Article

DNA methylation profiling reveals novel biomarkers and important roles for DNA methyltransferases in prostate cancer

Department of Genetics, Stanford University, Stanford, CA 94305, USA.
Genome Research (Impact Factor: 14.63). 04/2011; 21(7):1017-27. DOI: 10.1101/gr.119487.110
Source: PubMed

ABSTRACT

Candidate gene-based studies have identified a handful of aberrant CpG DNA methylation events in prostate cancer. However, DNA methylation profiles have not been compared on a large scale between prostate tumor and normal prostate, and the mechanisms behind these alterations are unknown. In this study, we quantitatively profiled 95 primary prostate tumors and 86 benign adjacent prostate tissue samples for their DNA methylation levels at 26,333 CpGs representing 14,104 gene promoters by using the Illumina HumanMethylation27 platform. A 2-class Significance Analysis of this data set revealed 5912 CpG sites with increased DNA methylation and 2151 CpG sites with decreased DNA methylation in tumors (FDR < 0.8%). Prediction Analysis of this data set identified 87 CpGs that are the most predictive diagnostic methylation biomarkers of prostate cancer. By integrating available clinical follow-up data, we also identified 69 prognostic DNA methylation alterations that correlate with biochemical recurrence of the tumor. To identify the mechanisms responsible for these genome-wide DNA methylation alterations, we measured the gene expression levels of several DNA methyltransferases (DNMTs) and their interacting proteins by TaqMan qPCR and observed increased expression of DNMT3A2, DNMT3B, and EZH2 in tumors. Subsequent transient transfection assays in cultured primary prostate cells revealed that DNMT3B1 and DNMT3B2 overexpression resulted in increased methylation of a substantial subset of CpG sites that showed tumor-specific increased methylation.

Download full-text

Full-text

Available from: Devin Absher
  • Source
    • "The most frequently mutated genes in primary prostate cancers are SPOP, TP53, FOXA1, and PTEN (Barbieri et al., 2012). Only recently has the spectrum of epigenetic changes in prostate cancer genomes been explored (Bö rno et al., 2012; Friedlander et al., 2012; Kim et al., 2011; Kobayashi et al., 2011; Mahapatra et al., 2012). Importantly, no studies have comprehensively integrated diverse omics data types to assess the robustness of previously defined subtypes and potentially prognostic alterations. "
    [Show abstract] [Hide abstract]
    ABSTRACT: Summary There is substantial heterogeneity among primary prostate cancers, evident in the spectrum of molecular abnormalities and its variable clinical course. As part of The Cancer Genome Atlas (TCGA), we present a comprehensive molecular analysis of 333 primary prostate carcinomas. Our results revealed a molecular taxonomy in which 74% of these tumors fell into one of seven subtypes defined by specific gene fusions (ERG, ETV1/4, and FLI1) or mutations (SPOP, FOXA1, and IDH1). Epigenetic profiles showed substantial heterogeneity, including an IDH1 mutant subset with a methylator phenotype. Androgen receptor (AR) activity varied widely and in a subtype-specific manner, with SPOP and FOXA1 mutant tumors having the highest levels of AR-induced transcripts. 25% of the prostate cancers had a presumed actionable lesion in the PI3K or MAPK signaling pathways, and DNA repair genes were inactivated in 19%. Our analysis reveals molecular heterogeneity among primary prostate cancers, as well as potentially actionable molecular defects.
    Full-text · Article · Nov 2015 · Cell
  • Source
    • "We sought to uncover molecular mechanisms behind aggressive prostate cancer by comparing DNA methylation profiles between benign prostate, indolent prostate cancer, and aggressive prostate cancer. DNA methylation is a compelling candidate for involvement in prostate cancer aggressiveness due to the comparatively low somatic mutation rate in prostate tumors (Taylor et al., 2010) and the reported overexpression of DNA methyltransferases in prostate cancer (Kobayashi et al., 2011). Two alternative ways to divide prostate cancers into aggressiveness groups for research are by outcomes (recurrence and/or prostate cancer specific mortality) or by histopathological grading. "
    [Show abstract] [Hide abstract]
    ABSTRACT: A critical need in understanding the biology of prostate cancer is characterizing the molecular differences between indolent and aggressive cases. Because DNA methylation can capture the regulatory state of tumors, we analyzed differential methylation patterns genome-wide among benign prostatic tissue and low-grade and high-grade prostate cancer and found extensive, focal hypermethylation regions unique to high-grade disease. These hypermethylation regions occurred not only in the promoters of genes but also in gene bodies and at intergenic regions that are enriched for DNA-protein binding sites. Integration with existing RNA-sequencing (RNA-seq) and survival data revealed regions where DNA methylation correlates with reduced gene expression associated with poor outcome. Regions specific to aggressive disease are proximal to genes with distinct functions from regions shared by indolent and aggressive disease. Our compendium of methylation changes reveals crucial molecular distinctions between indolent and aggressive prostate cancer.
    Full-text · Article · Nov 2015 · Cell Reports
  • Source
    • "TCGA cohorts analyzed revealed that four of the six CpGs analyzed are significantly hypermethylated in tumor samples. This confirms data seen in a recent high-throughput methylation array analysis of prostate tumors [22]. Treatment of cancer cell lines with a methyltransferase inhibitor (5-azadC) resulted in increased expression of CHD8 mRNA in LNCaP indicating DNA methylation plays a role in CHD8 regulation (Figure 2C). "
    [Show abstract] [Hide abstract]
    ABSTRACT: Abnormal expression and function of chromatin regulators results in the altered chromatin structure seen in cancer. The chromatin regulator CTCF, its cofactor CHD8, and antagonistic paralogue BORIS have wide-ranging effects on gene regulation. Their concurrent expression and regulation was examined in benign, localized, and metastatic prostate cancer (PCa) arrays with extended follow-up using an automated quantitative imaging system, VECTRA. Epithelial staining was quantified and compared against a range of clinicopathologic variables. CHD8 expression was decreased in HGPIN, localized, and metastatic PCa compared to benign (P < .001). CHD8 promoter hypermethylation, assessed by Quantitative Pyrosequencing, occurred in over 45% of primary cancers in this population as well as the TGCA database. Treatment of cell lines with the demethylating agent 5-Aza-2'-deoxycytidine reinduced expression. An interesting dichotomy for CHD8 was observed within primary cancers, with higher nuclear protein expression associated with adverse clinical outcomes including extracapsular extension (P = .007), presence of metastases (P = .025) and worse PSA-recurrence free survival (P = .048). CHD8 outperformed Gleason score and predicted biochemical failure within intermediate grade prostate cancers. The BORIS/CTCF expression ratio increased in localized (P = .03) and metastatic PCa (P = .006) and was associated with higher Gleason score (P = .02), increased tumor volume (P = .02) and positive margins (P = .04). Per cell heterogeneity of expression revealed all protein expression to be more heterogeneous in cancerous tissue (both P < .001), especially high grade (P < .01). In the first detailed analysis in cancer, a marked loss of CHD8 expression and increased BORIS/CTCF ratio indicate frequent disruption of CTCF and its effector genes in PCa. Copyright © 2014 Neoplasia Press, Inc. Published by Elsevier Inc. All rights reserved.
    Full-text · Article · Dec 2014 · Neoplasia (New York, N.Y.)
Show more