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Barnicle A, Seoighe C, Greally JM, Golden A, Egan LJ. Inflammation-associated DNA methylation patterns in epithelium of ulcerative colitis. Epigenetics 2017; 12:591-606. [PMID: 28557546 DOI: 10.1080/15592294.2017.1334023] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Aberrant DNA methylation patterns have been reported in inflamed tissues and may play a role in disease. We studied DNA methylation and gene expression profiles of purified intestinal epithelial cells from ulcerative colitis patients, comparing inflamed and non-inflamed areas of the colon. We identified 577 differentially methylated sites (false discovery rate <0.2) mapping to 210 genes. From gene expression data from the same epithelial cells, we identified 62 differentially expressed genes with increased expression in the presence of inflammation at prostate cancer susceptibility genes PRAC1 and PRAC2. Four genes showed inverse correlation between methylation and gene expression; ROR1, GXYLT2, FOXA2, and, notably, RARB, a gene previously identified as a tumor suppressor in colorectal adenocarcinoma as well as breast, lung and prostate cancer. We highlight targeted and specific patterns of DNA methylation and gene expression in epithelial cells from inflamed colon, while challenging the importance of epithelial cells in the pathogenesis of chronic inflammation.
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Affiliation(s)
- Alan Barnicle
- a Clinical Pharmacology, School of Medicine, National University of Ireland , Galway , Ireland.,b School of Mathematics, Statistics and Applied Mathematics, National University of Ireland , Galway , Ireland
| | - Cathal Seoighe
- b School of Mathematics, Statistics and Applied Mathematics, National University of Ireland , Galway , Ireland
| | - John M Greally
- c Center of Epigenomics and Department of Genetics (Division of Computational Genetics) , Albert Einstein College of Medicine, Morris Park Avenue , Bronx , NY , USA
| | - Aaron Golden
- b School of Mathematics, Statistics and Applied Mathematics, National University of Ireland , Galway , Ireland.,c Center of Epigenomics and Department of Genetics (Division of Computational Genetics) , Albert Einstein College of Medicine, Morris Park Avenue , Bronx , NY , USA.,d Department of Mathematical Sciences , Yeshiva University , 2495 Amsterdam Avenue, New York , NY , USA
| | - Laurence J Egan
- a Clinical Pharmacology, School of Medicine, National University of Ireland , Galway , Ireland
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Gainetdinov IV, Kapitskaya KY, Rykova EY, Ponomaryova AA, Cherdyntseva NV, Vlassov VV, Laktionov PP, Azhikina TL. Hypomethylation of human-specific family of LINE-1 retrotransposons in circulating DNA of lung cancer patients. Lung Cancer 2016; 99:127-30. [PMID: 27565927 DOI: 10.1016/j.lungcan.2016.07.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Revised: 05/12/2016] [Accepted: 07/05/2016] [Indexed: 02/06/2023]
Abstract
Circulating DNA has recently gained attention as a fast and non-invasive way to assess tumor biomarkers. Since hypomethylation of LINE-1 repetitive elements was described as one of the key hallmarks of tumorigenesis, we aimed to establish whether the methylation level of LINE-1 retrotransposons changes in cell-surface-bound fraction of circulating DNA (csbDNA) of lung cancer patients. Methylated CpG Island Recovery Assay (MIRA) coupled to qPCR-based quantitation was performed to assess integral methylation level of LINE-1 promoters in csbDNA of non-small cell lung cancer patients (n=56) and healthy controls (n=44). Deep sequencing of amplicons revealed that hypomethylation of LINE-1 promoters in csbDNA of lung cancer patients is more pronounced for the human-specific L1Hs family. Statistical analysis demonstrates significant difference in LINE-1 promoter methylation index between cancer patients and healthy individuals (ROC-curve analysis: n=100, AUC=0.69, p=0.0012) and supports the feasibility of MIRA as a promising non-invasive approach.
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Affiliation(s)
- Ildar V Gainetdinov
- Department of Genetics and Postgenomic Technologies, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.
| | - Kristina Yu Kapitskaya
- Department of Genetics and Postgenomic Technologies, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.
| | - Elena Yu Rykova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk State, Russia.
| | - Anastasia A Ponomaryova
- Tomsk Cancer Research Institute, National Research Tomsk Polytechnic University, Tomsk, Russia.
| | - Nadezda V Cherdyntseva
- Tomsk Cancer Research Institute, National Research Tomsk State University, Tomsk, Russia.
| | - Valentin V Vlassov
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia.
| | - Pavel P Laktionov
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Academician E.N. Meshalkin Novosibirsk Research Institute of Circulation Pathology, Novosibirsk, Russia Technical University, Novosibirsk, Russia.
| | - Tatyana L Azhikina
- Department of Genetics and Postgenomic Technologies, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.
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