Oosterveer, P.J. Fernandez-Marcos, H. Yamamoto, P.A. Andreux, P. Cettour-Rose, K. Gademann, C. Rinsch, K. Schoonjans, A. A. Sauve, J. Auwerx. The NAD+ precursor nicotinamide riboside enhances oxidative metabolism and protects against high-fat diet induced obesity. Cell Metabolism, 2012, 15, 838-847. P.A. Andreux, E.G. Williams, H. Koutnikova, R.H. Houtkooper, M.F. Champy, H. Henry, K. Schoonjans, R.W. Williams, J. Auwerx. Systems genetics of metabolism – the use of the BXD murine reference panel for multiscalar integration of traits. Cell 2012, 150, 1287-1299. P. Bai, C. Canto, H. Oudart, A. Brunyánszki, Y. Cen, C. Thomas, H. Yamamoto, A. Huber, B. Kiss, R.H. Houtkooper, K. Schoonjans, V. Schreiber, A.A. Sauve, J. Menissier-de Murcia, J. Auwerx PARP-1 inhibition increases mitochondrial metabolism through SIRT1 activation. Cell Metabolism, 2011, 13, 461-468. P. Bai, C. Canto, A. Brunyánszki, A. Huber, M. Szanto, Y. Cen, H. Yamamoto, S. Houten, B. Kiss, H. Oudart, P. Gergely, V. Schreiber, J. Menissier-de Murcia, A.A. Sauve, J. Auwerx. PARP-2 regulates SIRT1 expression and whole body energy expenditure. Cell Metabolism, 2011, 13, 450-460. J. Du, Y. Zhou, X. Su, J. J. Yu, S. Khan, H. Jiang, J. Kim, J. Woo, J. H. Kim, B. H. Choi, B. He, W. Chen, S. Zhang, R. A. Cerione, J. Auwerx, Q. Hao, H. Lin. Sirt5 Is an NAD-Dependent Protein Lysine Demalonylase and Desuccinylase. Science, 2011, 334, 806-809. H. Yamamoto, E.G. Williams, L. Mouchiroud, C. Canto, W. Fan, M. Downes, C. Heligon, G.D. Barish, B. Desvergne, R.M. Evans, K. Schoonjans, J. Auwerx. NCoR1 is a conserved physiological modulator of muscle mass and oxidative function. Cell, 2011, 147, 827-839. T.W.H. Pols, M. Nomura, T. Harach, G. Lo Sasso, M.H. Oosterveer, C. Thomas, G. Rizzo, A. Gioiello, L. Adorini, R. Pelliciari, J. Auwerx, K. Schoonjans. TGR5 activation inhibits atherosclerosis by reducing macrophage infiltration and lipid loading. Cell Metabolism, 2011, 14, 747-757.

Team Members Postdoctoral Fellows Taoufiq Harach Jo YoungSuk Giuseppe Lo Sasso Adriano Maida Laurent Mouchiroud Maaike Oosterveer Eija Pirinen Thijs Pols Sooraj Ratnakumar Dongryeol Ryu Matthias Stein Hiroyasu Yamamoto PhD Students Pénélope Andreux Virginija Jovaisaite Elena Katsyuba Mitsonura Nomura Evan Williams Pan Xu Julien Zaldivar Hongbo Zhang Master’s Student Adrienne Mottis Technicians Sabrina Bichet Thibaud Clerc Amandine Moriot-Signorino-Gelo Norman Moullan Administrative Assistant Valérie Stengel

IBI - Institute of Bioengineering

Oosterveer MH, Mataki C, Yamamoto H, Harach T, Moullan N, van Dijk TH, Ayuso E, Bosch F, Postic C, Groen AK, Auwerx J, Schoonjans K. LRH-1-dependent glucose sensing determines intermediary metabolism in liver. J. Clin. Invest, 2012, 122, 2817-2826.

Mice treated with resveratrol are protected from obesity.

EPFL School of Life Sciences - 2012 Annual Report

Baekkeskov Lab Steinunn Baekkeskov received her PhD in Biochemistry from the University of Copenhagen in 1984 identifying and characterizing target antigens of the autoimmune response that is 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. She has been a full professor at UCSF since 1998. In 2012 she became a part time visiting professor in the School of Life Sciences at EPFL.

Steinunn Baekkeskov Visiting Professor

Introduction

The Baekkeskov group studies how and why the pancreatic beta cell becomes a target of autoimmunity resulting in beta cell destruction and development of type 1 diabetes. Current research aims at elucidating the early events leading to autoimmunity towards the beta cell and how the process can be blocked or prevented.

Keywords

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

Results Obtained in 2012

Research in the Baekkeskov laboratory seeks to understand why the immune system erroneously mounts an immune response to some self proteins and how this process can be prevented. We study the autoantigen GAD65, which is targeted by the immune response associated with destruction of pancreatic beta cells and development of Type 1 Diabetes. GAD65, the smaller isoform of the GABA synthesizing enzyme, glutamic acid decarboxylase (GAD), is critical for fine tuning of GABA-ergic neurotransmission, while the highly homologous isoform of GAD, GAD67, synthesizes basic levels of GABA. GAD65 is unusually susceptible to becoming an autoantigen in the two cell types that express it, pancreatic beta cells and GABA-ergic neurons. Thus it is a primary autoantigen in both type 1 diabetes and a rare neurological disorder, stiff-man syndrome that affects GABA-ergic neurons. In contrast GAD67 is not an independent autoantigen in either disease. The two isoforms differ

mainly in the N-terminal region that controls membrane targeting and trafficking of the proteins. Our research focuses on elucidating the mechanisms of membrane association and trafficking pathways of GAD65 and how they differ for GAD67. A detailed understanding of the differences in the trafficking pathways of GAD65 and GAD67 may hold the key to why only GAD65 becomes a target of autoimmunity. While we know much about the mechanisms that mediate membrane association and trafficking of GAD65, more recently we have shown that two mechanisms govern membrane association of the GAD67. One mechanisms results in heterodimerisation with GAD65 and piggy-backing onto its the trafficking pathways, while the second mechanisms is independent of GAD65. Both mechanisms result in targeting of GAD67 to synaptic vesicle membranes. We have identified a sophisticated mechanism that controls the cycling of GAD65 between the Golgi compartment and the synaptic vesicle membranes, where it is needed for a rapid synthesis and secretion of GABA to meet a sudden increase in demand. This mechanism involves a cycle of palmitoylation/depalmitoylation of two cysteines, cys 30 and 45, in the N-terminal targeting domain, which are absent in GAD67. We have recently shown that induction of mild oxidative stress in beta cells results in GAD65 being excluded from its normal trafficking pathway. Thus the protein is blocked from entering the vesicular membrane pathway to synaptic vesicles. If beta cell stress continues, GAD65 can form large aggregates. We hypothesize that such aggregates would be highly immunogenic if released from damaged and/or apoptotic beta cells.

EPFL School of Life Sciences - 2012 Annual Report

Team Members

• What is the functional relevance of the acylation cycle in GAD65 for control of GABA-ergic mechanisms in neurons and pancreatic beta cells? • What is the mechanism involved in accumulation of GAD65 in conditions of beta cell oxidative stress? Is the block in the trafficking pathway to synaptic vesicle membranes due to oxidation of cys 30 and 45 to form a disulfide bridge and/ or inhibition of the palmtoylation transferase involved in palmitoylation of GAD65? Does a block in the acylation cycle due to accumulation of oxidized and aggregated GAD65 contribute to beta cells stress? Does aggregation of GAD65 increase its immunogenicity?

Postdoctoral Fellow Ed Phelps Lab Manager Miriella Pasquier

Administrative Assistant Marisa Marciano Wynn

IBI - Institute of Bioengineering

Current Questions:

Large dense core insulin secretory vesicles are visualized in primary rat beta cells by immunofluorescence staining and confocal microscopy. The diabetes autoantigen GAD-65 is found in vesicles separate from the insulin secretory system. Insulin (magenta), GAD-65 (green), and DNA (blue).

EPFL School of Life Sciences - 2012 Annual Report

Barrandon Lab http://ldcs.epfl.ch/

Yann Barrandon, MD-PhD, is joint professor in Stem Cell Dynamics at the EPFL and at the Lausanne University (Unil), and head of the Department of Experimental Surgery at the CHUV since 2002. He has made major contributions in basic epithelial stem cell biology and in stem cell therapy. Prof. Barrandon is a member of the EMBO and the Academia Europaea. He is also a member of the EPFL research committee, EPFL Ethical committee and of the Canton de Vaud Ethical committee. He was elected twice best teacher in Life Sciences at EPFL. In 2011, he co-founded gymetrics SA. Since 2012, he is “Initiative director” for the doctoral training cooperation initiative signed between the EPFL and A*Star Singapore.

Yann Barrandon

Full Professor Head of the Joint Chair of Stem Cell Dynamics EPFL – UNIL – CHUV Head of the Department of Experimental Surgery at the Lausanne University Hospital

Introduction

The laboratory of Stem Cell Dynamics at EPFL and Experimental Surgery at the CHUV has three main objectives that aim at improving cell and gene therapy using epithelial stem/progenitor cells: first, the laboratory would like to decipher the relationship between stem/progenitors cells of stratified epithelia, second to understand the impact of the physical environment on stem cell behavior and third to comprehend stem cell engraftment. The laboratory is a partner in three stem cell consortia within the EEC 7th framework program, aiming at the fundamentals of stem cells (EuroSyStem) and stem cell therapy (OptiStem and Betacelltherapy).

Keywords

Stem cell, plasticity, reprogramming, microenvironment, skin, epidermis, whisker, hair follicle, thymus, cornea, gene and cell therapy, translational medicine, regenerative medicine.

Results Obtained in 2012

Skin stem cells (epithelial and mesenchymal) can be extensively cultured and cloned, genetically manipulated and transplanted. Engraftment is the quintessence of stem cell behavior as it draws on all stem cell basic functions, i.e. homing, attachment, migration, proliferation, fate choice, renewal, differentiation and death. In homeostatic situation, these decisions are tightly controlled and influenced by the

microenvironment (the niche). In a disease, the microenvironment may be abnormal, damaged by a preconditioning treatment or even completely missing as in third degree burns of the skin or corneal deficiency. Hence, transplanted cultured stem cells in regenerative medicine have to adjust to an environment that is far from ideal, if not hostile. Surprisingly, little is known on how stem cells respond to a non-homeostatic microenvironment and engraftment mostly remains an uncontrolled process. Using the minipig as a model system, we have cultured autologous epidermal stem cells and transplanted them onto granulation tissue formed in response to skin surgical wounds excised to muscular fascia. We have demonstrated that the cultured autologous stem cells respond to the microenvironment of the grafting bed by favoring differentiation rather self-renewal or death. We are now screening for small molecules and factors that favor renewal of transplanted stem cells to improve engraftment. The laboratory of Stem Cell Dynamics is also using state-of-the art architecture, microtechnology, informatics and visualization technology to construct models that permit to virtually manipulate the microenvironment and predict the consequences of theses manipulations on stem cell behavior and organ function using the skin, the thymus and the cornea as model systems.

EPFL School of Life Sciences - 2012 Annual Report

Selected Publications

Hirata-Tominaga, K., Nakamura, T., Okumura, N., Kawasaki, S., Kay, E.P., Barrandon, Y., Koizumi, N, and Kinoshita, S. (2013). Corneal endothelial cell fate is maintained by LGR5 via the regulation of hedgehog and Wnt pathway. Stem Cells. Apr 3. doi: 10.1002/stem.1390. [Epub ahead of print]

Team Members

Senior scientists Rochat Ariane

Smith, E., Claudinot, S., Lehl, R., Pellegrinet, L., Barrandon, Y., and Radtke, F. (2012). Generation and Characterization of a Notch1 Signaling-Specific Reporter Mouse Line. Genesis. 50(9):700-10.

Postdoctoral Fellows Amici Alessandro Caillier-Veron Maïa Claudinot Stéphanie Droz-Georget Stéphanie Gonneau Christèle Grasset Nicolas Kanemitsu Michiko Maggioni Melissa Wasnick Roxana PhD Students Arlabosse Tiphaine Gorostidi François Graber Julien Maggioni Melissa Manti Pierluigi Mosig Johannes Muller Georges Pluchinotta Matteo Zaffalon Andrea

Rochat, A., Grasset, N., Gorostidi, F., Lathion Droz-Georget, S., and Barrandon, Y. (2012) Regeneration of epidermis from adult human keratinocyte stem cells. In Handbook of stem cells 2nd ed. Atalla and Lanza editors Elsevier. Vol 2 pp. 767-777.

Master’s Students De Lageneste Marine Hémon Diane Lai Quiwen Perseguers Marie-Noëlle

Bonfanti, P., Barrandon, Y., and Cossu, G. “Hearts and Bones”: (2012) The Ups and Downs of “Plasticity” in Stem Cell Bioloy EMBO Mol. Med. 4(5):353-61.

Visiting Student Tyler Haynes

Bonfanti, P., Claudinot, S., Amici, A.W., Farley, A., Blackburn, C.C, and Barrandon, Y. (2010). Microenvironmental reprogramming of thymic epithelial cells to skin multipotent stem cells. Nature 466(7309):978-82. (Press release) Commentary in Bilousova and Roop Cell Stem Cell 2010, 7: 419-420.

Technicians Burki Marco De Souza Olga Mercier Louis Savoy Dorinne

Nanba, D., Toki, F., Matsushita, N., Matsushita, S., Higashiyama, S. and Barrandon, Y. (2013). Actin Filament Dynampacts Keratinocyte Stem Cell Maintainance EMBO Mol. Med. 5(4):640-53. Barrandon, Y., Grasset, N., Zaffalon, A., Gorostidi, F., Claudinot, S., DrozGeorget, S.L., Nanba, D., and Rochat, A. (2012). Capturing epidermal stemness for regenerative medicine. Semin. Cell Dev. Biol. 23(8):937-944. 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., and Sommer, L. (2012). Sox10 promotes the formation and maintenance of giant congenital naevi and melanoma. Nature Cell Biol. 14(8):882-90.

IBI - Institute of Bioengineering

Administrative Assistants Guex Nathalie Savioz-Dayer Emmanuelle

Generation of epidermis, hair follicles and sebaceous glands from a serially cultured progeny of a single multipotent stem cell isolated from the upper constant region of a whisker follicle of an adult GFP rat. Cells were transplanted onto the back skin of a DsRed mouse pup and biopsy was obtained and sectioned 90 days later. Bar = 100 microns.

EPFL School of Life Sciences - 2012 Annual Report

Dal Peraro Lab http://lbm.epfl.ch/

Matteo Dal Peraro graduated in Physics at the University of Padua in 2000. He obtained his Ph.D. in Biophysics at the International School for Advanced Studies (SISSA, Trieste) in 2004. He received postdoctoral training at the University of Pennsylvania (Philadelphia) under the guidance of Prof. M. L. Klein. He was nominated Tenure Track Assistant Professor at the EPFL School of Life Sciences in late 2007, where he is heading the Laboratory for Biomolecular Modeling (LBM), within the Interfaculty Institute of Bioengineering (IBI).

Matteo Dal Peraro Tenure Track Assistant Professor

Introduction

We use molecular modeling techniques combined with high-performance computing and integrated with experimental inputs to investigate biological systems, in particular their function emerging from structure. Our main targets are bacterial and viral systems and their mechanism of resistance towards natural and clinical drugs. We also develop new multiscale schemes and models to extend the power of current molecular simulations to tackle problems such as the assembly of large macromolecular complexes and the design of remedies for pathogenic infections.

Keywords

Computational biophysics, biochemistry, and structural biology, bacteria and viruses, multiscale molecular simulations; macromolecular assembly, high-performance computing.

Results Obtained in 2012

The seamless integration of computational techniques and biophysical/biochemical measurements is an emerging and efficient strategy to extend our knowledge of biological function at the molecular level shedding light on features that are often experimentally inaccessible. Biomolecules assemble and cooperate in large complexes to achieve specific biological tasks. Owing to their size and complexity, their structure and dynamics are difficult to be investigated at atomistic resolution with current in vitro/in vivo methods. To enhance the effective resolution of molecular architecture and mechanism, we have recently introduced a new approach called Protein Optimization Workbench - POW (available at http://lbm.epfl.ch/resources) that uses a Particle Swarm Optimization (PSO) search guided by experimental-based restraints to characterize protein quaternary structure. Importantly, within this scheme it is possible to take into account the native flexibility of each protein subunit as extracted from molecular dynamics simulations. This is a key ingredient for the prediction of biologically functional assemblies when, upon oligomerization, subunits explore activated states undergoing significant conformational changes. We expect that, with the ever-growing sampling capabilities of current molecular dynamics simulations, this hybrid strategy will offer in the future an un-

precedented, robust and efficient way to address molecular assembly through dynamic modeling. During this year, we have worked at extending and improving our framework with new optimization engines, new experimentally based fitness functions and new applications to molecular assembly. Following this same integrative dynamic strategy, we have completed the modeling of the transmembrane (TM) core of the PhoQP two-component system, a signaling complex essential for bacterial virulence and cationic antimicrobial peptide resistance (see Figure 1). PhoQ is the histidine kinase chemoreceptor of this tandem machine and assembles in a homodimer conformation spanning the bacterial inner membrane. We obtained an atomistic model of the key TM domain assembled by using molecular simulations, validated by experimental cross-linking data (Figure 1A,B). A concerted displacement of the TM helices at the periplasmic side is found to modulate a rotation at the cytoplasmic end (Figure 1C), supporting the transduction of the chemical signal through a combination of scissoring and rotational movement of the TM helices. This mechanism is the key to understanding how the chemical stimuli sensed by the periplasmic sensor domain trigger, via the relay of the HAMP domain, the histidine auto-phosphorylation and kinase/phosphatase activity at the cytoplasmic end (Figure 1D) (PLoS Comput Biol 9(1): e1002878). PhoQ is embedded in the inner bacterial membrane. Therefore, interaction with anionic lipids, such as phosphophatidylglycerol and cardiolipin, is supposed to play a key role in the activity of PhoQ TCS and other membrane proteins interacting with at the bacterial membrane. In particular, cardiolipins have a unique dimeric structure for which we have developed an ab initio parameterization for molecular simulation consistent with commonly used force fields. The proposed models will contribute to study the assembly of more realistic bacterial and mitochondrial membranes and the investigation of the role of cardiolipins for the biophysical and biochemical properties of membranes and membrane-embedded proteins (J. Chem. Theory Comput., 2013, 9 (1), 670).

EPFL School of Life Sciences - 2012 Annual Report

Selected Publications

T. Lemmin, C. Soto, G. Clinthorne, W.L. DeGrado, M. Dal Peraro (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. G. Palermo, M. Stenta, A. Cavalli, M. Dal Peraro, M. De Vivo (2013) Molecular Simulations Highlight the Role of Metals in Catalysis and Inhibition of Type II Topoisomerase, J. Chem. Theory Comput., 9 (2), 857. T. Lemmin, C. Bovigny, D. Lançon, M. Dal Peraro. (2013) Cardiolipin Models for Molecular Simulations of Bacterial and Mitochondrial Membranes, J. Chem. Theory Comput., 9 (1):670–678. T. Hofmeyer, S. Schmelz, M. T. Degiacomi, M. Dal Peraro, M. Daneschdar, A. Scrima, J. van den Heuvel, D.W. Heinz and H. Kolmar (2013) Arranged Sevenfold: Structural Insights into the C-Terminal Oligomerization Domain of Human C4b-Binding Protein, J. Mol. Biol. 425, 1302–1317

Team Members Postdoctoral Fellows Luciano Abriata Davide Alemani Marco Stenta PhD Students Martina Audagnotto Christophe Bovigny Matteo Degiacomi Hassan Pezeshki Thomas Lemmin Enrico Spiga Adnimistrative Assistant Marie-France Radigois

S. Ittig, B. Lindner, M. Stenta, P. Manfredi, E. Zdorovenko, Y.A. Knirel, M. Dal Peraro, G.A. Cornelis and U. Zähringer (2012) The Lipopolysaccharide from Capnocytophaga canimorsus Reveals an Unexpected Role of the Core-Oligosaccharide in MD-2 Binding, PLoS Pathogens, 8(5):e1002667. A. Lakkaraju, L. Abrami, T. Lemmin, B. Kunz, S. Blaskovic, A. Kihara, M. Dal Peraro, F.G. van der Goot FG (2012) Palmitoylated calnexin is a key component of the ribosome-translocon complex, EMBO J, 7;31(7):1823-35. J. Sgrignani, A. Magistrato, M. Dal Peraro, et al. (2012) On the active site of mononuclear B1 metallo beta-lactamases: a computational study, J. Comp-Aided Mol. Des. 26(4): 425-435. B. Blasco, M. Stenta, L. Alonso-Sarduy, G. Dietler, M. Dal Peraro, S. Cole, F. Pojer (2011) Atypical DNA recognition mechanism used by the EspR virulence regulator of Mycobacterium tuberculosis, Molecular Microbiology, 82:251–264. I. Iacovache, M. Degiacomi, L. Pernot, M. Schiltz, M. Dal Peraro, F. G. van der Goot (2011) Folding of the pore-forming toxin aerolysin is catalyzed by the Cterminal propeptide, PLoS Pathogens 7(7):e1002135. M. Stenta and M. Dal Peraro (2011) An introduction to quantum chemical methods applied to drug design, Frontiers in Bioscience, E3(1):1061-1078.

IBI - Institute of Bioengineering

E. Khurana, R. Devane, M. Dal Peraro, M.L., Klein (2011) Computational study of drug binding to the membrane-bound tetrameric M2 peptide bundle from influenza A virus, Biochimica et Biophysica Acta (BBA) - Biomembranes, 1808:530.

Assembly of the Transmembrane Domain of E. coli PhoQ Histidine Kinase. (A,B) Structural validation using disulfide cross-linking scanning of MD-derived conformation of TM1-TM2 tetramer (see structural model in D). In the inset the correlation between the cross-linking (1-efficiency) (in black) and the MD-averaged Cα distance measured for the TM model structure (in red) is reported. (C) The free energy landscape defined by sampling interhelical distances between TM1 C-termini and TM2 N-termini is reported. The conformational change observed in the unbiased MD simulations (orange points) occurs along a free energy valley, which connects a main equilibrium state (F0) and a high-energy conformation, which can be associated with relevant states during the signaling process (F1, ~5 kcal/mol higher in free energy). (D) PhoQ TM1-TM2 assembly equilibrated in an all-atom membrane bilayer. PLoS Comp. Biol., 9(1): e1002878.

EPFL School of Life Sciences - 2012 Annual Report

Deplancke Lab http://deplanckelab.epfl.ch/

Bart Deplancke received his M.Sc. in bio-engineering from Ghent University (Belgium), and his PhD 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 as a tenure-track assistant professor where his group 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 software company Genohm SA.

Bart Deplancke Tenure Track Assistant Professor

Introduction

The LSBG is developing and using high-throughput sequencing, microfluidics, large-scale yeast screening, and computational approaches to characterize the regulatory code in Drosophila and mammals and to examine how variations in this code affect molecular and organismal diversity.

Keywords

Systems biology, gene regulatory network, transcription, quantitative genetics, mouse, Drosophila, yeast, genetic engineering, adipogenesis, genomic variation.

Results 2012

Genomic variation and its impact on gene expression in Drosophila melanogaster - One of the principal challenges in current biology is to understand the relationship between genetic and phenotypic variation. Despite its excellent track record as a premier model to understand genome function, no genome-wide variation data beyond single-nucleotide variants and microsatellites are currently available for D. melanogaster. Our lab therefore set out to generate a comprehensive, nucleotide-resolution catalogue of variants of various types (single-nucleotide, multi-nucleotide, and structural variants) using high-throughput sequencing for 39 wild-derived inbred D. melanogaster lines. For this purpose, we used our in-house developed algorithm, PrInSeS-G, which uses de novo local assembly to detect both SNP and non-SNP variants (1 bp-~10 kb) at single nucleotide resolution (Massouras et al., Nature Meth., 2010). We identified more than 2.8 million SNPs across all analyzed inbred fly lines. In addition, we detected 0.6 million indels (i.e. insertions or deletions), and 0.2 million complex variants, together accounting for more than half of the observed genomic variation (see Figure below). We used our variant data to provide novel insights into the regulatory architecture of gene expression variation in adult flies by mapping cis-expression quantitative trait loci (cis-eQTLs) for more than 2,000 genes. Interestingly, most associations are sexspecific, providing evidence for a decoupling of the genomic, regulatory architecture between males and females.

Absolute quantification of transcription factors during cellular differentiation using multiplexed targeted proteomics - The accurate and reproducible quantification of proteins within pathways or biological networks has been described as an essential requirement in life sciences or clinical research (Picotti and Aebersold, Nature Methods, 2012). For example, the biochemical and regulatory properties of transcription factors (TFs) which control gene expression within gene regulatory networks are largely dictated by their cellular (nuclear) abundance. Deriving absolute TF values is therefore of crucial importance to understand TF function. However, accurate TF copy number information has been notoriously difficult to acquire, owing to the low cellular concentration of many TFs. Consequently, only a handful of studies have so far provided estimates on the absolute in vivo abundance of animal TFs. Among the novel proteomic approaches enabling targeted, quantitative analyses, Selected Reaction Monitoring (SRM) has emerged as a powerful, analytical tool. Over the course of the last three years, our lab, together with the EPFL Proteomics Core Facility, has therefore invested significant efforts to develop a novel and sensitive SRM-based mass spectrometry assay, allowing the simultaneous measurement of copy numbers of up to 10 TFs. We applied this approach to profile the levels of key TFs in our model system of interest: adipogenesis. Specifically, we revealed that TF abundance differs dramatically (from 250 to >300,000 copies per nucleus), but that their dynamic range during fat cell differentiation varies at most five-fold. In collaboration with the Naef lab here at the EPFL, we also formulated a genome-wide TF DNA binding model to explain the significant increase in binding sites of the adipogenic master regulator PPARÎł during the final differentiation stage, despite a concurrent saturation in PPARÎł copy number. This model provides unique, quantitative insights into the relative contributions of binding energetics, copy number, and chromatin state in dictating TF DNA occupancy profiles.

EPFL School of Life Sciences - 2012 Annual Report

Selected Publications

Team Members

Raghav*, S.K., Waszak*, S.M., Krier, I., Isakova, A., Gubelmann, C., Mikkelsen, T.S., and Deplancke, B. (2012). Integrative genomics identifies SMRT as a gatekeeper of early adipogenesis through the transcription factors C/EBPβ and KAISO, Molecular Cell, 46:335-50. (*, first author)

PhD Students Carine Gubelmann Alina Isakova Irina Krier Andreas Massouras Rachana Pradhan Sebastian Waszak

Simicevic*, J., Schmid*, A.W., Gilardoni*, P., Zoller, B., Raghav, S.K., Krier, I., Gubelmann, C., Lisacek, F., Naef, F., Moniatte#, M., Deplancke#, B. Absolute copy number analysis of transcription factors during cellular differentiation using multiplexed targeted proteomics, Nature Methods, in press. (*, first author; #, corresponding author)

Deplancke#, B., Verstrepen#, K.J. (2012). Variable outcome of mutations. Science, 335:44-45. (#, corresponding author) LeMartelot*, G., Canella*, D., Symul*, L., Migliavacca*, E., Gilardi, F., Liechti, R., Martin, O., Harshman, K., Delorenzi, M., Desvergne, B., Herr, W., Deplancke, B., Schibler, U., Rougemont, J., Guex#, N., Hernandez#, N., Naef#, F., and the CycliX consortium. (2012) Genome-wide profiling of RNA polymerase II occupancy, associated histone marks, and mRNA accumulation reveal transcriptional and post-transcriptional mechanisms underlying circadian gene expression, PLoS Biology, 10:e1001442. (*, first author; #, corresponding author)

Postdoctoral Fellows Monica Albarca Paola Gilardoni Sunil Raghav Petra Schwalie

Scientific Assistants Jean-Daniel Feuz Wiebke Westphal Administrative assistant Marie-France Radigois

Schröter, C., Ares, S., Morelli, L.G., Isakova, A., Hens, K., Soroldoni, D., Gajewski, M., Jülicher, F., Maerkl, S.J., Deplancke, B., Oates, A.C. (2012). Topology and dynamics of the zebrafish segmentation clock core circuit, PLoS Biology, 10:e1001364. Hens, K., Feuz, J., Isakova, A., Iagovitina, A., Massouras, A., Bryois, J., Callaerts, P., Celniker, S.E., Deplancke, B. (2011). Automated protein-DNA interaction screening of Drosophila regulatory elements. Nature Methods, 8:1065-70. Perspective: Ozdemir, A., Stathopoulos, A. (2011). Exciting times: bountiful data to facilitate studies of cis-regulatory control. Nature Methods, 8:1016-17. Gubelmann, C., Gattiker, A., Massouras, A., Hens, K., Decouttere, F., Rougemont, J., Deplancke, B. (2011). GETPrime: a gene- or transcript-specific primer generator for qPCR. Database, bar040.

IBI - Institute of Bioengineering

Tabuchi*, T.M., Deplancke*, B., Osato, N., Zhu, L.J., Barrasa, M.I., Harrison, M.M., Horvitz, H.R., Walhout, A.J.M., Hagstrom, K.A. (2011). Chromosomebiased binding and gene regulation by the C. elegans DRM complex. PLoS Genetics,7: e1002074, 2011. (*, first author)

Number of base pairs affected by variants discovered per fly inbred line, with lines ordered by depth of coverage (green dotted line). The line “Berkeley” is the reference line. SNPs are shown in black/grey, insertions in red, deletions in blue, and complex variants in orange. (From Massouras et al., 2012)

EPFL School of Life Sciences - 2012 Annual Report

Hubbell Lab http://lmrp.epfl.ch/

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.

Jeffrey A. Hubbell

Full Professor Dean of the School of Life Sciences Merck-Serono Chair in Drug Delivery

Introduction

We design novel materials for applications in medicine such as drug delivery, 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 biology.

Keywords

Biomaterials, tissue engineering, protein engineering, extracellular matrix, immunoengineering, vaccines, tolerogenic vaccines.

Results Obtained in 2012

Regenerative medicine - The laboratory made exciting advances in engineering matrix-bound morphogens for conjugation in biomaterial matrices for tissue repair and regeneration. We had previously developed a biochemical approach to incorporate morphogenetic proteins into surgical matrices such as fibrin, two of which have now entered into clinical testing in bone repair and chronic wound healing in more than 500 patients in collaboration with corporate partners. We have further determined that display of growth factors, for example for inducting angiogenesis, proximal to adhesion promoting domains can induce synergistic signaling between the ligated growth factor receptor and the ligated adhesion receptor. We have used this concept to design second generation variants of a number of growth factors, for example for inducing angiogenesis, skin repair and bone repair, such that the variants display super-affinity for extracellular matrix molecules. We have shown that these engineered growth factors can induce more potent tissue repair and regeneration then their wildtype homologs. Vaccines and immunotherapeutics - In collaboration with the Laboratory for Lymphatic and Cancer Bioengineering (Prof. M.A. Swartz), the laboratory demonstrated that nanoparticles can be used as a vaccine platform for targeting cells in the lymph nodes draining dermal site and

the lung, in addition to secondary lymphoid tissues in the nasal cavity. This, combined with advanced design of the polymeric nanoparticle surfaces, has enabled a new generation of vaccines, highly stable and very economical, for use in both the developing and the developed world. The team has demonstrated that ultra-small particles, smaller than biological particles, can be swept into the lymphatics within a few minutes of injection, drain to the lymph nodes, and are collected there for antigen presentation. Particularly favorable antigen conjugation schemes were developed for promotion of MHC I presentation and induction of potent CD8+ T cell responses, very impressive protection of mice versus influenza and Mycobacterium tuberculosis challenge was demonstrated, much more impressive than with free antigen delivered with the same adjuvants. From a materials perspective, our focus is on self-assembling block copolymers that form polymer micelles, upon the surface of which antigens are conjugated, or polymer vesicles, in the core of which antigens are encapsulated. Given that our interest is in inducing cellular immunity for chronic disease, our materials are designed to enhance mechanisms of antigen cross-presentation. 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 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. This results in clonal deletion of both CD4+ and CD8+ T cells. 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.

EPFL School of Life Sciences - 2012 Annual Report

Selected Publications

Martino, M.M., Briquez, P.S., Ranga, A., Lutolf, M.P. & Hubbell, J.A. Heparinbinding 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 (2013). Garcia-Cordero, J.L., Nembrini, C., Stano, A., Hubbell, J.A. & Maerkl, S.J. A high-throughput nanoimmunoassay chip applied to large-scale vaccine adjuvant screening. Integrative biology : quantitative biosciences from nano to macro 5, 650-658 (2013). Vasdekis, A.E., Scott, E.A., O’Neil, C.P., Psaltis, D. & Hubbell, J.A. Precision intracellular delivery based on optofluidic polymersome rupture. ACS nano 6, 7850-7857 (2012). Swartz, M.A., Hirosue, S. & Hubbell, J.A. Engineering approaches to immunotherapy. Sci Transl Med 4, 148rv149 (2012). Stano, A., Nembrini, C., Swartz, M.A., Hubbell, J.A. & Simeoni, E. Nanoparticle size influences the magnitude and quality of mucosal immune responses after intranasal immunization. Vaccine 30, 7541-7546 (2012). Scott, E.A. et al. Dendritic cell activation and T cell priming with adjuvant- and antigen-loaded oxidation-sensitive polymersomes. Biomaterials 33, 6211-6219 (2012). Hubbell, J.A. & Chilkoti, A. Chemistry. Nanomaterials for drug delivery. Science 337, 303-305 (2012). Velluto, D., Thomas, S.N., Simeoni, E., Swartz, M.A. & Hubbell, J.A. PEG-bPPS-b-PEI micelles and PEG-b-PPS/PEG-b-PPS-b-PEI mixed micelles as non-viral vectors for plasmid DNA: tumor immunotoxicity in B16F10 melanoma. Biomaterials 32, 9839-9847 (2011). Nembrini, C. et al. From the Cover: Nanoparticle conjugation of antigen enhances cytotoxic T-cell responses in pulmonary vaccination. Proc. Natl. Acad. Sci. U. S. A. 108, E989-997 (2011). Martino, M.M. et al. Engineering the growth factor microenvironment with fibronectin domains to promote wound and bone tissue healing. Sci Transl Med 3, 100ra189 (2011).

Team Members

Postdoctoral Fellows Amiguet-Vercher Sandra Brubaker Carrie De LaPorte Laura Dane Karen Engelhardt, Eva-Maria Kontos Stephane Kourtis Iraklis Larsson Mattias Lorentz Kristen Mahou Redouan Rice Jeffrey Sancho Oltra Nuria Scott Evan Alexander Tortelli Federico Wilson David Scott

PhD Students Ahmadloo Hamideh Briquez Priscilla Damo Martina De Titta Alexandre Eby Jackson Grimm Alizée Julier Ziad Panagiotou Vasiliki Raghunathan Sandeep Stano Armando Vardar Elif Master Students Djahanbakhsh Rafiee Sarah Liu Alexandra Sibylle Fallet Léa Maillat Hasani-Sadrabadi Mohammad Mahdi Bachelor Students Kayser Stephanie Leahu Teodor Marchand Cynthia Internships Marion Boursier, France David Allen Roberts, USA Other Scientific Personnel Frey Peter Wandrey Christine Simeoni Eleonora Dessibourg Céline Quaglia Xavier Pasquier Miriella

IBI - Institute of Bioengineering

Administrative Assistant Bonzon Carol Anne

Antigen-specific tolerance in a mouse diabetes model. Upper left: a normal islet, with insulin in red. Upper right, a rejecting islet, with T cell in green; islet destruction is profound. Lower left: a rejecting islet in an animal in which the tolerogenic antigen is provided as a wild-type, free protein injected iv. Lower right: islet rejection is completely blocked by tolerizing with the same antigen, however fused to an antibody fragment that binds to erythrocytes.

EPFL School of Life Sciences - 2012 Annual Report

Jensen Lab http://jensenlab.epfl.ch/

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 Evolutionary Biology and Biological Anthropology, respectively, and was co-advised by Michael Nachman and Brian Charlesworth. Prof. Jensen earned his PhD in Molecular Biology & Genetics at Cornell University in 2006, co-advised by Charles Aquadro and Carlos Bustamante. He did his postdoc work as an NSF Bioinformatics Fellow at UCSD and UC Berkeley advised by Doris Bachtrog, Peter Andolfatto, and Rasmus Nielsen. He founded the Jensen Lab at the University of Massachusetts in 2009, and relocated the lab to EPFL in the Fall of 2011.

Jeffrey Jensen Tenure Track Assistant Professor

Introduction

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 natural populations, and between species. Under this over-arching theme, specific projects range from the development of Bayesian statistics for the estimation of demographic parameters, to Neanderthal genomics, to directly inferring the distribution of fitness effects of new mutations from experimental yeast data. Lab members work on both applied and theoretical problems in fields ranging from population genomics to medical genetics.

Keywords

Population genetics, molecular evolution, computational biology.

Results Obtained in 2012

In the molecular age, the relationship between gene sequence and selective effect has provided the fundamental link between genotype and phenotype with the notion of Darwinian fitness. Yet, despite great strides in molecular technologies, remarkably little is known about the genetic basis of phenotypic evolution, or of how selective pressures act to shape phenotypes. And thus questions fundamental to all of evolution biology remain largely unanswered: How many sites in the genome encode functions that are strongly maintained? Do most adaptive changes have a large effect on fitness, or is adaptation accomplished through many small steps? How many changes underlie adaptation to a novel selective pressure? And, indeed, what proportion of new, segregating, and fixed mutations are deleterious, neutral or beneficial? While lab members work on a variety of topics spanning population genetic theory, ecological genetics, and medical genomics, all united by the above questions - we highlight here three general themes of current focus.

Statistical inference in population genetics This line of research aims to identify adaptively important regions of the genome in an unbiased manner based on patterns of genetic variation - offering a genotype-first approach to identifying the action of positive selection. We design maximum likelihood and approximate Bayesian based methodology, with an interest towards both the identification of specific beneficial mutations as well as the estimation of the distribution of fitness effects - all with a particular focus on distinguishing selective from demographic forces. The evolution of cryptic coloration In collaboration with the Hoekstra Lab (Harvard University), we seek to investigate the evolutionary consequences of cryptic coloration in wild mouse populations. Pelage of the deer mouse, Peromyscus maniculatus, closely matches its substrate throughout its range, driven by natural selection for crypsis. This project takes advantage of a system in which the ecological context of phenotypic variation is well understood, and in which the genetic basis of the quantitative phenotype is largely controlled by a single gene of major effectâ&#x20AC;&#x201D;Agouti. This system represents an ideal scenario in which to address the long-standing debate regarding the means by which selection shapes natural populations following the advent of a novel selective pressure. Experimental dissection of fitness landscapes In collaboration with Dan Bolon (University of Massachusetts Medical School), we seek to systematically determine the fitness effects of all individual single-codon substitutions in yeast, utilizing a newly developed high throughput sequencing technology. Rather than drawing inference from fixed or polymorphic differences as in Peromyscus above, this project seeks to measure selection coefficients directly from new mutations. Specifically, we can for the first time empirically describe the relative proportions of deleterious, neutral, and beneficial mutations.

EPFL School of Life Sciences - 2012 Annual Report

Selected Publications

Shulha, H.P.*, J. Crisci*, D. Reshetov*, J.S. Tushir*, I. Cheung, R. Bharadwaj, H.J. Chou, I. Houston, C.J. Peter, A.C. Mitchell, W-D. Yah, R.H. Myers, J-f. Chen, T.M. Preuss, E. Rogaev#, J.D. Jensen#, Z. Weng#, and S. Akbarian#, 2012. Humanspecific histone methylation signatures at transcription start sites in prefrontal neurons. PLoS Biology 10(11): e1001427. * authors contributed equally, #corresponding authors Pavlidis, P., J.D. Jensen, W. Stephan, and A. Stamatakis, 2012. A critical assessment of story-telling: GO categories and the importance of validating genomic scans. Molecular Biology & Evolution 29(10): 3237-48. Domingues, V., Y.-P. Poh, B. Peterson, P. Pennings, J.D. Jensen, and H.E. Hoekstra, 2012. Evidence of adaptation from ancestral variation in young populations of beach mice. Evolution 66: 3209-23. Crisci, J., Y.-P. Poh, A. Bean, A. Simkin, and J.D. Jensen, 2012. Recent progress in polymorphism-based population genetic inference. Journal of Heredity 103: 287-96. Sinha, P., A. Dincer, D. Virgil, G. Xu, Y.-P. Poh, and J.D. Jensen, 2011. On detecting recent adaptive events using single genomes. Front. Gene. 2: 85-90. Crisci, J., A. Wong, J. Good, and J.D. Jensen, 2011. On characterizing adaptive events unique to modern humans. Genome Biology & Evolution 3: 791-8. Jensen, J.D. and D. Bachtrog, 2011. Characterizing the influence of effective population size on the rate of adaptation: Gillespie’s Darwin Domain. Genome Biology & Evolution 3: 687-701.

Team Members Senior Scientists Greg Ewing Anna Ferrer-Admetlla Matthieu Foll Postdoctoral Fellows Claudia Bank Lisha Mathew Yu-Ping Poh Cornelia Pokalyuk Nick Renzette Daniel Wegmann PhD Students Angela Bean Jessica Crisci Louise Ormond Alfred Simkin Master Student Hyunjin Shim Bioinformatician Shivani Mahajan Administrative Assistant Sophie Barret

IBI - Institute of Bioengineering

Hietpas, R.T., J.D. Jensen, and D.N.A. Bolon, 2011. Experimental dissection of a fitness landscape. Proc Natl Acad Sci USA 108: 7896-901.

The observed distribution of fitness effects of mutations observed directly from experimental studies in yeast (described in project III). For comparison, a cartoon of historically proposed population genetic models is given above. As shown – empirical observations give a remarkable fit to the Nearly-Neutral Theory of molecular evolution.

EPFL School of Life Sciences - 2012 Annual Report

Lutolf Lab http://lscb.epfl.ch/ Matthias Lutolf was trained as a Materials Engineer at ETH Zurich where he also carried out his Ph.D. studies on the development of a novel class of biomolecular materials for tissue engineering (awarded with ETH medal, 2004). From 2005 to 2007 and supported by fellowships from the Swiss National Science Foundation and Leukemia and Lymphoma Society, Lutolf was a Postdoc in the laboratory of Helen Blau at Stanford University, where he studied microenvironmental (â&#x20AC;&#x2DC;nicheâ&#x20AC;&#x2122;) regulation of adult stem cells. In 2007, Lutolf received a European Young Investigator (EURYI) award to start up his independent research at EPFL. Lutolf is associate editor of the new RSC Journal Biomaterials Science and editorial board member of the NPC Journal Scientific Reports.

Matthias P. Lutolf Tenure Track Assistant Professor

Introduction

Adult stem cells rapidly lose their potential when grown outside of their natural microenvironment, or niche, posing a substantial hurdle for their efficient clinical use. By interfacing stem cell biology, biomolecular engineering and microtechnology, a major goal in the Lutolf lab is to elucidate how niche signals control the behavior of adult stem cells, in particular hematopoietic stem cells. We address this question by developing functional artificial niches as tools to probe the biochemical and biophysical stem cell-niche cross-talk at the single cell level and in high-throughput.

Keywords

Stem cells, self-renewal, niche, single cell analysis, hydrogel engineering, microfluidics.

Results Obtained in 2012

One pertinent question the lab has been addressing is the regulation of mouse hematopoietic stem cell (HSC) fate decision-making. Despite a remarkable extent of knowledge regarding HSC biology, the mechanisms governing the long-term maintenance of their function are poorly understood. Compelling evidence shows that the niche plays the key role in regulating HSC function in vivo, but just how the stem cells remain quiescent and, upon activation, integrate the multiple niche signaling cues to either undergo self-renewal or commitment remains unknown. We have been tackling this key question by first identifying a minimal functional artificial HSC niche, i.e. by discovering candidate extrinsic factors that can influence in vitro HSC maintenance without loss of in vivo function, and then exploring their mechanisms of action. For example, a micro-engineered platform consisting of soft hydrogel microwell arrays with modular stiffness was developed where individual microwells can be functionalized with combinations of candidate biomolecules spotted by robotic technology. Using this novel platform, it is pos-

sible to probe the effect of key microenvironmental perturbations on the fate of virtually any (stem) cell type at single cell level and in high-throughput. We have successfully validated this system by studying niche-regulation of several adult stem cell populations including neural stem cells, mesenchymal progenitor cells and HSCs. Single mouse long-term HSCs (LT-HSC) were analyzed by time-lapse microscopy and showed distinct in vitro clonal proliferation kinetics in response to putative niche signaling cues. These experiments showed that specific single cell growth kinetics could be correlated with their long-term repopulation potential, the only definitive test of HSC function. To understand whether daughter cells generated by cell division of a mother LT-HSC keep their long-term multipotency or have committed, we utilized single cell multi-gene expression analysis to identify gene expression profiles associated with the most primitive stem and progenitor cell states in the mouse bone marrow. We identified several genes involved in regulating cell-cell interactions (e.g. Junctional adhesion molecule C, JAM3, a component of tight junctions) whose expression was significantly upregulated in LT-HSC versus ST-HSC and multipotent progenitors. We showed that these proteins are expressed at the cell surface and can be used as additional phenotypic markers of live LT-HSCs. We then used multigene expression analysis in combination with micromanipulation to analyze paired daughter cells of dividing single HSCs. In vitro divisions under serum-free conditions supplemented with well-known hematopoietic cytokines, that is, in the absence of a functional niche, resulted in significant downregulation of the key niche interaction genes. Interestingly, several of the analyzed genes appear to be differentially expressed in the two paired daughter cells suggesting asymmetric divisions. LT-HSC culture on artificial niches displaying the identified cell-cell interaction proteins show delayed cell cycle entry and maintenance of long-term blood reconstitution.

EPFL School of Life Sciences - 2012 Annual Report

Selected Publications

Roccio M, Schmitter D, Knobloch M, Okawa Y, Sage D, Lutolf MP*, Predicting stem cell fate changes by differential cell cycle progression patterns, Development, 140 (2): 459-70 (2012) Kobel S, Burri O, Griffa A., Girotra M, Seitz A, Lutolf MP*, Automated analysis of single cells in microfluidic traps, Lab on a Chip, 12 (16): 2843-9 (2012) Bichsel C, Gobaa S, Kobel S, Secondini C, Thalmann GN, Cecchini MG, Lutolf MP*, Diagnostic microchip to assay 3D colony-growth potential of captured circulating tumor cells, Lab on a Chip, 12 (13): 2313-6 (2012) Vannini N, Roch A, Griffa A, Naveiras O, Kobel S, Lutolf MP*, Identification of in vitro HSC fate regulators by differential lipid raft clustering, Cell Cycle, 11(8): 1535-43 (2012) Roccio M, Gobaa S, Lutolf MP*, High-throughput fate analysis of single neural stem cells in microarrayed artificial niches, Integrative Biology, 4 (4), 391-400 (2012) Pataky K, Braschler T, Negro A, Renaud P, Lutolf MP*, Brugger J*, Microdrop printing of soft matter into 3D tissue-like geometries, Advanced Materials, 24(3): 391-396 (2012) Gobaa S, Hoehnel S, Roccio M, Negro A, Kobel S, Lutolf MP*, Artificial niche microarrays for probing stem cell fate in high-throughput, Nature Methods, 8 (11): 949-55 (2011)

Team Members Postdoctoral Fellows Steffen Cosson Nikolce Gjorevski Samy Gobaa Olaia Naveiras Adrian Ranga Nicola Vannini

PhD Students Simone Allazetta Nathalie Brandenberg Mukul Girotra Sylke Hoehnel Laura Kolb Andrea Negro Yuya Okawa Adrian Ranga Aline Roch Yoji Tabata Master Student Jo’an Bardy Technician Vasco Campos Administrative Assistant Maria Fernandes Coelho

Kobel S, Lutolf MP*, Biomaterials meet Microfluidics: Building the next generation of artificial niches, Current Opinion in Biotechnology, 2, pp. 690-697 (2011) Ehrbar M*, Sala A, Lienemann P, Rizzi SC, Weber FE and Lutolf MP*, Elucidating the role of matrix stiffness in 3D cell migration and remodeling, Biophysical Journal, 100, 284-293 (2011)

IBI - Institute of Bioengineering

Allazetta S, Cosson S, Lutolf MP*, Programmable microfluidic patterning of protein gradients on hydrogels, Chemical Communications, 47 (1): 191-193 (2011)

Automated high-throughput screening of cell fate in near-physiological 3D artificial microenvironments (‘niches’). (A) A materials library is synthesized which is amenable to robotic liquid dispensing. (B) Cell-containing gel precursors are microarrayed as 3D ‘spots’ into 1536-well plates. (C) Upon cell culture, colony formation and phenotypes in 3D can be readily visualized, quantified to reveal novel regulatory mechanisms.

EPFL School of Life Sciences - 2012 Annual Report

Naef Lab http://naef-lab.epfl.ch/

Felix Naef studied theoretical physics at the ETHZ and obtained his PhD from the EPFL in 2000. He received postdoctoral training at the Center for Studies in Physics and Biology at the Rockefeller University (NYC). His research focuses on the study of biomolecular oscillators, modeling, and transcription regulation. He was promoted as Associate Professor at the EPFL School of Life Sciences in 2012 and is currently a member of the Institute of Bioengineering (IBI).

Felix Naef

Associate Professor

Introduction

Our lab is interested in quantitative, computational, and systems biology. We work on various problems including circadian biology, developmental patterning, gene expression networks, and stochastic transcription in single cells. To study these systems we combined theoretical, computational and experimental methods.

Keywords

Gene regulation, circadian transcription, chronobiology, circadian clock precision, fluctuations and bursting in gene expression.

Results Obtained in 2012

Circadian gene regulation in mouse liver. Interactions of cell-autonomous circadian oscillators with diurnal cycles govern the temporal compartmentalization of cell physiology in mammals. To understand the transcriptional and epigenetic basis of diurnal rhythms in mouse liver genomewide, we generated temporal DNA occupancy profiles by RNA polymerase II (Pol II), as well as profiles of the histone modifications H3K4me3 and H3K36me3. We used these data to quantify the relationships of phases and amplitudes between different marks. We found that rhythmic Pol II recruitment at promoters rather than rhythmic transition from paused to productive elongation underlies diurnal gene transcription, a conclusion further supported by modeling. Moreover, Pol II occupancy preceded mRNA accumulation by three hours, consistent with mRNA half-lives. Both methylation marks showed that the epigenetic landscape is highly dynamic and globally remodeled during the 24 hour cycle. While promoters of transcribed genes had trimethylated H3K4 even at their trough activity times, trimethylation levels reached their peak, on average, one

hour after Pol II. Meanwhile, rhythms in tri-methylation of H3K36 lagged transcription by three hours. Finally, modeling profiles of Pol II occupancy and mRNA accumulation identified three classes of genes: one showing rhythmicity both in transcriptional and mRNA accumulation, a second class with rhythmic transcription but flat mRNA levels, and a third with constant transcription but rhythmic mRNAs. The latter class emphasizes widespread temporally gated post-transcriptional regulation in the mouse liver. Stochastic transcription in single mammalian cells in response to endogenous stimuli. Mammalian genes are often transcribed discontinuously in the form of short bursts of RNA synthesis followed by longer silent periods. However, how these ‘on’ and ‘off’ transitions, together with the burst sizes, are modulated in single cells to increase gene expression upon stimulation is poorly characterized. By combining single cell time-lapse luminescence imaging with stochastic analysis of the time traces, we quantified the transcriptional responses of the endogenous connective tissue growth factor (ctgf) gene to different physiological stimuli, serum and TGF-b1. Both stimuli caused an acute increase in bursting. While TGF-b1 showed prolonged transcriptional activation, serum stimulation resulted in a large and temporally tight first burst of transcription, followed by a refractory period in the range of hours. Our study thus reveals how different physiological stimuli can trigger kinetically distinct transcriptional responses on the same gene promoter.

EPFL School of Life Sciences - 2012 Annual Report

Selected Publications

G. Le Martelot, D. Canella, L. Symul, E. Migliavacca, F. Gilardi, R. Liechti, O. Martin, K. Harshman, M. Delorenzi, B. Desvergne, W. Herr, B. Deplancke, U. Schibler, J. Rougemont, N. Guex, N. Hernandez, F. Naef, “Genome-Wide RNA Polymerase II Profiles and RNA Accumulation Reveal Kinetics of Transcription and Associated Epigenetic Changes During Diurnal Cycles”. PLoS Biol 10, e1001442 (2012). J. Morf, G. Rey, K. Schneider, M. Stratmann, J. Fujita, F. Naef, U. Schibler, “Coldinducible RNA-binding protein modulates circadian gene expression posttranscriptionally”, Science 338, 379 (2012). M. Stratmann, D. Suter, N. Molina, F. Naef, U. Schibler, “Circadian Dbp transcription relies on highly dynamic BMAL1-CLOCK interaction with E-boxes and requires the proteasome”, Molecular Cell, 48, 277 (2012). D. M. Suter, N. Molina, D. Gatfield, K. Schneider, U. Schibler*, F. Naef*, “Mammalian Genes Are Transcribed with Widely Different Bursting Kinetics”, Science 332, 472 (2011).

Team Members Postdoctoral Fellows Teresa Ferraro Nacho Molina Bhaswar Ghosh Jingkui Wang PhD Students Johannes Becker Jonathan Bieler Simon Blanchoud Rosamaria Cannavo Julia Cajan Jerome Mermet Damien Nicolas Jonathan Sobel Laura Symul Benjamin Zoller Administrative Assistant Sophie Barret

G. Rey, F. Cesbron, J. Rougemont, H. Reinke, M. Brunner, F. Naef*, “GenomeWide and Phase-Specific DNA-Binding Rhythms of BMAL1 Control Circadian Output Functions in Mouse Liver”, Plos Biology 9, (2011). J. Bieler, C. Pozzorini, F. Naef*, “Whole-embryo modeling of early segmentation in Drosophila identifies robust and fragile expression domains”, Biophys J 101, 287 (2011).

IBI - Institute of Bioengineering

I. Gyurjan, B. Sonderegger, F. Naef, D. Duboule, “Analysis of the dynamics of limb transcriptomes during mouse development.” BMC Dev Biol. 11(1):47 (2011).

Figure 1. Pol II, H3K4me3, and H3K36me3 genomic profiles of core circadian clock genes measured around the clock. A. The density profiles of Pol II (red), H3K4me3 (green), and H3K36me3 (blue) are indicated for the Bmal1 gene, with the thin lines above the profiles indicating the position-specific temporal maxima. The gene structure (RefSeq transcripts) is shown below the panel. The dashed lines starting with a circle and the arrows represent minima and maxima, respectively, of gene body Pol II occupancy (red), promoter H3K4me3 occupancy (green), and gene body H3K36me3 occupancy (blue), as estimated by cosine fits. Maximal in Pol II, H3K4me23, and H3K36me3 densities are reached at ZT21, ZT23, and ZT2. B. As in A, but for the RevErba(Nr1d1) gene. Maximal Pol II, H3K4me23, and H3K36me3 densities are reached at ZT6, ZT9, and ZT9.

EPFL School of Life Sciences - 2012 Annual Report

Swartz Lab http://swartz-lab.epfl.ch/

Melody Swartz is a Professor and Director of the Institute of Bioengineering (IBI), with a joint appointment in Cancer Research (ISREC). She trained at Johns Hopkins (BS) and M.I.T. (PhD) in Chemical Engineering, and Brigham & Women’s Hospital (postdoc). She spent four years as Asst. Professor at Northwestern Univ. before moving to the EPFL in 2003. Her research focuses on the lymphatic system, integrating several fields to elucidate the functional regulation and immunobiology of lymphatic vessels. In 2012, she was named a MacArthur Fellow.

Melody A. Swartz Full Professor Director of IBI

Introduction

The lymphatic system is an important regulator of tissue homeostasis including fluid and solute balance, inflammation, and immunity. We are fascinated by this network of vessels that drain fluid, antigens, and cells from the periphery, through the lymph nodes, and back into the blood. By uncovering its complex roles in immunity and tolerance, we hope to understand – and ultimately manipulate – its participation in cancer progression and metastasis. Thus, we aim to build a more comprehensive understanding of how various aspects of lymphatic function are coupled, as well as to develop novel therapeutic strategies to target lymphatic vessels for immunomodulation, e.g., in vaccine design and cancer immunotherapy.

Keywords

Lymphatic vessels, immunoengineering, tumor microenvironment, lymph node metastasis, interstitial flow, mechanobiology, biotransport phenomena.

Results Obtained in 2012

In 2012, we demonstrated an essential role of peripheral lymphatics in eliciting the timing and the quality of the immune response (Thomas et al, J. Immunol). Specifically, we found that humoral (antibody) responses, but not cellular immune responses, critically depends on dermal lymphatic drainage, and furthermore that adaptive tolerance following challenge could not be induced without lymphatics. We suggest that lymphatic drainage of fluid and antigens is critical to B cell immunity and maintenance of peripheral tolerance. We also discovered a new mechanism by which lymphatic endothelial cells (LECs) themselves can promote immunological tolerance, specifically in the context of cancer (Lund et al, Cell Rep.). In collaboration with Stephanie Hugues’ lab at the University of Geneva, we demonstrated that tumor-associated LECs can scavenge tumor antigens and cross-present them to T cells for subsequent deletional

tolerance. In this way, lymphatic vessels may limit the efficacy of immunotherapy aimed to activate host immunity against the tumor. These studies, among other recent reports, are helping to define the immunomodulatory roles of lymphatic vessels as well as the immunological functions of inflammationassociated lymphangiogenesis. Of course, these results bring interesting implications for cancer immunotherapy strategies. In collaboration with Jeff Hubbell’s lab (EPFL), we are finding improved cancer vaccine efficacy when targeted specifically to tumor-draining lymph nodes as compared with non-draining lymph nodes, presumably by replacing the tumor-primed, tolerogenic milieu of the draining lymph node with immune activation signals. In other areas of lymphatic-targeting nanoparticle vaccines, we have demonstrated that nanoparticle coupling of adjuvant gives more efficacy with lower doses, presumably because it concentrates the signal in the lymph node. We have also demonstrated similar effects of nanoparticlecoupled vaccines particularly when delivered to the lung, where mucosal immunity is enhanced with lower vaccine doses. Also in 2012, we continued to bring new fundamental understanding of how the lymphatic microenvironment affects interstitial function by virtue of driving interstitial flow. We explored how dendritic cells (DCs) interpret different types of cues in such a biomechanically complex environment, and demonstrated the importance of flow-mediated signals on lymphatic function; namely, its active transport mechanisms for water, solutes, proteins, and nanoparticles. We also furthered our understanding of autologous chemotaxis, a concept that our laboratory has put forth, in a model of glioma with CXCL12/CXCR4 signaling (Munson et al, Cancer Res.).

EPFL School of Life Sciences - 2012 Annual Report

Selected Publications

JM Munson, R.V. Bellamkonda, and M.A. Swartz (in press). Interstitial flow in a 3D microenvironment increases glioma invasion by a CXCR4-dependent mechanism. Cancer Res. (epub ahead of print). MA Swartz, S Hirosue, JA Hubbell (2012). Engineering approaches to immunotherapy. Sci. Transl. Med. 4:148rv9. SN Thomas, JM Rutkowski, M Pasquier, EL Kuan, K Alitalo, GJ Randolph, and MA Swartz (2012). Weak humoral immunity and acquired autoimmunity in mice with impaired dermal lymphatic drainage. J. Immunol. 189(5):2181-90. AW Lund, F.V. Duraes, S. Hirosue, S.N. Thomas, C. Nembrini, S. Hugues, and M.A. Swartz (2012). Tumor VEGF-C promotes immune tolerance and tumor antigen cross-presentation by lymphatics. Cell Reports 1(3): 191 - 199. Comment: Cancer Res. 72:1589-90, 2012; named “Best of Cell Reports 2012”. MA Swartz and AW Lund (2012). Lymphatic and interstitial flow in the tumor microenvironment: Linking tumor mechanobiology with lymph node immunity. Nature Rev. Cancer 12:210-219. M Ballester, C Nembrini, N Dhar, A de Titta, C de Piano, M Pasquier, E Simeoni, AJ van der Vlies, JD McKinney, JA Hubbell, and MA Swartz (2011). Nanoparticle conjugation and pulmonary delivery enhance the protective efficacy of Ag85B and CpG against tuberculosis. Vaccine 29:6959– 6966. U Haessler, M Pisano, M Wu, and MA Swartz (2011). Dendritic cell chemotaxis in 3D under defined chemokine gradients reveals differential response to CCL21 and CCL19. Proc. Natl. Acad. Sci. U.S.A. 108:5614-18. AC Shieh, HA Rozansky, B Hinz and MA Swartz (2011). Tumor cell invasion is promoted by interstitial flow-induced matrix priming by stromal fibroblasts. Cancer Res. 71(3):790-800.

Team Members Postdoctoral Fellows Dan Bonner Francesca Capotosti Catherine Card Witold Kilarski Amanda Lund Alexandra Magold Jennifer Munson Scott Ryan Oliver Edward Phelps

PhD Students Marie Ballester Alexandre de Titta Manuel Fankhauser Esra Güç Laura Jeanbart Iraklis Kourtis Marco Pisano Sandeep Raghunathan Marcela Rincon-Restrepo Valentina Triacca Ingrid van Mier Efthymia Vokali Master’s Students Sabrina Riedl (Erasmus) Lambert Potin Iro Oikonomidi Research Associate Sachiko Hirosue Technicians Véronique Borel Patricia Corthésy Henrioud Pasquier Miriella Interns/Trainees Luis Alonso Natacha Bordry Kathryn Hockemeyer Renata Mezyk-Kopecm PhD Le Thanh Tu Nguyen Amy Sessions Katherine Tschudi

IBI - Institute of Bioengineering

Administrative Assistant Ingrid Margot

In vitro 3D lymphangiogenesis assay showing lymphatic endothelial cells sprouting from dextran beads embedded within a fibrin gel (Image by Esra Guç).

EPFL School of Life Sciences - 2012 Annual Report

Wurm Lab http://lbtc.epfl.ch/

Florian M. Wurm obtained his PhD in Genetics at the University of Giessen, Germany. After having worked for 5 years at Hoechst AG in Marburg, he joined Harvard Medical School and then in 1986 he joined Genentech Inc., San Francisco, holding leading positions in Process Sciences. Since 1995 he is professor of Biotechnology at the EPFL, and he was appointed Visiting Professor at Jinan University in Guangzhou, China in 2008. He has published over 200 scientific papers and holds several patents. He is the founder and CSO of ExcellGene SA, a Swiss biotechnology company in Monthey, Valais.

Florian M. Wurm Full Professor

Introduction

Research at the LBTC is situated on the crossroads between biology and engineering, and it addresses the expression of recombinant proteins (r-proteins) from suspension cultures of mammalian cells, which is the major approach to therapeutic protein production. Mammalian cells are the most versatile and productive system for the manufacture of r-proteins. The major goal of the LBTC is the development of novel and/or improved tools for gene transfer to cultured mammalian cells and subsequent high-level expression of r-proteins from such cells in new and scalable production systems (bioreactors).

Keywords

Recombinant protein expression, mammalian cell culture, orbital shaking bioreactor, bioprocess control, gene transfer, DNA integration, stable cell line development, HEK293, CHO, insect cell culture.

Results Obtained in 2012

We are investigating two major thematic areas: (1) gene delivery, integration and expression in animal cells and their respective impacts on the host cells physiology and genetics (2) orbital shaking technology and novel bioreactor systems. The main results obtained in 2012 are summarized below. Transient gene expression and stable transgene integration. The transient transfection approach allows the expression of a fully glycosylated r-protein at high titres (up to 1 g/L for IgGs) only 1-2 weeks after gene cloning. Through a detailed analysis of the cellular uptake and disassembly of PEI-DNA complexes we were able to increase r-protein productivity from transiently transfected cells by maximizing the relative amount of plasmid DNA delivered at transfection. This knowledge allowed us to develop an optimized transfection protocol that sensibly reduces the overall production costs for r-proteins by transient expression. In collaboration with Prof. H.A. Klok, we evaluated a promising new polylysine-based polymer for gene delivery

in animal cells. In collaboration with Prof. Y. Tsybin, we characterized recombinant antibodies produced by transient gene expression and compared the glycosylation patterns with the same protein produced in stable cell lines. Stable integration of recombinant genes into the genome of a host cell was studied in the widely-used cell line Chinese hamster ovary (CHO). We investigated the cytogenetics of CHO-derived stable cell lines generated using different DNA delivery techniques, including transposonand lentivirus-mediated gene integration. Understanding transgene integration will allow us to develop strategies to prevent the widely-observed phenomenon of gene silencing, which lowers productivity in stable cell lines over time. We demonstrated that transposon-mediated DNA delivery is a very efficient method to obtain high-producing CHO cell lines, superior to cell lines generated by standard transfection. More recently, we extended our research to insect cell-based expression systems, and we are developing nonviral, scalable gene delivery methods for these hosts. The orbitally shaken bioreactor (OSR) technology for mammalian cell cultivation, designed in our lab has been scaledup to 1000 L. The fluid dynamics in orbitally shaken cylindrical vessels (with nominal volumes from 50 mL to 250 L) were studied in collaboration with Prof. A. Quarteroni (Chair of Modelling and Scientific Computing) and Dr. M. Farhat of the Hydraulic Machines Laboratory. A fluid dynamics model of the OSRs could be determined and tested. Further characterization of the OSR system and confirmation of the numerical simulation is ongoing. Overall, our research provided useful insights for understanding cell cultivation in suspension, gene integration and protein expression. These studies are of interest both in basic cellular biology and for their application in pharmaceutical biotechnology for the production of recombinant therapeutic proteins. Several products (tools and bioreactor systems) are on the market since a number of years that have been inspired, invented and generated by and with contributions of LBTC scientists.

EPFL School of Life Sciences - 2012 Annual Report

Selected Publications

Michel PO, Degen C, Hubert M, Baldi L, Hacker DL, Wurm FM. (2012) A NanoDrop-based method for rapid determination of viability decline in suspension cultures of animal cells. Anal Biochem 430(2):138–40. Kadlecova Z, Baldi L, Hacker D, Wurm FM, Klok H-A. (2012) Comparative study on the in vitro cytotoxicity of linear, dendritic, and hyperbranched polylysine analogues. Biomacromolecules 13(10):3127–37. Rajendra Y, Kiseljak D, Manoli S, Baldi L, Hacker DL, Wurm FM. (2012) Role of non-specific DNA in reducing coding DNA requirement for transient gene expression with CHO and HEK-293E cells. Biotechnol Bioeng 109(9):2271–8. Zagari F, Jordan M, Stettler M, Broly H, Wurm FM. (2012) Lactate metabolism shift in CHO cell culture: the role of mitochondrial oxidative activity. N Biotechnol 30(2):238-45. Kadlecova Z, Nallet S, Hacker DL, Baldi L, Klok H-A, Wurm FM. (2012) Poly(ethyleneimine)-Mediated Large-Scale Transient Gene Expression: Influence of Molecular Weight, Polydispersity and N-Propionyl Groups. Macromol Biosci 12(5):628–36. Rajendra Y, Kiseljak D, Baldi L, Hacker DL, Wurm FM. (2012) Reduced glutamine concentration improves protein production in growth-arrested CHODG44 and HEK-293E cells. Biotechnol Lett 34(4):619–26.

Team Members Senior Scientists Lucia Baldi David Hacker

Postdoctoral Fellow Patrik Olavi Michel PhD Students Sowmya Balasubramanian Divor Kiseljak Dominique Monteil Yashas Rajendra Xiao Shen Francesca Zagari Master Students Archita Chaudhary Fabrizio De Angelis Saroj Ghimire Bachelor/Project students Christophe Degen Ana Pitol Garcia Anne Catherine Portman Laboratory Support Veronika Knapkova

Tissot S, Michel PO, Hacker DL, Baldi L, De Jesus M, Wurm FM. (2012) k(L)a as a predictor for successful probe-independent mammalian cell bioprocesses in orbitally shaken bioreactors. N Biotechnol 29(3):387–94.

Trainees Mélanie Hubert Mélissa Vona

Discacciati M, Hacker D, Quarteroni A, Quinodoz S, Tissot S, Wurm FM. (2012) Numerical simulation of orbitally shaken viscous fluids with free surface. Int J Numer Meth Fluids 71(3): 294-315.

Technical Assistants Virginie Bachmann Ione Gutscher

IBI - Institute of Bioengineering

Administrative Assistant Fabienne Rudin

We studied the structure-activity relationship for various lots of linear poly(ethyleneimine) (PEI), a commonly used transfection reagent for the production of r-proteins by transient gene expression. PEI’s polydispersity and N-propionyl side groups contribute to its high transfection efficiency.

Co-affiliated Research Groups EPFL School of Life Sciences - 2012 Annual Report

Aminian Lab

- coaffiliated

http://lmam.epfl.ch/ Kamiar Aminian received his PhD degree in biomedical engineering in 1989 from Ecole Polytechnique Fédérale de Lausanne (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 currently the president of the 3D Analysis of Human Movement group on the International Society of Biomechanics. He is author of more than 350 scientific publications and holds more than 8 patents related to medical devices.

Kamiar Aminian

Adjunct Professor School of Engineering (STI)

Research Interests

The Laboratory of Movement Analysis and Measurement investigates human movement, physical activity and locomotion associated with health and disease. Performance or failure affecting the motor function is characterized in real world condition through a multidisciplinary approach involving wearable and implanted instrumentation, signal processing, biomechanics and clinical evaluation. In 2012, we performed gait analysis in more than 1800 subjects (elderly, Parkinson’s disease, cerebral palsy) with our foot worn system and defined a new concept of “foot signature” to classify diseases based on foot trajectories. We quantified the effect of soft tissue artifact on the actual 3D kinematics of the knee and to avoid this artefact we proposed a smart knee implant with internal kinematics sensors and evaluated its performance with a customised actuated knee simulator. We designed an inertial sensor based wearable system to quantify daily upper limbs mobility in patients with the cervical and shoulder disease. In sport, we proposed instrumented suits to estimate and validate kinematics, kinetics and coordination in ski jump and swimming which allowed further evaluations with Swiss Ski team and Lausanne Swimming Club. Our group participated also in measurements during the world alpine ski championship to evaluate the risk of injury by movement quantification. Finally, the patterns of physical activity were investigated in patients with pain and a new approach based on barcoding of physical activity was proposed to show the decrease of complexity of mobility pattern with pain. Based on the same approach we started to study the change of complexity in lifestyle activity of stroke patients and elderly subjects with fall risk.

Keywords

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

Selected Publications

Paraschiv-Ionescu A., Perruchoud C., Buchser E., Aminian K., (2012) Barcoding Human Physical Activity to Assess Chronic Pain Conditions, PLoS ONE 7(2), e32239. doi:10.1371/journal.pone.0032239.

Bagalà F., Becker C., Cappello A., Chiari L., Aminian K., Hausdorff JM., Zijlstra W., Klenk J., (2012) Evaluation of Accelerometer-Based Fall Detection Algorithms on Real-World Falls, PLoS ONE 7(5), e37062. doi:10.1371/journal. pone.0037062. Ganea, R., Paraschiv-Ionescu, A., Aminian, K. (2012) Detection and Classification of Postural Transitions in Real-World Conditions, IEEE Transactions on Neural Systems and Rehabilitation Engineering, 20(5), 688-696. Arami, A., Miehlbradt, J., Aminian, K. (2012) Accurate Internal-External Rotation Measurement in Total Knee Prosthesis: a magnetic solution, Journal of Biomechanics, 45(11), 2023-2027. Dadashi, F., Crettenand, F., Millet, G., Aminian, K. (2012) Front-crawl Instantaneous Velocity Estimation Using a Wearable Inertial Measurement Unit, Sensors, 12, 12927-12939. Chardonnens, J., Le Callennec, B., Favre, J., Cuendet, F., Gremion, G., and Aminian, K. (2012) Automatic measurement of key ski jumping phases and temporal events with a wearable system, Journal of Sports Sciences, 30(1), 53-61.

Team Members Scientist Anisoara Ionescu

Postdoctoral Fellows Hooman Dejnabadi Arash Salarian PhD Students Arash Arami Arnaud Barré Farzin Dadashi Julien Chardonnens Cyntia Duc Raluca Ganea Benoit Mariani Fabien Massé Hossein Rouhani Master’s Students Matthieu Hayoz Francois Curdy Technicians Jean Gramige Pascal Morel Administrative assistant Danielle Alvarez

EPFL School of Life Sciences - 2012 Annual Report

Fantner Lab

- coaffiliated

http://lbni.epfl.ch/ Georg Fantner is a Tenure Track Assistant Professor for bio-and nanoinstrumentation 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 microfabriaction. 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.

Georg Ernest Fantner Tenure Track Assistant Professor School of Engineering (STI)

Research Interests

Our research aims to advance nanoscale measurement technology for life-science applications, with a special focus on high-speed atomic force microscopy (HS-AFM). Towards this end, we work on the integration of high-speed AFM with super-resolution optical microscopy, micro-and 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 modelmembranes with nanometer resolution, and can observe changes two orders of magnitude faster than previously possible with AFM. This high spatial and temporal resolution allows us to study how membrane-disrupting toxins, such as antimicrobial peptides, pore-forming toxins and antimicrobial polymers interact with the membrane. This technique can also be applied to study the action of enzymes such as Topoisomerase II on DNA. 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 “sacrificialbond, hidden-length mechanism”, 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.

Selected Publications

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, 747–58. 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, 597–619. doi:10.3762/bjnano.3.70. Leitner, M., Fantner, G. E., Fantner, E. J., Ivanova, K., Ivanov, T., Rangelow, I., Ebner, A., et al. (2012). Increased imaging speed and force sensitivity for bio-applications with small cantilevers using a conventional AFM setup. Micron (Oxford, England : 1993), 43(12), 1399–407. doi:10.1016/j.micron.2012.05.007. Burns, D., Fantner, G. E., & Youcef-Toumi, K. (2012). Automatic lateral resonance identification from cantilever deflection information in high speed atomic force microscopy. ACC, 3240–3246. Retrieved from http://ieeexplore.ieee. org/xpls/abs_all.jsp?arnumber=6315085. Bozchalooi, I. S., Youcef-Toumi, K., Burns, D. J., & Fantner, G. E. (2011). Compensator design for improved counterbalancing in high speed atomic force microscopy. The Review of scientific instruments, 82(11), 113712. doi:10.1063/1.3663070. Burns, D. J., Youcef-Toumi, K., & Fantner, G. E. (2011). Indirect identification and compensation of lateral scanner resonances in atomic force microscopes. Nanotechnology, 22(31), 315701. doi:10.1088/0957-4484/22/31/315701.

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

IBI - Co-affiliated Research Groups

Keywords

Team Members Postdoctoral Fellows Jonathan Adams Blake Erickson

PhD Students Farnaz Behroozi Maja Dukic Nahid Hosseini Adrian Pascal Nievergelt Pascal Damian Odermatt Oliver Peric Administrative Assistant Ruth Fiaux

EPFL School of Life Sciences - 2012 Annual Report

Guiducci Lab

- coaffiliated

http://clse.epfl.ch/ Carlotta Guiducci holds a PhD in Electrical Engineering from the University of Bologna (I). She was a postdoc at the Nanobiophysics Lab at ESPCI ParisTech (F) since 2007. In 2006 she presented with Infineon Technologies the first CMOS chip for label-free electrical detection of DNA. In 2009, she joined the Institute of Bioengineering at EPFL as a Tenure-Track Assistant Professor. She is also affiliated to the EPFL Institute of Electrical Engineering. She is Associate Editor of the ACM JETC and reviewer of the main journals in the biosensor/ biochip field. She has 500 citations of her scientific work.

Carlotta Guiducci

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

Research Interests

The Laboratory of Life Sciences Electronics (CLSE) is committed to provide new fabrication solutions for heterogeneous integration and new sensing technologies to for the life science domain. At present, successful integration and miniaturization of e-biochips are hindered by the several issues, namely, the lack of cost-effective solutions for biochip-on chip stacking, the limited compatibility of standard microelectronic processes with chemical surface treatments and the lack of universal robust molecular probes to be coupled yet functional on solid-state surface. The group of Prof. Guiducci recently provided an innovative solution for the 3D integration of a disposable sensing microchip on a CMOS stack and developed a set of processes for the protection of the underlying electronics and for the improved robustness of the exposed biochip features. The research activity is also dedicated to the development and characterization of electronic micro and nanotransducers for label-free chemical and biological sensing such as hybrid field effect devices (electrochemical silicon and gold nanowires) and 3D microelectrodes for particles detection and characterization by electrical techniques (impedance sensing and electrorotation for application in the study of cell-protein interaction and cell characterization). Prof Guiducci is coordinator of the ISyPeM Nano-tera.ch project on therapeutic drug monitoring for personalized medicine. In this framework, the group develops aptamerbased label-free sensing approaches for the detection of small drug molecules such as efavirenz and imatinib.

Keywords

Drug monitoring, lab-on-a-chip, e-biochips, vertical silicon surfaces, nanosensors, microarrays, SPR micrfabrication, heterogeneous integration, aptamers, electrochemical impedance spectroscopy, nanowires.

Selected Publications

Temiz, Y., Ferretti, A., Leblebici, Y., Guiducci, C. (2012). A Comparative Study on Fabrication Techniques for On-Chip Micro- electrodes. Lab Chip. (12): 4920–4928.

Cagnin, S., Cimetta, E., Guiducci, C., Martini, P., Lanfranchi, G. (2012). Directly detect biological effects: overview on micro- and nano-technology tools for stem cells applications. Sensors 12(11): 15947-15982. Temiz, Y., Guiducci, C., Leblebici, Y. (2013). Post-CMOS Processing and 3D Integration Based on Dry-Film Lithography. Proc. IEEE Compon., Pack. and Manufact. Techno. (99): 1. Balasubramaniany, V., Ruediy, P.-F., Temiz, Y., Ferretti, A., Guiducci, C., Enz, C. (2013). A 0.18μm Biosensor Frontend based on 1/f Noise, Distortion Cancelation and Chopper Stabilization Techniques. Proc. IEEE Biomed. Circuits and Syst. (99): 1-14. Cappi, G., Accastelli, E., Cantale, V., 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: Chem. 176: 225-231. Bianchi, E., Rollo, E., Kilchenmann, S., Bellati, F. M., Accastelli, E., Guiducci, C. (2012). Detecting Particles Flowing through Interdigitated 3D Microelectrodes. Proc. IEEE EMBC: 5002-5005. Temiz, Y., Zervas, M., Guiducci, C., Leblebici, Y. (2011). Die-level TSV fabrication platform for CMOS-MEMS integration. Proc. Solid-State Sensors, Actuators and Microsyst. Conf. (TRANSDUCERS): 1799-1802. Temiz, Y., Kilchenmann, S., Leblebici, Y., Guiducci, C. (2011). 3D integration technology for lab-on-a-chip applications. Electr. Letters. 47(26): S22-S24.

Team Members Postdoctoral Fellows Elena Bianchi Fabio Spiga

PhD Students Enrico Accastelli Giulia Cappi Anna Ferretti Samuel Kilchenmann Enrica Rollo Interships Sarah Rafiee Djahanbakhsh Master’s Students Ketki Chawla Tania Palmieri Nadia Sarait Vertti Quintero Administrative Assistant Homeira Salimi

EPFL School of Life Sciences - 2012 Annual Report

Hatzimanikatis Lab

- coaffiliated

http://lcsb.epfl.ch/

Associate Professor School of Basic Sciences (SB)

Research Interests

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. We develop 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. Our research 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

Systems biotechnology, metabolic engineering, metabolism, proteomics, lipidomics.

Selected Publications

Racle J, Overney J and Hatzimanikatis V. (2012) A computational framework for the design of optimal protein synthesis. Biotechnol Bioeng. 109(8): 2127-2133. Soh KC, Miskovic L and Hatzimanikatis V. (2012) From network models to network responses: integration of thermodynamic and kinetic properties of yeast genome-scale metabolic networks. FEMS Yeast Res. 12(2):129-143. Brunk E, Neri M, Tavernelli I, Hatzimanikatis V and Rothlisberger U. (2012) Integrating computational methods to retrofit enzymes to synthetic pathways. Biotechnol Bioeng, 109(2): 572-582. Miskovic L and Hatzimanikatis V. (2011) Modeling of uncertainties in biochemical reactions. Biotechnol Bioeng. 108(2): 413-423. Singh A, Soh KC, Hatzimanikatis V and Gill RT. (2011) Manipulating redox and ATP balancing for improved production of succinate in E. coli. Metabol Eng. 13(1): 76-81.

Team members Postdoctoral Fellows Anirikh Chakrabarti Alexandros Kiparissides Georgios Savoglidis Marianne Seijo Katerina Zisaki PhD Students Stefano Andreozzi Meric Ataman Elizabeth Brunk James Clulow Noushin Hadadi Julien Racle Andrijana Radivojevic Maryam Sadat Zoee Keng Cher Soh Stepan Tymoshenko

IBI - Co-affiliated Research Groups

Vassily Hatzimanikatis

Vassily Hatzimanikatis received his Diploma (1991) in Chemical Engineering from the Uni Patras, his PhD (1996) and MS (1994) in Chemical Engineering from the California Institute of Technology. He has held the positions of Group leader (ETH Zurich), Senior research Scientist (DuPont and Cargill) and Assistant Professor (Northwestern University). Professor Hatzimanikatis has over 70 technical publications, three patents and patent applications and has given over 100 invited lectures. He is an Associate editor of the journals Biotechnology & Bioengineering , Metabolic Engineering, and Biotechnology Journal and is on the editorial advisory board of four biotechnology journals. Dr. Hatzimanikatis has received many awards including: DuPont Young Professor (2001-2003); the Jay Bailey Young Investigator Award in Metabolic Engineering (2002); AIMBE Fellow (2010); the ACS Gaden Award (2011).

Research Associate Ljubisa Miskovic Administrative Assistant Christine Kupper

EPFL School of Life Sciences - 2012 Annual Report

Ijspeert Lab

- coaffiliated

http://biorob.epfl.ch/ Auke Ijspeert is an associate professor at the EPFL in the Institute of Bioengineering, and head of the Biorobotics Laboratory. He is also 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

Auke Ijspeert

Associate Professor School of Engineering (STI)

Research Interests

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: (1) to program and design robots that exhibit motor skills with the same efficiency, adaptivity, and robustness as animals, and (2) to gain 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

Robotics, computational neuroscience, control of locomotion, central pattern generators, nonlinear dynamical systems, exoskeletons.

Selected Publications

A. J. Ijspeert, J. Nakanishi, H. Hoffmann, P. Pastor and S. Schaal. Dynamical Movement Primitives: Learning Attractor Models for Motor Behaviors, in 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. 29 (2), p. 308 – 320, 2013. R. Ronsse, N. Vitiello, T. Lenzi, J. van den Kieboom and M. C. Carrozza et al. Human-Robot Synchrony: Flexible Assistance Using Adaptive Oscillators, IEEE Transactions On Biomedical Engineering, vol. 58, p. 1001-1012, 2011. D. Ryczko, V. Charrier, A. Ijspeert and J.-M. Cabelguen. Segmental Oscillators in Axial Motor Circuits of the Salamander: Distribution and Bursting Mechanisms, Journal of Neurophysiology, vol. 104, p. 2677-2692, 2010. Ijspeert A.J., Central pattern generators for locomotion control in animals and robots: a review. Neural Networks, 21(4):642-653, 2008. Ijspeert A.J., Crespi A., Ryczko D., and Cabelguen J.M.. From swimming to walking with a salamander robot driven by a spinal cord model. Science, 315(5817):1416-1420, 2007.

Team Members

Postdoctoral Fellows Crespi Alessandro Gams Andrej Guyot Luc Karakasiliotis Konstantinos Möckel Rico Morel Yannick PhD Studnets Ajallooeian Mostafa Bicanski Andrej Bonardi Stéphane Gay Sébastien Knüsel Jérémie Pouya Soha Thiandackal Robin Tuleu Alexandre van den Kieboom Jesse Vespignani Massimo Administrative Assistant Fiaux Sylvie

EPFL School of Life Sciences - 2012 Annual Report

Johnsson Lab

- coaffiliated

http://lip.epfl.ch/

Kai Johnsson

Kai Johnsson is Professor at the Institute of Chemical Sciences and Engineering. His current research interests are the development and application of chemical approaches to study and manipulate protein function. Professor Johnsson has been Associate Editor of ACS Chemical Biology since 2005. He is member of the Editorial Advisory Board of Science, of the Research Council of the Swiss National Science Foundation and of a number of scientific journals. He is co-founder of Covalys Biosciences which was based on protein labeling technologies developed in his laboratory; these technologies are now available through New England BioLabs. He received the Prix APLE for the invention of the year 2003 of EPFL and the Novartis Lectureship Award 2012/13.

Full Professor School of Basic Sciences (SB)

Research Interests

The visualization and characterization of biologically relevant molecules and activities inside living cells continues to transform cell biology into a truly quantitative science. However, despite the spectacular achievements in some areas of cell biology, the majority of cellular processes still operate invisibly. Further progress will therefore depend increasingly on the development of new (fluorescent) sensors and chemical probes to target and characterize these activities. Our research addresses this need by developing and applying chemical approaches to observe and manipulate protein function in living cells. For example, we have introduced general methods for the covalent and specific labeling of fusion proteins with chemically diverse compounds that open up new ways of studying proteins (i.e. SNAP-tag, CLIP-tag and ACP-tag). We are pursuing the further development of such approaches and their application to biological problems that cannot be resolved by traditional approaches.

Selected Publications

C. Trefzer, H. S’kovierova, S. Buroni, A. Bobovska, S. Nenci, E. Molteni, F. Pojer, M. R. Pasca, V. Makarov, S. T. Cole, G. Riccardi, K. Mikusova, K. Johnsson, Benzothiazinones are suicide inhibitors of mycobacterial decaprenylphosphoryl-ß-D-ribofuranose 2’-oxidase (DprE1)” in J Am Chem Soc. (2012), vol. 134, pp. 912-915. A. Masharina, L. Reymond, D. Maure, K. Umezawa, K. Johnsson, A Fluorescent Sensor for GABA and Synthetic GABA(B) Receptor Ligands. J Am Chem Soc 134, 19026 (Nov 21, 2012). M. A. Brun, K. T. Tan, R. Griss, A. Kielkowska, L. Reymond, K. Johnsson, A Semisynthetic Fluorescent Sensor Protein for Glutamate. J Am Chem Soc 134, 7676 (May 9, 2012). C. Chidley, H. Haruki, M. G. Pedersen, E. Muller, K. Johnsson, A yeast-based screen reveals that sulfasalazine inhibits tetrahydrobiopterin biosynthesis. Nature Chem Biol 7, 375 (Jun, 2011). M. A. Brun, R. Griss, L. Reymond, K. T. Tan, J. Piguet, R. J. R. W. Peters, H. Vogel, K. Johnsson, Semisynthesis of Fluorescent Metabolite Sensors on Cell Surfaces. J Am Chem Soc 133, 16235 (Oct 12, 2011).

Currently, we are interested in the following topics:

• Identifying the protein targets of bioactive molecules. • Engineering of new protein functions for applications in functional proteomics. • Synthesis of new spectroscopic probes for applications in cell biology.

Keywords

Chemical biology, fluorescent protein sensors, drug target deconvolution, protein chemistry, protein engineering.

Team Members Postdoctoral Fellows Hirohito Haruki Katarina Gorska Grazvydas Lukinavicius Luc Reymond Keitaro Umezawa

IBI - Co-affiliated Research Groups

• Development of semisynthetic fluorescent sensor proteins to measure key metabolites in living cells.

PhD Students Cindy Fellay Rudolf Griss Miriam Grolund Petersen Birgit Mollwitz Alberto Schena Administrative Assistant Claudia Gasparini

EPFL School of Life Sciences - 2012 Annual Report

Jolles-Haeberli Lab

- coaffiliated

http://cbt.epfl.ch/

Brigitte Jolles-Haeberli

Adjunct Professor School of Engineering (STI) Director of Center of Translational Biomechanics

Brigitte Haeberli-Jolles graduated from the EPFL with a MSc Diploma of Professional Engineer in Microtechnology in 1990. In 1995 she obtained her MD, Swiss Federal Diploma of Medicine and her Doctoral thesis in Medicine with honors (UNIL). She then received the Diploma in Clinical Epidemiology in 2002 and successfully completed a Clinical Fellowship in Arthritis Surgery at the University of Toronto. She obtained also the FMH and Swiss Federal Diploma of Specialist in Orthopaedic Surgery and Traumatology. She was nominated Master of Teaching and Research (MER) in 2003 and in 2005, Assistant Professor (PD) at UNIL. In 2008 she was nominated Adjunct Professor (EPFL) where she heads the Interinstitutional Center of Translational Biomechanics (CBT). Dr. Jolles-Haeberli was nominated Associate Professor (UNIL) in 2010 where she is the Team leader for Knee Arthroplasty Surgery (CHUV-UNIL).

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

Keywords

Selected Publications

Jolles BM, Aminian K, Coley B, Pichonnaz C, Bassin JP, Leyvraz PF, Farron A. Objective evaluation of shoulder function using body-fixed sensors: a new way to detect early treatment failures? J Shoulder Elbow Surg. 2011; 20(7):1074-81. Jolles BM, Bogoch ER. Juvenile arthritis patients report favorable subjective outcomes of hip arthroplasty despite poor standard outcome scores. J Arthroplasty. 2012 Oct;27(9):1622-8. doi: 10.1016/j.arth.2012.02.024. Pichonnaz C, Bassin JP, Currat D, Martin E, Jolles BM. Bioimpedance for Oedema Evaluation after Total Knee Arthroplasty. Physiother Res Int. 2012 Nov 27. doi: 10.1002/pri.1540 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. 2012 Sep 17. Rouhani H, Favre J, Crevoisier X, Jolles BM, Aminian K. A comparison between joint coordinate system and attitude vector for multi-segment foot kinematics. J Biomech. 2012 Jul 26;45(11):2041-5. doi: 10.1016/j.jbiomech.2012.05.018. Jolles BM, Grzesiak A, Eudier A, Dejnabadi H, Voracek C, Pichonnaz C, Aminian K, Martin E. A randomised controlled clinical trial and gait analysis of fixedand mobile-bearing total knee replacements with a five-year follow-up. J Bone Joint Surg Br. 2012 May; 94(5):648-55. doi: 10.1302/0301-620X.94B5.27598.

Center Groups

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

Aminia Lab (LMAM) p. 72 Pioletti Lab (LBO) p. 84

Administrative Assistant Sabrina Martone

EPFL School of Life Sciences - 2012 Annual Report

Lacour Lab

- coaffiliated

http://lsbi.epfl.ch/ Stéphanie P. Lacour (PI) is 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. Her research focuses on the materials, technology and integration of soft bioelectronic interfaces including artificial skin, ultra-compliant neural electrodes for in vitro platforms as well as in vivo implants.

Stéphanie P. Lacour

Tenure Track Assistant Professor Bertarelli Foundation Chair in Neuroprosthetic Technology School of Engineering (STI)

The Laboratory for Soft Bioelectronics Interfaces (LSBI) explores how to shape traditionally rigid electronic circuits into conformable, skin-like formats. Our mission is to engineer and implement novel materials and technologies overcoming the “hard to soft” mechanical mismatch between man-made devices and biological tissues in order to provide improved biocompatibility and enhanced functionality of these hybrid interfaces. Tactile sensory skin - In 2012, we have optimized the design of a skin-like substrate, which can host microfabricated tactile sensor circuits. The engineered substrates can stretch and relax reversibly like human skin yet provide “safe” mechanical platforms for the most fragile electronic devices. The substrate is made of elastomers and photosensitive plastics. We have also developed the technology to produce ultra-compliant pressure microsensors made of elastomeric microcellular polymers and thin film metallization. The sensors have unique conformability and can be tuned to detect the lightest touch but also full weight body load. Polymeric neural interfaces - In vitro, we are testing the hypothesis that the behavior of cells may be altered by modulating the local mechanical microenvironment at the surface of an implant. In vivo, we are developing a range of neural electrodes embedded in soft polymers. We have produced first prototypes of flexible auditory brainstem implants, stretchable spinal cord electrode implants and nerve-like regenerative electrode implants. Acute and chronic evaluation of the neural interfaces is on-going.

Keywords

Microelectrode arrays, neural interfaces, stretchability, sensory neurons, neuroprosthesis, tactile sensors, polymers, thin films, biocompatibility, thin film electronics, micro/ nanofabrication.

Selected Publications

Granger N, Chew D, Fairhurst P, Fawcett JW, Lacour SP, Craggs M, Mosse CA, Donaldson N, Jeffery ND (2013). Use of an implanted sacral nerve stimulator to restore urine voiding in chronic paraplegic dogs. Journal of Veterinary Internal Medicine, 27:99-105. Delivopoulos E, Chew D, Minev IR, Fawcett JW, Lacour SP (2012). Concurrent recordings of bladder afferents from multiple nerves using a microfabricated PDMS microchannel electrode array. Lab on Chip. 12:2540-2551. Huang YY, Terentjev E, Oppenheim T, Lacour SP, Welland ME (2012). Fabrication and electromechanical characterization of near-field electrospun composite fibers. Nanotechnology. 23:105305. Liu Q, Ford KL, Langley RL, Robinson A, Lacour SP (2012). Elastic dipole antenna prepared with thin metal films on elastomeric substrate. Electronics Letters. 48:65-66. FitzGerald J.J., Lago N., Benmerah S., Serra J., Watling C.P., Cameron R.E., Tarte E., Lacour S.P., McMahon S.B. and Fawcett J.W. (2012). A regenerative microchannel neural interface for recording from and stimulating peripheral axons in vivo. Journal of Neural Engineering. 9:016010. Minev I.R., Chew D.J., Delivopoulos E., Fawcett J.W. and Lacour S.P. (2012). High sensitivity recording of afferent nerve activity using ultra-compliant microchannel electrodes: an acute in vivo validation. Journal of Neural Engineering. 9:026005. Lacour S.P., Graz I.M., Bauer S., Wagner S. (2011). Elastic components for prosthetic skin. Conf Proc IEEE Eng Med Biol Soc. 2011:8373-6.

Team Members

IBI - Co-affiliated Research Groups

Research Interests

Postdoctoral Fellows Ivan Minev Kate Musick Hugues Vandeparre PhD Students Anna Cyganowski Amelie Guex Cedric Paulou Alessia Romeo Douglas Watson Master’s Student Amélie Guex

Visiting PhD Student Maria-Teresa Francomano Administrative Assistant Carole Weissenberger

EPFL School of Life Sciences - 2012 Annual Report

Maerkl Lab

- coaffiliated

microfluidics.epfl.ch/

Sebastian Maerkl

Tenure Track Assistant Professor School of Engineering (STI)

Sebastian Maerkl received a B.S. degree in Biology and a second B.S. degree in Chemistry from Fairleigh-Dickinson University. He then joined the Biophysics and Biochemistry Option at Caltech as a graduate student and contributed to the early development of microfluidic technology. For his PhD thesis, 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 SSV-Ambition.

Research Interests

The Maerkl lab is principally interested in developing highly integrated microfluidic devices and applying these to pertinent problems in biology. Of particular interest to the lab are systems biology, synthetic biology, and diagnostics, which will benefit tremendously from the development of novel, high-throughput technologies. We are actively developing methods for single cell analysis in S.cerevisiae and S.pombe, as well as M.smegmatis in collaboration with the McKinney Lab (SV/GHI). Using these methods we are interested in characterizing global protein expression dynamics on the single cell level (S.cerevisiae), understand how genotypic variants affect fitness (S.pombe), and discover leads towards understanding and possibly counteracting bacterial persistence (M.smegmatis). The lab is also interested in understanding transcriptional regulatory networks by developing and characterizing promoter variants in vivo, as well as through the biophysical characterization of transcription factors in vitro. Here the lab recently developed a microfluidic platform capable of obtaining 768 parallel kinetic rate measurements of biological interactions. We are using synthetic biology approaches to synthesize and measure large promoter libraries, and we are interested in generating genetic networks in vitro. In diagnostics we have been developing microfluidic platforms able to measure biomarkers in hundreds to thousands of samples, reducing assay costs and increasing throughput by orders of magnitude compared to current state-of-the-art approaches.

Keywords

Microfluidics, systems biology, synthetic biology, diagnostics.

Selected Publications

Niederholtmeyer H. and Maerkl S.J. (2012). Real-time mRNA measurement during an in vitro transcription and translation reaction using binary probes. ACS Synthetic Biology, doi:10.1021/sb300104f. Rockel S., Hens K., Geertz M., Deplancke B. and Maerkl S.J. (2012). iSLIM: a comprehensive approach to mapping and characterizing gene regulatory networks. Nucleic Acids Research, doi:10.1093/nar/gks1323.

Garcia-Cordero J.L. and S.J. Maerkl. (2012). Multiplexed surface micropatterning of proteins with a pressure-modulated microfluidic button-membrane. Chem. Commun., doi:10.1039/C2CC37740C. Geertz M., Shore D., and Maerkl S.J. (2012). Massively parallel measurements of biomolecular interaction kinetics on a microfluidic device. Proc. Natl. Acad. Sci. USA, doi:10.1073/pnas.1206011109. Schroeter C., Ares S., Morelli L.G., Isakova A., Hens K.J.I., Gajewski M., Juelicher F., Maerkl S.J., Deplancke B. and Oates A. C. (2012). Ubiquitous dimerization and selective DNA binding determine the dynamics of the zebrafish segmentation clock’s core circuit. PLoS Biology, 10(7): e1001364. Rajkumar A.S. and Maerkl S.J. (2012). Rapid Synthesis Of Defined Eukaryotic Promoter Libraries. ACS Synthetic Biology, doi:10.1021/sb300045j. Schultzaberger R.K., Maerkl S.J., Kirsch J.F. and M.B. Eisen. (2012). Probing the Informational and Regulatory Plas- ticity of a Transcription Factor DNA-Binding Domain. PLoS Genetics, 8(3): e1002614. He B., Holloway A., Maerkl S.J. and Kreitman M. (2011) Does positive selection drive transcription factor binding site turnover? A test with Drosophila cisregulatory modules. PLoS Genetics, e1002053. Fidalgo L.M. and Maerkl S.J. (2011). A software–programmable microfluidic device for automated biology. LOC, 11(9), 1612-9.

Team Members Postdoctoral Fellows Jose Garcia-Cordero

PhD Students Matthew Blackburn Henrike Niederholtmeyer Jean-Bernard Nobs Arun Rajkumar Francesca Volpetti Kristina Woodruff Co-Advised PhD Students Johannes Becker Zuzana Tatarova Amanda Verpoorte Administrative Assistant Helen Chong

EPFL School of Life Sciences - 2012 Annual Report

Mermod Lab -

coaffiliated

http://www.unil.ch/biotech/page16861_en.html

Full Professor IBI-UNIL

Research Interests

Our translational research activities are focused on the elucidation of the mechanisms that control gene expression in mammals including humans, and to obtain reliable gene expression for medical use, for instance to express therapeutic proteins in the bioreactor in gene and cell-based therapies . Four research lines are currently being followed by the laboratory. • Gene regulation by cell growth factors upon tissue regeneration • Expression of genes of biotechnological interest in mammalian cells • Characterization and modeling of regulatory genomic regions in cancer • Development of more efficient and safer vectors for gene and stem cell-based therapies

Keywords

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

Selected Publications

Gaussin A., Modlich U., Bauche C., Niederländer N., Schambach A., Duros C., Artus A., Baum C., Cohen-Haguenauer O. and Mermod N. (2012). CTF/NF1 transcription factors act as a potent genetic insulator for integrating gene transfer vectors. Gene Ther., 19:15-24. Harraghy N., Farina M., Regamey A., Girod P.-A., and Mermod N. (2012). Using matrix attachment regions to improve recombinant protein production. Methods Mol. Biol., 801:93-110. Mernier G., Majocchi S., Mermod N. and Renaud P. (2012). In situ evaluation of single-cell lysis by cytosol extraction and observation through fluorescence decay and dielectrophoretic trapping time. Sensors Actuators B Chem., 166: 907-912 Buceta M., Galbete J.L., Kostic C., Arsenijevic Y., and Mermod N. (2011). Use of human MAR elements to improve retroviral vector production. Gene Ther. 18:7-13. Kerschgens J., Renaud S., Grasso L., Egener-Kuhn T., Delaloye J.F., Lehr H.A., Vogel H. and Mermod N. (2011). Detection and analysis of tumor suppressor AP2α DNA binding activity by protein-binding microarrays. PLOS One, 6:e22895.

Grandjean M., Girod P.-A., Calabrese D., Wicht M., Beckman J.S., Martinet D. and Mermod N. (2011). High-level transgene expression by homologous recombination-mediated gene transfer. Nucl. Acids Res., 39:e104. Pjanic M., Pjanic P., Schmid C., Ambrosini G., Gaussin A., Plasari G., Mazza C., Bucher P., and Mermod N. (2011). Nuclear factor I revealed as family of promoter binding transcription activators. BMC Genomics, 12:181.

Team Members Postdoctoral Fellows Niko Niederländer Stéphanie Renaud Stefania Puttini Niamh Harraghy Elena Aritonovska Maxime Albesa Solenne Bire PhD Students Ruthger van Zwieten Stefano Majocchi Deborah Ley Simone Edelmann Kaja Kostyrko Yaroslav Shcherba Matthias Contie Pavithra Iyer Research Fellow Xuan Luo Master’s student Arnaud Rivier Engineers, informaticians & bioinformaticians Thomas Junier Etienne Lançon Daniel Peter Technicians Yves Dusserre Jacqueline Masternak Armindo Texeira Ione Gutscher Apprentice Alessia Cochard Administrative Assistant Nassim Berberat

IBI - Co-affiliated Research Groups

Nicolas Mermod

Nic Mermod did his PhD on bacterial gene regulation and 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 fellow of the Swiss National Science Foundation, to become full professor and director of the Institute of Biotechnology. Nic heads a laboratory of 25 scientists at the Center for Biotechnology of the University of Lausanne and of the Swiss Institute of Technology Lausanne (EPFL). He is also co-founder of Selexis SA, a biotechnology company developing therapeutic-producing cell lines. His research bridges fundamental work on genomics and epigenetics to molecular biotechnology and gene and cell therapies. Prof. Mermod has authored a number of scientific publications and patents.

EPFL School of Life Sciences - 2012 Annual Report

Micera Lab

- coaffiliated

http://tne.epfl.ch/ Silvestro Micera is Associate Professor and Head of the Translational Neural Engineering Laboratory in 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.

Silvestro Micera

Associate Professor Center for Neuroprosthetics School of Engineering (STI)

Research Interests

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 kind of disabilities (spinal cord injury, stroke, amputation, etc.). In particular, the TNE lab aim is to be a technological bridge between basic science and clinical environment. Therefore, TNE novel technologies and approaches are designed and developed also starting from basic scientific knowledge in the field of neuroscience, neurology and geriatrics with the idea that better understanding means better development of clinical solutions. The lab is currently working with the University Hospital of Geneva (Prof. Guyot) to develop and validate a novel neuroprosthesis to restore vestibular functions in disabled subjects. The TNE is responsible for the integration and the assessment of performance of this device and collaborates on the clinical and neurophysiological characterization with clinical team. TNE is deeply involved in the activities led by Courtine’s team to develop a novel neuroprosthesis to restore locomotion using epidural electrical stimulation (EES). TNE works on novel models to better understanding EES, on novel control strategies to improve the performance of EES, and in several experiments to characterize cortical activities using intracortical electrodes during locomotion.

Selected Publications

Van den Brand R, Heutschi J, Barraud Q, DiGiovanna J, Bartholdi K, Huerlimann M, Friedli L, Vollenweider I, Moraud EM, Duis S, Dominici N, Micera S, Musienko P, Courtine G (2012). Restoring voluntary control of locomotion after paralyzing spinal cord injury. Science. 336:1182-5. Raspopovic S, Capogrosso M, Badia J, Navarro X, Micera S (2012). Experimental validation of a hybrid computational model for selective stimulation using transverse intrafascicular multichannel electrodes. IEEE Trans Neural Syst Rehabil Eng. 20:395-404. Panarese A, Colombo R, Sterpi I, Pisano F, Micera S (2012). Tracking motor improvement at the subtask level during robot-aided neurorehabilitation of stroke patients. Neurorehabil Neural Repair. 26:822-33. Tombini M, Rigosa J, Zappasodi F, Porcaro C, Citi L, Carpaneto J, Rossini PM, Micera S (2012). Combined analysis of cortical (EEG) and nerve stump signals improves robotic hand control. Neurorehabil Neural Repair. 26:275-81. Raspopovic S, Capogrosso M, Micera S (2011). A computational model for the stimulation of rat sciatic nerve using a transverse intrafascicular multichannel electrode. IEEE Trans Neural Syst Rehabil Eng. 19:333-44. Carpaneto J, Umiltà MA, Fogassi L, Murata A, Gallese V, Micera S, Raos V (2011). Decoding the activity of grasping neurons recorded from the ventral premotor area F5 of the macaque monkey. Neuroscience. 188:80-94.

Team Members Postdoctoral Fellows Jack DiGiovanna Stanisa Raspopovic

Professor Micera’s team also prepared all the devices and algorithms for the implantation of intraneural peripheral electrodes on an amputee (will happen in Rome in 2013), in order to develop a real-time bidirectional control of hand prostheses.

PhD Students Marco Bonizzato Marco Capogrosso (visiting) Martina Coscia (visiting) Andrea Crema Vidhi H. Desai (visiting) T. Khoa Nguyen Eduardo Martin Moraud Elvira Pirondini

Keywords

Research Assistant Federica Aprigliano

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

Master’s Students Florian Gothey Edoardo D’Anna Matteo Mancuso Administrative Assistant Jennifer Dinkleldein

EPFL School of Life Sciences - 2012 Annual Report

Millán Lab -

coaffiliated

http://cnbi.epfl.ch/ Prof. José del R. Millán holds the Defitech Chair at the École 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 brain-computer interfaces. Dr. Millán is an IEEE SMC Distinguished Lecturer.

José del Rocio Millán

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

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. Our neuroprostheses are explored in cooperation with clinical partners and disabled volunteers for the purpose of motor restoration, communication, entertainment and rehabilitation. A major highlight of 2012 was the final stretch of the European TOBI project that we have been coordinating since 2008. Remarkably, an important aspect of the project was to allow potential end-users to test our brain-controlled devices either at the involved research laboratories or at rehabilitation centers. More than 100 users suffering from motor impairments -due to stroke, spinal cord injury or neurodegenerative diseases- tested the designed prototypes.

Keywords

Brain-computer interfaces, neuroprosthetics, statistical machine learning, human-robot interaction, adaptive robotics, neuroscience, EEG, mental imagery.

Selected Publications

Lew E., Chavarriaga R., Silvoni S. and Millán J. d. R. (2012). Detection of self-paced reaching movement intention from EEG signals. Frontiers in neuroengineering. 5:13. Tzovara A., Murray M., Bourdaud N., Chavarriaga R., Millán J. d. R. and De Lucia M (2012). The timing of exploratory decision-making revealed by singletrial topographic EEG analyses. Neuroimage. 4:1959-69. Chavarriaga, R., Bayati, H., and Millán, J.d.R. (2012). Unsupervised adaptation for acceleration-based activity recognition: robustness to sensor displacement and rotation. Journal of Personal and Ubiquitous Computing, doi: 10.1007/s00779-011-0493-y. Leeb, R., Sagha, H., Chavarriaga, R., and Millán, J.d.R. (2011). A hybrid BCI based on the fusion of EEG and EMG Activities. Journal of Neural Engineering, 8:025011.

Müller-Putz, G.R., Breitwieser.,C., Cincotti, F., Leeb, R., Schreuder, M., Leotta, F., Tavella, M., Bianchi, L., Kreilinger, A., Ramsay, A., Rohm, M., Sagebaum, M., Tonin, L., Neuper, C. and Millán, J.d.R. (2011). Tools for Brain-Computer Interaction: A General Concept for a Hybrid BCI. Frontiers in Neuroinformatics, 5:30. doi: 10.3389/fninf.2011.00030. Carlson T. E., Tonin L., Leeb R., Rohm M., Rupp R., Al-Khodairy A. and Millán J. d. R. (2012). BCI Telepresence: A Six Patient Evaluation. TOBI Workshop lll: Bringing BCIs to End-Users: Facing the Challenge, Würzburg, Germany, March 20-22. Khaliliardali Z., Chavarriaga R., Gheorghe L.A. and Millán J. d. R. (2012). Detection of Anticipatory Brain Potentials during Car Driving. The 34th Annual International Conference of the Engineering in Medicine and Biology Society, San Diego, USA, Aug 28-Sep 1.

Team Members Postdoctoral Fellows Ricardo Chavarriaga Robert Leeb Tom Carlson Maria Laura Blefari Aleksander Sobolewski Sarah Degallier PhD Students Andrea Biasiucci Luca Tonin Serafeim Perdikis Mohit Kumar Goel Hesam Sagha Sareh Saeedi Michele Tavella Zahra Khaliliardali Marija Ušcumlic ` ` Huaijian Zhang Lucian Gheorghe Pierluca Borsò Michael Pereira Nicolas Bourdaud Eileen Lew

IBI - Co-affiliated Research Groups

Research Interests

Research Staff Marco Creatura Nicolas Beuchat Alberto Molina Master’s Student Abdolreza Madi Administrative Assistant Najate Guechoul

EPFL School of Life Sciences - 2012 Annual Report

Pioletti Lab

- coaffiliated

http://lbo.epfl.ch/

Dominique Pioletti received his Master in Physics and obtained his PhD in biomechanics in 1997 from the EPFL. He developed original constitutive laws taking into account viscoelasticity in large deformations. Then he did a post-doc at UCSD focusing on osteoblast reaction to different implant surface types. Since April 2006, Dominique Pioletti is appointed Assistant Professor tenure-track at the EPFL and is director of the Laboratory of Biomechanical Orthopedics.

Dominique P. Pioletti

Tenure Track Assistant Professor Center of Translational Biomechanics School of Engineering (STI)

Research Interests

Our research topics include biomechanics and tissue engineering of musculo-skeletal tissues; mechano-transduction in bone, and development of orthopedic implant as a drug delivery system. Prof. Pioletti is a pioneer in the development of orthopedic implants used as drug delivery systems. The drug is delivered either passively from the 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.

Keywords

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

Selected Publications

Voge,l A., Pioletti, D.P. (2012). Damping properties of the nucleus pulposus. Clinical Biomechanics. 27, 861-865. Darwich, S., Scaletta, C., Raffoul, W., Pioletti, D.P., Applegate, L.A. (2012). Epiphyseal chondro-progenitors provide a stable cell source for cartilage cell therapy. Cell Medicine, 4, 23-32. Terrier, A., Brighenti, V., Pioletti, D.P., Farron, A. (2012). Importance of polyethylene thickness in total shoulder arthroplasty: a finite element analysis. Clinical Biomechanics, 27, 443-448. Roshan Ghias, A., Vogel, A., Rakotomanana, L., Pioletti, D.P. (2011) Prediction of spatio-temporal bone formation in scaffold by diffusion equation. Biomaterials, 32, 7006-7012. Stadelmann, V. A., Bonnet, N., Pioletti, D.P. Combined effects of zoledronate and mechanical stimulation on bone adaptation in an axially loaded mouse tibia, Clinical Biomechanics, 26, 101-105.

Team Members Group Leader Alexandre Terrier

Postdoctoral Fellow Xabier Larrea PhD Students Jérôme Hollenstein Salim Darwich Philippe Abdel-Sayed Ulrike Kettenberger Mohamadreza Nassajian Moghadam Sohrab Emami-naini Chrsitoph Engelhardt Adeliya Latypova Tanja Hausherr Valérie Malfroy Camine Lab Assistant Sandra Jaccoud Engineers Francesc Levrero Florencio Julien Ston Master’s Students Yannick Devaud Christoph Wenger Valérie Malfroy-Camine Mohsen Afshar Gilles Michel Guillaume Pierret Sara Molins Raphaël Obrist Serge Metrailler Anouk Grandgeorge Annick Baur Valérie Parvex Jules Bourgon Administrative Assistant Virginie Kokocinski

Gortchacow, M., Wettstein, M., Pioletti, D.P., Terrier, A. (2011). A new technique to measure micromotion distribution around a cementless femoral stem, J Biomechanics, 44, 557-560. Roshan Ghias, A., Lambers, F., Gholam-Rezaee, M., Müller, R., Pioletti, D.P. (2011). In vivo loading increases mechanical properties of scaffold by affecting bone formation and bone resorption rates. Bone, 49, 1357-1364.

EPFL School of Life Sciences - 2012 Annual Report

Psaltis Lab

- coaffiliated

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

Demetri Psaltis

Full Professor Dean of the School of Engineering (STI)

The Optics laboratory focuses on biological imaging and optofluidics. Biological imaging deals with a variety of topics: phase conjugation through multimode fibers and biological tissues, imaging through biological media and nonlinear optics for bioparticle characterization. With optofluidics, we are focusing on developing technologies for energy harvesting purposes by leveraging the advantages of microfluidic systems. Biological imaging at a glance. • imaging techniques are used to improve detection of the type of cochlear damage. In preliminary studies, two-photon fluorescence microscopy is used to detect the damage on individual hair cells. • a high-resolution, lensless endoscope, minimally invasive, based on digital scanning, using phase conjugation through a multimode fiber was developed. • second harmonic generation (SHG) from nanoparticles for new types of imaging applications was studied. The coherent nature of SHG allows us to capture the complex radiated field information, thus allowing for many novel imaging applications, such as scan-free three-dimensional (3D) imaging, focusing and imaging through scattering media. • nonlinear imaging through Kerr media and object reconstruction after distortion in a non-linear media were studied. • a scanning confocal microscopy technique based on digital holography was developed. The data collected in this way contains all the necessary information to digitally produce three-dimensional images. Optofluidics - An interdisciplinary subject between optics and microfluidics, optofluidics has made substantial progress towards the integration of versatile optical functions into lab-on-a-chip systems. Integration and reconfigurability are its two major advantages. 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.

Selected Publications

Yang, X., 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. Goy, A., Psaltis, D. (2012). Digital confocal microscope. Optics Express. 20 (20): 22720-22727. Vasdekis, A.E., Evan, S., O’Neil, C., Psaltis, D., Hubbell, J. (2012). Precision intracellular delivery based on optofluidic polymersome rupture. ACS Nano. 6 (9): 7850-7857. Song, W., Vasdekis, A.E., Psaltis, D. (2012). Elastomer based tunable optofluidic devices. Lab on a Chip. 12 (19): 3590-3597. Erickson, D., Sinton, D., Psaltis, D., (2012). Optofluidics for energy applications. Nature Photonics. 5 (10): 583-590. Grange, R., Lanvin, T., Hsieh, C.L., Pu, Y., Psaltis, D. (2012). Imaging with second-harmonic radiation probes in living tissue. Biomedical Optics Express. 2 (9): 2532-2539.

Team Members Postdoctoral Fellows Alexandre Goy Jae-Woo Choi Marcin Zielinski Salma Farahi Wuzhou Song Ye Pu

PhD Students Grégoire Laporte Ioannis Papadopoulos Julien Cuennet Mohammad Hashemi Nicolino Stasio Thomas Lanvin Xin Yang Administrative Assistant Carole Loeffen Berthet

IBI - Co-affiliated Research Groups

Research Interests

EPFL School of Life Sciences - 2012 Annual Report

Radenovic Lab

- coaffiliated

http://lben.epfl.ch/

Aleksandra Radenovic earned a degree in physics from the University of Zagreb before joining Professor Giovanni Dietler’s. There she earned her Doctor of Sciences degree in 2003. She then undertook postdoctoral study at the University of California, Berkeley. From July 2008 she is an assistant tenure tracked professor at the Institute of Bioengineering.

Aleksandra Radenovic Tenure Track Assistant Professor School of Engineering (STI)

Research Interests

The research of the Laboratory of Nanoscale Biology focuses on developing tools and probes for single-molecule biophysics. The group uses optical tweezers, AFM, single-molecule fluorescence, PhotoActivated Light microscopy PALM and nanofabricated structures to study biomolecular systems and advance new nanotechnology. Current experimental work in our lab focuses on two interconnecting areas: Nanofabricated probes and platforms for single-molecule biophysics experiments including nanofabricated SHG nanocylinders, solid-state nanopores, local nanolectrodes for molecular sensing and sequencing. DNA nanotechnology. Our main focus is to implement DNA origami structures into nanoelectronics. We use grapheme nanoribbon templates onto which different DNA origami structures can self-assemble and would enable us to register individual molecular nanostructures, to electronically address them, and to integrate them into functional devices. Local probe studies of single biomolecules. For example RNA polymerase, DNA binding proteins, membrane proteins such G protein–coupled receptors (GPCRs).

Keywords

PALM, GPCRs, solid-state nanopores, single molecule, DNA sequencing, nanoelectrodes.

Cell-type-specific β2 adrenergic receptor clusters identified using photo-activated localization microscopy are not lipid raft related, but depend on actin cytoskeleton integrity, M. Scarselli, P.Annibale and A.Radenovic Journal of Biological Chemistry DOI 10.1074/jbc.M111.329912. Nonlinear Optical Response in Single Alkaline Niobate Nanowires, F. Dutto, C. Raillon, K.Schenk and A. Radenovic Nano Lett., 2011, 11 (6), pp 2517–2521. 5. Identification of clustering artifacts in photoactivated localization microscopy P. .Annibale, S. Vanni, M. Scarselli, U. Rothlisberger and A. Radenovic Nature Methods 8, 527–528 2011. Single-layer MoS2 transistors, B. Radisavljevic, A. Radenovic, J. Brivio, V. Giacometti, A. Kis1*, Nature Nanotechnology Volume:6,147–150 2011

Team Members Postdoctoral Fellows Traversi Floriano Steinbock Lorentz Ke Liu Hendrik Deschout

PhD Students Annibale Paolo Brando Serena Roman Bulushev Dutto Fabrizia Kayci Metin Raillon Camille Arun Shivanandan Roman Bulushev

Selected Publications

Master’s Students Garcia Cordero Erick Mattia Greco Michael Graf Swati Krishnan

Nanopore Detection of Single Molecule RNAP–DNA Transcription Complex, C. Raillon, P. Cousin, F. Traversi, N. Hernandez and A.Radenovic Nano Letters 2012 DOI 10.1021/nl3002827

Technician Lely Feletti

Controllable shrinking and shaping of glass nanocapilaries under electron irradiation, L.J. Steinbock, J.F. Steinbock and A. Radenovic Nano Letters 2013 DOI: 10.1021/nl400304y

Administrative Assistant Chong Helen

EPFL School of Life Sciences - 2012 Annual Report

Renaud Lab

- coaffiliated

http://lmis4.epfl.ch/ Philippe Renaud has a Ms in Theoretical Physics. He received his PhD in Physics in 1988 and did a postdoc at the University of California, Berkeley (1988-1989) and then at the IBM Research Laboratories in Zürich (1990-1991) on scanning probe microscopy and magnetism. In 1992, he move to the MEMS team of CSEM in Neuchâtel, developing microsensors. He was appointed in 1993 as professor at EPFL where he started research on microsystems and on BioMEMS. He is also Scientific Director of the EPFL Center of MicroNanotechnollogy (CMi).

Phillippe Renaud

Full Professor School of Engineering (STI)

The Renaud laboratory is doing research in BioMEMS, microfluidics, nanofluidics and bioelectronic implants. We use the diverse wafer-based microfabrication for the realization of our devices. We have a strong activity on microfluidics systems for handling, analyzing and culturing biological cells. We have studied novel methods in flow cytometry and cell sorting based on electrical impedance analysis and dielectric properties of the cells. We also develop micro-bioreactors for on-chip co-culture of cells in drug screening and toxicology applications. Research on basic nanofluidic phenomena is used for understanding molecular transport in nanochannels. The team is developing devices for bioelectronic implants such as micro-electrodes for neural recordings and stimulation, biomechanical sensors for eye pressure or articular implants.

Keywords

Biosensors, microfluidics, cell chips, microflow cytometry, medical devices.

Selected Publications

B. Eker, R. Meissner, A. Bertsch, K. Mehta and P. Renaud. Label-Free Recognition of Drug Resistance via Impedimetric Screening of Breast Cancer Cells, in PLoS ONE, vol. 8, num. 3, p. e57423.1-12, 2013. G. Mernier, R. Martinez Duarte, R. Lehal, F. Radtke and P. Renaud. Very High Throughput Electrical Cell Lysis and Extraction of Intracellular Compounds Using 3D Carbon Electrodes in Lab-on-a-Chip Devices, in Micromachines, vol. 3, num. 3, p. 574-581, 2012.

Position Synapses Heterogeneously in 3D Micropatterned Neural Cultures, in PLoS ONE, vol. 6, num. 10, p. e26187.1-12, 2011. N. Buffi, D. Merulla, J. Beutier, F. Barbaud and S. Beggah et al. Miniaturized bacterial biosensor system for arsenic detection holds great promise for making integrated measurement device, in Bioengineered Bugs, vol. 2, num. 5, p. 296-298, 2011. R. Meissner, B. Eker, H. Kasi, A. Bertsch and P. Renaud. Distinguishing druginduced minor morphological changes from major cellular damage via labelfree impedimetric toxicity screening, in Lab on a Chip, vol. 11, num. 14, p. 2352-2361, 2011.

Team Members Postdoctoral Fellows Jules Vandersarl Rodrigo Martinez Duarte Amélie Beduer Ludovica Colella Songmei Wu PhD Students David Bonzon Sophie Delasoie Fabien Wildhaber Yufei ren Pierre Joris Mojtaba Taghipoor Robert Meissner David Forcheler

L. Colella, C. Beyer, J. Froehlich, M. Talary and P. Renaud. Microelectrodebased dielectric spectroscopy of glucose effect on erythrocytes, in Bioelectrochemistry, vol. 85, p. 14-20, 2012.

Senior Scientists Arnaud Bertsch Harald van Lintel

A. Kunze, A. Valero, D. Zosso and P. Renaud. Synergistic NGF/B27 Gradients

Administrative Assistant Sylvie Clavel

IBI - Co-affiliated Research Groups

Research Interests

EPFL School of Life Sciences - 2012 Annual Report

Roke Lab

- coaffiliated

http://lbp.epfl.ch/ Sylvie Roke studied chemistry and physics at Utrecht University (NL, highest honors). She obtained a PhD degree from Leiden University (highest honors) in the field of nonlinear optics. She was awarded the LJ Oosterhoff prize 2003. In 2004 she graduated with highest honors and obtained an Alexander von Humboldt Fellowship. In 2005 she obtained a Max-Planck Group Leader position and Research Group. In 2006 she was awarded the Minerva Prize (FOM, NL) and in 2008 the Hertha Sponer prize (DPG, DE). In 2009 she obtained an ERC startup grant, and in 2010 she became a fellow of the Young Academy of the German Academy of Sciences. In April 2011 she started the Laboratory for fundamental BioPhotonics (LBP).

Sylvie Roke

Tenure Track Assistant Professor Julia Jacobi Chair in Photomedicine School of Engineering (STI)

Research Interests

Life occurs in three dimensions. Living cells and organelles, such as the nucleus, mitochondria and ribosomes require membranes for protection and as vital part of their production units. Viruses consist of capsides that can self-assemble into nanoscopic projectiles, ready to deliver DNA or RNA to the next willing host. These examples illustrate the complexity of small biological systems. For living matter, the ability to respond, adapt and reform according to the needs of the specific molecular environment is enormous. If we could harness those abilities, a huge leap in technological performance from the nano sciences to the life sciences becomes possible. Currently, our understanding of soft biological systems is mostly limited to macro- or microscopic theories. Molecular understanding is often absent. To change this and to arrive at tomorrows’ diagnostics we work on four main themes that are chosen to increase both our fundamental understanding and our technological abilities. • Development of theory and instrumentation for nonlinear light scattering / microscopy techniques to understand fundamental light matter interaction processes. • Molecular understanding of processes and interfaces in liquids and turbid media: aqueous systems • The investigation of structure and properties of biologically and medically relevant interfaces • Nonlinear optics applied to living systems Ultimately we want to develop a toolbox for tomorrow’s diagnosis for biomedical research, and bring molecular foundations to the understanding of biomedical processes.

Keywords

Nonlinear optics, biological imaging, light scattering, nanodroplets & particles, interfaces, water, membranes, surfactants.

Selected Publications

R. Vacha, S. Roke, P. (2012). Sodium Dodecyl Sulfate at Water-hydrophobic Interfaces: A Simulation Study. J. Phys. Chem B, 116, 11936-11942, DOI: 10.1021/jp304900z. KC. Jena, R. Scheu, S. Roke, P. (2012). Surface Impurities Are Not Responsible For the Charge on the Oil/Water Interface: A Comment. Angew. Chem. Int. Ed, DOI: 10.1002/anie.201204662. H. B. de Aguiar, R. Scheu, K. C. Jena, A. G. F. de Beer, S. Roke, P. (2012). Comparison of scattering and reflection SFG: a question of phase-matching. Phys. Chem. Chem. Phys, 14, 6826-6832. S. Roke, G. Gonella, P. (2012). Nonlinear Light Scattering and Spectroscopy of Particles and Droplets in Liquids. Annu Rev. Phys. Chem 63, 2012 :353–378. A. G. F. de Beer, J-S Samson, W. Hua, Z. Huang, X. Chen, H. C. Allen, and S. Roke, P. (2012). A direct comparison of Phase-Sensitive Vibrational Sum Frequency generation with the Maximum Entropy Method: a case study of water. J. Chem. Phys 135, 224701. H. B. de Aguiar, J.-S. Samson and S. Roke, P. (2011). Probing nanoscopic droplet interfaces in aqueous solution with vibrational sum-frequency scattering: a study of the effects of path length, droplet density and pulse energy. Chem. Phys. Lett, 512, 2011, 76-80. R. Vacha, S. Rick, P. Jungwirth, A. G. F. de Beer, H. B. de Aguiar, J-S Samson, and S. Roke, P. (2011). The structure and charge of water around a surfactant free oil in water emulsion. J. Am. Chem. Soc, 133 (26),10204–10210.

Team Members Postdoctoral Fellows Nikolaos Gomopoulos Kailash C. Jena Carlos Macias-Romero PhD Students Yixing Chen Cornelis Luetgebaucks Ekaterina Rostova Rüdiger Scheu Nikolay Smolentsev Administrative Assistant Rebecca Veselinov

EPFL School of Life Sciences - 2012 Annual Report

Stergiopulos Lab

- coaffiliated

http://lhtc.epfl.ch/ 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 140 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.

Nikos Stergiopulos

Full Professor School of Engineering (STI)

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 study also the interaction between the heart and arterial system and the resulting wave propagation phenomena, with the goal of understanding hypertension and aging and also for improving 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.

Keywords

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

Selected Publications

Yiallourou, T. I., Kroger, J. R., Stergiopulos, N., Maintz, D., Martin, B. A., & Bunck, A. C. (2012). Comparison of 4D phase-contrast MRI flow measurements to computational fluid dynamics simulations of cerebrospinal fluid motion in the cervical spine. PLoS One, 7(12), e52284. Villamarin, A., Roy, S., & Stergiopulos, N. (2012). Eye vessel compliance as a function of intraocular and arterial pressure and eye compliance. Invest Ophthalmol Vis Sci, 53(6), 2831-2836. Vardoulis, O., Papaioannou, T. G., & Stergiopulos, N. (2012). On the estimation of total arterial compliance from aortic pulse wave velocity. Ann Biomed Eng, 40(12), 2619-2626. Rezakhaniha, R., Agianniotis, A., Schrauwen, J. T., Griffa, A., Sage, D., Bouten, C. V., et al. (2012). Experimental investigation of collagen waviness and orientation in the arterial adventitia using confocal laser scanning microscopy. Biomech Model Mechanobiol, 11(3-4), 461-473.

Papaioannou, T. G., Vardoulis, O., & Stergiopulos, N. (2012). The “systolic volume balance” method for the noninvasive estimation of cardiac output based on pressure wave analysis. Am J Physiol Heart Circ Physiol, 302(10), H20642073. Martin, B. A., Reymond, P., Novy, J., Baledent, O., & Stergiopulos, N. (2012). A coupled hydrodynamic model of the cardiovascular and cerebrospinal fluid system. Am J Physiol Heart Circ Physiol, 302(7), H1492-1509.

Team Members Engineers & Technical Staff Christian Andrié Michel Bachmann Stephane Bigler Fabiana Fraga Laurent Mosimann

Scientific Collaborators & Postdoctoral Fellows Rodrigo Araujo Fraga Da Silva Bryn Martin Danielle Passos Silva Sylvain Roy PhD Students Aristotelis Agianniotis Thiresia Gialourou Orestis Vardoulis Adan Villamarin

IBI - Co-affiliated Research Groups

Research Interests

Masters Students Emilie Farine Maira Seidl Administrative Assistant Tamina Sissoko

EPFL School of Life Sciences - 2012 Annual Report

Van de Ville Lab

- coaffiliated

http://miplab.epfl.ch/

Dimitri Van De Ville

SNSF Professor School of Engineering (STI)

Dimitri Van De Ville received his MS and PhD in Computer Sciences from Ghent University, Belgium (1998, 2002) and did his postdoc at EPFL (2002-2005). He was a research associate and coordinator of the CIBM Signal Processing Unit at University of Geneva (2005-2009), awarded SNSF professorship (2009) and currently is a tenure-track assistant professor affiliated with EPFL and University of Geneva. Prof. Van De Ville chairs the Biomedical Image & Signal Processing Technical Committee of the IEEE Signal Processing Society and was an Associate Editor of IEEE Transactions on Image Processing (2006-2009) and Guest Editor of the Special Issue on Brain Decoding in Elsevier Pattern Recognition. Dr. Van De Ville was a recipient of the Pfizer Research Award 2012 in the category “Neurosciences and Diseases of the Nervous System”.

Research Interests

To advance our understanding of the human body, in particular of brain function in health and disorder using noninvasive imaging techniques. To that aim, we pursue the development and integration of innovative methodological tools from signal and image processing at various stages of the acquisition, processing, and analysis pipeline. The first highlight of our research is on temporal dynamics of spontaneous brain activity; e.g., we showed fractal organization of the rapid switching between scalp topographies in spontaneous EEG and how it interlinks with fMRI that is governed by slow hemodynamics. The second highlight is on the analysis of functional brain networks using multi-scale graph models and techniques from pattern recognition to interpret and predict cognitive and clinical conditions based on signatures of functional connectivity.

Keywords

Signal & image processing, neuroimaging, pattern recognition.

Selected Publications

Van De Ville, D., Jhooti, P., Haas, T., Kopel, R., Lovblad, K.-O. and Haller, S. (2013). Recovery of the Default Mode Network After Demanding Neurofeedback Training Occurs in Spatio-Temporally Segregated Subnetworks, NeuroImage, 63(4):1775-1781. Richiardi, J., Gschwind, M., Simioni, S., Annoni, J.-M., Greco, B., Hagmann, P., Schluep, M., Vuilleumier, P. and Van De Ville, D. (2013). Classifying Minimally Disabled Multiple Sclerosis Patients from Resting State Functional Connectivity, NeuroImage, 62(3):2021-2033. Boss, D., Hoffmann, A., Rappaz, B., Depeursinge, C., Magistretti, P. J., Van De Ville, D. and Marquet, P. (2012). Spatially-Resolved Eigenmode Decomposition of Red Blood Cells Membrane Fluctuations Questions the Role of ATP in Flickering. PLoS ONE, 7(8):e40667.

Gschwind, M.; Pourtois, G.; Schwartz, S.; Van De Ville, D. & Vuilleumier, P. (2012). White-Matter Connectivity between Face-Responsive Regions in the Human Brain. Cerebral Cortex, 22(7):1564-1576. Van De Ville, D. and Kocher, M. (2011). Non-Local Means with Dimensionality Reduction and SURE-Based Parameter Selection. IEEE Transactions on Image Processing, 20(9):2683-2690. Richiardi, J., Eryilmaz, H., Schwartz, S., Vuilleumier, P. and Van De Ville, D. (2011). Decoding Brain States from fMRI Connectivity Graphs, NeuroImage, 56(2):616-626. Karahanoglu, I., Bayram, I. and Van De Ville, D. (2011). A Signal Processing Approach to Generalized 1D Total Variation. IEEE Transactions on Signal Processing, 59(11):5265-5274.

Team Members Affiliated Scientist Melissa Saenz

Postdoctoral Fellows Ivana Balic Yury Koush Jonas Richiardi Frank Scharnowski PhD Students Zafer Dogan Soheil Faridi Isik Karahanoglu Jeffrey Kasten Rotem Kopel Nora Leonardi Master’s Students Nicolas Gninenko Yannik Messerli Thomas Zuppetti Administrative Assistant Ruth Fiaux

EPFL School of Life Sciences - 2012 Annual Report

Van den Bergh Lab -

coaffiliated

http://lpas.epfl.ch/PDT Hubert van den Bergh obtained a BA in chemistry at Williams College Massachusetts USA, a PhD in physical chemistry at Cambridge University UK, and did postdoctoral work in physics at the Max Planck Institut für Strömungsforschung in Göttingen Germany. He is professor at EPFL and a member of the Council of the Swiss National Science Foundation. He was awarded the prize of the Swiss Chemical Society, the Ruzicka Prize and the price of the Swiss Biomedical Technology Society.

Hubert van den Bergh Full Professor School of Engineering (STI)

The focus of the Medical Photonics Group at EPFL is on detecting and treating disease with the help of light. This is translational research and goes from the basic ideas to clinical tests, and in some cases introduction into the market. Our projects involve close collaboration between academic, clinical and industrial partners. Among others we have contributed significantly to the development of several drugs approved by the US FDA and the European medical authorities, such as VisudyneTM for the treatment of wet age-related macular degeneration (AMD) - with QLT and Novartis, and HexvixTM (Cysview) for the detection and removal of early stage bladder cancer – with Photocure and GE-Healthcare. We also developed an autofluorescence bronchoscope, DAFETM, for the detection of early lung cancer with Wolf GmbH. At present we are working on the optimization of drug mixtures using a stochastic method with an in vitro feedback loop. We are also developing several novel methods for drug delivery. The latter include a photodynamic leakage approach, which will soon enter clinical trials, and an approach with enzyme-activated nanoparticles, which is based on disease enhanced enzyme activity. Our preclinical tests are done in part on the chicken chorioallantoic membrane (CAM) model and using intravital microscopy on the nude mouse. Other contributions include a novel method for the separation of isotopes by laser-induced inhibition of condensation, which has led to the large scale separation of Uranium isotopes now in use at Wilmington NC by GE, Hitachi and Cameco.

Keywords

Fluorescence detection, translational research, drug development, drug delivery, combination strategies, cancer, neovascularization.

Selected Publications

Weiss, A., van den Bergh, H., Griffioen, A.W., Nowak-Sliwinska, P. (2012).Angiogenesis inhibition for improvement of photodynamic therapy; the revival of a promising idea. BBA Rev. Cancer, 1826(1):53-70. Nowak-Sliwinska, P., Weiss, A., van Beijnum, J.R., Wong, T., Lovisa, B., Ballini, J.P., van den Bergh, H., Griffioen, A.W. (2012). Angiostatic kinase inhibitors to sustain photodynamic angio-occlusion. J. Cell. Mol. Med., 16(7) :1553-62. Gabriel, D., Lange, D., Chobaz-Peclat, V., Zuluaga, M.F., Gurny, R., van den Bergh, H., Busso, H. Thrombin-sensitive dual fluorescence imaging and therapeutic agent for detection and treatment of synovial inflammation in murine rheumatoid arthritis. (2011). J Control Release 28;163(2): 178-86. Gabriel, D., Zuluaga, M.F., van den Bergh, H., Gurny, R. Lange, N. (2011). It is all about proteases: from drug delivery to in vivo imaging and photomedicine. Curr Med Chem.18(12) :1785-805. Nowak-Sliwinska, P., van Beijnum, J.R., Casini, A., Nazarov, A., van den Bergh, H., Wagnières, G., Dyson, P.J., Griffioen, A.W. Organomettalic ruthenium(II) arene compounds with anti-angiogenic activity. (2011). J. Med. Chem, 54:3895-3902. Debefve, E., Mithieux, F., Perentes, J.Y., Wang, Y., Cheng, C., Schaefer, S.C., Ruffieux, C., Ballini, J.P., Gonzalez, M., van den Bergh, H., Ris, H.B., Lehr, H.B., Krueger, T. (2011). Leukocyte-endothelial cell interaction is necessary for photodynamic therapy induced vascular permeabilization. Lasers Surg Med. 43(7):696-704.

Team Members Postdoctoral Fellows Sandrine Gay Veronika Huntosova Patrycja Nowak-Sliwinska Andreas Pitzschke Georges Wagnières Yaboo Wang Matthiau Zellweger

IBI - Co-affiliated Research Groups

Research Interests

Master’s Student Debora Bonvin Research Assistants Carla Martoccia Olivier Seydoux Andrea Weiss Administration Véronique Bauler

EPFL School of Life Sciences - 2012 Annual Report

GHI

Global Health Institute

Stewart Cole - Director

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 comprises eight 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. 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.

GHI - Global Health Institute

http://sv.epfl.ch/GHI

EPFL School of Life Sciences - 2012 Annual Report

Blokesch Lab http://blokesch-lab.epfl.ch/

Melanie Blokesch studied biology at Ludwig-Maximilians-University (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 Association for General and Applied Microbiology and the German Academy of Sciences Leopoldina. 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.

Melanie Blokesch Tenure Track Assistant Professor

Introduction

“How and why do bacteria evolve to become pathogens”? To address this question we study Vibrio cholerae, the causative agent of cholera, a disease that is still prevalent in developing countries. V. cholerae is a member of aquatic environments where the bacterium is able to induce a developmental program known as natural competence for transformation. This phenotype allows the bacterium to take up DNA from the surroundings and to recombine it into its genome. Our research focuses on the regulatory and mechanistic aspects of this DNA uptake process as a mode of horizontal gene transfer (HGT).

Keywords

Evolution of human pathogens, horizontal gene transfer, bacterial regulatory networks, environmental reservoirs.

Results Obtained in 2012

toinducer-1. Such small-molecule dependent regulation of natural competence resembles the pheromone-dependent regulation in Gram-positive bacteria but has never been demonstrated before for Gram-negative bacteria. Our results illustrate how V. cholerae enhances the probability of species-specific DNA uptake by coupling gene expression to the species-specific quorum sensing system. This could be beneficial for the DNA repair. In addition, we demonstrated for the first time that a population of V. cholerae responds uniformly with respect to competence induction without a bifurcation of subpopulations. However, around the biotic chitin surface, small molecules such as chitin-degradation products and quorum-sensing autoinducers are most likely not equally distributed resulting in non-synchronized and heterogeneous competence induction within the bacterial population.

Natural competence for transformation of Vibrio cholerae - Natural competence for transformation is one of three modes of HGT in bacteria. It was recently demonstrated that V. cholerae enters natural competence upon growth on chitinous surfaces. Chitin is the most abundant polymer in the aquatic environment, the natural reservoir of this organism. The phenomenon of chitin-induced natural competence is so far poorly understood.

In a recent study, we tested how chitin induction and QS are linked with respect to competence regulation using bacterial genetics and biochemical approaches. We identified a new transcriptional regulator whose expression is dependent on the presence of chitin as inducer as well as species-specific autoinducers. Using epistasis experiments we showed that this regulator plays a role upstream of a subset of essential competence genes.

Our main interest is to understand the link between the environmental niche of this bacterium and the induction of competence. This entails the elucidation of the regulatory network that drives this mode of HGT. In addition, understanding the DNA uptake process is of major importance and so far mostly based on hypothetical models.

Understanding the dynamics of DNA uptake in V. cholerae - In this project we aimed at investigating the composition of the DNA uptake machinery. We used cellular microbiology techniques to study the DNA uptake process. Using this approach we successfully visualized – for the first time – the competence-dependent chitin-induced type IV-like pilus. This pilus is thought to be the main machine of the DNA uptake complex. We also created translational fusion constructs between components of the DNA uptake machinery and fluorescent proteins (see Figure). Our data will help us in getting a better understanding of the mechanistic aspects of the DNA uptake process in naturally competent V. cholerae cells.

The regulatory network of natural competence / transformation of V. cholerae - The goal of this study was to elucidate how environmental signals foster natural competence and transformation. We studied the dependency of natural transformation on small molecules, (so-called autoinducers) produced by V. cholerae and other bacteria. We showed that chitin-induced natural competence and transformation is dependent on the species-specific cholera au-

EPFL School of Life Sciences - 2012 Annual Report

Selected Publications

Lo Scrudato M., Blokesch M. (2013) A transcriptional regulator linking quorum sensing and chitin induction to render Vibrio cholerae naturally transformable. Nucleic Acids Res. (Feb 4th) Borgeaud S., Blokesch M. (2013) Overexpression of the tcp gene cluster using the T7 RNA polymerase / promoter system and natural transformation-mediated genetic engineering of Vibrio cholerae. PLoS One 8: e53952. Seitz P., Blokesch M. (2012) Cues and regulatory pathways involved in natural competence and transformation in pathogenic and environmental Gram-negative bacteria. FEMS Microbiol. Rev.; (Aug 28th).

Team Members Postdoctoral Fellow Juliane Kühn PhD Students Mirella Lo Scrudato Patrick M. Seitz Technicians Sandrine Borgeaud Clémentine Thévoz Administrative assistant Marisa Marciano Wynn

Blokesch M. (2012) TransFLP – a method to genetically modify Vibrio cholerae based on natural transformation and FLP-recombination. J. Vis. Exp. 68, e3761. Lo Scrudato M., Blokesch M. (2012) The Regulatory Network of Natural Competence and Transformation of Vibrio cholerae. PLoS Genet. 8: e1002778. Blokesch M. (2012) Chitin colonization, chitin degradation, and chitin-induced natural competence of Vibrio cholerae are subject to catabolite repression. Environ. Microbiol., 14:1898-912. Suckow G., Seitz P., Blokesch M. (2011) Quorum Sensing Contributes to Natural Transformation of Vibrio cholerae in a Species-Specific Manner. J. Bacteriol. 193:4914-24. Contributed (collaborations): Hornung C., Poehlein A., Haack F.S., Schmidt M., Dierking K., Pohlen A., Schulenburg H., Blokesch M., et al. (2013). PLoS One 8: e55045. Rinaldo A., Bertuzzo E., Mari L., Righetto L., Blokesch M., Gatto M., Casagrandi R., Murray M., Vesenbeckh S.M. and Rodriguez-Iturbe I. (2012) Proc. Natl. Acad. Sci. USA, 109:6602-07. Rinaldo A., Blokesch M., Bertuzzo E., Mari L., Righetto L., Murray M., Gatto M., Casagrandi R., Rodriguez-Iturbe I. (2011) Ann. Intern. Med. 155: 403-404.

GHI - Global Health Institute

Bertuzzo E., Mari L., Righetto L., Gatto M., Casagrandi R., Blokesch M., Rodriguez-Iturbe I., Rinaldo A. (2011) Geophys. Res. Lett., 38:L06403.

A translational fusion of the competence protein ComEA and mCherry was visualized in naturally competent V. cholerae cells. The protein shows a typical pattern of periplasmatically-localized proteins (upper row). This localization pattern changed dramatically upon DNA uptake (lower row).

EPFL School of Life Sciences - 2012 Annual Report

Cole Lab http://cole-lab.epfl.ch/

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 industrialised nations. He has published over 270 scientific articles and received many national and international prizes and distinctions.

Stewart T. Cole Full Professor Director of GHI

Introduction

We are using a multidisciplinary approach to tackle major public health problems such as tuberculosis. Finding new drugs and understanding disease mechanisms are among our priorities.

Keywords

Tuberculosis, leprosy, drug discovery, pathogenesis.

Results Obtained in 2012

TB Drug Discovery - We are leading a major international initiative to discover new drugs for the treatment of tuberculosis (TB), the More Medicines for Tuberculosis Project, MM4TB, funded by the European Commission. In 2012, we completed successfully the preclinical testing of BTZ, a candidate drug that is nearing clinical trials. BTZ kills M. tuberculosis by forming a covalent adduct with cysteine 394 in the active site of its target, the essential flavoenzyme, decaprenyl phosphoryl-D-beta-D-ribose 2â&#x20AC;&#x2122; epimerase. The figure shows a close-up of the active site deduced from the crystal structure of the BTZ-DprE1 complex. We have also reinvestigated pyridomycin, an old, overlooked antibiotic and shown that it is highly active against M. tuberculosis. Pyridomycin was found to inhibit another essential enzyme involved in cell wall biogenesis, InhA. Like BTZ, pyridomycin is active against many multidrug resistant strains. Protein secretion and pathogenicity - The ESX-1 protein secretion system is the major virulence determinant operating in M. tuberculosis and has been lost by the live vaccine strains M. bovis BCG and M. microti. ESX-1 exports small helical-hairpin proteins belonging to the ESAT-6 family as

well as other effector proteins of unknown function. ESX1 mediates host cell entry of tubercle bacilli and triggers intercell spread. We are using an integrated approach involving biochemistry, genetics, X-ray crystallography and electron microscopy to establish the organization, architecture, structure and function of this ATP-driven secretory apparatus. A regulatory map of the M. tuberculosis genome - Gene regulation is being studied using chromatin-immunoprecipitation of DNA-binding proteins in conjunction with ultra-high-throughput sequencing to map regulatory sites on the genome. We have mapped all the RNA polymerase, NusA, SigF, EspR and PhoP binding sites in two different strains under different growth conditions. Regulatory information is being incorporated into TubercuList, the genome server dedicated to M. tuberculosis http://tuberculist.epfl. ch/, for which we are the official curators. Phylogeography of leprosy - Despite the highly successful implementation of multi-drug therapy by the World Health Organisation, leprosy remains a serious public health problem in several countries probably due to our inability to identify infectious cases early enough. We have developed and used an epidemiological tool based on single nucleotide polymorphisms to monitor transmission of the disease and found that in the Southern USA humans contract leprosy from contact with wild armadillos. In collaboration with WHO, we are also coordinating a worldwide effort to monitor the emergence of drug resistance.

EPFL School of Life Sciences - 2012 Annual Report

Zhang, M., Sala, C., Hartkoorn, R.C., Dhar, N., Mendoza-Losana, A., Cole, S.T., (2012). Streptomycin-starved Mycobacterium tuberculosis 18b, a drug discovery tool for latent tuberculosis. Antimicrobial agents and chemotherapy 56, 5782-5789. Neres, J., Pojer, F., Molteni, E., Chiarelli, L.R., Dhar, N., Boy-Rottger, S., Buroni, S., Fullam, E., Degiacomi, G., Lucarelli, A.P., Read, R.J., Zanoni, G., Edmondson, D.E., De Rossi, E., Pasca, M.R., McKinney, J.D., Dyson, P.J., Riccardi, G., Mattevi, A., Cole, S.T., Binda, C., (2012). Structural basis for benzothiazinonemediated killing of Mycobacterium tuberculosis. Science translational medicine 4, 150ra121. Lechartier, B., Hartkoorn, R.C., Cole, S.T., (2012). In vitro combination studies of Benzothiazinone lead compound BTZ043 against Mycobacterium tuberculosis. Antimicrobial agents and chemotherapy 56, 5790-5793. Hartkoorn, R.C., Sala, C., Uplekar, S., Busso, P., Rougemont, J., Cole, S.T., (2012). Genome-wide definition of the SigF regulon in Mycobacterium tuberculosis. Journal of bacteriology 194, 2001-2009. Hartkoorn, R.C., Sala, C., Neres, J., Pojer, F., Magnet, S., Mukherjee, R., Uplekar, S., Boy-Rottger, S., Altmann, K.H., Cole, S.T., (2012). Towards a new tuberculosis drug: pyridomycin - nature’s isoniazid. EMBO molecular medicine 4, 1032-1042. Fullam, E., Pojer, F., Bergfors, T., Jones, T.A., Cole, S.T., (2012). Structure and function of the transketolase from Mycobacterium tuberculosis and comparison with the human enzyme. Open biology 2, 110026. Chen, J.M., Boy-Rottger, S., Dhar, N., Sweeney, N., Buxton, R.S., Pojer, F., Rosenkrands, I., Cole, S.T., (2012). EspD is critical for the virulence-mediating ESX-1 secretion system in Mycobacterium tuberculosis. Journal of bacteriology 194, 884-893. Blasco, B., Chen, J.M., Hartkoorn, R., Sala, C., Uplekar, S., Rougemont, J., Pojer, F., Cole, S.T., (2012). Virulence regulator EspR of Mycobacterium tuberculosis is a nucleoid-associated protein. PLoS pathogens 8, e1002621.

Team Members Postdoctoral Fellows Andrej Benjak Jeffrey Chen Ruben Hartkoorn Raju Mukherjee Joao Neres Florence Pojer Jan Rybniker Claudia Sala Pushpendra Singh PhD Students Benjamin Blasco Gaëlle Kolly Benoit Lechartier Ye Lou Swapna Uplekar Ming Zhang Technicians Stefanie Boy-Röttger Philippe Busso Anthony Vocat Other Staff Jocelyne Lew Yaser Heidari Students Francesco Baccalà Joachim Bacoyannis Isobel Hambleton Mahé Raccaud Ofelia Sanchez Salinas Collaborations Luciana Silva Rodrigues Administrative Staff Suzanne Lamy

GHI - Global Health Institute

Selected Publications

BTZ043 binding to DprE1 and interactions with active site residues. The FAD cofactor is represented in yellow with nitrogen, oxygen, and phosphorous atoms colored in blue, red, and magenta, respectively. Water molecules are represented as red spheres. Dashed lines represent H-bonds

EPFL School of Life Sciences - 2012 Annual Report

Fellay Lab http://fellay-lab.epfl.ch/

Jacques Fellay is a medical scientist with expertise in infectious diseases and human genomics. He obtained his MD from the University of Lausanne in 2002 and was clinically trained in infectious diseases in Switzerland, before working on human genomics of infections at the Duke Center for Human Genome Variation from 2006 to 2010. Jacques Fellay joined the EPFL in April 2011 as an SNSF Professor, and is also a Visiting Physician at the Institute of Microbiology of UNIL/CHUV in Lausanne. In 2012, he was awarded the National Latsis Prize for his work on HIV and HCV host genomics.

Jacques Fellay SNSF Professor

Introduction

The focus of our research is the identification of host genetic factors influencing outcome after viral infections, with a major focus on HIV-1, hepatitis and respiratory viruses. The work in the Fellay lab includes both classical genetics of infection susceptibility that measures clinical outcome, and a novel approach investigating the imprint of human polymorphisms on viral genetic diversity.

Keywords

Human genomics, infectious diseases, HIV, Host-pathogen interactions, deep-sequencing, translational genomics, personalized medicine.

Results Obtained in 2012

Human genetic variation plays a key role in determining individual outcomes after exposure to infectious agents. The mission of our laboratory is to contribute to a better understanding of inter-individual differences in response to infections, using a range of genomic tools. Human genetic studies in HIV-1 disease - We use whole genome DNA genotyping and exome sequencing to search for human genetic variants that influence various aspects of HIV-1 disease. Resistance against infection was investigated in patients with hemophilia that were highly exposed to potentially contaminated blood products in the early days of the pandemic, yet remained seronegative. A large exome sequencing study is underway to explore the potential impact of rare genomic variants on HIV-1 control. We

also aim at understanding differences in chronic immune activation, a critical pathogenic mechanism in HIV-1 infection that leads to a slow exhaustion of immune responses, to increased viral replication in the activated T cells and to premature ageing. Host-pathogen genomic interactions - Advances in genomic technology and bioinformatics make it possible to acquire and combine large-scale host and pathogen genome information from the same infected individuals. We developed a novel strategy to explore the continuous struggle and complex interactions between human genetic variation and pathogen sequence diversity, as well as their respective impact on clinical outcome of infection. Using HIV-1 infection as a model, we explore the respective contributions of viral and human genetic variation to HIV-1 control. The method also highlights the sites of genomic conflict between the retrovirus and its human host. Exome sequencing in children with severe respiratory infections and in patients with fulminant hepatitis B infection - In these projects, we test the hypothesis that patients who develop unusually severe symptoms after common infections have rare genetic defects that confer particular susceptibility to specific viruses. Study participants are prospectively recruited in Swiss and Australian Intensive Care Units and Transplantation Centers, and are analyzed by exome and transcriptome sequencing.

EPFL School of Life Sciences - 2012 Annual Report

Selected Publications

Lane, J., McLaren, P.J., Dorrell, L., Shianna, K.V., Stemke, A., Pelak, K., Moore, S., Oldenburg, J., Alvarez-Roman, M.T., Angelillo-Scherrer, A., Boehlen, F., Bolton-Maggs, P.H.B., Brand, B., Brown, D., Chiang, E., Cid-Haro, A.R., Clotet, B., Collins, P., Colombo, S., Dalmau, J., Fogarty, P., Giangrande, P., Gringeri, A., Iyer, R., Katsarou, O., Kempton, C., Kuriakose, P., Lin, J., Makris, M., Manco-Johnson, M., Tsakiris, D.A., Martinez-Picado, J., Mauser-Bunschoten, E., Neff, A., Oka, S., Oyesiku, L., Parra, R., Peter-Salonen, K., Powell, J., Recht, M., Shapiro, A., Stine, K., Talks, K., Telenti, A., Wilde, J., Yee, T.T., Wolinsky, S.M., Martinson, J., Hussain, S.K., Bream, J.H., Jacobson, L.P., Carrington, M., Goedert, J.J., Haynes, B.F., McMichael, A.J., Goldstein, D.B. and Fellay, J. (2013). A genome-wide association study of resistance to HIV infection in highly exposed uninfected individuals with hemophilia A. Human Molecular Genetics. In press Apps, R., Qi, Y., Carlson, J.M., Chen, H., Gao, X., Thomas, R., Yuki, Y., Del Prete, G., Goulder, P., Brumme, Z.L., Brumme, C.J., John, M., Mallal, S., Nelson, G., Bosch, R., Heckerman, D., Stein, J., Soderberg, K.A., Moody, M.A., Denny, T.N., Zeng, X., Fang, J., Moffett, A., Lifson, J.D., Goedert, J.J., Buchbinder, S., Kirk, G.D., Fellay, J., McLaren, P.J., Deeks, S.G., Pereyra, F., Walker, B., Michael, N.L., Weintrob, A., Wolinsky, S., Liao, W. and Carrington, M. (2013). Opposing effects of HLA-C expression level in viral versus inflammatory disease. Science. In press

Team Members Postdoctoral Fellows Jérôme Lane Paul J. McLaren Staff Scientists Istvan Bartha Thomas Junier PhD Students Samira Asgari Ana Bittencourt Piccini Master’s student Florian Gilbert Administrative Assistant Marisa Marciano Wynn

Pillai, S.K., Abdel-Mohsen, M., Guatelli, J., Skasko, M., Monto, A., Fujimoto, K., Yukl, S., Greene, W.C., Kovari, H., Rauch, A., Fellay, J., Battegay, M., Hirschel, B., Witteck, A., Bernasconi, E., Ledergerber, B., Günthard, H.F. and Wong, J.K. (2012). Role of retroviral restriction factors in the interferon-α-mediated suppression of HIV-1 in vivo. Proc. Natl. Acad. Sci. U S A. 109(8):3035-40. Snoeck, J., Fellay, J., Bartha, I., Douek, D.C. and Telenti, A. (2011). Mapping of positive selection sites in the HIV genome in the context of RNA and protein structural constraints. Retrovirology 8(1):87. Pelak, K., Need, A.C., Fellay, J., Shianna, K.V., Feng, S., Urban, T.J., Ge, D., De Luca, A., Martinez-Picado, J., Wolinsky, S.M., Martinson, J.J., Jamieson, B.D., Bream, J.H., Martin, M.P., Borrow, P., Letvin, N.L., McMichael, A.J., Haynes, B.F., Telenti, A., Carrington, M., Goldstein, D.B. and Alter, G. (2011). Copy number variation of genes encoding killer cell immunoglobulin-like receptors and the control of HIV-1. PLoS Biology. 9(11):e1001208. Rotger, M., Dalmau, J., Rauch, A., McLaren, P.J., Bosinger, S., Battegay, M., Bernasconi, E., Descombes, P., Erkizia, I., Fellay, J., Hirschel, B., Miró, J.P., Palou, E., Vernazza, P., Woods, M., Günthard, H.F., de Bakker, P., Silvestri, G., MartinezPicado, J. and Telenti, A. (2011). Comparative analysis of genomic features of human HIV-1 infection and primate models of SIV infection. J. Clin. Invest. 121(6):2391-400.

GHI - Global Health Institute

Fellay, J., Frahm, N., Shianna, K.V., Cirulli, E.T., Casimiro, D.R., Robertson, M.N., Haynes, B.F., Geraghty, D.E., McElrath, M.J. and Goldstein, D.B. (2011). Host genetic determinants of T cell responses to the MRKAd5 HIV-1 gag/pol/nef vaccine in the Step trial. J. Infect. Dis. 203(6):773-9.

Manhattan plot summarizing human genetic determinants of HIV control identified in genomewide association studies: CCR5 delta 32 heterozygosity and HLA class I allelic variants.

EPFL School of Life Sciences - 2012 Annual Report

Harris Lab http://harris-lab.epfl.ch/

Nicola Harris

Nicola Harris was born in New Zealand and completed her Masters degree in physiology at Victoria University of Wellington in 1994. She then trained in the field of immunology, completing a PhD thesis at the Malaghan Institute of Medical Research Otago University, New Zealand. In 2002 she moved to Switzerland to complete further postdoctoral work 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 is currently employed as a tenure track Assistant Professor.

Tenure Track Assistant Professor

Introduction

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 and worms (helminths) 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; i) how the immune system can provide protection against intestinal helminths, and ii) 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

Immunology, intestine, soil-transmitted helminths, commensal bacteria, antibodies, Th2 immune responses, cytokines, allergy, vaccination

Results Obtained in 2012

As part of our earlier work we uncovered an essential role for antibodies in providing effective immunity against helminth parasites. We then expanded this project to investigate the mechanisms by which antibodies promote helminth killing. In 2012 we completed a project demonstrating a novel role for IgG1 and IgE antibodies in regulating the haematopoiesis of basophils. These data were highly interesting as they represent the first demonstration that antibodies can regulate the development of specific cell types in the bone marrow. However basophils were

found to only have a small role in attacking the helminth parasites. We therefore investigated the role of antibodies in activating other cell types and uncovered a role for these molecules in promoting the activation of macrophages and the adhesion of these cells to the parasitic larvae. Once adhered these cells were able to ‘paralyse’ the parasite and prevent it from completing its life-cylce within the mammalian host (Figure 1). In a separate project we investigated the impact of intestinal bacteria on intestinal immune responses and reported a crucial role for the intestinal cytokine TSLP in intestinal T cell responses. We could determine that intestinal bacteria lead to TSLP secretion, which in turn suppresses the development of inflammatory T cell responses and promotes regulatory T cell responses. TSLP thus represents a crucial cytokine involved in allowing intestinal homeostasis and preventing inflammatory bowel disease. 2012 also saw the initiation of a project aimed at investigating the interactions between intestinal helminths and commensal bacteria. As intestinal helminths and commensal bacteria inhabit the same environmental niche we considered it likely that these organisms interact with, and impact on, each other. In addition, intestinal helminths are well known to alter intestinal physiology, permeability, mucous secretion and the production of anti-microbial peptides⎯all of which may impact on bacterial survival and spatial organization. Preliminary findings from our laboratory indicated that helminth infection of mice does alter the abundance and diversity of intestinal bacteria, as well as impacting on the availability of immuno-modulatory metabolites. We are now recruiting new staff members to work in this exciting area.

EPFL School of Life Sciences - 2012 Annual Report

Selected Publications

Team Members

T. Herbst, J. Esser, M. Prati, M. Kulagin and R. Stettler et al. Antibodies and IL-3 support helminth-induced basophil expansion, in Proc Natl Acad Sci USA, vol. Epub ahead of print, (2012).

PhD Students Ilaria Mosconi Beatrice Volpe Luc Lebon

I Mosconi, M B Geuking, M M Zaiss, J C Massacand, C Aschwanden, C K C Kwong Chung, K D McCoy and N L Harris. Intestinal bacteria induce TSLP to promote mutualistic T-cell responses in Mucosal immunology, vol. Epub ahead of print, (2013).

K. Yadava, A. Sichelstiel, I. F. Luescher, L. P. Nicod and N. L. Harris et al. TSLP promotes influenza-specific CD8+ T-cell responses by augmenting local inflammatory dendritic cell function, in Mucosal immunology, vol. Epub ahead of print, (2012). T. B. Feyerabend, A. Weiser, A. Tietz, M. Stassen and N. Harris et al. Cre-mediated cell ablation contests mast cell contribution in models of antibody- and T cell-mediated autoimmunity, in Immunity, vol. 35, num. 5, p. 832-44, (2011). R. Duvoisin, M. A. Ayuk, G. Rinaldi, S. Suttiprapa and V. H. Mann et al. Human U6 promoter drives stronger shRNA activity than its schistosome orthologue in Schistosoma mansoni and human fibrosarcoma cells., in Transgenic research, (2011).

Postdoctoral Fellows Julia Esser Mario Zaiss Lalit Kumar Dubey

Master’s Student Lorianne Rey-Bellet Senior Technical Assistant Manuel Kulagin Technical Assistant Manuel Kulagin Administrative Assistant Marisa Marciano Wynn

T. Herbst, A. Sichelstiel, C. Schär, K. Yadava and K. Bürki et al. Dysregulation of Allergic Airway Inflammation in the Absence of Microbial Colonization, in American journal of respiratory and critical care medicine, vol. Epub ahead of print, (2011). C. Schaer, S. Hiltbrunner, B. Ernst, C. Mueller and M. Kurrer et al. HVEM Signalling Promotes Colitis, in PloS one, vol. 6, num. 4, p. e18495, (2011).

GHI - Global Health Institute

Infective larvae of the intestinal nematode Heligmosomoides polygyrus after co-culture with macrophages (left) or with macrophages in the presence of immune serum from protected mice (right).

EPFL School of Life Sciences - 2012 Annual Report

Lemaitre Lab http://lemaitrelab.epfl.ch/

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, he started his own laboratory on Drosophila immunity at the Centre Génétique Moléculaire (Gif-sur-Yvette, France). In 2007, he was appointed professor at EPFL.

Bruno Lemaitre Full Professor

Introduction

Our group uses the Drosophila and its powerful genetics as a model to analyse integrated physiological question at the organismal level. We currently have three main axis of research focussing on: • Drosophila immunity • Drosophila-Spiroplasma interaction • Drosophila gut function (including mucosal immunology)

Keywords

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

Results Obtained in 2012

Drosophila innate immunity - Insects possess efficient mechanisms for detecting and neutralizing microbial infection. The application of Drosophila genetics to decipher these mechanisms has generated insights into insect immunity and uncovered similarities with mammalian innate immune responses. Our research focuses on understanding mechanisms of microbial infection and corresponding host defence responses in Drosophila using genetic and genomic approaches. Our group employs genetic screens to identify novel factors regulating the immune response of Drosophila. These studies extend our understanding of how the Toll and Imd NF-κB pathways activate antimicrobial defense, as well as how the host recognizes and distinguishes between different microbial pathogens. We are also analyzing the strategies used by entomopathogenic bacteria to subvert the Drosophila innate immune system. The Drosophila-Spiroplasma interaction: a model for insect endosymbiont - Virtually every insect species harbours facultative bacterial endosymbionts (ex. Wolbachia, Buchnera) that are transmitted from females to their offspring. These symbionts play crucial roles in the biology of their hosts. Some manipulate host reproduction in order to spread within host populations. However, 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. Our project uses a broad range of approaches ranging from molecular genetics to genomics to dissect the molecular mechanisms underlying key features of the symbiosis, including vertical transmission, male killing, regulation of symbiont growth, and symbiont-mediated protection against pathogens. We believe that the fundamental knowledge generated on the Drosophila-Spiroplasma interaction will serve as a paradigm for other endosymbiontinsect 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 defence 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, such as the pancreas and the brain in mammals. Hence, far from being a passive tube exclusively concerned with digestion, the gut is emerging as a major regulator of multiple biological processes. The gut has also been a relatively understudied organ in Drosophila melanogaster. Using an integrated approach, we are studying the mechanisms that make the gut an efficient and interactive barrier despite its constant interactions with microbes. We also analyze the regulatory mechanisms that restore normal gut function upon challenge with bacteria. We have recently studied the role of intestinal stem cell in gut repair during bacterial infection. In parallel to these studies, we have generated a comprehensive atlas deciphering the morphological and functional properties of Drosophila gut compartments. In the follow-up to this study, we are now working on the gene regulatory networks that govern gut region identities, and understand their impact on various gut function such as immunity and digestive enzyme regulation.

EPFL School of Life Sciences - 2012 Annual Report

Selected Publications

Herren JK, Paredes JC, Schupfer F, and Lemaitre B. 2013. Vertical transmission of a Drosophila endosymbiont via cooption of the yolk transport and internalization machinery. MBio 4. Neyen C, Poidevin M, Roussel A. and Lemaitre B. 2012. Tissue- and ligandspecific sensing of gram-negative infection in drosophila by PGRP-LC isoforms and PGRP-LE. J Immunol 189: 1886-97. Osman D, Buchon N, Chakrabarti S, Huang YT, Su WC, Poidevin M, Tsai YC and Lemaitre B. 2012. Autocrine and paracrine unpaired signaling regulate intestinal stem cell maintenance and division. J Cell Sci 125: 5944-9. Broderick NA, Lemaitre B. 2012. Gut-associated microbes of Drosophila melanogaster. Gut Microbes 3: 307-21. Chakrabarti S, Liehl P, Buchon N. and Lemaitre B. 2012. Infection-induced host translational blockage inhibits immune responses and epithelial renewal in the Drosophila gut. Cell Host Microbe 12: 60-70. Paredes, J.C., Welchman, D.P., Poidevin, P. and Lemaitre, B. (2011) Negative regulation by Amidase PGRPs shapes the Drosophila antibacterial response and protects the fly from its own immune system. Immunity, Nov 23;35(5):770-9. Opota, O., Vallet-Gély, I., Vincentelli, R. , Kellenberger C., Iacovache, I.,Gonzalez, M. Roussel, A., van der Goot, F.G. and Lemaitre, B. (2011) Monalysin, a novel b-pore-forming toxin from the Drosophila pathogen Pseudomonas entomophila, contributes to host intestinal damage and lethality. PLoS Pathog. 2011 Sep;7(9):e1002259.

Team Members Postdoctoral Fellows Andrew Bretscher Guennaëlle Dieppois Claudine Neyen Dani Osman Zongzhao Zhai

PhD Students Olivier Binggeli Maroun Bou Sleiman Sveta Chakrabarti Wen Bin (Alfred) Chng Jeremy Herren Juan Paredes Technicians Jean-Philippe Boquete Fanny Schüpfer Christophe Rémondeulaz Apprentices Mégane Bozza Barbara Lecrinier Administrative Assistant Véronique Dijkstra

Kuraishi, T., Binggeli, O., Opota, O. Buchon, N. , and Lemaitre, B. (2011) Genetic evidence for a protective role of the peritrophic matrix against intestinal bacterial infection in Drosophila melanogaster. Proc Natl Acad Sci U S A. 2011 Sep 20;108(38):15966-71.

GHI - Global Health Institute

Herren, J. and Lemaitre B. (2011) Spiroplasma and host immunity: Activation of humoral immune responses increases endosymbiont load and susceptibility to certain bacterial pathogens in Drosophila melanogaster. Cell. Microbiology 13(9):1385-96.

Spiroplasma colonization of the germline. Spiroplasma use the yolk uptake machinery to colonize the germline ensuring vertical transmission. In this photo, Spiroplasma (stained in red) colonize the egg chamber (stained with phalloidin) during vitellogenesis.

EPFL School of Life Sciences - 2012 Annual Report

McKinney Lab http://mckinney-lab.epfl.ch/ John McKinney received his PhD from Rockefeller University (1994) for studies on cell cycle regulation in yeast. His postdoctoral studies at the Albert Einstein College of Medicine (1995-1998) were focused on persistence mechanisms in tuberculosis. He then returned to Rockefeller as an Assistant (1999-2004) and Associate (2004-2007) Professor. In 2007, the McKinney lab relocated to EPFL in order to establish a new research program at the interface of microbiology and microengineering. Prof. McKinney heads the Laboratory of Microbiology and Microsystems (LMIC) affiliated with the Global Health Institute (GHI) and the Institute of Bioengineering (IBI). He is the director of EPFLâ&#x20AC;&#x2122;s Doctoral Program in Biotechnology and Bioengineering (EDBB).

John McKinney Full Professor

Introduction

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. Better understanding of microbial individuality will lead to new strategies to eliminate subpopulations of bacteria that are refractory to antimicrobial therapy and host immunity.

Keywords

Microbiology, microengineering, microbial individuality, single-cell biology, time-lapse fluorescence microscopy, microfluidics, microelectromechanical systems (MEMS), mycobacteria, tuberculosis, persistence, antibiotics.

Results Obtained in 2012

Bacterial cells behave as individuals. Mutation and horizontal DNA transfer are important drivers of bacterial individuation, but these genetic events 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 fluorescence microscopy with custom-made microdevices to study the real-time dynamics of bacterial behavior at the single-cell level. Counter-Immune Mechanisms This project is focused on the mechanisms that M. tuberculosis deploys to resist elimination by the host immune response. We identified a signal transduction pathway that mediates bacterial resistance to immune-related stresses, including reactive oxygen and nitrogen species. We found

that resistance to these stresses is linked to regulation of a prominent family of cell wall proteins of unknown function. We are exploring the mechanistic role of these proteins in stress resistance and immune evasion In Vivo Metabolism This project is focused on the metabolic pathways required for growth and persistence of M. tuberculosis in the mammalian host. Computational modeling of M. tuberculosis metabolism has generated surprising new insights into the metabolic capabilities and vulnerabilities of M. tuberculosis, including the identification of a novel pathway for ATP production that is present only in mycobacteria. We are testing our computational findings in wetlab experiments. Antibiotic Tolerance This project is focused on cell-to-cell variation in antibioticmediated cell death and persistence. Our findings challenge conventional models of antibiotic mode of action, which postulate that growth rate determines cell fate (death or persistence) at the single-cell level. Instead, we find that the fate of individual cells is not correlated with growth kinetics but is instead linked to stochastic expression of death-modulating factors. We are studying the underlying mechanisms of stochastic gene expression and their impact on cell fate. Growth Dynamics This project is focused on the physiology of slow growth, which is a hallmark of persistent infections, and the scaling rules that link cell growth and cell cycle kinetics. We find that mycobacteria display extreme cell-to-cell variation in biomass doubling time, interdivision time, size at division, symmetry of division, duration of S phase, timing of S phase initiation, etc. These findings challenge the conventional notion that each cellâ&#x20AC;&#x2122;s phenotype is uniquely determined by the sum of its genotype and its environment. We are studying the mechanistic basis of cell-to-cell variation in cell division cycle kinetics.

EPFL School of Life Sciences - 2012 Annual Report

Selected Publications

Team Members

Tischler, A.D., Leistikow, R.L., Kirksey, M.A., Voskuil, M.I. and McKinney, J.D. (2013) Mycobacterium tuberculosis requires phosphate-responsive gene regulation to resist host immunity. Infect. Immun. 81(1): 317-328.

Postdoctoral Fellows Jean-Baptiste Bureau Tarun Chopra Zeljka Maglica Giulia Manina Isabella Santi

Wakamoto, Y., Dhar, N., Chait, R., Schneider, K., Signorino-Gelo, F., Leibler, S. and McKinney, J.D. (2013) Dynamic persistence of antibiotic-stressed mycobacteria. Science 339(6115): 91-95.

Gelman, E., McKinney, J.D. and Dhar N. (2012) Malachite green interferes with post-antibiotic recovery of mycobacteria. Antimicrob. Agents Chemother. 56(7): 3610-3614. Griffin, J.E., Pandey, A.K., Gilmore, S.A., Mizrahi, V., McKinney, J.D., Bertozzi, C.R. and Sassetti, C.M. (2012) Cholesterol catabolism by Mycobacterium tuberculosis requires transcriptional and metabolic adaptations. Chem. Biol. 19(2): 218-227. Neres, J., Pojer, F., Molteni, E., Chiarelli, L.R., Dhar, N., Boy-Röttger, S., Buroni, S., et al. (2012) Structural basis for benzothiazinone-mediated killing of Mycobacterium tuberculosis. Sci. Transl. Med. 4(150): 150ra121. Lemos, M.P., Rhee, K.Y. and McKinney, J.D. (2011) Expression of the leptin receptor outside of bone marrow-derived cells regulates tuberculosis control and lung macrophage MHC expression. J. Immunol. 187(7): 3776-3784.

Senior Staff Scientist Neeraj Dhar

PhD students Matthieu Delincé Cyntia De Piano Ekaterina Gelman Emre Özdemir Katrin Schneider Amanda Verpoorte Visiting Scientist Paul Murima Research Technician François Signorino-Gelo Administrative Assistant Suzanne Lamy

Lemos, M.P., McKinney, J.D. and Rhee, K.Y. (2011). Dispensability of surfactant proteins A and D in immune control of Mycobacterium tuberculosis infection following aerosol challenge of mice. Infect. Immun. 79(3): 1077-1085.

GHI - Global Health Institute

Kirksey, M.A., Tischler, A.D., Siméone, R., Hisert, K.B., Uplekar, S., Guilhot, C. and McKinney, J.D. (2011) Spontaneous phthiocerol dimycocerosate (PDIM) deficient variants of Mycobacterium tuberculosis are susceptible to interferonγ-mediated immunity. Infect. Immun. 79(7): 2829-2838.

Single-cell division cycle dynamics in mycobacteria. The cell division septum was visualized by fusing green fluorescent protein to a septum protein (Wag31); the DNA replisome was visualized by fusing red fluorescent protein to a replisome protein (DnaN). Using timelapse microfluidic-microscopy, we found that individual bacteria grow exponentially (as cells enlarge they grow faster) and the duration of the cell division cycle scales with the duration of S phase, suggesting a unique mechanism of cell cycle control.

EPFL School of Life Sciences - 2012 Annual Report

Trono Lab http://tronolab.epfl.ch/

After obtaining an M.D. from the University of Geneva and completing a clinical training in pathology, internal medicine and infectious diseases in Geneva and at Massachusetts General Hospital in Boston, Didier Trono embarked in a scientific career at the Whitehead Institute for Biomedical Research of MIT. In 1990, he joined the faculty of the Salk Institute for Biological Studies to launch a center for AIDS research. He 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.

Didier Trono Full Professor

Introduction

We have a long-standing interest for interactions between viral pathogens and their hosts and in the development of gene-based therapies. This drove us a few years ago to orient our research towards the field of epigenetics, initially to explore how higher species including humans control the hundreds of thousands of retroviruses that have invaded their genomes since the dawn of times. This work has allowed us to reveal how what we coined the KRAB’n’KAP system, which emerged some three hundred and fifty million years ago as a defense against these retroviral invaders, has now become a master regulator of mammalian homeostasis, and thus conditions innumerable aspects of human health and disease.

Keywords

Genetics, epigenetics, KRAB zinc finger proteins, KAP1, transcriptional regulation, retroelements, retroviruses imprinting, liver metabolism, sexual dimorphism, lymphohematopoietic system, erythropoiesis.

Results Obtained in 2012

About 1’200 of the 20’000 genes contained in the human genome encode for transcriptional regulators, including some four hundred KRAB-containing zinc finger proteins (KRABZFPs). KRAB-ZFPs are tetrapod-restricted sequence-specific DNA binding transcriptional repressors that act by triggering the formation of heterochromatin through their universal cofactor KAP1, and their genes have been subjected to intense positive selection during evolution. However, their functions were largely a terra incognita when we started exploring this question some ten years ago. We first found that KRAB/KAP regulation is the system responsible for silencing endogenous retroviruses (ERVs), and that it

also contributes to the maintenance of imprinting marks in embryonic stem cells. More recently, we revealed that the KRAB/ KAP-mediated control of ERVs is crucial, not just to prevent retrotransposition, but more broadly to safeguard the transcriptional dynamics of early embryos by repressing retroelement-based enhancers. We also demonstrated that KRAB’n’KAP is responsible for the early embryonic establishments of site-specific DNA methylation patterns that are subsequently maintained during development. In parallel, through a combination of conditional KAP1 knockout in the mouse, chromatin studies and transcription analyses, we determined that KRAB/KAP-mediated gene regulation has been co-opted to regulate events as diverse as the maturation and activation of B and T lymphocytes, the hepatic metabolism of drugs and xenobiotics, the management of behavioral stress, as well as many steps of hematopoiesis. For instance, it was known that lineage- and stage-specific transcription factors work in concert with chromatin modifiers to direct the differentiation of all blood cells. We found that hematopoietic-restricted deletion of Kap1 in the mouse results in severe hypoproliferative anemia, and that Kap1-deleted erythroblasts fail to induce mitophagy-associated genes and retained mitochondria. This is due to persistent expression of microRNAs targeting mitophagy transcripts, itself secondary to a lack of repression by stagespecific KRAB-ZFPs. We further found that the KRAB/KAP1microRNA regulatory cascade is evolutionary conserved, as it also controls mitophagy during human erythropoiesis. Thus, our work unveils a multilayered transcription regulatory system, where protein- and RNA-based repressors are super-imposed in combinatorial fashion to govern the timely triggering of an important differentiation event. The formidable modularity and robustness of such a regulatory system makes it likely that it serves to control many physiological events.

EPFL School of Life Sciences - 2012 Annual Report

Selected Publications

I. Barde, B. Rauwel, R. M. Marin-Florez, A. Corsinotti, E. Laurenti, S. Verp, S. Offner, J. Marquis, A. Kapopoulou, J. Vanicek and D. Trono (2013). A KRAB/ KAP1-miRNA cascade regulates erythropoiesis through stage-specific control of mitophagy. Science, e-pub on Science Express March 14. H.M. Rowe, M. Friedli, S. Offer, S. Verp, D. Mesnard, J. Marquis, T. Aktas and D. Trono (2013). De novo DNA methylation of endogenous retroviruses is shaped by KRAB-ZFPs/KAP1 and ESET. Development, 140: 519-529. H.M. Rowe, A. Kapopoulou, A. Corsinotti, L. Fasching, T.S. McFarlan, Y. Tarabay, S. Viville, J. Jakobsson, S.L. Pfaff and D. Trono (2013). TRIM28 repression of retrotransposons-based enhancers is necessary to preserve transcriptional dynamics in embryonic stem cells. Genome Res., e-pub. Jan 14. S. Quenneville, P. Turelli, K. Bojkowska, C. Raclot, S. Offner, A. Kapopoulou and D. Trono (2012). The KRAB/KAP1 system contributes to the early embryonic establishment of site-specific DNA methylation patterns maintained during development. Cell Reports, 2: 776-773. T.S. Macfarlan, W.D. Gifford, H. Rowe, S. Driscoll, D. Bonamomi, S.E. Andrews, K. Lettieri, A. Firth, O. Dinger, D. Trono and S.L. Pfaff (2012). LTR-linked zyogtic genes mark a transient totipotent population in ES cells. Nature, 487: 57-63. K. Bojkowska, F. Aloisio, M. Cassano, A. Kapopoulou, F. Santoni de Sio, N. Zangger, S. Offner, C. Cartoni, C. Thomas, S. Quenneville, K. Johnsson and D. Trono (2012). Liver-specific ablation of KRAB-associated protein 1 in mice leads to male-predominant hepatosteatosis and development of liver adenoma. Hepatology, 56: 1279-1290. F.R. Santoni de Sio, J. Masssacand, I. Barde, S. Offner, A. Corsinotti, A. Kapopoulou, K. Bojkowska, A. Dagkis, M. Fernandez, P. Ghia, J.H. Thomas, D. Pinschewer, N. Harris and D. Trono (2012). KAP1 regulates gene networks controlling B lymphoid differentiation and function. Blood, 119: 4675-4685. S. Quenneville, G. Verde, A. Corsinotti, A. Kapopoulou, J. Jakobsson, S. Offner, I. Baglivo, P.V. Pedone, G. Grimaldi, A. Riccio and D. Trono (2011). In embryonic stem cells, ZFP57/KAP1 recognize a methylated hexanucleotide to affect the chromatin and DNA methylation of imprinting control regions. Mol. Cell, 44: 361-372.

Team Members Senior Scientist Priscilla Turelli

Postdoctoral Fellows Isabelle Barde Marco Cassano Marc Friedli Michael Imbeault Julien Marquis Simon Quenneville Benjamin Rauwel Helen Mary Rowe Benyamin Yazdan Panah PhD Students Karolina Bojkowska Natali Castro Diaz Andrea Corsinotti Gabriella Ecco Annamaria Kauzlaric Flavia Marzetta Andrea Coluccio Bioinformaticians Adamandia Kapopoulou Yoann Mouscaz Visiting scientist Timothy Lane Technicians Sandra Offner Charlène Raclot Sonia Verp Administrative Assistant Séverine Reynard

GHI - Global Health Institute

Magic touch Our work on KRAB’n’KAP-mediated regulation of erythropoiesis reveals a multilayered transcription control system, where lineage- and stagespecific KRAB-ZFP (top) and microRNA (middle) repressors are superimposed in combinatorial fashion to tune the expression of several effector genes (bottom) along a same pathway, so as to allow for the timely triggering of an essential step of differentiation. This type of regulation, likely to be at play in a very high number of physiological events, is formidably modular and robust.

EPFL School of Life Sciences - 2012 Annual Report

Van der Goot Lab http://vdg.epfl.ch/

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 finally Full Professor at the EPFL in 2006, where she co-founded the Global Health Institute.

F. Gisou van der Goot Full Professor

Introduction

Our laboratory has three main focuses: 1) understanding the physiological and pathological roles of the anthrax toxin receptors, TEM8 and CMG2; 2) unraveling the molecular mechanisms responsible for Hyaline Fibromatosis syndrome, a rare genetic disease due to mutations in CMG2. 3) Our third focus is on the compartmentalization of mammalian cells and the function thereof. We are particularly interested in the architecture of the endoplasmic reticulum and how its complex structure relates to function.

Keywords

Anthrax toxin, systemic hyalinosis, hyaline fibromatosis, TEM8, CMG2, endoplasmic reticulum, palmitoylation.

Results Obtained in 2012

Consequences of Hyaline Fibromatosis Syndrome mutations - Hyaline Fibromatosis Syndrome (HFS) is a human genetic disease caused by mutations in the anthrax toxin receptor 2 (or cmg2) gene, which encodes a membrane protein thought to be involved in the homeostasis of the extracellular matrix. Little is known about the structure and function of the protein and the genotype-phenotype relationship of the disease. Mutations are found throughout the gene and can be classified in 4 classes, 2 of which we have previously characterized. This year we have focused on hotspot for frameshift mutations in exon 13 which accounts for sixty percent of patientâ&#x20AC;&#x2122;s mutations. We found using patient cells that these mutations lead to low CMG2 mRNA and undetectable protein levels. Ectopic expression of the proteins encoded by the mutated genes revealed that a 2 base insertion leads to the synthesis of a protein that is rapidly targeted to the ER associated degradation pathway due to the modified structure of the cytosolic tail, which instead of being hydrophilic and highly disordered as in wild type CMG2, is folded and exposes hydrophobic patches. In contrast, one base insertions lead a truncated protein that properly localizes to the plasma membrane and retains par-

tial function. We next found that targeting the non-sense mediated mRNA decay pathway in patient cells leads to a rescue of ANTXR2 protein in patients carrying 1 base insertions but not in those carrying 2 base insertions. This study highlights the importance of in depth analysis of the molecular consequences of specific patient mutations, which even when they occur at the same site, can have drastically different consequences. Anthrax toxin hijacks multivesicular endosomes for long term action in cells - Pathogens, and their products, are masters in exploiting the endocytic pathway of mammalian cells to their own benefit. An illustrative example is anthrax lethal toxin, which is targeted, through its receptor, to the intraluminal vesicles (ILVs) of multivesicular endosomes, into which it translocates its enzymatic subunit, the Lethal Factor (LF). LF is subsequently released into the cytosol via back-fusion of the ILVs with the limiting endosomal membrane. We found that the LF can persist in cells for over a week, following only 1 hour of toxin exposure. LF remains sheltered from degradation within the lumen of ILVs and is transmitted to daughter cells upon cell division. Due to slow but continuous release of LF to the cytosol and to the potency of the enzyme, this leads to efficient long-term toxin action. These findings not only explain the long known persistence of anthrax toxin during infection, but also have important implications in terms of immune response and potential therapeutic treatment. More over, the delivery of LF to daughter cells over several rounds of cell division reveals the unexpected stable nature of multivesicular endosomes.

EPFL School of Life Sciences - 2012 Annual Report

Selected publications

Deuquet J., Lausch E. , Guex N., Abrami L., Salvi S., Lakkaraju A., Ramirez MCM, Martignetti J.A., Rokicki D., Bonafe L., Superti-Furga A. and F. G. van der Goot (2011) Hyaline Fibromatosis Syndrome inducing mutations in the ectodomain of anthrax toxin receptor 2 can be rescued by proteasome inhibitors. EMBO Mol. Med. 3:208-221. Gonzalez, RM., Bischofberger, M., Frêche, B., Ho, S., Parton, R.G. and F.G. van der Goot (2011) Pore-forming toxins induce multiple cellular responses promoting survival. Cellular Microbiology Apr 26. doi: 10.1111/j.14625822.2011.01600.x. Iacovache, I. Degiacomi, M.T., Pernot, L., Ho, S., Schiltz, M., Dal Peraro, M.* and van der Goot, F. G.* (2011) Dual chaperone role of the C-terminal propeptide in folding and oligomerization of the pore-forming toxin aerolysin. PLoS Pathogen 7:e1002135. *Co-senior corresponding author Opota O., Vallet-Gély I., Kellenberger C., Vincentelli R., Iacovache I., Gonzales M. R., Roussel, A., van der Goot F.G. and Lemaitre B. (2011) Identification of a novel ß-pore-forming toxin required for the pathogenesis of Pseudomonas entomophila in Drosophila. PLoS Pathogen 7: e1002259.

Team Members Scientist Collaborator Laurence Abrami

Postdoctoral Fellows Mathieu Blanc Ioan Iacovache (till August 2012) Asvin Lakkaraju PhD Students Sanja Blaskovic Jérôme Bürgi Sarah Frieben Patrick Sandoz Shixu Yan Laboratory Assistants Sylvia Ho Béatrice Kunz Suzanne Salvi Administrative Assistants Carole Burget Geneviève Rossier

Deuquet, J., Lausch E., Superti-Furga, A. and F.G. van der Goot (2011) The dark side of capillary morphogenesis gene 2. EMBO J. 31 :3-13. Lakkaraju, A.K.K., Abrami, L., Lemmin,T., Blaskovi, S., Kunz,B., Kihara, A., Dal Peraro, M. and van der Goot, F.G. (2012) Palmitoylated calnexin is a key component of the ribosome-translocon complex. EMBO J. 31 : 1823-35. Rojek, J.M., Moraz, M-L., Pythoud, C., Rothenberger, S. van der Goot, F.G. and S. Kunz (2012) Binding of Lassa virus perturbs extracellular matrix-induced signal transduction via dystroglycan. Cellular Microbiology 14:1122-1134 Castanon, I. , L. Abrami, L. Holtzer, C. P. Heisenberg, F. G. van der Goot* and M. González–Gaitán* (2012) Anthrax Toxin Receptor 2a controls mitotic spindle positioning. Nature Cell Biology 15:28-39. *Co-senior corresponding author

GHI - Global Health Institute

Bischofberger M., Iacovache, I and van der Goot, F.G. (2012) Pathogenic PoreForming Proteins: Function and Host Response. Cell Host & Microbes 12:266-275.

CMG2 structure and HFS mutations. Schematic representation of the CMG2 structure. The vWA domain corresponds to the crystal structure (1tzn) and the Ig-like domain to our recently published model (Deuquet et al, 2011). (A) Residues in blue represent the N-glycosylation sites and cysteine residues are shown in yellow. (B) The position and identity of reported extracellular missense HFS mutations are mapped onto the CMG2 model. The figure was generated using UCSF Chimera© software (Pettersen et al, 2004).

EPFL School of Life Sciences - 2012 Annual Report

ISREC

Swiss Institute for Experimental Cancer Research

Douglas Hanahan - Director

ISREC has been centrally involved in the plans to create a new multi-institutional cancer center, involving EPFL, the University/Cantonal Hospital (CHUV), and the biomedical research faculty of the University of Lausanne (UNIL). Toward that end a series of community building efforts have been instituted and sponsored by ISREC, including a monthly faculty research talk and a day-long faculty retreat, each involving all interested faculty from CHUV, UNIL, and EPFL. In addition ISREC sponsored a two-day faculty plus staff research retreat, again involving all interested labs from the cancer community in Lausanne. ISREC has also inaugurated a monthly seminar series, the ‘Lola and John Grace Distinguished Lectures in Cancer Research’, which invites internationally prominent cancer researchers to present lectures on their latest research. The Grace Lecturers spend the lecture day at EPFL meeting with faculty and students, and then visit faculty at CHUV/UNIL on the following day. This series has been made possible through the visionary support of John and Lola Grace, who live in the region. And finally, following on from the exceptionally successful ISREC Symposium in 2011 on ‘The Hallmarks of Cancer’, planning for the next ISREC Symposium began in 2012. The next ISREC Symposium is scheduled for January 22-25, 2014, in the town of Crans Montana in the Valais, on the topic of “Metastatic colonization: microenvironments, mechanisms, and therapeutic targeting”.

ISREC - Swiss Institute for Experimental Cancer Research

The Swiss Institute for Experimental Cancer Research (ISREC) includes fifteen core and three joint faculty members, whose research programs variously focus on basic and translational cancer research, and on cancer-related cell and developmental biology. Details on most research programs can be found on the ISREC Institute web site (isrec.epfl.ch).

EPFL School of Life Sciences - 2012 Annual Report

Aguet Lab

http://aguet-lab.epfl.ch/

Michel Aguet, MD, held positions in academia and industry (associate professor at the Institute of Molecular Biology, University of Zürich; head of Molecular Oncology, Genentech, So. San Francisco) before he was appointed director of ISREC (1996-2009). He joined EPFL when ISREC became integrated into the School of Life Sciences and directs the National Center of Competence in Research (NCCR) in Molecular Oncology. In the past his research focused on interferon signaling. More recently his interest has shifted towards investigating the involvement of embryonic development pathways in cancer cell differentiation.

Michel Aguet Full Professor

Introduction

Our group recently observed in a mouse model of colon adenocarcinoma that inactivation of BCL9 proteins, which are part of the WNT/β-catenin transcriptional activation complex, results in abrogation of transcriptional signatures characteristic of stem cells and associated with tumor progression and drug resistance. The main focus of our current research is to explore whether inhibiting the function of these proteins in human colon cancer cells can revert such traits and may lead to a novel therapeutic approach.

Keywords

WNT pathway, BCL9/BCL9L, intestinal tumorigenesis, epithelial-mesenchymal transition, cancer stem cells, resistance to chemotherapy, drug target validation.

Results Obtained in 2012

Canonical WNT-signaling regulates critical processes during embryonic development and adult tissue renewal, and aberrant activation of this pathway is associated with colorectal and other cancers. Oncogenic mutations in the WNT pathway cause ligand-independent pathway activation, due to the inappropriate stabilization of β-catenin, leading to aberrant transcription of β-catenin/TCF target genes. WNT signals may result in different outcomes, dependent upon tissue origin and cellular context, and stimulate cell proliferation, as well as control cell fate and differentiation. WNT signaling has also been implicated in the regulation of epithelial-mesenchymal transition (EMT). EMT has been associated with invasive and metastatic tumor behavior, and there is growing evidence suggesting a relationship between EMT, the emergence of cancer stem cells (CSCs) and drug resistance. Targeting pathways that regulate EMT and/or CSC traits may therefore prove of particular clinical relevance, with regard to preventing invasion and metastasis, and for precluding the outgrowth of therapy-resistant tumor cells. We recently described phenotypic changes in a mouse model of colon adenocarcinoma suggesting that the WNT signaling components BCL9/BCL9L are critical for the ex-

pression of a subset of WNT target genes relevant to controlling EMT- and stem cell-associated traits. Current work aims primarily at extending our studies to human cell-based CRC (colon rectal cancer) models. We established a strategy to efficiently and specifically prevent the interaction between BCL9 proteins and β-catenin through conditional expression of a BCL9L-derived decoy protein. Preliminary gene expression profiling studies indicated that, similar to the mouse CRC model, suppression of BCL9/BCL9L-function in colon SW480 cells resulted in wide-ranging transcriptional perturbations including decreased expression of a stem cell signature accompanied by an increase in cell differentiation markers. These preliminary observations revealed that SW480 cells comprise phenotypically distinct subpopulations and point to a model whereby suppression of BCL9/ BCL9L provokes changes in cell state transitions, which over time alter the relative proportions of SW480 subpopulations, favoring more differentiated cell states. Ongoing work aims at corroborating this model and further validating that suppression of BCL9/BCL9L function attenuates WNT-mediated maintenance of stem cell traits and favors differentiation in populations enriched for CRC stem cells obtained through colosphere cultures of primary mouse and human CRC tissue. Encouraged by the therapeutic perspectives of inhibiting the BCL9/BCL9L-β-catenin interaction, we have established a protein-protein interaction assay to screen for candidate inhibitors. This time resolved fluorescence-based assay (HTRF) has been optimized for high throughput compound screening and tested with the help of the EPFL Biomolecular Screening Facility. Small scale screening of commercially available libraries resulted in the identification of a few hits, some of which could be validated. Based upon this proof of concept, HTS was launched at the European Screening Port in Hamburg and the Small Molecule Discovery Center at UCSF. Hit validation and optimization is carried out in collaboration with academic and industrial partners with expertise in structural biology and medicinal chemistry.

EPFL School of Life Sciences - 2012 Annual Report

Selected Publications

Christensen J., El-Gebali S., Natoli M., Sengstag T., Delorenzi M., Bentz S., Bouzourene H., Rumbo M., Felsani A., Siissalo S., Hirvonen J., Vila M.R., Saletti P., Aguet M., and Anderle P. (2012). Defining new criteria for selection of cellbased intestinal models using publicly available databases. BMC Genomics 13: 274-284. Valenta, T., Gay, M., Steiner, S., Draganova, K., Zemke, M., Hoffmans, R., Cinelli, P., Aguet, M., Sommer, L., and Basler, K. (2011). Probing transcription-specific outputs of beta-catenin in vivo. Genes & Dev. 25, 2631-2643. Deka, J., Wiedemann, N., Anderle, P., Murphy-Seiler, F., Bultinck, J., Eyckerman, S., Stehle, J.C., Andre, S., Vilain, N., Zilian, O., et al. (2010). Bcl9/Bcl9l Are Critical for Wnt-Mediated Regulation of Stem Cell Traits in Colon Epithelium and Adenocarcinomas. Cancer Res. 70, 6619-6628.

Team Members

Staff scientist & Scientific manager NCCR «Molecular Oncology» Juergen Deka Postdoctoral Fellows Frédérique Baruthio Patrick Rodriguez Norbert Wiedemann MD/PhD student Andreas Moor PhD student Norbert Wiedemann Technician Sylvie André

ISREC - Swiss Institute for Experimental Cancer Research

Administrative assistant NCCR «Molecular Oncology» Valérie Le Dréau

Consecutive histological sections of AOM/DSS induced mouse adenocarcinomas. Ablation of BCL9/BCL9L was induced in pre-established tumors using tamoxifen-regulated Cre-recombinase. The transcriptional down-regulation in BCL9/BCL9L-mutant tumors of mesenchymal traits including the intermediate filament protein, vimentin, was confirmed by immunohistochemistry and was accompanied by restoration of basement membrane integrity, indicating that the wild-type tumor phenotype was shifted towards a lower tumor grade. Areas in which BCL9 protein is still present, presumably due to inefficient tamoxifen permeation, show remains of the wild-type phenotype (arrows).

EPFL School of Life Sciences - 2012 Annual Report

Brisken Lab

http://brisken-lab.epfl.ch/

http://www.nccr-oncology.ch/

Cathrin Brisken received an MD and a PhD in Biophysics from the Georg August University of Göttingen in 1993. She did postdoctoral work at the Whitehead Institute, MIT, MA, USA and became a research scientist there in 1999. She was assistant professor at the MGH Cancer Center, Harvard University before joining the NCCR Molecular Oncology at ISREC in 2002 and EPFL in 2005. She is a member of IBCSG (International Breast Cancer Study Group) Biological Protocol Working Group, various Scientific Advisory Boards and the Hinterzartener Kreis”, cancer think tank of the German Science Foundation.

Cathrin Brisken

Associate Professor Dean of EPFL Doctoral School

Introduction

The female reproductive hormones control breast development and breast cancer formation. Our aim is to understand how the reproductive hormones interact with local signaling pathways to control proliferation and morphogenesis in the breast, and how these pathways in turn contribute to breast carcinogenesis. To address these questions in vivo, we have made extensive use of the mouse model, different mutant strains and powerful tissue recombination techniques. These approaches have allowed us to characterize the role of the reproductive hormones in mammary gland development and to identify several downstream mediators (Figure 1):

Figure 1: Schematic representation of mammary gland development (black) and our current working model of how various factors control different morphogenetic steps (color) based on our previous work.

Keywords

Breast cancer, hormones, breast tissue microstructures, progesterone, RANKL, Wnt4, denosumab (AMGEN).

Results Obtained in 2012

It has long been an open question whether the mechanisms important in the mouse mammary gland are of relevance to the human breast. Our understanding of how hormones act on the human breast has been hampered by the lack of model systems to study this question. When human breast cells are put into culture for laboratory studies, they loose the hormone receptors. Hence they become insensitive to hormones.

Through a longstanding collaboration with clinical colleagues, Prof. Wassim Raffoul (Plastic Surgery, CHUV) and Dr. Maryse Fiche (Pathology, CHUV) and Dr. Delaloye (Gynecology, CHUV), we regularly obtain normal human breast tissue from women who undergo reduction mammoplasty. We have developed procedures that allow us to obtain through careful dissociation of the freshly isolated human breast tissue little fragments, breast tissue microstructures. In these, the milk duct cells preserve all the contacts with their neighboring cells. They retain hormone receptors and most importantly, remain sensitive to hormones. Using these tissue structures we have shown that estrogen stimulates cell proliferation only in a subset of women. Progesterone on the other hand is a strong proliferative stimulus in most breast samples. Excitingly, two major factors we had shown to by essential for progesterone action in the mouse mammary gland are also made by human milk duct cells in response to progesterone : Wnt-4 and RANKL. RANKL is secreted by cells that have the progesterone receptor when progesterone levels in the blood are high. It talks to the neighboring cells and makes them proliferate. The protein is required as a mediator of the proliferative response to progesterone. These findings have important implications because an inhibitor for RANKL a drug called denosumab (AMGEN) is already available and currently used to treat various bone diseases. We and others are now exploring the possibility that this drug may help breast cancer patients.

EPFL School of Life Sciences - 2012 Annual Report

Selected Publications

Cimino D, De Pittà C, Orso F, Zampini M, Casara S, Penna E, Quaglino E, Forni M, Damasco C, Pinatel E, Ponzone R, Romualdi C, Brisken C, De Bortoli M, Biglia N, Provero P, Lanfranchi G, Taverna D. (2013). miR148b is a major coordinator of breast cancer progression in a relapse-associated microRNA signature by targeting ITGA5, ROCK1, PIK3CA, NRAS, and CSF1. FASEB J. 2013 Mar;27(3):1223-35. doi: 10.1096/fj.12-214692. Epub 2012 Dec 11. Dong J, Huang S, Caikovski M, Ji S, McGrath A, Custorio MG, Creighton CJ, Maliakkal P, Bogoslovskaia E, Du Z, Zhang X, Lewis MT, Sablitzky F, Brisken C, Li Y. (2011) ID4 regulates mammary gland development by suppressing p38MAPK activity. Development 138(23):5247-56. doi: 10.1242/dev.069203. Ayyanan A, Laribi O, Schuepbach-Mallepell S, Schrick C, Gutierrez M, Tanos T, Lefebvre G, Rougemont J, Yalcin-Ozuysal O, Brisken C. (2011). Perinatal exposure to bisphenol a increases adult mammary gland progesterone response and cell number. Mol Endocrinol. 25:1915-23. doi: 10.1210/me.2011-1129. Epub 2011 Sep 8. Reviews Tanos T, Rojo LJ, Echeverria P, Brisken C. (2012). ER and PR signaling nodes during mammary gland development. Breast Cancer Research. 2012 Jul 19;14(4):210. Rajaram RD, Brisken C. (2012). Paracrine signaling by progesterone. Molecular And Cellular Endocrinology 2012 Jun 24;357(1-2):80-90. doi: 10.1016/j. mce.2011.09.018. Epub 2011 Sep 16.

Team Members Senior Scientist Cécile Lebrand

Postdoctoral Fellows Georgios Sflomos Lucia Jimenez Rojo Marian Caikovski Renuga Devi Rajaram Tamara Tanos PhD Students Duje Buric Duygu Deniz Bas Yakir Guri Senior Technician Ayyanan Ayyakkannu Scientist Assistant Andreas Moor Technicians Maria Gutierrez Najera Mélanie Wirth Jean Halbert Technician Assistant Pinelopi Chatziemmanouil

ISREC - Swiss Institute for Experimental Cancer Research

Administrative Assistant Lisa Cessy

Immunofluorescence of human milk ducts, cells are revealed by nuclear staining (DAPI) in blue. A subset of cells expresses RANKL on their cell membrane (green). The RANKL secreting cells have the progesterone receptor in the nucleus (red) consistent with progesterone controlling the expression of RANKL protein.

EPFL School of Life Sciences - 2012 Annual Report

Constam Lab

http://constam-lab.epfl.ch/

Daniel Constam obtained his doctoral degree from ETH Zürich for studies on TGFβ isoforms in the central nervous system. In 1994, he moved to Harvard University as an EMBO postdoctoral fellow to investigate the regulation of TGFβ signaling by proprotein convertases. He joined ISREC as a group leader in 2000 and EPFL as Assistant Professor in 2005. He became an associate professor at the School of Life Sciences in 2007. Prof. Constam is interested in the molecular interactions between stem cells and their microenvironments that govern morphogenesis and tissue homeostasis.

Daniel Constam Associate Professor

Introduction

Identifying cues that guide the maturation of progenitor cells into functional tissues during development is important because incomplete differentiation increases the aggressiveness of tumor cells and limits the use of stem cellderived transplants in regenerative medicine. The Constam lab showed that signals regulating stem cell fates in the early mouse embryo are activated by secreted proteases from the microenvironment. They also found that signal transduction of mechanoreceptors that are mutated in polycystic kidney disease is tuned by miRNA-induced gene silencing mediated by the RNA-binding protein BICC1. Finding the targets of BICC1 may pave a way for improved monitoring or therapy of renal cysts.

Keywords

Development and cancer, stem cell fate, polycystic kidney disease, cilia and planar polarity signaling, protein processing and trafficking; microRNA.

Results Obtained in 2012

Proteolytic enzymes of the PCSK family of proprotein convertases are implicated to process various growth factor receptors, ligands, prohormones and other substrates in exocytic vesicles. However, live imaging and functional analysis in early mouse embryos revealed that PCSK6 (Pace4) and a shed form of PCSK3 (furin) are secreted by extraembryonic ectoderm to activate Nodal and possibly other stem cell factors in a paracrine manner. Therefore, and since localization determines which substrates can be cleaved, we began to systematically quantify individual PCSK activities in various subcellular compartments in cancer cell lines. We also investigated how the RNA-binding protein Bicc1 enables epithelial cells in the developing kidney to arrest proliferation and consolidate the tubular architecture of functional nephrons. Renal tubules derive from multipotent progenitors in metanephric mesenchyme that are induced by ureteric bud-derived Wnt signals to condensate and form renal vesicles. Mechanosensory complexes of polycystin-1 and polycystin-2 enable the subsequent elongation and maintenance of tubular structures, primarily by stimulating Ca2+ influx. Mutations in the corresponding PKD1 and

PKD2 genes cause autosomal dominant polycystic kidney disease (ADPKD), a chronic disorder that is characterized by the appearance of fluid-filled cysts. How Ca2+ suppresses cyst formation is incompletely understood, but an important role is to reduce the levels of cAMP by inhibiting the Ca2+-sensitive adenylate cyclases AC6 and AC5. Cysts also develop in mice and humans with mutations in Bicc1 (Fig. 1a). Bicc1 comprises 3 KH domains and a sterile alpha motif (SAM) that mediate RNA-binding and selfpolymerization, respectively. We found that Bicc1-/- mouse kidneys accumulate elevated levels of cAMP and of its synthetic enzyme AC6 (Fig. 1b). Furthermore, studies in kidney cell lines revealed that Bicc1 KH domains independently bind the 3’UTR of AC6 and the cognate miRNA miR-125a, whereas the SAM domain mediates their incorporation into a silencing complex with argonaute-2. By an analogous mechanism, Bicc1 also promoted silencing of a negative regulator of cAMP signaling, the protein kinase A (PKA) inhibitor (PKI)-α, by miR-27a. Bicc1 thus emerges as a novel regulator of miRNA target selection required together with polycystins to adjust the levels of cAMP and PKA activity to the demands of maturing renal epithelial cells and their tubular architecture (Fig. 1d). In cystic renal epithelial cells of ADPKD patients, elevated cAMP levels lead to sustained proliferation and fluid secretion. How polycystins are mechanically stimulated to enable renal tubule formation is unclear. In growth-arrested cells, polycystins localize to primary cilia that may sense urine flow, but hydrostatic and osmotic pressures also activate polycystins bound to filamentous actin. In Bicc1 mutant kidneys, we observed a striking loss of subapical filamentous actin (Fig. 1c). In addition, Bicc1 has been reported to protect PKD2 mRNA against silencing by miR-17, suggesting that Bicc1 also promotes mechanosensation. Independently of RNA binding domains, Bicc1 in addition can attenuate canonical Wnt signaling through an interaction with Dishevelled (Dvl/Dsh protein). Taken together, our findings place Bicc1 at the nexus between diverse extracellular inputs and the intracellular regulatory circuits that control the differentiation of immature epithelial cells into terminally differentiated, functional tubules.

EPFL School of Life Sciences - 2012 Annual Report

Selected Publications

Team Members

Kraus, M.R., Clauin, S., Pfister, Y., Di Maio, M., Ulinski, T., Constam, D., Bellanne-Chantelot, C., Grapin-Botton, A., 2012. Two mutations in human BICC1 resulting in WNT pathway hyperactivity associate with cystic renal dysplasia. Hum. Mutat. 33(1):86-90.

PhD Students Florian Bernet Chhavi Jain Lucia Leal-Esteban

Piazzon, N., Maisonneuve, C., Guilleret, I., Rotman, S., Constam, D.B., 2012. Bicc1 links the regulation of cAMP signaling in polycystic kidneys to microRNAinduced gene silencing. J. Mol. Cell. Biol. 4(6):398-408.

Staff Séverine Urfer-Beck Stéphane Baflast

Besnard, J., Ruda, G.F., Setola, V., Abecassis, K., Rodriguiz, R.M., Huang, X.P., Norval, S., Sassano, M.F., Shin, A.I., Webster, L.A., Simeons, F.R., Stojanovski, L., Prat, A., Seidah, N.G., Constam, D.B., Bickerton, G.R., Read, K.D., Wetsel, W.C., Gilbert, I.H., Roth, B.L., Hopkins, A.L., 2012. Automated design of ligands to polypharmacological profiles. Nature 492(7428):215-220.

Mesnard, D., Donnison, M., Fuerer, C., Pfeffer, P.L., Constam, D.B., 2011. The microenvironment patterns the pluripotent mouse epiblast through paracrine Furin and Pace4 proteolytic activities. Genes Dev. 25(17):1871-1880.

Postdoctoral Fellows Sylvain Bessonnard Prudence Donovan Christophe Fuerer Daniel Mesnard Nathalie Piazzon

Administrative Assistant Virginie Kokocinski

Susan-Resiga, D., Essalmani, R., Hamelin, J., Asselin, M.C., Benjannet, S., Chamberland, A., Day, R., Szumska, D., Constam, D., Bhattacharya, S., Prat, A., Seidah, N.G., 2011. Furin is the major processing enzyme of the cardiac-specific growth factor bone morphogenetic protein 10. J. Biol. Chem. 286(26):2278522794.

ISREC - Swiss Institute for Experimental Cancer Research

Turco, M.Y., Furia, L., Dietze, A., Fernandez Diaz, L., Ronzoni, S., Sciullo, A., Simeone, A., Constam, D., Faretta, M., Lanfrancone, L., 2012. Cellular Heterogeneity During Embryonic Stem Cell Differentiation to Epiblast Stem Cells is Revealed by the ShcD/RaLP Adaptor Protein. Stem Cells 30(11):2423-2436.

Figure 1. Renal tubule morphogenesis and suppression of cysts depend on Bicc1, a novel regulator of miRNA target selection that controls cAMP/PKA signaling a) Staining of a proximal tubule marker (LTL) in cystic Bicc1-/- and wild-type kidneys b) Levels of AC6 at day P0 and of cAMP (P4-11) in kidney extracts c) F-actin staining at P0 d) Bicc1 regulates gene silencing by miRNAs

EPFL School of Life Sciences - 2012 Annual Report

De Palma Lab http://depalma-lab.epfl.ch/

Michele De Palma Tenure Track Assistant Professor

Michele De Palma obtained his PhD from the University of Turin Medical School, where he studied the role of bone marrow-derived cells in tumor angiogenesis. He described a macrophage subset that promotes angiogenesis in tumors and regenerating tissues, the Tie2expressing macrophages (TEMs). He then joined the San Raffaele Institute in Milan to continue his studies on the interplay between macrophages and tumor angiogenesis, and to explore the potential of monocyte-based delivery of biotherapeutics to tumors. He received several awards from the American and European Societies of Gene Therapy, and a European Research Council Starting grant in 2009. In 2012, he was appointed Assistant Professor and group leader at the Swiss Institute for Experimental Cancer Research (ISREC). He is routinely invited to international conferences on the topics of angiogenesis, and inflammation and cancer.

Introduction

Macrophages are immune cells that can support tumor progression by several mechanisms, one of which is the promotion of angiogenesis (the growth of new blood vessels). Our laboratory investigates the mechanisms whereby macrophages control angiogenesis in mouse models of cancer. This is being studied primarily in mouse models of breast cancer, in which macrophages are genetically engineered to be visualized or depleted, or to modify their expression of both coding and non-coding RNAs of interest. We also investigate how macrophages modulate tumor responses to chemotherapy and antiangiogenic treatments, such as those targeting the vascular-endothelial growth factor (VEGF) or angiopoietin-2 (ANG2) pathways.

Keywords

Tumor-associated macrophage, angiogenesis, microRNA, TIE2, ANG2, VEGF, Antiangiogenic therapy, chemotherapy.

Results Obtained in 2012

We have recently established our new laboratory at ISREC. The main focus of the lab is to investigate the interactions between macrophages and other components of the tumor microenvironment â&#x20AC;&#x201C; tumor blood vessels in particular â&#x20AC;&#x201C; with the ultimate goal to identify therapeutic targets in the macrophages that could restrain their proangiogenic and protumoral functions. Current research interests in our laboratory include: Exploring novel mechanisms whereby perivascular macrophages promote tumor angiogenesis - Besides their production of growth factors and proteolytic enzymes that facilitate the growth and expansion of new blood vessels, TAMs may release microvesicles (MVs) that shuttle functional microRNAs to angiogenic endothelial cells, thus modulating angiogenesis. We are currently exploring this scenario by using genetic strategies that sense, squelch or enforce microRNA trafficking from macrophages to endothelial cells in tumors.

Analyzing the contribution of macrophages to tumor responses (and resistance) to anticancer therapies - Recent studies suggest that macrophages may help tumors resist different anticancer treatments. We are currently investigating how TAMs (tumor associated macrophages) modulate tumor responses to chemotherapy or antiangiogenic drugs either targeting the VEGF/VEGFR2 or ANG2/TIE2 signaling pathway. This will be pursued primarily by molecular profiling of distinct TAM subsets (along with other tumor-associated stromal cells) from both untreated and treated mouse tumors (breast, pancreatic neuro-endocrine, and lung cancer models). These studies may help identify novel targets for combination-based treatments as well as biomarkers of tumor response to antiangiogenic therapy. Molecular profiling of mouse TAMs will be extended to the analysis of human cancer specimens. Exploring the pro-fibrotic activity of macrophages in tumors - Macrophages are known to express several proteolytic and matrix-remodeling enzymes in tumors. Our gene expression studies also suggest that macrophages secrete several fibrous proteins, including selected collagens. We will investigate the significance of TAM-derived collagens for matrix biogenesis and angiogenesis in ad hoc mouse tumor models, and interrogate the involvement of ROCK2 in modulating the profibrotic activity of macrophages. In 2012, we have performed an extensive characterization of the microRNA profile of macrophage-derived MVs, and assayed their ability to vehicle functional microRNAs to endothelial cells. Current studies are aimed to investigate the significance of this process for tumor angiogenesis. Furthermore, we have analyzed the role of TAMs in modulating tumor responses to the taxane, paclitaxel, as well as antiangiogenic drugs targeting the VEGF and ANG2 pathways. This has been primarily studied in mouse models of breast cancer and pancreatic islet insulinoma. Our preliminary data suggest that TAMs limit the efficacy of such anticancer treatments, and current studies are addressing the molecular bases of this phenomenon.

EPFL School of Life Sciences - 2012 Annual Report

Selected Publications

Team Members

Squadrito, M. L., Etzodt, M., De Palma, M.*, Pittet, J. M.* (2013) MicroRNA-mediated control of macrophages and its implications for cancer. Trends Immunol. doi: 10.1016/j.it.2013.02.003.

PhD Students Daniela Biziato Caroline Baer

De Palma, M., and Lewis, C. E. (2013) Macrophage regulation of tumor responses to anticancer therapies. Cancer Cell. doi: 10.1016/j.ccr.2013.02.013.

Squadrito, M. L., Pucci, F., Magri, L., Moi, D., Gilfillan, G. D., Ranghetti, A., Casazza, A., Mazzone, M., Lyle, R., Naldini, L., and De Palma, M. miR-511-3p modulates genetic programs of tumor-associated macrophages. Cell Reports. 2012 Feb 23;1(2):141-154. Takeda, Y., Costa, S., Delamarre, E., Roncal, C., Leite De Oliveira, R., Squadrito, M.L., […], De Palma, M., and Mazzone, M. Macrophage skewing by PHD2 haplodeficiency prevents ischemia by inducing arteriogenesis. Nature. 2011 Nov 4;479:122-126.

Postdoctoral Fellows Mario Leonardo Squadrito Nicolò Rigamonti

Research Assistants Giuseppe Muraca Claudio Maderna Master Student Ece Kadioglu Administrative Assistant Christine Skaletzka

Welford, A.F., Biziato, D., Coffelt, S.B., Nucera, S., Fisher, M., Pucci, F., Di Serio, C., Naldini, L., De Palma, M.*, Tozer, G.M.* and Lewis, C.E.*. TIE2-Expressing Macrophages Limit the Therapeutic Efficacy of the Vascular Disrupting Agent, Combretastatin A4 Phosphate. J Clin Invest. 2011 May 2;121:1969-73. Mazzieri, R., Pucci, F., Moi, D., Zonari, E., Ranghetti, A., Berti, A., Politi, L.S., Gentner, B., Brown, J., Naldini, L., and De Palma, M. Targeting the ANG2/ TIE2 axis inhibits tumor growth and metastasis by impairing angiogenesis and disabling rebounds of proangiogenic myeloid cells. Cancer Cell. 2011 Apr 12;19(4):512-26.

ISREC - Swiss Institute for Experimental Cancer Research

Rolny, C., Mazzone, M., Tugues S, Laoui D, Johansson, I., Coulon, C., Squadrito, M. L., […], De Palma, M., Dewerchin, M., Claesson-Welsh, L., Carmeliet, P. HRG inhibits tumor growth and metastasis by inducing macrophage polarization and vessel normalization through downregulation of PlGF. Cancer Cell. 2011 Jan 18;19(1):31-44.

miRNA expression analysis of bone-marrow derived macrophages (BMDMs) and tumor-associated macrophages (TAMs). Heatmap indicating the expression level of 720 miRNAs in BMDMs, either treated with IL-4 or untreated, or TAMs fractionated into MRC1+ and CD11c+ subsets. Only miRNAs that were detectable in each macrophage type are displayed. Data represent the dCt values relative to U6, a highly expressed snRNA (n = 3 biological replicates).

EPFL School of Life Sciences - 2012 Annual Report

Duboule Lab

http://duboule-lab.epfl.ch/

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. Since 2001, he is also the director of the Swiss National Research Centre â&#x20AC;&#x2DC;Frontiers in Geneticsâ&#x20AC;&#x2122;. Prof. 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. He is an elected member of several academies and has received many awards, amongst which the Louis-Jeantet Prize for Medicine in 1998.

Denis Duboule

Full Professor EPFL & University of Geneva

Introduction

The aim of this research is to understand how genes are regulated during mammalian embryonic development. We are particularly interested to study the relationships that exist between genomic organization (e.g. gene topology) and the control of transcriptional activity, both at the genetic and epigenetic levels, by using one of the Hox gene locus as a paradigm. These genes are involved in many important processes during embryonic development, and are mis-regulated in a variety of human genetic syndromes. We thus hope to understand some basic rules of long-distance gene regulation, which will be extrapolated to other normal and pathological contexts.

Keywords

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

Results Obtained in 2012

SystemsHox.ch - an in vivo System Approach to Hox Genes Regulation in Vertebrates - We have continued to study the different kinds of long-range regulations that occur at the HoxD gene locus. In particular, we have localized and studied those enhancers controlling the expression of these genes during both proximal limb and caecum development. We have also studied the control of gene expression during the ontogenesis of the external genital organs, with enhancers located at the other side of the gene cluster,

i.e. together with the digit regulation (see figure below). In parallel, we have studied another level of gene regulation occurring at this locus, via the repression by polycomb group proteins and their effect upon the tri-methylation of H3K27. We have used a battery of deletion mutants in vivo to try and understand which sequences are able to recruit the PRC2 complex at this locus, very early on during embryonic development. However, the system appears more buffered than anticipated and hence compensatory mechanisms seem to take place. Long range regulation has also been studied by using FISH technologies, which has allowed to see the respective positions of various loci in cells either expressing or non-expressing these genes. Finally, we have terminated our functional studies on the effect of multiple inactivations of Hox gene clusters. These experiments have revealed the resurgence of pleisiomorphic characters suggesting an important role for the genes in the setting up of vertebrate morphologies, at the time of the 2R genome duplications.

EPFL School of Life Sciences - 2012 Annual Report

Selected Publications

T. Montavon, L. Thevenet and D. Duboule. Impact of copy number variations (CNVs) on long-range gene regulation at the HoxD locus, in Proceedings of the National Academy of Sciences, vol. 109, p. 20204-20211, 2012. J. Zakany and D. Duboule. A Genetic Basis for Altered Sexual Behavior in Mutant Female Mice, in Current Biology, vol. 22, num. 18, p. 1676-1680, 2012.

Team Members Postdoctoral Fellows Pierre Fabre Thomas Montavon Daan Noordermeer Maxence Vieux-Rochas

T. Montavon and D. Duboule. Landscapes and archipelagos: spatial organization of gene regulation in vertebrates, in Trends in Cell Biology, vol. 22, 347354, 2012.

PhD Students Guillaume Andrey Fabrice Darbellay Saskia Delpretti Nicolas Lonfat Patrick Schorderet

S. Delpretti, J. Zakany and D. Duboule. A function for all posterior Hoxd genes during digit development?, in Developmental dynamics : an official publication of the American Association of Anatomists, vol. 241, num. 4, p. 792-802, 2012.

Technician Elisabeth Joye

P. Tschopp, A. J. Christen and D. Duboule. Bimodal control of Hoxd gene transcription in the spinal cord defines two regulatory subclusters, in Development, vol. 139, p. 929-939, 2012.

Bioinformaticians Marion Leleu Yohan Mouscaz Anamaria Necsulea

N. Gheldof, M. Leleu, D. Noordermeer, J. Rougemont and A. Reymond. Detecting long-range chromatin interactions using the chromosome conformation capture sequencing (4C-seq) method, in Methods in molecular biology (Clifton, N.J.), p. 211-25, 2011.

Administrative Assistant Doris Sapin

ISREC - Swiss Institute for Experimental Cancer Research

S. Verp, M. Blom, M. Friedli, S. Delpretti and I. Barde et al. Lentiviral vectors mediated transgenesis., Transgenic Research, vol. 20, p. 1170-1170, Springer Verlag, 2011.

The same Hoxd genes are expressed in a collinear fashion during the development of both digits and external genitalia. The global regulatory organization of the murine HoxD locus in these secondary embryonic structures shows unexpected similarities (Left) Hoxd13 is the most strongly expressed gene of the cluster at the distal ends of limbs and in the genital bud (in situ hybridization, E13.5). (Right) Analysis of the spatial conformation of the HoxD cluster and its centromeric neighborhood using chromosome conformation capture (4C). The interactions profiles between Hoxd13 (red rectangle) and DNA fragments in the gene desert are shown for developing digits (top) and genitalia (bottom). Several regions contact Hoxd13 via chromatin looping in both developing genital tubercle and digits, others are specific for either one of these two structures. Altogether, however, the profiles are comparable.

EPFL School of Life Sciences - 2012 Annual Report

Gönczy Lab

http://gonczy-lab.epfl.ch/

Pierre Gönczy obtained his PhD in 1995 from The Rockefeller University (New York, USA) before joining the laboratory of Tony Hyman at the EMBL (Heidelberg, Germany) as a postdoctoral fellow in 1996. Professor Gönczy started his laboratory at ISREC in 2000 before joining the EPFL School of Life Sciences in 2005.

Pierre Gönczy Full Professor

Introduction

Accurate cell division is critical for proper development and for self-renewing tissues. We use a combination of biochemical, computational, cell biological, molecular genetic and functional genomic approaches to dissect the mechanisms governing fundamental cell division processes. We focus in particular on asymmetric cell division and centrosome duplication, two evolutionarily conserved processes that are critical for genome integrity and which can go awry in disease situations.

Keywords

Cell biology, developmental biology, cell division, centrosome duplication, spindle positioning, C. elegans, human cells.

Results Obtained in 2012

Asymmetric cell division - Asymmetric spindle positioning is important for cell diversity in metazoan organisms. Our earlier results lead us to propose a model in which asymmetric spindle positioning in C. elegans one-cell embryos, relies on a ternary complex (LIN-5/GPR-1/2/Gα) that anchors the minus-end directed microtubule motor dynein to the cell cortex. Together with microtubule depolymerization, dynein allows pulling forces to be exerted along astral microtubules, thus ensuring proper spindle positioning. During the year 2012, we significantly expanded our work on spindle positioning in human cells. In particular, analysis of fixed specimens and time-lapse microscopy experiments allowed us to demonstrate that membrane-bound dynein is both necessary and sufficient to direct spindle positioning. Moreover, we discovered that the distribution of NuMA, a GPR-1/2 homologue in human cells, is dynamic during mitosis and have begun to unravel the mechanisms by which this is regulated. Overall, our work increases the understanding of the mechanisms governing spindle positioning in metazoan organisms.

Centrosome duplication - The centriole and the related basal body are critical for the formation of cilia, flagella and centrosomes. Centrioles exhibit a universal nine-fold radial symmetric arrangement of microtubules imparted by a structure called the cartwheel. In collaboration with the laboratory of Michel Steinmetz (PSI, Villingen, Switzerland), we previously generated a structural model of the cartwheel, in which nine homodimers of SAS-6 proteins assemble into rings from which nine radial spokes radiate outwards. During the year 2012, we notably completed a comprehensive siRNA-based screen in human cells to identify novel genes required for proper centriole formation. Using a custom-developed algorithm for automatic counting of centrosomes, we identified and validated candidate genes whose inactivation prevents or instead enhances centriole formation. Furthermore, we utilized cryo-electron tomography to reveal the architecture of the exceptionally long cartwheel of the flagellate Trichonympha. We demonstrated that the cartwheel is a stack of central rings 22 nm in diameter that exhibit a vertical periodicity of 8.5 nm and which can accommodate 9 homodimers of SAS-6 proteins. Furthermore, we established that the spokes that emanate from two such rings associate into a layer, with a vertical periodicity of 17 nm on the cartwheel margin. Our findings suggest a step-wise model for cartwheel assembly and provide a unique map for understanding the mechanisms at the root of the universal 9-fold symmetry of centrioles.

EPFL School of Life Sciences - 2012 Annual Report

Selected Publications

Kotak, S., Busso, C. and Gönczy, P. (2012) Cortical dynein is critical for proper spindle positioning in human cells. J. Cell Biol. 199: 97-110. Guichard, P., Desfosses A., Maheshwari, A., Hachet, V., Dietrich, C., Brune, A., Ishikawa, T., Sachse, C., and Gönczy, P. (2012) Cartwheel architecture of Trichonympha basal body. Science 337: 6094. Hachet V., Busso C., Toya M., Sugimoto, A., Askjaer, P. and Gönczy, P. (2012) The nucleoporin Nup205/NPP-3 is lost near centrosomes at mitotic onset and can modulate the timing of this process in C. elegans embryos. Mol. Biol. Cell 23: 3111-3121. Mikeladze-Dvali, T., von Tobel L., Strnad P., Knott G., Leonhardt H., Schermelleh, L. and Gönczy P. (2012) Analysis of centriole elimination during C. elegans oogenesis. Development 139:1670-1679. Kitagawa, D., Kohlmaier G., Keller D., Strnad P., Balestra F.R., Flückiger, I. and Gönczy P. (2011). Spindle positioning in human cells relies on proper centriole formation and on the microcephaly proteins CPAP and STIL. J. Cell Sci. 124: 3884-3893. Thyagarajan K., Afshar K. and Gönczy P. (2011) Polarity Mediates Asymmetric Trafficking of the Gβ Heterotrimeric G Protein Subunit GPB-1 in C. elegans Embryos. Development 138: 2773-2782.

Team Members Postdoctoral Fellows Paul Guichard Virginie Hamel Hachet Sachin Kotak Aitana Neves da Silva Meritxell Orpinell Fernando Romero Balestra Benita Wolf PhD Students Simon Blanchoud Alessandro De Simone Zhou Fang Christian Gentili Debora Keller Zoltan Spiro Lukas von Tobel Technicians Coralie Busso Isabelle Fluckiger Administrative Assistant Nicole De Montmollin

Kitagawa, D., Flückiger, I., Polanowska J., Keller, D., Reboul, J. and Gönczy P. (2011) PP2A phosphatase acts upon SAS-5 to ensure centriole formation in C. elegans embryos. Dev. Cell 20: 550-562.

ISREC - Swiss Institute for Experimental Cancer Research

Kitagawa, D., Vakonanis, I., Olieric, N., Hilbert, M., Keller, D., Olieric, V., Bortfled, V., Erat, M.C., Flückiger, I., Gönczy P. and Steimetz, M.O. (2011) Structural basis of the 9-fold symmetry of centrioles. Cell 144: 364-375.

Portion of the proximal part of the basal body from Trichonympha determined by cryo-electron tomography followed by image reconstruction. The cartwheel, with the central hub and the nine radial spokes emanating from it, is shown in light blue. Other connected structures, including the nine microtubule triplets, are shown in purple.

EPFL School of Life Sciences - 2012 Annual Report

Hanahan Lab

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 from 1978-88 as graduate student and then as 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).

Douglas Hanahan

Full Professor Director of ISREC Merck-Serono Professor of Molecular Oncology

Introduction

The Hanahan group investigates tumor development and progression using mouse models of cancer that recapitulate important characteristics of human cancers, with strategic goals to elucidate pathogenic mechanisms and develop new therapeutic strategies for translation to clinical trials.

Keywords

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

models of pancreatic cancer (neuroendocrine and ductal), and well as of glioblastoma, melanoma, and breast cancer. Topics of investigation include mechanisms of: angiogenesis, adaptive/evasive resistance to anti-angiogenic therapy, invasion, and tumor metabolism. Additional research topics include the delineation of phenotypically distinctive molecular genetic subtypes of ostensibly similar tumors of the same type, cross-correlated between mouse models and human tumors.

Results Obtained in 2012

The Hanahan laboratory studies genetically engineered mouse models of de novo organ-specific carcinogenesis, seeking to define mechanisms of multi-step tumorigenesis and progression. The lab also performs mechanism-guided pre-clinical therapeutic trials involving function-targeted drugs and drug-combinations, aiming to assess functional importance of the target(s), identify adaptive resistance mechanisms that limits efficacy, and incentivize clinical trials involving such targeted drugs and combinatorial regimens. The laboratory is currently studying two mouse

EPFL School of Life Sciences - 2012 Annual Report

Selected Publications

Team Members

Shchors K, Nozawa H, Xu J, Rostker F, Swigart-Brown L, Evan G, & Hanahan D. Increased invasiveness of MMP-9-deficient tumors in two mouse models of neuroendocrine tumorigenesis. Oncogene. 2013 Jan 24;32(4):502-13. doi: 10.1038/onc.2012.60. Epub 2012 Mar 5.

Postdoctoral Fellows Elizabeth Allen Krisztian Homiisko Seiko Ishida Anguraj Sadanandam Ksenya Shchors Stephan Wullschleger

Hanahan D, & Coussens LM. Accessories to the crime: functions of cells recruited to the tumor microenvironment. Cancer Cell. 2012 Mar 20;21(3):309-22.

De Palma M, & Hanahan D. The biology of personalized cancer medicine: facing individual complexities underlying hallmark capabilities. Mol Oncol. 2012 Apr;6(2):111-27. doi: 10.1016/j.molonc.2012.01.011. Epub 2012 Feb 4. Collisson EA, Sadanandam A, Olson P, Gibb WJ, Truitt M, Gu S, Cooc J, Weinkle J, Kim GE, Jakkula L, Feiler HS, Ko AH, Olshen AB, Danenberg KL, Tempero MA, Spellman PT, Hanahan D, Gray JW. Subtypes of pancreatic ductal adenocarcinoma and their differing responses to therapy. Nat Med. 2011 Apr;17(4):500-3. doi: 10.1038/nm.2344. Epub 2011 Apr 3. PubMed PMID: 21460848. Allen E, Walters IB, Hanahan D. Brivanib, a dual FGF/VEGF inhibitor, is active both first and second line against mouse pancreatic neuroendocrine tumors developing adaptive/evasive resistance to VEGF inhibition. Clin Cancer Res. 2011 Aug 15;17(16):5299-310. doi: 10.1158/1078-0432.CCR-10-2847. Epub 2011 May 27. PubMed PMID: 21622725; PubMed Central PMCID: PMC3156934.

Sabbatical Professor Luisa Arispe-Aruela, UCLA

PhD Student Leanne Li Technical Staff Ehud Drori Estelle Maillard Mei-Wen Peng Administrative Assistant Laura Bischoff

Olson P, Chu GC, Perry SR, Nolan-Stevaux O, Hanahan D. Imaging guided trials of the angiogenesis inhibitor sunitinib in mouse models predict efficacy in pancreatic neuroendocrine but not ductal carcinoma. Proc Natl Acad Sci U S A. 2011 Dec 6;108(49):E1275-84. doi: 10.1073/pnas.1111079108. Epub 2011 Nov 14. PubMed PMID: 22084065; PubMed Central PMCID: PMC3241750.

ISREC - Swiss Institute for Experimental Cancer Research

De Palma M, Hanahan D. The biology of personalized cancer medicine: facing individual complexities underlying hallmark capabilities. Mol Oncol. 2012. Apr;6(2):111-27. doi: 10.1016/j.molonc.2012.01.011. Epub 2012 Feb 4. Review. PubMed PMID: 22360993.

Macrometastasis from a Rip1Tag2 mouse treated with anti-mTOR monotherapy - Long term treatment of a Rip1Tag2 mice with rapamycin, an mTOR inhibitor, resulted in a response phase followed by tumor progression and metastasis. Depicted is the image of a liver metastasis stained with anti-Tag antibody (green) that recognizes tumor cells, while anti-CD31 (red) reacts with the endothelial cells of the newly vascularized metastasis.

EPFL School of Life Sciences - 2012 Annual Report

Hantschel Lab

http://hantschel-lab.epfl.ch/

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 with Giulio Superti-Furga at the Research Center for Molecular Medicine of the Austrian Academy of Sciences in Vienna. In 2011, he was nominated Tenure Track Assistant Professor at the EPFL School of Life Sciences and was awarded the ISREC Foundation Chair in Translational Oncology.

Oliver Hantschel

Tenure Track Assistant Professor ISREC Foundation Chair in Translational Oncology

Introduction

The Hantschel laboratory is studying leukemias, which are cancers that are characterized by the overproduction of white blood cells. Most leukemias are fatal if not treated readily after diagnosis. Several changes in the genetic material of leukemia patients result in the expression of abnormal amounts or structurally altered proteins. We are trying to understand the signaling of these altered protein in order to identify additional ways by which tumor cells can be attacked and hope that these new insights can be translated into useful therapies for cancer patients.

Keywords

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

Results Obtained in 2012

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, 18 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, as 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 laboratory uses interdisciplinary approaches at the interface of protein biochemistry, medicine, structural biolo-

gy and chemical biology to study cancer cell signaling with the aim to find novel ways for therapeutic intervention. We are initially focusing on tyrosine kinase oncoproteins that play key roles in the pathogenesis of different leukemias and lymphomas, but also solid tumors. Projects in our research group include: • Development and validation of engineered high-affinity protein antagonists to target protein-protein interactions in oncogenic signaling networks. • Elucidation of the signaling mechanisms of BcrAbl interacting proteins in oncogenic transformation and leukemogenesis. • Comparative analysis of oncogenic kinase signaling networks using interaction- and phospho-proteomics approaches. • Studies on the specificity & molecular mechanism-of-action of small-molecule kinase inhibitors.ssssssssssssssssssssssssssssssssssssssssss In the past year, we have intensively studied the adapter protein Gab2 that is critical for the transmission of oncogenic signals in different leukemias. Gab2 serves as an assembly platform for proteins that mediate the activation of pathways leading to cell proliferation and inhibition of cell death, but the importance and contributions of individual pathway components and their hierarchy is not well understood, mainly because of a lack of selective inhibitors for individual signaling molecules. We have developed and characterized small engineered proteins that are tailored to bind very specifically to individual domains in complex signaling proteins and thereby prevent their activation. This approach will help us to understand which of the signaling pathways is critical for tumorigenesis and therefore worth to target. In addition to leukemias, the Gab2 pathways are also deregulated in other diseases, such as breast and lung cancer.

EPFL School of Life Sciences - 2012 Annual Report

Selected Publications

Grebien, F. *, Hantschel, O. *, Wojcik, J., Kaupe, I., Kovacic, B., Wyrzucki, A. M., Gish, G. D., Cerny-Reiterer, S., Koide, A., Beug, H., Pawson, T., Valent, P., Koide, S. and Superti-Furga, G. (2011). Targeting the SH2-kinase interface in Bcr-Abl inhibits leukemogenesis. Cell, 147(2), 306–319. Hantschel, O.*, Warsch, W.*, Eckelhart, E.*, Kaupe, I., Grebien, F., Wagner, K.U., Superti-Furga, G. and Sexl, V. (2012). BCR-ABL uncouples canonical JAK2STAT5 signaling in chronic myeloid leukemia. Nat. Chem. Biol., 8(3), 285-293. Hopkins, S.*, Linderoth, E.*, Hantschel, O., Suarez-Henriques, P., Pilia, G., Kendrick, H., Smalley, M.J., Superti-Furga, G. and Ferby, I. (2012). Mig6 is a sensor of EGF receptor inactivation that directly activates c-Abl to induce apoptosis during epithelial homeostasis. Dev. Cell, 23(3), 547-559 Review articles: Valent, P., Gastl, G., Geissler, K., Greil, R., Hantschel, O., Lang, A., Linkesch, W., Lion, T., Petzer, A.L., Pittermann, E., Pleyer, L., Thaler, J. and Wolf, D. (2012). Nilotinib as Frontline and Second-Line Therapy in Chronic Myeloid Leukemia: Open Questions. Crit. Rev. Oncol. Hemat., 82(3), 370-377.

Team Members Postdoctoral Fellow Sina Reckel PhD Students Emel Basak Gencer Orest Kuzyk Allan Lamontanara Technician Sandrine Georgeon Master’s Student Nicolas Desbaillets Administrative Assistant Christine Skaletzka

Hantschel, O. (2012). Allosteric Bcr-Abl inhibitors in Ph+ acute lymphoblastic leukemia: novel opportunities for drug combinations to overcome resistance. Haematologica, 97(2), 157-159. Hantschel, O., Grebien, F. and Superti-Furga, G. (2012). The growing arsenal of ATP-competitive and allosteric inhibitors of BCR-ABL. Cancer Res., 72(19), 4890-4895. Hantschel, O. (2012). Structure, regulation, signaling and targeting of Abl kinases in cancer. Genes&Cancer, 3(5-6), 436-446.

ISREC - Swiss Institute for Experimental Cancer Research

Lamontanara, A. J., Gencer, E. B., Kuzyk, O. and Hantschel, O. (2012) Mechanisms of resistance to BCR-ABL and other kinase inhibitors. Biochim. Biophys. Acta, in press.

Schematic representation of common point mutations in the Bcr-Abl kinase domain that cause imatinib resistance. Imatinib is shown as a stick model in grey, red balls indicate the location of individual point mutations. The Gly-rich loop and activation loop are colored in yellow and green.

EPFL School of Life Sciences - 2012 Annual Report

Huelsken Lab

http://huelsken-lab.epfl.ch/

Joerg Huelsken received his PhD in 1998 at the Humboldt University and did postdoctoral research at the Max-Delbrueck 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.

Joerg Huelsken

Associate Professor Debiopharm Chair in Signal Transduction in Oncogenesis

Introduction

The last years of cancer research have established the concept of cancer stem cells (CSC) as sub-population of cells within a tumor entirely responsible for long-term tumor growth. We now provide evidence that these cells are also essential for metastatic disease and characterize 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.

Keywords

Cancer stem cells, metastatic colonization, Hh signaling, stem cell niches

Results Obtained in 2012

We are just beginning to understand the immediate molecular mechanisms which allow tumor cells to colonize a secondary target site after extravasation ; it can however be expected that this process is fundamentally involved in the apparent inefficiency of metastasis. In a collaborative project between our lab and the group of Felix Naef, a novel technology was developed to identify tumor- vs. stroma specific expression changes in vivo. This uses classical xenograft experiments combined with a specifically adapted mRNA profiling analysis which allows distinguishing human tumor cells and surrounding mouse stroma from mixed samples of human and mouse cells. We utilized this system to identify changes that are induced in the local environment during the colonization of the liver by metastatic cancer cells from colon and pancreas. Liver is the main target organ for metastasis of these two tumor entities. This expression profiling has revealed that there are overall many similarities in the stromal responses of the target organ towards tumor cell seeding suggesting that this rather stereotype response should make targeting such stromal reactions easier. We find a variety of specific ECM (extracellular matrix) proteins to be strongly enhanced upon metastasis establishment. Interestingly, we were able to distinguish

an early response which characterizes the micro-metastasis stage and a late response during the macro-metastasis stage suggesting an evolution of the tumor micro-environment. Conversely, we observe an overall strong heterogeneity in the cancer cell transcriptome between the micro- and macro-metastasis stage which suggests unique adaptation and selection of tumor cells during metastatic colonization. Nevertheless, there exists common de-regulated genes when comparing the two different tumor entities, which supports the idea of tissue specific programs in metastasis. In order to cross-validate candidate genes that could be relevant for the human setting, we next built a database of published array studies with human cancer samples containing survival data. This facilitated the classification of potential candidates from the mouse studies according to their ability to distinguish patient groups of good and poor survival. One of the candidates we identified in this way as a potentially important contributor is the Hh signaling pathway. We find transient activation of the Hh pathway in the stroma of micrometastasis indicating that this signal may instruct the stroma to initiate formation of a supportive niche. Recent reports by de Sauvage and others revealed a paracrine requirement for Hh signaling in primary tumor formation of pancreatic cancers. However, no study has so far addressed whether this pathway is also involved in metastatic colonization. In our system, we find that Hh ligands are expressed by tumor cells. Conversely, the stroma upregulates Hh pathway components as well as known Hh target genes, demonstrating that Hh signaling is activated in the stroma adjacent to metastases (Figure). We currently aim to understand in detail what are the target cells of the tumor-derived Hh ligands, what is their response to activation of the pathway and how they interact with the tumor cells (or other stromal cells) to support metastasis formation.

EPFL School of Life Sciences - 2012 Annual Report

Selected Publications

Ordóñez-Morán, P., A. Irmisch, A. Barbachano, I. Chicote, S. Landolfi, J. Tabernero, J. Huelsken and A. Muñoz (2013). SPROUTY2 is a β-catenin and FOXO3a target gene indicative of poor prognosis in colon cancer. Oncogene, in print Irmisch, A. and J. Huelsken (2013). Metastasis: New insights into organ-specific extravasation and metastatic niches. Exp. Cell Res., in print Martinez, A.S. and J. Huelsken (2012). The niche under siege: novel targets for metastasis therapy. J. Intern. Med., in print Smartt, H.J.M., A. Greenhough, P. Ordóñez-Morán, M. Al-Kharusi, T.J. Collard, J.M. Mariadason, J. Huelsken, A.C. Williams, C. Paraskeva (2012). β-catenin negatively regulates expression of the prostaglandin transporter PGT in the normal intestinal epithelium and colorectal tumour cells: a role in the chemopreventive efficacy of aspirin? Br. J. Cancer 107:1514-7. Santamaria-Martínez*,A., I. Malanchi*, E. Susanto, H. Peng, H.A. Lehr, J.F. Delaloye and J. Huelsken (2012). Interactions between cancer stem cells and their niche govern metastatic colonization. Nature, 481, 85–89. *these two authors contributed equally

Team Members Postdoctoral Fellows Anja Irmisch Paloma Ordóñez Morán Albert Santamaria Martínez Patrick Schmidt PhD Students Jean-Paul Abbuehl Evelyn Susanto Zuzana Tartarova Caroline Urech Technicians Jonathan Bernard Fanny Cavat Pierre Dessen Nancy Hynes Administrative Assistant Ursula Winter

This article has been highlighted in: • Wang Z. and G. Ouyang (2012). Periostin: A Bridge between Cancer Stem Cells and Their Metastatic Niche. Cell Stem Cell. 10:111-2. • Oskarsson T. and J. Massagué (2011). Extracellular matrix players in metastatic niches. EMBO J. 31:254-6. Smartt H.J., A. Greenhough, P. Ordóñez-Morán, E. Talero, C.A. Cherry, C.A. Wallam, L. Parry, M. Al Kharusi, H.R. Roberts, J.M. Mariadason, A.R. Clarke, J. Huelsken, A.C. Williams, and C. Paraskeva (2011). β-catenin represses expression of the tumour suppressor 15-prostaglandin dehydrogenase in the normal intestinal epithelium and colorectal tumour cells. Gut, 61:1306-14.

ISREC - Swiss Institute for Experimental Cancer Research

Holowacz, T., J. Huelsken, D. Dufort, and D. van der Kooy (2011). Neural stem cells are increased after loss of β-catenin, but neural progenitors undergo cell death. Eur J Neurosci., 33:1366-75.

Pancreatic cancer cells metastasizing to the liver secrete Hh ligands to induce signaling in the nearby stroma. Stromal response is measured by a Ptc1lacZ knock in allele which marks activated cells in blue. The exact phenotype of these stromal cells and their role in metastatic spread is one focus of our current research. Metastatic nodule encircled and marked by “T”.

EPFL School of Life Sciences - 2012 Annual Report

Kühn Lab

http://kuhn-lab.epfl.ch/

Lukas Kühn graduated in biochemistry at the Swiss Federal Institute of Technology in Zürich (EPFZ). He received his PhD in 1979 for a thesis with Jean-Pierre Kraehenbuhl at the University of Lausanne. After postdoctoral work in Lausanne and with Frank Ruddle at Yale University, USA, he became group leader at ISREC in 1984, was promoted senior scientist in 1988 and “professeur titulaire” (adjunct professor) at EPFL in June 2008.

Lukas Kühn

Adjunct Professor

Introduction

We study the role of ferritin in iron physiology by analyzing mice with a conditional deletion of the ferritin H gene. Ferritin H is necessary for iron storage and detoxification. Its absence increases intracellular free iron and the formation of reactive oxygen species that modify proteins and DNA, a known cause of cancer. Part of our activities is also devoted to studying rapid mRNA degradation. Numerous transcription factors and signaling proteins are encoded by unstable mRNAs that ensure rapid adaptation and avoid over-expression.

Keywords

Conditional knock-out mice for ferritin H, oxidative cell damage, iron physiology, mRNA degradation, RNA-protein interactions.

Results Obtained in 2012

Analysis of ferritin H knock-out mice - Iron is essential for life and at the same time a hazard. Intracellular free iron catalyzes the formation of hydroxyl radicals, which cause cell damage and mutations in DNA. Body iron absorption from nutrients and intracellular free iron are accurately controlled to avoid iron excess or deprivation. Ferritin is a protein complex composed of ferritin H and L chains, which stores excess iron. We have generated mice in which we delete the ferritin H gene in various tissues using the Cre lox method. Our past studies show that ferritin H plays a major role in the protection against intracellular free iron and radical formation. This year we continued the investigation of ferritin H in macrophages using a Lysozyme-Cre mediated deletion. Macrophages did not suffer cell death after the deletion. Iron storage in spleen and liver was strongly diminished documenting the importance of macrophages in iron storage. Red blood cell counts, hematocrit, and hemoglobin levels were not affected indicating that ferritin is not required for iron recycling to hematopoietic cells. We have started to investigate whether iron retention after inflammation is altered in ferritin H deleted mice. In collaboration with Miguel Soares at the Gulbenkian Institute, Oeiras, Portugal, we found that malaria infection by

Plasmodium chabaudi was far more severe in mice with a ferritin H deletion than control mice. None of the deleted mice survived beyond 10 days. Upon re-expression in the liver from adenovirus vectors, wild-type ferritin H, but not a ferroxidase mutated version, restored tolerance to Plasmodium indicating that iron storage protected mice. Ferritin H mainly prevented free labile iron from sustaining the proapoptotic activation of c-Jun N-terminal kinase, a major cause of tissue damage during Plasmodium infection. Mechanisms of rapid mRNA degradation - We have studied rapid mRNA degradation as it occurs in a large number of mRNAs harboring instability elements in their 3’-untranslated regions (3’UTR). We take advantage of a Tet-off system in which destabilizing regions are tested behind stable GFP (green florescent protein) mRNA (Figure). With a scanning deletion approach we have identified destabilizing elements in mouse Rankl and human Bcl6 mRNA. Important sequences were defined with a 15-base precision. Both mRNAs harbor at least two instability elements at sequences that are highly conserved in evolution. In Rankl mRNA they do not conform to AU-rich elements, whereas in Bcl6 at least one element is a non-classical AU-rich region. We have further measured the interaction of candidate RNAbinding proteins with these 3’UTRs. We have also completed the delineation of rapid decay elements in mouse c-myc mRNA. Natural c-myc mRNA decays with a 30-min half-life, and this requires both the coding region and 3’UTR. The coding region alone confers a half-life of 40 min, while the 3’UTR alone a half-life of 80 min. Constructs in frame behind GFP and deletion analysis indicated that rapid decay requires three short elements in the last third of the coding region. Without these elements the half-life rose to 180 min. In contrast, a coding region determinant previously identified by others as a binding site for CRD-BP (Coding Region Determinant-Binding Protein), stabilized the mRNA in our assay. We further found that stop codons in front of the c-myc coding region inhibit mRNA degradation to a variable extent depending on whether translation can proceed or not to destabilizing elements.

EPFL School of Life Sciences - 2012 Annual Report

Vanoaica, L., Darshan, D., Richman, L., Schümann, K., and Kühn, L.C. (2010). Intestinal ferritin H is required for an accurate control of iron absorption. Cell Metabolism. 12:273-282. Gozzelino, R., Andrade, B.B., Larsen, R., Luz, N.F., Vanoaica, L., Seixas, E., Coutinho, A., Cardoso, S., Rebelo, S., Poli, M., Barral-Netto, M., Darshan, D., Kühn, L.C., and Soares, M.P. (2012). Metabolic adaptation to tissue iron overload confers tolerance to malaria. Cell Host Microbe. 12:693-704.

Team Members PhD Student Ramona Batschulat

Specialist technicians Larry Richman Solange Kharoubi Hess Administrative assistant Jennifer Luyet

ISREC - Swiss Institute for Experimental Cancer Research

Selected Publications

mRNA half-life was tested in mouse 3T3 cells with a transcriptional transactivator for the Tet-promoter and a vector expressing GFP fused to destabilizing 3’UTRs. After addition of doxycycline the transactivator is inactivated and fusion mRNA decays with first order kinetics (left panels). A typical experiment shows RNA half-life of GFP vector alone, with the mouse Rankl 3’UTR, or various deletion mutants thereof. A restricted region of the Rankl 3’UTR is required for mRNA instability (right table and panel).

EPFL School of Life Sciences - 2012 Annual Report

Lingner Lab

http://lingner-lab.epfl.ch/

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 START-fellowship 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.

Joachim Lingner Full Professor

Introduction

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 from chromosome rearrangements typically seen in cancer. Telomeres also serve as cellular clocks. They shorten in the absence of telomerase limiting cellular lifespan. In most cancers, telomerase is upregulated in order to counteract telomere shortening. Through the expression of telomerase, human cancer cells acquire an immortal phenotype.

Keywords

Telomeres, telomerase, noncoding RNA, TERRA, chromosome stability, cellular senescence, cancer, biochemistry, molecular biology, genetics.

Results Obtained in 2012

Telomerase mechanism and structure - Telomerase is the cellular reverse transcriptase synthesis telomeric repeats at the end of chromosomes using an internal RNA moiety as a template. We established a robust system for the expression of active human telomerase in HEK293T cells, purified telomerase and our collaborators from the Rhodes-lab (LMB-Cambridge) determined the first three-dimensional structure of active human telomerase by single particle electron microscopy of negatively stained samples (Sauerwald et al. 2013, in press). The structure reveals that human telomerase has a bilobal structure. Incubation of purified telomerase with colloidal gold labeled telomeric primers revealed that human telomerase can bind two DNA substrates, suggesting that telomerase functions as a dimer. The multimeric nature of telomerase was confirmed in biochemical experiments. We demonstrate that telomerase needs two active sites in order to be catalytically active; in other words, the data suggest that telomerase dimerization is essential for activity and that telomerase-dimers extend two telomeres (possibly the two sister telomeres) at the same time in parallel.

Regulation of telomerase at chromosome ends - In human cancer cells, telomerase is thought to extend individual chromosome ends once and only once per cell cycle. The mechanism for this restriction was unknown. We now provided data that support a role of the human CST complex in terminating telomerase activity. We demonstrated that human CST complex (CTC1-STN1-TEN1) inhibits telomerase activity through primer sequestration and physical interaction with the Pot1/Tpp11 telomerase processivity factor (Chen et al., 2012). Significantly CST-binding at telomeres increases during late S/G2 phase only upon telomerase action, coinciding with telomerase shut-off. Through binding of the telomerase-extended telomere, CST may limit telomerase action at individual telomeres to approximately one binding and extension event per cell cycle. In addition, CST may prepare fill-in synthesis of the C-strand by lagging strand polymerases. Indeed, human CST subunits stimulate DNA polymerase alpha-primase, and CST from S. cerevisiae has also been implicated in fill-in synthesis of the telomerase-extended telomeres. This CST-mediated switch from telomere elongation to fill-in synthesis, functioning autonomously at single chromosome ends, can ensure that every telomere is extended by telomerase once and only once during every cell cycle. Telomeric repeat containing RNA (TERRA) - Until recently, telomeres have been considered to be transcriptionally silent. However, we overturned this dogma demonstrating that mammalian and yeast telomeres possess gene-like properties in that they are transcribed into the long noncoding telomeric repeat containing RNA (TERRA). Last year we demonstrated in vivo that TERRA stimulates chromosome shortening by the telomere trimming enzyme exonuclease 1 (Pfeiffer and Lingner, 2012). Thus TERRA upregulation seems to promote cellular senescence. The involved molecular mechanisms are currently being investigated by studying newly identified TERRA interacting chromatin factors.

EPFL School of Life Sciences - 2012 Annual Report

Selected Publications

**Sauerwald A., **Sandin S., Cristofari G., Scheres S.H.W., *Lingner J., *Rhodes D. (2013). Structure of active, dimeric human telomerase. Nat. Struct. Mol. Biol. 20 : 454-460. Pfeiffer V., Lingner, J. (2013). Replication of telomeres and the regulation of telomerase. Contribution to “DNA replication” (Bell, S. D., Méchali, M., DePamphilis, M.L., Ed.), Cold Spring Harbor Laboratory Press. Gupta A., Sharma S., Reichenbach P., Marjavaara L., Nilsson A.K., Lingner J., Chabes A.R., Rothstein R., Chang M. (2013). Telomere length homeostasis responds to changes in dNTP pools. Genetics 193: 1095-1105. Chen L.Y., Redon S., Lingner J. (2012). The human CST complex is a terminator of telomerase activity. Nature, 488 : 540-544. Pfeiffer V., Lingner J. (2012). TERRA promotes telomere shortening through exonuclease 1-mediated resection of chromosome ends. PLoS genetics, 8 : e1002747. Chen L. Y., and Lingner, J. (2012). AUF1/HnRNP D RNA binding protein functions in telomere maintenance. Mol Cell, 47: 1-2.

Team Members Postdoctoral Fellows Eric Aeby Liuh-Yow Chen Sascha Feuerhahn Verena Pfeiffer Antonio Porro Sophie Redon Anselm Sauerwald Ivo Zemp

PhD Students Naga Raja Chappidi Alix Christen Jérôme Crittin Larissa Grolimund Andrea Panza (until 4/2012) Senior Lab Assistant Patrick Reichenbach Administrator Nicole de Montmollin

D’Ambrosio D., Reichenbach P., Micheli E., Alvino A., Franceschin M., Savino M., and Lingner J. (2012). Specific binding of telomeric G-quadruplexes by hydrosoluble perylene derivatives inhibits repeat addition processivity of human telomerase. Biochimie, 94 : 854-863. Iglesias N., Redon S., Pfeiffer V., Dees M., Lingner J*, Luke B*. (2011). Subtelomeric repetitive elements determine TERRA regulation by Rap1/Rif and Rap1/Sir complexes in yeast. EMBO Rep,12 : 587-593.

ISREC - Swiss Institute for Experimental Cancer Research

Ferreira H.C., Luke B., Schober H., Kalck V., Lingner J, Gasser SM. (2011). The PIAS homologue Siz2 regulates perinuclear telomere position and telomerase activity in budding yeast. Nat Cell Biol, 13 : 867-874.

Analysis of telomerase by single-particle EM. (a) Field view. (b–d) Reference-free 2D class averages. (e) 2D class averages. (f) Refined dimer. (g) Individual telomerase dimers in complex with (TTAGGG)2 bound to gold particles. (h) Dimer and binding sites. Scale bars, 50 nm (a) or 10 nm (b–d,g).

EPFL School of Life Sciences - 2012 Annual Report

Meylan Lab

http://meylan-lab.epfl.ch/

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 JĂźrg Tschopp. From 2007 to 2010, he worked as a postdoctoral fellow in the laboratory of Tyler Jacks, at the Koch Institute for Integrative Cancer Research, MIT, Cambridge MA, USA. In 2011, he established his research laboratory at ISREC, as a Swiss National Science Foundation Professor, and was appointed TenureTrack Assistant Professor at the end of 2012. His laboratory focuses on the molecular mechanisms that contribute to the development of non-small cell lung cancer.

Etienne Meylan Tenure-track Assistant Professor SNSF Professor

Introduction

Our goal is to understand different molecular mechanisms that critically contribute to the development and progression of lung cancer, the leading cause of cancer related deaths in the world. Currently, we focus on molecules and signaling pathways that are implicated in innate immunity, inflammation or glucose metabolism, and we want to comprehend their role during disease progression. We hope our discoveries will translate into knowledge-based preclinical and clinical trials to treat this devastating disease.

Keywords

Non-small cell lung cancer, NF-kappaB, glucose metabolism, glucose transporters, inflammation, innate immunity, mouse models of lung cancer.

Results Obtained in 2012

After its establishment in 2011, our laboratory has begun to investigate several aspects of non-small cell lung cancer (NSCLC) development, using human NSCLC cell lines, genetically-engineered mouse models, and tumor tissue samples. We currently focus on two principal research directions: (1) NF-kappaB signaling and (2) glucose metabolism. NF-kappaB signaling - Recent studies published by our lab and others have positioned NF-kappaB as a crucial pathway for the development and progression of non-small cell lung cancer, however the molecular mechanisms that control and are controlled by NF-kappaB, are mostly unknown. In our laboratory, we are using cell-based and in vivo approaches to elucidate how NF-kappaB signaling, directly in the tumor cells, controls tumor progression. In collaboration with the group of B. Hahn (Broad Institute and DFCI, Boston), an shRNA screen for NF-kappaB pathway genes was conducted, to identify synthetic lethal partners of on-

cogenic K-ras in lung tumor cells. Based on the results from this screen, we are currently validating the top hits using siRNAs and shRNAs in a larger number of NSCLC cell lines. Additionally, we began to explore the function of a G-protein coupled receptor, called Gprc5a, because published reports have suggested it to be a lung-specific tumor suppressor and inhibitor of the NF-kappaB signaling pathway. However, our preliminary data suggest that Gprc5a does not inhibit, but activates NF-kappaB. Additional in vitro and in vivo experiments should help understand the function of this protein in NF-kappaB signaling and lung tumorigenesis. Of note, to help investigate the role of various NF-kappaB components during lung tumor progression in vivo, and to be able to monitor tumor response to various drugs and drug combinations longitudinally, our laboratory acquired a micro-computed tomography (uCT) instrument, which was installed at the SV mouse facility in 2012. This instrument is now fully functional, and available to the EPFL research community; it has allowed us to follow the progression of the first mouse lung tumors obtained in the lab (Figure). Glucose metabolism. 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 have begun to analyze the regulation of various glucose transporters, and we explore their contribution to lung tumor progression. We hope that a better comprehension of the alterations in glucose metabolism by cancer cells will help design small molecule compounds that target specific components of glucose entry or glycolysis, in order to diminish tumor progression.

EPFL School of Life Sciences - 2012 Annual Report

Etzrodt, M., Cortez-Retamozo, V., Newton, A., Zhao, J., Ng, A., Wildgruber, M., Romero, P., Wurdinger, T., Xavier, R., Geissmann, F., Meylan, E., Nahrendorf, M., Swirski, F.K., Baltimore, D., Weissleder, R. and Pittet, M.J. (2012). Regulation of monocyte functional heterogeneity by miR-146a and Relb. Cell Rep. 1(4):317-24. Xue, W., Meylan, E., Oliver, T.G., Feldser, D.M., Winslow, M.M., Bronson, R. and Jacks, T. (2011). Response and resistance to NF-κB inhibitors in mouse models of lung adenocarcinoma. Cancer Discov. 1(3):236-247. Oliver, T.G., Meylan, E., Chang, G.P., Xue, W., Burke, J.R., Humpton, T.J., Hubbard, D., Bhutkar, A. and Jacks, T. (2011). Caspase-2-mediated cleavage of Mdm2 creates a p53-induced positive feedback loop. Mol Cell. 43(1):57-71.

Team Members PhD Students Mark Masin Jawahar Kopparam Master’s Student Laetitia Virard Technician Jessica Vazquez Administrator Christine Skaletzka

ISREC - Swiss Institute for Experimental Cancer Research

Selected Publications

In vivo imaging of a K-ras Lox-STOP-LoxG12D/WT; p53Flox/Flox mouse. Lungs were analyzed 12 (A) and 14 (B) weeks after tumor initiation. A red circle shows the same tumor, with the calculated volume. A white arrow shows another tumor. Resolution: 59 um voxel size, with respiratory gating.

EPFL School of Life Sciences - 2012 Annual Report

Radtke Lab

http://radtke-lab.epfl.ch/

Freddy Radtke graduated from University of Zürich in molecular biology in 1994 and continued with a postdoctoral fellowship at Genentech Inc. USA 1995-1996. He then did his postdoctoral work at ISREC Switzerland (1997-1999) and became an Assistant Member of the Ludwig Institute for Cancer Research from1999-2004, being promoted to Associate Member in 2004. Prof. Radtke then joined ISREC as a Senior Scientist in 2006, before joining EPFL in August 2006 as an associate professor. In August 2012, Dr. Radtke was promoted to full professor.

Freddy Radtke Full Professor

Introduction

We use mouse genetics to study the molecular mechanisms controlling self-renewal and differentiation of normal and cancer stem cells in the blood system as well as in epithelial tissues including the intestine and the epidermis. The basic principle of self-renewing tissues is to constantly produce cells from a stem cell reservoir. This pool gives rise to proliferating transient amplifying cells, which subsequently differentiate and migrate to the correct compartment. These processes have to be under stringent control mechanisms to ensure life-long tissue homeostasis. Their deregulation can lead to organ failure and/or cancer. Moreover, we are interested how inflammation influences tumor development and/or progression. Current attention is focused on the evolutionarily conserved Notch and Wnt signaling pathways, which play pleiotropic roles in different self-renewing tissues and cancer.

Keywords

Notch, Wnt, stem and progenitor cells, self-renewing tissues, differentiation, cancer, inflammation, genetic mouse models.

Results Obtained in 2012

TSLP mediated inflammation mediates tumor protection in skin carcinogenesis - For many years cancer has been seen predominantly as a cell autonomous process in which genetically transformed cells propagate the development of malignant neoplasms. However, today it is well established that tumor progression is strongly influenced by the interactions between neoplastic cells and its environment, including tumor associated fibroblasts and inflammatory cells. Inflammation can promote or inhibit cancer progression. We have addressed the role of the pro-inflammatory cytokine Thymic Stromal Lymphopoietin (TSLP) during skin carcinogenesis. Using conditional loss- and gain-of-function mouse models for Notch and Wnt signaling respectively, we demonstrate that TSLP mediated inflammation pro-

tects against cutaneous carcinogenesis by acting directly on CD4+ and CD8+ T cells. Genetic ablation of the TSLP receptor (TSLPR) perturbs T cell mediated protection and results in the accumulation of CD11b+Gr1+ myeloid cells. These promote tumor growth by secreting Wnt ligands and augmenting β-catenin signaling in the neighboring epithelium. Epithelial specific ablation of β-catenin prevents both carcinogenesis and the accumulation of CD11b+Gr1+ myeloid cells, suggesting tumor cells initiate a feed-forward loop that induces pro-tumorigenic inflammation. Optimization and preclinical validation of Notch signalling inhibitors for cancer therapy - The Notch signaling cascade is an evolutionary conserved pathway that is activated via cell-to-cell contact. During both development and postnatal life, Notch signaling regulates a broad spectrum of cellular processes including binary cell fate decisions, lineage commitment, proliferation and differentiation; the functional outcome of Notch signaling with respect to each of these processes is tissue/context dependent. In addition to its role in development and homeostasis, aberrant Notch signaling is associated with a variety of human cancers and it is thus an attractive therapeutic target for the treatment of malignancies. In light of this, we have established and performed a chemical compound screen to identify novel potential Notch inhibitors. Several of the compounds identified in this screen have now been exhaustively tested on a variety of human cancer cell lines, such as human T cell leukemias and breast cancer cells, and have exhibited remarkable anti-cancer activity. At present we are elucidating the mechanism of action of these compounds with respect to Notch inhibition and thus cancer cell growth. In addition, we have established xenograft mouse models of human cancers, thus enabling the efficacy of the compounds to be tested in vivo.

EPFL School of Life Sciences - 2012 Annual Report

Selected Publications

Di Piazza M., Nowell C., Durham AD., Koch U. and Radtke F. (2012). Loss of cutaneous TSLP dependent immune responses skews the balance from tumorprotective to tumor-promoting. Cancer Cell 2012 Oct16; 22(4):479-93. Smith E., Claudinot S., Lehal R., Pellegrinet L., Barrandon Y., and Radtke F. 2012. Generation and characterization of a notch1 signaling-specific reporter mouse line. Genesis. 2012 Sep; 50(9): 700-10. Epub 2012 May 3. Elyaman W, Bassil R, Bradshaw EM, Orent W, Lahoud Y, Zhu B, Radtke F., Yagita H., and Khoury SJ. (2012). Notch receptors and smad3 signaling cooperate in the induction of interleukin-9-producing T cells. Immunity 20;36(4):623-34. Epub 2012 Apr 12. Benedito R., Rocha SF., Woeste M., Zamykal M., Radtke F., Casanovas O., Duarte A., Pytowski B., and Adams RH. (2012) Notch-dependent VEGFR3 upregulation allows angiogenesis without VEGF-VEGFR2 signalling. Nature. 18;484(7392):110-4. Wong SH., Walker JA., Jolin HE., Grynan LF., Hams E., Camelo A., Barlow JL., Neill DR., Panova V., Koch U., Radtke F., Hardman CS., Hwang YY., Fallon PG., McKenzie AN. Transcription factor RORa is critical for nuocyte development. Nat Immunol. 22:13(3):229-36.

Team Members

Postdoctoral Fellows /Scientists Matteo Di Piazza Nicolas Fasnacht Ute Koch Rajwinder Lehal Craig Nowell PhD Students Marzia Armaro Monique Coersmeyer Chhavi Jain Fabian Junker Viktoria Reinmüller Bhushan Sarrode Silvia Wirth Technicians Christelle Dubey Marianne Nkosi Administrative Assistant Catherine Pache

Koch U. and Radtke F. (2011). Mechanisms of T Cell Development and Transformation. Annu.Rev.Cell.Biol. Nov 10;27:539-62. Varnum-Finney B, Halasz LM, Sun M, Gridley T, Radtke F, and Bernstein ID. (2011). Notch2 governs the rate of generation of mouse long- and short-term repopulating stem cells. J Clin Invest. 121(3):1207-16.

ISREC - Swiss Institute for Experimental Cancer Research

Pellegrinet L, Rodilla V, Liu Z, Chen S, Koch U, Espinosa L, Kaestner KH, Kopan R, Lewis J, and Radtke F. (2011). Dll1- and Dll4-mediated Notch signaling is required for homeostasis of intestinal stem cells. Gastroenterology. 2011 Apr;142(4):967-977.

Model for the role of the immune system in controlling inflammation and cancer upon loss of Notch signaling in the adult murine skin. Notch receptors are expressed in the suprabasal layer of the epidermis. Skin specific loss of Notch signaling leads keratinocytes to secrete high levels of TSLP that trigger massive inflammation and the development of an Alzheimer’s-like disease. Inflammation is characterized by dermal recruitment of mast cells, eosinophiles, CD11b+Gr1+ myeloid cells, and CD4+ and CD8+ T cells. Genetic removal of TSLPR in Notch mutant mice causes the development of skin tumors. T cells are absent from the tumor microenvironment whereas CD11b+Gr1+ myeloid cells accumulate. Together with stromal fibroblasts, CD11b+Gr1+ myeloid cells sustain Wnt dependent tumorigenesis.

EPFL School of Life Sciences - 2012 Annual Report

Simanis Lab

http://simanis-lab.epfl.ch/

Viesturs Simanis was awarded a degree in Biochemistry from Imperial College London. He carried out his doctoral studies with David Lane at Imperial College, London University, and postdoctoral studies with Paul Nurse (London and Oxford). Professor Simanis has been a group leader at ISREC since 1988. In 2006 he was appointed Associate Professor at the EPFL School of Life Sciences.

Viesturs Simanis Associate Professor

Introduction

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 the death of the cells, or alter their properties, which can contribute to the development of diseases such as cancer. We study cytokinesis, the division of cells, to understand how it is regulated and coordinated with other events in the cell cycle.

Keywords

Cell cycle, cytokinesis, meiosis, protein kinase, phosphatase, schizosaccharomyces pombe. signal transduction.

Results Obtained in 2012

We study the process of cytokinesis (cell division), using the S. pombe model system. Proper coordination of cytokinesis with other events of the cell cycle is essential. 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”, which is often lethal for both daughter cells, as imbalances in gene dosage are ill- tolerated. An NDR-kinase/GTPase 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.

Genetic analysis of SIN regulation - We performed a genetic screen to search for regulators of the SIN. First, we isolated extragenic suppressors of a conditional SIN mutant at its lowest restrictive temperature, to obtain suppressor mutants that require a low level of SIN kinase activity to restore division. They mapped to two genes; ppa2, the major catalytic subunit of PP2A, and ypa2, which is one of two S. pombe orthologues of the mammalian PTPA gene. Their phenotypes revealed roles for PP2A in both the spatial and temporal control of cytokinesis, and in the initiation of mitosis. Analysis of the S. pombe genome revealed the presence of a second PTPA-like gene, which we named ypa1. Both ypa1 and ypa2 are essential individually at low temperatures, and a double null mutant is inviable at any temperature. We are currently investigating the roles of the ypa1 and ypa2 proteins in the regulation of PP2A and other phosphatases in the cell. We also screened for mutants that depend upon constant, high levels of signalling by the GTPase spg1, and for mutants that influence the activity of spg1 in mitosis and meiosis. Analysis of these mutants is on-going. Modelling and the role of asymmetry in regulating the SIN In collaboration with the Unser lab (EPFL; Daniel Sage and Daniel Schmitter) we have developed a software package to perform automated 3D tracking and analysis of SPBs in mitosis. We are using it to analyse the behaviour of SIN proteins in normal and perturbed mitosis to determine the rules that govern the asymmetric association of SIN proteins with the SPBs in anaphase. In collaboration with the Xenarios lab (Swiss Institute for Bioinformatics; Anastasia Chasapi) we are using this information, and published data about the SIN to develop a model of SIN regulation, which we will use to perform in silico genetic manipulation of the SIN, to guide our wet-lab experiments.

EPFL School of Life Sciences - 2012 Annual Report

Selected Publications

Grallert A, Connolly Y, Smith DL, Simanis V, Hagan IM. The S. pombe cytokinesis NDR kinase Sid2 activates Fin1 NIMA kinase to control mitotic commitment through Pom1/Wee1 (2012). Nature Cell Biology. 14, 738-745. Goyal A, Simanis V. Characterisation of ypa1 and ypa2, the Schizosaccharomyces pombe orthologues of the peptidyl proyl isomerases that activate PP2A, reveals a role for Ypa2p in the regulation of cytokinesis. (2012) Genetics 190, 1235-1250. Goyal A, Takaine M, Simanis V, Nakano K. Dividing the spoils of growth and the cell cycle: The fission yeast as a model for the study of cytokinesis. (2011) Cytoskeleton 68, 69-88 (REVIEW).

Team Members Postdoctoral Fellows Krapp Andrea Wachowicz Paulina Phd Students Anupama Goyal Evelyn Lattmann Manuela Moraru Technician Elena Cano Del Rosario Summer Students Marcelle Arrigo Tunvez Boulic

ISREC - Swiss Institute for Experimental Cancer Research

Administrative Assistant Catherine Pache

The image shows two components of the fission yeast contractile ring during the late stages of mitosis. Cells were imaged at 90 sec intervals as the actomyosin ring contracted during cytokinesis. The individual red and green fluorescently tagged proteins and a merge are shown.

EPFL School of Life Sciences - 2012 Annual Report

Bucher Group

http://bucher-lab.epfl.ch/

Philipp Bucher 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 in 1991 to ISREC to continue his research in comparative molecular sequence analysis. In 1995, he was promoted senior scientist.

Philipp Bucher Group Leader

Introduction

We are interested in gene regulation in higher organisms. More specifically, we try to understand the molecular processes that turn on and off gene transcription within cells in response to internal and external stimuli. Being a computational group, we exclusively rely on public data for our own research. We also develop databases and computer programs that help bench biologists to interpret their own data. Finally, we collaborate with experimental researchers in and outside of EPFL on applied projects related to gene regulatory defects in human diseases.

Keywords

Gene regulation, ChIP-Seq data analysis, bioinformatics algorithms, ultraconserved non-coding elements.

Results Obtained in 2012

We are currently pursuing two main research directions. One consists of using various kinds of sequencing-based epigenetic profiling data for studying gene regulatory processes. The other one focuses on so-called ultraconserved non-coding elements, DNA sequences which are almost 100% identical among all vertebrate species. Both projects have as a common goal to crack the still largely enigmatic regulatory code of our genome. For the analysis of epigenetic data, we are developing new algorithms to extract chromatin signatures from epigenetic profiling data and to classify these signatures into functional categories. An example is the ChIPnorm algorithm, developed in collaboration with Bernard Moret’s group from the Computer & Communication Sciences School, which serves to identify genomic regions that carry different levels of histone modifications in different cell types. We also applied our know-how and in-house developed method in several research collaborations. For instance, with Anne Grapin-Botton we generated an in vivo binding map of transcription factor Ptf1a from ChIP-Seq data.

parative genomics method to infer interactions between proteins. Extending this approach to cis-regulatory elements, we analyzed the retention patterns of UCNEs after the whole genome duplication (WGD) that happened in teleost fishes. It needs to be mentioned in this context, that most UCNEs occur as part large genomic regulatory blocks (GRBs), which may span several genes, but are supposed to control a single target gene typically encoding a transcription factor. The main finding of our study was that UCNEs of the same GRB are retained together at one chromosomal location after WGD, indicating that these elements interact with each other and function in a highly cooperative manner. The same principle can be used to establish regulatory interactions between UCNEs and target genes (see Figure). Besides research, our group also develops and maintains bioinformatics databases and web servers. Our best known resource is the Eukaryotic Promoter Database (EPD) which has been maintained for more than 25 years. Perhaps equally important nowadays is the ChIP-Seq server which allows users not only to analyze their own data but also to explore a growing collection of public datasets. Last year, the server-resident ChIP-Seq database has more than doubled in size as a result of the massive release of public data by the ENCODE consortium. During 2012, we made public UCNEbase, a database of ultraconserved non-coding elements and genomic regulatory blocks. UCNEbase currently provides information on the evolution and genomic organization of s 4351 UCNEs in 240 GRBs across 18 completely sequence vertebrate genomes. Its content is provided as a collections of custom tracks that can be viewed in a UCSC browser window (see Figure).

In order to gain insights into the function of ultraconserved sequence elements (UCNEs), we have applied a new setting of so-called genomic context analysis, which is a com-

EPFL School of Life Sciences - 2012 Annual Report

Selected Publications

Team Members

Nair, N.U., Sahu, A.D., Bucher, P. and Moret, B.M. (2012). ChIPnorm: a statistical method for normalizing and identifying differential regions in histone modification ChIP-seq libraries. PLoS One 7(8):e39573.

PhD Student Slavica Dimitrieva

Dimitrieva, S. and Bucher, P. (2012). Genomic context analysis reveals dense interaction network between vertebrate ultraconserved non-coding elements. Bioinformatics 28(18):i395-i401.

Dimitrieva, S. and Bucher, P. (2012). Practicality and time complexity of a sparsified RNA folding algorithm. J. Bioinform. Comput. Biol. 10(2):1241007.

Postdoctoral Fellows Giovanna Ambrosini René Dreos Sunil Kumar Rouaïda Cavin Périer

Administrative Assistant Sophie Barret

Thompson, N., Gésina, E., Scheinert, P., Bucher, P. and Grapin-Botton, A. (2012). RNA profiling and chromatin immunoprecipitation-sequencing reveal that PTF1a stabilizes pancreas progenitor identity via the control of MNX1/HLXB9 and a network of other transcription factors. Mol Cell Biol. 32(6):1189-1199. Cradickm T.J., Ambrosini, G., Iseli, C., Bucher, P. and McCaffrey, A.P. (2011). ZFN-site searches genomes for zinc finger nuclease target sites and off-target sites. BMC Bioinformatics. 2011 May 13;12:152. Bussotti, G., Raineri, E., Erb, I., Zytnicki, M., Wilm, A., Beaudoing, E., Bucher, P. and Notredame C. (2011). BlastR--fast and accurate database searches for noncoding RNAs. Nucleic Acids Res. 39(16):6886-6895. Meylan, S., Groner, A.C., Ambrosini, G., Malani, N., Quenneville, S., Zangger, N., Kapopoulou, A., Kauzlari,c A., Rougemont, J., Ciuffi, A., Bushman, F.D., Bucher, P. and Trono, D. (2011). A gene-rich, transcriptionally active environment and the pre-deposition of repressive marks are predictive of susceptibility to KRAB/KAP1-mediated silencing. BMC Genomics 12:378.

ISREC - Swiss Institute for Experimental Cancer Research

Pjanic, M., Pjanic, P., Schmid, C., Ambrosini, G., Gaussin, A., Plasari, G,. Mazza, C., Bucher, P. and Mermod, N. (2011). Nuclear factor I revealed as family of promoter binding transcription activators. BMC Genomics 12:181.

Ultraconserved non-coding elements in the genomic regulatory block surrounding the estrogen-related receptor gamma (ESRRG) gene. (A) UCSC genome browser snapshot of the human ESRRG region with custom tracks from UCNEbase showing the conservation of individual UCNEs in different vertebrate species. (B) Retention pattern of UCNEs in the two orthologous regions of the zebrafish genome. Being a transcription factor, ESRRG is considered the most likely target gene of the block. However, the retention pattern in zebrafish suggests that one UCNE controls the TGF beta rather than the ESRRG gene.

EPFL School of Life Sciences - 2012 Annual Report

Knowles

- Translational Research

Jonathan Knowles Full Professor

Research Interests

Jonathan Knowles was named as Professor of Translational Research at EPFL, Sciences de la Vie at the beginning of 2010. From the beginning of 2013 he has continued his work at EPFL as a Professor Emeritus. He is working to help better establish translational research, the critical bridge between bench and bedside at EPFL and other partners in Switzerland and abroad. His interests span all aspects of technology and fundamental biological science particularly in the context of how they could be applied to help patients now, or in the future, and he interacts with a number of groups at EPFL to help bring this about. He believes that better public-private partnerships are essential to bring the advances of technology to society. Dr. Knowles was Head of Group Research and Member of the Executive Committee at Roche for 15 years until the end of 2009. He was a member of the Genentech Board for 12 years and a member of the Chugai Board for seven years. Dr. Knowles was also the chairman of the Corporate Governance Committee of Genentech. From 1987 to 1997, he was director of the Glaxo Institute for Molecular Biology in Geneva, a privately funded Research Institute with an excellent academic publication record. From 1992 until 1997 until he moved to Roche, Jonathan Knowles was the head of the European Research Division and head of the Glaxo Genetics Initiative.

dustry Associations) and was the founding chairman of the Board of the Innovative Medicines Initiative, a unique public-private partnership between 28 Pharmaceutical companies, the European Commission and over one hundred of European academic centres with a budget of more than 2 billion Euros over five years. Jonathan Knowles is a Member of the European Molecular Biology Organization and also holds a Distinguished Professorship in Personalized Medicine at FIMM (Institute for Molecular Medicine Finland) at the University of Helsinki. He has been appointed to a Visiting Chair at the University of Oxford and is a Visiting Fellow of Pembroke College Cambridge. In 2011, Jonathan Knowles was appointed as a Trustee of Cancer Research UK, one of the worlds leading Cancer Research organisations. He remains very excited by the short term prospects for more personalised medicine through molecular diagnostics, especially for the treatment of cancer, as he believes this is the best and perhaps only way in which effective new therapies can be created and used. Contact: jonathan.knowles@epfl.ch

He was for 5 years the Chairman of the Research Directorsâ&#x20AC;&#x2122; Group of EFPIA (European Federation of Pharmaceutical In-

EPFL School of Life Sciences - 2012 Annual Report

Tanner - Swiss TPH http://www.swisstph.ch

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.

Marcel Tanner

External Adjunct Professor Swiss TPH Insitute, Basel Director

Keywords

Epidemiology, public health, vaccines, drugs and diagnostics.

Research Interests

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 host-pathogen 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.

sponses to infection with M. ulcerans and the development 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 optimized. Various subunit vaccine formulations have been used to immunize mice and analyzed for the induction of humoral and cellular immune responses. They are currently tested for protective efficacy. The biannual report of Swiss TPH: http://www.swisstph.ch/about-us/publications/biennialreport/biennial-report-2011-2012.html

The three main mycobacterial pathogens: Mycobacterium tuberculosis, M. leprae and M. ulcerans are the causative agents of the human diseases tuberculosis, leprosy and Buruli ulcer, respectively. These pathogens are all being intensively investigated as part of the GHI-SwissTPH collaboration. These disease-specific joint activities are complemented by collaborations in the fields of lipidomics and bioinformatics.

External Adjunct Professors

Work in vaccinology is concentrated on the emerging disease Buruli ulcer and involves studying the immune re-

EPFL School of Life Sciences - 2012 Annual Report

Molinari Group

http://www.irb.ch/protein-folding/

Maurizio Molinari earned a PhD in Biochemistry at the ETH-Zurich in 1995. He worked as a postdoctoral fellow in the laboratories of Cesare Montecucco (Padua, 1996-1997) and of Ari Helenius (Zurich, 1998-2000). Since October 2000, he is group leader at the IRB in Bellinzona. Dr. Molinari has received the Science Award 2002 from the Foundation for study of neurodegenerative diseases, the Kiwanis Club Award 2002 for Medical Science, the Friedrich-Miescher Award 2006 and the Research Award Aetas 2007. Since 2008, Dr. Molinari is Adjunct Professor at the EPFL. September 2012 he has been nominated commissary for chemistry and biology teaching at the High Schools in Cantone Ticino and since January 2013 he is member of the Research Committee at the Università della Svizzera Italiana.

Maurizio Molinari

External Adjunct Professor Institute for Research in Biomedicine Bellinzona

Introduction

peptides enhances the content of EDEM1 and OS-9 by inhibiting their SEL1L:LC3-I-mediated clearance from the ER thereby selectively rising ERAD activity in the absence of UPR induction. The aim of this project is to identify the chaperones/enzymes whose intraluminal level is regulated by ERAD tuning, and to characterize the mechanisms regulating their segregation from long-lived chaperones that are retained in the bulk ER. Since the vesicular export of select ERAD factors from the ER is hijacked by pathogens (see next project), the characterization of the mechanisms regulating ERAD tuning and the identification of the cellular proteins involved in this process might lead to the identification of potential targets for anti-viral therapies (Bernasconi et al. Mol Cell 2012).

Keywords

ERAD Tuning: Hijacking by Viral Pathogens - In collaboration with F. Reggiori and C. de Haan (Utrecht University), we have established that Coronaviruses (CoV) hijack the host cell ERAD tuning machinery during their infection cycle. In fact, the mouse hepatitis virus (MHV), a prototype CoV, co-opts the ER-derived vesicles containing EDEM1, OS-9, SEL1L and LC3-I, the EDEMosomes, and uses them as a scaffold to build viral replication and transcription complexes. MHV replication is significantly impaired upon silencing of SEL1L and LC3, which are required for EDEM1 and OS-9 segregation from the ER. Our data highlight the biological relevance of a novel COPII-independent ER export pathway, which is hijacked by mammalian pathogens. Furthermore, before our reports (Calì et al. BBRC 2008 and Reggiori et al. Cell Host Microbe 2010), LC3-I was simply considered as a cytosolic precursor of the autophagosomal protein LC3-II. By revealing the role of LC3-I in ERAD tuning and in cell infection by CoV, our studies show for the first time an autophagy-independent function of this ubiquitin-like protein (Bernasconi et al. Mol Cell 2012; Bernasconi et al Autophagy 2012).

The endoplasmic reticulum (ER) is site of synthesis for proteins destined to the extracellular space, the plasma membrane and the endocytic and secretory organelles. Foldingdefective polypeptides are transported to the cytosol for proteasomal degradation. Defective protein folding causes “loss-of-function” and “gain-of-toxic-function” diseases. 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 or should be destroyed. Particular emphasis is on the characterization of responses (transcriptional or post translational) activated by cells expressing folding-defective polypeptides. Cell Biology, conformational diseases, endoplasmic reticulum; ERAD tuning, folding enzymes molecular chaperones; protein Folding, quality control and degradation, UPR.

Results Obtained in 2012

ERAD Tuning: Regulation of the ERAD Activity in Mammalian Cells - Adaptation of the ER folding and degradation activities to long-lasting changes in cargo load is regulated at the transcriptional level by activation of the unfolded protein response (UPR). UPR activation has a latency period of several hours. Hence, it is unsuited to rapidly respond to fluctuations in misfolded proteins load in the ER. Posttranslational mechanisms have much shorter latency, since they do not depend on gene transcription and translation. In particular, we showed that at steady state the complex comprising the type-I ER protein SEL1L and the cytosolic protein LC3-I acts as an ERAD (Endoplasmic-reticulumassociated protein degradation) tuning receptor regulating the COPII-independent vesicle-mediated removal of the luminal ERAD regulators EDEM1 and OS-9 from the ER (Figure). Luminal expression of folding-defective poly-

EPFL School of Life Sciences - 2012 Annual Report

Selected Publications

Team Members

Bernasconi, R., Noack, J. and Molinari, M. (2012) Unconventional roles of nonlipidated LC3 in ERAD tuning and coronavirus infection. Autophagy. 8, 1534-1536.

PhD Students Giorgia Brambilla Pisoni Jessica Merulla Julia Noack

Hebert, D. N. and Molinari, M. (2012). Flagging and docking: dual roles for N-glycans in protein quality control and cellular proteostasis. Trends Biochem Sci. 37, 404-410.

Bernasconi, R., Galli, ., Noack, J., Bianchi, S., de Haan, C.A.M., Reggiori, F. and Molinari, M. (2012). Role of the SEL1L:LC3-I Complex as an ERAD Tuning Receptor in the Mammalian ER. Mol Cell. 46, 809-819. Galli, C., Bernasconi, R., Soldà, T., Calanca, V. and Molinari, M. (2011). Malectin Participates in a Backup Glycoprotein Quality Control Pathway in the Mammalian ER. PLoS ONE 6, e16304. Bernasconi, R. and Molinari, M. (2011). ERAD and ERAD Tuning: Disposal of Cargo and of ERAD Regulators from the Mammalian ER. Curr. Opin. in Cell Biol. 23, 176-183.

Postdoctoral Fellow Riccardo Bernasconi

Senior Scientists Elisa Fasana Carmela Galli Tatiana Soldà Visiting Scientists Tim Beltraminelli (Uni-Lausanne) Elettra Bernasconi (Liceo Lugano) Gaia Codoni (ZHDK ,Zurich) Sarah Motta (Uni-Zurich) Oliver Sulmoni (Uni-Lausanne, CH)

Marroquin, O.B., Cordero, M.I., Setola, V., Bianchi, S., Galli, C., Bouche, N. Mlynarik, V. Gruetter, R., Sandi, C., Bensadoun, J.-C., Molinari, M. and Aebischer, P. (2011). Chronic Delivery of Antibody Fragments Using Immunoisolated Cell Implants as a Passive Vaccination Tool. PLoS ONE 6, e18268.

External Adjunct Professors

Reggiori, F., deHaan, C.A.M. and Molinari, M. (2011). The Unconventional Use of LC3 by Coronaviruses through the Alleged Subversion of the ERAD Tuning Pathway. Viruses 3, 1610-1623.

ERAD regulation by misfolded proteins. A) Unused dislocation machineries are disassembled and the individual component are segregated (e.g., vesiclemediated release of SEL1L, EDEM1 and OS-9 from the ER) or degraded. B) Misfolded proteins engage ERAD factors thereby preserving ERAD complexes..

EPFL School of Life Sciences - 2012 Annual Report

Rainer Group

www.unifr.ch/inph/vclab/

Gregor Rainer received a Diploma in Experimental Physics from the University of Vienna in 1994, a Ph.D. in Systems Neuroscience from the Massachusetts Institute of Technology in 1999 and a Habilitation in behavioural Neurobiology from Eberhard-Karls-University TĂźbingen in 2003. Among his awards are a EURYI grant from the European Science Foundation, an APART scholarship from the Austrian Academy of Sciences, a prize for outstanding teaching from the TĂźbingen graduate school in Neurosciences and the Otto Hahn Medal from the Max Planck Society.

Gregor Rainer

External Adjunct Professor University of Fribourg

Introduction

The visual cognition laboratory focuses on the neurophysiology of the visual system, most notably the primary and extrastriate visual cortex. We are interested in understanding how cortex represents and learns about visual stimuli in the environment, and how these functions can be influenced or enhanced by stimulation of cholinergic centers in the basal forebrain. We are also studying visually based behaviours, using visual stimuli as well as artificial stimulation delivered to visual cortex. Our work is primarily geared towards development of scientific knowledge with relevance for improving medical devices for visual neuroprosthetics or deep brain stimulation.

Keywords

Deep brain stimulation, visual neuroprosthetics, visual cortex.

Results Obtained in 2012

Laminar specificity of cholinergic neuromodulation in the visual cortex - Acetylcholine is an important neuromodulator involved in cognitive function. We examined the effects of layer-specific cholinergic drug application in the tree shrew primary visual cortex during visual stimulation with drifting grating stimuli of varying contrast and orientation. Nicotinic receptor activation enhanced the contrast response in the granular input layer of the cortex, while tending to reduce neural selectivity for orientation across all cortical layers. Muscarinic activation modestly enhanced the contrast response across cortical layers, and tended to improve orientation tuning. Our results indicate that laminar position plays a crucial part in functional consequences of cholinergic stimulation, consistent with the differential distribution of cholinergic receptors. Nicotinic receptors function to enhance sensory representations arriving in the cortex, whereas muscarinic receptors act to boost the cortical computation of orientation tuning. Our findings suggest close homology between cholinergic mechanisms in tree shrew and primate visual cortices.

Novelty preference in tree shrew - Recognition memories are formed during perceptual experience and allow subsequent recognition of previously encountered objects as well as their distinction from novel objects. As a consequence, novel objects are generally explored longer than familiar objects by many species. We have examined novelty preference using the NOR task in tree shrew. After three object familiarization sessions, tree shrews exhibited robust preference for novel objects on the test day. This was accompanied by a significant reduction in familiar object exploration time, occurring largely between the first and second day of object familiarization. By contrast, tree shrews did not show a significant preference for the novel object after a one-session object familiarization. Nonetheless, they spent significantly less time exploring the familiar object on the test day compared to the object familiarization day, indicating that they did maintain a memory trace for the familiar object. Our study revealed different time courses for familiar object habituation and emergence of novelty preference, suggesting that novelty preference is dependent on well-consolidated memory of the competing familiar object. Neuropeptides in the visual system - Endogenous neuropeptides, acting as neurotransmitters or hormones in the brain, carry out important functions including neural plasticity, metabolism and angiogenesis. We target three important parts of the visual system: the primary visual cortex (V1), lateral geniculate nucleus (LGN) and superior colliculus (SC). We identified a total of 52 peptides from the tree shrew visual system. A total of 26 peptides, for example GAV and neuropeptide K were identified in the visual system for the first time. We observed generally lower abundance of peptides in the LGN compared to V1 and SC. Consistently, a number of individual peptides showed high abundance in V1 (such as neuropeptide Y or somatostatin 28) and in SC (such as somatostatin 28 AA1-12). This study provides the first in-depth characterization of peptides in the mammalian visual system. These findings now permit the investigation of neuropeptide-regulated mechanisms of visual perception.

EPFL School of Life Sciences - 2012 Annual Report

Selected Publications

Petruzziello F, Fouillen L, Wadenstein H, Kretz R, Andren P, Rainer G, Zhang X. Extensive characterization of Tupaia belangeri Neuropeptidome using an integrated Mass Spectrometry Approach. J Proteome Res 11(2): 886-896 (2012). Liebe S., Hoerzer G., Logothetis N.K., Rainer G. Theta coupling between V4 and prefrontal cortex predicts visual short-term memory performance. Nat Neurosci 15(3): 456-464 (2012). Bhattacharyya A., Biessmann F., Veit J., Kretz R., Rainer G. Functional and laminar dissociations between muscarinic and nicotinic cholinergic neuromodulation in the tree shrew primary visual cortex. Eur J Neurosci 35(8): 1270-1280 (2012).

Team Members Postdoctoral Fellow Xiaozhe Zhang

PhD Students Anwesha Bhattacharyya Julia Veit Abbas Khani Filomena Petruzziello Paolo Pretto Mohammed Faiz Jayakrishnan Nair Jordan Poirot

Ranc V., Petruzziello F., Kretz R., Argandona E., Zhang X., Rainer G. Broad characterization of endogenous peptides in the tree shrew visual system. J Prot 75(9): 2526-35 (2012). Zhang, X., Petruzziello F., Zani F., Fouillen L., Andren P., Solinas G., Rainer G. High identification rates of endogenous neuropeptides from mouse brain. J Proteome Res 11(5):2819-27 (2012). Khani A., Rainer G. Recognition memory in tree shrew (Tupaia belangeri) after repeated familiarization sessions. Behav Proc 90: 364-371 (2012). Falasca S., Petruzziello F., Kretz R., Rainer G., Zhang X. Analysis of Multiple Quaternary Ammonium Compounds in the Brain Using Tandem Capillary Column Separation and High Resolution Mass Spectrometric Detection. J Chrom A 1241:46-51 (2012). Pretto P., Bresciani J.P.,Rainer G, BĂźlthoff H.H. Foggy perception slows us down. E-Life DOI: 10.7554/eLife.00031 (2012).

External Adjunct Professors

A simplified version of the primary visual cortex laminar microcircuit including nicotinic and muscarinic cholinergic receptors.

EPFL School of Life Sciences - 2012 Annual Report

Schorderet Group www.irovision.ch/

After attending medical school at the Universities of Fribourg and Geneva, Dr Schorderet obtained an FMH in Pediatrics. He then trained in medical genetics at the University of Washington, Center for Inherited Diseases in Seattle, USA, where he was appointed research assistant professor. On his return to Switzerland, he developed the Unit of Molecular Genetics of the CHUV and later was appointed head of the Division of Medical Genetics. He obtained a FMH in Medical Genetics and a FAMH in analyses in Medical Genetics. In 2003, Dr. Schorderet was appointed director of the Institute of Research in Ophthalmology (IRO) in Sion. He is a member of the SV faculty since 2005.

Daniel Schorderet

External Adjunct Professor Institute for Reserch in Ophthalmology (IRO), Sion Director

Introduction

The Institute for Research in Ophthalmology (IRO) develops research in various aspects of vision, from understanding the development of the eye in animal models like the zebrafish and the mouse to identifying new genes and characterizing their molecular and cellular pathways for better diagnosis and treatment. Through various Swiss and international collaborations, IRO is shaping a new way in providing molecular diagnosis and understanding the inherited conditions behind some of the diseases leading to blindness.

anophthalmia, we contributed to the identification of GPR179, a new gene responsible for congenital stationary night blindness. Genotype-phenotype correlations are difficult to establish for many diseases. However, our in-depth analysis of patients with various forms of blinding disorders allowed us to make progress in diseases such as recurrent corneal erosion, retinal pattern dystrophy, anophthalmia and retinitis pigmentosa. We also continued our work on the characterization of the various pathways involved in retinal degeneration and showed that autophagy was involved in many of them.

Keywords

Blindness, genetics of eye diseases, retinitis pigmentosa, glaucoma, age-related macular degeneration, diabetic retinopathy, gene identification, next-generation sequencing.

Results Obtained in 2012

At IRO, research centers around 4 axes: identification of new genes, understanding their function, developing animal models of eye diseases and new therapeutic tools. Using the new mapping technology based on next-generation sequencing, we have continued our search for new genes in ophthalmic disorders, both in-house and through collaboration. After discovering the gene for Waardenburg

EPFL School of Life Sciences - 2012 Annual Report

Selected Publications

Team Members

Métrailler S, Schorderet DF, Cottet S (2012). Early apoptosis of rod photoreceptors in Rpe65-/-mice is associated with the upregulated expression of lysosomalmediated autophagic genes. Exp Eye Res 96:70-81.

PhD Students Séverine Hamann Fabienne Marcelli Lionel Page Gaëtan Pinton Fatima Taki Désirée von Alpen

Slavotinek A, Chao R, Vacik T, Yahyavi M, Abouzeid H, Bardakjian T, Schneider A, Shaw G, Sherr EH, Lemke G, Youssef M, Schorderet DF (2012). VAX1 mutation associated with microphthalmia, corpus callosum agenesis and orofacial clefting – the first description of a VAX1 phenotype in humans. Human Mutation, 33(2):364-368.

Vaclavik V, Tran HV, Gaillard MC, Schorderet DF, Munier FL (2012). Pattern dystrophy with high Intrafamilial variability associated with Y141C mutation in the Peripherin/RDS gene and successful treatment of subfoveal CNV related to multifocal pattern type with anti-VEGF (ranibizumab) intravitreal injections. Retina, 32(9):1942-1949. Klionsky DJ et al (2012). Guidelines for the use and interpretation of assays for monitoring autophagy. Autophagy 8(4):445-544. H. Abouzeid, Youssef MA, Bayoumi N, ElShakankiri N, Marzouk E, Hauser P, Schorderet DF (2012). RAX Gene and Anophthalmia in Human: Evidence of Brain Anomalies. Molecular Vision, 18:1449-1456. Escher P, Tran HV, Vaclavik V, Borruat FX, Schorderet DF and Francis L. Munier (2012). Double Concentric Autofluorescence Ring in NR2E3-p.G56R-linked Autosomal Dominant Retinitis Pigmentosa. Invest. Ophthalmol Vis Sci 53(8):4754-4764. Boisset G, and Schorderet DF (2012). Zebrafish hmx1 promotes retinogenesis. Exp Eye Res 105:34-42.

Postdoctoral Fellows Gaëlle Boisset Arnaud Boulling Anne Oberson Nathalie Produit Leila Tiab

Research Associate Nathalie Allaman-Pillet Laboratory Technicians Céline Agosti Martine Emery Tatiana Favez Carole Herkenne Sylviane Métrailler Loriane Moret Angélique Schmid Administrative Assistants Pascale Evéquoz Sandra Théodoloz

External Adjunct Professors

Abouzeid H, Boisset G, Favez T, Youssef M, Marzouk I, Shakankiry N, Bayoumi N, Descombes P, Agosti C, Munier FL, Schorderet DF (2011). Mutations in the SPARC-related modular calcium-binding protein 1 gene, SMOC1, cause Waardenburg anophthalmia syndrome. Am J Hum Genet 88(1):92-98.

Zebrafish larvae at 5 days post fertilization showing on the left a wild-type animal and on the right a fish treated with a morpholino against the SMOC1 gene responsible for the Waardenburg anophthalmia/ microphthalmia syndrome. The morphant shows a smaller eye (microphthalmia) and a cleft in the retina (coloboma), both findings that can be observed in human patients with this syndrome. Bars representing diameters of the wildtype eye are reported on the morphant eye to show size variation.

EPFL School of Life Sciences - 2012 Annual Report

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 state-of-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. 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://unil.ch/dafl).

Core Facilities & Technology Platforms

The following pages describe the Life Sciences-related core facilities and technology platforms currently available at the EPFL School of Life Sciences.

EPFL School of Life Sciences - 2012 Annual Report

Bioelectron Microscopy - Bio-EM http://cime.epfl.ch/bio-em/

Team Members Facility Head Graham Knott

Postdoctoral Researchers Davide Demurtas Bohumil Maco Corrado Cali Technicians Marie Croisier Stéphanie Rosset

Introduction

The BioEM Facility provides life scientists at the EPFL and the lemanic area with electron microscopy services, training and support. As part of the Centre of Electron Microscopy (CIME) this platform has a wide range of techniques available for analysing biological structures at high resolution. This includes scanning and transmission electron microscopy, using both ambient and cryo temperatures during the preparation processes. Recently, there have been increasing numbers of projects that require the correlation of information gathered using light with electron microscopy imaging. This has meant the development of new tools and protocols for targeting specific regions in cells for imaging with electrons. These methods have also been adapted for the different 3D imaging approaches in which the facility specializes, using either serial section TEM (Transmission electron microscopy), or focussed ion beam scanning electron microscopy.

Services and Technologies • Transmission electron microscopy • Cryo transmission electron microscopy • Scanning electron microscopy • Focussed ion beam scanning electron microscopy • Correlated light and electron microscopy • Resin embedding • Semithin sectioning • Ultrathin sectioning • Serial sectioning • Cryosectioning and immunolabelling • Pre-embedding immuno labelling • Negative staining • Critical point drying • High pressure freezing • Plunge freezing • Low temperature, and freeze substitution embedding

Selected Publications

Gaugler, M.N., Genc, O., Bobela, W., Mohanna, S., Ardah, M.T., El-Agnaf, O.M., Cantoni, M., Bensadoun, J.C., Schneggenburger, R., Knott, G.W., Aebischer, P., and Schneider, B.L. (2012). Nigrostriatal overabundance of α-synuclein leads to decreased vesicle density and deficits in dopamine release that correlate with reduced motor activity. Acta Neuropathol 123, 653-669. Mikeladze-Dvali, T., von Tobel, L., Strnad, P., Knott, G., Leonhardt, H., Schermelleh, L., and Gönczy, P. (2012). Analysis of centriole elimination during C. elegans oogenesis. Development 139, 1670-1679. Knott, G., Rosset, S., and Cantoni, M. (2011). Focussed ion beam milling and scanning electron microscopy of brain tissue. J Vis Exp , e2588. Kreshuk, A., Straehle, C.N., Sommer, C., Koethe, U., Cantoni, M., Knott, G., and Hamprecht, F.A. (2011). Automated detection and segmentation of synaptic contacts in nearly isotropic serial electron microscopy images. PLoS One 6, e24899. Sznitman, R., Lucchi, A., Pjescic-Emedji, N., Knott, G., and Fua, P. (2012). Efficient scanning for EM based target localization. Med Image Comput Comput Assist Interv 15, 337-344.

Contact Information: Graham Knott Station 19, EPFL CH-1015 Lausanne Tel: +41 (0) 21 693 1862 graham.knott@epfl.ch

EPFL School of Life Sciences - 2012 Annual Report

BioImaging & Optics - BIOP http://biop.epfl.ch/

Team Members Facility Head Arne Seitz

Collaborators José Artacho Olivier Burri Mathias Fournier Romain Guiet Thierry Laroche Adminstrative Assistant Maureen Ochsner

The Bioimaging and Optics platform (PT-BIOP) is located in the faculty of Life Science (SV) at the Ecole Polytechnique Fédérale de Lausanne (EPFL) and part of a network of core facilities at the institute. The general idea of the platform is to provide state of the art light microscopes and even more important expertise to solve challenging (biological) questions with modern light-microscopy. Currently a broad range of instruments are available in the facility: starting 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). Scientists who want to make use of the available equipment are trained by the PT-BIOP staff so that they can use the instruments independently or under the supervision of the staff. Additionally there is a strong competence and necessary computer power to perform image processing. The idea is to link the image analysis with the image acquisition as early as possible as only this approach guarantees optimal scientific results. The microscopes and the image analysis capabilities can be used by scientists of the faculty and the EPFL and are also available to scientist coming from outside the EPFL.

Services and Technologies

Selected Publications

BKobel SA, Burri O, Griffa A, Girotra M, Seitz A, Lutolf MP. (2012). Automated analysis of single stem cells in microfluidic traps. Lab Chip. 12(16):2843-9. Seitz A, Terjung S, Zimmermann T, Pepperkok R. (2012) Quantifying the influence of yellow fluorescent protein photoconversion on acceptor photobleaching-based fluorescence resonance energy transfer measurements. J Biomed Opt. 17(1):011010. Bélanger M, Yang J, Petit JM, Laroche T, Magistretti PJ, Allaman I. (2011). Role of the glyoxalase system in astrocyte-mediated neuroprotection. J Neurosci. 31(50):18338-52. Terjung, S., Walter, T., Seitz, A., Neumann, B., Pepperkok, R., and Ellenberg, J. (2010) High-throughput microscopy using live mammalian cells, Cold Spring Harbor Protocols, pdb top84. Maurel, D., Banala, S., Laroche, T., and Johnsson, K. (2010) Photoactivatable and photoconvertible fluorescent probes for protein labeling, ACS Chem Biol 5, 507-516.

Contact Information: Arne Seitz AI 0240 Station 19, EPFL CH-1015 Lausanne Tel: +41 (0) 21 693 9618 Fax: +41 (0) 21 693 9585 arne.seitz@epfl.ch

Core Facilities & Technology Platforms

Introduction

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

EPFL School of Life Sciences - 2012 Annual Report

Bioinformatics & Biostatistics - BBCF http://bbcf.epfl.ch/

Team Members Facility Head Jacques Rougemont

Postdoctoral Fellows Solenne Carat Fabrice David Kyle Gustafson Julia di Iulio Philippe Jacquet Marion Leleu Scientiﬁc Assistants Sara Benmohammed Julien Delafontaine Yohan Jarosz Adamandia Kapopoulou Bara’ah Khubieh Yoann Mouscaz Lucas Sinclair Administrative Assistant Sophie Barret

Introduction / Services and Technologies

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 development of data management pipelines for new high-throughput technologies (e.g. high-density arrays, high-throughput sequencers) and for the statistical planning in complex experimental designs. The BBCF also helps researchers in the areas of 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, and in particular the Vital-IT high performance computing center.

Selected Publications

Uplekar, S., Rougemont, J., Cole, S. T. & Sala, C. (2013) High-resolution transcriptome and genome-wide dynamics of RNA polymerase and NusA in Mycobacterium tuberculosis. Nucleic Acids Research 41:961–977. Le Martelot, G. et al. Genome-Wide RNA Polymerase II Profiles and RNA Accumulation Reveal Kinetics of Transcription and Associated Epigenetic Changes During Diurnal Cycles. (2012). PLoS Biol 10:e1001442. Lee, K. P. et al. Spatially and genetically distinct control of seed germination by phytochromes A and B. (2012). Genes Dev 26:1984–1996. Rougemont, J. & Naef, F. Computational Analysis of Protein-DNA Interactions from ChIP-seq Data. (2012). Methods Mol Biol 786:263–273. Gheldof, N., Leleu, M., Noordermeer, D., Rougemont, J. & Reymond, A. Detecting Long-Range Chromatin Interactions Using the Chromosome Conformation Capture Sequencing (4C-seq) Method. (2012). Methods Mol Biol 786:211–225.

Contact Information: Jacques Rougemont Station 15, EPFL CH-1015, Lausanne +41 (0)21 693 9573 jacques.rougemont@epfl.ch

EPFL for all material published in this report info.sv@epfl.ch

EPFL School of Life Sciences - 2012 Annual Report

Biomolecular Screening - BSF http://bsf.epfl.ch/

Team Members Facility Head Gerardo Turcatti

Scientists Billy Breton Marc Chambon Ruud van Deursen Benjamin Rappaz

Introduction

The BSF provides access to EPFL, NCCR-Chemical Biology and SystemsX.ch researchers to the infrastructure, expertise and collections of molecules required for performing medium to high throughput molecular screening assays. In the frame of the NCCR-Chemical Biology, the BSF leads the project ACCESS with the main mission to become the platform for Academic Chemical Screens in Switzerland. In addition, the BSF is pursuing an innovative and focused research program with industrial partners in screening or drug discovery-linked areas. Most of the incoming projects are related to Chemical Biology, Systems Biology or disease-oriented research in particular in the areas of Cancer, Infectious Diseases and Neurobiology. Our multidisciplinary laboratory provides scientists with adequate screening instrumentation, stateof-the-art technologies and compounds collections for applications ranging from the probing of cellular pathways to the broad area of bioactive compounds research. We perform our automated screens in 96 and 384 well plates for the following two main categories of assays: • Screening of chemicals for a variety of biochemical target-based and cellular assays using large, chemically diverse collections • RNA interference (RNAi) cellular screens for probing gene function using collections of small interfering RNAs (siRNAs) targeting the human genome.

Services and Technologies

• Access to instrumentation dedicated to microplates and cell culture facilities • Assay development and validation for HTS • Assay automation and statistical validations • Pilot screening • Primary screening campaigns • Hits confirmation • Dose response assays • Secondary screens • Compound storage and management of collections • Image processing for high content screening read-outs

• Data management using in-house developed Laboratory Implementation Management System (LIMS). • Cheminformatics Research BSF funded research in drug discovery-related areas through industry-academia grants: «Bridge to Industry» project (BIP) grant, SystemsX. High content screening by digital holographic imaging. Lyncée Tec HCS - BSF - LNDC - CHUV, two years CTI grant. A digital holographic microscope for label-free High Content Screening.

Selected Publications

Makhlouf Brahmi, M., Portmann, C., D’Ambrosio, Danilo., Woods,T. M., Banfi, D., Reichenbach, P., Da Silva, L., Baudat, E., Turcatti, G., Lingner J., and Gademann, K. (2012).Telomerase Inhibitors from Cyanobacteria: Isolation and Synthesis of Sulfoquinovosyl Diacylglycerols from Microcystis aeruguinosa PCC 7806, Chemistry - A European Journal. Epub ahead of print. Kühn, J., Shaffer, E., Mena, J., Breton, B., Parent, J., Rappaz, B., Chambon, M., Emery, Y., Magistretti, P., Depeursinge, C., and Turcatti, G. (2012) Label-Free Cytotoxicity Screening Assay by Digital Holographic Microscopy, ASSAY and Drug Development Technologies. Epub ahead of print. Takahashi-Umebayashi, M., Pineau, L., Hannich, T., Zumbuehl, A., Doval, D. A., Matile, S., Heinis, C., Turcatti, G., Loewith, R., Roux, A., lien, Reymond, L., Johnsson, K., and Riezman, H. (2011) Chemical Biology Approaches to Membrane Homeostasis and Function, CHIMIA International Journal for Chemistry 65, 849-852.

Contact Information: Gerardo Turcatti, MER Station 15, EPFL CH-1015 Lausanne Switzerland Tel: +41-(0)21 693 9666 gerardo.turcatti@epfl.ch

Core Facilities & Technology Platforms

Assistants Nathalie Ballanfat Sandra Borel Julien Bortoli Manuel Bueno Antoine Gibelin

EPFL School of Life Sciences - 2012 Annual Report

Flow Cytometry - FCCF http://fccf.epfl.ch/

Team Members Facility Head Miguel Garcia

Collaborators Telma Lopes Laetitia Roh Administrative Assistant Ursula Winter

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. Sorting allows us to capture and collect cells of interest for further analysis. The FCCF mission is to provide comprehensive flow cytometric analysis and sorting including instrumentation, technical and professional assistance, training and consultation.

Services and Technologies

The Flow Cytometry Core Facility from EPFL is equipped with five self-service cytometers. For cell sorting, the facility has two high-speed BLS2 cell sorters; one BD FACSAria II SORP & one MoFlo Astrios. The Core Facility also operates an automated immunomagnetic bead cell separator from Miltenyi Biotec MACS® Technology. The LSRII (Becton Dickinson) is a 5 lasers benchtop analyser capable of 18 colour, forward and side scatter analysis, equipped with a PC and DIVA digital acquisition software system. The Accuri C6 is equipped with 2 lasers and 4 active detectors to allow maximum flexibility for easy experimental design. This machine is also equipped with a plate reader (CSampler) The Cyan ADP (Beckman Coulter) is a 3-laser benchtop analyser capable of 9 colour, forward and side scatter analysis, equipped with a PC and Summit digital acquisition software system.

The FACSAria (Becton Dickinson) is a 5 laser high-speed sorter capable of 18 colour, forward and side scatter analysis. It is equipped with DIVA digital acquisition software system and ACDU. The MoFlo Astrios (Beckman Coulter) is a 4-laser sorter capable of 17 colour, forward and side scatter analysis. It is equipped with Summit acquisition software system. Flow Cytometry Core Facility services • Cell sorting • User training on machines and software • Help with acquisition and data analysis • Advice on cell preparation • Interpretation of results • Help with manuscript preparation; i.e. figures, materials and methods

Contact Information: Miguel Garcia EPFL / SV_PTECH / PTCF AI 0147 Sation 15 EPFL CH – 1015 Lausanne Tel: +41 21 693 0901 miguel.garcia@epfl.ch

The AutoMACS Pro is a fully automated bench-top sorter that can be used to perform sterile bulk sorts. Designed for ultra high-speed positive selection as well as depletion, the AutoMACS Pro can isolate virtually any cell type.

EPFL School of Life Sciences - 2012 Annual Report

Histology -

HCF & Comparative Pathology

http://hcf.epfl.ch/

Team Members Facility Head Jessica Sordet-Dessimoz Collaborators Gian-Filippo Mancini Nathalie Müller Agnès Hautier Veterinary pathologist Alessandra Piersigilli Administrative Assistant Maureen Ochsner

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 nothing without the expertise of a specialist in veterinarian pathology helping researchers analyzing their slides.

Services and Technologies

On one hand, the facility assists researchers in the setting up and optimizing of histological approaches specific for each scientific project. Members of the SV faculty can be trained on the available instruments like microtomes or cryostats and have then access to them for their own experiments. Furthermore a large panel of secondary antibodies are titrated and provided to the researchers by the service. On the other hand technicians of the facility 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 or cresyl violet among others. Several stains are running on the Prisma automate from Sakura • Setup and optimization of immunohistochemistry and immunofluorescence protocols manually as well as automated (Ventana Discovery xT)

Pathology service Pathology support is provided by professionals that underwent formal postgraduate training in veterinary anatomic pathology officially acknowledged by board certification of specialty. These professionals are trained to interpret morphologic changes within organs and tissues processed through the variety of histology techniques. Appropriate interpretation of tissue changes implies proper recognition of tissue abnormalities and pathologic processes of diseases that manifest as morphologic changes observable in histological preparations. The service provides the following activities: • Consulting, at the study design level for issues related to pathology investigation • Phenotyping, whole body or organ targeted for genetically engineered animals • Analysis (morphology), of histological preparations • Support, in reporting pathology data for manuscript preparation and grant application

Core Facilities & Technology Platforms

Introduction

• Diagnostics. Post mortem examination of diseased animals within the colony.

Contact Information: Jessica Sordet-Dessimoz EPFL SV PTH AI 0342 Station 19, EPFL 1015 Lausanne +41 (0)21 693 0962 info.hcf@epfl.ch

• Detection of mRNA and miRNA using cold probes on the Discovery xT automate from Roche-Ventana.

EPFL School of Life Sciences - 2012 Annual Report

Proteomics - PCF http://pcf-ptp.epfl.ch/

Team Members Facility Head Marc Moniatte

Collaborators Diego Chiappe Florence Armand Adrian Schmid Research Assistants Romain Hamelin Jonathan Paz-Montoya Administrative Assistant Maureen Ochsner

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. Today it is possible to get quantitative information about thousands of proteins in one experiment allowing researchers to 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 helps 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 QQQ LC-ESI-MS/MS and 1 MALDITOF/TOF instruments. Two ion trap instruments of the facility are also accessible in other EPFL labs. The bioinformatics analysis pipeline includes Mascot, Xtandem! SEQUEST and Peaks servers for matching MS data with protein sequence databases and data post-treatment tools like Maxquant, Perseus, Proteome 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 Relative Quantification by SILAC or Labelfree Quantitative Analysis on collaborative basis. • Protein

separation

FPLC

and

HPLC.

Contributes also to collaborative based services requiring heavy involvement of both parties like: • Accurate protein quantification by SRM-MRM. • Localization and eventually quantification of PTM’s other than phosphorylation. • Lipid mixtures profiling. Maintains tight collaboration with other proteomics facilities (UNIL-PAF, UNIGE-PCF, UNIBE) within a network called Repp-SO and with computer science and bioinformatics research centers (Vital-IT, SIB, etc..).

Selected Publications

Hirsch V, Kinnear C, Moniatte M, Rothen-Rutishauser B, Clift MJD, Fink A. (2013) Surface charge of polymer coated SPIONs influences the serum protein adsorption, colloidal stability and subsequent cell interaction in vitro. Nanoscale 2012 Dec DOI: 10.1039/C2NR33134A. Bosshard F, Armand F, Hamelin R, Kohn T. (2012) Human adenovirus sunlight and UVC inactivation mechanisms as examined by qPCR and quantitative proteomics. Appl. Environ. Microbiol. 2012 Dec DOI: 10.1128/AEM.03457-12. Dastidar EG, Dayer G, Holland ZM, Dorin-Semblat D, Claes A, Chêne A, Sharma A, Hamelin R, Moniatte M, Lopez-Rubio J-J, Scherf A, Doerig C. (2012) Involvement of Plasmodium falciparum protein kinase CK2 in the chromatin assembly pathway. BMC Biology Jan;10(1):5.

Contact Information: Marc Moniatte AI 0149 Station 15, EPFL CH-1015, Lausanne +41 (0)21 693 17 53 marc.moniatte@epfl.ch

• Protein/Peptide Molecular Weight Measurements by Mass Spectrometry. • Mass Spectrometry based Protein/Peptide Identification from Gel or Solution.

EPFL School of Life Sciences - 2012 Annual Report

Protein Crystallography - PCRYCF http://pcrycf.epfl.ch/

Team Members Facility Head Florence Pojer

Technical Assistant Gabriella Cuanoud Administrative Assistant Manuelle Mary

The Protein Crystallography Core Facility provides instrumentation and expertise at every stage of the structure determination process for non-crystallography 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 X-ray crystal screening, data collection, data processing and structure determination and analysis are provided. X-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. Presently, it is possible for a non-crystallographer to access this technology thanks to automation and a variety of commercially available kits as well as to the more user friendly and 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 proteins of choice.

Services and Technologies

The Protein Crystallography Core Facility provides the EPFL community with:

• Data processing using popular packages such as XDS and Mosflm. • Structure determination using molecular replacement, MAD and SAD techniques. • Structure refinement, fitting and analysis using ccp4i and Phenix software. • Deposition of structures in the protein database. • Preparation of images for publication using PyMol software.

Selected Publications

Towards a new tuberculosis drug: pyridomycin - nature’s isoniazid. Hartkoorn RC et al. (2012), EMBO Mol Med. Structural basis for benzothiazinone-mediated killing of Mycobacterium tuberculosis. Neres J. et al. (2012) Sci Transl Med. Structure and function of the transketolase from Mycobacterium tuberculosis and comparison with the human enzyme. Fullam E, et al. (2012) Open Biol.: 251-64.

Contact Information: Florence Pojer SV 3827 Station 19, EPFL CH-1015 Lausanne Tel: +41 (0)21 693 1772 +41 (0)21 693 1839 florence.pojer@epfl.ch

Core Facilities & Technology Platforms

Introduction

• 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 xray source and synchrotrons.

EPFL School of Life Sciences - 2012 Annual Report

Protein Expression - PECF http://pecf.epfl.ch/

Team Members Facility Head David Hacker

Collaborator Sarah Thurnheer

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 (HEK293) cells in suspension at volumetric scales from 5 mL to 15 L using orbitally shaken bioreactors. For transient protein production in mammalian cells, we have a number of expression vectors available. With the same technical approach, we are also capable of producing virus vectors such as adeno associated virus. 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. Cultures at volumetric scales up to 15 L are possible. Expression vectors based on piggybac transposon-mediated gene delivery are available to our clients. We produce monoclonal antibodies by scale-up of existing hybridoma cell lines. Serum-free suspension cultures based on mixing by orbital shaking can be used for a scale-up to 2 liters. When using E. coli as a host for protein production, the scales of operation range from 100 mL – 20 L. Induced protein production at low temperatures is feasible. We also provide services in protein recovery, mainly by affinity chromatography of antibodies and tagged proteins (Fc, 6X his, FLAG and GST) produced in either mammalian cells or E. coli.

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

Kadlecova, Z., Baldi, L., Hacker, D., Wurm, F.M., and Klok, H.A. (2012). Comparative study on the in vitro cytotoxicity of linear, dendritic, and hyperbranched polylysine analogues. Biomacromolecules 13(10):3127-3137. Rajendra, Y., Kiseljak, D., Manoli, S., Baldi, L., Hacker, D.L., and Wurm, F.M. (2012). Role of non-specific DNA in reducing coding DNA requirement for transient gene expression with CHO and HEK-293E cells. Biotechnol. Bioeng. 109(9):2271-2278. Kadlecova, Z., Nallet, S., Hacker, D.L., Baldi, L., Klok, H.A., and Wurm, F.M. (2012). Poly(ethyleneimine)-mediated large-scale transient gene expression: influence of molecular weight, polydispersity and N-propionyl groups. Macromol. Biosci.12(5):628-636. Baldi, L., Hacker, D.L., Meerschman, C., and Wurm, F.M. (2012). Large-scale transfection of mammalian cells. Methods Mol. Biol. 801:13-26. Tissot, S., Michel, P.O., Hacker, D.L., Baldi, L., De Jesus, M., and Wurm, F.M. (2012). k(L)a as a predictor for successful probe-independent mammalian cell bioprocesses in orbitally shaken bioreactors. N. Biotechnol. 29(3):387-394.

Contact Information: David Hacker Station 6 EPFL-SV-PECF CH J2 496 CH-1015 Lausanne Tel: +41 (0)21 693 6142 david.hacker@epfl.ch

EPFL School of Life Sciences - 2012 Annual Report

Transgenic - TCF http://tcf.epfl.ch/

Team Members Facility Head Isabelle Barde

Collaborators Michelle Blom Sabrina Guichard Amandine Moriot Signorino – Gelo Sandra Offner Sonia Verp

Introduction

Services and Technologies

We offer a centralized resource and state-of-the-art technology for the generation of transgenic animals. We can perform direct pronuclear injection of DNA in the mouse oocyte, which has been the standard method of trangenesis for more than three decades.

In progress: • ES mediated transgenesis, • ES cells microinjection into blastocysts.

As an attractive alternative, we are one of the very few platforms that provides a fast and efficient way to generate transgenic animals through the use of lentiviral vectors. Lentivector-mediated transgenesis is relatively easy to perform and leads to high percentages of provirus-positive animals. Moreover, a wide variety of lentiviral vectors have been developed that can all be used in transgenic animals, thus allowing for a broad range of genetic manipulations including externally controllable expression and knockdown, the latter offering an economically advantageous alternative to stable knockout. In addition to this primary service, we also offer 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.

• Pronuclear injection: plasmids and BACs • Lentiviral vector mediated transgenesis • Vectorology • Lentiviral vectors production/titration • Cleaning of established mouse lines by embryo transfer. • Cryopreservation by sperm freezing

Selected Publications

Åkerblom M, Sachdeva R, Barde I, Verp S, Gentner B, Trono D, Jakobsson J. (2012). MicroRNA-124 is a subventricular zone neuronal fate determinant. J Neurosci. Jun 27;32(26):8879-89. Groner AC, Tschopp P, Challet L, Dietrich JE, Verp S, Offner S, Barde I, Rodriguez I, Hiiragi T, Trono D. (2012). The Krüppel-associated box repressor domain can induce reversible heterochromatization of a mouse locus in vivo. J Biol Chem. Jul 20;287(30):25361-9. Bojkowska K, Santoni de Sio F, Barde I, Offner S, Verp S, Heinis C, Johnsson K, Trono D.(2011). Measuring in vivo protein half-life. Chem Biol. Jun 24;18(6):805-15. Montavon T, Soshnikova N, Mascrez B, Joye E, Thevenet L, Splinter E, de Laat W, Spitz F, Duboule D. (2011). A regulatory archipelago controls Hox genes transcription in digits. Cell Nov 23;147(5):1132-45.

Contact Information

Core Facilities & Technology Platforms

Genetic manipulation of rodents through the generation of transgenic animals is a procedure of paramount importance for biomedical research, either to address fundamental questions or to develop preclinical models of human diseases.

Isabelle Barde AI 3351 Station 19 EPFL CH-1015 Lausanne Tel: +41 (0)21 693 1702 isabelle.barde@epfl.ch

For long term preservation of a mouse line of particular interest, we now propose cryopreservation by sperm freezing via the JAX® Sperm Cryo Kit. The advantage of this technique is that it is standardized and requires only 2 competent male breeders.

EPFL School of Life Sciences - 2012 Annual Report

Phenotyping Unit - CPG-UDP Team Members CPG – Head Xavier Warot

CPG – UDP Managers Philippe Cettour-Rose Raphaël Doenlen Laboratory Assistants Arnaud Bichat Cristina Cartoni Sébastien Lamy Adeline Langla Elodie Schneider Marion Varet Collaborators Sybil Bron Sebastian Koenig Christine Pehm Trainee Céline Waldvogel

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 gene of interest. The clinical phenotyping unit of the Center of PhenoGenomics 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-ofthe-art equipment to enable cardio-metabolic, biochemical 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 for doing so from the scientific expertise of Prof. Johan Auwerx and Prof. Carmen Sandi, both experts in their respective fields of expertise, namely cardio-metabolism and neurobiology. 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.

Services and Technologies

We offer tests in the different scientific fields mentioned in the opposite figure. A series of tests can be combined in a pipeline in order to answer questions related to a given topic such as neurodegenerative diseases, obesity or diabetes.

Selected Publications

Cantó C, Houtkooper RH, Pirinen E, Youn DY, Oosterveer MH, Cen Y, Fernandez-Marcos PJ, Yamamoto H, Andreux PA, Cettour-Rose P, Gademann K, Rinsch C, Schoonjans K, Sauve AA, Auwerx J. (2012). The NAD(+) precursor nicotinamide riboside enhances oxidative metabolism and protects against high-fat diet-induced obesity. Cell Metabolism. 15(6):838-847. Houtkooper RH, Argmann C, Houten SM, Cantó C, Jeninga EH, Andreux PA, Thomas C, Doenlen R, Schoonjans K, Auwerx J. (2011). The metabolic footprint of aging in mice. Science Report. 1:134. Marcaletti S, Thomas C, Feige JN. (2011). Exercise Performance Tests in Mice. Current Protocols in Mouse Biology. 1:141-154. Thomas C, Marcaletti S, Feige JN. (2011). Assessment of Spontaneous Locomotor and Running Activity in Mice. Current Protocols in Mouse Biology. 1:185-198.

Contact Information: Raphael Doenlen: UDP manager Tel: +41 (0)21 693 0953 raphael.doenlen@epfl.ch Xavier Warot CPG Head Tel: +41 (0)21 693 1869 xavier.warot@epfl.ch

Core Facilities & Technology Platforms

EPFL School of Life Sciences - 2012 Annual Report

Silas Goodman

10th edition 2012/2013 Produced and edited by the EPFL School of Life Sciences Printed at the EPFL “Atelier de Reprographie” Editor: Alice Emery-Goodman With many thanks to Bruno Liardon (photographs & cover design), Roland Chabloz, and Harald Hirling for their help and support!

EPFL for all material published in this report info.sv@epfl.ch