Arul Chinnaiyan is searching for gene fusions that drive the formation of solid tumors, with the ultimate goal of improving the early diagnosis and therapy of common cancers.
Role of Gene Fusions in Cancer Progression
Gene fusions are a hallmark of cancer progression. Typically, these gene fusions are created when chromosomes inappropriately swap pieces of genetic material. The hybrid proteins produced by fused genes are associated with particularly aggressive forms of several cancers. The goal of this project is to understand the formation and function of cancer gene fusions using multiple approaches. These gene fusions would be characterized using state-of-the-art microscopy and molecular biology tools. The functional consequences of these gene fusions would be studied using cell biology approaches. For additional information on our projects, please see our recent publications (Mani et al., Science, 2009; Mani & Chinnaiyan, Nature Reviews Genetics, 2010; Mani et al., Cancer Research, 2011).
Students will learn a wide variety of cell biology, molecular biology, and microscopy techniques. The cell biology techniques include standard cell culture, invasion, and proliferation assays. The molecular biology techniques include RNA/plasmid isolation, complementary DNA synthesis, quantitative real-time PCR, chromatin immunoprecipitation assay, and Western blotting. The microscopy techniques involve image acquisition and analysis using state-of-the-art Zeiss Axioplan microscopes. In addition, students will get exposed to next-generation sequencing methodologies.
Characterization of Novel Long Noncoding RNA in Prostate Cancer
Despite improvements in medical treatments over the past three decades, prostate cancer remains the second most common cause of cancer death among U.S. men. According to the National Cancer Institute, ~241,000 prostate cancer diagnoses and ~28,000 related deaths of American men were estimated in 2012. Androgen deprivation, surgery, and/or radiotherapy in combination with chemotherapy are primary treatment modalities for patients with localized disease; however, patients who progress to aggressive hormone-refractory disease have high mortality rates. The molecular mechanisms that contribute to the progression of localized disease into an aggressive form and the availability of reliable prognostic markers of disease progression remain elusive. Long noncoding RNAs (lncRNAs) are polyadenylated RNA species that do not code for proteins. lncRNAs are known to play a role in a wide variety of cellular processes, including X-chromosome inactivation and pluripotency in stem cells, and in cancer progression. Using high-throughput sequencing and bioinformatics analysis, we have identified several lncRNAs that are upregulated in patients with prostate cancer. The goal of this project is to characterize these prostate lncRNAs to better understand their role in prostate cancer progression.
Students will design primers to validate expression of lncRNA in prostate cancer cell lines. Once validated, lncRNA will be further characterized to determine the exon structure. lncRNA will then be cloned and the functional role will be determined in prostate cancer cell lines. This project will introduce students to cell and molecular biology techniques such as RNA isolation, complementary DNA preparation, PCR, qualitative PCR, and cell culture.
Role of MMSET (WHSC1): An Oncogenic Histone Methyl Transferase in Prostate Cancer
MMSET (WHSC1 or NSD2) is a SET domain containing histone methyltransferease overexpressed in prostate cancer. This project investigates the role of MMSET in androgen signaling pathways leading to transcriptional activation of androgen receptor target genes. Students will learn cell culture, RNA isolation, cell transfection, quantitative PCR, Western blotting, and in vitro cytotoxicity assays.