51
|
Li D, Fan J, Li Z, Xu C. DNA methylation dynamics in the rat EGF gene promoter after partial hepatectomy. Genet Mol Biol 2014; 37:439-43. [PMID: 25071410 PMCID: PMC4094617 DOI: 10.1590/s1415-47572014000300017] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2013] [Accepted: 03/18/2014] [Indexed: 11/23/2022] Open
Abstract
Epidermal growth factor (EGF), a multifunctional growth factor, is a regulator in a wide variety of physiological processes. EGF plays an important role in the regulation of liver regeneration. This study was aimed at investigating the methylation level of EGF gene throughout liver regeneration. DNA of liver tissue from control rats and partial hepatectomy (PH) rats at 10 time points was extracted and a 354 bp fragment including 10 CpG sites from the transcription start was amplified after DNA was modified by sodium bisulfate. The result of sequencing suggested that methylation ratio of four CpG sites was found to be significantly changed when PH group was compared to control group, in particular two of them were extremely striking. mRNA expression of EGF was down-regulated in total during liver regeneration. We think that the rat EGF promoter region is regulated by variation in DNA methylation during liver regeneration.
Collapse
Affiliation(s)
- Deming Li
- Key Laboratory for Cell Differentiation Regulation , Xinxiang , China . ; College of Life Science , Henan Normal University , Xinxiang , China
| | - Jinyu Fan
- Key Laboratory for Cell Differentiation Regulation , Xinxiang , China . ; College of Life Science , Henan Normal University , Xinxiang , China
| | - Ziwei Li
- Key Laboratory for Cell Differentiation Regulation , Xinxiang , China . ; College of Life Science , Henan Normal University , Xinxiang , China
| | - Cunshuan Xu
- Key Laboratory for Cell Differentiation Regulation , Xinxiang , China . ; College of Life Science , Henan Normal University , Xinxiang , China
| |
Collapse
|
52
|
Liang L, Cookson WOC. Grasping nettles: cellular heterogeneity and other confounders in epigenome-wide association studies. Hum Mol Genet 2014; 23:R83-8. [PMID: 24927738 PMCID: PMC4170720 DOI: 10.1093/hmg/ddu284] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Platform technologies for measurement of CpG methylation at multiple loci across the genome have made ambitious epigenome-wide association studies affordable and practicable. In contrast to genetic studies, which estimate the effects of structural changes in DNA, and transcriptomic studies, which measure genomic outputs, epigenetic studies can access states of regulation of genome function in particular cells and in response to specific stimuli. Although many factors complicate the interpretation of epigenetic variation in human disease, cell-specific methylation patterns and the cellular heterogeneity present in peripheral blood and tissue biopsies are anticipated to cause the most problems. In this review, we suggest that the difficulties may be exaggerated and we explore how cellular heterogeneity may be embraced with appropriate study designs and analytical tools. We further suggest that systematic mapping of the loci influenced by age, sex and genetic polymorphisms will bring important biological insights as well as improved control of epigenome-wide association studies.
Collapse
Affiliation(s)
- Liming Liang
- Department of Epidemiology and Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, USA and
| | - William O C Cookson
- National Heart and Lung Institute, Imperial College London, London SW3 6LY, UK
| |
Collapse
|
53
|
Bujko M, Musialik E, Olbromski R, Przestrzelska M, Libura M, Pastwińska A, Juszczyński P, Zwierzchowski L, Baranowski P, Siedlecki JA. Repetitive genomic elements and overall DNA methylation changes in acute myeloid and childhood B-cell lymphoblastic leukemia patients. Int J Hematol 2014; 100:79-87. [PMID: 24841671 DOI: 10.1007/s12185-014-1592-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Revised: 04/25/2014] [Accepted: 04/28/2014] [Indexed: 12/30/2022]
Abstract
Aberrant epigenetic regulation is a hallmark of neoplastic cells. Increased DNA methylation of individual genes' promoter regions and decreases in overall DNA methylation level are both generally observed in cancer. In solid tumors, this global DNA hypomethylation is related to reduced methylation of repeated DNA elements (REs) and contributes to genome instability. The aim of the present study was to assess methylation level of LINE-1 and ALU REs and total 5-methylcytosine (5metC) content in adult acute myeloid leukemia (AML) (n = 58), childhood B-cell acute lymphoblastic leukemia (ALL) (n = 32), as the most frequent acute leukemias in two age categories and in normal adult bone marrow and children's blood samples. DNA pyrosequencing and ELISA assays were used, respectively. Global DNA hypomethylation was not observed in leukemia patients. Results revealed higher DNA methylation of LINE-1 in AML and ALL samples compared to corresponding normal controls. Elevated methylation of ALU and overall 5metC level were also observed in B-cell ALL patients. Differences of REs and global DNA methylation between AML cytogenetic-risk groups were observed, with the lowest methylation levels in intermediate-risk/cytogenetically normal patients. B-cell ALL is characterized by the highest DNA methylation level compared to AML and controls and overall DNA methylation is correlated with leukocyte count.
Collapse
Affiliation(s)
- Mateusz Bujko
- Department of Molecular and Translational Oncology, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, W.K. Roentgena 5, 02-781, Warsaw, Poland,
| | | | | | | | | | | | | | | | | | | |
Collapse
|
54
|
Varela-Rey M, Iruarrizaga-Lejarreta M, Lozano JJ, Aransay AM, Fernandez AF, Lavin JL, Mósen-Ansorena D, Berdasco M, Turmaine M, Luka Z, Wagner C, Lu SC, Esteller M, Mirsky R, Jessen KR, Fraga MF, Martínez-Chantar ML, Mato JM, Woodhoo A. S-adenosylmethionine levels regulate the schwann cell DNA methylome. Neuron 2014; 81:1024-1039. [PMID: 24607226 PMCID: PMC3960855 DOI: 10.1016/j.neuron.2014.01.037] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/14/2014] [Indexed: 10/25/2022]
Abstract
Axonal myelination is essential for rapid saltatory impulse conduction in the nervous system, and malformation or destruction of myelin sheaths leads to motor and sensory disabilities. DNA methylation is an essential epigenetic modification during mammalian development, yet its role in myelination remains obscure. Here, using high-resolution methylome maps, we show that DNA methylation could play a key gene regulatory role in peripheral nerve myelination and that S-adenosylmethionine (SAMe), the principal methyl donor in cytosine methylation, regulates the methylome dynamics during this process. Our studies also point to a possible role of SAMe in establishing the aberrant DNA methylation patterns in a mouse model of diabetic neuropathy, implicating SAMe in the pathogenesis of this disease. These critical observations establish a link between SAMe and DNA methylation status in a defined biological system, providing a mechanism that could direct methylation changes during cellular differentiation and in diverse pathological situations.
Collapse
Affiliation(s)
- Marta Varela-Rey
- CIC bioGUNE, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Bizkaia Technology Park, Derio, 48160 Bizkaia, Spain
| | - Marta Iruarrizaga-Lejarreta
- CIC bioGUNE, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Bizkaia Technology Park, Derio, 48160 Bizkaia, Spain
| | - Juan José Lozano
- Bioinformatic Platform, CIBERehd, Centre Esther Koplovitz (CEK), C/Rosselló 153 Subsuelo, 08036 Barcelona, Spain
| | - Ana María Aransay
- CIC bioGUNE, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Bizkaia Technology Park, Derio, 48160 Bizkaia, Spain
| | - Agustín F Fernandez
- Cancer Epigenetics Laboratory, Instituto Universitario de Oncología del Principado de Asturias (IUOPA-HUCA), Universidad de Oviedo, 33006 Oviedo, Spain
| | - José Luis Lavin
- CIC bioGUNE, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Bizkaia Technology Park, Derio, 48160 Bizkaia, Spain
| | - David Mósen-Ansorena
- CIC bioGUNE, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Bizkaia Technology Park, Derio, 48160 Bizkaia, Spain
| | - María Berdasco
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, 09908 Catalonia, Spain
| | - Marc Turmaine
- Department of Cell and Developmental Biology, University College London, Gower Street, London WC1E 6BT, UK
| | - Zigmund Luka
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232-0146, USA
| | - Conrad Wagner
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232-0146, USA
| | - Shelly C Lu
- Division of Gastrointestinal and Liver Diseases, USC Research Center for Liver Diseases, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Manel Esteller
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, 09908 Catalonia, Spain; Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, 08010 Catalonia, Spain
| | - Rhona Mirsky
- Department of Cell and Developmental Biology, University College London, Gower Street, London WC1E 6BT, UK
| | - Kristján R Jessen
- Department of Cell and Developmental Biology, University College London, Gower Street, London WC1E 6BT, UK
| | - Mario F Fraga
- Cancer Epigenetics Laboratory, Instituto Universitario de Oncología del Principado de Asturias (IUOPA-HUCA), Universidad de Oviedo, 33006 Oviedo, Spain; Department of Immunology and Oncology, National Center for Biotechnology, CNB-CSIC, Cantoblanco, E-28049Madrid, Spain
| | - María L Martínez-Chantar
- CIC bioGUNE, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Bizkaia Technology Park, Derio, 48160 Bizkaia, Spain; Biochemistry and Molecular Biology Department, University of the Basque Country (UPV/EHU), P.O. Box 644, E-48080 Bilbao, Spain
| | - José M Mato
- CIC bioGUNE, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Bizkaia Technology Park, Derio, 48160 Bizkaia, Spain
| | - Ashwin Woodhoo
- CIC bioGUNE, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Bizkaia Technology Park, Derio, 48160 Bizkaia, Spain; IKERBASQUE, Basque Foundation for Science, 48011 Bilbao, Spain.
| |
Collapse
|
55
|
Kar S, Parbin S, Deb M, Shilpi A, Sengupta D, Rath SK, Rakshit M, Patra A, Patra SK. Epigenetic choreography of stem cells: the DNA demethylation episode of development. Cell Mol Life Sci 2014; 71:1017-32. [PMID: 24114325 PMCID: PMC11113617 DOI: 10.1007/s00018-013-1482-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Revised: 09/12/2013] [Accepted: 09/16/2013] [Indexed: 12/17/2022]
Abstract
Reversible DNA methylation is a fundamental epigenetic manipulator of the genomic information in eukaryotes. DNA demethylation plays a very significant role during embryonic development and stands out for its contribution in molecular reconfiguration during cellular differentiation for determining stem cell fate. DNA demethylation arbitrated extensive make-over of the genome via reprogramming in the early embryo results in stem cell plasticity followed by commitment to the principal cell lineages. This article attempts to highlight the sequential phases and hierarchical mode of DNA demethylation events during enactment of the molecular strategy for developmental transition. A comprehensive knowledge regarding the pattern of DNA demethylation during embryogenesis and organogenesis and study of the related lacunae will offer exciting avenues for future biomedical research and stem cell-based regenerative therapy.
Collapse
Affiliation(s)
- Swayamsiddha Kar
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, Odisha 769008 India
| | - Sabnam Parbin
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, Odisha 769008 India
| | - Moonmoon Deb
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, Odisha 769008 India
| | - Arunima Shilpi
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, Odisha 769008 India
| | - Dipta Sengupta
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, Odisha 769008 India
| | - Sandip Kumar Rath
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, Odisha 769008 India
| | - Madhumita Rakshit
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, Odisha 769008 India
| | - Aditi Patra
- Additional Block Animal Health Centre, Veterinary Office, Oodlabari, Malbazar, Jalpaiguri, West Bengal India
| | - Samir Kumar Patra
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, Odisha 769008 India
| |
Collapse
|
56
|
Rodriguez RM, Suarez-Alvarez B, Salvanés R, Huidobro C, Toraño EG, Garcia-Perez JL, Lopez-Larrea C, Fernandez AF, Bueno C, Menendez P, Fraga MF. Role of BRD4 in hematopoietic differentiation of embryonic stem cells. Epigenetics 2014; 9:566-78. [PMID: 24445267 DOI: 10.4161/epi.27711] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The bromodomain and extra terminal (BET) protein family member BRD4 is a transcriptional regulator, critical for cell cycle progression and cellular viability. Here, we show that BRD4 plays an important role in embryonic stem cell (ESC) regulation. During differentiation of ESCs, BRD4 expression is upregulated and its gene promoter becomes demethylated. Disruption of BRD4 expression in ESCs did not induce spontaneous differentiation but severely diminished hematoendothelial potential. Although BRD4 regulates c-Myc expression, our data show that the role of BRD4 in hematopoietic commitment is not exclusively mediated by c-Myc. Our results indicate that BRD4 is epigenetically regulated during hematopoietic differentiation ESCs in the context of a still unknown signaling pathway.
Collapse
Affiliation(s)
- Ramon M Rodriguez
- Cancer Epigenetics Laboratory; Instituto Universitario de Oncología del Principado de Asturias (IUOPA); HUCA; Universidad de Oviedo; Oviedo, Spain; Department of Immunology; Hospital Universitario Central de Asturias; Oviedo, Spain
| | | | - Ruben Salvanés
- Department of Immunology; Hospital Universitario Central de Asturias; Oviedo, Spain
| | - Covadonga Huidobro
- Cancer Epigenetics Laboratory; Instituto Universitario de Oncología del Principado de Asturias (IUOPA); HUCA; Universidad de Oviedo; Oviedo, Spain; MRC Human Genetics Unit; Institute of Genetics and Molecular Medicine; University of Edinburgh; Western General Hospital; Edinburgh, UK
| | - Estela G Toraño
- Cancer Epigenetics Laboratory; Instituto Universitario de Oncología del Principado de Asturias (IUOPA); HUCA; Universidad de Oviedo; Oviedo, Spain
| | - Jose L Garcia-Perez
- Department of Human DNA Variability; Pfizer-University of Granada and Andalusian Government Center for Genomics and Oncology (GENYO); Granada, Spain
| | - Carlos Lopez-Larrea
- Department of Immunology; Hospital Universitario Central de Asturias; Oviedo, Spain; Fundacion Renal "Íñigo Álvarez de Toledo"; Madrid, Spain
| | - Agustin F Fernandez
- Cancer Epigenetics Laboratory; Instituto Universitario de Oncología del Principado de Asturias (IUOPA); HUCA; Universidad de Oviedo; Oviedo, Spain
| | - Clara Bueno
- Josep Carreras Leukemia Research Institute; Barcelona, Spain; Centre for Genomics and Oncological Research (GENYO); Pfizer/University of Granada/Andalusian Government; Granada, Spain
| | - Pablo Menendez
- Josep Carreras Leukemia Research Institute; Barcelona, Spain; Instituciò Catalana de Reserca i Estudis Avançats (ICREA); Barcelona, Spain
| | - Mario F Fraga
- Cancer Epigenetics Laboratory; Instituto Universitario de Oncología del Principado de Asturias (IUOPA); HUCA; Universidad de Oviedo; Oviedo, Spain; Department of Immunology and Oncology; Centro Nacional de Biotecnología/CNB-CSIC; Cantoblanco; Madrid, Spain
| |
Collapse
|
57
|
|
58
|
Vitaloni M, Pulecio J, Bilic J, Kuebler B, Laricchia-Robbio L, Izpisua Belmonte JC. MicroRNAs contribute to induced pluripotent stem cell somatic donor memory. J Biol Chem 2013; 289:2084-98. [PMID: 24311783 DOI: 10.1074/jbc.m113.538702] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Induced pluripotent stem cells (iPSCs) maintain during the first few culture passages a set of epigenetic marks and metabolites characteristic of their somatic cell of origin, a concept defined as epigenetic donor memory. These residual somatic features are lost over time after extensive culture passaging. Therefore, epigenetic donor memory may be responsible for the higher differentiation efficiency toward the tissue of origin observed in low passage iPSCs versus high passage iPSC or iPSCs derived from a different tissue source. Remarkably, there are no studies on the relevance of microRNA (miRNA) memory following reprogramming, despite the established role of these molecules in the context of pluripotency and differentiation. Using hematopoietic progenitors cells as a model, we demonstrated that miRNAs play a central role in somatic memory retention in iPSCs. Moreover, the comparison of the miRNA expression profiles among iPSCs from different sources allowed for the detection of a set of candidate miRNAs responsible for the higher differentiation efficiency rates toward blood progenitors observed in low passage iPSCs. Combining bioinformatic predictive algorithms with biological target validation, we identified miR-155 as a key player for the in vitro differentiation of iPSC toward hematopoietic progenitors. In summary, this study reveals that during the initial passages following reprogramming, iPSCs maintained the expression of a miRNA set exclusive to the original somatic population. Hence the use of these miRNAs might hold a direct application toward our understanding of the differentiation process of iPSCs toward hematopoietic progenitor cells.
Collapse
Affiliation(s)
- Marianna Vitaloni
- From the Center for Regenerative Medicine in Barcelona, 08003 Barcelona, Spain and
| | | | | | | | | | | |
Collapse
|
59
|
Hematopoietic stem and progenitor cells acquire distinct DNA-hypermethylation during in vitro culture. Sci Rep 2013; 3:3372. [PMID: 24284763 PMCID: PMC3842544 DOI: 10.1038/srep03372] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Accepted: 11/11/2013] [Indexed: 01/08/2023] Open
Abstract
Hematopoietic stem and progenitor cells (HPCs) can be maintained invitro, but the vast majority of their progeny loses stemness during culture. In this study, we compared DNA-methylation (DNAm) profiles of freshly isolated and culture-expanded HPCs. Culture conditions of CD34+ cells - either with or without mesenchymal stromal cells (MSCs) - had relatively little impact on DNAm, although proliferation is greatly increased by stromal support. However, all cultured HPCs - even those which remained CD34+ - acquired significant DNA-hypermethylation. DNA-hypermethylation occurred particularly in up-stream promoter regions, shore-regions of CpG islands, binding sites for PU.1, HOXA5 and RUNX1, and it was reflected in differential gene expression and variant transcripts of DNMT3A. Low concentrations of DNAm inhibitors slightly increased the frequency of colony-forming unit initiating cells. Our results demonstrate that HPCs acquire DNA-hypermethylation at specific sites in the genome which is relevant for the rapid loss of stemness during in vitro manipulation.
Collapse
|
60
|
Genome-wide methylation analyses of primary human leukocyte subsets identifies functionally important cell-type-specific hypomethylated regions. Blood 2013; 122:e52-60. [PMID: 24159175 DOI: 10.1182/blood-2013-05-503201] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
DNA methylation is an important mechanism by which gene transcription and hence cellular function are regulated. Here, we provide detailed functional genome-wide methylome maps of 5 primary peripheral blood leukocyte subsets including T cells, B cells, monocytes/macrophages, and neutrophils obtained from healthy individuals. A comparison of these methylomes revealed highly specific cell-lineage and cell-subset methylation profiles. DNA hypomethylation is known to be permissive for gene expression and we identified cell-subset-specific hypomethylated regions (HMRs) that strongly correlate with gene transcription levels suggesting these HMRs may regulate corresponding cell functions. Single-nucleotide polymorphisms associated with immune-mediated disease in genome-wide association studies preferentially localized to these cell-specific regulatory HMRs, offering insight into pathogenesis by highlighting cell subsets in which specific epigenetic changes may drive disease. Our data provide a valuable reference tool for researchers aiming to investigate the role of DNA methylation in regulating primary leukocyte function in health and immune-mediated disease.
Collapse
|
61
|
DNA methylation profiling of the fibrinogen gene landscape in human cells and during mouse and zebrafish development. PLoS One 2013; 8:e73089. [PMID: 23991173 PMCID: PMC3749180 DOI: 10.1371/journal.pone.0073089] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2013] [Accepted: 07/17/2013] [Indexed: 11/19/2022] Open
Abstract
The fibrinogen genes FGA, FGB and FGG show coordinated expression in hepatocytes. Understanding the underlying transcriptional regulation may elucidate how their tissue-specific expression is maintained and explain the high variability in fibrinogen blood levels. DNA methylation of CpG-poor gene promoters is dynamic with low methylation correlating with tissue-specific gene expression but its direct effect on gene regulation as well as implications of non-promoter CpG methylation are not clear. Here we compared methylation of CpG sites throughout the fibrinogen gene cluster in human cells and mouse and zebrafish tissues. We observed low DNA methylation of the CpG-poor fibrinogen promoters and of additional regulatory elements (the liver enhancers CNC12 and PFE2) in fibrinogen-expressing samples. In a gene reporter assay, CpG-methylation in the FGA promoter reduced promoter activity, suggesting a repressive function for DNA methylation in the fibrinogen locus. In mouse and zebrafish livers we measured reductions in DNA methylation around fibrinogen genes during development that were preceded by increased fibrinogen expression and tri-methylation of Histone3 lysine4 (H3K4me3) in fibrinogen promoters. Our data support a model where changes in hepatic transcription factor expression and histone modification provide the switch for increased fibrinogen gene expression in the developing liver which is followed by reduction of CpG methylation.
Collapse
|
62
|
Johnson AA, Akman K, Calimport SRG, Wuttke D, Stolzing A, de Magalhães JP. The role of DNA methylation in aging, rejuvenation, and age-related disease. Rejuvenation Res 2013; 15:483-94. [PMID: 23098078 DOI: 10.1089/rej.2012.1324] [Citation(s) in RCA: 232] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
DNA methylation is a major control program that modulates gene expression in a plethora of organisms. Gene silencing through methylation occurs through the activity of DNA methyltransferases, enzymes that transfer a methyl group from S-adenosyl-L-methionine to the carbon 5 position of cytosine. DNA methylation patterns are established by the de novo DNA methyltransferases (DNMTs) DNMT3A and DNMT3B and are subsequently maintained by DNMT1. Aging and age-related diseases include defined changes in 5-methylcytosine content and are generally characterized by genome-wide hypomethylation and promoter-specific hypermethylation. These changes in the epigenetic landscape represent potential disease biomarkers and are thought to contribute to age-related pathologies, such as cancer, osteoarthritis, and neurodegeneration. Some diseases, such as a hereditary form of sensory neuropathy accompanied by dementia, are directly caused by methylomic changes. Epigenetic modifications, however, are reversible and are therefore a prime target for therapeutic intervention. Numerous drugs that specifically target DNMTs are being tested in ongoing clinical trials for a variety of cancers, and data from finished trials demonstrate that some, such as 5-azacytidine, may even be superior to standard care. DNMTs, demethylases, and associated partners are dynamically shaping the methylome and demonstrate great promise with regard to rejuvenation.
Collapse
Affiliation(s)
- Adiv A Johnson
- Department of Physiological Sciences, University of Arizona, Tucson, AZ, USA
| | | | | | | | | | | |
Collapse
|
63
|
Rodríguez-Rodero S, Fernández AF, Fernández-Morera JL, Castro-Santos P, Bayon GF, Ferrero C, Urdinguio RG, Gonzalez-Marquez R, Suarez C, Fernández-Vega I, Fresno Forcelledo MF, Martínez-Camblor P, Mancikova V, Castelblanco E, Perez M, Marrón PI, Mendiola M, Hardisson D, Santisteban P, Riesco-Eizaguirre G, Matías-Guiu X, Carnero A, Robledo M, Delgado-Álvarez E, Menéndez-Torre E, Fraga MF. DNA methylation signatures identify biologically distinct thyroid cancer subtypes. J Clin Endocrinol Metab 2013; 98:2811-21. [PMID: 23666970 DOI: 10.1210/jc.2012-3566] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
OBJECTIVE The purpose of this study was to determine the global patterns of aberrant DNA methylation in thyroid cancer. RESEARCH DESIGN AND METHODS We have used DNA methylation arrays to determine, for the first time, the genome-wide promoter methylation status of papillary, follicular, medullary, and anaplastic thyroid tumors. RESULTS We identified 262 and 352 hypermethylated and 13 and 21 hypomethylated genes in differentiated papillary and follicular tumors, respectively. Interestingly, the other tumor types analyzed displayed more hypomethylated genes (280 in anaplastic and 393 in medullary tumors) than aberrantly hypermethylated genes (86 in anaplastic and 131 in medullary tumors). Among the genes indentified, we show that 4 potential tumor suppressor genes (ADAMTS8, HOXB4, ZIC1, and KISS1R) and 4 potential oncogenes (INSL4, DPPA2, TCL1B, and NOTCH4) are frequently regulated by aberrant methylation in primary thyroid tumors. In addition, we show that aberrant promoter hypomethylation-associated overexpression of MAP17 might promote tumor growth in thyroid cancer. CONCLUSIONS Thyroid cancer subtypes present differential promoter methylation signatures, and nondifferentiated subtypes are characterized by aberrant promoter hypomethylation rather than hypermethylation. Additional studies are needed to determine the potential clinical interest of the tumor subtype-specific DNA methylation signatures described herein and the role of aberrant promoter hypomethylation in nondifferentiated thyroid tumors.
Collapse
MESH Headings
- Adenocarcinoma, Follicular/genetics
- Adenocarcinoma, Follicular/metabolism
- Adenocarcinoma, Follicular/pathology
- Carcinoma/genetics
- Carcinoma/metabolism
- Carcinoma/pathology
- Carcinoma, Medullary/genetics
- Carcinoma, Medullary/metabolism
- Carcinoma, Medullary/pathology
- Carcinoma, Neuroendocrine
- Carcinoma, Papillary/genetics
- Carcinoma, Papillary/metabolism
- Carcinoma, Papillary/pathology
- Cell Line, Tumor
- Cohort Studies
- DNA Methylation
- Down-Regulation
- Genome-Wide Association Study
- Humans
- Neoplasm Proteins/genetics
- Neoplasm Proteins/metabolism
- Oligonucleotide Array Sequence Analysis
- Promoter Regions, Genetic
- Thyroid Cancer, Papillary
- Thyroid Carcinoma, Anaplastic
- Thyroid Gland/metabolism
- Thyroid Gland/pathology
- Thyroid Neoplasms/genetics
- Thyroid Neoplasms/metabolism
- Thyroid Neoplasms/pathology
- Tissue Banks
- Tumor Cells, Cultured
- Up-Regulation
Collapse
Affiliation(s)
- Sandra Rodríguez-Rodero
- Department of Endocrinology and Nutrition, Instituto Universitario de Oncología del Principado de Asturias, Hospital Universitario Central de Asturias, 33006 Oviedo, Spain
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
64
|
Tzenaki N, Papakonstanti EA. p110δ PI3 kinase pathway: emerging roles in cancer. Front Oncol 2013; 3:40. [PMID: 23459844 PMCID: PMC3585436 DOI: 10.3389/fonc.2013.00040] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2012] [Accepted: 02/12/2013] [Indexed: 12/11/2022] Open
Abstract
Class IA PI3Ks consists of three isoforms of the p110 catalytic subunit designated p110α, p110β, and p110δ which are encoded by three separate genes. Gain-of-function mutations on PIK3CA gene encoding for p110α isoform have been detected in a wide variety of human cancers whereas no somatic mutations of genes encoding for p110β or p110δ have been reported. Unlike p110α and p110β which are ubiquitously expressed, p110δ is highly enriched in leukocytes and thus the p110δ PI3K pathway has attracted more attention for its involvement in immune disorders. However, findings have been accumulated showing that the p110δ PI3K plays a seminal role in the development and progression of some hematologic malignancies. A wealth of knowledge has come from studies showing the central role of p110δ PI3K in B-cell functions and B-cell malignancies. Further data have documented that wild-type p110δ becomes oncogenic when overexpressed in cell culture models and that p110δ is the predominant isoform expressed in some human solid tumor cells playing a prominent role in these cells. Genetic inactivation of p110δ in mice models and highly-selective inhibitors of p110δ have demonstrated an important role of this isoform in differentiation, growth, survival, motility, and morphology with the inositol phosphatase PTEN to play a critical role in p110δ signaling. In this review, we summarize our understanding of the p110δ PI3K signaling pathway in hematopoietic cells and malignancies, we highlight the evidence showing the oncogenic potential of p110δ in cells of non-hematopoietic origin and we discuss perspectives for potential novel roles of p110δ PI3K in cancer.
Collapse
Affiliation(s)
- Niki Tzenaki
- Department of Biochemistry, School of Medicine, University of Crete Heraklion, Greece
| | | |
Collapse
|
65
|
Rodriguez RM, Suarez-Alvarez B, Salvanés R, Muro M, Martínez-Camblor P, Colado E, Sánchez MA, Díaz MG, Fernandez AF, Fraga MF, Lopez-Larrea C. DNA methylation dynamics in blood after hematopoietic cell transplant. PLoS One 2013; 8:e56931. [PMID: 23451113 PMCID: PMC3579934 DOI: 10.1371/journal.pone.0056931] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2012] [Accepted: 01/16/2013] [Indexed: 12/20/2022] Open
Abstract
Epigenetic deregulation is considered a common hallmark of cancer. Nevertheless, recent publications have demonstrated its association with a large array of human diseases. Here, we explore the DNA methylation dynamics in blood samples during hematopoietic cell transplant and how they are affected by pathophysiological events during transplant evolution. We analyzed global DNA methylation in a cohort of 47 patients with allogenic transplant up to 12 months post-transplant. Recipients stably maintained the donor’s global methylation levels after transplant. Nonetheless, global methylation is affected by chimerism status. Methylation analysis of promoters revealed that methylation in more than 200 genes is altered 1 month post-transplant when compared with non-pathological methylation levels in the donor. This number decreased by 6 months post-transplant. Finally, we analyzed methylation in IFN-γ, FASL, IL-10, and PRF1 and found association with the severity of the acute graft-versus-host disease. Our results provide strong evidence that methylation changes in blood are linked to underlying physiological events and demonstrate that DNA methylation analysis is a viable strategy for the study of transplantation and for development of biomarkers.
Collapse
Affiliation(s)
- Ramon M. Rodriguez
- Cancer Epigenetics Laboratory, Instituto Universitario de Oncología del Principado de Asturias (IUOPA), HUCA, Universidad de Oviedo, Oviedo, Spain
| | | | - Rubén Salvanés
- Department of Immunology, Hospital Universitario Central de Asturias, Oviedo, Spain
| | - Manuel Muro
- Department of Immunology, Hospital Virgen de la Arrixaca, Murcia, Spain
| | | | - Enrique Colado
- Department of Hematology, Hospital Universitario Central de Asturias, Oviedo, Spain
| | - Miguel Alcoceba Sánchez
- Servicio de Hematología y Hemoterapia, Hospital Universitario de Salamanca, Salamanca, Spain
| | - Marcos González Díaz
- Servicio de Hematología y Hemoterapia, Hospital Universitario de Salamanca, Salamanca, Spain
| | - Agustin F. Fernandez
- Cancer Epigenetics Laboratory, Instituto Universitario de Oncología del Principado de Asturias (IUOPA), HUCA, Universidad de Oviedo, Oviedo, Spain
| | - Mario F. Fraga
- Cancer Epigenetics Laboratory, Instituto Universitario de Oncología del Principado de Asturias (IUOPA), HUCA, Universidad de Oviedo, Oviedo, Spain
- Department of Immunology and Oncology, Centro Nacional de Biotecnologıa/CNB-CSIC, Cantoblanco, Madrid, Spain
- * E-mail: (MFF); (CLL)
| | - Carlos Lopez-Larrea
- Department of Immunology, Hospital Universitario Central de Asturias, Oviedo, Spain
- Fundación Renal “Iñigo Álvarez de Toledo”, Madrid, Spain
- * E-mail: (MFF); (CLL)
| |
Collapse
|
66
|
Abstract
DNA methylation is among the best studied epigenetic modifications and is essential to mammalian development. Although the methylation status of most CpG dinucleotides in the genome is stably propagated through mitosis, improvements to methods for measuring methylation have identified numerous regions in which it is dynamically regulated. In this Review, we discuss key concepts in the function of DNA methylation in mammals, stemming from more than two decades of research, including many recent studies that have elucidated when and where DNA methylation has a regulatory role in the genome. We include insights from early development, embryonic stem cells and adult lineages, particularly haematopoiesis, to highlight the general features of this modification as it participates in both global and localized epigenetic regulation.
Collapse
|
67
|
Abstract
Acute myeloid leukemia (AML) is characterized by dysregulated gene expression and abnormal patterns of DNA methylation; the relationship between these events is unclear. Many AML patients are now being treated with hypomethylating agents, such as decitabine (DAC), although the mechanisms by which it induces remissions remain unknown. The goal of this study was to use a novel stromal coculture assay that can expand primary AML cells to identify the immediate changes induced by DAC with a dose (100nM) that decreases total 5-methylcytosine content and reactivates imprinted genes (without causing myeloid differentiation, which would confound downstream genomic analyses). Using array-based technologies, we found that DAC treatment caused global hypomethylation in all samples (with a preference for regions with higher levels of baseline methylation), yet there was limited correlation between changes in methylation and gene expression. Moreover, the patterns of methylation and gene expression across the samples were primarily determined by the intrinsic properties of the primary cells, rather than DAC treatment. Although DAC induces hypomethylation, we could not identify canonical target genes that are altered by DAC in primary AML cells, suggesting that the mechanism of action of DAC is more complex than previously recognized.
Collapse
|
68
|
Guibert S, Weber M. Functions of DNA Methylation and Hydroxymethylation in Mammalian Development. Curr Top Dev Biol 2013; 104:47-83. [DOI: 10.1016/b978-0-12-416027-9.00002-4] [Citation(s) in RCA: 125] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
|
69
|
Mayol G, Martín-Subero JI, Ríos J, Queiros A, Kulis M, Suñol M, Esteller M, Gómez S, Garcia I, de Torres C, Rodríguez E, Galván P, Mora J, Lavarino C. DNA hypomethylation affects cancer-related biological functions and genes relevant in neuroblastoma pathogenesis. PLoS One 2012; 7:e48401. [PMID: 23144874 PMCID: PMC3492354 DOI: 10.1371/journal.pone.0048401] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2012] [Accepted: 10/01/2012] [Indexed: 02/06/2023] Open
Abstract
Neuroblastoma (NB) pathogenesis has been reported to be closely associated with numerous genetic alterations. However, underlying DNA methylation patterns have not been extensively studied in this developmental malignancy. Here, we generated microarray-based DNA methylation profiles of primary neuroblastic tumors. Stringent supervised differential methylation analyses allowed us to identify epigenetic changes characteristic for NB tumors as well as for clinical and biological subtypes of NB. We observed that gene-specific loss of DNA methylation is more prevalent than promoter hypermethylation. Remarkably, such hypomethylation affected cancer-related biological functions and genes relevant to NB pathogenesis such as CCND1, SPRR3, BTC, EGF and FGF6. In particular, differential methylation in CCND1 affected mostly an evolutionary conserved functionally relevant 3′ untranslated region, suggesting that hypomethylation outside promoter regions may play a role in NB pathogenesis. Hypermethylation targeted genes involved in cell development and proliferation such as RASSF1A, POU2F2 or HOXD3, among others. The results derived from this study provide new candidate epigenetic biomarkers associated with NB as well as insights into the molecular pathogenesis of this tumor, which involves a marked gene-specific hypomethylation.
Collapse
Affiliation(s)
- Gemma Mayol
- Developmental Tumor Biology Laboratory, Hospital Sant Joan de Déu, Fundación Sant Joan de Déu, Barcelona, Spain
| | - José I. Martín-Subero
- Department of Anatomic Pathology, Pharmacology and Microbiology, University of Barcelona, Barcelona, Spain
| | - José Ríos
- Laboratory of Biostatistics and Epidemiology, Universitat Autònoma de Barcelona, Barcelona, Spain
- Clinical Pharmacology Service, IDIBAPS, Hospital Clinic, Barcelona, Spain
| | - Ana Queiros
- Department of Anatomic Pathology, Pharmacology and Microbiology, University of Barcelona, Barcelona, Spain
| | - Marta Kulis
- Hematopathology Unit, Hospital Clinic, Barcelona, Spain
| | - Mariona Suñol
- Department of Pathology, Hospital Sant Joan de Déu, Barcelona, Spain
| | - Manel Esteller
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL),L'Hospitalet, Barcelona, Spain
- Department of Physiological Sciences II, School of Medicine, University of Barcelona, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Soledad Gómez
- Developmental Tumor Biology Laboratory, Hospital Sant Joan de Déu, Fundación Sant Joan de Déu, Barcelona, Spain
| | - Idoia Garcia
- Developmental Tumor Biology Laboratory, Hospital Sant Joan de Déu, Fundación Sant Joan de Déu, Barcelona, Spain
| | - Carmen de Torres
- Developmental Tumor Biology Laboratory, Hospital Sant Joan de Déu, Fundación Sant Joan de Déu, Barcelona, Spain
| | - Eva Rodríguez
- Developmental Tumor Biology Laboratory, Hospital Sant Joan de Déu, Fundación Sant Joan de Déu, Barcelona, Spain
| | - Patricia Galván
- Developmental Tumor Biology Laboratory, Hospital Sant Joan de Déu, Fundación Sant Joan de Déu, Barcelona, Spain
| | - Jaume Mora
- Developmental Tumor Biology Laboratory, Hospital Sant Joan de Déu, Fundación Sant Joan de Déu, Barcelona, Spain
| | - Cinzia Lavarino
- Developmental Tumor Biology Laboratory, Hospital Sant Joan de Déu, Fundación Sant Joan de Déu, Barcelona, Spain
- * E-mail:
| |
Collapse
|
70
|
Lee ST, Xiao Y, Muench MO, Xiao J, Fomin ME, Wiencke JK, Zheng S, Dou X, de Smith A, Chokkalingam A, Buffler P, Ma X, Wiemels JL. A global DNA methylation and gene expression analysis of early human B-cell development reveals a demethylation signature and transcription factor network. Nucleic Acids Res 2012; 40:11339-51. [PMID: 23074194 PMCID: PMC3526268 DOI: 10.1093/nar/gks957] [Citation(s) in RCA: 88] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The epigenetic changes during B-cell development relevant to both normal function and hematologic malignancy are incompletely understood. We examined DNA methylation and RNA expression status during early B-cell development by sorting multiple replicates of four separate stages of pre-B cells derived from normal human fetal bone marrow and applied high-dimension DNA methylation scanning and expression arrays. Features of promoter and gene body DNA methylation were strongly correlated with RNA expression in multipotent progenitors (MPPs) both in a static state and throughout differentiation. As MPPs commit to pre-B cells, a predominantly demethylating phenotype ensues, with 79% of the 2966 differentially methylated regions observed involving demethylation. Demethylation events were more often gene body associated rather than promoter associated; predominantly located outside of CpG islands; and closely associated with EBF1, E2F, PAX5 and other functional transcription factor (TF) sites related to B-cell development. Such demethylation events were accompanied by TF occupancy. After commitment, DNA methylation changes appeared to play a smaller role in B-cell development. We identified a distinct development-dependent demethylation signature which has gene expression regulatory properties for pre-B cells, and provide a catalog reference for the epigenetic changes that occur in pre-B-cell leukemia and other B-cell-related diseases.
Collapse
Affiliation(s)
- Seung-Tae Lee
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA 94158, USA
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
71
|
Sproul D, Kitchen RR, Nestor CE, Dixon JM, Sims AH, Harrison DJ, Ramsahoye BH, Meehan RR. Tissue of origin determines cancer-associated CpG island promoter hypermethylation patterns. Genome Biol 2012; 13:R84. [PMID: 23034185 PMCID: PMC3491412 DOI: 10.1186/gb-2012-13-10-r84] [Citation(s) in RCA: 131] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2012] [Revised: 07/13/2012] [Accepted: 10/03/2012] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Aberrant CpG island promoter DNA hypermethylation is frequently observed in cancer and is believed to contribute to tumor progression by silencing the expression of tumor suppressor genes. Previously, we observed that promoter hypermethylation in breast cancer reflects cell lineage rather than tumor progression and occurs at genes that are already repressed in a lineage-specific manner. To investigate the generality of our observation we analyzed the methylation profiles of 1,154 cancers from 7 different tissue types. RESULTS We find that 1,009 genes are prone to hypermethylation in these 7 types of cancer. Nearly half of these genes varied in their susceptibility to hypermethylation between different cancer types. We show that the expression status of hypermethylation prone genes in the originator tissue determines their propensity to become hypermethylated in cancer; specifically, genes that are normally repressed in a tissue are prone to hypermethylation in cancers derived from that tissue. We also show that the promoter regions of hypermethylation-prone genes are depleted of repetitive elements and that DNA sequence around the same promoters is evolutionarily conserved. We propose that these two characteristics reflect tissue-specific gene promoter architecture regulating the expression of these hypermethylation prone genes in normal tissues. CONCLUSIONS As aberrantly hypermethylated genes are already repressed in pre-cancerous tissue, we suggest that their hypermethylation does not directly contribute to cancer development via silencing. Instead aberrant hypermethylation reflects developmental history and the perturbation of epigenetic mechanisms maintaining these repressed promoters in a hypomethylated state in normal cells.
Collapse
Affiliation(s)
- Duncan Sproul
- Breakthrough Breast Cancer Research Unit and Division of Pathology, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, UK
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, UK
| | - Robert R Kitchen
- Breakthrough Breast Cancer Research Unit and Division of Pathology, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, UK
- Yale University School of Medicine, Department of Molecular Biophysics & Biochemistry and Department of Psychiatry, 266 Whitney Ave, New Haven, CT 06511, USA
| | - Colm E Nestor
- Breakthrough Breast Cancer Research Unit and Division of Pathology, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, UK
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, UK
| | - J Michael Dixon
- Breakthrough Breast Cancer Research Unit and Division of Pathology, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, UK
| | - Andrew H Sims
- Breakthrough Breast Cancer Research Unit and Division of Pathology, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, UK
| | - David J Harrison
- Breakthrough Breast Cancer Research Unit and Division of Pathology, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, UK
- University of St Andrews School of Medicine, Medical and Biological Sciences Building, University of St Andrews, North Haugh, St Andrews KY16 9TF, UK
| | - Bernard H Ramsahoye
- Breakthrough Breast Cancer Research Unit and Division of Pathology, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, UK
- Centre for Molecular Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, UK
| | - Richard R Meehan
- Breakthrough Breast Cancer Research Unit and Division of Pathology, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, UK
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, UK
| |
Collapse
|
72
|
Differential DNA methylation in purified human blood cells: implications for cell lineage and studies on disease susceptibility. PLoS One 2012; 7:e41361. [PMID: 22848472 PMCID: PMC3405143 DOI: 10.1371/journal.pone.0041361] [Citation(s) in RCA: 741] [Impact Index Per Article: 61.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2012] [Accepted: 06/20/2012] [Indexed: 02/07/2023] Open
Abstract
Methylation of cytosines at CpG sites is a common epigenetic DNA modification that can be measured by a large number of methods, now even in a genome-wide manner for hundreds of thousands of sites. The application of DNA methylation analysis is becoming widely popular in complex disorders, for example, to understand part of the “missing heritability”. The DNA samples most readily available for methylation studies are derived from whole blood. However, blood consists of many functionally and developmentally distinct cell populations in varying proportions. We studied whether such variation might affect the interpretation of methylation studies based on whole blood DNA. We found in healthy male blood donors there is important variation in the methylation profiles of whole blood, mononuclear cells, granulocytes, and cells from seven selected purified lineages. CpG methylation between mononuclear cells and granulocytes differed for 22% of the 8252 probes covering the selected 343 genes implicated in immune-related disorders by genome-wide association studies, and at least one probe was differentially methylated for 85% of the genes, indicating that whole blood methylation results might be unintelligible. For individual genes, even if the overall methylation patterns might appear similar, a few CpG sites in the regulatory regions may have opposite methylation patterns (i.e., hypo/hyper) in the main blood cell types. We conclude that interpretation of whole blood methylation profiles should be performed with great caution and for any differences implicated in a disorder, the differences resulting from varying proportions of white blood cell types should be considered.
Collapse
|
73
|
Suarez-Alvarez B, Rodriguez RM, Fraga MF, López-Larrea C. DNA methylation: a promising landscape for immune system-related diseases. Trends Genet 2012; 28:506-14. [PMID: 22824525 DOI: 10.1016/j.tig.2012.06.005] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2012] [Revised: 06/13/2012] [Accepted: 06/20/2012] [Indexed: 01/31/2023]
Abstract
During hematopoiesis, a unique hematopoietic stem cell (HSC) from the bone marrow gives rise to a subset of mature blood cells that directs all the immune responses. Recent studies have shown that this well-defined, hierarchical process is regulated in part by epigenetic mechanisms. Changes in the DNA methylation profile have a critical role in the division of these stem cells into the myeloid and lymphoid lineages and in the establishment of a specific phenotype and functionality in each terminally differentiated cell type. In this review, we describe how the DNA methylation patterns are modified during hematopoietic differentiation and what their role is in cell plasticity and immune function. An in-depth knowledge of these epigenetic mechanisms will help clarify how cell type-specific gene programs are established, and how they can be leveraged in the development of novel strategies for treating immune system-related pathologies.
Collapse
|
74
|
Huidobro C, Fernandez AF, Fraga MF. Aging epigenetics: causes and consequences. Mol Aspects Med 2012; 34:765-81. [PMID: 22771540 DOI: 10.1016/j.mam.2012.06.006] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2012] [Accepted: 06/27/2012] [Indexed: 12/26/2022]
Abstract
Growth and development of higher organisms are regulated by the orchestrated change of epigenetic marks over time. In addition, there is also an epigenetic variation without any apparent role in development that is thought to be the result of the stochastic accumulation of epigenetic errors. The process depends on genetic and environmental factors and, when it takes place in adult stem cells, it could play an important role in aging, although the underlying molecular mechanisms are still largely unknown.
Collapse
Affiliation(s)
- Covadonga Huidobro
- Cancer Epigenetics Laboratory, Instituto Universitario de Oncología del Principado de Asturias (IUOPA), HUCA, Universidad de Oviedo, Oviedo, Spain
| | | | | |
Collapse
|
75
|
De novo DNA methyltransferases: oncogenes, tumor suppressors, or both? Trends Genet 2012; 28:474-9. [PMID: 22704242 DOI: 10.1016/j.tig.2012.05.006] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2012] [Revised: 05/17/2012] [Accepted: 05/18/2012] [Indexed: 11/23/2022]
Abstract
Aberrant promoter DNA hypermethylation of tumor suppressor genes is a hallmark of cancer. This alteration is largely dependent on the action of de novo DNA methyltransferases (DNMTs) early during tumor progression, which supports the oncogenic role for these enzymes. However, recent research has identified several inactivating mutations of de novo DNMTs in various types of tumor. In addition, it has been shown that loss of de novo DNA methylation activity at advanced tumor stages leads to the promoter DNA demethylation-dependent expression of specific oncogenes. These new data support the notion that de novo DNMTs also have an important role in the maintenance of DNA methylation and suggest that, in addition to acting as oncogenes, they also behave as tumor suppressors. This potential dual role might have clinical implications, as DNMTs are currently considered bona fide targets in cancer therapy.
Collapse
|
76
|
Isoform-selective induction of human p110δ PI3K expression by TNFα: identification of a new and inducible PIK3CD promoter. Biochem J 2012; 443:857-67. [PMID: 22375552 PMCID: PMC3328000 DOI: 10.1042/bj20112214] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
PI3Ks (phosphoinositide 3-kinases) are signalling molecules and drug targets with important biological functions, yet the regulation of PI3K gene expression is poorly understood. Key PI3Ks are the class IA PI3Ks that consist of a catalytic subunit (p110α, p110β and p110δ) in complex with a p85 regulatory subunit. Whereas p110α and p110β are ubiquitously expressed, high levels of p110δ are mainly found in white blood cells, with most non-leucocytes expressing low levels of p110δ. In the present paper we report that TNFα (tumour necrosis factor α) stimulation induces p110δ expression in human ECs (endothelial cells) and synovial fibroblasts, but not in leucocytes, through transcription start sites located in a novel promoter region in the p110δ gene (PIK3CD). This promoter is used in all cell types, including solid tumour cell lines that express p110δ, and is activated by TNFα in ECs and synovial fibroblasts. We further present a detailed biochemical and bioinformatic characterization of p110δ gene regulation, demonstrating that PIK3CD has distinct promoters, some of which can be dynamically activated by pro-inflammatory mediators. This is the first molecular identification of a PI3K promoter under the control of acute extracellular stimulation.
Collapse
|
77
|
Li Y, Chen G, Ma L, Ohms SJ, Sun C, Shannon MF, Fan JY. Plasticity of DNA methylation in mouse T cell activation and differentiation. BMC Mol Biol 2012; 13:16. [PMID: 22642378 PMCID: PMC3386888 DOI: 10.1186/1471-2199-13-16] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2011] [Accepted: 05/29/2012] [Indexed: 01/09/2023] Open
Abstract
Background Circulating CD4+ T helper cells are activated through interactions with antigen presenting cells and undergo differentiation into specific T helper cell subsets depending on the type of antigen encountered. In addition, the relative composition of the circulating CD4+ T cell population changes as animals mature with an increased percentage of the population being memory/effector type cells. Results Here, we report on the highly plastic nature of DNA methylation at the genome-wide level as T cells undergo activation, differentiation and aging. Of particular note were the findings that DNA demethylation occurred rapidly following T cell activation and that all differentiated T cell populations displayed lower levels of global methylation than the non-differentiated population. In addition, T cells from older mice had a reduced level of DNA methylation, most likely explained by the increase in the memory/effector cell fraction. Although significant genome-wide changes were observed, changes in DNA methylation at individual genes were restricted to specific cell types. Changes in the expression of enzymes involved in DNA methylation and demethylation reflect in most cases the changes observed in the genome-wide DNA methylation status. Conclusion We have demonstrated that DNA methylation is dynamic and flexible in CD4+ T cells and changes rapidly both in a genome-wide and in a targeted manner during T cell activation, differentiation. These changes are accompanied by parallel changes in the enzymatic complexes that have been implicated in DNA methylation and demethylation implying that the balance between these opposing activities may play a role in the maintaining the methylation profile of a given cell type but also allow flexibility in a cell population that needs to respond rapidly to environmental signals.
Collapse
Affiliation(s)
- Yan Li
- College of Animal Science & Technology, Northwest A&F University, Yangling Shaanxi 712100, P. R. China
| | | | | | | | | | | | | |
Collapse
|
78
|
Auclair G, Weber M. Mechanisms of DNA methylation and demethylation in mammals. Biochimie 2012; 94:2202-11. [PMID: 22634371 DOI: 10.1016/j.biochi.2012.05.016] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2012] [Accepted: 05/15/2012] [Indexed: 12/18/2022]
Abstract
Cytosine methylation is an epigenetically propagated DNA modification that can modify how the DNA molecule is recognized and expressed. DNA methylation undergoes extensive reprogramming during mammalian embryogenesis and is directly linked to the regulation of pluripotency and cellular identity. Studying its regulation is also important for a better understanding of the many diseases that show epigenetic deregulations, in particular, cancer. In the recent years, a lot of progress has been made to characterize the profiles of DNA methylation at the genome level, which revealed that patterns of DNA methylation are highly dynamic between cell types. Here, we discuss the importance of DNA methylation for genome regulation and the mechanisms that remodel the DNA methylome during mammalian development, in particular the involvement of the rediscovered modified base 5-hydroxymethylcytosine.
Collapse
Affiliation(s)
- Ghislain Auclair
- UMR 7242, Biotechnology and Cell Signalling, Université de Strasbourg, CNRS, ESBS, Bd Sébastien Brant, BP 10413, 67412 Illkirch Cedex, France
| | | |
Collapse
|
79
|
Khulan B, Cooper WN, Skinner BM, Bauer J, Owens S, Prentice AM, Belteki G, Constancia M, Dunger D, Affara NA. Periconceptional maternal micronutrient supplementation is associated with widespread gender related changes in the epigenome: a study of a unique resource in the Gambia. Hum Mol Genet 2012; 21:2086-101. [PMID: 22307237 DOI: 10.1093/hmg/dds026] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
In addition to the genetic constitution inherited by an organism, the developmental trajectory and resulting mature phenotype are also determined by mechanisms acting during critical windows in early life that influence and establish stable patterns of gene expression. This is the crux of the developmental origins of health and disease hypothesis that suggests undernutrition during gestation and infancy predisposes to ill health in later life. The hypothesis that periconceptional maternal micronutrient supplementation might affect fetal genome-wide methylation within gene promoters was explored in cord blood samples from offspring of Gambian women enrolled into a unique randomized, double blind controlled trial. Significant changes in the epigenome in cord blood DNA samples were further explored in a subset of offspring at 9 months. Gender-specific changes related to periconceptional nutritional supplementation were identified in cord blood DNA samples, some of which showed persistent changes in infant blood DNA samples. Significant effects of periconceptional micronutrient supplementation were also observed in postnatal samples which were not evident in cord blood. In this Gambian population, the increased death rate of individuals born in nutritionally poor seasons has been related to infection and it is of interest that we identified differential methylation at genes associated with defence against infection and immune response. Although the sample size was relatively small, these pilot data suggest that periconceptional nutrition in humans is an important determinant of newborn whole genome methylation patterns but may also influence postnatal developmental patterns of gene promoter methylation linking early with disease risk.
Collapse
Affiliation(s)
- Batbayar Khulan
- Mammalian Molecular Genetics Group, Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK
| | | | | | | | | | | | | | | | | | | |
Collapse
|
80
|
Ramos-Mejía V, Montes R, Bueno C, Ayllón V, Real PJ, Rodríguez R, Menendez P. Residual expression of the reprogramming factors prevents differentiation of iPSC generated from human fibroblasts and cord blood CD34+ progenitors. PLoS One 2012; 7:e35824. [PMID: 22545141 PMCID: PMC3335819 DOI: 10.1371/journal.pone.0035824] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2012] [Accepted: 03/22/2012] [Indexed: 12/11/2022] Open
Abstract
Human induced pluripotent stem cells (hiPSC) have been generated from different tissues, with the age of the donor, tissue source and specific cell type influencing the reprogramming process. Reprogramming hematopoietic progenitors to hiPSC may provide a very useful cellular system for modelling blood diseases. We report the generation and complete characterization of hiPSCs from human neonatal fibroblasts and cord blood (CB)-derived CD34+ hematopoietic progenitors using a single polycistronic lentiviral vector containing an excisable cassette encoding the four reprogramming factors Oct4, Klf4, Sox2 and c-myc (OKSM). The ectopic expression of OKSM was fully silenced upon reprogramming in some hiPSC clones and was not reactivated upon differentiation, whereas other hiPSC clones failed to silence the transgene expression, independently of the cell type/tissue origin. When hiPSC were induced to differentiate towards hematopoietic and neural lineages those hiPSC which had silenced OKSM ectopic expression displayed good hematopoietic and early neuroectoderm differentiation potential. In contrast, those hiPSC which failed to switch off OKSM expression were unable to differentiate towards either lineage, suggesting that the residual expression of the reprogramming factors functions as a developmental brake impairing hiPSC differentiation. Successful adenovirus-based Cre-mediated excision of the provirus OKSM cassette in CB-derived CD34+ hiPSC with residual transgene expression resulted in transgene-free hiPSC clones with significantly improved differentiation capacity. Overall, our findings confirm that residual expression of reprogramming factors impairs hiPSC differentiation.
Collapse
Affiliation(s)
- Verónica Ramos-Mejía
- Centre Pfizer-Universidad de Granada-Junta de Andalucía for Genomics, Oncological Research (GENyO), Granada, Spain
- * E-mail: (VR); (PM)
| | - Rosa Montes
- Centre Pfizer-Universidad de Granada-Junta de Andalucía for Genomics, Oncological Research (GENyO), Granada, Spain
| | - Clara Bueno
- Centre Pfizer-Universidad de Granada-Junta de Andalucía for Genomics, Oncological Research (GENyO), Granada, Spain
| | - Verónica Ayllón
- Centre Pfizer-Universidad de Granada-Junta de Andalucía for Genomics, Oncological Research (GENyO), Granada, Spain
| | - Pedro J. Real
- Centre Pfizer-Universidad de Granada-Junta de Andalucía for Genomics, Oncological Research (GENyO), Granada, Spain
| | - René Rodríguez
- Centre Pfizer-Universidad de Granada-Junta de Andalucía for Genomics, Oncological Research (GENyO), Granada, Spain
| | - Pablo Menendez
- Centre Pfizer-Universidad de Granada-Junta de Andalucía for Genomics, Oncological Research (GENyO), Granada, Spain
- * E-mail: (VR); (PM)
| |
Collapse
|
81
|
Commentaries on Viewpoint: Epigenetic regulation of the ACE gene might be more relevant to endurance physiology than the I/D polymorphism. J Appl Physiol (1985) 2012; 112:1084-5. [DOI: 10.1152/japplphysiol.00065.2012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
|
82
|
Feil R, Fraga MF. Epigenetics and the environment: emerging patterns and implications. Nat Rev Genet 2012; 13:97-109. [PMID: 22215131 DOI: 10.1038/nrg3142] [Citation(s) in RCA: 1163] [Impact Index Per Article: 96.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Epigenetic phenomena in animals and plants are mediated by DNA methylation and stable chromatin modifications. There has been considerable interest in whether environmental factors modulate the establishment and maintenance of epigenetic modifications, and could thereby influence gene expression and phenotype. Chemical pollutants, dietary components, temperature changes and other external stresses can indeed have long-lasting effects on development, metabolism and health, sometimes even in subsequent generations. Although the underlying mechanisms remain largely unknown, particularly in humans, mechanistic insights are emerging from experimental model systems. These have implications for structuring future research and understanding disease and development.
Collapse
Affiliation(s)
- Robert Feil
- Institute of Molecular Genetics (IGMM), CNRS UMR-5535 and University of Montpellier, 1919 route de Mende, 34293 Montpellier, France. robert.feil@igmm. cnrs.fr
| | | |
Collapse
|
83
|
Abstract
Epigenetic phenomena in animals and plants are mediated by DNA methylation and stable chromatin modifications. There has been considerable interest in whether environmental factors modulate the establishment and maintenance of epigenetic modifications, and could thereby influence gene expression and phenotype. Chemical pollutants, dietary components, temperature changes and other external stresses can indeed have long-lasting effects on development, metabolism and health, sometimes even in subsequent generations. Although the underlying mechanisms remain largely unknown, particularly in humans, mechanistic insights are emerging from experimental model systems. These have implications for structuring future research and understanding disease and development.
Collapse
Affiliation(s)
- Robert Feil
- Institute of Molecular Genetics (IGMM), CNRS UMR-5535 and University of Montpellier, 1919 route de Mende, 34293 Montpellier, France. robert.feil@igmm. cnrs.fr
| | | |
Collapse
|