Characterization of copy number aberrations and epigenetic modifications in prostate cancer
Year: 2010
Type: dissertation
Abstract: Prostate cancer (PCa) is the most common epithelial cancer and second leading cause of cancer death among men in the US. Prostate cancer tumorigenesis is associated with numerous molecular events including transcriptomic, epigenetic, and copy number alterations. In this thesis, we characterized two major types of genome-wide events to understand their global implications and contributions in PCa. First, we assessed genome-wide copy number variations (CNVs) using array comparative genomic hybridization of laser-capture microdissected prostate cancer samples representing multiple stages of PCa progression. Minimal common regions (MCR) of CNVs, including novel regions, were defined for each sample type. Integrative analysis of MCRs with matched gene expression profiles revealed genes with coordinated CNV and altered transcript expression during PCa progression. We also identified MCRs that distinguished PCa samples harboring or lacking an ETS gene fusion. Secondly, we characterized genome-wide DNA methylation patterns, an epigenetic mark known to repress gene transcription. We employed a novel technology termed Methylplex-Next Generation Sequencing (M-NGS) which uses methylation sensitive restriction enzymes to enrich methylated genomic regions. The performance of M-NGS to characterize global methylation was tested in LNCaP prostate cancer and PrEC benign prostate epithelial cells. Multiple techniques, including bisulfite sequencing, validated the results. Detailed analyses revealed diverse promoter methylation patterns which correlated with transcriptional repression. Interestingly, integration of DNA methylation and H3K4me3 ChIP-Seq data in LNCaP identified differential epigenetic regulation of specific transcript isoforms. We next employed M-NGS to characterize PCa tissue samples. We identified 2,481 cancer-specific methylated regions, including WFDC2 promoter methylation, which served as a PCa biomarker and was validated on an independent tissue cohort. Finally we used a 3-way integrative analysis of these genome-wide events and identified regions with co-occurrence of copy number gain/loss and DNA methylation, associated with aberrant gene expression in PCa. In summary, this thesis work presents a comprehensive analyses of genome-wide copy number and methylation changes and its global implications on transcriptional regulation for the first time in prostate cancer. The datasets generated here will be a valuable public resource for genome-wide analysis in the future.
Author: Jung H. Kim
Language: English
Subfield: Cancer Research
Domain: Life Sciences
Open Access status: green
OpenAlex ID: W2152620230