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Peters TJ, Buckley MJ, Chen Y, Smyth GK, Goodnow CC, Clark SJ. Calling differentially methylated regions from whole genome bisulphite sequencing with DMRcate. Nucleic Acids Res 2021; 49:e109. [PMID: 34320181 PMCID: PMC8565305 DOI: 10.1093/nar/gkab637] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 05/31/2021] [Accepted: 07/19/2021] [Indexed: 11/12/2022] Open
Abstract
Whole genome bisulphite sequencing (WGBS) permits the genome-wide study of single molecule methylation patterns. One of the key goals of mammalian cell-type identity studies, in both normal differentiation and disease, is to locate differential methylation patterns across the genome. We discuss the most desirable characteristics for DML (differentially methylated locus) and DMR (differentially methylated region) detection tools in a genome-wide context and choose a set of statistical methods that fully or partially satisfy these considerations to compare for benchmarking. Our data simulation strategy is both biologically informed-employing distribution parameters derived from large-scale consortium datasets-and thorough. We report DML detection ability with respect to coverage, group methylation difference, sample size, variability and covariate size, both marginally and jointly, and exhaustively with respect to parameter combination. We also benchmark these methods on FDR control and computational time. We use this result to backend and introduce an expanded version of DMRcate: an existing DMR detection tool for microarray data that we have extended to now call DMRs from WGBS data. We compare DMRcate to a set of alternative DMR callers using a similarly realistic simulation strategy. We find DMRcate and RADmeth are the best predictors of DMRs, and conclusively find DMRcate the fastest.
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Affiliation(s)
- Timothy J Peters
- The Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, NSW 2010, Australia.,UNSW Sydney, Sydney 2052, Australia
| | - Michael J Buckley
- The Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, NSW 2010, Australia.,UNSW Sydney, Sydney 2052, Australia
| | - Yunshun Chen
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia.,Department of Medical Biology, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Gordon K Smyth
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia.,School of Mathematics and Statistics, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Christopher C Goodnow
- The Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, NSW 2010, Australia.,School of Medical Sciences and Cellular Genomics Futures Institute, UNSW Sydney, NSW 2052, Australia
| | - Susan J Clark
- The Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, NSW 2010, Australia.,St. Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, NSW 2010, Australia
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Yang B, Yang ZG, Gao B, Shao GG, Li GH. 5-Aza-CdR can reverse gefitinib resistance caused by DAPK gene promoter methylation in lung adenocarcinoma cells. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2015; 8:12961-12966. [PMID: 26722491 PMCID: PMC4680436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Accepted: 09/25/2015] [Indexed: 06/05/2023]
Abstract
To explore the relationship between death associated protein kinase (DAPK) gene promoter methylation and gefitinib resistance in Lung adenocarcinoma cell lines. EGFR-mutation lung adenocarcinoma cell lines PC9 and the gefitinib-resistant with T790M Mutation cell lines PC9/GR were chosen as cell models, and PC9/GR were treated with 5-aza-CdR (1 μmol/L). The experiments were divided into three groups: PC9 group, PC9/GR group and PC9/GR with 5-Aza-CdR pretreatment group. Treat three groups cell with different concentrations gefitinib, the cell proliferation was determined by MTT assay. The apoptotic rates were detected by flow cytometry. The methylation of DAPK gene promoter region was examined by methylation-specific PCR (MSP). The expressions of DAPK protein were detected by Western blot. MTT results showed that the half maximal inhibitory concentration (IC50) of PC9 and PC9/GR cell lines increase from 0.12 μmol/L to 8.52 μmol/L. But after treated with 5-aza-CdR, the IC50 of PC9/GR cell lines decrease to 4.35 μmol/L, and the resistance index (RI) decrease from 71 to 36 (P<0.05). Flow cytometry results showed that the apoptosis rate were 24.80% ± 0.28%, 12.70% ± 0.31%, 19.8% ± 0.15% respectively. MSP results showed that DAPK gene promoter region was un-methylated in PC9 cells and methylated in PC9/GR cells, when treated with 5-aza-CdR, DAPK gene promoter region was partly methylated in PC9/GR cells (P<0.05). Western blot results showed that the levels of DAPK protein were reduced significantly in PC9/GR cell lines compared with PC9, and after treated with 5-aza-CdR, the expression levels of DAPK protein in PC9/GR were increased (P<0.05). In conclusion, DAPK gene promoter methylation may contribute to the downregulation of DAPK gene and protein, and consequently affect the sensitivity of gefitinib in lung adenocarcinoma lines, induced gefitinib resistance. But 5-Aza-CdR can reverse gefitinib resistance by demethylation of DAPK gene promoter.
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Affiliation(s)
- Bo Yang
- Department of Thoracic Surgery, The First Bethune Hospital of Jilin University Changchun 13000, Jilin, China
| | - Zhi-Guang Yang
- Department of Thoracic Surgery, The First Bethune Hospital of Jilin University Changchun 13000, Jilin, China
| | - Bao Gao
- Department of Thoracic Surgery, The First Bethune Hospital of Jilin University Changchun 13000, Jilin, China
| | - Guo-Guang Shao
- Department of Thoracic Surgery, The First Bethune Hospital of Jilin University Changchun 13000, Jilin, China
| | - Guang-Hu Li
- Department of Thoracic Surgery, The First Bethune Hospital of Jilin University Changchun 13000, Jilin, China
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