title: Aberrant DNA methylation of WNT pathway genes in the development and progression of CIMP-negative colorectal cancer.
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.
authors.affiliation: a Molecular Medicine Research Group , Hungarian Academy of Sciences , Budapest , Hungary.
authors.forename: Orsolya
authors.initials: O
authors.lastname: Galamb
authors.affiliation: b 2nd Department of Internal Medicine , Semmelweis University , Budapest , Hungary.
authors.forename: Alexandra
authors.initials: A
authors.lastname: Kalmár
authors.affiliation: b 2nd Department of Internal Medicine , Semmelweis University , Budapest , Hungary.
authors.forename: Bálint
authors.initials: B
authors.lastname: Péterfia
authors.affiliation: c Department of Physics of Complex Systems , Eötvös Loránd University , Budapest , Hungary.
authors.forename: István
authors.initials: I
authors.lastname: Csabai
authors.affiliation: c Department of Physics of Complex Systems , Eötvös Loránd University , Budapest , Hungary.
authors.forename: András
authors.initials: A
authors.lastname: Bodor
authors.affiliation: c Department of Physics of Complex Systems , Eötvös Loránd University , Budapest , Hungary.
authors.forename: Dezső
authors.initials: D
authors.lastname: Ribli
authors.affiliation: d 1st Department of Pathology and Experimental Cancer Research , Semmelweis University , Budapest , Hungary.|e Tumor Progression Research Group , Hungarian Academy of Sciences - Semmelweis University , Budapest , Hungary.
authors.forename: Tibor
authors.initials: T
authors.lastname: Krenács
authors.affiliation: b 2nd Department of Internal Medicine , Semmelweis University , Budapest , Hungary.
authors.forename: Árpád V
authors.initials: ÁV
authors.lastname: Patai
authors.affiliation: a Molecular Medicine Research Group , Hungarian Academy of Sciences , Budapest , Hungary.
authors.forename: Barnabás
authors.initials: B
authors.lastname: Wichmann
authors.affiliation: b 2nd Department of Internal Medicine , Semmelweis University , Budapest , Hungary.
authors.forename: Barbara Kinga
authors.initials: BK
authors.lastname: Barták
authors.affiliation: b 2nd Department of Internal Medicine , Semmelweis University , Budapest , Hungary.
authors.forename: Kinga
authors.initials: K
authors.lastname: Tóth
authors.affiliation: a Molecular Medicine Research Group , Hungarian Academy of Sciences , Budapest , Hungary.
authors.forename: Gábor
authors.initials: G
authors.lastname: Valcz
authors.affiliation: f Department of Medical Oncology , Dana-Farber Cancer Institute , Boston , MA , USA.
authors.forename: Sándor
authors.initials: S
authors.lastname: Spisák
authors.affiliation: a Molecular Medicine Research Group , Hungarian Academy of Sciences , Budapest , Hungary.|b 2nd Department of Internal Medicine , Semmelweis University , Budapest , Hungary.
authors.forename: Zsolt
authors.initials: Z
authors.lastname: Tulassay
authors.affiliation: a Molecular Medicine Research Group , Hungarian Academy of Sciences , Budapest , Hungary.
authors.forename: Béla
authors.initials: B
authors.lastname: Molnár
mesh_terms: D000236:Adenoma / Q000235:genetics* / Q000378:metabolism / Q000473:pathology; D000368:Aged; D014408:Biomarkers, Tumor / Q000235:genetics / Q000378:metabolism; D015179:Colorectal Neoplasms / Q000235:genetics* / Q000378:metabolism / Q000473:pathology; D019175:DNA Methylation; D005260:Female; D056426:Genetic Loci; D015894:Genome, Human; D006801:Humans; D008297:Male; D008875:Middle Aged; D011401:Promoter Regions, Genetic; D060449:Wnt Signaling Pathway
chemical_list: D014408:Biomarkers, Tumor
keywords: APC; Adenoma; WNT signaling pathway; colorectal cancer; gene expression; promoter and gene body methylation; whole methylome analysis; β-catenin mutation