The centromere is an essential component of the cellular machinery required for the faithful segregation of chromosomes during mitosis, a process that is significantly dysregulated in cancer. Though accurate centromeric assembly is vital for maintaining genomic stability and ensuring accurate cell division, the role centromeres play in cancer biology remains understudied. The highly repetitive underlying sequence that makes up the genomic landscape has made annotation of the centromeric region very difficult, leaving the study of centromere genomics and epigenomics as one of the last frontiers in the quest towards a more complete understanding of the human genome. New methodologies that can navigate the repetitive nature of centromeric sequences are thus required to effectively study centromere genetics and molecular biology in the context of cancer. We have developed novel bioinformatics tools that allow us to survey gene expression across large data sets to ascertain cancer specific expression of target genes. Our group has additionally developed a quantitative PCR assay to detect chromosome-specific centromeric sequences, with a focus on detecting ?-satellite repeats, which are the hallmark of centromeres. Further, we have identified significant overexpression of the centromeric H3 histone variant CENPA in prostate cancer. Preliminary studies suggest that CENPA knockdown in prostate cancer cells limits their ability to proliferate. Centromeric ?-satellite RNAs (CeASaRs) are known to modulate CENPA function, and we can demonstrate enrichment of specific CeASaRs when comparing prostate cancer to benign prostatic tissue. This enrichment was validated using our chromosome specific qPCR assay in whole cell RNA extracts from prostate cancer and prostatic epithelial cell lines. In view of the above, we hypothesize that centromeres represent a functionally important molecular signature that can drive prostate cancer biology. We will investigate in detail the functions of CENPA and CeASaRs in the context of prostate cancer, through deep sequencing, bioinformatics approaches, cell culture techniques and mouse models. Specifically, modulating CENPA expression in prostate cancer cell lines through overexpression and knockdown studies in cell culture and xenograft transplants will enable us to demonstrate the biological relevance of CENPA to prostate cancer. Additionally, northern blots, RACE, and long read technology available to us through the PacBio RS II platform will assist us in navigating the highly repetitive landscape of centromeric sequences. The importance of these specific CeASaRs in driving prostate cell proliferation, along with CENPA, will then be explored. These studies will shed light on a largely unexplored area in biology and in cancer research, with the potential to inform novel therapeutic approaches.
The centromere, a structure that is essential for the faithful segregation of chromosomes, remains largely understudied in cancer due to technologic limitations in our ability to resolve the highly repetitive sequence characteristic of centromeric DNA. The goal of this project is to utilize novel centromere-focused methodologies to investigate the hypothesis that centromeres represent an unexplored molecular signature that may drive prostate cancer biology.
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