Aberrant DNA methylation of WNT pathway genes in the development and progression of CIMP-negative colorectal cancer

O. Galamb, Alexandra Kalmár, Bálint Péterfia, I. Csabai, András Bodor, Dezső Ribli, T. Krenács, Árpád V. Patai, Barnabás Wichmann, Barbara Kinga Barták, Kinga Tóth, Gábor Valcz, S. Spisák, Z. Tulassay, B. Molnár

Research output: Contribution to journalArticle

22 Citations (Scopus)

Abstract

The WNT signaling pathway has an essential role in colorectal carcinogenesis and progression, which involves a cascade of genetic and epigenetic changes. We aimed to analyze DNA methylation affecting the WNT pathway genes in colorectal carcinogenesis in promoter and gene body regions using whole methylome analysis in 9 colorectal cancer, 15 adenoma, and 6 normal tumor adjacent tissue (NAT) samples by methyl capture sequencing. Functional methylation was confirmed on 5-aza-2′-deoxycytidine-treated colorectal cancer cell line datasets. In parallel with the DNA methylation analysis, mutations of WNT pathway genes (APC, β-catenin/CTNNB1) were analyzed by 454 sequencing on GS Junior platform. Most differentially methylated CpG sites were localized in gene body regions (95% of WNT pathway genes). In the promoter regions, 33 of the 160 analyzed WNT pathway genes were differentially methylated in colorectal cancer vs. normal, including hypermethylated AXIN2, CHP1, PRICKLE1, SFRP1, SFRP2, SOX17, and hypomethylated CACYBP, CTNNB1, MYC; 44 genes in adenoma vs. NAT; and 41 genes in colorectal cancer vs. adenoma comparisons. Hypermethylation of AXIN2, DKK1, VANGL1, and WNT5A gene promoters was higher, while those of SOX17, PRICKLE1, DAAM2, and MYC was lower in colon carcinoma compared to adenoma. Inverse correlation between expression and methylation was confirmed in 23 genes, including APC, CHP1, PRICKLE1, PSEN1, and SFRP1. Differential methylation affected both canonical and noncanonical WNT pathway genes in colorectal normal-adenoma-carcinoma sequence. Aberrant DNA methylation appears already in adenomas as an early event of colorectal carcinogenesis.

Original languageEnglish
Pages (from-to)1-15
Number of pages15
JournalEpigenetics
DOIs
Publication statusAccepted/In press - Jun 30 2016

Fingerprint

DNA Methylation
Colorectal Neoplasms
Adenoma
Genes
Methylation
APC Genes
Body Regions
Carcinogenesis
decitabine
Carcinoma
Catenins
Genetic Promoter Regions
Epigenomics
Neoplasms
Colon
Cell Line
Mutation

Keywords

  • Adenoma
  • APC
  • colorectal cancer
  • gene expression
  • promoter and gene body methylation
  • whole methylome analysis
  • WNT signaling pathway
  • β-catenin mutation

ASJC Scopus subject areas

  • Molecular Biology
  • Cancer Research

Cite this

Aberrant DNA methylation of WNT pathway genes in the development and progression of CIMP-negative colorectal cancer. / Galamb, O.; Kalmár, Alexandra; Péterfia, Bálint; Csabai, I.; Bodor, András; Ribli, Dezső; Krenács, T.; Patai, Árpád V.; Wichmann, Barnabás; Barták, Barbara Kinga; Tóth, Kinga; Valcz, Gábor; Spisák, S.; Tulassay, Z.; Molnár, B.

In: Epigenetics, 30.06.2016, p. 1-15.

Research output: Contribution to journalArticle

Galamb, O. ; Kalmár, Alexandra ; Péterfia, Bálint ; Csabai, I. ; Bodor, András ; Ribli, Dezső ; Krenács, T. ; Patai, Árpád V. ; Wichmann, Barnabás ; Barták, Barbara Kinga ; Tóth, Kinga ; Valcz, Gábor ; Spisák, S. ; Tulassay, Z. ; Molnár, B. / Aberrant DNA methylation of WNT pathway genes in the development and progression of CIMP-negative colorectal cancer. In: Epigenetics. 2016 ; pp. 1-15.
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