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

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Homo sapiens

PROVIDER: GSE110538 | GEO | 2018/04/09

REPOSITORIES: GEO

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

Project description:Background: Sessile 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.Methods: We 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.Results: Our 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.Conclusions: This 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.

| S-EPMC5873940 | biostudies-literature

Active BRAF-V600E is the key player in generation of a sessile serrated polyp-specific DNA methylation profile (WGBS data set)

Project description:Screening and surveillance of colorectal cancers (CRCs) using advanced colonoscopy technologies have significantly reduced the incidence and mortality rates of CRCs in recent years. However, a significant portion of CRCs are still remained undiagnosed, especially those involving sessile serrated adenomas/polyps (SSA/P), most likely due to their flat shape and the excessive amounts of secreted mucin that cover the polyps, making them invisible for colonoscopy. Here, a potential alternative solution is the application of molecular markers enabling unambiguous characterization of SSPs. However, full implementation of this strategy requires availability of robust markers which are still lacking. In this work by comprehensive molecular analysis of several malignant and normal samples at the genome, methylome and transcriptome levels we show that activating mutation of BRAF-V600E drives the generation of a unique SSP-specific DNA methylation profile. As the result a robust set of DNA methylation markers showing significant (~3 to 30 fold) increase in their methylation levels, exclusively in SSP samples, are introduced. These markers can be of important clinical relevance, especially in early diagnosis of SSPs using non-invasive approaches such as fecal DNA testing.

2018-04-09 | GSE110537 | GEO

Active BRAF-V600E is the key player in generation of a sessile serrated polyp-specific DNA methylation profile (RNA-seq data set)

2018-04-09 | GSE110536 | GEO

Active BRAF-V600E is the key player in generation of a sessile serrated polyp-specific DNA methylation profile (Exome-seq data set)

2018-04-09 | GSE110535 | GEO

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

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

| PRJNA433947 | ENA

Active BRAF-V600E is the key player in generation of a sessile serrated polyp-specific DNA methylation profile (WGBS data set)

Project description:Active BRAF-V600E is the key player in generation of a sessile serrated polyp-specific DNA methylation profile (WGBS data set)

| PRJNA433957 | ENA

Active BRAF-V600E is the key player in generation of a sessile serrated polyp-specific DNA methylation profile (RNA-seq data set)

Project description:Active BRAF-V600E is the key player in generation of a sessile serrated polyp-specific DNA methylation profile (RNA-seq data set)

| PRJNA433955 | ENA

Active BRAF-V600E is the key player in generation of a sessile serrated polyp-specific DNA methylation profile (Exome-seq data set)

Project description:Active BRAF-V600E is the key player in generation of a sessile serrated polyp-specific DNA methylation profile (Exome-seq data set)

| PRJNA433956 | ENA

Endoscopic recognition of the sessile serrated polyp to cancer sequence.

Project description: Not available

| S-EPMC5991804 | biostudies-literature

Polyp Detection Rate as a Surrogate for Adenoma and Sessile Serrated Adenoma/Polyp Detection Rates.

Project description:IntroductionQuality measures for colonoscopy such as adenoma detection rate (ADR) have been proposed to be surveilled for ensuring minimum standards. However, its direct measurement is time consuming and often neglected. Extrapolating ADR and other quality measures from polyp detection rate (PDR) can be a pragmatic alternative.ObjectiveTo determine quotients for estimating ADR and sessile serrated adenoma/polyp detection rate (SSA/P-DR) from PDR in an Australian cohort.MethodsConsecutive adult patient colonoscopies during a 1-year period were retrospectively assessed in a single Australian tertiary endoscopy center. Adenoma detection quotient (ADQ) and SSA/P detection quotient (SSA/P-DQ) were defined as the division of ADR and SSA/P-DR by PDR, respectively. The primary outcome was the number of procedures to achieve a stable cumulative ADQ and SSA/P-DQ. Secondary outcomes included evaluation of ADQ and SSA/P-DQ in different subsets.ResultsIn total, 2,657 colonoscopies were performed by 15 endoscopists in 2016. The ADR, SSA/P-DR, and PDR found were 32.2, 6.7, and 47.3%, respectively. The ADQ and SSA/P-DQ values found were 0.68 and 0.14, respectively. After approximately 500 procedures, both ADQ and SSA/P-DQ became stable. Interclass correlation coefficient (ICC) for the prediction of ADR from ADQ was excellent for all endoscopists that performed >177 procedures in that year (ICC 0.84).ConclusionsADQ and SSA/P-DQ values were consistent when over 500 procedures were analyzed. ADQ had an excellent correlation with ADR when >177 procedures per endoscopist were evaluated.

| S-EPMC7445665 | biostudies-literature

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