GHI - Annual Report 2014 by EPFL School of Life Sciences

EPFL School of Life Sciences GHI - Global Health Institute Report 2014

EPFL School of Life Sciences - 2014 Annual Report

GHI

Global Health Institute

The research portfolio at the GHI includes a balanced mixture of basic and translational work. Mechanisms of host-pathogen interactions and innate and acquired immunity against disease are being studied using multidisciplinary approaches. A unique feature of the GHI is its ability to tackle crucial world health issues by harnessing cutting edge technologies developed elsewhere at EPFL to underpin research on diagnostics, drugs and vaccines as well as disease mechanisms. Prominent amongst these are the nanotechnologies, micro-engineering and bioinformatics. Aware of the impact of the microbiota on human health, the GHI is actively developing new programs in this area. http://sv.epfl.ch/GHI

Stewart Cole - Director

GHI - Global Health Institute

Since its foundation in 2006, the Global Health Institute (GHI) has contributed to the understanding, diagnosis, prevention and treatment of infectious diseases, which account for half of the deaths in the developing world and claim 18 million human lives every year. The GHI is comprised of nine groups, all engaged in different facets of research linked to human health but with strong emphasis on diseases of truly global importance such as HIV/AIDS and tuberculosis. The current workforce comprises ~120 students, postdoctoral-fellows, technicians and scientists, representing more than 25 different nations.

EPFL School of Life Sciences - 2014 Annual Report

Ablasser Lab Andrea Ablasser

Tenure-track Assistant Professor

http://ablasserlab.epfl.ch

Introduction

After graduating in medicine at the University of Munich, Germany in 2008, Andrea Ablasser moved to the University of Bonn to do her post-doctoral research which focused on understanding innate nucleic acid sensing mechanism that lead to an antiviral immune response. In 2014, the Ablasser lab was opened as part of the Global Health Institute in the School of Life Sciences of the EPFL.

The innate immune system is the first line of defense against pathogen infection. Central to this task are so called pattern recognition receptors, which allow the cells of the immune system to sense the presence of microbes and to respond accordingly. Our research focus is centered on delineating intracellular nucleic acid sensing pathways, which constitute one major innate sensing strategy during viral and bacterial infection. During infection viral or bacterial DNA or RNA is detected in the cytosol of host cells by distinct nucleic acid sensors, which upon activation lead to the induction of antiviral and pro-inflammatory gene expression. Recently, it was shown that the cytosolic nucleotidyltransferase cyclic GMP AMP synthase (cGAS) is the major receptor for intracellular DNA, which upon activation leads to the synthesis of a second messenger cyclic dinucleotide, cyclic GMP-AMP (cGAMP). This second messenger molecule in turn stimulates the endoplasmic reticulum protein Stimulator of Interferon Genes (STING) to trigger downstream signaling. In our previous work we characterized the nature of the second messenger cGAMP, which represents an unorthodox molecule that is composed of a 2`-5` and a 3`-5`phosphodiester linkage. Intriguingly, we have recently described that this second messenger system takes advantage of gap junction mediated cGAMP transfer to propagate an antiviral immune response rapidly towards neighboring cells. Of note, the two-receptor system of cGAS and STING not only plays a pivotal role during pathogen infection, but it also seems to be key in mediating stress responses by sensing endogenous DNA species that arise during tissue damage and cell death.

Focus for 2015

One major focus of our current work is centered on the pathogen Mycobacterium tuberculosis (Mtb), the causative agent of Tuberculosis. As such it is known that intracellular detection of mycobacterium-derived products is key for the initiation of an innate immune response. But while the receptors responsible for the inflammatory part of the innate immune response had been identified, the sensor system responsible for activation of the type I interferon pathway after infection with Mtb remained elusive. Ongoing work from our laboratory in collaboration with the laboratory of Stewart Cole now demonstrates that the cGAS-STING pathway is essential for mounting type I interferon production upon infection with Mtb. For the future we now aim to understand the precise molecular mechanism that underlies the activation of intracellular DNA sensing mechanism in the setting of Mtb infection in more detail. Another focus of our current research is to delineate the cause of the rare, congenital autoimmune disease Aicardi-GoutiĂ¨res Syndrome (AGS). Previously we had demonstrated that DNA sensing through cGAS plays a key role in the initiation of this complex autoimmune disorder. We are now trying to understand the molecular mechanism of cGAS activation and we are aiming at identifying agents that block the cGAS-STING pathway, which could serve as a novel therapeutic opportunity for AGS patients.

Keywords

Innate immunology, antiviral immunity, Type I Interferons, nucleic acid sensing.

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EPFL School of Life Sciences - 2014 Annual Report

Team Members Postdoctoral Fellows Muhammet Fatih Gülen Michael Heymann

PhD Student Simone Haag

Technician Sonia Garcia

Administrative Assistant Marisa Marciano Wynn

GHI - Global Health Institute

Schematic representation of the activation of the innate immune system through virus sensing mechanisms that activate IFN and ISG production in the infected as well as neighboring cells. The secreted IFNs, in turn induce the production of the full set of ISGs as well as other genes.

Selected Publications » » » » »

Ablasser A, Hemmerling I, Schmid-Burgk JL, Behrendt R, Roers A, Hornung V. TREX1-deficiency triggers cell-autonomous immunity in a cGAS-dependent manner.Journal of Immunology. 2014 Jun 15;192(12):5993-7. Ablasser A, Schmid-Burgk JL , Hemmerling I, Horvath G, Schmidt T, Latz E, Hornung V. Cell intrinsic immunity spreads to bystander cells via the intercellular transfer of cGAMP.Nature. 2013 Nov 28;503(7477):530-4. Ablasser A, Goldeck M, Cavlar T, Deimling T, Witte G, Röhl I, Hopfner K-P, Ludwig J, Hornung V. cGAS produces a 2´-5´-linked cyclic dinucleotide second messenger that activates STING.Nature 2013 Jun 20;498(7454):380-4. Civril F, Deimling T, de Oliveira Mann C. C, Ablasser A, Moldt M, Witte G, Hornung V, Hopfner K-P. Structural mechanism of cytosolic DNA sensing by cGAS.Nature 2013 Jun 20;498(7454):332-7. Hornung V, Hartmann R, Ablasser A, Hopfner K.-P. OAS and cGAS: unifying concepts in the sensing and signaling in response to cytosolic RNA and DNA.Nature Reviews Immunology. 2014 Aug;14(8):521-8.

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Blokesch Lab Melanie Blokesch

Tenure-track Assistant Professor

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

Introduction and Lab Description

Melanie Blokesch studied biology at Ludwig-MaximiliansUniversity (LMU) in Munich, Germany. In 2004 she obtained her PhD degree with highest honor from the LMU Munich based on her work on bacterial hydrogen production and metalloenzyme maturation. Her thesis was honored by the German Academy of Sciences Leopoldina and the German Association for General and Applied Microbiology. From 2005 to 2009 she worked as a postdoctoral fellow at Stanford University (USA) before being appointed as tenure-track assistant professor within the School of Life Sciences of EPFL.

The research of our group focuses on the question “How and why do bacteria evolve to become facultative human pathogens ?” Our model organism is Vibrio cholerae, the causative agent of cholera. Cholera is still widespread around the globe with up to 5 million cases every year. As the infection is linked to contaminated water, cholera is primarily a disease of developing countries. The goal of our research is to link the ecology of the organism with the epidemiology of the disease in order to learn more about the pathogen’s evolution. V. cholerae is a normal member of aquatic habitats and is often found associated with small crustaceans as part of the zooplankton. Under these conditions V. cholerae is able to induce a developmental program known as natural competence for genetic transformation, which allows the bacterium to take up free DNA from the surroundings and to recombine the DNA into its own genome. Natural competence for transformation is one out of three modes of horizontal gene transfer and therefore contributes to the spread of antibiotic resistance cassettes, virulence genes, and pathogenicity islands. During the last years we have focused on the regulatory circuits driving natural competence in V. cholerae in order to understand the environmental factors governing this process. More recently, we also started investigating the DNA uptake process itself. DNA uptake involves a macromolecular complex, which we are studying using cell biology-based approaches. Apart from these topics we are also interested in the interaction of V. cholerae with free-living amoebae and the role that virulence factors play in this context.

Keywords

Horizontal gene transfer, evolution of human pathogens, bacterial regulatory networks, cholera, environmental hosts.

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Results Obtained in 2014

Localization and visualization of the DNA uptake machinery DNA uptake machineries are generally not well understood. We therefore investigated the mechanistic aspects of the DNA uptake process. To do so, we genetically engineered V. cholerae to enable visualization of the subcellular localization of the essential competence protein ComEA. We showed that upon the addition of external DNA to competent cells, ComEA re-localized and formed discrete foci, which co-localized with the incoming DNA. Next, we used bacterial genetic approaches to better understand the shuffling role of ComEA between the outside of the cells and the inner membrane of the bacterium. Finally, we used timelapse microscopy imaging to visualize DNA uptake in real time. Our data strongly suggest that DNA uptake is promoted through ratcheting and entropic forces associated with ComEA binding. Killing for DNA: The type VI secretion system of Vibrio cholerae fosters horizontal gene transfer V. cholerae is considered an important model organism for elucidating virulence regulation. In this context, the involvement of quorum sensing (QS) and a predatory killing device (the type VI secretion system, T6SS) have been extensively studied even though the T6SS is considered to be “silent” (under laboratory conditions) in pandemic V. cholerae isolates. Much less is known about the bacterium’s environmental lifestyle, where it often associates with the chitinous surfaces of small crustaceans. We recently showed that the chitin and QS-dependent competence regulon includes the T6SS-encoding gene cluster and that the T6SS contributes to enhanced horizontal gene transfer by means of natural transformation. Moreover, we used live-cell imaging to visualize the T6SS-mediated killing of prey cells and the subsequent uptake of their DNA by predator cells. Our results indicate that the chitin-dependent induction of the T6SS enhances horizontal gene transfer by deliberate killing of neighboring non-immune cells and absorption up of their DNA (see Figure).

EPFL School of Life Sciences - 2014 Annual Report

Team Members Postdoctoral Fellows David Adams Milena Jaskolska Lisa Metzger Charles Van der Henst

PhD Student Noémie Matthey

Technicians Sandrine Borgeaud Tiziana Scrignari

Administrative Assistant Marisa Marciano Wynn

GHI - Global Health Institute

Horizontal gene transfer is achieved through deliberate killing of prey cells. Competence-induced V. cholerae (predator; red) were mixed with prey cells (green) and imaged. The appearance of rounded and lysed prey is followed by absorption of the released DNA by the predator (indicated by the arrows).

Selected Publications » Borgeaud S., Metzger L.C., Scrignari T., and Blokesch M. (2015) The type VI secretion system of Vibrio cholerae fosters horizontal gene transfer. Science, 347:63-67. » Lo Scrudato M., Borgeaud S., Blokesch M. (2014) Regulatory elements involved in the expression of competence genes in naturally transformable Vibrio cholerae. BMC Microbiol., 14: 327. » Kühn J., Finger F., Bertuzzo E., Borgeaud S., Gatto M., Rinaldo A., Blokesch M. (2014) Glucose- but not rice-based oral rehydration therapy enhances the production of virulence determinants in the human pathogen Vibrio cholerae. PLoS Negl. Trop. Dis., 8: e3347. » Seitz P., Blokesch M. (2014) DNA transport across the outer and inner membrane of naturally transformable Vibrio cholerae is spatially but not temporally coupled. mBio, 5:e01409-14. » Metzger L.C., Blokesch M. (2014) Composition of the DNA-uptake complex of Vibrio cholerae. Mob. Genet. Element., 4: e28142. » Seitz P., Pezeshgi Modarres H., Borgeaud S., Bulushev R.D., Steinbock L.J., Radenovic A., Dal Peraro M., Blokesch M. (2014) ComEA Is Essential for the Transfer of External DNA into the Periplasm in Naturally Transformable Vibrio cholerae Cells. PLoS Genet., 10: e1004066. » Venkova-Canova T., Baek J.H., FitzGerald P.C., Blokesch M., Chattoraj D.K. (2013) Evidence for two Different Regulatory Mechanisms Linking Replication and Segregation of Vibrio cholerae Chromosome II. PLoS Genet., 9: e1003579. » Seitz P., Blokesch M. (2013) DNA-uptake machinery of naturally competent Vibrio cholerae. Proc. Natl. Acad. Sci. USA, 110:17987-92. » Lo Scrudato M., Blokesch M. (2013) A transcriptional regulator linking quorum sensing and chitin induction to render Vibrio cholerae naturally transformable. Nucleic Acids Res., 41: 3644-58.

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EPFL School of Life Sciences - 2014 Annual Report

Cole Lab

Stewart T. Cole

Full Professor - Director of the Global Health Institute - GHI

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

Introduction

Professor Stewart Cole is an internationally acclaimed authority on the pathogenicity, drug resistance, evolution and genomics of the tubercle and leprosy bacilli. His laboratory is currently focused on discovering new drugs to treat tuberculosis. The findings of his research are of direct relevance to public health and disease-control in both the developing world and the industrialized nations. He has published over 300 scientific articles and been honored by many professional prizes, decorations and awards.

The Cole laboratory, UPCOL, is using a multidisciplinary approach to tackle major public health problems such as tuberculosis (TB), Buruli ulcer and leprosy. The laboratory is home to experts in genomics, functional genomics, bioinformatics, biochemistry, chemistry, chemical biology, molecular microbiology, cellular microbiology and structural biology. Using genome biology as a platform we are actively involved in discovering new drugs to treat TB and believe that knowledge gained through discovery must be broadly and swiftly disseminated. Given the global importance of the TB problem, we are trying to strike the correct balance between competition and collaboration. As part of a major, international collaboration UPCOL is leading the More Medicines for Tuberculosis (MM4TB) integrated project from the European Commissionâ&#x20AC;&#x2122;s Seventh Framework Program. The goal of MM4TB is to validate pharmacologically five new TB drug targets and to discover at least one family of compounds for development as a drug candidate. In this context, we have discovered many interesting leads for development including the natural product, pyridomycin, the thienopyrimidines, the carboxyquinoxalines and, above all, the benzothiazinone (BTZ) series. The latter gave rise to PBTZ169, a highly potent drug candidate that irreversibly inhibits an essential enzyme called DprE1, which plays a critical role in the biogenesis of the mycobacterial cell wall. The preclinical development of PBTZ169 is being undertaken by the not-for-profit foundation Innovative Medicines for Tuberculosis (iM4TB), an EPFL spin-off.

Keywords

Tuberculosis, leprosy, drug discovery, pathogenesis.

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Results Obtained in 2014

TB Drug Discovery Among our most notable achievements was solving the crystal structure of the flavoenzyme DprE1 in complex with BTZ043 and PBTZ169. This explains how these inhibitors act and provides a template for further rational drug design. We have also shown that PBTZ169 is compatible with all leading TB drugs and drug candidates and thus has the potential for inclusion in a new combination therapy. Protein secretion and pathogenicity The ESX-1 secretion system, the major virulence determinant of M. tuberculosis, is required for the export of small helical-hairpin proteins from the ESAT-6 family as well as other effector proteins of unknown function. We are using an integrated approach to elucidate the organization, architecture, structure and function of this ATP-driven secretory apparatus. The EspB protein has been shown to bind bioactive phospholipids with prominent roles in eukaryotic cell signaling and to act independently of ESAT-6. A regulatory map of the M. tuberculosis genome We are studying gene regulation by using chromatin-immunoprecipitation of DNA-binding proteins in conjunction with high-throughput sequencing to localize the various binding sites along the genome. We mapped all the RNA polymerase, NusA and EspR binding sites in two different strains in the log and stationary phases of growth. Regulatory information is displayed in TubercuList, http://tuberculist.epfl.ch/. Phylogeography of leprosy Despite the successful implementation of multidrug therapy, leprosy remains a serious public health problem in several countries. We have developed an epidemiological tool that employs SNP (single nucleotide polymorphism) analysis of M. leprae, to monitor transmission of the disease. We retraced the spread of leprosy in the Middle Ages from skeletal remains (Figure). Together with the WHO, we are also monitoring the emergence of drug resistance worldwide.

EPFL School of Life Sciences - 2014 Annual Report

Team Members Postdoctoral Fellows Andrej Benjak Jeffrey Chen Ruben Hartkoorn Raju Mukherjee Florence Pojer Jan Rybniker Claudia Sala Pushpendra Singh

PhD Students Charlotte Avanzi Benjamin Blasco Gaëlle Kolly Benoit Lechartier Lou Ye Zhang Ming Nina Odermatt

Master’s Student Stéphanie Cherbuin

Technicians Stefanie Boy-Röttger Philippe Busso Anthony Vocat

Administrative Assistants Suzanne Dubsky Cécile Prébandier

GHI - Global Health Institute

Skull of leprosy victim SK2 from Winchester, UK, circa 1270 used as source of ancient M. leprae DNA for genome sequence analysis (Schuenemann et al. 2013. Science 341: 179-183.)

Selected Publications » Chen, J.M., Zhang, M., Rybniker, J., Boy-Rottger, S., Dhar, N., Pojer, F., and Cole, S.T., 2013. Mycobacterium tuberculosis EspB binds phospholipids and mediates EsxA-independent virulence. Molecular Microbiology 89: 11541166. » Chen, J.M., Zhang, M., Rybniker, J., Basterra, L., Dhar, N., Tischler, A.D., Pojer, F., and Cole, S.T., 2013. Phenotypic profiling of Mycobacterium tuberculosis EspA point mutants reveals that blockage of ESAT-6 and CFP-10 secretion in vitro does not always correlate with attenuation of virulence. Journal of Bacteriology 195: 5421-5430. » Hartkoorn, R.C., Pojer, F., Read, J.A., Gingell, H., Neres, J., Horlacher, O.P., Altmann, K.H., and Cole, S.T., 2014. Pyridomycin bridges the NADH- and substrate-binding pockets of the enoyl reductase InhA. Nature Chemical Biology 10: 96-98. » Schuenemann, V.J., Singh, P., Mendum, T.A., Krause-Kyora, B., Jager, G., Bos, K.I., Herbig, A., Economou, C., Benjak, A., Busso, P., Nebel, A., Boldsen, J.L., Kjellstrom, A., Wu, H., Stewart, G.R., Taylor, G.M., Bauer, P., Lee, O.Y., Wu, H.H., Minnikin, D.E., Besra, G.S., Tucker, K., Roffey, S., Sow, S.O., Cole, S.T., Nieselt, K., and Krause, J., 2013. Genome-wide comparison of medieval and modern Mycobacterium leprae. Science 341: 179-183. » Uplekar, S., Rougemont, J., Cole, S.T., and Sala, C., 2013. High-resolution transcriptome and genome-wide dynamics of RNA polymerase and NusA in Mycobacterium tuberculosis. Nucleic Acids Research 41: 961977. » Zumla, A., Nahid, P., and Cole, S.T., 2013. Advances in the development of new tuberculosis drugs and treatment regimens. Nature Reviews Drug Discovery 12: 388-404.

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EPFL School of Life Sciences - 2014 Annual Report

Fellay Lab Jacques Fellay

SNSF Professor

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

Introduction

Jacques Fellay is a medical scientist with expertise in infectious diseases and human genomics. He obtained an MD from the University of Lausanne and a PhD from the University of Utrecht. Jacques Fellay joined the EPFL in April 2011 as an SNSF Professor; he is also a Group Leader at the Swiss Institute of Bioinformatics and a Visiting Physician at the Service of Infectious Diseases of the CHUV in Lausanne. In 2012, he was awarded the National Latsis Prize for his work on HIV and HCV host genomics.

Research in the Fellay lab focuses on human genomics of infection. Using a range of contemporary DNA and RNA analysis strategies, we explore the genetic roots of inter-individual differences in response to infectious agents. The work in the lab includes both classical genetics of infection susceptibility that measures clinical outcome, and a novel approach investigating the imprint of human polymorphisms on pathogen genetic diversity. In an effort to identify rare genetic variants conferring extreme susceptibility to specific infections, we use a combination of exome and RNA sequencing in patients with unusually severe clinical presentations upon infection with HIV, hepatitis B virus and respiratory viruses, as well as in children with bacterial sepsis. Candidate genes and variants are then genetically validated and functionally characterized. Our group is leading a large international project that aims at understanding how human genetic variation impacts HIV control. In collaboration with >25 cohorts or centers, we have collected genome-wide genotyping data on ~11,000 HIV infected individuals with clinical follow-up, allowing an unprecedented description of the impact of common genetic variants on HIV disease. To improve understanding of human-virus interactions at the genomic level, we also developed an innovative strategy to simultaneously analyze host and pathogen genetic variation. We are currently applying it to HIV, hepatitis C virus, cytomegalovirus and Epstein Barr virus infections. Finally, we collaborate with colleagues from the EPFL I&C Faculty to develop innovative solutions for genomic privacy, an essential trust-building component on the road toward genomic-based medicine.

Results Obtained in 2014

The past 2 years have seen important progress in our work on HIV host genomics. We coordinate the International Collaboration for the Genomics of HIV (ICGH), which has three main goals 1) To identify common genetic markers (>1% frequency) associating with HIV disease progression 2) To identify likely causal variants underlying associated regions through fine-mapping and 3) To quantify the proportion of variation in HIV disease progression that can be attributed to host genetics (heritability). Meta-analyses of HIV acquisition and HIV control phenotypes have been completed. In addition, we are investigating the influence of rare polymorphisms that occur within genes. This project uses exome sequencing to identify mutations that alter protein sequence (missense, frameshift and nonsense) and test them for an impact on HIV viral load individually (i.e. a single variant), in combination within a gene (i.e. burden of variation) and across relevant gene sets (i.e. gene networks). Currently we have obtained and analyzed exome sequence data on ~1,000 HIV infected patients. We also developed an online compendium of host genomic data in HIV biology and disease (www.guavah.org). This intuitive web interface allows queries and supports validation of the rapidly growing body of host genomic information pertinent to HIV research. After the publication of our joint analysis of human and viral genomes (Bartha et al, 2013), we further developed the genome-to-genome strategy, notably by using it for other chronic viral diseases. This pioneering work also allowed us to start new academic and industrial collaborations. We have been working on different aspects of genomic privacy in strong collaboration with the group of Prof JP Hubaux (EPFL IC). In particular, studies aiming at protecting and evaluating genomic privacy in medical tests and personalized medicine have resulted in a number of conference papers and patents.

Keywords

Human genomics, infectious diseases, host-pathogen interactions, deep-sequencing, translational genomics, genomic privacy, personalized medicine.

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Team Members Postdoctoral Fellows Paul McLaren Istvan Bartha Christian Hammer Nimisha Chaturvedi Thomas Junier

PhD Students Samira Asgari Ana Bittencourt Petar Scepanovic Christian Thorball

Master’s Student Caroline Perraudin

Administrative Assistant Marisa Marciano Wynn

GHI - Global Health Institute

Results of human-HIV “genometo-genome” association analyses (from Bartha et al, 2013). Associations between (A) human SNPs and HIV viral load (B) human SNPs and HIV amino acids; (C) HLA class I genes and associated SNPs in the region (D) Associations projected on the HIV proteome.

Selected Publications » » » » »

Regoes RR, McLaren PJ, Battegay M, Bernasconi E, Calmy A, Günthard HF, Hoffmann M, Rauch A, Telenti A and Fellay J. (2014). Disentangling human tolerance and resistance against HIV. PLoS Biology. 12(9):e1001951. Rausell A, Mohammadi P, McLaren PJ, Xenarios I, Fellay J and Telenti A. (2014) Analysis of stop-gain and frameshift variants in human innate immunity genes. PLoS Computational Biology. 10(7):e1003757. Bartha I, McLaren PJ, Ciuffi A, Fellay J and Telenti A. (2014). GuavaH: A compendium of host genomic data in HIV biology and disease. Retrovirology. 11(1):6. Bartha I, Carlson JM, Brumme CJ, McLaren PJ, Brumme ZL, et al. (2013) A Genome-to-Genome Analysis of Associations between Human Genetic Variation, HIV-1 Sequence Diversity, and Viral Control. eLife. 2:e01123. McLaren PJ, Coulonges C, Ripke S, van den Berg L, Buchbinder S, et al. (2013) Association Study of Common Genetic Variants and HIV-1 Acquisition in 6,300 Infected Cases and 7,200 Controls. PLoS Pathogens. 9(7): e1003515. » Lane J, McLaren PJ, Dorrell L, Shianna KV, Stemke A, et al. (2013) A genome-wide association study of resistance to HIV infection in highly exposed uninfected individuals with hemophilia A. Human Molecular Genetics. 22(9):1903-1910. » Apps R, Qi Y, Carlson JM, Chen H, Gao X, et al. (2013) Opposing effects of HLA-C expression level in viral versus inflammatory disease. Science. 340(6128):87-91.

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EPFL School of Life Sciences - 2014 Annual Report

Harris Lab Nicola Harris

Associate Professor

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

Introduction

Nicola Harris was born in New Zealand where she completed her undergraduate studies and PhD thesis. In 2002 she moved to Switzerland as a postdoctoral fellow where she worked with Hans Hengartner and the Nobel Laureate Rolf Zinkernagel at the Institute for Experimental Immunology, University of Zurich. In July 2005 she joined the ETH Zurich as an Assistant Professor and in August 2009 she moved to the Global Health Institute, Department of Life Sciences, EPFL where she was recently promoted to the position of Associate Professor.

The intestinal mucosa represents an extensive interface between the body and the external environment that is constantly exposed to environmental micro-organisms. Amongst these commensal bacteria are present in vast numbers (1012 per gram of intestinal contents) in all individuals at all times. Worms (helminths) can also establish chronic infections within our intestines and were present in a near ubiquitous manner throughout mammalian evolution. Today intestinal helminths still infect approximately 1/3 of the world’s population, with the heaviest infections found in children living in poor communities within developing countries. Our work aims to investigate: • how the immune system can provide protection against heavy burdens of intestinal helminths, and • how intestinal helminths and/or commensal bacteria can modulate the responsiveness of our immune system. In regard to the latter aim we would like to understand why and how reduced exposure to specific intestinal bacteria species and/or intestinal helminths can predispose towards increased autoimmune and allergic diseases.

Keywords

Mucosal immunology, intestinal helminths, intestinal microbiota, allergy.

Results Obtained in 2014

As part of our earlier work we uncovered an essential role for antibodies in providing effective immunity against helminth parasites. In 2013-2014 we expanded on these findings to show that these antibodies function by activated macrophages to attach to and paralyze these large multicellular parasites. We also identified the antibody isotype and host receptors involved in this response and found a very surprisingly role for antibodies normally associated with bacterial but not helminth infection. We are now investigating the regulation of protective antibody production following helminth infection with the hope of building better strategies for vaccine development in the future. We also noted a novel role for antibody-cellular interactions in regulating wound healing following helminth infection. Wound healing forms an integral arm of the host response to helminths as these large multicellular organisms migrate through various tissues causing widespread damage. Our findings indicate that the immune response functions not just to attack these larvae but also to promote tissue repair. This latter work in on-going and we hope to publish our findings in early 2015. In a separate project we investigated how mammals regulate the extent and type of immune responses occurring in the gut and identified two important innate cytokines, TSLP and IL-1 as key factors in the decision as to whether to raise a pro or anti-inflammatory response against intestinal bacteria and helminths respectively. This work is now complete and we are currently focusing our efforts on understanding how responses in the lymphoid organs, particularly those of non-immune stromal cells, regulate the extent of immune activation. 2013-4 also saw continuation of a project aimed at investigating the interactions between intestinal helminths and commensal bacteria. This project has revealed an ability of helminths to regulate inflammatory diseases such as allergy indirectly through alterations to intestinal bacteria and we expect to publish these novel findings in the upcoming year.

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Team Members PhD Students Luc Lebon Ilaria Mosconi Alexis Rapin Beatrice Volpe

Master’s Students Marion Chassouant Jade Sternberg Morgan Study

Administrative Assistant Caroline Rheiner

GHI - Global Health Institute

Postdoctoral Fellows Julia Esser-von Bieren Lalit Kumar Dubey Duncan Sutherland Mario Zaiss

Cover Image for the Journal of Immunology Feb 1st 2015: Motility of the infective larval stage of the intestinal helminth Heligmosomoides polygyrus bakeri shown in temporal color code (120 frames, 60 seconds).

Selected Publications » Esser-von Bieren J, Volpe B, Kulagin M, Sutherland DB, Guiet R, Seitz A, Marsland BJ, Verbeek JS, Harris NL. (2015). Antibody-Mediated Trapping of Helminth Larvae Requires CD11b and Fcγ Receptor I. J Immunol. 1;194(3):1154-63 » Zaph C, Cooper PJ, Harris NL. (2014). Mucosal immune responses following intestinal nematode infection. Parasite Immunol. 36(9):439-52. Review. » Trompette A, Gollwitzer ES, Yadava K, Sichelstiel AK, Sprenger N, Ngom-Bru C, Blanchard C, Junt T, Nicod LP, Harris NL, Marsland BJ. (2014). Gut microbiota metabolism of dietary fiber influences allergic airway disease and hematopoiesis. Nat Med. 20(2):159-66. » Esser-von Bieren, Julia; Mosconi, Ilaria; Guiet, Romain; Piersigilli, Alessandra; Volpe, Beatrice; Chen, Fei; Gause, William C.; Seitz, Arne; Verbeek, J. Sjef; Harris, Nicola. (2013). Antibodies Trap Tissue Migrating Helminth Larvae and Prevent Tissue Damage by Driving IL-4Rα-Independent Alternative Differentiation of Macrophages. Plos Pathogens. 9(11) e1003771. » Zaiss, Mario M.; Maslowski, Kendle M.; Mosconi, Ilaria; Guenat, Nadine; Marsland, Benjamin J.; Harris, Nicola L. (2013). IL-1β Suppresses Innate IL-25 and IL-33 Production and Maintains Helminth Chronicity. PLoS pathogens. 9(8) e1003531 » Mosconi, I.; Geuking, M. B.; Zaiss, M. M.; Massacand, J. C.; Aschwanden, C.; Kwong Chung, C. K. C.; Mccoy, K. D.; Harris, N. L. (2013). Intestinal bacteria induce TSLP to promote mutualistic T-cell responses. Mucosal Immunol. (6)6: 157-67 » Yadava K, Sichelstiel A, Luescher IF, Nicod LP, Harris NL, Marsland BJ. (2013). TSLP promotes influenza-specific CD8+ T-cell responses by augmenting local inflammatory dendritic cell function. Mucosal Immunol. 6(1):83-92

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EPFL School of Life Sciences - 2014 Annual Report

Lemaitre Lab Bruno Lemaitre

Full Professor - Director of the Doctoral Program in Molecular Life Sciences (EDMS)

http://lemaitrelab.epfl.ch/

Introduction

Our group uses Drosophila and its powerful genetics as a model to analyze integrated physiological questions at the organismal level. We currently have three main axes of researches focusing on:

Bruno Lemaitre obtained his PhD in 1992 with Dario Coen at the University Pierre and Marie Curie (Paris) on the P element transposition in Drosophila. Next, he joined the laboratory of Jules Hoffmann (Strasbourg, France) as a research associate where he began a genetic dissection of the Drosophila antimicrobial response. In 1998, Dr Lemaitre started his own laboratory on Drosophila immunity at the Centre Génétique Moléculaire (Gif-sur-Yvette, France). In 2007, he was appointed professor at EPFL.

Drosophila innate immunity Our research focuses on understanding mechanisms of microbial infection and corresponding host defense responses in Drosophila. Our current project is to delete systematically all genes belonging to large immune gene families both individually and collectively. We are especially interested in the molecular mechanisms underlying phagocytosis and encapsulation, two poorly characterized insect immune defenses. The Drosophila-Spiroplasma interaction: a model for insect endosymbiont Virtually every species of insect harbors facultative bacterial endosymbionts (ex. Wolbachia,) that are transmitted from females to their offspring. These symbionts play crucial roles in the biology of their hosts manipulating reproduction and protecting from pathogens. In spite of growing interest in endosymbionts, very little is known about the molecular mechanisms underlying most endosymbiont-insect interactions. Our laboratory analyses the interaction between Drosophila and its endosymbiont Spiroplasma poulsonii. We believe that the knowledge generated on the Drosophila-Spiroplasma interaction will serve as a paradigm for other endosymbiont-insect interactions that are less amenable to genetic studies. The digestive tract: an interactive barrier Aside from its central role in digesting and absorbing nutrients, the inner lining of the digestive tract must also serve as the first line of defense against a wide variety of pathogens. The gut is also a major source of neuronal and endocrine signals able to modulate nutrient storage or food intake by regulating the activity of other organs. Using an integrated approach, we are studying the mechanisms that make the gut an efficient and interactive barrier despite its constant interactions with microbes.

Keywords

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

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Results Obtained in 2014

Drosophila innate immunity The melanization reaction is a major immune response in Arthropods and involves the rapid synthesis of a black pigment, melanin, at the site of infection and injury. In a recent study, we have generated flies carrying deletions in the prophenoloxidases 1 and 2 genes and by analyzing these mutations alone and in combination, we have demonstrated the importance of melanization in combating microbial infection (Bingelli et al., 2014). We have also analyzed the impact of the gut microbiota on the intestinal epithelium. Our study shows that the microbiota affects gut morphology through their impacts on epithelial renewal rate, cellular spacing, and the composition of different cell types in the epithelium. Thus, the influence of the microbiota at large has far reaching effects on host physiology (Broderick et al., 2014; Buchon et al., 2014). The Drosophila-Spiroplasma interaction: a model for insect endosymbiont We have recently shown that the proliferation of the Drosophila endosymbiont Spiroplasma is limited by the availability of hemolymph lipids. This feature limits endosymbiont over-proliferation under conditions of host nutrient limitation (Herren et al., 2014). We have also deciphered the mechanism of vertical transmission by showing that Spiroplasma coopts the yolk transport and uptake machinery to colonize the germ line and ensure efficient vertical transmission (Herren et al., 2013). The uptake of yolk is a female germ line-specific feature and therefore an attractive target for co-option by endosymbionts that need to maintain high fidelity maternal transmission. The digestive tract: an interactive barrier We recently provided an atlas of the Drosophila adult midgut uncovering a fine-grained compartmentalization. We also revealed the role of intestinal stem cell in gut repair during bacterial infection (Buchon et al., 2013; 2014). Our laboratory is now working on the gene regulatory networks that govern gut regional identity and how regionalization affects various gut function such as immunity and digestive enzyme regulation. In this line we have recently demonstrated that the TGF-ß/Activin pathway functions as a carbohydrate- sensing mechanism in the adult Drosophila midgut to regulate digestive enzyme expression (Chng et al., 2014).

EPFL School of Life Sciences - 2014 Annual Report

Team Members Postdoctoral Fellows Anna Dostalova Igor Iatsenko Dani Osman Elodie Ramond Samuel Rommelaere Zongzhao Zhai

PhD Students Maroun Bou Sleiman Wen Bin (Alfred) Chng Jan Dudzic Mario Gonzalo Garcia Arraez Juan Paredes

Masters Student Laurent Alter

Technicial Support Jean-Philippe Boquete Christophe Rémondeulaz Fanny Schüpfer Tiffany Thébault

Administrative Assistant Véronique Dijkstra

GHI - Global Health Institute

Shown are wild-type (left) and eater deficient (right) transgenic Drosophila larvae expression GFP in hemocytes. Many hemocytes are sessile attached to inner parts of the cuticle (left). We have recently shown that formation of the sessile hematopoietic niche is disrupted in the eater mutant that affects a gene of the EGF repeat Nimrod family (right). Credit photo: Andrew Brestcher.

Selected Publications » » » » » » » » »

Binggeli, O., Neyen, C., Poidevin, M., and Lemaitre, B. (2014). Prophenoloxidase activation is required for survival to microbial infections in Drosophila. PLoS pathogens 10, e1004067. Broderick, N.A., Buchon, N., and Lemaitre, B. (2014). Microbiota-induced changes in Drosophila melanogaster host gene expression and gut morphology. mBio 5, e01117-01114. Chakrabarti, S., Poidevin, M., and Lemaitre, B. (2014). The Drosophila MAPK p38c regulates oxidative stress and lipid homeostasis in the intestine. PLoS genetics 10, e1004659. Chng, W.B., Bou Sleiman, M.S., Schupfer, F., and Lemaitre, B. (2014). Transforming growth factor beta/activin signaling functions as a sugar-sensing feedback loop to regulate digestive enzyme expression. Cell reports 9, 336-348. Herren, J.K., Paredes, J.C., Schupfer, F., Arafah, K., Bulet, P., and Lemaitre, B. (2014). Insect endosymbiont proliferation is limited by lipid availability. eLife 3, e02964. Buchon, N., Osman, D., David, F.P., Fang, H.Y., Boquete, J.P., Deplancke, B., and Lemaitre, B. (2013b). Morphological and molecular characterization of adult midgut compartmentalization in Drosophila. Cell reports 3, 1725-1738. Herren, J.K., Paredes, J.C., Schupfer, F., and Lemaitre, B. (2013). Vertical transmission of a Drosophila endosymbiont via cooption of the yolk transport and internalization machinery. mBio 4. Lemaitre, B., and Girardin, S.E. (2013). Translation inhibition and metabolic stress pathways in the host response to bacterial pathogens. Nature reviews. Microbiology 11, 365-369. Lemaitre, B., and Miguel-Aliaga, I. (2013). The digestive tract of Drosophila melanogaster. Annual review of genetics 47, 377-404.

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EPFL School of Life Sciences - 2014 Annual Report

McKinney Lab John McKinney

Full Professor - Director of the Doctoral Program in Biotechnology & Bioengineering (EDBB)

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

Introduction

John McKinney received his PhD from The Rockefeller University in 1994 for studies on eukaryotic cell cycle regulation. His postdoctoral studies at the Albert Einstein College of Medicine were focused on tuberculosis (1995-1998). Prof. McKinney headed the Laboratory of Infection Biology at Rockefeller University from 1999-2007. Since 2007, Prof. McKinney heads the Laboratory of Microbiology and Microsystems at EPFL. He is the director of EPFLâ&#x20AC;&#x2122;s Doctoral Program in Biotechnology and Bioengineering (EDBB) and is affiliated also with the Institute of Biotechnology (IBI).

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Research in the McKinney lab is focused on understanding the mechanistic basis of microbial individuality, defined as cell-to-cell phenotypic variation that is not attributable to genetic or environmental differences. A deeper understanding of this phenomenon will lead to new strategies to eliminate subpopulations of bacteria that are refractory to antimicrobial therapy and host immunity. Our interdisciplinary research program comprises equal parts microbiology and microengineering. In particular, we seek to design, develop, and apply new microfabricated tools for singlecell microbiology, combined with advanced imaging techniques based on optical and atomic force microscopy.

Keywords

Microbiology, microengineering, microbial individuality, single-cell biology, time-lapse microscopy, atomic force microscopy, microelectromechanical systems, microfluidics, mycobacteria, persistence, antibiotics.

Results Obtained in 2014

Bacterial cells behave as individuals. Mutation and horizontal DNA transfer are important drivers of bacterial individuation, but these genetic changes are relatively rare. At much higher frequencies, genetically identical cells display metastable variation in growth rates, response kinetics, stress resistance, and other quantitative phenotypes. These cell-to-cell differences arise from non-genetic sources, such as stochastic fluctuations in gene expression and asymmetric partitioning of components during cell division. Temporal variation at the single-cell level generates phenotypic diversity at the population level. This diversity is critical for bacterial persistence in changing environments because it ensures that some individuals will survive potentially lethal stresses that would otherwise extinguish the population. Our research focuses on the pathogenic species Mycobacterium tuberculosis. We use time-lapse optical and atomic force microscopy and custom-made microfabricated devices (microfluidics and MEMS) to study the real-time dynamics of bacterial behavior at the single-cell level.

EPFL School of Life Sciences - 2014 Annual Report

Team Members Senior Staff Scientist Neeraj Dhar

Postdoctoral Fellows Alex Eskandarian Giulia Manina Paul Murima

PhD Students Matthieu Delincé Oleg Mikhajlov Katrin Schneider Joëlle Ven Amanda Verpoorte

Masters Students Laurent Alter Coralie Boulet Kunal Sharma Thomas Simonet Gaëlle Thurre

Information Technologist: Olivia Mariana Research Technician François Signorino-Gelo Administrative Assistant Cécile Prébandier

GHI - Global Health Institute

Mycobacterium tuberculosis bacilli expressing a fluorescent reporter of single-cell ribosomal RNA production rates (green is high, red is low), which correlate with single-cell growth rates. See: Manina G, Dhar N, McKinney JD (2015) Cell Host Microbe 17(1): 32-46.

Selected Publications » Manina G, Dhar N, McKinney JD (2015) Stress and host immunity amplify Mycobacterium tuberculosis heterogeneity and induce non-growing metabolically active forms. Cell Host Microbe 17(1): 32-46. » Vaubourgeix J, Lin G, Dhar N, Chenouard N, Jiang X, Botella H, Lupoli T, Mariani O, Yang G, Ouerfelli O, Unser M, Schnappinger D, McKinney JD, Nathan C (2015) Stressed mycobacteria use the chaperone ClpB to sequester irreversibly oxidized proteins asymmetrically within and between cells. Cell Host Microbe PMID: 25620549. » Dhar N, Dubee V, Ballell L, Cuinet G, Hugonnet JE, Signorino-Gelo F, Barros D, Arthur M, McKinney JD (2015) Rapid cytolysis of Mycobacterium tuberculosis by faropenem, an orally available beta-lactam antibiotic. Antimicrob Agents Chemother 59(2): 1308-1319. » Chopra T, Hamelin R, Armand F, Chiappe D, Moniatte M, McKinney JD (2014) Quantitative mass spectrometry reveals plasticity of metabolic networks in Mycobacterium smegmatis. Mol Cell Proteomics 13(11): 3014-3028. » Elitas M, Martinez-Duarte R, Dhar N, McKinney JD, Renaud P (2014) Dielectrophoresis-based purification of antibiotic-treated bacterial subpopulations. Lab Chip 14(11): 1850-1857. » Santi I, Dhar N, Bousbaine D, Wakamoto Y, McKinney JD (2013) Single-cell dynamics of the chromosome replication and cell division cycles in mycobacteria. Nature Commun 4: 2470. » Wakamoto Y, Dhar N, Chait R, Schneider K, Signorino-Gelo F, Leibler S, McKinney JD (2013) Dynamic persistence of antibiotic-stressed mycobacteria. Science 339(6115): 91-95. » Tischler AD, Leistikow RL, Kirksey MA, Voskuil MI, McKinney JD (2013) Mycobacterium tuberculosis requires phosphate-responsive gene regulation to resist host immunity. Infect Immun 81(1): 317-328.

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EPFL School of Life Sciences - 2014 Annual Report

Trono Lab Didier Trono

Full Professor

http://tronolab.epfl.ch/

Introduction

After obtaining an M.D. from the University of Geneva and completing clinical training in pathology, internal medicine and infectious diseases in Geneva and at Massachusetts General Hospital, Didier Trono started a scientific career at the Whitehead Institute of MIT. In 1990, he joined the Salk Institute in San Diego to launch a center for AIDS research. Prof. Trono moved back to Europe seven years later, before taking the reins of the newly created EPFL School of Life Sciences, which he directed from 2004 to 2012. His research has long gravitated around interactions between viruses and their hosts and the development of tools for gene therapy. This led him to epigenetics, the current focus of his labâ&#x20AC;&#x2122;s investigation.

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More than half of the human genome is derived from transposable elements (TEs), most of them retrotransposons that spread by the copy-andpaste mechanism used by retroviruses. These endogenous retroelements (EREs) are essential motors of evolution, which can disrupt, activate or repress genes, move pieces of chromosomes around, and serve as hot spots for genetic recombination. The resulting mutations can either be evolutionarily advantageous or deleterious, and whether for their inactivation or their exaptation, transposable elements are under tight epigenetic control established from the earliest stages of embryogenesis. Our research explores this delicate equilibrium between transposable elements and their hosts, and investigates how these genetic invaders and their controlling mechanisms impact on the development, the physiology and the evolution of higher organisms, and how their deregulation can affect human health.

Keywords

Transposable elements, retroviruses, epigenetics, gene expression, stem cells, evolution.

Results Obtained in 2014

A few years ago, we discovered that the early embryonic control of endogenous retroviruses is mediated by KRAB-containing zinc finger proteins (KRABZFPs), a large family of tetrapod-restricted transcriptional repressors that act by recruiting inducers of heterochromatin and DNA methylation via their cofactor KAP1 (KRAB-associated protein 1). More recently, we found that KRAB-ZFPs are collectively responsible for silencing in an evolutionally dynamic fashion, a much broader range of TEs than previously thought, and that they exert as a consequence a marked influence on the transcriptional networks of human embryonic stem cells. We also demonstrated that, whereas the early embryonic silencing of EREs is a highly orderly process, their transcriptional control is profoundly altered during the reprogramming of somatic cells to induced pluripotent stem cells (iPSCs). This deregulation of EREs may be partly necessary for achieving pluripotency, but owing to its stochastic nature it likely decreases the overall efficiency of reprogramming. Furthermore it confers iPSCs with a great degree of epigenetic heterogeneity, and is a potential source of phenotypic anomalies for these cells. We also pursued our exploration of the functions and mechanisms of action of the KRAB/KAP1 system in somatic tissues. Adding to our previous results indicating that it is an essential regulator of the homeostasis of higher vertebrates, we unveiled that this system influences events as crucial as muscle differentiation and multiple steps of hematopoiesis. Through these experiments, we discovered that KAP1 can switch from a co-repressor to a co-activator state through phosphorylation, and that it can partake in multilayered transcription regulatory cascades, where protein- and RNA-based repressors are super-imposed in combinatorial fashion to govern the timely triggering of important physiological processes.

EPFL School of Life Sciences - 2014 Annual Report

Team Members Senior Scientist Priscilla Turelli

Postdoctoral Fellows Isabelle Barde Marco Cassano Marc Friedli Michael Imbeault Suk Min Jang Benjamin Rauwel Carmen Unzu

PhD Students Natali Castro Diaz Gabriella Ecco Pierre-Yves Helleboid Alexandra Iouranova Annamaria Kauzlaric Flavia Marzetta Andrea Coluccio

Master Student Marcelle Arrigo Bioinformaticians Julien Duc Evarist Planet

Technicians Sandra Offner Charlène Raclot Sonia Verp Administrative Assistant Séverine Reynard

GHI - Global Health Institute

Evolutionally dynamic control and co-option of transposable elements. New elements are partially controlled by RNA interference or cytidine deamination by APOBEC proteins, leaving room for some retrotransposition. Transcriptional repressors of the KRABZFP family eventually emerge that block the spread of these elements and partake in their domestication. Many EREs completely decay through genetic drift.

Selected Publications » Singh, K., Cassano, M., Planet, E., Soji, S., Jang, S.M., Sohi, G., Faralli, H., Choi, J., Youn, H.-D., Dillworth, J.D & Trono, D. (2015). A KAP1 phosphorylation switch controls MyoD function during skeletal muscle differentiation. Genes & Dev, in press. » Friedli, M. & Trono, D. (2015). The developmental control of transposable elements and the evolution of higher species. Ann Rev Cell Dev Bio, in press. Castro-Diaz, N., Friedli, M. & Trono, D. (2015). Drawing a fine line on endogenous retroelement activity. Mob Genet Elements, online Feb. 3. » Turelli, P., Castro-Diaz, N., Marzetta, F., Kapopoulou, A., Raclot, C., Duc, J., Tieng, V., Quenneville, S. & Trono, D. (2014). Interplay of TRIM28 and DNA methylation in controlling human endogenous retroelements. Genome Res 24, 1260-70. » Imbeault, M. & Trono, D. (2014). As Time Goes by: KRABs Evolve to KAP Endogenous Retroelements. Dev Cell 31, 257-8. » Friedli, M., Turelli, P., Kapopoulou, A., Rauwel, B., Castro-Diaz, N., Rowe, H.M., Ecco, G., Unzu, C., Planet, E., Lombardo, A., Mangeat, B., Wildhaber, B.E., Naldini, L. & Trono, D. (2014). Loss of transcriptional control over endogenous retroelements during reprogramming to pluripotency. Genome Res 24, 1251-9. » Castro-Diaz, N., Ecco, G., Coluccio, A., Kapopoulou, A., Yazdanpanah, B., Friedli, M., Duc, J., Jang, S.M., Turelli, P. & Trono, D. (2014). Evolutionally dynamic L1 regulation in embryonic stem cells. Genes Dev 28, 1397-409. » Rowe, H.M., Kapopoulou, A., Corsinotti, A., Fasching, L., Macfarlan, T.S., Tarabay, Y., Viville, S., Jakobsson, J., Pfaff, S.L. & Trono, D. (2013). TRIM28 repression of retrotransposon-based enhancers is necessary to preserve transcriptional dynamics in embryonic stem cells. Genome Res 23, 452-61. » Rowe, H.M., Friedli, M., Offner, S., Verp, S., Mesnard, D., Marquis, J., Aktas, T. & Trono, D. (2013). De novo DNA methylation of endogenous retroviruses is shaped by KRAB-ZFPs/KAP1 and ESET. Development 140, 519-29. » Barde, I., Rauwel, B., Marin-Florez, R.M., Corsinotti, A., Laurenti, E., Verp, S., Offner, S., Marquis, J., Kapopoulou, A., Vanicek, J. & Trono, D. (2013). A KRAB/KAP1-miRNA cascade regulates erythropoiesis through stage-specific control of mitophagy. Science 340, 350-3.

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EPFL School of Life Sciences - 2014 Annual Report

Van der Goot Lab F. Gisou van der Goot

Full Professor - Dean of the School of Life Sciences

http://vdg.epfl.ch/

Introduction

The general interest of our laboratory is to understand how biological membranes compartmentalize space, in 3D but also 2D; how shape is used to specify function; how transmission of information across membranes can be mediated. These over arching questions are addressed through the following main focuses: Gisou van der Goot studied engineering at the Ecole Centrale de Paris, then did a PhD in Molecular Biophysics at the Nuclear Energy Research Center, Saclay, France, followed by a postdoc at the European Molecular Biology Laboratory (EMBL) in Heidelberg. She started her own group in 1994 in the department of Biochemistry, University of Geneva, became Associate professor at the Faculty of Medicine (Univ. Geneva) in 2001 and Full Professor at the EPFL in 2006, where she cofounded the Global Health Institute. In 2014, she was appointed Dean of the School of Life Sciences.

• To understand how mammalian cell are compartmentalized, how compartmentalization of specific membranes is achieved and how this is related to function. We are particularly interested in the architecture of the endoplasmic reticulum and how palmitoylation, a uniquely reversible lipidation of proteins, regulates organelle structure and function by targeting key proteins. • To understand the physiological and pathological roles of the anthrax toxin receptors, TEM8 and CMG2. These two single spanning membrane proteins are well known to enable intoxication by anthrax but are poorly understood with respect to their role in communicating with the extracellular matrix. They are also palmitoylated and represent a useful model system to study this post-translationnal modification. • To unravel the molecular mechanisms responsible for Hyaline Fibromatosis and GAPO syndromes. These two rare genetic diseases are the result of mutations in the anthrax toxin receptor.

Keywords

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

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Results Obtained in 2014

Over the last few years, the laboratory has undergone a major change in focus, shifting the efforts from the study of bacterial toxins to studying how protein palmitoylation affects protein structure and functions and how cells make use of this reversible lipidation mechanism to organize the endomembrane system and generate compartments/domains with specific function. Major effort has been devoted to implementing high through putanalysis methods to study palmitoyl proteomes under various conditions and to establish a knowledge based database for palmitoylated proteins: SwissPalm. Since little is known about the regulations and dynamics of protein palmitoylation, we have chosen a set of key ER proteins as model proteins. In particular the ER chaperone calnexin, a type I membrane proteins harbouring a large lectin chaperone domain in the ER lumen and a 90 residue cytosolic tail that mediates unexpected functions such as association with the ribosome translocon complex and as well as signalling. We have combined experiment analysis with mathematical modelling (Coll. V. Hatzimanikatis, EPFL, Basic Sciences), to understand the dynamics and regulation of the calnexin palmitoylation cycle and how if affects function. This has also led us to study the enzyme that we have found palmitoylate scalnexin, DHHC6. We could also establish that DHHC6 is itself palmitoylated, providing the first evidence for palmitoylation cascades, reminiscent of phosphorylation cascades. On-going efforts are devoted to complexify the model, to evolve towards a complete model of the ER palmitoylation network. We have also pursued our studies to understand the physiological functions of the anthrax toxin receptors and the consequences of Hyaline Fibromatosis Syndrome mutations (HFS). Over the last 2 years, our focus has been to determine whether anthrax toxin receptors are actually receptors for a specific extracellular matrix component. We are particularly interested in determining how, mechanistically, the proteins are capable of transmitting information regarding the extracellular matrix to the interior of the cell and for what purpose. In these studies we combine analysis of CMG2 WT and mutants in tissue culture cells, the study of patient derived cells as well as the study of cmg2 KO mice.

EPFL School of Life Sciences - 2014 Annual Report

Team Members Scientist Collaborator Laurence Abrami

Postdoctoral Fellows Nicole Andenmatten Mathieu Blanc Sanja Blaskovic Elsa Perrody Oksana Sergeeva Maria Eugenia Zaballa

PhD Students Jérôme Bürgi Tiziano Dallavilla Mustafa Demir Sarah Friebe Patrick Sandoz Shixu Yan

Laboratory Assistants Sylvia Ho Béatrice Kunz

Administrative Assistant Geneviève Rossier

GHI - Global Health Institute

Schematic Representation of the Long-Term and Long-Distance LF Delivery Modes Anthrax LT is internalized via a dynamin-dependent pathway and delivered to early endosomes. There, the toxin-receptor complex is sorted into nascent ILVs. Anthrax PA forms a channel into the membrane of the ILV and translocates LF into the lumen. LF, encapsulated in the ILVs, is transported in a microtubule-dependent manner to later stages of the endocytic pathway. There, two fates are observed: LF is either delivered to the cytosol, presumably by back fusion, over periods of days, or LF-containing ILVs are released into the extracellular medium as exosomes. These exosomes can be taken up by naïve recipient cells via an ATR-independent dynamin-dependent mechanism. LF is subsequently released into the cytosol of the recipient cell in a Tgs101- and Alix-dependent manner (inspired by Raposo and Stoorvogel, 2013).

Selected publications » Abrami, L., Brandi, L., Moayeri, M., Brown, M. J., and Krantz, B. A. et al. (2013). Hijacking Multivesicular Bodies Enables Long-Term and Exosome-Mediated Long-Distance Action of Anthrax Toxin. Cell Reports. vol. 5, num. 4, p. 986-996. » Lakkaraju, A. K. and van der Goot, F.G. (2013). Calnexin Controls the STAT3-Mediated Transcriptional Response to EGF. Molecular Cell. vol. 51, num. 3, p. 386-396. » Yan, S. E., Lemmin, T., Salvi, S., Lausch, E. and Superti-Furga, A. D. Rokicki, M.D. Peraro, and F.G. van der Goot (2013). In-depth analysis of hyaline fibromatosis syndrome frameshift mutations at the same site reveal the necessity of personalized therapy. Human mutation. vol. 34, num. 7, p. 1005-17. » Castanon, I., Abrami, L., Holtzer, L., Heisenberg, C. P. van der Goot F. G.* and M. González–Gaitán*. (2013). Anthrax toxin receptor 2a controls mitotic spindle positioning. Nature Cell Biology. (15): 28-39. * Co-senior corresponding author » Degiacomi M.T. #, Iacovache I.#, Pernot L., Chami M., Kudryashev M., Stahlberg H., van der Goot F.G.* and Dal Peraro M. * (2013) The molecular assembly of the aerolysin pore reveals a unique swirling membraneinsertion mechanism. Nature Chemical Biology 9:623-9. doi: 10.1038/nchembio.1312 * Co-senior corresponding author » Blaskovic, S., Blanc, M. and van der Goot, F. G. (2013). What does S-palmitoylation do to membrane proteins? The FEBS journal. vol. 280, num. 12, p. 2766-74.

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