An experimental and bioinformatic toolbox for functional epigenomics and its application to epigenetically making and breaking a cancer cell

Informazioni relative al progetto

EpigenomeProgramming

ID dell’accordo di sovvenzione: 679146

DOI

10.3030/679146

Progetto chiuso

Data della firma CE 26 Aprile 2016

Data di avvio 1 Dicembre 2016

Data di completamento 30 Novembre 2021

Finanziato da

• EXCELLENT SCIENCE - European Research Council (ERC)

Costo totale

€ 1 281 205,00

Contributo UE

€ 1 281 205,00

Coordinato da

CEMM - FORSCHUNGSZENTRUM FUER MOLEKULARE MEDIZIN GMBH
Austria

CORDIS fornisce collegamenti ai risultati finali pubblici e alle pubblicazioni dei progetti ORIZZONTE.

I link ai risultati e alle pubblicazioni dei progetti del 7° PQ, così come i link ad alcuni tipi di risultati specifici come dataset e software, sono recuperati dinamicamente da .OpenAIRE .

Pubblicazioni

Peer reviewed articles (30)

Selective Mediator dependence of cell-type-specifying transcription

Autori: Martin G. Jaeger, Björn Schwalb, Sebastian D. Mackowiak, Taras Velychko, Alexander Hanzl, Hana Imrichova, Matthias Brand, Benedikt Agerer, Someth Chorn, Behnam Nabet, Fleur M. Ferguson, André C. Müller, Andreas Bergthaler, Nathanael S. Gray, James E. Bradner, Christoph Bock, Denes Hnisz, Patrick Cramer, Georg E. Winter
Pubblicato in: Nature Genetics, Numero 52/7, 2020, Pagina/e 719-727, ISSN 1061-4036
Editore: Nature Publishing Group
DOI: 10.1038/s41588-020-0635-0

Disturbed mitochondrial dynamics in CD8+ TILs reinforce T cell exhaustion

Autori: Yi-Ru Yu, Hana Imrichova, Haiping Wang, Tung Chao, Zhengtao Xiao, Min Gao, Marcela Rincon-Restrepo, Fabien Franco, Raphael Genolet, Wan-Chen Cheng, Camilla Jandus, George Coukos, Yi-Fan Jiang, Jason W. Locasale, Alfred Zippelius, Pu-Ste Liu, Li Tang, Christoph Bock, Nicola Vannini, Ping-Chih Ho
Pubblicato in: Nature Immunology, Numero 21/12, 2020, Pagina/e 1540-1551, ISSN 1529-2908
Editore: Nature Publishing Group
DOI: 10.1038/s41590-020-0793-3

Single-cell RNA-seq with spike-in cells enables accurate quantification of cell-specific drug effects in pancreatic islets

Autori: Brenda Marquina-Sanchez, Nikolaus Fortelny, Matthias Farlik, Andhira Vieira, Patrick Collombat, Christoph Bock, Stefan Kubicek
Pubblicato in: Genome Biology, Numero 21/1, 2020, ISSN 1474-760X
Editore: BioMed Central
DOI: 10.1186/s13059-020-02006-2

SARS-CoV-2 mutations in MHC-I-restricted epitopes evade CD8 + T cell responses

Autori: Benedikt Agerer, Maximilian Koblischke, Venugopal Gudipati, Luis Fernando Montaño-Gutierrez, Mark Smyth, Alexandra Popa, Jakob-Wendelin Genger, Lukas Endler, David M. Florian, Vanessa Mühlgrabner, Marianne Graninger, Stephan W. Aberle, Anna-Maria Husa, Lisa Ellen Shaw, Alexander Lercher, Pia Gattinger, Ricard Torralba-Gombau, Doris Trapin, Thomas Penz, Daniele Barreca, Ingrid Fae, Sabine Wenda,
Pubblicato in: Science Immunology, Numero 6/57, 2021, Pagina/e eabg6461, ISSN 2470-9468
Editore: American Association for the Advancement of Science
DOI: 10.1126/sciimmunol.abg6461

Genomic epidemiology of superspreading events in Austria reveals mutational dynamics and transmission properties of SARS-CoV-2

Autori: Alexandra Popa, Jakob-Wendelin Genger, Michael D. Nicholson, Thomas Penz, Daniela Schmid, Stephan W. Aberle, Benedikt Agerer, Alexander Lercher, Lukas Endler, Henrique Colaço, Mark Smyth, Michael Schuster, Miguel L. Grau, Francisco Martínez-Jiménez, Oriol Pich, Wegene Borena, Erich Pawelka, Zsofia Keszei, Martin Senekowitsch, Jan Laine, Judith H. Aberle, Monika Redlberger-Fritz, Mario Karolyi,
Pubblicato in: Science Translational Medicine, Numero 12/573, 2020, Pagina/e eabe2555, ISSN 1946-6234
Editore: American Association for the Advancement of Science
DOI: 10.1126/scitranslmed.abe2555

High-content CRISPR screening

Autori: Bock C, Datlinger P, Chardon F, Coelho MA, Dong MB, Lawson KA, Lu T, Maroc1 L, Norman TM, Song B, Stanley G, Chen S, Garnett M, Li1 W, Moffat J, Qi LS, Shapiro RS, Shendure J, Weissman JS, Zhuang X
Pubblicato in: Nature Reviews Methods Primers, 2022, ISSN 2662-8449
Editore: Nature Publishing Group
DOI: 10.1038/s43586-021-00093-4

Single-cell transcriptomics combined with interstitial fluid proteomics defines cell type–specific immune regulation in atopic dermatitis

Autori: Thomas B. Rojahn, Vera Vorstandlechner, Thomas Krausgruber, Wolfgang M. Bauer, Natalia Alkon, Christine Bangert, Felix M. Thaler, Farzaneh Sadeghyar, Nikolaus Fortelny, Victoria Gernedl, Katharina Rindler, Adelheid Elbe-Bürger, Christoph Bock, Michael Mildner, Patrick M. Brunner
Pubblicato in: Journal of Allergy and Clinical Immunology, Numero 146/5, 2020, Pagina/e 1056-1069, ISSN 0091-6749
Editore: Mosby Inc.
DOI: 10.1016/j.jaci.2020.03.041

Ultra-high-throughput single-cell RNA sequencing and perturbation screening with combinatorial fluidic indexing

Autori: Paul Datlinger, André F. Rendeiro, Thorina Boenke, Martin Senekowitsch, Thomas Krausgruber, Daniele Barreca, Christoph Bock
Pubblicato in: Nature Methods, Numero 18/6, 2021, Pagina/e 635-642, ISSN 1548-7091
Editore: Nature Publishing Group
DOI: 10.1038/s41592-021-01153-z

Acute BAF perturbation causes immediate changes in chromatin accessibility

Autori: Sandra Schick, Sarah Grosche, Katharina Eva Kohl, Danica Drpic, Martin G. Jaeger, Nara C. Marella, Hana Imrichova, Jung-Ming G. Lin, Gerald Hofstätter, Michael Schuster, André F. Rendeiro, Anna Koren, Mark Petronczki, Christoph Bock, André C. Müller, Georg E. Winter, Stefan Kubicek
Pubblicato in: Nature Genetics, Numero 53/3, 2021, Pagina/e 269-278, ISSN 1061-4036
Editore: Nature Publishing Group
DOI: 10.1038/s41588-021-00777-3

Single-Cell RNA Sequencing Analysis Reveals a Crucial Role for CTHRC1 (Collagen Triple Helix Repeat Containing 1) Cardiac Fibroblasts After Myocardial Infarction

Autori: Adrián Ruiz-Villalba, Juan P. Romero, Silvia C. Hernández, Amaia Vilas-Zornoza, Nikolaus Fortelny, Laura Castro-Labrador, Patxi San Martin-Uriz, Erika Lorenzo-Vivas, Paula García-Olloqui, Marcel Palacio, Juan José Gavira, Gorka Bastarrika, Stefan Janssens, Ming Wu, Elena Iglesias, Gloria Abizanda, Xabier Martinez de Morentin, Miren Lasaga, Nuria Planell, Christoph Bock, Diego Alignani, Gema Me
Pubblicato in: Circulation, Numero 142/19, 2020, Pagina/e 1831-1847, ISSN 0009-7322
Editore: Lippincott Williams & Wilkins Ltd.
DOI: 10.1161/circulationaha.119.044557

DNA methylation heterogeneity defines a disease spectrum in Ewing sarcoma

Autori: 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 Álava, Katharina Schallmoser, Dirk Strunk, Beate Rinner, Bernadette Liegl-Atzwa
Pubblicato in: Nature Medicine, Numero 23/3, 2017, Pagina/e 386-395, ISSN 1078-8956
Editore: Nature Publishing Group
DOI: 10.1038/nm.4273

An ERK-Dependent Feedback Mechanism Prevents Hematopoietic Stem Cell Exhaustion

Autori: Christian Baumgartner, Stefanie Toifl, Matthias Farlik, Florian Halbritter, Ruth Scheicher, Irmgard Fischer, Veronika Sexl, Christoph Bock, Manuela Baccarini
Pubblicato in: Cell Stem Cell, Numero 22/6, 2018, Pagina/e 879-892.e6, ISSN 1934-5909
Editore: Cell Press
DOI: 10.1016/j.stem.2018.05.003

Pooled CRISPR screening with single-cell transcriptome readout

Autori: Paul Datlinger, André F Rendeiro, Christian Schmidl, Thomas Krausgruber, Peter Traxler, Johanna Klughammer, Linda C Schuster, Amelie Kuchler, Donat Alpar, Christoph Bock
Pubblicato in: Nature Methods, Numero 14/3, 2017, Pagina/e 297-301, ISSN 1548-7091
Editore: Nature Publishing Group
DOI: 10.1038/nmeth.4177

Coloc-stats: a unified web interface to perform colocalization analysis of genomic features

Autori: 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
Pubblicato in: Nucleic Acids Research, Numero 46/W1, 2018, Pagina/e W186-W193, ISSN 0305-1048
Editore: Oxford University Press
DOI: 10.1093/nar/gky474

VCF.Filter: interactive prioritization of disease-linked genetic variants from sequencing data

Autori: Heiko Müller, Raul Jimenez-Heredia, Ana Krolo, Tatjana Hirschmugl, Jasmin Dmytrus, Kaan Boztug, Christoph Bock
Pubblicato in: Nucleic Acids Research, Numero 45/W1, 2017, Pagina/e W567-W572, ISSN 0305-1048
Editore: Oxford University Press
DOI: 10.1093/nar/gkx425

Assessment of established techniques to determine developmental and malignant potential of human pluripotent stem cells

Autori: 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
Pubblicato in: Nature Communications, Numero 9/1, 2018, ISSN 2041-1723
Editore: Nature Publishing Group
DOI: 10.1038/s41467-018-04011-3

The DNA methylation landscape of glioblastoma disease progression shows extensive heterogeneity in time and space

Autori: 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,
Pubblicato in: Nature Medicine, Numero in press, 2018, ISSN 1078-8956
Editore: Nature Publishing Group
DOI: 10.1038/s41591-018-0156-x

RnBeads 2.0: comprehensive analysis of DNA methylation data

Autori: Fabian Müller, Michael Scherer, Yassen Assenov, Pavlo Lutsik, Jörn Walter, Thomas Lengauer, Christoph Bock
Pubblicato in: Genome Biology, Numero 20/1, 2019, ISSN 1474-760X
Editore: BMC
DOI: 10.1186/s13059-019-1664-9

Epigenomics and Single-cell Sequencing Define a Developmental Hierarchy in Langerhans Cell Histiocytosis

Autori: 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
Pubblicato in: Cancer Discovery, 2019, Pagina/e CD-19-0138, ISSN 2159-8274
Editore: American Association for Cancer Research Inc.
DOI: 10.1158/2159-8290.cd-19-0138

Combined chemosensitivity and chromatin profiling prioritizes drug combinations in CLL

Autori: 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
Pubblicato in: Nature Chemical Biology, Numero 15/3, 2019, Pagina/e 232-240, ISSN 1552-4450
Editore: Nature Publishing Group
DOI: 10.1038/s41589-018-0205-2

Functional Dissection of the Enhancer Repertoire in Human Embryonic Stem Cells

Autori: Tahsin Stefan Barakat, Florian Halbritter, Man Zhang, André F. Rendeiro, Elena Perenthaler, Christoph Bock, Ian Chambers
Pubblicato in: Cell Stem Cell, Numero 23/2, 2018, Pagina/e 276-288.e8, ISSN 1934-5909
Editore: Cell Press
DOI: 10.1016/j.stem.2018.06.014

Colocalization analyses of genomic elements: approaches, recommendations and challenges

Autori: Chakravarthi Kanduri, Christoph Bock, Sveinung Gundersen, Eivind Hovig, Geir Kjetil Sandve
Pubblicato in: Bioinformatics, Numero 35/9, 2018, Pagina/e 1615-1624, ISSN 1367-4803
Editore: Oxford University Press
DOI: 10.1093/bioinformatics/bty835

DNA Methylation Dynamics of Human Hematopoietic Stem Cell Differentiation

Autori: 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
Pubblicato in: Cell Stem Cell, Numero 19/6, 2016, Pagina/e 808-822, ISSN 1934-5909
Editore: Cell Press
DOI: 10.1016/j.stem.2016.10.019

Systematic characterization of BAF mutations provides insights into intracomplex synthetic lethalities in human cancers

Autori: 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
Pubblicato in: Nature Genetics, Numero 51/9, 2019, Pagina/e 1399-1410, ISSN 1061-4036
Editore: Nature Publishing Group
DOI: 10.1038/s41588-019-0477-9

Chromatin mapping and single-cell immune profiling define the temporal dynamics of ibrutinib response in CLL

Autori: 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
Pubblicato in: Nature Communications, Numero 11/1, 2020, ISSN 2041-1723
Editore: Nature Publishing Group
DOI: 10.1038/s41467-019-14081-6

Structural cells are key regulators of organ-specific immune responses

Autori: Thomas Krausgruber, Nikolaus Fortelny, Victoria Fife-Gernedl, Martin Senekowitsch, Linda C. Schuster, Alexander Lercher, Amelie Nemc, Christian Schmidl, André F. Rendeiro, Andreas Bergthaler, Christoph Bock
Pubblicato in: Nature, Numero 583/7815, 2020, Pagina/e 296-302, ISSN 0028-0836
Editore: Nature Publishing Group
DOI: 10.1038/s41586-020-2424-4

Multimodal analysis of cell-free DNA whole-genome sequencing for pediatric cancers with low mutational burden

Autori: Peter Peneder, Adrian M. Stütz, Didier Surdez, Manuela Krumbholz, Sabine Semper, Mathieu Chicard, Nathan C. Sheffield, Gaelle Pierron, Eve Lapouble, Marcus Tötzl, Bekir Ergüner, Daniele Barreca, André F. Rendeiro, Abbas Agaimy, Heidrun Boztug, Gernot Engstler, Michael Dworzak, Marie Bernkopf, Sabine Taschner-Mandl, Inge M. Ambros, Ola Myklebost, Perrine Marec-Bérard, Susan Ann Burchill, Berna
Pubblicato in: Nature Communications, Numero 12/1, 2021, ISSN 2041-1723
Editore: Nature Publishing Group
DOI: 10.1038/s41467-021-23445-w

Knowledge-primed neural networks enable biologically interpretable deep learning on single-cell sequencing data

Autori: Nikolaus Fortelny, Christoph Bock
Pubblicato in: Genome Biology, Numero 21/1, 2020, ISSN 1474-760X
Editore: BioMed Central
DOI: 10.1186/s13059-020-02100-5

Spontaneously Resolved Atopic Dermatitis Shows Melanocyte and Immune Cell Activation Distinct From Healthy Control Skin

Autori: Katharina Rindler, Thomas Krausgruber, Felix M. Thaler, Natalia Alkon, Christine Bangert, Harald Kurz, Nikolaus Fortelny, Thomas B. Rojahn, Constanze Jonak, Johannes Griss, Christoph Bock, Patrick M. Brunner
Pubblicato in: Frontiers in Immunology, Numero 12, 2021, ISSN 1664-3224
Editore: Frontiers Media S.A.
DOI: 10.3389/fimmu.2021.630892

The Organoid Cell Atlas

Autori: Christoph Bock, Michael Boutros, J. Gray Camp, Laura Clarke, Hans Clevers, Juergen A. Knoblich, Prisca Liberali, Aviv Regev, Anne C. Rios, Oliver Stegle, Hendrik G. Stunnenberg, Sarah A. Teichmann, Barbara Treutlein, Robert G. J. Vries
Pubblicato in: Nature Biotechnology, Numero 39/1, 2021, Pagina/e 13-17, ISSN 1087-0156
Editore: Nature Publishing Group
DOI: 10.1038/s41587-020-00762-x

Diritti di proprietà intellettuale

Patent (1)

METHOD FOR SEQUENCING RNA OLIGONUCLEOTIDES

Numero candidatura/pubblicazione: 20 20074985
Data: 2020-09-07
Candidato/i: CEMM - FORSCHUNGSZENTRUM FUER MOLEKULARE MEDIZIN GMBH