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

Abstract

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, hypomethylated 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 hypermethylation 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.

The DNA hypermethylation phenotype of colorectal cancer liver metastases resembles that of the primary colorectal cancers.

“…We recently investigated the DNA methylomes of precancerous and cancerous colorectal lesions [13]. In addition to our extensive characterization of the hypermethylation phenotype of gene regulatory genomic regions in both types of tumor, we also confirmed the presence in these lesions of another classical tumor-associated change in the methylome: widespread hypomethylation.…”

“…As detailed in the Methods section, we then compared the primary CRC methylomes characterized with MBDE with the results obtained in other primary CRCs using TE [13]. As shown in emerged as significantly hypomethylated only with TE.…”

“…In a previous study [13], we used targeted bisulfite sequencing (SeqCapEpi CpGiant protocol, Roche, Basel, Switzerland) to assess DNA methylation in three CRCs (all microsatellite-stable and CpG island methylator phenotype-negative) and matched samples of normal mucosa (ArrayExpress accession number: E-MTAB-6949). The results of those experiments were compared with those obtained in the present study with MBD-capture sequencing, to identify potential strengths and weaknesses of the two enrichment methods for CRC methylome characterization.…”

“…During embryogenesis, the DNA methylome undergoes profound remodeling, with the removal and addition of methyl groups at cytosine bases, primarily those making up CpG dinucleotides. These changes are associated with markedly modified gene-expression (although the mechanisms underlying this association are still incompletely understood) [9][10][11][12][13], and play pivotal roles in the processes of cellular differentiation and organ specification [14,15]. Once the large intestine methylome is established, however, it is chemically stable and faithfully maintained by 4 mitotic inheritance for the life of the individual.…”

The DNA hypermethylation phenotype of colorectal cancer liver metastases resembles that of the primary colorectal cancers.

“…During embryogenesis, the DNA methylome undergoes profound remodeling, with the removal and addition of methyl groups at cytosine bases, primarily those making up CpG dinucleotides. These changes are associated with markedly modified gene-expression (although the mechanisms underlying this association are still incompletely understood) [9][10][11][12][13], and play pivotal roles in the processes of cellular differentiation and organ specification [14,15]. Once the large intestine methylome is established, however, it is chemically stable and faithfully maintained by mitotic inheritance for the life of the individual.…”