1
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Li L, Zhang D, Cao X. EBF1, PAX5, and MYC: regulation on B cell development and association with hematologic neoplasms. Front Immunol 2024; 15:1320689. [PMID: 38318177 PMCID: PMC10839018 DOI: 10.3389/fimmu.2024.1320689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 01/08/2024] [Indexed: 02/07/2024] Open
Abstract
During lymphocyte development, a diverse repertoire of lymphocyte antigen receptors is produced to battle against pathogens, which is the basis of adaptive immunity. The diversity of the lymphocyte antigen receptors arises primarily from recombination-activated gene (RAG) protein-mediated V(D)J rearrangement in early lymphocytes. Furthermore, transcription factors (TFs), such as early B cell factor 1 (EBF1), paired box gene 5 (PAX5), and proto-oncogene myelocytomatosis oncogene (MYC), play critical roles in regulating recombination and maintaining normal B cell development. Therefore, the aberrant expression of these TFs may lead to hematologic neoplasms.
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Affiliation(s)
- Li Li
- Immune Mechanism and Therapy of Major Diseases of Luzhou Key Laboratory, School of Basic Medical Sciences, Southwest Medical University, Luzhou, China
| | - Daiquan Zhang
- Department of Traditional Chinese Medicine, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Xinmei Cao
- Immune Mechanism and Therapy of Major Diseases of Luzhou Key Laboratory, School of Basic Medical Sciences, Southwest Medical University, Luzhou, China
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2
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Jang JY, Hwang I, Pan H, Yao J, Alinari L, Imada E, Zanettini C, Kluk MJ, Wang Y, Lee Y, Lin HV, Huang X, Di Liberto M, Chen Z, Ballman KV, Cantley LC, Marchionni L, Inghirami G, Elemento O, Baiocchi RA, Chen-Kiang S, Belvedere S, Zheng H, Paik J. A FOXO1-dependent transcription network is a targetable vulnerability of mantle cell lymphomas. J Clin Invest 2022; 132:160767. [PMID: 36282572 PMCID: PMC9753996 DOI: 10.1172/jci160767] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 10/21/2022] [Indexed: 12/24/2022] Open
Abstract
Targeting lineage-defined transcriptional dependencies has emerged as an effective therapeutic strategy in cancer treatment. Through screening for molecular vulnerabilities of mantle cell lymphoma (MCL), we identified a set of transcription factors (TFs) including FOXO1, EBF1, PAX5, and IRF4 that are essential for MCL propagation. Integrated chromatin immunoprecipitation and sequencing (ChIP-Seq) with transcriptional network reconstruction analysis revealed FOXO1 as a master regulator that acts upstream in the regulatory TF hierarchy. FOXO1 is both necessary and sufficient to drive MCL lineage commitment through supporting the lineage-specific transcription programs. We further show that FOXO1, but not its close paralog FOXO3, can reprogram myeloid leukemia cells and induce B-lineage gene expression. Finally, we demonstrate that cpd10, a small molecule identified from an enriched FOXO1 inhibitor library, induces a robust cytotoxic response in MCL cells in vitro and suppresses MCL progression in vivo. Our findings establish FOXO1 inhibition as a therapeutic strategy targeting lineage-driven transcriptional addiction in MCL.
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Affiliation(s)
| | - Inah Hwang
- Department of Pathology and Laboratory Medicine and
| | - Heng Pan
- Caryl and Israel Englander Institute for Precision Medicine, Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York, USA
| | - Jun Yao
- Department of Molecular and Cellular Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Lapo Alinari
- Division of Hematology, Department of Internal Medicine, College of Medicine, The Ohio State University, Columbus, Ohio, USA
| | - Eddie Imada
- Department of Pathology and Laboratory Medicine and
| | | | - Michael J. Kluk
- Department of Pathology and Laboratory Medicine and,Sandra and Edward Meyer Cancer Center, Weill Medical College of Cornell University, New York, New York, USA
| | - Yizhe Wang
- Department of Pathology and Laboratory Medicine and
| | - Yunkyoung Lee
- Forkhead BioTherapeutics Inc., New York, New York, USA
| | - Hua V. Lin
- Forkhead BioTherapeutics Inc., New York, New York, USA
| | | | - Maurizio Di Liberto
- Department of Pathology and Laboratory Medicine and,Sandra and Edward Meyer Cancer Center, Weill Medical College of Cornell University, New York, New York, USA
| | - Zhengming Chen
- Sandra and Edward Meyer Cancer Center, Weill Medical College of Cornell University, New York, New York, USA.,Division of Biostatistics, Department of Population Health Sciences, and
| | - Karla V. Ballman
- Sandra and Edward Meyer Cancer Center, Weill Medical College of Cornell University, New York, New York, USA.,Division of Biostatistics, Department of Population Health Sciences, and
| | - Lewis C. Cantley
- Sandra and Edward Meyer Cancer Center, Weill Medical College of Cornell University, New York, New York, USA.,Department of Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Luigi Marchionni
- Department of Pathology and Laboratory Medicine and,Sandra and Edward Meyer Cancer Center, Weill Medical College of Cornell University, New York, New York, USA
| | - Giorgio Inghirami
- Department of Pathology and Laboratory Medicine and,Sandra and Edward Meyer Cancer Center, Weill Medical College of Cornell University, New York, New York, USA
| | - Olivier Elemento
- Caryl and Israel Englander Institute for Precision Medicine, Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York, USA.,Sandra and Edward Meyer Cancer Center, Weill Medical College of Cornell University, New York, New York, USA
| | - Robert A. Baiocchi
- Division of Hematology, Department of Internal Medicine, College of Medicine, The Ohio State University, Columbus, Ohio, USA
| | - Selina Chen-Kiang
- Department of Pathology and Laboratory Medicine and,Sandra and Edward Meyer Cancer Center, Weill Medical College of Cornell University, New York, New York, USA
| | | | - Hongwu Zheng
- Department of Pathology and Laboratory Medicine and
| | - Jihye Paik
- Department of Pathology and Laboratory Medicine and,Sandra and Edward Meyer Cancer Center, Weill Medical College of Cornell University, New York, New York, USA
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3
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Miller HE, Montemayor D, Abdul J, Vines A, Levy SA, Hartono SR, Sharma K, Frost B, Chédin F, Bishop AJR. Quality-controlled R-loop meta-analysis reveals the characteristics of R-loop consensus regions. Nucleic Acids Res 2022; 50:7260-7286. [PMID: 35758606 PMCID: PMC9303298 DOI: 10.1093/nar/gkac537] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Accepted: 06/16/2022] [Indexed: 12/13/2022] Open
Abstract
R-loops are three-stranded nucleic acid structures formed from the hybridization of RNA and DNA. While the pathological consequences of R-loops have been well-studied to date, the locations, classes, and dynamics of physiological R-loops remain poorly understood. R-loop mapping studies provide insight into R-loop dynamics, but their findings are challenging to generalize. This is due to the narrow biological scope of individual studies, the limitations of each mapping modality, and, in some cases, poor data quality. In this study, we reprocessed 810 R-loop mapping datasets from a wide array of biological conditions and mapping modalities. From this data resource, we developed an accurate R-loop data quality control method, and we reveal the extent of poor-quality data within previously published studies. We then identified a set of high-confidence R-loop mapping samples and used them to define consensus R-loop sites called 'R-loop regions' (RL regions). In the process, we identified a stark divergence between RL regions detected by S9.6 and dRNH-based mapping methods, particularly with respect to R-loop size, location, and colocalization with RNA binding factors. Taken together, this work provides a much-needed method to assess R-loop data quality and offers novel context regarding the differences between dRNH- and S9.6-based R-loop mapping approaches.
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Affiliation(s)
- Henry E Miller
- Department of Cell Systems and Anatomy, UT Health San Antonio, San Antonio, TX, USA.,Greehey Children's Cancer Research Institute, UT Health San Antonio, San Antonio, TX, USA.,Bioinformatics Research Network, Atlanta, GA, USA
| | - Daniel Montemayor
- Department of Medicine, UT Health San Antonio, San Antonio, TX, USA.,Center for Precision Medicine, UT Health San Antonio, San Antonio, TX, USA
| | - Jebriel Abdul
- Bioinformatics Research Network, Atlanta, GA, USA.,Department of Biology, University of Ottawa, Ottawa, Canada
| | - Anna Vines
- Bioinformatics Research Network, Atlanta, GA, USA.,Faculty of Arts, University of Bristol, Bristol, U.K
| | - Simon A Levy
- Department of Cell Systems and Anatomy, UT Health San Antonio, San Antonio, TX, USA.,Bioinformatics Research Network, Atlanta, GA, USA.,Sam & Ann Barshop Institute for Longevity & Aging Studies, UT Health San Antonio, San Antonio, TX, USA.,Glenn Biggs Institute for Alzheimer's and Neurodegenerative Diseases, UT Health San Antonio, San Antonio, TX, USA
| | - Stella R Hartono
- Department of Molecular and Cellular Biology, UC Davis, Davis, CA, USA
| | - Kumar Sharma
- Department of Medicine, UT Health San Antonio, San Antonio, TX, USA.,Center for Precision Medicine, UT Health San Antonio, San Antonio, TX, USA
| | - Bess Frost
- Department of Cell Systems and Anatomy, UT Health San Antonio, San Antonio, TX, USA.,Sam & Ann Barshop Institute for Longevity & Aging Studies, UT Health San Antonio, San Antonio, TX, USA.,Glenn Biggs Institute for Alzheimer's and Neurodegenerative Diseases, UT Health San Antonio, San Antonio, TX, USA
| | - Frédéric Chédin
- Department of Molecular and Cellular Biology, UC Davis, Davis, CA, USA
| | - Alexander J R Bishop
- Department of Cell Systems and Anatomy, UT Health San Antonio, San Antonio, TX, USA.,Greehey Children's Cancer Research Institute, UT Health San Antonio, San Antonio, TX, USA.,May's Cancer Center, UT Health San Antonio, San Antonio, TX, USA
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4
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Liu T, Salguero P, Petek M, Martinez-Mira C, Balzano-Nogueira L, Ramšak Ž, McIntyre L, Gruden K, Tarazona S, Conesa A. PaintOmics 4: new tools for the integrative analysis of multi-omics datasets supported by multiple pathway databases. Nucleic Acids Res 2022; 50:W551-W559. [PMID: 35609982 PMCID: PMC9252773 DOI: 10.1093/nar/gkac352] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Revised: 04/22/2022] [Accepted: 04/25/2022] [Indexed: 01/02/2023] Open
Abstract
PaintOmics is a web server for the integrative analysis and visualisation of multi-omics datasets using biological pathway maps. PaintOmics 4 has several notable updates that improve and extend analyses. Three pathway databases are now supported: KEGG, Reactome and MapMan, providing more comprehensive pathway knowledge for animals and plants. New metabolite analysis methods fill gaps in traditional pathway-based enrichment methods. The metabolite hub analysis selects compounds with a high number of significant genes in their neighbouring network, suggesting regulation by gene expression changes. The metabolite class activity analysis tests the hypothesis that a metabolic class has a higher-than-expected proportion of significant elements, indicating that these compounds are regulated in the experiment. Finally, PaintOmics 4 includes a regulatory omics module to analyse the contribution of trans-regulatory layers (microRNA and transcription factors, RNA-binding proteins) to regulate pathways. We show the performance of PaintOmics 4 on both mouse and plant data to highlight how these new analysis features provide novel insights into regulatory biology. PaintOmics 4 is available at https://paintomics.org/.
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Affiliation(s)
- Tianyuan Liu
- Department of Mechanical Engineering, School of Engineering, Cardiff University, Cardiff, UK
| | - Pedro Salguero
- Department of Applied Statistics, Operations Research and Quality, Universitat Politècnica de València, Valencia, Spain
| | - Marko Petek
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | | | | | - Živa Ramšak
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Lauren McIntyre
- Department of Molecular Genetics and Microbiology, Genetics Institute, University of Florida, Gainesville, USA
| | - Kristina Gruden
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Sonia Tarazona
- Department of Applied Statistics, Operations Research and Quality, Universitat Politècnica de València, Valencia, Spain
| | - Ana Conesa
- Institute for Integrative Systems Biology, Spanish National Research Council (CSIC), Paterna, Spain
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, USA
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5
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Ramamoorthy S, Kometani K, Herman JS, Bayer M, Boller S, Edwards-Hicks J, Ramachandran H, Li R, Klein-Geltink R, Pearce EL, Grün D, Grosschedl R. EBF1 and Pax5 safeguard leukemic transformation by limiting IL-7 signaling, Myc expression, and folate metabolism. Genes Dev 2020; 34:1503-1519. [PMID: 33004416 PMCID: PMC7608749 DOI: 10.1101/gad.340216.120] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 09/11/2020] [Indexed: 12/11/2022]
Abstract
In this study, Ramamoorthy et al. investigate EBF1 and PAX5 combined haploinsufficiency in the development of a B-ALL phenotype in mice. Using transcriptional and metabolomic profiling, the authors report that EBF1 and Pax5 may safeguard early stage B cells from transformation to B-ALL by limiting IL-7 signaling, folate metabolism, and Myc expression. EBF1 and PAX5 mutations are associated with the development of B progenitor acute lymphoblastic leukemia (B-ALL) in humans. To understand the molecular networks driving leukemia in the Ebf1+/−Pax5+/− (dHet) mouse model for B-ALL, we interrogated the transcriptional profiles and chromatin status of leukemic cells, preleukemic dHet pro-B, and wild-type pro-B cells with the corresponding EBF1 and Pax5 cistromes. In dHet B-ALL cells, many EBF1 and Pax5 target genes encoding pre-BCR signaling components and transcription factors were down-regulated, whereas Myc and genes downstream from IL-7 signaling or associated with the folate pathway were up-regulated. We show that blockade of IL-7 signaling in vivo and methotrexate treatment of leukemic cells in vitro attenuate the expansion of leukemic cells. Single-cell RNA-sequencing revealed heterogeneity of leukemic cells and identified a subset of wild-type pro-B cells with reduced Ebf1 and enhanced Myc expression that show hallmarks of dHet B-ALL cells. Thus, EBF1 and Pax5 may safeguard early stage B cells from transformation to B-ALL by limiting IL-7 signaling, folate metabolism and Myc expression.
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Affiliation(s)
- Senthilkumar Ramamoorthy
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Kohei Kometani
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Josip S Herman
- Laboratory of Single-Cell Biology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany.,International Max Planck Research School, University of Freiburg, 79104 Freiburg, Germany
| | - Marc Bayer
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany.,International Max Planck Research School, University of Freiburg, 79104 Freiburg, Germany
| | - Sören Boller
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Joy Edwards-Hicks
- Department of Immunometabolism, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Haribaskar Ramachandran
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Rui Li
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Ramon Klein-Geltink
- Department of Immunometabolism, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Erika L Pearce
- Department of Immunometabolism, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Dominic Grün
- Laboratory of Single-Cell Biology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany.,Center for Integrative Biological Signaling Studies (CIBSS), University of Freiburg, 79104 Freiburg, Germany
| | - Rudolf Grosschedl
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
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6
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Gomez-Cabrero D, Tarazona S, Ferreirós-Vidal I, Ramirez RN, Company C, Schmidt A, Reijmers T, Paul VVS, Marabita F, Rodríguez-Ubreva J, Garcia-Gomez A, Carroll T, Cooper L, Liang Z, Dharmalingam G, van der Kloet F, Harms AC, Balzano-Nogueira L, Lagani V, Tsamardinos I, Lappe M, Maier D, Westerhuis JA, Hankemeier T, Imhof A, Ballestar E, Mortazavi A, Merkenschlager M, Tegner J, Conesa A. STATegra, a comprehensive multi-omics dataset of B-cell differentiation in mouse. Sci Data 2019; 6:256. [PMID: 31672995 PMCID: PMC6823427 DOI: 10.1038/s41597-019-0202-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 09/02/2019] [Indexed: 12/30/2022] Open
Abstract
Multi-omics approaches use a diversity of high-throughput technologies to profile the different molecular layers of living cells. Ideally, the integration of this information should result in comprehensive systems models of cellular physiology and regulation. However, most multi-omics projects still include a limited number of molecular assays and there have been very few multi-omic studies that evaluate dynamic processes such as cellular growth, development and adaptation. Hence, we lack formal analysis methods and comprehensive multi-omics datasets that can be leveraged to develop true multi-layered models for dynamic cellular systems. Here we present the STATegra multi-omics dataset that combines measurements from up to 10 different omics technologies applied to the same biological system, namely the well-studied mouse pre-B-cell differentiation. STATegra includes high-throughput measurements of chromatin structure, gene expression, proteomics and metabolomics, and it is complemented with single-cell data. To our knowledge, the STATegra collection is the most diverse multi-omics dataset describing a dynamic biological system.
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Affiliation(s)
- David Gomez-Cabrero
- Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), IdiSNA, Pamplona, Spain
- Unit of Computational Medicine, Department of Medicine, Solna, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
- Science for Life Laboratory, Solna, Sweden
| | - Sonia Tarazona
- Department of Applied Statistics, Operations Research and Quality, Universitat Politècnica de València, Valencia, Spain
| | - Isabel Ferreirós-Vidal
- MRC London Institute of Medical Sciences, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Du Cane Road, London, W12 0NN, UK
| | - Ricardo N Ramirez
- Department of Developmental and Cell Biology and Center for Complex Biological Systems, University of California, Irvine, CA, USA
| | - Carlos Company
- Chromatin and Disease Group, Cancer Epigenetics and Biology Programme (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), 08908 L'Hospitalet de Llobregat, Barcelona, Spain
| | - Andreas Schmidt
- Protein Analysis Unit, Biomedical Center, Ludwig Maximilian University of Munich, Munich, Germany
| | - Theo Reijmers
- Division of Analytical Biosciences, Leiden Academic Center for Drug Research, Leiden University, Leiden, The Netherlands
| | | | - Francesco Marabita
- Unit of Computational Medicine, Department of Medicine, Solna, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Javier Rodríguez-Ubreva
- Chromatin and Disease Group, Cancer Epigenetics and Biology Programme (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), 08908 L'Hospitalet de Llobregat, Barcelona, Spain
| | - Antonio Garcia-Gomez
- Chromatin and Disease Group, Cancer Epigenetics and Biology Programme (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), 08908 L'Hospitalet de Llobregat, Barcelona, Spain
| | - Thomas Carroll
- MRC London Institute of Medical Sciences, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Du Cane Road, London, W12 0NN, UK
| | - Lee Cooper
- MRC London Institute of Medical Sciences, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Du Cane Road, London, W12 0NN, UK
| | - Ziwei Liang
- MRC London Institute of Medical Sciences, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Du Cane Road, London, W12 0NN, UK
| | - Gopuraja Dharmalingam
- MRC London Institute of Medical Sciences, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Du Cane Road, London, W12 0NN, UK
| | - Frans van der Kloet
- Centre for Human Metabolomics, Faculty of Natural Sciences, North-West University (Potchefstroom Campus), Potchefstroom, South Africa
| | - Amy C Harms
- Division of Analytical Biosciences, Leiden Academic Center for Drug Research, Leiden University, Leiden, The Netherlands
| | - Leandro Balzano-Nogueira
- Microbiology and Cell Science Department, Institute for Food and Agricultural Research, Genetics Institute, University of Florida, Gainesville, Florida, USA
| | - Vincenzo Lagani
- Computer Science Department, University of Crete, Heraklion, Greece
- Institute of Chemical Biology, Ilia State University, Tbilisi, Georgia, United States
| | - Ioannis Tsamardinos
- Institute of Chemical Biology, Ilia State University, Tbilisi, Georgia, United States
- Gnosis Data Analysis PC, Heraklion, Greece
| | - Michael Lappe
- QIAGEN Aarhus A/S, Silkeborgvej 2, 8000, Aarhus, Denmark
| | | | - Johan A Westerhuis
- Centre for Human Metabolomics, Faculty of Natural Sciences, North-West University (Potchefstroom Campus), Potchefstroom, South Africa
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Thomas Hankemeier
- Division of Analytical Biosciences, Leiden Academic Center for Drug Research, Leiden University, Leiden, The Netherlands
| | - Axel Imhof
- Protein Analysis Unit, Biomedical Center, Ludwig Maximilian University of Munich, Munich, Germany
| | - Esteban Ballestar
- Chromatin and Disease Group, Cancer Epigenetics and Biology Programme (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), 08908 L'Hospitalet de Llobregat, Barcelona, Spain
| | - Ali Mortazavi
- Department of Developmental and Cell Biology and Center for Complex Biological Systems, University of California, Irvine, CA, USA
| | - Matthias Merkenschlager
- MRC London Institute of Medical Sciences, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Du Cane Road, London, W12 0NN, UK.
| | - Jesper Tegner
- Unit of Computational Medicine, Department of Medicine, Solna, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.
- Science for Life Laboratory, Solna, Sweden.
- Biological and Environmental Sciences and Engineering Division, Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia.
| | - Ana Conesa
- Microbiology and Cell Science Department, Institute for Food and Agricultural Research, Genetics Institute, University of Florida, Gainesville, Florida, USA.
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