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

EPFL School of Life Sciences - 2012 Annual Report

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

Jeffrey A. Hubbell - Dean of Life Sciences

Introduction

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

EPFL School of Life Sciences - 2012 Annual Report

Table Of Contents

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

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

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

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

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

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

Auwerx - Schoonjans Lab..........................................................................................................50 Baekkeskov Lab.........................................................................................................................52 Barrandon Lab...........................................................................................................................54 Dal Peraro Lab...........................................................................................................................56 Deplancke Lab..........................................................................................................................58 Hubbell Lab...............................................................................................................................60 Jensen Lab.................................................................................................................................62 Lutolf Lab..................................................................................................................................64 Naef Lab....................................................................................................................................66 Swartz Lab.................................................................................................................................68 Wurm Lab.................................................................................................................................70

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

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

EPFL School of Life Sciences - 2012 Annual Report

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

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

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

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

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

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

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

Introduction

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

EPFL School of Life Sciences - 2012 Annual Report

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

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

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

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

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

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

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

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

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

EPFL School of Life Sciences - 2012 Annual Report

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

Olaia Naveiras (IBI) - Jose Carreras Junior Investigator

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Career Fellowship

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

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

Swiss Final, Zurich.

Hilal Lashuel (BMI) - World Economic Forum Honoree

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Switzerland participants, CERN, Geneva. Muralidhar -

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

Foundation Scientific Prize

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

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

Hubbell - PERL Prizes

European Molecular Biology Organization.

Denis Duboule (ISREC) - US National Academy election.

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

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Hubbell - Vigier Prizes

Daan

Noordermeer

(ISREC)

Junior

Douglas Hanahan (ISREC) - 2012 Award for Cancer

Debiopharm

Research from the Fondazione San Salvatore, Lugano, CH

Group™ Prize

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

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

- 2012 MacArthur Foundation

Council (ERC) Starting Grants

A ug

Fellow

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

Jacques Fellay (GHI) - National Latsis Prize

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

Melanie Blokesch (GHI) - Best Teaching Evaluation prize

Olaf Blanke (BMI) - Cloëtta Foundation Prize

Introduction

Friedemann Zenken (BMI) - Teaching Assistant IC Award

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Swiss League Against Cancer

Joerg Huelsken (ISREC) - Robert Wenner Prize by the

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Ambition prize

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

EPFL School of Life Sciences - 2012 Annual Report

Undergraduate Studies The Life Sciences curriculum aims to educate a new generation of engineers who can master the technical and scientific skills needed for studying life processes and developing the biomedical technologies of tomorrow. This educational program, established under the direction of Prof. William F. Pralong, M. D., is unique in Switzerland and Europe. Bachelor’s Program (3 years) The first two years provide basic courses followed throughout the EPFL, such as analysis, linear algebra, physics, chemistry (general and organic), statistics and numerical methods. Specific courses in Life Sciences begin with biochemistry, cellular, molecular biology, biophysics, computer sciences, and biothermodynamics. In the first two years, life sciences courses make up less than 20% of the total academic load. In the third year, engineering courses (signals and systems, electronic and electrical systems) and typical life sciences courses such as genetics and genomics, immunology, developmental biology, bio-computing, systems biology via the study of human physiology are integrated. Physiology also gives the opportunity to integrate the engineering and biological knowledge acquired up to this point. During this year, the students also fine tune their training by choosing some specific credits to better prepare themselves for one of the orientations offered in our masters’ programs. This includes a bachelor project either in bioengineering, in bio-computing, in biomedical technologies, in neurosciences, or in molecular medicine.

Master’s Programs (2 years)

The Master’s in Life Science and Technology includes several specializations. Among these are Neurosciences and Neuroengineering, Molecular Medicine and System Biology. Each specialization is made up of 19 credits of optional courses selected under the supervision of a mentor. Students aiming to focus their training on interdisciplinary subjects will have the possibilities to choose different minors such as Biocomputing and Computational Neurosciences. The Master’s in Bioengineering is organized in collaboration with STI, and provides classical courses in bioengineering; in addition students can chose different possible orientations through the choice of a minor such as Biomedical Technologies (STI), Biocomputing (I&C) or Neuroprosthetics. Each minor requires taking 30 specific credits chosen under the guidance of a mentor. The minors, as indicated, are organized within the different schools at EPFL. Bertrand Rey - photographer

Both degree programs share some common basic curriculum that aims to provide students with the knowledge of the modern technologies used in the life sciences such as imaging, bio-computing and optical systems applied to biology, etc.... In addition, courses in management, economics, applied laws and ethics for the life sciences are offered. A large portion of the master’s program (60 credits) can be dedicated to laboratory work and projects. http://ssv.epfl.ch/

EPFL School of Life Sciences - 2012 Annual Report

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

Neuroscience (EDNE) provides its stu-

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

ch/edne

Biotechnology and Bioengineering (EDBB) prepares doctoral students

to become leaders in the fast-growing academic and industrial biotechnology and bioengineering sectors by providing a depth of knowledge and competence in their specific research areas as well as a breadth of knowledge in biology, bioengineering, and biotechnology. Focus areas include: biomolecular engineering and biomaterials; cell, tissue, and process engineering; stem cell biotechnology; orthopaedic engineering; microtechnology and nanotechnology; biomechanics and mechanobiology; molecular and cellular biophysics; computational biology; genomics and proteomics; advanced biomedical imaging and image processing. http:// phd.epfl.ch/edbb

Molecular Life Sciences (EDMS) aims at providing doctoral students with the education necessary to become leaders in biological research, implementing the latest state of the art. The combination of laboratory based research with access to modern technological platforms, coursework, in-house seminars, national and international conferences, etc., forms the basis of this education. The programâ&#x20AC;&#x2122;s themes include cell biology, developmental biology, biochemistry & biophysics, molecular genetics, cancer research, microbiology, host-pathogen interactions, immunology, systems biology, computational biology, human genetics, stem cells and metabolism. The EDMS PhD program offers exciting PhD positions to talented and ambitious young researchers.

Introduction

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

EPFL School of Life Sciences - 2012 Annual Report

SV Doctoral Graduates

Introduction

EPFL School of Life Sciences - 2012 Annual Report

SV Masters Graduates Master Bioengineering Graduates 2012

Master Life Sciences & Technology Graduates 2012

EPFL School of Life Sciences - 2012 Annual Report

Introduction

School of Life Sciences at a Glance

Centers

EPFL School of Life Sciences - 2012 Annual Report

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

Director: Prof. Henry Markram Introduction

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

Keywords

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

Description of BBP activities & results 2012

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

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

EPFL School of Life Sciences - 2012 Annual Report

Team Members

Selected Publications

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

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

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

of selected touch between neurons.

locations

Centers

Illustration

EPFL School of Life Sciences - 2012 Annual Report

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

Director: Prof. Rolf Gruetter

From Mouse to Patient History of the Center

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

2012 Highlights • 115 publications • 1 starting ERC grant

Mission and Aim

The CIBMseeks to advance our understanding of biomedical processes in health and disease, focusing on mechanisms of normal functioning, pathogenic mechanisms, characterization of disease onset prior to structural damage, metabolic and functional consequences of gene expression, and non-invasive insights into disease processes under treatment. The research uses model systems ranging from transgenic animals to human subjects (“from mouse to man”) and fosters multi-disciplinary collaboration between basic science, biomedical science and clinical applications. The goal is to advance biomedical imaging, i.e. functional and metabolic imaging, while addressing biomedical questions of importance at the same time. This is accomplished by establishing a research network in imaging science to enhance biomedical research capabilities of the founding institutions and beyond, as well as within the CIBM.

Contact

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

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EPFL School of Life Sciences - 2012 Annual Report

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

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

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

A selection of images from all seven research cores.

Centers

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

EPFL School of Life Sciences - 2012 Annual Report

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

Director: Prof. Olaf Blanke

Introduction

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

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

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EPFL School of Life Sciences - 2012 Annual Report

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

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

Selected Publications:

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

Centers

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

EPFL School of Life Sciences - 2012 Annual Report

ISREC

Swiss Institute for Experimental Cancer Research

Douglas Hanahan - Director

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

ISREC - Swiss Institute for Experimental Cancer Research

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

EPFL School of Life Sciences - 2012 Annual Report

Aguet Lab

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

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

Michel Aguet Full Professor

Introduction

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

Keywords

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

Results Obtained in 2012

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

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

EPFL School of Life Sciences - 2012 Annual Report

Selected Publications

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

Team Members

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

ISREC - Swiss Institute for Experimental Cancer Research

Administrative assistant NCCR «Molecular Oncology» Valérie Le Dréau

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

EPFL School of Life Sciences - 2012 Annual Report

Brisken Lab

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

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

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

Cathrin Brisken

Associate Professor Dean of EPFL Doctoral School

Introduction

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

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

Keywords

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

Results Obtained in 2012

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

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

EPFL School of Life Sciences - 2012 Annual Report

Selected Publications

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

Team Members Senior Scientist Cécile Lebrand

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

ISREC - Swiss Institute for Experimental Cancer Research

Administrative Assistant Lisa Cessy

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

EPFL School of Life Sciences - 2012 Annual Report

Constam Lab

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

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

Daniel Constam Associate Professor

Introduction

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

Keywords

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

Results Obtained in 2012

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

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

EPFL School of Life Sciences - 2012 Annual Report

Selected Publications

Team Members

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

PhD Students Florian Bernet Chhavi Jain Lucia Leal-Esteban

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

Staff Séverine Urfer-Beck Stéphane Baflast

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

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

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

Administrative Assistant Virginie Kokocinski

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

ISREC - Swiss Institute for Experimental Cancer Research

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

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

EPFL School of Life Sciences - 2012 Annual Report

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

Michele De Palma Tenure Track Assistant Professor

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

Introduction

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

Keywords

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

Results Obtained in 2012

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

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

EPFL School of Life Sciences - 2012 Annual Report

Selected Publications

Team Members

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

PhD Students Daniela Biziato Caroline Baer

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

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

Postdoctoral Fellows Mario Leonardo Squadrito Nicolò Rigamonti

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

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

ISREC - Swiss Institute for Experimental Cancer Research

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

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

EPFL School of Life Sciences - 2012 Annual Report

Duboule Lab

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

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

Denis Duboule

Full Professor EPFL & University of Geneva

Introduction

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

Keywords

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

Results Obtained in 2012

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

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

EPFL School of Life Sciences - 2012 Annual Report

Selected Publications

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

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

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

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

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

Technician Elisabeth Joye

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

Bioinformaticians Marion Leleu Yohan Mouscaz Anamaria Necsulea

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

Administrative Assistant Doris Sapin

ISREC - Swiss Institute for Experimental Cancer Research

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

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

EPFL School of Life Sciences - 2012 Annual Report

Gönczy Lab

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

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

Pierre Gönczy Full Professor

Introduction

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

Keywords

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

Results Obtained in 2012

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

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

EPFL School of Life Sciences - 2012 Annual Report

Selected Publications

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

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

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

ISREC - Swiss Institute for Experimental Cancer Research

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

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

EPFL School of Life Sciences - 2012 Annual Report

Hanahan Lab

Douglas Hanahan, born in Seattle, Washington, USA, received a bachelorâ&#x20AC;&#x2122;s degree in Physics from MIT (1976), and a Ph.D. in Biophysics from Harvard (1983). He worked at Cold Spring Harbor Laboratory in New York from 1978-88 as graduate student and then as group leader. From 1988-2010 he was on the faculty of the Department of Biochemistry & Biophysics at UCSF in San Francisco. He has been elected to the American Academy of Arts & Sciences (2007), the Institute of Medicine (USA) (2008), the US National Academy of Science (2009), and EMBO (2010). In 2011, Hanahan received an honorary degree from the University of Dundee (UK).

Douglas Hanahan

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

Introduction

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

Keywords

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

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

Results Obtained in 2012

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

EPFL School of Life Sciences - 2012 Annual Report

Selected Publications

Team Members

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

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

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

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

Sabbatical Professor Luisa Arispe-Aruela, UCLA

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

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

ISREC - Swiss Institute for Experimental Cancer Research

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

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

EPFL School of Life Sciences - 2012 Annual Report

Hantschel Lab

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

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

Oliver Hantschel

Tenure Track Assistant Professor ISREC Foundation Chair in Translational Oncology

Introduction

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

Keywords

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

Results Obtained in 2012

Protein kinases are involved in almost all aspects of oncogenesis. The inhibition of particular aberrantly activated kinases is considered to be beneficial for cancer treatment for numerous tumor types. Over the past ten years, 18 different inhibitors of a few oncogenic driver kinases in haematological and solid tumor types have received regulatory approval and entered clinical practice. Despite remarkable clinical responses that could be achieved in selected diseases, it is now well-established that most kinase inhibitors merely improve progression-free survival, but not overall survival. The main reasons is the development of drug resistance, often caused by point mutations in the targeted kinase that prevents or inhibits drug binding. Moreover, as it is difficult to develop highly selective kinase inhibitors, as there are more than 500 kinases in humans with a conserved sequence and structure. Therefore, side effects caused by the inhibition of off-target kinases may also limit its clinical utility. The laboratory uses interdisciplinary approaches at the interface of protein biochemistry, medicine, structural biolo-

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

EPFL School of Life Sciences - 2012 Annual Report

Selected Publications

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

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

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

ISREC - Swiss Institute for Experimental Cancer Research

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

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

EPFL School of Life Sciences - 2012 Annual Report

Huelsken Lab

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

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

Joerg Huelsken

Associate Professor Debiopharm Chair in Signal Transduction in Oncogenesis

Introduction

The last years of cancer research have established the concept of cancer stem cells (CSC) as sub-population of cells within a tumor entirely responsible for long-term tumor growth. We now provide evidence that these cells are also essential for metastatic disease and characterize the interaction between stem cells and their environment as an essential factor for metastatic growth. Understanding in detail the communication between cancer cells and surrounding stroma will help to define new therapeutic options to block spreading of cancer to secondary sites.

Keywords

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

Results Obtained in 2012

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

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

EPFL School of Life Sciences - 2012 Annual Report

Selected Publications

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

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

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

ISREC - Swiss Institute for Experimental Cancer Research

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

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

EPFL School of Life Sciences - 2012 Annual Report

Kühn Lab

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

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

Lukas Kühn

Adjunct Professor

Introduction

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

Keywords

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

Results Obtained in 2012

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

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

EPFL School of Life Sciences - 2012 Annual Report

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

Team Members PhD Student Ramona Batschulat

Specialist technicians Larry Richman Solange Kharoubi Hess Administrative assistant Jennifer Luyet

ISREC - Swiss Institute for Experimental Cancer Research

Selected Publications

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

EPFL School of Life Sciences - 2012 Annual Report

Lingner Lab

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

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

Joachim Lingner Full Professor

Introduction

The physical ends of chromosomes, known as telomeres, play critical roles in cancer development, other age-related disorders and short telomere syndromes. Telomeres protect chromosomes from degradation and from chromosome rearrangements typically seen in cancer. Telomeres also serve as cellular clocks. They shorten in the absence of telomerase limiting cellular lifespan. In most cancers, telomerase is upregulated in order to counteract telomere shortening. Through the expression of telomerase, human cancer cells acquire an immortal phenotype.

Keywords

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

Results Obtained in 2012

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

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

EPFL School of Life Sciences - 2012 Annual Report

Selected Publications

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

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

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

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

ISREC - Swiss Institute for Experimental Cancer Research

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

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

EPFL School of Life Sciences - 2012 Annual Report

Meylan Lab

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

Etienne Meylan received a PhD in Life Sciences from the University of Lausanne in 2006, for his work on innate immunity performed in the laboratory of JĂźrg Tschopp. From 2007 to 2010, he worked as a postdoctoral fellow in the laboratory of Tyler Jacks, at the Koch Institute for Integrative Cancer Research, MIT, Cambridge MA, USA. In 2011, he established his research laboratory at ISREC, as a Swiss National Science Foundation Professor, and was appointed TenureTrack Assistant Professor at the end of 2012. His laboratory focuses on the molecular mechanisms that contribute to the development of non-small cell lung cancer.

Etienne Meylan Tenure-track Assistant Professor SNSF Professor

Introduction

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

Keywords

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

Results Obtained in 2012

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

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

EPFL School of Life Sciences - 2012 Annual Report

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

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

ISREC - Swiss Institute for Experimental Cancer Research

Selected Publications

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

EPFL School of Life Sciences - 2012 Annual Report

Radtke Lab

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

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

Freddy Radtke Full Professor

Introduction

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

Keywords

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

Results Obtained in 2012

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

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

EPFL School of Life Sciences - 2012 Annual Report

Selected Publications

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

Team Members

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

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

ISREC - Swiss Institute for Experimental Cancer Research

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

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

EPFL School of Life Sciences - 2012 Annual Report

Simanis Lab

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

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

Viesturs Simanis Associate Professor

Introduction

Cell division is essential for the propagation of all organisms. If the fidelity of the processes involved in cell division is reduced, there is an increased risk that errors will occur in the transmission of genetic information from a cell to its daughters; this can result in the death of the cells, or alter their properties, which can contribute to the development of diseases such as cancer. We study cytokinesis, the division of cells, to understand how it is regulated and coordinated with other events in the cell cycle.

Keywords

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

Results Obtained in 2012

We study the process of cytokinesis (cell division), using the S. pombe model system. Proper coordination of cytokinesis with other events of the cell cycle is essential. If a cell divides without segregating its DNA, the outcome is a dead cell devoid of chromosomal DNA and a cell with increased ploidy, which is genetically less stable than a normal cell. Alternatively, if cytokinesis is triggered before chromosome segregation has been completed, then the nucleus may be “cut”, which is often lethal for both daughter cells, as imbalances in gene dosage are ill- tolerated. An NDR-kinase/GTPase signalling network known as the SIN (septation initiation network) acts at multiple points during cytokinesis. Failure of SIN signalling results in the production of multinucleated cells that die, while inappropriate activation of the SIN promotes cytokinesis from any cell cycle stage.

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

EPFL School of Life Sciences - 2012 Annual Report

Selected Publications

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

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

ISREC - Swiss Institute for Experimental Cancer Research

Administrative Assistant Catherine Pache

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

EPFL School of Life Sciences - 2012 Annual Report

Bucher Group

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

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

Philipp Bucher Group Leader

Introduction

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

Keywords

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

Results Obtained in 2012

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

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

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

EPFL School of Life Sciences - 2012 Annual Report

Selected Publications

Team Members

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

PhD Student Slavica Dimitrieva

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

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

Postdoctoral Fellows Giovanna Ambrosini René Dreos Sunil Kumar Rouaïda Cavin Périer

Administrative Assistant Sophie Barret

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

ISREC - Swiss Institute for Experimental Cancer Research

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

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

EPFL School of Life Sciences - 2012 Annual Report

Knowles

- Translational Research

Jonathan Knowles Full Professor

Research Interests

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

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

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

EPFL School of Life Sciences - 2012 Annual Report

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

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

Marcel Tanner

External Adjunct Professor Swiss TPH Insitute, Basel Director

Keywords

Epidemiology, public health, vaccines, drugs and diagnostics.

Research Interests

Swiss TPH (Swiss Tropical and Public Health Institute) and the EPFL School of Life Sciences are collaborating with the goal to bring together complementary expertise of the two institutions in research on host-pathogen interaction in infectious and chronic diseases and the development of new diagnostics, drugs and vaccines. Besides the collaboration in research, exchanges of teaching faculty and students within the MSc courses is continuing.

sponses to infection with M. ulcerans and the development of vaccine candidates. These activities rely heavily on the BSL3 animal facilities at the GHI. A mouse model for Buruli ulcer has been successfully established and optimized. Various subunit vaccine formulations have been used to immunize mice and analyzed for the induction of humoral and cellular immune responses. They are currently tested for protective efficacy. The biannual report of Swiss TPH: http://www.swisstph.ch/about-us/publications/biennialreport/biennial-report-2011-2012.html

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

External Adjunct Professors

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

EPFL School of Life Sciences - 2012 Annual Report

Molinari Group

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

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

Maurizio Molinari

External Adjunct Professor Institute for Research in Biomedicine Bellinzona

Introduction

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

Keywords

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

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

Results Obtained in 2012

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

EPFL School of Life Sciences - 2012 Annual Report

Selected Publications

Team Members

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

PhD Students Giorgia Brambilla Pisoni Jessica Merulla Julia Noack

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

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

Postdoctoral Fellow Riccardo Bernasconi

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

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

External Adjunct Professors

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

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

EPFL School of Life Sciences - 2012 Annual Report

Rainer Group

www.unifr.ch/inph/vclab/

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

Gregor Rainer

External Adjunct Professor University of Fribourg

Introduction

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

Keywords

Deep brain stimulation, visual neuroprosthetics, visual cortex.

Results Obtained in 2012

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

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

EPFL School of Life Sciences - 2012 Annual Report

Selected Publications

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

Team Members Postdoctoral Fellow Xiaozhe Zhang

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

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

External Adjunct Professors

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

EPFL School of Life Sciences - 2012 Annual Report

Schorderet Group www.irovision.ch/

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

Daniel Schorderet

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

Introduction

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

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

Keywords

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

Results Obtained in 2012

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

EPFL School of Life Sciences - 2012 Annual Report

Selected Publications

Team Members

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

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

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

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

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

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

External Adjunct Professors

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

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