2011 EPFL SV Annual Report by EPFL School of Life Sciences

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EPFL School of Life Sciences - 2011 Annual Report

Preamble Whether paving the way to personalized medicine or meeting our planet’s environmental challenges, trans-disciplinary approaches will be the key to research and education in the life sciences. It is with a true pioneering spirit that our school is geared to train a new breed of engineers/scientists endowed with quantitative and integrative skills. In accordance with this objective, our close to fifty research groups push for holistic approaches that span a range of disciplines from functional genomics to high-tech bio-engineering, and from computer neurosciences to structural modeling. A bachelor degree (Life Sciences and Technology), two masters degrees (Life Sciences and Technology; Bioengineering), and three Ph.D. programs (Biotechnology and Bioengineering; Neurosciences; Molecular Life Sciences), constitute the educational arms of our school, hosting some six hundred students from all geographic and scientific horizons. Our first classes of Engineers in Life Sciences and Technology are now in the greater world. In 2011, our faculty further increased its team of ERC grant recipients to a total of 12 (9 seniors, 4 juniors), launched the Center for Neuroprosthetics in association with the School of Engineering, held its first SV Research Day for the wider EPFL community, and established very productive interactions with its new neighbor, the Nestlé Institute for Health Sciences. These are exciting times to be at the EPFL School of Life Sciences! Didier Trono, M.D. Professor & Dean of the School of Life Sciences Ecole Polytechnique Fédérale de Lausanne (Switzerland)

Introduction

http://sv.epfl.ch

EPFL School of Life Sciences - 2011 Annual Report

Table Of Contents

INTRO

Main Scientific Events..................................................................................................................6 Public-Oriented Events................................................................................................................6 Honors-Awards-Announcements.................................................................................................7 Undergraduate Studies.................................................................................................................8 Graduate Studies.........................................................................................................................8 School of Life Sciences at a Glance.............................................................................................9 Congratulations to our PhD Grads!............................................................................................10

Core Facilities & Technology Platforms............................................................................13 Bioelectron Microscopy.............................................................................................................14 BioImaging & Optics.................................................................................................................15 Bioinformatics & Biostatistics.....................................................................................................16 Biomolecular Screening.............................................................................................................17 Flow Cytometry ........................................................................................................................18 Histology ..................................................................................................................................19 Proteomics.................................................................................................................................20 Protein Crystallography..............................................................................................................21 Protein Expression.....................................................................................................................22 Transgenic ................................................................................................................................23 Phenotyping Unit.......................................................................................................................24

BMI - Brain Mind Institute...............................................................................................27 Aebischer Lab............................................................................................................................28 Blanke Lab.................................................................................................................................30 Fraering Lab...............................................................................................................................32 Gerstner Lab..............................................................................................................................34 Hadjikhani Group......................................................................................................................36 Herzog Lab................................................................................................................................38 Lashuel Lab...............................................................................................................................40 Luthi-Carter Lab . ................................................................................................................42 Magistretti Lab...........................................................................................................................44 Markram Lab.............................................................................................................................46 Moore Lab.................................................................................................................................48 Petersen Lab..............................................................................................................................50 Sandi Lab...................................................................................................................................52 Schneggenburger Lab................................................................................................................54 Blue Brain Project......................................................................................................................56

IBI - Institute of Bioengineering.......................................................................................59 Auwerx - Schoonjans Lab..........................................................................................................60 Barrandon Lab...........................................................................................................................62 Dal Peraro Lab...........................................................................................................................64 Deplancke Lab..........................................................................................................................66 Hubbell Lab...............................................................................................................................68 Lutolf Lab..................................................................................................................................70 Naef Lab....................................................................................................................................72 Swartz Lab.................................................................................................................................74 Wurm Lab.................................................................................................................................76

Co-affiliated Research Groups.........................................................................................78 Aminian Lab..............................................................................................................................78 Fantner Lab . .............................................................................................................................79 Guiducci Lab.............................................................................................................................80

EPFL School of Life Sciences - 2011 Annual Report

Hatzimanikatis Lab....................................................................................................................81 Ijspeert Lab................................................................................................................................82 Johnsson Lab.............................................................................................................................83 Jolles-Haeberli Lab ...................................................................................................................84 Lacour Lab ...............................................................................................................................85 Maerkl Lab ...............................................................................................................................86 Mermod Lab..............................................................................................................................87 Millán Lab ................................................................................................................................88 Pioletti Lab ...............................................................................................................................89 Psaltis Lab ................................................................................................................................90 Radenovic Lab . ........................................................................................................................91 Roke Lab ..................................................................................................................................92 Stergiopulos Lab .......................................................................................................................93 Van de Ville Lab . ......................................................................................................................94 Van den Bergh Lab ...................................................................................................................95

GHI - Global Health Institute..........................................................................................97 Blokesch Lab.............................................................................................................................98 Cole Lab..................................................................................................................................100 Doerig Lab...............................................................................................................................102 Fellay Lab................................................................................................................................104 Harris Lab................................................................................................................................106 Lemaitre Lab............................................................................................................................108 McKinney Lab.........................................................................................................................110 Trono Lab................................................................................................................................112 Van der Goot Lab....................................................................................................................114

ISREC - Swiss Institute for Experimental Cancer Research......................................117 Aguet Lab................................................................................................................................118 Beard Lab................................................................................................................................120 Brisken Lab..............................................................................................................................122 Constam Lab............................................................................................................................124 De Palma Lab..........................................................................................................................126 Duboule Lab............................................................................................................................128 Gönczy Lab.............................................................................................................................130 Grapin-Botton Lab...................................................................................................................132 Hanahan Lab...........................................................................................................................134 Hantschel Lab..........................................................................................................................136 Huelsken Lab .........................................................................................................................138 Kühn Lab.................................................................................................................................140 Lingner Lab..............................................................................................................................142 Meylan Lab..............................................................................................................................144 Radtke Lab...............................................................................................................................146 Simanis Lab.............................................................................................................................148 Bucher Group..........................................................................................................................150

Other Professors............................................................................................................152 Knowles...................................................................................................................................153 Molinari Group........................................................................................................................154 Rainer Group...........................................................................................................................156 Schorderet Group....................................................................................................................158 Tanner.....................................................................................................................................160

Introduction

Welcome To Our New Collaborators!............................................................................161

EPFL School of Life Sciences - 2011 Annual Report

Main Scientific Events

INTRO

March 14th - 15th: A Symposium on Stress, the Social Brain and Psychopathology was organized by Prof. Sandi (BMI) which brought together international leading scientists to discuss work done on human and animal models. The meeting was attended by over 100 participants. May 2nd - 3rd: Experts from India and Switzerland were brought together for a Indo-Swiss Symposium on Infectious Diseases hosted by the GHI. India and Switzerland share many common interests in the fields of science and medicine and both countries have exceptional expertise in the areas of HIV/AIDS, malaria and tuberculosis, human diseases of global importance. May 30th: A one day symposium was organized by the GHI called GMS 2011 “Gut Microbiota in Health and Disease”. Areas such as microbial communities (ecology, metabolism) and mucosal immunology were presented and discussed by young international experts in the field. July 4th to August 26th: The 2011 International Summer Research Program for undergraduate students welcomed 26 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. September 7th - 10th: The annual Life Sciences Symposium was hosted by ISREC, on the theme “Hallmarks and Horizons of Cancer”, with a world-class roster of speakers. The symposium was a resounding success, with well over 600 applicants. The 2011 Debiopharm Life Sciences Award was given to Professor Stefano Piccolo, from the University of Padua, Italy.

Public-Oriented Events March: The SV labs welcomed 10 enthusiastic high school students from all corners of Switzerland under the framework of La Science Appelle les Jeunes! (Schweizer Jugend forscht!) These students experienced first-hand lab work and completed and presented a mini-project. http://fr.sjf.ch/index.cfm March: The undergraduate (or Bachelor-Master) teaching section in Life Sciences and Technologies participated in the EPFL Prospective Students Days and welcomed more than 150 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 November. More information : http://ssv.epfl.ch/gymnasiens June 8th: The first SV Research Day was held with the theme of “Towards Personalised Medicine”. Non-bio EPFL scientists were cordially invited to attend.

EPFL School of Life Sciences - 2011 Annual Report

Honors-Awards-Announcements February: The EPFL, has joined with AstraZeneca, Sanofi-Aventis, the Universities of Pavia, Uppsala and Cambridge, and 19 other research groups from 13 different countries, to form the More Medicines for Tuberculosis (MM4TB) consortium, which aims to develop new drugs for successful and shorter treatment of Tuberculosis (TB). This consortium is led by TB expert Professor Stewart Cole (GHI). March: On World Tuberculosis Day (24 March 2011), Dr Neeraj Dhar, senior scientist within the research group of Prof. John McKinney (GHI) received the “2011 Swiss TB Award” from the Swiss Foundation for Tuberculosis Research. March: Prof. Melody A. Swartz (IBI), Head of the Laboratory of Lymphatic and Cancer Bioengineering, together with Prof. Stephanie Hugues, Department of Pathology and Immunology at the University of Geneva won one of the 2011 Leenaards Foundation’s Scientific Prizes for their project on an emerging therapeutic approach to destroy cancer cells by activating the body’s immune system. April: Tej Tadi, PhD student in Prof. Olaf Blanke’s lab (BMI), was awarded two prizes: the “Lausanne Entrepreneurship Region” PERL Prize for his start-up “MindMaze” and one of EPFL’s prestigious PhD prizes, the Chorofas Award. April: PhD student Alireza Roshan Ghias from the Laboratory of Biomechanical Orthopedics (Director Prof. Dominique Pioletti, IBI), was awarded the Swiss Bone Mineral Society’s President Award for an outstanding publication (European Cell and Materials) in 2010. May: Douglas Hanahan (ISREC) was awarded an honorary degree from the University of Dundee, Scotland, UK. September: Denis Duboule (ISREC) received the Annual Prize of the Fondation pour Genève and the EPFL Polysphere Prize for teaching in Life Sciences. September: Etienne Meylan (ISREC) was honored with a Debiopharm Group Junior Life Sciences Award. October: Congratulations to Prof. Carl Petersen (BMI) for his European Research Council (ERC) Advanced Grant. October: Patrick Aebischer (BMI) has received a Dr. Honoris Causa from the Ecole Polytechnique of the University of Montreal. October: Henning Sprekeler, PostDoc from Prof. Gerstner’s Computational Neuroscience Lab (BMI), received the very prestigious Berstein Award that will allow him to start his own research group in Germany. October: José del R. Millán (IBI) received the IEEE Nobert Wiener Award for “seminal and pioneering contributions to non-invasive brain-computer interfaces, in particular brain-controlled robots, wheelchairs and prostheses”, at the IEEE International Conference on Systems, Man, and Cybernetics. November: Harvard Medical School and Ecole Polytechnique Fédérale de Lausanne (EPFL) launched a Joint Program to “Improve Quality of Life for People With Neurological Disabilities” joining forces to combine neuroscience and engineering in order to alleviate human suffering caused by such neurological disabilities as paralysis and deafness. Collaboration on six pioneering neuroengineering projects was made possible by a grant from the Bertarelli Foundation.

Introduction

November: The Zonta Award was presented to Stéphanie Lacour (IBI) for her work on creating an electronic artificial skin which could help repair nerves that have been severed due to a serious accident.

EPFL School of Life Sciences - 2011 Annual Report

Undergraduate Studies

INTRO

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 orientations. Among these are neurosciences, molecular medicine, and bio-computing. Each orientation is made up of 30 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 bio-computing, computing neurosciences and neuroprosthetics. 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), biotechnology(SB), bio-computing (I&C), or neuroprosthetics. Each minor requires taking 30 specific credits chosen under the guidance of a mentor. The minors, as indicated, are organized within the different schools at EPFL. Both degree programs share some common basic curriculum that aims to provide students with the knowledge of the modern technologies used in the life sciences such as imaging, bio-computing and optical systems applied to biology, etc.... In addition, courses in management, economics, applied laws and ethics for the life sciences are offered. A large portion of the master’s program (60 credits) can be dedicated to laboratory work and projects. http://ssv.epfl.ch/

Graduate Studies

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 twice a year through a competitive selection procedure.

The Doctoral Program in Biotechnology and Bioengineering aims at providing doctoral students with the education

necessary to be leaders in the fast-growing industrial and academic biotechnology and bioengineering sectors, i.e. a depth of knowledge and competence in their specific research area as well as a breadth of knowledge in biology, bioengineering and biotechnology. These program themes include: genomics and proteomics, biomolecular engineering and biomaterials, stem cell biotechnology, cell and process engineering, biochemical engineering, orthopaedic engineering, biomechanics, mechanobiology, cell biophysics, computational biology, biomedical imaging as well as molecular, cell and tissue engineering. http://phd.epfl.ch/edbb

The Doctoral Program in Neuroscience provides its students with training from the genetic to the behavioural level including molecular, cellular, cognitive, and computational neuroscience. Students enroll in the highly dynamic and interdisciplinary environment of the BMI-EPFL of the SV. The program is further strengthened by research and training opportunities in collaboration with the Universities of Lausanne and Geneva. ‘http://phd.epfl.ch/edne The Doctoral Program in Molecular Life Sciences is a joint program between the Swiss Institute for Experimental Cancer Research (ISREC-EPFL) and the Global Health Institute (GHI-EPFL). The program provides training and research opportunities to highly motivated doctoral students in key areas of modern biology. http://phd.epfl.ch/edms/en

Introduction

Doctoral programs EDBB EDMS EDNE

Teaching Sec+on BA/MA programs

ISREC

Global Health Ins+tute

(interfacultary SV-‐STI)

Ins+tute of Bioengineering

Brain Mind Ins+tute

postdocs, PhD students

all professors

Teaching Commission

General Services

techn. & administra+ve personnel

BA/MA students

Professors

Core Facili+es

Dean s Oﬃce

Educa+on Deleg.

representatives

School Council

Faculty Assembly

School Directory Board 4 full prof.

Directors +

Research Deleg.

Dean

EPFL School of Life Sciences - 2011 Annual Report

School of Life Sciences at a Glance

EPFL School of Life Sciences - 2011 Annual Report

INTRO

Congratulations to our PhD Grads! Mr. Alessandro Wataru Amici

EDBB

Prof. Yann Barrandon

The Role of LEKTI in Fate Determination of Keratinocyte Stem Cells

Ms. Julie Deuquet Ariosa

EDBB

Prof. Gisou van der Goot

Molecular mechanisms underlying Hyaline Fibromatosis Syndrome

Ms. Elena Aritonovska

EDMS

Prof. Joachim Lingner

Insight into the Regulation of Telomerase Access to Telomeres by Shelterin Proteins

Mr Maxime Baud*

EDNE

Prof. P. Magistretti/ Dr J.-M. Petit

The Impact of Sleep Fragmentation on Sleep Homeostasis, Brain and Peripheral Energy Metabolism and Spatial Learning

Ms. Alexandra Bezler

EDMS

Prof. Pierre Gönczy

Mutual Inhibition Between the Anaphase-promoting Complex and the Spindle Assembly Checkpoint in C. Elegans Embryos

Mr. Jorge Castro

EDNE

Prof. Carmen Sandi

Psychobiological Vulnerability to Stress: Behavioral Traits and Neurobiological Mechanisms

Mr. Philippe Coune

EDNE

Prof. P. Aebischer/ Dr B.Schneider

Alpha-Synuclein Effects at the ER-to-Golgi Level and Potential Biomarkers in Rat Models of the Early Phase of Parkinson's Disease

Mr. Sebastian Dieguez

EDNE

Prof. Olaf Blanke

Bodily Ownership: Tactile, Visual and Motor Mechanisms

Ms. Anja Dietze

EDMS

Prof. Daniel Constam

Role of Nodal Processing in Pluripotent Progenitors

Mr. Thomas d'Eysmond

EDBB

Prof. Felix Naef

On the Precision of Circadian Oscillators

Mr. Rodrigo Manuel Gonzalez EDBB

Prof. Gisou van der Goot Cellular Responses to Bacterial Pore-Forming Toxins

Ms. Chiara Greggio

EDMS

Definition of in Vitro Microenvironments to Prof. Anne Grapin-Botton Characterize and Control Pancreatic Progenitor Expansion and Differentiation

Ms. Anna Claire Groner

EDBB

Prof. Didier Trono

Studies on KRAB/KAP1-mediated long-range repression and its potential as a tool

Ms. Yunyun Han

EDNE

Prof. Ralf Schneggenburger

RIM Determines Ca2+ Channel Density and Vesicle Docking at the Presynaptic Active Zone

Mr. Lukas Heydrich*

EDNE

Prof. Olaf Blanke

Turning Body and Self Inside Out: Extero- and Interoceptive Signal Integration in Temporo-Parietal and Insular Cortex

Ms. Jemila Houacine

EDNE

Prof. Patrick Fraering

The Gamma-Secretase-Mediated Proteolytic Processing of APP C-Terminal Fragments as a Therapeutic Target for Alzheimer's Disease

Ms. Mircea Ioan Iacovache

EDBB

Prof. Gisou van der Goot

Folding and Structure of the Pore Forming Toxin Aerolysin

Mr Asif Jan

EDNE

Prof. H.Markram/ Dr F.Schürmann

A Pipeline Based Approach for Experimental Neuroscience Data Management

Ms. Ana Jovicic

EDNE

Prof. Ruth Luthi-Carter

Unique Cell-Type-Specific Distributions and Functions of Brain MicroRNAs

Ms. Susanna Eveliina Kallioinen

EDMS

Prof. Daniel Constam

Activin Signalling in Human Melanoma Cells

EPFL School of Life Sciences - 2011 Annual Report

Mr. Georges Khazen

EDNE

Prof. Henry Markram

Predictive Engineering the Membrane Composition of Neocortical Neurons

Mr. Stephane Kontos

EDBB

Prof. Jeffrey Hubbell

Engineering erythrocyte affinity for improved pharmacokinetics and immune tolerogenesis

Ms. Kristen Lorentz

EDBB

Prof. Jeffrey Hubbell

Biofunctional Scaffold Design for Soft Tissue Regeneration

Ms. Alexandra Magold

EDNE

Prof. Patrick Fraering

Gamma-Secretase Dependent Gene Expression: A Potential New Focus of Alzheimer's Disease Research

Mr. Nicolas Marcille

EDNE

Prof. Wulfram Gerstner

Models of Evidence Integration in Rapid Decision Making Processes

Mr. Mikaël Martino

EDBB

Prof. Jeffrey Hubbell

Engineering of Signaling Microenvironments with Fibronectin Fragments to Enhance Tissue Regeneration

Mr. Lionel Ambroise Micol*

EDBB

Prof. Jeffrey Hubbell

Hydrogels for Urinary Tract Tissue Engineering

Mr. Richard Naud

EDNE

Prof. Wulfram Gerstner

The Dynamics of Adapting Neurons

Mr. Luca Pellegrinet

EDMS

Prof. Freddy Radtke

The Intestinal Epithelium: Role of Notch Signaling

Ms. Emilda Pino

EDNE

Prof. P. Aebischer/ Dr B. Schneider

Role of the FoxO3a Transcription Factor in alphasynuclein Induced Neurodegeneration

Mr. Rubin Berek Pisarek

EDBB

Prof. Jeffrey Hubbell

New/Surface-Modified Biocompatible Polymer for ICD Lead Insulation

Ms. Caroline Poisson

EDMS

Prof. Freddy Radtke

The Microenvironment and the Cell Differentiation Status Influence the Outcome of Notch-Induced Malignancy

Ms. Carolyn Yong Pullin

EDBB

Prof. Melody Swartz

In Vitro Lymphatic Endothelial Morphogenesis: Molecular vs. Biophysical Regulation

Mr. Ranjan Rajnish

EDNE

Prof. Henry Markram

Mr. Lehal Rajwinder

EDMS

Prof. Freddy Radtke

Mr. Srikanth Ramaswamy

EDNE

Prof. Henry Markram/ Dr S. Hill

Emergent Properties of in silico Synaptic Transmission in a Model of the Rat Neocortical Column

Mr. Guillaume Rey

EDMS

Prof. Felix Naef

On the Relationship Between Protein-DNA Interactions and Circadian Gene Expression in Mouse Liver

Mr. Tej Tadi

EDNE

Prof. Olaf Blanke

Neural Mechanisms of the Embodied Self Merging Virtual Reality and Electrical Neuroimaging

Ms. Kalyani Thyagarajan

EDMS

Prof. Pierre Gönczy

Asymmetric Spindle Positioning and Intracellular Trafficking in C. elegans Embryos

Ms. Stéphanie Tissot

EDBB

Prof. Florian Wurm

OrbShake Bioreactors for Mammalian Cell Cultures: Engineering and Scale-up

Mr. Norbert Wiedemann

EDMS

Prof. Michel Aguet

Role of BcI9 and BcI9I in Homeostasis, Regeneration and Tumorigenesis of the Gastrointestinal Epithelium

Engineering Neuron Models: from Ion Channels to Electrical Behavior Identification and Preclinical Validation of Novel Inhibitors of the Notch Pathway

*MD-PhD" UNIL-EPFL joint degrees EDMS - Molecular Life sciences

Introduction

EDBB - Biotechnology and Bioengineering EDNE - Neuroscience

EPFL School of Life Sciences - 2011 Annual Report

Core Facilities & Technology Platforms In its goal to offer maximal support to its students and scientists in their training and research capabilities, EPFL and its School of Life Sciences have made a significant investment over the past years to establish state-of-the-art technology platforms and core facilities. These facilities are directed and managed by dedicated teams of highly trained and experienced staff and are run on a fee-for-service basis. They offer training, access to technology, assistance with experimental design and high level data analysis, and collaborations. The platforms are also involved in the School’s undergraduate and graduate teaching programs. In addition, scientists from our School of Life Sciences closely collaborate with other services in the Lemanic region, including the ‘Center for Biomedical Imaging’ (http://www.cibm.ch) and the ‘Lausanne Genomics Technologies Facility’ (http://unil.ch/dafl).

Core Facilities & Technology Platforms

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

CORE

EPFL School of Life Sciences - 2011 Annual Report

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

Team Members Facility Head Graham Knott

Postdoctoral researchers Natalya Korogod Bohumil Maco Scientists Davide Demurtas Corrado Cali Technicians Marie Croisier Stéphanie Rosset

Introduction

The Bio Electron Microscopy Facility (BioEM) is located in the Faculty of Life Science (SV), and also in the Interdisciplinary Centre of Electron Microscopy (CIME). It provides both services and training to researchers at the EPFL who need to image their biological samples at high resolution. This begins with specific sample preparation techniques, carried out in the preparation laboratories, and then a range of different imaging approaches using either scanning or transmission electron microscopes. These machines are specially suited to biological samples and during 2011, the facility expanded its range of imaging technology with the acquisition of two new transmission electron microscopes; one for ambient temperature imaging, and the other for imaging frozen samples. Other additions during the past year also include the installation of a new high-pressure freezer for instantaneously freezing living material.

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

Selected Publications

Knott, Graham, Stéphanie Rosset, and Marco Cantoni. «Focussed Ion Beam Milling and Scanning Electron Microscopy of Brain Tissue.» Journal of visualized experiments : JoVE , no. 53 (2011) Lucchi, A, K Smith, R Achanta, G Knott, and P Fua. «Supervoxel-Based Segmentation of Mitochondria in EM Image Stacks with Learned Shape Features.» IEEE transactions on medical imaging (2011) Straehle, C N, U Köthe, G Knott, and F A Hamprecht. «Carving: Scalable Interactive Segmentation of Neural Volume Electron Microscopy Images.» Med Image Comput Comput Assist Interv 14, no. Pt 1 (2011): 653-60. Kreshuk, Anna, Christoph N Straehle, Christoph Sommer, Ullrich Koethe, Marco Cantoni, Graham Knott, and Fred A Hamprecht. «Automated Detection and Segmentation of Synaptic Contacts in Nearly Isotropic Serial Electron Microscopy Images.» PloS one 6, no. 10 (2011). Cantoni, M. Genoud, C., Hébert, C., Knott, GW. (2010). Large volume, isotropic, 3D imaging of cell structure on the nanometer scale. Microscopy and Analysis 24 (4).

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

EPFL School of Life Sciences - 2011 Annual Report

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

Team Members Facility Head Arne Seitz

Collaborators José Artacho Olivier Burri Mathias Fournier Romain Guiet Thierry Laroche

The Bioimaging and Optics platform (PT-BIOP) is located in the faculty of Life Science (SV) at the Ecole Polytechnique Fédérale de Lausanne (EPFL) and is part of a network of core facilities at the institute. The general idea of the platform is to provide state of the art light microscopes and even more importantly, expertise to solve challenging (biological) questions with modern light-microscopy. Currently a broad range of instruments ranging from simple wide-field imaging systems over standard point-scanning confocal microscopes up to a high-end 2-Photon-excitation microscope are available in the facility. Scientists who want to make use of the available equipment are trained by the PT-BIOP staff so that they can use the instruments independently or under the supervision of the staff. Additionally there is a strong competence and necessary computer power to perform image processing. The idea is to link the image analysis with the image acquisition as early as possible as only this approach guarantees optimal scientific results. The microscopes and the image analysis capabilities can be used by scientists of the faculty and the EPFL but are also available to scientist coming from outside the EPFL.

Services and Technologies • Wide-field transmission and fluorescent microscopes • Life cell imaging microscopes

Selected Publications

Bélanger M, Yang J, Petit JM, Laroche T, Magistretti PJ, Allaman I. Role of the glyoxalase system in astrocyte-mediated neuroprotection. J Neurosci. (2011) 31(50):18338-52. Terjung, S., Walter, T., Seitz, A., Neumann, B., Pepperkok, R., and Ellenberg, J. (2010) High-throughput microscopy using live mammalian cells, (2010) Cold Spring Harbor Protocols, pdb top84. Maurel, D., Banala, S., Laroche, T., and Johnsson, K. (2010) Photoactivatable and photoconvertible fluorescent probes for protein labeling, ACS Chem Biol 5, 507-516. Kobel, S., Limacher, M., Gobaa, S., Laroche, T., and Lutolf, M. P. (2009) Micropatterning of hydrogels by soft embossing, Langmuir 25, 8774-8779. Lefort S., Tomm C., Floyd Sarria J.C., Petersen C.C. (2009) The excitatory neuronal network of the C2 barrel column in mouse primary somstosensory cortex, Neuron 61, 301-316. Emmenlauer, M., Ronneberger, O., Ponti, A., Schwarb, P., Griffa, A., Filippi, A., Nitschke, R., Driever, W., and Burkhardt, H. (2009) XuvTools: free, fast and reliable stitching of large 3D datasets, J Microsc 233, 42-60.

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

Core Facilities & Technology Platforms

Introduction

• Single and multiple-beam confocal microscopes • 2P microscope • High resolution and super resolution microscope (will be available in 2012) • Image Processing tools (commercially available and/or custom built)

EPFL School of Life Sciences - 2011 Annual Report

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

Team Members Facility Head Jacques Rougemont Post doctoral Solenne Carat Fabrice David Julia di Iulio Gregory Lefebvre Marion Leleu Scientific assistants Julien Delafontaine Yohan Jarosz Bara’ah Khubieh Frederick Ross Lucas Sinclair Administrative Assistant Sophie Barret

Introduction and Services and Technologies

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

Selected Publications

Ayyanan, A., Laribi, O., Schuepbach-Mallepell, S., Schrick, C., Gutierrez, M., Tanos, T., Lefebvre, G., et al. (2011). Perinatal exposure to bisphenol a increases adult mammary gland progesterone response and cell number. Molecular Endocrinology, 25(11), 1915–1923. Huber, A., French, S. L., Tekotte, H., Yerlikaya, S., Stahl, M., Perepelkina, M. P., Tyers, M., et al. (2011). Sch9 regulates ribosome biogenesis via Stb3, Dot6 and Tod6 and the histone deacetylase complex RPD3L. The EMBO journal, 30(15), 3052–3064. Rey, G., Cesbron, F., Rougemont, J., Reinke, H., Brunner, M., & Naef, F. (2011). Genome-wide and phase-specific DNA-binding rhythms of BMAL1 control circadian output functions in mouse liver. PLoS Biology, 9(2), e1000595. Leleu, M., Lefebvre, G., & Rougemont, J. (2010). Processing and analyzing ChIP-seq data: from short reads to regulatory interactions. Briefings In Functional Genomics, 9(5-6), 466–476. Preti, M., Ribeyre, C., Pascali, C., Bosio, M. C., Cortelazzi, B., Rougemont, J., Guarnera, E., et al. (2010). The telomere-binding protein Tbf1 demarcates snoRNA gene promoters in Saccharomyces cerevisiae. Molecular Cell, 38(4), 614–620. Rowe, H. M., Jakobsson, J., Mesnard, D., Rougemont, J., Reynard, S., Aktas, T., Maillard, P. V., et al. (2010). KAP1 controls endogenous retroviruses in embryonic stem cells. Nature, 463(7278), 237–240.

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

Noordermeer, D., Leleu, M., Splinter, E., Rougemont, J., de Laat, W., & Duboule, D. (2011). The dynamic architecture of Hox gene clusters. Science, 334(6053), 222–225. Truman, R. W., Singh, P., Sharma, R., Busso, P., Rougemont, J., Paniz-Mondolfi, A., Kapopoulou, A., et al. (2011). Probable zoonotic leprosy in the southern United States. The New England Journal of Medicine, 364(17), 1626–1633.

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

EPFL School of Life Sciences - 2011 Annual Report

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

Team Members Facility Head Gerardo Turcatti

Scientists Damiano Banfi Marc Chambon Ruud van Deursen Assistants Nathalie Ballanfat Manuel Bueno Miquel Busquets Julien Mena

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

Services and Technologies

• Access to instrumentation dedicated to microplates and cell culture facilities • Assay development and validation for HTS • Assay automation and statistical validations • Pilot screening • Primary screening campaigns • Hits confirmation • Dose response assays • Secondary screens

• Compound storage and management of collections • Image processing for high content screening read-outs • Data management using in-house developed Laboratory Implementation Management System (LIMS). • Cheminformatics

Selected Publications

Takahashi-Umebayashi, M., Pineau, L., Hannich, T., Zumbuehl, A., Doval, D. A., Matile, S., Heinis, C., Turcatti, G., Loewith, R., Roux, A., lien, Reymond, L., Johnsson, K., and Riezman, H. (2011) Chemical Biology Approaches to Membrane Homeostasis and Function, CHIMIA International Journal for Chemistry 65, 849-852. Magnet, S., Hartkoorn, R. C., Székely, R., Pató, J., Triccas, J. A., Schneider, P., Szántai-Kis, C., Orfi, L., Chambon, M., Banfi, D., Bueno, M., Turcatti, G., Kéri, G., and Cole, S. T. (2010) Leads for antitubercular compounds from kinase inhibitor library screens, Tuberculosis 90, 354-360. Kobel, S., Valero, A., Latt, J., Renaud, P., and Lutolf, M. (2010) Optimization of microfluidic single cell trapping for long-term on-chip culture, Lab on a Chip 10, 857-863. Gormley, N.; Boutell, J., Turcatti, G.,Barnes, G. (2010). Preparation of nucleic acid templates for solid phase amplification. Patent number: US2010041561. Ouertatani-Sakouhi, H., El-Turk, F., Fauvet, B., Cho, M.-K., Pinar Karpinar, D., Le Roy, D., Dewor, M., Roger, T., Bernhagen, J., Calandra, T., Zweckstetter, M., and Lashuel, H. A. (2010) Identification and Characterization of Novel Classes of Macrophage Migration Inhibitory Factor (MIF) Inhibitors with Distinct Mechanisms of Action, Journal of Biological Chemistry 285, 26581-26598.

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

Core Facilities & Technology Platforms

Introduction

CORE

EPFL School of Life Sciences - 2011 Annual Report

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

Team Members Facility Head Miguel Garcia

Collaborators Gonzalo Tapia Sintia Winkler Administrative Assistant Ursula Winter

Introduction

Flow cytometry is a technology that simultaneously measures and then analyzes multiple physical characteristics of single particles, usually cells, as they flow in a fluid stream through a beam of light. Sorting allows us to capture and collect cells of interest for further analysis. Our mission is to provide comprehensive flow cytometric analysis and sorting including instrumentation, technical and professional assistance, training.

Services and Technologies

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

quick and quantitative analysis of red & green expression, apoptosis, cell viability, cell count, and much more. The AutoMACS Pro is a fully automated bench-top sorter that can be used to perform sterile bulk sorts. Designed for ultra high-speed positive selection as well as depletion, the AutoMACS Pro can isolate virtually any cell type. The FACSVantage DIVA (BD) is a 3-laser sorter capable of 8 colour, forward and side scatter analysis. It is equipped with DIVA digital acquisition software system. The FACSAria (BD) is a 5 laser high-speed sorter capable of 18 colour, forward and side scatter analysis. It is equipped with DIVA digital acquisition software system and ACDU. Services : • Cell sorting • User training • Help with acquisition and data analysis • Experiment design & manuscript • Advice on cell preparation • Interpretation of results • Consulting

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

The TaliTM Image Cytometer is a 3-channel (bright field, green & red fluorescence) benchtop assay platform giving a

EPFL School of Life Sciences - 2011 Annual Report

Histology -

HCF & Comparative Pathology

http://hcf.epfl.ch

Team Members Facility Head Jessica Sordet-Dessimoz Collaborators Gian-Filippo Mancini Nathalie Müller Agnès Hautier Veterinary pathologist Fabio Aloisio Administrative Assistant Ursula Winter

Introduction

Histology involves the use of a set of techniques to examine the morphology, architecture and composition of tissues. The tissue samples are processed for the study of structures seen under the microscope, also called microscopic anatomy, as opposed to gross anatomy which involves structures that can be observed with the naked eye. The histology core facility is a competence pole which provides expertise in those analyses as well as routine work for researchers. All the techniques would be nothing without the expertise of a specialist in veterinarian pathology who has been hired in 2011 to help researchers analyzing their slides.

Pathology service Pathology support is provided by professionals that underwent formal postgraduate training in veterinary anatomic pathology officially acknowledged by board certification of specialty. These professionals are trained to interpret morphologic changes within organs and tissues processed through the variety of histology techniques. Appropriate interpretation of tissue changes implies proper recognition of tissue abnormalities and pathologic processes of diseases that manifest as morphologic changes observable in histological preparations.

Services and Technologies

The service provides the following activities:

On the other hand technicians of the facility perform work for researchers: • Tissue processing to frozen, paraffin or resin sections • Histological stains like the standard Hematoxyline and eosin and routine stains like Masson’s trichrome or cresyl violet among others. The standard stains are running on the Prisma automate from Sakura • Setup and optimization of immunohistochemistry and immunofluorescence protocols • Detection of mRNA and miRNA using cold probes on the Discovery xT automate from Roche-Ventana.

• Consulting, at the study design level for issues related to pathology investigation • Phenotyping, whole body or organ targeted for genetically engineered animals • Analysis (morphology), of histological preparations

Core Facilities & Technology Platforms

On one hand, the facility assists researchers in the setting up and optimizing of histological approaches specific for each scientific project. Members of the SV faculty can be trained on the available instruments like microtomes or cryostats and have then access to them for their own experiments. Furthermore a large panel of secondary antibodies are titrated and provided to the researchers by the service.

• Support, in reporting pathology data for manuscript preparation and grant application • Diagnostics. Post mortem examination of diseased animals within the colony.

Contact Information: Jessica Sordet-Dessimoz EPFL SV PTH AI 0342 Station 19 1015 Lausanne +41 (0)21 693 0962 info.hcf@epfl.ch

CORE

EPFL School of Life Sciences - 2011 Annual Report

Proteomics - PCF http://pcf-ptp.epfl.ch/

Team Members Facility Head Marc Moniatte

Collaborators Diego Chiappe Florence Armand Adrian Schmid Research Assistants Romain Hamelin Jonathan Paz-Montoya Administrative Assistant Sophie Barret

Introduction

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

Services and Technologies

Instrumentation The PCF-PTP laboratory is currently equipped with sample preparation and fractionation devices (HPLC, FPLC, pI) and several mass spectrometers coupled to liquid chromatography: 3 Orbitraps, 2 ion traps, and 2 QQQ LC-ESI-MS/MS and 1 MALDI-TOF/TOF instruments. The bioinformatics analysis pipeline includes Mascot, Xtandem! SEQUEST and Peaks servers for matching MS data with protein sequence databases and data post-treatment tools like Maxquant, Perseus, Proteome Discoverer, PinPoint and Scaffold for protein identification validation and pipelining of quantitative studies. Services The PCF-PTP has implemented several complementary workflows for protein analysis and offers an increasing palette of services... • Protein/Peptide Molecular Weight Measurements by Mass Spectrometry. • Mass Spectrometry based Protein/Peptide Identification from Gel or Solution. • Protein Relative Quantification by SILAC or Label-free Quantitative Analysis on collaborative basis.

Contributes also to collaborative based services requiring heavy involvement of both parties like: • Accurate protein quantification by SRM-MRM. • Localization and eventually quantification of PTM’s other than phosphorylation. • Lipid mixtures profiling. Maintains tight collaboration with other proteomics facilities (UNIL-PAF, UNIGE-PCF, UNIBE) within a network called Repp-SO and with computer science and bioinformatics research centers (Vital-IT, SIB, etc..).

Selected Publications

Dastidar EG, Dayer G, Holland ZM, Dorin-Semblat D, Claes A, Chêne A, Sharma A, Hamelin R, Moniatte M, Lopez-Rubio J-J, Scherf A, Doerig C. (2012) Involvement of Plasmodium falciparum protein kinase CK2 in the chromatin assembly pathway. BMC Biology Jan;10(1):5. Sicard A, Semblat J, Doerig C, Hamelin R, Sicard, A., Semblat, J. P., Doerig, C., Hamelin, R., Moniatte, M., Dorin-Semblat, D., Spicer, J. A., Srivastava, A., Retzlaff, S., Heussler, V., and Waters, A. P. (2011) Activation of a PAK-MEK signalling pathway in malaria parasite-infected erythrocytes, Cell Microbiol. Jun;13(6):836-845. Schmid, A. W., Condemi, E., Tuchscherer, G., Chiappe, D., Mutter, M., Vogel, H., Moniatte, M., and Tsybin, Y. O. (2011) Tissue transglutaminase mediated glutamine deamidation of beta-amyloid peptide increases peptide solubility, whereas enzymatic cross-linking and peptide fragmentation may serve as molecular triggers for rapid peptide aggregation, J. Biol. Chem. Apr 8;286(14):12172-88. Paleologou KE, Oueslati A, Shakked G, Rospigliosi CC, Kim H-Y, Lamberto GR, Fernandez CO, Schmid A, Chegini F, Gai WP, Chiappe D, Moniatte M, Schneider BL, Aebischer P, Eliezer D, Zweckstetter M, Masliah E, Lashuel HA. (2010) Phosphorylation at S87 Is Enhanced in Synucleinopathies, Inhibits {alpha}Synuclein Oligomerization, and Influences Synuclein-Membrane Interactions. J. Neurosci, Mar;30(9):3184–3198. With acknowledgements Kitagawa D, Flückiger I, Polanowska J, Keller D, Reboul J, Gönczy P. (2011) PP2A phosphatase acts upon SAS-5 to ensure centriole formation in C. elegans embryos. Dev. Cell. Apr 19; 20(4):550-62

Contact Information: Dr. Marc Moniatte Station 15, CH-1015, Lausanne +41 (0)21 693 17 53 marc.moniatte@epfl.ch

• Protein separation by FPLC and HPLC.

EPFL School of Life Sciences - 2011 Annual Report

Protein Crystallography - PCRYCF http://pcrycf.epfl.ch

Team Members Facility Head Florence Pojer

Collaborator Larry Richman

Introduction

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

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

Selected Publications

Mollwitz B., Brun E., Schmitt S., Pojer F., Bannwarth M.,Rothlisberger U., Schiltz M.; Johnsson K. (2012). Directed evolution of the suicide protein O6-alkylguanine-DNA alkyltransferase for increased reactivity results in an alkylated protein with exceptional stability Biochemistry. Biochemistry 51(5):986-94. Blasco B, Stenta M, Alonso-Sarduy L, Dietler G, Peraro MD, Cole ST, Pojer F.* (2011). Atypical DNA recognition mechanism used by the EspR virulence regulator of Mycobacterium tuberculosis. Molecular Microbiology 82(1):251-64.

Contact Information: Florence Pojer SV 3533 Station 19 EPFL CH-1015 Lausanne Tel: +41 (0)21 693 1772 +41 (0)21 693 1839 florence.pojer@epfl.ch

Core Facilities & Technology Platforms

Services and Technologies

The Protein Crystallography Core Facility provides the EPFL community with: • Advice on larger-scale protein expression and purification, if required. • Set-up of crystallization screens using commercial and facility-made conditions. • Optimization of crystals. • Data collection of quality crystals at facility xray source and synchrotrons. • Data processing using popular packages such as XDS and Mosflm. • Structure determination using molecular replacement, MAD and SAD techniques. • Structure refinement, fitting and analysis using ccp4i and Phenix software.

CORE

EPFL School of Life Sciences - 2011 Annual Report

Protein Expression - PECF http://pecf.epfl.ch/

Team Members Facility Head David Hacker

Collaborator Sarah Thurnheer

Introduction

The objective of the PECF is to provide recombinant proteins, rapidly and at low cost, to EPFL researchers. Both cultivated mammalian cells and E. coli are used as production hosts. One of our main activities is recombinant protein production by transient transfection of Chinese hamster ovary (CHO) or human embryo kidney (HEK293) cells in suspension at volumetric scales from 5 mL to 15 L using orbitally shaken bioreactors. For transient protein production in mammalian cells, we have a number of expression vectors available. With the same technical approach, we are also capable of producing virus vectors such as adeno associated virus. We also produce proteins from existing recombinant cell lines developed by our clients. This may involve adapting the cell line to serum-free suspension culture. Cultures at volumetric scales up to 15 L are possible. Expression vectors based on piggybac transposon-mediated gene delivery are available to our clients. We produce monoclonal antibodies by scale-up of existing hybridoma cell lines. Serum-free suspension cultures based on mixing by orbital shaking can be used for a scale-up to 2 liters. When using E. coli as a host for protein production, the scales of operation range from 100 mL – 20 L. Induced protein production at low temperatures is feasible. We also provide services in protein recovery, mainly by affinity chromatography of antibodies and tagged proteins (Fc, 6X his, FLAG and GST) produced in either mammalian cells or E. coli.

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

Selected Publications

Matasci M, Baldi L, Hacker DL, Wurm FM. 2011. The PiggyBac transposon enhances the frequency of CHO stable cell line generation and yields recombinant lines with superior productivity. Biotechnol Bioeng. 108(9):2141-50. Rajendra Y, Kiseljak D, Baldi L, Hacker DL, Wurm FM. 2011. A simple highyielding process for transient gene expression in CHO cells. J Biotechnol. 153(1-2):22-6. Tissot S, Oberbek A, Reclari M, Dreyer M, Hacker DL, Baldi L, Farhat M, Wurm FM. 2011. Efficient and reproducible mammalian cell bioprocesses without probes and controllers? N Biotechnol 28(4):382-90. Xie Q, Michel PO, Baldi L, Hacker DL, Zhang X, Wurm FM. 2011. TubeSpin bioreactor 50 for the high-density cultivation of Sf-9 insect cells in suspension. Biotechnol Lett. 33(5):897-902. Wurm FM, Hacker D. 2011. First CHO genome. Nat Biotechnol 29(8):718-20. Oberbek A, Matasci M, Hacker DL, Wurm FM. 2011. Generation of stable, high-producing CHO cell lines by lentiviral vector-mediated gene transfer in serum-free suspension culture. Biotechnol Bioeng. 108(3):600-10.

Contact Information: David Hacker Station 6 EPFL CH J2 496 CH-1015 Lausanne Tel: +41 (0)21 693 6142 david.hacker@epfl.ch

EPFL School of Life Sciences - 2011 Annual Report

Transgenic - TCF

http://jahia-prod.epfl.ch/cms/site/tcf

Team Members Facility Head Isabelle Barde

Collaborators Blom Michelle Guichard Sabrina Offner Sandra Eloise Verp Sonia

Introduction

Services and Technologies

We offer a centralized resource and state-of-the-art technology for the generation of transgenic animals. We can perform direct pronuclear injection of DNA in the mouse oocyte, which has been the standard method of trangenesis for more than three decades.

Selected Publications

As an attractive alternative, we are one of the very few platforms that provides a fast and efficient way to generate transgenic animals through the use of lentiviral vectors. Lentivector-mediated transgenesis is relatively easy to perform and leads to high percentages of provirus-positive animals. Moreover, a wide variety of lentiviral vectors have been developed that can all be used in transgenic animals, thus allowing for a broad range of genetic manipulations including externally controllable expression and knockdown, the latter offering an economically advantageous alternative to stable knockout. In addition to this primary service, we also offer general support in both vector design and lentiviral vector production and titration, as our expertise in lentiviral vectors has become of general interest for many other applications than transgenesis. An important variable that affects the results of mouse studies is the sanitary status of the animals. Taking advantage of our expertise in embryo manipulation, we also propose the rederivation of mouse transgenic lines as a routine service. This procedure allows cleaning and hosting of a wide range of mouse lines in the SPF area of the EPFL animal house.

• Pronuclear injection: plasmids and BACs • Lentiviral vector mediated transgenesis • Vectorology • Lentiviral vectors production/titration • Rederivation by embryo transfer • Cryopreservation by sperm freezing • In progress: ES mediated transgenesis.

Barde I, Laurenti E, Verp S, Wiznerowicz M, Offner S, Viornery A, Galy A, Trumpp A, Trono D. (2011). Lineage- and stage-restricted lentiviral vectors for the gene therapy of chronic granulomatous disease. Gene Ther. (11):1087-97. Robyr D, Friedli M, Gehrig C, Arcangeli M, Marin M, Guipponi M, Farinelli L, Barde I, Verp S, Trono D, Antonarakis SE.(2011). Chromosome conformation capture uncovers potential genome-wide interactions between human conserved non-coding sequences. PLoS One. 6(3):e17634. Friedli M, Barde I, Arcangeli M, Verp S, Quazzola A, Zakany J, Lin-Marq N, Robyr D, Attanasio C, Spitz F, Duboule D, Trono D, Antonarakis SE. (2010). A systematic enhancer screen using lentivector transgenesis identifies conserved and non-conserved functional elements at the Olig1 and Olig2 locus. PLoS One.;5(12):e15741. Barde I, Salmon P, Trono D. (2010). Production and titration of lentiviral vectors. Curr Protoc Neurosci.;Chapter 4:Unit 4.21. Meyer K, Marquis J, Trüb J, Nlend Nlend R, Verp S, Ruepp MD, Imboden H, Barde I, Trono D, Schümperli D. (2009). Rescue of a severe mouse model for spinal muscular atrophy by U7 snRNA-mediated splicing modulation. Hum Mol Genet. 18(3):546-55.

Contact Information

Core Facilities & Technology Platforms

Genetic manipulation of rodents through the generation of transgenic animals is a procedure of paramount importance for biomedical research, either to address fundamental questions or to develop preclinical models of human diseases.

Isabelle Barde AI 3351 Station 19 EPFL CH-1015 Lausanne Tel: +41 (0)21 693 1702 isabelle.barde@epfl.ch

For long term preservation of a mouse line of particular interest, we now propose cryopreservation by sperm freezing via the JAX® Sperm Cryo Kit. The advantage of this technique is that it is standardized and requires only 2 competent male breeders.

CORE

EPFL School of Life Sciences - 2011 Annual Report

Phenotyping Unit - CPG-UDP /

Team Members CPG – Head Xavier Warot

CPG – UDP Managers Philippe Cettour-Rose Raphaël Doenlen Laboratory Assistants Arnaud Bichat Cristina Cartoni Sébastien Lamy Adeline Langla Marion Varet Animal Care Takers Christine Pehm

Introduction

The development of genetic tools for the manipulation of the mouse genome has led to the creation of numerous and sophisticated mouse models. The in-depth characterization of the phenotype of these mouse lines is crucial to decipher the roles of the gene of interest. The clinical phenotyping unit of the Center of PhenoGenomics is composed of highly interactive service platforms including clinical chemistry laboratory, metabolic and functional exploration platform, behavior and cognition exploration platform. The UDP provides a range of state-ofthe-art equipment to enable cardio-metabolic, biochemical and behavioural exploration of mouse models. We offer different types of support to the users of the platform, going from general support and training in protocols establishment to full completion of tests and analysis. We benefit for doing so from the scientific expertise of Prof. Johan Auwerx and Prof. Carmen Sandi, both authorities in their respective fields, namely cardio-metabolism and neurobiology. The UDP is part of the animal facility barrier unit, and encompasses a working area constituted of housing, testing and analysis rooms. The mouse models are housed in individual ventilated cages and maintained at a conventional sanitary status. The UDP equipment has been chosen to ensure a high level of flexibility for the tests that can be performed. Additionally, most of experiments can be run by fully programmable and automated interfaces and thus the impact of experimental interventions by the researcher over the experimental period is reduced.

Services and Technologies

We offer tests in the different scientific fields mentioned in the figure. A series of tests can be combined in a pipeline in order to answer questions related to a given topic such as neurodegenerative diseases or obesity or diabetes.

Selected Publications

Houtkooper RH, Argmann C, Houten SM, Cantó C, Jeninga EH, Andreux PA, Thomas C, Doenlen R, Schoonjans K, Auwerx J. (2011). The metabolic footprint of aging in mice. Sci Rep. 1:134. Marcaletti S, Thomas C, Feige JN. (2011). Exercise Performance Tests in Mice. Current Protocols in Mouse Biology. 1:141-154. Thomas C, Marcaletti S, Feige JN. (2011). Assessment of Spontaneous Locomotor and Running Activity in Mice. Current Protocols in Mouse Biology. 1:185198.

Contact Information:

Philippe Cettour-Rose : Cardio-metabolism Manager Tel: +41 (0)21 693 0984 philippe.cettour-rose@epfl.ch Raphael Doenlen: Neurobiology Manager Tel: +41 (0)21 693 0953 raphael.doenlen@epfl.ch Xavier Warot Tel: +41 (0)21 693 1869 xavier.warot@epfl.ch

Core Facilities & Technology Platforms

EPFL School of Life Sciences - 2011 Annual Report

BMI - Brain Mind Institute The mission of the Brain Mind Institute (BMI) is to understand the fundamental principles of brain function in health and disease, by using and developing unique experimental, theoretical, technological and computational approaches. The scientific challenge addressed by the BMI consists of connecting different levels of analysis of brain activity, such that cognitive functions can be understood as a manifestation of specific brain processes; specific brain processes as emerging from the collective activity of thousands of cells and synapses; synaptic and neuronal activity in turn as emerging properties of the biophysical and molecular mechanisms of cellular compartments. Understanding information processing in the brain and its higher emerging properties is arguably one of the major challenges in the life sciences. Research at the BMI focuses on three main areas: i) Molecular neurobiology and mechanisms of neurodegeneration ii) Molecular and cellular mechanisms of synapse and microcircuit function up to the behavioural level and including metabolic aspects; iii) Sensory perception and cognition in humans. In all areas, the BMI strives to integrate knowledge gained by multidisciplinary approaches and across different disciplines and research laboratories. Finally, underlying all levels of analysis, research at BMI is characterized by a sustained interest in pathological processes. In order to achieve these scientific goals, the Brain Mind Institute benefits from a unique academic environment: • An institute organized as a network of independent laboratories reflecting complementary technological approaches; each laboratory collaborates with several others within the institute in addition to cross-disciplinary interactions on campus. • A campus that stands out as a premier technological university in engineering, computer science and basic sciences. • An intimate collaboration with the Blue Brain Project which stands out as one of the most challenging neuroscience simulation and data basing projects worldwide. • A proximity to and joint affiliations of our faculty with top university hospitals in Lausanne and Geneva in particular for projects related to cognition and neurodegenerative diseases. • A new initiative in neuroprosthetics to which the BMI is strongly committed that will further the collaboration with engineering sciences by a host of inspiring common projects.

BMI - Brain Mind Institute

A feature of the Brain Mind Institute is that several faculty members have strong expertise in physics or mathematics; this holds not only for theoretical but also for experimental neuroscience. In this way, the Brain Mind Institute reflects the mission of the School of Life Science: to provide a life science curriculum with a strong emphasis on quantitative approaches. As far as teaching is concerned, the BMI Faculty is committed to provide a comprehensive and formal training in neuroscience from the undergraduate to the graduate levels. http://bmi.epfl.ch

EPFL School of Life Sciences - 2011 Annual Report

Aebischer Lab http://len.epfl.ch

BMI

Patrick Aebischer was trained as an MD (1980) and a Neuroscientist (1983) at the University of Geneva and Fribourg in Switzerland. From 1984 to 1992, he worked as a Faculty member at Brown University in Providence (USA). In 1991, he became the chairman of the Section of Artificial Organs, Biomaterials and Cellular Technology of the Division of Biology and Medicine of Brown University. In the fall of 1992, he returned to Switzerland as a Professor and Director of the Surgical Research Division and Gene Therapy Center at the Centre Hospitalier Universitaire Vaudois in Lausanne. In 1999, Patrick Aebischer was nominated President of EPFL by the Swiss Federal Council. He took office on March 17th, 2000. He is the founder of 3 biotech companies.

Patrick Aebischer Full Professor President of EPFL

Introduction

Our laboratory is involved in understanding the cause of neurodegenerative diseases of the central nervous system (CNS) and design effective treatments to slow down the progression of neuronal degeneration. We develop new technologies for animal modelling of the disease and comprehensive analysis of the degenerative process, and investigate therapies based on genes and compounds. Recently developed viral vectors show unprecedented efficacy to deliver genetic information to the CNS and correct the molecular defects leading to devastating conditions such as fatal neuromuscular diseases. In addition, viral vectors can be used to introduce pathogenic genes in adult neurons and thereby generate rodent models to decipher the molecular mechanisms leading to complex brain disorders such as Parkinson’s and Alzheimer’s diseases.

Keywords

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

Results Obtained in 2011

Adeno-associated viral vectors (AAV) have a remarkable capacity to broadly diffuse in the CNS and transfer genes to non-dividing cells, such as neurons and astrocytes. Based on this technology, our lab develops therapies against neuromuscular disorders such as amyotrophic lateral sclerosis (ALS) and spinal muscular atrophy (SMA). Harnessing the ability of AAV vectors to distally target neurons via axonal processes, we have generated specific vectors and explored routes of administration to transduce motor neurons across the entire spinal cord. In particular, we have used this approach to deliver miRNA-based silencing instructions against mutated human SOD1, a protein involved in familial forms of ALS. Specific vectors were generated to lower SOD1 levels in both neurons and astrocytes, two cell types crucially implicated in ALS pathogenesis. We are currently assessing the neuroprotective effect of this gene therapy approach in the G93ASOD1 mouse model for ALS.

For Alzheimer’s disease, we used AAV vectors to express the amyloid precursor (APP) and tau genes in the mouse brain and develop rodent models of the pathology that show accumulations of the pathogenic proteins and degenerative effects. In collaboration with the Paul Scherrer Institute at Villigen, our laboratory was involved in developing novel imaging approaches to assess amyloid plaque pathology, an histopathological signature of Alzheimer’s disease. Quantitative assessment of amyloid pathology in the mouse brain was achieved using coherent X-ray tomography. In the frame of Parkinson’s disease, the animal model based on AAV-mediated overexpression of human α synuclein previously established in our laboratory was used to explore particular aspects of the on going pathology. We found that α-synuclein accumulation leads to deficient dopamine neurotransmission in the striatum, preceding overt neurodegeneration. Defects in dopamine neurotransmission contribute to the apparition of motor symptoms in these animals. In addition, these functional defects are linked to impairments in the secretory pathway of the diseased neurons. We are currently exploring these aspects of the AAV α-synuclein model to design symptomatic and neuroprotective treatments that may better address the pathological features observed in these animals. In addition, adenoviral vectors for the expression of the G2019S mutated form of LRRK2 in dopaminergic neurons of the substantia nigra recapitulate neurodegenerative features consistent with the prevalent forms of LRRK2-associated Parkinson’s disease. We are currently exploring innovative therapeutic approaches that aim at preventing neuronal degeneration. In this context, we develop bioactive cellular implants for the chronic delivery of recombinant antibodies. This approach may find application for passive immunization against the pathogenic proteins implicated in neurodegenerative disorders.

EPFL School of Life Sciences - 2011 Annual Report

Aebischer P. Philanthropy: The price of charity, Nature, 481:260, 2012. Ciron C., Lengacher S., Dusonchet J., Aebischer P., Schneider B.L., Sustained expression of PGC-1α in the rat nigrostriatal system selectively impairs dopaminergic function, Hum Mol Genet., 21:1861-76, 2012. P.G. Coune, J.C. Bensadoun, P. Aebischer, B.L. Schneider, Rab1A Over-Expression Prevents Golgi Apparatus Fragmentation and Partially Corrects Motor Deficits in an Alpha-Synuclein Based Rat Model of Parkinson’s Disease, Journal Parkinsons Dis., 1:373-387, 2011. O. Marroquin Belaunzaran, C. Campana, M. I. Cordero, V. Setola, S. Bianchi, C. Galli, N. Bouche, V. Mlynarik, R. Gruetter, C. Sandi, J.-C. Bensadoun, M. Molinari, P. Aebischer, Chronic Delivery of Antibody Fragments Using Immunoisolated Cell Implants as a Passive Vaccination Tool, Plos One, 6:e18268, 2011 . K. Löw, P. Aebischer, Use of viral vectors to create animal models for Parkinson’s disease, Neurobiol. Dis., 2011. J. Dusonchet, O. Kochubey, K. Stafa, S.M. Young Jr., R. Zufferey, D.J. Moore, B.L. Schneider, P. Aebischer, A rat model of progressive nigral neurodegeneration induced by the Parkinson’s disease-associated G2019S mutation in LRRK2, J Neurosci, 31:907-12, 2011. C. Towne, V. Setola, B.L. Schneider, P. Aebischer, Neuroprotection by Gene Therapy Targeting Mutant SOD1 in Individual Pools of Motor Neurons Does not Translate into Therapeutic Benefit in fALS Mice, Mol Ther, 19:274-83, 2011. Neurodegenerative Disorders: Gene Therapy on Clinical Trial, P. Aebischer. Frontiers in Neuroscience, vol. 4, p. 138-139, 2010. C. Towne, B.L. Schneider, D. Kieran, DE Redmond Jr, P. Aebischer, Efficient transduction of non-human primate motor neurons after intramuscular delivery of recombinant AAV serotype 6, Gene Ther, 17:141-6, 2010. K. Langou, A. Moumen, C. Pellegrino, J. Aebischer, I. Medina, P. Aebischer, C. Raoul, AAV-mediated expression of wild-type and ALS-linked mutant VAPB selectively triggers death of motoneurons through a Ca2+-dependent ER-associated pathway, J Neurochem, 114:795-809, 2010.

Team Members Research Associates Bernard Schneider

Postdoctoral Fellows Julianne Aebischer Matthias Cacquevel Carine Ciron David Genoux Karin Löw Veronica Setola PhD students Philippe Coune Wojciech Bobela Elisabeth Dirren Aurélien Lathuilière Emilda Pino Lu Zheng Master’s students Marc Godbille Dominique Rubi Technicians Aline Aebi Philippe Colin Fabienne Pidoux Vivianne Padrun Christel Sadeghi Delphine Ernst (visiting) Marc-Antoine Perrenoud (visiting) Jonas Carrel (visiting Visiting Students Pamela Valdes Katherine Li (SRP) Maria Zamfir Administrative Assistant: Ursula Alves-Zwahlen

BMI - Brain Mind Institute

Selected publications

(A) Histology of an amyloid plaque generated in the mouse hippocampus by injection of an AAV vector encoding mutated human APP. Three-dimensional plaque imaging by coherent X-ray tomography in the 5xFAD Alzheimer’s mouse model: X-ray plaque imaging (B) is compared with the classical thioflavin S histology (C). D shows cortical amyloid deposition. Figure adapted from: Imaging brain amyloid deposition using grating-based differential phase contrast tomography. Pinzer BR, Cacquevel M, Modregger P, McDonald SA, Bensadoun JC, Thuering T, Aebischer P, Stampanoni M. Neuroimage. 2012

EPFL School of Life Sciences - 2011 Annual Report

Blanke Lab http://lnco.epfl.ch

Olaf Blanke

BMI

Olaf Blanke is director of the Center for Neuroprosthetics at the Ecole Polytechnique Fédérale de Lausanne (EPFL), holds the Bertarelli Foundation Chair in Cognitive Neuroprosthetics, and is consultant neurologist at the Department of Neurology (Geneva University Hospital). He received his MD and PhD in neurophysiology from the Free University of Berlin. Blanke’s research targets the brain mechanisms of body perception, corporeal awareness and self-consciousness, applying paradigms from cognitive science, neuroscience, neuroimaging, robotics, and virtual reality in healthy subjects and neurological patients. His two main goals are to understand and control neural own body representations to develop a neurobiological model of self-consciousness and to apply these findings in the emerging field of cognitive and systems neuroprosthetics.

Associate Professor

Introduction

The Laboratory of Cognitive Neuroscience targets the functional and neural mechanisms of body perception, corporeal awareness and self-consciousness. Projects rely on the investigation of healthy subjects and neurological patients by combining psychophysical and cognitive paradigms with state of the art neuroimaging techniques such as intracranial EEG, surface EEG, and fMRI. Our interdisciplinary expertise – bridging neurology, epileptology, intracranial electrophysiology, cognitive science, and neuroimaging – also includes engineering-based approaches to cognitive science: a virtual reality (VR) neuroimaging platform with a portable high-density EEG system, a vestibular stimulation platform with an integrated high-density EEG system, and several haptic platforms for neuroscience robotics in conjunction with fMRI. Next to studying the brain mechanisms of body perception, cognition, and self-consciousness, we actively pursue our translational neurorehabilitation research and interdisciplinary fields of virtual reality, presence research, brain-computer interfaces.

Results Obtained in 2011

A major development and result in 2011 was the description of a novel robotic stimulation device that can be used jointly with non-invasive brain imaging in humans (3T magnetic resonance imaging). The device was built in collaboration with the Laboratory of Prof Roger Gassert (ETH Zurich) and allowed us to describe for the first time the brain mechanisms in temporo-parietal cortex related to key aspects of bodily self-consciousness (self-location; firstperson perspective) (Ionta et al., 2011). We have further developed the MRI-compatible robot (Duenas et al., 2011), which is currently involved in a number of ongoing behavioral and brain imaging projects.

Keywords

Multisensory integration, sensorimotor, neuroscience robotics, perception, neuroprosthetics, temporo-parietal cortex, bodily awareness, self-consciousness, self-location, first-person perspective, neuroimaging, fMRI, EEG, neuropsychology, cognitive neuroscience, neurology, virtual reality, vestibular system, mental imagery. Brain region in temporo-parietal cortex reflecting robotically-controlled changes in self-location in healthy participants using fMRI (red region) and neurologically-induced changes in self-location in neurological patients (blue region).

EPFL School of Life Sciences - 2011 Annual Report

Selected Publications

Arzy, S., Collette, S., Wissmeyer, M., Lazeyras, F., Kaplan, P. W., & Blanke, O. (2011). Psychogenic amnesia and self-identity: a multimodal functional investigation. European Journal of Neurology 18, 1422-1425. Arzy, S., Mohr, C., Molnar-Szakacs, I., & Blanke, O. (2011). Schizotypal perceptual aberrations of time: correlation between score, behavior and brain activity. PLoS One 6, e16154. Dieguez, S., Scherer, J., & Blanke, O. (2011). My face through the lookingglass: The effect of mirror reversal on reflection size estimation. Consciousness & Cognition 20, 1452-1459. Dueñas, J., Chapuis, C., Pfeiffer, C., Martuzzi, R., Ionta, S., Blanke, O., et al. (2011). Neuroscience robotics to investigate multisensory integration and bodily awareness. Engineering in Medicine and Biology Society (EMBC) IEEE 8348-8352. Hansel, A., Lenggenhager, B., von Kanel, R., Curatolo, M., & Blanke, O. (2011). Seeing and identifying with a virtual body decreases pain perception. Eur J Pain 15, 874-879. Ionta, S., Heydrich, L., Lenggenhager, B., Mouthon, M., Fornari, E., Chapuis, D., et al. (2011). Multisensory mechanisms in temporo-parietal cortex support self-location and first-person perspective. Neuron 70, 363-374.

Team Members Postdoctoral Fellows Kanayama Noriaki Llobera Mahy Joan Martuzzi Roberto Salomon Roy Prsa Mario Bolomey Léandre Garipelli Gangadhar Palluel Estelle Herbelin Bruno Ionta Silvio Van Elk Michiel

PhD students Berger Steve Michel Jimenez Rezende Danilo Pfeiffer Christian Kaliuzhna Mariia Pozeg Polona Marclay Samuel Monnard Guillaume Evans Nathaniel Gale Steven Administrative Assistant Gordana Kokorus

Lenggenhager, B., Halje, P., & Blanke, O. (2011). Alpha band oscillations correlate with illusory self-location induced by virtual reality. Eur J Neurosci, 33, 1935-1943. Lopez, C., & Blanke, O. (2011). The thalamocortical vestibular system in animals and humans. Brain Res Rev. 67, 119-146. Lopez, C., Mercier, M. R., Halje, P., & Blanke, O. (2011). Spatiotemporal dynamics of visual vertical judgments: early and late brain mechanisms as revealed by high-density electrical neuroimaging. Neuroscience 181, 134-149. Palluel, E., Aspell, J. E., & Blanke, O. (2011). Leg muscle vibration modulates bodily self-consciousness: integration of proprioceptive, visual, and tactile signals. J Neurophysiol, 105(5), 2239-2247. van Elk, M., & Blanke, O. (2011a). Manipulable objects facilitate cross-modal integration in peripersonal space. PLoS One 6, e24641.

BMI - Brain Mind Institute

van Elk, M., & Blanke, O. (2011b). The relation between body semantics and spatial body representations. Acta psychologica, 138, 347-358.

fMRI-compatible neuroscience robotics. The robotic device is placed in the MR scanner. The device’s structure with ultrasonic motors, linear guides and stroking spheres is shown.

EPFL School of Life Sciences - 2011 Annual Report

Fraering Lab

http://fraering-lab.epfl.ch

Patrick Fraering

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

Tenure Track Assistant Professor Merck-Sorono Chair in Neuroscience

Introduction

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

Keywords

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

Results Obtained in 2011

Mercury is a direct and potent γ-secretase inhibitor affecting Notch processing and embryonic development. Prenatal exposure to mercury causes neurodevelopmental and neurological pathologies in infants, such as microcephaly and mental retardation. Since γ-secretase and the Notch pathway regulate neuronal differentiation and survival during development, and since Notch receptor signaling relies on cleavage by γ-secretase, we investigated mercury effects on γ-secretase in vitro and in vivo. We found that mercury inhibits Notch processing in a γ-secretase cell-free assay and in embryos collected from adult Drosophila melanogaster treated with mercury. This was accompanied by severe neurodevelopmental abnormalities in embryos. Our findings provide first evidence that mercury is a direct and potent γ-secretase inhibitor and suggest that disruption of the Notch pathway contributes to mercury-induced toxicity in the nervous system. Selective neutralization of APP-C99 with monoclonal antibodies reduces the production of Alzheimer’s Aβ peptides. Recent phase 3 clinical trials testing γ-secretase inhibitors revealed unwanted side effects likely attributed to impaired

Notch cleavage, critically involved in cell fate regulation. We developed a new therapeutic approach to reduce Aβ production with monoclonal antibodies selectively targeting the Amyloid-β Precursor Protein C-terminal fragment, without affecting other γ-secretase functions. These antibodies, generated by immunizing mice with recombinant human APP-C99 adopting a native conformation, bound accessible N- or C-terminal epitopes of this substrate and led to reduced Aβ levels in vitro and in vivo. Processing of the synaptic cell-adhesion molecule neurexin3β by Alzheimer’s disease α- and γ-secretases. Neurexins (NRXNs) and Neuroligins (NLGNs) are synaptic cell adhesion molecules having essential roles in the assembly and maturation of synapses into fully functional units. We found that the α-secretase metalloprotease TACE/ADAM17 and γ-secretase can sequentially process neurexin-3β (NRXN3β), leading to the formation of two final products: a ~80 kDa N-terminal extracellular domain (sNRXN3β) and ~12 kDa C-terminal intracellular domain (NRXN3β-ICD), with both of them being potentially implicated in the regulation of NRXNs and NLGNs functions at the synapses. Importantly, we found that this processing is altered by several mutations in presenilin-1 (PS1, the catalytic subunit of the γ-secretase) that cause early-onset familial Alzheimer’s disease (FAD). Alzheimer’s disease-linked mutations in Presenilin-1 result in a drastic loss of activity in purified γ-secretase complexes. Mutations linked to FAD are found most frequently in PSEN1, the gene encoding PS1. We took advantage of a mouse embryonic fibroblast cell line lacking PS1 and PS2 to purify human γ-secretase complexes with the pathogenic PS1 mutants L166P, ΔE9, or P436Q. The functional characterization of these complexes revealed that all PS1 FADlinked mutations caused a drastic reduction of Aβ and APP intracellular domain productions in vitro. Our findings support the view that PS1 mutations lead to a strong γ-secretase loss-of-function phenotype associated with an increased Aβ1-42/Aβ1-40 ratio, two mechanisms that are potentially involved in the pathogenesis of AD.

EPFL School of Life Sciences - 2011 Annual Report

Selected Publications

J. Houacine, T. Bolmont, L. Aeschbach, M. Oulad-Abdelghani, and PC. Fraering. (2012). Selective neutralization of APP-C99 with monoclonal antibodies reduce the production of Alzheimer’s Aβ peptides. Neurobiol Aging. 2012 Feb 6. M. Cacquevel, L. Aeschbach, J. Houacine, and PC. Fraering. (2012). Alzheimer’s disease-linked mutations in Presenilin-1 result in a drastic loss of activity in purified γ-secretase complexes. Plos One, In press. JR Alattia, T. Kuraishi, I. Chang, B. Lemaître, and PC. Fraering. (2011). Methylmercury is a direct and potent γ-secretase inhibitor affecting Notch processing and embryonic development. FASEB Jul;25(7):2287-95. Bot N, Schweizer C, Ben Halima S, and Fraering PC. (2011). Processing of the synaptic cell-adhesion molecule neurexin-3b by Alzheimer’s disease α- and γ-secretases. J Biol Chem. Jan 28;286(4):2762-73. F. Wu, C. Schweizer, N. Rudinskiy, DM. Taylor, A. Kazantsev, R. Luthi-Carter and PC. Fraering. (2010). Novel γ-secretase inhibitors uncover a common nucleotide-binding site in JAK3, SIRT2 and PS1. FASEB, Jul;24(7):2464-74.

Team Members Postdoctoral Fellows Jean-René Alattia Claude Schweizer Tristan Bolmont Nathalie Bot PhD students Jemila Houacine Mitko Dimitrov Isabelle, Magold Sebastien Mosser Magda Palcynska Master’s Student Andrzej Fligier Techician Lorene Aeschbach Administrative Assistant Caroline Rheiner

BMI - Brain Mind Institute

Model for the processing of APP-C99 by γ-secretase. Monoclonal antibodies targeting the substrate prevent its binding to the enzyme (I), and/or preclude its entrance in the cavity of the enzyme (II), and/or block the release of the Aβ product (III). Green star: substrate binding site; red star: catalytic site.

EPFL School of Life Sciences - 2011 Annual Report

Gerstner Lab http://lcn1.epfl.ch

BMI

Wulfram Gerstner is Director of the Laboratory of Computational Neuroscience LCN at the EPFL. He studied physics at the universities of Tubingen and Munich and received a PhD from the Technical University of Munich. His research in computational neuroscience concentrates on models of spiking neurons and spike-timing dependent plasticity, on the problem of neuronal coding in single neurons and populations, as well as on the role of spatial representation for navigation of rat-like autonomous agents. He currently has a joint appointment at the School of Life Sciences and the School of Computer and Communications Sciences at the EPFL. He teaches courses for physicists, computer scientists, mathematicians, and life scientists.

Wulfram Gerstner

Full Professor Life Sciences and Computer & Communication Sciences

Introduction

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

Keywords

Modeling, Hebbian learning, spike-timing dependent plasticity, simulation, spiking neuron models.

Results Obtained in 2011

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

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

EPFL School of Life Sciences - 2011 Annual Report

Selected Publications

T. Vogels, H. Sprekeler, F. Zenke, C. Clopath and W. Gerstner, (2011),Inhibitory Plasticity Balances Excitation and Inhibition in Sensory Pathways and Memory Networks, Science, Vol. 334, Nr. 6062, pp. 1569-1573. R. Naud, F. Gerhard, S. Mensi and W. Gerstner, (2011),Improved Similarity Measures for Small Sets of Spike Trains, Neural Computation, Vol. 23, Nr. 12, pp. 3016-3069. H. Markram, W. Gerstner and P.J. Sjöström, (2011), A history of spike-timingdependent plasticity, Frontiers in Synaptic Neuroscience, Vol. 3, Nr. 4, pp. 1-24. F. Gerhard, R. Haslinger and G. Pipa, (2011), Applying the Multivariate TimeRescaling Theorem to Neural Population Models., Neural Computation, Vol. 23, Nr. 6, pp. 1452-1483. F. Gerhard, G. Pipa, B. Lima, S. Neuenschwander and W. Gerstner, (2011), Extraction of network topology from multi-electrode recordings: Is there a smallworld effect?, Frontiers in Computational Neuroscience, Vol. 5, Nr. 4, pp. 1-13. Hennequin, G., Gerstner, W., Pfister, J-P. (2010). STDP in adaptive neurons gives close-to-optimal information transmission Frontiers in computational neuroscience, 4(143). Frémaux, N., Sprekeler, H., Gerstner, W. (2010). Functional Requirements for Reward-Modulated Spike-Timing-Dependent Plasticity. Journal of Neuroscience 30(40):13326-13337.

Team Members Postdoctoral Fellows Richard Naud Kerstin Preuschoff Tim Vogels

PhD students Mohammadjavad Faraji Nicolas Fremaux Felipe Gerhard Guillaume Hennequin Danilo Jimenez Rezende Skander Mensi Richard Naud Christian Pozzorini Alex Seeholzer Carlos Stein Christian Tomm Friedemann Zenke Lorric Ziegler Research Assistants William Podlaski Hesam Setareh Administrative Assistant Chantal Mellier

BMI - Brain Mind Institute

Clopath, C., Büsing, L., Vasilaki, E., Gerstner, W. (2010). Connectivity reflects coding: a model of voltage-based STDP with homeostasis. Nature Neuroscience, 13(3):344–35.

Hand movement simulated in a learning net of spiking neurons.

EPFL School of Life Sciences - 2011 Annual Report

Hadjikhani Group http://sv.epfl.ch/faculty

BMI

Nouchine Hadjikhani completed her studies and her doctorate of medicine at the University of Lausanne. After a postdoc at the Karolinska Institute in Stockholm, she continued her career as a brain imaging research in Boston, at the Martinos Center for Biomedical Imaging, Massachusetts General Hospital, where she is now Associate Professor in Radiology at Harvard Medical School. Since 2006, she also has been holding a position as SNF Professor at the Brain Mind Institute at EPFL.

Nouchine Hadjikhani SNSF Professor

Introduction

The theme of our research is the neuroanatomical bases of emotional, social and cognitive difficulties in autism. Our lab is also interested in examining the pathophysiology and the possible role of the cerebellum in migraine.

Keywords

Functional and anatomical brain imaging, cognition, emotion, autism, plasticity, migraine, cerebellum.

Results Obtained in 2011

Our lab has been working at not only performing research on autism spectrum disorders, but also on informing the public about this condition, and organize meeting with parentsâ&#x20AC;&#x2122; associations to provide a better understanding of autism. In collaboration with the team of Genetics at the CHUV and the Center for Integrative Genomics at UNIL, we were in 2010 the recipients of the Leenaards prize for Scientific research. The project awarded will study the phenotype, including behavioral, anatomical and functional profile, of a newly described copy number variant of the chromosome 16p11.2, strongly associated with autism and obesity. From this collaboration, a paper has already been pub-

lished in Nature describing for the first time an association between a genetical microdeletion and obesity. Our collaboration has also lead to the award of a Synergia grant, extending our research to an animal model. Autism spectrum disorders (ASD) are characterized by difficulties in social interactions, and in emotion expression. We are pursuing to understand of the neuroanatomical and functional bases of this disorder. Our data show that there is a delay in the maturation in the white matter connection in the brain of individuals with autism. We also demonstrated the impact to specifically cueing autistic individuals to look at the eyes in faces both for behavioral performance and for brain activation in areas involved in social cognition and emotion. In parallel, we are pursuing, in collaboration with our group at the Harvard Medical School in Boston, our research on migraine, its physiopathology and its long-term effect on the brain.

EPFL School of Life Sciences - 2011 Annual Report

Selected Publications

Granziera C, Daducci A, Meskaldji D, Roche A, Maeder P, Michel P, Hadjikhani N, Sorensen G, Frackowiak R, Thiran J.P., Meuli R, Krueger G. A new early and automated MRI-based predictor of motor improvement after stroke Neurology 2012; in press. Van den Stock J, Vandenbulke M, Zh Qi, Hadjikhani N, de Gelder B. Developmental prosopagnosia in a patient with hypoplasia of the vermis cerebelli. Neurology 2012, in press. Van der Zwaag W, Da Costa S, Zurcher N.R, Adams R.B, Hadjikhani N. A 7 Tesla fMRI study of amygdala response to fearful faces. Brain Topogr. 2012; in press. Donnelly N, Zurcher N, Cornes K, Snyder J, Naik P, Hadwin J, Hadjikhani N. Discriminating grotesque from typical faces: evidence from the Thatcher illusion. PLoS One. 2011;6(8):e23340. Mainero C, Boshyan J, Hadjikhani N. Altered functional resting-state connectivity in the periacqueductal gray networks in migraine. Annals of Neurology. 2011;70(2):838-845.

Team Members Postdoctoral Fellows Cristina Granziera Loyse Hippolyte Ophélie Rogier PhD Student Nicole Zürcher Master’s Students Elvira Pirondini Lorenzo Casari Research Coordinator Karine Métrailler Scientific Collaborators Anthony Lissot Anne Maillard Torsten Ruest Administrative Assistant Carole Burget

Adams RB, Franklin RG, Kveraga K, Ambady N, Kleck RE, Whalen P, Hadjikhani N, Nelson AJ. Amygdala responses to averted vs direct gaze fear vary as a function of presentation speed. Soc Cogn Affect Neurosci 2011;Epub ahead of print. . Granziera C, Hadjikhani N, et al. In vivo imaging of the structural core of Papez circuit in humans. NeuroReport. 2011;22(5):227-31. Jacquemont S, et al. Epigenetic modification of the FMR1 gene in fragile X leads to a differential response to the mGluR5 antagonist AFQ056. Science Transl Med. 2011;3:64ra1. Adams RB Jr, Franklin RG Jr, Rule NO, Freeman JB, Kveraga K, Hadjikhani N, Yoshikawa S, Ambady N. Culture, Gaze and the neural processing of fear expressions. Soc Cogn Affect Neurosci 2010 5(2-3) :340-8. Hadjikhani N. Serotonin, pregnancy and increased autism prevalence: is there a link? Medical Hypotheses 2010;74(5):880-32.

BMI - Brain Mind Institute

Walters RG, Jacquemont S. et al., A novel highly-penetrant form of obesity due to microdeletions on chromosome 16p11.2, Nature 463, 2010, 671-675.

Perspectives on the brain

EPFL School of Life Sciences - 2011 Annual Report

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

BMI

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

Michael Herzog Associate Professor

Introduction

In humans, vision is the most important sensory modality. Surprisingly, the mechanisms of even the simplest forms of visual processing, such as spotting a pen on a cluttered desk, are largely unknown. For this reason, robots are still “object blind”. Our research aims to understand how and why humans can cope with visual tasks so remarkably well.

Keywords

Vision research, spatio-temporal vision, schizophrenia research, psychophysics, TMS, EEG, modelling.

Results Obtained in 2011

Vision is not retinotopic, i.e., we perceive the world in Euclidian coordinates independent of eye and head movements. When we turn our heads, the world remains stable even though the image of the world rotates on the retina. To study how the information on our retinae is transformed into the Euclidian framework, we have developed a number of paradigms for non-retinotopic vision in the last years. Here, we used these paradigms to show that attention is processed retinotopically (Boi et al., 2011; Aydin et al., 2011b) and we characterized non-retinotopic feature integration in more detail. The population of the developed world is aging faster than at any time before. In Europe, for example, the percentage of people of age 65 and older will increase from 17.4% in 2010 to 30.0% in 2060 (European Demography Report 2010, European Commission). Aging affects all kinds of

human functions even in the absence of age-related diseases such as Alzheimer’s and Parkinson’s. Age-related visual deficits occur on the level of the eye (optical deficits), the visual cortex (perceptual deficits), and in higher cortical areas (cognitive deficits). Whereas optical and cognitive deficits are widely studied, little is known about the effects of aging on perception. We have developed a test for visual aging which is little affected by optical deficits and is not related to cognitive and motor functions and potential deficits (Roinishvili et al., 2011). With this paradigm and high density EEG recordings, we have shown that healthy elderly use very different brain areas to solve the visual task than younger controls (see figure below and Plomp et al., 2011). Healthy elderly (ELD) and younger controls (CON) performed a visual discrimination task in four conditions (vernier, long SOA, short SOA, mask only). We recorded high density EEG. On the left, global field power is shown in the four conditions for ELD and CON separately. Global field power (GFP) is an overall measure of brain activity. It is obvious, that brain activity of elderly is strongly diminished. For example, at 200ms after stimulus onset, a strong GFP peak occurs in the controls but not in the elderly. On the right, maps are shown that correspond to single electrode activity. Obviously, elderly show, particularly at around 200ms, clearly different maps than controls (compare maps 3 and 5). Our observations suggest that in most conditions, elderly use very different brain areas to solve the visual tasks than younger controls.

EPFL School of Life Sciences - 2011 Annual Report

Selected Publications

Boi M, Vergeer M, Ögmen H, Herzog MH (2011) Nonretinotopic Exogenous Attention. Current Biology, 21(20), p1732-1737. Plomp G, Kunchulia M, Herzog MH (2011) Age-related changes in visually evoked electrical brain activity. Hum Brain Mapp. doi: 10.1002/hbm.21273. Roinishvili M, Chkonia E, Stroux A, Brand A, Herzog MH (2011) Combining vernier acuity and visual backward masking as a sensitive test for visual temporal deficits in aging research. Vision Research, 51(4), p417-423. Boi M, Ögmen H, Herzog MH (2011) Motion and tilt aftereffects occur largely in retinal, not in object, coordinates in the Ternus-Pikler display. Journal of Vision, 11(3):7, p1-11. Sayim B, Westheimer G, Herzog MH (2011) Quantifying target conspicuity in contextual modulation by visual search. Journal of Vision, 11(1):6, p1-11. Rüter J, Francis G, Frehe P, Herzog MH (2011) Testing dynamical models of vision. Vision Research, 51(3), p343-351. Chkonia E., Roinishvili M., Makhatadze N., Tsverava L., Stroux A., Neumann K., Herzog M.H., Brand A. (2010). The shine-through masking paradigm is a potential endophenotype of schizophrenia. PLoS ONE, 5(12), e14268.

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

PhD Students Marco Boi Vitaly Chicherov Lukasz Grzeczkowski Mauro Manassi Johannes Rueter Izabela Szumska Evelina Thunell Master Students Julianne Grainger Michel Akselrod Aurelie Papilloud Engineer Marc Repnow Administrative Assistant Laure Dayer

Aydin M, Herzog MH, Ögmen H (2011a) Barrier effects in non-retinotopic feature attribution. Vision Research, 51(16), p1861-1871.

BMI - Brain Mind Institute

Aydin M, Herzog MH, Ögmen H (2011b) Attention modulates spatio-temporal grouping. Vision Research, 51(4), p435-446.

Neural responses for elderly (ELD) and controls (CON) are highly different. From: Plomp G, Kunchulia M, Herzog MH (2011) Age-related changes in visually evoked electrical brain activity. Hum Brain Mapp. doi: 10.1002-hbm.21273.

EPFL School of Life Sciences - 2011 Annual Report

Lashuel Lab

http://lashuel-lab.epfl.ch

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Hilal A. Lashuel received his B.Sc. degree in chemistry from the City University of New York in 1994 and his PhD in bio-organic chemistry from Texas A&M University in 2000. In 2001, he moved to Harvard Medical School and the Brigham and Women’s Hospital as a research fellow in the Center for Neurologic Diseases where he was later promoted to an instructor in neurology. In 2005 Dr. Lashuel joined the Brain Mind Institute as a tenure track assistant professor and was promoted in 2011 to an associate professor.

Hilal Lashuel

Associate Professor

Introduction

Current research efforts in our laboratory cover the following topics: (1) Elucidating the molecular and cellular determinants underlying amyloid-β and α-synuclein (α-syn) aggregation and toxicity in Alzheimer’s diseases and Parkinson’s disease (PD) and related disorders. (2) Elucidating the structural basis of amyloid-associated toxicity by correlating the structural properties of defined aggregates in the amyloid pathway to their toxicity in primary neuronal cultures; (3) Developing innovative chemical approaches and novel tools to monitor and control protein folding/ misfolding and self-assembly in vitro and in vivo with spatial and temporal resolution; (4) Understanding the role of post-translational modifications in the pathogenesis of neurodegenerative diseases; (5) Identifying and validating new therapeutic targets for treating PD.

Keywords

Neurodegeneration, Parkinson’s disease, Alzheimer’s disease, chemical biology, amyloid, aggregation, toxicity, fibrils, phosphorylation, kinases, post-translational modifications, semisynthesis.

Results Obtained in 2011

The role of post-translational modifications (PTMs) in the pathogenesis of Parkinson’s disease and related disorders: Detailed understanding of the role of each PTM in α-syn aggregation and toxicity remains elusive, because the natural enzymes involved in regulating these modifications remain unknown. Towards addressing this knowledge gap, our laboratory has developed and optimized for the first time multiple efficient synthetic and semisynthetic approaches that enable site-specific introduction of single or multiple PTMs into α-syn and used these homogeneously modified forms of α-syn to elucidate the effect of all disease-associated modification on the structure, aggregation, membrane binding and subcellular localization of α-syn. Our studies have provided novel insight into the role of diseases-associated phosphorylation, ubiquitination of α-syn in regulating the structure, aggregation, and membrane binding of α-syn in vitro.

Ubiquitination: The directed site-specific ubiquitination of α-syn at a single or multiple lysine residues has not been possible. To address this problem, we developed, in collaboration with the Brik laboratory a semisynthetic strategy by combining cysteine- and d-mercaptolysine-based methods for native chemical ligation (NCL) for the site-specific incorporation of ubiquitin and the preparation and characterization of highly homogenous monoubiquitinated forms of α-syn. Our results provide strong evidence in support of the hypothesis that the N-terminal ubiquitination of α-syn stabilizes the monomeric form of the protein and thus prevents its oligomerization and fibrillogenesis. Phosphorylation: Whether phosphorylation enhances or protects against α-syn toxicity in vivo remains unknown. To assess the effect of phosphorylation at S87, we investigated the cellular and behavioral effect of overexpression of wild-type (WT), S87A, and S87E α-syn to block or to mimic S87 phosphorylation, respectively, in the substantia nigra of rats using recombinant adeno-associated vectors. Our results revealed that WT and S87A overexpression induced α-syn aggregation, loss of dopaminergic neurons, and fiber pathology. These neuropathological effects correlated well with the induction of hemi-parkinsonian motor symptoms. Strikingly, overexpression of the phosphomimic mutant S87E did not show any toxic effect on dopaminergic neurons and resulted in significantly less α-syn aggregates, dystrophic fibers, and motor impairment. Together, our data demonstrate that mimicking phosphorylation at S87 inhibits α-syn aggregation and protects against α-syn-induced toxicity in vivo, suggesting that phosphorylation at this residue could play an important role in controlling α-syn neuropathology. In addition, our results provide strong evidence for a direct correlation between α-syn-induced neurotoxicity, fiber pathology, and motor impairment and the extent of α-syn aggregation in vivo, suggesting that lowering α-syn levels and/or blocking its aggregation are viable therapeutic strategies for the treatment of PD and related synucleinopathies.

EPFL School of Life Sciences - 2011 Annual Report

Selected Publications

Yu L, Prudent M, Fauvet B, Lashuel HA* and Girault H* “Phosphorylation of α-syn at Y125 and S129 alters its metal binding properties: Implications for understanding the role of a-synuclein in the pathogenesis of Parkinson’s disease and related disorders”. ACS Chem. Neurosci. 2011 2, 667–675. Jan A, Adolfsson O, Allaman I, Buccarello AL, Magistretti PJ, Pfeifer A, Muhs A, Lashuel HA*, “Aβ42 neurotoxicity is mediated by ongoing nucleated polymerization process rather than by discrete Aβ42 species”. J. Biol. Chem. 2011, 286(10):8585-96. Hejjaoui H, Haj-Yahya M, Kumar KS, Brik A* and Lashuel HA* “Towards elucidating the role of ubiquitination in the pathogenesis of Parkinson’s disease using semisynthetic ubquitinated α-syn”. Angew Chem Int Ed. 2011, 10;50(2):405-9. Paleologou KE., Oueslati Abid, Kim H-Y, Lamberto GR., Rospigliosi CC., Schmid A., Chiappe D., Moniatte M., Eliezer D., Zweckstetter M., Masliah E. Lashuel HA*.” Phosphorylation at S87 is enhanced in synucleinopathies, inhibits alphasynuclein oligomerization, and influences synuclein-membrane interactions” J. Neuroscience, 2010, 3;30(9):3184-98. Siman P, Blatt O, Moyal T, Danieli T, Lebendiker M, Lashuel HA, Friedler A, Brik A. “Chemical synthesis and expression of the HIV-1 Rev Protein” ChemBiochem. 2011, 2;12(7):1097-104.

Team Members Postdoctoral Fellows Baillie Mark Burai Ritwik Mahul Mellier Anne-Laure Oueslati Abid Wang Zheming PhD Students Ansaloni Annalisa Desobry Carole Fares Bilal Fauvet Bruno Hejjaoui Mirva Mbefo Kamdem Martial Vercruysse Filip Master’s Student Ashrafi Amer Research Associates Jordan Nathalie Perrin John Administrative Assistants Favre Sandrine Bouchet Stéphanie

Elturk, Fauvet B, Ouertatani-Sakouhi, Lugari A, Betzi S, Roche P, Morelli X and Lashuel HA*. “ An integrative in silico methodologies for the identification of small molecule inhibitors of Macrophage Migration Inhibitory factor”. J. Bioorg. Chem. 2010, 18(14):5425-40. Butterfied SM and Lashuel HA*. “Amyloidogenic protein-membrane interactions: mechanistic insights from model systems”. Angewandte Chemie Int Ed. 2010, 49, 5628-5654. Oueslati A¥, Fournier M¥, and Lashuel HA*. “Role of post-translational modifications in modulating α-syn structure, aggregation and toxicity: implications for Parkinson’s disease pathogenesis and therapies”. Prog Brain Res. 2010;183C:115-145.

BMI - Brain Mind Institute

Our group works at the interface of chemistry and biology to bring to bear the power of chemistry, biophysics, proteomic engineering, and neurobiology to address many of the key outstanding questions and technical challenges in the field of neurodegenerative research.

EPFL School of Life Sciences - 2011 Annual Report

Luthi-Carter Lab http://lngf.epfl.ch/

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Ruth Luthi-Carter obtained her PhD from Johns Hopkins University and conducted a postdoctoral fellowship at Harvard University’s MassGeneral Institute for Neurodegenerative Diseases, where she was promoted to the rank of Instructor. She joined the Brain Mind Institute as an Assistant Professor in 2003. Prof. Luthi-Carter is an international leader in the application of transcriptomic profiling approaches to understand neurodegenerative diseases and has led several large international consortium projects on HD. Her innovative, unbiased gene expression analysis strategies have established novel paradigms for the implementation of transcriptomic data, and have been successful in elucidating many important new facets of normal and disease-related neuronal function.

Ruth Luthi-Carter Tenure Track Assistant Professor

Introduction

The Laboratory of Functional Neurogenomics (LNGF) uses high-throughput gene expression profiling and other molecular approaches to elucidate new aspects of brain function and neurodegenerative disease. We use this approach to study the diverse effects of pharmacologic agents and disease-causing proteins on the expression of the entire mammalian genome, allowing us understand which molecules might be responsible for a particular brain-related process. Our research focuses primarily on Huntington’s disease (HD), and the function of the striatum and cerebral cortex, the brain regions involved in HD. Other research interests include brain aging, neural cell type-specific aspects of gene expression, and the development of new tools for gene expression analysis and drug discovery. Understanding diseases with known causes like HD has been viewed as a unique opportunity to elucidate universal mechanisms of neurodegeneration and explore their possible treatment, and we believe that a neuroprotective treatment for Huntington’s disease might not only benefit patients with this disorder, but also be applicable to other, more prevalent diseases.

Keywords

Neurodegenerative disease, Huntington’s disease, striatum, cerebral cortex, motor cortex, aging.

Results Obtained in 2011

This year we continued to make important progress in our search for new therapeutic targets for Huntington’s disease and in developing novel methodologies for improving analyses of gene expression data. 1) Unveiling of Population-Specific Expression Analysis (PSEA), a method to deconvolute molecular expression data into contributions from individual cell types. Many human diseases are accompanied by histological changes of affected tissues. When performing molecular profiling of such tissues, sample heterogeneity and chang-

es in the cellular composition can obscure and confound the identification of disease-related effects. In order to address this problem, we developed a computational method to resolve gene expression measured in samples of varying composition into the contributions from individual cell populations. This novel method allows identification of cell population-specific changes. We have recently unveiled the PSEA method and its application to human neurodegenerative disease in a publication in Nature Methods (Kuhn et al., 2011). 2) New insights from HD-regulated genes: RGS2 RNA profiling yields valuable information on how cells respond to toxic stimuli. In some cases, changes in gene expression are part a compensatory program, whereas, in others, they are detrimental to the cell. Molecules showing increased and decreased expression can generally be parsed into pathological versus protective changes through examining their contributions to health or toxicity in model systems. These analyses discriminate HD-regulated genes into etiologic, compensatory, and bystander effects (see Figure). Using this approach, we have recently discovered that expression levels of the G-protein signaling regulator RGS2 are inversely correlated with neuronal survival in HD: reversing HD-induced decreases in RGS2 expression enhanced mutant huntingtin’s neurotoxicity, while further decreasing RGS2 using RNAi was neuroprotective. We also discovered a putative mechanism for the RGS2 inhibition’s effect, comprising the activation of the HD-neuroprotective MAP kinase ERK. Our results support the perspective that some changes, even early changes, in gene expression represent compensatory responses of cells to limit diseaserelated neurotoxicity. These recent data also suggest that inhibition of RGS2 may be a rational strategy to achieve neuroprotection in HD (Seredenina et al., 2011).

EPFL School of Life Sciences - 2011 Annual Report

Selected Publications

Kuhn, A., Thu, D., Waldvogel, H., Faull, R.L.M. and Luthi-Carter, R. Populationspecific expression analysis (PSEA) detect molecular changes in human diseased brain. Nature Methods 8:945-947. Jiang, M., Wang, J., Fu, J., Du, L., Jeong, H., West, T., Xiang, L., Peng, Q., Hou, Z., Cai, H., Seredenina, T., Arbez, N., Zhu, S., Sommers, K., Qian, J., Zhang, J., Mori, S., Yang, X.W., Tamashiro, K.L., Aja, S., Moran, T.H., Luthi-Carter, R., Martin, B., Maudsley, S., Mattson, M.P., Cichewicz, R.H., Ross, C.A., Holtzman, D.M., Krainc, D., Duan, W. Neuroprotective role of Sirt1 in mammalian models of Huntington’s disease through activation of multiple Sirt1 targets. Nature Medicine 18:153-158. Seredenina, T., Gokce, O. and Luthi-Carter, R. Decreased striatal RGS2 expression is neuroprotective in Huntington’s disease (HD) and exemplifies a compensatory aspect of HD-induced gene regulation. PLoS ONE e22231. Labbadia, J.P. Labbadia, Cunliffe, H., Weiss, A., Katsyuba, E., Sathasivam, K., Seredenina, T., Woodman, B., Moussaoui, S., Frentzel, S., Luthi-Carter, R., Paganetti, P. and Bates, G.P. Altered chromatin architecture underlies progressive impairment of the heat shock response in Huntington’s disease mice. J. Clin. Invest. 121:3306-3319.

Team Members Postdoctoral Fellows Asad Jan Roger Moser Tamara Seredenina David Taylor Doris Chu Voo Thu Erwann Vieu Phd Students Ana Jovicic Irina Krier Technicians Maria De Fatima Rey Lely Feletti Project Students Elias Gebara Elena Katsyuba Julien Fransisco Zaldivar-Jolissaint Administrative Assistant Laure Dayer

Luthi-Carter, R., Taylor, D., Pallos, J., Lambert, E., Amore, A., Parker, A., Moffitt, H., Smith, D.L., Runne, H., Gokce, O., Kuhn, A., Xiang, Z., Maxwell, M.M., Reeves, S.A., Bates, G.P., Neri, C., Thompson, L.M., Marsh, J.L., Kazantsev, A.G. (2010) SIRT2 inhibition achieves neuroprotection by decreasing sterol biosynthesis. Proc. Natl. Acad. Sci. U.S.A. 107:7927-7932. Gambazzi, L., Gokce, O., Seredenina, T., Katsyuba, E. Runne, H., Markram, H., Giugliano, M. and Luthi-Carter, R. (2010) Diminished activity-dependent BDNF expression underlies cortical neuron microcircuit hypoconnectivity resulting from exposure to mutant huntingtin fragments. J. Pharmacol. Exp. Ther. 335:13-22. Seredenina, T. and Luthi-Carter, R. (2012) What have we learned from gene expression profiles in Huntington’s disease? Neurobiol. Dis. 45:83-98. [Review article]

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Luthi-Carter, R. and Kazantsev, A.G. (2010) SIRT2-mediated neuroprotection and cholesterol dyshomeostasis in Huntington’s disease. Proc. Natl. Acad. Sci. U.S.A. 107:E144. [Letter]

Functional significance of Huntington’s disease-related gene expression changes. The large number of gene expression changes associated with Huntington’s disease can be divided into three categories based on their effects on the disease process (caused by mutant huntingtin (Htt-QQQ)): some are detrimental and mediate neurodegeneration (red); others arise from compensatory responses that counteract mutant Htt toxicity (green); a third subset may be without a functional effect, as judged from the fact that restoring their levels to normal has no apparent impact on disease phenotype (blue).

EPFL School of Life Sciences - 2011 Annual Report

Magistretti Lab http://lndc.epfl.ch/

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Director of the Brain Mind Institute at EPFL and of the Center for Psychiatric Neuroscience of the University of Lausanne/CHUV. Internationally recognized leader in the field of brain energy metabolism and glia biology. His group has discovered some of the mechanisms that underlie the coupling between neuronal activity and energy consumption by the brain. Since October 2010, director of NCCR SYNAPSY - “The synaptic bases of mental diseases”. Recipient of the Theodore-Ott Prize (1997). International Chair (2007-2008) at the Collège de France, Paris. Since 2010 IBRO Secretary General.

Pierre Magistretti

Full Professor Joint Chair EPFL/UNIL-CHUV

Introduction

We investigate the cellular and molecular mechanisms of brain energy metabolism, in particular the interactions between neurons and astrocytes and the role of this interaction in normal brain function (e.g. learning and memory), as well as dysfunction.

Keywords

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

Results Obtained in 2011

Neuroenergetics (Mireille Bélanger and Igor Allaman) Our group and others have contributed to demonstrate that glucose metabolism in astrocytes is predominantly glycolytic, while oxidative metabolism characterizes neurons. We hypothesize that this limited capacity of neurons to increase their glycolytic rate could be a lower ability to detoxify methylglyoxal (MeG), a toxic by-product of glycolysis. Indeed, the production of MeG in a cell is proportional to the rate of glycolysis as it is estimated that between 0.1% to 0.4% of the glucose entering the glycolytic pathway is inevitably metabolized in the form of MeG. MeG accumulation induces cellular damage (e.g. formation of “advanced glycation end products”, AGEs) leading to apoptosis in different cell types including neurons . The glyoxalase system is the most important pathway for the detoxification of MeG. We observed that both enzymes composing the glyoxalase system (glyoxalase-1 and glyoxalase-2) were highly expressed in primary mouse astrocytes compared to neurons, which translated into higher enzymatic activity rates in astrocytes (9.9-fold and 2.5-fold respectively). The presence of a highly efficient glyoxalase system in astrocytes was associated with lower accumulation of AGEs compared to neurons, a greater resistance to methylglyoxal toxicity, and the capacity to protect neurons against methylglyoxal in a co-culture system. In addition, we observed that glyoxalase-1 down-regulation, using RNA interference strategies, resulted in a loss of viability in neurons, but

not in astrocytes. Interestingly, we were able to demonstrate that stimulation of neuronal glycolysis via lentiviralmediated over-expression of 6-phosphofructose-2-kinase/ fructose-2,6-bisphosphatase-3 to result in increased methylglyoxal levels and AGEs formation. As a whole our observations suggest that the poor glycolytic capacity of neurons as compared to astrocytes may be related to weaker defense mechanisms against MeG toxicity. Accordingly, the neuroenergetic specialization taking place between these two cell types may serve as a protective mechanism against methylglyoxal-induced neurotoxicity. Neurophotonic project Neurons are known to be excitable cells, essentially through variations of their membrane potential, which occur through ionic influx and outflux between the cytosol and the extracellular medium. To do that, these cells possess several transmembrane proteins involved in ionic fluxes, such as voltage-gated ion channels or ligand-gated ion channel, in particular glutamatergic receptors (NMDA and AMPA receptors) whose activation is known to be linked with water diffusion and consequent volume changes. Digital Holographic Microscopy (DHM) is not only a non-invasive optical imaging technique that provides quantitative phase images of living cells but also quantitative monitoring of the phase signal by DHM was a simple label-free method to study the effects of glutamate on neuronal optical responses. We have shown that a short application of glutamate (30mM; 30s) produced the following three distinct optical responses in mouse primary cortical neurons in culture, predominantly mediated by NMDA receptors: biphasic, reversible decrease (RD) and irreversible decrease (ID) responses. Furthermore, we are interested in studying cell volume regulation mechanisms in astrocytes that are closely related to neuronal activity. With a combined DHM/Epifluorescence setup, we are investigating astrocyte cell swelling and ion dynamics in vitro in response to glutamate application and exposure to elevated potassium levels.

EPFL School of Life Sciences - 2011 Annual Report

Selected Publications

Team Members

Allaman I, Gavillet M, Bélanger M, Laroche T, Viertl D, Lashuel HA, Magistretti PJ. Amyloid-beta aggregates cause alterations of astrocytic metabolic phenotype: impact on neuronal viability. J Neurosci. 30(9):3326-38 (2010).

Scientists Igor Allaman Nicolas Aznavour Stéphane Chamot Zhizhong Dong Hubert Fiumelli Pascal Jourdain Sylvain Lengacher Pierre Marquet Jean-Marie Petit Jiangyan Yang

Brunet JF, Allaman I, Magistretti PJ, Pellerin L. Glycogen metabolism as a marker of astrocyte differentiation. J Cereb Blood Flow Metab. 30(1):51-5 (2010).

Jolivet R, Allaman I, Pellerin L, Magistretti PJ, Weber B. Comment on recent modeling studies of astrocyte-neuron metabolic interactions. J Cereb Blood Flow Metab. 30(12):1982-6 (2010). N. Pavillon, A. Benke, D. Boss, C. Moratal, J. Kühn, P. Jourdain, C. Depeursinge, P. J. Magistretti, and P. Marquet, “Cell Morphology and Intracellular Ionic Homeostasis explored with a Multimodal Approach combining Epifluorescence and Digital Holographic Microscopy,” J. Biophotonics 3, 432–436 (2010). Bélanger M, Allaman I, Magistretti PJ. Differential effects of pro- and antiinflammatory cytokines alone or in combinations on the metabolic profile of astrocytes. J Neurochem. 116(4):564-76 (2011). Allaman I, Bélanger M, Magistretti PJ. Astrocyte-neuron metabolic relationships: for better and for worse. Trends Neurosci. 34(2):76-87 (2011). Allaman I, Fiumelli H, Magistretti PJ, Martin JL. Fluoxetine regulates the expression of neurotrophic/growth factors and glucose metabolism in astrocytes. Psychopharmacology (Berl). 216(1):75-84 (2011). Lavoie S, Allaman I, Petit JM, Do KQ, Magistretti PJ. Altered glycogen metabolism in cultured astrocytes from mice with chronic glutathione deficit; relevance forneuroenergetics in schizophrenia. PLoS One. 6(7):e22875 (2011). Bélanger M, Allaman I, Magistretti PJ. Brain energy metabolism: focus on astrocyte- neuron metabolic cooperation. Cell Metab. 14(6):724-38 (2011). Bélanger M, Yang J, Petit JM, Laroche T, Magistretti PJ, Allaman I. Role of the glyoxalase system in astrocyte-mediated neuroprotection. J Neurosci. 31(50):18338-52 (2011).

Senior Scientist Gabriele Grenningloh

Postdoctoral Fellows Jonas Kühn Mireille Bélanger PhD Students Maxime Baud Daniel Boss Elena Migacheva Julia Parafita Monika Saxena Manuel Zenger Master’s Student Anna Mikhaleva Technicians Cendrine Barrière Aurélie Calame Joel Gyger Evelyne Ruchti Administrative Assistant Egizia Carbone

BMI - Brain Mind Institute

P. Jourdain, N. Pavillon, C. Moratal, D. Boss, B. Rappaz, C. Depeursinge, P. Marquet, and P. J. Magistretti, “Transmembrane water fluxes in neurons revealed by Digital Holographic Microscopy: application to the study of glutamate ionotropic receptors and of the co-transporters KCC2 and NKCC1,” J. Neurosci. 31, 11,846–11,854 (2011).

High expression of Glo-1 in astrocytes of the mouse cerebral cortex. Coronal sections of mouse brain were immunostained with Glo-1 and with the astrocytic marker GFAP. Glo-1 immunoreactivity is located in the cell body and processes along the GFAP+ filaments.

EPFL School of Life Sciences - 2011 Annual Report

Markram Lab http://bmi.epfl.ch

Henry Markram

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Henry Markram is a professor of the Laboratory for Neural Microcircuitry and director of the Blue Brain Project, which he founded in 2005. He studied medicine and neuroscience at the University of Cape Town and obtained his Ph.D. in Neuroscience at the Weizmann Institute of Science. He worked at the Max Planck Institute, NIH, and WIS. In 2002 he moved to the EPFL to form and direct the Brain Mind Institute. He received numerous awards and published over a 100 papers. He discovered numerous principles governing the architecture of the neocortex (e.g. innate assemblies) and brain plasticity (e.g. Spike Timing Dependent Plasticity, STDP) and proposed the Lego Theory of Memory. He co-developed models of synapses and plasticity, the theory of Liquid Computing, and Intense World Theory of Autism. His is currently mobilizing an international effort to launch the Human Brain Project.

Full Professor

Introduction

The Laboratory of Neural Microcircuitry (LNMC) is dedicated to understanding the structure, function and plasticity of the microcircuitry of the neocortex, the outer, most evolved layer of the mammalian brain. In humans the neocortex constitutes more than 80% of the brain. A detailed description of cortical circuits, their neural constituents at the cellular and synaptic level is a fundamental requirement for understanding the mechanism involved in perception, attention, decision-making, memory formation, higher cognition and complex behaviors. We focus on the rodent (mice and rats) brain.

Keywords

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

Results Obtained in 2011

To investigate these neocortical microcircuits, we developed state of art technologies including 12 patch-clamp recordings to dissect circuits, single cell RT-PCR to identify genes expressed in specific cells, dynamic patch-clamp to electrically lesion ion channels, multi-electrode recording and stimulation to study the evoked responses of microcircuits in brain slices, automated patch-clamp to study ion channel kinetics. Using these techniques, we tracked the development of the layer 5 pyramidal neuron [1], discovered effective electrical stimuli that are most useful for modeling neurons [2], discovered that neurons are sensitive to the electrical fields generated by other neurons [3], characterized and databased the biophysics of ion channels expressed in cell lines [4], showed that a brief burst in one neuron causes self-inhibition and correlates the surrounding neurons [5], and discovered that the synaptic connectivity between neurons is largely innately determined causing neurons to be clustered in an experience independent manner [6]. In our work on autism, we achieved an even greater level of unification of all findings on autism and described this in The Intense World Theory of Autism [7]. The discovery of innate neural assemblies was a significant recent finding [6]. This study involved the first ever 12 patch-clamp recordings of layer 5 pyramidal neurons. We found that the con-

nectivity between neurons followed a clustering rule where the connection probability and strength of connectivity between any two neurons is positively correlated to the number of their common neighbors. These innate assemblies are independent of experience and hence we proposed that they arise innately during development. The states of the synapses within innate assemblies were not suitable for acquiring new memories, and we therefore proposed that they are elementary building blocks of the neocortex that represent genetically programmed knowledge. We therefore proposed the Lego Theory of Memory [8] where we all have the same types of lego blocks (which would explain why we all perceive the world in the same way), but we can combine them differently during life (which would explain our unique history of memories). The second important discovery related to ephaptic coupling of neurons [2]. Apart form direct synaptic transmission, it has been speculated that neurons may be influenced by external electrical fields (so-called, LFPs). We used the 12 patch system to record from one neuron and generated electrical fields around the recorded neuron. We found that cortical pyramidal cells are indeed sensitive to the electrical fields generated by other neurons. This finding has enormous potential significance because it means that neurons can become synchronized by waves of these fields throughout the brain without any direct synaptic communication. The third important discovery related to how a neuron should be probed to extract the mechanisms governing its behavior [3]. We have devised a novel theoretical framework validated experimentally for objectively selecting the stimuli that best unravel the neuronâ&#x20AC;&#x2122;s dynamics. The general framework that we propose paves the way for defining, evaluating and standardizing effective electrical probing of neurons and thus lays the foundation for a much deeper understanding of neuronal behavior. We also presently invest considerable effort into developing a new method to obtain the single cell transcriptome (all genes expressed in a single cell), which we believe will allow us to map the neuronal diversity of the brain and predict structural and functional properties of the brain. We are also completing a series of experiments on the animal model of autism exploring how the environment influences the progression of autism.

EPFL School of Life Sciences - 2011 Annual Report

Selected Publications

Romand S, Wang Y, Toledo-Rodriguez M, Markram H. Morphological development of thick-tufted layer V pyramidal cells in the rat somatosensory cortex. Front Neuroanat. 2011, 17;5:5. (1) Anastassiou CA, Perin R, Markram H, Koch C. Ephaptic coupling of cortical neurons. Nature Neurosci. 2011;14(2):217-23. (2) Druckmann S, Berger TK, Schürmann F, Hill S, Markram H, Segev I. Effective stimuli for constructing reliable neuron models. PLoS Comput Biol. 2011;7(8):e1002133. (3) Ranjan R, Khazen G, Gambazzi L, Ramaswamy S, Hill SL, Schürmann F, Markram H. Channelpedia: an integrative and interactive database for ion channels. Front Neuroinform. 2011;5:36. (4) Berger TK, Silberberg G, Perin R, Markram H. Brief bursts self-inhibit and correlate the pyramidal network. PLoS Biol. 2010;8(9). (5) Perin R, Berger TK, Markram H. A synaptic organizing principle for cortical neuronal groups. PNAS, 2011;108(13):5419-24. (6) Markram K, Markram H. The intense world theory - a unifying theory of the neurobiology of autism. Front Hum Neurosci. 2010;4:224. (7) Markram H, Perin R. Innate neural assemblies for lego memory. Front Neural Circuits. 2011;5:6. 2011. (8)

Team Members Group leaders Abdeladim Elhamdani Kamila Markram Jesper Ryge Postdoctoral Fellows Emmanuelle Logette Rodrigo Perin Séverine Petitprez Maurizio Pezzoli Susana Camacho PhD Students Vincent Delattre Monica Favre Jean-Pierre Ghobril Shruti Muralidhar Rajnish Ranjan Master’s Students Michela Abele Micheal Schartner Technicians Deborah La Mendola Julie Meystre Chantal Moratal Clément Murgues Coraly Pernet Apprentice Eliott Mutrux Researchers Harald Holze Ying Shi Visiting researcher Costas Anastassiou Internships Dimitri Christodoulou Stéphanie Davis Olivier Hagens Mirija Herzog Cécile Prébandier Louis Wessels

BMI - Brain Mind Institute

Administrative Assistant Christiane Debono

Multi-neuron patch-clamp: A, biocytin labeling of 12 neurons recorded simultaneously; B, Region of the brain from which brain slices where obtained and neurons recorded; C, 3D anatomical reconstruction of 12 recorded pyramidal neurons.

EPFL School of Life Sciences - 2011 Annual Report

Moore Lab

http://moorelab.epfl.ch

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

Darren Moore Tenure Track Assistant Professor

Introduction

a simple model in the baker’s yeast, Saccharomyces cerevisiae, to further understand the molecular pathobiology of LRRK2 and we have used this model to identify genes that can modify LRRK2-dependent phenotypes. One of these gene products, the GTPase-activating protein ArfGAP1, interacts with LRRK2 and regulates its enzymatic activity and neuronal toxicity whereas ArfGAP1 also serves as a novel substrate of phosphorylation by LRRK2. Finally, our research is attempting to clarify the mechanisms underlying neuronal cell death induced by mutated LRRK2 and here we continue to focus on the role of mitochondrial dysfunction, autophagy, neuronal morphology and proteins or protein complexes that interact with, or are phosphorylated by, LRRK2.

Keywords

In 2011 we continued to focus on the ATP13A2 protein. Genetic mutations in ATP13A2 cause familial PD and Kufor-Rakeb syndrome, a juvenile-onset, autosomal recessive disorder characterized by pallido-pyramidal neurodegeneration with severe parkinsonism and dementia. ATP13A2 is a novel P 5 -type ATPase protein which is thought to transport cations across intracellular vesicular membranes in an ATP-dependent manner. We are attempting to understand the normal function of ATP13A2 in neurons, and we are also creating disease models based upon gene disruption or silencing to replicate the effects of recessive “lossof-function” mutations.

The Laboratory of Molecular Neurodegenerative Research investigates the pathophysiology of Parkinson’s disease, a chronic neurodegenerative movement disorder. Our laboratory investigates the normal biological function and pathological dysfunction of various proteins, that when genetically mutated, cause an inherited (familial) form of Parkinson’s disease. Our mission is to understand the molecular mechanisms and pathways through which disease-associated mutations in these proteins cause neuronal damage and neurodegeneration. We aim to use this information in the long term to develop novel therapies and neuroprotective strategies to delay or prevent this devastating disease. Parkinson’s disease, parkinsonism, neurodegeneration, genetic mutations, disease models, neuronal cell death, LRRK2, alpha-synuclein, ATP13A2, parkin, VPS35, therapeutic targets, mouse models.

Results Obtained in 2011

The Moore laboratory focuses its investigations on a number of gene products that when mutated cause familial Parkinson’s disease (PD), including leucine-rich repeat kinase 2 (LRRK2), alpha-synuclein, parkin, ATP13A2 and VPS35. Mutations in the LRRK2, alpha-synuclein and VPS35 genes cause autosomal dominant forms of PD, whereas parkin and ATP13A2 mutations cause autosomal recessive PD. Mutations in the LRRK2 gene were discovered in 2004 and we have been working over the years to model the pathogenic effects of these dominant mutations. In 2011, we continued to develop and phenotype a collection of novel transgenic mice that we created to over express diseaseassociated mutated forms of human LRRK2 protein in the brain. These transgenic models develop some key features of PD with advanced age and will prove extremely useful for understanding how LRRK2 mutations cause neurodegenerative disease. We also conducted genetic interaction studies in mice to reveal that alpha-synuclein-related neuropathology that develops in transgenic mice occurs independent of LRRK2 expression. We recently developed

We are also interested in the role of the E3 ubiquitin ligase, parkin, in mitochondrial function. Genetic mutations in parkin cause early-onset, autosomal recessive PD. Recent studies have shown that parkin translocates to damaged mitochondria to mediate their removal by autophagy (termed mitophagy). We have recently established that parkin can mediate the ubiquitination and proteasomal degradation of mitofusin 1, a protein that normally promotes mitochondrial fusion. Our studies reveal some of the molecular details underlying parkin-dependent mitophagy and support a model whereby, during mitochondrial damage, parkin inhibits mitochondrial fusion through degradation of mitofusin 1 to limit mitochondrial refusion and thereby isolate damaged mitochondria for removal by mitophagy.

EPFL School of Life Sciences - 2011 Annual Report

Selected Publications

Tsika E, Moore DJ. Mechanisms of LRRK2-mediated neurodegeneration. Curr. Neurol. Neurosci. Rep. 2012, Epub Mar 24. Daher JPL, Pletnikova O, Biskup S, Musso A, Gellhaar S, Galter D, Troncoso JC, Lee MK, Dawson TM, Dawson VL, Moore DJ. Neurodegenerative phenotypes in an A53T ?-synuclein transgenic mouse model are independent of LRRK2. Hum. Mol. Genet. 2012,Epub Mar 7. Stafa K, Trancikova A, Webber PJ, Glauser L, West AB, Moore DJ. GTPase activity and neuronal toxicity of Parkinson’s disease-associated LRRK2 is regulated by ArfGAP1. PLoS Genet. 2012, 8: e1002527. Ramonet D, Podhajska A, Stafa K, Sonnay S, Trancikova A, Tsika E, Pletnikova O, Troncoso JC, Glauser L, Moore DJ. PARK9-associated ATP13A2 localizes to intracellular acidic vesicles and regulates cation homeostasis and neuronal integrity. Hum. Mol.Genet. 2012, 21: 1725-43. Trancikova A, Tsika E, Moore DJ. Mitochondrial dysfunction in genetic animal models of Parkinson’s disease. Antioxid. Redox Signal. 2012, 16: 896-919.

Team Members Post doctoral Fellows Roger Moser Alzbeta Trancikova Elpida Tsika PhD Students Alice Biosa Alessandra Musso Agata Podhajska Klodjan Stafa Master’s Students Duygu Deniz Bas Caroline Shi-Yan Foo Meghna Kannan Sarah Sonnay Anastasia Vishnevetsky Laboratory technician Liliane Glauser Administrative assistant Caroline Rheiner

Glauser L, Sonnay S, Stafa K, Moore DJ. Parkin promotes the ubiquitination & degradation of the mitochondrial fusion factor mitofusin 1. J. Neurochem. 2011, 118: 636-45. Ramonet D, Daher JPL, Lin BM, Stafa K, Kim J, Banerjee R, Westerlund M, Pletnikova O, Glauser L, Yang L, Liu Y, Swing DA, Beal MF, Troncoso JC, McCaffery JM, Jenkins NA, Copeland NG, Galter D, Thomas B, Lee MK, Dawson TM, Dawson VL, Moore DJ. Dopaminergic neuronal loss, reduced neurite complexity and autophagic abnormalities in transgenic mice expressing G2019S mutant LRRK2. PLoS One 2011, 6: e18568. Dusonchet J, Kochubey O, Stafa K, Young SM, Zufferey R, Moore, DJ, Schneider BL, Aebischer, P. A rat model of progressive nigral neurodegeneration induced by the Parkinson’s disease-associated G2019S mutation in LRRK2. J. Neurosci. 2011, 31(3): 907-12.

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Xiong Y, Coombes CE, Kilaru A, Li X, Gitler AD, Bowers WJ, Dawson VL, Dawson TM, Moore DJ. GTPase activity plays a key role in the pathobiology of LRRK2. PLoS Genetics 2010, 6(4):e1000902.

Models of familial Parkinson’s disease: (A) phospho-proteome profiling, (B) dopaminergic neuronal loss, (C) accumulation of autophagosomes, in LRRK2 transgenic mice. (D) Adenoviral-mediated LRRK2 expression in cultured dopaminergic neurons (TH). Lower panel: protein architecture of LRRK2.

EPFL School of Life Sciences - 2011 Annual Report

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

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Carl Petersen obtained a BA in Physics from Oxford University in 1992 and his PhD from Cambridge University in 1996 studying calcium signalling under the supervision of Prof. Michael Berridge. As a postdoctoral fellow he worked with Prof. Roger Nicoll investigating synaptic transmission and plasticity at the University of California San Francisco (1996-1998) and with Prof. Bert Sakmann studying neocortical circuits underlying sensory processing at the Max Planck Institute for Medical Research in Heidelberg (1999-2003). Carl Petersen currently investigates the synaptic mechanisms of sensory perception at the Brain Mind Institute of the EPFL, which he joined in 2003 as an Assistant Professor and in 2010 was promoted to Associate Professor.

Carl Petersen

Associate Professor

Introduction

The Laboratory of Sensory Processing aims to obtain a causal and mechanistic understanding of sensory perception and associative learning at the level of individual neurons and their synaptic interactions within complex neural circuits of the mammalian brain. Our experiments investigate tactile sensory perception in the mouse whisker sensorimotor system.

Keywords

Sensory perception, active sensing, motor control, rewardbased learning, whole-cell recordings, optogenetics, voltage-sensitive dye imaging, two-photon microscopy.

Results Obtained in 2011

Active Touch (Crochet et al., 2011): Sensory information is actively gathered by animals, but the synaptic mechanisms driving neuronal circuit function during active sensory processing are poorly understood. In this study, we investigated the synaptically driven membrane potential dynamics during active whisker sensation using whole-cell recordings from layer 2/3 pyramidal neurons in the primary somatosensory barrel cortex of behaving mice. Although whisker contact with an object evoked rapid depolarization in all neurons, these touch responses only drove action potentials in 10% of the cells. Such sparse coding was ensured by cell-specific reversal potentials of the touch-evoked response that were hyperpolarized relative to action potential threshold for most neurons. Intercontact interval profoundly influenced touch-evoked postsynaptic potentials, interestingly without affecting the peak membrane potential of the touch response. Dual whole-cell recordings indicated highly correlated membrane potential dynamics during active touch. Sparse action potential firing within synchronized cortical layer 2/3 microcircuits therefore appears to robustly signal each active touch response.

sory perception. Synaptic transmission between identified neurons within neocortical microcircuits has mainly been studied in brain slice preparations in vitro. In this study, we investigated brain-state-dependent neocortical synaptic interactions in vivo by combining the specificity of optogenetic stimulation with the precision of whole-cell recordings from postsynaptic excitatory glutamatergic neurons and GFP-labeled inhibitory GABAergic neurons targeted through two-photon microscopy. Channelrhodopsin-2 (ChR2) stimulation of excitatory layer 2/3 barrel cortex neurons evoked larger and faster depolarizing postsynaptic potentials and more synaptically driven action potentials in fast-spiking (FS) GABAergic neurons compared to both non-fast-spiking (NFS) GABAergic neurons and postsynaptic excitatory pyramidal neurons located within the same neocortical microcircuit. The number of action potentials evoked in ChR2-expressing neurons showed low trial-totrial variability, but postsynaptic responses varied strongly with near-linear dependence upon spontaneously driven changes in pre-stimulus membrane potential. Postsynaptic responses in excitatory neurons had reversal potentials, which were hyperpolarized relative to action potential threshold and were therefore inhibitory. Reversal potentials measured in postsynaptic GABAergic neurons were close to action potential threshold. Postsynaptic inhibitory neurons preferentially fired synaptically driven action potentials from spontaneously depolarized network states, with stronger state-dependent modulation in NFS GABAergic neurons compared to FS GABAergic neurons. Inhibitory neurons appear to dominate neocortical microcircuit function, receiving stronger local excitatory synaptic input and firing more action potentials compared to excitatory neurons. In mouse layer 2/3 barrel cortex, we propose that strong state-dependent recruitment of inhibitory neurons drives competition among excitatory neurons enforcing sparse coding.

In vivo optogenetic probing of cortical synaptic microcircuits (Mateo et al., 2011): Synaptic interactions between excitatory and inhibitory neocortical neurons are important for mammalian sen-

EPFL School of Life Sciences - 2011 Annual Report

Selected Publications

Mateo C, Avermann M, Gentet LJ, Zhang F, Deisseroth K, Petersen CCH (2011) In vivo optogenetic stimulation of neocortical excitatory neurons drives brainstate-dependent inhibition. Curr Biol 21: 1593-1602. Crochet S, Poulet JFA, Kremer Y, Petersen CCH (2011) Synaptic mechanisms underlying sparse coding of active touch. Neuron 69: 1160-1175. Petersen CCH (2011) Voltage-sensitive dye imaging of cortical spatiotemporal dynamics in awake behaving mice. Chapter in ‘Imaging in neuroscience’. Edited by Fritjof Helmchen and Arthur Konnerth. Published by Cold Spring Harbor Laboratory Press. Matyas F, Sreenivasan V, Marbach F, Wacongne C, Barsy B, Mateo C, Aronoff R, Petersen CCH (2010) Motor control by sensory cortex. Science 330: 12401243. Gentet LJ, Avermann M, Matyas F, Staiger JF, Petersen CCH (2010) Membrane potential dynamics of GABAergic neurons in the barrel cortex of behaving mice. Neuron 65: 422-435.

Team Members Postdoctoral Fellows Sylvain Crochet Emmanuel Eggermann Luc Gentet Natalya Korogod Yves Kremer Alexandros Kyriakatos Szabolcs Olah Shankar Sachidhanandam Nadia Urbain Takayuki Yamashita PhD Students Aurelie Pala Varun Sreenivasan Administrative Assistants Séverine Janot Monica Navarro

Aronoff R, Matyas F, Mateo C, Ciron C, Schneider B, Petersen CCH (2010) Longrange connectivity of mouse primary somatosensory barrel cortex. Eur J Neurosci 31: 2221-2233.

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Grinvald A, Petersen CCH (2010) Imaging the dynamics of neocortical population activity in behaving and freely moving mammals. Chapter in ‘Membrane potential imaging in the nervous system’. Edited by Marco Canepari and Dejan Zecevic. Published by Springer.

The light-gated ion channel, Channelrhodopsin-2(ChR2-YFP), was expressed in excitatory layer 2/3 (L2/3) neurons of mouse barrel cortex using a lentivirus. Blue light evoked depolarisation and action potential firing in ChR2-expressing neurons recorded in vivo. Adapted from Mateo et al., 2011.

EPFL School of Life Sciences - 2011 Annual Report

Sandi Lab

http://lgc.epfl.ch/

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Carmen Sandi investigates how stress affects brain function, behavior and cognition, with a recent strong interest in understanding stress effects in social behaviors and aggression. Her work has been pioneering in implicating stress hormones and cell adhesion molecules in memory formation and psychopathology. Currently, she is the Chief Editor of the journal Frontiers in Behavioral Neuroscience, Scientific Advisor at the European College of Neuropsychopharmacology, the President of the European Brain and Behavior Society (EBBS) and the Coordinator of the FP7 EU Project MemStick. Prof. Sandi joined the EPFL in 2003 and was promoted to full professor in 2012.

Carmen Sandi Full Professor

Introduction/Results Obtained in 2011

Evidence for biological roots in the transgenerational transmission of intimate partner violence Intimate partner violence is a ubiquitous and devastating phenomenon for which effective interventions and a clear etiological understanding are still lacking. A major risk factor for violence perpetration is childhood exposure to violence, prompting the proposal that social learning is a major contributor to the transgenerational transmission of violence. Using an animal model devoid of human cultural factors, we showed that male rats became highly aggressive against their female partners as adults after exposure to non-social stressful experiences in their youth. Their offspring also showed increased aggression towards females in the absence of postnatal father-offspring interaction or any other exposure to violence. Both the females that cohabited with the stressed males and those that cohabited with their male offspring showed behavioral, physiological and neurobiological symptoms resembling the alterations described in abused and depressed women. With the caution required when translating animal work to humans, our findings extend current psychosocial explanations of the transgenerational transmission of intimate partner violence by strongly suggesting an important role for biological factors.

We are currently investigating the modulatory role of personality traits in the prediction of social hierarchy outcome in rodents and humans. We have identified anxiety trait as a key modulatory factor in the development of either subordinate or dominant status. Our results highlight interactions between the GABAergic and mesolimbic dopaminergic systems as the critical substrates. The impact of developmental stress on aggression Stress is an important risk factor for a wide variety of psychopathological alterations. In particular, adverse experiences during childhood and adolescence have been associated with the development of psychiatric disorders. We have developed an animal model that recapitulates alterations in orbitofrontal-amygdala interactions observed in humans. We found changes in serotonergic pathways and their epigenetic control in the long-term effects of stress, along with alterations in impulsive behaviors and cognitive bias towards social threats and adversity.

Keywords

Stress, anxiety, aocial hierarchy, aggression, transgenerational mechanisms, epigenetics, early life trauma.

Stress, Personality Traits and Social Hierarchies â&#x20AC;&#x201C; Neurobiological Mechanisms Social hierarchies are highly relevant for both individualsâ&#x20AC;&#x2122; behavior and physical and mental health, as well as for the well-being of societies. Given that once established, hierarchies tend to be quite stable, the outcome of an initial encounter between two or more individuals can have important consequences for future behavioral interactions and fitness. Our previous work has characterized the effect of stress in the establishment of social hierarchies and identified key neurobiological mechanisms translating stress effects.

EPFL School of Life Sciences - 2011 Annual Report

Selected Publications

Team Members

Conboy L., Varea E., Castro J.E., Sakouhi-Ouertatani H., Calandra T., Lashuel H. and Sandi C. (2011) Macrophage migration inhibitory factor (MIF) is critically involved in basal and fluoxetine-stimulated adult hippocampal cell proliferation and in anxiety, depression and memory related behaviours. Molecular Psychiatry 16: 533-547.

External Employee Maria Isabel Cordero

Postdoctoral Fellows Martina Fantin Fiona Hollis Guillaume Poirier Ricardo Ramires Yannick Sevelinge Michael van der Kooij

Kraev I., Henneberger C., Rossetti C., Conboy L., Kohler L.B., Fantin M., Jennings A., Venero C., Popov V., Rusakov D., Stewart M.G., Bock E., Berezin V. and Sandi C. (2011) A peptide mimetic targeting of trans-homophilic NCAM binding sites promotes spatial learning and synaptic plasticity in the hippocampus. PloS One, 6(8): e23433. doi:10.1371/journal.pone.0023433.

PhD Students Stamatina Tzanoulinou Vandana Veenit

Bisaz R., Schachner M. and Sandi C. (2011) Causal evidence for the involvement of the neural cell adhesion molecule, NCAM, in chronic stress-induced cognitive impairments. Hippocampus 21: 56-71.

Lab Technicians Christelle Albac CĂŠline Fournier Jocelyn Grosse Coralie Siegmund Olivia Zanolettir

Cuesto G., Enriquez-Barreto L., Carames C., Cantarero M., Gasull X., Sandi C., Ferrus A., Acebes A. and Morales M. (2011) PI3K activation controls synaptogenesis and spinogenesis in hippocampal neurons. Journal of Neuroscience 31: 2721-2733. Sandi C. (2011) Glucocorticoids act on glutamatergic pathways to affect memory processes. Trends in Neuroscience 34: 165-176. Luksys G. and Sandi C.* (2011) Neural mechanisms and computations underlying stress effects on learning and memory. Current Opinion in Neurobiology, Epub ahead of print, PMID: 21501959. Sandi C. (2011) Healing anxiety disorders with glucocorticoids. Proc. Natl. Acad. Sci. USA 108: 6343-6344. Conboy L. and Sandi C. (2010) Stress at learning facilitates memory formation by regulating AMPA receptor trafficking through a glucocorticoid action. Neuropsychopharmacology 35: 674-685. Salehi B., Cordero M.I. and Sandi C. (2010) Learning under stress: The invertedU-shape function revisited, Learning & Memory 17:522-530.

Master Student Xavier Fontana

Trainees Eleni Batzianouli Lejla Colic Hussein Khdour Manila Loi Laura Lozano Emil Polny Zhiva Skachokova Students Nicolas Chatel Elise Gehring Damien Huzard Alain Jacot-Guillarmod Chenyu Lin Martin Vogel Administrative Assistant Barbara Goumaz

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Timmer M., Cordero M.I., Sevelinge Y. and Sandi C. (2011) Evidence for a role of oxytocin receptors in the long-term establishment of dominance hierarchies. Neuropsychopharmacology, doi:10.1038/ npp.2011.125.

Expression of the immediate early gene c-fos in the rat brain after stress challenge.

EPFL School of Life Sciences - 2011 Annual Report

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

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Ralf Schneggenburger obtained a PhD in Biology at the University of Göttingen in 1993. During post-doctoral stages at the University of Saarland and at the Ecole Normale Supérieure (1994 - 1996), he investigated the role of glutamate receptors in neuronal Ca2+ signaling. As a postdoctoral fellow and as a Research Group Leader at the Max-Planck Institute for biophysical Chemistry (Göttingen, 1996- 2005), he developed a research program in transmitter release mechanisms, and presynaptic plasticity. In 2005, he was appointed as Associate Professor at EPFL and has since then been leading the Laboratory for Synaptic Mechanisms at the Brain Mind Institute. In 2012, he was promoted to Full Professor.

Ralf Schneggenburger Full Professor

Introduction

terminals. Furthermore, re-expressed Syt2 fully rescued a more than 500-fold reduction of Ca2+-evoked transmitter release in Syt2 knock-out mice. This allowed us to begin a structure-function analysis of Syt2 function under direct control of presynaptic Ca2+ concentrations as afforded by the calyx of Held synapse. Our data shows that Syt2, and in analogy Syt1 in forebrain synapses, triggers a fast phase of release which is highly non-linearly dependent on the intracellular Ca2+ concentration, [Ca2+]i (a 4th power relation between [Ca2+]i and release). At the same time, we found that Syt2 suppresses release evoked by low [Ca2+]i elevations, and spontaneous release. This “release clamping” function involves a different part of the Syt2 protein, and probably an interaction with a yet unidentified Ca2+ sensor for slow release. The feasibility of virus-mediated rescue of Synaptotagmin function at the calyx of Held synapse will be the basis for future studies investigating the molecular and biophysical mechanisms of the highly nonlinear Ca2+ dependence of vesicle fusion.

Keywords

In a separate study in 2011, we used Cre-lox mediated conditional removal of floxed genes in mice, to study the role of RIM proteins for presynaptic Ca2+ channels and transmitter release. RIM (for Rab3-interacting molecule) is coded by two major genes (Rim1, 2). In a collaborative research effort, we produced auditory-system specific conditional RIM1/2 knock-out mice, in which mouse survival was not impaired (Han et al., 2011). This allowed us to study the function of RIM proteins in direct presynaptic recordings at the calyx of Held. We found that RIM proteins are necessary to achieve a high density of presynaptic Ca2+ channels, and for vesicle docking at the active zone (Han et al., 2011). The conditional mouse knock-out approach at the calyx of Held synapse will be invaluable for future studies investigating functional parameters of presynaptic proteins.

The main interest of the lab lies in understanding the cellular and molecular mechanisms of neuronal communication at synapses. Nerve cells are arranged in intricate neuronal networks, and communicate with each other at synapses, the contact points between a pre- and postsynaptic neuron pair. Synaptic transmission is mediated by transmitter release in a process of SNARE-protein mediated vesicle fusion, which is controlled by intracellular Ca2+ ions on time scales of a millisecond or less. We also investigate how the functional properties of synapses, including synaptic strength and speed of transmitter release, are specified during the development of neuronal circuits. Understanding the molecular mechanisms of synaptic transmission and synapse development is important to gain insight into neuronal network function, and forms the basis for understanding the pathophysiology of neuropsychiatric and neurodegenerative disorders, many of which represent diseases of the synapse. Synaptic transmission, nerve terminal, neurotransmitter, exocytosis, short-term plasticity, synapse development.

Results Obtained in 2011

We use an exceptionally large synapse located in the auditory pathway, the calyx of Held, at which we can gain excellent access to the physiology of the presynaptic nerve terminal. In 2011, we could study the function of the Ca2+ sensor protein, Synaptotagmin-2 (Syt2), in triggering a fast phase of vesicle fusion, as well as in suppressing background spontaneous release (Kochubey and Schneggenburger 2011). This study was made possible by adapting methods of virus-mediated protein overexpression in specific mouse brain circuits (see Figure). We found that recombinantly expressed Syt2 is correctly targeted to nerve terminals, including the large calyx of Held

EPFL School of Life Sciences - 2011 Annual Report

Selected Publications

Kochubey O., Lou X., Schneggenburger R. (2011) Regulation of transmitter release by Ca2+ and synaptotagmin: insights form a large CNS synapse. Trends Neurosci. 34(5), 237-246. Kochubey O., Schneggenburger R. (2011) Synaptotagmin increases the dynamic range of synapses by driving Ca2+-evoked release and by clamping a nearlinear remaining Ca2+ sensor. Neuron. 2011 Feb 24;69(4):736-48. Han, Y., Kaeser, P.S., Südhof, T.C., Schneggenburger, R. (2011) RIM Determines Ca2+ Channel Density and Vesicle Docking at the Presynaptic Active Zone. Neuron 69 : 304-316. Beurg, M., Michalski, N., Safieddine, S., Bouleau, Y., Schneggenburger, R., Chapman, E. R., Petit, C., and Dulon, D. (2010). Control of exocytosis by synaptotagmins and otoferlin in auditory hair cells. J. Neuroscience 30, 1328113290. Xiao, L., Han, Y., Runne, H., Murray, H., Kochubey, O., Lüthi-Carter, R. and Schneggenburger, R. (2010) Developmental expression of Synaptotagmin isoforms in single calyx of Held-generating neurons. Mol Cell Neurosci 44: 374-85.

Team Members Postdoctoral Fellows Norbert Babai Naila Ben Fredj Olexiy Kochubey Nicolas Michalski Le Xiao Phd Students Ozgür Genc Enida Gjoni Yunyun Han Elin Kronander Shovan Naskar Technicians Heather Murray Jessica Perritaz Administrative Assistant Laure Dayer

BMI - Brain Mind Institute

Müller, M., Goutman, J. D., Kochubey O., Schneggenburger R. (2010). Interaction between facilitation and depression at a large CNS synapse reveals mechanisms of short-term plasticity. J Neurosci 30(6): 2007-2016.

Virus-mediated protein overexpression in the auditory system. An adenovirus vector drove the expression of GFP (green) and Syt2 (red); note that Syt2 protein was specifically targeted to nerve terminals. Taken from Kochubey and Schneggenburger 2011, Neuron.

EPFL School of Life Sciences - 2011 Annual Report

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

Henry Markram

BMI

Full Professor Director BBP

Introduction

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 seventh 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.

Keywords

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

Results Obtained in 2011

2011 was a year of important change for the Blue Brain Project. Due to the mandate of the ETH Board the project prepared itself for future growth and sustainability. In that regard several senior researchers and engineers came on board to bring the project on the road from the proof-ofconcept work of the previous years to a state where the facility can be eventually available for the wider community. To accommodate this growth, the project moved to its new space in the Quartier Innovation, where all the efforts can be effectively coordinated in a tailored space. On the scientific side, several important results where published during the year. On the one hand, the previously published series of technical publications on establishing a data-driven, automatic workflow to modeling detailed conductance-based models of individual cells has been complemented with two PLoS Computational Biology studies. In one of them, the method was successfully applied to create and validate the most comprehensive model

of a layer 5 pyramidal cell to date, capable of reproducing multiple somatic and dendritic experimental properties in a unifying model. Secondly, the method was used to explore in silico which experimental stimulation protocol is most effective to constrain detailed models. Furthermore, in the publication of Khazen et al., we were able to show informatically that a neuron’s features, such as its cortical layer, morphological type and electrical class are informative about the expression of certain gene combinations. Based on the classification data alone, we could predict previously measured ion channel patterns with 78 per cent accuracy. When we added in a subset of data about the ion channels to the classification data, we were able to boost that accuracy to 87 per cent for the more commonly occurring neuronal types. Systematically testing which ion channels were the most informative about others, allowed us to extract logical rules as to which channels co-express or which exclude each other in the different cell types. Lastly, the year 2011 saw intensive and exciting efforts for the preparation for a 10 year FET Flagship project: in the context of the Human Brain Project – Preparatory Study (HBP-PS) - a one year EU-funded Coordinating Action, nearly three hundred experts in neuroscience, medicine and computing came together to develop a new “ICT-accelerated” vision for brain research and its applications. The Human Brain Project should lay the technical foundations for a new model of ICT-based brain research, driving integration between data and knowledge from different disciplines, and catalyzing a community effort to achieve a new understanding of the brain, new treatments for brain disease and new brain-like computing technologies. The selection process for the FET Flagship candidates continues in 2012.

EPFL School of Life Sciences - 2011 Annual Report

Selected Publications

Team Members

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

Project Managers Buncic Nenad Marc-Oliver Gewaltig Sean Hill Eilif Muller Julian Shillcock

Khazen G, Hill S L, Schürmann F, and Markram H (2012). Combinatorial Expression Rules of Ion Channel Genes in Juvenile Rat (Rattus norvegicus) Neocortical Neurons, PLoS One. 2012;7(4):e34786. Epub 2012 Apr 11.

Ramaswamy S, Hill SL, King JG, Schürmann F, Wang Y, Markram H (2012). 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. Lasserre S, Hernando J, Hill S, Schürmann F, Anasagasti PM, Abou-Jaoudé G and Markram H (2012). A Neuron Membrane Mesh Representation for Visualization of Electrophysiological Simulations, IEEE Transactions on Visualization and Computer Graphics, 18(2):214-217. Hay E., Hill S., Schürmann F., Markram H, Segev I (2011). Models of Neocortical Layer 5b Pyramidal Cells Capturing a Wide Range of Dendritic and Perisomatic Active Properties. PLoS Computational Biology 7(7): e1002107. doi:10.1371/journal.pcbi.1002107. Druckmann S, Berger TK, Schürmann F, Hill S, Markram H and Segev I (2011), Effective stimuli for constructing reliable neuron models, Plos Computational Biology, 7(8): e1002133. doi:10.1371/journal.pcbi.1002133. Hines M, Kumar S and Schürmann F (2011). Comparison of neuronal spike exchange methods on a Blue Gene/P supercomputer. Front. Comput. Neurosci. 5:49. doi: 10.3389/fncom.2011.00049. Ranjan R, Khazen G, Gambazzi L, Ramaswamy S, Hill SL, Schürmann F, and Markram H (2011). Channelpedia: an integrative and interactive database for ion channels, Front. Neuroinform. 5:36. doi: 10.3389/fninf.2011.00036.

General Project Manager Felix Schürmann

Senior Science Writer Richard Walker Operations Alejandro Schiliuk Postdoctoral Fellows Guy Antoine Atenekeng Ahmet Bilgili Joe Graham Daniel Keller Sébastien Lasserre Martin Telefont Werner Van Geit Research Assistants Marija Rakonjac Melissa Cochrane Engineers Marwan Abd Ellah Carlos Aguado Sanchez Athanassia Chalimoudra Jean-Denis Courcol Fabien Delalondre Stefan Eilemann Valentin Haenel John Kenyon (till March) James Gonzalo King Bruno Ricardo Magalhaes Gabriel Mateescu Jeff Muller Keerthan Muthurasa Barthélémy Von Haller PhD Students Georges Khazen (till August) Srikanth Ramaswamy Rajnish Ranjan Michael Reimann Renaud Richardet Farhan Tauheed Anirudh Vij Interns Damien Drix Michael Hull Elizabeth Ottens Dmimitri Probst Anna Traussnig Matthew Perich Visiting Researcher Prof. Yun Wang Visiting Professor Prof. Karlheinz Wilhelm Meier

BMI - Brain Mind Institute

Administration Claire Devillers (CHUV) Christian Fauteux Catherine Hanriot Amanda Pingree

Visualization of the unifying model of a cortical column of a young rat. In false colors indicated are the different morphological types of cells.

EPFL School of Life Sciences - 2011 Annual Report

IBI - Institute of Bioengineering The Institute of Bioengineering (IBI) sits at the interface of the life sciences and of engineering, being situated in both the School of Life Sciences and the School of Engineering and reporting to both deans. This dual affiliation allows great diversity in hiring faculty from different backgrounds and with different research perspectives, all focused on basic biological sciences using quantitative and systems analyses, as well as translating the biological and biochemical sciences into therapeutics and diagnostics. The dual affiliation also provides a rich educational environment, both at the BS/MS and PhD levels, especially since a joint MS program in Bioengineering has come into effect in the fall of 2010, shared between the two Schools. In pursuit of basic biological mechanisms, IBI faculty investigate questions such as: • How the cellular micro-environment controls cellular differentiation and morphogenetic processes; • How stem cell processes, such as self-renewal and differentiation, are determined; • How cell migration and trafficking in complex environments is modulated; • How complex biological networks such as metabolism, gene expression and protein trafficking are regulated, as well as transmitted and evolved within populations; • How biophysical and biomolecular signals interact in controlling cellular behavior; • How fundamental biophysical processes are at work at the single-molecule and nano scales, and in 3-dimensional soft biological systems. Our goal is to transform knowledge gained from our studies into clinical applications. To that end, the IBI faculty develops novel technologies in areas including: • Delivery of small molecule drugs, proteins and DNA, based on synthetic and biosynthetic biomaterials; • Materials in bio-nanotechnology; • Immunotherapy based on active biomolecules and nanomaterials; • Novel molecules for photodynamic therapy; • Tissue engineering for therapeutics; • Interventional and diagnostic biomedical micro-devices and image processing tools; • Biosensors and neuro-electrodes; • Soft bioelectronic (“electronic skin”) and brain-machine interfaces; • Sensory and motor neuroprosthetics;

IBI - Institute of Bioengineering

• Biorobotics, biomechanics and cardiovascular modelling; • Rehabilitation monitoring based on movement or gait measurement and assessment; • Biotechnology for therapeutic protein production; As well as innovative physiological modelling based on biomolecular and stem cell approaches; http://ibi.epfl.ch

EPFL School of Life Sciences - 2011 Annual Report

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

IBI

Johan Auwerx, MD, PhD and Kristina Schoonjans, PhD use a systems physiology approach to understand metabolic homeostasis and the pathogenesis of common metabolic diseases.

Johan Auwerx Full Professor NestlĂŠ Chair in Energy Metabolism

Kristina Schoonjans Adjunct Professor

Introduction

The research of the Laboratory of Integrative and Systems Physiology aims to understand how regulatory proteins, including nuclear receptors, membrane receptors and transcriptional cofactors, act as sensors for molecules of nutritional, metabolic or pharmacological origin, and translate this into altered gene expression and protein patterns affecting metabolic function.

Keywords

Aging, c.elegans, diabetes, genetics, metabolism, metabolic disease, phenogenomics, transcription.

Results Obtained in 2011

Our laboratory was among the pioneers to unravel the wide-ranging implications of the peroxisome proliferatoractivated receptors (PPARs) - PPARa, PPARb/d, and PPARg - in cardio-metabolic control. Importantly, we discovered an association between the PPARg Pro12Ala gene variant with type 2 diabetes and obesity, long before the era of genome-wide association studies, and as such identified the first gene tied with common complex metabolic disease. Furthermore, we identified many new target genes and mapped several of the pathways controlled by PPAR signaling, including those involved in glucose homeostasis, lipid and lipoprotein metabolism, inflammation, bone homeostasis, and cancer. We also established how the enterohepatic nuclear receptors - farnesoid X receptor, liver receptor homolog-1 and short heterodimer partner - govern hepatic lipid and bile acid metabolism, regulate intestinal substrate absorption and cell proliferation, and control male and female fertility. We furthermore identified bile acids as endocrine regulators of energy expenditure, glucose homeostasis, and immune modulation, through the activation of a novel GPCR, TGR5. This work on bile acid signaling, revealed a protective role for bile acids against the development of type 2 diabetes and atherosclerosis and sparked a paradigm shift that transformed bile acids, known to be lipid solubilizers in the gut, to versatile endocrine signals that impact almost any aspect of physiology.

More recently, our research has been on the role of transcriptional cofactors in the control of metabolic homeostasis, in general, and of mitochondrial function, in particular. We were amongst the leading groups that established that a yin-yang between corepressors - the nuclear receptor corepressor 1 (NCoR1) and the sirtuin family of deacetylases - and coactivators - the PPARg coactivator 1a (PGC1a), the steroid receptor coactivators 2 and 3 (SRC-2 and -3) and GCN5 - fine-tunes transcriptional networks that control oxidative metabolism. We showed that increased cellular NAD+ levels during energy stress, activate SIRT1 to deacetylate and induce the activity of PGC-1a, the master controller of mitochondrial function. This process, together with reduced activity of NCoR1 favors oxidative metabolism, thereby enhancing the use of stored energy during caloric restriction. These processes are reversed by excessive energy intake, when the activity of AMP-activated kinase and SIRT1 is attenuated due to high intracellular ATP and low NAD+ levels. A high fat diet, furthermore induces the expression of the acetyltransferases, SRC-3 and GCN5, while concomitantly reducing SIRT1 levels. One result is the acetylation and inhibition of PGC1a, which in turn attenuates mitochondrial activity. Furthermore, NCoR1 is activated, accentuating the decreased transcription of genes governing mitochondrial activity, ultimately enabling the storage of excess calories in times of excessive intake. Our work has established that complex transcriptional networks convert signals associated with caloric intake and cellular energy status into changes of chromatin state and transcription. This alters mitochondrial function and whole body metabolic homeostasis. As such, our research paved the way for novel preventive and therapeutic strategies for these common diseases. Examples of drugs for which our research contributed significantly to clinical development are the fibrates (through PPARa), thiazolidinediones (through PPARg), PPARb/d agonists, bile acid derivatives (through both TGR5 and FXR), and AMPK agonists, such as resveratrol (which activates SIRT1).

EPFL School of Life Sciences - 2011 Annual Report

Noriega, L., Feige, J., Canto, C., Yamamoto, H., Yu, J., Herman, M., Mataki, C., Kahn, B.B., Auwerx, J. (2011) CREB and ChREBP oppositely regulate SIRT1 expression in response to energy availability. EMBO Reports 12:1069-1076. Du, J., Zhou, Y., Su, X., Yu, J. J., Khan, S., Jiang, H., Kim, J., Woo, J., Kim, J. H., Choi, B. H., He, B., Chen, W., Zhang, S., Cerione, R. A., Auwerx, J., Hao, Q., Lin, H. (2011) Sirt5 Is an NAD-Dependent Protein Lysine Demalonylase and Desuccinylase. Science 334: 806-809. Pols, T.W.H., Nomura, M., Harach, T., Lo Sasso, G., Oosterveer, M.H., Thomas, C., Rizzo, G., Gioiello, A., Adorini, L., Pelliciari, R., Auwerx, J., Schoonjans, K. (2011) TGR5 activation inhibits atherosclerosis by reducing macrophage infiltration and lipid loading. Cell Metabolism 14:747-757. Bai, P., Canto, C., Brunyánszki, A., Huber, A., Szanto, M., Cen, Y., Yamamoto, H., Houten, S., Kiss, B., Oudart, H., Gergely, P., Schreiber, V., Menissier-de Murcia, J., Sauve, A.A., Auwerx, J. (2011) PARP-2 regulates SIRT1 expression and whole body energy expenditure. Cell Metabolism 13:450-460. Bai, P., Canto, C., Oudart, H., Brunyánszki, A., Cen, Y., Thomas, C., Yamamoto, H., Huber, A., Kiss, B., Houtkooper, R.H., Schoonjans, K., Schreiber, V., Sauve, A.A., Menissier-de Murcia, J., Auwerx, J. (2011) PARP-1 inhibition increases mitochondrial metabolism through SIRT1 activation. Cell Metabolism 13: 461-468.

Team Members Postdoctoral Fellows Carles Canto Pablo Fernandez-Marcos Taoufiq Harach Riekelt Houtkooper Ellen Jeninga Giuseppe Lo Sasso Adriano Maida Laurent Mouchiroud Maaike Oosterveer Eija Pirinen Thijs Pols Dongryeol Ryu Matthias Stein Hiroyasu Yamamoto Jiujiu Yu PhD Students Pénélope Andreux Elena Katsyuba Mitsonura Nomura Evan Williams Master’s Student Adrienne Mottis

Yamamoto, H., Williams, E.G., Mouchiroud, L., Canto, C., Fan, W., Downes, C. Heligon, Barish, G.D., Desvergne, B., Evans, R.M., Schoonjans, K., Auwerx, J. (2011) NCoR1 is a conserved physiological modulator of muscle mass and oxidative function. Cell 147 :827-839.

Technicians Sabrina Bichet Thibaud Clerc Amandine Moriot-Signorino-Gelo Norman Moullan

Houtkooper, R.H., Williams, R.W., Auwerx, J. (2010). Metabolic networks of longevity. Cell 142 :9-14. Canto, C., Jiang, L.Q., Desmukh, A.S., Mataki, C., Coste, A., Lagouge, M., Zierath, J., Auwerx, J. (2010). The interdependence of AMPK and SIRT1 for metabolic adaptation to fasting and excercise in skeletal muscle. Cell Metabolism 11:213-219.

Administrative Assistant Valérie Stengel

IBI - Institute of Bioengineering

Selected Publications

Mice treated with resveratrol are protected from obesity.

EPFL School of Life Sciences - 2011 Annual Report

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

IBI

Yann Barrandon, MD-PhD, is joint professor in Stem Cell Dynamics at the EPFL and at the Lausanne University (Unil), and head of the Department of Experimental Surgery at the CHUV. He has made major contributions in basic epithelial stem cell biology and in stem cell therapy. Prof. Barrandon is a principal investigator in several European Commission stem cell consortia (EuroSystem, Optistem and BetacellTherapy). Professor Barrandon is a member of the EMBO and the Academia Europaea. He was elected twice best teacher in Life Sciences at EPFL. He is also a member of the EPFL research committee, EPFL Ethical committee and the Canton de Vaud Ethical committee. In 2011, he co-founded gyMETRICS SA.

Yann Barrandon

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

Introduction

The laboratory of Stem Cell Dynamics at EPFL and Experimental Surgery at the CHUV pursues three main objectives aiming at improving cell and gene therapy using epithelial stem/progenitor cells: first, the laboratory would like to decipher the basic relationship between stem/progenitors cells of stratified epithelia and p63 expressing cells, second to understand the impact of the environment on stem cell behavior and third to comprehend stem cell engraftment. The laboratory is a partner in three stem cell consortia within the EEC 7th framework program, aiming at the fundamentals of stem cells (EuroSyStem) and stem cell therapy (OptiStem and BetaCellTherapy).

Keywords

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

Results Obtained in 2011

Within tissue stem cells, the skin is privileged because it’s stem cells (epithelial and mesenchymal) can be extensively cultivated and cloned, genetically manipulated and transplanted in laboratory animals, but also in human. We have demonstrated that all stratified epithelia of the rat, independent of their primary germ line origin (e.g. the endodermal esophagus or the ectodermal cornea), contain clonogenic stem cells that can respond to skin morphogenetic signals by forming epidermis, sebaceous glands and functional hair follicles in serial transplantation. Furthermore, we have demonstrated that the thymus, which has a unique 3D structure that does not resemble that of a simple or stratified epithelium, contains a population of clonogenic epithelial cells with the astonishing capability to adopt the fate of bona fide multipotent stem cells of the hair follicle when exposed to skin morphogenetic signals, a property maintained in serial transplantation. Gene profiling experiments have demonstrated that several transcription factors

important for thymic identity were either down-regulated or silenced in thymic epithelial cells recovered from skin (Bonfanti et al., Nature 2010). This clearly represents a crossing of lineage boundaries, an increase in potency and the demonstration that adult stem/progenitor cells can be robustly reprogrammed by microenvironmental cues. Engraftment is the quintessence of stem cell behavior as it draws on all stem cell basic functions, i.e. homing, attachment, migration, proliferation, fate choice, renewal, differentiation and death. In a normal situation, these decisions are tightly controlled and influenced by the microenvironment (the niche), but in therapy, the microenvironment may be diseased, damaged by the preconditioning treatment, or even completely missing as in third degree burns or limbal deficiency. Hence, transplanted stem cells have to adapt to an environment that is far from ideal, if not hostile. Surprisingly, little is known on engraftment that remains more a lottery than a scientifically controlled process. We have demonstrated that transplanted stem cells respond to adverse conditions by favoring differentiation rather self-renewal or death (Grasset et al., submitted). We are now using state-of-the art architecture, informatics and visualization technology to construct models that will allow us to virtually manipulate stem cell behavior and predict the consequences on organ function using the skin, the thymus and the cornea as model systems. We have also completed our studies 1- on the role of small variation of temperature on stem cell behavior and demonstrated that it signals through mTOR wired to TRPVs (Brouard et al., submitted), 2- on a single stem cell strategy for ex vivo gene therapy of Recessive Dystrophic Epidermal Bullosa (Lathion Droz-Georget et al., submitted), 3- on the plasticity of stratified epithelial cells (Claudinot et al., submitted), 4- on the characterization of the clonogenic epithelial cells in human thymus (Magggioni et al., in preparation), and 5- on the organization of actin filaments which predicts the response of human clonogenic epidermal keratinocytes to epidermal growth factor (Nanba et al., submitted).

EPFL School of Life Sciences - 2011 Annual Report

Selected Publications

Smith E, Claudinot S, Lehl R, Pellegrinet L, Barrandon Y, Radtke F. Generation and Characterization of a Nothc1 Signaling-Specific Reporter Mouse Line. (April 2012) Genesis, epub ahead of print. Rochat A, Grasset N, Gorostidi F. Lathion Droz-Georget S, Barrandon Y. Regeneration of epidermis from adult human keratinocyte stem cells. (2012) In Handbook of stem cells A. Atalla and R. Lanza coordinating editors Elsevier. In press. Bonfanti P, Barrandon Y, Cossu G. “Hearts and Bones”: The Ups and Downs of “Plasticity” in Stem Cell Bioloy (2012) EMBO Molecular Medicine 4, 1-9 . Grasset, N, Barrandon Y, Hug K, Hermeren G. Issues beyond the debate on the moral status of the embryo, in Translational Stem Cell Research, pp. 45-53, Eds Springer Verlag, New York, 2011. Bonfanti, P., Claudinot, S., Amici, A.W., Farley, A., Blackburn, C.C, Barrandon, Y. (2010). Microenvironmental reprogramming of thymic epithelial cells to skin multipotent stem cells. Nature 466, 978-982. Majo, F., Rochat, A., Nicolas, M., Abou Jaoudé, G., Barrandon, Y. (2008). Oligopotent stem cells are distributed throughout the ocular surface. Nature 456, 250-254. Epub 2008 Oct 1. Research Highlights in Nature Reports Stem Cells Epub Oct 9, 2008. (press release). Majo F., Rochat A, Nicolas M, Abou Jaoude G, Barrandon Y, Location of corneal epithelial stem cells Reply, Nature, 463 (7284), 11, 2010. Gurtner, G. C., Werner, S., Barrandon, Y., Longaker, M. T. (2008). Wound repair and regeneration. Nature 453: 314-321.

Team Members Senior scientists Brouard Michel Rochat Ariane

Postdoctoral Fellows Amici Alessandro Caillier-Veron Maïa Claudinot Stéphanie Droz-Georget Stéphanie Gonneau Christèle Grasset Nicolas Kanemitsu Michiko Volorio Christelle Wasknick Roxana PhD Students Gorostidi François Graber Julien Maggioni Melissa Manti Pierluigi Mosig Johannes Muller Georges Pluchinotta Matteo Zaffalon Andrea Master’s Students Muller Georges Pluchinotta Matteo Zaffalon Andrea Hémon Diane De Lageneste Marine Richter Solange Technicians Mercier Louis Vermot Steeve Clinical Trial Collaborator Savioz-Dayer Emmanuelle Supporting Staff Mercier Louis Vermot Steeve

IBI - Institute of Bioengineering

Administrative Assistants Guex Nathalie Savioz-Dayer Emmanuelle

Cultured neuron isolated from a trigeminal ganglion of a mouse, TUJ1 immunostaining; 10x magnification

EPFL School of Life Sciences - 2011 Annual Report

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

IBI

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

Matteo Dal Peraro Tenure Track Assistant Professor

Introduction

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

Keywords

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

Results Obtained in 2011

In the past decade, the advances of computational biophysics and biochemistry have permitted to extend our knowledge of biological function at the molecular level shedding light on features that are often experimentally inaccessible. Proteins often assemble in large macromolecular complexes to achieve a specific biological task. Unfortunately, owing to their size and complexity, the structure of these machines is difficult to be determined at atomistic resolution. Thus, the ability to reliably predict the conformation of multimeric assemblies is desirable. To address this issue we developed a new approach called POW (Protein Optimization Workbench) that uses a Particle Swarm Optimization (PSO) search guided by experimental-based restraints to characterize protein quaternary structure. We showed how, by exploiting a limited set of known experimental restraints, our method can successfully (i) predict the arrangement of a variety of protein assemblies according to a predefined symmetry, and (ii) sample the conformation of protein-protein binary complexes (see Figure). In addition, the inclusion of the native flexibility of each protein subunit is a key ingredient for the prediction of biologically functional assemblies. The advantage of this ap-

proach is that assembly prediction is performed using an ensemble of physically plausible structures. Upon definition of a list of geometric restraints and a specific symmetry, a PSO search tries to arrange the elements belonging to a conformational database in a multimeric assembly so that all restraints are respected, and steric clashes avoided. Geometric restraints can be typically provided by low resolution electron density maps or experiments such as cross-linking disulfide scanning, mutagenesis, FRET, etc. If necessary, POW can assemble a multimer on a given substrate. A small set of representative solutions, typically less than ten, is returned by clustering the accepted solutions. This process is usually very fast (less than 5 minutes on an average workstation), and can produce a small ensemble of solutions being sufficiently good to generate biologically sound working hypotheses, and act as seeds for further optimization steps using more computationally expensive techniques. This scheme has been recently used to model the heptameric soluble form of pore-forming toxin aerolysin from Aeromonas hydrophila (in collaboration with the van der Goot Lab at EPFL). The model is based on the high-resolution X-ray structure of aerolysin monomer and the lowresolution cryo-EM map of the heptamer. The same strategy has been used to determine the membrane-embedded basal body (namely the complex between YscD and YscJ) of the multi-MDa type III secretion system from Yersinia enterocolitica. The PSO engine in our software is not sensitive to the kind of imposed symmetry, thus implementing other common symmetries (such as helical or icosaedral) is trivial, and is part of our future development plans. Moreover, improvements on (i) the fitness function with the inclusion of a broader set of geometric restraints, and/or (ii) the energy scoring with the use of more accurate molecular mechanics potentials will certainly contribute to enhance the quality of the final predicted assemblies and eventually address the prediction of protein-protein interactions in large macromolecular networks.

EPFL School of Life Sciences - 2011 Annual Report

Selected Publications

B. Blasco, M. Stenta, L. Alonso-Sarduy, G. Dietler, M. Dal Peraro, S. Cole, F. Pojer (2011) Atypical DNA recognition mechanism used by the EspR virulence regulator of Mycobacterium tuberculosis, Molecular Microbiology, 82:251–264. I. Iacovache, M. Degiacomi, L. Pernot, M. Schiltz, M. Dal Peraro, F. G. van der Goot (2011) Folding of the pore-forming toxin aerolysin is catalyzed by the Cterminal propeptide, PLoS Pathogens 7(7):e1002135. M. Stenta and M. Dal Peraro (2011) An introduction to quantum chemical methods applied to drug design, Frontiers in Bioscience, E3(1):1061-1078. S. Wagner, M. Stenta, L. C. Metzger, M. Dal Peraro and G. R. Cornelis, (2010) Length control of the injectisome needle requires only one molecule of Yop secretion protein P (YscP), Proc. Natl. Acad. Sci. USA, 107(31):13860-13865.

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

M.H. Ho, M. De Vivo, M. Dal Peraro, and M. L. Klein, (2010) Understanding the Effect of Magnesium Ion Concentration on the Catalytic Activity of Ribonuclease H through Computation: Does a Third Metal Binding Site Modulate Endonuclease Catalysis, J. Am. Chem. Soc., 132:13702-13712. E. Khurana, R. H. Devane, M. D. Peraro and M. L. Klein (2010). Computational study of drug binding to the membrane-bound tetrameric M2 peptide bundle from influenza A virus, Biochimica et Biophysica Acta (BBA) - Biomembranes, 1808:530–537.

IBI - Institute of Bioengineering

D. Alemani, F. Collu, M. Cascella and M. Dal Peraro, (2010) A nonradial coarsegrained potential for proteins produces naturally stable secondary structure elements, Journal of Chemical Theory and Computation, 6(1):315-324.

(Left box) POW workflow. (Right) Best symmetrical rigid assembly predictions (in yellow) superposed to known X-ray crystal structures (in blue) of a representative set of symmetric assemblies.

EPFL School of Life Sciences - 2011 Annual Report

Deplancke Lab

http://deplanckelab.epfl.ch/

IBI

Bart Deplancke performed his undergraduate and M.Sc. studies in bio-engineering at Ghent University (Belgium), after which he pursued a Ph.D. in Immunobiology with Dr. Rex Gaskins at the University of Illinois (Urbana-Champaign, USA). He then teamed up for his post-doctoral studies with Dr. Marian Walhout, first in the laboratory of Dr. Marc Vidal at the Dana-Farber Cancer Institute of Harvard Medical School and later at the University of Massachusetts Medical School where Marian established her own laboratory, to study the structural and dynamic properties of gene regulatory networks. At the end of 2007, he started his own Laboratory of Systems Biology and Genetics at the EPFL as a tenure track assistant professor.

Bart Deplancke Tenure Track Assistant Professor

Introduction/Results 2011

Automated protein-DNA interaction screening of Drosophila regulatory elements The LSBG developed during the last two years an automated platform that enables the high-throughput protein-DNA interaction screening of Drosophila regulatory elements of interest (Hens et al., Nature Methods, 2011). Because of the availability of a high-quality genome sequence and many genetic tools, Drosophila has one of the best characterized metazoan genomes in terms of functionally annotated regulatory elements. Yet for most of these, it is still not known which the interacting TFs are. The ability to screen annotated regulatory elements for interacting TFs should therefore be of great value for the Drosophila community. To evaluate the efficacy of this platform, we screened six well-characterized regulatory elements and identified 33 TFâ&#x20AC;&#x201C;DNA interactions of which many were previously unidentified. To simultaneously validate these interactions and locate the binding sites of involved TFs, we implemented a powerful microfluidics-based approach, MARE (MITOMI-based Analysis of Regulatory Elements), that allows us to retrieve DNA occupancy data for each TF throughout the respective target DNA elements. Using MARE, we observed site-specific DNA binding for ~80% of the detected TFs. Importantly, we also biologically validated several interactions and identified two new regulators of sine oculis gene expression and hence eye development. This work has been well appreciated by the Drosophila community as reflected by the fact that over a dozen labs have already sent students to our lab to perform protein-DNA interaction screens. An integrative genomics study to dissect the gene regulatory mechanisms underlying adipogenesis In the last couple of years, our Lab has invested substantial efforts to elucidate the molecular function of Nuclear Receptor Co-Repressor 2 (NCoR2, or also known as Silencing Mediator of Retinoic acid and Thyroid hormone receptor (SMRT)) during adipogenesis (Raghav et al., Molecular Cell, in press). SMRT is a member of the family of transcriptional

co-regulators, which complement the function of TFs by acting as sensors of upstream regulatory signals, as such modulating the interaction between TFs and the basal transcriptional machinery. So far, most of our time has been devoted to elucidate the role of co-activators (e.g. p300, CBP) since they provide a more convenient experimental read-out, i.e. that of gene activation. Consequently, knowledge about the role and importance of their transcriptional counterparts, i.e. co-repressors, is still in its infancy, despite the fact that several have already been implicated in a wide range of biological processes. A striking example is SMRT, which, among many other biological processes, has been shown to repress terminal white fat cell differentiation. To elucidate the regulatory role of the co-regulator SMRT during adipogenesis, we first performed genome-wide DNAbinding profiling revealing that this co-repressor, in contrast to what may have been expected, is predominantly located in active chromatin regions and that most distal SMRT binding events are lost after differentiation induction. We found that promoter-proximal tethering of SMRT in pre-adipocytes is primarily mediated by the ZBT TF KAISO through the TCTCGCGAGA site (see graphical abstract), one of the most conserved motifs in mammalian promoters. Further characterization revealed that KAISO, similar to SMRT, accelerates the cell cycle and increases fat accumulation upon knockdown, identifying KAISO as a novel adipogenic repressor that likely modulates the mitotic clonal expansion phase of this process. We found that SMRT-bound promoter-distal sites tend to overlap with C/EBPb-bound regions, which become occupied by pro-adipogenic transcription factors after SMRT clearance. This reveals a role for SMRT of masking enhancers from pro-adipogenic factors in pre-adipocytes.

Keywords

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

EPFL School of Life Sciences - 2011 Annual Report

Selected Publications

S.K. Raghav*, S.M. Waszak*, I. Krier, A. Isakova, C. Gubelmann, T.S. Mikkelsen, and B. Deplancke. Integrative genomics identifies SMRT as a gatekeeper of early adipogenesis through the transcription factors C/EBPb and KAISO, Molecular Cell, in press. B. Deplancke, K.J. Verstrepen. Variable outcome of mutations. Science, 335:4445, 2012. K. Hens, J. Feuz, B. Deplancke. A high-throughput gateway-compatible yeast one-hybrid screen to detect protein-DNA interactions. Methods in Molecular Biology, 786:335-55, 2012. S. Raghav, B. Deplancke. Genome-wide profiling of DNA binding proteins using barcode-based multiplex Solexa sequencing. Methods in Molecular Biology, 786:247-62, 2012. K. Hens, J Feuz, A. Isakova, A. Iagovitina, A. Massouras, J. Bryois, P. Callaerts, S.E. Celniker, B. Deplancke. Automated protein-DNA interaction screening of Drosophila regulatory elements. Nature Methods, 8:1065-70, 2011.

Team Members Postdoctoral Fellows Monica Albarca Korneel Hens Sunil Raghav PhD Students Julia Cajan Carine Gubelmann Alina Isakova Irina Krier GrĂŠgoire Laporte Andreas Massouras Jovan Simicevic Sebastian Waszak Scientific assistants Jean-Daniel Feuz Wiebke Westphal Administrative assistant Marie-France Radigois

C. Gubelmann, A. Gattiker, A. Massouras, K. Hens, F. Decouttere, J. Rougemont, B. Deplancke. GETPrime: a gene- or transcript-specific primer generator for qPCR. Database, bar040, 2011. T.M. Tabuchi*, B. Deplancke*, N. Osato, L.J. Zhu, M.I. Barrasa, M.M. Harrison, H.R. Horvitz, A.J.M. Walhout, K.A. Hagstrom. Chromosome-biased binding and gene regulation by the C. elegans DRM complex. PLoS Genetics,7: e1002074, 2011. (*, shared first authorship). A. Massouras, K. Hens, C. Gubelmann, S. Uplekar, F. Decouttere, J. Rougemont, S.T. Cole, B. Deplancke. PrInSeS: Primer-Initiated Sequence Synthesis. Nature Methods, 7:485-6, 2010.

IBI - Institute of Bioengineering

A. Massouras, F. Decouttere, K. Hens, B. Deplancke. WebPrInSeS: automated full-length clone sequence identification and verification using high-throughput sequencing data. Nucleic Acids research, 38:W378-84, 2010.

Graphical abstract of the molecular role of the co-repressor SMRT during terminal white fat cell differentiation.

EPFL School of Life Sciences - 2011 Annual Report

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

IBI

Jeffrey Hubbell was trained as a chemical engineer from Kansas State University (B.S.) and Rice University (Ph.D.) in the United States. Previous to moving to Lausanne, he was on the faculty at the Swiss Federal Institute of Technology Zurich, at the California Institute of Technology, and at the University of Texas in Austin. He is author of more than 250 papers in peer-reviewed journals and inventor on more than 100 patents. He is a member of the National Academy of Engineering, USA.

Jeffrey A. Hubbell

Full Professor Director of IBI Merck-Serono Chair in Drug Delivery

Introduction

We design novel materials for investigation of basic cell biological phenomena such as stem cell self-renewal and differentiation and applications in medicine such as drug delivery, regenerative medicine, and vaccination. We focus on examples where novel materials are necessary to solve the problem, thus working at the interface between materials science and biology.

Keywords

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

Results Obtained in 2011

Regenerative medicine: The laboratory made exciting advances in engineering matrix-bound morphogens for conjugation in biomaterial matrices for tissue repair and regeneration. We had previously developed a biochemical approach to incorporate morphogenetic proteins into surgical matrices such as fibrin, two of which have now entered into clinical testing in bone repair and chronic wound healing in more than 500 patients in collaboration with corporate partners. We have further developed this concept, engineering extracellular matrix proteins, based on fibronectin and other extracellular matrix proteins, to comprise a promiscuous growth factor-binding domain proximal to an integrin-binding domain. The growth factor-binding domain was observed to bind to more than 20 growth factors from very diverse families. From the reverse perspective, we have identified domains from growth factors that are capable of binding a very diverse collection of extracellular matrix proteins. Using these two approaches, we can on the one hand engineer a matrix-based material scaffold to bind to a wide variety of growth factors, or we can engineer a particular growth factor to bind to a wide variety of extracellular matrix-based scaffold materials. We are exploring these approaches in the context of angiogenesis, chronic wound repair, bone repair, nerve repair and hair cell regeneration.

Vaccines and immunotherapeutics: In collaboration with the Laboratory for Lymphatic and Cancer Bioengineering (Prof. M.A. Swartz), the laboratory demonstrated that nanoparticles can be used as a vaccine platform for targeting cells in the lymph nodes draining dermal site and the lung, in addition to secondary lymphoid tissues in the nasal cavity. This, combined with advanced design of the polymeric nanoparticle surfaces, has enabled a new generation of vaccines, highly stable and very economical, for use in both the developing and the developed world. The team has demonstrated that ultra-small particles, smaller than biological particles, can be swept into the lymphatics within a few minutes of injection, drain to the lymph nodes, and are collected there for antigen presentation. Particularly favorable antigen conjugation schemes were developed for promotion of MHC I presentation and induction of potent CD8+ T cell responses, very impressive protection of mice versus influenza and Mycobacterium tuberculosis challenge was demonstrated, much more impressive than with free antigen delivered with the same adjuvants. From a materials perspective, our focus is on self-assembling block copolymers that form polymer micelles, upon the surface of which antigens are conjugated, or polymer vesicles, in the core of which antigens are encapsulated. Given that our interest is in inducing cellular immunity for chronic disease, our materials are designed to enhance mechanisms of antigen cross-presentation. In addition to inducing cellular immunity, we are also keenly interested in protein engineering approaches to tolerize versus cellular immunity, harnessing the tolerogenic antigen presentation that occurs with antigen from apoptotic cells yet using simple engineered antigen forms that are clinically tractable. We have shown that antigens can be engineered to bind in situ to erythrocytes, and that this leads to antigen deposition in antigen presenting cells in the liver and spleen very efficiently, the antigen circulating on the erythrocyte until it is cleared in the liver and spleen as it ages. This results in clonal deletion of both CD4+ and CD8+ T cells.

EPFL School of Life Sciences - 2011 Annual Report

Selected Publications

Stano, A. et al. PPS nanoparticles as versatile delivery system to induce systemic and broad mucosal immunity after intranasal administration. Vaccine 29, 804812 (2011). Nembrini, C. et al. From the Cover: Nanoparticle conjugation of antigen enhances cytotoxic T-cell responses in pulmonary vaccination. Proc. Natl. Acad. Sci. U. S. A. 108, E989-997 (2011). Martino, M.M. et al. Engineering the growth factor microenvironment with fibronectin domains to promote wound and bone tissue healing. Sci Transl Med 3, 100ra189 (2011). van der Vlies, A.J., O’Neil, C.P., Hasegawa, U., Hammond, N. & Hubbell, J.A. Synthesis of pyridyl disulfide-functionalized nanoparticles for conjugating thiolcontaining small molecules, peptides, and proteins. Bioconj. Chem. 21, 653662 (2010). Martino, M.M. & Hubbell, J.A. The 12th-14th type III repeats of fibronectin function as a highly promiscuous growth factor-binding domain. FASEB J. 24, 47114721 (2010). Kontos, S. & Hubbell, J.A. Improving protein pharmacokinetics by engineering erythrocyte affinity. Mol Pharm 7, 2141-2147 (2010). Hubbell, J.A. Drug development: Longer-lived proteins. Nature 467, 1051-1052 (2010). Hirosue, S., Kourtis, I.C., van der Vlies, A.J., Hubbell, J.A. & Swartz, M.A. Antigen delivery to dendritic cells by poly(propylene sulfide) nanoparticles with disulfide conjugated peptides: Cross-presentation and T cell activation. Vaccine 28, 7897-7906 (2010). Velluto, D., Thomas, S.N., Simeoni, E., Swartz, M.A. & Hubbell, J.A. PEG-bPPS-b-PEI micelles and PEG-b-PPS/PEG-b-PPS-b-PEI mixed micelles as non-viral vectors for plasmid DNA: tumor immunotoxicity in B16F10 melanoma. Biomaterials 32, 9839-9847 (2011). Vasdekis, A.E., O’Neil, C.P., Hubbell, J.A. & Psaltis, D. Microfluidic assays for DNA manipulation based on a block copolymer immobilization strategy. Biomacromolecules 11, 827-831 (2010).

Team Members Postdoctoral fellows Brubaker Carrie De LaPorte Laura Dane Karen Engelhardt Eva-Maria Hasegawa Urara Kontos Stephane Lorentz Kristen Martino Mikaël Mochizuki Mayumi Nembrini Chiara Patterson Jennifer Rice Jeffrey Sancho Oltra Nuria Scott Evan Alexander Tortelli Federico Van der Vlies André Velluto Diana

PhD students Ahmadloo Hamideh Damo Martina De Titta Alexandre Eby Jackson Julier Ziad Kourtis Iraklis Larsson Hans Mattias Mahou Redouan Micol Lionel Panagiotou Vasiliki Pisarek Rubin Berek Raghunathan Sandeep Schütz Catherine Stano Armando Vardar Elif Master students Briquez Priscilla Djahanbakhsh Rafiee Sarah Liu Alexandra Bachelor students Courthion Hervé Desbaillets Nicolas Kayser Stephanie Leahu Teodor Maillat Léa Internships Boyer David, France David Allen Roberts, USA Ferreira Daniela, Portugal Hopkins Amy, USA Neubauer Stefanie, Germany Other scientific personnel Frey Peter Wandrey Christine Simeoni Eleonora Dessibourg Céline Quaglia Xavier Pasquier Miriella

IBI - Institute of Bioengineering

Administrative Assistant Bonzon Carol Anne

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

EPFL School of Life Sciences - 2011 Annual Report

Lutolf Lab http://lscb.epfl.ch/

IBI

Matthias Lutolf was trained as a Materials Engineer at ETH Zurich where he also carried out his Ph.D. studies on the development of a novel class of biomolecular materials for tissue engineering (awarded with ETH medal, 2004). In 2005, Lutolf joined the Baxter Laboratory in Stem Cell Biology at Stanford University to work on hematopoietic stem cells; research sponsored by Swiss National Science Foundation and Leukemia and Lymphoma Society fellowships. In 2007 Lutolf won a European Young Investigator (EURYI) award to start up his independent research at EPFL.

Matthias P. Lutolf Tenure Track Assistant Professor

Introduction

Results Obtained in 2011

eral adult stem cell populations including neural stem cells, mesenchymal progenitor cells and HSCs. Single mouse long-term HSCs (LT-HSC) were analyzed by time-lapse microscopy and showed distinct in vitro clonal proliferation kinetics in response to putative niche signaling cues. These experiments showed that specific single cell growth kinetics could be correlated with their long-term repopulation potential, the only definitive test of HSC function. Interestingly, we also found that very early (i.e. after one hour in culture) changes in lipid raft distribution on single HSCs could serve as an indicator of the quiescent and activated state of HSCs. Extrinsic factors that decreased the lipid raft clustering slowed down cell cycle kinetics, while factors that increased clustering led to faster and more synchronous cell cycling.

For example, a micro-engineered platform consisting of soft hydrogel microwell arrays with modular stiffness was developed where individual microwells can be functionalized with combinations of candidate biomolecules spotted by robotic technology. Using this novel platform, it is possible to probe the effect of key micro-environmental perturbations on the fate of virtually any stem cell type at single cell level and in high-throughput. We have successfully validated this system by studying niche-regulation of sev-

To understand whether daughter cells generated by cell division of a mother LT-HSC keep their long-term multipotency or have committed, we utilized single cell multi-gene expression analysis to identify gene expression profiles associated with the most primitive stem and progenitor cell states in the mouse bone marrow. Apart from the CDK inhibitor p57 we found several genes involved in regulating cell-cell interactions (e.g. Junctional adhesion molecule C, JAM3, a component of tight junctions) whose expression was significantly upregulated in LT-HSC versus ST-HSC and multipotent progenitors. We showed that these proteins are expressed at the cell surface and can be used as additional phenotypic markers of live LT-HSCs. We then used multigene expression analysis in combination with micromanipulation to analyze paired daughter cells of dividing single HSCs. In vitro divisions under serum-free conditions supplemented with well-known hematopoietic cytokines, that is, in the absence of a functional niche, resulted in significant downregulation of the key niche interaction genes. Interestingly, several of the analyzed genes appear to be differentially expressed in the two paired daughter cells suggesting asymmetric divisions. Preliminary LT-HSC culture experiments on artificial niches displaying the identified cell-cell interaction proteins such as JAM3 show delayed cell cycle entry and maintenance of an LT-HSC-like gene expression profile.

Adult stem cells can hardly be grown in a culture dish (‘ex vivo’), posing a substantial hurdle for their clinical use. By merging biomaterials science with microfabrication technologies, the Lutolf laboratory develops and applies innovative bioengineering tools to probe and manipulate single stem cell behavior in vitro in an unprecedented fashion. These technologies are expected to have the potential to be translated into clinical settings.

Keywords

Stem cells, self-renewal, single cell analysis, niche, hydrogel engineering, microfluidics. One question the lab has been pursuing using this paradigm is the regulation of mouse hematopoietic stem cell (HSC) fate decision-making. That is to say, despite a remarkable extent of knowledge regarding the biology of hematopoietic stem cells (HSCs), the mechanisms governing the long-term maintenance of their function have not been elucidated. Compelling evidence shows that the microenvironment, or niche, plays the key role in regulating HSC function in vivo, but just how the stem cells remain quiescent and, upon activation, integrate the multiple niche signaling cues to either undergo self-renewal or commitment remains unknown. We have been tackling this crucial question by first identifying a minimal functional artificial HSC niche, i.e. by discovering candidate extrinsic factors that can influence in vitro HSC maintenance without loss of in vivo function, and then exploring their mechanisms of action.

EPFL School of Life Sciences - 2011 Annual Report

Selected Publications

Gobaa S, Hoehnel S, Roccio M, Negro A, Kobel S, Lutolf MP*, Artificial niche microarrays for probing stem cell fate in high-throughput, Nature Methods, 2011 Oct 9;8(11):949-55. (highlighted by a News & Views from F. Watt and J. Burdick). Kobel S, Lutolf MP*, Biomaterials meet Microfluidics: Building the next generation of artificial niches, Current Opinion in Biotechnology, 2, pp. 690-697 (2011). Ehrbar M*, Sala A, Lienemann P, Rizzi SC, Weber FE and Lutolf MP*, Elucidating the role of matrix stiffness in 3D cell migration and remodeling, Biophysical Journal, 100, 284-293 (2011). Allazetta S, Cosson S, Lutolf MP*, Programmable microfluidic patterning of protein gradients on hydrogels, Chemical Communications, 47 (1): 191-193 (2011). Gilbert PM, Havenstrite KL, Sacco A, Leonardi N, Peggy Kraft, Nguyen NK, Lutolf MP, and Blau HM (2010). Matrix rigidity regulates skeletal muscle stem cell self-renewal in culture, Science, 329 (5995): 1078 – 1081. Mosiewicz, K., Johnsson, K. and Lutolf, M.P. (2010). Phosphopantetheinyl Transferase-Catalyzed Formation of Bioactive Hydrogels for Tissue Engineering, JACS, 132 (17): 5972–5974. Kobel, S. and Lutolf, M.P.*, High-throughput methods to define complex stem cell niches, Biotechniques, Vol. 48, No. 4, pp. ix–xxii (2010)

Team Members Postdoctoral Fellows Samy Gobaa Marta Roccio Nicola Vannini Olaia Naveiras PhD Students Simone Allazetta Steffen Cosson Mukul Girotra Sylke Hoehnel Andrea Negro Yuya Okawa Adrian Ranga Aline Roch Master Students Ryan Erickson Sonia Hallen Luc Gervais Mbida Teodor Leahu Technician Vasco Campos Administrative Assistant Maria Fernandes Coelho

IBI - Institute of Bioengineering

Kobel, S., Valero, A., Latt, J. Renaud, P., and Lutolf, M.P. (2010). Optimization of microfluidic single cell trapping for long-term on-chip culture, Lab on a Chip, 10: 857 - 863.

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

EPFL School of Life Sciences - 2011 Annual Report

Naef Lab

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

IBI

Felix Naef studied theoretical physics at the ETHZ and obtained his PhD from the EPFL in 2000. He received postdoctoral training at the Center for Studies in Physics and Biology at the Rockefeller University (NYC). His research focuses on the study of biomolecular oscillators, modeling, and transcription regulation. He was nominated Tenure Track Assistant Professor at the EPFL School of Life Sciences in 2005. He is currently a member of the Institute of Bioengineering (IBI).

Felix Naef

Tenure Track Assistant Professor

Introduction

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

Keywords

Gene regulation, chronobiology, circadian rhythms, stochastic gene expression.

Results Obtained in 2011

Circadian gene regulation in mouse liver. The circadian clock is a timing system that allows organisms to keep behavioral, physiological, and cellular rhythms in resonance with daily environmental cycles. In mammals, such clocks use transcriptional regulatory loops in which the heterodimeric transcription factor BMAL1/CLOCK plays a central role. Recently, we performed the first comprehensive time series analysis of the binding profiles of the core circadian transcription factor BMAL1 in a complex tissue, namely the mouse liver (Rey et al, 2011). The mouse liver has been a prime model in circadian biology showing high amplitude rhythms; moreover, it has high relevance to study the timely issue of how the clock interacts with metabolism. The approach used ultra-high throughput sequencing (UHTS) combined with chromatin immuno-precipitation (ChIP) assays and bioinformatics modeling to characterize the rhythmic DNA-binding and its role in controlling circadian gene transcription and accumulation. Our temporal analysis revealed widespread daily rhythms in DNA-binding with maximum levels at midday. BMAL1 targets clearly indicated a circadian function in carbohydrate and lipid metabolism, mediated via nuclear receptors. Moreover, detailed in vitro and in cellulo assays elucidated the role of cooperative interactions at E1-E2 enhancer sites. Our results strengthened BMAL1â&#x20AC;&#x2122;s primary function as master regulator of the core circadian oscillator, while it is implicated more weakly in a variety of hepatic output functions.

Stochastic transcription in single mammalian cells. This work lies at the interface of circadian transcription regulation and basic transcription biology. Our previous discovery of cell-autonomous transcriptional circadian oscillations in 2004 (Nagoshi et al., 2004) used a single gene promoter (RevErba) with a relatively long-lived (half-live of ~3 hours) fluorescent reporter (venus-YPF). The question then arose as to what temporal patterns in transcription can be found in a mammalian cell when measured (i) in unbiased fashion (genome-wide); and (ii) using a shorter lived reporter such that rhythms of shorter period (ultradian frequencies) or transcriptional discontinuities (transcriptional bursting) could be characterized. In Suter et al., 2011, we provided a systematic and quantitative time-lapse study of transcriptional bursting in mammalian cells using high temporal resolution measurements of transcription in individual cells. Specifically, we discovered how discontinuous transcription of mammalian genes leads to broad spectra of temporal bursting in mRNA synthesis. To obtain these results, we monitored transcription at high temporal resolution by designing chromosomally integrated vectors encoding a destabilized luciferase in combination with ultrasensitive bioluminescence microscopy. We then developed a novel mathematical framework that combines a stochastic model of transcription with Bayesian inference to (i) calibrate model parameters, and (ii) compute the statistical properties of switching times in gene activity. This revealed gene-specific transcription burst sizes, switching rates, and we discovered refractory periods of variable duration in the inactive state. Relevant to chronobiology, we found that the circadian transcription of the Bmal1 gene is accompanied by an ultradian frequency band in the range of two hours, which persisted after treatment with TSA (resulting in a state of hyper-acetylated histones and transcriptionally permissive chromatin).

EPFL School of Life Sciences - 2011 Annual Report

Selected Publications

D. M. Suter, N. Molina, D. Gatfield, K. Schneider, U. Schibler*, F. Naef*, “Mammalian Genes Are Transcribed with Widely Different Bursting Kinetics”, Science 332, 472 (2011). G. Rey, F. Cesbron, J. Rougemont, H. Reinke, M. Brunner, F. Naef*, “GenomeWide and Phase-Specific DNA-Binding Rhythms of BMAL1 Control Circadian Output Functions in Mouse Liver”, Plos Biology 9, (2011). J. Bieler, C. Pozzorini, F. Naef*, “Whole-embryo modeling of early segmentation in Drosophila identifies robust and fragile expression domains”, Biophys J 101, 287 (2011). I. Gyurjan, B. Sonderegger, F. Naef, D. Duboule, “Analysis of the dynamics of limb transcriptomes during mouse development.” BMC Dev Biol. 11(1):47 (2011). G. Stoll, M. Bischofberger, J. Rougemont, F. Naef*, “Stabilizing patterning in the Drosophila segment polarity network by selecting models in silico”, Biosystems 102, 3 (2010).

Team Members Postdoctoral Fellows Teresa Ferraro Nacho Molina Bhaswar Ghos PhD Students Mirko Bischofberger Guillaume Rey Thomas d’Eysmond Simon Blanchoud Jonathan Bieler Laura Symul Julia Cajan Johannes Becker Benjamin Zoller Rosamaria Cannavo Jerome Mermet Administrative Assistant Sophie Barret

M. Preti, C. Ribeyre, C. Pascali, M. C. Bosio, B. Cortelazzi, J. Rougemont, E. Guarnera, F. Naef, D. Shore, G. Dieci, “The Telomere-Binding Protein Tbf1 Demarcates snoRNA Gene Promoters in Saccharomyces cerevisiae”, Molecular Cell 38, 614 (2010).

IBI - Institute of Bioengineering

S. Blanchoud, Y. Budirahardja, F. Naef*, P. Gonczy*, “ASSET: A Robust Algorithm for the Automated Segmentation and Standardization of Early Caenorhabditis elegans Embryos”, Developmental Dynamics 239, 3285 (2010).

Transcription of individual mammalian genes shows refractory period in gene re-activation. A) two single-cell bioluminescence traces form the same clone. B) Signal deconvolution. C) Duration of ‘off’ state shows peaked distribution. D) Minimal model of gene transcription needs three-states.

EPFL School of Life Sciences - 2011 Annual Report

Swartz Lab

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

IBI

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

Melody A. Swartz Full Professor

Introduction

The lymphatic system is an important regulator of fluid balance, innate immunity and peripheral tolerance. We are fascinated by this network of vessels that drain fluid, antigens, and cells from the periphery, through the lymph nodes, and back into the blood. By uncovering its complex roles in immunity and tolerance, we hope to understand – and ultimately manipulate – its participation in cancer progression and metastasis.

Keywords

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

Results Obtained in 2011

In 2011, we contributed new fundamental understanding of how the lymphatic microenvironment affects immunity and cancer, and how dendritic cells (DCs) interpret different types of cues in this biomechanically complex environment. We also contributed to the mechanobiology of lymphatic endothelium, demonstrating the importance of flow on lymphatic function – namely, its active transport mechanisms for water, solutes, proteins, and nanoparticles.

way, lymphatic endothelium can directly protect the tumor against host immune responses, and may limit the efficacy of immunotherapy aimed to activate host immunity against the tumor. This has implications for cancer immunotherapy strategies. In collaboration with Jeff Hubbell’s lab (EPFL), we are finding improved cancer vaccine efficacy when targeted specifically to tumor-draining lymph nodes, presumably by replacing the tumor-primed, tolerogenic milieu of the tumor-draining lymph node with immune activation signals. In other areas of lymphatic-targeting nanoparticle vaccines, we have demonstrated that nanoparticle coupling of adjuvant gives more efficacy with lower doses, presumably because it concentrates the signal in the lymph node. We have also demonstrated similar effects of nanoparticlecoupled vaccines particularly when delivered to the lung, where mucosal immunity is enhanced with lower vaccine doses.

We showed that tumor-associated lymphatic hyperplasia, both in the tumor and its draining lymph node, plays important immune regulatory roles that can protect the tumor from even pre-existing host immunity. In collaboration with Stephanie Hugues’s lab at the University of Geneva, we demonstrated that lymphatic endothelial cells in the tumor microenvironment can scavenge tumor antigens and crosspresent them for subsequent CD8 T cell deletion. In this

EPFL School of Life Sciences - 2011 Annual Report

Selected Publications

JD Shields, I.C. Kourtis, AA Tomei, J. Roberts, and MA Swartz (2010). Induction of lymphoid-like stroma and immune escape by tumors that express the chemokine CCL21. Science. 328(5979):749-52. (comment: “Perspectives,” Science 328:697-7, 2010; “Research Highlights,” Nature Rev. Cancer, 10(5):292, 2010). DO Miteva, JB Dixon, W Kilarski, JM Rutkowski, JD Shields, and MA Swartz (2010). Transmural flow modulates cell and fluid transport functions of lymphatic endothelium: A potential early cue for inflammation. Circ. Res. 106(5):920-31. JM Rutkowski, CE Markhus, C.C. Gyenge, K. Alitalo, H. Wiig, and MA Swartz (2010). Dermal collagen and fat accumulation correlate with tissue swelling and hydraulic conductivity in murine lymphedema. Am J Pathol. 176(3):1122-9. S Hirosue, IC Kourtis, AJ van der Vlies, JA Hubbell*, and MA Swartz* (2010). Antigen delivery to dendritic cells by poly (propylene sulfide) nanoparticles with disulfide conjugated peptides: Cross-presentation and T cell activation. Vaccine 28:7897-7906. JA Pedersen, S. Lichter, and MA Swartz (2010). Cells in 3D matrices under interstitial flow: Effects of pericellular matrix alignment on cell shear stress and drag forces. J Biomech 43:900-905. U Haessler, M Pisano, M Wu, and MA Swartz (2011). Dendritic cell chemotaxis in 3D under defined chemokine gradients reveals differential response to CCL21 and CCL19. Proc. Natl. Acad. Sci. U.S.A. 108:5614-18. AC Shieh, HA Rozansky, B Hinz and MA Swartz (2011). Tumor cell invasion is promoted by interstitial flow-induced matrix priming by stromal fibroblasts. Cancer Res. 71(3):790-800. SN Thomas, AJ van der Vlies, CP O’Neil, SS Yu, TD Giorgio, MA Swartz*, and JA Hubbell* (2011). Engineering complement activation on polypropylene sulfide vaccine nanoparticles. Biomaterials 32(8):2194-203. AC Shieh and MA Swartz (2011). Regulation of tumor invasion by interstitial fluid flow. Physical Biol. 8: 015012. M Ballester, C Nembrini, N Dhar, A de Titta, C de Piano, M Pasquier, E Simeoni, AJ van der Vlies, JD McKinney, JA Hubbell, and MA Swartz (2011). Nanoparticle conjugation and pulmonary delivery enhance the protective efficacy of Ag85B and CpG against tuberculosis. Vaccine 29:6959– 6966.

Team Members Postdoctoral Fellows Francesca Capotosti Witold Kilarski Amanda Lund Alexandra Magold Munson Jennifer Scott Ryan Oliver Jeremy Teo Susan Thomas

PhD Students Marie Ballester Marie Alexandre de Titta Manuel Fankhauser Esra Güç Laura Jeanbart Iraklis Kourtis Marco Pisano Sandeep Raghunathan Marcela Rincon-Restrepo Valentina Triacca Vokali Efthymia Master’s Students Iro Oikonomidi Sabrina Riedl Efthymia Vokali Research Associate Sachiko Hirosue Technicians Borel Véronique Corthésy Henrioud Patricia Foretay Didier Pasquier Miriella Visiting Fellows/Trainee Vidya Raghavan Vanessa Kennedy Renata Mezyk-Kopec Tú Nguyen Le Thanh (Trainee) Administrative Assistant Ingrid Margot

IBI - Institute of Bioengineering

C Nembrini, A Stano, KY Dane, M Ballester, A van der Vlies, BJ Marsland, MA Swartz*, and JA Hubbell* (2011). Nanoparticle conjugation of antigen enhances cytotoxic T cell responses in pulmonary vaccination. Proc. Natl. Acad. Sci. U.S.A. 108(44):E989-97 (*=equal contribution).

Human primary lymphatic endothelial cells exposed to physiological flow show extensive microtubular networks (green). Blue: cell nuclei, purple: podoplanin, red: F-actin red. Photo credit: Dr. Isabelle Magold.

EPFL School of Life Sciences - 2011 Annual Report

Wurm Lab

http://lbtc.epfl.ch/

IBI

Florian M. Wurm obtained his PhD in Genetics at the University of Giessen, Germany. After having worked for 5 years at Hoechst AG in Marburg, Florian joined Harvard Medical School and then in 1986 he joined Genentech Inc., San Francisco, holding leading positions in Process Sciences. Since 1995 he is professor of Biotechnology at the EPFL, and in 2008 he was appointed Visiting Professor at Jinan University in Guangzhou, China. He has published more than 200 scientific papers and holds more than 10 patents. He is the founder and CSO of ExcellGene SA, a Swiss biotechnology company in Monthey, Valais.

Florian M. Wurm Full Professor

Introduction

Research at the LBTC is situated on the crossroads between biology and engineering, and it addresses the expression of recombinant proteins from suspension cultures of mammalian cells, which is the major approach to therapeutic protein production. Mammalian cells are the most versatile and productive system for the manufacture of recombinant proteins. The major goal of the Laboratory of Cellular Biotechnology is the development of novel and/or improved tools for gene transfer to cultured mammalian cells and subsequent high-level expression of recombinant proteins from such cells in innovative and scalable production systems (bioreactors). We are investigating two major thematic areas: (1) gene delivery, integration and expression in animal cells and their respective impacts on the host cells physiology and genetics (2) orbital shaking technology and novel bioreactor systems.

Keywords

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

Results Obtained in 2011

Transient gene expression and stable transgene integration. The transient transfection approach allows to express a fully glycosylated recombinant protein at high titers (up to 1 g/L for IgGs in HEK-293 cells) only 2-3 weeks after gene cloning. We have studied the cellular uptake and disassembly of PEI-DNA complexes in mammalian cells, and by combining our knowledge of cellular metabolism in suspension cultures with our most recent results, we were able to increase recombinant protein productivity from transiently transfected cells. To study the stable integration of recombinant genes into the genome of a host cell we have focused on the Chinese hamster ovary cell line (CHO), which is the most widely used cell line in the industry. We have inves-

tigated the cytogenetics of CHO-derived stable cell lines generated using different DNA delivery techniques, including transposon-mediated and lentivirus-mediated gene integration. Understanding transgene integration at the molecular level will allow us to develop strategies to prevent the widely observed phenomenon of gene silencing, which lowers productivity in cell clones over time. We demonstrated that transposon (integrase) mediated DNA delivery is a very efficient method to generate high producing, stable CHO cell lines, and we proved the superiority of this technology compared to other gene transfer approaches. More recently, we extended our research to insect cells-based expression systems, and we are developing non-viral, scalable gene delivery methods for these hosts. The orbitally shaken (OrbShake) bioreactor technology for mammalian cell cultivation, designed in our lab, has been scaled-up to 1â&#x20AC;&#x2122;000 L. Orbitally shaken cylindrical vessels (with nominal volumes from 50 mL to 250 L) are being extensively studied in order to characterize the hydrodynamics of this type of agitated systems. A scale-up factor for the OrbShake bioreactors could be determined by mixing time analysis in small-scale experiments. In collaborations with Prof. Alfio Quarteroni (Chair of Modelling and Scientific Computing) and Dr. Mohamed Farhat of the Laboratory of Hydraulic Machines, a fluid dynamics model of the OrbShake bioreactor could be determined and tested. Overall, our research provided useful insights for understanding cell cultivation in suspension, gene integration and protein expression. These studies are of general interest in cellular biology and biotechnology.

EPFL School of Life Sciences - 2011 Annual Report

Rajendra Y., Kiseljak D., Baldi L., Hacker D. L. and Wurm F. M. (2011) Reduced glutamine concentration improves protein production in growth-arrested CHODG44 and HEK-293E cells. Biotechnology Letters, vol 34 (4): 619-626. Wurm F. M. and Hacker D.L. (2011) First CHO genome. Nature Biotechnology, vol 29 (8): 718-720. Tissot S., Oberbek A., Reclari M., Dreyer M., Hacker D. L. et al. (2011) Efficient and reproducible mammalian cell bioprocesses without probes and controllers? New Biotechnology, vol 28 (4): 382-390. Matasci M., Baldi L., Hacker D. L. and Wurm F. M. (2011) The PiggyBac transposon enhances the frequency of CHO stable cell line generation and yields recombinant lines with superior productivity and stability. Biotechnology and Bioengineering, vol 108 (9): 2141-2150. Rajendra Y., Kiseljak D., Baldi L., Hacker D. L. and Wurm F. M. (2011) A simple high-yielding process for transient gene expression in CHO cells. Journal of Biotechnology, vol 153 (1-2): 22-26. Xie Q., Michel P. O., Baldi L., Hacker D. L., Zhang X. and and Wurm F. M. (2011) TubeSpin bioreactor 50 for the high-density cultivation of Sf-9 insect cells in suspension. Biotechnology Letters, vol 33 (5): 897-902. Oberbek A, Matasci M, Hacker DL, Wurm FM. (2011) Generation of stable, high-producing CHO cell lines by lentiviral vector-mediated gene transfer in serum-free suspension culture. Biotechnol Bioeng vol 108 (3): 600-10. Wulhfard S, Baldi L, Hacker DL, Wurm F. (2010) Valproic acid enhances recombinant mRNA and protein levels in transiently transfected Chinese hamster ovary cells. J Biotechnol vol 148 (2-3): 128-32. Zhang XW, Garcia IF, Baldi L, Hacker DL, Wurm FM. (2010) Hyperosmolarity enhances transient recombinant protein yield in Chinese hamster ovary cells. Biotechnol Lett vol 32 (11): 1587-1592. Tissot S, Farhat M, Hacker DL, Anderlei T, Kühner M, Comninellis C, Wurm F. (2010). Determination of a scale-up factor from mixing time studies in orbitally shaken bioreactors. Biochem Eng J vol 52 (2-3): 181-186.

Team Members Senior Scientists Lucia Baldi David Hacker

Postdoctoral Fellow Patrik Olavi Michel PhD Students Sowmya Balasubramanian Divor Kiseljak Dominique Monteil Yashas Rajendra Xiao Shen Stéphanie Tissot Francesca Zagari Master Students Archita Chaudhary Riad Gacem Guillaume Lüthi Joao Pereira Ghimire Saroj Giulia Tontodonati Exchange Student Jake Yeung Laboratory Support Ione Gutscher Veronika Knapkova Trainees Clara Douet Sarah Grezet Mélanie Hubert Samjhana Thapa Technical Assistants Virginie Bachmann Gilles Broccard Administrative Assistant Fabienne Rudin

IBI - Institute of Bioengineering

Selected Publications

Chromosome spread of CHO K1 cell analyzed by confocal microscopy after staining with YOYO-1 (491/509). 3-D image reconstructed from 23 images (0.04 μm per section) (Picture from PO Michel)

Co-affiliated Research Groups EPFL School of Life Sciences - 2011 Annual Report

Aminian Lab -

coaffiliated

http://lmam.epfl.ch/

IBI

Kamiar Aminian received the M.S. degree in electrical engineering in 1982, the Ph.D degree in biomedical engineering in 1989 and the Postgraduate degree on technical computing in 1993 from EPFL. He is currently Professor of Medical Instrumentation and the Director of the Laboratory of Movement Analysis and Measurement in the Institute of Bioengineering of EPFL. He is a member of the International Society of Posture and Gait Research, the Institute of Electrical and Electronics Engineers, the European Society of Movement Analysis in Adults and Children, the Prevention of Falls Network Europe, the Intentional Society of Biomechanics and the future president of the 3D analysis of the human movement group.

Kamiar Aminian

Adjunct Professor School of Engineering (STI)

Research Interests

The Laboratory of Movement Analysis and Measurement investigates fundamental functions in human movement, sport science and locomotion that relate to health and disease. Performance or failure affecting the motor function is characterized in real world condition through a multidisciplinary approach involving wearable and implanted instrumentation, signal processing, biomechanics and clinical evaluation. This involves the design of advanced algorithms for the long-term monitoring and analysis of physical behaviour, measurement of 3D joint kinematics and kinetics of the movement and estimation of spatio-temporal parameters of locomotion. In sport science, performance evaluation is particularly studied in snow sports and aquatic locomotion. In clinics, the outcomes consist particularly to characterize failure affecting motor functions by identifying relevant disease/health related features hidden in human biomechanical signals. Based on these features new metrics are defined and validated to provide early diagnosis and objective clinimetry for outcome evaluation in orthopaedics and aging, to assess the change of motor function with pain, to detect motor failure in movement disorder such as stroke and Parkinson disease, and to analyse the frailty behaviour in elderly population in order to investigate appropriate intervention for disease prevention and rehabilitation.

Selected Publications

Rouhani, H., Favre, J., Crevoisier, X., and Aminian, K. (2011) Ambulatory measurement of ankle kinetics for clinical applications, Journal of Biomechanics, 44, 2712-2718. Aissaoui, R., Ganea, R., & Aminian, K. (2011). Conjugate momentum estimate using non-linear dynamic model of the sit-to-stand correlates well with accelerometric surface data. Journal of Biomechanics, 44(6), 1073-1077. Ganea, R., Paraschiv-Ionescu, A., Büla, C., Rochat, S., Aminian, K. (2011) Multiparametric Evaluation of Sit-to-Stand and Stand-to-Sit Transitions in Elderly People, Medical Engineering & Physics (33), 1086-1093. Rouhani, H., Favre, J., Crevoisier, X., & Aminian, K. (2011). Outcome evaluation of ankle osteoarthritis treatments: Plantar pressure analysis during long-distance walking, Clinical Biomechanics, 26(4), 397-404.

Mariani, B., Hoskovec, C., Rochat, S., Büla, C., Penders, J., & Aminian, K. (2010). 3D gait assessment in young and elderly subjects using foot-worn inertial sensors. Journal of Biomechanics, 43(15), 2999-3006. Favre, J., Crevoisier, X., Jolles, B. M., & Aminian, K. (2010). Evaluation of a mixed approach combining stationary and wearable systems to monitor gait over long distance. Journal of Biomechanics, 43(11), 2196-2202. Salarian, A., Horak, F. B., Zampieri, C., Carlson-Kuhta, P., Nutt, J. G., & Aminian, K. (2010). ITUG, a sensitive and reliable measure of mobility. IEEE Transactions on Neural Systems and Rehabilitation Engineering, 18(3), 303-310. Rouhani, H., Favre, J., Crevoisier, X., & Aminian, K. (2010). Ambulatory assessment of 3D ground reaction force using plantar pressure distribution. Gait and Posture, 32(3), 311-316.

Team Members Scientist Anisoara Ionescu

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

EPFL School of Life Sciences - 2011 Annual Report

Fantner Lab -

coaffiliated

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

Georg Fantner

Tenure Track Assistant Professor School of Engineering (STI)

Our research aims to advance nanoscale measurement technology for life-science applications, with a special focus on high-speed atomic force microscopy (HS-AFM). Towards this end, we work on the integration of high-speed AFM with super-resolution optical microscopy, micro-and nano-fluidics for high throughput AFM sample handling and NEMS cantilever design. Using these new technologies we study the structure of cell membranes and lipid modelmembranes with nanometer resolution, and can observe changes two orders of magnitude faster than previously possible with AFM. This high spatial and temporal resolution allows us to study how membrane-disrupting toxins, such as antimicrobial peptides, pore-forming toxins and antimicrobial polymers interact with the membrane. This technique can also be applied to study the action of enzymes such as Topoisomerase II on DNA. Other research interests include molecular interactions in organic/inorganic composites such as bone, and their contribution to bone fracture toughness. In bone, we have found a molecular level energy dissipation mechanism called the “sacrificialbond, hidden-length mechanism”, which protects bone against the formation of micro-fractures. Currently we are studying which factors (such as age and disease) can influence the sacrificial bonds, and if this mechanism is a potential target for therapeutic approaches against osteoporosis.

Selected Publications

Bozchalooi, I. S., Youcef-Toumi, K., Burns, D. J., & Fantner, G. E. (2011). Compensator design for improved counterbalancing in high speed atomic force microscopy. The Review of scientific instruments, 82(11), 113712. doi:10.1063/1.3663070.

Fantner, Georg E, Barbero, R. J., Gray, D. S., & Belcher, A. M. (2010). Kinetics of antimicrobial peptide activity measured on individual bacterial cells using highspeed atomic force microscopy. Nature nanotechnology, 5(4), 280-5. Nature Publishing Group. doi:10.1038/nnano.2010.29. Nam, Y. S., Shin, T., Park, H., Magyar, A. P., Choi, K., Fantner, G., Nelson, K. a, et al. (2010). Virus-templated assembly of porphyrins into light-harvesting nanoantennae. Journal of the American Chemical Society, 132(5), 1462-3. doi:10.1021/ja908812b.

Team Members Postdoctoral Fellows Jonathan Adams Blake Erickson PhD Students Maja Dukic Maksim Kazanskii Pascal Odermatt Master’s Students Cyrus Rashti Oliver Peric

IBI - Co-affiliated Research Groups

Research Interests

Administrative Assistant Ruth Fiaux

Burns, D. J., Youcef-Toumi, K., & Fantner, G. E. (2011). Indirect identification and compensation of lateral scanner resonances in atomic force microscopes. Nanotechnology, 22(31), 315701. doi:10.1088/0957-4484/22/31/315701.

EPFL School of Life Sciences - 2011 Annual Report

Guiducci Lab

- coaffiliated

http://clse.epfl.ch/

Carlotta Guiducci

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

Carlotta Guiducci holds a PhD in Electrical Engineering from the University of Bologna (I). She was a postdoc at the Nanobiophysics Lab at ESPCI ParisTech (F) sine 2007. In 2006 she presented with Infineon Technologies the first CMOS chip for DNA label- free electrical detection. In 2009, she joined the Institute of Bioengineering at EPFL, as Tenure-Track Assistant Professor with a double appointment at the Institute of Electrical Engineering. Since 2009, she coordinate the ISyPeM Nano-tera.ch project on therapeutic drug monitoring for personalized medicine. Recently, she served as invited lecturer at the IEEE Solid-State Circuits Conference and she was interviewed by the Journal Electronics Letters on the present and future role of semiconductor technologies in the health care area. She is Associate Editor of the ACM JETC.

Research Interests

The development of biochips based on the present and future electronic technologies of CMOS entails enormous potential and challenges. The Laboratory of Life Sciences Electronics (CLSE) is committed to providing new process technologies and measurements techniques to fully exploit the possibilities offered by electronics and microtechnologies in the life science domain. The team consists of an enthusiastic group of engineers in microtechnologies and electronics, bioengineers and pure biologists committed to address some of the key issues in the field of electronic biochips, such as wet environment compatibility, the integration of nanosensors and the development of devices for personalized medicine. In particular, we focus on micromachining and 3D integration solutions to enhance the robustness of the biochip surface, to develop hybrid electronic biochips with disposable parts and to develop microchannels with conductive pillars. Our technologies for electrode-based systems are applied to membrane-amyloids interaction studies and to cell-adhesion assays. Nanosensors such as silicon nanowires and plasmonic nanoislands are characterized and compared to standard sensing techniques for real-time label-free molecular detection. In the framework of the ISyPeM nano-tera.ch project, the laboratory addresses the development of aptamer-based sensor systems for the detection of small drugs in blood and for the personalized drug dose adjustment based on therapeutic drug monitoring approaches.

Selected Publications

Temiz, Y.; Kilchenmann, S.; Leblebici, Y.; Guiducci, C., “3D integration technology for lab-on-a-chip applications,” Electronics Letters, vol.47, no.26, pp.S22S24, December 22 2011. Temiz, Y.; Zervas, M.; Guiducci, C.; Leblebici, Y., “Die-level TSV fabrication platform for CMOS-MEMS integration,” Solid-State Sensors, Actuators and Microsystems Conference (TRANSDUCERS), 2011 16th International, vol., no., pp.1799-1802, 5-9 June 2011.

Guiducci, C.; Temiz, Y.; Leblebici, Y.; Accastelli, E.; Ferretti, A.; Cappi, G.; Bianchi, E., “Integrating bio-sensing functions on CMOS chips,” Circuits and Systems (APCCAS), 2010 IEEE Asia Pacific Conference on, vol., no., pp.548-551, 6-9 Dec. 2010. Bianchi, E., Boschetti, F., Dubini, G., and Guiducci, C. (2010). Model of an Interdigitated Microsensor to Detect and Quantify Cells Flowing in a Test Chamber. Proc. of the 6th annual COMSOL Conference, Paris, France, November 17-19 2010. Temiz, Y., Ferretti, A., Accastelli, E., Leblebici, Y., and Guiducci, C. (2010). Robust Microelectrodes Developed for Improved Stability in Electrochemical Characterization of Biomolecular Layers . Proc. of the 9th Annual IEEE Sensors Conference (Sensors’10), pages 1051-1055, Hawaii, USA, November 1-4, 2010. Guiducci, C., Temiz, Y., Leblebici, Y., Accastelli, E., Ferretti, A., Cappi, G., and Bianchi, E. (2010). Integrating Bio-sensing Functions on CMOS Chips, Proc. of Asia Pacific Conference on Circuits and Systems, Kuala Lumpur, Malaysia, December 6 – 9, 2010.

Team Members Postdoctoral Fellows Fabio Mario Spiga Elena Bianchi

PhD Students Enrico Accastelli Giulia Cappi Anna Ferretti Samuel Kilchenmann Yuksel Temiz Interships Enrica Rollo Valeiria Davì Marco Spinsanti Master’s Students Nadia Sarait Vertti Sophie Crettaz Administrative Assistant Homeira Salimi

IBI

EPFL School of Life Sciences - 2011 Annual Report

Hatzimanikatis Lab -

coaffiliated

http://lcsb.epfl.ch/

Associate Professor School of Basic Sciences (BS)

Research Interests

The Laboratory of Computational Systems Biotechnology (LCSB) focuses on the development of mathematical models and systems engineering frameworks for accelerating the design and purposeful manipulation of complex cellular processes. LCSB develops expertise in the formulation of mathematical models of cellular processes, in process systems engineering methods for the integration, and in the analysis of experimental information from different levels. As most of this information in biological systems is partial and it is subject to uncertainty, researchers in LCSB develop methods that can account quantitatively for the uncertainty in the available information and can provide guidance on solving problems in biotechnology and medicine. LCSB is one of the leading laboratories in the study of energetics and thermodynamics of complex cellular processes. Research in LCSB has also pioneered the development of computational methods for the discovery of novel metabolic pathways for metabolic engineering and synthetic biology. The applications areas of research in LCSB are: metabolic engineering and metabolic diseases, bioenergetics, protein synthesis, lipidomics, and drug discovery for infectious diseases.

Selected Publications

Integrating computational methods to retrofit enzymes to synthetic pathways. Brunk E, Neri M, Tavernelli I, Hatzimanikatis V and Rothlisberger U. Biotechnol Bioeng, EPUB 28 Sep 2011. Modeling of uncertainties in biochemical reactions. Miskovic L and Hatzimanikatis V. Biotechnol Bioeng, 108(2), 413-423 (2011). Manipulating redox and ATP balancing for improved production of succinate in E. coli. Singh A, Soh KC, Hatzimanikatis V and Gill RT. Metabol Eng, 13(1), 76-81 (2011). Thermodynamic Calculations for Biochemical Transport and Reaction Processes in Metabolic Networks. Stefan JJ, Kuemmel A, Hatzimanikatis V, Beard DA, and Heinemann M. Biophys J, 99 (10), 3139-3144 (2010). DREAMS of metabolism, Soh KC and Hatzimanikatis V, Trends Biotech, 28 (10), 501-508 (2010).

Production of biofuels and biochemical: in need of an ORACLE. Miskovic L and Hatzimanikatis V. Trends Biotech, 28 (8), 391-397 (2010). Network thermodynamics in the post-genomic era. Soh KC and Hatzimanikatis V. Curr Opin Microbiol., 13 (3), 350-357 (2010). In silico feasibility of novel biodegradaion pathways for 1,2,4-trichlorobenzene. Finley SD, Broadbelt LJ, and Hatzimanikatis V. BMC Sys Biol, 4:7, doi:10.1186/1752-0509-4-7 (2010). The Origins of Time-Delay in Template Biopolymerization Processes. Mier-y-Teran L, Silber M and Hatzimanikatis V, PLoS Comp Biol, Apr 1;6(4):e1000726 (2010). Discovery and analysis of novel metabolic pathways for the biosynthesis of industrial chemicals: 3-hydroxypropanoate. Henry CS, Broadbelt LJ and Hatzimanikatis V. Biotechnol Bioeng, 106(3), 462-473 (2010).

Team members Postdoctoral fellows Ho Ki Fung Georgios Savoglidis Marianne Seijo Katerina Zisaki

PhD students Mahdi Alemohammad Stefano Andreozzi Elizabeth Brunk James Clulow Noushin Hadadi Julien Racle Andrijana Radivojevic Maryam Sadat Zoee Keng Cher Soh Stepan Tymoshenko

IBI - Co-affiliated Research Groups

Vassily Hatzimanikatis

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

Research Associate Ljubisa Miskovic Bachelor/Master Students Flavien Morel Pascal Sutter Administrative Assistant Christine Kupper

EPFL School of Life Sciences - 2011 Annual Report

Ijspeert Lab -

coaffiliated

http://biorob.epfl.ch/

IBI

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

Auke Ijspeert

Associate Professor School of Engineering (STI)

Research Interests

Our research is at the intersection of robotics and computational neuroscience. It addresses the topics of movement control, sensorimotor coordination, and learning in autonomous robots with multiple degrees of freedom (from snake robots to quadruped robots to humanoid robots). Our ambition is two-fold: (1) to program and design robots that exhibit motor skills with the same efficiency, adaptivity, and robustness as animals, and (2) to get a better understanding of the functioning of animals using numerical simulation and robots as scientific tools. Together with neurobiologists (Jean-Marie Cabelguen and Sten Grillner), we have developed mathematical models of the neural circuits controlling locomotion in lower vertebrates. We have demonstrated how a primitive neural circuit for swimming like the one found in the lamprey can be extended by phylogenetically more recent limb oscillatory centers to explain the ability of salamanders to switch between swimming and walking. These models have been tested in an innovative salamander-like robot capable of swimming and walking. We also develop a dynamical systems approach for controlling movements in robots. For instance, we designed the concept of dynamical movement primitives: nonlinear dynamical systems with well-defined attractor properties that can learn demonstrated discrete or rhythmic movements. Our methods are applied to various robots (quadruped, humanoid and reconfigurable modular robots) and more recently to lower limb exoskeletons for patients with locomotor deficiencies.

Selected Publications

R. Ronsse, N. Vitiello, T. Lenzi, J. van den Kieboom and M. C. Carrozza et al. Human-Robot Synchrony: Flexible Assistance Using Adaptive Oscillators, IEEE Transactions On Biomedical Engineering, vol. 58, p. 1001-1012, 2011. S. Dégallier Rochat, L. Righetti, S. Gay and A. Ijspeert. Towards simple control for complex, autonomous robotic applications: Combining discrete and rhythmic motor primitives, Autonomous Robots, vol. 31, num. 2, p. 155-181, 2011.

D. Ryczko, V. Charrier, A. Ijspeert and J.-M. Cabelguen. Segmental Oscillators in Axial Motor Circuits of the Salamander: Distribution and Bursting Mechanisms, Journal of Neurophysiology, vol. 104, p. 2677-2692, 2010. S. Dégallier and A. Ijspeert. Modeling Discrete and Rhythmic Movements through Motor Primitives: A Review, Biological Cybernetics, vol. 103, num. 4, p. 319-338, 2010. A. Spröwitz, S. Pouya, S. Bonardi, J. van den Kieboom, R. Möckel, A. Billard, P. Dillenbourg, A.J. Ijspeert. Roombots: Reconfigurable Robots for Adaptive Furniture, IEEE Computational Intelligence Magazine, 5(3): 20-32, 2010. Ijspeert A.J., Central pattern generators for locomotion control in animals and robots: a review. Neural Networks, 21(4):642-653, 2008. Buchli J., Righetti L., and Ijspeert A.J.. Frequency Analysis with a Nonlinear Dynamical System, Physica D, 237: 1705–1718, 2008. Sproewitz A., Moeckel R., Maye J., Ijspeert A.J., Learning to move in modular robots using central pattern generators and online optimization. International Journal of Robotics Research. 27(3-4):423-443, 2008. Ijspeert A.J., Crespi A., Ryczko D., and Cabelguen J.M.. From swimming to walking with a salamander robot driven by a spinal cord model. Science, 315(5817):1416-1420, 2007. Righetti L., Buchli, J. and Ijspeert A.J.: Dynamic Hebbian learning in adaptive frequency oscillators, Physica D, 216(2), 2006 pp 269-281.

Team Members

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

EPFL School of Life Sciences - 2011 Annual Report

Johnsson Lab

- coaffiliated

http://lip.epfl.ch/

Kai Johnnson

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

Full Professor School of Basic Sciences (SB)

Research Interests

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

Selected Publications

“A yeast-based screen reveals that sulfasalazine inhibits tetrahydrobiopterin biosynthesis” Christopher Chidley, Hirohito Haruki, Miriam Gronlund Pedersen, Evelyne Muller, Kai Johnsson, Nature Chemical Biology, 7, 375-83 (2011). “Semisynthesis of fluorescent metabolite sensors on cell surfaces” Matthias A. Brun, Rudolf Griss, Luc Reymond, Kui-Thong Tan, Joachim Piguet , Ruud Peters, Horst Vogel, Kai Johnsson, J. Am. Chem. Soc., 133, 16235-42 (2011). “Benzothiazinones are prodrugs that covalently modify the decaprenylphosphoryl-ß-D-ribose 2’-epimerase DprE1 of Mycobacterium tuberculosis” Claudia Trefzer, Monica Rengifo-Gonzalez, Marlon J. Hinner, Patricia Schneider, Vadim Makarov, Stewart T. Cole, Kai Johnsson, J. Am. Chem. Soc., 132,13663-5 (2010). “A Targetable and Highly Sensitive Calcium Indicator based on BODIPY-fluorophore” Mako Kamiya, Kai Johnsson, Analytical Chemistry, 82, 6472-9 (2010). “Photoactivatable and photoconvertible fluorescent probes for protein labeling” Damien Maurel, Sambashiva Banala, Thierry Laroche, Kai Johnsson, ACS Chemical Biology 5, 507-16 (2010).

Currently, we are interested in the following topics:

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

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

IBI - Co-affiliated Research Groups

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

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

EPFL School of Life Sciences - 2011 Annual Report

Jolles-Haeberli Lab

- coaffiliated

http://cbt.epfl.ch/

IBI

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

Brigitte Jolles-Haeberli

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

Research Interests

We promote and support the transfer of findings from the basic science laboratory to clinical application with a strong relationship between clinicians and engineers for each specific project. We develop medical devices and wearable systems to characterize human mobility and locomotion in daily conditions. Based on these instruments, we provide objective clinical metrics for diagnosis and outcome evaluation of treatments as well as useful parameters to increase sport performances. We also carry out work in tissue engineering of musculoskeletal tissues, implant and joints biomechanics, drug delivery systems and mechanobiology. A combination of biomechanical and biological approaches is used to describe and understand different clinical problems of interest such as bone loss following total joint arthroplasty, arthritis or intervertebral disc degeneration. Based on these analyses, original solutions are developed such as fetal cell therapy, scaffolds with high mechanical properties or orthopaedic implants used as drug delivery systems.

Hirt-Burri N, Ramelet AA, Raffoul W, de Buys Roessingh A, Scaletta C, Pioletti D, Applegate LA. Biologicals and fetal cell therapy for wound and scar management. Dermatol. 2011;2011:549870. Roshan-Ghias A, Lambers FM, Gholam-Rezaee M, MĂźller R, Pioletti DP. In vivo loading increases mechanical properties of scaffold by affecting bone formation and bone resorption rates. Bone. 2011 Dec;49(6):1357-64.

Center Groups Aminia Lab Pioletti Lab

Administrative Assistant Sabrina Martone

Selected Publications

Favre J, Crevoisier X, Jolles BM, Aminian K. Evaluation of a mixed approach combining stationary and wearable systems to monitor gait over long distance. J Biomech. 2010; 43(11): 2196-202. Rouhani H, Favre J, Crevoisier X, Jolles BM, Aminian K. Segmentation of foot and ankle complex based on kinematic criteria.Comput Methods Biomech Biomed Engin. 2011; 14(9):773-81. Jolles BM, Aminian K, Coley B, Pichonnaz C, Bassin JP, Leyvraz PF, Farron A. Objective evaluation of shoulder function using body-fixed sensors: a new way to detect early treatment failures? J Shoulder Elbow Surg. 2011; 20(7):1074-81.

EPFL School of Life Sciences - 2011 Annual Report

Lacour Lab

- coaffiliated

http://lsbi.epfl.ch/ Stéphanie P. Lacour is an Assistant Professor at the EPFL, affiliated with the Institutes of Microengineering and Bioengineering. She received her PhD in Electrical Engineering from INSA de Lyon, France, and completed postdoctoral research at Princeton University, USA and the University of Cambridge, UK. She has pioneered the development of stretchable electronics, demonstrating elastic metallization and the first stretchable electronic circuit, and was named to the “Top 35 Innovators under the age of 35” by MIT Technology Review in 2006. She was awarded a University Research Fellowship from the Royal Society in 2007 and the Zonta Award in 2011 for her research achievement as a young female academic.

Stéphanie P. Lacour

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

The Laboratory for Soft Bioelectronics Interfaces (LSBI) explores how to shape traditionally rigid electronic circuits into conformable, skin-like formats. Our mission is to engineer and implement novel materials and technologies overcoming the “hard to soft” mechanical mismatch between man-made devices and biological tissues. We currently have two main activities: tactile electronic skins and soft neural electrodes. Both systems are fabricated using standard microfabrication processes but adapted to mechanically compliant silicone substrate. Tactile e-skins are designed to conform a robotic or prosthetic hand and provide distributed sensory feedback (pressure, shear and strain). Ultra-compliant neural electrodes are designed for in vitro platforms combining mechanical stimulation and electrophysiology, surface microelectrode arrays to conform the surface of the spinal cord or the brainstem, and regenerative peripheral nerve implants.

Selected Publications

Delivopoulos D., Chew D., Minev I.R., Fawcett J.W. and Lacour S.P. (2012) Concurrent recordings of bladder afferents from multiple nerves using a microfabricated PDMS microchannel electrode array. Lab on Chip, 2012, DOI: 10.1039/C2LC21277C. FitzGerald J.J., Lago N., Benmerah S., Serra J., Watling C.P., Cameron R.E., Tarte E., Lacour S.P., McMahon S.B. and Fawcett J.W. (2012) A regenerative microchannel neural interface for recording from and stimulating peripheral axons in vivo. Journal of Neural Engineering 9:016010. Minev I.R., Chew D.J., Delivopoulos E., Fawcett J.W. and Lacour S.P. (2012) High sensitivity recording of afferent nerve activity using ultra-compliant microchannel electrodes: an acute in vivo validation. Journal of Neural Engineering 9:026005.

Lacour S.P., Graz I.M., Bauer S., Wagner S. (2011) Elastic components for prosthetic skin. Conf Proc IEEE Eng Med Biol Soc. 2011 8373-6. Graz I.M., Cotton D.P.J., Robinson A., Lacour S.P. (2011) Silicone substrate with in situ relief for stretchable thin-film transistors. Applied Physics Letters, 98:124101. Lacour S.P., Benmerah S., Tarte E., FitzGerald J., Serra J., McMahon S., Fawcett J., Graudejus O.,Yu Z. and Morrison III B. (2011) Flexible and stretchable micro-electrodes for in vitro and in vivo neural interfaces, Medical & Biological Engineering & Computing 48, 945-954.

Team Members

Postdoctoral Fellows Katherine Musick Tom Oppenheim Hugues Vandeparre Evangelos Delivopoulos Atif Aziz Adam Robinson

IBI - Co-affiliated Research Groups

Research Interests

PhD students Ivan Minev Cédric Paulou Alessia Romeo Masters Student Amélie Guex Administrative Assistant Carole Weissenberger

EPFL School of Life Sciences - 2011 Annual Report

Maerkl Lab

- coaffiliated

http://lbnc.epfl.ch/

IBI

Sebastian Maerkl obtained a PhD degree from the California Institute of Technology in 2008. His thesis on “Microfluidic Large Scale Integration and its Application to Systems Biology” received the Demetriades-Tsafka-Kokkalis Prize for the best Caltech PhD thesis in Biotechnology. In the same year, Prof. Maerkl accepted a tenure track assistant professorship at the EPFL, where he is currently running a lab consisting of 3 Post-Docs and 6 PhD students. Prof. Maerkl coaches the EPFL iGEM team and teaches a masters level course on Genome & Network Architecture.

Sebastian Maerkl

Tenure Track Assistant Professor School of Engineering (STI)

Research Interests

The Maerkl lab is principally interested in developing highly integrated microfluidic devices and applying these to pertinent problems in biology. Of particular interest to the lab are systems biology, synthetic biology, and diagnostics, which will benefit tremendously from the development of novel, high-throughput technologies. We are actively developing methods for single cell analysis in S.cerevisiae and S.pombe, as well as M.smegmatis in collaboration with the McKinney Lab (SV/GHI). Using these methods, we are interested in characterizing global protein expression dynamics on the single cell level (S.cerevisiae), understand how genotypic variants affect fitness (S.pombe), and discover leads towards understanding and possibly counteracting bacterial persistence (M.smegmatis). The lab is also interested in understanding transcriptional regulatory networks by developing and characterizing promoter variants in vivo, as well as through the biophysical characterization of transcription factors in vitro.

Team Members Postdoctoral Fellows Luis Miguel Fidalgo Jose Garcia-Cordero

PhD Students Matthew Blackburn Nicolas Denervaud Henrike Niederholtmeyer Jean-Bernard Nobs Arun Rajkumar Sylvie Rockel Administrative Assistant Helen Chong

Selected Publications

Schultzaberger R.K., Maerkl S.J., Kirsch J.F. and M.B. Eisen (2012). ”Probing the Informational and Regulatory Plas- ticity of a Transcription Factor DNA-Binding Domain.” accepted to PLoS Genetics.. He B., Holloway A., Maerkl S.J., and Kreitman M. (2011). “Does positive selection drive transcription factor binding site turnover? A test with Drosophila cisregulatory modules.” PLOS Genetics 7(4): e1002053. Fidalgo L.M., and Maerkl S.J. (2011). “A software-programmable microfluidic device for automated biology.” Lab on a Chip 11: 1612-19. Geertz M., and Maerkl S.J. (2010). “Experimental strategies for studying transcription factor-DNA binding specificities.” Briefings in Functional Genomics doi:10.1093/bfgp/elq023. Maerkl S.J. (2010). “Next generation microfluidic platforms for high-throughput protein biochemistry.” Current Opinion in Biotechnology 22(1): 59-65.

EPFL School of Life Sciences - 2011 Annual Report

Mermod Lab -

coaffiliated

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

Full Professor IBI-UNIL

Research Interests

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

Team Members Postdoctoral Fellows Niko Niederländer Stéphanie Renaud Stefania Puttini Niamh Harraghy Elena Aritonovska Christophe Debonneville Maxime Albesa PhD students Ruthger van Zwieten Stefano Majocchi Deborah Ley Simone Edelmann Kaja Kostyrko Yaroslav Shcherba Matthias Contie

• Characterization and modeling of regulatory genomic regions in cancer

Master’s student Arnaud Rivier

• Development of more efficient and safer vectors for gene and stem cell-based therapies

Engineers Etienne Lançon

Plasari G, Edelmann S, Hogger F, Dusserre Y, Mermod N and Calabrese A. (2010) Nuclear Factor I-C regulates TGF-beta-dependent hair follicle cycling. J Biol. Chem. 285:34115–34125.

Technicians and informaticians Yves Dusserre Jacqueline Masternak Ionie Gutscher Armindo Texeira Daniel Peter

Buceta M, Galbete JL, Kostic C, Arsenijevic Y, and Mermod N. (2011). Use of human MAR elements to improve retroviral vector production. Gene Ther. 18:7-13.

Apprentice Alessia Cochard

Kerschgens J, Renaud S, Grasso L, Egener-Kuhn T, Delaloye JF, Lehr HA, Vogel H and Mermod N. (2011). Detection and analysis of tumor suppressor AP-2α DNA binding activity by protein-binding microarrays. PLOS One, 6:e22895.

Administrative Assistant Nassim Berberat

Selected Publications

IBI - Co-affiliated Research Groups

Nicolas Mermod

Nic Mermod did his PhD on bacterial gene regulation and environmental biotechnology with Ken Timmis at the University of Geneva. As a postdoc with Bob Tjian at the University of California at Berkeley, he identified and characterized some of the first mammalian transcription factors. He then joined the University of Lausanne as an assistant Professor fellow of the Swiss National Science Foundation, to become full professor and director of the Institute of Biotechnology. Nic heads a laboratory of 25 scientists at the Center for Biotechnology of the University of Lausanne and of the Swiss Institute of Technology Lausanne (EPFL). He is also co-founder of Selexis SA, a biotechnology company developing therapeutic-producing cell lines. His research bridges fundamental work on genomics and epigenetics to molecular biotechnology and gene and cell therapies. Nic has authored a number of scientific publications and patents.

Pjanic M, Pjanic P, Schmid C, Ambrosini G, Gaussin A, Plasari G, Mazza C, Bucher P, and Mermod N. (2011). Nuclear factor I revealed as family of promoter binding transcription activators. BMC Genomics, 12:181. Grandjean M, Girod P-A, Calabrese D, Wicht M, Beckman JS, Martinet D and Mermod N. (2011). High-level transgene expression by homologous recombination-mediated gene transfer. Nucl. Acids Res., 39:e104. Harraghy N, Regamey A, Girod PA, and Mermod N. (2011). Identification of a potent MAR element from the mouse genome and assessment of its activity in stable and transient transfections. J. Biotechnol. 154:11-20.

EPFL School of Life Sciences - 2011 Annual Report

Millán Lab

- coaffiliated

http://cnbi.epfl.ch/

IBI

José del R. Millán explores the use of brain signals for multimodal interaction and, in particular, the development of brain-controlled robots and neuroprostheses. In this multidisciplinary research effort, Dr. Millán is bringing together his pioneering work on the two fields of brain-machine interfaces (BMI) and adaptive intelligent robotics. He received his Ph.D. in computer science from the Univ. Politècnica de Catalunya (Barcelona, Spain) in 1992. Among other honors, his research on BMI was nominated finalist of the European Descartes Prize 2001 and he has been named Research Leader 2004 by the journal Scientific American for his work on brain-controlled robots.

José del Rocio Millán

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

Research Interests

The Defitech Foundation Chair in Non-Invasive BrainMachine Interface (CNBI) carries out research on the direct use of human brain signals for controlling devices and interacting with the environment. In this multidisciplinary research, CNBI is bringing together its pioneering work in the two fields of brain-machine interfaces and adaptive intelligent robotics. A brain-machine interface (BMI) monitors a subject’s brain activity, extracts specific features from the brain signals that reflect his/her intent, and translates these features into actions —such as moving a wheelchair or selecting a letter from a virtual keyboard, without use of muscles or peripheral nerves. CNBI focuses on non-invasive methods for recording brain activity, in particular using electroencephalographic (EEG) signals recorded from electrodes placed on the scalp. The goal of CNBI is to develop principled methods to design intelligent brain-actuated devices that people can efficiently operate them in a natural and intuitive manner over long periods of time. Such neuroprosthetic devices allow interaction by exploiting brain signals associated to different aspects of voluntary behavior.

Selected Publications

A. Tzovara, M. Murray, N. Bourdaud, R. Chavarriaga, J. d. R. Millán and M. De Lucia. The timing of exploratory decision-making revealed by single-trial topographic EEG analyses. Neuroimage, vol. 4, num. 1, 2012. R. Leeb, H. Sagha, R. Chavarriaga and J. d. R. Millán. A hybrid BCI based on the fusion of EEG and EMG activities.in Journal of Neural Engineering, vol. 8, num. 2, 2011. G. R. Müller-Putz, C. Breitwieser, F. Cincotti, R. Leeb, M. Schreuder, F. Leotta, M. Tavella, L. Bianchi, A. Kreilinger, A. Ramsay, M. Rohm, M. Sagebaum, L. Tonin, C. Neuper and J. d. R. Millán. Tools for brain-computer interaction: a general concept for a hybrid BCI. in Frontiers in Neuroinformatics, vol. 5, num. 30, 2011.

A. Biasiucci, R. Chavarriaga Lozano, B.Hamner, R. Leeb, F. Pichiorri, F. De Vico Fallani, D. Mattia and J. d.. R. Millán. Combining Discriminant and Topographic Information in BCI: Preliminary, Results on Stroke Patients. IEEE EMBS Conference on Neural Engineering, Cancún, Mexico, April 27 - May 1, 2011. G. Garipelli, R. Chavarriaga and J. d. R. Millán. Single Trial Recognition of Anticipatory Slow Cortical Potentials: The Role of Spatio-Spectral Filtering. IEEE EMBS Conference on Neural Engineering, Cancun, Mexico, April 27-May 1, 2011.

Team Members Senior Post doctoral Fellow Ricardo Chavarriaga Postdoctoral Fellows Tom Carlson Sarah Degallier Robert Leeb Aleksander Sobolewski PhD Students Andrea Biasiucci Nicolas Bourdaud Zahra Khaliliardali Mohit K. Goel Eileen Y.L. Lew Serafeim Perdikis Sareh Saeidi Hesam Sagha Michele Tavella Luca Tonin Marija Uscumlic Huaijian Zhang Visiting Researcher Lucian Gheorghe Administrative Assistant Najate Guechoul

L. Tonin, T. E. Carlson, R. Leeb and J. d. R. Millán. Brain-Controlled Telepresence Robot by Motor-Disabled People. IEEE Engineering in Medicine and Biology Society (EMBC’11), Boston, USA, 2011.

EPFL School of Life Sciences - 2011 Annual Report

Pioletti Lab

- coaffiliated

http://lbo.epfl.ch/ Dominique Pioletti received his Master in Physics and obtained his PhD in biomechanics in 1997 from the EPFL. He developed original constitutive laws taking into account viscoelasticity in large deformations. Then he did a post-doc at UCSD focusing on osteoblast reaction to different implant surface types. Since April 2006, Dominique Pioletti is appointed Assistant Professor tenure-track at the EPFL and is director of the Laboratory of Biomechanical Orthopedics. His research topics include biomechanics and tissue engineering of musculo-skeletal tissues; mechano-transduction in bone; development of orthopedic implant as drug delivery system.

Dominique P. Pioletti

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

The research interests of the LBO are in the fields of tissue engineering, joint and implant biomechanics, mechano-transduction, and drug delivery system. By combining these different fields, we use biomechanics to functionalize tissue engineering scaffolds and drug delivery systems for musculo-skeletal applications. The final goal of our research is to translate the obtained results into clinical applications. We have been pioneer in the development of orthopedic implant as drug delivery system. In particular, we have developed a technique allowing to decrease the peri-implant bone loss following the implantation of a prosthesis. This result is now translated into a clinical product with the collaboration of a large orthopedic company. In parallel, we have developed different strategies for bone or cartilage tissue engineering. The originality of our approach is to combine the intrinsic in vivo mechanical loading to the development of scaffold with the goal of rendering the scaffold more osteoinductive for the bone application.

Selected Publications

Roshan Ghias A., Vogel A., Rakotomanana L., Pioletti D.P. Prediction of spatiotemporal bone formation in scaffold by diffusion equation. Biomaterials, 32, 7006-7012, 2011. Stadelmann V. A., Bonnet N., Pioletti D.P. Combined effects of zoledronate and mechanical stimulation on bone adaptation in an axially loaded mouse tibia, Clinical Biomechanics, 26, 101-105, 2011. Roshan Ghias A., Lambers F., Gholam-Rezaee M., Müller R., Pioletti D.P. In vivo loading increases mechanical properties of scaffold by affecting bone formation and bone resorption rates. Bone, 49, 1357-1364, 2011. Gortchacow M, Wettstein M., Pioletti D.P. Terrier A. A new technique to measure micromotion distribution around a cementless femoral stem, J Biomechanics, 44, 557-560, 2011. Blecha L.D., Rakotomanana L., Razafimaheri F., Terrier A., Pioletti D.P. Mechanical interaction between cells and fluid for bone tissue engineering scaffold: modulation of the interfacial shear stress. J Biomechanics, 43, 933-937, 2010.

Team Members Group leaders Alexandre Terrier

Postdoctoral Fellows Xabier Larrea Hicham Majd Lab assistants Sandra Jaccoud Corinne Scaletta (UNIL/CHUV) Engineers Tanja Hausherr Damien Joss Patricia Scheuber Julien Ston PhD students Philippe Abdel-sayed Salim Darwich Christoph Anselm Engelhardt Sohrab Emami Naeini Michael Gortchacow Anthony Grognuz (UNIL/CHUV) Jérôme Hollenstein (UCSD) Ulrike Kettenberger Adeliya Latypova Mohamdreza Nassajian Moghadam Alireza Roshan Ghias Marion Röthlisberger Arne Vogel Medical Advisors Martin Broome, P.D. Xavier Crevoisier, P.D. Alain Farron Brigitte Jolles-Haeberli Wassim Raffoul Hannes Rudiger, P.D. Constantin Schizas. P.D. Pierre-Yves Zambelli

IBI - Co-affiliated Research Groups

Research Interests

Administrative Assistant Virginie Kokocinski

Krattinger N., Applegate L.A., Biver E., Pioletti D.P., Caverzasio J. Regulation of proliferation and differentiation of human fetal bone cells. e Cells Materials, 21, 46-58, 2011.

EPFL School of Life Sciences - 2011 Annual Report

Psaltis Lab

- coaffiliated

http://lo.epfl.ch/

IBI

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

Demetri Psaltis

Full Professor Dean of the School of Engineering (STI)

Research Interests

Holography is the most persistent thread in Demetri Psaltis’ research. It goes back to his PhD thesis work on invariant pattern recognition using the Mellin transform which he demonstrated holographically. His work on optical neural networks (which originated as collaboration with Nabil Farhat) established a link between adaptive volume holography and Hebbian learning in the nervous system. His work on holographic memories in the late 80’s and early 90’s spearheaded the rebirth of the field. His recent work on holographic filters for telecommunications and other applications was featured on the cover of Science in November 2002 and it has led to commercialization of this technology. In recent years, Demetri Psaltis’ research has moved towards nonlinear optics.

Team Members Post-doctoral Fellows Andreas Vasdekis Jae-Woo Choi Marcin Zielinski Salma Farahi Ye PU PhD students Alexandre Goy Grégoire Laporte Ioannis Papasopoulos Julien Cuennet Thomas Lanvin Wuzhou Song Xin Yang Administrative Assistant Carole Berthet

Selected Publications

“Optofluidics for energy applications”, Erickson D, Sinton D, Psaltis D - Nature Photonics, Vol. 5, pp. 583-590, October 2011. “Imaging withsecond-harmonic radiation probes in living tissue” Grange R, Lanvin T, Hsieh CL, Pu Y, Psaltis D - Biomedical Optics Express, Vol. 2, pp. 2532-2539, August 2011. “Imaging with second-harmonic radiation probes in living tissue” Grange R, Lanvin T, Hsieh CL, Pu Y, Psaltis D - Biomedical Optics Express, Vol. 2, pp. 2532-2539, August 2011. “Optofluidic modulator based on peristaltic nematogen microflows” J.G.Cuennet**, A.E. Vasdekis*, L. De Sio, Psaltis D. (*Equivalent first authors) – Nature Photonics, Vol5, pp 234-238, February 2011. “Nonlinear optical properties of core-shell nanocavities for enhanced secondharmonic generation” - Pu Y, Grange R, Hsieh CL, Psaltis D - Physical Review Letters, Vol. 104, Art. 207402, May 2010. “Coherent anti-Stokes Raman holography for chemically selective single-shot nonscanning 3D imaging” Shi K, Li H, Xu Q, Psaltis D, Liu Z - Physical Review Letters, Vol. 104, Art. 093902, March 2010.

EPFL School of Life Sciences - 2011 Annual Report

Radenovic Lab -

coaffiliated

http://lben.epfl.ch/

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

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

Research Interests

The research of the Laboratory of Nanoscale Biology focuses on developing tools and probes for single-molecule biophysics. The group uses optical tweezers, AFM, singlemolecule fluorescence, PhotoActivated Light microscopy PALM and nanofabricated structures to study biomolecular systems and advance new nanotechnology techniques. Current experimental work in our lab focuses on two interconnecting areas: Nanofabricated probes and platforms for single-molecule biophysics experiments: Including nanofabricated SHG nanocylinders, solid-state nanopores, local nanolectrodes for molecular sensing and sequencing. Local probe studies of single biomolecules: For example RNA polymerase, DNA binding proteins, membrane proteins such G protein–coupled receptors (GPCRs).

Team Members Postdoctoral Fellows Husale Sudhir Scarselli Marco Steinbock Lorentz Traversi Floriano PhD Students Annibale Paolo Brando Serena Dutto Fabrizia Kayci Metin Raillon Camille Arun Shivanandan Master’s students Garcia Cordero Eric Mattia Greco Administrative Assistant Chong Helen

Selected Publications

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

IBI - Co-affiliated Research Groups

Identification of clustering artifacts in photoactivated localization microscopy P. .Annibale, S. Vanni, M. Scarselli, U. Rothlisberger and A. Radenovic Nature Methods (2011). Single-layer MoS2 transistors B. Radisavljevic, A. Radenovic, J. Brivio, V. Giacometti, A. Kis1* Nature Nanotechnology Volume:6,147–150 (2011) cover article Nonlinear Optical Response in Single Alkaline Niobate Nanowires F. Dutto, C. Raillon, K.Schenk and A. Radenovic Nano Letters., 2011, 11 (6), pp 2517–252. Quantitative Photo Activated Localization Microscopy: unraveling the effects of photoblinking P. Annibale, S. Vanni, M. Scarselli, U. Rothlisberger and A. Radenovic PloS One July 2011, Volume 6, Issue 7, e2267.

EPFL School of Life Sciences - 2011 Annual Report

Roke Lab -

coaffiliated

http://lbp.epfl.ch/

Sylvie Roke

IBI

Sylvie Roke received her bachelor’s degree in chemistry and physics at Utrecht University (NL, highest honors) and her PhD degree from Leiden University (highest honors) in the field of nonlinear optics. In 2005 she obtained a Max-Planck Group Leader position and Research Group. Professor Roke was awarded an ERC startup grant (2009), and in 2010 she became a fellow of the Young Academy of the German Academy of Sciences. In April 2011 she started the Laboratory for Fundamental BioPhotonics (LBP) as a tenure track Assistant Professor at the EPFL, School of Engineering. She has been awarded the LJ Oosterhoff prize (2003), an Alexander von Humboldt Fellowship (2005), the Minerva Prize (FOM, NL, 2006) and the Hertha Sponer prize (DPG, DE,2008).

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

Research Interests

Life occurs in three dimensions. Living cells and organelles, such as the nucleus, mitochondria and ribosomes require membranes for protection and as vital part of their production units. Viruses consist of capsides that can self assemble into nanoscopic projectiles, ready to deliver DNA or RNA to the next willing host. This illustrates the complexity of small biological systems. The ability to respond, adapt and reform according to the needs of the specific molecular environment is enormous. If we could harness those abilities a huge leap in technological performance from the nanosciences to the life sciences is possible. Currently our understanding of soft biological systems is limited to macro- or microscopic theories. Molecular understanding is often absent. To change this and to arrive at tomorrows’ diagnostics we work on four main themes: • The investigation of structure and properties of biologically and medically relevant interfaces (supported lipid bilayers, biopolymer interfaces, water, protein-surface interactions). • Development of theory for nonlinear light scattering techniques to understand fundamental light matter interaction processes. • Development of experimental methods for nonlinear light scattering and microscopy. These techniques are ‘tomorrows’ diagnostics’ for biomedical research. IV. In-situ probing of nanodroplets, liposomes, and biological or living systems with particular interest in interfaces, ultrafast processes, and 3D self-assembly.

Selected Publications

Vacha, R., Rick S., Jungwirth P., de Beer A. G. F., de Aguiar H. B., Samson J-S and Roke S. The structure and charge of water around a surfactant free oil in water emulsion. J. Am. Chem. Soc 2011, 133 (26),10204–10210. de Beer A. G. F., Samson J-S, Hua W., Huang Z., Chen X., Allen H. C. and Roke S. A direct comparison of Phase-Sensitive Vibrational Sum Frequency generation with the Maximum Entropy Method: a case study of water. J. Chem. Phys 135, 224701 (2011).

de Beer A. G. F., Roke S. and Dadap J. I. Second-order nonlinear light scattering: of arbitrarily shaped particles. J. Opt. Soc. Am. B 2011, 28, 1374-1384 . Strader M. L., de Aguiar H. B., de Beer A. G. F. and Roke S. Direct detection of vesicle bilayer asymmetry in catanionic vesicles using vibrational sum frequency scattering. Soft Matter 2011, 7 (10), 4959 – 4963 . de Aguiar H. B., Strader M. L., de Beer A. G. F. and Roke S. Surface structure of SDS Surfactant and oil at the oil-in-water droplet liquid/liquid interface: A manifestation of a non-equilibrium surface state. J. Phys. Chem. B 2011, 115, 2970-2978 . de Beer A. G. F., Campen R. K. and Roke S. Separating surface structure and surface charge with second-harmonic and sum-frequency scattering. Phys. Rev. B, 2010, 82, 235431. de Aguiar H. B., de Beer A. G. F., Strader M. L. and Roke S. The Interfacial Tension of Nanoscopic Oil Droplets in Water Is Hardly Affected by SDS Surfactant. J. Am. Chem. Soc 2010, 132, 2122-2123. de Beer A. G. F. and Roke S. Obtaining molecular orientation from second harmonic and sum frequency scattering experiments: angular distribution and polarization dependence. J. Chem. Phys 2010, 132, 234702-1-8.

Team Members Postdoctoral Fellows Nikolaos Gomopoulos Kailash C. Jena Carlos Macias-Romero PhD Students Yixing Chen Cornelis Luetgebaucks Ekaterina Rostova Rüdiger Scheu Qinchao Sun Research Assistants Benjamin Hamner Guillaume Monnard Administrative Assistant Dominique Widmer

EPFL School of Life Sciences - 2011 Annual Report

Stergiopulos Lab -

coaffiliated

http://lhtc.epfl.ch/ Nikos Stergiopulos studied Mechanical Engineering at the National Technical University of Athens, Greece and obtained his Ph.D. in Biomedical Engineering from Iowa State University in 1990. His research interests are Hemodynamics, Cardiovascular Mechanics and Medical Implant Technology. He has authored more than 120 publications and holds more than 15 patents in medical technology. He co-founded EndoArt, world leader in telemetric implants for the treatment of congenital heart disease and morbid obesity, Antlia SA, developer of implantable drug delivery pumps and Rheon Medical, developer of the implantable shunt for the surgical treatment of glaucoma.

Nikos Stergiopulos

Full Professor School of Engineering (STI)

Research Interests

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

Selected Publications

Tsamis A, Rachev A, and Stergiopulos N. A constituent-based model of age-related changes in conduit arteries. Am J Physiol Heart Circ Physiol 301: H12861301, 2011. Reymond P, Bohraus Y, Perren F, Lazeyras F, and Stergiopulos N. Validation of a patient-specific one-dimensional model of the systemic arterial tree. Am J Physiol Heart Circ Physiol 301: H1173-1182, 2011.

Team Members Engineer Stéphane Bigle

Scientific collaborators & Postdoctoral Fellows Luciano Capettini Rafaela Fernandes da Silva Dimitrios Kontaxakis Bryn Martin Sylvain Roy PhD students Aristotelis Agianniotis Thiresia Gialourou Orestis Vardoulis Adan Villamarin Masters students Olivier Frémont Vu Thanh-Hieu Nguyen Eline Coppens Administrative Assistant Tamina Sissoko

Rezakhaniha R, Fonck E, Genoud C, and Stergiopulos N. Role of elastin anisotropy in structural strain energy functions of arterial tissue. Biomech Model Mechanobiol 10: 599-611, 2011.

IBI - Co-affiliated Research Groups

Augsburger L, Reymond P, Rufenacht DA, and Stergiopulos N. Intracranial stents being modeled as a porous medium: flow simulation in stented cerebral aneurysms. Ann Biomed Eng 39: 850-863, 2011. Rezakhaniha R, Agianniotis A, Schrauwen JT, Griffa A, Sage D, Bouten CV, van de Vosse FN, Unser M, and Stergiopulos N. Experimental investigation of collagen waviness and orientation in the arterial adventitia using confocal laser scanning microscopy. Biomech Model Mechanobiol 11: 461-473, 2011.

EPFL School of Life Sciences - 2011 Annual Report

Van de Ville Lab

- coaffiliated

http://miplab.epfl.ch/

Dimitri Van De Ville

SNSF Professor School of Engineering (STI)

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

Research Interests

To advance our understanding of the human body, in particular of brain function in health and disorder using noninvasive imaging techniques. To that aim, we pursue the development and integration of innovative methodological tools from signal and image processing at various stages of the acquisition, processing, and analysis pipeline. The first highlight of our research is on temporal dynamics of spontaneous brain activity; e.g., we showed fractal organization of the rapid switching between scalp topographies in spontaneous EEG and how it interlinks with fMRI that is governed by slow hemodynamics. We also develop advanced regularization techniques that exploit prior knowledge of the neurovascular system that dominates hemodynamic-related imaging techniques. The second highlight is on the analysis of functional brain networks using multi-scale graph models and techniques from pattern recognition to interpret and predict cognitive and clinical conditions based on signatures of functional connectivity. Finally, we are looking into new approaches to MR spectroscopic imaging and source imaging from boundary measurements such as in ultrasound tomography and photo-acoustic imaging.

Selected Publications

Van De Ville, D., Britz, J., and Michel, C. M. (2010). EEG Microstate Sequences in Healthy Humans at Rest Reveal Scale-Free Dynamics. Proc. Natl. Acad. Sci. U S A. 107(42), 18179-18184. Binzoni, T., Seelamantula, C. S., and Van De Ville, D. (2010). A Fast Time-Domain Algorithm for the Assessment of Tissue Blood Flow in Laser-Doppler Flowmetry. Physics in Medicine and Biology, 55, N383-N394. Britz, J., Van De Ville, D. and Michel, C. M. (2010) BOLD Correlates of EEG Topography Reveal Rapid Resting-State Network Dynamics. NeuroImage, 52, 1162-1170.

Richiardi, J., Eryilmaz, H., Schwartz, S., Vuilleumier, P. and Van De Ville, D. (2011) Decoding Brain States from fMRI Connectivity Graphs. NeuroImage, 56, 616-626. Van De Ville, D. , Kocher, M. (2011) Non-Local Means with Dimensionality Reduction and SURE-Based Parameter Selection. IEEE Transactions on Image Processing, 20, 2683-2690. Karahanoglu, I., Bayram, I. and Van De Ville, D. (2011) A Signal Processing Approach to Generalized 1D Total Variation. IEEE Transactions on Signal Processing, 59, 5265-5274. Khalidov, I., Fadili, J., Lazeyras, F., Van De Ville, D. and Unser, M. (2011) Activelets: Wavelets for Sparse Representation of Hemodynamic Responses. Signal Processing, 91, 2810-2821.

Team Members Postdoctoral Fellows Ivana Balic Yury Koush Jonas Richiardi Frank Scharnowski Yves Wiaux PhD students Zafer Dogan Soheil Faridi Isik Karahanoglu Jeffrey Kasten Rotem Kopel Nora Leonardi Master’s students Romain Pirson Ahmed Abdulkadir Hamid Behjat Administrative Assistant Ruth Fiaux

IBI

EPFL School of Life Sciences - 2011 Annual Report

Van den Bergh Lab -

coaffiliated

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

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

Hubert van den Bergh has contributed in the fields of basic chemical kinetics (including the development of the T-jump method in the gas-phase and molecular beam investigations of the cage effect), laser- and beam-induced chemical vapor deposition, and air pollution studies (modeling and measurements). The atmospheric measurements by LIDAR include a Raman system for measuring H2O vapor and temperature that was delivered to the Swiss Meteorological Institute for routine daily round the clock measurements. Other contributions include a novel method for the separation of isotopes by laser-induced inhibition of condensation, which has led to the large scale separation of Uranium isotopes now in use at Wilmington NC by GE, Hitachi and Cameco. Contributions to photomedicine include part of the development of Visudyne® technology for the treatment of wet age-related macular degeneration (FDA approval in 2000) with Novartis and QLT, the development of Hexvix® for the detection and removal of early stage bladder cancer (FDA approval in 2010) with Photocure and GE Healthcare, and the development of a fluorescence endoscope with Wolf GmbH in Germany.

Selected Publications

Gabriel D., Zuluaga M.F., van den Bergh H., Gurny R., and Lange N. (Accepted). It is all about proteases: from drug delivery to in vivo imaging and photomedicine, Current Medical Chemistry. Nowak-Sliwinska P., Ballini J.-P., Wagnières G., van den Bergh H.. (2010). Processing of fluorescence angiograms for the quantification of vascular effects induced by anti-angiogenic agents in the CAM model, Microvascular Research, 79, 21-28.

Debefve E., Cheng C., Schaefer S.C., Yan H., Ballini J.-P., van den Bergh H., Lehr H.-A., Ris H.-B., and Krueger T. (2010). Photodynamic therapy induces selective extravasation of macromolecules : Insights using intravital microcospy, Journal of Photochem. and Photobiol. B ; Biology 98, 69-76. Lovisa B., Jichlinski P., Weber B.C., Aymon D., van den Bergh H., and Wagnières G. (2010). High-magnification vascular imaging to reject false-positive sites in situ during Hexvix ® fluorescence cystoscopy, Journal of Biomedical Optics, 15(5), 051606, 1-8. Gabrecht T., Lovisa B., van den Bergh H., and Wagnières G. (2009). Autofluorescence bronchoscopy: quantification of inter-patient variations of fluorescence intensity intensity, Lasers in Medical Sciences, 24(1), 45-51. Gabriel D., Busso N., So A., van den Bergh H., Gurny R. and Lange N. (2009). Thrombin-sensitive photodynamic agents : A novel strategy for selective synovectomy in rheumatoid arthritis, Journal of Controlled Release, vol.138, (3), 225-234.

Team Members Postdoctoral Fellows Thomas Braschler Elodie Debefve Sandrine Gay Blaise Lovisa Karine Mondon Senthil Kumar Rajendran Patrycja Nowak-Sliwinska Magdalena Swiderska Georges Wagnières Yaboo Wang

IBI - Co-affiliated Research Groups

Research Interests

PhD Students Gilles Kratzer Cédric Paulou

Nowak-Sliwinska P., van Beijnum J.R., van Berkel M., van den Bergh H. and Griffioen A.W. (2010). Vascular regrowth following photodynamic therapy in the chicken embryo chorioallantoic membrane, Angiogenesis, 13, 281-292.

Master’s Students Deborah Forte Stephanie Kappel Carla Martoccia Vincent Mazoyer Andrea Weiss

Cheng C., Debefve E., Haouala A., Andrejevic Blant S., Krueger T., Ballini J.-P., Peters S., Decosterd L.-A., van den Bergh H., Wagnières G., Perentes Y., and Ris H.-B. (2010). Photodynamic therapy selectively enhances liposomal Doxorubicin uptake in sarcoma tumors to rodent lungs, Lasers in Surgery and Medicine, 42, 391-399.

Administration Véronique Bauler Roxane Mischler

EPFL School of Life Sciences - 2011 Annual Report

GHI - Global Health Institute Since its foundation in 2006, the Global Health Institute (GHI) has been contributing to the understanding, diagnosis, prevention and treatment of infectious diseases, which account for half of the deaths in the developing world and still claim 18 million human lives every year. The GHI comprises 9 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, tuberculosis and malaria. The current workforce comprises ~120 students, postdoctoral-fellows, technicians and scientists, representing 28 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 at EPFL and elsewhere. Among these the nanotechnologies, micro-engineering and informatics are proving particularly powerful at underpinning drug discovery and vaccinology as well as more mechanistic research.

GHI - Global Health Institute

http://sv.epfl.ch/GHI

EPFL School of Life Sciences - 2011 Annual Report

Blokesch Lab

http://blokesch-lab.epfl.ch

GHI

Melanie Blokesch studied biology at Ludwig-Maximilians-University in Munich, Germany, graduating with a major in microbiology. 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 doctoral dissertation was honored by the German Association for General and Applied Microbiology and the German Academy of Sciences Leopoldina. In 2005 she joined the group of Dr. Gary Schoolnik within the Department of Microbiology and Immunology at Stanford University, USA as a postdoctoral fellow. In 2009, Melanie Blokesch joined the Global Health Institute within the School of Life Sciences of EPFL as a tenure-track Assistant Professor.

Melanie Blokesch Tenure Track Assistant Professor

Introduction

There is increasing concern about the (re-)emergence of infectious agents and the threat this poses to human health. Knowledge of how bacteria acquire pathogenic traits is of fundamental importance. Our research focuses on evolution mediated by horizontal gene transfer and is exemplified using the human pathogen Vibrio cholerae, the causative agent of the disease cholera, as a model organism.

Keywords

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

Results Obtained in 2011

The human pathogen Vibrio cholerae is an aquatic bacterium often encountered in rivers, estuaries and coastal regions. Within this environmental niche, the bacterium often associates with the chitinous exoskeleton of zooplankton. Upon colonization of these chitinous surfaces, V. cholerae switches on a developmental program known as natural competence for genetic transformation. Natural competence for transformation is a mode of horizontal gene transfer that allows bacteria to acquire new genes derived from free DNA, which is released by other members of the community. The evolutionary consequences could be that the bacterial recipient becomes better adapted to its environmental niche or, in a worst-case scenario, more pathogenic for man. Regulation of natural competence for transformation and DNA uptake In this project we studied the dependency of natural transformation on the so-called autoinducers produced by V. cholerae. More specifically, we showed that chitin-induced natural competence and transformation is strongly enhanced or even dependent on the species-specific cholera autoinducer -1 (CAI-1). In contrast, the universal interspecies autoinducer AI-2 of V. cholerae plays a negligible role. We illustrated that in the absence of either one of the two autoinducer-synthases, natural transformation is completely abolished in this organism. Such a small-molecule dependent regulation of natural competence and transformation

resembles the competence pheromone-dependent regulation in Gram-positive bacteria. Additionally, we provided evidence that V. cholerae does not distinguish between species-specific and species-unspecific DNA at the level of the DNA uptake process. This is in contrast to certain other Gram-negative bacteria, such as Neisseria gonorrhoeae and Haemophilus influenzae; both of these organisms only take up species-specific DNA via the recognition of DNA uptake sequences. More generally, these results illustrate how V. cholerae enhances the probability of species-specific DNA uptake by coupling gene expression required for natural transformation to the species-specific quorum sensing autoinducer. This could be beneficial for the repair of defective genes. We also followed up on the complex regulatory circuit of natural competence using transcriptional reporter fusions and single-cell microscopy. This allowed us to distinguish between population-wide transcriptional profiles and those genes that are only transcribed in distinct subpopulations. The results of this study show that, under optimal conditions, all members within a V. cholerae population acquire the competence state. However, in an aquatic environment, a combination of different ecological factors might lead to heterogeneity in the competence phenotype. Therefore, we investigated the role of extracellular and intracellular signalling molecules with respect to competence induction. We illustrated that at least three interconnected signalling cascades are required for competence induction, which are based on bacterial metabolism and group behavior. Natural transformation of Vibrio cholerae as a tool As we know that V. cholerae becomes naturally transformable and can take up free DNA from the environment upon chitin induction, we went on to use this phenomenon as a tool to genetically manipulate these bacteria. We established experimental setups to knock-in and knock-out genomic islands, genes, and promoter regions, respectively, using chitin-induced natural transformation in combination with the yeast Flp recombination system.

EPFL School of Life Sciences - 2011 Annual Report

Selected Publications

Blokesch M. (2012) TransFLP – a method to genetically modify V. cholerae based on natural transformation and FLP-recombination – accepted for publication in J. Vis. Exp. – Blokesch M. (2012) Chitin colonization, chitin degradation, and chitin-induced natural competence of Vibrio cholerae are subject to catabolite repression. Environ. Microbiol., published online Jan 6th, 2012. 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. De Souza Silva O., Blokesch M. (2010) Genetic manipulation of Vibrio cholerae by combining natural transformation with FLP recombination. Plasmid, 64: 186-195.

Team Members Postdoctoral Fellow Juliane Kühn PhD Students Mirella Lo Scrudato Patrick M. Seitz Gaia F. M. Suckow Technicians Sandrine Borgeaud Olga de Souza Silva Administrative assistant Marisa Marciano Wynn

Marvig R. L., Blokesch M. (2010) Natural transformation of Vibrio cholerae as a tool-optimizing the procedure. BMC Microbiol. 10:155. In collaboration with Prof. Dr. Andrea Rinaldo / ECHO laboratory ENAC, EPFL: Rinaldo A., Bertuzzo E., Mari L., Righetto L., Blokesch M., Gatto M., Casagrandi R., Murray M., Vesenbeckh S., Rodriguez-Iturbe I. (2012) Reassessment of the 2010-2011 Haiti cholera outbreak and rainfall-driven multi-season projections – accepted for publication in Proc. Natl. Acad. Sci. USA – Rinaldo A., Blokesch M., Bertuzzo E., Mari L., Righetto L., Murray M., Gatto M., Casagrandi R., Rodriguez-Iturbe I. (2011) A transmission model of the 2010 cholera epidemic in Haiti. 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) Prediction of the spatial evolution and effects of control measures for the unfolding Haiti cholera outbreak. Geophys. Res. Lett., 38:L06403.

Vibrio cholerae lives in association with chitinous plankton, which foster exchange of genetic material via horizontal gene transfer (HGT). In the figure the colonization of a chitin bead is shown. The bacteria carry fluorescent reporter fusions to monitor expression of genes involved in HGT.

EPFL School of Life Sciences - 2011 Annual Report

Cole Lab

http://cole-lab.epfl.ch

GHI

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 2011

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 2011, we successfully completed work on the back-up series to our candidate drug BTZ043 by developing a derivative with a better selectivity index and in vivo efficacy. BTZ043 kills M. tuberculosis by forming a covalent adduct with the essential enzyme decaprenyl-phosphoryl-beta-D-ribose 2â&#x20AC;&#x2122;-epimerase, which produces decaprenyl-phosphoryl-D-arabinose (DPA), a key component of the mycobacterial cell wall. We have extended our studies to other enzymes in the DPA pathway and made conditional knock-down mutants and begun structural analysis. The figure shows the 3D structure of one such enzyme, transketolase, acting at an early stage in the pathway. We have also extensively characterized another new antitubercular agent, pyridomycin.

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.

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. ESX-1 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.

EPFL School of Life Sciences - 2011 Annual Report

Selected Publications

EspD Is Critical for the Virulence-Mediating ESX-1 Secretion System in Mycobacterium tuberculosis. J. M. Chen, S. Boy-Röttger, N. Dhar, N. Sweeney, R. S. Buxton, F. Pojer, I. Rosenkrands and S. T. Cole. Journal of bacteriology, vol. 194, num. 4, p. 884-93, 2011. Comparative genomics of Esx genes from clinical isolates of Mycobacterium tuberculosis provides evidence for gene conversion and epitope variation. S. Uplekar, B. Heym, V. Friocourt, J. Rougemont and S. T. Cole. Infection and immunity, vol. 79, num. 10, p. 4042-9, 2011. Probable zoonotic leprosy in the southern United States. R. W. Truman, P. Singh, R. Sharma, P. Busso, J. Rougemont, A. Paniz-Mondolfi, A. Kapopoulou, S. Brisse, D. M. Scollard, T. P. Gillis and S. T. Cole. The New England journal of medicine, vol. 364, num. 17, p. 1626-33, 2011. Molecular drug susceptibility testing and genotyping of Mycobacterium leprae strains from South America. P. Singh, P. Busso, A. Paniz-Mondolfi, N. Aranzazu, M. Monot, N. Honore, A. de Faria Fernandes Belone, M. Virmond, M. E. Villarreal-Olaya, C. Rivas and S. T. Cole. Antimicrobial agents and chemotherapy, vol. 55, num. 6, p. 2971-3, 2011. ESAT-6 secretion-independent impact of ESX-1 genes espF and espG1 on virulence of Mycobacterium tuberculosis. D. Bottai, L. Majlessi, R. Simeone, W. Frigui, C. Laurent, P. Lenormand, J. Chen, I. Rosenkrands, M. Huerre, C. Leclerc, S. T. Cole and R. Brosch. The Journal of infectious diseases, vol. 203, num. 8, p. 1155-64, 2011. Atypical DNA recognition mechanism used by the EspR virulence regulator of Mycobacterium tuberculosis. B. Blasco, M. Stenta, L. Alonso-Sarduy, G. Dietler, M. Dal Peraro, S. T. Cole and F. Pojer. Molecular Microbiology, vol. 2011, num. 82, p. 251–264, 2011. A Simple Model for Testing Drugs against Non-replicating Mycobacterium tuberculosis. C. Sala, N. Dhar, R. C. Hartkoorn, M. Zhang, Y. H. Ha, P. Schneider and S. T. Cole. Antimicrobial agents and chemotherapy, vol. 54, num. 10, p. 4150-8, 2010.

Team Members Postdoctoral Fellows Jeffrey Chen Ruben Hartkoorn Joao Neres Sophie Magnet Raju Mukherjee Florence Pojer Jan Rybniker Claudia Sala Pushpendra Singh PhD Students Benjamin Blasco Gaëlle Kolly Benoit Lechartier Swapna Uplekar Ming Zhang Technicians Stefanie Boy-Röttger Philippe Busso Administrative Staff Suzanne Lamy Other Staff Jocelyne Lew Wareed Ahmed Luis Solans Bernad Yaser Heidari Students Joachim De Jonghe Mack Su Ofelia Sanchez Salinas Collaborations Sudhir Sinha

GHI - Global Health Institute

Sigma Factor F does not Prevent Rifampin Inhibition of RNA Polymerase or Cause Rifampin Tolerance in Mycobacterium tuberculosis. R. C. Hartkoorn, C. Sala, S. J. Magnet, J. M. Chen, F. Pojer and S. T. Cole. Journal of bacteriology, vol. 192 num. 20, p. 5472-9. 2010.

Structural model of the M. tuberculosis transketolase dimer with one monomer represented as surface and coloured by B-factor and the second monomer as a cartoon with the domains colored as follows: magenta, domain I; orange, domain II; green, domain III; red, linkers 1, 2.

EPFL School of Life Sciences - 2011 Annual Report

Doerig Lab

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

Christian Doerig

GHI

After a PhD in molecular virology at ISREC and a post-doc on Herpes simplex virus, Christian Doerig turned to malaria research in 1992. He pioneered Plasmodium kinomics, bringing internationally recognized contributions to the fields of signal transduction, cell cycle control and kinome characterization in malaria parasites, and has served as the coordinator of three EU consortia in this area in Framework Programmes FP5, 6, and 7. Having been nominated “Directeur de Recherche” at Inserm in 2001, he established the first Inserm lab in the UK, at the Glasgow-based Wellcome Trust Centre for Molecular Parasitology, and was awarded an Honorary Professorship form the University of Glasgow in 2005. His team moved to EPFL in 2009, where it remained until 2011, when he was appointed Head of the Department of Microbiology at Monash University, Melbourne, Australia.

Directeur de Recherche Inserm EPFL - INSERM Joint Laboratory

Introduction

Our research programme focuses on the role of protein phosphorylation in the life cycle of the human malaria parasite Plasmodium falciparum. The long term objectives are (i) to elucidate the organisation and function of phosphosignalling pathways controlling proliferation and development of the parasite in the human and mosquito hosts, and (ii) to identify protein kinase inhibitors as leads for antimalarial drug discovery. Soon after the publication of the P. falciparum genome sequence, we produced a seminal paper identifying the parasite’s 85-enzyme kinome (Ward et al., BMC Genomics, 2004), which provided a basis for subsequent work in functional characterization of individual protein kinases. Active collaborations have been established with industrial and academic partners to implement drug discovery activities based on kinase inhibition.

Keywords

Malaria, Plasmodium, kinomics, protein kinase, signalling.

Results Obtained in 2011

2011 has seen the publication of a number of studies, including: •

•

A kinome-wide reverse genetics study that took several years to complete, because of the difficulties associated with P. falciparum genetic manipulations. We determined which protein kinases are essential for parasite survival in the human blood; in parallel, a global phosphoproteomic analysis of blood stage parasites was performed in collaboration with Prof. A. Tobin (University of Leicester). Together, these studies, published in Nature Communications, provide new insights into Plasmodium functional kinomics and permit prioritization of potential targets for drug discovery. A pilot interactomics/proteomics study performed in collaboration with the EPFL Proteomics Facility (published in BMC Biology), where immune-complexes purified from transgenic parasite lines expressing an epitope-tagged version of the parasite’s casein kinase 2 (PfCK2) were analysed my mass spectrometry

to gain insight into the cellular function of the enzyme. We identified chromatin assembly as a major process regulated by PfCK2; this approach is now being implemented in a kinome-wide approach. •

A series of pharmacology and immune-detection experiments (performed in collaboration with Kinexus, a company specializing in phosphosignaling) demonstrating a crucial role of kinases from the host erythrocyte for parasite survival. We showed that a phosphosignaling pathway of the erythrocyte is strongly activated by infection with the parasite, and that this activation is required for parasite proliferation. These observations have considerable implications in the context of strategies for antimalarial drug discovery (Cellular Microbiology, 2011, EPFL and Glasgow University press releases)

•

The finding that PfARK1, a homologue of the mammalian Aurora kinases regulating cell division, is required for parasite proliferation. Tagging the endogenous Pfark-1 gene with the green fluorescent protein revealed a dynamic recruitment of Pfark-1 at duplicated spindle pole bodies (the plasmodial equivalents of the centrosome) and enabled us to directly demonstrate that nuclei within a single P. falciparum schizont divide asynchronously. This provides new insights into the cell cycle control of malaria parasites and highlights the parasite’s Aurora kinases as potential targets for malaria chemotherapy(Molecular Microbiology, 2011).

The Inserm-EPFL Joint Laboratory closed on the 31st October 2011, after three productive years at the GHI. Prof. Christian Doerig (christian.doerig@monash.edu.) is now the Head of the Department of Microbiology at Monash University and continues his research there on malaria kinomics. Collaborations established with EPFL laboratories will continue, notably with the Proteomics Facility. Everyone in the Inserm-EPFL Joint laboratory has found new host laboratories (for the Inserm staff) or new employment (for non-Inserm staff). For details of their whereabouts see http://doerig-lab.epfl.ch/

EPFL School of Life Sciences - 2011 Annual Report

Selected Publications

Talevich, E., Tobin, A., Kannan, N. and Doerig, C. An evolutionary perspective on the kinome of malaria parasites. Philosoph. Transact. B, in press. Ghosh Dastidar, E., Dayer, G., Holland, Z., Dorin-Semblat, D., Claes, A., Chêne, A., Sharma, A., Hamelin, R., Moniatte, M., Lopez-Rubio, J., Scherf, A. and Doerig, C. (2012) Involvement of Plasmodium falciparum protein casein kinase 2 in the chromatin assembly pathway. BMC Biology 10:5. Solyakov, L., Halbert, J., Graciotti, M, Semblat, J.P. , Dorin-Semblat, D., Bottrill A., Mistry, S., Abdi, A., Fennell, C., Demarta, C., Bouza, Y., Nivez, M.P., Eschenlauer, S., Lama, T., Reininger, L., Agrawal, S., Kern, S., Pradel, G., Alam, M.M., Tobin, A.B and Doerig, C. (2011) Global kinomic and phospho-proteomic analyses of the human malaria parasite Plasmodium falciparum. Nature Communications 2:565. Sicard, A., Semblat, J.P., Doerig, C.M., Hamelin, R., Moniatte. M., Spicer, J.A., Srivastava, A., Retzlaff, S., Heussler, V., Waters, A.P. and Doerig, C. (2011) Activation of a PAK-MEK pathway in malaria parasite-infected erythrocytes. Cell. Microbiol.13: 836-845.

Team Members Inserm Luc Reininger Dominique Dorin-Semblat Postdoctoral Fellow Jean-Philippe Semblat Master’s students Guillem Dayer Claudia Demarta Technicians Jean Halbert Audrey Sicard Administrative Assistant Marisa Marciano Wynn

Reininger, L., Wilkes, J., Bourgade, H., Miranda-Saavedra, D. and Doerig, C. (2011) An essential Aurora-related kinase transiently associates with spindle pole bodies during Plasmodium falciparum erythrocytic schizogony. Mol. Microbiol. 79: 205-221. Zhang, M., Fennell, C., Ranford-Cartwright, L., Doerig, C., Nussenzweig, R.S., Sullivan Fr, W., Ménard, R., Winzeler, E.A. and Nussenzweig. V. Mechanism of latency in malaria sporozoites. (2010) J. Exp. Med. 207:1465-1474. Doerig, C and Tobin, A. (2010) Parasite protein kinases: at home and abroad. Cell Host Microbe 8:305-307. Doerig, C. and Billker, O. (2010) A parasite calcium switch and Achilles’ heel revealed. Nature Struct. Mol. Biol. 17 :541-543.

GHI - Global Health Institute

A multi-nucleated Plasmodium falciparum schizont expressing GFP-tagged PfARK1. Nuclei are stained in blue. Three of these nuclei display a pair of green dots indicating recruitment of GFP-PfARK1 at the spindle pole bodies located at nuclear periphery. (For more details see Reininger et al., Molecular Microbiology 79: 205-221, 2011). Photograph by Luc Reininger.

EPFL School of Life Sciences - 2011 Annual Report

Fellay Lab

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

GHI

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 moving in 2006 to Duke University, where he worked on human genomics of infections in David Goldsteinâ&#x20AC;&#x2122;s Center for Human Genome Variation. Jacques Fellay joined the EPFL in April 2011 as an SNSF Professor. He is also a Visiting Physician at the Institute of Microbiology of UNIL/CHUV in Lausanne.

Jacques Fellay SNSF Professor

Introduction

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.

Keywords

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

Results Obtained in 2011

Genomic analysis of children with severe respiratory infections In the pediatric population, viral infections of the lower respiratory tract are usually mild and self-limiting, but severe disease sometimes occurs, resulting in the hospitalization of 1-2% of each birth cohort and in the admission to an intensive care unit of about 10% of hospitalized patients. In this project, we test the hypothesis that children who develop unusually severe symptoms after banal respiratory infection have rare genetic defects that confer particular susceptibility to respiratory viruses. Study participants are prospectively recruited in Swiss and Australian Intensive Care Units, and are analyzed by exome and transcriptome sequencing.

Host-pathogen genomic interactions The most recent 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. Human genetic studies in HIV disease We use DNA genotyping and sequencing approaches to search for human genetic variants that influence various aspects of HIV disease, in the context of several national and international collaborations. Resistance against infection is investigated in patients with hemophilia that were highly exposed to potentially contaminated blood products in the early days of the pandemic, yet remained seronegative. 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 complications like cardio-vascular diseases.

EPFL School of Life Sciences - 2011 Annual Report

Selected Publications

Team Members

Pelak K, Need AC, Fellay J, et al. (2011). Copy number variation of genes encoding killer cell immunoglobulin-like receptors and the control of HIV-1. PLoS Biology; 9(11):e1001208.

PhD Students Samira Asgari Istvan Bartha

Rauch A and Fellay J (2011). Personalized Hepatitis C Therapy: Opportunities and Pitfalls. Expert Review of Molecular Diagnostics; 11(2):127-9.

Master’s student Florian Gilbert

Rotger M, Dalmau J, Rauch A, et al. (2011). Comparative analysis of genomic features of human HIV-1 infection and primate models of SIV infection. Journal of Clinical Investigations; 121(6):2391-400.

Administrative Assistant Marisa Marciano Wynn

Snoeck J, Fellay J, Bartha I, Douek DC, 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.

Postdoctoral Fellows Jérôme Lane Paul J. McLaren Thomas Junier

Fellay J, Frahm N, Shianna KV, et al. (2011). Host genetic determinants of T cell responses to the MRKAd5 HIV-1 gag/pol/nef vaccine in the Step trial. Journal of Infectious Diseases; 203(6):773-9. Petrovski S, Fellay J, Shianna KV, et al. (2011). Common Human Genetic Variants and HIV-1 susceptibility: A genome-wide survey in a homogeneous African population. AIDS; 25(4):513-8. Fellay J, Thompson AJ, Ge D, et al. (2010). ITPA gene variants protect against anemia in patients treated for chronic hepatitis C. Nature; 464(7287):405-8.

GHI - Global Health Institute

Fellay J, Shianna KV, Telenti A, and Goldstein DB (2010). Host Genetics and HIV-1: the final phase? PLoS Pathogens; 6(10):e1001033.

Associations between human polymorphisms and ribavirin-induced anemia: genomic overview of the 20q13 region including the genome-wide significant associated variants and the ITPA gene (adapted from Nature 2010).

EPFL School of Life Sciences - 2011 Annual Report

Harris Lab

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

Nicola Harris

GHI

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 (1012 per gram of intestinal contents) in all individuals at all times. Worms (helminths) can also establish chronic infections within our intestines and were present in a near ubiquitous manner throughout mammalian evolution. Today intestinal helminths still infect approximately 1/3 of the world’s population, with the heaviest infections found in children living in poor communities within developing countries. Our work aims to investigate: i) how the immune system can provide protection against heavy burdens of 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 2011

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 and in 2011 we completed a project demonstrating a novel role for IgG1 and IgE antibodies in regulating the haematopoiesis of basophils. We additionally

demonstrated that antibody-laden basophils played a small but significant role in the killing of helminth larvae. More recently we have established that antibodies also function to promote the activation and recruitment of so called ‘alternatively’ activated macrophages. Such macrophages are postulated to contribute to helminth killing and the means by which they achieve this, plus the impact of antibodies on these cells, is currently the subject of ongoing investigation in our laboratory. 2011 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 indicate 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. To investigate the impact of these changes on the host response against the helminth we have now developed a model of germ-free helminth infection which involves the hatching of helminth larvae using the auxotrophic HA107 E. coli (that can not replicate in germ-free mice). Initial experiments using this system are now underway and we hope to report on the consequences of helminth-bacterial interactions in 2012.

EPFL School of Life Sciences - 2011 Annual Report

Selected Publications

Santoni de Sio FR, Massacand J, Barde I, Offner S, Corsinotti A, Kapopoulou A, Bojkowska K, Dagklis A, Fernandez M, Ghia P, Thomas JH, Pinschewer D, Harris N, Trono D. KAP1 regulates gene networks controlling mouse B lymphoid cell differentiation and function, Blood. 2012 Apr 3. [Epub ahead of print) Feyerabend TB, Weiser A, Tietz A, Stassen M, Harris N, Kopf M, Radermacher P, Möller P, Benoist C, Mathis D, Fehling HJ, Rodewald HR. Cre-mediated cell ablation contests mast cell contribution in models of antibody- and T cell-mediated autoimmunity, Immunity, vol. 35, num. 5, p. 832-44, 2011. Duvoisin R, Ayuk MA, Rinaldi G, Suttiprapa S, Mann VH, Lee CM, Harris N, Brindley PJ.. Human U6 promoter drives stronger shRNA activity than its schistosome orthologue in Schistosoma mansoni and human fibrosarcoma cells, Transgenic research, 2011.

Team Members Postdoctoral Fellows Julia Esser Mario Zaiss PhD Student Ilaria Mosconi Master’s Student Nadine Guenat Senior Technical Assistant Manuel Kulagin Administrative Assistant Marisa Marciano Wynn

Herbst T, Sichelstiel A, Schär C, Yadava K, Bürki K, Cahenzli J, McCoy K, Marsland BJ, Harris NL. Dysregulation of Allergic Airway Inflammation in the Absence of Microbial Colonization, American Journal of Respiratory and Critical Care Medicine, Jul 15;184(2):198-205. 2011. Schaer C, Hiltbrunner S, Ernst B, Mueller C, Kurrer M, Kopf M, Harris NL. HVEM Signalling Promotes Colitis, PloS one, Apr 18;6(4):e18495., 2011. N. Harris and W. C. Gause. To B or not to B: B cells and the Th2-type immune response to helminths, Trends in Immunology, vol. 32, num. 2, p. 80-8, 2011.

GHI - Global Health Institute

N. L. Harris. Advances in helminth immunology: optimism for future vaccine design?, Trends in Parasitology, Jul;27(7):288-93. 2011.

The picture depicts macrophages surrounding the larval stage of the murine intestinal helminth Heligmosomoides polygyrus bakeri.

EPFL School of Life Sciences - 2011 Annual Report

Lemaitre Lab

http://lemaitrelab.epfl.ch/

GHI

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 has developed an integrated approach of hostpathogen interactions in model insect Drosophila analysing the basis of microbial infection and corresponding host defence responses using both genetic and genomic tools.

Keywords

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

Results Obtained in 2011

The gut is the major interface between microbes and their animal hosts. The gut epithelial cells are armed with efficient immune defenses to combat invasion and colonization by pathogens. However, the gut also harbors a flora of commensal bacteria, with potentially beneficial effects for the host, which must be tolerated without a chronic and harmful immune response. In recent years Drosophila has emerged as a powerful model to dissect host-pathogen interactions, leading to the paradigm of antimicrobial peptide regulation by the Toll and Imd signaling pathways. The strength of this model derives from the availability of powerful and cost effective genetic and genomic tools as well as the high degree of similarities to vertebrate innate immunity. However, in spite of growing interest in gut mucosal immunity generally, very little is known about the immune response of the Drosophila gut.

the peritrophic matrix and (iii) maintenance of gut homeostasis through regulation of stem cell activity are all essential elements of the gut defense to infection. We have also started to investigate the role of the Drosophila microbiota on the gut immune response and intestinal homeostasis. We first showed that the Drosophila microbiota affect at basal levels the immune and gut stem cell activities. Interestingly, the chronic stimulation of stem cell by the indigenous microbiota is stronger in old flies (due to higher bacterial count) and lead to defects in gut morphogenesis. Moreover, we have shown that an important role of Amidase Peptidoglycan Recognition Protein is to prevent deleterious immune responses by the indigenous microbiota by scavenging peptidoglycan, the elicitors of the Imd pathway. Our current project extends from a sensu-stricto analysis of the gut immune response by addressing the impact of infection on gut renewal and physiology. This project is in line with the renewed interest in the study of gut-bacteria interactions in both mammals and insects. We believe that the fundamental knowledge generated on Drosophila gut immunity will serve as a paradigm of epithelial immune reactivity and have broader impacts on our comprehension of animal immune defense mechanisms and gut homeostasis.

Using a genetic approach, my laboratory has started to investigate the molecular mechanisms underlying gut immune responses in Drosophila. Our studies have already indicated that (i) production of antibacterial peptides through the Imd pathway, (ii) physical barrier provided by

EPFL School of Life Sciences - 2011 Annual Report

Selected Publications

Buchon N, Broderick NA, Kuraishi T, and Lemaitre B. (2010). The EGFR pathway coordinates Drosophila stem cell proliferation and gut remodeling in response to infection. BMC Biol. 2010 Dec 22;8(1):152. Alattia JR, Kuraishi T, Dimitrov M, Chang I, Lemaitre B, Fraering PC. Mercury is a direct and potent {gamma}-secretase inhibitor affecting Notch processing and development in Drosophila. FASEB J. 2011 Jul;25(7):2287-95. 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. 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 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 -pore-forming toxin from the Drosophila pathogen Pseudomonas entomophila, contributes to host intestinal damage and lethality. PLoS Pathog. 2011 Sep;7(9):e1002259. 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, 23;35(5):770-9.

Team Members Postdoctoral Fellows Nichole Broderick Nicolas Buchon Guennalle Diepois Claudine Neyen Dani Osman

PhD Students Olivier Biggeli Wen Bin (Alfred) Chng Sveta Chakrabarti Jeremy Herren Juan Paredes Lab Technicians Jean-Philippe Boquete Fanny Schüpfer Christophe Remondeulaz Master’s Student Maroun Bou Sleiman Apprentices Mégane Bozza Barbara Lecrinier Administrative Assistant Véronique Dijkstra-Bulliard

Vallet-Gely I, Opota O, Boniface A, Novikov A, Lemaitre B. (2010) A secondary metabolite acting as a signaling molecule controls Pseudomonas entomophila virulence. Cell Microbiol. 2010 Nov;12(11):1666-7.

GHI - Global Health Institute

Zaidman-Remy, A., Poidevin, M., Herve, M., Welchman, D.P., Paredes, J.C., Fahlander, C., Steiner, H., Mengin-Lecreulx, D., and Lemaitre B. (2011). Drosophila immunity: analysis of PGRP-SB1 expression, enzymatic activity and function. PLoS One 6(2): e17231.

Section of the Drosophila midgut: Image depicting a crosssection of the Drosophila gut with muscle in red (Phaloidin), the brush border in green (reporter-GFP) and nuclei in blue (DAPI).

EPFL School of Life Sciences - 2011 Annual Report

McKinney Lab

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

GHI

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, he 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 in EPFLâ&#x20AC;&#x2122;s Global Health Institute.

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, real-time single-cell analysis, timelapse fluorescence microscopy, microfluidics, microelectromechanical systems (MEMS), tuberculosis, persistence, antibiotics.

Results Obtained in 2011

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 timelapse 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 - 2011 Annual Report

Selected Publications

Team Members

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.

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

Gelman, E., McKinney, J.D. and Dhar N. (2012) Malachite green interferes with post-antibiotic recovery of mycobacteria. Antimicrob. Agents Chemother. (in press).

Griffin, J.E., Pandey, A.K., Gilmore, S.A., Mizrahi, V., McKinney, J.D., Bertozzi, C.R. and Sassetti, C.M. (2011) Cholesterol catabolism by Mycobacterium tuberculosis requires transcriptional and metabolic adaptations. Chem. Biol. 19(2): 218-227. Ballester, M., Nembrini, C., Dhar, N., de Titta, A., de Piano, C., Pasquier, M., Simeoni, E., van der Vlies, A.J., McKinney, J.D., Hubbell, J.A. and Swartz, M.A. (2011) Nanoparticle conjugation and pulmonary delivery enhance the protective efficacy of Ag85B and CpG against tuberculosis. Vaccine 29(40): 69596966. 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.

Senior Staff Scientist Neeraj Dhar

PhD students Matthieu Delincé Cyntia De Piano Meltem Elitas Ekaterina Gelman Manisha Lotlikar Emre Özdemir 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. Tischler, A.D. and McKinney, J.D. (2011) Bacterial strategies for survival in the host. In The Immune Response to Infection (ed. Kaufmann, S.H.E., Rouse, B.T. and Sacks, D.L.) ASM Press, Washington DC, pp. 425-440. Dhar, N. and McKinney, J. (2010). Mycobacterium tuberculosis persistence mutants identified by screening in isoniazid-treated mice. Proc. Natl. Acad. Sci. U S A 107(27): 12275-12280.

GHI - Global Health Institute

Tischler, A.D. and McKinney, J.D. (2010). Contrasting persistence strategies in Salmonella and Mycobacterium. Curr. Opin. Microbiol. 13(1): 93-99.

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 - 2011 Annual Report

Trono Lab

http://tronolab.epfl.ch

GHI

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 in 2004.

Didier Trono

Full Professor Dean of the School of Life Sciences

Introduction

After a long involvement in the study of interactions between viral pathogens and their hosts and the development of gene-based therapies, our laboratory shifted a few years ago to the field of epigenetics, when we became interested in exploring a true terra incognita of mammalian biology, the roles and mechanisms of action of KRAB-containing zinc finger proteins (KRAB-ZFPs). Our ongoing work demonstrates that this tetrapod-specific family of transcriptional regulators initially evolved as a line of defense against retroviral invaders, to become understood today as a master regulator of mammalian homeostasis.

Keywords

Genetics, epigenetics, KRAB zinc finger proteins, KAP1, transcriptional regulation, retroelements, imprinting, liver metabolism, sexual dimorphism, lympho-hematopoietic system.

Results Obtained in 2011

About 1â&#x20AC;&#x2122;200 of the 20â&#x20AC;&#x2122;000 genes contained in the human genome encode for transcriptional regulators, including some four hundred KRAB-ZFPs. Sequence-specific DNA binding transcriptional repressors that act by triggering the formation of heterochromatin through their universal cofactor KAP1, KRABZFPs have been subjected to intense positive selection during evolution, suggesting their engagement in some genetic conflict. Confirming this prediction, we reported last year that KRAB-ZFPs and their cofactor KAP1 are responsible for the early embryonic silencing of endogenous retroviruses. This year, we revealed how a highly conserved member of the family, ZFP57, is responsible for the maintenance of imprinting marks in embryonic stem cells. Imprinting is a process restricted to placental mammals, which results in the parental allele-specific expression of a few dozen genes important notably for metabolic regulation and neurological development. We demonstrated that ZFP57, KAP1 and associated effectors bind selectively to the H3K9me3-bearing, DNA methylated allele of ICRs (imprinting control regions) in embryonic stem (ES) cells. KAP1 deletion induced a loss of heterochromatin marks at ICRs, while deleting ZFP57 or DNA methyltransferases (DNMTs) led to ICR DNA demethylation. Accordingly, we found ZFP57 and KAP1 associated with DNMTs and the hemimethylated DNA-binding NP95. We finally identified the methylated TGCCmeGC hexa-

nucleotide as the motif recognized by ZFP57 in all ICRs as well as in several dozen of additional loci, several of which at least are ZFP57-dependently methylated in ES cells. These results significantly advance our understanding of imprinting, and suggest a general mechanism for the protection of specific loci against the wave of DNA demethylation that affects the mammalian genome during the first few days of embryogenesis. These data nicely illustrate the crucial role of KRAB/KAP1mediated regulation at the earliest stage of development. In parallel, we have been exploring the functions fulfilled by this system in adulthood. We had previously determined that, in the forebrain, KAP1 regulates behavioral susceptibility to stress. Through a combination of conditional KAP1 knockout in the mouse, in vivo chromatin and transcription studies as well as a broad range of tissue culture-based experiments and in silico analyses, we now have determined that KRAB/KAP1-mediated gene regulation is critical for events as diverse as the maturation and activation of B and T lymphocytes, for several steps of hematopoietic differentiation and for liver metabolism. Interestingly, the liver is characterized by sexually dimorphic gene expression translating into sex-specific differences in lipid, drug, steroid hormone and xenobiotic metabolism, with distinct responses of males and females to environmental challenges. Liver-specific KAP1 knockout in the mouse led to sexually dimorphic phenotypic disturbances, including male-restricted steatosis and hepatic tumors. This correlated with sex-specific transcriptional dysregulation of a wide range of metabolic genes, notably those involved in retinol and sex hormone processing as well as in detoxification, with chromatin immunoprecipitation followed by deep sequencing indicating that many of these genes are direct targets of the KRAB/KAP1 repression system. These results identify KRAB/KAP1-mediated transcriptional regulation as a central event in the metabolic control of hormones, drugs and xenobiotics in the liver, and further link disturbances in these processes with hepatic carcinogenesis. A long-term objective of these studies is to ask whether polymorphism in KRAB-ZFP genes or their targets might underlay inter-individual differences in susceptibility to human diseases, for instance ones reminiscent of the phenotypes of mice in which KAP1 is inactivated in specific organs.

EPFL School of Life Sciences - 2011 Annual Report

Selected Publications

Team Members

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 regualtes gene networks controlling B lymphoid differentiation and function. Blood, (E-pub ahead of print).

Postdoctoral Fellows Isabelle Barde Marco Cassano Marc Friedli Michael Imbeault Julien Marquis Simon Quenneville Benjamin Rauwel Helen Mary Rowe Francesca Santoni de Sio Benyamin Yazdan Panah

K. Bojkowska, F. Aloisio, M. Cassano, A. Kapopoulou, F. Santoni de Sio, N. Zangger, S. Offner, C. Cartoni, C. Thomas, S. Quenneveille, 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, in press.

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. S. Meylan, A. Groner, G. Ambrosini, N. Malani, S. Quenneville, N. Zangger, A. Kapopoulou, A. Kauzlaric, J. Rougemont, A. Ciuffi, F.D. Bushman, P. Bucher and D. Trono (2011). A gene-rich, transcriptionally active environment and the predeposition of repressive marks are predictive of susceptibility to KRAB/KAP1mediated silencing. BMC Genomics, 12: 378.

Senior Scientist Priscilla Turelli

PhD Students Karolina Bojkowska Natali Castro Diaz Andrea Corsinotti Gabriella Ecco Anna Groner Annamaria Kauzlaric Flavia Marzetta

K. Bojkowska, F. Santoni de Sio, I. Barde, S. Offner, S. Verp, C. Hienis, K. Johnsson and D. Trono (2011). Measuring in vivo protein half-life. Chem. Biol., 18: 805-815.

Bioinformaticians Adamandia Kapopoulou Yoann Mouscaz

H.M. Rowe and D. Trono (2011). Dynamic control of endogenous retroelements during development. Virology, 411: 273-287.

Technicians Sandra Offner Charlène Raclot Sonia Verp

D. Trono, C. Van Lint, C. Rouzioux, E. Verdin, F. Barré-Sinoussi, T.-W. Chun and N. Chomont (2010). HIV persistence and the prospect of long-term drug-free remission in HIV-infected individuals. Science, 329: 174-180.

Administrative Assistant Séverine Reynard

V. Busskamp, J. Duebel, D. Balya, M. Fradot, T. James, S. Siegert, A.C. Groner, E. Cabuy, V. Forster, M. Seeliger, M. Biel, P. Humphries, S. Mohand-Said, D. Trono, K. Deisseroth, J.A. Sahel, S. Picaud and B. Roska (2010). Genetic reactivation of cone photoreceptors restores visual responses in Retinitis pigmentosa. Science, 329: 413-417. A.C. Groner, S. Meylan, A. Ciuffi, N. Zangger, G. Ambrosini, N. Dénervaud, Philipp Bucher and D. Trono (2010). KRAB-zinc finger proteins and KAP1 can mediate long-range transcriptional repression through heterochromatin spreading. PLoS Genetics, 6: e1000869. H. Rowe, J. Jakobsson, D. Mesnard, J. Rougemont, S. Reynard, T. Aktas, P.V. Maillard, H. Layard-Liesching, S. Verp, J. Marquis. F. Spitz, D.B. Constam and D. Trono (2010). KAP1 controls endogenous retroviruses in embryonic stem cells. Nature, 463: 237-240.

GHI - Global Health Institute

Model of ZFP57/KAP1-mediated maintenance of imprinting marks in ESC. ZFP57 binds to the TGCCmeGC methylated hexanucleotide in ICRs and recruits KAP1, which serves as a scaffold for indicated chromatin modifiers and DNA methyltransferases, ensuring that imprinted alleles resist that genome-wide wave of demethylation that takes place during this period (See Quenneville et al., Mol. Cell 2011).

EPFL School of Life Sciences - 2011 Annual Report

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

GHI

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 2011

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. Through the analysis of 4 patients, we identified 3 novel mutants and determined their effects at the cellular level. Using a variety of approaches (biochemical, morphological and functional), we could show that missense mutations that map to the extracellular von Willebrand domain or the Ig-like domain lead to folding defects and thereby to retention of the mutated protein in the endoplasmic reticulum. Mutations in the Ig-like domain, the structure of which we have modeled, prevent proper disulfide bond formation and are more efficiently targeted to ER associated degradation. Importantly, we found that CMG2 can be rescued in fibroblasts of some HFS patients by treatment with a proteasome inhibitor that is in clinical trials and that rescued mutant CMG2 is then properly transported to the plasma membrane and is functional. Our work shows that the ER folding and degradation pathway components are promising drug targets for HFS.

Regulation of endoplasmic reticulum function by palmitoyltransferases The endoplasmic reticulum (ER) is the largest intracellular organelle of mammalian cells. It fulfills major functions such as folding and quality control of membrane and secreted proteins, lipid biosynthesis and calcium storage. This diversity of functions is accompanied by a complex 3D architecture, the maintenance of which is essential, since alterations lead to disease. How this architecture is generated, how proteins localize to specific subdomains and how structure and functions are coordinated is poorly understood. We are interested in the potential role of palmitoyltransferases in these processes. We found that a major ER chaperone, the transmembrane protein calnexin involved in the folding of glycoproteins such as CMG2, is palmitoylated and that this modification, which occurs on 2 juxtamembranous sites, is essential for the chaperone to perform its function. We determined, using RNAi and overexpression screening, that the modification is mediated by a single enzyme, DHHC6, and that none of the other 16 ER DHHC enzymes can compensate for DHHC6 loss. More specifically, modification of calnexin by DHHC6 drives the formation of an actin-stabilized super complex, comprising calnexin, the sec61 translocon, the oligosaccharyl transferase complex responsible for Nglycosylation and the TRAP complex. This super complex (figure ) is essential for proper handling of newly synthesized glycoproteins, which, as they emerge from the ribosome through the translocon pore, acquire their sugars and are assisted by calnexin to prevent aggregation during folding. Palmitoylation thus ensures that the chaperone is in the right place at the right time, so that in the competition between folding and aggregation, the former is more efficient. Our aim is to extend these studies to other palmitoylated ER proteins to obtain a systems understanding of the ER palmitoylation network.

EPFL School of Life Sciences - 2011 Annual Report

Selected publications

Team Members

Deuquet, J., Lausch E., Superti-Furga, A. and F.G. van der Goot (2012) The dark side of capillary morphogenesis gene 2. EMBO J. 31:3-13.

Postdoctoral Fellows Michal Feldman Asvin Lakkaraju Julie Deuquet Ioan Iacovache

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. (in press) .

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. 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. 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.

Scientist Collaborator Laurence Abrami

PhD Students Sanja Blaskovic Jérôme Bürgi Sarah Frieben Yan Shixu Laboratory Assistants Sylvia Ho Béatrice Kunz Suzanne Salvi Administrative Assistants Carole Burget Geneviève Rossier

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. Abrami, L., Kunz, B. and van der Goot, F.G. (2010) Anthrax toxin triggers the activation of src like kinases to mediates its own uptake. Proc Natl Acad Sci USA 107:1420-1424. Iacovache, I. Biasini, M., Kowal, J., Kukulski, W., Chami, M. van der Goot, F.G., Engel, A. and Rémigy, R.W. (2010) The 2DX robot: a membrane protein 2D crystallization Swiss Army knife. J. Struct. Biol. 169:370-378. Abrami, L., Bischofberger M, Kunz, B., Groux, R. and van der Goot, F.G. (2010) Endocytosis of the anthrax toxin is mediated by clathrin, actin and unconventional adaptors PLoS Pathogen 6(3): e1000792.

GHI - Global Health Institute

Iacovache, I, Bischofberger M. and van der Goot, F.G. (2010) Structure and assembly of pore-forming proteins. Current Opinion in Structural Biology 20:241-246.

Schematic representation of the Ribosome-translocon-oligosacharyl transferase-calnexin super complex. Calnexin is then positioned to efficiently grab nascent glycoproteins as they emerge from the translocon pore, acquire their N-linked glycan from which the 2 external glucoses have been trimmed.

EPFL School of Life Sciences - 2011 Annual Report

ISREC - Swiss Institute for Experimental Cancer Research The Swiss Institute for Experimental Cancer Research (ISREC) has seen a year of continuing progress and development in 2011. Three new assistant professors - Oliver Hantschel, Etienne Meylan, and Michele De Palma – established their laboratories in the Life Sciences Building (SV) on the EPFL campus and are already active members of the Life Sciences and Cancer Communities at EPFL and in Lausanne at large. Joerg Huelsken was promoted to the position of Associate Professor with tenure. Professor Peter Beard retired but remains involved in teaching in the School of Life Sciences. The annual Life Sciences Symposium, hosted by ISREC, was held September 7-10, 2011. The topic was on “Hallmarks and Horizons of Cancer”, with a world-class roster of speakers. The symposium was a resounding success, with well over 600 applicants, of which some 525 were accommodated. The program continues to be available for review at http://isrec2011.epfl.ch/. The Next ISREC Symposium is scheduled for January 22-25, 2014, in Crans Montana, on the topic of “Metastatic colonization: microenvironments, mechanisms, and therapeutic targeting”. Several ISREC faculty received honors and awards in 2011: Denis Duboule received the Annual Prize of the Fondation pour Genève and the EPFL Polysphere Prize for teaching in Life Sciences. Etienne Meylan was honored with a Debiopharm Group Junior Life Sciences Award for 2011. Michele De Palma received an award from the Anna Fuller Fund. Douglas Hanahan was awarded an honorary degree from the University of Dundee, Scotland, UK.

ISREC - Swiss Institute for Experimental Cancer Research

ISREC’s faculty maintains a balanced emphasis on fundamental research into biological systems and basic and translational cancer research, seeking to elucidate mechanisms that on the one hand are subverted to facilitate tumor growth and progression, and on the other orchestrate normal biological processes in development and organ function. ISREC continues to contribute to the missions of EPFL in teaching undergraduate and graduate students, and in mentoring young scientists toward careers in academics and biotechnology. ISREC remains the home base for the Swiss National Center of Competence in Research (NCCR) in Molecular Oncology, which is focused on characterizing the complex organization and functional importance of the tumororgan microenvironment, in model systems and in clinical samples. The institute is significantly involved on behalf of the EPFL in the design and implementation of a new multi-institutional regional cancer center, involving the University of Lausanne, its Hospital and biomedical faculty, the (independent) ISREC Foundation, and in turn other regional institutions. This new cancer center will seek, via trans-disciplinary collaborations between scientists, bioengineers, and clinicians, to discover and then translate knowledge about mechanisms of the disease into improved treatments for human cancer. http://sv.epfl.ch/page-37991.html

ISREC

EPFL School of Life Sciences - 2011 Annual Report

Aguet Lab

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

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

Michel AGUET Full Professor

Introduction

Our group recently observed in a mouse model of colon adenocarcinoma that inactivation of Bcl9/Bcl9l, two genes involved in the Wnt pathway, results in abrogation of traits characteristic of stem cells and associated with invasiveness and drug resistance. The main focus of our current research is to explore whether inhibiting the function of these genes in human cancer cells can revert such traits and may lead to a novel therapeutic approach.

Keywords

Wnt pathway, Bcl9/Bcl9l, intestinal tumorigenesis, epithelial-mesenchymal transition, cancer stem cells, drug target validation.

Results Obtained in 2011

Canonical Wnt-signaling regulates critical processes during embryonic development and adult tissue renewal, and aberrant activation of this pathway is associated with colorectal and other cancers. Oncogenic mutations in the Wnt pathway cause ligand-independent pathway activation, due to the inappropriate stabilization of β-catenin, leading to aberrant transcription of β-catenin/TCF target genes. Wnt signals may result in different outcomes, dependent upon tissue origin and cellular context, and stimulate cell proliferation, as well as control cell fate and differentiation. Wnt signaling has also been implicated in the regulation of epithelial-mesenchymal transition (EMT). EMT has been associated with invasive and metastatic tumor behavior, and there is growing evidence suggesting a relationship between EMT, the emergence of cancer stem cells (CSCs) and drug resistance. Targeting pathways that regulate EMT and/or CSC traits may therefore prove of particular clinical relevance, with regard to preventing invasion and metastasis, and for precluding the outgrowth of therapy-resistant tumor cells. We recently described phenotypic changes in a mouse model of colon adenocarcinoma suggesting that the Wnt signaling components Bcl9/Bcl9l mediate a subprogram of the Wnt pathway (Deka et al., 2010). Thus, a subset of

Wnt target genes associated with a mesenchymal phenotype, intestinal stem cells and colon cancer progression was strongly down-regulated in Bcl9/Bcl9l-mutant tumors. Consistent with the EMT state of wild-type tumor cells, the basement membrane appeared disintegrated as assessed by laminin staining, whereas Bcl9/Bcl9l-mutant tumor cells were aligned on a contiguous laminin membrane. Followup experiments showed that the EMT phenotype observed in this tumor model is dependent upon continuous Bcl9/ Bcl9l expression and can be abrogated when ablation of Bcl9/Bcl9l is induced in established tumors. Collectively, these observations indicate that Bcl9/Bcl9l are critical for the expression of a subset of Wnt target genes relevant to controlling EMT- and stem cell-associated traits. Our current research focuses on validating these observations in human Wnt-activated cancers. We have therefore generated Wnt-activated human colon cancer cell lines in which BCL9/BCL9L function is abrogated through conditional expression of dominant-negative Wnt signaling components and assess to what extent phenotypic alterations observed in the mouse adenocarcinoma model can be recapitulated in these cell lines in vitro as well as in xenografts. In particular, our studies aim at validating the interaction of BCL9/BCL9L and its partner protein β-catenin as a potential therapeutic target to attenuate metastatic dissemination and enhance susceptibility to chemotherapy. The interface between BCL9/BCL9L and β-catenin is structurally well characterized and appears potentially drugable. We are collaborating with the group of Prof. Leonardo Scapozza to identify small compound inhibitors of this interaction through molecular docking and have also established a physical screening assay. A first medium throughput screen carried out at the EPFL Biomolecular Screening Facility provided hits that are currently validated in secondary binding, biochemical and cell-based assays, as well as proof for the feasibility of larger scale screens that are currently carried out with external partners.

EPFL School of Life Sciences - 2011 Annual Report

Selected Publications

Brack, A.S., Murphy-Seiler, F., Hanifi, J., Deka, J., Eyckerman, S., Keller, C., Aguet, M., and Rando, T.A. (2009). BCL9 is an essential component of canonical Wnt signaling that mediates the differentiation of myogenic progenitors during muscle regeneration. Dev. Biol. 335, 93-105. Deka, J., Wiedemann, N., Anderle, P., Murphy-Seiler, F., Bultinck, J., Eyckerman, S., Stehle, J.C., Andre, S., Vilain, N., Zilian, O., et al. (2010). Bcl9/Bcl9l Are Critical for Wnt-Mediated Regulation of Stem Cell Traits in Colon Epithelium and Adenocarcinomas. Cancer Res. 70, 6619-6628. Valenta, T., Gay, M., Steiner, S., Draganova, K., Zemke, M., Hoffmans, R., Cinelli, P., Aguet, M., Sommer, L., and Basler, K. (2011). Probing transcription-specific outputs of beta-catenin in vivo. Genes & Dev. 25, 2631-2643.

Team Members

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

ISREC - Swiss Institute for Experimental Cancer Research

Administrative assistant NCCR «Molecular Oncology» Léonore Golay-Miauton

Immunofluorescence staining of mouse colon adenocarcinomas. Wild-type tumor cells stain for the mesenchymal filament vimentin (green) and show a discontinuous basement membrane (laminin; red). Bcl9/Bcl9l-mutant tumor cells express no vimentin and are aligned on a continuous laminin layer.

ISREC

EPFL School of Life Sciences - 2011 Annual Report

Beard Lab

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

Peter Beard studied mathematics, physics and chemistry at the University of Glasgow. After graduating in biochemistry, he moved to the Imperial Cancer Research Fund Laboratories and obtained his PhD from University College London. He then worked at Stanford University at the time the idea of gene cloning was first being tested. After initially joining the Virology group at ISREC, he subsequently became a member of the senior scientific staff and was appointed as EPFL Titular Professor in 2008. Since July 2011 he is EPFL Professor Emeritus.

Peter Martin Beard Professor Emeritus

Introduction

Our laboratory has been studying the relation between small viruses with DNA genomes and cancer. Some cancers, for example cervical carcinoma, are caused by viruses of this type â&#x20AC;&#x201C; human papillomaviruses. On the other hand, we also have worked on the use of a different class of viruses to specifically target tumour cells, an approach termed oncosuppressive virotherapy.

Keywords

Adeno-associated virus, papillomavirus, cancer, DNA damage response, cell cycle, cell death.

Results Obtained in 2011

Viral targeting of cancer cells We have used the helper-dependent parvovirus adeno-associated virus (AAV) as a biological probe to study DNA damage signalling pathways in cancer cells. We found that infection with AAV, wild- type or UV-inactivated, triggers a damage response that can lead to death of p53-defective tumour cells. AAV therefore provides a unique opportunity to study this response without actually damaging the cellular DNA. Understanding the tumour-suppressive activity of AAV may lead to novel approaches to cancer therapy. Why are transformed cells more susceptible to AAV infection than normal cells? In U2OS osteosarcoma cells, AAV2 can initiate part of its replicative cycle in the absence of helper virus, leading to production of the cytotoxic viral Rep proteins; this does not occur in untransformed cells. While testing whether the cellular innate antiviral defences control this susceptibility we found that AAV2 induces type I IFN production and release in normal human fibroblasts, but not in the U2OS tumour cells. This permissiveness is in large part due to impairment of the viral sensing machinery in U2OS cells. Toll-like receptor 9 (TLR9) is an intracellular sensor that detects AAV2 and triggers the antiviral state in AAV-infected normal cells. Thus, the ability to sense the AAV genome and the innate antiviral host cell response are crucial events that control the infectivity of this parvovirus.

Infection of osteosarcoma cells by adeno-associated virus: cells in a bone-like matrix show reduced susceptibility to AAV. We set out to test whether growing osteosarcoma cells in a bone-like matrix that more resembles in vivo conditions changes their sensitivity to AAV infection. Matrices, or scaffolds, were prepared using nano-particulate hydroxyapatite and chitosan. After equilibrating with medium, cells were added and their growth and osteogenic differentiation observed. Osteosarcoma cells (U2OS) growing on plates or in matrices were infected with AAV in parallel. Cells on plates allowed the early steps of infection and extensive Rep production, as previously noted. Although the cells in matrices displayed widespread cell-associated virus by immunofluorescence, they expressed little or no Rep proteins. These results suggest that while osteosarcoma cells growing in plates permit the initial phase of AAV infection, the same cells when incorporated into a bone-like matrix do not. Although more work will be needed to determine the stage at which the apparent block occurs, the results are consistent with the notion that the cellular context, on plates or in a more in vivo-like environment, can have a striking effect on the vulnerability to infection. What are the cellular changes, on top of papillomavirus infection, that lead to cervical cancer? Although human papillomavirus (HPV) infection is an important factor in the development of cervical cancer, this infection is not sufficient. Additional cellular changes are required and we have been studying the role of a candidate for one of these changes, the Hedgehog (Hh) signalling pathway. Components of the Hh pathway are expressed in cervical cancer cells, indicating the possibility of an autocrine Hh signalling loop in these cells. Furthermore, inhibition of Hh signalling pathway reduces survival of cervical cell lines and induces apoptosis. The Shh ligand induces cell proliferation and promotes cell migration in some cervical cell lines. Our results indicate that Hh signalling has a pro-survival and protective role in cervical cancer cells, and suggest that inhibiting this pathway may contribute to therapy against cervical cancer.

EPFL School of Life Sciences - 2011 Annual Report

Fragkos, M. and Beard, P. (2011) Mitotic catastrophe occurs in the absence of apoptosis in p53-null cells with a defective G1 checkpoint. PLoS ONE Vol. 6: Issue 8 e22946. Laredj, L.N. and Beard, P. (2011) Adeno-associated virus activates an innate immune response in normal human cells but not osteosarcoma cells. J. Virol. 85 : 13133–13143. Ingemarsdotter C, Keller D, Beard P. (2010) The DNA damage response to nonreplicating adeno-associated virus: Centriole overduplication and mitotic catastrophe independent of the spindle checkpoint. Virology 400:271-86. Fragkos M, Jurvansuu J, Beard P. (2009) H2AX is required for cell cycle arrest via the p53/p21 pathway. Mol Cell Biol. 29:2828-40.

Team Members Postdoctoral Fellows Leila Laredj Ivana Samarzija Technician Nicole Paduwat Trainee Sangeeta Dey Bachelor’s students Manon Muller Katarina Damjanovic Administrative assistant Geneviève Massy

ISREC - Swiss Institute for Experimental Cancer Research

Selected Publications

A three-dimensional artificial bone-like scaffold for the culture of osteosarcoma cells.

ISREC

EPFL School of Life Sciences - 2011 Annual Report

Brisken Lab

http://brisken-lab.epfl.ch

http://www.nccr-oncology.ch

Cathrin Brisken received an MD and a PhD in Biophysics from the University of Göttingen in 1993. She worked as a postdoc and research scientist at the Whitehead Institute, MIT, Cambridge, USA. She was assistant professor at the MGH Cancer Center, Harvard University before joining the NCCR Molecular Oncology at ISREC in 2002. In 2005 she was appointed Tenure Track Assistant Professor at EPFL and then promoted to Associate Professor in 2012. Cathrin Brisken is a member of various scientific advisory boards and of the “Hinterzartener Kreis”, the DFG cancer think tank.

Cathrin Brisken Associate Professor

Introduction

Breast cancer strikes one out of eight women in Switzerland. A woman’s risk to get breast cancer is linked to her life time exposure to hormones. Early pregnancies have a protective effect and breast cancer risk increases with the number of menstrual cycles experienced prior to a first pregnancy. Hormones also influence the course of the disease. We study how hormones control the breast in vivo, in particular the mechanisms by which they elicit cell proliferation and changes in structure of the breast tissue, to gain insights into the genesis of the disease and to develop new preventive and therapeutic strategies. We have established the role of estrogens, progesterone and prolactin in mammary gland development (summarized in scheme 1).

Scheme 1: Schematic representation of the hormonal control of mammary gland development (black) based on our previous work.

Keywords

Breast cancer, hormones, bisphenol A, paracrine signaling

Results Obtained in 2011

Does breast cancer begin in utero ? Perinatal exposure to bisphenol A increases adult mammary gland progesterone response & cell number Bisphenol A (BPA, 2,2,-bis (hydroxyphenyl) propane), originally synthesized as a chemical estrogen, is a high-volume chemical with a global production of 3 million tons per year. It is utilized, to manufacture food and beverage containers from which it can leach out. Uptake is mostly via food and drinks as well as dental fillings and skin contact with thermal paper, widely used for receipts. It has been

detected in different body fluids in 90% of people examined in the US. To date, regulatory bodies in the US and EU support safety of low dose BPA exposure, defined as ≤ 5 mg/kg-body weight (bw)/day. A number of studies in rodents raise the concern that exposure to low doses of BPA may have developmental effects in various hormone responsive organs, including the mammary gland, with potential consequences for public health. The hypothesis that perinatal exposure to hormonally active compounds may affect breast cancer risk has been put forward. It is supported by observations made on women exposed to diethylbestrol (DES) in utero. This estrogenic compound was widely administered to pregnant women in the 1950s and 1960s. The FDA banned DES when uterine exposure to the drug was linked to clear cell vaginal adenocarcinoma in teenage girls. Recently, DES daughters were found to have an almost two fold higher breast cancer risk after age 40. To assess whether perinatal exposure to low dose BPA in environmentally relevant conditions affects the mammary gland, we mimicked human exposure, most of which occurs by mouth via food and beverage containers, by adding BPA to the drinking water of breeding C57Bl6 mice. We tested a range of doses below those used in standard toxicology testing (5 mg/kg-bw/d). We find that perinatal exposure to environmentally-relevant has dose-dependent effects on the mammary gland. It results in long term changes : it affects the response to estrogens during puberty and alters the response to progesterone with increased mammary epithelial cell numbers in adult females similar to that elicited by DES exposure. Molecularly, we identify increased induction of the central mediators of progesterone function, wnt-4 and RANKL. Hence, perinatal exposure to environmentally relevant doses of BPA has long-term effects on the mammary gland with implications for breast cancer risk that need to be carefully evaluated.

EPFL School of Life Sciences - 2011 Annual Report

Selected Publications

Team Members

Ayyanan, A., Laribi, O., Schuepbach-Mallepell, S., Schrick, C., Gutierrez, M., Tanos, T., Lefebvre, G., Rougemont, J., Yalcin-Ozuysal, O,. Brisken, C. (2011) Perinatal exposure to bisphenol A increases adult mammary gland progesterone response and cell number Mol. Endocrinol. 25(11): 1915-23.

Graduate Student Buric Duje

Dong J, Huang S, Caikovski M, Ji S, McGrath A, Custorio MG, Creighton CJ, Maliakkal P, Bogoslovskaia E, Du Z, Zhang X, Lewis MT, Sablitzky F, Brisken C, Li Y. (2011). ID4 regulates mammary gland development by suppressing p38MAPK activity. Development 138(23): 5247-56.

Hu, B. Lefort, K., Qiu, W., Nguyen, B. C., Rajaram, R., Castillo, E., He, F., Chen, Y., Angel, P., Brisken, C., Dotto, G. P. (2010). Control of hair follicle cell fate by underlying mesenchyme through a CSL -Wnt5a-FoxN1 regulatory axis. Genes and Development, 15(24): 1519-32. Battula, V. L., Evans, K., Hollier, B. G., Shi, Y., Marini, F.C., Ayyanan, A., Brisken, C., Michael Andreeff, M., Mani, S. A. (2010). Epithelial-to-Mesenchymal Transition Generates Functional Mesenchymal Stem/Stromal Cells Stem Cells, 28(8):1435-45.

Postdoctoral Fellows Jimenez Rojo Lucia, Rajaram Renuga Devi Tamara Tanos Caikovski Marian

MD/PhD Student Guri Yakir Senior Technician Ayyanan Ayyakkannu Technician Gutierrez Najera Maria Halber Jean Administrative Assistant Cepeda Lisa

Yang, C., Chen, L., Li, C., Lynch, M. C., Brisken, C., Schmidt, E. V. (2010). Cyclin D1 enhances the response to estrogen and progesterone by regulating progesterone receptor expression. Mol Cell Biol. 30(12):3111-25. Yalçın-Özuysal, O., Fiche, M., Guitierrez, M., Wagner, K. U., Raffoul, W., Brisken, C. (2010). Antagonistic roles of Notch and p63 in controlling mammary epithelial cell fates. Cell Death Differ,17(10):1600-12. Beleut, M., Rajaram, R., Caikovski, M., Ayyanan, A., Germano, D., Choi, Y., Schneider, P., Brisken, C. (2010). Two distinct mechanisms underlie progesterone-induced proliferation in the mammary gland. Proc Natl Acad Sci U S A. 2010 Feb 16;107(7):2989-94. Booth BW, Boulanger CA, Anderson LH, Jimenez-Rojo L, Brisken C, Smith GH. (2010) Amphiregulin mediates self-renewal in an immortal mammary epithelial cell line with stem cell characteristics. Exp Cell Res. 2010 Feb 1;316(3):422-32.

ISREC - Swiss Institute for Experimental Cancer Research

Reviews : Rajaram, R. , Brisken, C., (2011). Paracrine signaling by progesterone. Mol Cell Endocrinol. Sept 16 epub. Tanos, T.,Brisken, C., (2011). High hopes for RANKL. Will the mouse model live up to its promise? Breast Cancer Research, 11(6): 306.

Bisphenol A: Top: Consumer products that contain bisphenol A. Bottom: Chemical structure of 17-β-estradiol, bisphenol A and DES all of which interact with the estrogen receptor.

ISREC

EPFL School of Life Sciences - 2011 Annual Report

Constam Lab

http://constam-lab.epfl.ch

Daniel Constam received his doctoral degree from ETH ZĂźrich for studying the immunoregulatory cytokine TGF in the central nervous system (1993). In 1994, he became an EMBO postdoctoral fellow at Harvard University where he investigated the regulation of TGF signaling by proprotein convertases during embryogenesis. He joined ISREC as a group leader in 2000 and EPFL in 2005, where he was appointed associate professor at the School of Life Sciences in 2007. His general interest is in elucidating molecular interactions between stem and progenitor cells and their microenvironments and how they effectuate normal tissue morphogenesis.

Daniel Constam Associate Professor

Introduction

Both during normal development and in solid tumors, secreted proteins of the TGF and Wnt families can mediate pro- or anti-differentiation signals. Our aim is to elucidate how the morphogenetic potential of such signals is harnessed, especially to balance pluripotency and lineage restriction during the initial stages of normal mammalian embryogenesis, but also in other contexts such as the developing kidney or pancreas. A current focus is on live imaging of secreted endoproteases of the proprotein convertase family that regulate TGF signals of Nodal and its coreceptor Cripto in adjacent pluripotent cells. We also study the regulation of miRNA-mediated mRNA silencing by Bicc1. We showed that this RNA-binding protein is required to orient motile cilia that bias Nodal signaling to the left side during left-right patterning of the visceral organs. In addition, deletion of Bicc1 induced cystic growth in renal and pancreatic tubules. Identification of relevant Bicc1 target RNAs provides a new approach to study the etiology of polycystic kidney diseases.

Keywords

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

Results Obtained in 2011

In implanted blastocysts, expression of the TGF family member Nodal in the inner cell mass sustains pluripotency and suppresses neural differentiation of its derivative, the epiblast, until autoregulatory feedback establishes distinct Nodal activity thresholds to induce mesoderm and endoderm formation. Feedback regulation relies on a complex with the coreceptor Cripto and signalling receptors that stimulate Smad2 and Smad3 transcription factors following proteolytic removal of an inhibitory propeptide from the Nodal precursor protein. It is crucial, therefore, to know when and where the Nodal precursor is activated.

Nodal processing involves overlapping activities of the endoproteases Furin and Pace4. These and related proprotein convertases in general are thought to process various growth factors, hormones, adhesion molecules and metalloproteases in exocytic vesicles. However, rather than being coexpressed with Nodal and Cripto in the epiblast, Furin and Pace4 are transcribed in adjacent extraembryonic lineages, suggesting Furin and Pace4 may act in a paracrine fashion. To test this, transgenes encoding fluorescent GFP fusions were specifically expressed in the trophoblast. Both FurinGFP and Pace4GFP reached the epiblast and significantly rescued Nodal function in Furin-/-;Pace4-/- double knockout (DKO) embryos. To monitor their range of action, we used a cell surface-linked indicator of proteolysis (CLIP) where the cleavage motif RQRR links cyan fluorescent protein to citrine at the plasma membrane (Fig. 1A). Imaging of CLIP transgenic embryos revealed that eCFP was efficiently cleaved off in wild-type but not in DKO epiblasts. However, expressing FurinGFP or Pace4GFP in the extraembryonic ectoderm restored CLIP processing in DKO epiblasts to levels comparable to those in Furin+/-;Pace4+/- double heterozygotes (Fig. 1B, C). Thus, secreted Furin and Pace4 activities directly act on remote target cells (Fig. 1D). Imaging will be useful to explore physiological functions of these and possibly other secreted proteases also in other contexts. We also studied the RNA-binding protein Bicc1 and its new role in miRNA-mediated silencing. Targeted deletion of mouse Bicc1 induces polycystic kidney disease combined with visceral situs defects. In collaboration with colleagues at EPFL and Paris University Pierre & Marie Curie (UPMC), we now identified the first human BICC1 mutations associated with unilateral renal cysts in heterozygous pediatric patients. We previously reported that Bicc1 attenuates canonical Wnt signaling at the level of Dishevelled, albeit independently of RNA binding domains. Ongoing studies explore the regulation and function of direct target RNAs. We also developed sensitive assays to delineate how human BICC1 mutations affect these and other downstream targets.

EPFL School of Life Sciences - 2011 Annual Report

Selected Publications

Mesnard, D., M. Donnison, C. Fuerer, P.L. Pfeffer, and D.B. Constam (2011). The microenvironment patterns the pluripotent mouse epiblast through paracrine Furin and Pace4 proteolytic activities. Genes Dev. 25:1871-1880. Kraus, M.R., S. Clauin, Y. Pfister, M. Di Maio, T. Ulinski, D. Constam, C. Bellanne-Chantelot, and A. Grapin-Botton (2011). Two mutations in human BICC1 resulting in WNT pathway hyperactivity associate with cystic renal dysplasia. Hum. Mutat. 33(1):86-90. Susan-Resiga, D., R. Essalmani, J. Hamelin, M.C. Asselin, S. Benjannet, A. Chamberland, R. Day, D. Szumska, D. Constam, S. Bhattacharya, A. Prat, and N.G. Seidah (2011). Furin is the major processing enzyme of the cardiac-specific growth factor bone morphogenetic protein 10. J. Biol. Chem. 286:2278522794. Mesnard, D., and Constam, D.B. (2010). Imaging proprotein convertase activities and their regulation in the implanting mouse blastocyst. J. Cell Biol. 191(1):129-139.

Team Members Postdoctoral Fellows Bruno Filippi Christophe Fuerer Daniel Mesnard Nathalie Piazzon PhD Students Anja Dietze Susanna Kallioinen Chhavi Jain Florian Bernet Staff Séverine Urfer-Beck Stéphane Baflast Administrative Assistant Virginie Kokocinski

ISREC - Swiss Institute for Experimental Cancer Research

Rowe, H. M., Jakobsson, J., Mesnard, D., Rougemont, J., Reynard, S., Aktas, T., Maillard, P. V., Layard-Liesching, H., Verp, S., Marquis, J., Spitz, F., Constam, D. B., and Trono, D. (2010) ‘KAP1 controls endogenous retroviruses in embryonic stem cells’, Nature 463(7278): 237-240.

Imaging FurinGFP and Pace4GFP and their activities. Transgenic (tg) Furin and Pace4 are secreted apically or basally by ExE (A, arrows) and rescue cleavage of the reporter substrate CLIP in Furin; Pace4 double knockout (DKO) epiblasts (B-D), consistent with a paracrine role in Nodal processing (E).

ISREC

EPFL School of Life Sciences - 2011 Annual Report

De Palma Lab http://people.epfl.ch/michele.depalma

Michele De Palma

Michele De Palma obtained his Ph.D. in 2004 at the University of Turin Medical School, Italy, where he developed with Dr. Naldini genetic vectors and transgenic mouse models to study the role of bone marrow-derived cells to tumor angiogenesis. He described a macrophage subset that promotes angiogenesis in tumors and regenerating tissues, the Tie2-expressing macrophages (TEMs). He then moved to the San Raffaele-Telethon Institute for Gene Therapy (TIGET) in Milan to continue his studies on the interplay between macrophages and tumor angiogenesis, and to explore the potential of monocyte-based delivery of biotherapeutics to tumors. He received several awards from the American and European Societies of Gene Therapy, and in 2009 he obtained a European Research Council Starting grant. In 2011, he was appointed Assistant Professor at the School of Life Sciences, EPFL.

Tenure Track Assistant Professor

Introduction

We have recently established our new laboratory at ISREC. The main focus of the lab is to investigate the interactions between macrophages and other components of the tumor microenvironment – tumor blood vessels in particular – with the ultimate goal to identify therapeutic targets in the macrophages that could restrain their proangiogenic and protumoral functions.

Keywords

Tumor-associated macrophage; Angiogenesis; microRNA; TIE2; Angiopoietin-2 (ANG2); Antiangiogenic therapy.

Results Obtained in 2011

It is now well established that macrophages foster tumor progression by diverse mechanisms, one of which is the promotion of angiogenesis. We have previously identified a perivascular macrophage subset (TIE2+ macrophages) with marked proangiogenic activity, and contributed to elucidating the molecular and functional heterogeneity of tumor-associated macrophages (TAMs) in mouse models of cancer. During the year 2011, we have clarified the importance of the angiopoietin-2 (ANG2)/TIE2 axis for macrophage-mediated tumor angiogenesis (Mazzieri et al., Cancer Cell 2011), and identified a novel miRNA, miR-511-3p, which modulates TAM’s protumoral genetic programs (Squadrito et al., Cell Reports 2012). We have also shown, in collaboration with Prof Claire Lewis (Sheffield, UK), that TIE2+ TAMs modulate tumor responses to vascular disrupting agents by protecting tumor blood vessels from the effects of the drug (Welford et al., J Clin Invest 2011). Current research interests in our laboratory include:

cells, thus modulating angiogenesis. We are currently exploring this scenario by using genetic strategies that sense, squelch or enforce microRNA trafficking from macrophages to endothelial cells in tumors. Analyzing the contribution of macrophages to tumor responses (and resistance) to antiangiogenic therapy. Recent studies suggest that macrophages may help tumors resist different anticancer treatments. We are currently investigating how TAMs modulate tumor responses to antiangiogenic drugs either targeting the VEGF/VEGFR2 or ANG2/ TIE2 signaling pathway. This will be pursued primarily by molecular profiling of distinct TAM subsets (along with other tumor-associated stromal cells) from both untreated and treated mouse tumors (breast, pancreatic neuro-endocrine, and lung cancer models). These studies may help identify novel targets for combination-based treatments as well as biomarkers of tumor response to antiangiogenic therapy. Molecular profiling of mouse TAMs will be extended to the analysis of human cancer specimens. Exploring the pro-fibrotic activity of macrophages in tumors. Macrophages are known to express several proteolytic and matrix-remodeling enzymes in tumors. Our gene expression studies also suggest that macrophages secrete several fibrous proteins, including selected collagens. We will investigate the significance of TAM-derived collagens for matrix biogenesis and angiogenesis in ad hoc mouse tumor models, and interrogate the involvement of ROCK2 in modulating the profibrotic activity of macrophages.

Exploring novel mechanisms whereby perivascular macrophages promote tumor angiogenesis. Besides their production of endothelial growth factors and proteolytic enzymes that facilitate the growth and expansion of new blood vessels, TAMs may release microvesicles that shuttle functional microRNAs to angiogenic endothelial

EPFL School of Life Sciences - 2011 Annual Report

Selected Publications

Squadrito, M. L., Pucci, F., Magri, L., Moi, D., Gilfillan, G. D., Ranghetti, A., Casazza, A., Mazzone, M., Lyle, R., Naldini, L., and De Palma, M. miR-511-3p modulates genetic programs of tumor-associated macrophages. Cell Reports. 2012 Feb 23;1(2):141-154. Takeda, Y., Costa, S., Delamarre, E., Roncal, C., Leite De Oliveira, R., Squadrito, M.L., […], De Palma, M., and Mazzone, M.Macrophage skewing by PHD2 haplodeficiency prevents ischemia by inducing arteriogenesis. Nature. 2011 Nov 4;479:122-126. Welford, A.F.*, Biziato, D.*, Coffelt, S.B., Nucera, S., Fisher, M., Pucci, F., Di Serio, C., Naldini, L., De Palma, M.§, Tozer, G.M.§ and Lewis, C.E.§. TIE2-Expressing Macrophages Limit the Therapeutic Efficacy of the Vascular Disrupting Agent, Combretastatin A4 Phosphate. J Clin Invest. 2011 May 2;121:1969-73. *: Equal Contribution. §: Co-senior & co-corresponding authors.

Team Members Postdoctoral Fellows Mario Leonardo Squadrito Nicolò Rigamonti PhD Students Daniela Biziato Caroline Baer Research Assistants Giuseppe Muraca Claudio Maderna Administrative Assistant Christine Skaletzka

Mazzieri, R., Pucci, F., Moi, D., Zonari, E., Ranghetti, A., Berti, A., Politi, L.S., Gentner, B., Brown, J., Naldini, L., and De Palma, M. Targeting the Angiopoietin-2/TIE2 axis Inhibits Tumor Progression and Metastasis by Impairing Angiogenesis and Disabling Rebounds of Proangiogenic Myeloid Cells. Cancer Cell. 2011 Apr 12;19(4):512-26. Rolny, C., Mazzone, M., Tugues S, Laoui D, Johansson I, Coulon C, Squadrito ML, […], De Palma, M., Dewerchin, M., Claesson-Welsh, L., Carmeliet, P. HRG inhibits tumor growth and metastasis by inducing macrophage polarization and vessel normalization through downregulation of PlGF. Cancer Cell. 2011 Jan 18;19(1):31-44.

ISREC - Swiss Institute for Experimental Cancer Research

Andreu, P., Johansson, M., Affara, N. I., Pucci, F., Tan, T., Junankar, S., Korets, L., Lam, J., Tawfik, D., DeNardo, D. G., Naldini, L., de Visser, K. E., De Palma, M., and Coussens, L. M. FcRγ activation regulates inflammation-associated squamous carcinogenesis. Cancer Cell. 2010 Feb 17;17(2):121-134.

Lewis lung carcinoma tumor blood vessels visualized by Microfill perfusion.

ISREC

EPFL School of Life Sciences - 2011 Annual Report

Duboule Lab

http://duboule-lab.epfl.ch

Denis Duboule earned his PhD in Biology in 1984. He is currently Professor of Developmental Genetics and Genomics at the EPFL and at the department of Genetics and Evolution of the University of Geneva. Since 2001, he is also the director of the Swiss National Research Centre â&#x20AC;&#x2DC;Frontiers in Geneticsâ&#x20AC;&#x2122;. Duboule has a long-standing interest in the function and regulation of Hox genes, a family of genes responsible for the organization and evolution of animal body plans. He is an elected member of several academies and has received many awards, amongst which the Louis-Jeantet Prize for Medicine in 1998.

Denis Duboule

Full Professor EPFL & University of Geneva

Introduction

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

Keywords

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

emerges. To this aim, we looked at the development of digits, of the proximal part of the limbs (forearms and forelegs), the external genital organs as well as of the caecum, an organ specific for vertebrate animals eating vegetals. While all these contexts implement related regulatory mechanisms, important differences are observed, which illustrate the evolution of these large-scale regulatory circuits. We hope that their fine genetic and biochemical dissections will allow us to reconstruct their emergence and thus lead to a better understanding of the relationships between morphological variations and genome structure/regulation. We have also started to implement FISH technology to try and combine our genetic and biochemical analyses with an optical approach of how this particular locus behaves in space, under these various contexts.

Results Obtained in 2011

SystemsHox.ch; an in vivo System Approach to Hox Genes Regulation in Vertebrates. We would like to understand the relationships between genomic topology and the control of transcription, using the HoxD locus as a paradigm. We have continued to study the different kinds of long-range regulations that occur at the HoxD locus. In particular, we have analyzed in detail the collinear activation process, which leads Hox genes to be activated in time, one after the other following their genomic neighborhood. We discovered that this cis-acting process is closely associated with modifications in the general chromatin architecture of the locus. We have also investigated the regulation at work in various developing tissues where these genes are required, to try and see if a generic logic

EPFL School of Life Sciences - 2011 Annual Report

Selected Publications

Di-Poï, N., Montoya-Burgos, J., Miller, H., Pourquie, O., Milinkovitch, M. and Duboule, D. (2010) Changes in Hox genes’ structure and function during the evolution of the squamate body plan. Nature, 464, 99-103. Woltering J.M. and Duboule D (2010) The origin of digits : expression patterns versus regulatory mechanisms. Dev. Cell 18, 526-532.

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

Soshnikova N., Montavon, T., Leleu, M., Galjart, N. and Duboule D. (2010) Functional analysis of CTCF during mammalian limb development. Dev. Cell, 19, 819-830.

PhD students Guillaume Andrey Saskia Delpretti Nicolas Lonfat Patrick Schorderet

Tschopp P. and Duboule D. (2011) A regulatory ‘landscape effect’ over the HoxD cluster. Dev. Biol. 351, 288-96.

Technician Elisabeth Joye

Schorderet, P and Duboule, D. (2011) Structural and functional differences in the long non coding RNA HOTAIR in mouse and human. PLoS Genet 7(5): e1002071. Tschopp P., Fraudeau, N., Béna, F. and Duboule D. (2011) Reshuffling genomic landscapes and the impact of regulatory evolution upon neo-functionalization. Proc. Natl. Acad. Sci. USA, 108: 10632-10637.

Bioinformatician Marion Leleu Yohan Mouscaz Administrative Assistant Doris Sapin

Montavon, T., Soshnikova, N., Mascrez, B., Joye, E., Thevenet, L., Splinter, E., de Laat, W., Spitz, F. and Duboule D. (2011). A regulatory archipelago controls controls Hoxd gene expression in developing digits. Cell, 147, 1132-1145. Gyurjan, I., Sonderegger, B., Naef, F. and Duboule, D. (2011) Dynamic analysis of limb transcriptomes during mouse development. BMC Developmental Biology 2011, 11 :47. Noordermeer, D., Leleu, M., Splinter, E., Rougemont, J., De Laat, W. and Duboule, D. (2011) The dynamic architecture of Hox gene clusters. Science, 334, 222-225.

ISREC - Swiss Institute for Experimental Cancer Research

Tschopp, P. and Duboule, D. (2011) A genetic approach to the transcriptional regulation of Hox gene clusters. Ann. Rev. Genet. 45, 145-166.

Hoxd genes onset in the early limb bud: Early limb buds were harvested and prepared for various biochemical experiments. 4C-sequencing (Black plot) revealed a large region telomeric to the HoxD cluster interacting with Hoxd9 promoter, the most expressed Hoxd gene in this tissue (see: In Situ Hybridistion (ISH) of Hoxd9). This large region is decorated with an enhancer-associated mark: H3K27 Acetylation (Green plot). In addition an enhancer screen covering this portion of the genome revealed 3 CNSs eliciting strong transcriptional output of a reporter gene (lacZ) in limb buds. Altogether these data argue for an archipelago-like type of regulation of Hoxd genes during early limb bud development.

ISREC

EPFL School of Life Sciences - 2011 Annual Report

Gönczy Lab

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

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

Pierre Gönczy Full Professor

Introduction

Accurate cell division is fundamental for the correct execution of development and for self-renewing tissues. To better understand the mechanisms governing fundamental cell division processes, we use a unique combination of biochemical, computational, cell biological, molecular genetic and functional genomic approaches.

Keywords

Cell biology, developmental biology, centrosome duplication, asymmetric cell division, C. elegans

Results Obtained in 2011

The bulk of our effort have been directed towards better understanding the mechanisms governing asymmetric cell division and centrosome duplication. Asymmetric cell division. Asymmetric spindle positioning during cell division is critical for cell diversity in metazoan organisms. Our previous work led to a working model whereby asymmetric spindle positioning in C. elegans one-cell stage embryos relies on a ternary complex (LIN-5/GPR-1/2/Ga) that recruits the minus-end directed microtubule motor dynein to the cell cortex. Together with microtubule depolymerization, dynein allows pulling forces to be exerted along astral microtubules, thus ensuring proper spindle positioning. We had established that inactivation of the protein phosphatase complex PPH-6/SAPS-1 decreases pulling forces in C. elegans embryos, which correlates with diminished cortical GPR-1/2 and LIN-5. Mass-spectrometry analysis revealed that PPH-6/SAPS-1 associates with the Aurora-A kinase AIR1, and we found that mislocalization of AIR-1 likely explains the reduction in pulling forces in embryos depleted of PPH-6/ SAPS-1. Moreover, we found that Aurora-A is also required for spindle positioning in human cells, suggesting broad evolutionary conservation. We expanded our work on spindle positioning in human cells. We thus uncovered that levels of the ternary complex NuMA/LGN/Ga are critical for spindle positioning. Moreover, our study demonstrated that dynein is both necessary

and sufficient at the plasma membrane to direct spindle positioning. These findings help clarify the mechanisms by which the presence of dynein at the cell cortex dictates spindle positioning in metazoan organisms. Centrosome duplication. Centrioles exhibit a universal ninefold radial symmetry. In collaboration with the laboratory of Michel Steinmetz (PSI, Villingen, Switzerland), we established that oligomers of SAS-6 proteins are critical for this nine-fold radial symmetry. We found that SAS-6 proteins form rod-shaped homodimers that interact in a pair-wise fashion through their N-terminal domains to form oligomers. The team generated a structural model in which nine homodimers assemble into a ring from which nine coiled-coil rod domains radiate outwards, and found that such structures can self-assemble in vitro. These findings establish a structural basis of the universal nine-fold symmetry of centrioles. The Gönczy Lab also performed a genome-wide functional genomic siRNA-based screen in human cells to identify novel genes required for proper centriole formation. Using a custom-developed algorithm for automatic counting of centrosomes, the lab identified several candidate genes whose inactivation prevents or instead enhances centriole formation. We are in the process of performing secondary screens to validate these candidate genes. An investigation of the differential inheritance of centrioles in the germ line has also begun in the lab. Whereas in most proliferating cells the single centrosome present early in the cell cycle duplicates once per cell cycle, centrioles are eliminated during oogenesis but maintained during spermatogenesis. We set out to investigate the mechanisms governing centriole elimination in C. elegans oogenesis. The lab established that centrioles are eliminated in the diplotene stage of the meiotic cell cycle. Moreover, we discovered that the helicase CGH-1 promotes centriole elimination. Furthermore, using mutants in the sex determination pathway, we found that the karyotype of the germ cells plays a critical role for timely centriole elimination. These findings set the stage for a mechanistic dissection of centriole elimination during oogenesis in a metazoan organism.

EPFL School of Life Sciences - 2011 Annual Report

Selected Publications

Kitagawa, D., Kohlmaier G., Keller D., Strnad P., Balestra F.R., Flückiger, I. and Gönczy P. Spindle positioning in human cells relies on proper centriole formation and on the microcephaly proteins CPAP and STIL. J. Cell Sci. 124: 38843893 (2011). Thyagarajan K., Afshar K. and Gönczy P. Polarity Mediates Asymmetric Trafficking of the Gb Heterotrimeric G Protein Subunit GPB-1 in C. elegans Embryos. Development 138: 2773-2782 (2011). Kitagawa, D., Flückiger, I., Polanowska J., Keller, D., Reboul, J. and Gönczy P. PP2A phosphatase acts upon SAS-5 to ensure centriole formation in C. elegans embryos. Dev. Cell 20: 550-562 (2011). Kitagawa, D., Vakonanis, I., Olieric, N., Hilbert, M., Keller, D., Olieric, V., Bortfled, V., Erat, M.C., Flückiger, I., Gönczy P. and Steimetz, M.O. Structural basis of the 9-fold symmetry of centrioles. Cell 144: 364-375 (2011). Blanchoud S., Budirahardja Y., Naef F. and Gönczy P. ASSET: a robust algorithm for the automated segmentation and standardization of early C. elegans embryos. Dev. Dynamics 239:3285-3296. (2010) . Bezler A. and Gönczy P. Mutual antagonism between the Anaphase Promoting Complex and the Spindle Assembly Checkpoint contributes to mitotic timing in C. elegans. Genetics 186:1271-83 (2010) .

Team Members Postdoctoral Fellows Katayoun Afshar Paul Guichard Virginie Hamel Hachet Sachin Kotak Meritxell Orpinell Fernando Romero Balestra PhD Students Alexandra Bezler Simon Blanchoud Zhou Fang Christian Gentili Debora Keller Zoltan Spiro Kalyani Thyagarajan Lukas von Tobel Technicians Coralie Busso Isabelle Fluckiger Administrative Assistant Nicole De Montmollin

ISREC - Swiss Institute for Experimental Cancer Research

Regulation of cortical contractility and spindle positioning by the protein phosphatase 6 PPH-6 in one-cell stage C. elegans embryos. Development 137:237247 (2010).

Evolution of the cortical GFP-PAR-2 domain during asymmetric division of one-cell stage C. elegans embryo. Time is displayed along the Y axis (early: top), the embryo circumference along the X axis (posterior: center). Warmer colors indicate higher levels of GFP-PAR-2.

ISREC

EPFL School of Life Sciences - 2011 Annual Report

Grapin-Botton Lab http://grapinbotton-lab.epfl.ch/

Anne Grapin-Botton studied developmental biology of the nervous system in Paris (France) with Nicole Le Douarin and received her PhD in 1995. She carried out postdoctoral work with Doug Melton in Harvard University (Cambridge, USA) and joined ISREC as an associate scientist in 2001. In September 2005 she was appointed tenure track assistant professor in the School of Life Sciences at EPFL. Recently, she moved to Denmark to assume the position of Professor of Molecular and Cellular Biology in the new Danish Stem Cell center of the University of Copenhagen.

Anne Grapin-Botton Tenure Track Assistant Professor

Introduction

Our goal is to understand how the pancreas forms during development. The long term medical purpose is to use this information to generate replacement cells for patients suffering from diabetes and to understand pancreatic cancer progression.

Keywords

Development, embryo, pancreas, diabetes, endoderm, Wnt, Planar cell polarity, patterning, beta-cell, chick, mouse, architecture

Results Obtained in 2011

Regulation of pancreas organogenesis: role of the bHLH transcription factors Ptf1a and Ngn3. We investigated the mechanisms by which Ptf1a maintains and expands pancreas progenitors. We compared the transcriptome of early pancreas progenitors lacking Ptf1a to that of wild type progenitors and analyzed the chromatin regions bound by Ptf1a using ChiP-sequencing. Our experiments show that Ptf1a directly regulates a very large number of effector genes. However, its activities are also relayed by a network of 5 crucial transcription factors which regulate each other, thereby robustly maintaining pancreas progenitors (Thompson et al., 2012). Pancreas progenitors differentiate into exocrine cells and multiple endocrine cells whose main function is the regulation of glucose homeostasis. The transcription factor Ngn3 is absolutely necessary to generate endocrine cell and to promote their migration from the epithelium. We recently identified targets of Ngn3 which mediate its ability to trigger migration (Gouzi et al., 2011) and differentiation. In particular we found that Ngn3 induces planar cell polarity genes and are currently using mouse mutants for this pathway to study its function during development. Regulation of endocrine differentiation by intercellular communication pathways The differentiation of specific endocrine cells in the pancreas is controlled by distinct transcription factors. We recently found that β-cell differentiation does not proceed in a deterministic manner, but that it is regulated by communication between cells through the canonical and non-canonical Wnt pathways. Direct interferences with canonical Wnt signaling show that this pathway must be blocked for β-cells to differ-

entiate. Interferences with the non-canonical Wnt-planar polarity pathway have the opposite outcome. Moreover, inversin truncation mutants behave as overactive alleles resulting in decreased canonical Wnt signaling and increased β-cell differentiation. Our study suggests that the frequent type 2 diabetes risk alleles of the Wnt pathway component TCF7L2 may increase disease susceptibility by reducing the emergence of beta cells in embryos. Impaired endocrine differentiation upon mutation of a new putative Maturity Onset Diabetes of the Young (MODY5) gene Together with the Constam lab, we observed that inactivation of the RNA-binding protein Bicaudal C1 (Bicc1) in mice leads to kidney cyst formation as well as pancreatic cysts and reduced endocrine differentiation leading to glucose intolerance. The mechanisms by which Bicc1 inactivation causes these phenotypes, show that Bicc1 regulates PKD2 leading to cyst formation in kidney and pancreas and that reduction of Ngn3 levels and activity triggers the re-routing of endocrine progenitors to exocrine fates. Since Bicc1 knock-out mice were strikingly similar to human MODY5 syndrome, with a team of geneticists led by Dr C. Bellanné-Chantelot, we identified patients with kidney dysplasia that carry Bicc1 mutations (Kraus et al., 2011). The sequencing of more patients is ongoing to evaluate the link with MODY5-type diabetes. Significance of this work for diabetes Although the function of the pancreas in controlling glucose homeostasis is compensated by insulin injection in diabetic patients, the physiological effects are inexact and too variable. Among approaches that are currently being explored to find a cure for diabetes are the isolation and propagation of embryonic or adult stem cells that can be engineered to produce endocrine hormones and then transplanted to patients. Our experiments are aimed at identifying the critical cellular transcription factors, signaling molecules and niche that are sufficient to transform cells, including ES and iPS cells, into β-cells. To assist diabetes therapy, we developed optical coherence microscopy in collaboration with the Lasser laboratory (EPFL) to image islets of Langerhans live in normal and diabetic mice (Villiger et al., 2009 and 2010). We also developed a 3D in vitro model that recapitulates mouse pancreas development that we are currently adapting to establish a model of human pancreas development (See figure).

EPFL School of Life Sciences - 2011 Annual Report

Thompson, N., Gésina, E., Scheinert, P., Bucher, P. and Grapin-Botton, A. (2012) Mechanisms of pancreas progenitor maintenance by Ptf1a are revealed by RNA profiling and ChIP sequencing. Mol. Cell Biol. 32(6):1189-99. Boutant M, Ramos OH, Tourrel-Cuzin C, Movassat J, Ilias A, Vallois D, Planchais J, Pégorier JP, Schuit F, Petit PX, Bossard P, Maedler K, Grapin-Botton A, VasseurCognet M. (2012) COUP-TFII Controls Mouse Pancreatic β-Cell Mass through GLP-1-β-Catenin Signaling Pathways. PLoS One. 7(1):e30847. R-C Kraus, M., Clauin, S., Pfister,Y., Di Maïo, M., Ulinski, T., Constam, D., Bellanné-Chantelot, C. and Grapin-Botton, A. (2011) Two mutations in human BICC1 resulting in Wnt pathway hyperactivity associate with cystic renal dysplasia. Human Mutation 33(1):86-90. Gouzi, M.; Kim, Y.H., Katsumoto, K., Johansson, K. and Grapin-Botton, A. (2011) Neurogenin3 initiates stepwise delamination of differentiating endocrine cells during pancreas development. Dev. Dyn. 240(3):589-604. Villiger, M, Goulley, J, Martin-Williams, EJ, Grapin-Botton, A and Lasser, T. (2010) Towards high resolution optical imaging of beta cells in vivo. Curr Pharm Des. 16:1595-608.

Team Members

Postdoctoral Fellows Filippo De Franceschi Keiichi Katsumoto Yung Hae Kim David Martin Marine Rentler-Courdier-Kraus PhD Students Corinne Berclaz Cédric Cortijo Chiara Greggio Laurence Lemaire Research Associate Nancy Thompson Technician Yvan Pfister Administrative Assistant Anne-Marie Rodel

ISREC - Swiss Institute for Experimental Cancer Research

Selected Publications

A new 3D in vitro model that recapitulates pancreas development from few starting cells.

ISREC

EPFL School of Life Sciences - 2011 Annual Report

Hanahan Lab

Douglas Hanahan, born in Seattle, Washington, USA, received a bachelorâ&#x20AC;&#x2122;s degree in Physics from MIT (1976), and a Ph.D. in Biophysics from Harvard (1983). He worked at Cold Spring Harbor Laboratory in New York from 1978-88 as graduate student and then as group leader. From 1988-2010 he was on the faculty of the Department of Biochemistry & Biophysics at UCSF in San Francisco. He has been elected to the American Academy of Arts & Sciences (2007), the Institute of Medicine (USA) (2008), the US National Academy of Science (2009), and EMBO (2010).

Douglas Hanahan

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

Introduction

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

Keywords

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

ma, melanoma, and breast cancer. Topics of investigation currently include mechanisms of angiogenesis, of adaptive/ evasive resistance to anti-angiogenic therapy, of invasion, and of tumor metabolism. Additional topics include the delineation of phenotypically distinctive molecular genetic subtypes of ostensibly similar tumors of the same type, cross correlated between mouse models and human, exemplified in a recent publication in pancreatic ductal adenocarcinoma (Collison et al 2011) and now extended to pancreatic neuroendocrine tumors and other tumor types.

Results Obtained in 2011

The Hanahan lab continues to investigate genetically engineered mouse models of de novo organ-specific carcinogenesis, seeking to define mechanisms of multi-step tumorigenesis and progression. The lab also performs mechanism-guided pre-clinical therapeutic trials involving function-targeted drugs, aiming to probe roles and functional importance, identify adaptive resistance that limits efficacy, and as appropriate incentivize clinical trials involving such targeted drugs and combinatorial regimens. The laboratory is currently studying two mouse models of pancreatic cancer (neuroendocrine and ductal), glioblasto-

EPFL School of Life Sciences - 2011 Annual Report

Selected Publications

Olson P, Chu GC, Perry SR, Nolan-Stevaux O, Hanahan D. (2011). Imaging guided trials of the angiogenesis inhibitor sunitinib in mouse models predict efficacy in pancreatic neuroendocrine but not ductal carcinoma. PNAS USA.108: E1275-1284. Xie L, Duncan MB, Pahler J, Sugimoto H, Martino M, Lively J, Mundel T, Soubasakos M, Rubin K, Takeda T, Inoue M, Lawler J, Hynes RO, Hanahan D, Kalluri R. (2011). Counterbalancing angiogenic regulatory factors control the rate of cancer progression and survival in a stage-specific manner. PNAS USA.108: 9939-9944. Allen E, Walters IB, Hanahan D. (2011). Brivanib, a dual FGF/VEGF inhibitor, is active both first and second line against mouse pancreatic neuroendocrine tumors developing adaptive/evasive resistance to VEGF inhibition. Clin Cancer Res. 17: 5299-5310. Collisson EA, Sadanandam A, Olson P, Gibb WJ, Truitt M, Gu S, Cooc J, Weinkle J, Kim GE, Jakkula L, Feiler HS, Ko AH, Olshen AB, Danenberg KL, Tempero MA, Spellman PT, Hanahan D, Gray JW. (2011). Subtypes of pancreatic ductal adenocarcinoma and their differing responses to therapy. Nat Med. 17(4):500-503.

Team Members Postdoctoral Fellows Elizabeth Allen Ke Cheng Krisztian Homiisko Seiko Ishida Anguraj Sadanandam Ksenya Shchors Stephan Wullschleger PhD Students Nicola Brindle Leanne Li Technical Staff Ehud Drori Estelle Maillard Mei-Wen Peng Administrative Assistants Jennifer Brady Stéphanie Bouchet Laura Bischoff

Tuveson D, Hanahan D. (2011). Translational medicine: Cancer lessons from mice to humans. Nature. 471: 316-317.

ISREC - Swiss Institute for Experimental Cancer Research

Hanahan D, Weinberg RA. Hallmarks of cancer: the next generation. Cell.144 :646674. Review.

A ‘heatmap’ of genome-wide gene expression profiles reveals that subsets of ostensibly similar pancreatic neuroendocrine tumors (PNET) cluster together in distinctive groups, both mouse and human, according to their patterns of differential gene expression. The ‘cross filtering’ of mouse and human datasets focuses congruent changes that may represent significant functional determinants of tumor phenotypes. The results reveal heretofore unappreciated molecular subtypes, one of which is selectively associated with liver metastasis in both human PNET and the mouse model. (Figure courtesy of Dr. A. Sadanandam, unpublished.)

ISREC

EPFL School of Life Sciences - 2011 Annual Report

Hantschel Lab

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

Oliver Hantschel studied biochemistry at the University of Regensburg and at Rockefeller University in New York City. He received his PhD in 2004 from the European Molecular Biology Laboratory in Heidelberg and did postdoctoral work with Giulio Superti-Furga at the Research Center for Molecular Medicine of the Austrian Academy of Sciences in Vienna. In 2011, he was nominated Tenure Track Assistant Professor at the EPFL School of Life Sciences and was awarded the ISREC Foundation Chair in Translational Oncology.

Olivier Hantschel

Tenure Track Assistant Professor ISREC Foundation Chair Translational Oncology

Introduction

The Bcr-Abl tyrosine kinase and its small-molecule inhibitors, such as imatinib served as a paradigmatic case for modern targeted cancer therapy. Bcr-Abl is formed by a reciprocal chromosomal translocation event (t9;22 (q34;q11)) that leads to the fusion of the breakpoint cluster region (BCR) gene and the Abelson tyrosine kinase (ABL1), thereby generating a de-regulated, constitutively activated tyrosine kinase. Expression of Bcr-Abl is considered to be sufficient for the transformation of hematopoietic stem cells leading to chronic myeloid leukemia (CML) in humans and a CML-like myeloproliferative disorder in mice. The central role of Bcr-Abl in the pathophysiology of CML led to the development of the highly-specific Bcr-Abl inhibitor imatinib (Gleevec) that is now the frontline therapy for CML in all disease stages and induces durable complete cytogenetic responses in many patients in the chronic phase of CML. However, a proportion of patients does not achieve an adequate response to imatinib (now commonly referred to as ‘primary’ imatinib resistance), depending on the disease stage when patients are diagnosed. In addition, the occurrence of ‘secondary’ imatinib resistance, primarily caused by point mutations in the Abl tyrosine kinase domain, leads to patient relapse and disease progression and triggered the development of the second-generation inhibitors nilotinib and dasatinib that target most imatinib resistant Bcr-Abl variants. However, the general shortcomings of primary and secondary resistance especially in advanced disease stages and long-term tolerability of Bcr-Abl inhibitors remain a major clinical problem. Together with the inability of current Bcr-Abl inhibitors to target leukemia stem cells, additional targets that are critical for Bcr-Abl action need to be identified and exploited for combination therapy in order to ultimately result in a curative strategy for CML rather than maintaining patients in remission.

approaches at the interface of protein biochemistry, medicine, structural biology and chemical biology to study cancer cell signaling with the aim of finding novel ways for therapeutic intervention.

Keywords

Leukemia, Oncoproteins, Tyrosine kinases, Kinase inhibitors, Protein engineering, Protein structures, Protein phosphorylation, Proteomics, Protein-protein interaction domains

Research Projects

1. Development and validation of engineered high-affinity protein antagonists to target critical protein-protein interactions in oncogenic tyrosine kinases. 2. Analysis of signaling domains in Abl fusion-oncoproteins using biochemical structure-function analysis, biophysical characterization and mouse models. 3. Elucidation of the signaling mechanisms of Bcr-Abl interacting proteins in oncogenic transformation and leukemogenesis. 4. Comparative analysis of oncogenic kinase signaling networks using proteomics and transcriptomics. 5. Studies on the specificity and molecular mechanism-ofaction of small-molecule kinase inhibitors.

With an initial strong focus on tyrosine kinase oncoproteins that play a key role in the pathogenesis of several different leukemias and lymphomas, we are using interdisciplinary

EPFL School of Life Sciences - 2011 Annual Report

Selected Publications

Grebien, F. *, Hantschel, O. *, Wojcik, J., Kaupe, I., Kovacic, B., Wyrzucki, A. M., Gish, G. D., Cerny-Reiterer, S., Koide, A., Beug, H., Pawson, T., Valent, P., Koide, S. and Superti-Furga, G. (2011). Targeting the SH2-kinase interface in Bcr-Abl inhibits leukemogenesis. Cell, 147(2), 306–319. Sherbenou, D.W.*, Hantschel, O.*, Kaupe, I., Willis, S., Bumm, T., Turaga, L., Lange, T., Dao, K.H., Press, R.D., Superti-Furga, G., Druker, B.J. and Deininger, M.W. (2010). BCR-ABL SH3-SH2 domain mutations in chronic myeloid leukemia patients on imatinib, Blood, 116(17), 3278-3285.

Team Members PhD Students Emel Basak Gencer Orest Kuzyk

Technician Sandrine Georgeon Administrative Assistant Christine Skaletzka

Wojcik, J., Hantschel, O., Grebien, F., Kaupe, I., Bennett, K.L., Barkinge, J., Jones, R.B., Koide, A., Superti-Furga, G. and Koide, S. (2010). A potent highly specific FN3 monobody inhibitor of the Abl SH2 domain. Nat. Struct. Mol. Biol., 17(4), 519-527. Review Articles: Hantschel, O., Grebien, F. and Superti-Furga, G. (2011). Targeting allosteric regulatory modules in oncoproteins: “Drugging the Undruggable”. Oncotarget, 2(11), 828-829.

ISREC - Swiss Institute for Experimental Cancer Research

Valent, P., Gastl, G., Geissler, K., Greil, R., Hantschel, O., Lang, A., Linkesch, W., Lion, T., Petzer, A.L., Pittermann, E., Pleyer, L., Thaler, J. and Wolf, D. (2011). Nilotinib as Frontline and Second-Line Therapy in Chronic Myeloid Leukemia: Open Questions. Crit. Rev. Oncol. Hemat. , in press (PMID: 21903413).

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

ISREC

EPFL School of Life Sciences - 2011 Annual Report

Huelsken Lab

http://huelsken-lab.epfl.ch

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

Joerg Huelsken

Associate Professor Debiopharm Chair in Signal Transduction in Oncogenesis

Introduction

Years of cancer research have established the concept of cancer stem cells (CSC) as sub-population of cells within a tumor entirely responsible for long-term tumor growth. We now provide evidence that these cells are also essential for metastatic disease and characterize the interaction between stem cells and their environment as an essential factor for metastatic growth. In particular one component of the extracellular matrix was identified which presents a promising target to block spreading of cancer to secondary sites.

Keywords Stem cells, Cancer stem cells, Stem cell niches, Wnt signaling, Metastatic colonization

Results Obtained in 2011

In the last few years, we and others have identified hierarchical organization as a basic principle which applies not only to normal tissues but also to tumors. This has led to the identification of so-called cancer stem cells which are essential for initiating tumor growth and long-term tumor maintenance. We have now expanded this concept and shown that these rare cancer stem cells are also essential for metastatic progression. Moreover, we found that niche signals, i.e. signalling molecules and extracellular matrix components produced by surrounding stromal cells, participate in the control of cancer stem cell function and play an important role in expanding these stem cells. We furthermore found that such niche derived signals are of particular importance during the early phases of metastatic colonization, when cancer cells leave the primary niche and are suddenly exposed to a new environment. Cancer stem cells appear to critically depend on a â&#x20AC;&#x153;knownâ&#x20AC;? set of signaling molecules present at the primary site, however missing in the new environment. Consequently, infiltrating cancer cells attempt to re-program the target organ to generate a supportive niche. Since this is hardly ever successful, many disseminated cancer cells fail to initiate growth at a secondary site. This is in line with earlier reports which

described metastasis formation as an overall very inefficient process. Consequently, we were able to show that genetic ablation of essential niche components can render the body resistant to metastasis formation, even when challenged with large amounts of cancer cells. This clearly demonstrates that targeting the stem cell - niche communication could emerge as a viable approach to metastasis prevention and intervention. It is in particular the early metastatic colonization phase that can be expected to be sensitive to therapeutic intervention as the dependence of the cancer stem cell for niche signals is highest. We suggest that targeting the stroma-derived cancer stem cell niche holds the promise to be less prone to rapid genetic changes in cancer cells and therefore could turn out as a favorable regimen to avoid resistance and therapy escape. We have developed antibodies which can target stem cell niche molecules and interfere with cancer stem cell expansion. We are optimistic that such antibody-mediated therapies can be further developed and may be used for the benefit of cancer patients in the future.

EPFL School of Life Sciences - 2011 Annual Report

Selected Publications

Ordóñez-Morán P and J. Huelsken (2012). Lrig1: a new master regulator of epithelial stem cells. EMBO J., advance online publication. Malanchi*, I., A. Santamaria-Martínez*, E. Susanto, H. Peng, H.A. Lehr, J.F. Delaloye and J. Huelsken (2012). Interactions between cancer stem cells and their niche govern metastatic colonization. Nature, 481, 85–89. *these two authors contributed equally. This article has been highlighted in: • Wang Z. and G. Ouyang (2012). Periostin: A Bridge between Cancer Stem Cells and Their Metastatic Niche. Cell Stem Cell. 10, 111-2. • Oskarsson T. and J. Massagué (2011). Extracellular matrix players in metastatic niches. EMBO J. 31:254-6. • This article has been recommended in “Faculty of 1000” as “Must Read” by Ian Macara, Valerie Horsley, Eric Sahai, and Ana Tadeu. Smartt H.J., A. Greenhough, P. Ordóñez-Morán, E. Talero, C.A. Cherry, C.A. Wallam, L. Parry, M. Al Kharusi, H.R. Roberts, J.M. Mariadason, A.R. Clarke, J. Huelsken, A.C. Williams, and C. Paraskeva (2011). β-catenin represses expression of the tumour suppressor 15-prostaglandin dehydrogenase in the normal intestinal epithelium and colorectal tumour cells. Gut, advanced online publication.

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

Holowacz, T., J. Huelsken, D. Dufort, and D. van der Kooy (2011). Neural stem cells are increased after loss of β-catenin, but neural progenitors undergo cell death. Eur J Neurosci., 33, 1366-75. Jeannet, G., C. Boudousquié, N. Gardiol, J. Kang, J. Huelsken, and W. Held (2010). Essential role of the Wnt pathway effector Tcf-1 for the establishment of functional CD8 T cell memory. Proc Natl Acad Sci USA, 107, 9777-82.

ISREC - Swiss Institute for Experimental Cancer Research

Hussenet, T., J. Exinger, S. Dali, B. Jost, D. Dembelé, C. Thibault, J. Huelsken, E. Brambilla and S. du Manoir (2010). SOX-2 is a new oncogene activated by recurrent 3q26.3 amplifications in lung Squamous Cell Carcinomas. PLOS One, 5:e8960.

Tumour cells grow in a supportive niche prepared by stromal fibroblast. Extracellular matrix deposition (red) by primary lung fibroblast (violet) will enable breast cancer cells (green) to grow in an otherwise hostile environment.

ISREC

EPFL School of Life Sciences - 2011 Annual Report

Kühn Lab

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

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

Lukas Kühn

Adjunct Professor

Introduction

We study the role of ferritin in iron physiology by analyzing mice with a conditional deletion of the ferritin H gene. Ferritin H is necessary for iron storage and detoxification. Its absence increases intracellular free iron and the formation of reactive oxygen species that modify proteins and DNA, a known cause of cancer. By exploring iron-mediated oxidative damage, we gather basic information on consequences of iron overload as it occurs in the hereditary disease of hemochromatosis. Part of our activities is also devoted to studying rapid mRNA degradation.

Keywords

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

Results Obtained in 2011

Analysis of ferritin H knock-out mice Iron is essential for life and at the same time a hazard. Intracellular free iron catalyzes the formation of hydroxyl radicals, which cause cell damage and mutations in DNA. Body iron absorption from nutrients and intracellular free iron are accurately controlled to avoid iron excess or deprivation. In the human population, an excess of iron is observed in patients with idiopathic hemochromatosis. It is accompanied by tissue damage in liver, heart and pancreas, and can be the cause of liver cancer. Ferritin is a protein complex composed of ferritin H and L chains, which stores excess free iron. We have generated mouse strains in which we can conditionally delete the ferritin H gene in various tissues using the Cre lox method. Our current studies show that ferritin H plays a major role in the protection against intracellular free iron and oxidative radical formation. This year we have revisited the importance of the ferritin H gene in lymphocytes. A few years ago we had noticed that the Mx-Cre mediated ferritin H gene deletion in bone marrow provoked a reduction in the number of mature B and T cells. We have now confirmed these findings by analyzing the ferritin H gene deletion with B-cell specific CD19-Cre mice, as well as T-cell specific CD4-Cre mice. In both cases we found a similar reduction of lymphocytes as previously observed with the Mx-

Cre mediated deletion. The loss of cells was correlated with a high intracellular free iron pool and an increased fraction of cells showing mitochondrial depolarization. This condition leads to an increased cell death that affects preferentially mature B cells and T cells beyond the CD4+/CD8+ stage. We have also started to study the importance of ferritin H in macrophages using a LysM-Cre mediated deletion. Unlike lymphocytes, macrophages do not suffer cell death after the deletion. Iron storage in spleen and liver was strongly diminished showing that macrophages represent the major body iron storage sites. However, iron recycling from senescent erythrocytes, which are degraded in macrophages, was not affected, and deleted mice showed no changes in their hematocrit, red blood cell counts and hemoglobin levels. Finally, in collaboration with Patrick Fraering at the BMI, we have initiated deletion studies on ferritin H in the brain by Emx1-Cre known to be active in the cortex and hypothalamus during development. The mice were readily born and showed a normal phenotype at young age. However, the mice died spontaneously between 7 and 19 weeks of increasing hydrocephaly. Phenotypic alterations were clearly visible in brain sections (Figure). We found that the ferritin H was deleted not only in the cortex and hypothalamus, but also the ependymal epithelium of the choroid plexus. This cell layer is thought to be important for ion exchange and liquid flow between circulation and cerebrospinal fluid. It seems possible that the hydrocephalus is a consequence of a local damage at the choroid plexus due to the ferritin H deletion. Mechanisms of rapid mRNA degradation In parallel we study rapid mRNA degradation as it occurs in a large number of mRNAs that harbor instability elements, such as AU-rich sequences, in their 3’-untranslated regions. We have mainly made progress towards locating destabilizing elements in the short-lived mRNAs of c-Myc, RankL and Bcl6.

EPFL School of Life Sciences - 2011 Annual Report

Selected Publications

Vanoaica, L., Darshan, D., Richman, L., Schümann, K., and Kühn, L.C. (2010). Intestinal ferritin H is required for an accurate control of iron absorption. Cell Metabolism. 12:273-282.

Team Members Postdoctoral Fellow Claude Schweizer PhD Student Ramona Batschulat Specialist technician Larry Richman

ISREC - Swiss Institute for Experimental Cancer Research

Administrative assistant Geneviève Massy

Whole brain sections of 7-week old Fthlox/lox control mice (A, C) and FthD/D deleted mice (B, D). Sagittal sections (A, B) are stained with Luxol fast blue and cresyl violet. Coronal sections (C, D) across frontal cortex and striatum are H&E-stained. Ferritin H deleted mice show an enlarged volume of lateral ventricles and reduced cortex thickness.

ISREC

EPFL School of Life Sciences - 2011 Annual Report

Lingner Lab

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

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

Joachim Lingner Full Professor

Introduction

Telomeres are the nucleoprotein structure at the ends of eukaryotic chromosomes. They protect chromosome ends from DNA repair activities. In addition, telomeres function as cellular clocks. With the doubling of chromosomes, which precedes cell division, telomeres get shorter. When reaching a critical length, short telomeres elicit a DNA damage response which instructs the cells to stop dividing. Such cells are called senescent. Senescence occurs in order to suppress uncontrolled cell growth and the formation of life-threatening tumors. Telomerase is the cellular reverse transcriptase, which counteracts telomere shortening. Its expression is tightly regulated during human development, being expressed only during early embryogenesis, in germ cells and in some stem cells. Telomerase is also expressed in tumors, equipping cancer cells with an immortal phenotype. Our laboratory studies telomerase structure and mechanism. We are trying to elucidate how in cancer cells the telomerase enzyme is regulated at chromosome ends by telomere binding proteins and by TERRA, a large non-coding (lnc) RNA which is transcribed at telomeres. We are also studying the regulation of TERRA and its roles in remodeling telomeric chromatin structure.

Keywords

Telomeres, telomerase, long noncoding RNA, TERRA, cellular senescence, genome stability

Results Obtained in 2011

Activation and recruitment of telomerase to chromosome ends Activation and recruitment of telomerase to chromosome ends are not well understood in complex eukaryotes including humans. Therefore, we developed assays to measure association of human telomerase with chromosome ends by chromatin immunoprecipitation, and our collaborators from the Terns-lab (University of Georgia) could for the first time detect human telomerase at chromosome ends by fluorescence in situ hybridization. We defined two critical steps that are required for telomerase maturation. First, we could show that Cajal bodies, subnuclear structures implicated in ribonucleoprotein assembly are critical for

telomerase maturation and the recruitment to telomeres. Second, through down-regulation of telomere binding proteins by RNA interference, we identified that the shelterin components TPP1 in association with TIN2 recruit human telomerase to chromosome ends to allow their extension in S phase of the cell cycle. Recently, we have also identified the human CST-complex, previously implicated in telomere protection and DNA metabolism, as regulator of telomerase activity. Regulation and function of TERRA lncRNA We discovered in eutherian mammals and in the yeast Saccharomyces cerevisiae that telomeres are transcribed into a lnc RNAs termed TERRA. We demonstrated that human TERRA functions as a potent mixed-type inhibitor of telomerase binding to the template sequence of the telomerase RNA in addition to interacting with the telomerase reverse transcriptase polypeptide. We found that the propensity of TERRA to act as an inhibitor of human telomerase is modulated by TERRA binding proteins. In S. cerevisiae we demonstrated that TERRA is regulated by telomere-binding proteins in a chromosome-end-specific manner that is dependent on subtelomeric repetitive DNA elements. At telomeres that contain only so-called X-elements, the telomeric Rap1-protein recruits the Sir2/3/4 and Rif1/2 complexes to repress transcription in addition to promoting Rat1-nuclease-dependent TERRA degradation. At telomeres that contain Yâ&#x20AC;&#x2122; elements, however, Rap1 represses TERRA through recruitment of Rif1 and Rif2. We mapped TERRA promoters and replaced it with a drug-regulatable promoter in order to modulate telomere transcription. This analysis established that TERRA induces telomere shortening in vivo in cis, at the chromosome end from which it is expressed. Genetic analysis indicates that TERRA promotes telomere shortening even in cells that lack telomerase, through activation of a nuclease which we have identified as Exonuclease I. Overall our data indicate that telomere transcription can regulate telomere length and cellular lifespan through the regulation of telomerase and through stimulation of nucleolytic processing activities at chromosome ends.

EPFL School of Life Sciences - 2011 Annual Report

Selected Publications

Pfeiffer, V, and Lingner J. TERRA Promotes Telomere Shortening through Exonuclease 1-mediated Resection of Chromosome Ends. PloS Genetics, in press. D’Ambrosio, D, Reichenbach, P, Mecheli, E, Alvino, A, Franceschin, M, Savino, M, and Lingner J. Specific binding of telomeric G-quadruplexes by hydrosoluble perylene derivatives inhibits repeat addition processivity of human telomerase. Biochimie 2012, 94: 854-863. Iglesias N, Redon S, Pfeiffer V, Dees M, Lingner J*, Luke B*. Subtelomeric repetitive elements determine TERRA regulation by Rap1/Rif and Rap1/Sir complexes in yeast. EMBO Rep 2011;12:587-93. *co-corresponding authors. Ferreira HC, Luke B, Schober H, Kalck V, Lingner J, Gasser SM. The PIAS homologue Siz2 regulates perinuclear telomere position and telomerase activity in budding yeast. Nat Cell Biol 2011; 13: 867-74. Redon S, Reichenbach P, Lingner J. The non-coding RNA TERRA is a natural ligand and direct inhibitor of human telomerase. Nucleic Acids Research 2010;38:5797-806.

Team Members Postdoctoral Fellows Eric Aeby Liuh-Yow Chen Sascha Feuerhahn Verena Pfeiffer Antonio Porro Sophie Redon Anselm Sauerwald Ivo Zemp PhD Students Alix Christen Jérôme Crittin Larissa Grolimund Andrea Panza Senior Lab Assistant Patrick Reichenbach Administrator Nicole de Montmollin

Porro A, Feuerhahn S, Reichenbach P, Lingner J. Molecular dissection of telomeric repeat-containing RNA biogenesis unveils the presence of distinct and multiple regulatory pathways. Mol Cell Biol 2010;30:4808-17. Feuerhahn S, Iglesias N, Panza A, Porro A, Lingner J. TERRA biogenesis, turnover and implications for function. FEBS Lett 2010;584:3812-8.

ISREC - Swiss Institute for Experimental Cancer Research

*Abreu E, *Aritonovska E, Reichenbach P, Cristofari, G, Culp, B, Terns, RM, **Lingner, J., and **Terns, MP. *co-first authors; **co-corresponding authors. TIN2-tethered TPP1 recruits human telomerase to telomeres in vivo. Mol Cell Biol 2010;30:2971-82.

Telomere binding proteins, TERRA and telomerase at chromosome ends. In S. cerevisiae (upper panel), telomerase is recruited to telomeres through Est1 and Cdc13. In humans (lower panel), telomerase recruitment requires Tpp1 and Tin2. TERRA and CST are also implicated in telomerase control.

ISREC

EPFL School of Life Sciences - 2011 Annual Report

Meylan Lab

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

Etienne Meylan received a PhD in Life Sciences from the University of Lausanne in 2006, for his work on innate immunity performed in the laboratory of Jürg Tschopp. From 2007 to 2010, he worked as a postdoctoral fellow in the laboratory of Tyler Jacks, at the Koch Institute for Integrative Cancer Research, MIT, Cambridge USA. In 2011, he established his research laboratory at ISREC, as a Swiss National Science Foundation Professor. His laboratory focuses on the molecular mechanisms that contribute to the development of non-small cell lung cancer.

Etienne Meylan SNSF Professor

Introduction

Our goal is to understand different molecular mechanisms that critically contribute to the development and progression of lung cancer, the leading cause of cancer related deaths in the world. We hope our discoveries will translate into knowledge-based preclinical and clinical trials to treat this devastating disease.

Keywords

Non-small cell lung cancer, mouse models, NF-kappaB, glucose metabolism

effect). However, altered glucose metabolism in cancer cells is only recently being re-evaluated. In our laboratory, we have begun to analyze the expression of various genes implicated in glycolysis, and how they are regulated during lung tumor progression. We identified that certain glucose transporters are aberrantly expressed in lung tumor cells, especially in higher-grade areas (see figure). We are hopeful that a better comprehension of alterations in glucose metabolism by cancer cells will help design small molecule compounds that target specific components of glycolysis or related pathways.

Results Obtained in 2011

During the year of 2011, the laboratory of Etienne Meylan was established, to investigate several aspects of non-small cell lung cancer development, using genetically-engineered mouse models, human cell lines and tissue samples. Two directions of research have been taken: (1) NF-kappaB signaling and (2) glucose metabolism. NF-kappaB signaling – Recent studies published by our laboratory and others have positioned NF-kappaB as a crucial pathway for the development and progression of non-small cell lung cancer, however the molecular mechanisms that control and are controlled by NF-kappaB are mostly unknown. We are using cell-based and in vivo approaches to elucidate how NF-kappaB signaling, directly in the tumor epithelial cells, controls tumor progression. Glucose metabolism – Otto Warburg described in 1924 that cancer cells produce lactate even in normoxic conditions, and thus exhibit altered glucose metabolism (the Warburg

EPFL School of Life Sciences - 2011 Annual Report

Selected Publications

Xue W, Meylan E, Oliver TG, Feldser DM, Winslow MM, Bronson R, Jacks T. (2011) Response and resistance to NF-?B inhibitors in mouse models of lung adenocarcinoma. Cancer Discov. 1(3): 236-247. Oliver TG, Meylan E, Chang GP, Xue W, Burke JR, Humpton TJ, Hubbard D, Bhutkar A, Jacks T. (2011) Caspase-2-mediated cleavage of Mdm2 creates a p53induced positive feedback loop. Mol Cell. 43(1): 57-71.

Team Members PhD Students Mark Masin Jawahar Kopparam Masterâ&#x20AC;&#x2122;s Student Laetitia Virard Technician Jessica Vazquez

ISREC - Swiss Institute for Experimental Cancer Research

Administrator Christine Skaletzka

Aberrant expression of glucose transporters in lung cancer. The expression of a glucose transporter was assessed by immunohistochemistry, from a lung tumor of a Kras(G12D)/WT; p53Flox/Flox mouse. The higher-grade area, as defined by nuclear atypia, is enriched for the presence of the transporter.

ISREC

EPFL School of Life Sciences - 2011 Annual Report

Radtke Lab

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

Freddy Radtke graduated from the University of ZĂźrich in molecular biology in 1994 and continued with a postdoctoral fellowship at Genentech Inc. USA (1995-1996) followed by a postdoctoral position at ISREC Switzerland 1997-1999. Prof. Radtke then became an Assistant Member of the Ludwig Institute for Cancer Research in 1999 and was promoted to Associate Member in 2004. He then joined ISREC as a Senior Scientist in 2006 before joining EPFL in August 2006 as an Associate Professor.

Freddy Radtke Associate Professor

Introduction

My group uses mouse genetics to study the molecular mechanisms controlling self-renewal and differentiation of normal and cancer stem cells in the blood system as well as in epithelial tissues including the intestine and the epidermis. The basic principle of self-renewing tissues is that they constantly produce cells from a stem cell reservoir that gives rise to proliferating transient amplifying cells, which subsequently differentiate and migrate to the correct compartment. These processes have to be under stringent control mechanisms to ensure life-long tissue homeostasis and their deregulation can lead to organ failure and/or cancer. Current attention is focused on the evolutionarily conserved Notch and Wnt signaling pathways, which play pleiotropic roles in different self-renewing tissues and cancer. The general concept is that a better understanding of the mechanisms controlling stem maintenance versus differentiation may lead to the identification of novel therapeutic targets, as well as improving strategies to manipulate these players during tumorigenesis.

Keywords

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

Results Obtained in 2011

Delta-like 1 and Delta-like 4 mediated Notch signaling are essential for intestinal stem cell homeostasis The intestinal epithelium is a self-renewing tissue with a high turn over rate and cellular processes such as proliferation, migration and cell death have to be under stringent control to ensure homeostasis of the tissue. The epithelium of the small intestine consists of four principal cell types: absorptive enterocytes, mucus secreting goblet cells, antimicrobial Paneth cells, and hormone secreting enteroendocrine cells. While most differentiated cell types reside within the villus, post-mitotic Paneth cells together with proliferating Lgr5+ stem and progenitor cells localize to the crypt compartment. We previously showed that Notch signaling (mediated by Notch 1 and 2) is essential for the maintenance of crypt progenitors. Ablation of Notch signal-

ing results in a rapid and massive conversion of proliferative crypt cells into post-mitotic goblet cells demonstrating that Notch is required for the high turn over and homeostasis of the intestinal epithelium. More recently, we performed lineage-tracing experiments combined with tissue specific gene targeting to show that Notch signaling is also occurring at the level of Lgr5+ stem cells and is important for their maintenance. Furthermore, we identified Delta-like 1 and 4 as the physiological Notch ligands of the small and the large intestine (Figure). Loss of cutaneous TSLP dependent immune responses skews the balance of inflammation from tumor-protective to tumor-promoting Inflammation can promote or inhibit cancer progression. We have addressed the role of the pro-inflammatory cytokine Thymic Stromal Lymphopoietin (TSLP) during skin carcinogenesis. Using conditional loss- and gain-of-function mouse models for Notch and Wnt signaling respectively, we demonstrate that TSLP mediated inflammation protects against cutaneous carcinogenesis by acting directly on CD4+ and CD8+ T cells. Genetic ablation of the TSLP receptor (TSLPR) perturbs T cell mediated protection and results in the accumulation of CD11b+ Gr1+ myeloid cells. These promote tumor growth by secreting Wnt ligands and augmenting b-catenin signaling in the neighboring epithelium. Epithelial specific ablation of b-catenin prevents both carcinogenesis and the accumulation of CD11b+Gr1+ myeloid cells, suggesting tumor cells initiate a feed-forward loop that induces pro-tumorigenic inflammation.

EPFL School of Life Sciences - 2011 Annual Report

Selected Publications

Koch U. and Radtke F. Mechanisms of T Cell Development and Transformation. Annu.Rev.Cell.Biol. Nov 10;27:539-62. (2011). Varnum-Finney B, Halasz LM, Sun M, Gridley T, Radtke F, and Bernstein ID.Notch2 governs the rate of generation of mouse long- and short-term repopulating stem cells, J Clin Invest. 2011 Mar; 121(3):1207-16. Pellegrinet L, Rodilla V, Liu Z, Chen S, Koch U, Espinosa L, Kaestner KH, Kopan R, Lewis J, and Radtke F. (2011). Dll1- and Dll4-mediated Notch signaling is required for homeostasis of intestinal stem cells. Gastroenterology. 2011 Jan 13. Jeannet R, Mastio J, Macias-Garcia A, Oravecz A, Ashworth T, Geimer Le Lay AS, Jost B, Le Gras S, Ghysdael J, Gridley T, Honjo T, Radtke F, Aster JC, Chan S, Kastner P. (2010) Oncogenic activation of the Notch1 gene by deletion of its promoter in Ikaros-deficient T-ALL. Blood. Dec 16;116(25):5443-54. Wendorff, A.A., Koch U., Wunderlich T, Wirth S., Dubey D., Br端ning J., MacDonald H.R. and Radtke F. (2010) Hes1 is a critical but context-dependent mediator of canonical Notch signaling in lymphocyte development and T-ALL. Immunity Nov 24; 33 (5):671-84.

Team Members

Postdoctoral Fellows /Scientists Matteo Di Piazza Nicolas Fasnacht Ute Koch Craig Nowell PhD Students Marzia Armaro Monique Coersmeyer Fabian Junker Rajwinder Lehal Luca Pellegrinet Viktoria Reinm端ller Bhushan Sarode Silvia Wirth Technicians Christelle Dubey Olivier Randin Administrative Assistant Catherine Pache

Di-Po誰 N, Koch U, Radtke F, and Duboule D. (2010) Additive and global functions of HoxA cluster genes in mesoderm derivatives. Dev Biol. May 15;341(2):488-98. Dumortier A, Durham AD, Di Piazza M, Vauclair S, Koch U, Ferrand G, Ferrero I, Demehri S, Song LL, Farr AG, Leonard WJ, Kopan R, Miele L, Hohl D, Finke D, and Radtke F. (2010) Atopic dermatitis-like disease and associated lethal myeloproliferative disorder arise from loss of notch signaling in the murine skin. PLoS One. Feb 18;5(2):e9258.

ISREC - Swiss Institute for Experimental Cancer Research

Radtke F, Fasnacht N, Macdonald HR. (2010) Notch signaling in the immune system. Immunity. Jan 29;32(1):14-27.

A. Schematic diagram of an intestinal crypt-villus axis of the small intestine. B. Intestinal physiological ligands DL1 and DL4 mediate Notch signaling through Notch1 (N1) and Notch 2 (N2) to regulate and maintain intestinal stem and progenitor cell fates.

ISREC

EPFL School of Life Sciences - 2011 Annual Report

Simanis Lab

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

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

Viesturs Simanis Associate Professor

Introduction

If the fidelity of the processes involved in cell division is reduced, there is an increased risk that errors will occur in the transmission of genetic information from a cell to its daughters; this can results in the death of the cells, or alter their properties, which can contribute to the development of diseases such as cancer. We study cytokinesis, the division of cells, to understand how it is regulated and coordinated with other events in the cell cycle, using the fission yeast model system. We focus upon the septation initiation network (SIN), a signalling pathway that regulates cytokinesis in vegetative cells and spore formation in meiosis. The SIN is comprised of three protein kinases, which are anchored at the poles of the mitotic spindle by a tripartite scaffold. Ectopic activation of the SIN triggers cytokinesis from any stage of the cell cycle, emphasizing the need for it to be regulated correctly. The use of a simple, genetically tractable system such as fission yeast allows us to analyse SIN regulation using a combination of genetics, and cell and molecular biology.

Keywords

Cell cycle / Schizosaccharomyces pombe / Cytokinesis / Protein kinase / Protein Phosphatase / Meiosis

Results Obtained in 2011

Identification of regulators of the SIN (Anupama Goyal, Evelyn Lattmann). We have used a variety of genetic screening approaches to identify regulators of the SIN, including the isolation of mutants dependent upon high levels of SIN signalling for viability, and isolation of extragenic suppressors of SIN mutants. The thesis work of Anupama Goyal involved characterisation of the two PP2A activator proteins of fission yeast. PP2A holoenzyme activity is regulated in part by peptidyl proline isomerases (PTPAs), which activate the catalytic subunit. S. pombe has two PTPA orthologues ypa1 and ypa2. In this study we show that Ypa1p and Ypa2p have independent, essential roles at low temperature. The ma-

jor isoform, Ypa2p, regulates cytokinesis at multiple levels. First, by influencing the position of the division site; second, by regulating septation initiation network signalling, which is involved in assembly and constriction of the contractile ring; third, by controlling the completion of cell separation. Furthermore, Ypa2p also affects cell morphology and the timing of mitotic entry. Anupama obtained her PhD degree in February 2012. Evelyn Lattmann has been working on regulators of the SIN isolated in a screen for spg1-dependent mutants. She has obtained novel alleles of known components of the SIN, and has also been characterizing a novel mutant that blocks septation if SIN signalling is elevated. We are presently analysing the gene defined by this mutation, to determine its role in regulation of the SIN. The role of dma1 in meiosis: (Andrea Krapp, Elena Cano). Meiosis is a specialised form of the cell cycle that gives rise to haploid gametes. In S. pombe, the products of meiosis are four spores, which are formed by encapsulation of the four meiosis II nuclei within the cytoplasm of the zygote that was produced by fusion of the mating cells. We investigated the role of the SIN regulator dma1p in meiosis, and discovered that though both meiotic divisions occur in the absence of dma1p, asci frequently contain fewer than four spores, which are larger than in wild-type meiosis. Staining with DAPI indicates the one or more nuclei do not become encapsulated within a spore. The spores that are produced have viability comparable to a wild-type spores, and the vast majority are haploid. Imaging of forespore membrane formation in living cells indicates that in the absence of dma1p, all SPBs initiate spore formation, but the process proceeds aberrantly on some SPBs. Our current studies are directed to finding substrates and regulators of dma1p in meiosis.

EPFL School of Life Sciences - 2011 Annual Report

Goyal A, Simanis V. Characterisation of ypa1 and ypa2, the Schizosaccharomyces pombe orthologues of the peptidyl proyl isomerases that activate PP2A, reveals a role for Ypa2p in the regulation of cytokinesis.Genetics (in press). Goyal A, Takaine M, Simanis V, Nakano K. Dividing the spoils of growth and the cell cycle: The fission yeast as a model for the study of cytokinesis. (2011) Cytoskeleton 68, 69-88. Krapp A., Cano Del Rosario E., and Simanis V. The role of Schizosaccharomyces pombe dma1 in spore formation during meiosis. (2010) Journal of Cell Science. 123 3284 - 3293.

Team Members Postdoctoral Fellows Krapp Andrea Wachowicz Paulina Phd Students Goyal Anupama Lattmann Evelyn Technician Elena Cano Del Rosario Administrative Assistant Catherine Pache

ISREC - Swiss Institute for Experimental Cancer Research

Selected Publications

The phenotype of a cold-sensitive mutant of PP2A. 1 is a cell with an eccentrically placed septum. 2 is cells with lagging chromosomes. 3 shows a pair of cells that have failed to separate, one of which has initiated the subsequent mitosis. 4 is a cell with aberrant morphology. Bar=10 mm.

ISREC

EPFL School of Life Sciences - 2011 Annual Report

Bucher Group

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

Philipp Bucher was first trained as a molecular biologist at the University of ZĂźrich, and subsequently received his PhD in computational biology at the Weizmann Institute of Science in Israel. He then worked as a postdoctoral fellow with Sam Karlin at Stanford University before he moved in 1991 to ISREC to continue his research in comparative molecular sequence analysis. In 1995, he was promoted senior scientist.

Philipp Bucher Group Leader

Introduction

New technologies allow for comprehensive characterization of the molecular processes that cause a healthy cell to become cancerous. These technologies produce vast amounts of data. We develop computational methods that will help to extract insights and knowledge from such data.

have studied their fate after the whole genome duplication event that has occurred in teleost fishes. The retention patterns observed in five completely sequenced fish genomes can possibly provide important clues about cis-regulatory interactions between such elements.

Cancer can be considered a gene regulatory disease. Normal regulation of genes permits the development and maintenance of a healthy human being. Abnormal regulation leads to various diseases. Cancer cells are maintained in a specific pathological state by gene regulatory circuits. Transcription factors are key elements of such circuits in that they control the expression of other genes while themselves being regulated by the products of genes. Our research aims at an understanding of transcriptional regulatory mechanisms in general, but with a particular focus on those which are affected by genetic lesions that cause cancer.

We are also interested in the use of molecular profiling data for medical diagnostic applications. In previous years, we tested several machine learning approaches to predict survival of breast cancer patients from microarray-based gene expression data. Last year we used our experience gained in this work to diagnose Acute Myeloid Leukaemia from flow cytometry data. The training and test data for this projects were provided by the FlowCAP consortium (Flow Cytometry: Critical Assessment of Population Identification Methods) as part of a machine learning challenge organized by the DREAM project (Dialogue for Reverse Engineering Assessments and Methods).

Keywords

Besides research, our group also develops and maintains bioinformatics databases and web servers. Last year, we have introduced a completely redesigned version of the 25 year old Eukaryotic Promoter Database EPD, with greatly increased coverage of the human and mouse genomes. The new resource is automatically compiled from so-called mass genome annotation data (ChIP-Seq and RNA-Seq) stored in a local repository. A special effort was made to offer powerful visualization tools for exploring the epigenetic environment (nucleosome positions, histone modifications, DNA methylation) of selected promoters (see Figure). Moreover, in collaboration with bio-engineers in the USA, we developed a new web server called ZFN-site which can be used to search genomes for target and off-target sites of zinc finger nuclease. Such enzymes are important genetic engineering tools for site-directed mutagenesis in large genomes.

Bioinformatics, Computational genomics, transcriptional regulation, ChIP-Seq data analysis, molecular diagnostics.

Results Obtained in 2011

We are currently pursuing two main research directions. One consists of using epigenetic profiles to classify gene regulatory regions, and to infer their activity status during development and across tissues. The other one focuses on so-called ultraconserved elements, DNA sequences which are almost 100% identical among all vertebrate species. Both projects have as a common goal to crack the still largely enigmatic regulatory code of our genome. For the analysis of epigenetic data, we have developed a probabilistic algorithm to extract prototypical patterns of histone modifications around in vivo transcription factor binding sites. The application of this new method to recently published ChIP-Seq data unambiguously confirmed earlier speculations that some transcription factors bind to nucleosome-free regions whereas others bind to DNA that is wrapped around nucleosomes. In order to gain insights into the function of ultraconserved sequence elements, we

EPFL School of Life Sciences - 2011 Annual Report

Selected Publications

Cradickm T.J., Ambrosini, G., Iseli, C., Bucher, P. and McCaffrey, A.P. (2011). ZFN-site searches genomes for zinc finger nuclease target sites and off-target sites. BMC Bioinformatics. 2011 May 13;12:152. Bussotti, G., Raineri, E., Erb, I., Zytnicki, M., Wilm, A., Beaudoing, E., Bucher, P. and Notredame C. (2011). BlastR--fast and accurate database searches for noncoding RNAs. Nucleic Acids Res. 39(16):6886-6895.

Team Members Postdoctoral Fellow René Dreos PhD Students Slavica Dimitrieva Administrative Assistant Sophie Barret

Meylan, S., Groner, A.C., Ambrosini, G., Malani, N., Quenneville, S., Zangger, N., Kapopoulou, A., Kauzlari,c A., Rougemont, J., Ciuffi, A., Bushman, F.D., Bucher, P. and Trono, D. (2011). A gene-rich, transcriptionally active environment and the pre-deposition of repressive marks are predictive of susceptibility to KRAB/KAP1-mediated silencing. BMC Genomics 12:378. Pjanic, M., Pjanic, P., Schmid, C., Ambrosini, G., Gaussin, A., Plasari, G,. Mazza, C., Bucher, P. and Mermod, N. (2011). Nuclear factor I revealed as family of promoter binding transcription activators. BMC Genomics 12:181. Jacques-Antoine Gauthier, J.-A., Widmer, D.E., Bucher, P. and Notredame, C. (2010). Multichannel sequence analysis applied to social science data. Sociological Methodology 40(1):1–38. Schmid, C.D. and Bucher, P. (2010). MER41 repeat sequences contain inducible STAT1 binding sites. PLoS One 5:e11425. Ait-Lounis, A., Bonal, C., Seguín-Estévez, Q., Schmid, C.D., Bucher, P., Herrera, P.L., Durand, B., Meda, P. and Reith, W. (2010). The transcription factor Rfx3 regulates betacell differentiation, function, and glucokinase expression. Diabetes 59(7): 1674-1685.

ISREC - Swiss Institute for Experimental Cancer Research

Groner, A.C., Meylan, S., Ciuffi, A., Zangger, N., Ambrosini, G., Dénervaud, N., Bucher, P. and Trono, D. (2010). KRAB-zinc finger proteins and KAP1 can mediate long-range transcriptional repression through heterochromatin spreading. PLoS Genet. 6(3):e1000869.

Epigenetic context of the human MGMT promoter displayed by the new EPD viewer in a UCSC browser window. The picture shows the location of transcription start sites, the abundances of two promoter-specific histone variants, the methylaton status of the DNA and the distribution of RNA polymerase II. The DNA methylation status of the MGMT promoter in certain cancer types is currently evaluated as a predictive marker for therapy choice.

EPFL School of Life Sciences

–

2011 Annual Report

Other SV Professors and Newcomer Professors

EPFL School of Life Sciences - 2011 Annual Report

Knowles

-Translational Research

Jonathan Knowles Full Professor

Research Interests

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

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

He was for 5 years the Chairman of the Research Directorsâ&#x20AC;&#x2122; Group of EFPIA (European Federation of Pharmaceutical Industry Associations) and was the founding chairman of the

EPFL School of Life Sciences - 2011 Annual Report

Molinari Group http://www.irb.ch/

ADJ

Maurizio Molinari earned a PhD in Biochemistry at the ETH-Zurich in 1995. He worked as a postdoctoral fellow in the laboratories of Cesare Montecucco (Padua, 1996-1997) and of Ari Helenius (Zurich, 1998-2000). Since October 2000, he is group leader at the IRB in Bellinzona. Dr. Molinari has received the Science Award 2002 from the Foundation for Study of Neurodegenerative Diseases, the Kiwanis Club Award 2002 for Medical Science, the Friedrich-Miescher Award 2006 and the Research Award Aetas 2007. Since 2008, Dr. Molinari is Adjunct Professor at the EPFL.

Maurizio Molinari

External Adjunct Professor Institute for Research in Biomedicine Bellinzona

Introduction

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

Keywords

Cell biology, protein folding, quality control and degradation, endoplasmic reticulum; molecular chaperones, folding enzymes, conformational diseases.

Results Obtained in 2011

ERAD Tuning: The Selective Clearance of ERAD Regulators from the ER Lumen-Several regulators of ERAD have shorter half-life compared to conventional ER chaperones. At steady state, they are selectively removed from the ER in a series of poorly defined events that we named ERAD tuning (Bernasconi and Molinari 2011). In an environment, the ER, where folding and disposal of newly synthesized cargo polypeptides are in kinetic competition, ERAD tuning sets ERAD activity at levels that do not interfere with

completion of ongoing folding programs and is therefore crucial to maintain cellular proteostasis. We have identified the complex comprising a type-I ER protein and the cytosolic protein LC3-I as an ERAD tuning receptor that regulates the COPII-independent vesicle-mediated removal of the luminal ERAD regulators EDEM1 and OS-9 from the ER (Submitted). Hijacking of ERAD Tuning by Viral Pathogens: the unconventional role of non-lipidated LC3-The COPII-independent vesicle-mediated removal of EDEM1 and OS-9 from the ER is hijacked by Coronaviruses (CoV) during their infection cycle and crucially depends on LC3-I, a cytosolic, ubiquitin-like protein. Before our reports (Calì et al 2008 and Reggiori et al 2010), LC3-I was simply considered as a cytosolic precursor of the autophagosomal protein LC3II. By revealing the role of LC3-I in ERAD tuning and in cell infection by CoV, our studies show for the first time an autophagy-independent function of this protein (deHaan et al. 2010, Reggiori et al. 2011). Malectin-We have functionally characterized Malectin, a novel ER-resident, stress-induced lectin binding di-glucosylated oligosaccharides displayed on newly synthesized polypeptides. Malectin shows prolonged association with misfolded protein conformers, consistent with a crucial role in ER quality control (Galli et al. 2011). Alzheimer’s Disease (AD)-In collaboration with the group of Patrick Aebischer, we have developed a novel technique for chronic in situ delivery of antibodies as an alternative to passive vaccination strategies. A polymer device loaded with genetically engineered C2C12 cells was implanted in the brain parenchyma of APP23 transgenic mice. Implanted cells supported secretion of single chain antibodies to the amyloid precursor protein, thereby preventing deposition of toxic Abeta aggregates. This substantially contrasted the worsening of behavioral, anxiety and memory defects, which are hallmarks of progressive AD (Marroquin et al. 2011).

EPFL School of Life Sciences - 2011 Annual Report

Selected Publications

Bernasconi, R., Soldà, T., Galli, C., Pertel, T., Luban, J. and Molinari, M. (2010) Cyclosporine A-Sensitive, Cyclophilin B-Dependent Endoplasmic ReticulumAssociated Degradation. PLoS ONE 5, e13008. Aebi, M., Bernasconi, R., Clerc, S. and Molinari, M. (2010) N-Glycan Structures: Recognition and Processing in the ER. TIBS 35, 74-82. Bernasconi, R., Galli, C., Calanca, V., Nakajima, T. and Molinari, M. (2010) Stringent Requirement for HRD1, SEL1L and OS-9/XTP3-B for Disposal of ERAD-LS Substrates. J. Cell Biol. 188, 223-235.

Team Members Post doctoral Riccardo Bernasconi PhD Students Jessica Merulla Julia Noack Senior Scientists Elisa Fasana Carmela Galli Tatiana Soldà

-Highlights in J. Cell Biol 188, 176.

Reggiori, F., Monastyrska, I., Verheije, M.H., Calì, T., Ulasli, M., Bianchi, S., Bernasconi, R., deHaan, C.H.M. and Molinari, M. (2010) Coronaviruses Hijack the LC3-I-Positive EDEMosome, ER-Derived vesicles Exporting Short-Lived ERAD Regulators, for Replication. Cell Host & Microbe 7, 500-508. -Highlights in Cell Host & Microbe 7, 424-426. -Editors’ Choice in Science 329, 14. -Leading Edge, Microbiology Select in Cell 142, 5. -Recommended by the Faculty of 1000.

de Haan, C.A.M., Molinari, M. and Reggiori, F. (2010) Autophagy-Independent LC3 Function in Vesicular Traffic. Autophagy 6, 994-996. Hebert, D.N. Bernasconi, R. and Molinari, M. (2010) ERAD Substrates: Which Way Out? Semin. Cell Dev. Biol. 21, 526-532. Galli, C., Bernasconi, R., Soldà, T., Calanca, V. and Molinari, M. (2011) Malectin Participates in a Backup Glycoprotein Quality Control Pathway in the Mammalian ER. PLoS ONE 6, e16304. Bernasconi, R. and Molinari, M. (2011) ERAD and ERAD Tuning: Disposal of Cargo and of ERAD Regulators from the Mammalian ER. Curr. Opin. in Cell Biol. 23, 176-183. Marroquin, O.B., Cordero, M.I., Setola, V., Bianchi, S., Galli, C., Bouche, N. Mlynarik, V. Gruetter, R., Sandi, C., Bensadoun, J.-C., Molinari, M. and Aebischer, P. (2011) Chronic Delivery of Antibody Fragments Using Immunoisolated Cell Implants as a Passive Vaccination Tool. PLoS ONE 6, e18268. Reggiori, F., deHaan, C.A.M. and Molinari, M. (2011) The Unconventional Use of LC3 by Coronaviruses through the Alleged Subversion of the ERAD Tuning Pathway. Viruses 3, 1610-1623.

External Adjunct Professors

A, Receptor-mediated exported from the ER of ERAD regulators, which is hijacked by CoV for replication. B, Misfolded polypeptides inhibit the receptor-mediated clearance of ERAD factors from the ER. This results in UPR-independent enhancement of the intraluminal concentration of ERAD regulators.

EPFL School of Life Sciences - 2011 Annual Report

Rainer Group www.unifr.ch/inph/vclab

ADJ

Gregor Rainer obtained a Diploma in experimental physics from the University of Vienna, and then completed a Ph.D. at the Massachusetts Institute of Technology in systems neuroscience. Following nine years of experience as postdoc and research group leader at the Max Planch Institute for biological cybernetics in TĂźbingen, he joined the faculty of medicine at the University of Fribourg in 2008 and was subsequently appointed adjunct professor at EPFL.

Gregor Rainer

External Adjunct Professor University of Fribourg

Introduction

Research in the Visual Cognition Laboratory encompasses the study of higher cognitive functions in the mammalian visual system, with a focus on cholinergic neuromodulation. We use analysis of behavior during various visually based tasks, multi-channel recording of neurons and field potentials and quantitative neuropeptide analyses using mass spectrometry.

Keywords

Visual system, cortex, neural plasticity, learning, acetylcholine.

Results Obtained in 2011

One line of investigation has focused on plasticity of representations in higher level visual cortex in primates. We have recently published findings related to how inferior temporal cortex neurons mediate categorization of faces belonging to the own species compared to other species faces. We found that the inter-species boundary in the neural representation was shifted towards the own species, showing that visual experience with members of the own species profoundly affects memory representation. In a related pharmacological study, we have shown that cholinergic activation is crucial for the performance of categorization tasks. We have also examined the relation between the local field potential and spiking activity in different parts of the visual processing hierarchy. We found close correspondence between these signals in prefrontal but not visual cortex, a finding that is of importance for the interpretation of neural mass signals in humans. We have performed detailed laminar recordings in primary visual cortex in tree

shrews, examining layer-specific aspects of temporal and feature selective neural activity. Of particular interest is the high temporal fidelity of tree shrew visual cortical neurons to transient visual stimulation, which is clearly visible as response bursts following each visual transient. Detailed laminar specific information about temporal aspects of visual responses is crucial for obtaining a mechanistic understanding of information flow in cortex. Finally, we have established a database based on nano-flow liquid chromatography and mass spectrometry analysis of brain tissue data. We have described a large number of neuropeptides in the tree shrew brain, which provides a tool for investigating functional changes in neuropeptide regulation during cholinergic activation.

EPFL School of Life Sciences - 2011 Annual Report

Selected Publications

Team Members

Rainer G. Allocating attention in rank-ordered groups. Neuron 70(1):5-7 (2011).

PhD Students Anwesha Bhattacharyya Julia Veit Abbas Khani Filomena Petruzziello Sara Falasca Vaclav Ranc

Hoerzer GM, Liebe S, Schloegl A, Logothetis NK and Rainer G Directed coupling in local field potentials of macaque V4 during visual short-term memory revealed by multivariate autoregressive models. Front.Comput. Neurosci. 4:14 (2010).

Chablais F, Veit J, Rainer G, Jazwinska A. The zebrafish heart regenerates after cryoinjury-induced myocardial infarction. BMC Dev Biol. 7;11(1):21 (2011).

Post doctoral Xiaozhe Zhang

Sigala R, Logothetis NK, Rainer G. Own-species bias in the representations of monkey and human face categories in the primate temporal lobe. J Neurophysiol 105: 2740-2752 (2011). Liebe S, Logothetis NK, Rainer G. Dissociable effects of natural image structure and color on LFP and spiking activity in the lateral prefrontal cortex and extrastriate visual area V4. J Neurosci 31(28):10215-10227 (2011). Veit J, Bhattacharyya A, Kretz R, Rainer G. Neural response dynamics of spiking and local field potential activity depend on CRT monitor refresh-rate in the tree shrew primary visual cortex J Neurophysiol 106: 2303-2313 (2011). Aggelopoulos NC, Liebe S, Logothetis NK, Rainer G. Cholinergic control of visual ategorization in macaques. Front Behav Neurosci 5 (73): 1-10 (2011).

External Adjunct Professors

Petruzziello F, Fouillen L, Wadenstein H, Kretz R, Andren P, Rainer G, Zhang XJ. Extensive characterization of Tupaia belangeri Neuropeptidome using an integrated Mass Spectrometry Approach. J Proteome Res dx.doi.org/10.1021/ pr200709 (2011).

Each refresh monitor causes a distinct visual transient in primary visual cortex (V1) of the tree shrew. The stimulus is shown between 0 to 80ms (vertical dashed bars) at a refresh rate of 120Hz in this example. The neural response latency is around 25ms.

EPFL School of Life Sciences - 2011 Annual Report

Schorderet Group www.irovision.ch

ADJ

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

Daniel Schorderet

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

Introduction

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

particularly during the formation of the digits. Recently, we identified mutations in a transporter that was exchanging magnesium for calcium in the retina and the teeth. Taken together, these results pinpoint the importance of calcium/ magnesium homeostasis in the development of the eye. We also associated mutations in PRSS56, a proteinase with trypsin-like serine protease activity, with posterior microphthalmia, a particular form of microphthalmia. This leads us to hypothesize that proteins of the sclera need to be digested to allow for correct expansion of the eye globe.

Keywords

Blindness, genetics of eye diseases, retinitis pigmentosa, glaucoma, age-related macular degeneration, diabetic retinopathy.

Results Obtained in 2011

At IRO, research centers around 4 axes: identification of new genes, understanding their function, developing animal models of eye diseases and new therapeutic tools. Anophthalmia /microphthalmia, a disease in which children are born with no or very small, non functional eyes, has recently emerged as one of the main research areas in gene identification in my laboratory. In 2011, we identified two new genes, SMOC1 in Waardenburg-anophthalmia syndrome and PRSS56 in posterior microphthalmia. These two genes illustrate two different pathways leading to small eyes. SMOC1, a calcium-binding protein, is assumed to interact with calcium signaling both in the retinal progenitors during eye development, and in bone formation, more

EPFL School of Life Sciences - 2011 Annual Report

Selected Publications

Team Members

Gal A et al. Autosomal recessive posterior microphthalmos is caused by mutations in PRSS56, a gene encoding a trypsin-like serine protease. Am J Hum Genet, 88(3):382-390,2011.

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

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

Emery M, Schorderet DF, Roduit R. Acute hypoglycemia induces retinal cell death in mouse. Plos ONE, 6(6):e21586,2011. Escher P, Schorderet DF, Cottet S. Altered expression of t he transcription factor Mef2c during retinal degeneration in Rpe65-/- mice. Invest. Ophthalmol Vis Sci, 52(8):5933-40,2011. Kotoulas A, Kokotas H, Kopsidas K, Droutsas K, Grigoriadou M, Bajrami H, Schorderet DF, Petersen M. A novel PIKFYVE mutation in fleck corneal dystrophy. Molec Vision 17:2776-2781,2011. Le Carré J, Schorderet DF, Cottet S. Altered expression of β-galactosidase-1-like protein 3 (Glb1l3) in the retinal pigment epithelium (RPE)-specific 65-kDa protein knock-out mouse model of Leber’s congenital amaurosis. Mol Vis 17:128797,2011. Ouechtati F et al. Clinical and genetic investigation of a large Tunisian family with complete achromatopsia: identification of a new nonsense mutation in GNAT2 gene. J Hum Genet. 56(1):22-8, 2011.

Research Associates Nathalie Allaman-Pillet Raphaël Roduit

PhD Students Séverine Hamann Fabienne Marcelli Lionel Page Gaëtan Pinton Désirée von Alpen Linda Wicht Laboratory technicians Céline Agosti Martine Emery Tatiana Favez Carole Herkenne Sylviane Métrailler Loriane Moret Administrative Assistants Pascale Evéquoz Sandra Théodoloz

Normal retina

Retina, 5 days post injury. Necrotic cells are observed at the site of the injury indicated by the arrow. No retinal layers are identifiable.

External Adjunct Professors

Neuroregeneration in the retina of an adult zebrafish after local external injury.

Retina, 100 days post injury. Retina is almost completely regenerated (arrow). The various retinal layers can be observed.

Tanner

EPFL School of Life Sciences - 2011 Annual Report

http://www.swisstph.ch

ADJ

Marcel Tanner

External Adjunct Professor Swiss TPH Insitute, Basel Director

Keywords

Epidemiology, public health, vaccines, drugs and diagnostics.

Research Interests

Swiss TPH (Tropical and Public Health Institute) and the EPFL School of Life Sciences are collaborating with the goal to bring together complementary expertise of the two institutions in research on host-pathogen interaction in infectious and chronic diseases and the development of new diagnostics, drugs and vaccines. Besides the collaboration in research, exchanges of teaching faculty and students within the MSc courses continued. Joint research activities with pathogenic mycobacteria and nematodes as target pathogens have been initiated. These disease-specific joint activities are complemented by collaborations in the fields of lipidomics and bioinformatics. The nematodes comprise a plethora of pathogens of medical, veterinary, and agricultural importance. Most of the pathogenic nematodes are difficult to maintain in the lab and their life-cycles cannot be completed in vitro. The freeliving nematode Caenorhabditis elegans, widely used as a model in developmental biology, provides an attractive tool for identification of novel anthelmintics and for functional characterization of the existing ones. Medium-throughput in vitro screening of chemical libraries against C. elegans

have been initiated in order to identify novel anthelmintic scaffolds and synthetic lethal compounds against drugresistant nematodes. Other collaborations between EPFL and Swiss TPH are focused on the mycobacterial pathogens Mycobacterium tuberculosis and M. ulcerans, the etiologic agents of tuberculosis and Buruli ulcer. Facilitated by access to the BSL3 laboratories at the GHI, a mouse model for Buruli ulcer has been established and will be used for the assessment of vaccine and drug candidates. In tuberculosis, it is planned to jointly investigate the human and bacterial genetic factors contributing to the immune reconstitution inflammatory syndrome (IRIS) in HIV-coinfected tuberculosis (TB) patients. The biannual report of Swiss TPH: http://www.swisstph.ch/fileadmin/user_upload/Pdfs/Biennial_Reports/Br_2009-10_full.pdf

EPFL School of Life Sciences - 2011 Annual Report

Welcome To Our New Collaborators!

Former Home Institution University of Zurich, Department of Neurology EPFL School of Life Sciences (BMI) since December 2011 Keywords Neurorehabilitation, neuroregeneration, neuroprosthetics, locomotion, spinal cord injury

GrĂŠgoire Courtine Associate Professor IRP Chair on Spinal Cord Repair

Former Home Institution University of Massachusetts EPFL School of Life Sciences (IBI) since October 2011 Keywords: Population genetics, evolutionary biology, statistical inference.

Jeffrey D. Jensen

New Collaborators

Tenure Track Assistant Professor

EPFL School of Life Sciences - 2011 Annual Report

9th edition 2011/2012 Produced and edited by the EPFL School of Life Sciences Printed at the EPFL “Atelier de Reprographie” Editor: Alice Emery-Goodman With many thanks to Bruno Liardon (photographs & cover design), Timothy Goodman (photographs), Roland Chabloz, and Harald Hirling for their help and support!