Active BRAF-V600E is the key player in generation of a sessile serrated polyp-specific DNA methylation profile

Abstract

BackgroundSessile serrated polyps (SSPs) have emerged as important precursors for a large number of sporadic colorectal cancers. They are difficult to detect during colonoscopy due to their flat shape and the excessive amounts of secreted mucin that cover the polyps. The underlying genetic and epigenetic basis for the emergence of SSPs is largely unknown with existing genetic studies confined to a limited number of oncogenes and tumor suppressors. A full characterization of the genetic and epigenetic landscape of SSPs would provide insight into their origin and potentially offer new biomarkers useful for detection of SSPs in stool samples.MethodsWe used a combination of genome-wide mutation detection, exome sequencing and DNA methylation profiling (via methyl-array and whole-genome bisulfite sequencing) to analyze multiple samples of sessile serrated polyps and compared these to familial adenomatous polyps.ResultsOur analysis revealed BRAF-V600E as the sole recurring somatic mutation in SSPs with no additional major genetic mutations detected. The occurrence of BRAF-V600E was coincident with a unique DNA methylation pattern revealing a set of DNA methylation markers showing significant (~3 to 30 fold) increase in their methylation levels, exclusively in SSP samples. These methylation patterns effectively distinguished sessile serrated polys from adenomatous polyps and did so more effectively than parallel gene expression profiles.ConclusionsThis study provides an important example of a single oncogenic mutation leading to reproducible global DNA methylation changes. These methylated markers are specific to SSPs and could be of important clinical relevance for the early diagnosis of SSPs using non-invasive approaches such as fecal DNA testing.

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

“…Global hypomethylation of the genome is also a common feature of tumorigenesis, and it was clearly evident in both cADNs and CIMP(-) colon cancers. It has also been reported in a single SSA/P investigated with whole-genome bisulfite sequencing (Dehghanizadeh et al, 2018). However, our data indicate that SSA/Ps and CIMP(+) cancers are generally spared from the wave of demethylation that occurs during conventional colorectal tumorigenesis (at least within the 80.5 Mb area of the genome we investigated).…”

“…Dehghanizadeh et al recently attempted to explore this uncharted territory using a microarraybased assay to assess methylation at ~450,000 CpG sites (Dehghanizadeh et al, 2018). However, the series of precancerous lesions they studied included only 5 SSA/Ps (archival samples: fresh or FFPE) and 3 cADNs (all from patients with familial polyposis), and, with the exception of one of the SSA/Ps, none of the precancerous lesions were accompanied by a paired sample of normal mucosa.…”

“…Not only are they the most stable of known epigenetic marks, (Bird, 1978) , (Wu & Zhang, 2014) they also occur early in tumorigenesis (Feinberg et al, 2006, Issa, 2014, Jones & Baylin, 2007, Menigatti, Cattaneo et al, 2009, Menigatti, Staiano et al, 2013, Menigatti, Truninger et al, 2009, Suzuki, Watkins et al, 2004. Furthermore, differentially methylated regions of the genome far outnumber gene mutations in precancerous colon tumors, and they tend to be found across most lesions (unlike mutations, which are likely to be tumor subset-specific (Dehghanizadeh, Khoddami et al, 2018, Lin, Raju et al, 2017, Nikolaev, Sotiriou et al, 2012).…”

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

“…Dehghanizadeh et al recently attempted to explore this uncharted territory using a microarraybased assay to assess methylation at~450,000 CpG sites [41]. However, the series of precancerous Age 70 83 70 74 60 85 57 72 46 66 72 72 85 59 69 67 68 57 53 71 64 65 65 78 52 77 67 79 63 71 55 24 54 45 63 59 74 55 55 49 71 24 58 52 59 57 72 55 68 72 68 86 84 78 77 69 64 64 78 probably reflecting their different frequencies of KRAS mutations.…”

“…Not only are they the most stable of known epigenetic marks [33,34], they also occur early in tumorigenesis [9][10][11][35][36][37][38]. Furthermore, differentially methylated regions of the genome far outnumber gene mutations in precancerous colon tumors, and they tend to be found across most lesions (unlike mutations, which are likely to be tumor subset-specific [39][40][41]).…”