EPFL-SV GHI Annual Report 2012 by EPFL School of Life Sciences

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

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

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

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).