201
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Abstract
Epstein-Barr virus (EBV) infection is associated with several distinct hematological and epithelial malignancies, e.g., Burkitt lymphoma, Hodgkin lymphoma, nasopharyngeal carcinoma, gastric carcinoma, and others. The association with several malignant tumors of local and worldwide distribution makes EBV one of the most important tumor viruses. Furthermore, because EBV can cause posttransplant lymphoproliferative disease, transplant medicine has to deal with EBV as a major pathogenic virus second only to cytomegalovirus. In this review, we summarize briefly the natural history of EBV infection and outline some of the recent advances in the pathogenesis of the major EBV-associated neoplasms. We present alternative scenarios and discuss them in the light of most recent experimental data. Emerging research areas including EBV-induced patho-epigenetic alterations in host cells and the putative role of exosome-mediated information transfer in disease development are also within the scope of this review. This book contains an in-depth description of a series of modern methodologies used in EBV research. In this introductory chapter, we thoroughly refer to the applications of these methods and demonstrate how they contributed to the understanding of EBV-host cell interactions. The data gathered using recent technological advancements in molecular biology and immunology as well as the application of sophisticated in vitro and in vivo experimental models certainly provided deep and novel insights into the pathogenetic mechanisms of EBV infection and EBV-associated tumorigenesis. Furthermore, the development of adoptive T cell immunotherapy has provided a novel approach to the therapy of viral disease in transplant medicine and hematology.
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Affiliation(s)
- Janos Minarovits
- Faculty of Dentistry, Department of Oral Biology and Experimental Dental Research, University of Szeged, Tisza Lajos krt. 64, H-6720, Szeged, Hungary.
| | - Hans Helmut Niller
- Institute of Medical Microbiology and Hygiene, University of Regensburg, D-93053, Regensburg, Germany
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202
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Mitchell SM, Ho T, Brown GS, Baker RT, Thomas ML, McEvoy A, Xu ZZ, Ross JP, Lockett TJ, Young GP, LaPointe LC, Pedersen SK, Molloy PL. Evaluation of Methylation Biomarkers for Detection of Circulating Tumor DNA and Application to Colorectal Cancer. Genes (Basel) 2016; 7:E125. [PMID: 27983717 PMCID: PMC5192501 DOI: 10.3390/genes7120125] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Revised: 11/03/2016] [Accepted: 11/29/2016] [Indexed: 12/29/2022] Open
Abstract
Solid tumors shed DNA into circulation, and there is growing evidence that the detection of circulating tumor DNA (ctDNA) has broad clinical utility, including monitoring of disease, prognosis, response to chemotherapy and tracking tumor heterogeneity. The appearance of ctDNA in the circulating cell-free DNA (ccfDNA) isolated from plasma or serum is commonly detected by identifying tumor-specific features such as insertions, deletions, mutations and/or aberrant methylation. Methylation is a normal cell regulatory event, and since the majority of ccfDNA is derived from white blood cells (WBC), it is important that tumour-specific DNA methylation markers show rare to no methylation events in WBC DNA. We have used a novel approach for assessment of low levels of DNA methylation in WBC DNA. DNA methylation in 29 previously identified regions (residing in 17 genes) was analyzed in WBC DNA and eight differentially-methylated regions (DMRs) were taken through to testing in clinical samples using methylation specific PCR assays. DMRs residing in four genes, BCAT1, GRASP, IKZF1 and IRF4, exhibited low positivity, 3.5% to 7%, in the plasma of colonoscopy-confirmed healthy subjects, with the sensitivity for detection of ctDNA in colonoscopy-confirmed patients with colorectal cancer being 65%, 54.5%, 67.6% and 59% respectively.
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Affiliation(s)
- Susan M Mitchell
- CSIRO Food and Nutrition, P.O. Box 52, North Ryde, NSW 1670, Australia.
| | - Thu Ho
- CSIRO Food and Nutrition, P.O. Box 52, North Ryde, NSW 1670, Australia.
| | - Glenn S Brown
- CSIRO Food and Nutrition, P.O. Box 52, North Ryde, NSW 1670, Australia.
| | - Rohan T Baker
- Clinical Genomics Pty Ltd., North Ryde, NSW 2113, Australia.
| | | | - Aidan McEvoy
- Clinical Genomics Pty Ltd., North Ryde, NSW 2113, Australia.
| | - Zheng-Zhou Xu
- CSIRO Food and Nutrition, P.O. Box 52, North Ryde, NSW 1670, Australia.
| | - Jason P Ross
- CSIRO Food and Nutrition, P.O. Box 52, North Ryde, NSW 1670, Australia.
| | - Trevor J Lockett
- CSIRO Food and Nutrition, P.O. Box 52, North Ryde, NSW 1670, Australia.
| | - Graeme P Young
- Flinders Centre for Innovation in Cancer, Flinders University of South Australia, GPO Box 2100, Adelaide, SA 5001, Australia.
| | | | | | - Peter L Molloy
- CSIRO Food and Nutrition, P.O. Box 52, North Ryde, NSW 1670, Australia.
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203
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Paul DS, Teschendorff AE, Dang MA, Lowe R, Hawa MI, Ecker S, Beyan H, Cunningham S, Fouts AR, Ramelius A, Burden F, Farrow S, Rowlston S, Rehnstrom K, Frontini M, Downes K, Busche S, Cheung WA, Ge B, Simon MM, Bujold D, Kwan T, Bourque G, Datta A, Lowy E, Clarke L, Flicek P, Libertini E, Heath S, Gut M, Gut IG, Ouwehand WH, Pastinen T, Soranzo N, Hofer SE, Karges B, Meissner T, Boehm BO, Cilio C, Elding Larsson H, Lernmark Å, Steck AK, Rakyan VK, Beck S, Leslie RD. Increased DNA methylation variability in type 1 diabetes across three immune effector cell types. Nat Commun 2016; 7:13555. [PMID: 27898055 PMCID: PMC5141286 DOI: 10.1038/ncomms13555] [Citation(s) in RCA: 119] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2016] [Accepted: 10/04/2016] [Indexed: 02/06/2023] Open
Abstract
The incidence of type 1 diabetes (T1D) has substantially increased over the past decade, suggesting a role for non-genetic factors such as epigenetic mechanisms in disease development. Here we present an epigenome-wide association study across 406,365 CpGs in 52 monozygotic twin pairs discordant for T1D in three immune effector cell types. We observe a substantial enrichment of differentially variable CpG positions (DVPs) in T1D twins when compared with their healthy co-twins and when compared with healthy, unrelated individuals. These T1D-associated DVPs are found to be temporally stable and enriched at gene regulatory elements. Integration with cell type-specific gene regulatory circuits highlight pathways involved in immune cell metabolism and the cell cycle, including mTOR signalling. Evidence from cord blood of newborns who progress to overt T1D suggests that the DVPs likely emerge after birth. Our findings, based on 772 methylomes, implicate epigenetic changes that could contribute to disease pathogenesis in T1D.
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Affiliation(s)
- Dirk S. Paul
- Medical Genomics, UCL Cancer Institute, University College London, London WC1E 6BT, UK
- Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Strangeways Research Laboratory, Cambridge CB1 8RN, UK
| | - Andrew E. Teschendorff
- CAS Key Lab of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
- Statistical Cancer Genomics, UCL Cancer Institute, University College London, London WC1E 6BT, UK
| | - Mary A.N. Dang
- The Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, UK
| | - Robert Lowe
- The Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, UK
| | - Mohammed I. Hawa
- The Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, UK
| | - Simone Ecker
- Medical Genomics, UCL Cancer Institute, University College London, London WC1E 6BT, UK
| | - Huriya Beyan
- The Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, UK
| | - Stephanie Cunningham
- The Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, UK
| | - Alexandra R. Fouts
- Barbara Davis Center for Childhood Diabetes, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
| | - Anita Ramelius
- Department of Clinical Sciences, Lund University, Skåne University Hospital, SE-20502 Malmö, Sweden
| | - Frances Burden
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0PT, UK
- National Health Service Blood and Transplant, Cambridge Biomedical Campus, Cambridge CB2 0PT, UK
| | - Samantha Farrow
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0PT, UK
- National Health Service Blood and Transplant, Cambridge Biomedical Campus, Cambridge CB2 0PT, UK
| | - Sophia Rowlston
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0PT, UK
- National Health Service Blood and Transplant, Cambridge Biomedical Campus, Cambridge CB2 0PT, UK
| | - Karola Rehnstrom
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0PT, UK
- National Health Service Blood and Transplant, Cambridge Biomedical Campus, Cambridge CB2 0PT, UK
| | - Mattia Frontini
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0PT, UK
- National Health Service Blood and Transplant, Cambridge Biomedical Campus, Cambridge CB2 0PT, UK
- British Heart Foundation Centre of Excellence, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - Kate Downes
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0PT, UK
- National Health Service Blood and Transplant, Cambridge Biomedical Campus, Cambridge CB2 0PT, UK
| | - Stephan Busche
- Department of Human Genetics, McGill University, Montreal, Québec, Canada H3A 0G1
- McGill University and Genome Quebec Innovation Centre, Montreal, Québec, Canada H3A 0G1
| | - Warren A. Cheung
- Department of Human Genetics, McGill University, Montreal, Québec, Canada H3A 0G1
- McGill University and Genome Quebec Innovation Centre, Montreal, Québec, Canada H3A 0G1
| | - Bing Ge
- Department of Human Genetics, McGill University, Montreal, Québec, Canada H3A 0G1
- McGill University and Genome Quebec Innovation Centre, Montreal, Québec, Canada H3A 0G1
| | - Marie-Michelle Simon
- Department of Human Genetics, McGill University, Montreal, Québec, Canada H3A 0G1
- McGill University and Genome Quebec Innovation Centre, Montreal, Québec, Canada H3A 0G1
| | - David Bujold
- Department of Human Genetics, McGill University, Montreal, Québec, Canada H3A 0G1
- McGill University and Genome Quebec Innovation Centre, Montreal, Québec, Canada H3A 0G1
| | - Tony Kwan
- Department of Human Genetics, McGill University, Montreal, Québec, Canada H3A 0G1
- McGill University and Genome Quebec Innovation Centre, Montreal, Québec, Canada H3A 0G1
| | - Guillaume Bourque
- Department of Human Genetics, McGill University, Montreal, Québec, Canada H3A 0G1
- McGill University and Genome Quebec Innovation Centre, Montreal, Québec, Canada H3A 0G1
| | - Avik Datta
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Ernesto Lowy
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Laura Clarke
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Emanuele Libertini
- Medical Genomics, UCL Cancer Institute, University College London, London WC1E 6BT, UK
| | - Simon Heath
- CNAG-CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), Baldiri Reixac 4, 08028 Barcelona, Spain
- Universitat Pompeu Fabra, Plaça de la Mercè 10, 08002 Barcelona, Spain
| | - Marta Gut
- CNAG-CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), Baldiri Reixac 4, 08028 Barcelona, Spain
- Universitat Pompeu Fabra, Plaça de la Mercè 10, 08002 Barcelona, Spain
| | - Ivo G Gut
- CNAG-CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), Baldiri Reixac 4, 08028 Barcelona, Spain
- Universitat Pompeu Fabra, Plaça de la Mercè 10, 08002 Barcelona, Spain
| | - Willem H. Ouwehand
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0PT, UK
- National Health Service Blood and Transplant, Cambridge Biomedical Campus, Cambridge CB2 0PT, UK
- British Heart Foundation Centre of Excellence, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
- Human Genetics, Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Tomi Pastinen
- Department of Human Genetics, McGill University, Montreal, Québec, Canada H3A 0G1
- McGill University and Genome Quebec Innovation Centre, Montreal, Québec, Canada H3A 0G1
| | - Nicole Soranzo
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0PT, UK
- Human Genetics, Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Sabine E. Hofer
- Department of Pediatrics, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Beate Karges
- Division of Endocrinology and Diabetes, RWTH Aachen University, 52074 Aachen, Germany
- German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany
| | - Thomas Meissner
- German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany
- Department of General Pediatrics, Neonatology and Pediatric Cardiology, University Children's Hospital, Heinrich Heine University of Düsseldorf, 40225 Düsseldorf, Germany
| | - Bernhard O. Boehm
- Division of Endocrinology, Department of Internal Medicine I, Ulm University Medical Centre, 89081 Ulm, Germany
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 636921, Singapore
- Imperial College London, London SW7 2AZ, UK
| | - Corrado Cilio
- Department of Clinical Sciences, Lund University, Skåne University Hospital, SE-20502 Malmö, Sweden
| | - Helena Elding Larsson
- Department of Clinical Sciences, Lund University, Skåne University Hospital, SE-20502 Malmö, Sweden
| | - Åke Lernmark
- Department of Clinical Sciences, Lund University, Skåne University Hospital, SE-20502 Malmö, Sweden
| | - Andrea K. Steck
- Barbara Davis Center for Childhood Diabetes, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
| | - Vardhman K. Rakyan
- The Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, UK
| | - Stephan Beck
- Medical Genomics, UCL Cancer Institute, University College London, London WC1E 6BT, UK
| | - R. David Leslie
- The Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, UK
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204
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Ventham NT, Kennedy NA, Adams AT, Kalla R, Heath S, O'Leary KR, Drummond H, Wilson DC, Gut IG, Nimmo ER, Satsangi J. Integrative epigenome-wide analysis demonstrates that DNA methylation may mediate genetic risk in inflammatory bowel disease. Nat Commun 2016; 7:13507. [PMID: 27886173 PMCID: PMC5133631 DOI: 10.1038/ncomms13507] [Citation(s) in RCA: 142] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 10/11/2016] [Indexed: 02/06/2023] Open
Abstract
Epigenetic alterations may provide important insights into gene-environment interaction in inflammatory bowel disease (IBD). Here we observe epigenome-wide DNA methylation differences in 240 newly-diagnosed IBD cases and 190 controls. These include 439 differentially methylated positions (DMPs) and 5 differentially methylated regions (DMRs), which we study in detail using whole genome bisulphite sequencing. We replicate the top DMP (RPS6KA2) and DMRs (VMP1, ITGB2 and TXK) in an independent cohort. Using paired genetic and epigenetic data, we delineate methylation quantitative trait loci; VMP1/microRNA-21 methylation associates with two polymorphisms in linkage disequilibrium with a known IBD susceptibility variant. Separated cell data shows that IBD-associated hypermethylation within the TXK promoter region negatively correlates with gene expression in whole-blood and CD8+ T cells, but not other cell types. Thus, site-specific DNA methylation changes in IBD relate to underlying genotype and associate with cell-specific alteration in gene expression.
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Affiliation(s)
- N. T. Ventham
- Gastrointestinal Unit, Centre for Genomics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 6XU, UK
| | - N. A. Kennedy
- Gastrointestinal Unit, Centre for Genomics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 6XU, UK
| | - A. T. Adams
- Gastrointestinal Unit, Centre for Genomics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 6XU, UK
| | - R. Kalla
- Gastrointestinal Unit, Centre for Genomics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 6XU, UK
| | - S. Heath
- CNAG-CRG, Centro Nacional de Análisis Genómico, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, Barcelona 08028, Spain
- Universitat Pompeu Fabra (UPF), Barcelona 08002, Spain
| | - K. R. O'Leary
- Gastrointestinal Unit, Centre for Genomics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 6XU, UK
| | - H. Drummond
- Gastrointestinal Unit, Centre for Genomics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 6XU, UK
| | - D. C. Wilson
- Department of Child Life and Health, University of Edinburgh, Edinburgh EH9 1UW, UK
| | - I. G. Gut
- CNAG-CRG, Centro Nacional de Análisis Genómico, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, Barcelona 08028, Spain
- Universitat Pompeu Fabra (UPF), Barcelona 08002, Spain
| | - E. R. Nimmo
- Gastrointestinal Unit, Centre for Genomics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 6XU, UK
| | - J. Satsangi
- Gastrointestinal Unit, Centre for Genomics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 6XU, UK
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205
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Lio CW, Zhang J, González-Avalos E, Hogan PG, Chang X, Rao A. Tet2 and Tet3 cooperate with B-lineage transcription factors to regulate DNA modification and chromatin accessibility. eLife 2016; 5. [PMID: 27869616 PMCID: PMC5142813 DOI: 10.7554/elife.18290] [Citation(s) in RCA: 106] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2016] [Accepted: 11/18/2016] [Indexed: 12/30/2022] Open
Abstract
Ten-eleven translocation (TET) enzymes oxidize 5-methylcytosine, facilitating DNA demethylation and generating new epigenetic marks. Here we show that concomitant loss of Tet2 and Tet3 in mice at early B cell stage blocked the pro- to pre-B cell transition in the bone marrow, decreased Irf4 expression and impaired the germline transcription and rearrangement of the Igκ locus. Tet2/3-deficient pro-B cells showed increased CpG methylation at the Igκ 3' and distal enhancers that was mimicked by depletion of E2A or PU.1, as well as a global decrease in chromatin accessibility at enhancers. Importantly, re-expression of the Tet2 catalytic domain in Tet2/3-deficient B cells resulted in demethylation of the Igκ enhancers and restored their chromatin accessibility. Our data suggest that TET proteins and lineage-specific transcription factors cooperate to influence chromatin accessibility and Igκ enhancer function by modulating the modification status of DNA.
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Affiliation(s)
- Chan-Wang Lio
- Division of Signaling and Gene Expression, San Diego, United States
| | - Jiayuan Zhang
- Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences and Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | | | - Patrick G Hogan
- Division of Signaling and Gene Expression, San Diego, United States
| | - Xing Chang
- Division of Signaling and Gene Expression, San Diego, United States.,Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences and Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Sanford Consortium for Regenerative Medicine, San Diego, United States
| | - Anjana Rao
- Division of Signaling and Gene Expression, San Diego, United States.,Sanford Consortium for Regenerative Medicine, San Diego, United States.,Department of Pharmacology, University of California, San Diego, San Diego, United States.,Moores Cancer Center, University of California, San Diego, San Diego, United States
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206
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Schuyler RP, Merkel A, Raineri E, Altucci L, Vellenga E, Martens JHA, Pourfarzad F, Kuijpers TW, Burden F, Farrow S, Downes K, Ouwehand WH, Clarke L, Datta A, Lowy E, Flicek P, Frontini M, Stunnenberg HG, Martín-Subero JI, Gut I, Heath S. Distinct Trends of DNA Methylation Patterning in the Innate and Adaptive Immune Systems. Cell Rep 2016; 17:2101-2111. [PMID: 27851971 PMCID: PMC5889099 DOI: 10.1016/j.celrep.2016.10.054] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 06/17/2016] [Accepted: 09/12/2016] [Indexed: 01/15/2023] Open
Abstract
DNA methylation and the localization and post-translational modification of nucleosomes are interdependent factors that contribute to the generation of distinct phenotypes from genetically identical cells. With 112 whole-genome bisulfite sequencing datasets from the BLUEPRINT Epigenome Project, we analyzed the global development of DNA methylation patterns during lineage commitment and maturation of a range of immune system effector cells and the cancers that arise from them. We show clear trends in methylation patterns that are distinct in the innate and adaptive arms of the human immune system, both globally and in relation to consistently positioned nucleosomes. Most notable are a progressive loss of methylation in developing lymphocytes and the consistent occurrence of non-CG methylation in specific cell types. Cancer samples from the two lineages are further polarized, suggesting the involvement of distinct lineage-specific epigenetic mechanisms. We anticipate broad utility for this resource as a basis for further comparative epigenetic analyses.
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Affiliation(s)
- Ronald P Schuyler
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, Barcelona 08028, Spain; Universitat Pompeu Fabra (UPF), Barcelona 08002, Spain
| | - Angelika Merkel
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, Barcelona 08028, Spain; Universitat Pompeu Fabra (UPF), Barcelona 08002, Spain
| | - Emanuele Raineri
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, Barcelona 08028, Spain; Universitat Pompeu Fabra (UPF), Barcelona 08002, Spain
| | - Lucia Altucci
- Dipartimento di Biochimica Biofisica e Patologia Generale, Seconda Università degli Studi di Napoli, Vico Luigi de Crecchio 7, Napoli 80138, Italy
| | - Edo Vellenga
- Department of Hematology, University of Groningen and University Medical Center Groningen, PO Box 30001, 9700 RB Groningen, the Netherlands
| | - Joost H A Martens
- Department of Molecular Biology, Radboud University, Faculty of Science, Nijmegen Centre for Molecular Life Sciences, 6500 HB Nijmegen, the Netherlands
| | - Farzin Pourfarzad
- Department of Blood Cell Research, Sanquin Research and Landsteiner Laboratory, Academic Medical Center, University of Amsterdam, Plesmanlaan 125, 1066 CX Amsterdam, the Netherlands
| | - Taco W Kuijpers
- Department of Blood Cell Research, Sanquin Research and Landsteiner Laboratory, Academic Medical Center, University of Amsterdam, Plesmanlaan 125, 1066 CX Amsterdam, the Netherlands; Emma Children's Hospital, Academic Medical Center, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
| | - Frances Burden
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Long Road, CB2 0PT Cambridge, UK; National Health Service (NHS) Blood and Transplant, Cambridge Biomedical Campus, Long Road, CB2 0PT Cambridge, UK
| | - Samantha Farrow
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Long Road, CB2 0PT Cambridge, UK; National Health Service (NHS) Blood and Transplant, Cambridge Biomedical Campus, Long Road, CB2 0PT Cambridge, UK
| | - Kate Downes
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Long Road, CB2 0PT Cambridge, UK; National Health Service (NHS) Blood and Transplant, Cambridge Biomedical Campus, Long Road, CB2 0PT Cambridge, UK
| | - Willem H Ouwehand
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Long Road, CB2 0PT Cambridge, UK; National Health Service (NHS) Blood and Transplant, Cambridge Biomedical Campus, Long Road, CB2 0PT Cambridge, UK; British Heart Foundation Centre of Excellence, University of Cambridge, Cambridge Biomedical Campus, Long Road, CB2 0QQ Cambridge, UK; Department of Human Genetics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1HH Cambridge, UK
| | - Laura Clarke
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD Cambridge, UK
| | - Avik Datta
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD Cambridge, UK
| | - Ernesto Lowy
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD Cambridge, UK
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD Cambridge, UK
| | - Mattia Frontini
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Long Road, CB2 0PT Cambridge, UK; National Health Service (NHS) Blood and Transplant, Cambridge Biomedical Campus, Long Road, CB2 0PT Cambridge, UK; British Heart Foundation Centre of Excellence, University of Cambridge, Cambridge Biomedical Campus, Long Road, CB2 0QQ Cambridge, UK
| | - Hendrik G Stunnenberg
- Department of Molecular Biology, Radboud University, Faculty of Science, Nijmegen Centre for Molecular Life Sciences, 6500 HB Nijmegen, the Netherlands
| | - José I Martín-Subero
- Department of Anatomic Pathology, Pharmacology and Microbiology, University of Barcelona, Institut d'Investigacions Biomédiques August Pi i Sunyer (IDIBAPS), Barcelona 08036, Spain
| | - Ivo Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, Barcelona 08028, Spain; Universitat Pompeu Fabra (UPF), Barcelona 08002, Spain
| | - Simon Heath
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, Barcelona 08028, Spain; Universitat Pompeu Fabra (UPF), Barcelona 08002, Spain.
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207
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Queirós AC, Beekman R, Vilarrasa-Blasi R, Duran-Ferrer M, Clot G, Merkel A, Raineri E, Russiñol N, Castellano G, Beà S, Navarro A, Kulis M, Verdaguer-Dot N, Jares P, Enjuanes A, Calasanz MJ, Bergmann A, Vater I, Salaverría I, van de Werken HJG, Wilson WH, Datta A, Flicek P, Royo R, Martens J, Giné E, Lopez-Guillermo A, Stunnenberg HG, Klapper W, Pott C, Heath S, Gut IG, Siebert R, Campo E, Martín-Subero JI. Decoding the DNA Methylome of Mantle Cell Lymphoma in the Light of the Entire B Cell Lineage. Cancer Cell 2016; 30:806-821. [PMID: 27846393 PMCID: PMC5805090 DOI: 10.1016/j.ccell.2016.09.014] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Revised: 07/18/2016] [Accepted: 09/19/2016] [Indexed: 01/17/2023]
Abstract
We analyzed the in silico purified DNA methylation signatures of 82 mantle cell lymphomas (MCL) in comparison with cell subpopulations spanning the entire B cell lineage. We identified two MCL subgroups, respectively carrying epigenetic imprints of germinal-center-inexperienced and germinal-center-experienced B cells, and we found that DNA methylation profiles during lymphomagenesis are largely influenced by the methylation dynamics in normal B cells. An integrative epigenomic approach revealed 10,504 differentially methylated regions in regulatory elements marked by H3K27ac in MCL primary cases, including a distant enhancer showing de novo looping to the MCL oncogene SOX11. Finally, we observed that the magnitude of DNA methylation changes per case is highly variable and serves as an independent prognostic factor for MCL outcome.
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Affiliation(s)
- Ana C Queirós
- Departamento de Fundamentos Clínicos, Universitat de Barcelona, Barcelona 08036, Spain
| | - Renée Beekman
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona 08036, Spain
| | - Roser Vilarrasa-Blasi
- Departamento de Fundamentos Clínicos, Universitat de Barcelona, Barcelona 08036, Spain
| | - Martí Duran-Ferrer
- Departamento de Fundamentos Clínicos, Universitat de Barcelona, Barcelona 08036, Spain
| | - Guillem Clot
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona 08036, Spain
| | - Angelika Merkel
- Centro Nacional de Análisis Genómico, Parc Científic de Barcelona, Barcelona 08028, Spain
| | - Emanuele Raineri
- Centro Nacional de Análisis Genómico, Parc Científic de Barcelona, Barcelona 08028, Spain
| | - Nuria Russiñol
- Departamento de Fundamentos Clínicos, Universitat de Barcelona, Barcelona 08036, Spain; Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona 08036, Spain
| | - Giancarlo Castellano
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona 08036, Spain
| | - Sílvia Beà
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona 08036, Spain
| | - Alba Navarro
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona 08036, Spain
| | - Marta Kulis
- Departamento de Fundamentos Clínicos, Universitat de Barcelona, Barcelona 08036, Spain
| | - Núria Verdaguer-Dot
- Departamento de Fundamentos Clínicos, Universitat de Barcelona, Barcelona 08036, Spain; Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona 08036, Spain
| | - Pedro Jares
- Departamento de Fundamentos Clínicos, Universitat de Barcelona, Barcelona 08036, Spain; Unidad de Genómica, IDIBAPS, Barcelona 08036, Spain
| | | | | | - Anke Bergmann
- Institute of Human Genetics, Christian-Albrechts University, Kiel 24105, Germany; Department of Pediatrics, Christian-Albrechts University & University Hospital Schleswig-Holstein, Kiel 24105, Germany
| | - Inga Vater
- Institute of Human Genetics, Christian-Albrechts University, Kiel 24105, Germany
| | - Itziar Salaverría
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona 08036, Spain
| | - Harmen J G van de Werken
- Department of Cell Biology, Erasmus MC, Rotterdam 3015 CN, the Netherlands; Cancer Computational Biology Center, Erasmus MC, Rotterdam 3015 CN, the Netherlands; Department of Urology, Erasmus MC, Rotterdam 3015 CN, the Netherlands
| | - Wyndham H Wilson
- Lymphoid Malignancies Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Avik Datta
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK
| | - Romina Royo
- Joint Program on Computational Biology, Barcelona Supercomputing Center (BSC) and Institute of Research in Biomedicine (IRB), Barcelona Science Park, Barcelona 08034, Spain
| | - Joost Martens
- Molecular Biology, NCMLS, FNWI, Radboud University, Nijmegen 6500 HB, the Netherlands
| | - Eva Giné
- Servicio de Hematología, Hospital Clínic, IDIBAPS, Barcelona 08036, Spain
| | | | - Hendrik G Stunnenberg
- Molecular Biology, NCMLS, FNWI, Radboud University, Nijmegen 6500 HB, the Netherlands
| | - Wolfram Klapper
- Hematopathology Section and Lymph Node Registry, Christian-Albrecht University, Kiel 24105, Germany
| | - Christiane Pott
- Second Medical Department, University Hospital Schleswig-Holstein, Kiel 24116, Germany
| | - Simon Heath
- Centro Nacional de Análisis Genómico, Parc Científic de Barcelona, Barcelona 08028, Spain
| | - Ivo G Gut
- Centro Nacional de Análisis Genómico, Parc Científic de Barcelona, Barcelona 08028, Spain
| | - Reiner Siebert
- Institute of Human Genetics, Christian-Albrechts University, Kiel 24105, Germany
| | - Elías Campo
- Departamento de Fundamentos Clínicos, Universitat de Barcelona, Barcelona 08036, Spain; Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona 08036, Spain; Unidad de Hematopatología, Servicio de Anatomía Patológica, Hospital Clínic, Barcelona 08036, Spain
| | - José I Martín-Subero
- Departamento de Fundamentos Clínicos, Universitat de Barcelona, Barcelona 08036, Spain; Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona 08036, Spain.
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208
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Mansouri L, Rosenquist R. Unraveling the DNA Methylome in Mantle Cell Lymphoma: New Insights into the Cellular Origin. Cancer Cell 2016; 30:665-667. [PMID: 27846388 DOI: 10.1016/j.ccell.2016.10.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Our understanding of the DNA methylome and its impact on cancer evolution and disease progression is rapidly evolving. In this issue of Cancer Cell, Queirós et al. provide a detailed characterization of the DNA methylome in mantle cell lymphoma and reveal novel molecular subtypes, potentially with different cellular origins.
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Affiliation(s)
- Larry Mansouri
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, 751 85 Uppsala, Sweden
| | - Richard Rosenquist
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, 751 85 Uppsala, Sweden.
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209
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Arribas AJ, Bertoni F. Methylation patterns in marginal zone lymphoma. Best Pract Res Clin Haematol 2016; 30:24-31. [PMID: 28288713 DOI: 10.1016/j.beha.2016.09.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Revised: 09/16/2016] [Accepted: 09/19/2016] [Indexed: 02/07/2023]
Abstract
Promoter DNA methylation is a major regulator of gene expression and transcription. The identification of methylation changes is important for understanding disease pathogenesis, for identifying prognostic markers and can drive novel therapeutic approaches. In this review we summarize the current knowledge regarding DNA methylation in MALT lymphoma, splenic marginal zone lymphoma, nodal marginal zone lymphoma. Despite important differences in the study design for different publications and the existence of a sole large and genome-wide methylation study for splenic marginal zone lymphoma, it is clear that DNA methylation plays an important role in marginal zone lymphomas, in which it contributes to the inactivation of tumor suppressors but also to the expression of genes sustaining tumor cell survival and proliferation. Existing preclinical data provide the rationale to target the methylation machinery in these disorders.
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Affiliation(s)
- Alberto J Arribas
- Lymphoma & Genomics Research Program, Institute of Oncology Research (IOR), Bellinzona, Switzerland.
| | - Francesco Bertoni
- Lymphoma & Genomics Research Program, Institute of Oncology Research (IOR), Bellinzona, Switzerland; Oncology Institute of Southern Switzerland (IOSI), Bellinzona, Switzerland.
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210
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Durek P, Nordström K, Gasparoni G, Salhab A, Kressler C, de Almeida M, Bassler K, Ulas T, Schmidt F, Xiong J, Glažar P, Klironomos F, Sinha A, Kinkley S, Yang X, Arrigoni L, Amirabad A, Ardakani F, Feuerbach L, Gorka O, Ebert P, Müller F, Li N, Frischbutter S, Schlickeiser S, Cendon C, Fröhler S, Felder B, Gasparoni N, Imbusch C, Hutter B, Zipprich G, Tauchmann Y, Reinke S, Wassilew G, Hoffmann U, Richter A, Sieverling L, Chang HD, Syrbe U, Kalus U, Eils J, Brors B, Manke T, Ruland J, Lengauer T, Rajewsky N, Chen W, Dong J, Sawitzki B, Chung HR, Rosenstiel P, Schulz M, Schultze J, Radbruch A, Walter J, Hamann A, Polansky J. Epigenomic Profiling of Human CD4+ T Cells Supports a Linear Differentiation Model and Highlights Molecular Regulators of Memory Development. Immunity 2016; 45:1148-1161. [DOI: 10.1016/j.immuni.2016.10.022] [Citation(s) in RCA: 130] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Revised: 06/22/2016] [Accepted: 07/22/2016] [Indexed: 12/21/2022]
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211
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Singh SK, Lupo PJ, Scheurer ME, Saxena A, Kennedy AE, Ibrahimou B, Barbieri MA, Mills KI, McCauley JL, Okcu MF, Dorak MT. A childhood acute lymphoblastic leukemia genome-wide association study identifies novel sex-specific risk variants. Medicine (Baltimore) 2016; 95:e5300. [PMID: 27861356 PMCID: PMC5120913 DOI: 10.1097/md.0000000000005300] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Childhood acute lymphoblastic leukemia (ALL) occurs more frequently in males. Reasons behind sex differences in childhood ALL risk are unknown. In the present genome-wide association study (GWAS), we explored the genetic basis of sex differences by comparing genotype frequencies between male and female cases in a case-only study to assess effect-modification by sex.The case-only design included 236 incident cases of childhood ALL consecutively recruited at the Texas Children's Cancer Center in Houston, Texas from 2007 to 2012. All cases were non-Hispanic whites, aged 1 to 10 years, and diagnosed with confirmed B-cell precursor ALL. Genotyping was performed using the Illumina HumanCoreExome BeadChip on the Illumina Infinium platform. Besides the top 100 statistically most significant results, results were also analyzed by the top 100 highest effect size with a nominal statistical significance (P <0.05).The statistically most significant sex-specific association (P = 4 × 10) was with the single nucleotide polymorphism (SNP) rs4813720 (RASSF2), an expression quantitative trait locus (eQTL) for RASSF2 in peripheral blood. rs4813720 is also a strong methylation QTL (meQTL) for a CpG site (cg22485289) within RASSF2 in pregnancy, at birth, childhood, and adolescence. cg22485289 is one of the hypomethylated CpG sites in ALL compared with pre-B cells. Two missense SNPs, rs12722042 and 12722039, in the HLA-DQA1 gene yielded the highest effect sizes (odds ratio [OR] ∼ 14; P <0.01) for sex-specific results. The HLA-DQA1 SNPs belong to DQA1*01 and confirmed the previously reported male-specific association with DQA1*01. This finding supports the proposed infection-related etiology in childhood ALL risk for males. Further analyses revealed that most SNPs (either direct effect or through linkage disequilibrium) were within active enhancers or active promoter regions and had regulatory effects on gene expression levels.Cumulative data suggested that RASSF2 rs4813720, which correlates with increased RASSF2 expression, may counteract the suppressor effect of estrogen-regulated miR-17-92 on RASSF2 resulting in protection in males. Given the amount of sex hormone-related mechanisms suggested by our findings, future studies should examine prenatal or early postnatal programming by sex hormones when hormone levels show a large variation.
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Affiliation(s)
- Sandeep K. Singh
- Department of Environmental and Occupational Health, Robert Stempel College of Public Health and Social Work, Florida International University, Miami, FL
- Department of Biological Sciences, Florida International University, Miami, FL
| | - Philip J. Lupo
- Department of Pediatrics, Section of Hematology-Oncology, Texas Children's Cancer Center
| | - Michael E. Scheurer
- Department of Pediatrics, Section of Hematology-Oncology, Baylor College of Medicine, Houston, TX
| | - Anshul Saxena
- Department of Health Promotion and Disease Prevention, Robert Stempel College of Public Health and Social Work, Florida International University, Miami, FL
| | - Amy E. Kennedy
- Division of Cancer Control and Population Sciences, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Boubakari Ibrahimou
- Department of Biostatistics, Robert Stempel College of Public Health and Social Work, Florida International University, Miami, FL
| | | | - Ken I. Mills
- Centre for Cancer Research and Cell Biology (CCRCB), Queen's University Belfast, Belfast, UK
| | - Jacob L. McCauley
- Dr. John T. Macdonald Foundation, Department of Human Genetics, John P. Hussman Institute for Human Genomics, Biorepository Facility, Center for Genome Technology University of Miami, Miller School of Medicine
| | - Mehmet Fatih Okcu
- Department of Pediatrics, Section of Hematology-Oncology, Baylor College of Medicine, Houston, TX
| | - Mehmet Tevfik Dorak
- Department of Epidemiology, Robert Stempel College of Public Health and Social Work, Florida International University, Miami, FL
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212
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Genetic evolution in chronic lymphocytic leukaemia. Best Pract Res Clin Haematol 2016; 29:67-78. [PMID: 27742073 DOI: 10.1016/j.beha.2016.08.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Revised: 06/30/2016] [Accepted: 08/04/2016] [Indexed: 11/21/2022]
Abstract
Next-generation sequencing provides a comprehensive understanding of the genomic, epigenomic and transcriptomic underpinnings of chronic lymphocytic leukaemia. Recent studies have uncovered new drivers, including mutations in non-coding regions, and signalling pathways whose role in cancer was previously unknown or poorly understood. Moreover, massive scale epigenomics and transcriptomics have supplied the foundations for the cellular origin of the disease. Some drivers could be targeted pharmacologically, and the ability to detect mutations present in minority subclones might even allow treatment before clonal selection occurs, thus preventing disease refractoriness. As our understanding broadens and ongoing technological innovation propels new achievements, we will certainly learn how to apply it in our daily practice.
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213
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Barwick BG, Scharer CD, Bally AP, Boss JM. Plasma cell differentiation is coupled to division-dependent DNA hypomethylation and gene regulation. Nat Immunol 2016; 17:1216-1225. [PMID: 27500631 PMCID: PMC5157049 DOI: 10.1038/ni.3519] [Citation(s) in RCA: 106] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Accepted: 06/23/2016] [Indexed: 12/16/2022]
Abstract
The epigenetic processes that regulate antibody-secreting plasma cells are not well understood. Here, analysis of plasma cell differentiation revealed DNA hypomethylation of 10% of CpG loci that were overrepresented at enhancers. Inhibition of DNA methylation enhanced plasma cell commitment in a cell-division-dependent manner. Analysis of B cells differentiating in vivo stratified by cell division revealed a fivefold increase in mRNA transcription coupled to DNA hypomethylation. Demethylation occurred first at binding motifs for the transcription factors NF-κB and AP-1 and later at those for the transcription factors IRF and Oct-2 and was coincident with activation and differentiation gene-expression programs in a cell-division-dependent manner. These data provide mechanistic insight into cell-division-coupled transcriptional and epigenetic reprogramming and suggest that DNA hypomethylation reflects the cis-regulatory history of plasma cell differentiation.
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Affiliation(s)
- Benjamin G. Barwick
- Department of Microbiology & Immunology Emory University School of Medicine Atlanta, GA, USA
| | - Christopher D. Scharer
- Department of Microbiology & Immunology Emory University School of Medicine Atlanta, GA, USA
| | - Alexander P.R. Bally
- Department of Microbiology & Immunology Emory University School of Medicine Atlanta, GA, USA
| | - Jeremy M. Boss
- Department of Microbiology & Immunology Emory University School of Medicine Atlanta, GA, USA
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214
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Ammerpohl O, Scheufele S, Siebert R. Analysen epigenetischer Marker aus Liquid Biopsies: Informationen von jenseits des Genoms. MED GENET-BERLIN 2016. [DOI: 10.1007/s11825-016-0093-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Zusammenfassung
Die Analyse epigenetischer Marker aus Liquid Biopsies erlaubt Einblicke in physiologische und pathologische Prozesse im Körper einer Person, die über die reine Sequenzinformation hinausgehen. Insbesondere das DNA-Methylierungsmuster sowie die Expressionsmuster von mRNA und ncRNA sind aus Liquid Biopsies erfassbar. Damit werden ganze Gruppen neuer potenzieller Biomarker einer nicht invasiven und ökonomischen Diagnostik zugänglich. Darüber hinaus und im Gegensatz zur reinen DNA-Sequenzanalyse von Liquid Biopsies erlaubt die hohe Gewebespezifität epigenetischer Marker auch die Bestimmung der Herkunft der analysierten Nukleinsäuren z. B. in Bezug auf ein betroffenes Organ. Angesichts der fallenden Kosten für Sequenzierungen und des technologischen Fortschritts, der die Nachweisgrenzen immer weiter zu immer sensitiveren Anwendungen verschiebt, könnten epigenetische Untersuchungen aus Liquid Biopsies den Trend zu einer Individualisierung in der Medizin weiter forcieren.
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Affiliation(s)
- Ole Ammerpohl
- Aff1 grid.9764.c 0000000121539986 Institut für Humangenetik Christian‑Albrechts‑Universität zu Kiel Schwanenweg 24 24105 Kiel Deutschland
- Aff2 grid.412468.d 0000000406462097 Universitätsklinikum Schleswig-Holstein Campus Kiel Kiel Deutschland
- Aff3 grid.452624.3 Airway Research Center North (ARCN) German Center for Lung Research (DZL) Gießen Deutschland
| | - Swetlana Scheufele
- Aff1 grid.9764.c 0000000121539986 Institut für Humangenetik Christian‑Albrechts‑Universität zu Kiel Schwanenweg 24 24105 Kiel Deutschland
- Aff2 grid.412468.d 0000000406462097 Universitätsklinikum Schleswig-Holstein Campus Kiel Kiel Deutschland
- Aff3 grid.452624.3 Airway Research Center North (ARCN) German Center for Lung Research (DZL) Gießen Deutschland
| | - Reiner Siebert
- Aff3 grid.452624.3 Airway Research Center North (ARCN) German Center for Lung Research (DZL) Gießen Deutschland
- Aff4 grid.6582.9 0000000419369748 Institut für Humangenetik Universität Ulm Albert-Einstein-Allee 11 89081 Ulm Deutschland
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215
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Teschendorff AE, Zheng SC, Feber A, Yang Z, Beck S, Widschwendter M. The multi-omic landscape of transcription factor inactivation in cancer. Genome Med 2016; 8:89. [PMID: 27562343 PMCID: PMC4997779 DOI: 10.1186/s13073-016-0342-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 08/05/2016] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Hypermethylation of transcription factor promoters bivalently marked in stem cells is a cancer hallmark. However, the biological significance of this observation for carcinogenesis is unclear given that most of these transcription factors are not expressed in any given normal tissue. METHODS We analysed the dynamics of gene expression between human embryonic stem cells, fetal and adult normal tissue, as well as six different matching cancer types. In addition, we performed an integrative multi-omic analysis of matched DNA methylation, copy number, mutational and transcriptomic data for these six cancer types. RESULTS We here demonstrate that bivalently and PRC2 marked transcription factors highly expressed in a normal tissue are more likely to be silenced in the corresponding tumour type compared with non-housekeeping genes that are also highly expressed in the same normal tissue. Integrative multi-omic analysis of matched DNA methylation, copy number, mutational and transcriptomic data for six different matching cancer types reveals that in-cis promoter hypermethylation, and not in-cis genomic loss or genetic mutation, emerges as the predominant mechanism associated with silencing of these transcription factors in cancer. However, we also observe that some silenced bivalently/PRC2 marked transcription factors are more prone to copy number loss than promoter hypermethylation, pointing towards distinct, mutually exclusive inactivation patterns. CONCLUSIONS These data provide statistical evidence that inactivation of cell fate-specifying transcription factors in cancer is an important step in carcinogenesis and that it occurs predominantly through a mechanism associated with promoter hypermethylation.
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Affiliation(s)
- Andrew E Teschendorff
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Chinese Academy of Sciences, Shanghai Institute for Biological Sciences, 320 Yue Yang Road, Shanghai, 200031, China.
- Statistical Cancer Genomics, UCL Cancer Institute, University College London, Paul O'Gorman Building, 72 Huntley Street, London, WC1E 6BT, UK.
- Department of Women's Cancer, University College London, 74 Huntley Street, London, WC1E 6BT, UK.
| | - Shijie C Zheng
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Chinese Academy of Sciences, Shanghai Institute for Biological Sciences, 320 Yue Yang Road, Shanghai, 200031, China
| | - Andy Feber
- Medical Genomics, UCL Cancer Institute, University College London, Paul O'Gorman Building, 72 Huntley Street, London, WC1E 6BT, UK
| | - Zhen Yang
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Chinese Academy of Sciences, Shanghai Institute for Biological Sciences, 320 Yue Yang Road, Shanghai, 200031, China
| | - Stephan Beck
- Medical Genomics, UCL Cancer Institute, University College London, Paul O'Gorman Building, 72 Huntley Street, London, WC1E 6BT, UK
| | - Martin Widschwendter
- Department of Women's Cancer, University College London, 74 Huntley Street, London, WC1E 6BT, UK
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216
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Lim YC, Chia SY, Jin S, Han W, Ding C, Sun L. Dynamic DNA methylation landscape defines brown and white cell specificity during adipogenesis. Mol Metab 2016; 5:1033-1041. [PMID: 27689016 PMCID: PMC5034609 DOI: 10.1016/j.molmet.2016.08.006] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Revised: 08/07/2016] [Accepted: 08/10/2016] [Indexed: 12/20/2022] Open
Abstract
OBJECTIVE DNA methylation may be a stable epigenetic contributor to defining fat cell lineage. METHODS We performed reduced representation bisulfite sequencing (RRBS) and RNA-seq to depict a genome-wide integrative view of the DNA methylome and transcriptome during brown and white adipogenesis. RESULTS Our analysis demonstrated that DNA methylation is a stable epigenetic signature for brown and white cell lineage before, during, and after differentiation. We identified 31 genes whose promoters were significantly differentially methylated between white and brown adipogenesis at all three time points of differentiation. Among them, five genes belong to the Hox family; their expression levels were anti-correlated with promoter methylation, suggesting a regulatory role of DNA methylation in transcription. Blocking DNA methylation with 5-Aza-cytidine increased the expression of these genes, with the most prominent effect on Hoxc10, a repressor of BAT marker expression. CONCLUSIONS Our data suggest that DNA methylation may play an important role in lineage-specific development in adipocytes.
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Affiliation(s)
- Yen Ching Lim
- School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China; Cardiovascular and Metabolic Disorders Program, Duke-NUS Graduate Medical School, 8 College Road, Singapore 169857, Singapore
| | - Sook Yoong Chia
- Cardiovascular and Metabolic Disorders Program, Duke-NUS Graduate Medical School, 8 College Road, Singapore 169857, Singapore
| | - Shengnan Jin
- School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Weiping Han
- Singapore Bioimaging Consortium, Agency for Science, Technology and Research (A*STAR), Singapore 138667, Singapore
| | - Chunming Ding
- School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China.
| | - Lei Sun
- Cardiovascular and Metabolic Disorders Program, Duke-NUS Graduate Medical School, 8 College Road, Singapore 169857, Singapore; Institute of Molecular and Cell Biology, 61 Biopolis Drive, Proteos, Singapore 138673, Singapore.
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217
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Kim S, Eliot M, Koestler DC, Houseman EA, Wetmur JG, Wiencke JK, Kelsey KT. Enlarged leukocyte referent libraries can explain additional variance in blood-based epigenome-wide association studies. Epigenomics 2016; 8:1185-92. [PMID: 27529193 DOI: 10.2217/epi-2016-0037] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
AIM We examined whether variation in blood-based epigenome-wide association studies could be more completely explained by augmenting existing reference DNA methylation libraries. MATERIALS & METHODS We compared existing and enhanced libraries in predicting variability in three publicly available 450K methylation datasets that collected whole-blood samples. Models were fit separately to each CpG site and used to estimate the additional variability when adjustments for cell composition were made with each library. RESULTS Calculation of the mean difference in the CpG-specific residual sums of squares error between models for an arthritis, aging and metabolic syndrome dataset, indicated that an enhanced library explained significantly more variation across all three datasets (p < 10(-3)). CONCLUSION Pathologically important immune cell subtypes can explain important variability in epigenome-wide association studies done in blood.
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Affiliation(s)
- Stephanie Kim
- Department of Epidemiology, Brown University School of Public Health, Providence, RI 02912, USA.,Department of Environmental Health, Boston University School of Public Health, Boston, MA 02118, USA
| | - Melissa Eliot
- Department of Epidemiology, Brown University School of Public Health, Providence, RI 02912, USA
| | - Devin C Koestler
- Department of Biostatistics, University of Kansas Medical Center, Kansas City, KA 66160, USA
| | - Eugene A Houseman
- Oregon State University College of Public Health & Human Sciences, Corvallis, OR 97331, USA
| | - James G Wetmur
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - John K Wiencke
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA 94158, USA
| | - Karl T Kelsey
- Department of Epidemiology, Brown University School of Public Health, Providence, RI 02912, USA.,Department of Laboratory Medicine & Pathology, Brown University, Providence, RI 02912, USA
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218
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Lin X, Barton S, Holbrook JD. How to make DNA methylome wide association studies more powerful. Epigenomics 2016; 8:1117-29. [PMID: 27052998 PMCID: PMC5066141 DOI: 10.2217/epi-2016-0017] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Accepted: 03/23/2016] [Indexed: 02/06/2023] Open
Abstract
Genome-wide association studies had a troublesome adolescence, while researchers increased statistical power, in part by increasing subject numbers. Interrogating the interaction of genetic and environmental influences raised new challenges of statistical power, which were not easily bested by the addition of subjects. Screening the DNA methylome offers an attractive alternative as methylation can be thought of as a proxy for the combined influences of genetics and environment. There are statistical challenges unique to DNA methylome data and also multiple features, which can be exploited to increase power. We anticipate the development of DNA methylome association study designs and new analytical methods, together with integration of data from other molecular species and other studies, which will boost statistical power and tackle causality. In this way, the molecular trajectories that underlie disease development will be uncovered.
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Affiliation(s)
- Xinyi Lin
- Singapore Institute for Clinical Sciences (SICS), Agency for Science & Technology Research (A*STAR), Brenner Centre for Molecular Medicine, 30 Medical Drive, 117609, Singapore
| | - Sheila Barton
- MRC Lifecourse Epidemiology Unit, Faculty of Medicine, University of Southampton, Southampton, SO16 6YD, UK
| | - Joanna D Holbrook
- Singapore Institute for Clinical Sciences (SICS), Agency for Science & Technology Research (A*STAR), Brenner Centre for Molecular Medicine, 30 Medical Drive, 117609, Singapore
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219
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Abstract
Mammalian embryonic development is a tightly regulated process that, from a single zygote, produces a large number of cell types with hugely divergent functions. Distinct cellular differentiation programmes are facilitated by tight transcriptional and epigenetic regulation. However, the contribution of epigenetic regulation to tissue homeostasis after the completion of development is less well understood. In this Review, we explore the effects of epigenetic dysregulation on adult stem cell function. We conclude that, depending on the tissue type and the epigenetic regulator affected, the consequences range from negligible to stem cell malfunction and disruption of tissue homeostasis, which may predispose to diseases such as cancer.
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220
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Suelves M, Carrió E, Núñez-Álvarez Y, Peinado MA. DNA methylation dynamics in cellular commitment and differentiation. Brief Funct Genomics 2016; 15:443-453. [PMID: 27416614 DOI: 10.1093/bfgp/elw017] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
DNA methylation is an essential epigenetic modification for mammalian development and is crucial for the establishment and maintenance of cellular identity. Traditionally, DNA methylation has been considered as a permanent repressive epigenetic mark. However, the application of genome-wide approaches has allowed the analysis of DNA methylation in different genomic contexts, revealing a more dynamic regulation than originally thought, as active DNA methylation and demethylation occur during cell fate commitment and terminal differentiation. Recent data provide insights into the contribution of different epigenetic factors, and DNA methylation in particular, to the establishment of cellular memory during embryonic development and the modulation of cell type-specific gene regulation programs to ensure proper differentiation. This review summarizes published data regarding DNA methylation changes along lineage specification and differentiation programs. We also discuss the current knowledge about DNA methylation alterations occurring in physiological and pathological conditions such as aging and cancer.
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221
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Klutstein M, Nejman D, Greenfield R, Cedar H. DNA Methylation in Cancer and Aging. Cancer Res 2016; 76:3446-50. [PMID: 27256564 DOI: 10.1158/0008-5472.can-15-3278] [Citation(s) in RCA: 540] [Impact Index Per Article: 67.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 03/14/2016] [Indexed: 12/26/2022]
Abstract
DNA methylation is known to be abnormal in all forms of cancer, but it is not really understood how this occurs and what is its role in tumorigenesis. In this review, we take a wide view of this problem by analyzing the strategies involved in setting up normal DNA methylation patterns and understanding how this stable epigenetic mark works to prevent gene activation during development. Aberrant DNA methylation in cancer can be generated either prior to or following cell transformation through mutations. Increasing evidence suggests, however, that most methylation changes are generated in a programmed manner and occur in a subpopulation of tissue cells during normal aging, probably predisposing them for tumorigenesis. It is likely that this methylation contributes to the tumor state by inhibiting the plasticity of cell differentiation processes. Cancer Res; 76(12); 3446-50. ©2016 AACR.
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Affiliation(s)
- Michael Klutstein
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hebrew University Medical School, Jerusalem, Israel
| | - Deborah Nejman
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hebrew University Medical School, Jerusalem, Israel
| | - Razi Greenfield
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hebrew University Medical School, Jerusalem, Israel
| | - Howard Cedar
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hebrew University Medical School, Jerusalem, Israel.
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222
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Abstract
PURPOSE OF REVIEW The interplay between lipids and epigenetic mechanisms has recently gained increased interest because of its relevance for common diseases and most notably atherosclerosis. This review discusses recent advances in unravelling this interplay with a particular focus on promising approaches and methods that will be able to establish causal relationships. RECENT FINDINGS Complementary approaches uncovered close links between circulating lipids and epigenetic mechanisms at multiple levels. A characterization of lipid-associated genetic variants suggests that these variants exert their influence on lipid levels through epigenetic changes in the liver. Moreover, exposure of monocytes to lipids persistently alters their epigenetic makeup resulting in more proinflammatory cells. Hence, epigenetic changes can both impact on and be induced by lipids. SUMMARY It is the combined application of technological advances to probe epigenetic modifications at a genome-wide scale and methodological advances aimed at causal inference (including Mendelian randomization and integrative genomics) that will elucidate the interplay between circulating lipids and epigenetics. Understanding its role in the development of atherosclerosis holds the promise of identifying a new category of therapeutic targets, since epigenetic changes are amenable to reversal.
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Affiliation(s)
- Koen F Dekkers
- aMolecular Epidemiology section bDepartment of Cardiology, Leiden University Medical Center, Leiden, The Netherlands
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223
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Tissue-specific DNA demethylation is required for proper B-cell differentiation and function. Proc Natl Acad Sci U S A 2016; 113:5018-23. [PMID: 27091986 DOI: 10.1073/pnas.1604365113] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
There is ample evidence that somatic cell differentiation during development is accompanied by extensive DNA demethylation of specific sites that vary between cell types. Although the mechanism of this process has not yet been elucidated, it is likely to involve the conversion of 5mC to 5hmC by Tet enzymes. We show that a Tet2/Tet3 conditional knockout at early stages of B-cell development largely prevents lineage-specific programmed demethylation events. This lack of demethylation affects the expression of nearby B-cell lineage genes by impairing enhancer activity, thus causing defects in B-cell differentiation and function. Thus, tissue-specific DNA demethylation appears to be necessary for proper somatic cell development in vivo.
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224
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Mazor T, Pankov A, Song JS, Costello JF. Intratumoral Heterogeneity of the Epigenome. Cancer Cell 2016; 29:440-451. [PMID: 27070699 PMCID: PMC4852161 DOI: 10.1016/j.ccell.2016.03.009] [Citation(s) in RCA: 143] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Revised: 03/11/2016] [Accepted: 03/14/2016] [Indexed: 02/06/2023]
Abstract
Investigation into intratumoral heterogeneity (ITH) of the epigenome is in a formative stage. The patterns of tumor evolution inferred from epigenetic ITH and genetic ITH are remarkably similar, suggesting widespread co-dependency of these disparate mechanisms. The biological and clinical relevance of epigenetic ITH are becoming more apparent. Rare tumor cells with unique and reversible epigenetic states may drive drug resistance, and the degree of epigenetic ITH at diagnosis may predict patient outcome. This perspective presents these current concepts and clinical implications of epigenetic ITH, and the experimental and computational techniques at the forefront of ITH exploration.
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Affiliation(s)
- Tali Mazor
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA 94158, USA
| | - Aleksandr Pankov
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA 94158, USA
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA 94158, USA
| | - Jun S. Song
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA 94158, USA
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Champaign, IL 61801, USA
- Department of Physics, University of Illinois at Urbana-Champaign, Champaign, IL 61801, USA
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Champaign, IL 61801, USA
| | - Joseph F. Costello
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA 94158, USA
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225
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Rodríguez-Cortez VC, Del Pino-Molina L, Rodríguez-Ubreva J, López-Granados E, Ballestar E. Dissecting Epigenetic Dysregulation of Primary Antibody Deficiencies. J Clin Immunol 2016; 36 Suppl 1:48-56. [PMID: 26984849 DOI: 10.1007/s10875-016-0267-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 03/07/2016] [Indexed: 01/04/2023]
Abstract
Primary antibody deficiencies (PADs), the most prevalent inherited primary immunodeficiencies (PIDs), are associated with a wide range of genetic alterations (both monogenic or polygenic) in B cell-specific genes. However, correlations between the genotype and clinical manifestations are not evident in all cases indicating that genetic interactions, environmental and epigenetic factors may have a role in PAD pathogenesis. The recent identification of key defects in DNA methylation in common variable immunodeficiency as well as the multiple evidences on the role of epigenetic control during B cell differentiation, activation and during antibody formation highlight the importance of investing research efforts in dissecting the participation of epigenetic defects in this group of diseases. This review focuses on the role of epigenetic control in B cell biology which can provide clues for the study of potential novel pathogenic defects involved in PADs.
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Affiliation(s)
- Virginia C Rodríguez-Cortez
- Chromatin and Disease Group, Cancer Epigenetics and Biology Programme (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), 08908 L'Hospitalet de Llobregat, Barcelona, Spain
| | - Lucia Del Pino-Molina
- Clinical Immunology Department, University Hospital La Paz, Paseo de la Castellana 261, 28046, Madrid, Spain
- Physiopathology of Lymphocytes in Immunodeficiencies Group, IdiPAZ Institute for Health Research, Paseo de la Castellana 261, 28046, Madrid, Spain
| | - 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
| | - Eduardo López-Granados
- Clinical Immunology Department, University Hospital La Paz, Paseo de la Castellana 261, 28046, Madrid, Spain
- Physiopathology of Lymphocytes in Immunodeficiencies Group, IdiPAZ Institute for Health Research, Paseo de la Castellana 261, 28046, Madrid, Spain
| | - Esteban Ballestar
- Chromatin and Disease Group, Cancer Epigenetics and Biology Programme (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), 08908 L'Hospitalet de Llobregat, Barcelona, Spain.
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226
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Muñoz-López Á, van Roon EHJ, Romero-Moya D, López-Millan B, Stam RW, Colomer D, Nakanishi M, Bueno C, Menendez P. Cellular Ontogeny and Hierarchy Influence the Reprogramming Efficiency of Human B Cells into Induced Pluripotent Stem Cells. Stem Cells 2016; 34:581-7. [PMID: 26850912 DOI: 10.1002/stem.2303] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Revised: 12/28/2015] [Accepted: 01/08/2016] [Indexed: 01/21/2023]
Abstract
Although B cells have been shown to be refractory to reprogramming into pluripotency, induced pluripotent stem cells (iPSCs) have been very recently generated, at very low efficiency, from human cord blood (CB)- and peripheral blood (PB)-derived CD19+CD20 + B cells using nonintegrative tetracistronic OSKM-expressing Sendai Virus (SeV). Here, we addressed whether cell ontogeny and hierarchy influence the reprogramming efficiency of the B-cell compartment. We demonstrate that human fetal liver (FL)-derived CD19 + B cells are 110-fold easier to reprogram into iPSCs than those from CB/PB. Similarly, FL-derived CD34+CD19 + B progenitors are reprogrammed much easier than mature B cells (0.46% vs. 0.11%). All FL B-cell iPSCs carry complete VDJH rearrangements while 55% and 45% of the FL B-progenitor iPSCs carry incomplete and complete VDJH rearrangements, respectively, reflecting the reprogramming of developmentally different B progenitors (pro-B vs. pre-B) within a continuous differentiation process. Finally, our data suggest that successful B-cell reprogramming relies on active cell proliferation, and it is MYC-dependent as identical nonintegrative polycistronic SeV lacking MYC (OSKL or OSKLN) fail to reprogram B cells. The ability to efficiently reprogram human fetal primary B cells and B precursors offers an unprecedented opportunity for studying developmental B-lymphopoiesis and modeling B-cell malignances.
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Affiliation(s)
- Álvaro Muñoz-López
- Josep Carreras Leukemia Research Institute (IJC) and School of Medicine, Department of Biomedicine, University of Barcelona, Barcelona, Spain
| | - Eddy H J van Roon
- Department of Pediatric Oncology/Hematology, Erasmus MC-Sophia Children's Hospital, Rotterdam, The Netherlands
| | - Damià Romero-Moya
- Josep Carreras Leukemia Research Institute (IJC) and School of Medicine, Department of Biomedicine, University of Barcelona, Barcelona, Spain
| | - Belén López-Millan
- Josep Carreras Leukemia Research Institute (IJC) and School of Medicine, Department of Biomedicine, University of Barcelona, Barcelona, Spain
| | - Ronald W Stam
- Department of Pediatric Oncology/Hematology, Erasmus MC-Sophia Children's Hospital, Rotterdam, The Netherlands
| | - Dolors Colomer
- Hematopathology Unit, Department of Anatomic Pathology, Hospital Clinic, IDIBAPS, Barcelona, Spain
| | - Mahito Nakanishi
- Research Center for Stem Cell Engineering and National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraka, Japan
| | - Clara Bueno
- Josep Carreras Leukemia Research Institute (IJC) and School of Medicine, Department of Biomedicine, University of Barcelona, Barcelona, Spain
| | - Pablo Menendez
- Josep Carreras Leukemia Research Institute (IJC) and School of Medicine, Department of Biomedicine, University of Barcelona, Barcelona, Spain.,Instituciò Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
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227
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Aran D, Abu-Remaileh M, Levy R, Meron N, Toperoff G, Edrei Y, Bergman Y, Hellman A. Embryonic Stem Cell (ES)-Specific Enhancers Specify the Expression Potential of ES Genes in Cancer. PLoS Genet 2016; 12:e1005840. [PMID: 26886256 PMCID: PMC4757527 DOI: 10.1371/journal.pgen.1005840] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Accepted: 01/12/2016] [Indexed: 11/18/2022] Open
Abstract
Cancers often display gene expression profiles resembling those of undifferentiated cells. The mechanisms controlling these expression programs have yet to be identified. Exploring transcriptional enhancers throughout hematopoietic cell development and derived cancers, we uncovered a novel class of regulatory epigenetic mutations. These epimutations are particularly enriched in a group of enhancers, designated ES-specific enhancers (ESSEs) of the hematopoietic cell lineage. We found that hematopoietic ESSEs are prone to DNA methylation changes, indicative of their chromatin activity states. Strikingly, ESSE methylation is associated with gene transcriptional activity in cancer. Methylated ESSEs are hypermethylated in cancer relative to normal somatic cells and co-localized with silenced genes, whereas unmethylated ESSEs tend to be hypomethylated in cancer and associated with reactivated genes. Constitutive or hematopoietic stem cell-specific enhancers do not show these trends, suggesting selective reactivation of ESSEs in cancer. Further analyses of a hypomethylated ESSE downstream to the VEGFA gene revealed a novel regulatory circuit affecting VEGFA transcript levels across cancers and patients. We suggest that the discovered enhancer sites provide a framework for reactivation of ES genes in cancer.
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Affiliation(s)
- Dvir Aran
- Developmental Biology and Cancer Research, The Institute for Medical Research Israel-Canada (IMRIC), The Hebrew University-Hadassah Medical School, Jerusalem, Israel
- Institute for Computational Health Sciences, University of California, San Francisco, California, United States of America
| | - Monther Abu-Remaileh
- Developmental Biology and Cancer Research, The Institute for Medical Research Israel-Canada (IMRIC), The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Revital Levy
- Developmental Biology and Cancer Research, The Institute for Medical Research Israel-Canada (IMRIC), The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Nurit Meron
- Developmental Biology and Cancer Research, The Institute for Medical Research Israel-Canada (IMRIC), The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Gidon Toperoff
- Developmental Biology and Cancer Research, The Institute for Medical Research Israel-Canada (IMRIC), The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Yifat Edrei
- Developmental Biology and Cancer Research, The Institute for Medical Research Israel-Canada (IMRIC), The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Yehudit Bergman
- Developmental Biology and Cancer Research, The Institute for Medical Research Israel-Canada (IMRIC), The Hebrew University-Hadassah Medical School, Jerusalem, Israel
- * E-mail: (YB); (AH)
| | - Asaf Hellman
- Developmental Biology and Cancer Research, The Institute for Medical Research Israel-Canada (IMRIC), The Hebrew University-Hadassah Medical School, Jerusalem, Israel
- * E-mail: (YB); (AH)
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228
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Abstract
Aberrant DNA methylation is a characteristic feature of cancer including blood malignancies. Mutations in the DNA methylation regulators DNMT3A, TET1/2 and IDH1/2 are recurrent in leukemia and lymphoma. Specific and distinct DNA methylation patterns characterize subtypes of AML and lymphoma. Regulatory regions such as promoter CpG islands, CpG shores and enhancers show changes in methylation during transformation. However, the reported poor correlation between changes in methylation and gene expression in many mouse models and human studies reflects the complexity in the precise molecular mechanism for why aberrant DNA methylation promotes malignancies. This review will summarize current concepts regarding the mechanisms behind aberrant DNA methylation in hematopoietic malignancy and discuss its importance in cancer prognosis, tumor heterogeneity and relapse.
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Affiliation(s)
- Maria Guillamot
- Howard Hughes Medical Institute and Department of Pathology, NYU School of Medicine, New York, NY, 10016, USA; Laura and Isaac Perlmutter Cancer Center and Helen L. and Martin S. Kimmel Center for Stem Cell Biology, NYU School of Medicine, New York, NY, 10016, USA
| | - Luisa Cimmino
- Howard Hughes Medical Institute and Department of Pathology, NYU School of Medicine, New York, NY, 10016, USA; Laura and Isaac Perlmutter Cancer Center and Helen L. and Martin S. Kimmel Center for Stem Cell Biology, NYU School of Medicine, New York, NY, 10016, USA
| | - Iannis Aifantis
- Howard Hughes Medical Institute and Department of Pathology, NYU School of Medicine, New York, NY, 10016, USA; Laura and Isaac Perlmutter Cancer Center and Helen L. and Martin S. Kimmel Center for Stem Cell Biology, NYU School of Medicine, New York, NY, 10016, USA
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229
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DNA methylation dynamics during B cell maturation underlie a continuum of disease phenotypes in chronic lymphocytic leukemia. Nat Genet 2016; 48:253-64. [PMID: 26780610 DOI: 10.1038/ng.3488] [Citation(s) in RCA: 212] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Accepted: 12/17/2015] [Indexed: 12/14/2022]
Abstract
Charting differences between tumors and normal tissue is a mainstay of cancer research. However, clonal tumor expansion from complex normal tissue architectures potentially obscures cancer-specific events, including divergent epigenetic patterns. Using whole-genome bisulfite sequencing of normal B cell subsets, we observed broad epigenetic programming of selective transcription factor binding sites coincident with the degree of B cell maturation. By comparing normal B cells to malignant B cells from 268 patients with chronic lymphocytic leukemia (CLL), we showed that tumors derive largely from a continuum of maturation states reflected in normal developmental stages. Epigenetic maturation in CLL was associated with an indolent gene expression pattern and increasingly favorable clinical outcomes. We further uncovered that most previously reported tumor-specific methylation events are normally present in non-malignant B cells. Instead, we identified a potential pathogenic role for transcription factor dysregulation in CLL, where excess programming by EGR and NFAT with reduced EBF and AP-1 programming imbalances the normal B cell epigenetic program.
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230
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Cell-Cycle-Dependent Reconfiguration of the DNA Methylome during Terminal Differentiation of Human B Cells into Plasma Cells. Cell Rep 2015; 13:1059-71. [DOI: 10.1016/j.celrep.2015.09.051] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Revised: 07/06/2015] [Accepted: 09/17/2015] [Indexed: 01/22/2023] Open
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231
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Kretzmer H, Bernhart SH, Wang W, Haake A, Weniger MA, Bergmann AK, Betts MJ, Carrillo-de-Santa-Pau E, Doose G, Gutwein J, Richter J, Hovestadt V, Huang B, Rico D, Jühling F, Kolarova J, Lu Q, Otto C, Wagener R, Arnolds J, Burkhardt B, Claviez A, Drexler HG, Eberth S, Eils R, Flicek P, Haas S, Humme M, Karsch D, Kerstens HH, Klapper W, Kreuz M, Lawerenz C, Lenzek D, Loeffler M, López C, MacLeod RA, Martens JH, Kulis M, Martín-Subero JI, Möller P, Nage I, Picelli S, Vater I, Rohde M, Rosenstiel P, Rosolowski M, Russell RB, Schilhabel M, Schlesner M, Stadler PF, Szczepanowski M, Trümper L, Stunnenberg HG, Küppers R, Ammerpohl O, Lichter P, Siebert R, Hoffmann S, Radlwimmer B. DNA methylome analysis in Burkitt and follicular lymphomas identifies differentially methylated regions linked to somatic mutation and transcriptional control. Nat Genet 2015; 47:1316-1325. [PMID: 26437030 PMCID: PMC5444523 DOI: 10.1038/ng.3413] [Citation(s) in RCA: 101] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Accepted: 09/08/2015] [Indexed: 12/14/2022]
Abstract
Although Burkitt lymphomas and follicular lymphomas both have features of germinal center B cells, they are biologically and clinically quite distinct. Here we performed whole-genome bisulfite, genome and transcriptome sequencing in 13 IG-MYC translocation-positive Burkitt lymphoma, nine BCL2 translocation-positive follicular lymphoma and four normal germinal center B cell samples. Comparison of Burkitt and follicular lymphoma samples showed differential methylation of intragenic regions that strongly correlated with expression of associated genes, for example, genes active in germinal center dark-zone and light-zone B cells. Integrative pathway analyses of regions differentially methylated in Burkitt and follicular lymphomas implicated DNA methylation as cooperating with somatic mutation of sphingosine phosphate signaling, as well as the TCF3-ID3 and SWI/SNF complexes, in a large fraction of Burkitt lymphomas. Taken together, our results demonstrate a tight connection between somatic mutation, DNA methylation and transcriptional control in key B cell pathways deregulated differentially in Burkitt lymphoma and other germinal center B cell lymphomas.
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Affiliation(s)
- Helene Kretzmer
- Transcriptome Bioinformatics, LIFE Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany
- Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany
- Bioinformatics Group, Department of Computer Science, University of Leipzig, Leipzig, Germany
- German ICGC MMML-Seq-project
| | - Stephan H. Bernhart
- Transcriptome Bioinformatics, LIFE Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany
- Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany
- Bioinformatics Group, Department of Computer Science, University of Leipzig, Leipzig, Germany
- German ICGC MMML-Seq-project
| | - Wei Wang
- German Cancer Research Center (DKFZ), Division Molecular Genetics, Heidelberg, Germany
| | - Andrea Haake
- German ICGC MMML-Seq-project
- Institute of Human Genetics, Christian-Albrechts-University, Kiel, Germany
| | - Marc A. Weniger
- German ICGC MMML-Seq-project
- Institute of Cell Biology (Cancer Research), University of Duisburg-Essen, Essen, Germany
| | - Anke K. Bergmann
- Institute of Human Genetics, Christian-Albrechts-University, Kiel, Germany
- Department of Pediatrics, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
- BLUEPRINT project
| | - Matthew J. Betts
- Cell Networks, Bioquant, University of Heidelberg, Heidelberg, Germany
| | - Enrique Carrillo-de-Santa-Pau
- BLUEPRINT project
- Structural Biology and BioComputing Programme, Spanish National Cancer Research Center (CNIO), Madrid, Spain
| | - Gero Doose
- Transcriptome Bioinformatics, LIFE Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany
- Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany
- Bioinformatics Group, Department of Computer Science, University of Leipzig, Leipzig, Germany
- German ICGC MMML-Seq-project
| | - Jana Gutwein
- Institute of Human Genetics, Christian-Albrechts-University, Kiel, Germany
| | - Julia Richter
- German ICGC MMML-Seq-project
- Institute of Human Genetics, Christian-Albrechts-University, Kiel, Germany
| | - Volker Hovestadt
- German Cancer Research Center (DKFZ), Division Molecular Genetics, Heidelberg, Germany
| | - Bingding Huang
- Deutsches Krebsforschungszentrum Heidelberg (DKFZ), Division Theoretical Bioinformatics, Heidelberg, Germany
| | - Daniel Rico
- BLUEPRINT project
- Structural Biology and BioComputing Programme, Spanish National Cancer Research Center (CNIO), Madrid, Spain
| | - Frank Jühling
- Transcriptome Bioinformatics, LIFE Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany
- Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany
- Bioinformatics Group, Department of Computer Science, University of Leipzig, Leipzig, Germany
| | - Julia Kolarova
- Institute of Human Genetics, Christian-Albrechts-University, Kiel, Germany
| | - Qianhao Lu
- Cell Networks, Bioquant, University of Heidelberg, Heidelberg, Germany
| | - Christian Otto
- Transcriptome Bioinformatics, LIFE Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany
- Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany
- Bioinformatics Group, Department of Computer Science, University of Leipzig, Leipzig, Germany
| | - Rabea Wagener
- German ICGC MMML-Seq-project
- Institute of Human Genetics, Christian-Albrechts-University, Kiel, Germany
| | - Judith Arnolds
- Department of Otorhinolaryngology, University of Duisburg-Essen, Essen, Germany
| | - Birgit Burkhardt
- German ICGC MMML-Seq-project
- University Hospital Muenster - Pediatric Hematology and Oncology, Münster Germany
| | - Alexander Claviez
- German ICGC MMML-Seq-project
- Department of Pediatrics, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Hans G. Drexler
- Leibniz-Institut DSMZ, German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Sonja Eberth
- German ICGC MMML-Seq-project
- Leibniz-Institut DSMZ, German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
- Department of Hematology and Oncology, Georg-Augusts-University of Göttingen, Göttingen, Germany
| | - Roland Eils
- German ICGC MMML-Seq-project
- Deutsches Krebsforschungszentrum Heidelberg (DKFZ), Division Theoretical Bioinformatics, Heidelberg, Germany
- Institute of Pharmacy and Molecular Biotechnology, Bioquant, University of Heidelberg, Heidelberg, Germany
| | - Paul Flicek
- BLUEPRINT project
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Siegfried Haas
- German ICGC MMML-Seq-project
- Friedrich-Ebert Hospital Neumuenster, Clinics for Haematology, Oncology and Nephrology, Neumünster, Germany
| | - Michael Humme
- German ICGC MMML-Seq-project
- Institute of Pathology, Charité – University Medicine Berlin, Berlin, Germany
| | - Dennis Karsch
- German ICGC MMML-Seq-project
- Department of Internal Medicine II: Hematology and Oncology, University Medical Centre, Campus Kiel, Kiel, Germany
| | - Hinrik H.D. Kerstens
- BLUEPRINT project
- Radboud University, Department of Molecular Biology, Faculty of Science, Nijmegen, Netherlands
| | - Wolfram Klapper
- German ICGC MMML-Seq-project
- Hematopathology Section, Christian-Albrechts-University, Kiel, Germany
| | - Markus Kreuz
- German ICGC MMML-Seq-project
- BLUEPRINT project
- Institute for Medical Informatics Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
| | - Chris Lawerenz
- German ICGC MMML-Seq-project
- Deutsches Krebsforschungszentrum Heidelberg (DKFZ), Division Theoretical Bioinformatics, Heidelberg, Germany
| | - Dido Lenzek
- German ICGC MMML-Seq-project
- Institute of Pathology, Charité – University Medicine Berlin, Berlin, Germany
| | - Markus Loeffler
- German ICGC MMML-Seq-project
- BLUEPRINT project
- Institute for Medical Informatics Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
| | - Cristina López
- German ICGC MMML-Seq-project
- Institute of Human Genetics, Christian-Albrechts-University, Kiel, Germany
| | - Roderick A.F. MacLeod
- Leibniz-Institut DSMZ, German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Joost H.A. Martens
- BLUEPRINT project
- Radboud University, Department of Molecular Biology, Faculty of Science, Nijmegen, Netherlands
| | - Marta Kulis
- BLUEPRINT project
- Radboud University, Department of Molecular Biology, Faculty of Science, Nijmegen, Netherlands
| | - José Ignacio Martín-Subero
- BLUEPRINT project
- Departamento de Anatomía Patológica, Farmacología y Microbiología, Universitat de Barcelona, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Peter Möller
- German ICGC MMML-Seq-project
- Institute of Pathology, Medical Faculty of the Ulm University, Ulm, Germany
| | - Inga Nage
- German ICGC MMML-Seq-project
- Institute of Human Genetics, Christian-Albrechts-University, Kiel, Germany
| | - Simone Picelli
- German Cancer Research Center (DKFZ), Division Molecular Genetics, Heidelberg, Germany
| | - Inga Vater
- German ICGC MMML-Seq-project
- Institute of Human Genetics, Christian-Albrechts-University, Kiel, Germany
| | - Marius Rohde
- German ICGC MMML-Seq-project
- University Hospital Giessen, Pediatric Hematology and Oncology, Giessen, Germany
| | - Philip Rosenstiel
- German ICGC MMML-Seq-project
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, Kiel, Germany
| | - Maciej Rosolowski
- German ICGC MMML-Seq-project
- Institute for Medical Informatics Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
| | - Robert B. Russell
- Cell Networks, Bioquant, University of Heidelberg, Heidelberg, Germany
| | - Markus Schilhabel
- German ICGC MMML-Seq-project
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, Kiel, Germany
| | - Matthias Schlesner
- German ICGC MMML-Seq-project
- Deutsches Krebsforschungszentrum Heidelberg (DKFZ), Division Theoretical Bioinformatics, Heidelberg, Germany
| | - Peter F. Stadler
- Transcriptome Bioinformatics, LIFE Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany
- Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany
- Bioinformatics Group, Department of Computer Science, University of Leipzig, Leipzig, Germany
- German ICGC MMML-Seq-project
- RNomics Group, Fraunhofer Institute for Cell Therapy and Immunology IZI, Leipzig, Germany
- Santa Fe Institute, Santa Fe, New Mexico, United States of America
- Max-Planck-Institute for Mathematics in Sciences, Leipzig, Germany
| | | | - Lorenz Trümper
- German ICGC MMML-Seq-project
- Department of Hematology and Oncology, Georg-Augusts-University of Göttingen, Göttingen, Germany
| | - Hendrik G. Stunnenberg
- BLUEPRINT project
- Radboud University, Department of Molecular Biology, Faculty of Science, Nijmegen, Netherlands
| | - Ralf Küppers
- German ICGC MMML-Seq-project
- Institute of Cell Biology (Cancer Research), University of Duisburg-Essen, Essen, Germany
- BLUEPRINT project
| | - Ole Ammerpohl
- German ICGC MMML-Seq-project
- Institute of Human Genetics, Christian-Albrechts-University, Kiel, Germany
| | - Peter Lichter
- German ICGC MMML-Seq-project
- German Cancer Research Center (DKFZ), Division Molecular Genetics, Heidelberg, Germany
| | - Reiner Siebert
- German ICGC MMML-Seq-project
- Institute of Human Genetics, Christian-Albrechts-University, Kiel, Germany
- BLUEPRINT project
| | - Steve Hoffmann
- Transcriptome Bioinformatics, LIFE Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany
- Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany
- Bioinformatics Group, Department of Computer Science, University of Leipzig, Leipzig, Germany
- German ICGC MMML-Seq-project
- BLUEPRINT project
| | - Bernhard Radlwimmer
- German ICGC MMML-Seq-project
- German Cancer Research Center (DKFZ), Division Molecular Genetics, Heidelberg, Germany
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232
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McGinn S, Bauer D, Brefort T, Dong L, El-Sagheer A, Elsharawy A, Evans G, Falk-Sörqvist E, Forster M, Fredriksson S, Freeman P, Freitag C, Fritzsche J, Gibson S, Gullberg M, Gut M, Heath S, Heath-Brun I, Heron AJ, Hohlbein J, Ke R, Lancaster O, Le Reste L, Maglia G, Marie R, Mauger F, Mertes F, Mignardi M, Moens L, Oostmeijer J, Out R, Pedersen JN, Persson F, Picaud V, Rotem D, Schracke N, Sengenes J, Stähler PF, Stade B, Stoddart D, Teng X, Veal CD, Zahra N, Bayley H, Beier M, Brown T, Dekker C, Ekström B, Flyvbjerg H, Franke A, Guenther S, Kapanidis AN, Kaye J, Kristensen A, Lehrach H, Mangion J, Sauer S, Schyns E, Tost J, van Helvoort JMLM, van der Zaag PJ, Tegenfeldt JO, Brookes AJ, Mir K, Nilsson M, Willcocks JP, Gut IG. New technologies for DNA analysis--a review of the READNA Project. N Biotechnol 2015; 33:311-30. [PMID: 26514324 DOI: 10.1016/j.nbt.2015.10.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 10/17/2015] [Indexed: 01/09/2023]
Abstract
The REvolutionary Approaches and Devices for Nucleic Acid analysis (READNA) project received funding from the European Commission for 41/2 years. The objectives of the project revolved around technological developments in nucleic acid analysis. The project partners have discovered, created and developed a huge body of insights into nucleic acid analysis, ranging from improvements and implementation of current technologies to the most promising sequencing technologies that constitute a 3(rd) and 4(th) generation of sequencing methods with nanopores and in situ sequencing, respectively.
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Affiliation(s)
- Steven McGinn
- CEA - Centre National de Génotypage, 2, rue Gaston Cremieux, 91057 Evry Cedex, France
| | - David Bauer
- The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Thomas Brefort
- Comprehensive Biomarker Center GmbH, Im Neuenheimer Feld 583, D-69120 Heidelberg, Germany
| | - Liqin Dong
- The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Afaf El-Sagheer
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, UK; Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Rd, Oxford OX1 3TA, UK; Chemistry Branch, Department of Science and Mathematics, Faculty of Petroleum and Mining Engineering, Suez University, Suez 43721, Egypt
| | - Abdou Elsharawy
- Institute of Clinical Molecular Biology, Christian-Albrechts-University (CAU), Am Botanischen Garten 11, D-24118 Kiel, Germany; Faculty of Sciences, Division of Biochemistry, Chemistry Department, Damietta University, New Damietta City, Egypt
| | - Geraint Evans
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, Parks Road, Oxford OX1 3PU, UK
| | - Elin Falk-Sörqvist
- Department of Immunology, Genetics, and Pathology, Science for Life Laboratory, Uppsala University, Sweden
| | - Michael Forster
- Institute of Clinical Molecular Biology, Christian-Albrechts-University (CAU), Am Botanischen Garten 11, D-24118 Kiel, Germany
| | | | - Peter Freeman
- University of Leicester, University Road, Leicester LE1 7RH, UK
| | - Camilla Freitag
- Department of Physics, University of Gothenburg, SE-412 96 Gothenburg, Sweden
| | - Joachim Fritzsche
- Department of Applied Physics, Chalmers University of Technology, Kemivägen 10, 412 96 Göteborg, Sweden
| | - Spencer Gibson
- University of Leicester, University Road, Leicester LE1 7RH, UK
| | - Mats Gullberg
- Olink AB, Dag Hammarskjölds väg 52A, 752 37 Uppsala, Sweden
| | - Marta Gut
- Centro Nacional de Análisis Genómico (CNAG-CRG), Center for Genomic Regulation, C/Baldiri Reixac 7, 08028 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Simon Heath
- Centro Nacional de Análisis Genómico (CNAG-CRG), Center for Genomic Regulation, C/Baldiri Reixac 7, 08028 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Isabelle Heath-Brun
- Centro Nacional de Análisis Genómico (CNAG-CRG), Center for Genomic Regulation, C/Baldiri Reixac 7, 08028 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Andrew J Heron
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, England, UK
| | - Johannes Hohlbein
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, Parks Road, Oxford OX1 3PU, UK
| | - Rongqin Ke
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Box 1031, Se-171 21 Solna, Sweden; Department of Immunology, Genetics, and Pathology, Science for Life Laboratory, Uppsala University, Sweden
| | - Owen Lancaster
- University of Leicester, University Road, Leicester LE1 7RH, UK
| | - Ludovic Le Reste
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, Parks Road, Oxford OX1 3PU, UK
| | - Giovanni Maglia
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, England, UK
| | - Rodolphe Marie
- DTU Nanotech, Oerstedsplads Building 345 East, 2800, Kongens Lyngby, Denmark
| | - Florence Mauger
- CEA - Centre National de Génotypage, 2, rue Gaston Cremieux, 91057 Evry Cedex, France
| | - Florian Mertes
- Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195 Berlin, Germany
| | - Marco Mignardi
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Box 1031, Se-171 21 Solna, Sweden; Department of Immunology, Genetics, and Pathology, Science for Life Laboratory, Uppsala University, Sweden
| | - Lotte Moens
- Department of Immunology, Genetics, and Pathology, Science for Life Laboratory, Uppsala University, Sweden
| | | | - Ruud Out
- FlexGen BV, Galileiweg 8, 2333 BD Leiden, The Netherlands
| | | | - Fredrik Persson
- Department of Physics, University of Gothenburg, SE-412 96 Gothenburg, Sweden
| | - Vincent Picaud
- CEA-Saclay, Bât DIGITEO 565 - Pt Courrier 192, 91191 Gif-sur-Yvette Cedex, France
| | - Dvir Rotem
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, England, UK
| | - Nadine Schracke
- Comprehensive Biomarker Center GmbH, Im Neuenheimer Feld 583, D-69120 Heidelberg, Germany
| | - Jennifer Sengenes
- CEA - Centre National de Génotypage, 2, rue Gaston Cremieux, 91057 Evry Cedex, France
| | - Peer F Stähler
- Comprehensive Biomarker Center GmbH, Im Neuenheimer Feld 583, D-69120 Heidelberg, Germany
| | - Björn Stade
- Institute of Clinical Molecular Biology, Christian-Albrechts-University (CAU), Am Botanischen Garten 11, D-24118 Kiel, Germany
| | - David Stoddart
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, England, UK
| | - Xia Teng
- FlexGen BV, Galileiweg 8, 2333 BD Leiden, The Netherlands
| | - Colin D Veal
- University of Leicester, University Road, Leicester LE1 7RH, UK
| | - Nathalie Zahra
- University of Leicester, University Road, Leicester LE1 7RH, UK
| | - Hagan Bayley
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, England, UK
| | - Markus Beier
- Comprehensive Biomarker Center GmbH, Im Neuenheimer Feld 583, D-69120 Heidelberg, Germany
| | - Tom Brown
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, UK; Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Rd, Oxford OX1 3TA, UK
| | - Cees Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft, The Netherlands
| | - Björn Ekström
- Olink AB, Dag Hammarskjölds väg 52A, 752 37 Uppsala, Sweden
| | - Henrik Flyvbjerg
- DTU Nanotech, Oerstedsplads Building 345 East, 2800, Kongens Lyngby, Denmark
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University (CAU), Am Botanischen Garten 11, D-24118 Kiel, Germany
| | - Simone Guenther
- Thermo Fisher Scientific Frankfurter Straße 129B, 64293 Darmstadt, Germany
| | - Achillefs N Kapanidis
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, Parks Road, Oxford OX1 3PU, UK
| | - Jane Kaye
- HeLEX - Centre for Health, Law and Emerging Technologies, Nuffield Department of Population Health, University of Oxford, Old Road Campus, Oxford OX3 7LF, UK
| | - Anders Kristensen
- DTU Nanotech, Oerstedsplads Building 345 East, 2800, Kongens Lyngby, Denmark
| | - Hans Lehrach
- Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195 Berlin, Germany
| | - Jonathan Mangion
- Thermo Fisher Scientific Frankfurter Straße 129B, 64293 Darmstadt, Germany
| | - Sascha Sauer
- Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195 Berlin, Germany
| | - Emile Schyns
- PHOTONIS France S.A.S. Avenue Roger Roncier, 19100 Brive B.P. 520, 19106 BRIVE Cedex, France
| | - Jörg Tost
- CEA - Centre National de Génotypage, 2, rue Gaston Cremieux, 91057 Evry Cedex, France
| | | | - Pieter J van der Zaag
- Philips Research Laboratories, High Tech Campus 11, 5656 AE Eindhoven, The Netherlands
| | - Jonas O Tegenfeldt
- Division of Solid State Physics and NanoLund, Lund University, Box 118, 22100 Lund, Sweden
| | | | - Kalim Mir
- The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Mats Nilsson
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Box 1031, Se-171 21 Solna, Sweden; Department of Immunology, Genetics, and Pathology, Science for Life Laboratory, Uppsala University, Sweden
| | - James P Willcocks
- Oxford Nanopore Technologies, Edmund Cartwright House, 4 Robert Robinson Avenue, Oxford Science Park, Oxford OX4 4GA, UK
| | - Ivo G Gut
- Centro Nacional de Análisis Genómico (CNAG-CRG), Center for Genomic Regulation, C/Baldiri Reixac 7, 08028 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain.
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233
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Relton CL, Hartwig FP, Davey Smith G. From stem cells to the law courts: DNA methylation, the forensic epigenome and the possibility of a biosocial archive. Int J Epidemiol 2015; 44:1083-93. [PMID: 26424516 PMCID: PMC5279868 DOI: 10.1093/ije/dyv198] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The growth in epigenetics continues to attract considerable cross-disciplinary interest, apparently representing an opportunity to move beyond genomics towards the goal of understanding phenotypic variability from molecular through organismal to the societal level. The epigenome may also harbour useful information about life-time exposures (measured or unmeasured) irrespective of their influence on health or disease, creating the potential for a person-specific biosocial archive . Furthermore such data may prove of use in providing identifying information, providing the possibility of a future forensic epigenome . The mechanisms involved in ensuring that environmentally induced epigenetic changes perpetuate across the life course remain unclear. Here we propose a potential role of adult stem cells in maintaining epigenetic states provides a useful basis for formulating such epidemiologically-relevant concepts.
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Affiliation(s)
- Caroline L Relton
- MRC Integrative Epidemiology Unit, School of Social & Community Medicine, University of Bristol, Bristol, UK
| | | | - George Davey Smith
- MRC Integrative Epidemiology Unit, School of Social & Community Medicine, University of Bristol, Bristol, UK
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