2011 ISREC Annual Report by EPFL School of Life Sciences

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

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

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

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

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

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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/

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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

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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

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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