CRISPR Knockout Identifies New Biomarkers for PARP Inhibitor Resistance in Prostate Cancer

A new analysis using CRISPR screens has revealed insights that could help better explain which patients with prostate cancer are most likely to respond to poly (ADP-ribose) polymerase (PARP) inhibitors.

The report builds on the knowledge that patients with BRCA1/2 mutations are highly sensitive to PARP inhibitors by identifying new genes whose presence or absence appears to have a significant impact on the success of PARP inhibitor therapy. The study was published in Nature Communications.

About 10% of people with primary prostate cancer and a quarter of people with metastatic prostate cancer have at least 1 DNA damage response (DDR) gene alteration, wrote the study authors. These alterations could be a therapeutic vulnerability, they said.

“In particular, defects in homologous recombination repair (HRR) render cells highly sensitive to inhibition of PARP,” the authors wrote.

Two PARP inhibitors—olaparib (Lynparza) and rucaparib (Rubraca)—have been approved by the FDA to treat metastatic castration-resistant prostate cancer (mCRPC), and the data from the trials for those and other PARP inhibitors suggests that BRCA1/2-deficient tumors are highly sensitive to this class of drug.

“However, genomic alterations in other DNA damage response genes have not been consistently predictive of clinical response to PARP inhibition,” the investigators explained.

They therefore decided to use genome-wide CRISPR knockout screens to see whether other types of mutations might also affect PARP outcomes in prostate cancer. They used 4 BRCA1/2-proficient cell lines to identify genes that conferred PARP inhibitor sensitivity or resistance when deleted. The analysis led to several insights.

The investigators found that deletion of MMS22L greatly enhances sensitivity to PARP inhibitors because it disrupts RAD51 recruitment, which is required for HRR. They noted that as many as 14% of people with prostate cancer have MMS22L deletion.

“Given the considerable number of prostate cancer patients with MMS22L deletion detected by next-generation sequencing or DNA in situ hybridization-based assays, this genomic alteration may be a valuable biomarker for PARP inhibition despite the fact that the response is TP53-dependent,” they wrote.

The authors also found that CHEK2 was associated with resistance, rather than sensitivity, to PARP inhibition, although they said combining PARP inhibition with ataxia telangiectasia and Rad3-related protein (ATR) inhibition could overcome that resistance.

“In order to survive PARP inhibition, cancer cells rely more on ATR checkpoint to slow down cell cycle and reduce replication stress for repairing double-strand breaks (DSBs),” they wrote. “ATR inhibition increases replication origin firing and DNA synthesis despite the presence of PARP inhibitor–induced replication fork gaps, leading to the progressive accumulation of DSBs.”

The authors added that ATR inhibition can disrupt RAD51 loading to stalled replication forks and DSBs in PARP inhibitor–resistant BRCA1-deficient cells.

They said their findings offer a systematic view of the genetic determinants and mechanisms associated with resistance to PARP inhibitors in patients with prostate cancer, potentially expanding the number of biomarkers used to personalize therapy. In addition, they said they may have found a new way to overcome PARP inhibitor resistance.

“Simultaneous suppression of ATR and PARP may be a preferred strategy to overcome PARP inhibition resistance,” they concluded.

Reference

Tsujino T, Takai T, Hinohara K, et al. CRISPR screens reveal genetic determinants of PARP inhibitor sensitivity and resistance in prostate cancer. Nat Commun. Published online January 17, 2023. doi:10.1038/s41467-023-35880-y