Research Projects

Epigenetic alterations are known to play a critical role in prostate cancer (PCa) pathogenesis and progression, e.g., DNA hypermethylation of the tumor suppressor genes' regulatory region, i.e., GSTP1 and RASSF1A, is known to be an early event. With recent advancements, cell-free DNA (cfDNA) profiling has been used for tumor molecular subtyping, monitoring metastases, and guiding treatment. Likewise, methylation profiling of cfDNA is considered a promising and potentially reliable tool for liquid biopsy. Using our Epic-Array methylation data of Indian PCa patients, we aim to develop a 6-probe panel for hypermethylated loci, which will be used as a diagnostic test for patients’ cfDNA using Digital Droplet PCR. Briefly, the ratio of DNA methylation-positive droplets and DNA-methylation negative droplets would be used to statistically assess the specificity, sensitivity, and AUC score. This will be the first cfDNA methylation-based assay designed for the diagnosis of PCa among Indian patients. Integrating hypermethylated loci and TF binding sites (TFBS) using JASPAR, we found PATZ1 binding sites enriched in hypermethylated CpG loci. PATZ1 plays a key role in stemness and neuroepithelial tumors, thus, we sought to investigate its functional significance in PCa. Our preliminary data show that PATZ1 is positively associated with repressive epigenetic modifiers and ERG in PCa patients. Nonetheless, the mechanistic underpinnings of PATZ1 as a repressive TF and its associated transcriptional machinery are yet to be explored. We propose to employ CRISPR-Cas9 loss-of-function studies to decipher the oncogenic potential of PATZ1 using cell-based assays and xenograft experiments and unravel the potential interdependency between PATZ1 and ERG. We will also decipher the PATZ1-interactome using immunoprecipitation-mass spectroscopy and uncover its interaction with repressive epigenetic modifiers. Finally, the role of PATZ1 as an immunomodulator of the tumor microenvironment will be examined, and leads will be considered for designing immunotherapeutic strategies. Next, we integrated DEGs and hypomethylated genes, resulting in a list of 134 upregulated genes, of which GMEB2 appeared as a top gene. GMEB2 is known to modulate transactivation of the glucocorticoid receptor (GR) signaling. Whole-exome sequencing (WES) data in our PCa cohort also revealed GMEB2 to be copy-number amplified. We hypothesize that GMEB2 might play a critical role in the advancement of PCa to the aggressive stage of Neuroendocrine PCa. Hence, we propose investigating the functional impact of GMEB2 in PCa progression, resistance to anti-androgens, and transdifferentiation to Neuroendocrine prostate cancer. Next, we will decipher the crosstalk and dependencies in the AR-GR-GMEB2 signaling axis. Proteome and phosphoproteomic profiling of GMEB2 engineered cells will unravel the underlying mechanism of GMEB2-mediated oncogenicity, its role in anti-androgen resistance, and NEPC onset.