Aging related methylation influences the gene expression of key control genes in colorectal cancer and adenoma

• Published in: World journal of gastroenterology : WJG Vol. 22; no. 47; pp. 10325 - 10340
• Main Author: Orsolya Galamb Alexandra Kalmár Barbara Kinga Barták árpád V Patai Katalin Leiszter Bálint Péterfia Barnabás Wichmann Gábor Valcz Gábor Veres Zsolt Tulassay Béla Molnár
• Format: Journal Article
• Language: English
• Published: United States Baishideng Publishing Group Inc 21.12.2016
• Subjects: Adenoma - genetics; Adenoma - pathology; Adolescent; Adult; Aged; Aged, 80 and over; Aging - genetics; Basic Study; Biomarkers, Tumor - genetics; Biopsy; Carcinoma - genetics; Carcinoma - pathology; Case-Control Studies; Child; Child, Preschool; Colorectal Neoplasms - genetics; Colorectal Neoplasms - pathology; CpG Islands; DNA Methylation; Epigenesis, Genetic; Female; Gene Expression Profiling - methods; Gene Expression Regulation, Neoplastic; Humans; Infant; Intercellular Signaling Peptides and Proteins - genetics; Male; Membrane Proteins - genetics; Middle Aged; Oligonucleotide Array Sequence Analysis; Polymerase Chain Reaction; Promoter Regions, Genetic; Epigenetic clock; Colorectal cancer; Aging; DNA methylation; Adenoma; Secreted frizzled related protein 1; Epigenetic drift
• ISSN: 1007-9327; 2219-2840
• DOI: 10.3748/wjg.v22.i47.10325

AIM To analyze colorectal carcinogenesis and age-related DNA methylation alterations of gene sequences associated with epigenetic clock CpG sites. METHODS In silico DNA methylation analysis of 353 epigenetic clock Cp G sites published by Steve Horvath was performed using methylation array data for a set of 123 colonic tissue samples (64 colorectal cancer(CRC), 42 adenoma, 17 normal; GEO accession number: GSE48684)Among the differentially methylated agerelated genes, secreted frizzled related protein 1(SFRP1) promoter methylation was further investigated in colonic tissue from 8 healthy adults, 19 normal children, 20 adenoma and 8 CRC patients using bisulfite-specific PCR followed by methylation-specific high resolution melting(MS-HRM) analysis. m RNA expression of age-related 'epigenetic clock' genes was studied using Affymetrix HGU133 Plus2.0 whole transcriptome data of 153 colonic biopsy samples(49 healthy adult, 49 adenoma, 49 CRC, 6 healthy children)(GEO accession numbers: GSE37364, GSE10714, GSE4183, GSE37267). Whole promoter methylation analysis of genes showing inverse DNA methylationgene expression data was performed on 30 colonic samples using methyl capture sequencing.RESULTS Fifty-seven age-related Cp G sites including hypermethylated PPP1R16 B, SFRP1, SYNE1 and hypomethylated MGP, PIPOX were differentially methylated between CRC and normal tissues(P < 0.05, ?β≥ 10%). In the adenoma vs normal comparison, 70 CpG sites differed significantly, including hypermethylated DKK3, SDC2, SFRP1, SYNE1 and hypomethylated CEMIP, SPATA18(P < 0.05, ?β≥ 10%). In MS-HRM analysis, the SFRP1 promoter region was significantly hypermethylated in CRC(55.0% ± 8.4 %) and adenoma tissue samples(49.9% ± 18.1%) compared to normal adult(5.2% ± 2.7%) and young(2.2% ± 0.7%) colonic tissue(P < 0.0001). DNA methylation of SFRP1 promoter was slightly, but significantly increased in healthy adults compared to normal young samples(P < 0.02). This correlated with significantly increased SFRP1 m RNA levels in children compared to normal adult samples(P < 0.05). In CRC tissue the mR NA expression of 117 agerelated genes were changed, while in adenoma samples 102 genes showed differential expression compared with normal colonic tissue(P < 0.05, logF C > 0.5). The change of expression for several genes including SYNE1, CLEC3 B, LTBP3 and SFRP1, followed the same pattern in aging and carcinogenesis, though not for all genes(e.g., MGP). CONCLUSION Several age-related DNA methylation alterations can be observed during CRC development and progression affecting the m RNA expression of certain CRC- and adenoma-related key control genes.