EpigenomeProgramming SIGNED
An experimental and bioinformatic toolbox for functional epigenomics and its application to epigenetically making and breaking a cancer cell
Total Cost €
0EC-Contrib. €
0Partnership
0Views
0EpigenomeProgramming project word cloud
Explore the words cloud of the EpigenomeProgramming project. It provides you a very rough idea of what is the project "EpigenomeProgramming" about.
Project "EpigenomeProgramming" data sheet
The following table provides information about the project.
| Coordinator |
CEMM - FORSCHUNGSZENTRUM FUER MOLEKULARE MEDIZIN GMBH
Organization address contact info |
| Coordinator Country | Austria [AT] |
| Project website | https://cemm.at/research/funding/international-funding/erc-starting-grant-epigenomeprogramming/ |
| Total cost | 1˙281˙205 € |
| EC max contribution | 1˙281˙205 € (100%) |
| Programme |
1. H2020-EU.1.1. (EXCELLENT SCIENCE - European Research Council (ERC)) |
| Code Call | ERC-2015-STG |
| Funding Scheme | ERC-STG |
| Starting year | 2016 |
| Duration (year-month-day) | from 2016-12-01 to 2021-11-30 |
Partnership
Take a look of project's partnership.
| # | ||||
|---|---|---|---|---|
| 1 | CEMM - FORSCHUNGSZENTRUM FUER MOLEKULARE MEDIZIN GMBH | AT (WIEN) | coordinator | 1˙281˙205.00 |
Map
Project objective
Epigenetic alterations can be detected in all cancers and in essentially every patient. Despite their prevalence, the concrete functional roles of these alterations are not well understood, for two reasons: First, cancer samples tend to carry many correlated epigenetic alterations, making it difficult to statistically distinguish relevant driver events from those that co-occur for other reasons. Second, we lack tools for targeted epigenome editing that could be used to validate biological function in perturbation and rescue experiments.
The proposed project strives to overcome these limitations through experimental and bioinformatic methods development, with the ambition of making and breaking cancer cells in vitro by introducing defined sets of epigenetic alterations. We will focus on leukemia as our “model cancer” (given its low mutation rate, frequent defects in epigenetic regulators, and availability of excellent functional assays), but the concepts and methods are general. In Aim 1, we will generate epigenome profiles for a human knockout cell collection comprising 100 epigenetic regulators and use the data to functionally annotate thousands of epigenetic alterations observed in large cancer datasets. In Aim 2, we will develop an experimental toolbox for epigenome programming using epigenetic drugs, CRISPR-assisted recruitment of epigenetic modifiers for locus-specific editing, and cell-derived guide RNA libraries for epigenome copying. Finally, in Aim 3 we will explore epigenome programming (methods from Aim 2) of candidate driver events (predictions from Aim 1) with the ultimate goal of converting cancer cells into non-cancer cells and vice versa.
In summary, this project will establish a broadly applicable methodology and toolbox for dissecting the functional roles of epigenetic alterations in cancer. Moreover, successful creation of a cancer that is driven purely by epigenetic alterations could challenge our understanding of cancer as a genetic disease.
Publications
| year | authors and title | journal | last update |
|---|---|---|---|
| 2020 |
André F. Rendeiro, Thomas Krausgruber, Nikolaus Fortelny, Fangwen Zhao, Thomas Penz, Matthias Farlik, Linda C. Schuster, Amelie Nemc, Szabolcs Tasnády, Marienn Réti, Zoltán Mátrai, Donát Alpár, Csaba Bödör, Christian Schmidl, Christoph Bock Chromatin mapping and single-cell immune profiling define the temporal dynamics of ibrutinib response in CLL published pages: , ISSN: 2041-1723, DOI: 10.1038/s41467-019-14081-6 |
Nature Communications 11/1 | 2020-02-05 |
| 2019 |
Sandra Schick, André F. Rendeiro, Kathrin Runggatscher, Anna Ringler, Bernd Boidol, Melanie Hinkel, Peter Májek, Loan Vulliard, Thomas Penz, Katja Parapatics, Christian Schmidl, Jörg Menche, Guido Boehmelt, Mark Petronczki, André C. Müller, Christoph Bock, Stefan Kubicek Systematic characterization of BAF mutations provides insights into intracomplex synthetic lethalities in human cancers published pages: 1399-1410, ISSN: 1061-4036, DOI: 10.1038/s41588-019-0477-9 |
Nature Genetics 51/9 | 2020-02-04 |
| 2019 |
Fabian Müller, Michael Scherer, Yassen Assenov, Pavlo Lutsik, Jörn Walter, Thomas Lengauer, Christoph Bock RnBeads 2.0: comprehensive analysis of DNA methylation data published pages: , ISSN: 1474-760X, DOI: 10.1186/s13059-019-1664-9 |
Genome Biology 20/1 | 2020-01-29 |
| 2019 |
Christian Schmidl, Gregory I. Vladimer, André F. Rendeiro, Susanne Schnabl, Thomas Krausgruber, Christina Taubert, Nikolaus Krall, Tea Pemovska, Mohammad Araghi, Berend Snijder, Rainer Hubmann, Anna Ringler, Kathrin Runggatscher, Dita Demirtas, Oscar Lopez de la Fuente, Martin Hilgarth, Cathrin Skrabs, Edit Porpaczy, Michaela Gruber, Gregor Hoermann, Stefan Kubicek, Philipp B. Staber, Medhat Sheh Combined chemosensitivity and chromatin profiling prioritizes drug combinations in CLL published pages: 232-240, ISSN: 1552-4450, DOI: 10.1038/s41589-018-0205-2 |
Nature Chemical Biology 15/3 | 2020-01-29 |
| 2019 |
Florian Halbritter, Matthias Farlik, Raphaela Schwentner, Gunhild Jug, Nikolaus Fortelny, Thomas Schnoller, Hanja Pisa, Linda Christina Schuster, Andrea Reinprecht, Thomas Czech, Johannes Gojo, Wolfgang Holter, Milen Minkov, Wolfgang M Bauer, Ingrid Simonitsch-Klupp, Christoph Bock, Caroline Hutter Epigenomics and Single-cell Sequencing Define a Developmental Hierarchy in Langerhans Cell Histiocytosis published pages: CD-19-0138, ISSN: 2159-8274, DOI: 10.1158/2159-8290.cd-19-0138 |
Cancer Discovery | 2020-01-29 |
| 2017 |
Paul Datlinger, André F Rendeiro, Christian Schmidl, Thomas Krausgruber, Peter Traxler, Johanna Klughammer, Linda C Schuster, Amelie Kuchler, Donat Alpar, Christoph Bock Pooled CRISPR screening with single-cell transcriptome readout published pages: 297-301, ISSN: 1548-7091, DOI: 10.1038/nmeth.4177 |
Nature Methods 14/3 | 2020-01-29 |
| 2017 |
Heiko Müller, Raul Jimenez-Heredia, Ana Krolo, Tatjana Hirschmugl, Jasmin Dmytrus, Kaan Boztug, Christoph Bock VCF.Filter: interactive prioritization of disease-linked genetic variants from sequencing data published pages: W567-W572, ISSN: 0305-1048, DOI: 10.1093/nar/gkx425 |
Nucleic Acids Research 45/W1 | 2020-01-29 |
| 2018 |
Johanna Klughammer1,37, Barbara Kiesel2,3,37, Thomas Roetzer3,4, Nikolaus Fortelny1, Amelie Nemc1,
Karl-Heinz Nenning5, Julia Furtner3,6, Nathan C. Sheffield7, Paul Datlinger1, Nadine Peter3,4,
Martha Nowosielski8,9, Marco Augustin10, Mario Mischkulnig2,3, Thomas Ströbel3,4, Donat Alpar1,
Bekir Ergüner1, Martin Senekowitsch1, Patrizia Moser11, Christian F. Freyschlag12,
Johannes Kerschbaumer12, Claudius Thomé12, Astrid E. Grams13, Günther Stockhammer8,
Melitta Kitzwoegerer14, Stefan Oberndorfer15, Franz Marhold16, Serge Weis17, Johannes Trenkler18,
Johanna Buchroithner19, Josef Pichler20, Johannes Haybaeck21,22, Stefanie Krassnig21, Kariem M. Ali23,
Gord von Campe23, Franz Payer24, Camillo Sherif25, Julius Preiser26, Thomas Hauser27, Peter A. Winkler27,
Waltraud Kleindienst28, Franz Würtz29, Tanisa Brandner-Kokalj29, Martin Stultschnig30,
Stefan Schweiger31, Karin Dieckmann3,32, Matthias Preusser3,33, Georg Langs6, Bernhard Baumann10,
Engelbert Knosp2,3, Georg Widhalm2,3, Christine Marosi3,33, Johannes A. Hainfellner3,4,
Adelheid Woehrer3,4,38* and Christoph Bock The DNA methylation landscape of glioblastomadisease progression shows extensiveheterogeneity in time and space published pages: , ISSN: 1078-8956, DOI: 10.1038/s41591-018-0156-x |
Nature Medicine in press | 2020-01-29 |
| 2018 |
Thomas F. Allison1,2, Peter W. Andrews 1, Yishai Avior3, Ivana Barbaric1, Nissim Benvenisty3,
Christoph Bock 4,5,6, Jennifer Brehm7, Oliver Brüstle8, Ivan Damjanov 9, Andrew Elefanty10,11, Daniel Felkner7,
Paul J. Gokhale1, Florian Halbritter 4, Lyn E. Healy12,13, Tim X. Hu 14, Barbara B. Knowles15,16,
Jeanne F. Loring 17, Tenneille E. Ludwig7, Robyn Mayberry10,11, Suzanne Micallef10,11, Jameelah S. Mohamed14,
Franz-Josef Müller 18,19, Christine L. Mummery20, Norio Nakatsuji21, Elizabeth S. Ng10,11, Steve K.W. Oh22,
Orla O’Shea12, Martin F. Pera23,24,25,26,27, Benjamin Reubinoff28, Paul Robson 14,29,30, Janet Rossant 31,32,
Bernhard M. Schuldt19, Davor Solter16,33, Koula Sourris10,11, Glyn Stacey12,34, Edouard G. Stanley10,11,
Hirofumi Suemori35, Kazutoshi Takahashi36 & Shinya Yamanaka36,37 Assessment of established techniques to determine developmental and malignant potential of human pluripotent stem cells published pages: , ISSN: 2041-1723, DOI: 10.1038/s41467-018-04011-3 |
Nature Communications 9/1 | 2020-01-29 |
| 2018 |
Verhaak, Roel; Consortium, The Glioma Glioma Through the Looking GLASS: the Glioma Longitudinal Analysis consortium, molecular evolution of diffuse gliomas published pages: , ISSN: 1522-8517, DOI: 10.1101/196139 |
Neuro-Oncology 1 | 2020-01-29 |
| 2017 |
Nathan C Sheffield, Gaelle Pierron, Johanna Klughammer, Paul Datlinger, Andreas Schönegger, Michael Schuster, Johanna Hadler, Didier Surdez, Delphine Guillemot, Eve Lapouble, Paul Freneaux, Jacqueline Champigneulle, Raymonde Bouvier, Diana Walder, Ingeborg M Ambros, Caroline Hutter, Eva Sorz, Ana T Amaral, Enrique de Ãlava, Katharina Schallmoser, Dirk Strunk, Beate Rinner, Bernadette Liegl-Atzwanger, Berthold Huppertz, Andreas Leithner, Gonzague de Pinieux, Philippe Terrier, Valérie Laurence, Jean Michon, Ruth Ladenstein, Wolfgang Holter, Reinhard Windhager, Uta Dirksen, Peter F Ambros, Olivier Delattre, Heinrich Kovar, Christoph Bock, Eleni M Tomazou DNA methylation heterogeneity defines a disease spectrum in Ewing sarcoma published pages: 386-395, ISSN: 1078-8956, DOI: 10.1038/nm.4273 |
Nature Medicine 23/3 | 2020-01-29 |
| 2018 |
Boris Simovski, Chakravarthi Kanduri, Sveinung Gundersen, Dmytro Titov, Diana Domanska, Christoph Bock, Lara Bossini-Castillo, Maria Chikina, Alexander Favorov, Ryan M Layer, Andrey A Mironov, Aaron R Quinlan, Nathan C Sheffield, Gosia Trynka, Geir K Sandve Coloc-stats: a unified web interface to perform colocalization analysis of genomic features published pages: W186-W193, ISSN: 0305-1048, DOI: 10.1093/nar/gky474 |
Nucleic Acids Research 46/W1 | 2020-01-29 |
| 2018 |
Christian Baumgartner, Stefanie Toifl, Matthias Farlik, Florian Halbritter, Ruth Scheicher, Irmgard Fischer, Veronika Sexl, Christoph Bock, Manuela Baccarini An ERK-Dependent Feedback Mechanism Prevents Hematopoietic Stem Cell Exhaustion published pages: 879-892.e6, ISSN: 1934-5909, DOI: 10.1016/j.stem.2018.05.003 |
Cell Stem Cell 22/6 | 2020-01-29 |
| 2018 |
Chakravarthi Kanduri, Christoph Bock, Sveinung Gundersen, Eivind Hovig, Geir Kjetil Sandve Colocalization analyses of genomic elements: approaches, recommendations and challenges published pages: 1615-1624, ISSN: 1367-4803, DOI: 10.1093/bioinformatics/bty835 |
Bioinformatics 35/9 | 2020-01-29 |
| 2016 |
Matthias Farlik, Florian Halbritter, Fabian Müller, Fizzah A. Choudry, Peter Ebert, Johanna Klughammer, Samantha Farrow, Antonella Santoro, Valerio Ciaurro, Anthony Mathur, Rakesh Uppal, Hendrik G. Stunnenberg, Willem H. Ouwehand, Elisa Laurenti, Thomas Lengauer, Mattia Frontini, Christoph Bock DNA Methylation Dynamics of Human Hematopoietic Stem Cell Differentiation published pages: 808-822, ISSN: 1934-5909, DOI: 10.1016/j.stem.2016.10.019 |
Cell Stem Cell 19/6 | 2020-01-29 |
| 2018 |
Tahsin Stefan Barakat, Florian Halbritter, Man Zhang, André F. Rendeiro, Elena Perenthaler, Christoph Bock, Ian Chambers Functional Dissection of the Enhancer Repertoire in Human Embryonic Stem Cells published pages: 276-288.e8, ISSN: 1934-5909, DOI: 10.1016/j.stem.2018.06.014 |
Cell Stem Cell 23/2 | 2020-01-29 |
Are you the coordinator (or a participant) of this project? Plaese send me more information about the "EPIGENOMEPROGRAMMING" project.
For instance: the website url (it has not provided by EU-opendata yet), the logo, a more detailed description of the project (in plain text as a rtf file or a word file), some pictures (as picture files, not embedded into any word file), twitter account, linkedin page, etc.
Send me an email (fabio@fabiodisconzi.com) and I put them in your project's page as son as possible.
Thanks. And then put a link of this page into your project's website.
The information about "EPIGENOMEPROGRAMMING" are provided by the European Opendata Portal: CORDIS opendata.