CRISPR/Cas9 screens identify LIG1 as a sensitizer of PARP inhibitors in castration-resistant prostate cancer

Abstract

DNA repair; Oncology; Prostate cancer

Reparació de l'ADN; Oncologia; Càncer de pròstata

Reparación del ADN; Oncología; Cáncer de próstata

PARP inhibitors (PARPi) have received regulatory approval for the treatment of several tumors, including prostate cancer (PCa), and demonstrate remarkable results in the treatment of castration-resistant prostate cancer (CRPC) patients characterized by defects in homologous recombination repair (HRR) genes. Preclinical studies showed that DNA repair genes (DRG) other than HRR genes may have therapeutic value in the context of PARPi. To this end, we performed multiple CRISPR/Cas9 screens in PCa cell lines using a custom sgRNA library targeting DRG combined with PARPi treatment. We identified DNA ligase 1 (LIG1), essential meiotic structure-specific endonuclease 1 (EME1), and Fanconi anemia core complex associated protein 24 (FAAP24) losses as PARPi sensitizers and assessed their frequencies from 3% to 6% among CRPC patients. We showed that concomitant inactivation of LIG1 and PARP induced replication stress and DNA double-strand breaks, ultimately leading to apoptosis. This synthetic lethality (SL) is conserved across multiple tumor types (e.g., lung, breast, and colorectal), and its applicability might be extended to LIG1-functional tumors through a pharmacological combinatorial approach. Importantly, the sensitivity of LIG1-deficient cells to PARPi was confirmed in vivo. Altogether, our results argue for the relevance of determining the status of LIG1 and potentially other non-HRR DRG for CRPC patient stratification and provide evidence to expand their therapeutic options.

This work received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement no. 648670 to FD), from MIUR FARE (DiVERrSE, R16Z7PSLHN to FD), from the Fondazione Trentina per la Ricerca sui Tumori (to FD), from AIRC Investigator Grant (ID 29370 to FD), from AIRC fellowship for Italy (29926-2023 to GF), from the Prostate Cancer Foundation Young Investigator Award (19YOUN16 to FL), from Fundacion AECC (LABAE20019MATE to JM), and from the European Regional Development Fund (ERDF) 2014–2020 (to Department CIBIO Core Facilities). The FDADF laboratory is supported by: ERC advanced grant (TELORNAGING—835103); AIRC-IG (21762); Telethon (GGP17111); AIRC 5×1000 (21091); Progetti di Ricerca di Interesse Nazionale (PRIN) 2015“ATR and ATM-mediated control of chromosome integrity and cell plasticity”*(2015SJLMB); Progetti di Ricerca di Interesse Nazionale (PRIN) 2017 “RNA and Genome Instability”;(2017NWEXEP) Progetto AriSLA 2021“DDR & ALS” (FG_24/2020); POR FESR 2014-2020 Regione Lombardia (InterSLA project) (DSB.AD004.294); FRRB—Fondazione Regionale per la Ricerca Biomedica—under the frame of EJP RD, the European Joint Programme on Rare Diseases with funding from the European Union’s Horizon 2020 research and innovation program under the EJP RD COFUND-EJP NO 825575 (EJPRD19-206); cofunding European Union – Next Generation EU, in the context of The National Recovery and Resilience Plan, Investment Partenariato Esteso PE8 “Conseguenze e sfide dell’invecchiamento,” Project Age-It (Aging Well in an Aging Society) GAE 492 PNRR PE_8 SPOKE 2; NRR-CN3 “National Center for Gene Therapy and Drugs based on RNA Technology”; ERC POC TELOVACCINE – 101113229; Telethon GMR23T2007. FC laboratory was supported by #NEXTGENERATIONEU (NGEU) and funded by the Italian MUR, National Recovery and Resilience Plan (NRRP), project Investment PE8 - Project Age-It: “Ageing Well in an Ageing Society” (D.R. 1557 11.10.2022).