Pluto Bioinformatics

GSE127904: Systematic characterization of epigenetic modifying enzymes identifies KDM3B as a key regulator in castration resistant prostate cancer

Bulk RNA sequencing

Androgen deprivation therapy (ADT) is the standard care for prostate cancer patients who fail surgery and radiotherapy. While initially effective, the cancer almost always recurs into a more aggressive Castration Resistant Prostate Cancer (CRPC). Despite the existing evidence on the role of epigenetic modifiers in CRPC, only a handful of enzymes have been tested. In this study, we conducted a systematic shRNA library screen, focusing of epigenetic modifiers linked to stem-cell reprogramming, in LNCaP-abl cells, a model of CRPC. Amongst the shRNA hits, KDM3B, a histone H3K9 demethylase, was identified to have the most significant anti-proliferative effect on LNCaP-abl cells. KDM3B CRISPR/Cas9 knockout phenocopied the shRNA treatment, proving the observed phenotype was not due to shRNA off-target effects. Interestingly, this decrease in proliferation was remarkably specific to androgen-independent cells. Additionally, genetic rescue experiment showed that only enzymatically active KDM3B recovers the phenotype. No alterations in the cell cycle distribution or expression of AR downstream effectors were observed, but RNASeq revealed subtle changes in the genes expression profile for cells treated with KDM3A shRNA, including in metabolome-related enzymes such as ARG2, RDH11. However, metabolomic analysis in KDM3B knockout cells showed little change overall compared to untreated cells. Interestingly, we observed a decrease in the availability of amino acids in the absence of KDM3B which requires further investigation. Overall, our studies are the first ones to show the specificity of KDM3B in CRPC. SOURCE: Nathan,Allan,Lack (nlack@prostatecentre.com) - University of British Columbia