351
|
Yang IV, Pedersen BS, Liu A, O'Connor GT, Teach SJ, Kattan M, Misiak RT, Gruchalla R, Steinbach SF, Szefler SJ, Gill MA, Calatroni A, David G, Hennessy CE, Davidson EJ, Zhang W, Gergen P, Togias A, Busse WW, Schwartz DA. DNA methylation and childhood asthma in the inner city. J Allergy Clin Immunol 2015; 136:69-80. [PMID: 25769910 DOI: 10.1016/j.jaci.2015.01.025] [Citation(s) in RCA: 156] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Revised: 01/21/2015] [Accepted: 01/23/2015] [Indexed: 01/15/2023]
Abstract
BACKGROUND Epigenetic marks are heritable, influenced by the environment, direct the maturation of T lymphocytes, and in mice enhance the development of allergic airway disease. Thus it is important to define epigenetic alterations in asthmatic populations. OBJECTIVE We hypothesize that epigenetic alterations in circulating PBMCs are associated with allergic asthma. METHODS We compared DNA methylation patterns and gene expression in inner-city children with persistent atopic asthma versus healthy control subjects by using DNA and RNA from PBMCs. Results were validated in an independent population of asthmatic patients. RESULTS Comparing asthmatic patients (n = 97) with control subjects (n = 97), we identified 81 regions that were differentially methylated. Several immune genes were hypomethylated in asthma, including IL13, RUNX3, and specific genes relevant to T lymphocytes (TIGIT). Among asthmatic patients, 11 differentially methylated regions were associated with higher serum IgE concentrations, and 16 were associated with percent predicted FEV1. Hypomethylated and hypermethylated regions were associated with increased and decreased gene expression, respectively (P < 6 × 10(-12) for asthma and P < .01 for IgE). We further explored the relationship between DNA methylation and gene expression using an integrative analysis and identified additional candidates relevant to asthma (IL4 and ST2). Methylation marks involved in T-cell maturation (RUNX3), TH2 immunity (IL4), and oxidative stress (catalase) were validated in an independent asthmatic cohort of children living in the inner city. CONCLUSIONS Our results demonstrate that DNA methylation marks in specific gene loci are associated with asthma and suggest that epigenetic changes might play a role in establishing the immune phenotype associated with asthma.
Collapse
Affiliation(s)
- Ivana V Yang
- Department of Medicine, University of Colorado, School of Medicine, Aurora, Colo; Departments of Pediatrics and Medicine, National Jewish Health, Denver, Colo
| | - Brent S Pedersen
- Department of Medicine, University of Colorado, School of Medicine, Aurora, Colo
| | - Andrew Liu
- Departments of Pediatrics and Medicine, National Jewish Health, Denver, Colo
| | - George T O'Connor
- Department of Medicine, Boston University School of Medicine, Boston, Mass
| | | | - Meyer Kattan
- Columbia University Medical Center, New York, NY
| | | | | | | | - Stanley J Szefler
- Department of Pediatrics, Children's Hospital Colorado and University of Colorado, School of Medicine, Aurora, Colo
| | - Michelle A Gill
- University of Texas, Southwestern Medical Center, Dallas, Tex
| | | | | | - Corinne E Hennessy
- Department of Medicine, University of Colorado, School of Medicine, Aurora, Colo
| | - Elizabeth J Davidson
- Department of Medicine, University of Colorado, School of Medicine, Aurora, Colo
| | - Weiming Zhang
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado, Aurora, Colo
| | - Peter Gergen
- National Institute of Allergy and Infectious Diseases, Bethesda, Md
| | - Alkis Togias
- National Institute of Allergy and Infectious Diseases, Bethesda, Md
| | - William W Busse
- Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, Wis
| | - David A Schwartz
- Department of Medicine, University of Colorado, School of Medicine, Aurora, Colo; Departments of Pediatrics and Medicine, National Jewish Health, Denver, Colo; Department of Immunology, University of Colorado, Aurora, Colo.
| |
Collapse
|
352
|
Lee ST, Muench MO, Fomin ME, Xiao J, Zhou M, de Smith A, Martín-Subero JI, Heath S, Houseman EA, Roy R, Wrensch M, Wiencke J, Metayer C, Wiemels JL. Epigenetic remodeling in B-cell acute lymphoblastic leukemia occurs in two tracks and employs embryonic stem cell-like signatures. Nucleic Acids Res 2015; 43:2590-602. [PMID: 25690899 PMCID: PMC4357708 DOI: 10.1093/nar/gkv103] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
We investigated DNA methylomes of pediatric B-cell acute lymphoblastic leukemias (B-ALLs) using whole-genome bisulfite sequencing and high-definition microarrays, along with RNA expression profiles. Epigenetic alteration of B-ALLs occurred in two tracks: de novo methylation of small functional compartments and demethylation of large inter-compartmental backbones. The deviations were exaggerated in lamina-associated domains, with differences corresponding to methylation clusters and/or cytogenetic groups. Our data also suggested a pivotal role of polycomb and CTBP2 in de novo methylation, which may be traced back to bivalency status of embryonic stem cells. Driven by these potent epigenetic modulations, suppression of polycomb target genes was observed along with disruption of developmental fate and cell cycle and mismatch repair pathways and altered activities of key upstream regulators.
Collapse
Affiliation(s)
- Seung-Tae Lee
- Department of Epidemiology and Biostatistics, University of California at San Francisco, San Francisco, CA 94158, USA Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul 120752, Republic of Korea
| | - Marcus O Muench
- Blood Systems Research Institute, University of California at San Francisco, San Francisco, CA 94158, USA Liver Center and Department of Laboratory Medicine, University of California at San Francisco, San Francisco, CA 94158, USA
| | - Marina E Fomin
- Blood Systems Research Institute, University of California at San Francisco, San Francisco, CA 94158, USA
| | - Jianqiao Xiao
- Department of Epidemiology and Biostatistics, University of California at San Francisco, San Francisco, CA 94158, USA
| | - Mi Zhou
- Department of Epidemiology and Biostatistics, University of California at San Francisco, San Francisco, CA 94158, USA
| | - Adam de Smith
- Department of Epidemiology and Biostatistics, University of California at San Francisco, San Francisco, CA 94158, USA
| | - José I Martín-Subero
- Unidad de Hematopatología, Servicio de Anatomía Patológica, Hospital Clínic, Universitat de Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona 08036, Spain
| | - Simon Heath
- Centro Nacional de Análisis Genómico, Parc Científic de Barcelona, Barcelona 08036, Spain
| | - E Andres Houseman
- Department of Public Health, Oregon State University, Corvallis, OR, 97331 USA
| | - Ritu Roy
- Cancer Research Institute, University of California at San Francisco, San Francisco, CA 94158, USA
| | - Margaret Wrensch
- Department of Neurological Surgery, University of California at San Francisco, San Francisco, CA 94158, USA
| | - John Wiencke
- Department of Neurological Surgery, University of California at San Francisco, San Francisco, CA 94158, USA
| | - Catherine Metayer
- Division of Epidemiology, School of Public Health, University of California at Berkeley, Berkeley, CA 94720, USA
| | - Joseph L Wiemels
- Department of Epidemiology and Biostatistics, University of California at San Francisco, San Francisco, CA 94158, USA Department of Neurological Surgery, University of California at San Francisco, San Francisco, CA 94158, USA
| |
Collapse
|
353
|
Wang LQ, Chim CS. DNA methylation of tumor-suppressor miRNA genes in chronic lymphocytic leukemia. Epigenomics 2015; 7:461-73. [PMID: 25650645 DOI: 10.2217/epi.15.6] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
DNA methylation is one of the most important epigenetic modifications of the genome involved in the regulation of numerous cellular processes through gene silencing without altering DNA sequences. miRNAs, a class of single-stranded noncoding RNAs of 19-25 nucleotides in length, function as post-transcriptional regulators of gene expression leading to mRNA cleavage or translational repression of their corresponding target protein-coding genes. Recently, dysregulation of tumor suppressor miRNAs mediated by promoter DNA hypermethylation is implicated in human cancers, including B-cell chronic lymphocytic leukemia (CLL). Moreover, it appears that methylated miRNA genes could be potential biomarkers for CLL diagnosis or therapy. This review will highlight the role of aberrant methylation of miRNA genes in the pathogenesis of CLL.
Collapse
Affiliation(s)
- Lu Qian Wang
- Department of Medicine, Queen Mary Hospital, The University of Hong Kong, Hong Kong
| | - Chor Sang Chim
- Department of Medicine, Queen Mary Hospital, The University of Hong Kong, Hong Kong
| |
Collapse
|
354
|
Agirre X, Castellano G, Pascual M, Heath S, Kulis M, Segura V, Bergmann A, Esteve A, Merkel A, Raineri E, Agueda L, Blanc J, Richardson D, Clarke L, Datta A, Russiñol N, Queirós AC, Beekman R, Rodríguez-Madoz JR, San José-Enériz E, Fang F, Gutiérrez NC, García-Verdugo JM, Robson MI, Schirmer EC, Guruceaga E, Martens JHA, Gut M, Calasanz MJ, Flicek P, Siebert R, Campo E, Miguel JFS, Melnick A, Stunnenberg HG, Gut IG, Prosper F, Martín-Subero JI. Whole-epigenome analysis in multiple myeloma reveals DNA hypermethylation of B cell-specific enhancers. Genome Res 2015; 25:478-87. [PMID: 25644835 PMCID: PMC4381520 DOI: 10.1101/gr.180240.114] [Citation(s) in RCA: 99] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Accepted: 01/22/2015] [Indexed: 12/20/2022]
Abstract
While analyzing the DNA methylome of multiple myeloma (MM), a plasma cell neoplasm, by whole-genome bisulfite sequencing and high-density arrays, we observed a highly heterogeneous pattern globally characterized by regional DNA hypermethylation embedded in extensive hypomethylation. In contrast to the widely reported DNA hypermethylation of promoter-associated CpG islands (CGIs) in cancer, hypermethylated sites in MM, as opposed to normal plasma cells, were located outside CpG islands and were unexpectedly associated with intronic enhancer regions defined in normal B cells and plasma cells. Both RNA-seq and in vitro reporter assays indicated that enhancer hypermethylation is globally associated with down-regulation of its host genes. ChIP-seq and DNase-seq further revealed that DNA hypermethylation in these regions is related to enhancer decommissioning. Hypermethylated enhancer regions overlapped with binding sites of B cell-specific transcription factors (TFs) and the degree of enhancer methylation inversely correlated with expression levels of these TFs in MM. Furthermore, hypermethylated regions in MM were methylated in stem cells and gradually became demethylated during normal B-cell differentiation, suggesting that MM cells either reacquire epigenetic features of undifferentiated cells or maintain an epigenetic signature of a putative myeloma stem cell progenitor. Overall, we have identified DNA hypermethylation of developmentally regulated enhancers as a new type of epigenetic modification associated with the pathogenesis of MM.
Collapse
Affiliation(s)
- Xabier Agirre
- Area de Oncología, Centro de Investigación Médica Aplicada (CIMA), Universidad de Navarra, 31008 Pamplona, Spain;
| | - Giancarlo Castellano
- Unidad de Hematopatología, Servicio de Anatomía Patológica, Hospital Clínic, Universitat de Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain
| | - Marien Pascual
- Area de Oncología, Centro de Investigación Médica Aplicada (CIMA), Universidad de Navarra, 31008 Pamplona, Spain
| | - Simon Heath
- Centro Nacional de Análisis Genómico, Parc Científic de Barcelona, 08028 Barcelona, Spain
| | - Marta Kulis
- Unidad de Hematopatología, Servicio de Anatomía Patológica, Hospital Clínic, Universitat de Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain
| | - Victor Segura
- Unidad de Bioinformática, Centro de Investigación Médica Aplicada (CIMA), Universidad de Navarra, 31008 Pamplona, Spain
| | - Anke Bergmann
- Institute of Human Genetics, Christian-Albrechts-University, 24105 Kiel, Germany
| | - Anna Esteve
- Centro Nacional de Análisis Genómico, Parc Científic de Barcelona, 08028 Barcelona, Spain
| | - Angelika Merkel
- Centro Nacional de Análisis Genómico, Parc Científic de Barcelona, 08028 Barcelona, Spain
| | - Emanuele Raineri
- Centro Nacional de Análisis Genómico, Parc Científic de Barcelona, 08028 Barcelona, Spain
| | - Lidia Agueda
- Centro Nacional de Análisis Genómico, Parc Científic de Barcelona, 08028 Barcelona, Spain
| | - Julie Blanc
- Centro Nacional de Análisis Genómico, Parc Científic de Barcelona, 08028 Barcelona, Spain
| | - David Richardson
- European Bioinformatics Institute, European Molecular Biology Laboratory, Cambridge, CB10 1SD, United Kingdom
| | - Laura Clarke
- European Bioinformatics Institute, European Molecular Biology Laboratory, Cambridge, CB10 1SD, United Kingdom
| | - Avik Datta
- European Bioinformatics Institute, European Molecular Biology Laboratory, Cambridge, CB10 1SD, United Kingdom
| | - Nuria Russiñol
- Unidad de Hematopatología, Servicio de Anatomía Patológica, Hospital Clínic, Universitat de Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain
| | - Ana C Queirós
- Unidad de Hematopatología, Servicio de Anatomía Patológica, Hospital Clínic, Universitat de Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain
| | - Renée Beekman
- Unidad de Hematopatología, Servicio de Anatomía Patológica, Hospital Clínic, Universitat de Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain
| | - Juan R Rodríguez-Madoz
- Area de Oncología, Centro de Investigación Médica Aplicada (CIMA), Universidad de Navarra, 31008 Pamplona, Spain
| | - Edurne San José-Enériz
- Area de Oncología, Centro de Investigación Médica Aplicada (CIMA), Universidad de Navarra, 31008 Pamplona, Spain
| | - Fang Fang
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medical College, New York, New York 10065, USA
| | | | - José M García-Verdugo
- Department of Cellular Morphology, University of Valencia, Unidad Mixta CIPF-UVEG, CIBERNED, 46100 Valencia, Spain
| | - Michael I Robson
- The Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, EH9 3BF, United Kingdom
| | - Eric C Schirmer
- The Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, EH9 3BF, United Kingdom
| | - Elisabeth Guruceaga
- Unidad de Bioinformática, Centro de Investigación Médica Aplicada (CIMA), Universidad de Navarra, 31008 Pamplona, Spain
| | - Joost H A Martens
- Department of Molecular Biology, Faculty of Science, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen, 6500 HB Nijmegen, The Netherlands
| | - Marta Gut
- Centro Nacional de Análisis Genómico, Parc Científic de Barcelona, 08028 Barcelona, Spain
| | - Maria J Calasanz
- Departamento de Genética, Universidad de Navarra, 31008 Pamplona, Spain
| | - Paul Flicek
- European Bioinformatics Institute, European Molecular Biology Laboratory, Cambridge, CB10 1SD, United Kingdom
| | - Reiner Siebert
- Institute of Human Genetics, Christian-Albrechts-University, 24105 Kiel, Germany
| | - Elías Campo
- Unidad de Hematopatología, Servicio de Anatomía Patológica, Hospital Clínic, Universitat de Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain
| | - Jesús F San Miguel
- Clínica Universidad de Navarra, Universidad de Navarra, 31008 Pamplona, Spain
| | - Ari Melnick
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medical College, New York, New York 10065, USA
| | - Hendrik G Stunnenberg
- Department of Molecular Biology, Faculty of Science, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen, 6500 HB Nijmegen, The Netherlands
| | - Ivo G Gut
- Centro Nacional de Análisis Genómico, Parc Científic de Barcelona, 08028 Barcelona, Spain
| | - Felipe Prosper
- Area de Oncología, Centro de Investigación Médica Aplicada (CIMA), Universidad de Navarra, 31008 Pamplona, Spain; Clínica Universidad de Navarra, Universidad de Navarra, 31008 Pamplona, Spain
| | - José I Martín-Subero
- Unidad de Hematopatología, Servicio de Anatomía Patológica, Hospital Clínic, Universitat de Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain;
| |
Collapse
|
355
|
Wong AI, Lo YD. Noninvasive fetal genomic, methylomic, and transcriptomic analyses using maternal plasma and clinical implications. Trends Mol Med 2015; 21:98-108. [DOI: 10.1016/j.molmed.2014.12.006] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Revised: 12/12/2014] [Accepted: 12/18/2014] [Indexed: 01/01/2023]
|
356
|
Rodríguez D, Bretones G, Arango JR, Valdespino V, Campo E, Quesada V, López-Otín C. Molecular pathogenesis of CLL and its evolution. Int J Hematol 2015; 101:219-28. [PMID: 25630433 DOI: 10.1007/s12185-015-1733-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2014] [Accepted: 01/14/2015] [Indexed: 12/11/2022]
Abstract
In spite of being the most prevalent adult leukemia in Western countries, the molecular mechanisms driving the establishment and progression of chronic lymphocytic leukemia (CLL) remain largely unknown. In recent years, the use of next-generation sequencing techniques has uncovered new and, in some cases, unexpected driver genes with prognostic and therapeutic value. The mutational landscape of CLL is characterized by high-genetic and epigenetic heterogeneity, low mutation recurrence and a long tail of cases with undefined driver genes. On the other hand, the use of deep sequencing has also revealed high intra-tumor heterogeneity and provided a detailed picture of clonal evolution processes. This phenomenon, in which aberrant DNA methylation can also participate, appears to be tightly associated to poor outcomes and chemo-refractoriness, thus providing a new subject for therapeutic intervention. Hence, and having in mind the limitations derived from the CLL complexity thus described, the application of massively parallel sequencing studies has unveiled a wealth of information that is expected to substantially improve patient staging schemes and CLL clinical management.
Collapse
Affiliation(s)
- David Rodríguez
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología-IUOPA, Universidad de Oviedo, 33006, Oviedo, Spain
| | | | | | | | | | | | | |
Collapse
|
357
|
Gutierrez-Arcelus M, Ongen H, Lappalainen T, Montgomery SB, Buil A, Yurovsky A, Bryois J, Padioleau I, Romano L, Planchon A, Falconnet E, Bielser D, Gagnebin M, Giger T, Borel C, Letourneau A, Makrythanasis P, Guipponi M, Gehrig C, Antonarakis SE, Dermitzakis ET. Tissue-specific effects of genetic and epigenetic variation on gene regulation and splicing. PLoS Genet 2015; 11:e1004958. [PMID: 25634236 PMCID: PMC4310612 DOI: 10.1371/journal.pgen.1004958] [Citation(s) in RCA: 140] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2013] [Accepted: 12/16/2014] [Indexed: 12/14/2022] Open
Abstract
Understanding how genetic variation affects distinct cellular phenotypes, such as gene expression levels, alternative splicing and DNA methylation levels, is essential for better understanding of complex diseases and traits. Furthermore, how inter-individual variation of DNA methylation is associated to gene expression is just starting to be studied. In this study, we use the GenCord cohort of 204 newborn Europeans’ lymphoblastoid cell lines, T-cells and fibroblasts derived from umbilical cords. The samples were previously genotyped for 2.5 million SNPs, mRNA-sequenced, and assayed for methylation levels in 482,421 CpG sites. We observe that methylation sites associated to expression levels are enriched in enhancers, gene bodies and CpG island shores. We show that while the correlation between DNA methylation and gene expression can be positive or negative, it is very consistent across cell-types. However, this epigenetic association to gene expression appears more tissue-specific than the genetic effects on gene expression or DNA methylation (observed in both sharing estimations based on P-values and effect size correlations between cell-types). This predominance of genetic effects can also be reflected by the observation that allele specific expression differences between individuals dominate over tissue-specific effects. Additionally, we discover genetic effects on alternative splicing and interestingly, a large amount of DNA methylation correlating to alternative splicing, both in a tissue-specific manner. The locations of the SNPs and methylation sites involved in these associations highlight the participation of promoter proximal and distant regulatory regions on alternative splicing. Overall, our results provide high-resolution analyses showing how genome sequence variation has a broad effect on cellular phenotypes across cell-types, whereas epigenetic factors provide a secondary layer of variation that is more tissue-specific. Furthermore, the details of how this tissue-specificity may vary across inter-relations of molecular traits, and where these are occurring, can yield further insights into gene regulation and cellular biology as a whole. In order to better understand how genetic differences between individuals can cause diseases, it is crucial to understand how genetic variants affect cellular functions in the different tissues that compose the human body. From the umbilical cord of 195 newborn babies, we previously obtained three different cell-types: fibroblasts, T-cells and immortalized B-cells. From every individual in each cell type we measured four features across the genome: 1) genetic differences, 2) DNA methylation, an epigenetic modification of DNA that can affect its functional state, 3) gene expression—the amount of gene activity, 4) alternative splicing—which of the different versions of a gene is manifested. We find thousands of genetic variants of the DNA sequence that affect methylation, gene expression, and splicing. We show that while these genetic effects often affect multiple cell-types, the strength of these effects varies between cell-types. Also epigenetic methylation marks of DNA associate to gene expression and particularly often to splicing. Since abnormalities in gene expression, DNA methylation and alternative splicing are associated to diseases, it is important to continue studying how these traits are inter-related and affected by genetic variation across cell-types.
Collapse
Affiliation(s)
- Maria Gutierrez-Arcelus
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
- Institute of Genetics and Genomics in Geneva (iGE3), Geneva, Switzerland
- Swiss Institute of Bioinformatics (SIB), Geneva, Switzerland
| | - Halit Ongen
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
- Institute of Genetics and Genomics in Geneva (iGE3), Geneva, Switzerland
- Swiss Institute of Bioinformatics (SIB), Geneva, Switzerland
| | - Tuuli Lappalainen
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
- Institute of Genetics and Genomics in Geneva (iGE3), Geneva, Switzerland
- Swiss Institute of Bioinformatics (SIB), Geneva, Switzerland
| | - Stephen B. Montgomery
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
- Departments of Pathology and Genetics, Stanford University, Stanford, California, United States of America
| | - Alfonso Buil
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
- Institute of Genetics and Genomics in Geneva (iGE3), Geneva, Switzerland
- Swiss Institute of Bioinformatics (SIB), Geneva, Switzerland
| | - Alisa Yurovsky
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
- Institute of Genetics and Genomics in Geneva (iGE3), Geneva, Switzerland
- Swiss Institute of Bioinformatics (SIB), Geneva, Switzerland
| | - Julien Bryois
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
- Institute of Genetics and Genomics in Geneva (iGE3), Geneva, Switzerland
- Swiss Institute of Bioinformatics (SIB), Geneva, Switzerland
| | - Ismael Padioleau
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
- Institute of Genetics and Genomics in Geneva (iGE3), Geneva, Switzerland
- Swiss Institute of Bioinformatics (SIB), Geneva, Switzerland
| | - Luciana Romano
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
- Institute of Genetics and Genomics in Geneva (iGE3), Geneva, Switzerland
- Swiss Institute of Bioinformatics (SIB), Geneva, Switzerland
| | - Alexandra Planchon
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
- Institute of Genetics and Genomics in Geneva (iGE3), Geneva, Switzerland
- Swiss Institute of Bioinformatics (SIB), Geneva, Switzerland
| | - Emilie Falconnet
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
- Institute of Genetics and Genomics in Geneva (iGE3), Geneva, Switzerland
| | - Deborah Bielser
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
- Institute of Genetics and Genomics in Geneva (iGE3), Geneva, Switzerland
| | - Maryline Gagnebin
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
- Institute of Genetics and Genomics in Geneva (iGE3), Geneva, Switzerland
| | - Thomas Giger
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Christelle Borel
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Audrey Letourneau
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
- Institute of Genetics and Genomics in Geneva (iGE3), Geneva, Switzerland
| | - Periklis Makrythanasis
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
- Institute of Genetics and Genomics in Geneva (iGE3), Geneva, Switzerland
| | - Michel Guipponi
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
- Institute of Genetics and Genomics in Geneva (iGE3), Geneva, Switzerland
| | - Corinne Gehrig
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
- Institute of Genetics and Genomics in Geneva (iGE3), Geneva, Switzerland
| | - Stylianos E. Antonarakis
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
- Institute of Genetics and Genomics in Geneva (iGE3), Geneva, Switzerland
- * E-mail: (SEA); (ETD)
| | - Emmanouil T. Dermitzakis
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
- Institute of Genetics and Genomics in Geneva (iGE3), Geneva, Switzerland
- Swiss Institute of Bioinformatics (SIB), Geneva, Switzerland
- Center of Excellence in Genomic Medicine Research, KingAbdulaziz University, Jeddah, Saudi Arabia
- * E-mail: (SEA); (ETD)
| |
Collapse
|
358
|
Ecker S, Pancaldi V, Rico D, Valencia A. Higher gene expression variability in the more aggressive subtype of chronic lymphocytic leukemia. Genome Med 2015; 7:8. [PMID: 25632304 PMCID: PMC4308895 DOI: 10.1186/s13073-014-0125-z] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Accepted: 12/18/2014] [Indexed: 12/31/2022] Open
Abstract
Background Chronic lymphocytic leukemia (CLL) presents two subtypes which have drastically different clinical outcomes, IgVH mutated (M-CLL) and IgVH unmutated (U-CLL). So far, these two subtypes are not associated to clear differences in gene expression profiles. Interestingly, recent results have highlighted important roles for heterogeneity, both at the genetic and at the epigenetic level in CLL progression. Methods We analyzed gene expression data of two large cohorts of CLL patients and quantified expression variability across individuals to investigate differences between the two subtypes using different measures and statistical tests. Functional significance was explored by pathway enrichment and network analyses. Furthermore, we implemented a random forest approach based on expression variability to classify patients into disease subtypes. Results We found that U-CLL, the more aggressive type of the disease, shows significantly increased variability of gene expression across patients and that, overall, genes that show higher variability in the aggressive subtype are related to cell cycle, development and inter-cellular communication. These functions indicate a potential relation between gene expression variability and the faster progression of this CLL subtype. Finally, a classifier based on gene expression variability was able to correctly predict the disease subtype of CLL patients. Conclusions There are strong relations between gene expression variability and disease subtype linking significantly increased expression variability to phenotypes such as aggressiveness and resistance to therapy in CLL. Electronic supplementary material The online version of this article (doi:10.1186/s13073-014-0125-z) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Simone Ecker
- Structural Biology and Biocomputing Programme, Spanish National Cancer Research Center (CNIO), 28029 Madrid, Spain
| | - Vera Pancaldi
- Structural Biology and Biocomputing Programme, Spanish National Cancer Research Center (CNIO), 28029 Madrid, Spain
| | - Daniel Rico
- Structural Biology and Biocomputing Programme, Spanish National Cancer Research Center (CNIO), 28029 Madrid, Spain
| | - Alfonso Valencia
- Structural Biology and Biocomputing Programme, Spanish National Cancer Research Center (CNIO), 28029 Madrid, Spain
| |
Collapse
|
359
|
Xu J, He G, Zhu J, Zhou X, St Clair D, Wang T, Xiang Y, Zhao Q, Xing Q, Liu Y, Wang L, Li Q, He L, Zhao X. Prenatal nutritional deficiency reprogrammed postnatal gene expression in mammal brains: implications for schizophrenia. Int J Neuropsychopharmacol 2015; 18:pyu054. [PMID: 25522397 PMCID: PMC4360220 DOI: 10.1093/ijnp/pyu054] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Epidemiological studies have identified prenatal exposure to famine as a risk factor for schizophrenia, and animal models of prenatal malnutrition display structural and functional brain abnormalities implicated in schizophrenia. METHODS The offspring of the RLP50 rat, a recently developed animal model of prenatal famine malnutrition exposure, was used to investigate the changes of gene expression and epigenetic modifications in the brain regions. Microarray gene expression analysis was carried out in the prefrontal cortex and the hippocampus from 8 RLP50 offspring rats and 8 controls. MBD-seq was used to test the changes in DNA methylation in hippocampus depending on prenatal malnutrition exposure. RESULTS In the prefrontal cortex, offspring of RLP50 exhibit differences in neurotransmitters and olfactory-associated gene expression. In the hippocampus, the differentially-expressed genes are related to synaptic function and transcription regulation. DNA methylome profiling of the hippocampus also shows widespread but systematic epigenetic changes; in most cases (87%) this involves hypermethylation. Remarkably, genes encoded for the plasma membrane are significantly enriched for changes in both gene expression and DNA methylome profiling screens (p = 2.37×10(-9) and 5.36×10(-9), respectively). Interestingly, Mecp2 and Slc2a1, two genes associated with cognitive impairment, show significant down-regulation, and Slc2a1 is hypermethylated in the hippocampus of the RLP50 offspring. CONCLUSIONS Collectively, our results indicate that prenatal exposure to malnutrition leads to the reprogramming of postnatal brain gene expression and that the epigenetic modifications contribute to the reprogramming. The process may impair learning and memory ability and result in higher susceptibility to schizophrenia.
Collapse
Affiliation(s)
- Jiawei Xu
- *These authors contributed equally to this work
| | - Guang He
- *These authors contributed equally to this work
| | | | | | | | | | | | | | | | | | | | | | - Lin He
- Children's Hospital and Institutes of Biomedical Sciences, Fudan University, Shanghai, China (Drs Xu, Zhou, T. Wang, Xiang, Xing, Liu, L. Wang, Li, L. He and X. Zhao); Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, China (Drs Xu, G. He, Zhou, T. Wang, Xiang, Q. Zhao, Xing, Liu, L.Wang, Li, L. He and X. Zhao); Center for Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Shanghai, China (Dr Xu); Cancer Epigenetics and Gene Therapy Program, Shanghai Cancer Institute, Shanghai Jiao Tong University, Shanghai, China (Dr Zhu); Department of Mental Health, University of Aberdeen, Scotland (Dr St Clair).
| | - Xinzhi Zhao
- Children's Hospital and Institutes of Biomedical Sciences, Fudan University, Shanghai, China (Drs Xu, Zhou, T. Wang, Xiang, Xing, Liu, L. Wang, Li, L. He and X. Zhao); Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, China (Drs Xu, G. He, Zhou, T. Wang, Xiang, Q. Zhao, Xing, Liu, L.Wang, Li, L. He and X. Zhao); Center for Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Shanghai, China (Dr Xu); Cancer Epigenetics and Gene Therapy Program, Shanghai Cancer Institute, Shanghai Jiao Tong University, Shanghai, China (Dr Zhu); Department of Mental Health, University of Aberdeen, Scotland (Dr St Clair).
| |
Collapse
|
360
|
Lessard S, Beaudoin M, Benkirane K, Lettre G. Comparison of DNA methylation profiles in human fetal and adult red blood cell progenitors. Genome Med 2015; 7:1. [PMID: 25606059 PMCID: PMC4298057 DOI: 10.1186/s13073-014-0122-2] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Accepted: 12/09/2014] [Indexed: 11/21/2022] Open
Abstract
Background DNA methylation is an epigenetic modification that plays an important role during mammalian development. Around birth in humans, the main site of red blood cell production moves from the fetal liver to the bone marrow. DNA methylation changes at the β-globin locus and a switch from fetal to adult hemoglobin production characterize this transition. Understanding this globin switch may improve the treatment of patients with sickle cell disease and β-thalassemia, two of the most common Mendelian diseases in the world. The goal of our study was to describe and compare the genome-wide patterns of DNA methylation in fetal and adult human erythroblasts. Methods We used the Illumina HumanMethylation 450 k BeadChip to measure DNA methylation at 402,819 CpGs in ex vivo-differentiated erythroblasts from 12 fetal liver and 12 bone marrow CD34+ donors. Results We identified 5,937 differentially methylated CpGs that overlap with erythroid enhancers and binding sites for erythropoiesis-related transcription factors. Combining this information with genome-wide association study results, we show that erythroid enhancers define particularly promising genomic regions to identify new genetic variants associated with fetal hemoglobin (HbF) levels in humans. Many differentially methylated CpGs are located near genes with unanticipated roles in red blood cell differentiation and proliferation. For some of these new candidate genes, we confirm the correlation between DNA methylation and gene expression levels in red blood cell progenitors. We also provide evidence that DNA methylation and genetic variation at the β-globin locus independently control globin gene expression in adult erythroblasts. Conclusions Our DNA methylome maps confirm the widespread dynamic changes in DNA methylation that occur during human erythropoiesis. These changes tend to happen near erythroid enhancers, further highlighting their importance in erythroid regulation and HbF production. Finally, DNA methylation may act independently of the transcription factor BCL11A to repress fetal hemoglobin production. This provides cues on strategies to more efficiently re-activate HbF production in sickle cell disease and β-thalassemia patients. Electronic supplementary material The online version of this article (doi:10.1186/s13073-014-0122-2) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Samuel Lessard
- Montreal Heart Institute, 5000 Bélanger Street, Montréal, Québec H1T 1C8 Canada ; Faculté de Médecine, Université de Montréal, 2900 Boul. Édouard-Montpetit, Montréal, Québec H3T 1J4 Canada
| | - Mélissa Beaudoin
- Montreal Heart Institute, 5000 Bélanger Street, Montréal, Québec H1T 1C8 Canada
| | - Karim Benkirane
- Hôpital Maisonneuve-Rosemont, 5415 Boul. de l'Assomption, Montréal, Québec H1T 2M4 Canada
| | - Guillaume Lettre
- Montreal Heart Institute, 5000 Bélanger Street, Montréal, Québec H1T 1C8 Canada ; Faculté de Médecine, Université de Montréal, 2900 Boul. Édouard-Montpetit, Montréal, Québec H3T 1J4 Canada
| |
Collapse
|
361
|
Shahjahani M, Mohammadiasl J, Noroozi F, Seghatoleslami M, Shahrabi S, Saba F, Saki N. Molecular basis of chronic lymphocytic leukemia diagnosis and prognosis. Cell Oncol (Dordr) 2015; 38:93-109. [PMID: 25563586 DOI: 10.1007/s13402-014-0215-3] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/23/2014] [Indexed: 12/31/2022] Open
Abstract
BACKGROUNDS Chronic lymphocytic leukemia (CLL) is the most common type of leukemia in adults and is characterized by a clonal accumulation of mature apoptosis-resistant neoplastic cells. It is also a heterogeneous disease with a variable clinical outcome. Here, we present a review of currently known (epi)genetic alterations that are related to the etiology, progression and chemo-refractoriness of CLL. Relevant literature was identified through a PubMed search (1994-2014) of English-language papers using the terms CLL, signaling pathway, cytogenetic abnormality, somatic mutation, epigenetic alteration and micro-RNA. RESULTS CLL is characterized by the presence of gross chromosomal abnormalities, epigenetic alterations, micro-RNA expression alterations, immunoglobulin heavy chain gene mutations and other genetic lesions. The expression of unmutated immunoglobulin heavy chain variable region (IGHV) genes, ZAP-70 and CD38 proteins, the occurrence of chromosomal abnormalities such as 17p and 11q deletions and mutations of the NOTCH1, SF3B1 and BIRC3 genes have been associated with a poor prognosis. In addition, mutations in tumor suppressor genes, such as TP53 and ATM, have been associated with refractoriness to conventional chemotherapeutic agents. Micro-RNA expression alterations and aberrant methylation patterns in genes that are specifically deregulated in CLL, including the BCL-2, TCL1 and ZAP-70 genes, have also been encountered and linked to distinct clinical parameters. CONCLUSIONS Specific chromosomal abnormalities and gene mutations may serve as diagnostic and prognostic indicators for disease progression and survival. The identification of these anomalies by state-of-the-art molecular (cyto)genetic techniques such as fluorescence in situ hybridization (FISH), comparative genomic hybridization (CGH), single nucleotide polymorphism (SNP) microarray-based genomic profiling and next-generation sequencing (NGS) can be of paramount help for the clinical management of these patients, including optimal treatment design. The efficacy of novel therapeutics should to be tested according to the presence of these molecular lesions in CLL patients.
Collapse
Affiliation(s)
- Mohammad Shahjahani
- Department of Hematology and Blood Banking, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | | | | | | | | | | | | |
Collapse
|
362
|
Spruijt CG, Vermeulen M. DNA methylation: old dog, new tricks? Nat Struct Mol Biol 2015; 21:949-54. [PMID: 25372310 DOI: 10.1038/nsmb.2910] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Accepted: 09/30/2014] [Indexed: 12/17/2022]
Abstract
DNA methylation is an epigenetic modification that is generally associated with repression of transcription initiation at CpG-island promoters. Here we argue that, on the basis of recent high-throughput genomic and proteomic screenings, DNA methylation can also have different outcomes, including activation of transcription. This is evidenced by the fact that transcription factors can interact with methylated DNA sequences. Furthermore, in certain cellular contexts, genes containing methylated promoters are highly transcribed. Interestingly, this uncoupling between methylated DNA and repression of transcription seems to be particularly evident in germ cells and pluripotent cells. Thus, contrary to previous assumptions, DNA methylation is not exclusively associated with repression of transcription initiation.
Collapse
Affiliation(s)
- Cornelia G Spruijt
- Department of Molecular Cancer Research, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Michiel Vermeulen
- 1] Department of Molecular Cancer Research, University Medical Center Utrecht, Utrecht, the Netherlands. [2] Department of Molecular Biology, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, the Netherlands. [3] Cancer Genomics Netherlands, the Netherlands
| |
Collapse
|
363
|
Yang IV, Schwartz DA. Epigenetics of idiopathic pulmonary fibrosis. Transl Res 2015; 165:48-60. [PMID: 24746870 PMCID: PMC4182166 DOI: 10.1016/j.trsl.2014.03.011] [Citation(s) in RCA: 94] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Revised: 03/18/2014] [Accepted: 03/21/2014] [Indexed: 12/15/2022]
Abstract
Idiopathic pulmonary fibrosis (IPF) is a complex lung disease of unknown etiology. Development of IPF is influenced by both genetic and environmental factors. Recent work by our and other groups has identified strong genetic predisposition factors for the development of pulmonary fibrosis, and cigarette smoke remains the most strongly associated environmental exposure risk factor. Gene expression profiling studies of IPF lung have taught us quite a bit about the biology of this fatal disease, and those of peripheral blood have provided important biomarkers. However, epigenetic marks may be the missing link that connects the environmental exposure in genetically predisposed individuals to transcriptional changes associated with disease development. Moreover, epigenetic marks represent a promising therapeutic target for IPF. In this review, the disease is introduced, genetic and gene expression studies in IPF are summarized, exposures relevant to IPF and known epigenetic changes associated with cigarette smoke exposure are discussed, and epigenetic studies conducted so far in IPF are summarized. Limitations, challenges, and future opportunities in this field are also discussed.
Collapse
Affiliation(s)
- Ivana V Yang
- Department of Medicine, University of Colorado School of Medicine, Aurora, Colo; Department of Epidemiology, Colorado School of Public Health, Aurora, Colo.
| | - David A Schwartz
- Department of Medicine, University of Colorado School of Medicine, Aurora, Colo; Department of Immunology, University of Colorado School of Medicine, Aurora, Colo
| |
Collapse
|
364
|
García-Muñoz R, Feliu J, Llorente L. The top ten clues to understand the origin of chronic lymphocytic leukemia (CLL). J Autoimmun 2015; 56:81-6. [DOI: 10.1016/j.jaut.2014.10.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2012] [Revised: 10/12/2014] [Accepted: 10/18/2014] [Indexed: 11/24/2022]
|
365
|
Dominguez PM, Shaknovich R. Epigenetic function of activation-induced cytidine deaminase and its link to lymphomagenesis. Front Immunol 2014; 5:642. [PMID: 25566255 PMCID: PMC4270259 DOI: 10.3389/fimmu.2014.00642] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Accepted: 12/02/2014] [Indexed: 01/16/2023] Open
Abstract
Activation-induced cytidine deaminase (AID) is essential for somatic hypermutation and class switch recombination of immunoglobulin (Ig) genes during B cell maturation and immune response. Expression of AID is tightly regulated due to its mutagenic and recombinogenic potential, which is known to target not only Ig genes, but also non-Ig genes, contributing to lymphomagenesis. In recent years, a new epigenetic function of AID and its link to DNA demethylation came to light in several developmental systems. In this review, we summarize existing evidence linking deamination of unmodified and modified cytidine by AID to base-excision repair and mismatch repair machinery resulting in passive or active removal of DNA methylation mark, with the focus on B cell biology. We also discuss potential contribution of AID-dependent DNA hypomethylation to lymphomagenesis.
Collapse
Affiliation(s)
- Pilar M Dominguez
- Division of Hematology and Oncology, Weill Cornell Medical College , New York, NY , USA
| | - Rita Shaknovich
- Division of Hematology and Oncology, Weill Cornell Medical College , New York, NY , USA ; Department of Pathology and Laboratory Medicine, Weill Cornell Medical College , New York, NY , USA
| |
Collapse
|
366
|
Strefford JC. The genomic landscape of chronic lymphocytic leukaemia: biological and clinical implications. Br J Haematol 2014; 169:14-31. [PMID: 25496136 DOI: 10.1111/bjh.13254] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Chronic lymphocytic leukaemia (CLL) remains at the forefront of the genetic analysis of human tumours, principally due its prevalence, protracted natural history and accessibility to suitable material for analysis. With the application of high-throughput genetic technologies, we have an unbridled view of the architecture of the CLL genome, including a comprehensive description of the copy number and mutational landscape of the disease, a detailed picture of clonal evolution during pathogenesis, and the molecular mechanisms that drive genomic instability and therapeutic resistance. This work has nuanced the prognostic importance of established copy number alterations, and identified novel prognostically relevant gene mutations that function within biological pathways that are attractive treatment targets. Herein, an overview of recent genomic discoveries will be reviewed, with associated biological and clinical implications, and a view into how clinical implementation may be facilitated.
Collapse
Affiliation(s)
- Jonathan C Strefford
- Cancer Genomics, Academic Unit of Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| |
Collapse
|
367
|
Landau DA, Clement K, Ziller MJ, Boyle P, Fan J, Gu H, Stevenson K, Sougnez C, Wang L, Li S, Kotliar D, Zhang W, Ghandi M, Garraway L, Fernandes SM, Livak KJ, Gabriel S, Gnirke A, Lander ES, Brown JR, Neuberg D, Kharchenko PV, Hacohen N, Getz G, Meissner A, Wu CJ. Locally disordered methylation forms the basis of intratumor methylome variation in chronic lymphocytic leukemia. Cancer Cell 2014; 26:813-825. [PMID: 25490447 PMCID: PMC4302418 DOI: 10.1016/j.ccell.2014.10.012] [Citation(s) in RCA: 269] [Impact Index Per Article: 26.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/04/2014] [Revised: 09/16/2014] [Accepted: 10/24/2014] [Indexed: 01/01/2023]
Abstract
Intratumoral heterogeneity plays a critical role in tumor evolution. To define the contribution of DNA methylation to heterogeneity within tumors, we performed genome-scale bisulfite sequencing of 104 primary chronic lymphocytic leukemias (CLLs). Compared with 26 normal B cell samples, CLLs consistently displayed higher intrasample variability of DNA methylation patterns across the genome, which appears to arise from stochastically disordered methylation in malignant cells. Transcriptome analysis of bulk and single CLL cells revealed that methylation disorder was linked to low-level expression. Disordered methylation was further associated with adverse clinical outcome. We therefore propose that disordered methylation plays a similar role to that of genetic instability, enhancing the ability of cancer cells to search for superior evolutionary trajectories.
Collapse
MESH Headings
- B-Lymphocytes/metabolism
- CpG Islands
- DNA Methylation
- Epigenesis, Genetic
- Gene Expression Regulation, Leukemic
- Genetic Variation
- Genome, Human
- Humans
- Leukemia, Lymphocytic, Chronic, B-Cell/genetics
- Leukemia, Lymphocytic, Chronic, B-Cell/pathology
- Molecular Sequence Data
- Sequence Analysis, DNA
- Sulfites/chemistry
Collapse
Affiliation(s)
- Dan A Landau
- Cancer Vaccine Center, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Broad Institute, Cambridge, MA 02139, USA
| | - Kendell Clement
- Broad Institute, Cambridge, MA 02139, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Harvard-MIT Division of Health Sciences and Technology, Cambridge, MA 02139, USA
| | - Michael J Ziller
- Broad Institute, Cambridge, MA 02139, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | | | - Jean Fan
- Center for Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | | | - Kristen Stevenson
- Department of Biostatistics and Computational Biology, Dana Farber Cancer Institute, Boston, MA 02115, USA
| | | | - Lili Wang
- Cancer Vaccine Center, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Shuqiang Li
- Fluidigm, South San Francisco, CA 94080, USA
| | - Dylan Kotliar
- Cancer Vaccine Center, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Wandi Zhang
- Cancer Vaccine Center, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | | | - Levi Garraway
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Broad Institute, Cambridge, MA 02139, USA
| | - Stacey M Fernandes
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | | | | | | | | | - Jennifer R Brown
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Donna Neuberg
- Department of Biostatistics and Computational Biology, Dana Farber Cancer Institute, Boston, MA 02115, USA
| | - Peter V Kharchenko
- Center for Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA; Division of Hematology/Oncology, Children's Hospital, Boston, MA 02115, USA
| | - Nir Hacohen
- Broad Institute, Cambridge, MA 02139, USA; Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Gad Getz
- Broad Institute, Cambridge, MA 02139, USA; Cancer Center and Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Alexander Meissner
- Broad Institute, Cambridge, MA 02139, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA.
| | - Catherine J Wu
- Cancer Vaccine Center, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Division of Hematology/Oncology, Children's Hospital, Boston, MA 02115, USA.
| |
Collapse
|
368
|
DNA hydroxymethylation profiling reveals that WT1 mutations result in loss of TET2 function in acute myeloid leukemia. Cell Rep 2014; 9:1841-1855. [PMID: 25482556 DOI: 10.1016/j.celrep.2014.11.004] [Citation(s) in RCA: 207] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Revised: 10/04/2014] [Accepted: 11/04/2014] [Indexed: 12/21/2022] Open
Abstract
Somatic mutations in IDH1/IDH2 and TET2 result in impaired TET2-mediated conversion of 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC). The observation that WT1 inactivating mutations anticorrelate with TET2/IDH1/IDH2 mutations in acute myeloid leukemia (AML) led us to hypothesize that WT1 mutations may impact TET2 function. WT1 mutant AML patients have reduced 5hmC levels similar to TET2/IDH1/IDH2 mutant AML. These mutations are characterized by convergent, site-specific alterations in DNA hydroxymethylation, which drive differential gene expression more than alterations in DNA promoter methylation. WT1 overexpression increases global levels of 5hmC, and WT1 silencing reduced 5hmC levels. WT1 physically interacts with TET2 and TET3, and WT1 loss of function results in a similar hematopoietic differentiation phenotype as observed with TET2 deficiency. These data provide a role for WT1 in regulating DNA hydroxymethylation and suggest that TET2 IDH1/IDH2 and WT1 mutations define an AML subtype defined by dysregulated DNA hydroxymethylation.
Collapse
|
369
|
Bianchi G, Ghobrial IM. Biological and Clinical Implications of Clonal Heterogeneity and Clonal Evolution in Multiple Myeloma. CURRENT CANCER THERAPY REVIEWS 2014; 10:70-79. [PMID: 25705146 PMCID: PMC4334389 DOI: 10.2174/157339471002141124121404] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Clonal heterogeneity and clonal evolution have emerged as critical concepts in the field of oncology over the past four decades, largely thanks to the implementation of novel technologies such as comparative genomic hybridization, whole genome/exome sequencing and epigenetic analysis. Along with the identification of cancer stem cells in the majority of neoplasia, the recognition of intertumor and intratumor variability has provided a novel perspective to understand the mechanisms behind tumor evolution and its implication in terms of treatment failure and cancer relapse or recurrence. First hypothesized over two decades ago, clonal heterogeneity and clonal evolution have been confirmed in multiple myeloma (MM), an incurable cancer of plasma cells, almost universally preceded by a pre-malignant conditioned named monoclonal gammopathy of undetermined significance (MGUS). The genetic events and molecular mechanisms underlying such evolution have been difficult to dissect. Moreover, while a role for the bone marrow microenvironment in supporting MM cell survival, proliferation and drug-resistance has been well established, whether it is directly involved in driving evolution from MGUS to MM is at present unclear. We present in this review a historical excursus on the concepts of clonal heterogeneity and clonal evolution in MM with a special emphasis on their role in the progression from MGUS to MM; the contribution of the microenvironment; and the clinical implications in terms of resistance to treatment and disease relapse/recurrence.
Collapse
Affiliation(s)
- Giada Bianchi
- Dana-Farber Cancer Institute, Department of Medical Oncology, Harvard Medical School, 450 Brookline Avenue, Boston, MA 02215, USA
| | - Irene M Ghobrial
- Dana-Farber Cancer Institute, Department of Medical Oncology, Harvard Medical School, 450 Brookline Avenue, Boston, MA 02215, USA
| |
Collapse
|
370
|
Yang X, Han H, De Carvalho DD, Lay FD, Jones PA, Liang G. Gene body methylation can alter gene expression and is a therapeutic target in cancer. Cancer Cell 2014; 26:577-90. [PMID: 25263941 PMCID: PMC4224113 DOI: 10.1016/j.ccr.2014.07.028] [Citation(s) in RCA: 785] [Impact Index Per Article: 78.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/18/2013] [Revised: 03/18/2014] [Accepted: 07/29/2014] [Indexed: 02/08/2023]
Abstract
DNA methylation in promoters is well known to silence genes and is the presumed therapeutic target of methylation inhibitors. Gene body methylation is positively correlated with expression, yet its function is unknown. We show that 5-aza-2'-deoxycytidine treatment not only reactivates genes but decreases the overexpression of genes, many of which are involved in metabolic processes regulated by c-MYC. Downregulation is caused by DNA demethylation of the gene bodies and restoration of high levels of expression requires remethylation by DNMT3B. Gene body methylation may, therefore, be an unexpected therapeutic target for DNA methylation inhibitors, resulting in the normalization of gene overexpression induced during carcinogenesis. Our results provide direct evidence for a causal relationship between gene body methylation and transcription.
Collapse
Affiliation(s)
- Xiaojing Yang
- Department of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Han Han
- Department of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Daniel D De Carvalho
- The Princess Margaret Cancer Centre, University Health Network, Toronto ON M5G 1L7, Canada; Department of Medical Biophysics, University of Toronto, Toronto ON M5G 2M9, Canada
| | - Fides D Lay
- Department of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Peter A Jones
- Department of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA.
| | - Gangning Liang
- Department of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA.
| |
Collapse
|
371
|
Divergence of gene body DNA methylation and evolution of plant duplicate genes. PLoS One 2014; 9:e110357. [PMID: 25310342 PMCID: PMC4195714 DOI: 10.1371/journal.pone.0110357] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Accepted: 09/22/2014] [Indexed: 01/24/2023] Open
Abstract
It has been shown that gene body DNA methylation is associated with gene expression. However, whether and how deviation of gene body DNA methylation between duplicate genes can influence their divergence remains largely unexplored. Here, we aim to elucidate the potential role of gene body DNA methylation in the fate of duplicate genes. We identified paralogous gene pairs from Arabidopsis and rice (Oryza sativa ssp. japonica) genomes and reprocessed their single-base resolution methylome data. We show that methylation in paralogous genes nonlinearly correlates with several gene properties including exon number/gene length, expression level and mutation rate. Further, we demonstrated that divergence of methylation level and pattern in paralogs indeed positively correlate with their sequence and expression divergences. This result held even after controlling for other confounding factors known to influence the divergence of paralogs. We observed that methylation level divergence might be more relevant to the expression divergence of paralogs than methylation pattern divergence. Finally, we explored the mechanisms that might give rise to the divergence of gene body methylation in paralogs. We found that exonic methylation divergence more closely correlates with expression divergence than intronic methylation divergence. We show that genomic environments (e.g., flanked by transposable elements and repetitive sequences) of paralogs generated by various duplication mechanisms are associated with the methylation divergence of paralogs. Overall, our results suggest that the changes in gene body DNA methylation could provide another avenue for duplicate genes to develop differential expression patterns and undergo different evolutionary fates in plant genomes.
Collapse
|
372
|
Shaknovich R, De S, Michor F. Epigenetic diversity in hematopoietic neoplasms. Biochim Biophys Acta Rev Cancer 2014; 1846:477-84. [PMID: 25240947 DOI: 10.1016/j.bbcan.2014.09.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Revised: 09/09/2014] [Accepted: 09/11/2014] [Indexed: 12/31/2022]
Abstract
Tumor cell populations display a remarkable extent of variability in non-genetic characteristics such as DNA methylation, histone modification patterns, and differentiation levels of individual cells. It remains to be elucidated whether non-genetic heterogeneity is simply a byproduct of tumor evolution or instead a manifestation of a higher-order tissue organization that is maintained within the neoplasm to establish a differentiation hierarchy, a favorable microenvironment, or a buffer against changing selection pressures during tumorigenesis. Here, we review recent findings on epigenetic diversity, particularly heterogeneity in DNA methylation patterns in hematologic malignancies. We also address the implications of epigenetic heterogeneity for the clonal evolution of tumors and discuss its effects on gene expression and other genome functions in cancer.
Collapse
Affiliation(s)
- Rita Shaknovich
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medical College, New York, NY 10021, USA; Division of Immunopathology, Department of Pathology, Weill Cornell Medical College, New York, NY 10021, USA
| | - Subhajyoti De
- Department of Medicine, University of Colorado School of Medicine, Aurora, CO 80045, USA; University of Colorado Cancer Center, Aurora, CO 80045, USA
| | - Franziska Michor
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Harvard School of Public Health, Boston, MA 02215, USA; Department of Biostatistics, Harvard School of Public Health, Boston, MA 02215, USA.
| |
Collapse
|
373
|
Báez A, Álvarez-Laderas I, Piruat JI, Caballero-Velázquez T, Barbado MV, Millán-Uclés Á, Medrano M, García-Guerrero E, Sánchez-Abarca LI, Pérez-Simón JA. The CD27 + memory B cells display changes in the gene expression pattern in elderly individuals. Immunology 2014; 144:395-404. [PMID: 25196729 PMCID: PMC4557676 DOI: 10.1111/imm.12381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Revised: 07/30/2014] [Accepted: 08/27/2014] [Indexed: 11/27/2022] Open
Abstract
Memory B cells (MBCs) have a very long life-span as compared to naïve B cells (NBCs), remaining viable for years. It could predispose them to suffer misbalances in the gene expression pattern at the long term, which might be involved in the development of age-related B-cell disorders. In order to identify genes whose expression might change during life, we analyzed the gene expression patterns of CD27- NBCs versus CD27+ MBCs in young and old subjects. Using microarray assays we observed that the expression pattern of CD27- NBCs versus CD27+ MBCs is significantly different. Furthermore, in order to evaluate the age effect, we compared the gene expression pattern of young versus aged subjects in both cell populations. Interestingly, we did not find significant differences in the CD27- NBC population between young and aged individuals, whereas we found 925 genes differentially expressed in CD27+ MBCs. Among these genes, 193 were also differentially expressed in CD27+ MBCs as compared to CD27- NBCs, most of them involved in cell survival, cell growth and proliferation, cellular development and gene expression. We conclude that gene expression profiles of CD27- NBCs and CD27+ MBCs are different. Moreover, whereas the gene expression pattern of CD27+ MBCs varies with age, the same does not happen in CD27- NBCs. This suggests that MBCs undergo time-dependent changes which could underlie a higher susceptibility to dysfunction with age. This article is protected by copyright. All rights reserved.
Collapse
Affiliation(s)
- Alicia Báez
- Haematology Department, Institute of Biomedicine of Seville (IBIS), University Hospital Virgen del Rocio/CSIC/University of SevilleSeville, Spain
| | - Isabel Álvarez-Laderas
- Haematology Department, Institute of Biomedicine of Seville (IBIS), University Hospital Virgen del Rocio/CSIC/University of SevilleSeville, Spain
| | - José I Piruat
- Haematology Department, Institute of Biomedicine of Seville (IBIS), University Hospital Virgen del Rocio/CSIC/University of SevilleSeville, Spain
| | - Teresa Caballero-Velázquez
- Haematology Department, Institute of Biomedicine of Seville (IBIS), University Hospital Virgen del Rocio/CSIC/University of SevilleSeville, Spain
| | - María Victoria Barbado
- Haematology Department, Institute of Biomedicine of Seville (IBIS), University Hospital Virgen del Rocio/CSIC/University of SevilleSeville, Spain
| | - África Millán-Uclés
- Haematology Department, Institute of Biomedicine of Seville (IBIS), University Hospital Virgen del Rocio/CSIC/University of SevilleSeville, Spain
| | - Mayte Medrano
- Haematology Department, Institute of Biomedicine of Seville (IBIS), University Hospital Virgen del Rocio/CSIC/University of SevilleSeville, Spain
| | - Estefanía García-Guerrero
- Haematology Department, Institute of Biomedicine of Seville (IBIS), University Hospital Virgen del Rocio/CSIC/University of SevilleSeville, Spain
| | - Luis Ignacio Sánchez-Abarca
- Haematology Department, Institute of Biomedicine of Seville (IBIS), University Hospital Virgen del Rocio/CSIC/University of SevilleSeville, Spain
| | - José Antonio Pérez-Simón
- Haematology Department, Institute of Biomedicine of Seville (IBIS), University Hospital Virgen del Rocio/CSIC/University of SevilleSeville, Spain
| |
Collapse
|
374
|
Abstract
The comparison of DNA methylation patterns across cancer types (pan-cancer methylome analyses) has revealed distinct subgroups of tumors that share similar methylation patterns. Integration of these data with the wealth of information derived from cancer genome profiling studies performed by large international consortia has provided novel insights into the cellular aberrations that contribute to cancer development. There is evidence that genetic mutations in epigenetic regulators (such as DNMT3, IDH1/2 or H3.3) mediate or contribute to these patterns, although a unifying molecular mechanism underlying the global alterations of DNA methylation has largely been elusive. Knowledge gained from pan-cancer methylome analyses will aid the development of diagnostic and prognostic biomarkers, improve patient stratification and the discovery of novel druggable targets for therapy, and will generate hypotheses for innovative clinical trial designs based on methylation subgroups rather than on cancer subtypes. In this review, we discuss recent advances in the global profiling of tumor genomes for aberrant DNA methylation and the integration of these data with cancer genome profiling data, highlight potential mechanisms leading to different methylation subgroups, and show how this information can be used in basic research and for translational applications. A remaining challenge is to experimentally prove the functional link between observed pan-cancer methylation patterns, the associated genetic aberrations, and their relevance for the development of cancer.
Collapse
Affiliation(s)
- Tania Witte
- Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heid elberg, Germany
| | - Christoph Plass
- Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heid elberg, Germany
| | - Clarissa Gerhauser
- Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heid elberg, Germany
| |
Collapse
|
375
|
Fleischer T, Frigessi A, Johnson KC, Edvardsen H, Touleimat N, Klajic J, Riis ML, Haakensen VD, Wärnberg F, Naume B, Helland A, Børresen-Dale AL, Tost J, Christensen BC, Kristensen VN. Genome-wide DNA methylation profiles in progression to in situ and invasive carcinoma of the breast with impact on gene transcription and prognosis. Genome Biol 2014. [PMID: 25146004 PMCID: PMC4165906 DOI: 10.1186/s13059-014-0435-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Ductal carcinoma in situ (DCIS) of the breast is a precursor of invasive breast carcinoma. DNA methylation alterations are thought to be an early event in progression of cancer, and may prove valuable as a tool in clinical decision making and for understanding neoplastic development. RESULTS We generate genome-wide DNA methylation profiles of 285 breast tissue samples representing progression of cancer, and validate methylation changes between normal and DCIS in an independent dataset of 15 normal and 40 DCIS samples. We also validate a prognostic signature on 583 breast cancer samples from The Cancer Genome Atlas. Our analysis reveals that DNA methylation profiles of DCIS are radically altered compared to normal breast tissue, involving more than 5,000 genes. Changes between DCIS and invasive breast carcinoma involve around 1,000 genes. In tumors, DNA methylation is associated with gene expression of almost 3,000 genes, including both negative and positive correlations. A prognostic signature based on methylation level of 18 CpGs is associated with survival of breast cancer patients with invasive tumors, as well as with survival of patients with DCIS and mixed lesions of DCIS and invasive breast carcinoma. CONCLUSIONS This work demonstrates that changes in the epigenome occur early in the neoplastic progression, provides evidence for the possible utilization of DNA methylation-based markers of progression in the clinic, and highlights the importance of epigenetic changes in carcinogenesis.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Vessela N Kristensen
- Department of Genetics, Institute for Cancer Research, OUS Radiumhospitalet, Montebello, Oslo, 0310, Norway.
| |
Collapse
|
376
|
A B-cell epigenetic signature defines three biologic subgroups of chronic lymphocytic leukemia with clinical impact. Leukemia 2014; 29:598-605. [DOI: 10.1038/leu.2014.252] [Citation(s) in RCA: 100] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Revised: 08/01/2014] [Accepted: 08/11/2014] [Indexed: 11/09/2022]
|
377
|
Fleischer T, Frigessi A, Johnson KC, Edvardsen H, Touleimat N, Klajic J, Riis ML, Haakensen VD, Wärnberg F, Naume B, Helland A, Børresen-Dale AL, Tost J, Christensen BC, Kristensen VN. Genome-wide DNA methylation profiles in progression to in situ and invasive carcinoma of the breast with impact on gene transcription and prognosis. Genome Biol 2014; 15:435. [PMID: 25146004 DOI: 10.1186/preaccept-2333349012841587] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Accepted: 08/08/2014] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Ductal carcinoma in situ (DCIS) of the breast is a precursor of invasive breast carcinoma. DNA methylation alterations are thought to be an early event in progression of cancer, and may prove valuable as a tool in clinical decision making and for understanding neoplastic development. RESULTS We generate genome-wide DNA methylation profiles of 285 breast tissue samples representing progression of cancer, and validate methylation changes between normal and DCIS in an independent dataset of 15 normal and 40 DCIS samples. We also validate a prognostic signature on 583 breast cancer samples from The Cancer Genome Atlas. Our analysis reveals that DNA methylation profiles of DCIS are radically altered compared to normal breast tissue, involving more than 5,000 genes. Changes between DCIS and invasive breast carcinoma involve around 1,000 genes. In tumors, DNA methylation is associated with gene expression of almost 3,000 genes, including both negative and positive correlations. A prognostic signature based on methylation level of 18 CpGs is associated with survival of breast cancer patients with invasive tumors, as well as with survival of patients with DCIS and mixed lesions of DCIS and invasive breast carcinoma. CONCLUSIONS This work demonstrates that changes in the epigenome occur early in the neoplastic progression, provides evidence for the possible utilization of DNA methylation-based markers of progression in the clinic, and highlights the importance of epigenetic changes in carcinogenesis.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Vessela N Kristensen
- Department of Genetics, Institute for Cancer Research, OUS Radiumhospitalet, Montebello, Oslo, 0310, Norway.
| |
Collapse
|
378
|
Carmona FJ, Davalos V, Vidal E, Gomez A, Heyn H, Hashimoto Y, Vizoso M, Martinez-Cardus A, Sayols S, Ferreira HJ, Sánchez-Mut JV, Morán S, Margelí M, Castella E, Berdasco M, Stefansson OA, Eyfjord JE, Gonzalez-Suarez E, Dopazo J, Orozco M, Gut IG, Esteller M. A comprehensive DNA methylation profile of epithelial-to-mesenchymal transition. Cancer Res 2014; 74:5608-19. [PMID: 25106427 DOI: 10.1158/0008-5472.can-13-3659] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Epithelial-to-mesenchymal transition (EMT) is a plastic process in which fully differentiated epithelial cells are converted into poorly differentiated, migratory and invasive mesenchymal cells, and it has been related to the metastasis potential of tumors. This is a reversible process and cells can also eventually undergo mesenchymal-to-epithelial transition. The existence of a dynamic EMT process suggests the involvement of epigenetic shifts in the phenotype. Herein, we obtained the DNA methylomes at single-base resolution of Madin-Darby canine kidney cells undergoing EMT and translated the identified differentially methylated regions to human breast cancer cells undergoing a gain of migratory and invasive capabilities associated with the EMT phenotype. We noticed dynamic and reversible changes of DNA methylation, both on promoter sequences and gene-bodies in association with transcription regulation of EMT-related genes. Most importantly, the identified DNA methylation markers of EMT were present in primary mammary tumors in association with the epithelial or the mesenchymal phenotype of the studied breast cancer samples.
Collapse
Affiliation(s)
- F Javier Carmona
- Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute, L'Hospitalet de Llobregat; Barcelona, Spain
| | - Veronica Davalos
- Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute, L'Hospitalet de Llobregat; Barcelona, Spain
| | - Enrique Vidal
- Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute, L'Hospitalet de Llobregat; Barcelona, Spain
| | - Antonio Gomez
- Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute, L'Hospitalet de Llobregat; Barcelona, Spain
| | - Holger Heyn
- Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute, L'Hospitalet de Llobregat; Barcelona, Spain
| | - Yutaka Hashimoto
- Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute, L'Hospitalet de Llobregat; Barcelona, Spain
| | - Miguel Vizoso
- Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute, L'Hospitalet de Llobregat; Barcelona, Spain
| | - Anna Martinez-Cardus
- Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute, L'Hospitalet de Llobregat; Barcelona, Spain
| | - Sergi Sayols
- Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute, L'Hospitalet de Llobregat; Barcelona, Spain
| | - Humberto J Ferreira
- Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute, L'Hospitalet de Llobregat; Barcelona, Spain
| | - Jose V Sánchez-Mut
- Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute, L'Hospitalet de Llobregat; Barcelona, Spain
| | - Sebastián Morán
- Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute, L'Hospitalet de Llobregat; Barcelona, Spain
| | | | - Eva Castella
- Pathology Department, Hospital Germans Trias i Pujol, Badalona, Spain
| | - Maria Berdasco
- Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute, L'Hospitalet de Llobregat; Barcelona, Spain
| | - Olafur A Stefansson
- Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute, L'Hospitalet de Llobregat; Barcelona, Spain
| | - Jorunn E Eyfjord
- Cancer Research Laboratory, Faculty of Medicine, University of Iceland, Reykjavik, Iceland. Department of Medicine, University of Iceland, Reykjavik, Iceland
| | - Eva Gonzalez-Suarez
- Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute, L'Hospitalet de Llobregat; Barcelona, Spain
| | - Joaquín Dopazo
- Department of Bioinformatics, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain. CIBER de Enfermedades Raras (CIBERER), Valencia, Spain. Functional Genomics Node (INB) at CIPF, Valencia, Spain
| | - Modesto Orozco
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona, Spain. Joint IRB-BSC Research Program on Computational Biology, Barcelona, Spain. Barcelona Supercomputing Center, Barcelona, Spain. Department of Biochemistry and Molecular Biology, University of Barcelona, Barcelona, Spain
| | - Ivo G Gut
- Centre Nacional d'Anàlisi Genòmica (CNAG), Barcelona, Spain
| | - Manel Esteller
- Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute, L'Hospitalet de Llobregat; Barcelona, Spain. Department of Physiological Sciences II, School of Medicine, University of Barcelona, Barcelona, Spain. Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.
| |
Collapse
|
379
|
Dreidax D, Bannert S, Henrich KO, Schröder C, Bender S, Oakes CC, Lindner S, Schulte JH, Duffy D, Schwarzl T, Saadati M, Ehemann V, Benner A, Pfister S, Fischer M, Westermann F. p19-INK4d inhibits neuroblastoma cell growth, induces differentiation and is hypermethylated and downregulated in MYCN-amplified neuroblastomas. Hum Mol Genet 2014; 23:6826-37. [PMID: 25104850 DOI: 10.1093/hmg/ddu406] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Uncontrolled cell cycle entry, resulting from deregulated CDK-RB1-E2F pathway activity, is a crucial determinant of neuroblastoma cell malignancy. Here we identify neuroblastoma-suppressive functions of the p19-INK4d CDK inhibitor and uncover mechanisms of its repression in high-risk neuroblastomas. Reduced p19-INK4d expression was associated with poor event-free and overall survival and neuroblastoma risk factors including amplified MYCN in a set of 478 primary neuroblastomas. High MYCN expression repressed p19-INK4d mRNA and protein levels in different neuroblastoma cell models with conditional MYCN expression. MassARRAY and 450K methylation analyses of 105 primary neuroblastomas uncovered a differentially methylated region within p19-INK4d. Hypermethylation of this region was associated with reduced p19-INK4d expression. In accordance, p19-INK4d expression was activated upon treatment with the demethylating agent, 2'-deoxy-5-azacytidine, in neuroblastoma cell lines. Ectopic p19-INK4d expression decreased viability, clonogenicity and the capacity for anchorage-independent growth of neuroblastoma cells, and shifted the cell cycle towards the G1/0 phase. p19-INK4d also induced neurite-like processes and markers of neuronal differentiation. Moreover, neuroblastoma cell differentiation, induced by all-trans retinoic acid or NGF-NTRK1-signaling, activated p19-INK4d expression. Our findings pinpoint p19-INK4d as a neuroblastoma suppressor and provide evidence for MYCN-mediated repression and for epigenetic silencing of p19-INK4d by DNA hypermethylation in high-risk neuroblastomas.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Sven Lindner
- Department of Pediatric Oncology and Hematology, University Children's Hospital, Essen, Germany
| | - Johannes H Schulte
- Department of Pediatric Oncology and Hematology, University Children's Hospital, Essen, Germany
| | - David Duffy
- Systems Biology Ireland, Conway Institute of Biomolecular and Biomedical Research and School of Medicine and Medical Science, University College Dublin, Ireland
| | - Thomas Schwarzl
- Systems Biology Ireland, Conway Institute of Biomolecular and Biomedical Research and School of Medicine and Medical Science, University College Dublin, Ireland
| | - Maral Saadati
- Division of Biostatistics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Volker Ehemann
- Department of Pathology, University of Heidelberg, Heidelberg, Germany and
| | - Axel Benner
- Division of Biostatistics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Matthias Fischer
- Department of Pediatric Oncology and Center for Molecular Medicine Cologne (CMMC), University Children's Hospital, Cologne, Germany
| | | |
Collapse
|
380
|
García-Muñoz R, Llorente L. Chronic lymphocytic leukaemia: could immunological tolerance mechanisms be the origin of lymphoid neoplasms? Immunology 2014; 142:536-50. [PMID: 24645778 PMCID: PMC4107664 DOI: 10.1111/imm.12285] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2014] [Revised: 03/06/2014] [Accepted: 03/13/2014] [Indexed: 12/12/2022] Open
Abstract
Immunological tolerance theory in chronic lymphocytic leukaemia (CLL): we suggest that B cells that express B-cell receptors (BCR) that recognize their own BCR epitopes are viewed by immune system as 'dangerous cells'. BCR autonomous signalling may induce constant receptor editing and mistakes in allelic exclusion. The fact that whole BCR recognizes a self-antigen or foreing antigen may be irrelevant in early B cell development. In early B cells, autonomous signalling induced by recognition of the BCR's own epitopes simulates an antigen-antibody engagement. In the bone marrow this interaction is viewed as recognition of self-molecules and induces receptor editing. In mature B cells autonomous signalling by the BCR may promote 'reversible anergy' and also may correct self-reactivity induced by the somatic hypermutation mechanisms in mutated CLL B cells. However, in unmutated CLL B cells, BCR autonomous signalling in addition to self-antigen recognition augments B cell activation, proliferation and genomic instability. We suggest that CLL originates from a coordinated normal immunologic tolerance mechanism to destroy self-reactive B cells. Additional genetic damage induced by tolerance mechanisms may immortalize self-reactive B cells and transform them into a leukemia.
Collapse
Affiliation(s)
| | - Luis Llorente
- Department of Immunology and Rheumatology, Instituto Nacional de Ciencias Médicas y Nutrición Salvador ZubiránMéxico City, México
| |
Collapse
|
381
|
The tissue is the issue: improved methylome analysis from paraffin-embedded tissues by application of the HOPE technique. J Transl Med 2014; 94:927-33. [PMID: 24933424 DOI: 10.1038/labinvest.2014.79] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Revised: 04/25/2014] [Accepted: 05/14/2014] [Indexed: 01/07/2023] Open
Abstract
Alterations in the DNA methylome are characteristic for numerous diseases and a typical hallmark of cancer. Therefore, DNA methylation is currently under investigation in research labs and has also entered diagnostics. Recently, protocols like the BeadChip technology have become commercially available to study DNA methylation in an array format and semiquantitative fashion. However, it is known that fixation of the sample material with formalin prior to BeadChip analysis can affect the results. In this study we compared the influence of fixation on the outcome of BeadChip analysis. From six patients each a lung cancer tissue sample and a corresponding tumor-free lung tissue sample were collected. The samples were separated into three pieces. One piece of each sample was fixed with formalin, another one by the non-cross-linking HOPE technique (Hepes-glutamic acid buffer mediated Organic solvent Protection Effect). Subsequently, both became paraffin embedded. As a reference, the remaining third piece was cryopreserved. In addition we used three adenocarcinoma cell lines (H838, A549, and H1650) to validate the results from patient tissues. We show that using the HOPE technique instead of formalin largely prevents the introduction of formalin-fixation related artifacts. An ANOVA analysis significantly separated HOPE- and cryopreserved from formalin-fixed samples (FDR<0.05), while differences in the methylation data obtained from HOPE-fixed and cryopreserved material were minor. Consequently, HOPE fixation is superior to formalin fixation if a subsequent BeadChip analysis of paraffin-embedded sample material is intended.
Collapse
|
382
|
Jeong M, Goodell MA. New answers to old questions from genome-wide maps of DNA methylation in hematopoietic cells. Exp Hematol 2014; 42:609-17. [PMID: 24993071 PMCID: PMC4137036 DOI: 10.1016/j.exphem.2014.04.008] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Revised: 04/17/2014] [Accepted: 04/22/2014] [Indexed: 01/10/2023]
Abstract
DNA methylation is a well-studied epigenetic modification essential for efficient cellular differentiation. Aberrant DNA methylation patterns are a characteristic feature of cancer, including myeloid malignancies such as acute myeloid leukemia. Recurrent mutations in DNA-modifying enzymes were identified in acute myeloid leukemia and linked to distinct DNA methylation signatures. In addition, discovery of Tet enzymes provided new mechanisms for the reversal of DNA methylation. Advances in base-resolution profiling of DNA methylation have enabled a more comprehensive understanding of the methylome landscape in the genome. This review will summarize and discuss the key questions in the function of DNA methylation in the hematopoietic system, including where and how DNA methylation regulates diverse biological processes in the genome as elucidated by recent studies.
Collapse
Affiliation(s)
- Mira Jeong
- Stem Cells and Regenerative Medicine Center, Department of Pediatrics and Molecular & Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Margaret A. Goodell
- Stem Cells and Regenerative Medicine Center, Department of Pediatrics and Molecular & Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| |
Collapse
|
383
|
|
384
|
Abstract
Over the past few years, massively parallel sequencing technologies have revealed with high resolution the tremendous genetic and epigenetic heterogeneity in chronic lymphocytic leukemia (CLL). We have learned how the molecular architecture differs not only between affected individuals but also within samples and over time. These insights have catalyzed our understanding of the pathobiology of CLL and point to critical signaling pathways in the development and progression of the disease. Several key driver alterations have been identified, which serve to refine prognostic schemata but also to inspire the development of new therapeutic strategies. Ongoing advances in technology promise to further elucidate the molecular basis of CLL, and this knowledge is anticipated to aid us in understanding and addressing the clinical challenge presented by the vast variability in the clinical course of patients with CLL.
Collapse
MESH Headings
- Chromosome Aberrations
- Epigenomics
- Genetic Heterogeneity
- Genome/genetics
- Humans
- Leukemia, Lymphocytic, Chronic, B-Cell/genetics
- Leukemia, Lymphocytic, Chronic, B-Cell/pathology
- Leukemia, Lymphocytic, Chronic, B-Cell/therapy
- Receptors, Antigen, B-Cell/genetics
- Receptors, Antigen, B-Cell/metabolism
- Signal Transduction/genetics
Collapse
Affiliation(s)
- Michaela Gruber
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA; Broad Institute, Cambridge, MA; Department of Internal Medicine I, Division of Haematology and Haemostaseology, Medical University of Vienna, Vienna, Austria
| | - Catherine J Wu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA; Broad Institute, Cambridge, MA; Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA.
| |
Collapse
|
385
|
Itonaga H, Imanishi D, Wong YF, Sato S, Ando K, Sawayama Y, Sasaki D, Tsuruda K, Hasegawa H, Imaizumi Y, Taguchi J, Tsushima H, Yoshida S, Fukushima T, Hata T, Moriuchi Y, Yanagihara K, Miyazaki Y. Expression of myeloperoxidase in acute myeloid leukemia blasts mirrors the distinct DNA methylation pattern involving the downregulation of DNA methyltransferase DNMT3B. Leukemia 2014; 28:1459-66. [PMID: 24457336 DOI: 10.1038/leu.2014.15] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Accepted: 12/19/2013] [Indexed: 12/21/2022]
Abstract
Myeloperoxidase (MPO) has been associated with both a myeloid lineage commitment and favorable prognosis in patients with acute myeloid leukemia (AML). DNA methyltransferase inhibitors (decitabine and zeburaline) induced MPO gene promoter demethylation and MPO gene transcription in AML cells with low MPO activity. Therefore, MPO gene transcription was directly and indirectly regulated by DNA methylation. A DNA methylation microarray subsequently revealed a distinct methylation pattern in 33 genes, including DNA methyltransferase 3 beta (DNMT3B), in CD34-positive cells obtained from AML patients with a high percentage of MPO-positive blasts. Based on the inverse relationship between the methylation status of DNMT3B and MPO, we found an inverse relationship between DNMT3B and MPO transcription levels in CD34-positive AML cells (P=0.0283). In addition, a distinct methylation pattern was observed in five genes related to myeloid differentiation or therapeutic sensitivity in CD34-positive cells from AML patients with a high percentage of MPO-positive blasts. Taken together, the results of the present study indicate that MPO may serve as an informative marker for identifying a distinct and crucial DNA methylation profile in CD34-positive AML cells.
Collapse
MESH Headings
- Antigens, CD34/metabolism
- Bone Marrow/pathology
- Bone Marrow Cells/metabolism
- Bone Marrow Cells/pathology
- CCAAT-Enhancer-Binding Proteins/genetics
- Cell Line, Tumor
- Cluster Analysis
- DNA (Cytosine-5-)-Methyltransferases/genetics
- DNA (Cytosine-5-)-Methyltransferases/metabolism
- DNA Methylation
- Epigenesis, Genetic
- Gene Expression Profiling
- Gene Expression Regulation, Leukemic
- Humans
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/metabolism
- Leukemia, Myeloid, Acute/pathology
- Mutation
- Nuclear Proteins/genetics
- Nucleophosmin
- Peroxidase/genetics
- Peroxidase/metabolism
- fms-Like Tyrosine Kinase 3/genetics
- DNA Methyltransferase 3B
Collapse
Affiliation(s)
- H Itonaga
- 1] Department of Hematology, Atomic Bomb Disease and Hibakusya Medicine Unit, Atomic Bomb Disease Institute, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan [2] Department of Hematology, Sasebo City General Hospital, Sasebo, Japan
| | - D Imanishi
- Department of Hematology, Atomic Bomb Disease and Hibakusya Medicine Unit, Atomic Bomb Disease Institute, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Y-F Wong
- Laboratory for Stem Cell Biology, RIKEN Center for Development Biology, Kobe, Japan
| | - S Sato
- Department of Hematology, Sasebo City General Hospital, Sasebo, Japan
| | - K Ando
- Department of Hematology, Atomic Bomb Disease and Hibakusya Medicine Unit, Atomic Bomb Disease Institute, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Y Sawayama
- Department of Hematology, Atomic Bomb Disease and Hibakusya Medicine Unit, Atomic Bomb Disease Institute, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - D Sasaki
- Department of Laboratory Medicine, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - K Tsuruda
- Department of Laboratory Medicine, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - H Hasegawa
- Department of Laboratory Medicine, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Y Imaizumi
- Department of Hematology, Atomic Bomb Disease and Hibakusya Medicine Unit, Atomic Bomb Disease Institute, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - J Taguchi
- Department of Hematology, Atomic Bomb Disease and Hibakusya Medicine Unit, Atomic Bomb Disease Institute, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - H Tsushima
- Department of Hematology, Sasebo City General Hospital, Sasebo, Japan
| | - S Yoshida
- Department of Internal Medicine, National Hospital Organization Nagasaki Medical Center, Ohmura, Japan
| | - T Fukushima
- School of Health Sciences, University of the Ryukyus, Nishihara, Japan
| | - T Hata
- Department of Hematology, Atomic Bomb Disease and Hibakusya Medicine Unit, Atomic Bomb Disease Institute, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Y Moriuchi
- Department of Hematology, Sasebo City General Hospital, Sasebo, Japan
| | - K Yanagihara
- Department of Laboratory Medicine, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Y Miyazaki
- Department of Hematology, Atomic Bomb Disease and Hibakusya Medicine Unit, Atomic Bomb Disease Institute, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| |
Collapse
|
386
|
Kita Y, Vincent K, Natsugoe S, Berindan-Neagoe I, Calin GA. Epigenetically regulated microRNAs and their prospect in cancer diagnosis. Expert Rev Mol Diagn 2014; 14:673-83. [PMID: 24914586 DOI: 10.1586/14737159.2014.925399] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Epigenetic alterations have been reported to deregulate the expression of many transcripts, including noncoding RNAs that have no apparent protein-coding capacity. Recently, as the result of numerous studies focused on miRNAs, novel sequencing technologies have made available the transcription profile of the entire human genome. miRNAs as drivers of tumor-suppressive and oncogenic functions have been found to be dysregulated in numerous cancer types. However, the functions of epigenetically regulated genetic elements other than protein-coding genes are still a matter of debate. In this review, the authors focus mainly on describing the epigenetic regulation of miRNAs in cancer. They also discuss the role of miRNAs as potential diagnostic and/or prognostic biomarkers.
Collapse
Affiliation(s)
- Yoshiaki Kita
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | | | | | | |
Collapse
|
387
|
Prange KHM, Singh AA, Martens JHA. The genome-wide molecular signature of transcription factors in leukemia. Exp Hematol 2014; 42:637-50. [PMID: 24814246 DOI: 10.1016/j.exphem.2014.04.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Revised: 04/22/2014] [Accepted: 04/23/2014] [Indexed: 01/08/2023]
Abstract
Transcription factors control expression of genes essential for the normal functioning of the hematopoietic system and regulate development of distinct blood cell types. During leukemogenesis, aberrant regulation of transcription factors such as RUNX1, CBFβ, MLL, C/EBPα, SPI1, GATA, and TAL1 is central to the disease. Here, we will discuss the mechanisms of transcription factor deregulation in leukemia and how in recent years next-generation sequencing approaches have helped to elucidate the molecular role of many of these aberrantly expressed transcription factors. We will focus on the complexes in which these factors reside, the role of posttranslational modification of these factors, their involvement in setting up higher order chromatin structures, and their influence on the local epigenetic environment. We suggest that only comprehensive knowledge on all these aspects will increase our understanding of aberrant gene expression in leukemia as well as open new entry points for therapeutic intervention.
Collapse
Affiliation(s)
- Koen H M Prange
- Department of Molecular Biology, Faculty of Science, Nijmegen Centre for Molecular Life Sciences, Radboud University, Nijmegen, The Netherlands
| | - Abhishek A Singh
- Department of Molecular Biology, Faculty of Science, Nijmegen Centre for Molecular Life Sciences, Radboud University, Nijmegen, The Netherlands
| | - Joost H A Martens
- Department of Molecular Biology, Faculty of Science, Nijmegen Centre for Molecular Life Sciences, Radboud University, Nijmegen, The Netherlands.
| |
Collapse
|
388
|
Heyn H. A symbiotic liaison between the genetic and epigenetic code. Front Genet 2014; 5:113. [PMID: 24822056 PMCID: PMC4013453 DOI: 10.3389/fgene.2014.00113] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2014] [Accepted: 04/15/2014] [Indexed: 01/30/2023] Open
Abstract
With rapid advances in sequencing technologies, we are undergoing a paradigm shift from hypothesis- to data-driven research. Genome-wide profiling efforts have given informative insights into biological processes; however, considering the wealth of variation, the major challenge still remains in their meaningful interpretation. In particular sequence variation in non-coding contexts is often challenging to interpret. Here, data integration approaches for the identification of functional genetic variability represent a possible solution. Exemplary, functional linkage analysis integrating genotype and expression data determined regulatory quantitative trait loci and proposed causal relationships. In addition to gene expression, epigenetic regulation and specifically DNA methylation was established as highly valuable surrogate mark for functional variance of the genetic code. Epigenetic modification has served as powerful mediator trait to elucidate mechanisms forming phenotypes in health and disease. Particularly, integrative studies of genetic and DNA methylation data have been able to guide interpretation strategies of risk genotypes, but also proved their value for physiological traits, such as natural human variation and aging. This Review seeks to illustrate the power of data integration in the genomic era exemplified by DNA methylation quantitative trait loci. However, the model is further extendable to virtually all traceable molecular traits.
Collapse
Affiliation(s)
- Holger Heyn
- Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute Barcelona, Spain
| |
Collapse
|
389
|
Peters SL, Hlady RA, Opavska J, Klinkebiel D, Pirruccello SJ, Talmon GA, Sharp JG, Wu L, Jaenisch R, Simpson MA, Karpf AR, Opavsky R. Tumor suppressor functions of Dnmt3a and Dnmt3b in the prevention of malignant mouse lymphopoiesis. Leukemia 2014; 28:1138-42. [PMID: 24292811 DOI: 10.1038/leu.2013.364] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- S L Peters
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, USA
| | - R A Hlady
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE, USA
| | - J Opavska
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE, USA
| | - D Klinkebiel
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Nebraska Medical Center, Omaha, NE, USA
| | - S J Pirruccello
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, USA
| | - G A Talmon
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, USA
| | - J G Sharp
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, USA
| | - L Wu
- Department of Microbiology and Molecular Genetics, Rutgers New Jersey Medical School, Cancer Center, Newark, NJ, USA
| | - R Jaenisch
- Whitehead Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - M A Simpson
- Department of Biochemistry, University of Nebraska, Lincoln, NE, USA
| | - A R Karpf
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE, USA
| | - R Opavsky
- 1] Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, USA [2] Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE, USA [3] Center for Lymphoma and Leukemia Research, University of Nebraska Medical Center, Omaha, NE, USA
| |
Collapse
|
390
|
Nagarajan RP, Zhang B, Bell RJ, Johnson BE, Olshen AB, Sundaram V, Li D, Graham AE, Diaz A, Fouse SD, Smirnov I, Song J, Paris PL, Wang T, Costello JF. Recurrent epimutations activate gene body promoters in primary glioblastoma. Genome Res 2014; 24:761-74. [PMID: 24709822 PMCID: PMC4009606 DOI: 10.1101/gr.164707.113] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Accepted: 02/05/2014] [Indexed: 01/09/2023]
Abstract
Aberrant DNA hypomethylation may play an important role in the growth rate of glioblastoma (GBM), but the functional impact on transcription remains poorly understood. We assayed the GBM methylome with MeDIP-seq and MRE-seq, adjusting for copy number differences, in a small set of non-glioma CpG island methylator phenotype (non-G-CIMP) primary tumors. Recurrent hypomethylated loci were enriched within a region of chromosome 5p15 that is specified as a cancer amplicon and also encompasses TERT, encoding telomerase reverse transcriptase, which plays a critical role in tumorigenesis. Overall, 76 gene body promoters were recurrently hypomethylated, including TERT and the oncogenes GLI3 and TP73. Recurring hypomethylation also affected previously unannotated alternative promoters, and luciferase reporter assays for three of four of these promoters confirmed strong promoter activity in GBM cells. Histone H3 lysine 4 trimethylation (H3K4me3) ChIP-seq on tissue from the GBMs uncovered peaks that coincide precisely with tumor-specific decrease of DNA methylation at 200 loci, 133 of which are in gene bodies. Detailed investigation of TP73 and TERT gene body hypomethylation demonstrated increased expression of corresponding alternate transcripts, which in TP73 encodes a truncated p73 protein with oncogenic function and in TERT encodes a putative reverse transcriptase-null protein. Our findings suggest that recurring gene body promoter hypomethylation events, along with histone H3K4 trimethylation, alter the transcriptional landscape of GBM through the activation of a limited number of normally silenced promoters within gene bodies, in at least one case leading to expression of an oncogenic protein.
Collapse
Affiliation(s)
- Raman P. Nagarajan
- Brain Tumor Research Center, Department of Neurosurgery, Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, California 94143, USA
| | - Bo Zhang
- Department of Genetics, Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri 63108, USA
| | - Robert J.A. Bell
- Brain Tumor Research Center, Department of Neurosurgery, Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, California 94143, USA
| | - Brett E. Johnson
- Brain Tumor Research Center, Department of Neurosurgery, Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, California 94143, USA
| | - Adam B. Olshen
- Brain Tumor Research Center, Department of Neurosurgery, Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, California 94143, USA
| | - Vasavi Sundaram
- Department of Genetics, Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri 63108, USA
| | - Daofeng Li
- Department of Genetics, Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri 63108, USA
| | - Ashley E. Graham
- Department of Microbiology and Immunology, University of California San Francisco, California 94143, USA
| | - Aaron Diaz
- Institute for Human Genetics, University of California San Francisco, California 94143, USA
| | - Shaun D. Fouse
- Brain Tumor Research Center, Department of Neurosurgery, Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, California 94143, USA
| | - Ivan Smirnov
- Brain Tumor Research Center, Department of Neurosurgery, Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, California 94143, USA
| | - Jun Song
- Institute for Human Genetics, University of California San Francisco, California 94143, USA
| | - Pamela L. Paris
- Department of Urology, Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, California 94143, USA
| | - Ting Wang
- Department of Genetics, Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri 63108, USA
| | - Joseph F. Costello
- Brain Tumor Research Center, Department of Neurosurgery, Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, California 94143, USA
| |
Collapse
|
391
|
Santacruz R, Villamor N, Aymerich M, Martínez-Trillos A, López C, Navarro A, Rozman M, Beà S, Royo C, Cazorla M, Colomer D, Giné E, Pinyol M, Puente XS, López-Otín C, Campo E, López-Guillermo A, Delgado J. The prognostic impact of minimal residual disease in patients with chronic lymphocytic leukemia requiring first-line therapy. Haematologica 2014; 99:873-80. [PMID: 24700492 PMCID: PMC4008107 DOI: 10.3324/haematol.2013.099796] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Accepted: 12/31/2013] [Indexed: 12/13/2022] Open
Abstract
A proportion of patients with chronic lymphocytic leukemia achieve a minimal residual disease negative status after therapy. We retrospectively evaluated the impact of minimal residual disease on the outcome of 255 consecutive patients receiving any front-line therapy in the context of a detailed prognostic evaluation, including assessment of IGHV, TP53, NOTCH1 and SF3B1 mutations. The median follow-up was 73 months (range, 2-202) from disease evaluation. The median treatment-free survival durations for patients achieving a complete response without or with minimal residual disease, a partial response and no response were 76, 40, 11 and 11 months, respectively (P<0.001). Multivariate analysis revealed that three variables had a significant impact on treatment-free survival: minimal residual disease (P<0.001), IGHV status (P<0.001) and β2-microglobulin levels (P=0.012). With regards to overall survival, factors predictive of an unfavorable outcome were minimal residual disease positivity (P=0.014), together with advanced age (P<0.001), unmutated IGHV status (P=0.001), TP53 mutations (P<0.001) and elevated levels of β2-microglobulin (P=0.003). In conclusion, for patients requiring front-line therapy, achievement of minimal residual disease negativity is associated with significantly prolonged treatment-free and overall survival irrespective of other prognostic markers or treatment administered.
Collapse
MESH Headings
- Adult
- Aged
- Aged, 80 and over
- Antineoplastic Combined Chemotherapy Protocols/therapeutic use
- Follow-Up Studies
- Humans
- Induction Chemotherapy
- Leukemia, Lymphocytic, Chronic, B-Cell/diagnosis
- Leukemia, Lymphocytic, Chronic, B-Cell/drug therapy
- Leukemia, Lymphocytic, Chronic, B-Cell/genetics
- Leukemia, Lymphocytic, Chronic, B-Cell/mortality
- Male
- Middle Aged
- Mutation
- Neoplasm Staging
- Neoplasm, Residual/genetics
- Neoplasm, Residual/pathology
- Prognosis
- Treatment Outcome
Collapse
|
392
|
Abstract
One major goal of cancer genome sequencing is to identify key genes and pathways that drive tumor pathogenesis. Although many studies have identified candidate driver genes based on recurrence of mutations in individual genes, subsets of genes with nonrecurrent mutations may also be defined as putative drivers if they affect a single biological pathway. In this fashion, we previously identified Wnt signaling as significantly mutated through large-scale massively parallel DNA sequencing of chronic lymphocytic leukemia (CLL). Here, we use a novel method of biomolecule delivery, vertical silicon nanowires, to efficiently introduce small interfering RNAs into CLL cells, and interrogate the effects of 8 of 15 mutated Wnt pathway members identified across 91 CLLs. In HEK293T cells, mutations in 2 genes did not generate functional changes, 3 led to dysregulated pathway activation, and 3 led to further activation or loss of repression of pathway activation. Silencing 4 of 8 mutated genes in CLL samples harboring the mutated alleles resulted in reduced viability compared with leukemia samples with wild-type alleles. We demonstrate that somatic mutations in CLL can generate dependence on this pathway for survival. These findings support the notion that nonrecurrent mutations at different nodes of the Wnt pathway can contribute to leukemogenesis.
Collapse
|
393
|
Zhang R, Zhao C, Xiong Z, Zhou X. Pathway bridge based multiobjective optimization approach for lurking pathway prediction. BIOMED RESEARCH INTERNATIONAL 2014; 2014:351095. [PMID: 24949437 PMCID: PMC4052696 DOI: 10.1155/2014/351095] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Accepted: 03/16/2014] [Indexed: 11/26/2022]
Abstract
Ovarian carcinoma immunoreactive antigen-like protein 2 (OCIAD2) is a protein with unknown function. Frequently methylated or downregulated, OCIAD2 has been observed in kinds of tumors, and TGFβ signaling has been proved to induce the expression of OCIAD2. However, current pathway analysis tools do not cover the genes without reported interactions like OCIAD2 and also miss some significant genes with relatively lower expression. To investigate potential biological milieu of OCIAD2, especially in cancer microenvironment, a nova approach pbMOO was created to find the potential pathways from TGFβ to OCIAD2 by searching on the pathway bridge, which consisted of cancer enriched looping patterns from the complicated entire protein interactions network. The pbMOO approach was further applied to study the modulator of ligand TGFβ1, receptor TGFβR1, intermediate transfer proteins, transcription factor, and signature OCIAD2. Verified by literature and public database, the pathway TGFβ1-TGFβR1-SMAD2/3-SMAD4/AR-OCIAD2 was detected, which concealed the androgen receptor (AR) which was the possible transcription factor of OCIAD2 in TGFβsignal, and it well explained the mechanism of TGFβ induced OCIAD2 expression in cancer microenvironment, therefore providing an important clue for the future functional analysis of OCIAD2 in tumor pathogenesis.
Collapse
Affiliation(s)
- Rengjing Zhang
- Electrical and Computer Engineering Department, Texas A&M University, College Station, TX 77840, USA
| | - Chen Zhao
- Radiology Comprehensive Cancer Center Cancer Biology, Wake Forest University, Winston-Salem, NC 27103, USA
| | - Zixiang Xiong
- Electrical and Computer Engineering Department, Texas A&M University, College Station, TX 77840, USA
| | - Xiaobo Zhou
- Radiology Comprehensive Cancer Center Cancer Biology, Wake Forest University, Winston-Salem, NC 27103, USA
| |
Collapse
|
394
|
Mertens D, Stilgenbauer S. Prognostic and Predictive Factors in Patients With Chronic Lymphocytic Leukemia: Relevant in the Era of Novel Treatment Approaches? J Clin Oncol 2014; 32:869-72. [DOI: 10.1200/jco.2013.53.8421] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Affiliation(s)
- Daniel Mertens
- Ulm University, Ulm; German Cancer Research Center, Heidelberg, Germany
| | | |
Collapse
|
395
|
Agathangelidis A, Vardi A, Baliakas P, Stamatopoulos K. Stereotyped B-cell receptors in chronic lymphocytic leukemia. Leuk Lymphoma 2014; 55:2252-61. [DOI: 10.3109/10428194.2013.879715] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
|
396
|
Villamor N, López-Guillermo A, López-Otín C, Campo E. Next-generation sequencing in chronic lymphocytic leukemia. Semin Hematol 2014; 50:286-95. [PMID: 24246696 DOI: 10.1053/j.seminhematol.2013.09.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The use of next-generation sequencing (NGS) has expanded our knowledge of the genomic alterations in chronic lymphocytic leukemia (CLL) and provides new tools for analyzing leukemic clonal architecture. Recent studies have demonstrated substantial differences in genomic alterations between mutated and unmutated IGHV subgroups, which reflect distinct molecular pathways and mutagenic mechanisms in the pathogenesis of the disease. The mutational profile of CLL can be characterized by a relatively low number of somatic mutations per case, few recurrent mutations at moderate frequency (5%-15%) and a long tail of recurrent lower frequency somatic mutations. Functional and clinical studies of novel mutations have uncovered new mechanisms involved in the pathogenesis of the disease, revealing new insights into CLL molecular evolution that could ultimately translate into improvements in the management of patients. The clonal architecture of CLL shows striking heterogeneity between patients, which could have important clinical implications. In summary, NGS studies of CLL are expanding our fundamental knowledge on the molecular mechanisms involved in the pathogenesis of the disease and offering new perspectives for the clinical management of the patients.
Collapse
Affiliation(s)
- Neus Villamor
- Unitat d'Hematopatologia, Servei d'Anatomia Patològica, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.
| | | | | | | |
Collapse
|
397
|
Tsagaratou A, Rao A. TET proteins and 5-methylcytosine oxidation in the immune system. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2014; 78:1-10. [PMID: 24619230 DOI: 10.1101/sqb.2013.78.020248] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
DNA methylation in the form of 5-methylcytosine (5mC) is essential for normal development in mammals and influences a variety of biological processes, including transcriptional regulation, imprinting, and the maintenance of genomic stability. The recent discovery of TET proteins, which oxidize 5mC to 5-hydroxymethylcytosine, 5-formylcytosine, and 5-carboxylcytosine, has changed our understanding of the process of DNA demethylation. Here, we summarize our current knowledge of the roles of DNA methylation and TET proteins in cell differentiation and function. The intensive research on this subject has so far focused primarily on embryonic stem (ES) cells and neurons. In addition, we summarize what is known about DNA methylation in T-cell function.
Collapse
Affiliation(s)
- Ageliki Tsagaratou
- La Jolla Institute for Allergy and Immunology, La Jolla, California 92037
| | - Anjana Rao
- La Jolla Institute for Allergy and Immunology, La Jolla, California 92037 Department of Pharmacology, University of California, San Diego, La Jolla, California 92093-0636 Sanford Consortium for Regenerative Medicine, La Jolla, California 92037
| |
Collapse
|
398
|
Oakes CC, Claus R, Gu L, Assenov Y, Hüllein J, Zucknick M, Bieg M, Brocks D, Bogatyrova O, Schmidt CR, Rassenti L, Kipps TJ, Mertens D, Lichter P, Döhner H, Stilgenbauer S, Byrd JC, Zenz T, Plass C. Evolution of DNA methylation is linked to genetic aberrations in chronic lymphocytic leukemia. Cancer Discov 2014; 4:348-61. [PMID: 24356097 PMCID: PMC4134522 DOI: 10.1158/2159-8290.cd-13-0349] [Citation(s) in RCA: 116] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Although clonal selection by genetic driver aberrations in cancer is well documented, the ability of epigenetic alterations to promote tumor evolution is undefined. We used 450k arrays and next-generation sequencing to evaluate intratumor heterogeneity and evolution of DNA methylation and genetic aberrations in chronic lymphocytic leukemia (CLL). CLL cases exhibit vast interpatient differences in intratumor methylation heterogeneity, with genetically clonal cases maintaining low methylation heterogeneity and up to 10% of total CpGs in a monoallelically methylated state. Increasing methylation heterogeneity correlates with advanced genetic subclonal complexity. Selection of novel DNA methylation patterns is observed only in cases that undergo genetic evolution, and independent genetic evolution is uncommon and is restricted to low-risk alterations. These results reveal that although evolution of DNA methylation occurs in high-risk, clinically progressive cases, positive selection of novel methylation patterns entails coevolution of genetic alteration(s) in CLL.
Collapse
MESH Headings
- Aged
- Chromosomes, Human
- CpG Islands
- DNA Methylation
- Disease Progression
- Epigenesis, Genetic
- Female
- Gene Expression Regulation, Leukemic
- Genetic Heterogeneity
- Genome, Human
- Genomic Instability
- Humans
- Leukemia, Lymphocytic, Chronic, B-Cell/diagnosis
- Leukemia, Lymphocytic, Chronic, B-Cell/genetics
- Leukemia, Lymphocytic, Chronic, B-Cell/pathology
- Male
- Middle Aged
Collapse
Affiliation(s)
- Christopher C. Oakes
- Division of Epigenomics and Cancer Risk Factors, National Center for Tumor Diseases (NCT), The German Cancer Research Center (DKFZ)
| | - Rainer Claus
- Division of Epigenomics and Cancer Risk Factors, National Center for Tumor Diseases (NCT), The German Cancer Research Center (DKFZ)
- Department of Medicine, University of Freiburg Medical Center, Freiburg
| | - Lei Gu
- Division of Epigenomics and Cancer Risk Factors, National Center for Tumor Diseases (NCT), The German Cancer Research Center (DKFZ)
- Division of Theoretical Bioinformatics, National Center for Tumor Diseases (NCT), The German Cancer Research Center (DKFZ)
| | - Yassen Assenov
- Division of Epigenomics and Cancer Risk Factors, National Center for Tumor Diseases (NCT), The German Cancer Research Center (DKFZ)
| | - Jennifer Hüllein
- Department of Translational Oncology, National Center for Tumor Diseases (NCT), The German Cancer Research Center (DKFZ)
| | - Manuela Zucknick
- Division of Biostatistics, National Center for Tumor Diseases (NCT), The German Cancer Research Center (DKFZ)
| | - Matthias Bieg
- Division of Theoretical Bioinformatics, National Center for Tumor Diseases (NCT), The German Cancer Research Center (DKFZ)
| | - David Brocks
- Division of Epigenomics and Cancer Risk Factors, National Center for Tumor Diseases (NCT), The German Cancer Research Center (DKFZ)
| | - Olga Bogatyrova
- Division of Epigenomics and Cancer Risk Factors, National Center for Tumor Diseases (NCT), The German Cancer Research Center (DKFZ)
| | - Christopher R. Schmidt
- Division of Epigenomics and Cancer Risk Factors, National Center for Tumor Diseases (NCT), The German Cancer Research Center (DKFZ)
| | - Laura Rassenti
- Department of Medicine, University of California at San Diego Moores Cancer Center, La Jolla, California
| | - Thomas J. Kipps
- Department of Medicine, University of California at San Diego Moores Cancer Center, La Jolla, California
| | - Daniel Mertens
- Division of Molecular Genetics, National Center for Tumor Diseases (NCT), The German Cancer Research Center (DKFZ)
- Department of Internal Medicine III, University of Ulm, Ulm
| | - Peter Lichter
- Division of Molecular Genetics, National Center for Tumor Diseases (NCT), The German Cancer Research Center (DKFZ)
- The German Cancer Consortium, Germany
| | - Hartmut Döhner
- Department of Internal Medicine III, University of Ulm, Ulm
| | | | - John C. Byrd
- Division of Hematology, The Ohio State University, Columbus, Ohio
| | - Thorsten Zenz
- Division of Epigenomics and Cancer Risk Factors, National Center for Tumor Diseases (NCT), The German Cancer Research Center (DKFZ)
- Department of Medicine V, University of Heidelberg, Heidelberg
| | - Christoph Plass
- Division of Epigenomics and Cancer Risk Factors, National Center for Tumor Diseases (NCT), The German Cancer Research Center (DKFZ)
- The German Cancer Consortium, Germany
| |
Collapse
|
399
|
Wagner JR, Busche S, Ge B, Kwan T, Pastinen T, Blanchette M. The relationship between DNA methylation, genetic and expression inter-individual variation in untransformed human fibroblasts. Genome Biol 2014; 15:R37. [PMID: 24555846 PMCID: PMC4053980 DOI: 10.1186/gb-2014-15-2-r37] [Citation(s) in RCA: 315] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Accepted: 02/20/2014] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND DNA methylation plays an essential role in the regulation of gene expression. While its presence near the transcription start site of a gene has been associated with reduced expression, the variation in methylation levels across individuals, its environmental or genetic causes, and its association with gene expression remain poorly understood. RESULTS We report the joint analysis of sequence variants, gene expression and DNA methylation in primary fibroblast samples derived from a set of 62 unrelated individuals. Approximately 2% of the most variable CpG sites are mappable in cis to sequence variation, usually within 5 kb. Via eQTL analysis with microarray data combined with mapping of allelic expression regions, we obtained a set of 2,770 regions mappable in cis to sequence variation. In 9.5% of these expressed regions, an associated SNP was also a methylation QTL. Methylation and gene expression are often correlated without direct discernible involvement of sequence variation, but not always in the expected direction of negative for promoter CpGs and positive for gene-body CpGs. Population-level correlation between methylation and expression is strongest in a subset of developmentally significant genes, including all four HOX clusters. The presence and sign of this correlation are best predicted using specific chromatin marks rather than position of the CpG site with respect to the gene. CONCLUSIONS Our results indicate a wide variety of relationships between gene expression, DNA methylation and sequence variation in untransformed adult human fibroblasts, with considerable involvement of chromatin features and some discernible involvement of sequence variation.
Collapse
Affiliation(s)
- James R Wagner
- McGill University School of Computer Science, Rm 318, 3480 University Street, Montreal, Québec H3A 0E9, Canada
| | - Stephan Busche
- Department of Human Genetics, McGill University, 740 Dr. Penfield Avenue, Room 6202, Montréal, Québec H3A 0G1, Canada
- Génome Québec Innovation Centre, 740 Dr. Penfield Avenue, Room 6202, Montréal, Québec H3A 0G1, Canada
| | - Bing Ge
- Génome Québec Innovation Centre, 740 Dr. Penfield Avenue, Room 6202, Montréal, Québec H3A 0G1, Canada
| | - Tony Kwan
- Department of Human Genetics, McGill University, 740 Dr. Penfield Avenue, Room 6202, Montréal, Québec H3A 0G1, Canada
- Génome Québec Innovation Centre, 740 Dr. Penfield Avenue, Room 6202, Montréal, Québec H3A 0G1, Canada
| | - Tomi Pastinen
- Department of Human Genetics, McGill University, 740 Dr. Penfield Avenue, Room 6202, Montréal, Québec H3A 0G1, Canada
- Génome Québec Innovation Centre, 740 Dr. Penfield Avenue, Room 6202, Montréal, Québec H3A 0G1, Canada
| | - Mathieu Blanchette
- McGill University School of Computer Science, Rm 318, 3480 University Street, Montreal, Québec H3A 0E9, Canada
| |
Collapse
|
400
|
Saito Y, Tsuji J, Mituyama T. Bisulfighter: accurate detection of methylated cytosines and differentially methylated regions. Nucleic Acids Res 2014; 42:e45. [PMID: 24423865 PMCID: PMC3973284 DOI: 10.1093/nar/gkt1373] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Analysis of bisulfite sequencing data usually requires two tasks: to call methylated cytosines (mCs) in a sample, and to detect differentially methylated regions (DMRs) between paired samples. Although numerous tools have been proposed for mC calling, methods for DMR detection have been largely limited. Here, we present Bisulfighter, a new software package for detecting mCs and DMRs from bisulfite sequencing data. Bisulfighter combines the LAST alignment tool for mC calling, and a novel framework for DMR detection based on hidden Markov models (HMMs). Unlike previous attempts that depend on empirical parameters, Bisulfighter can use the expectation-maximization algorithm for HMMs to adjust parameters for each data set. We conduct extensive experiments in which accuracy of mC calling and DMR detection is evaluated on simulated data with various mC contexts, read qualities, sequencing depths and DMR lengths, as well as on real data from a wide range of biological processes. We demonstrate that Bisulfighter consistently achieves better accuracy than other published tools, providing greater sensitivity for mCs with fewer false positives, more precise estimates of mC levels, more exact locations of DMRs and better agreement of DMRs with gene expression and DNase I hypersensitivity. The source code is available at http://epigenome.cbrc.jp/bisulfighter.
Collapse
Affiliation(s)
- Yutaka Saito
- Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan, Japan Science and Technology Agency, CREST, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan and Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655, USA
| | | | | |
Collapse
|