Colorectal cancer early methylation biomarkers

FADDA, ANTONIO;GENTILINI, ORESTE DAVIDE;MOI, LOREDANA;Barault, L.;Zavattari, C.;SULAS, PIA;LEONI, VERA PIERA;ZORCOLO, LUIGI;De Miglio, M. R.;Varesco, L.;Columbano, A.;Di Nicolantonio, F.;ZAVATTARI, PATRIZIA

2016-01-01

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Abstract

Distinct molecular pathways characterized by both genetic mutations and epigenetic alterations are implicated in colorectal cancer (CRC) development. However, which pathways are critical and the stage at which the alterations occur remain elusive. To identify significant methylation differences between tumoral and nontumoral tissue we analyzed over 480k CpG loci and performed a transcriptomic analysis on 18 human CRCs, 21 adenomas and normal mucosa. The results of gene ontology analysis of transcripts showing altered methylation, both in CRCs and adenomas, identified novel pathways so far not associated with CRC development. Remarkably, alteration of the same gene promoters was observed in adenomas, suggesting that aberrant methylation of specific pathways might drive the tumorigenic process. Transcriptomic analysis and qRT­PCR of selected genes showed downregulation in CRC samples of genes involved in pathways regulated by altered methylated genes. From the crosscomparison analysis between CRCs and adenomas methylation alterations we identified 74 CpG islands as early biomarkers of CRC carcinogenesis. This set was successfully crossvalidated using methylation data online available from 518 CRC, 52 adenomas and 121 non tumoral mucosa samples. The hypermethylation of 3 selected CpG islands was also replicated in 38 CRC vs peritumoral samples and in stool DNA from the same patients and in 50 circulating tumoral DNAs. In conclusion, the results of the present study identified a panel of genes with altered methylation in both adenomas and CRCs and, most intriguingly, raised the possibility of their identification as biomarkers