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Whole-blood DNA Methylation Markers for Risk Stratification in Colorectal Cancer Screening: A Systematic Review. Cancers (Basel) 2019; 11:cancers11070912. [PMID: 31261771 PMCID: PMC6678372 DOI: 10.3390/cancers11070912] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 06/25/2019] [Accepted: 06/26/2019] [Indexed: 12/24/2022] Open
Abstract
DNA methylation profiles within whole-blood samples have been reported to be associated with colorectal cancer (CRC) occurrence and might enable risk stratification for CRC. We systematically reviewed and summarized studies addressing the association of whole-blood DNA methylation markers and risk of developing CRC or its precursors. We searched PubMed and ISI Web of Knowledge to identify relevant studies published until 12th November 2018. Two reviewers independently extracted data on study population characteristics, candidate genes, methylation measurement methods, methylation levels of patients in comparison to healthy controls, p-values, and odds ratios of the markers. Overall, 19 studies reporting 102 methylation markers for risk assessment of colorectal neoplasms met our inclusion criteria. The studies mostly used Methylation Specific Polymerase Chain Reaction (MS-PCR) for assessing the methylation status of a defined set of genes. Only two studies applied array-based genome-wide assays to assess the methylation levels. Five studies incorporated panels consisting of 2–10 individual methylation markers to assess their potential for stratifying the risk of developing colorectal neoplasms. However, none of these associations was confirmed in an independent cohort. In conclusion, whole-blood DNA methylation markers may be useful as biomarkers for risk stratification in CRC screening, but reproducible risk prediction algorithms are yet to be established by large scale epigenome-wide studies with thorough validation of results in prospective study cohorts including large screening populations. The possibilities of enhancing predictive power by combining methylation data with polygenetic risk scores and environmental risk factors need to be explored.
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Clare CE, Brassington AH, Kwong WY, Sinclair KD. One-Carbon Metabolism: Linking Nutritional Biochemistry to Epigenetic Programming of Long-Term Development. Annu Rev Anim Biosci 2019; 7:263-287. [DOI: 10.1146/annurev-animal-020518-115206] [Citation(s) in RCA: 104] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
One-carbon (1C) metabolism comprises a series of interlinking metabolic pathways that include the methionine and folate cycles that are central to cellular function, providing 1C units (methyl groups) for the synthesis of DNA, polyamines, amino acids, creatine, and phospholipids. S-adenosylmethionine is a potent aminopropyl and methyl donor within these cycles and serves as the principal substrate for methylation of DNA, associated proteins, and RNA. We propose that 1C metabolism functions as a key biochemical conduit between parental environment and epigenetic regulation of early development and that interindividual and ethnic variability in epigenetic-gene regulation arises because of genetic variants within 1C genes, associated epigenetic regulators, and differentially methylated target DNA sequences. We present evidence to support these propositions, drawing upon studies undertaken in humans and animals. We conclude that future studies should assess the epigenetic effects of cumulative (multigenerational) dietary imbalances contemporaneously in both parents, as this better represents the human experience.
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Affiliation(s)
- Constance E. Clare
- School of Biosciences, University of Nottingham, Sutton Bonington, Leicestershire LE12 5RD, United Kingdom
| | - Amey H. Brassington
- School of Biosciences, University of Nottingham, Sutton Bonington, Leicestershire LE12 5RD, United Kingdom
| | - Wing Yee Kwong
- School of Biosciences, University of Nottingham, Sutton Bonington, Leicestershire LE12 5RD, United Kingdom
| | - Kevin D. Sinclair
- School of Biosciences, University of Nottingham, Sutton Bonington, Leicestershire LE12 5RD, United Kingdom
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Ma HS, Wang EL, Xu WF, Yamada S, Yoshimoto K, Qian ZR, Shi L, Liu LL, Li XH. Overexpression of DNA (Cytosine-5)-Methyltransferase 1 (DNMT1) And DNA (Cytosine-5)-Methyltransferase 3A (DNMT3A) Is Associated with Aggressive Behavior and Hypermethylation of Tumor Suppressor Genes in Human Pituitary Adenomas. Med Sci Monit 2018; 24:4841-4850. [PMID: 30002361 PMCID: PMC6069575 DOI: 10.12659/msm.910608] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Background Alteration of DNA methylation of tumor suppressor genes (TSGs) is one of the most consistent epigenetic changes in human cancers. DNMTs play several important roles in DNA methylation and development of cancers. Regarding DNMTs protein expressions, little is known about the clinical significance and correlation with promoter methylation status of TSGs in human pituitary adenomas. Material/Methods We analyzed the protein expression of 3 DNMTs using immunohistochemistry and assessed DNA hypermethylation of RASSF1A, CDH13, CDH1, and CDKN2A (p16) in 63 pituitary adenomas. We examined associations between DNMTs expression and clinicopathological features or promoter methylation status of TSGs. Results Overexpression of DNMTs was detected in pituitary adenomas. Frequencies of DNMT1 overexpression were significantly higher in macroadenomas, invasive tumors, and grade III and IV tumors. DNMT3A was frequently detected in invasive tumors and grade IV tumors. In addition, DNMT1 and DNMT3A were frequently detected in high-methylation tumors. Furthermore, in multivariate logistic regression, the significant association between DNMT1 or DNMT3A and high-methylation status persisted after adjusting for clinicopathological features. Conclusions Our findings suggested that tumor overexpression of DNMT1 and DNMT3A is associated with tumor aggressive behavior and high-methylation status in pituitary adenomas. Our data support a possible role of DNMT1 and DNMT3A in TSG promoter methylation leading to pituitary adenoma invasion and suggest that inhibition of DNMTs has the potential to become a new therapeutic approach for invasive pituitary adenoma.
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Affiliation(s)
- Hou-Shi Ma
- Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou, Zhejiang, China (mainland).,Zhejiang Provincial Key Laboratory of Applied Enzymology, Yangtze Delta Region Institute of Tsinghua University, Jiaxing, Zhejiang, China (mainland)
| | - Elaine Lu Wang
- Department of Human Pathology, Institute of Health Biosciences, University of Tokushima Graduate School, Tokushima City, Tokushima, Japan.,Department of Legal Medicine, Kanazawa Medical University, Uchinada, Ishikawa, Japan
| | - Wen-Fei Xu
- Zhejiang Provincial Key Laboratory of Applied Enzymology, Yangtze Delta Region Institute of Tsinghua University, Jiaxing, Zhejiangb, China (mainland)
| | - Shozo Yamada
- Department of Neurosurgery, Toranomon Hospital, Tokyo, Japan
| | - Katsuhiko Yoshimoto
- Department of Medical Pharmacology, Institute of Health Biosciences, University of Tokushima Graduate School, Tokushima City, Tokushima, Japan
| | - Zhi Rong Qian
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Long Shi
- Zhejiang Provincial Key Laboratory of Applied Enzymology, Yangtze Delta Region Institute of Tsinghua University, Jiaxing, Zhejiang, China (mainland)
| | - Li-Li Liu
- Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou, Zhejiang, China (mainland)
| | - Xu-Hui Li
- Zhejiang Provincial Key Laboratory of Applied Enzymology, Yangtze Delta Region Institute of Tsinghua University, Jiaxing, Zhejiang, China (mainland)
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El Bairi K, Tariq K, Himri I, Jaafari A, Smaili W, Kandhro AH, Gouri A, Ghazi B. Decoding colorectal cancer epigenomics. Cancer Genet 2018; 220:49-76. [PMID: 29310839 DOI: 10.1016/j.cancergen.2017.11.001] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 11/01/2017] [Accepted: 11/06/2017] [Indexed: 02/07/2023]
Abstract
Colorectal cancer (CRC) is very heterogeneous and presents different types of epigenetic alterations including DNA methylation, histone modifications and microRNAs. These changes are considered as characteristics of various observed clinical phenotypes. Undoubtedly, the discovery of epigenetic pathways with novel epigenetic-related mechanisms constitutes a promising advance in cancer biomarker discovery. In this review, we provide an evidence-based discussing of the current understanding of CRC epigenomics and its role in initiation, epithelial-to-mesenchymal transition and metastasis. We also discuss the recent findings regarding the potential clinical perspectives of these alterations as potent biomarkers for CRC diagnosis, prognosis, and therapy in the era of liquid biopsy.
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Affiliation(s)
- Khalid El Bairi
- Independent Research Team in Cancer Biology and Bioactive Compounds, Mohamed 1(st) University, Oujda, Morocco.
| | - Kanwal Tariq
- B-10 Jumani Center, Garden East, Karachi 74400, Pakistan
| | - Imane Himri
- Laboratory of Biochemistry, Faculty of Sciences, Mohamed I(st) Universiy, Oujda, Morocco; Delegation of the Ministry of Health, Oujda, Morocco
| | - Abdeslam Jaafari
- Laboratoire de Génie Biologique, Equipe d'Immunopharmacologie, Faculté des Sciences et Techniques, Université Sultan Moulay Slimane, Beni Mellal, Maroc
| | - Wiam Smaili
- Centre de Génomique Humaine, Faculté de Médecine et de Pharmacie, Université Mohamed V, Rabat, Maroc; Département de Génétique Médicale, Institut National d'Hygiène, Rabat, Maroc
| | - Abdul Hafeez Kandhro
- Department of Biochemistry, Healthcare Molecular and Diagnostic Laboratory, Hyderabad, Pakistan
| | - Adel Gouri
- Laboratory of Medical Biochemistry, Ibn Rochd University Hospital, Annaba, Algeria
| | - Bouchra Ghazi
- National Laboratory of Reference, Faculty of Medicine, Mohammed VI University of Health Sciences (UM6SS), Casablanca, Morocco
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Integrative modelling of tumour DNA methylation quantifies the contribution of metabolism. Nat Commun 2016; 7:13666. [PMID: 27966532 PMCID: PMC5171841 DOI: 10.1038/ncomms13666] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 10/24/2016] [Indexed: 12/29/2022] Open
Abstract
Altered DNA methylation is common in cancer and often considered an early event in tumorigenesis. However, the sources of heterogeneity of DNA methylation among tumours remain poorly defined. Here we capitalize on the availability of multi-platform data on thousands of human tumours to build integrative models of DNA methylation. We quantify the contribution of clinical and molecular factors in explaining intertumoral variability in DNA methylation. We show that the levels of a set of metabolic genes involved in the methionine cycle is predictive of several features of DNA methylation in tumours, including the methylation of cancer genes. Finally, we demonstrate that patients whose DNA methylation can be predicted from the methionine cycle exhibited improved survival over cases where this regulation is disrupted. This study represents a comprehensive analysis of the determinants of methylation and demonstrates the surprisingly large interaction between metabolism and DNA methylation variation. Together, our results quantify links between tumour metabolism and epigenetics and outline clinical implications.
Altered DNA methylation is a feature of cancer and between-patient variability is prevalent. Here, the authors integrate data on thousands of human tumours, and find that expression levels of methionine metabolism genes are predictive of methylation features, and that the breakdown of this relationship is a negative prognostic marker.
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Ho V, Ashbury JE, Taylor S, Vanner S, King WD. Genetic and epigenetic variation in the DNMT3B and MTHFR genes and colorectal adenoma risk. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2016; 57:261-8. [PMID: 27062459 DOI: 10.1002/em.22010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 02/15/2016] [Indexed: 06/05/2023]
Abstract
Polymorphisms in DNMT3B and MTHFR have been implicated in cancer etiology; however, it is increasingly clear that gene-specific DNA methylation also affects gene expression. A cross-sectional study (N = 272) investigated the main and joint effects of polymorphisms and DNA methylation in DNMT3B and MTHFR on colorectal adenoma risk. Polymorphisms examined included DNMT3B c.-6-1045G > T, and MTHFR c.665C > T and c.1286A > C. DNA methylation of 66 and 28 CpG sites in DNMT3B and MTHFR, respectively, was quantified in blood leukocytes using Sequenom EpiTYPER®. DNA methylation was conceptualized using two approaches: (1) average methylation and (2) unsupervised principal component analysis to identify variables that represented methylation around the transcription start site and the gene coding area of both genes. Logistic regression was used to estimate odds ratios (ORs) and 95% confidence intervals (CIs) associated with the main and joint effects of polymorphisms and DNA methylation. DNA methyltransferase 3B (DNMT3B) TT versus GG/GT genotypes was associated with increased colorectal adenoma risk (OR = 2.12; 95% CI: 1.03-4.34). In addition, increasing DNA methylation in the gene-coding area of DNMT3B was associated with higher risk of colorectal adenomas (OR = 1.34; 95% CI: 1.01-1.79 per SD). In joint effect analyses, synergistic effects were observed among those with both the DNMT3B TT genotype and higher DNMT3B methylation levels compared to those with GT/GG genotypes and lower methylation levels (OR = 4.19; 95% CI: 1.45-12.13 for average methylation; OR = 4.26; 95%CI: 1.31-13.87 for methylation in the transcription start site). This research provides novel evidence that genetic and epigenetic variations contribute to colorectal adenoma risk, precursor to the majority of colorectal cancer (CRC).
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Affiliation(s)
- Vikki Ho
- University of Montreal Hospital Research Centre (CRCHUM), Tour Saint-Antoine, Montréal, Québec, Canada
| | - Janet E Ashbury
- Department of Public Health Sciences, Second Floor Carruthers Hall, Queen's University, Kingston, Ontario, Canada
| | - Sherryl Taylor
- Department of Medical Genetics, Medical Sciences Building, University of Alberta, Edmonton, Alberta, Canada
| | - Stephen Vanner
- Gastrointestinal Diseases Research Unit (GIDRU), Queen's University, Kingston General Hospital, Kingston, Ontario, Canada
| | - Will D King
- Department of Public Health Sciences, Second Floor Carruthers Hall, Queen's University, Kingston, Ontario, Canada
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Ho V, Ashbury JE, Taylor S, Vanner S, King WD. Quantification of gene-specific methylation of DNMT3B and MTHFR using sequenom EpiTYPER®. Data Brief 2015; 6:39-46. [PMID: 26759827 PMCID: PMC4683340 DOI: 10.1016/j.dib.2015.11.039] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Revised: 11/09/2015] [Accepted: 11/16/2015] [Indexed: 11/29/2022] Open
Abstract
Among 272 patients undergoing a screening colonoscopy, DNA methylation of DNMT3B and MTHFR, genes encoding enzymes critical to one-carbon metabolism, was quantified in blood leukocytes using Sequenom EpiTYPER®. DNA methylation was quantified in 66 and 28 CpG sites of DNMT3B and MTHFR respectively, and conceptualized using two approaches. First, measures representing average methylation across all CpG sites were created. Second, unsupervised principal component (PC) analysis was used as a pattern derivation and data-reduction approach, to develop two summary variables (PC1 and PC2). These two summary variables represented methylation around the transcription start site (PC1) and in the gene-coding area (PC2) for both DNMT3B and MTHFR. The data contained in this article presents the variation of methylation levels for individual CpG sites within the DNMT3B and MTHFR genes and possible correlations uncovered using PC analysis. The data are related to the research article “Gene-specific DNA methylation of DNMT3B and MTHFR and colorectal adenoma risk” in Mutation Research – Fundamental and Molecular Mechanisms of Mutagenesis.
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Affiliation(s)
- Vikki Ho
- Department of Public Health Sciences, Queen's University Kingston, Ontario, Canada K7L3N6
| | - Janet E Ashbury
- Department of Public Health Sciences, Queen's University Kingston, Ontario, Canada K7L3N6
| | - Sherryl Taylor
- Department of Medical Genetics, University of Alberta, Edmonton, Alberta, Canada T6G 2R3
| | - Stephen Vanner
- Gastrointestinal Diseases Research Unit (GIDRU), Queen's University, Kingston, Ontario, Canada K7L3N6
| | - Will D King
- Department of Public Health Sciences, Queen's University Kingston, Ontario, Canada K7L3N6
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