title: Comparison of genome-wide DNA methylation in urothelial carcinomas of patients with and without arsenic exposure.
abstract: BACKGROUND
  Arsenic is a well-documented carcinogen of human urothelial carcinoma (UC) with incompletely understood mechanisms.
  
  
  OBJECTIVE
  This study aimed to compare the genome-wide DNA methylation profiles of arsenic-induced UC (AsUC) and non-arsenic-induced UC (Non-AsUC), and to assess associations between site-specific methylation levels and cumulative arsenic exposure.
  
  
  METHODS
  Genome-wide DNA methylation profiles in 14 AsUC and 14 non-AsUC were analyzed by Illumina Infinium methylation27 BeadChip and validated by bisulfite pyrosequencing. Mean methylation levels (β¯) in AsUC and non-AsUC were compared by their ratio (β¯ ratio) and difference (Δβ¯). Associations between site-specific methylation levels in UC and cumulative arsenic exposure were examined.
  
  
  RESULTS
  Among 27,578 methylation sites analyzed, 231 sites had β¯ ratio >2 or <0.5 and 45 sites had Δβ¯ >0.2 or <-0.2. There were 13 sites showing statistically significant (q<0.05) differences in β¯ between AsUC and non-AsUC including 12 hypermethylation sites in AsUC and only one hypermethylation site in non-AsUC. Significant associations between cumulative arsenic exposure and DNA methylation levels of 28 patients were observed in nine CpG sites of nine gens including PDGFD (Spearman rank correlation, 0.54), CTNNA2 (0.48), KCNK17 (0.52), PCDHB2 (0.57), ZNF132 (0.48), DCDC2 (0.48), KLK7 (0.48), FBXO39 (0.49), and NPY2R (0.45). These associations remained statistically significant for CpG sites in CTNNA2, KLK7, NPY2R, ZNF132 and KCNK17 in 20 non-smoking women after adjustment for tumor stage and age.
  
  
  CONCLUSIONS
  Significant associations between cumulative arsenic exposure and methylation level of CTNNA2, KLK7, NPY2R, ZNF132 and KCNK17 were found in smoking-unrelated urothelial carcinoma. Arsenic exposure may cause urothelial carcinomas through the hypermethylation of genes involved in cell adhesion, proteolysis, transcriptional regulation, neuronal pathway, and ion transport. The findings of this study, which are limited by its small sample size and moderate dose-response relation, remain to be validated by further studies with large sample sizes.
authors.affiliation: Graduate Institute of Life Science, National Defense Medical Center, Taipei, Taiwan; Genomics Research Center, Academia Sinica, Taipei, Taiwan; Molecular and Genomic Epidemiology Center, China Medical University Hospital, Taichung, Taiwan; China Medical University, Taichung, Taiwan.
authors.forename: Tse-Yen
authors.initials: TY
authors.lastname: Yang
authors.affiliation: Genomics Research Center, Academia Sinica, Taipei, Taiwan.
authors.forename: Ling-I
authors.initials: LI
authors.lastname: Hsu
authors.affiliation: College of Medicine, National Yang-Ming University Hospital, Taipei, Taiwan.
authors.forename: Allen W
authors.initials: AW
authors.lastname: Chiu
authors.affiliation: Department of Urology, College of Medicine, National Taiwan University, Taipei, Taiwan.
authors.forename: Yeong-Shiau
authors.initials: YS
authors.lastname: Pu
authors.affiliation: Department of Urology, College of Medicine, National Taiwan University, Taipei, Taiwan.
authors.forename: Sheng-Hsin
authors.initials: SH
authors.lastname: Wang
authors.affiliation: Genomics Research Center, Academia Sinica, Taipei, Taiwan.
authors.forename: Ya-Tang
authors.initials: YT
authors.lastname: Liao
authors.affiliation: Graduate Institute of Oncology, National Taiwan University, Taipei, Taiwan.
authors.forename: Meei-Maan
authors.initials: MM
authors.lastname: Wu
authors.affiliation: Division of General Surgery, Department of Urology, Shuang Ho Hospital, Taipei Medical University, New Taipei City, Taiwan; Graduate Institute of Clinical Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan.
authors.forename: Yuan-Hung
authors.initials: YH
authors.lastname: Wang
authors.affiliation: Department of Medical Research, National Taiwan University Hospital, Taipei, Taiwan.
authors.forename: Chin-Hao
authors.initials: CH
authors.lastname: Chang
authors.affiliation: Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan.
authors.forename: Te-Chang
authors.initials: TC
authors.lastname: Lee
authors.affiliation: Graduate Institute of Life Science, National Defense Medical Center, Taipei, Taiwan; Genomics Research Center, Academia Sinica, Taipei, Taiwan; Graduate Institute of Epidemiology and Preventive Medicine, National Taiwan University, Taipei, Taiwan. Electronic address: chencj@gate.sinica.edu.tw.
authors.forename: Chien-Jen
authors.initials: CJ
authors.lastname: Chen
mesh_terms: D000368:Aged; D001151:Arsenic / Q000009:adverse effects*; D002277:Carcinoma / Q000209:etiology* / Q000235:genetics* / Q000378:metabolism; D016022:Case-Control Studies; D019175:DNA Methylation / Q000235:genetics; D004781:Environmental Exposure / Q000009:adverse effects; D005260:Female; D015894:Genome, Human; D055106:Genome-Wide Association Study; D006801:Humans; D008297:Male; D008875:Middle Aged; D012044:Regression Analysis; D017422:Sequence Analysis, DNA; D014571:Urologic Neoplasms / Q000209:etiology* / Q000235:genetics* / Q000378:metabolism
chemical_list: D001151:Arsenic
keywords: Arsenic; AsUC; CAE; Cumulative Arsenic Exposure; DAVID; DNA methylation; GOTerm_BP; KEGG; Kyoto encyclopedia of genes and genomes; S-adenosyl methionine; SAM; Spearman rank correlation coefficients; UC; Urothelial carcinoma; arsenic related urothelial carcinoma; cumulative arsenic exposure; database for annotation, visualization and integrated discovery; difference in mean β value; gene ontogeny term biological processes; mean β value; non-AsUC; non-arsenic related urothelial carcinoma; rS; urothelial carcinoma; β value