The proto CpG island methylator phenotype of sessile serrated adenomas/polyps

Sessile serrated adenomas/polyps (SSA/Ps) are the putative precursors of the ˜20% of colon cancers with the CpG island methylator phenotype (CIMP), but their molecular features are poorly understood. We used high-throughput analysis of DNA methylation and gene expression to investigate the epigenetic phenotype of SSA/Ps. Fresh-tissue samples of 17 SSA/Ps and (for comparison purposes) 15 conventional adenomas (cADNs)—each with a matched sample of normal mucosa— were prospectively collected during colonoscopy (total no. samples analyzed: 64). DNA and RNA were extracted from each sample. DNA was subjected to bisulfite next-generation sequencing to assess methylation levels at ˜2.7 million CpG sites located predominantly in gene regulatory regions and spanning 80.5Mb (˜2.5% of the genome); RNA was sequenced to define the samples’ transcriptomes. An independent series of 61 archival lesions was used for targeted verification of DNA methylation findings. Compared with normal mucosa samples, SSA/Ps and cADNs exhibited markedly remodeled methylomes. In cADNs, hypo methylated regions were far more numerous (18,417 vs 4288 in SSA/Ps) and rarely affected CpG islands/shores. SSA/Ps seemed to have escaped this wave of demethylation. Cytosine hyper methylation in SSA/Ps was more pervasive (hypermethylated regions: 22,147 vs 15,965 in cADNs; hypermethylated genes: 4938 vs 3443 in cADNs) and more extensive (region for region), and it occurred mainly within CpG islands and shores. Given its resemblance to the CIMP typical of SSA/Ps’ putative descendant colon cancers, we refer to the SSA/P methylation phenotype as proto-CIMP . Verification studies of six hypermethylated regions (3 SSA/P-specific and 3 common) demonstrated the high potential of DNA methylation markers for predicting the diagnosis of SSA/Ps and cADNs. Surprisingly, proto-CIMP in SSA/Ps was associated with upregulated gene expression (n=618 genes vs 349 that were downregulated); downregulation was more common in cADNs (n=712 vs 516 upregulated genes). The epigenetic landscape of SSA/Ps differs markedly from that of cADNs. These differences are a potentially rich source of novel tissue-based and noninvasive biomarkers that can add precision to the clinical management of the two most frequent colon-cancer precursors. ### Author contributions G.M. and H.R.P. designed research; H.R.P. and A.M.O. performed research; S.O. and H.R.P. analyzed data; F.C., H.H., M.S., S.V., L.A., and F.B. performed tissue sample and clinical data collection; G.T., A.W., and P.K. reviewed histology; H.R.P. and G.M. wrote the paper. We thank Martin Roszkowski, Vera van der Weijden, Hadi Gharibi, Anette Hunziker, Catharine Aquino, and Brigitta Tomlinson for their technical support, help, and productive discussions, and Marian Everett Kent for editing the manuscript. Abbreviations : cADNs : Conventional adenomas CIMP : CpG island methylator phenotype DMCs : Differentially methylated cytosines DMRs : Differentially methylated regions FFPE : Formalin-fixed, paraffin-embedded IGV : Integrative genomics viewer MDS : Multidimensional scaling MMR : DNA-mismatch repair PRC2 : Polycomb repressive complex 2 SSA/Ps : Sessile serrated adenomas/polyps TSAs : Traditional serrated adenomas TSS : Transcription start site WHO : World Health Organization