Chromosome-wide mapping of DNA methylation patterns in normal and malignant prostate cells reveals pervasive methylation of gene-associated and conserved intergenic sequences

Yegnasubramanian, Srinivasan; Wu, Zhijin; Haffner, Michael C.; Esopi, David; Aryee, Martin J.; Badrinath, Raghav; He, Tony L.; Morgan, James D.; Carvalho, Benilton; Zheng, Qizhi; Marzo, Angelo M. De; Irizarry, Rafael A.; Nelson, William G.

doi:10.1186/1471-2164-12-313

Cited by 65 publications

(63 citation statements)

References 46 publications

(65 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…(18,19) Briefly, DNA was sonicated, end-repaired, and ligated to SOLiD P1 and P2 sequencing adaptors lacking 5' phosphate groups, using the NEBNext DNA Library Prep Set for SOLiD according to the manufacturer's recommended protocol (NEB). Libraries were then nick-translated with Platinum Taq polymerase and divided into two fractions: an enriched methylated fraction that was subjected to isolation and elution of CpG-methylated library fragments by using MBD2-MBD-bound magnetic beads as described previously,(19) and a total input fraction that was left unenriched. These fractions were then amplified using 4–6 cycles for the total input, and 10–12 cycles for the enriched methylated fractions according to the NEBNext DNA Library Prep Set for SOLiD kit (NEB).…”

Section: Methodsmentioning

confidence: 99%

A Novel Functional Splice Variant of AKT3 Defined by Analysis of Alternative Splice Expression in HPV-Positive Oropharyngeal Cancers

et al. 2017

Self Cite

View full text Add to dashboard Cite

The incidence of HPV-related oropharyngeal squamous cell carcinoma (OPSCC) has increased more than 200% in the past 20 years. Recent genetic sequencing efforts have elucidated relevant genes in head and neck cancer, but HPV-related tumors have consistently shown few DNA mutations. In this study, we sought to analyze alternative splicing events (ASE) that could alter gene function independent of mutations. To identify ASE unique to HPV-related tumors, RNA sequencing was performed on 46 HPV-positive OPSCC and 25 normal tissue samples. A novel algorithm using outlier statistics on RNA-sequencing junction expression identified 109 splicing events, which were confirmed in a validation set from the Cancer Genome Atlas (TCGA). Because the most common type of splicing event identified was an alternative start site (39%), MBD-seq genome-wide CpG methylation data were analyzed for methylation alterations at promoter regions. ASE in six genes showed significant negative correlation between promoter methylation and expression of an alternative transcriptional start site, including AKT3. The novel AKT3 transcriptional variant and methylation changes were confirmed using qRT-PCR and qMSP methods. In vitro silencing of the novel AKT3 variant resulted in significant growth inhibition of multiple head and neck cell lines, an effect not observed with wild type AKT3 knockdown. Analysis of ASE in HPV-related OPSCC identified multiple alterations likely involved in carcinogenesis, including a novel, functionally active transcriptional variant of AKT3. Our data indicate that ASEs represent a significant mechanism of oncogenesis with untapped potential for understanding complex genetic changes that result in development of cancer.

show abstract

Section: Methodsmentioning

confidence: 99%

A Novel Functional Splice Variant of AKT3 Defined by Analysis of Alternative Splice Expression in HPV-Positive Oropharyngeal Cancers

et al. 2017

Self Cite

View full text Add to dashboard Cite

show abstract

“…Evidence for DNA methylation changes on enhancers in cancer comes from several studies in breast, cervical, lung and prostate cancer [29–32]. Gains and losses in H3K4 monomethylation (H3K4me1) on many enhancers have been reported in colon cancer [33] and similar findings were reported for changes in the DNA accessibility pattern on cis-regulatory elements in various cancers [34].…”

Section: Indirect Evidence Of Enhancer Malfunction In Diseasementioning

confidence: 80%

Enhancer deregulation in cancer and other diseases

Herz

2016

BioEssays

View full text Add to dashboard Cite

Summary Mutations in enhancer-associated chromatin-modifying components and genomic alterations in non-coding regions of the genome occur frequently in cancer and other diseases pointing to the importance of enhancer fidelity to ensure proper tissue homeostasis. In this review, I will use specific examples to discuss how mutations in chromatin-modifying factors might affect enhancer activity of disease-relevant genes. I will then consider direct evidence from single nucleotide polymorphisms, small insertions or deletions but also larger genomic rearrangements such as duplications, deletions, translocations and inversions of specific enhancers to demonstrate how they have the ability to impact enhancer activity of disease genes including oncogenes and tumor suppressor genes. Considering that the scientific community only fairly recently has begun to focus its attention on “enhancer malfunction” in disease, I propose that multiple new enhancer-regulated and disease-relevant processes will be uncovered in the near future that will constitute the mechanistic basis for novel therapeutic avenues.

show abstract

“…Moreover, a combined assay for GSTP1 and APC hypermethylation have great potential for detecting PCa in clinical samples up to 100 % sensitivity [3,4].…”

Section: Genomics/epigenetic and Snpsmentioning

confidence: 99%