Molecular Biology and Genetics PhD Thesis Defense by Hilal Saraç

KOÇ UNIVERSITY

GRADUATE SCHOOL OF SCIENCES & ENGINEERING

MOLECULAR BIOLOGY AND GENETICS

PhD THESIS DEFENSE BY HİLAL SARAÇ

Title: The Role of KDM3B in Castration Resistant Prostate Cancer

Speaker: Hilal SARAÇ

Time: August 7th, 2018, 10:00

Place: SNA A52

Koç University

Rumeli Feneri Yolu

Sariyer, Istanbul

Thesis Committee Members:

Asst. Prof. Nathan LACK, Advisor (Koç University, Molecular Biology and Genetics)

Asst. Prof. Tamer ÖNDER (Koç University, Molecular Biology and Genetics)

Asst. Prof. Serkan KIR (Koç University, Molecular Biology and Genetics)

Assoc. Prof. N.C. Tolga EMRE (Boğaziçi University, Molecular Biology and Genetics)

Dr. Akane KAWAMURA (University of Oxford, Radcliffe Department of Medicine)

Abstract:

Prostate cancer (PCa) is an extremely common disease. Androgen Deprivation Therapy (ADT) is the standard of care for patients who fail surgery or radiotherapy. While initially successful, the cancer almost recurs into a more aggressive Castration Resistant Prostate Cancer (CRPC) state.

Extensive evidence has shown that CRPC is dynamically regulated by epigenetic modifying enzymes. Yet despite this importance, only a small subset of histone modifying enzymes have been tested in CRPC. Therefore, in an effort to understand what other epigenetic modifiers play role in the mechanism of CRPC, we conducted an shRNA screen with 122 shRNAs (>2 shRNA per target) against different epigenetic modifying enzymes in LNCaP-abl cells, a model of CRPC. We found out that knock-down of KDM3B, a H3K9me2 demethylase, dramatically decreased proliferation. We validated this phenotype by using CRISPR/Cas9 mediated KDM3B knock-out. Importantly, overexpression of KDM3B could rescue the phenotype. The effect of KDM3B was found to be remarkably specific to androgen-independent cells as downregulation of KDM3B did not alter the proliferation of other prostate cell lines. Interestingly, cell cycle distribution remained the same after KDM3B knock-down.

To characterize the role of KDM3B in CRPC, we performed RNA-seq at two different time points and found out that only a small number of genes were differentially expressed in shKDM3B. Among them, ARG2 and RDH11 looked very interesting. Surprisingly, our GSEA results revealed G2/M check-point enrichment in LNCaP-abl cells when KDM3B was knocked-down. We also did ChIP-seq to investigate genome-wide recruitment of KDM3B in LNCaP-abl cells. While additional studies our needed, our findings suggested that KDM3B binding was rather dispersed in the cells. Finally, we also examined the translational potential of KDM3B by testing knockdown or knockout in xenograft studies. However, we did not detect any significant difference between control and KDM3B knock-down/out tumours.

In conclusion, our data suggests that KDM3B is important for the proliferation of CRPC cells and its histone demethylase activity is required for its role in CRPC. Further studies are needed to better understand the role of KDM3B in CRPC to provide better treatment strategies.