Title: CancerEpiSys – Integrative analysis of epigenetic networks that determine the chronic lymphocytic leukemia disease state

Type Dataset Jan-Philipp Mallm, Murat Iskar, Naveed Ishaque, Sabrina J. Kugler, Jose M. Muino, Vladimir Teif, Lara Klett, Alexandra M. Poos, Sebastian Großmann, Fabian Erdel, Daniele Tavernari, Sandra D. Koser, Sabrina Schumacher, Benedikt Brors, Rainer König, Daniel Remondini, Stephan Stilgenbauer, Peter Lichter, Martin Vingron, Marc Zapatka, Daniel Mertens, Karsten Rippe (2018): CancerEpiSys – Integrative analysis of epigenetic networks that determine the chronic lymphocytic leukemia disease state. Zenodo. Dataset. https://zenodo.org/record/1161179

Authors: Jan-Philipp Mallm (Division of Chromatin Networks, German Cancer Research Center (DKFZ) and Bioquant, Heidelberg, Germany) ; Murat Iskar (Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany) ; Naveed Ishaque (Division of Theoretical Bioinformatics and Heidelberg Center for Personalized Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany) ; Sabrina J. Kugler (Mechanisms of Leukemogenesis, German Cancer Research Center (DKFZ), Heidelberg, Germany & Department of Internal Medicine III, University of Ulm, Germany) ; Jose M. Muino (Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany) ; Vladimir Teif (School of Biological Sciences, University of Essex, Colchester, UK) ; Lara Klett (Division of Chromatin Networks, German Cancer Research Center (DKFZ) and Bioquant, Heidelberg, Germany) ; Alexandra M. Poos (Integrated Research and Treatment Center, Center for Sepsis Control and Care (CSCC), Jena University Hospital, Jena, Germany and Network Modeling, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute Jena, Germany) ; Sebastian Großmann (Division of Chromatin Networks, German Cancer Research Center (DKFZ) and Bioquant, Heidelberg, Germany) ; Fabian Erdel (Division of Chromatin Networks, German Cancer Research Center (DKFZ) and Bioquant, Heidelberg, Germany) ; Daniele Tavernari (Division of Chromatin Networks, German Cancer Research Center (DKFZ) and Bioquant, Heidelberg, Germany) ; Sandra D. Koser (Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany) ; Sabrina Schumacher (Division of Chromatin Networks, German Cancer Research Center (DKFZ) and Bioquant, Heidelberg, Germany) ; Benedikt Brors (Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany) ; Rainer König (Integrated Research and Treatment Center, Center for Sepsis Control and Care (CSCC), Jena University Hospital, Jena, Germany and Network Modeling, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute Jena, Germany) ; Daniel Remondini (Department of Physics and Astronomy, Bologna University, Italy) ; Stephan Stilgenbauer (Department of Internal Medicine III, Ulm University, Germany) ; Peter Lichter (Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany) ; Martin Vingron (Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany) ; Marc Zapatka (Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany) ; Daniel Mertens (Mechanisms of Leukemogenesis, German Cancer Research Center (DKFZ), Heidelberg, Germany & Department of Internal Medicine III, University of Ulm, Germany) ; Karsten Rippe (Division of Chromatin Networks, German Cancer Research Center (DKFZ) and Bioquant, Heidelberg, Germany) ;

Links

• Item record in Zenodo
• Digital object URL

Summary

A public repository of data processed for Mallm, Iskar, Ishaque et. al. 2018 Linking aberrant chromatin features in chronic lymphocytic leukemia to deregulated transcription factor networks

Website: http://www.cancerepisys.org/cancerepisys/index.html

Github: https://github.com/CancerEpiSys/Mallm-et-al-processing-scripts

Research mission

CancerEpiSys is a BMBF funded research project with the CancerSys program that dissects the epigenetic networks associated with chronic lymphocytic leukemia (CLL) to develop novel diagnostic and therapeutic approaches for the disease. It has been initiated based on the emerging view that signals encoded in the DNA sequence, epigenetic modifications (e.g. DNA methylation, post-translational histone modifications), non-coding RNAs and nucleosome positioning are not independently regulated properties. Rather, these chromatin features are governed by an interconnected network of molecular processes that determine the cellular gene expression program. Any errors that occur in the interplay of these factors can lead to aberrant gene regulation associated with cancer. To rationalize the mode of action of novel ‘epigenetic’ drugs in cancer therapy that change properties of this network, we will dissect experimentally and mathematically the interdependence of these processes, focusing on CLL.

The main objectives of CancerEpiSys are: (i) deciphering the relation of DNA sequence, epigenetic modifications, nucleosome positioning and aberrant gene expression in CLL, (ii) the identification of epigenetic network morphologies that describe the response to the epigenetic drugs panobinostat and 3-deazaneplanocin (DZNep) that inhibit histone deacetylases and methyltransferases, (iii) the characterization of epigenetic markers and chromatin features of CLL patient subgroups, and (iv) the integration of results into an analysis scheme for the epigenetic aberrations most relevant for prognostication, prediction of treatment relapse and stratification of patients with respect to therapeutic options. Moreover, our results will inform novel therapeutic approaches that target gene-expression programs at the epigenetic level to sensitize cancer cells towards apoptosis and anti-growth signals.

More information

• DOI: 10.5281/zenodo.1161179
• Language: en

Subjects

• CLL, Leukemia, epigenetic networks, single cell, ATAC-seq, DNA methylation, Whole genome bisulfite sequencing, ChIP-seq, strand specific RNA-seq, panobinostat, HDAC

Dates

• Publication date: 2018
• Issued: February 26, 2018

Rights

• https://creativecommons.org/licenses/by-nc/4.0/legalcode Creative Commons Attribution Non Commercial 4.0 International
• info:eu-repo/semantics/openAccess Open Access

Format

electronic resource

Relateditems