1
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Zaiou M. Peroxisome Proliferator-Activated Receptor-γ as a Target and Regulator of Epigenetic Mechanisms in Nonalcoholic Fatty Liver Disease. Cells 2023; 12:cells12081205. [PMID: 37190114 DOI: 10.3390/cells12081205] [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: 03/11/2023] [Revised: 04/17/2023] [Accepted: 04/19/2023] [Indexed: 05/17/2023] Open
Abstract
Peroxisome proliferator-activated receptor-γ (PPARγ) belongs to the superfamily of nuclear receptors that control the transcription of multiple genes. Although it is found in many cells and tissues, PPARγ is mostly expressed in the liver and adipose tissue. Preclinical and clinical studies show that PPARγ targets several genes implicated in various forms of chronic liver disease, including nonalcoholic fatty liver disease (NAFLD). Clinical trials are currently underway to investigate the beneficial effects of PPARγ agonists on NAFLD/nonalcoholic steatohepatitis. Understanding PPARγ regulators may therefore aid in unraveling the mechanisms governing the development and progression of NAFLD. Recent advances in high-throughput biology and genome sequencing have greatly facilitated the identification of epigenetic modifiers, including DNA methylation, histone modifiers, and non-coding RNAs as key factors that regulate PPARγ in NAFLD. In contrast, little is still known about the particular molecular mechanisms underlying the intricate relationships between these events. The paper that follows outlines our current understanding of the crosstalk between PPARγ and epigenetic regulators in NAFLD. Advances in this field are likely to aid in the development of early noninvasive diagnostics and future NAFLD treatment strategies based on PPARγ epigenetic circuit modification.
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Affiliation(s)
- Mohamed Zaiou
- Institut Jean-Lamour, Université de Lorraine, UMR 7198 CNRS, 54505 Vandoeuvre-les-Nancy, France
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2
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Occean JR, Yang N, Sun Y, Dawkins MS, Munk R, Belair C, Dar S, Anerillas C, Wang L, Shi C, Dunn C, Bernier M, Price NL, Kim JS, Cui CY, Fan J, Bhattacharyya M, De S, Maragkakis M, deCabo R, Sidoli S, Sen P. Gene body DNA hydroxymethylation restricts the magnitude of transcriptional changes during aging. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.15.528714. [PMID: 36824863 PMCID: PMC9949049 DOI: 10.1101/2023.02.15.528714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
DNA hydroxymethylation (5hmC) is the most abundant oxidative derivative of DNA methylation (5mC) and is typically enriched at enhancers and gene bodies of transcriptionally active and tissue-specific genes. Although aberrant genomic 5hmC has been implicated in many age-related diseases, the functional role of the modification in aging remains largely unknown. Here, we report that 5hmC is stably enriched in multiple aged organs. Using the liver and cerebellum as model organs, we show that 5hmC accumulates in gene bodies associated with tissue-specific function and thereby restricts the magnitude of gene expression changes during aging. Mechanistically, we found that 5hmC decreases binding affinity of splicing factors compared to unmodified cytosine and 5mC, and is correlated with age-related alternative splicing events, suggesting RNA splicing as a potential mediator of 5hmC's transcriptionally restrictive function. Furthermore, we show that various age-related contexts, such as prolonged quiescence and senescence, are partially responsible for driving the accumulation of 5hmC with age. We provide evidence that this age-related function is conserved in mouse and human tissues, and further show that the modification is altered by regimens known to modulate lifespan. Our findings reveal that 5hmC is a regulator of tissue-specific function and may play a role in regulating longevity.
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Affiliation(s)
- James R Occean
- Laboratory of Genetics and Genomics, National Institute on Aging, NIH, Baltimore, MD
| | - Na Yang
- Laboratory of Genetics and Genomics, National Institute on Aging, NIH, Baltimore, MD
| | - Yan Sun
- Department of Biochemistry, Albert Einstein School of Medicine, Bronx, NY
| | - Marshall S Dawkins
- Laboratory of Genetics and Genomics, National Institute on Aging, NIH, Baltimore, MD
| | - Rachel Munk
- Laboratory of Genetics and Genomics, National Institute on Aging, NIH, Baltimore, MD
| | - Cedric Belair
- Laboratory of Genetics and Genomics, National Institute on Aging, NIH, Baltimore, MD
| | - Showkat Dar
- Laboratory of Genetics and Genomics, National Institute on Aging, NIH, Baltimore, MD
| | - Carlos Anerillas
- Laboratory of Genetics and Genomics, National Institute on Aging, NIH, Baltimore, MD
| | - Lin Wang
- Laboratory of Genetics and Genomics, National Institute on Aging, NIH, Baltimore, MD
| | - Changyou Shi
- Laboratory of Genetics and Genomics, National Institute on Aging, NIH, Baltimore, MD
| | - Christopher Dunn
- Flow Cytometry Unit, National Institute on Aging, NIH, Baltimore, MD
| | - Michel Bernier
- Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, MD
| | - Nathan L Price
- Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, MD
| | - Julie S Kim
- Department of Biochemistry, Albert Einstein School of Medicine, Bronx, NY
| | - Chang-Yi Cui
- Laboratory of Genetics and Genomics, National Institute on Aging, NIH, Baltimore, MD
| | - Jinshui Fan
- Computational Biology and Genomics Core, Laboratory of Genetics and Genomics, National Institute on Aging, NIH, Baltimore, MD
| | | | - Supriyo De
- Computational Biology and Genomics Core, Laboratory of Genetics and Genomics, National Institute on Aging, NIH, Baltimore, MD
| | - Manolis Maragkakis
- Laboratory of Genetics and Genomics, National Institute on Aging, NIH, Baltimore, MD
| | - Rafael deCabo
- Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, MD
| | - Simone Sidoli
- Department of Biochemistry, Albert Einstein School of Medicine, Bronx, NY
| | - Payel Sen
- Laboratory of Genetics and Genomics, National Institute on Aging, NIH, Baltimore, MD
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3
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Santos RDS, Hirth CG, Pinheiro DP, Bezerra MJB, Silva-Fernandes IJDL, Paula DSD, Alves APNN, Moraes Filho MOD, Moura ADAA, Lima MVA, Pessoa CDÓ, Furtado CLM. HPV infection and 5mC/5hmC epigenetic markers in penile squamous cell carcinoma: new insights into prognostics. Clin Epigenetics 2022; 14:133. [PMID: 36284309 PMCID: PMC9597985 DOI: 10.1186/s13148-022-01360-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 10/09/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Penile cancer is one of the most aggressive male tumors. Although it is preventable, the main etiologic causes are lifestyle behaviors and viral infection, such as human papillomavirus (HPV). Long-term epigenetic changes due to environmental factors change cell fate and promote carcinogenesis, being an important marker of prognosis. We evaluated epidemiological aspects of penile squamous cell carcinoma (SCC) and the prevalence of HPV infection using high-risk HPV (hrHPV) and p16INK4A expression of 224 participants. Global DNA methylation was evaluated through 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC). RESULTS The incidence of HPV was 53.2% for hrHPV and 22.32% for p16INK4a. hrHPV was not related to systemic or lymph node metastasis and locoregional recurrence, nor influenced the survival rate. P16INK4a seems to be a protective factor for death, which does not affect metastasis or tumor recurrence. Lymph node and systemic metastases and locoregional recurrence increase the risk of death. An increased 5mC mark was observed in penile SCC regardless of HPV infection. However, there is a reduction of the 5hmC mark for p16INK4a + (P = 0.024). Increased 5mC/5hmC ratio (> 1) was observed in 94.2% of penile SCC, irrespective of HPV infection. Despite the increase in 5mC, it seems not to affect the survival rate (HR = 1.06; 95% CI 0.33-3.38). CONCLUSIONS P16INK4a seems to be a good prognosis marker for penile SCC and the increase in 5mC, an epigenetic mark of genomic stability, may support tumor progression leading to poor prognosis.
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Affiliation(s)
- Renan da Silva Santos
- grid.8395.70000 0001 2160 0329Drug Research and Development Center, Department of Physiology and Pharmacology, Federal University of Ceará, Fortaleza, Brazil
| | | | - Daniel Pascoalino Pinheiro
- grid.8395.70000 0001 2160 0329Drug Research and Development Center, Department of Physiology and Pharmacology, Federal University of Ceará, Fortaleza, Brazil
| | | | | | - Dayrine Silveira de Paula
- grid.8395.70000 0001 2160 0329Department of Dental Clinic, Faculty of Pharmacy, Dentistry and Nursing, Federal University of Ceará, Fortaleza, Brazil
| | - Ana Paula Negreiros Nunes Alves
- grid.8395.70000 0001 2160 0329Drug Research and Development Center, Postgraduate Program in Translational Medicine, Federal University of Ceará, Fortaleza, Brazil ,grid.8395.70000 0001 2160 0329Department of Dental Clinic, Faculty of Pharmacy, Dentistry and Nursing, Federal University of Ceará, Fortaleza, Brazil
| | - Manoel Odorico de Moraes Filho
- grid.8395.70000 0001 2160 0329Drug Research and Development Center, Department of Physiology and Pharmacology, Federal University of Ceará, Fortaleza, Brazil ,grid.8395.70000 0001 2160 0329Drug Research and Development Center, Postgraduate Program in Translational Medicine, Federal University of Ceará, Fortaleza, Brazil
| | | | - Marcos Venício Alves Lima
- Laboratory of Pathology, Cancer Institute of Ceará, Fortaleza, Brazil ,Laboratory of Molecular Biology and Genetics, Cancer Institute of Ceará, Fortaleza, Brazil
| | - Claudia do Ó Pessoa
- grid.8395.70000 0001 2160 0329Drug Research and Development Center, Department of Physiology and Pharmacology, Federal University of Ceará, Fortaleza, Brazil
| | - Cristiana Libardi Miranda Furtado
- grid.8395.70000 0001 2160 0329Drug Research and Development Center, Postgraduate Program in Translational Medicine, Federal University of Ceará, Fortaleza, Brazil ,grid.412275.70000 0004 4687 5259Experimental Biology Center, University of Fortaleza, Fortaleza, Brazil
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4
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Vachher M, Bansal S, Kumar B, Yadav S, Burman A. Deciphering the role of aberrant DNA methylation in NAFLD and NASH. Heliyon 2022; 8:e11119. [PMID: 36299516 PMCID: PMC9589178 DOI: 10.1016/j.heliyon.2022.e11119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 07/30/2022] [Accepted: 10/12/2022] [Indexed: 11/15/2022] Open
Abstract
The global incidence of nonalcoholic fatty liver disease (NAFLD) is mounting incessantly, and it is emerging as the most frequent cause of chronic and end stage liver disorders. It is the starting point for a range of conditions from simple steatosis to more progressive nonalcoholic steatohepatitis (NASH) and associated hepatocellular carcinoma (HCC). Dysregulation of insulin secretion and dyslipidemia due to obesity and other lifestyle variables are the primary contributors to establishment of NAFLD. Onset and progression of NAFLD is orchestrated by an interplay of metabolic environment with genetic and epigenetic factors. An incompletely understood mechanism of NAFLD progression has greatly hampered the progress in identification of novel prognostic and therapeutic strategies. Emerging evidence suggests altered DNA methylation pattern as a key determinant of NAFLD pathogenesis. Environmental and lifestyle factors can manipulate DNA methylation patterns in a reversible manner, which manifests as changes in gene expression. In this review we attempt to highlight the importance of DNA methylation in establishment and progression of NAFLD. Development of novel diagnostic, prognostic and therapeutic strategies centered around DNA methylation signatures and modifiers has also been explored.
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5
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Włodarczyk M, Nowicka G, Ciebiera M, Ali M, Yang Q, Al-Hendy A. Epigenetic Regulation in Uterine Fibroids-The Role of Ten-Eleven Translocation Enzymes and Their Potential Therapeutic Application. Int J Mol Sci 2022; 23:2720. [PMID: 35269864 PMCID: PMC8910916 DOI: 10.3390/ijms23052720] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 02/23/2022] [Accepted: 02/25/2022] [Indexed: 02/01/2023] Open
Abstract
Uterine fibroids (UFs) are monoclonal, benign tumors that contain abnormal smooth muscle cells and the accumulation of extracellular matrix (ECM). Although benign, UFs are a major source of gynecologic and reproductive dysfunction, ranging from menorrhagia and pelvic pain to infertility, recurrent miscarriage, and preterm labor. Many risk factors are involved in the pathogenesis of UFs via genetic and epigenetic mechanisms. The latter involving DNA methylation and demethylation reactions provide specific DNA methylation patterns that regulate gene expression. Active DNA demethylation reactions mediated by ten-eleven translocation proteins (TETs) and elevated levels of 5-hydroxymethylcytosine have been suggested to be involved in UF formation. This review paper summarizes the main findings regarding the function of TET enzymes and their activity dysregulation that may trigger the development of UFs. Understanding the role that epigenetics plays in the pathogenesis of UFs may possibly lead to a new type of pharmacological fertility-sparing treatment method.
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Affiliation(s)
- Marta Włodarczyk
- Department of Biochemistry and Pharmacogenomics, Faculty of Pharmacy, Medical University of Warsaw, Banacha 1B, 02-097 Warsaw, Poland;
- Centre for Preclinical Research, Medical University of Warsaw, Banacha 1B, 02-097 Warsaw, Poland
| | - Grażyna Nowicka
- Department of Biochemistry and Pharmacogenomics, Faculty of Pharmacy, Medical University of Warsaw, Banacha 1B, 02-097 Warsaw, Poland;
- Centre for Preclinical Research, Medical University of Warsaw, Banacha 1B, 02-097 Warsaw, Poland
| | - Michał Ciebiera
- The Center of Postgraduate Medical Education, Second Department of Obstetrics and Gynecology, 01-809 Warsaw, Poland;
| | - Mohamed Ali
- Clinical Pharmacy Department, Faculty of Pharmacy, Ain Shams University, Cairo 11566, Egypt;
- Department of Obstetrics and Gynecology, University of Chicago, Chicago, IL 60637, USA; (Q.Y.); (A.A.-H.)
| | - Qiwei Yang
- Department of Obstetrics and Gynecology, University of Chicago, Chicago, IL 60637, USA; (Q.Y.); (A.A.-H.)
| | - Ayman Al-Hendy
- Department of Obstetrics and Gynecology, University of Chicago, Chicago, IL 60637, USA; (Q.Y.); (A.A.-H.)
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6
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Xu L, Zhou Y, Chen L, Bissessur AS, Chen J, Mao M, Ju S, Chen L, Chen C, Li Z, Zhang X, Chen F, Cao F, Wang L, Wang Q. Deoxyribonucleic Acid 5-Hydroxymethylation in Cell-Free Deoxyribonucleic Acid, a Novel Cancer Biomarker in the Era of Precision Medicine. Front Cell Dev Biol 2021; 9:744990. [PMID: 34957093 PMCID: PMC8703110 DOI: 10.3389/fcell.2021.744990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 11/29/2021] [Indexed: 11/13/2022] Open
Abstract
Aberrant methylation has been regarded as a hallmark of cancer. 5-hydroxymethylcytosine (5hmC) is recently identified as the ten-eleven translocase (ten-eleven translocase)-mediated oxidized form of 5-methylcytosine, which plays a substantial role in DNA demethylation. Cell-free DNA has been introduced as a promising tool in the liquid biopsy of cancer. There are increasing evidence indicating that 5hmC in cell-free DNA play an active role during carcinogenesis. However, it remains unclear whether 5hmC could surpass classical markers in cancer detection, treatment, and prognosis. Here, we systematically reviewed the recent advances in the clinic and basic research of DNA 5-hydroxymethylation in cancer, especially in cell-free DNA. We further discuss the mechanisms underlying aberrant 5hmC patterns and carcinogenesis. Synergistically, 5-hydroxymethylation may act as a promising biomarker, unleashing great potential in early cancer detection, prognosis, and therapeutic strategies in precision oncology.
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Affiliation(s)
- Ling Xu
- Department of Surgical Oncology, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, China.,School of Medicine, Zhejiang University, Hangzhou, China
| | - Yixin Zhou
- Department of Thyroid and Breast Surgery, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Luqiao, China
| | - Lijie Chen
- Department of Thyroid and Breast Surgery, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Luqiao, China
| | - Abdul Saad Bissessur
- Department of Surgical Oncology, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, China.,School of Medicine, Zhejiang University, Hangzhou, China
| | - Jida Chen
- Department of Surgical Oncology, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, China
| | - Misha Mao
- Department of Surgical Oncology, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, China.,School of Medicine, Zhejiang University, Hangzhou, China
| | - Siwei Ju
- Department of Surgical Oncology, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, China.,School of Medicine, Zhejiang University, Hangzhou, China
| | - Lini Chen
- Department of Surgical Oncology, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, China.,School of Medicine, Zhejiang University, Hangzhou, China
| | - Cong Chen
- Department of Surgical Oncology, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, China.,School of Medicine, Zhejiang University, Hangzhou, China
| | - Zhaoqin Li
- Department of Surgical Oncology, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, China.,School of Medicine, Zhejiang University, Hangzhou, China
| | - Xun Zhang
- Department of Surgical Oncology, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, China.,School of Medicine, Zhejiang University, Hangzhou, China
| | - Fei Chen
- Department of Surgical Oncology, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, China.,School of Medicine, Zhejiang University, Hangzhou, China
| | - Feilin Cao
- Department of Thyroid and Breast Surgery, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Luqiao, China
| | - Linbo Wang
- Department of Surgical Oncology, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, China
| | - Qinchuan Wang
- Department of Surgical Oncology, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, China
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7
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Molecular Tumor Subtypes of HPV-Positive Head and Neck Cancers: Biological Characteristics and Implications for Clinical Outcomes. Cancers (Basel) 2021; 13:cancers13112721. [PMID: 34072836 PMCID: PMC8198180 DOI: 10.3390/cancers13112721] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 05/24/2021] [Accepted: 05/27/2021] [Indexed: 01/18/2023] Open
Abstract
Until recently, research on the molecular signatures of Human papillomavirus (HPV)-associated head and neck cancers mainly focused on their differences with respect to HPV-negative head and neck squamous cell carcinomas (HNSCCs). However, given the continuing high incidence level of HPV-related HNSCC, the time is ripe to characterize the heterogeneity that exists within these cancers. Here, we review research thus far on HPV-positive HNSCC molecular subtypes, and their relationship with clinical characteristics and HPV integration into the host genome. Different omics data including host transcriptomics and epigenomics, as well as HPV characteristics, can provide complementary viewpoints. Keratinization, mesenchymal differentiation, immune signatures, stromal cells and oxidoreductive processes all play important roles.
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8
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Bordin DL, Lirussi L, Nilsen H. Cellular response to endogenous DNA damage: DNA base modifications in gene expression regulation. DNA Repair (Amst) 2021; 99:103051. [PMID: 33540225 DOI: 10.1016/j.dnarep.2021.103051] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 01/15/2021] [Accepted: 01/18/2021] [Indexed: 12/19/2022]
Abstract
The integrity of the genetic information is continuously challenged by numerous genotoxic insults, most frequently in the form of oxidation, alkylation or deamination of the bases that result in DNA damage. These damages compromise the fidelity of the replication, and interfere with the progression and function of the transcription machineries. The DNA damage response (DDR) comprises a series of strategies to deal with DNA damage, including transient transcriptional inhibition, activation of DNA repair pathways and chromatin remodeling. Coordinated control of transcription and DNA repair is required to safeguardi cellular functions and identities. Here, we address the cellular responses to endogenous DNA damage, with a particular focus on the role of DNA glycosylases and the Base Excision Repair (BER) pathway, in conjunction with the DDR factors, in responding to DNA damage during the transcription process. We will also discuss functions of newly identified epigenetic and regulatory marks, such as 5-hydroxymethylcytosine and its oxidative products and 8-oxoguanine, that were previously considered only as DNA damages. In light of these resultsthe classical perception of DNA damage as detrimental for cellular processes are changing. and a picture emerges whereDNA glycosylases act as dynamic regulators of transcription, placing them at the intersection of DNA repair and gene expression modulation.
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Affiliation(s)
- Diana L Bordin
- Department of Clinical Molecular Biology, University of Oslo, 0318, Oslo, Norway; Department of Clinical Molecular Biology (EpiGen), Akershus University Hospital, 1478, Lørenskog, Norway
| | - Lisa Lirussi
- Department of Clinical Molecular Biology, University of Oslo, 0318, Oslo, Norway; Department of Clinical Molecular Biology (EpiGen), Akershus University Hospital, 1478, Lørenskog, Norway
| | - Hilde Nilsen
- Department of Clinical Molecular Biology, University of Oslo, 0318, Oslo, Norway; Department of Clinical Molecular Biology (EpiGen), Akershus University Hospital, 1478, Lørenskog, Norway.
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9
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Liu S, de Medeiros MC, Fernandez EM, Zarins KR, Cavalcante RG, Qin T, Wolf GT, Figueroa ME, D'Silva NJ, Rozek LS, Sartor MA. 5-Hydroxymethylation highlights the heterogeneity in keratinization and cell junctions in head and neck cancers. Clin Epigenetics 2020; 12:175. [PMID: 33203436 PMCID: PMC7672859 DOI: 10.1186/s13148-020-00965-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 11/03/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Head and neck squamous cell carcinoma (HNSCC) is the sixth most prevalent cancer worldwide, with human papillomavirus (HPV)-related HNSCC rising to concerning levels. Extensive clinical, genetic and epigenetic differences exist between HPV-associated HNSCC and HPV-negative HNSCC, which is often linked to tobacco use. However, 5-hydroxymethylation (5hmC), an oxidative derivative of DNA methylation and its heterogeneity among HNSCC subtypes, has not been studied. RESULTS We characterized genome-wide 5hmC profiles in HNSCC by HPV status and subtype in 18 HPV(+) and 18 HPV(-) well-characterized tumors. Results showed significant genome-wide hyper-5hmC in HPV(-) tumors, with both promoter and enhancer 5hmC able to distinguish meaningful tumor subgroups. We identified specific genes whose differential expression by HPV status is driven by differential hydroxymethylation. CDKN2A (p16), used as a key biomarker for HPV status, exhibited the most extensive hyper-5hmC in HPV(+) tumors, while HPV(-) tumors showed hyper-5hmC in CDH13, TIMP2, MMP2 and other cancer-related genes. Among the previously reported two HPV(+) subtypes, IMU (stronger immune response) and KRT (more keratinization), the IMU subtype revealed hyper-5hmC and up-regulation of genes in cell migration, and hypo-5hmC with down-regulation in keratinization and cell junctions. We experimentally validated our key prediction of higher secreted and intracellular protein levels of the invasion gene MMP2 in HPV(-) oral cavity cell lines. CONCLUSION Our results implicate 5hmC in driving differences in keratinization, cell junctions and other cancer-related processes among tumor subtypes. We conclude that 5hmC levels are critical for defining tumor characteristics and potentially used to define clinically meaningful cancer patient subgroups.
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Affiliation(s)
- Siyu Liu
- Department of Computational Medicine and Bioinformatics, University of Michigan, 100 Washtenaw Ave., Ann Arbor, MI, 48109-2218, USA
| | | | - Evan M Fernandez
- Department of Computational Medicine and Bioinformatics, University of Michigan, 100 Washtenaw Ave., Ann Arbor, MI, 48109-2218, USA
| | - Katie R Zarins
- Department of Environmental Health Sciences, University of Michigan, Ann Arbor, MI, 48109, USA
| | | | - Tingting Qin
- Department of Computational Medicine and Bioinformatics, University of Michigan, 100 Washtenaw Ave., Ann Arbor, MI, 48109-2218, USA
| | - Gregory T Wolf
- Department of Otolaryngology-Head and Neck Surgery, Michigan Medicine, Ann Arbor, MI, 48109, USA
| | - Maria E Figueroa
- Department of Human Genetics and Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA
| | - Nisha J D'Silva
- Department of Periodontics and Oral Medicine, University of Michigan, Ann Arbor, MI, 48104, USA
| | - Laura S Rozek
- Department of Environmental Health Sciences, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Maureen A Sartor
- Department of Computational Medicine and Bioinformatics, University of Michigan, 100 Washtenaw Ave., Ann Arbor, MI, 48109-2218, USA. .,Department of Biostatistics, University of Michigan, Ann Arbor, MI, 48109, USA.
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10
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Hyun J, Jung Y. DNA Methylation in Nonalcoholic Fatty Liver Disease. Int J Mol Sci 2020; 21:ijms21218138. [PMID: 33143364 PMCID: PMC7662478 DOI: 10.3390/ijms21218138] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Revised: 10/28/2020] [Accepted: 10/28/2020] [Indexed: 12/12/2022] Open
Abstract
Nonalcoholic fatty liver disease (NAFLD) is a widespread hepatic disorder in the United States and other Westernized countries. Nonalcoholic steatohepatitis (NASH), an advanced stage of NAFLD, can progress to end-stage liver disease, including cirrhosis and liver cancer. Poor understanding of mechanisms underlying NAFLD progression from simple steatosis to NASH has limited the development of effective therapies and biomarkers. An accumulating body of studies has suggested the importance of DNA methylation, which plays pivotal roles in NAFLD pathogenesis. DNA methylation signatures that can affect gene expression are influenced by environmental and lifestyle experiences such as diet, obesity, and physical activity and are reversible. Hence, DNA methylation signatures and modifiers in NAFLD may provide the basis for developing biomarkers indicating the onset and progression of NAFLD and therapeutics for NAFLD. Herein, we review an update on the recent findings in DNA methylation signatures and their roles in the pathogenesis of NAFLD and broaden people’s perspectives on potential DNA methylation-related treatments and biomarkers for NAFLD.
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Affiliation(s)
- Jeongeun Hyun
- Institute of Tissue Regeneration Engineering (ITREN), Dankook University, Cheonan 31116, Korea;
- Department of Nanobiomedical Science and BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan 31116, Korea
- Department of Biomaterials Science, College of Dentistry, Dankook University, Cheonan 31116, Korea
- Cell and Matter Institute, Dankook University, Cheonan 31116, Korea
| | - Youngmi Jung
- Department of Integrated Biological Science, Pusan National University, Pusan 46241, Korea
- Department of Biological Sciences, Pusan National University, Pusan 46241, Korea
- Correspondence: ; Tel.: +82-51-510-2262
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11
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Armstrong MJ, Jin Y, Allen EG, Jin P. Diverse and dynamic DNA modifications in brain and diseases. Hum Mol Genet 2020; 28:R241-R253. [PMID: 31348493 DOI: 10.1093/hmg/ddz179] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 07/17/2019] [Accepted: 07/18/2019] [Indexed: 12/17/2022] Open
Abstract
DNA methylation is a class of epigenetic modification essential for coordinating gene expression timing and magnitude throughout normal brain development and for proper brain function following development. Aberrant methylation changes are associated with changes in chromatin architecture, transcriptional alterations and a host of neurological disorders and diseases. This review highlights recent advances in our understanding of the methylome's functionality and covers potential new roles for DNA methylation, their readers, writers, and erasers. Additionally, we examine novel insights into the relationship between the methylome, DNA-protein interactions, and their contribution to neurodegenerative diseases. Lastly, we outline the gaps in our knowledge that will likely be filled through the widespread use of newer technologies that provide greater resolution into how individual cell types are affected by disease and the contribution of each individual modification site to disease pathogenicity.
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Affiliation(s)
- Matthew J Armstrong
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, GA, USA
| | - Yulin Jin
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, GA, USA
| | - Emily G Allen
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, GA, USA
| | - Peng Jin
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, GA, USA
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12
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Rodríguez-Aguilera JR, Ecsedi S, Goldsmith C, Cros MP, Domínguez-López M, Guerrero-Celis N, Pérez-Cabeza de Vaca R, Chemin I, Recillas-Targa F, Chagoya de Sánchez V, Hernández-Vargas H. Genome-wide 5-hydroxymethylcytosine (5hmC) emerges at early stage of in vitro differentiation of a putative hepatocyte progenitor. Sci Rep 2020; 10:7822. [PMID: 32385352 PMCID: PMC7210258 DOI: 10.1038/s41598-020-64700-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 04/15/2020] [Indexed: 12/23/2022] Open
Abstract
A basic question linked to differential patterns of gene expression is how cells reach different fates despite using the same DNA template. Since 5-hydroxymethylcytosine (5hmC) emerged as an intermediate metabolite in active DNA demethylation, there have been increasing efforts to elucidate its function as a stable modification of the genome, including a role in establishing such tissue-specific patterns of expression. Recently we described TET1-mediated enrichment of 5hmC on the promoter region of the master regulator of hepatocyte identity, HNF4A, which precedes differentiation of liver adult progenitor cells in vitro. Here, we studied the genome-wide distribution of 5hmC at early in vitro differentiation of human hepatocyte-like cells. We found a global increase in 5hmC as well as a drop in 5-methylcytosine after one week of in vitro differentiation from bipotent progenitors, at a time when the liver transcript program is already established. 5hmC was overall higher at the bodies of overexpressed genes. Furthermore, by modifying the metabolic environment, an adenosine derivative prevents 5hmC enrichment and impairs the acquisition of hepatic identity markers. These results suggest that 5hmC could be a marker of cell identity, as well as a useful biomarker in conditions associated with cell de-differentiation such as liver malignancies.
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Affiliation(s)
- Jesús Rafael Rodríguez-Aguilera
- Department of Cellular Biology and Development, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México (UNAM), Circuito Exterior s/n, Ciudad Universitaria, Coyoacán, 04510, Cd. Mx., Mexico
| | - Szilvia Ecsedi
- Institute of Biology Valrose (iBV), The National Center for Scientific Research (CNRS) - National Institute of Health and Medical Research (Inserm), Université Côte d'Azur, Nice, France
| | - Chloe Goldsmith
- Department of Immunity, Virus and Inflammation. Cancer Research Centre of Lyon (CRCL), Inserm U 1052, CNRS UMR 5286, Université de Lyon, Centre Léon Bérard, 28 rue Laennec, 69373, Lyon, CEDEX 08, France
| | - Marie-Pierre Cros
- Molecular Mechanisms and Biomarkers Group, International Agency for Research on Cancer (IARC), 150 Cours Albert Thomas, 69008, Lyon, France
| | - Mariana Domínguez-López
- Department of Cellular Biology and Development, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México (UNAM), Circuito Exterior s/n, Ciudad Universitaria, Coyoacán, 04510, Cd. Mx., Mexico
| | - Nuria Guerrero-Celis
- Department of Cellular Biology and Development, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México (UNAM), Circuito Exterior s/n, Ciudad Universitaria, Coyoacán, 04510, Cd. Mx., Mexico
| | - Rebeca Pérez-Cabeza de Vaca
- Department of Cellular Biology and Development, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México (UNAM), Circuito Exterior s/n, Ciudad Universitaria, Coyoacán, 04510, Cd. Mx., Mexico
- Division of Biomedical Research, Centro Médico Nacional "20 de noviembre", ISSSTE, San Lorenzo 502, Benito Juárez, 03100, Cd. Mx., Mexico
| | - Isabelle Chemin
- INSERM U1052, CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon Université Claude Bernard, Lyon, France
| | - Félix Recillas-Targa
- Department of Molecular Genetics, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México (UNAM), Circuito Exterior s/n, Ciudad Universitaria, Coyoacán, 04510, Cd. Mx., Mexico
| | - Victoria Chagoya de Sánchez
- Department of Cellular Biology and Development, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México (UNAM), Circuito Exterior s/n, Ciudad Universitaria, Coyoacán, 04510, Cd. Mx., Mexico.
| | - Héctor Hernández-Vargas
- Department of Immunity, Virus and Inflammation. Cancer Research Centre of Lyon (CRCL), Inserm U 1052, CNRS UMR 5286, Université de Lyon, Centre Léon Bérard, 28 rue Laennec, 69373, Lyon, CEDEX 08, France.
- Department of Translational Research and Innovation. Centre Léon Bérard, 28 rue Laennec, 69373, Lyon, CEDEX 08, France.
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13
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Mahmood AM, Dunwell JM. Evidence for novel epigenetic marks within plants. AIMS GENETICS 2019; 6:70-87. [PMID: 31922011 PMCID: PMC6949463 DOI: 10.3934/genet.2019.4.70] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 12/07/2019] [Indexed: 12/21/2022]
Abstract
Variation in patterns of gene expression can result from modifications in the genome that occur without a change in the sequence of the DNA; such modifications include methylation of cytosine to generate 5-methylcytosine (5mC) resulting in the generation of heritable epimutation and novel epialleles. This type of non-sequence variation is called epigenetics. The enzymes responsible for generation of such DNA modifications in mammals are named DNA methyltransferases (DNMT) including DNMT1, DNMT2 and DNMT3. The later stages of oxidations to these modifications are catalyzed by Ten Eleven Translocation (TET) proteins, which contain catalytic domains belonging to the 2-oxoglutarate dependent dioxygenase family. In various mammalian cells/tissues including embryonic stem cells, cancer cells and brain tissues, it has been confirmed that these proteins are able to induce the stepwise oxidization of 5-methyl cytosine to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and finally 5-carboxylcytosine (5caC). Each stage from initial methylation until the end of the DNA demethylation process is considered as a specific epigenetic mark that may regulate gene expression. This review discusses controversial evidence for the presence of such oxidative products, particularly 5hmC, in various plant species. Whereas some reports suggest no evidence for enzymatic DNA demethylation, other reports suggest that the presence of oxidative products is followed by the active demethylation and indicate the contribution of possible TET-like proteins in the regulation of gene expression in plants. The review also summarizes the results obtained by expressing the human TET conserved catalytic domain in transgenic plants.
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Affiliation(s)
- Asaad M Mahmood
- Department of Biology, College of Education, University of Garmian, Kalar, KRG/Iraq
| | - Jim M Dunwell
- School of School of Agriculture, Policy and Development, University of Reading, Reading, Berkshire, UK
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14
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Zhang Q, Zheng S, Wang S, Jiang Z, Xu S. The Effects of Low Selenium on DNA Methylation in the Tissues of Chickens. Biol Trace Elem Res 2019; 191:474-484. [PMID: 30737629 DOI: 10.1007/s12011-019-1630-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 01/01/2019] [Indexed: 12/12/2022]
Abstract
DNA methylation is involved in epigenetic mechanisms associated with gene suppression, and its abnormalities lead to gene instability and disease development. As an essential trace element in humans and animals, selenium (Se) is also associated with abnormal changes in DNA methylation. However, the effect of low Se on DNA methylation in avian tissues has not been reported. In the current study, chickens were fed a low-Se diet (0.033 mg Se/kg) or supplemented with 0.15 mg Se/kg as selenite for up to 55 days. DNA methylation levels were examined by high-performance liquid chromatography (HPLC). DNA methyltransferases (DNMTs) and methyl-DpG-binding domain protein 2 (MBD2) mRNA levels were examined through the applications of RT-PCR. The experiment aims to explore the relationship between low Se and DNA methylation. The results showed that total DNA methylation levels in the muscle tissues, brain, immune tissues, and liver of the low-selenium diet group were decreased compared with the control group. The degree of DNA methylation reduction in different tissues from largest to smallest was liver > cerebellum > thymus > brain > spleen ≥ leg muscles > pectoral muscles > bursa of Fabricius > thalamus > wing muscles. DNMT1, DNMT3A, and DNMT3B mRNA expression levels of the low-selenium diet group were decreased compared with those in the control group. The mRNA expression of the MBD2 gene was increased. The results indicate that low Se can reduce the DNA methylation levels of tissues, especially within the liver. These conclusions provide a basis for exploring the pathogenesis of selenium deficiency from the perspective of DNA methylation and create a new basis for comparative medicine.
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Affiliation(s)
- Qiaojian Zhang
- College of Veterinary Medicine, Northeast Agricultural University, 600 Changjiang Road, Harbin, 150030, People's Republic of China
| | - Shufang Zheng
- College of Veterinary Medicine, Northeast Agricultural University, 600 Changjiang Road, Harbin, 150030, People's Republic of China
| | - Shengchen Wang
- College of Veterinary Medicine, Northeast Agricultural University, 600 Changjiang Road, Harbin, 150030, People's Republic of China
| | - Zhihui Jiang
- College of Veterinary Medicine, Northeast Agricultural University, 600 Changjiang Road, Harbin, 150030, People's Republic of China.
| | - Shiwen Xu
- College of Veterinary Medicine, Northeast Agricultural University, 600 Changjiang Road, Harbin, 150030, People's Republic of China.
- Key Laboratory of the Provincial Education Department of Heilongjiang for Common Animal Disease Prevention and Treatment, College of Veterinary Medicine, Northeast Agricultural University, Harbin, 150030, People's Republic of China.
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15
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DNA Hydroxymethylation at the Interface of the Environment and Nonalcoholic Fatty Liver Disease. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2019; 16:ijerph16152791. [PMID: 31387232 PMCID: PMC6695744 DOI: 10.3390/ijerph16152791] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Revised: 08/02/2019] [Accepted: 08/03/2019] [Indexed: 12/25/2022]
Abstract
Non-alcoholic fatty liver disease (NAFLD) is one of the most prevalent forms of chronic liver disorders among adults, children, and adolescents, and a growing epidemic, worldwide. Notwithstanding the known susceptibility factors for NAFLD, i.e., obesity and metabolic syndrome, the exact cause(s) of this disease and the underlying mechanisms of its initiation and progression are not fully elucidated. NAFLD is a multi-faceted disease with metabolic, genetic, epigenetic, and environmental determinants. Accumulating evidence shows that exposure to environmental toxicants contributes to the development of NAFLD by promoting mitochondrial dysfunction and generating reactive oxygen species in the liver. Imbalances in the redox state of the cells are known to cause alterations in the patterns of 5-hydroxymethylcytosine (5hmC), the oxidative product of 5-methylcytosine (5mC), thereby influencing gene regulation. The 5hmC-mediated deregulation of genes involved in hepatic metabolism is an emerging area of research in NAFLD. This review summarizes our current knowledge on the interactive role of xenobiotic exposure and DNA hydroxymethylation in the pathogenesis of fatty liver disease. Increasing the mechanistic knowledge of NAFLD initiation and progression is crucial for the development of new and effective strategies for prevention and treatment of this disease.
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16
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Slynko A, Benner A. Statistical methods for classification of 5hmC levels based on the Illumina Inifinium HumanMethylation450 (450k) array data, under the paired bisulfite (BS) and oxidative bisulfite (oxBS) treatment. PLoS One 2019; 14:e0218103. [PMID: 31194780 PMCID: PMC6563990 DOI: 10.1371/journal.pone.0218103] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 05/27/2019] [Indexed: 12/22/2022] Open
Abstract
Hydroxymethylcytosine (5hmC) methylation is a well-known epigenetic mark that is involved in gene regulation and may impact genome stability. To investigate a possible role of 5hmC in cancer development and progression, one must be able to detect and quantify its level first. In this paper, we address the issue of 5hmC detection at a single base resolution, starting with consideration of the well-established 5hmC measure Δβ and, in particular, with an analysis of its properties, both analytically and empirically. Then we propose several alternative hydroxymethylation measures and compare their properties with those of Δβ. In the absence of a gold standard, the (pairwise) resemblance of those 5hmC measures to Δβ is characterized by means of a similarity analysis and relative accuracy analysis. All results are illustrated on matched healthy and cancer tissue data sets as derived by means of bisulfite (BS) and oxidative bisulfite converting (oxBS) procedures.
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Affiliation(s)
- Alla Slynko
- Department of Statistics and Actuarial Science, University of Waterloo, Waterloo, Canada
- * E-mail:
| | - Axel Benner
- Division of Biostatistics, German Cancer Research Center, Heidelberg, Germany
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17
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Pfeifer GP, Szabó PE. Gene body profiles of 5-hydroxymethylcytosine: potential origin, function and use as a cancer biomarker. Epigenomics 2018; 10:1029-1032. [PMID: 30052061 PMCID: PMC6190241 DOI: 10.2217/epi-2018-0066] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Affiliation(s)
- Gerd P Pfeifer
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI, 49503, USA
| | - Piroska E Szabó
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI, 49503, USA
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18
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Thomson JP, Meehan RR. Affinity-Based Enrichment Techniques for the Genome-Wide Analysis of 5-Hydroxymethylcytosine. Methods Mol Biol 2018; 1708:679-696. [PMID: 29224170 DOI: 10.1007/978-1-4939-7481-8_35] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Since its initial characterization in 2009 there has been a great degree of interest in comparative profiling of 5-hydroxymethylcytosine (5hmC) nucleotides in vertebrate DNA. Through a host of genome-wide studies the distribution of 5hmC has been mapped in a range of cell lines, tissue types and organisms; the majority of which have been generated through affinity-based methods for 5hmC enrichment. Although recent advances in the field have resulted in the ability to investigate the levels of both methylated and hydroxymethylated cytosines at single base resolution, such studies are still relatively cost-prohibitive as well as technically challenging. As such affinity-based methods for the enrichment of 5hmC-modified DNA fragments represent a cost-effective and highly informative method for profiling 5hmC residency in genomic DNA. Here we will outline protocols for two independent affinity based methods to generate 5hmC enriched fractions for subsequent locus specific and genome-wide analysis; immunoprecipitation using highly specific 5hmC antibodies as well as a chemical capture based method.
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Affiliation(s)
- John P Thomson
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road, Edinburgh, EH4 2XU, UK
| | - Richard R Meehan
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road, Edinburgh, EH4 2XU, UK.
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19
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Chen Z, Shi X, Guo L, Li Y, Luo M, He J. Decreased 5-hydroxymethylcytosine levels correlate with cancer progression and poor survival: a systematic review and meta-analysis. Oncotarget 2018; 8:1944-1952. [PMID: 27911867 PMCID: PMC5352110 DOI: 10.18632/oncotarget.13719] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2016] [Accepted: 09/14/2016] [Indexed: 11/30/2022] Open
Abstract
Ten-eleven translocation (TET) enzymes catalyze the oxidation of 5-methylcytosine (5-mC) to 5-hydroxymethylcytosine (5-hmC) and then to 5-formylcytosine (5-fC) and 5-carboxylcytosine (5-caC), resulting in genomic DNA demethylation. Decreased 5-hmC levels have been reported in a variety of cancers, and loss of 5-hmC might be considered an epigenetic hallmark of cancer. However, the prognostic value of decreased 5-hmC in cancers remain controversial. Here, a systematic review was performed by conducting an electronic search of PubMed, EMBASE, Web of Science and the Cochrane Library. Finally, ten studies with a total of 1736 patients with cancer were included in the present study. Negative/low 5-hmC levels were significantly associated with lymph node metastasis [OR=2.20, 95% CI=1.23-3.96, P=0.008] and advanced TNM stage [OR=2.89, 95% CI=1.21-6.92, P=0.017]. More importantly, negative/low 5-hmC levels were significantly associated with poor prognosis of cancer patients [overall survival: HR=1.76, 95% CI=1.41-2.11, P < 0.001; disease free survival: HR=1.28, 95% CI=0.60-1.96, P < 0.001]. The results of this meta-analysis indicate that decreased 5-hmC levels are an indicator of poor survival of cancer patients. Given variability related to ethnicity, cancer types and detection methods, additional well-designed studies with larger sample sizes are required to further confirm our findings.
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Affiliation(s)
- Zhaoli Chen
- Department of Thoracic Surgery, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Xuejiao Shi
- Department of Thoracic Surgery, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Lanwei Guo
- Department of Cancer Epidemiology, Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Henan Office for Cancer Control and Research, Zhengzhou, China
| | - Yuan Li
- Department of Thoracic Surgery, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Mei Luo
- Department of Thoracic Surgery, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Jie He
- Department of Thoracic Surgery, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences, Beijing, China
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20
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Ohara A, Takahashi Y, Kondo M, Okuda Y, Takeda S, Kushida M, Kobayashi K, Sumida K, Yamada T. Candidate genes responsible for early key events of phenobarbital-promoted mouse hepatocellular tumorigenesis based on differentiation of regulating genes between wild type mice and humanized chimeric mice. Toxicol Res (Camb) 2017; 6:795-813. [PMID: 30090543 PMCID: PMC6062386 DOI: 10.1039/c7tx00163k] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 08/23/2017] [Indexed: 12/12/2022] Open
Abstract
Phenobarbital (PB) is a nongenotoxic hepatocellular carcinogen in rodents. PB induces hepatocellular tumors by activating the constitutive androstane receptor (CAR). Some previous research has suggested the possible involvement of epigenetic regulation in PB-promoted hepatocellular tumorigenesis, but the details of its molecular mechanism are not fully understood. In the present study, comprehensive analyses of DNA methylation, hydroxymethylation and gene expression using microarrays were performed in mouse hepatocellular adenomas induced by a single 90 mg kg-1 intraperitoneal injection dose of diethylnitrosamine (DEN) followed by 500 ppm PB in the diet for 27 weeks. DNA modification and expression of hundreds of genes are coordinately altered in PB-induced mouse hepatocellular adenomas. Of these, gene network analysis showed alterations of CAR signaling and tumor development-related genes. Pathway enrichment analysis revealed that differentially methylated or hydroxymethylated genes belong mainly to pathways involved in development, immune response and cancer cells in contrast to differentially expressed genes belonging primarily to the cell cycle. Furthermore, overlap was evaluated between the genes with altered expression levels with 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) alterations in mouse hepatocellular adenoma induced by DEN/PB and the genes with altered expression levels in the liver of CD-1 mice or humanized chimeric mice treated with PB for 7 days. With the integration of transcriptomic and epigenetic approaches, we detected candidate genes responsible for early key events of PB-promoted mouse hepatocellular tumorigenesis. Interestingly, these genes did not overlap with genes altered by the PB treatment of humanized chimeric mice, thus suggesting a species difference between the effects of PB in mouse and human hepatocytes.
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Affiliation(s)
- Ayako Ohara
- Environmental Health Science Laboratory , Sumitomo Chemical Co. , Ltd. , 1-98 , 3-Chome , Kasugade-Naka , Konohana-ku , Osaka 554-8558 , Japan . ; ; Tel: +81-66466-5322
| | - Yasuhiko Takahashi
- Environmental Health Science Laboratory , Sumitomo Chemical Co. , Ltd. , 1-98 , 3-Chome , Kasugade-Naka , Konohana-ku , Osaka 554-8558 , Japan . ; ; Tel: +81-66466-5322
| | - Miwa Kondo
- Environmental Health Science Laboratory , Sumitomo Chemical Co. , Ltd. , 1-98 , 3-Chome , Kasugade-Naka , Konohana-ku , Osaka 554-8558 , Japan . ; ; Tel: +81-66466-5322
| | - Yu Okuda
- Environmental Health Science Laboratory , Sumitomo Chemical Co. , Ltd. , 1-98 , 3-Chome , Kasugade-Naka , Konohana-ku , Osaka 554-8558 , Japan . ; ; Tel: +81-66466-5322
| | - Shuji Takeda
- Environmental Health Science Laboratory , Sumitomo Chemical Co. , Ltd. , 1-98 , 3-Chome , Kasugade-Naka , Konohana-ku , Osaka 554-8558 , Japan . ; ; Tel: +81-66466-5322
| | - Masahiko Kushida
- Environmental Health Science Laboratory , Sumitomo Chemical Co. , Ltd. , 1-98 , 3-Chome , Kasugade-Naka , Konohana-ku , Osaka 554-8558 , Japan . ; ; Tel: +81-66466-5322
| | - Kentaro Kobayashi
- Environmental Health Science Laboratory , Sumitomo Chemical Co. , Ltd. , 1-98 , 3-Chome , Kasugade-Naka , Konohana-ku , Osaka 554-8558 , Japan . ; ; Tel: +81-66466-5322
| | - Kayo Sumida
- Environmental Health Science Laboratory , Sumitomo Chemical Co. , Ltd. , 1-98 , 3-Chome , Kasugade-Naka , Konohana-ku , Osaka 554-8558 , Japan . ; ; Tel: +81-66466-5322
| | - Tomoya Yamada
- Environmental Health Science Laboratory , Sumitomo Chemical Co. , Ltd. , 1-98 , 3-Chome , Kasugade-Naka , Konohana-ku , Osaka 554-8558 , Japan . ; ; Tel: +81-66466-5322
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21
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Deng M, Ren C, Liu Z, Zhang G, Wang F, Wan Y. Epigenetic Status of H19-Igf2 Imprinted Genes and Loss of 5-Hydroxymethylcytosine in the Brain of Cloned Goats. Cell Reprogram 2017; 19:199-207. [PMID: 28350187 DOI: 10.1089/cell.2016.0049] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
In mammals, the imprinted genes play vital roles in development and are generally controlled by DNA methylation at imprinting control regions (ICRs). Recently, it was discovered that 5-hydroxymethylcytosine (5-hmC) is a stable epigenetic modification; however, its functions in cloned animal genomes have not yet been fully elucidated. In this study, we interrogated and quantified the 5-hmC levels in the brain of cloned goats and discovered upregulation of Uhrf1 (p < 0.001), Dnmt1 (p < 0.05), Dnmt3a (p < 0.05), Igf2 (p < 0.01), and H19 (p < 0.05) and downregulation of Dnmt3b (p < 0.001), Tet1 (p < 0.001), Tet2 (p < 0.05), Tet3 (p < 0.001), Mecp2 (p < 0.05), and Igf2r (p < 0.05) in deceased cloned goat tissues compared with the normal controls. We demonstrated that DNA methylation was increased at H19 ICR (51.33% ± 2.03% vs. 93.07% ± 3.06%; p < 0.01) and that DNA was hypomethylated at Igf2 ICR (4.57% ± 1.48% vs. 7.63% ± 1.83%; p > 0.05) in the brain of deceased cloned goats. Finally, we showed that within the cloned goat brain genome, the amount of genome-wide 5-hmC was significantly decreased (0.083% ± 0.026% vs. 0.024% ± 0.007%; p < 0.05), whereas the 5-hmC levels within H19 and Igf2 CCGG sites were not significantly altered (0.17% ± 0.09% vs. 0.03% ± 0.01%; p > 0.05) in the brain of deceased cloned goats. Our data bring further experimental evidence regarding the abnormalities in 5-hmC and advance our current understanding of the role of 5-hmC in cloned animals.
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Affiliation(s)
- Mingtian Deng
- Jiangsu Livestock Embryo Engineering Laboratory, College of Animal Science and Technology, Nanjing Agricultural University , Nanjing, China
| | - Caifang Ren
- Jiangsu Livestock Embryo Engineering Laboratory, College of Animal Science and Technology, Nanjing Agricultural University , Nanjing, China
| | - Zifei Liu
- Jiangsu Livestock Embryo Engineering Laboratory, College of Animal Science and Technology, Nanjing Agricultural University , Nanjing, China
| | - Guomin Zhang
- Jiangsu Livestock Embryo Engineering Laboratory, College of Animal Science and Technology, Nanjing Agricultural University , Nanjing, China
| | - Feng Wang
- Jiangsu Livestock Embryo Engineering Laboratory, College of Animal Science and Technology, Nanjing Agricultural University , Nanjing, China
| | - Yongjie Wan
- Jiangsu Livestock Embryo Engineering Laboratory, College of Animal Science and Technology, Nanjing Agricultural University , Nanjing, China
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22
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Abstract
Since its "re-discovery" in 2009, there has been significant interest in defining the genome-wide distribution of DNA marked by 5-hydroxymethylation at cytosine bases (5hmC). In recent years, technological advances have resulted in a multitude of unique strategies to map 5hmC across the human genome. Here we discuss the wide range of approaches available to map this modification and describe in detail the affinity based methods which result in the enrichment of 5hmC marked DNA for downstream analysis.
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Affiliation(s)
- John P Thomson
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, The University of Edinburgh, Crewe Road, Edinburgh, EH4 2XU, UK
| | - Colm E Nestor
- The Centre for Individualized Medication, Linköping University Hospital, Linköping University, Linköping, SE-58185, Sweden
| | - Richard R Meehan
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, The University of Edinburgh, Crewe Road, Edinburgh, EH4 2XU, UK.
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23
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Thomson JP, Meehan RR. The application of genome-wide 5-hydroxymethylcytosine studies in cancer research. Epigenomics 2016; 9:77-91. [PMID: 27936926 DOI: 10.2217/epi-2016-0122] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Early detection and characterization of molecular events associated with tumorgenesis remain high priorities. Genome-wide epigenetic assays are promising diagnostic tools, as aberrant epigenetic events are frequent and often cancer specific. The deposition and analysis of multiple patient-derived cancer epigenomic profiles contributes to our appreciation of the underlying biology; aiding the detection of novel identifiers for cancer subtypes. Modifying enzymes and co-factors regulating these epigenetic marks are frequently mutated in cancers, and as epigenetic modifications themselves are reversible, this makes their study very attractive with respect to pharmaceutical intervention. Here we focus on the novel modified base, 5-hydoxymethylcytosine, and discuss how genome-wide 5-hydoxymethylcytosine profiling expedites our molecular understanding of cancer, serves as a lineage tracer, classifies the mode of action of potentially carcinogenic agents and clarifies the roles of potential novel cancer drug targets; thus assisting the development of new diagnostic/prognostic tools.
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Affiliation(s)
- John P Thomson
- MRC Human Genetics Unit, Institute of Genetics & Molecular Medicine, University of Edinburgh, Crewe Road, Edinburgh, EH4 2XU, UK
| | - Richard R Meehan
- MRC Human Genetics Unit, Institute of Genetics & Molecular Medicine, University of Edinburgh, Crewe Road, Edinburgh, EH4 2XU, UK
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24
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Costa LDA, da Silva ICB, Mariz BALA, da Silva MB, Freitas-Ribeiro GM, de Oliveira NFP. Influence of smoking on methylation and hydroxymethylation levels in global DNA and specific sites of KRT14 , KRT19 , MIR-9-3 and MIR-137 genes of oral mucosa. Arch Oral Biol 2016; 72:56-65. [DOI: 10.1016/j.archoralbio.2016.08.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Revised: 06/08/2016] [Accepted: 08/10/2016] [Indexed: 12/14/2022]
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25
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Li X, Liu Y, Salz T, Hansen KD, Feinberg A. Whole-genome analysis of the methylome and hydroxymethylome in normal and malignant lung and liver. Genome Res 2016; 26:1730-1741. [PMID: 27737935 PMCID: PMC5131824 DOI: 10.1101/gr.211854.116] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 10/12/2016] [Indexed: 12/11/2022]
Abstract
DNA methylation at the 5-position of cytosine (5mC) is an epigenetic modification that regulates gene expression and cellular plasticity in development and disease. The ten-eleven translocation (TET) gene family oxidizes 5mC to 5-hydroxymethylcytosine (5hmC), providing an active mechanism for DNA demethylation, and it may also provide its own regulatory function. Here we applied oxidative bisulfite sequencing to generate whole-genome DNA methylation and hydroxymethylation maps at single-base resolution in human normal liver and lung as well as paired tumor tissues. We found that 5hmC is significantly enriched in CpG island (CGI) shores while depleted in CGIs themselves, especially in active genes, which exhibit a bimodal distribution of 5hmC around CGI that corresponds to H3K4me1 modifications. Hydroxymethylation on promoters, gene bodies, and transcription termination regions (TTRs) showed strong positive correlation with gene expression within and across tissues, suggesting that 5hmC is a marker of active genes and could play a role in gene expression mediated by DNA demethylation. Comparative analysis of methylomes and hydroxymethylomes revealed that 5hmC is significantly enriched in both tissue-specific DMRs (t-DMRs) and cancer-specific DMRs (c-DMRs), and 5hmC is negatively correlated with methylation changes, especially in non-CGI-associated DMRs. These findings revealed novel reciprocity between epigenetic markers at CGI shores corresponding to differential gene expression in normal tissues and matching tumors. Overall, our study provided a comprehensive analysis of the interplay between the methylome, hydroxymethylome, and histone modifications during tumorigenesis.
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Affiliation(s)
- Xin Li
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Yun Liu
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA.,The Ministry of Education Key Laboratory of Metabolism and Molecular Medicine, Fudan University, Shanghai, China, 200032.,Department of Biochemistry and Molecular Biology, Shanghai Medical College, Fudan University, Shanghai, China, 200032
| | - Tal Salz
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Kasper D Hansen
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA.,McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA.,Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland 21205, USA
| | - Andrew Feinberg
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA.,Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA.,Department of Biomedical Engineering, Johns Hopkins Whiting School of Engineering, Baltimore, Maryland 21205, USA.,Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland 21205, USA
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26
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Shahal T, Green O, Hananel U, Michaeli Y, Shabat D, Ebenstein Y. Simple and cost-effective fluorescent labeling of 5-hydroxymethylcytosine. Methods Appl Fluoresc 2016; 4:044003. [PMID: 28192296 DOI: 10.1088/2050-6120/4/4/044003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The nucleobase 5-hydroxymethylcytosine (5-hmC), a modified form of cytosine, is an important epigenetic mark related to regulation of gene expression. 5-hmC levels are highly dynamic during early development and are modulated during the progression of neurodegenerative disease and cancer. We describe a spectroscopic method for the global quantification of 5-hmC in genomic DNA. This method relies on the enzymatic glucosylation of 5-hmC, followed by a glucose oxidation step that results in the formation of aldehyde moieties that are covalently linked to a fluorescent reporter by oxime ligation. The fluorescence intensity of the labeled sample is directly proportional to its 5-hmC content. We show that this simple and cost-effective technique is suitable for quantification of 5-hmC content in different mouse tissues.
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27
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Hack LM, Dick AL, Provençal N. Epigenetic mechanisms involved in the effects of stress exposure: focus on 5-hydroxymethylcytosine. ENVIRONMENTAL EPIGENETICS 2016; 2:dvw016. [PMID: 29492296 PMCID: PMC5804530 DOI: 10.1093/eep/dvw016] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2016] [Revised: 06/03/2016] [Accepted: 06/11/2016] [Indexed: 05/31/2023]
Abstract
5-hydroxymethylcytosine (5hmC) is a recently re-discovered transient intermediate in the active demethylation pathway that also appears to play an independent role in modulating gene function. Epigenetic marks, particularly 5-methylcytosine, have been widely studied in relation to stress-related disorders given the long-lasting effect that stress has on these marks. 5hmC is a good candidate for involvement in the etiology of these disorders given its elevated concentration in mammalian neurons, its dynamic regulation during development of the central nervous system, and its high variability among individuals. Although we are unaware of any studies published to date examining 5 hmC profiles in human subjects who have developed a psychiatric disorder after a life stressor, there is emerging evidence from the animal literature that 5hmC profiles are altered in the context of fear-conditioning paradigms and stress exposure, suggesting a possible role for 5hmC in the biological underpinnings of stress-related disorders. In this review, the authors examine the available approaches for profiling 5hmC and describe their advantages and disadvantages as well as discuss the studies published thus far investigating 5hmC in the context of fear-related learning and stress exposure in animals. The authors also highlight the global versus locus-specific regulation of 5hmC in these studies. Finally, the limitations of the current studies and their implications are discussed.
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Affiliation(s)
- Laura M. Hack
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany
- Department of Psychiatry and Behavioral Sciences, Emory University Medical School, Atlanta, GA, USA
| | - Alec L.W. Dick
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany
| | - Nadine Provençal
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany
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28
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Nestor CE, Lentini A, Hägg Nilsson C, Gawel DR, Gustafsson M, Mattson L, Wang H, Rundquist O, Meehan RR, Klocke B, Seifert M, Hauck SM, Laumen H, Zhang H, Benson M. 5-Hydroxymethylcytosine Remodeling Precedes Lineage Specification during Differentiation of Human CD4(+) T Cells. Cell Rep 2016; 16:559-570. [PMID: 27346350 DOI: 10.1016/j.celrep.2016.05.091] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Revised: 03/24/2016] [Accepted: 05/22/2016] [Indexed: 12/17/2022] Open
Abstract
5-methylcytosine (5mC) is converted to 5-hydroxymethylcytosine (5hmC) by the TET family of enzymes as part of a recently discovered active DNA de-methylation pathway. 5hmC plays important roles in regulation of gene expression and differentiation and has been implicated in T cell malignancies and autoimmunity. Here, we report early and widespread 5mC/5hmC remodeling during human CD4(+) T cell differentiation ex vivo at genes and cell-specific enhancers with known T cell function. We observe similar DNA de-methylation in CD4(+) memory T cells in vivo, indicating that early remodeling events persist long term in differentiated cells. Underscoring their important function, 5hmC loci were highly enriched for genetic variants associated with T cell diseases and T-cell-specific chromosomal interactions. Extensive functional validation of 22 risk variants revealed potentially pathogenic mechanisms in diabetes and multiple sclerosis. Our results support 5hmC-mediated DNA de-methylation as a key component of CD4(+) T cell biology in humans, with important implications for gene regulation and lineage commitment.
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Affiliation(s)
- Colm E Nestor
- Centre for Personalized Medicine, Department of Pediatrics, Faculty of Medicine, Linköping University, 581 85 Linköping, Sweden.
| | - Antonio Lentini
- Centre for Personalized Medicine, Department of Pediatrics, Faculty of Medicine, Linköping University, 581 85 Linköping, Sweden
| | - Cathrine Hägg Nilsson
- Centre for Personalized Medicine, Department of Pediatrics, Faculty of Medicine, Linköping University, 581 85 Linköping, Sweden
| | - Danuta R Gawel
- Centre for Personalized Medicine, Department of Pediatrics, Faculty of Medicine, Linköping University, 581 85 Linköping, Sweden
| | - Mika Gustafsson
- Bioinformatics, Department of Physics, Chemistry and Biology, Linköping University, 581 83 Linköping, Sweden
| | - Lina Mattson
- Centre for Personalized Medicine, Department of Pediatrics, Faculty of Medicine, Linköping University, 581 85 Linköping, Sweden
| | - Hui Wang
- MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Olof Rundquist
- Centre for Personalized Medicine, Department of Pediatrics, Faculty of Medicine, Linköping University, 581 85 Linköping, Sweden
| | - Richard R Meehan
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road, Edinburgh EH4 2XU, UK
| | | | | | - Stefanie M Hauck
- Research Unit Protein Science, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, 85764 Neuherberg, Germany
| | - Helmut Laumen
- Else Kröner-Fresenius-Center for Nutritional Medicine, Chair of Nutritional Medicine, MRI and ZIEL, Technische Universität München, 85354 Freising-Weihenstephan, Germany; German Center for Diabetes Research (DZD), Clinical Cooperation Group Nutrigenomics and Type 2 Diabetes at the Helmholtz Zentrum München, 85764 Neuherberg, Germany; Technische Universität München, 85354 Freising-Weihenstephan, Germany
| | - Huan Zhang
- Centre for Personalized Medicine, Department of Pediatrics, Faculty of Medicine, Linköping University, 581 85 Linköping, Sweden
| | - Mikael Benson
- Centre for Personalized Medicine, Department of Pediatrics, Faculty of Medicine, Linköping University, 581 85 Linköping, Sweden.
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29
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Thomson JP, Ottaviano R, Unterberger EB, Lempiäinen H, Muller A, Terranova R, Illingworth RS, Webb S, Kerr ARW, Lyall MJ, Drake AJ, Wolf CR, Moggs JG, Schwarz M, Meehan RR. Loss of Tet1-Associated 5-Hydroxymethylcytosine Is Concomitant with Aberrant Promoter Hypermethylation in Liver Cancer. Cancer Res 2016; 76:3097-108. [PMID: 27197233 PMCID: PMC5021200 DOI: 10.1158/0008-5472.can-15-1910] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Accepted: 03/09/2016] [Indexed: 12/17/2022]
Abstract
Aberrant hypermethylation of CpG islands (CGI) in human tumors occurs predominantly at repressed genes in the host tissue, but the preceding events driving this phenomenon are poorly understood. In this study, we temporally tracked epigenetic and transcriptomic perturbations that occur in a mouse model of liver carcinogenesis. Hypermethylated CGI events in the model were predicted by enrichment of the DNA modification 5-hydroxymethylcytosine (5hmC) and the histone H3 modification H3K27me3 at silenced promoters in the host tissue. During cancer progression, selected CGIs underwent hypo-hydroxymethylation prior to hypermethylation, while retaining H3K27me3. In livers from mice deficient in Tet1, a tumor suppressor involved in cytosine demethylation, we observed a similar loss of promoter core 5hmC, suggesting that reduced Tet1 activity at CGI may contribute to epigenetic dysregulation during hepatocarcinogenesis. Consistent with this possibility, mouse liver tumors exhibited reduced Tet1 protein levels. Similar to humans, DNA methylation changes at CGI in mice did not appear to be direct drivers of hepatocellular carcinoma progression, rather, dynamic changes in H3K27me3 promoter deposition correlated strongly with tumor-specific activation and repression of transcription. Overall, our results suggest that loss of promoter-associated 5hmC in liver tumors licenses reprograming of DNA methylation at silent CGI during progression. Cancer Res; 76(10); 3097-108. ©2016 AACR.
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Affiliation(s)
- John P Thomson
- MRC Human Genetics Unit at the Institute of Genetics and Molecular Medicine at the University of Edinburgh, Edinburgh, United Kingdom
| | - Raffaele Ottaviano
- MRC Human Genetics Unit at the Institute of Genetics and Molecular Medicine at the University of Edinburgh, Edinburgh, United Kingdom
| | - Elif B Unterberger
- Department of Toxicology, Institute of Experimental and Clinical Pharmacology and Toxicology, University of Tübingen, Tübingen, Germany
| | - Harri Lempiäinen
- Preclinical Safety, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Arne Muller
- Preclinical Safety, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Remi Terranova
- Preclinical Safety, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Robert S Illingworth
- MRC Human Genetics Unit at the Institute of Genetics and Molecular Medicine at the University of Edinburgh, Edinburgh, United Kingdom
| | - Shaun Webb
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Alastair R W Kerr
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Marcus J Lyall
- University/BHF Centre for Cardiovascular Science, University of Edinburgh, Edinburgh, United Kingdom
| | - Amanda J Drake
- University/BHF Centre for Cardiovascular Science, University of Edinburgh, Edinburgh, United Kingdom
| | - C Roland Wolf
- Medical Research Institute, University of Dundee, Ninewells Hospital & Medical School, Dundee, United Kingdom
| | - Jonathan G Moggs
- Preclinical Safety, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Michael Schwarz
- Department of Toxicology, Institute of Experimental and Clinical Pharmacology and Toxicology, University of Tübingen, Tübingen, Germany.
| | - Richard R Meehan
- MRC Human Genetics Unit at the Institute of Genetics and Molecular Medicine at the University of Edinburgh, Edinburgh, United Kingdom.
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30
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Zhang R, Lin H. 5-hydroxymethylcytosine: A new marker for early detection of digestive system tumors? Shijie Huaren Xiaohua Zazhi 2016; 24:1213-1219. [DOI: 10.11569/wcjd.v24.i8.1213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
5-methylcytosine (5-mc) has been recognized as an important epigenetic modification in mammalian genomic DNA. Studies have revealed that TET (ten-eleven translocation) protein family could catalyze the conversion of 5-mc into 5-hydroxyme-thylcytosine (5-hmc), which is now widely recognized as the sixth base in the genome. Recent reports showed that the level of 5-hmc was decreased in digestive system tumors, indicating that 5-hmc may be a useful epigenetic biomarker for the early diagnosis of gastrointestinal tumors. To better understand the roles of TET and 5-hmc, this article will elucidate the function of TET protein and the connections between 5-hmc and digestive system tumors.
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31
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Wang XL, Song SH, Wu YS, Li YL, Chen TT, Huang ZY, Liu S, Dunwell TL, Pfeifer GP, Dunwell JM, Wamaedeesa R, Ullah I, Wang Y, Hu SN. Genome-wide mapping of 5-hydroxymethylcytosine in three rice cultivars reveals its preferential localization in transcriptionally silent transposable element genes. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:6651-63. [PMID: 26272901 PMCID: PMC4715260 DOI: 10.1093/jxb/erv372] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
5-Hydroxymethylcytosine (5hmC), a modified form of cytosine that is considered the sixth nucleobase in DNA, has been detected in mammals and is believed to play an important role in gene regulation. In this study, 5hmC modification was detected in rice by employing a dot-blot assay, and its levels was further quantified in DNA from different rice tissues using liquid chromatography-multistage mass spectrometry (LC-MS/MS/MS). The results showed large intertissue variation in 5hmC levels. The genome-wide profiles of 5hmC modification in three different rice cultivars were also obtained using a sensitive chemical labelling followed by a next-generation sequencing method. Thousands of 5hmC peaks were identified, and a comparison of the distributions of 5hmC among different rice cultivars revealed the specificity and conservation of 5hmC modification. The identified 5hmC peaks were significantly enriched in heterochromatin regions, and mainly located in transposable elements (TEs), especially around retrotransposons. The correlation analysis of 5hmC and gene expression data revealed a close association between 5hmC and silent TEs. These findings provide a resource for plant DNA 5hmC epigenetic studies and expand our knowledge of 5hmC modification.
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Affiliation(s)
- Xi-liang Wang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China Graduate University of Chinese Academy of Sciences, Yuquan Road, Beijing 100039, China
| | - Shu-hui Song
- Core Genomic Facility, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Yong-Sheng Wu
- Mudanjiang Youbo Pharmaceutical Co., Ltd, Heilongjiang 157011, China
| | - Yu-Li Li
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China Core Genomic Facility, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China Graduate University of Chinese Academy of Sciences, Yuquan Road, Beijing 100039, China
| | - Ting-ting Chen
- Core Genomic Facility, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhi-yuan Huang
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha 410125, China
| | - Shuo Liu
- Environmental Toxicology Graduate Program, University of California, Riverside, CA 92521, USA
| | | | - Gerd P Pfeifer
- Beckman Research Institute, City of Hope Medical Centre, Duarte, CA 91010, USA
| | - Jim M Dunwell
- School of Agriculture, Policy and Development, University of Reading, Earley Gate, Reading RG6 6AR, UK
| | - Raheema Wamaedeesa
- School of Agriculture, Policy and Development, University of Reading, Earley Gate, Reading RG6 6AR, UK
| | - Ihsan Ullah
- School of Agriculture, Policy and Development, University of Reading, Earley Gate, Reading RG6 6AR, UK Agricultural Biotechnology Research Institute, Faisalabad 38000, Pakistan
| | - Yinsheng Wang
- Environmental Toxicology Graduate Program, University of California, Riverside, CA 92521, USA Department of Chemistry, University of California, Riverside, CA 92521, USA
| | - Song-nian Hu
- Core Genomic Facility, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
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32
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Jankowska AM, Millward CL, Caldwell CW. The potential of DNA modifications as biomarkers and therapeutic targets in oncology. Expert Rev Mol Diagn 2015; 15:1325-37. [PMID: 26394702 DOI: 10.1586/14737159.2015.1084229] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Knowledge of epigenetic alterations in cancer is rapidly increasing due to the development of genome-wide techniques for their identification. DNA methylation is the best understood epigenetic adaptation and disease-specific aberrant DNA methylation is a well-recognized hallmark of cancer. Recently, novel modifications, including 5-hydroxymethylation have been described, adding a new layer of complexity to understanding the epigenetic machinery and their role in cancer. There have been significant advances in techniques for the discovery and validation of DNA methylation- and hydroxymethylation-based biomarkers, each with its own advantages and limitations. With the advent of new profiling technologies, the ever-growing list of genes that show epigenetic alterations, particularly DNA methylation, emphasizes the role of these changes for early detection, diagnosis, prognosis, and prediction of response to therapies. While there are yet many challenges to the effective implementation of DNA-methylation/hydroxymethylation-based biomarkers and epigenetic therapeutics, the field is moving closer to the goal of defining personalized medicine.
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Affiliation(s)
- Anna M Jankowska
- a Lilly Research Laboratories, Eli Lilly and Company Corporate Center, Indianapolis, IN 46285 USA
| | - Carl L Millward
- a Lilly Research Laboratories, Eli Lilly and Company Corporate Center, Indianapolis, IN 46285 USA
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Pirola CJ, Scian R, Gianotti TF, Dopazo H, Rohr C, Martino JS, Castaño GO, Sookoian S. Epigenetic Modifications in the Biology of Nonalcoholic Fatty Liver Disease: The Role of DNA Hydroxymethylation and TET Proteins. Medicine (Baltimore) 2015; 94:e1480. [PMID: 26356709 PMCID: PMC4616643 DOI: 10.1097/md.0000000000001480] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The 5-Hydroxymethylcytosine (5-hmC) is an epigenetic modification whose role in the pathogenesis of metabolic-related complex diseases remains unexplored; 5-hmC appears to be prevalent in the mitochondrial genome. The Ten-Eleven-Translocation (TET) family of proteins is responsible for catalyzing the conversion of 5-methylcytosine to 5-hmC. We hypothesized that epigenetic editing by 5-hmC might be a novel mechanism through which nonalcoholic fatty liver disease (NAFLD)-associated molecular traits could be explained.Hence, we performed an observational study to explore global levels of 5-hmC in fresh liver samples of patients with NAFLD and controls (n = 90) using an enzyme-linked-immunosorbent serologic assay and immunohistochemistry. We also screened for genetic variation in TET 1-3 loci by next generation sequencing to explore its contribution to the disease biology. The study was conducted in 2 stages (discovery and replication) and included 476 participants.We observed that the amount of 5-hmC in the liver of both NAFLD patients and controls was relatively low (up to 0.1%); a significant association was found with liver mitochondrial DNA copy number (R = 0.50, P = 0.000382) and PPARGC1A-mRNA levels (R = -0.57, P = 0.04).We did not observe any significant difference in the 5-hmC nuclear immunostaining score between NAFLD patients and controls; nevertheless, we found that patients with NAFLD (0.4 ± 0.5) had significantly lower nonnuclear-5-hmC staining compared with controls (1.8 ± 0.8), means ± standard deviation, P = 0.028. The missense p.Ile1123Met variant (TET1-rs3998860) was significantly associated with serum levels of caspase-generated CK-18 fragment-cell death biomarker in the discovery and replication stage, and the disease severity (odds ratio: 1.47, 95% confidence interval: 1.10-1.97; P = 0.005). The p.Ile1762Val substitution (TET2-rs2454206) was associated with liver PPARGC1A-methylation and transcriptional levels, and Type 2 diabetes.Our results suggest that 5-hmC might be involved in the pathogenesis of NAFLD by regulating liver mitochondrial biogenesis and PPARGC1A expression. Genetic diversity at TET loci suggests an "epigenetic" regulation of programmed liver-cell death and a TET-mediated fine-tuning of the liver PPARGC1A-transcriptional program.
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Affiliation(s)
- Carlos J Pirola
- From the Department of Molecular Genetics and Biology of Complex Diseases, Institute of Medical Research A Lanari-IDIM, University of Buenos Aires-National Scientific and Technical Research Council (CONICET), Ciudad Autónoma de Buenos Aires, Argentina (CJP, RS, TFG); Biomedical Genomics and Evolution Laboratory, Ecology, Genetics and Evolution Department, Faculty of Science, IEGEBA, University of Buenos Aires-National Scientific and Technical Research Council (CONICET), Ciudad Autónoma de Buenos Aires, Argentina (HD, CR); Department of Pathology, Hospital Diego Thompson, San Martin, Buenos Aires, Argentina (JSM); Liver Unit, Medicine and Surgery Department, Hospital Abel Zubizarreta, Ciudad Autónoma de Buenos Aires, Argentina (GOC); and Department of Clinical and Molecular Hepatology, Institute of Medical Research A Lanari-IDIM, University of Buenos Aires-National Scientific and Technical Research Council (CONICET), Ciudad Autónoma de Buenos Aires, Argentina (RS, SS)
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Xiong J, Jiang HP, Peng CY, Deng QY, Lan MD, Zeng H, Zheng F, Feng YQ, Yuan BF. DNA hydroxymethylation age of human blood determined by capillary hydrophilic-interaction liquid chromatography/mass spectrometry. Clin Epigenetics 2015. [PMID: 26207150 PMCID: PMC4511989 DOI: 10.1186/s13148-015-0109-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Background Aging is a complex phenomenon and characterized by a progressive decline in physiology and function of adult tissues. However, it hasn’t been well established of the correlation between aging and global DNA methylation and hydroxymethylation that regulate the growth and development of higher organisms. Results We developed an on-line trapping/capillary hydrophilic-interaction liquid chromatography/electrospray ionization-mass spectrometry method for ultra-sensitive and simultaneous quantification of 5-methylcytosine (5-mC) and 5-hydroxymethylcytosine (5-hmC) in genomic DNA from human blood. Limits of detection for 5-mC and 5-hmC were 0.04 and 0.13 fmol, respectively. The imprecision and recovery of the method were determined with the relative standard deviations (RSDs) and relative errors being <11.2 and 14.0 %, respectively. We analyzed the contents of 5-mC and 5-hmC in genomic DNA of blood from 238 healthy people aged from 1 to 82 years. The results showed that 5-hmC content was significantly decreased and highly correlated with aging process, while 5-mC only showed slight correlation with age. We then established a DNA hydroxymethylation age model according to 5-hmC content with a mean absolute deviation (MAD) of approximate 8.9 years. We also calculated the mean relative error (MRE) using the predicted ages based on the age model and the chronological ages. The results showed that the MRE was 18.3 % for samples with ages from 20 to 82 years (95 % confidence interval, N = 190). Conclusions The global DNA hydroxymethylation represents a strong and reproducible mark of chronological age, which could be potentially applied in health assessment and prevention of diseases. The identification of biological or environmental factors that influence DNA hydroxymethylation aging rate may permit quantitative assessments of their impacts on health. Electronic supplementary material The online version of this article (doi:10.1186/s13148-015-0109-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jun Xiong
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of education), Department of Chemistry, Wuhan University, Wuhan, 430072 China
| | - Han-Peng Jiang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of education), Department of Chemistry, Wuhan University, Wuhan, 430072 China
| | - Chun-Yan Peng
- Center for Gene Diagnosis, Zhongnan Hospital of Wuhan University, Wuhan, 430071 China
| | - Qian-Yun Deng
- Center for Gene Diagnosis, Zhongnan Hospital of Wuhan University, Wuhan, 430071 China
| | - Meng-Dan Lan
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of education), Department of Chemistry, Wuhan University, Wuhan, 430072 China
| | - Huan Zeng
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of education), Department of Chemistry, Wuhan University, Wuhan, 430072 China
| | - Fang Zheng
- Center for Gene Diagnosis, Zhongnan Hospital of Wuhan University, Wuhan, 430071 China
| | - Yu-Qi Feng
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of education), Department of Chemistry, Wuhan University, Wuhan, 430072 China
| | - Bi-Feng Yuan
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of education), Department of Chemistry, Wuhan University, Wuhan, 430072 China
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35
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Miousse IR, Currie R, Datta K, Ellinger-Ziegelbauer H, French JE, Harrill AH, Koturbash I, Lawton M, Mann D, Meehan RR, Moggs JG, O'Lone R, Rasoulpour RJ, Pera RAR, Thompson K. Importance of investigating epigenetic alterations for industry and regulators: An appraisal of current efforts by the Health and Environmental Sciences Institute. Toxicology 2015; 335:11-9. [PMID: 26134581 DOI: 10.1016/j.tox.2015.06.009] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Revised: 06/15/2015] [Accepted: 06/23/2015] [Indexed: 12/20/2022]
Abstract
Recent technological advances have led to rapid progress in the characterization of epigenetic modifications that control gene expression in a generally heritable way, and are likely involved in defining cellular phenotypes, developmental stages and disease status from one generation to the next. On November 18, 2013, the International Life Sciences Institute (ILSI) Health and Environmental Sciences Institute (HESI) held a symposium entitled "Advances in Assessing Adverse Epigenetic Effects of Drugs and Chemicals" in Washington, D.C. The goal of the symposium was to identify gaps in knowledge and highlight promising areas of progress that represent opportunities to utilize epigenomic profiling for risk assessment of drugs and chemicals. Epigenomic profiling has the potential to provide mechanistic information in toxicological safety assessments; this is especially relevant for the evaluation of carcinogenic or teratogenic potential and also for drugs that directly target epigenetic modifiers, like DNA methyltransferases or histone modifying enzymes. Furthermore, it can serve as an endpoint or marker for hazard characterization in chemical safety assessment. The assessment of epigenetic effects may also be approached with new model systems that could directly assess transgenerational effects or potentially sensitive stem cell populations. These would enhance the range of safety assessment tools for evaluating xenobiotics that perturb the epigenome. Here we provide a brief synopsis of the symposium, update findings since that time and then highlight potential directions for future collaborative efforts to incorporate epigenetic profiling into risk assessment.
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Affiliation(s)
- Isabelle R Miousse
- Department of Environmental and Occupational Health, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Richard Currie
- Syngenta Jealotts Hill International Research Centre, Bracknell, Berkshire, UK
| | | | - Heidrun Ellinger-Ziegelbauer
- Toxicology, Bayer Pharma AG, Wuppertal, Germany; Member of the Innovative Medicines Initiative (IMI) BioMARkers & molecular tumor classification for non-genotoxic CARcinogenesis (MARCAR) consortium www.imi-marcar.eu
| | - John E French
- National Institute for Environmental Health Sciences, Division of the National Toxicology Program, Research Triangle Park, NC, USA
| | - Alison H Harrill
- Department of Environmental and Occupational Health, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Igor Koturbash
- Department of Environmental and Occupational Health, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | | | - Derek Mann
- Fibrosis Research Group, Institute of Cellular Medicine, Newcastle University, Newcastle Upon Tyne, UK
| | - Richard R Meehan
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK; Member of the Innovative Medicines Initiative (IMI) BioMARkers & molecular tumor classification for non-genotoxic CARcinogenesis (MARCAR) consortium www.imi-marcar.eu
| | - Jonathan G Moggs
- Discovery and Investigative Safety, Preclinical Safety, Novartis Institutes for Biomedical Research, Basel, Switzerland; Member of the Innovative Medicines Initiative (IMI) BioMARkers & molecular tumor classification for non-genotoxic CARcinogenesis (MARCAR) consortium www.imi-marcar.eu
| | - Raegan O'Lone
- ILSI Health and Environmental Sciences Institute, Washington, D.C., USA
| | - Reza J Rasoulpour
- Toxicology Environmental Research and Consulting, The Dow Chemical Company, Midland, MI, USA
| | | | - Karol Thompson
- Division of Applied Regulatory Science, OCP, CDER, US FDA, Silver Spring, MD, USA
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Thomson JP, Fawkes A, Ottaviano R, Hunter JM, Shukla R, Mjoseng HK, Clark R, Coutts A, Murphy L, Meehan RR. DNA immunoprecipitation semiconductor sequencing (DIP-SC-seq) as a rapid method to generate genome wide epigenetic signatures. Sci Rep 2015; 5:9778. [PMID: 25985418 PMCID: PMC4435000 DOI: 10.1038/srep09778] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2014] [Accepted: 03/02/2015] [Indexed: 02/02/2023] Open
Abstract
Modification of DNA resulting in 5-methylcytosine (5 mC) or 5-hydroxymethylcytosine (5hmC) has been shown to influence the local chromatin environment and affect transcription. Although recent advances in next generation sequencing technology allow researchers to map epigenetic modifications across the genome, such experiments are often time-consuming and cost prohibitive. Here we present a rapid and cost effective method of generating genome wide DNA modification maps utilising commercially available semiconductor based technology (DNA immunoprecipitation semiconductor sequencing; "DIP-SC-seq") on the Ion Proton sequencer. Focussing on the 5hmC mark we demonstrate, by directly comparing with alternative sequencing strategies, that this platform can successfully generate genome wide 5hmC patterns from as little as 500 ng of genomic DNA in less than 4 days. Such a method can therefore facilitate the rapid generation of multiple genome wide epigenetic datasets.
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Affiliation(s)
- John P Thomson
- MRC Human Genetics Unit at the Institute of Genetics and Molecular Medicine at the University of Edinburgh, Crewe Road, Edinburgh, EH4 2XU, UK
| | - Angie Fawkes
- Wellcome Trust Clinical Research Facility, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, UK
| | - Raffaele Ottaviano
- MRC Human Genetics Unit at the Institute of Genetics and Molecular Medicine at the University of Edinburgh, Crewe Road, Edinburgh, EH4 2XU, UK
| | - Jennifer M Hunter
- MRC Human Genetics Unit at the Institute of Genetics and Molecular Medicine at the University of Edinburgh, Crewe Road, Edinburgh, EH4 2XU, UK
| | - Ruchi Shukla
- MRC Human Genetics Unit at the Institute of Genetics and Molecular Medicine at the University of Edinburgh, Crewe Road, Edinburgh, EH4 2XU, UK
| | - Heidi K Mjoseng
- MRC Human Genetics Unit at the Institute of Genetics and Molecular Medicine at the University of Edinburgh, Crewe Road, Edinburgh, EH4 2XU, UK
| | - Richard Clark
- Wellcome Trust Clinical Research Facility, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, UK
| | - Audrey Coutts
- Wellcome Trust Clinical Research Facility, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, UK
| | - Lee Murphy
- Wellcome Trust Clinical Research Facility, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, UK
| | - Richard R Meehan
- MRC Human Genetics Unit at the Institute of Genetics and Molecular Medicine at the University of Edinburgh, Crewe Road, Edinburgh, EH4 2XU, UK
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Behnia F, Parets SE, Kechichian T, Yin H, Dutta EH, Saade GR, Smith AK, Menon R. Fetal DNA methylation of autism spectrum disorders candidate genes: association with spontaneous preterm birth. Am J Obstet Gynecol 2015; 212:533.e1-9. [PMID: 25687563 DOI: 10.1016/j.ajog.2015.02.011] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Revised: 01/24/2015] [Accepted: 02/09/2015] [Indexed: 11/18/2022]
Abstract
OBJECTIVE Autism spectrum disorder (ASD) is associated with preterm birth (PTB), although the reason underlying this relationship is still unclear. Our objective was to examine DNA methylation patterns of 4 ASD candidate genes in human fetal membranes from spontaneous PTB and uncomplicated term birth. STUDY DESIGN A literature search for genes that have been implicated in ASD yielded 14 candidate genes (OXTR, SHANK3, BCL2, RORA, EN2, RELN, MECP2, AUTS2, NLGN3, NRXN1, SLC6A4, UBE3A, GABA, AFF2) that were epigenetically modified in relation to ASD. DNA methylation in fetal leukocyte DNA in 4 of these genes (OXTR, SHANK3, BCL2, and RORA) was associated with PTB in a previous study. This study evaluated DNA methylation, transcription (reverse transcription polymerase chain reaction), and translation patterns (immunostaining and Western blot) in fetal membrane from term labor (n = 14), term not in labor (TNIL; n = 29), and spontaneous preterm birth (PTB; n = 27). Statistical analysis was performed with analysis of variance; a probability value of < .05 was significant. RESULTS Higher methylation of the OXTR promoter was seen in fetal membranes from PTB, compared with term labor or TNIL. No other gene showed any methylation differences among groups. Expression of OXTR was not different among groups, but the 70 kDa OXTR protein was seen only in PTB, and immunostaining was more intense in PTB amniocytes than term labor or TNIL. CONCLUSION Among the 4 genes that were studied, fetal membranes from PTB demonstrate differences in OXTR methylation and regulation and expression, which suggest that epigenetic alteration of this gene in fetal membrane may likely be indicating an in utero programing of this gene and serve as a surrogate in a subset of PTB. The usefulness of OXTR hypermethylation as a surrogate for a link to ASD should be further evaluated in longitudinal and in vitro studies.
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Affiliation(s)
- Fara Behnia
- Division of Maternal-Fetal Medicine and Perinatal Research, Department of Obstetrics and Gynecology, University of Texas Medical Branch, Galveston, TX
| | - Sasha E Parets
- Genetics and Molecular Biology Program, Emory University School of Medicine, Atlanta, GA
| | - Talar Kechichian
- Division of Maternal-Fetal Medicine and Perinatal Research, Department of Obstetrics and Gynecology, University of Texas Medical Branch, Galveston, TX
| | - Huaizhi Yin
- Division of Maternal-Fetal Medicine and Perinatal Research, Department of Obstetrics and Gynecology, University of Texas Medical Branch, Galveston, TX
| | - Eryn H Dutta
- Division of Maternal-Fetal Medicine and Perinatal Research, Department of Obstetrics and Gynecology, University of Texas Medical Branch, Galveston, TX
| | - George R Saade
- Division of Maternal-Fetal Medicine and Perinatal Research, Department of Obstetrics and Gynecology, University of Texas Medical Branch, Galveston, TX
| | - Alicia K Smith
- Genetics and Molecular Biology Program, Emory University School of Medicine, Atlanta, GA; Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA
| | - Ramkumar Menon
- Division of Maternal-Fetal Medicine and Perinatal Research, Department of Obstetrics and Gynecology, University of Texas Medical Branch, Galveston, TX.
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Nestor CE, Ottaviano R, Reinhardt D, Cruickshanks HA, Mjoseng HK, McPherson RC, Lentini A, Thomson JP, Dunican DS, Pennings S, Anderton SM, Benson M, Meehan RR. Rapid reprogramming of epigenetic and transcriptional profiles in mammalian culture systems. Genome Biol 2015; 16:11. [PMID: 25648825 PMCID: PMC4334405 DOI: 10.1186/s13059-014-0576-y] [Citation(s) in RCA: 111] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Accepted: 12/22/2014] [Indexed: 12/12/2022] Open
Abstract
Background The DNA methylation profiles of mammalian cell lines differ from those of the primary tissues from which they were derived, exhibiting increasing divergence from the in vivo methylation profile with extended time in culture. Few studies have directly examined the initial epigenetic and transcriptional consequences of adaptation of primary mammalian cells to culture, and the potential mechanisms through which this epigenetic dysregulation occurs is unknown. Results We demonstrate that adaptation of mouse embryonic fibroblasts to cell culture results in a rapid reprogramming of epigenetic and transcriptional states. We observed global 5-hydroxymethylcytosine (5hmC) erasure within three days of culture initiation. Loss of genic 5hmC was independent of global 5-methylcytosine (5mC) levels and could be partially rescued by addition of vitamin C. Significantly, 5hmC loss was not linked to concomitant changes in transcription. Discrete promoter-specific gains of 5mC were also observed within seven days of culture initiation. Against this background of global 5hmC loss we identified a handful of developmentally important genes that maintained their 5hmC profile in culture, including the imprinted loci Gnas and H19. Similar outcomes were identified in the adaption of CD4+ T cells to culture. Conclusions We report a dramatic and novel consequence of adaptation of mammalian cells to culture in which global loss of 5hmC occurs, suggesting rapid concomitant loss of methylcytosine dioxygenase activity. The observed epigenetic and transcriptional re-programming occurs much earlier than previously assumed, and has significant implications for the use of cell lines as faithful mimics of in vivo epigenetic and physiological processes. Electronic supplementary material The online version of this article (doi:10.1186/s13059-014-0576-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Colm E Nestor
- Centre for Individualised Medicine, Faculty of Health Sciences, Linköping University, Linköping, 581 83, Sweden. .,MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK.
| | - Raffaele Ottaviano
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK.
| | - Diana Reinhardt
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK.
| | - Hazel A Cruickshanks
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK.
| | - Heidi K Mjoseng
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK.
| | - Rhoanne C McPherson
- MRC Centre for Inflammation Research, Centre for Multiple Sclerosis Research and Centre for Immunity Infection and Evolution, University of Edinburgh, Edinburgh, EH16 4TJ, UK.
| | - Antonio Lentini
- Centre for Individualised Medicine, Faculty of Health Sciences, Linköping University, Linköping, 581 83, Sweden.
| | - John P Thomson
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK.
| | - Donncha S Dunican
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK.
| | - Sari Pennings
- Centre for Cardiovascular Science, Queen's Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh, EH16 4TJ, UK.
| | - Stephen M Anderton
- MRC Centre for Inflammation Research, Centre for Multiple Sclerosis Research and Centre for Immunity Infection and Evolution, University of Edinburgh, Edinburgh, EH16 4TJ, UK.
| | - Mikael Benson
- Centre for Individualised Medicine, Faculty of Health Sciences, Linköping University, Linköping, 581 83, Sweden.
| | - Richard R Meehan
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK.
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Cui Y, Gao D, Linghu E, Zhan Q, Chen R, Brock MV, Herman JG, Guo M. Epigenetic changes and functional study of HOXA11 in human gastric cancer. Epigenomics 2015; 7:201-13. [PMID: 25590359 DOI: 10.2217/epi.14.92] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
AIM To examine epigenetic changes and the function of HOXA11 in human gastric cancer (GC). MATERIALS & METHODS Seven GC cell lines, five cases of normal gastric mucosa and 112 cases primary GC samples were used in this study. RESULTS Expression of HOXA11 and lack of promoter region methylation were found in NCI-N87, MKN45, BGC823 and HGC27 cells. Loss of expression and complete methylation were found in AGS gastric cancer cells. Reduced expression and partial methylation were found in MGC803 and SGC7901 cells. Restoration of HOXA11 expression was induced by 5-aza-2'-deoxycytidine. HOXA11 was methylated in 81.25% (91/112) of primary GCs. The presence of methylation was associated with male gender, tumor size, tumor differentiation and lymph node metastasis (all p < 0.05). Restoration of HOXA11 expression reduced cell proliferation, invasion, migration and induced apoptosis and G2/M phase arrest. HOXA11 was found to inhibit Wnt signaling by upregulating NKD1 expression. CONCLUSION Epigenetic silencing of HOXA11 promotes GC proliferation, migration and invasion through activation of Wnt signaling.
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Affiliation(s)
- Yingying Cui
- Department of Gastroenterology & Hepatology, Chinese PLA General Hospital, Beijing, China
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40
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Abstract
Epigenetic control of gene expression programs is essential for normal organismal development and cellular function. Abrogation of epigenetic regulation is seen in many human diseases, including cancer and neuropsychiatric disorders, where it can affect disease etiology and progression. Abnormal epigenetic profiles can serve as biomarkers of disease states and predictors of disease outcomes. Therefore, epigenetics is a key area of clinical investigation in diagnosis, prognosis, and treatment. In this review, we give an overarching view of epigenetic mechanisms of human disease. Genetic mutations in genes that encode chromatin regulators can cause monogenic disease or are incriminated in polygenic, multifactorial diseases. Environmental stresses can also impact directly on chromatin regulation, and these changes can increase the risk of, or directly cause, disease. Finally, emerging evidence suggests that exposure to environmental stresses in older generations may predispose subsequent generations to disease in a manner that involves the transgenerational inheritance of epigenetic information.
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Affiliation(s)
- Emily Brookes
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115
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41
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Abstract
Combined with TCR stimuli, extracellular cytokine signals initiate the differentiation of naive CD4(+) T cells into specialized effector T-helper (Th) and regulatory T (Treg) cell subsets. The lineage specification and commitment process occurs through the combinatorial action of multiple transcription factors (TFs) and epigenetic mechanisms that drive lineage-specific gene expression programs. In this article, we review recent studies on the transcriptional and epigenetic regulation of distinct Th cell lineages. Moreover, we review current study linking immune disease-associated single-nucleotide polymorphisms with distal regulatory elements and their potential role in the disease etiology.
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Affiliation(s)
- Subhash K Tripathi
- Turku Centre for Biotechnology, University of Turku and
Åbo Akademi UniversityTurku, Finland
- National Doctoral Programme in Informational and
Structural BiologyTurku, Finland
- Turku Doctoral Programme of Molecular Medicine (TuDMM),
University of TurkuTurku, Finland
| | - Riitta Lahesmaa
- Turku Centre for Biotechnology, University of Turku and
Åbo Akademi UniversityTurku, Finland
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Ficz G, Gribben JG. Loss of 5-hydroxymethylcytosine in cancer: cause or consequence? Genomics 2014; 104:352-7. [PMID: 25179374 DOI: 10.1016/j.ygeno.2014.08.017] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Revised: 08/21/2014] [Accepted: 08/22/2014] [Indexed: 12/19/2022]
Abstract
Discovery of the enzymatic activity that catalyses oxidation of 5-methylcytosine (5mC) to generate 5-hydroxymethylcytosine (5hmC) mediated by the MLL (KMT2A) fusion partner TET1 has sparked intense research to understand the role this new DNA modification has in cancer. An unambiguous picture has emerged where tumours are depleted of 5hmC compared to corresponding normal tissue, but it is not known whether lack of 5hmC is a cause or a consequence of tumourigenesis. Experimental data reveals a dual tumour-suppressive and oncogenic role for TET proteins. Tet2 mutations are drivers in haematological malignancies but Tet1 had an oncogenic role in MLL-rearranged leukaemia, where Tet1 is overexpressed. Overexpression of Tet2 in melanoma cells re-established the 5hmC landscape and suppressed cancer progression but inhibiting Tet1 in non-transformed cells did not initiate cellular transformation. In this review we summarise recent findings that have shaped the current understanding on the role 5hmC plays in cancer.
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Affiliation(s)
- Gabriella Ficz
- Centre for Haemato-Oncology, Barts Cancer Institute, EC1M 6BQ London, UK.
| | - John G Gribben
- Centre for Haemato-Oncology, Barts Cancer Institute, EC1M 6BQ London, UK
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Hahn MA, Szabó PE, Pfeifer GP. 5-Hydroxymethylcytosine: a stable or transient DNA modification? Genomics 2014; 104:314-23. [PMID: 25181633 DOI: 10.1016/j.ygeno.2014.08.015] [Citation(s) in RCA: 90] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Revised: 08/13/2014] [Accepted: 08/15/2014] [Indexed: 12/16/2022]
Abstract
The DNA base 5-hydroxymethylcytosine (5hmC) is produced by enzymatic oxidation of 5-methylcytosine (5mC) by 5mC oxidases (the Tet proteins). Since 5hmC is recognized poorly by DNA methyltransferases, DNA methylation may be lost at 5hmC sites during DNA replication. In addition, 5hmC can be oxidized further by Tet proteins and converted to 5-formylcytosine and 5-carboxylcytosine, two bases that can be removed from DNA by base excision repair. The completed pathway represents a replication-independent DNA demethylation cycle. However, the DNA base 5hmC is also known to be rather stable and occurs at substantial levels, for example in the brain, suggesting that it represents an epigenetic mark by itself that may regulate chromatin structure and transcription. Focusing on a few well-studied tissues and developmental stages, we discuss the opposing views of 5hmC as a transient intermediate in DNA demethylation and as a modified DNA base with an instructive role.
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Affiliation(s)
- Maria A Hahn
- Beckman Research Institute, City of Hope, Duarte CA 91010, USA
| | - Piroska E Szabó
- Beckman Research Institute, City of Hope, Duarte CA 91010, USA
| | - Gerd P Pfeifer
- Beckman Research Institute, City of Hope, Duarte CA 91010, USA.
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44
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Epigenetically modified nucleotides in chronic heroin and cocaine treated mice. Toxicol Lett 2014; 229:451-7. [PMID: 25064621 DOI: 10.1016/j.toxlet.2014.07.023] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Revised: 07/21/2014] [Accepted: 07/22/2014] [Indexed: 12/19/2022]
Abstract
Epigenetic changes include the addition of a methyl group to the 5' carbon of the cytosine ring, known as DNA methylation, which results in the generation of the fifth DNA base, namely 5-methylcytosine. During active or passive demethylation, an intermediate modified base is formed, 5-hydroxymethylcytosine. We have currently quantified 5-methylcytosine and 5-hydroxymethylcytosine in the liver and brain of mice treated with cocaine or heroin, using liquid chromatography/tandem mass spectrometry (LC-MS/MS). Our results show that global 5-methylcytosine levels are not affected by heroin or cocaine administration, neither in the liver nor in the brain. However, 5-hydroxymethylcytosine levels are reduced in the liver following cocaine administration, while they are not affected by cocaine in the brain or by heroin administration in the liver and the brain. Elucidation of the epigenetic phenomena that takes place with respect to drug abuse and addiction, via quantitative analysis of different modified bases, may enable a better understanding of the underlying mechanisms and may lead to more personalized and effective treatment options.
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45
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DNA methylation of the allergy regulatory gene interferon gamma varies by age, sex, and tissue type in asthmatics. Clin Epigenetics 2014; 6:9. [PMID: 24891923 PMCID: PMC4041041 DOI: 10.1186/1868-7083-6-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Accepted: 05/08/2014] [Indexed: 12/30/2022] Open
Abstract
Background Asthma is associated with allergic sensitization in about half of all cases, and asthma phenotypes can vary by age and sex. DNA methylation in the promoter of the allergy regulatory gene interferon gamma (IFNγ) has been linked to the maintenance of allergic immune function in human cell and mouse models. We hypothesized that IFNγ promoter methylation at two well-studied, key cytosine phosphate guanine (CpG) sites (-186 and -54), may differ by age, sex, and airway versus systemic tissue in a cohort of 74 allergic asthmatics. Results After sampling buccal cells, a surrogate for airway epithelial cells, and CD4+ lymphocytes, we found that CD4+ lymphocyte methylation was significantly higher in children compared to adults at both CpG sites (P <0.01). Buccal cell methylation was significantly higher in children at CpG -186 (P = 0.03) but not CpG -54 (P = 0.66). Methylation was higher in males compared to females at both CpG sites in CD4+ lymphocytes (-186: P <0.01, -54: P = 0.02) but not buccal cells (-186: P = 0.14, -54: P = 0.60). In addition, methylation was lower in CD4+ lymphocytes compared to buccal cells (P <0.01) and neighboring CpG sites were strongly correlated in CD4+ lymphocytes (r = 0.84, P <0.01) and weakly correlated in buccal cells (r = 0.24, P = 0.04). At CpG -186, there was significant correlation between CD4+ lymphocytes and buccal cells (r = 0.24, P = 0.04) but not at CpG -54 (r = -0.03, P = 0.78). Conclusions These findings highlight significant age, sex, and tissue-related differences in IFNγ promoter methylation that further our understanding of methylation in the allergic asthma pathway and in the application of biomarkers in clinical research.
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Pfeifer GP, Xiong W, Hahn MA, Jin SG. The role of 5-hydroxymethylcytosine in human cancer. Cell Tissue Res 2014; 356:631-41. [PMID: 24816989 DOI: 10.1007/s00441-014-1896-7] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Accepted: 04/10/2014] [Indexed: 12/22/2022]
Abstract
The patterns of DNA methylation in human cancer cells are highly abnormal and often involve the acquisition of DNA hypermethylation at hundreds or thousands of CpG islands that are usually unmethylated in normal tissues. The recent discovery of 5-hydroxymethylcytosine (5hmC) as an enzymatic oxidation product of 5-methylcytosine (5mC) has led to models and experimental data in which the hypermethylation and 5mC oxidation pathways seem to be connected. Key discoveries in this setting include the findings that several genes coding for proteins involved in the 5mC oxidation reaction are mutated in human tumors, and that a broad loss of 5hmC occurs across many types of cancer. In this review, we will summarize current knowledge and discuss models of the potential roles of 5hmC in human cancer biology.
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Affiliation(s)
- Gerd P Pfeifer
- Beckman Research Institute, City of Hope Medical Center, 1500 East Duarte Road, Duarte, CA 91010, USA,
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