Genome-wide CRISPR screen reveals SLFN11 as a potent mediator of cisplatin sensitivity in muscle-invasive bladder cancer

Abstract

Bladder cancer is among the top ten most common cancer types in the world, with approximately 550,000 new cases annually. The highest burden of bladder cancer is currently on most developed communities across the world and an estimated 9,000 Canadians are diagnosed with bladder cancer each year. Cisplatin-based Neoadjuvant chemotherapy (NAC) followed by radical cystectomy in patients with muscle-invasive bladder cancer (MIBC) has been shown to improve five-year survival, and is therefore currently the first-line standard of care in patients. However, 60% of patients are inherently resistant to NAC at the time of cystectomy. While several mechanisms of cellular resistance to cisplatin have been proposed, the mechanisms presented thus far still do not offer and effective patient response prediction in the context of MIBC. There is therefore, an urgent and unmet need to determine clinically actionable mechanisms of cisplatin resistance. In order to elucidate mechanisms of resistant to cisplatin, the study presented in this thesis takes advantage of a pooled genome‐wide CRISPR knock‐out library targeting 19,114 protein coding genes with 76,441 synthetic guide RNAs (sgRNAs) which allows for an unbiased screen. Upon completion of the screen the top hit was validated in vitro (CRISPR knockout cell lines), in vivo (mouse models) and in patient tumour tissue samples by immunohistochemistry. A full-scale screen revealed that several genes involved in the pro-apoptotic pathway (such as CASP8, BAX, and TNFSFR10A) and cell cycle regulation have the potential to confer resistance to cisplatin when knocked out. For this study however, we validated the top hit from our screen - Schlafen 11 (SLFN11) - and established that the complete loss of SLFN11 confers a cisplatin resistant phenotype in MIBC. We further established that SLFN11 is involved in the regulation of cell cycle progression upon cisplatin challenge and does so via interactions with Mediator of DNA Damage Checkpoint 1 (MDC1) protein. Overall, the study presented here offers SLFN11 as a potential biomarker to aid in clinical decision making and to anticipate resistance to cisplatin-based NAC in MIBC. Furthermore, targeting SLFN11 associated pathways could allow for the development of combination therapies to be used in conjunction with cisplatin in the future.