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Chromatin dysregulation and DNA methylation at transcription start sites associated with transcriptional repression in cancers. Nat Commun 2019; 10:2188. [PMID: 31097695 PMCID: PMC6522544 DOI: 10.1038/s41467-019-09937-w] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 04/09/2019] [Indexed: 02/08/2023] Open
Abstract
Although promoter-associated CpG islands have been established as targets of DNA methylation changes in cancer, previous studies suggest that epigenetic dysregulation outside the promoter region may be more closely associated with transcriptional changes. Here we examine DNA methylation, chromatin marks, and transcriptional alterations to define the relationship between transcriptional modulation and spatial changes in chromatin structure. Using human papillomavirus-related oropharyngeal carcinoma as a model, we show aberrant enrichment of repressive H3K9me3 at the transcriptional start site (TSS) with methylation-associated, tumor-specific gene silencing. Further analysis identifies a hypermethylated subtype which shows a functional convergence on MYC targets and association with CREBBP/EP300 mutation. The tumor-specific shift to transcriptional repression associated with DNA methylation at TSSs was confirmed in multiple tumor types. Our data may show a common underlying epigenetic dysregulation in cancer associated with broad enrichment of repressive chromatin marks and aberrant DNA hypermethylation at TSSs in combination with MYC network activation. In tumours aberrant epigenetic modifications can alter the transcriptional state. Here, the authors identify a common tumour-specific shift to transcriptional repression associated with DNA methylation and chromatin dysregulation at the transcription start site.
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Woraruthai T, Charoenlap C, Hongsaprabhas C, Mutirangura A, Honsawek S. Alu hypermethylation and high oxidative stress in patients with musculoskeletal tumors. PeerJ 2018; 6:e5492. [PMID: 30128216 PMCID: PMC6098941 DOI: 10.7717/peerj.5492] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 07/27/2018] [Indexed: 01/13/2023] Open
Abstract
Background Alu is one of the non-autonomous element retrotransposons, constituting nearly 11% of the human DNA. Methylation changes of the Alu element can cause genomic instability, a hallmark of cancer development, ultimately leading to the development of cancer. Epigenetic factors may induce the aberrant methylation of Alu and also oxidative stress. However, current knowledge of Alu methylation and oxidative stress is limited. There are few studies that have evaluated Alu methylation and oxidative stress on musculoskeletal tumor progression. Therefore, the present study evaluated the status of Alu methylation in musculoskeletal (MS) tumor, adjacent tissues, and blood leukocytes from MS tumor subjects, as well as unaffected participants. Moreover, we also investigated the oxidative stress status in MS tumor subjects and the control participants and determined the correlation between Alu methylation in MS tumors and that in blood leukocytes. Methods Musculoskeletal tumors from musculoskeletal tumor patients (n = 40) were compared to adjacent tissues (n = 40). The blood leukocytes from musculoskeletal tumor patients were compared to the blood leukocytes from controls (n = 107). Alu methylation status was analyzed using quantitative combined bisulfite restriction analysis (COBRA). In addition, 8-hydroxy 2'-deoxyguanosine (8-OHdG) values were determined using enzyme-linked immunosorbent assay. Results Alu methylation values in MS tumors were statistically significantly higher than those in adjacent tissues (P = 0.035). Similarly, Alu methylation statuses in the blood leukocytes of MS tumor subjects were statistically greater than those of control participants (P < 0.001). Moreover, there was a positive association between Alu methylation levels in MS tumors and blood leukocytes (r = 0.765, P < 0.001). In addition, the highest tertile was significantly associated with the risk of MS tumors (OR = 14.17, 95% CI [5.08-39.51]; P < 0.001). The 8-OHdG values in MS tumors were statistically higher than in adjacent tissues (P < 0.001) and circulating 8-OHdG levels were substantially greater in MS tumor subjects than in the control participants (P < 0.001). Discussion These findings suggest that Alu methylation in blood leukocytes and plasma 8-OHdG might represent non-invasive biomarkers to help diagnose MS tumors. Therefore, Alu hypermethylation and high oxidative stress might be involved in the pathogenesis of the musculoskeletal tumors.
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Affiliation(s)
- Thamonwan Woraruthai
- Osteoarthritis and Musculoskeleton Research Unit, Department of Biochemistry, Faculty of Medicine, King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Chulalongkorn University, Bangkok, Thailand
| | - Chris Charoenlap
- Department of Orthopaedics, Vinai Parkpian Orthopaedic Research Center, Faculty of Medicine, King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Chulalongkorn University, Bangkok, Thailand
| | - Chindanai Hongsaprabhas
- Department of Orthopaedics, Vinai Parkpian Orthopaedic Research Center, Faculty of Medicine, King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Chulalongkorn University, Bangkok, Thailand
| | - Apiwat Mutirangura
- Center for Excellence in Molecular Genetics of Cancer & Human Diseases, Department of Anatomy, Faculty of Medicine, King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Chulalongkorn University, Bangkok, Thailand
| | - Sittisak Honsawek
- Osteoarthritis and Musculoskeleton Research Unit, Department of Biochemistry, Faculty of Medicine, King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Chulalongkorn University, Bangkok, Thailand
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Analysis of Microarray Data on Gene Expression and Methylation to Identify Long Non-coding RNAs in Non-small Cell Lung Cancer. Sci Rep 2016; 6:37233. [PMID: 27849024 PMCID: PMC5110979 DOI: 10.1038/srep37233] [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: 08/16/2016] [Accepted: 10/26/2016] [Indexed: 12/28/2022] Open
Abstract
To identify what long non-coding RNAs (lncRNAs) are involved in non-small cell lung cancer (NSCLC), we analyzed microarray data on gene expression and methylation. Gene expression chip and HumanMethylation450BeadChip were used to interrogate genome-wide expression and methylation in tumor samples. Differential expression and methylation were analyzed through comparing tumors with adjacent non-tumor tissues. LncRNAs expressed differentially and correlated with coding genes and DNA methylation were validated in additional tumor samples using RT-qPCR and pyrosequencing. In vitro experiments were performed to evaluate lncRNA’s effects on tumor cells. We identified 8,500 lncRNAs expressed differentially between tumor and non-tumor tissues, of which 1,504 were correlated with mRNA expression. Two of the lncRNAs, LOC146880 and ENST00000439577, were positively correlated with expression of two cancer-related genes, KPNA2 and RCC2, respectively. High expression of LOC146880 and ENST00000439577 were also associated with poor survival. Analysis of lncRNA expression in relation to DNA methylation showed that LOC146880 expression was down-regulated by DNA methylation in its promoter. Lowering the expression of LOC146880 or ENST00000439577 in tumor cells could inhibit cell proliferation, invasion and migration. Analysis of microarray data on gene expression and methylation allows us to identify two lncRNAs, LOC146880 and ENST00000439577, which may promote the progression of NSCLC.
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Richardson TG, Shihab HA, Hemani G, Zheng J, Hannon E, Mill J, Carnero-Montoro E, Bell JT, Lyttleton O, McArdle WL, Ring SM, Rodriguez S, Campbell C, Smith GD, Relton CL, Timpson NJ, Gaunt TR. Collapsed methylation quantitative trait loci analysis for low frequency and rare variants. Hum Mol Genet 2016; 25:4339-4349. [PMID: 27559110 PMCID: PMC5291201 DOI: 10.1093/hmg/ddw283] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 06/30/2016] [Accepted: 08/12/2016] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Single variant approaches have been successful in identifying DNA methylation quantitative trait loci (mQTL), although as with complex traits they lack the statistical power to identify the effects from rare genetic variants. We have undertaken extensive analyses to identify regions of low frequency and rare variants that are associated with DNA methylation levels. METHODS We used repeated measurements of DNA methylation from five different life stages in human blood, taken from the Avon Longitudinal Study of Parents and Children (ALSPAC) cohort. Variants were collapsed across CpG islands and their flanking regions to identify variants collectively associated with methylation, where no single variant was individually responsible for the observed signal. All analyses were undertaken using the sequence kernel association test. RESULTS For loci where no individual variant mQTL was observed based on a single variant analysis, we identified 95 unique regions where the combined effect of low frequency variants (MAF ≤ 5%) provided strong evidence of association with methylation. For loci where there was previous evidence of an individual variant mQTL, a further 3 regions provided evidence of association between multiple low frequency variants and methylation levels. Effects were observed consistently across 5 different time points in the lifecourse and evidence of replication in the TwinsUK and Exeter cohorts was also identified. CONCLUSION We have demonstrated the potential of this novel approach to mQTL analysis by analysing the combined effect of multiple low frequency or rare variants. Future studies should benefit from applying this approach as a complementary follow up to single variant analyses.
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Affiliation(s)
- Tom G Richardson
- MRC Integrative Epidemiology Unit (IEU), School of Social and Community Medicine, University of Bristol, Oakfield House, Oakfield Grove, Bristol, UK
| | - Hashem A Shihab
- MRC Integrative Epidemiology Unit (IEU), School of Social and Community Medicine, University of Bristol, Oakfield House, Oakfield Grove, Bristol, UK
| | - Gibran Hemani
- MRC Integrative Epidemiology Unit (IEU), School of Social and Community Medicine, University of Bristol, Oakfield House, Oakfield Grove, Bristol, UK
| | - Jie Zheng
- MRC Integrative Epidemiology Unit (IEU), School of Social and Community Medicine, University of Bristol, Oakfield House, Oakfield Grove, Bristol, UK
| | - Eilis Hannon
- University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Jonathan Mill
- University of Exeter Medical School, University of Exeter, Exeter, UK
- Institute of Psychiatry, King's College London, London, UK
| | - Elena Carnero-Montoro
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Jordana T Bell
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Oliver Lyttleton
- Avon Longitudinal Study of Parents and Children (ALSPAC) & School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - Wendy L McArdle
- Avon Longitudinal Study of Parents and Children (ALSPAC) & School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - Susan M Ring
- MRC Integrative Epidemiology Unit (IEU), School of Social and Community Medicine, University of Bristol, Oakfield House, Oakfield Grove, Bristol, UK
- Avon Longitudinal Study of Parents and Children (ALSPAC) & School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - Santiago Rodriguez
- Bristol Genetic Epidemiology Laboratories, School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - Colin Campbell
- Intelligent Systems Laboratory, University of Bristol, Bristol, UK
| | - George Davey Smith
- MRC Integrative Epidemiology Unit (IEU), School of Social and Community Medicine, University of Bristol, Oakfield House, Oakfield Grove, Bristol, UK
| | - Caroline L Relton
- MRC Integrative Epidemiology Unit (IEU), School of Social and Community Medicine, University of Bristol, Oakfield House, Oakfield Grove, Bristol, UK
| | - Nicholas J Timpson
- MRC Integrative Epidemiology Unit (IEU), School of Social and Community Medicine, University of Bristol, Oakfield House, Oakfield Grove, Bristol, UK
| | - Tom R Gaunt
- MRC Integrative Epidemiology Unit (IEU), School of Social and Community Medicine, University of Bristol, Oakfield House, Oakfield Grove, Bristol, UK
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Kim B, Bae H, Lee H, Lee S, Park JC, Kim KR, Kim SJ. Proton Beams Inhibit Proliferation of Breast Cancer Cells by Altering DNA Methylation Status. J Cancer 2016; 7:344-52. [PMID: 26918048 PMCID: PMC4747889 DOI: 10.7150/jca.13396] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 11/15/2015] [Indexed: 12/04/2022] Open
Abstract
Proton beam therapy has been gaining popularity in the management of a wide spectrum of cancers. However, little is known about the effect of proton beams on epigenetic alterations. In this study, the effects of proton beams on DNA methylation were evaluated in the breast cell lines MCF-10A and MCF-7. Pyrosequencing analysis of the long interspersed element 1 (LINE1) gene indicated that a few specific CpG sites were induced to be hypermethylated by proton beam treatment from 64.5 to 76.5% and from 57.7 to 60.0% (p < 0.05) in MCF-10A and MCF-7, respectively. Genome-wide methylation analysis identified “Developmental Disorder, Hereditary Disorder, Metabolic Disease” as the top network in the MCF-7 cell line. The proliferation rate significantly decreased in proton beam-treated cells, as judged by colony formation and cell proliferation assay. Upon treatment with the proton beam, expression of selected genes (MDH2, STYXL1, CPE, FAM91A1, and GPR37) was significantly changed in accordance with the changes of methylation level. Taken together, the findings demonstrate that proton beam-induced physiological changes of cancer cells via methylation modification assists in establishing the epigenetic basis of proton beam therapy for cancer.
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Affiliation(s)
- Byungtak Kim
- 1. Department of Life Science, Dongguk University-Seoul, Goyang, Korea
| | - Hansol Bae
- 1. Department of Life Science, Dongguk University-Seoul, Goyang, Korea
| | - Hyunkyung Lee
- 1. Department of Life Science, Dongguk University-Seoul, Goyang, Korea
| | - Seungyeon Lee
- 1. Department of Life Science, Dongguk University-Seoul, Goyang, Korea
| | - Jeong Chan Park
- 2. Korea Multi-purpose Accelerator Complex, Korea Atomic Energy Research Institute, Gyeongju, Korea
| | - Kye Ryung Kim
- 2. Korea Multi-purpose Accelerator Complex, Korea Atomic Energy Research Institute, Gyeongju, Korea
| | - Sun Jung Kim
- 1. Department of Life Science, Dongguk University-Seoul, Goyang, Korea
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Claudin11 Promoter Hypermethylation Is Frequent in Malignant Melanoma of the Skin, but Uncommon in Nevus Cell Nevi. Cancers (Basel) 2015. [PMID: 26198249 PMCID: PMC4586767 DOI: 10.3390/cancers7030834] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Epigenetic inactivation of tumor-related genes is an important characteristic in the pathology of human cancers, including melanomagenesis. We analyzed the epigenetic inactivation of Claudin 11 (CLDN11) in malignant melanoma (MM) of the skin, including six melanoma cell lines, 39 primary melanoma, 41 metastases of MM and 52 nevus cell nevi (NCN). CLDN11 promoter hypermethylation was found in 19 out of 39 (49%) of the primary MM and in 21 out of 41 (51%) of the MM metastases, but only in eight out of 52 (15%) of NCN (p = 0.001 and p = 0.0003, respectively). Moreover, a significant increase in the methylation level of CLDN11 from primary melanomas to MM metastases was revealed (p = 0.003). Methylation of CLDN11 was significantly more frequent in skin metastases (79%) compared to brain metastases (31%; p = 0.007). CLDN11 methylation was also found in five out of six MM cell lines (83%) and its promoter hypermethylation correlated with a reduced expression. Treatment of MM cell lines with a DNA methylation inhibitor reactivated CLDN11 transcription by its promoter demethylation. In summary, CLDN11 proved to be an epigenetically inactivated tumor related gene in melanomagenesis, and analysis of CLDN11 methylation level represents a potential tool for assisting in the discrimination between malignant melanoma and nevus cell nevi.
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