Annual report - ISREC 15-16 by EPFL School of Life Sciences

ISREC

Swiss Institute for Experimental Cancer Research The Swiss Institute for Experimental Cancer Research (ISREC) has continued its contributions to the School of Life Sciences at EPFL, via cutting-edge research, mentoring young scientists, and classroom teaching. In addition, ISREC is playing a key role in the new Swiss Cancer Center Lausanne, a joint venture with the University of Lausanne and its Hospital and Medical Center (CHUV). This new cancer center, announced in January 2013, has a mission statement to become the first comprehensive cancer center is Switzerland, as defined by depth and breadth in basic and translational cancer research, in clinical research and clinical trials of new therapies, and excellent care of cancer patients. ISREC, with 15 faculty research groups focused on cancer research or fundamental cell and developmental biology, brings exceptional strength and talent to this new cancer center. ISREC has been centrally involved in community-building initiatives for the SCCL, including a series of annual faculty-only and faculty plus staff retreats, held in the spring and fall, respectively. Both retreats - initiated in 2013 and continued annually henceforth under the excellent stewardship of Etienne Meylan (ISREC, SV, EPFL) and Olivier Michielin (CHUV, UNIL) – have proved successful at building bridges across the multiple sites in Lausanne that house cancer-related faculty. The Lola and John Grace Distinguished Lectures in Cancer Research – sponsored by the Grace family – bring in eminent cancer scientists for a once-monthly lecture at EPFL that is televised to the CHUV and Biopole/Epalinges sites of the SCCL. In addition, ISREC sponsors a monthly faculty-only research presentation, and a weekly informal seminar series for ISREC students and postdocs. Douglas Hanahan - Director

Denis Duboule was recently elected to the prestigious College de France, established in Paris in 1530, a society consisting of 52 members whose endeavors span the pursuit and public dissemination of knowledge across the spectrum of academic disciplines. Michele de Palma and Oliver Hantschel were awarded highly competitive ERC Consolidator Grants. On the occasion of the EPFL graduation ceremony - the Magistrale 2016 - Etienne Meylan received the EPFL Life Sciences Teaching Prize, ‘For excellence of his teaching judged from the last 3 years’. http://sv.epfl.ch/ISREC

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Brisken Lab Cathrin Brisken - Associate Professor

Cathrin Brisken received her MD and her PhD degree in Biophysics from the Georg August University of Göttingen, Germany. She completed her postdoctoral work in cancer biology with Dr. R.A. Weinberg at the Whitehead Institute of Biomedical Research in Cambridge, MA, USA. She previously held appointments at the Cancer Center of the Massachusetts General Hospital, Harvard Medical School, Boston and the Swiss Institute for Experimental Cancer Research (ISREC). Dr. Brisken is member of the International Breast Cancer Study Group (IBCSG) Biological Protocol Working Group. She served as Dean of EPFL Doctoral School (more than 2000 PhD students in 18 PhD programs), as member of the Hinterzartener Kreis, the oncology think-tank associated with the German Science Foundation, and numerous Swiss, European, and AACR committees. She co-founded the International Cancer Prevention Institute and is member of the AACRWomen in Cancer Research Council (2016-2019).

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Introduction

Results Obtained

Research in Dr. Brisken’s laboratory focuses on the cellular and molecular underpinnings of estrogen and progesterone receptor signaling in the breast and the respective roles of these hormones and hormonally active compounds in carcinogenesis. The aim is to understand how recurrent exposures to endogenous and exogenous hormones contribute to breast carcinogenesis in order to better prevent and treat the disease. The laboratory has pioneered in vivo approaches to genetically dissect the role of the reproductive hormones in driving mouse mammary gland development and shown how they control intercellular communication. Dr. Brisken’s group has developed ex vivo and humanized mouse models using patient samples to study hormone action in human tissues in normal settings and during disease progression.

Progesterone and Wnt4 control mammary stem cells via myoepithelial crosstalk Ovarian hormones increase breast cancer risk by poorly understoood mechanisms. We reveal that progesterone receptor (PR) signaling controls mammary epithelial stem cells through Wnt-4. Wnt-4 is secreted by PR positive luminal cells and activates canonical wnt signaling in basal cells.

Keywords Hormones, mammary gland development, breast carcinogenesis, paracrine signaling, estrogen, progesterone, RANKL, Wnt-4, stem cells, preclinical xenograft models

A preclinical model for ERα positive (ER+) breast cancer Ninety percent of new drugs in oncology fail, partly because the preclinical models used to test them are not adequate. Breast cancer is the leading cause of cancer-related death among women worldwide and we lack in vivo models for the ER+ subtypes, which represent more than 75% of all cases. We show that ER+ tumor cells can be successfully established as xenografts when injected into the milk ducts of immunocompromised mice. Traditional grafting into subcutaneous fat induces TGFβ/SLUG signaling and basal differentiation and prevents in vivo growth. Intraductally, SLUG is suppressed and ER+ tumor cells grow like their clinical counterparts. Disease progression with invasion and metastasis can now be studied in a physiologic endocrine milieu. The in vivo function of the secreted metalloproteinases ADAMTS18 We generated Adamts18-deficient mice and demonstrated a 100% penetrant eye defect resulting from leakage of lens material through the lens capsule. Adamts18 is also required for bronchiolar branching and vaginal opening. Thus, the orphan protease is essential in the development of distinct tissues and the new mouse strain is likely to be useful for investigating ADAMTS18 function in human disease, particularly in the contexts of infertility and carcinogenesis.

ISREC - Swiss Institute for Experimental Cancer Research

Team Members Postdoctoral Fellows

Georgios Sflomos Stéphanie Cagnet (until mid 2016) Csaba Lazlo PhD Students

Dalya Ataca Rachel Jeitziner Valentina Scabia Marie Shamseddin Lab Manager

Ayyakkannu Ayyanan Technicians

Laura Battista Administrative Assistants

Magali Frainier Tissue section from an intraductal xenograft’s hormone receptor positive breast cancer, stained for fibrillar collagen networks.

Selected Publications » Ataca, D., Caikovski M., Piersigilli, A., Moulin, A., Benarafa, C.; Earp, S.E., Guri, Y., Kostic, C., Arsenivic, Y., Soininen, R., Apte, S.S., Brisken, C. (2016) Adamts18 deletion results in distinct developmental defects and provides a model for congenital disorders of lens, lung, and female reproductive tract development. Biol Open. 2016 Nov 15; 5(11):1585-1594. » Sflomos, G., Dormoy, V., T. Metsalu, T., Jeitziner, R., Battista, L., Scabia, V., Raffoul, W., Delaloye, J.-F., Treboux, A., Vilo,J., Fiche, M., Ayyanan, A., Brisken C. (2016) A robust preclinical model for ERα positive breast cancer points to the mammary epithelial microenvironment as critical determinant of luminal phenotype and hormone response. Cancer Cell, 29(3): 407-422 » Procopio, MG., Laszlo, C., Al Labban, D., Kim, D., Bordignon, P., Jo, SH., Goruppi, S., Menietti, E., Ostano, P., Ala, U., Provero, P., Hoetzenecker, W., Neel, V., Kilarski, W., Swartz, M., Brisken C, Lefort, K., Dotto, G. P. (2015) Combined CSL and p53 downregulation promotes cancer-associated fibroblast activation. Nature Cell Biol 17(9):1193-204. » Dobrolecki LE, Airhart SD, Alferez DG, Aparicio S, Behbod F, Bentires-Alj M, Brisken C, Bult CJ, Cai S, Clarke RB, Dowst H, Ellis MJ, Gonzalez-Suarez E, Iggo RD, Kabos P, Li S, Lindeman GJ, Marangoni E,

McCoy A, Meric-Bernstam F, Piwnica-Worms H, Poupon MF, Reis-Filho J, Sartorius CA, Scabia V, Sflomos G, Tu Y, Vaillant F, Visvader JE, Welm A, Wicha MS, Lewis MT. Patient-derived xenograft (PDX) models in basic and translational breast cancer research. Cancer Metastasis Rev. 2016 Dec; 35(4): 547-573 » Brisken C., Hess, K., Jeitziner, R. (2015) Progesterone and overlooked endocrine pathways in breast cancer pathogenesis. Endocrinology, 156(10):3442-50. » Brisken C., Ataca, D., (2015) Endocrine hormones and local signals during the development of the mouse mammary gland. Wiley Interdiscip Rev Dev Biol. 4(3):181-95. » Sflomos, G., Shamsheddin, M. , Brisken C. (2015) An ex vivo model to study hormone action in the human breast. J Vis Exp. (95): e52436

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Constam Lab Daniel B. Constam - Associate Professor

Daniel Constam obtained his doctoral degree from ETH ZĂźrich. After postdoctoral studies at Harvard University as an EMBO fellow, he became an ISREC group leader in 2000 and associate professor at the EPFL School of Life Sciences in 2007. His lab studies signaling pathways that direct stem cell differentiation in development and cancer.

constam-lab.epfl.ch

Introduction

Results Obtained

Using genetic and biochemical approaches, we investigate how proprotein convertase family and their substrates govern stem and progenitor cell renewal and differentiation in the mammalian embryo, and how cancer cells redeploy them for tumor progression. Such road maps of progenitor cell differentiation are important both for regenerative medicine and to find ways to reduce tumor aggressiveness. We have shown that proprotein convertases control TGFÎ˛related activities and other master regulators of early lineage differentiation. However, what determines the substrate specificities and paracrine range of action of these proteases during development and in cancer is unclear. To address this, we generated convertase gene deletions and high resolution live imaging probes that reveal when and where these enzymes are active in normal and cancerous cells and tissues.

The first lineage decision in mammalian embryos occurs at the morula stage when outer cells become polarized by asymmetric contacts and activate the transcription factor YAP to form trophectoderm. By contrast, symmetric contacts of the adhesion molecule E-cadherin in inner cells inhibit this pathway and maintain the pluripotency of the cells that will form all body parts.

Several cancer hallmarks are shared by heritable polycystic kidney diseases. In such patients, renal epithelial tubule cells or their progenitors are reprogrammed to form fluid-filled cysts as they fail to protrude functional primary cilia into the tubule lumen to sense urine flow and possibly other stimuli. We study the role of the RNA-binding protein Bicc1 in signal transduction pathways such as Wnt, PKA and mTOR that control cell growth, repair and metabolism upand/or downstream of primary cilia.

Keywords Protease imaging, mRNA silencing, stem cells, cancer, polycystic kidney diseases

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Our PC7 gene knockout and live imaging showed that Furin and PC7 jointly initiate morula compaction at least in part by stimulating E-cadherin cleavage and stability, thus identifying the most upstream regulators of ICM formation known to date. However, a related convertase (Pace4) was activated a few hours later specifically in outer cells and significantly compensated for combined loss of Furin and PC7. Thus, during inner cell mass formation, E-cadherin precursor processing involves not only one but as many as three functionally overlapping proprotein convertases that are dynamically regulated. Ongoing work addresses whether other substrates rely on fewer PC family members for cleavage due to differential trafficking, and whether their processing in specific subcompartments would be a viable cancer drug target. Mutations in Bicc1 instigate cysts in kidney and pancreas. Our candidate search for the first direct targets identified AC6 and PKI mRNAs that affect cAMP signaling. However, why cAMP accumulates in polycystic kidney disease patients with ciliary defects is unclear. To elucidate how Bicc1 enables mRNA silencing, we modeled the structure of its SAM domain. In this model, the SAM organizes Bicc1 as a helical polymer with RNA binding sites arrayed at the surface. In line with this prediction, the bpk mutant Bicc1 allele and point mutations blocking SAM polymerization abolished the localization and silencing of associated reporter mRNA in cytoplasmic Bicc1 foci (Fig. 1). Whether Bicc1 polymerization is regulated by cilia or vice versa is under investigation.

ISREC - Swiss Institute for Experimental Cancer Research

Team Members Postdoctoral Fellows

Simon Fortier Benjamin Rothé PhD Students

Teresa Didonna Olivier Dubey Lucia Leal-Esteban Pierpaolo Ginefra Administrative Assistants & Technicians

Manuela Isenschmid Virginie Kokocinski Séverine Urfer Nancy Thompson

n -stained cyst-lining cells of bpk mutant polycystic mouse kidneys ( ), isoform A of Bicc1 is not polymerized by its SAM domain in cytoplasmic foci ( - ). nrichment of Bicc (pink) and bound mR (yellow) in foci is also inhibited if polymerization is blocked by point mutation (mutD, - ).

Selected Publications » Bessonnard, S., Mesnard, D. and Constam, D.B. (2015) PC7 and the related proteases Furin and Pace4 regulate E-cadherin function during blastocyst formation. J. Cell Biol. 210(7): 1185-1197. » Ellis, P., Burbridge, S., Soubes, S., Ohyama, K., Ben-Haim, N., Chen, C., Dale, K., Shen, M.M., Constam, D. and Placzek, M. (2015) ProNodal acts via FGFR3 to govern duration of Shh expression in the prechordal mesoderm. Development 142(22): 3821-3832. » Lemaire, L. A., Goulley, J., Kim, Y. H., Carat, S., Jacquemin, P., Rougemont, J., Constam, D.B. and Grapin-Botton, A. (2015) Bicaudal C1 promotes pancreatic NEUROG3+ endocrine progenitor differentiation and ductal morphogenesis. Development 142(5): 858-870. » Piazzon, N., Bernet, F., Guihard, L., Leonhard, W. N., Urfer, S., Firsov, D., Chehade, H., Vogt, B., Piergiovanni, S., Peters, D. J., Bonny, O. and Constam, D.B. (2015) Urine Fetuin-A is a biomarker of autosomal dominant polycystic kidney disease progression. J. Trans. Med. 13(1): 103. » Rothe, B., Leal-Esteban, L., Bernet, F., Urfer, S., Doerr, N., Weimbs, T., Iwaszkiewicz, J. and Constam, D.B. (2015) Bicc1 polymerization regulates the localization and silencing of bound mRNA. Mol. Cell. Biol. 35(19): 3339-3353. » Minocha, S., Bessonnard, S., Sung, T.L., Moret, C., Constam, D.B., and Herr, W. (2016) Epiblast-specific loss of HCF-1 leads to failure in anterior-posterior axis specification. Dev. Biol. 418: 75-88.

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De Palma Lab Michele De Palma - Tenure-Track Assistant Professor

Miki De Palma graduated in Biology (1999) and obtained a PhD degree in cell biotechnologies (2004) from the University of Torino Medical School, Italy, with a thesis on the regulation of tumor angiogenesis by bone-marrowderived cells. He performed post-doctoral training (20052008) at the Telethon Institute for Gene Therapy in Milan, where he developed strategies for engineering monocytes and reprogramming them into antitumoral immune cells. He was appointed group leader at the San Raffaele Institute, Milan, in 2008 (tenured in 2011), and joined ISREC/EPFL in 2012. He serves on the advisory boards of several international journals, including Science Translational Medicine and Cell Reports.

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Introduction

Results Obtained

Our lab has contributed to elucidating the pro-angiogenic functions of monocytes/macrophages in mouse models of cancer, as well as the molecular and functional heterogeneity of macrophages in both experimental and human tumors. We have also characterized VEGF-independent modes of tumor angiogenesis, and illustrated the therapeutic opportunities afforded by inhibiting angiopoietin signaling in de novo models of metastatic cancer. Currently, we employ genetic cancer models and cell-engineering strategies, largely based on lentiviral gene transfer, to dissect the interactions among macrophages, blood vessels and T cells in tumors, primarily by focusing on angiogenic signaling, immune checkpoints, microRNA regulation, and secreted exosomes. By tackling these processes, we aim to reprogram the immunosuppressive tumor microenvironment to a form that facilitates the deployment of anti-tumor immunity and enhances the efficacy of anticancer therapies.

In one recent study, we identified a mechanism regulating the immunosuppressive functions of macrophages in tumors. Tumor-associated macrophages (TAMs) largely express an alternatively activated (or M2) phenotype, which entails immunosuppressive and tumor-promoting capabilities. Reprogramming TAMs toward a classically activated (M1) phenotype may thwart tumor-associated immunosuppression and unleash anti-tumor immunity. We found that conditional deletion of the microRNA (miRNA)-processing enzyme DICER in macrophages prompts M1-like TAM programming, which is characterized by hyperactive interferon (IFN)-γ/STAT1 signaling. This rewiring abated the immunosuppressive capacity of TAMs and fostered the recruitment of activated cytotoxic T lymphocytes (CTLs) to the tumors. CTL-derived IFN-γ exacerbated M1 polarization of Dicer1-deficient TAMs and inhibited tumor growth. Remarkably, we found that DICER deficiency in TAMs negated the anti-tumoral effects of macrophage depletion by anti-CSF1R antibodies, and enabled complete tumor eradication by PD-1 checkpoint blockade or CD40 agonistic antibodies. Finally, we showed that the genetic rescue of Let-7 miRNA activity in Dicer1-deficient TAMs was sufficient to partly restore their M2-like phenotype and decrease tumor-infiltrating CTLs. These findings indicate that DICER/Let-7 activity opposes IFN-γ-induced, immunostimulatory M1-like TAM activation, with potential therapeutic implications.

Current research topics include: 1. Engineered dendritic cell vaccines for cancer immunotherapy; 2. microRNA regulation of macrophage activation in tumors; 3. Anti-angiogenesis as a tumor-conditioning strategy for improving cancer immunotherapy; 4. Mechanisms of tumor resistance to antiangiogenic therapy; 5. Tumor-derived exosomes and cancer progression.

Keywords Cancer, macrophage, angiogenesis, microRNA, exosome, immunotherapy, lentiviral vector.

ISREC - Swiss Institute for Experimental Cancer Research

Team Members Postdoctoral Fellows

Mario Leonardo Squadrito Martina Scmittnaegel Ioanna Keklikoglou Florent Duval Chiara Cianciaruso PhD Students

Caroline Baer Ece Kadioglu Technicians

Celine Wyse Danielle Thompson Antonino Cassará Axel Bellotti Administrative Assistants

Soledad Andany

he figure shows specific labeling of tumor-associated macrophages ( s green) in m mG mice, which express GFP upon re-mediated recombination. he yz2re transgene was used to induce macrophage-specific GFP activation. he yz2re transgene was also used to conditionally delete Dicer in s (see publication Baer et al., at ell Biol., 20 ).

Selected Publications » Baer, C., Squadrito, M.L., Laoui, D., Thompson, D., Hansen, S.K., Kiialainen, A., Hoves, S., Ries, C.H., Ooi, C.-H. and De Palma, M. (2016) Suppression of microRNA activity amplifies IFN-γ-induced macrophage activation and promotes anti-tumor immunity. Nat Cell Biol. 18(7): 790–802. » Cianciaruso, C., Phelps, E.A., Pasquier, M., [...], Swartz, M.A., De Palma, M., Hubbell, J.A., Baekkeskov, S. (2016) Primary human and rat β-cells release the intracellular autoantigens GAD65, IA-2, and proinsulin in exosomes together with cytokine-induced enhancers of immunity. Diabetes 66(2):460-473. » He, H., Mack, J.J., Güç, E., Warren, C.M., Squadrito, M.L., Kilarski, W.W., Baer, C., Freshman, R.D., McDonald, A.I., Ziyad, S., Swartz, M.A., De Palma, M. and Iruela-Arispe ML. (2016) Perivascular macrophages limit permeability. Arterioscler Thromb Vasc Biol. 36(11):2203-2212. » Wallerius, M., Wallmann, T., Bartish, M., […], De Palma, M., Ostman, A., Andersson J. and Rolny, C. (2016). Guidance molecule SEMA3A restricts tumor growth by differentially regulating the proliferation of

tumor-associated macrophages. Cancer Res. 76(11):3166-3178. » Galletti, G., Scielzo, C., Barbaglio, F., […], De Palma, M., Caligaris-Cappio, F. and Bertilaccio, M.T.S. (2016) Targeting macrophages sensitizes chronic lymphocytic leukemia to apoptosis and inhibits disease progression. Cell Rep. 14(7):1748-1760. » Ferri, F., Parcelier, A., Petit, V., [...], De Palma, M., Davidson, I., Rousselet, G. and Romeo, P.H. (2015) TRIM33 switches off Ifnb1 gene transcription during the late phase of macrophage activation. Nat Commun. 6:8900. » Hughes, R., Qian, B.-Z., Muthana, M., […], Joyce, J.A., De Palma, M., Pollard, J.W. and Lewis, C.E. (2015) Perivascular M2 macrophages stimulate tumor relapse after chemotherapy. Cancer Res. 75(17):3479-3491.

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Duboule Lab Denis Duboule - Full Professor

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’. 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 such as the National Academy of Sciences USA and the Royal Society and has received many awards, amongst which the Louis-Jeantet Prize for Medicine.

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duboule-lab.epfl.ch

Introduction

Results Obtained

Our laboratory has started operating at EPFL during 2007. Its major aim is to study principles of mammalian embryological development by using the recent tools of functional genomics. A special focus is given to those similarities and differences that exist between the embryological development of vertebrates (to whom mammals belong) and those of other animals (invertebrates), from whom vertebrates derive. To achieve this task, we use the developing mouse embryo in vivo as an experimental system, and try and apply the methodology developed following the sequencing of complex genomes. Our major aim is the understanding of the regulation of a critical family of transcription factors during the construction of the animal body plan, referred to as architect genes (the Hox gene family). These genes have a special interest in the study of both our ontogenesis (our development as individuals) and our phylogeny (our origin as a group of individuals) and the detailed understanding of their regulations and functions will be an important step in our understanding of our own histories. More recently, in collaboration with the Martinez-Arias (Cambridge) and Lutolf (EPFL) laboratories, we have started a new research program using in vitro grown organoids as models of mouse embryos.

Over the past two years, progresses have been made in several lines of research. Importantly, by using biochemical, genetic and epigenetic approaches, we have finally obtained a fair understanding of the collinear mechanism at work during limb development, a project that started in 1989 with the discovery of this intriguing phenomenon. We deciphered the chromatin structure around the HoxA and HoxD gene clusters and reported that they both had evolved related topologically associating domains (TADs) regulatory organization, likely implying that such a structure was already present in an ancestor animal that only had one gene cluster. During 2015, we have terminated a series of experiments whose aim was to determine which mechanism implements the transition between the regulation from one such TAD to the other, and we demonstrated that the Hox13 proteins themselves are involved in this important switch either by repressing the telomeric, or by activating the centromeric regulation. These opposite effects of the same proteins explain how these two regulations are exclusive from another and hence how the transition between the forearm and the hands is organized, with the mesopodial articulation (the wrist) in between. In the same context, we have shown how regulations in this system could be hi-jacked to serve another purpose in the course of evolution, as illustrated by the necessary function of these genes during the emergence of the mammary glands.

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

In parallel with these molecular studies, we have well progressed in our projects to try and better visualize the spatial organization of these genetic loci, as well as their long-range contacts with other genomic loci, either in expressing tissues, or in tissues where these genes are silent. In the former case, we set up a collaboration with the Sulyana Manley laboratory from the school of physics at EPFL, to try and picture the gene cluster by using STORM microscopy at very high resolution, in comparison with either SIM or more ‘classical’ FISH technology.

ISREC - Swiss Institute for Experimental Cancer Research

Team Members Postdoctoral Fellows

Pierre Fabre Nayuta Yakushiji Christopher Bolt Lucille Delisle PhD Students

Fabrice Darbellay Rita Amândio Technicians

Elisabeth Brönimann-Joye Trainees

ripartite interactions between oxd and regulatory islands. D D -F oxd and two regulatory islands. B uantifications showing variations in the distribution of physical distances between oxd and island or island , or island and island . c eatmap showing the distribution of tripartite interactions including at least oxd .

Ben Mormann, Fullbright fellow Athimed El Taher, stage Master Célia Bochaton, stage Master Hosted Ambizione Fellow

Anamaria Necsulea

Administrative Assistants

Gordana Favre

Selected Publications » Amândio, A.R., Necsulea, A., Joye, E., Mascrez, B. and Duboule, D. (2016) Hotair is dispensible for mouse development. PLoS Genet. 12(12):e1006232 » Schep, R., Necsulea, A., Rodríguez-Carballo, E., Guerreiro, I., Andrey, G., Nguyen Huynh, T.H., Marcet, V., Zákány, J., Duboule, D. and Beccari, L. (2016) Control of Hoxd gene transcription in the mammary bud by hijacking a preexisting regulatory landscape. Proc Natl Acad Sci USA 113(48):E7720-E7729. » Guerreiro, I., Gitto, S., Novoa, A., Codourey, J., Nguyen Huynh, T.H., Gonzalez, F., Milinkovitch, M.C., Mallo, M. and Duboule, D. (2016) Reorganisation of Hoxd regulatory landscapes during the evolution of a snake-like body plan. Elife 5. pii: e16087. » Beccari, L., Yakushiji-Kaminatsui, N., Woltering, J.M., Necsulea, A., Lonfat, N., Rodríguez-Carballo, E., Mascrez, B., Yamamoto, S., Kuroiwa, A. and Duboule D. (2016) A role for HOX13 proteins in the regulatory switch between TADs at the HoxD locus. Genes Dev. 30(10):1172-1186. » Darbellay, F. and Duboule, D. (2016) Topological domains, metagenes, and the emergence of pleiotropic regulations at Hox loci. Curr Top Dev Biol. 116:299-314. » Fabre, P.J, Benke, A., Manley, S. and Duboule, D. (2015) Visualizing the HoxD Gene Cluster at the Nanoscale Level. Cold Spring Harb Symp Quant Biol. 80:9-16.

» Fabre, P.J., Benke, A., Joye, E., Nguyen Huynh, T.H., Manley, S. and Duboule D. (2015) Nanoscale spatial organization of the HoxD gene cluster in distinct transcriptional states. Proc Natl Acad Sci USA 112(45):13964-13969. » Woltering, J.M. and Duboule, D. (2015) Tetrapod axial evolution and developmental constraints; Empirical underpinning by a mouse model. Mech Dev. 138 Pt 2:64-72. » Lonfat, N. and Duboule, D. (2015) Structure, function and evolution of topologically associating domains (TADs) at HOX loci. FEBS Lett. 589(20 Pt A):2869-2876. » Vieux-Rochas, M., Fabre, P.J., Leleu, M., Duboule, D. and Noordermeer, D. (2015) Clustering of mammalian Hox genes with other H3K27me3 targets within an active nuclear domain. Proc Natl Acad Sci USA. 112(15):4672-4677.

151

Gönczy Lab Pierre Gönczy - Full Professor

Pierre Göncyz obtained his PhD from The Rockefeller University (New York City, USA) in 1995. Thereafter, he conducted postdoctoral work at the EMBL (Heidelberg, Germany), before starting his laboratory in Lausanne in 2000 at ISREC, joining EPFL in 2005.

gonczy-lab.epfl.ch

Introduction

Results Obtained

We are interested in understanding fundamental cell division processes and focus on two in particular: centriole assembly and asymmetric division. To uncover the underlying mechanisms, we use a combination of genetic, functional genomic, biochemical, proteomic and cell biological approaches, primarily in C. elegans embryos and human cells.

We pursued our multidisciplinary research program to gain insights notably into the mechanisms of centriole assembly, as well as of centrosome positioning, in particular during asymmetric division. Two studies illustrating our efforts are highlighted below.

Centriole formation: Centrioles are evolutionarily conserved organelles essential for the assembly of cilia, flagella, and centrosomes, and which are characterized by a 9-fold radial symmetry of microtubules. We and others identified five proteins required for centriole formation in C. elegans, which are likewise crucial in other organisms. In collaboration with the Steinmetz laboratory, we discovered that one of these protein families (SAS-6 proteins) forms 9-fold symmetric rings at the root of the 9-fold symmetry of centrioles. Asymmetric cell division: Asymmetric division is crucial for generating diversity during development and stem cell lineages, and relies notably on proper positioning of the mitotic spindle. We and others showed that spindle positioning requires an evolutionary conserved ternary complex, which anchors the minus end directed motor protein complex dynein at the cell cortex. There, dynein is thought to generate pulling forces on astral microtubules that emanate from the spindle poles, thus positioning the mitotic spindle.

Keywords Cell biology, developmental biology, mitosis, centriole assembly, spindle positioning, C. elegans, human cells.

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Persistence of paternal centrioles The two gametes contribute differently to the zygote at fertilization. Apart from the genetic material, the oocyte contributes the bulk of cytoplasmic constituents, whereas in most animal species the sperm contributes two centrioles. How long such paternally contributed centrioles persist in the developing embryo was not known in any system. We set out to track the fate of paternally contributed centriolar components in C. elegans embryos. Our analysis revealed that several evolutionarily conserved centriolar components exhibit exceptional persistence over many cell cycles in the embryo. These findings raise the intriguing possibility that centrioles could act as information carrier, and that paternal centrioles may contribute information to the zygote. See Balestra et al.; 2015. Centrosome separation The two centrosomes present at the onset of mitosis must separate accurately to ensure proper bipolar spindle assembly. The minus-end directed motor dynein plays a key role in centrosome separation, but the underlying mechanisms remained elusive. We addressed these questions in the one-cell C. elegans embryo using a combination of 3D time-lapse microscopy and computational modeling. Our analysis revealed that centrosome separation is powered by the joint action of dynein at the nuclear envelope and at the cell cortex. We demonstrated that dynein at the cell cortex acts as a crosslinker that transmits polarized actomyosin cortical flows initiated by the centrosomes earlier in the cell cycle. This novel mechanism elegantly couples the early events of cell polarization with centrosome separation, thus ensuring faithful cell division. See also De Simone et al.; 2016.

ISREC - Swiss Institute for Experimental Cancer Research

Team Members Postdoctoral Fellows

Niccolò Banterle George Hatzopoulos Kerstin Klinkert Marie Pierron Jian Qiu Benita Wolf PhD Students

Radek Jankele Melina Scholze Veronika Villimova Technicians

Coralie Busso Isabelle Fluckiger omputer simulation of centrosome separation in . elegans embryo. perm (blue disk) and oocyte (dark green disk) pronuclei are shown. he two centrosomes (small green disks) nucleate microtubules (white lines). Dynein motors at the surface of pronuclei (blue points) or the cell cortex (red points) bind microtubules, exert force on them, and thus separate centrosomes.

Administrative Assistants

Nicole De Montmollin

Selected Publications » Graciotti M., Fang Z., Johnsson K. and Gönczy, P. (2016) Chemical genetic screen identified natural products that modulate centriole number. Chembiochem 17: 2063-2074.

» Sharma A., Aher A., Dynes N.J., Frey D., Katrukha E.A., Jaussi R., Grigoriev I., Croisier M., Kammerer R.A., Akhmanova A., Gönczy P. and Steinmetz M.O. (2016) Centriolar CPAP/SAS-4 imparts slow processive microtubule growth. Dev Cell 37: 362-376. » » » » »

De Simone A., Nédélec F. and Gönczy P. (2016) Dynein transmits polarized actomyosin cortical flows to promote centrosome separation. Cell Rep 14: 2250-2262. Gönczy, P. (2015) Centrosomes and cancer: revisiting a long-standing relationship. Nat Rev Cancer 15(11): 639-52. Neves, A., Busso, C. and Gönczy, P. (2015) Cellular hallmarks reveal restricted aerobic metabolism at thermal limits. Elife 4: e04810. Balestra, F.R., von Tobel, L. and Gönczy, P. (2015) Paternally contributed centrioles exhibit exceptional persistence in C. elegans embryos. Cell Res 25: 642-644. Blanchoud, S., Busso, C., Naef, F. and Gönczy, P. (2015) Quantitative analysis and modeling probes polarity establishment in C. elegans embryos. Biophysical J 108: 799-809.

153

Hanahan Lab Douglas Hanahan - Full Professor - Director of Swiss Institute of Experimental Cancer Research (ISREC)

Douglas Hanahan, born in Seattle, Washington, USA, received a bachelor’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 (1978-88) initially as a graduate student and then as a 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).

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Introduction

Results Obtained

The Hanahan group investigates tumor development and progression using genetically engineered mouse models of cancer that recapitulate important characteristics of human cancers, with strategic goals to elucidate pathogenic mechanisms underlying multi-step tumorigenesis and malignant progression, and to develop new therapeutic strategies based on knowledge of mechanism for translation toward clinical trials aiming to improve the treatment of human cancers. Currently the lab focuses on melanoma, glioblastoma, and pancreatic, breast, and cervical cancers. Topics include mechanistic studies on acquired capabilities – hallmarks of cancer – including the capabilities for ‘invasion and metastasis’ and ‘evading immune destruction’. A crosscutting theme is the role of the heterotypic tumor microenvironment and the accessory cells that collaborate with cancer cells to manifest malignant disease. In addition, the lab is studying mechanisms of adaptive resistance to therapies targeting these and other hallmark capabilities, which represent fascinating perturbations into corrupted regulatory systems, and offer potential avenues to circumvent such drug resistance with combinatorial therapies.

The lab has made exciting progress on multiple fronts during 2015/16. We have, for example: • Reported that glioblastoma brain cancers are hypersensitive to drugs that elevate the cellular recycling system called autophagy to levels that cause cell death, impairing tumor progression, and that such autophagyassociated cell death can be instigated by repurposing two classes of clinically approved drugs, originally developed to be anti-depressants or anti-coagulants, which are now appreciated to hyper-stimulate autophagy (Shchors et al, Cancer Cell, 2015). • Extended this concept, where in on-going studies we have found that these autophagy-inducing drugs can be combined with anti-angiogenic therapy, producing added benefit, exemplifying a conceptual strategy of co-targeting distinct hallmarks of cancer, aiming to limit adaptive resistance to cancer therapies (unpublished). • Reported that pancreatic neuroendocrine tumors can be defined as two molecular subtypes, of which one is preferentially associated with metastasis (Sadanandam et al, 2015, and unpublished). • Described a new form of adaptive resistance to anti-angiogenic therapy - metabolic symbiosis - whereby cancer cells, faced with vascular insufficiency, adopt compartmentalized metabolic states to share limited supplies of blood-borne glucose, with one instead utilizing as fuel lactate that is produced by the other’s metabolism of glucose (Allen et al Cell Reports, 2016). • Investigated mechanisms of resistance to cancer immunotherapy, using a mouse model of cervical carcinoma induced by the HPV16 oncogenes, wherein multiple micro-environmental barriers to infiltration and killing by cytotoxic T cells are implicated. In the context of a Sinergia grant and two pharma collaborations, we are characterizing the immune barriers and testing mechanism-based therapies in logical combinations, seeking to break down the barriers and unleash efficacious immunotherapy (unpublished).

Keywords Cancer mechanisms & therapeutic targeting, mouse models of cancer; tumor microenvironment.

ISREC - Swiss Institute for Experimental Cancer Research

Team Members Postdoctoral Fellows

Krisztian Homicsko Iacovos Michael Courtney Thomas Stephan Wullschleger Qian (Sophia) Zeng PhD Students

Gabriele Galliverti (joint M. Swartz) Julie Scotton Sadegh Saghafina Technical Staff

Sylvie André Balfast Mei-Wen Peng Bruno Torchia Sebastien Lamy Lab Manager etabolic symbiosis induced by anti-angiogenic therapy. ascular regression elicits reorganization of tumors into a hypoxic compartment that is glycolytic and a normoxic compartment that imports and metabolizes lactate. nhibition of m R disrupts this symbiosis ( llen et al., ell Reports 20 ).

Ehud Drori

Visiting Students

Agata Mlynska

Administrative Assistants

Diane Cevat Dorothée Demeester

Selected Publications » Shchors, K. Massaras, A. and Hanahan, D. (2015) Dual targeting of the autophagic regulatory circuitry in gliomas with repurposed drugs elicits cell-lethal rates of autophagy and therapeutic benefit. Cancer Cell 28: 456-471. » Sadanandam, A., Wullschleger, S., Lyssiotis, C., Grötzinger, C., Barbi, S., Bersani, S., Körner, J., Wafy, I., Mafficini, A., Lawlor, R.T., Asara, J., Bläker, H., Cantley, L.C., Wiedenmann, B., Aldo Scarpa, S. and Hanahan, D. (2015) Pancreatic neuroendocrine tumors: cross-species analysis reveals molecular subtypes with distinctive metastatic, developmental, and metabolic characteristics. Cancer Discovery 5: 1296-1313. » Hanahan, D. and Weinberg, R.A. (2016) The hallmarks of cancer: Perspectives for cancer medicine. In “The Oxford Textbook of Oncology, 3rd edition”, eds. Kerr, D., Haller, D., Van De Velde, C., Baumann, M, &

Saijo, N.; Oxford University Press, Oxford, UK. » Hanahan, D. and Weinberg, R.A. (2016) Biological Hallmarks of Cancer. In “Holland-Frei Cancer Medicine, Ninth Edition”, eds. Bast Jr., R.C., Croce, C.M., Hait, W., Hong, W.K., Kufe, D.W., Pollock, R.E., Weichselbaum, R.R., & Holland, J.F.; John Wiley & Sons, Hoboken, USA. » Allen, E., Mieville, P., Warren, C.M., Li, L., Peng, M.-W., and Hanahan, D. (2016) Metabolic symbiosis enables adaptive resistance to anti-angiogenic therapy that is dependent on mTOR signaling. Cell Reports 15: 1144-1460.

155

Hantschel Lab Douglas Hanahan - Tenure-Track Assistant Professor - ISREC Foundation Chair for Translational Oncology

Oliver Hantschel studied biochemistry in Regensburg and New York, received his PhD in 2004 from EMBL Heidelberg and did postdoctoral work at the Center for Molecular Medicine in Vienna. In 2010, he obtained his Venia Docendi (Habilitation) in Experimental Haematology from the Medical University of Vienna and joined EPFL in 2011.

Introduction

Results Obtained

Protein kinases are strongly involved in oncogenesis. The inhibition of aberrantly activated kinases is considered to be beneficial for cancer treatment. Since 2001, 30 inhibitors of a few oncogenic driver kinases in haematological and solid tumors have entered clinical practice. Despite remarkable clinical responses that could be achieved in selected diseases, most kinase inhibitors merely improve progression-free survival, but not overall survival, which is due to various mechanisms of evasive and adaptive resistance. Moreover, it is difficult to develop highly selective kinase inhibitors, as there are more than 500 kinases in humans with a conserved structure. Therefore, side effects caused by the inhibition of off-target kinases may limit its clinical utility. The Hantschel lab studies oncogenic kinase signaling by using interdisciplinary approaches at the interface of biochemistry, proteomics, chemical biology and protein engineering with the aim to identify innovative ways for therapeutic intervention.

Despite the success of ATP-competitive kinase inhibitors, the development of secondary drug resistance severely blunted initial clinical responses in most cases. In addition, only few human protein kinases have been targeted with the required degree of specificity by inhibitors targeting the ATP binding pocket of the protein kinase domain. An alternative strategy is the identification and targeting of sites other than the ATP binding pocket that are critical for kinase activity and that may down-modulate oncogenicity. This may provide an alternative handle to provide more specific kinase inhibitors, as the targeted site would be unique to only a few kinases and could decrease the overall incidence of drug resistance. We have demonstrated that the SH2 domain of the cytoplasmic tyrosine kinases oncoproteins ABL and FES acts as an allosteric activator, which is critical for high kinase activation and oncogenicity.

Main research avenues include: • Structure-function analysis of protein kinases • Targeting of intracellular protein-protein interactions and posttranslational modifications with engineered high-affinity protein antagonists • Analysis of oncogenic signaling networks using interaction- and phospho-proteomics. • Mechanism-of-action and specificity studies of kinase inhibitors

Keywords Leukemia, kinase inhibitors, protein engineering, phosphorylation, proteomics.

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Based on the promising results we have embarked on a systematic survey of most classes of cytoplasmic tyrosine kinases for allosteric activation that may be mediated by their modular protein interaction domains, e.g. SH2 and SH3 domains (see Figure). Using both quantitative in vitro enzymological assays with purified kinases (from bacterial, insect cell and mammalian expression systems), structure-function analysis as well as models in cancer cells, we have mapped such novel allosteric interactions and currently study their molecular mechanism-of-action. This provides the rationale for the functional testing of these interactions in cancer models with the prospect of their targeting with engineered protein inhibitors (monobodies) and small molecule chemical inhibitors. Our work provides important insight into the regulation of a large class of therapeutically important protein kinases, may identify additional targetable sites and provide the framework for future cancer drug development efforts.

ISREC - Swiss Institute for Experimental Cancer Research

Team Members Postdoctoral Fellows

Tim Kükenshöner Allan Lamontanara Gregory Mann Sina Reckel Timothy Reichart PhD Students

Daniel Duarte Grégory La Sala Nadine Schmit Research Technician

Sandrine Georgeon Apprentice

Sara Pereira n cytoplasmic tyrosine kinases ( s), protein interaction domains (P D) are involved in autoinhibition. pon oncogenic activation, P Ds contribute to allosteric activation of s and increase substrate recruitment. ngineered proteins or drugs can be used to disrupt allosteric activation.

Administrative Assistants

Christine Skaletzka

Selected Publications » Wojcik, J., Lamontanara, A.J., Grabe, G., Koide, A., Akin, L., Gerig, B., Hantschel, O. and Koide, S. (2016) High-affinity monobody inhibitors directed to the SH2-kinase interface of Bcr-Abl. J. Biol. Chem. 291(16):8836-8847.

» Maxson, J.E., Abel, M.L., Wang, J., Deng, X., Reckel, S., Luty, S.B., Sun, H., Gorenstein, J., Hughes, S., Bottomly, D., Wilmot, B., McWeeney, S.K., Radich, J., Hantschel, O., Middleton, R.E., Gray, N.S., Druker, B.J. and Tyner, J.W. (2016) Identification and characterization of tyrosine kinase nonreceptor 2 mutations in leukemia through integration of kinase inhibitor screening and genomic analysis. Cancer Res. 76(1): 127-138. » Reckel, S. and Hantschel, O. (2015) Kinase regulation in Mycobacterium tuberculosis: variations on a theme. Structure 23(6): 975-976. » Lorenz, S., Deng, P., Hantschel, O., Superti-Furga, G. and Kuriyan, J. (2015). Crystal structure of an SH2-kinase construct of c-Abl and effect of the SH2 domain on kinase activity. Biochem. J. 468(2): 283-291. » Hantschel, O. (2015) Unexpected off-targets and paradoxical pathway activation by kinase inhibitors. ACS Chem. Biol. 10(1) : 234-245.

157

Huelsken Lab Joerg Huelsken - Associate Professor

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

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Introduction

Results Obtained

Cancer stem cells (CSC) or tumor-initiating cells have been identified as subpopulation of tumor cells at the origin of cancer development and as a major driver for long-term tumor growth, tumor progression and metastasis. We are studying the biology of these cells with an emphasis on their interaction with other tumor cells and with the tumor stroma. In particular the role of cancer stem cells in the control of anti-tumor immune reactions has been a major topic of our research in recent years. Based on the principles we have learned from detailed analysis of pre-clinical tumor models, we are currently exploring several novel therapeutic options to interfere with these cells. We concentrate on breast and colon cancers for which we were able to show that eliminating cancer stem cells can cure disease even in advanced stages of cancer progression.

Most cancers, even in an advanced stage, resemble their tissue of origin indicating that tumor cells maintain parts of the normal differentiation program of their non-transformed ancestors. We now identified the homeobox transcription factor HoxA5 as an important inducer of intestinal epithelial differentiation. In colon cancer, HoxA5 is down-regulated during cancer progression, but when re-activated can induce loss of the cancer stem cell phenotype and can strikingly block-tumor growth and metastasis in vivo. HoxA5 is interconnected with the Wnt pathway in a negative feedback loop which ensures definitive bimodal fate decisions enforcing cells to halt cell cycling and exit the stem cell pool. Since HoxA5 expression can be triggered by retinoids, this may allow to treat colon cancer patients by Hox-mediated elimination of cancer stem cells.

Keywords Cancer stem cells, immunotherapy

metastatic

colonization,

differentiation

therapy,

Apart from generating all other tumor cells, we now find that cancer stem cells have an important function in controlling anti-tumor immune responses. For breast cancer, we have identified mechanisms which enable cancer stem cells to induce an immune suppressive microenvironment. This appears to be in particular important during metastatic seeding when a small number of cancer stem cells arrives in a new target organ and has to modify the stroma to become tumor-supportive. An important aspect of this ability of cancer stem cells is their immanent resistance to cell death which makes them withstand a number of hostile influences from the tumor stroma. We are working to decompose this immune suppressive activity in order to design targeted strategies for metastasis prevention which overcome these resistance mechanisms.

ISREC - Swiss Institute for Experimental Cancer Research

Team Members Postdoctoral Fellows

Laurent Beziaud PhD Students

Luisa Spisak Maxim Norkin Mathieu Girardin Nicolas Desbaillets Zuzana Tartarova Visiting Scientists

Jean-Paul Abbuehl Paloma Ordóñez Morán Technician

Pierre Dessen Administrative Assistants

Fanny Cavat

ancer initiation in the intestinal epithelium of the pre-clinical cancer model P lox lox, a fre uently mutated tumor suppressor gene in human colorectal cancers, can be prevented by treatment with vitamin (retinoic acid). his enforces differentiation of cancer stem cells preventing cancer growth.

Selected Publications » Natalia Lugli, N., V.S. Dionellis, P. Ordonez-Moran, I. Kamileri, S.K. Sotiriou, J. Huelsken, T. Halazonetis (2017). Enhanced rate of acquisition of point mutations in mouse intestinal adenomas compared to normal tissue. Cell Reports, in press. » Khurana, S., S. Schouteden, A. Santamaria-Martinez, J. Huelsken, A. Lacy-Hulbert, C. Verfaillie (2016). Outside-in integrin signaling regulates stemness and ageing of hematopoietic stem cells. Nature Commun 7:13500. » Tatárová, Z., J.P. Abbuehl, S. Maerkl and J. Huelsken (2016). Microfluidic co-culture platform to quantify chemotaxis of primary stem cells. Lab Chip, 16:1934-45. » » » »

Diderich, P., D. Bertoldo, P. Dessen, M. Khan, I. Pizzitola, W. Held, J. Huelsken, C. Heinis (2016). Phage selection of chemically stabilized -helical peptide ligands. ACS Chem Biol, 11:1422-7. Bertoldo, D., M. Khan, P. Dessen, W. Held, J. Huelsken, C. Heinis (2016).Phage Selection of Peptide Macrocycles against β-Catenin to Interfere with Wnt Signaling. Chem Med Chem., 11:834-9. Ordóñez-Morán, P., Dafflon, C., Imajo, M., Nishida, E., Huelsken, J. (2015). HoxA5 counteracts stem cell traits by inhibiting Wnt signalling in colorectal cancer. Cancer Cell, 28:815-29. Chiacchiera, F. , Rossi, A., Jammula, S., Piunti, A., Scelfo, A., Ordóñez-Morán, P., Huelsken, J., Koseki, H., Pasini, D. (2015). Polycomb complex PRC1 preserves intestinal stem cell identity by sustaining Wnt/ßcatenin transcriptional activity. Cell Stem Cell 18:91-103.

159

Lingner Lab Joachim Lingner - Full Professor

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 STARTfellowship 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.

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Introduction

Results Obtained

Telomeres are nucleoprotein structures at the ends of eukaryotic chromosomes. They have crucial functions as tumor suppressors and they protect chromosome ends from degradation and rearrangements. Telomere length and chromatin defects cause telomeropathies, which are characterized by damage in highly proliferative tissues early in life. Telomeres also serve as cellular clocks. They shorten in normal human cells with every round of DNA replication due to the DNA end replication problem and the absence of telomerase. Short telomeres elicit a DNA damage response triggering a permanent cell cycle arrest termed cellular senescence. Thus, the replicative potential of primary human cells is limited. While cellular senescence may contribute to organismal aging, it is beneficial to restrain the growth of pre-cancerous lesions. During progression towards malignancy, senescence is overcome by mutations in cell cycle regulators such as p53 and pRB. Furthermore, cancer cells acquire mutations that reactivate the telomerase enzyme, which stabilizes telomere length. Through telomerase activation, cancer cells acquire an immortal phenotype representing a cancer hallmark. Our laboratory combines telomeric chromatin analysis by mass spectrometry, biochemistry and molecular genetics to study the function, the dynamics and maintenance of telomere structures in normal development and disease.

Oxidative damage of telomeres can promote cancer, cardiac failure, and muscular dystrophy. Specific mechanisms protecting telomeres from oxidative damage had not been described. In collaboration with Viesturs Simanis, we analyzed telomeric chromatin composition by QTIP (Nat Comm. 4, 2848 (2013); Methods 114, 28 (2017)) during the cell cycle and showed that the antioxidant enzyme peroxiredoxin 1 (PRDX1) is enriched at telomeres during S phase (Cell Reports 17, 3107 (2016)). Deletion of the PRDX1 gene leads to damage of telomeric DNA upon oxidative stress, revealing a protective function of PRDX1 against oxidative damage. We also found that oxidized nucleotide or DNA substrates cause premature chain termination when incorporated by telomerase. Thus, PRDX1 safeguards telomeres from oxygen radicals to counteract telomere damage and preserve telomeric DNA for elongation by telomerase. The telomeric shelterin protein TRF2 suppresses the DNA damage response (DDR) and this function has been attributed to its abilities to trigger t-loop formation or to prevent massive decompaction and loss of density of telomeric chromatin. In collaboration with the group of Suliana Manley, we applied stochastic optical reconstruction microscopy (STORM) to measure the sizes and shapes of functional human telomeres of different lengths and dysfunctional telomeres that elicit a DDR (Genes & Dev, in press). Telomeres have an ovoid appearance with considerable plasticity in shape. Depletion of TRF2, TRF1 or both affected the sizes of only a small subset of telomeres. Co-staining of telomeres with DDR markers further revealed that the majority of DDR-signaling telomeres retained a normal size. Thus DDR signaling at telomeres does not require decompaction. We propose that telomeres are monitored by the DDR-machinery in the absence of telomere expansion and that the DDR is triggered by changes at the molecular level in structure and protein composition.

Keywords Telomeres, TERRA long noncoding RNA, chromatin, cellular senescence, telomeropathies.

ISREC - Swiss Institute for Experimental Cancer Research

Team Members Postdoctoral Fellows

Eric Aeby Wareed Ahmed Reyes Babiano Marianna Feretzaki Galina Glousker Gérald Lossaint Sophie Redon PhD Students

Jana Majerska Anna-Sophia Reis Patricia Renck-Nunes Aleksandra Vancevska Technician

Thomas Lunardi Administrative Assistants

Nicole de Montmollin

Quantitative telomeric chromatin isolation protocol (QTIP). (a) ork ow of P. (b) ffects of RF2-depletion at telomeres. (c) omparison of telomeric protein composition at long versus short telomeres. ee Grolimund, eby et al., ature ommunications 2 (20 ) for details.

Selected Publications » Aeby, E. and Lingner, J. (2015) ALT telomeres get together with nuclear receptors. Cell 160(5): 811-813. » Azzalin, C.M. and Lingner, J. (2015) Telomere functions grounding on TERRA firma. Trends Cell Biol. 25(1): 29-36. » » » » »

*Aeby, E., *Ahmed, W., Redon, S., Simanis, V. and Lingner, J. (2016) Peroxiredoxin 1 protects telomeres from oxidative damage and preserves telomeric DNA for extension by telomerase. Cell Rep (17): 3107-3114. Lossaint, G. and Lingner, J. (2017) TZAP or not to zap telomeres. Science 355: 578-579. Feretzaki, M. and Lingner, J. (2017) A practical qPCR approach to detect TERRA, the elusive telomeric repeat-containing RNA. Methods 114: 39-45. Majerská, J., Redon, S. and Lingner, J. (2017) Quantitative telomeric chromatin isolation protocol for human cells. Methods 114: 28-38. *Vancesca, A., *Douglass, K.M., Pfeiffer, V., **Manley, S. and **Lingner, J. (2017) The telomeric DNA damage response occurs in the absence of chromatin decompaction. Genes & Dev, in press

161

Meylan Lab Etienne Meylan - Tenure-Track Assistant Professor - SNSF Professor

Etienne Meylan received a PhD in Life Sciences from the University of Lausanne in 2006. From 2007 to 2010, he was a postdoc at MIT, Cambridge USA. In 2011, he established his laboratory at ISREC as a SNSF Professor and since 2013 as Tenuretrack Assistant Professor. His laboratory focuses on the molecular mechanisms that contribute to the development of lung cancer..

Introduction

Results Obtained

In our laboratory, we study signalling pathways that regulate crucial aspects of tumor metabolism or immunology. Our efforts are currently focused on nonsmall cell lung cancer (NSCLC), the principal type of lung cancer, which is the leading cause of cancer related deaths worldwide in women and men.

In 2015 and 2016 we have continued our work on glucose transporter GLUT3, and have begun to investigate GLUT1 in NSCLC.Based on our previous findings of GLUT3 being a target gene of the epithelial-mesenchymal transition (EMT) transcription factor ZEB1, we decided to explore how EMT perturbation would affect GLUT3 expression and, by extension, glucose metabolism in NSCLC. To address these points, we used KrasLSL-G12D/WT; p53Flox/Flox mouse models of lung adenocarcinoma, where we increased or decreased the expression of an EMT transcription factor. Upon sacrifice, these lung tumors were isolated, and are currently under molecular and histopathological analysis. During our characterization of GLUT3 expression in tumor cells, we made the interesting observations that tumor cell lines from a rare pediatric liver cancer, hepatoblastoma, express GLUT3 to very high levels. This prompted us to interrogate how GLUT3 is regulated in tumor cells from this malignancy, and if knowledge can be gained about the metabolism of these tumors. Experiments with cultured cells as well as actual human tumor tissue samples are ongoing.

We use combinations of in vitro cellular systems, bioinformatics analyses and genetically-engineered mouse models of human cancer as well as human tissue specimens to accomplish our goal: to better understand how this malignancy develops and progresses to a fatal disease. An initial focus in our laboratory was to comprehend the molecular mechanisms explaining the regulation and function of a high affinity glucose transporter in NSCLC, GLUT3. Currently, we are expanding our research activities toward a more global understanding of pathways regulating the tumor environment. Hopefully, our projects will enable us to identify new vulnerabilities of this cancer, which could be amenable to future therapies to combat it. We have also developed a new line of research on hepatoblastoma, a rare childhood liver cancer where we identified GLUT3 expression being strongly elevated.

Keywords Lung cancer, mouse models, glucose metabolism, tumor immunology

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We have also continued our investigations of signalling pathways that impact lung tumor development, and highlighted two proteins, RIP4 and RANKL, which are both known to be potent activators of NF-kappaB signalling, a pathway promoting lung cancer development. Through genetic or pharmacologic-based experiments, we modified their expression or activity directly in vivo, to reveal their function in the development of NSCLC. The consequences of RIP4 or RANKL blockade on tumor cells and the immune microenvironment are currently being investigated. In parallel, we have elaborated a sophisticated methodology to extract and analyse in an unbiased manner the complex immune microenvironment of lung tumors from our mouse models. Hopefully, these analyses will provide new information about immune cell types causally linked to tumor progression.

ISREC - Swiss Institute for Experimental Cancer Research

Team Members Postdoctoral Fellows

Pierre-Benoit Ancey Julien Faget Jawahar Kopparam PhD Students

Caroline Contat Svenja Groeneveld Technician

Jessica Vazquez Silvia Sabatino (apprentice) Bioinformatician

Nadine Zangger

Masterâ&#x20AC;&#x2122;s Students

Bernard Moret

Administrative Assistants

Christine Skaletzka

General experimental setting tumors are initiated by intratracheal virus- re, where a second gene or shR of interest can be added for study. icro- reveals lung tumors a few months after initiation. t sacrifice, tumors are collected individually and prepared for multiple analyses.

163

Oricchio Lab Elisa Oricchio - Tenure-Track Assistant Professor - ISREC Foundation Chair for Translational Oncology

In November 2014, Elisa Oricchio was appointed as tenure track Assistant Professor at ISREC/EPFL. Prof. Oricchio graduated in Genetics with highest honor in 2004 and obtained a PhD in 2008 at the National Italian Institute of Health in Rome Italy. In Sept 2008, she joined the group of Dr. HG Wendel at Memorial Sloan Kettering (NY, USA) as a post-doc. Her research work focused on the genetics of Lymphoma exploring innovative therapeutic approaches.

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Introduction

Results Obtained

Research in Oricchio laboratory focuses on the genetics of lymphoma and its translation into new therapies. Lymphoma is a heterogeneous disease characterized by multiple genomic alterations. We combine genomic analyses of human tumors with functional in vivo studies using mosaic models of lymphomas to functionally annotate genes of interest. Moreover, we directly compare the impact of different genetic lesions on therapy response using highly controlled experimental systems that resemble the design of clinical trials in a physiological context. Our ultimate goal is to exploit our genetic and biological studies for the design of new therapeutic strategies.

The research activity in the lab focuses on the lymphoma biology and recently we started a new project on Primitive Neuro-Ectodermal Tumors. We have 3 main projects ongoing in the lab. Project 1. Identify novel therapeutic targets in Follicular and Diffuse Large B-cell lymphoma. We used an inducible CRISPR/Cas9 library targeting more than ~500 kinases to identify new essential targets in DLBCL lymphoma. We found that loss of specific kinases regulating B-cell receptor and mTOR signaling strongly impair B-cell proliferation. Moreover, we uncovered an unexpected synthetic lethal interaction between inhibition of B-cell receptor signaling and SRC- family kinases prompting the possibility to test new rational combination therapies. Project 2. Identify chromosomal structural changes dictate by epigenetic and copy number alterations. Follicular lymphoma development is driven by multiple genomic alterations, including frequently mutated epigenetic modifiers (e.g. EZH2) and several copy number changes. The EZH2 gain of function mutation Y641X increases the H3K27me3 levels altering the heterochromatin organization and blocking the expression of several genes. Now, we are defining how epigenetic changes influence tri-dimensional organization of the genome. To analyze the chromosomal structural organization, we are using highthroughput Chromosome Conformation Capture method (Hi-C). We recently completed Hi-C analysis in lymphoma cell lines and in our preliminary data, we identified that the expression of several genes is concordantly regulated within specific chromosomal domains and is epigenetically controlled. Project 3. Define epigenetic and metabolic alterations in Primitive NeuroEctodermal Tumors (PNET). We developed a new in vivo model to study PNET pathogenesis. Our model is based on primary human neural precursor originated from induced pluripotent stem cells (human-iPS). We reported that PNET are dependent on MYC activity and genetic MYC inhibition alters the expression of metabolic genes such as PKM2 and LDHA and blocks cell proliferation. Now, we are exploring metabolic and epigenetic changes associated with PNET development. We are analyzing public available DNA methylation profile in PNET patients and we obtained in vivo preliminary data of the metabolic changes associated with these tumors.

Keywords Cancer genetics, mouse models, therapy

ISREC - Swiss Institute for Experimental Cancer Research

Team Members Post doctoral

Sungalee Stephanie PhD Students

Battistello Elena Donaldson Maria Technician

Katanayeva Natalya Administrative Assistants

Demeester Dorothée

Design and analysis of a genome editing screen using rispr to identify new therapeutic targets for lymphoma treatment.

Selected Publications » Boice, M., Salloum, D., Mourcin, F., Sanghvi, V., Amin, R., Oricchio, E., Jiang, M., Mottok, A., Denis-Lagache, N., Ciriello, G., Tam, W., Teruya-Feldstein, J., de Stanchina, E., Chan, W.C., Malek, S.N., Ennishi, D., Brentjens, R.J., Gascoyne, R.D., Cogné, M., Tarte, K. and Wendel, H.G. (2016) Loss of the HVEM tumor suppressor in lymphoma and restoration by modified CAR-T cells. Cell 167(2): 405-418. » Oricchio, E., Papapetrou, E.P., Lafaille, F., Ganat, Y.M., Kriks, S., Mark, W.H., Teruya-Feldstein, J., Huse, J.T., Reuter, V., Sadelain, M., Studer, L. and Wendel, H.G. (2014) A cell engineering strategy to enhance the

safety of stem cell therapies. Cell Report 8: 1677-1685. » Goldgur, Y., Susi, P., Karelehto, E., Sanmark, H., Lamminmäki, U., Oricchio, E., Wendel, H.G., Nikolov, D.B. and Himanen, J.P. (2014) Generation and characterization of a single-chain anti-EphA2 antibody. Growth Factors 32(6): 214-222. » Oricchio, E., Ciriello, G., Schatz, J.H., Jiang, M., Heguy, A., Viale, A., de Stanchina, E., Teruya-Feldstein, J., Sander, C., Wayne, T., Seshan, V.E., Chaganti,,R.S.K. and Wendel, H.G. (2014) Frequent disruption of the RB pathway in indolent follicular lymphoma suggests a new combination therapy. J Exp. Med. 211(7): 1379-1391.

165

Radtke Lab Freddy Radtke - Full Professor

Freddy Radtke graduated from the University of ZĂźrich in molecular biology 1994, a postdoctoral fellowship at Genentech Inc. USA 19951996 was followed by a postdoctoral position at ISREC Switzerland 1997-1999; Assistant Member of the Ludwig Institute for Cancer Research 1999-2004 promoted to Associate Member in 2004; joined ISREC as Senior Scientist in 2006, before joining EPFL in August 2006 as associate professor; promoted to full professor in 2012.

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Introduction

Results Obtained

Our group is interested in the molecular mechanisms controlling tissue selfrenewal, differentiation and cancer. The basic principle of self-renewing tissues is that they continuously produce cells from a stem cell reservoir that gives rise to proliferating transient amplifying cells, which subsequently differentiate and migrate to the correct compartment. These processes have to be tightly regulated to ensure life-long homeostasis. Developmental signaling pathways such as Notch and Wnt signaling have been shown to play important roles in regulating self-renewing tissues. Moreover, these pathways are often deregulated during tumorigenesis due to mutations in key elements involved in these pathways. Using mouse genetics we study the role of evolutionarily conserved signaling pathways under physiological and pathological situations to gain a better understanding of their role in cancer. In addition, the lab optimizes and validates potential drug development candidates that target developmental signaling pathways to assess their mode of action and their efficacy in pre-clinical cancer models and in primary human tumor samples. The goal is to develop these drug development candidates further for clinical proof of concept in human studies. Another aspect of our current research is to study the influence of inflammation for tumor progression.

Dicer1 imparts essential survival cues in Notch driven T-ALL via miR-21 mediated tumor suppressor Pdcd4 repression: The modulatory function of individual miRNAs in Notch driven T-ALLs has recently been established. Although pro-tumorigenic and tumor-suppressive miRNAs are implicated in disease onset in murine models of Notch-driven T cell leukemia, whether Dicer1-processed miRNAs are essential for Notchdriven T-ALL was unknown. We showed that Dicer1-processed miRs are essential at all stages of T-ALL development and maintenance. Lineage tracing experiments revealed that Dicer1 deficiency led to the induction of apoptosis in T-ALL cells whereas cell cycle progression remained unaltered. Through microarray-based miRNA profiling, we identified miR-21 as a previously unrecognized miRNA deregulated in both mouse and human T-ALL. We demonstrated that miR-21 regulates T-ALL cell survival via repression of the tumor suppressor Pdcd4.

Keywords Cancer, leukemia, stem cells, differentiation, immunity, notch, Wnt, preclinical drug development and trials.

Chronic inflammation imposes aberrant stem cell fate via mechanotransduction : Chronic inflammation is associated with a variety of pathological conditions in epithelial tissues, including cancer, metaplasia and aberrant wound healing. We have delineated the effect of chronic inflammation on epithelial stem cells using the corneal epithelium as a model tissue. We demonstrated that chronic inflammation indirectly regulates stem cell fate choice by altering the mechanical properties of the surrounding microenvironment. Subsequently, aberrant mechanotransduction in corneal epithelial stem/progenitor cells induces epidermal differentiation via elevated -catenin signaling. Corneal differentiation can be restored using small molecule inhibitors of mechanotransduction. Collectively, this study demonstrates that chronic inflammation and mechanotransduction are linked and act to elicit pathological responses in epithelial stem cells. This therefore establishes a new mechanism by which chronic inflammation can contribute to disease.

ISREC - Swiss Institute for Experimental Cancer Research

Team Members Senior Scientists & Post Doctoral

Ute Koch Markus Germann Rajwinder Lehal Alain Kfouri Charlotte Urech Nadine Zangger PhD Students

Mateusz Antoszewski Linlin Cao Delphine Harduin Technician

Christelle Dubey Pasqualina Magliano Marianne Nkosi Administrative Assistants

Catherine Pache he schematic depicts the essential function of Dicer mediated miR biogenesis for induction and maintenance of otch-driven cell acute lymphoblastic leukemia ( ) as well as novel signaling axis involving miR-2 and the tumor suppressor Pdcd that is essential for survival of cells.

Selected Publications » Chennupati, V., Koch, U., Coutaz, M., Scarpellino, L., Tacchini-Cottier, F., Luther, S.A., Radtke, F., Zehn, D. and MacDonald, H.R. (2016) Notch signaling regulates the homeostasis of tissue-restricted innate-like T

cells. J Immunol 197: 771.782. » Gamrekelashvili, J., Giagnorio, R., Jussofie, J., Soehnlein, O., Duchene, J., Briseño, C.G., Ramasamy, S.K., Krishnasamy, K., Limbourg, A., Kapanadze, T., Ishifune, C., Hinkel, R., Radtke, F., Strobl, L.J., Zimber-Strobl, U., Napp, L.C., Bauersachs, J., Haller, H., Yasutomo, K., Kupatt, C., Murphy, K.M., Adams, R.H., Weber, C. and Limbourg, F.P. (2016) Regulation of monocyte cell fate by blood vessels mediated by Notch signaling. Nat Commun 7: 12597. » Nowell, C,S., Odermatt, P,D., Azzolin, L., Hohnel, S., Wagner, E.F., Fantner, G.E., Lutolf, M.P., Barrandon, Y., Piccolo, S. and Radtke, F. (2016) Chronic inflammation imposes aberrant cell fate in regenerating

epithelia via mechanotrunsdaction. Nature Cell Biology 18(2):168-180. » Bernier-Latmani, J., Cisravvsky, C., Demir, C.S., Bruand, M., Jaquet, M., Davanture, S., Ragusa, S., Siegert, S., Dormond, O.l., Benedito, R., Radtke, F., Luther, S.A. and Petrova, T.V. (2015) DLL4 promotes continuous adult intestinal lacteal regeneration and dietary fat transport. J Clin Invest 125(12): 4572-4586. » Urech-Varenne, C., Radtke, F*. and Heinis, C*. (2015) Phage selection of bycyclic peptide ligands of the Notch1 receptor. CheMedChem 10(10):1754-1761. » Junker, F., Chabloz, A., Koch, U. and Radtke, F. (2015) Dicer1 imparts essential survival cues in Notch-driven T-ALL via miR-21-mediated tumor suppressor Pdcd4 repression. BLOOD 126(8): 993-1004. » López-Arribillaga, E., Rodilla, V., Pellegrinet, L., Guiu, J., Iglesias, M., Roman, A.C., Gutarra, S., González, S., Muñoz-Cánoves, P., Fernández-Salguero, P., Radtke, F., Bigas, A. and Espinosa, L. (2015) Bmi1 regulates murine intestinal stem cell proliferation and self-renewal downstream of Notch. Development 142(1): 41-50.

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Simanis Lab Viesturs Simanis - Associate Professor

Viesturs Simanis studied Biochemistry at Imperial College, graduating with a First Class Honours Degree in 1980. He did his Ph.D. studies with Professor Sir David Lane, at Imperial College London (awarded 1984). He did his postdoctoral studies with Professor Sir Paul Nurse, at ICRF in London, and the Department of Microbiology in Oxford (1984 to 1988). He then moved to the Swiss Institute for Experimental Cancer Research in Lausanne (Switzerland), as a junior, then senior group leader (1988 to 2006). He was appointed Associate Professor at EPFL in 2006.

simanis-lab.epfl.ch

Introduction

Results Obtained

Cell division requires duplication of the genome followed by segregation of one copy to each daughter cell and cytokinesis. Errors in these events can result in cell death, or alter the cellâ&#x20AC;&#x2122;s behaviour, which can contribute to the development of diseases such as cancer. We use S. pombe model to study cytokinesis, the final event of the cell cycle. Our goal is to understand how cytokinesis is regulated and coordinated with other events in the cell cycle. In S. pombe a GTPase-regulated NDR-kinase signalling network known as the Septation Initiation Network (SIN) 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. The SIN is considered to be the functional counterpart of the mammalian Hippo signalling pathway, which regulates growth and proliferation. The SIN also plays a role in meiosis, where is it essential for generating the spores/ gametes following completion of the two meiotic divisions. Our primary tools are forward and reverse genetics, combined with cell biology and biochemical analysis. Our goal is to identify regulators and targets of the SIN in mitosis and meiosis.

Association of SIN proteins with the spindle pole bodies (SPBs) during mitosis is important for SIN regulation. We used semi-automated image analysis (with the Unser lab, EPFL) to study SIN proteins localisation in wild-type and mutant cells. This analysis uncovered new facets of SIN regulation. First, the association of Cdc7p with the SPBs in early mitosis is asymmetric, favouring the new SPB. This requires Plo1p activity, and is unaffected by mutations that influence Cdc7p asymmetry in anaphase. Second, Cdc7p asymmetry in anaphase B is promoted by the 14-3-3 protein Rad24p, but delayed by the DYRK-family kinase Pom1p and the spindle assembly checkpoint. Finally, some SIN proteins show dynamic localisation patterns in early mitosis, which then become fixed in anaphase B. We are now investigating the molecular basis underlying the transition between the two states of the SIN.

Keywords Cytokinesis, cell division, meiosis, mitosis, signal transduction, yeast

In a companion study in collaboration with the Xenarios lab (SIB-UNIL), we adopted a Boolean modelling approach to describe the qualitative behaviour of the SIN and predict the behaviour of compound mutants that had not yet been constructed. Our extended Boolean model of the SIN comprised most SIN components and regulators as individual, experimentally malleable nodes. We used CDK activity levels as control nodes for the simulation of SIN related events in different stages of the cell cycle. The model was optimized using single knock-out experiments of known phenotypic effect as a training set, and was able to correctly predict a double knock-out test set. Moreover, the model made in silico predictions that have been validated in vivo, providing new insights into the regulation and hierarchical organization of the SIN. We also collaborated with the Lingner lab (EPFL SV) to study the protein composition of telomeres at different cell cycle stages. This study revealed that peroxiredoxin1 associates with telomeres maximally during S-phase and helps protect telomeres from oxidative damage.

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ISREC - Swiss Institute for Experimental Cancer Research

Team Members Post Doctoral Fellows

Andrea Krapp

PhD Students

Claudia Melcarne Manuela Moraru (graduated Oct. 2016) Technician

Elena Cano del Rosario Administrative Assistants

Catherine Pache

he image of the scaffold dc p-GFP illustrates progress from interphase (single PB) to mitosis as a kymograph. he vertical axis is time, the horizontal represents PB position. he inter- PB distance decreases as the nuclei move to the middle of the daughter cells after spindle disassembly. n wild-type cells, R contraction begins at maximal PB separation. he three phases of mitosis are shown to the right of the image. he early and late states of the are shown to the right of the image. he early state re uires Plo p activity, and is characterised by faint protein signals and unstable association of dc p and id p with the PBs. he late state does not re uire Plo p, but depends upon pg p and td p. t is characterised by asymmetric localisation of some proteins. he gradient between them indicates the fact that the precise timing of the transition varies from cell to cell

Selected Publications » Aeby, E., Ahmed, W., Redon, S., Simanis, V. and Lingner, J. (2016) Peroxiredoxin 1 protects telomeres from oxidative damage and preserves telomeric DNA for extension by telomerase. Cell Reports 17:3107 - 3114.

» Chasapi, A., Wachowicz, P., Niknejad, A., Collin, P., Krapp, A., Cano, E., Simanis, V. and Xenarios, I. (2015) An extended, Boolean model of the septation initiation network in S.Pombe provides insights into its regulation. PLoS One 10: e0134214. (co-corresponding author) » Simanis, V. (2015) Pombe’s thirteen - control of fission yeast cell division by the septation initiation network. Journal of Cell Science 128: 1465-1474. » Wachowicz, P., Chasapi, A., Krapp, A., Cano Del Rosario, E., Schmitter, D., Sage, D., Unser, M., Xenarios, I., Rougemont, J. and Simanis, V. (2015) Analysis of S. pombe SIN protein association to the SPB reveals two genetically separable states of the SIN. Journal of Cell Science 128: 741-754.

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Bucher Lab Philipp Bucher - Group Leader

Philipp Bucher was 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 to ISREC where he was promoted senior scientist in 2001.

bucher-lab.epfl.ch

Introduction

Results Obtained

New technologies allow for comprehensive characterization of the molecular changes that cause a healthy cell to become cancerous. These technologies produce vast amounts of data. We develop computational methods that will help to extract insights and knowledge from such data. Our main focus is on gene regulation. Transcription factors are key elements of regulatory circuits that control gene expression. We are interested in the molecular processes that guide transcription factors to their target sites, in a developmental stage- and tissue-specific manner, and we are studying these processes by using computational approaches in conjunction with highthroughput functional genomics data such as CAGE and ChIP-Seq data. We are further interested in the use of molecular profiling data for medical diagnosis. To this end we develop and test machine learning methods in the framework of open prediction challenges organized by the DREAM and sbv IMPROVER consortia. Besides research, our group develops and maintains bioinformatics databases and web servers. Our best known resource is the Eukaryotic Promoter Database EPD, created in 1986 and regularly updated since then. The ChIPseq server features web-based programs to access and analyze a large collection of public functional genomics data sets. The Signal Search Analysis (SSA) and PWMTools server offer DNA motif discovery and search tools. These three resources are tightly interlinked and together form a comprehensive web-based platform for gene regulatory regions analysis.

Research Building cell differentiation trees from ChIP-seq data. Following up on previous joint work with Bernard Moret’s group we successfully applied a new tree building algorithm to histone modification data from ENCODE. The novelty of this algorithms is that it can assign samples to internal nodes of a tree corresponding to the common progenitors of more differentiated cell types. Building transcription factor specificity models from high-throughput experimental data: We successfully adapted a computational pipeline originally developed for protein binding microarray (PBM) to be used with highthroughput data generated with SMiLE-seq (Selective Microfluidics-based Ligand Enrichment followed by sequencing) technology recently developed in Bart Deplancke’s lab. Promoter analysis: Making use of large volumes of recently published transcription start and nucleosome mapping data, we carried out a comparative study on the role of positioned nucleosomes in promoter regions in five model organisms. Our results show that the so-called +1 nucleosome plays an active role in transcription start site selection in those promoters that lack a core promoter element such as a TATA-box, initiator or DPE. Annotation of SNPs with regard to TF binding potential. We developed a computational pipeline to identify all common variants that change the predicted affinity of a transcription factor binding site in the human genome. The resulting catalogue will be used to interpret histone modification profiles from a GWAS study carried by the SysGenetiX consortium.

Keywords Computational genomics, epigenetics, molecular diagnostics and machine learning

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Bioinformatics resources The Eukaryotic Promoter database EPDnew was extended to three new model organisms: Arabidopsis thaliana, Saccharomyces cerevisiae and Schizosaccharomyces pombe. Several new feature has been added to the ChIP-seq server, including an application that generates genomic feature correlation plots in form of heatmaps and allows export of the corresponding numerical data in a format appropriate for follow-up analyses by statistics software packages such as R.

ISREC - Swiss Institute for Experimental Cancer Research

Team Members Postdoctoral Fellows

Giovanna Ambrosini René Dreos Sunil Kumar Rouayda Cavin Périer PhD Students

Romain Groux Administrative Assistants

Sophie Barret

nput form and results page of the P can server. pper right nput form. enter left se uence logo of the position weight matrix entered. Bottom results page with action buttons for saving the match list, for extracting surrounding D se uences or sending the results to another web application.

Selected Publications » Dreos, R., Ambrosini, G., Périer Cavin, R. and Bucher P. (2015). The Eukaryotic Promoter Database: expansion of EPDnew and new promoter analysis tools. Nucleic Acids Res. 43(Database issue):D92-D96. » Ambrosini. G., Dreos, R. and Bucher, P. (2015). Principles of ChIP-seq data analysis illustrated with examples. Genomics Comp. Biol. 1(1):e22.

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Editor: Laurence Mauro Many thanks to Friedrich Beermann, Lucia Baldi, Dietrich Reinhard, Sacha Sidjanski, Harald Hirling and Roland Chabloz at the Repro for their help and support!

12th edition 2015/2016 Produced and edited by the EPFL School of Life Sciences Printed at the EPFL “Atelier de Reprographie”

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