Uncovering mechanisms of PARP inhibitor resistance in IDH1-mutant cancers via serial tumor transplantation and genome wide CRISPR-Cas9 knockout screen

Over the last two decades, novel cancer therapies have targeted genetic profiles identified through whole exome sequencing data, including mutations in the homology-directed repair (HDR) proteins breast cancer-associated genes 1 and 2 (BRCA1 and BRCA2), as well as cancer-linked mutations in isocitrate dehydrogenase (IDH), an essential tricarboxylic acid cycle enzyme. Our group and others recently reported that cancers harboring IDH1/2 mutations have defective recruitment of HDR factors to sites of DNA damage due to changes in chromatin dynamics and consequent sensitivity to poly(ADP-ribose) polymerase inhibitors (PARPi). These findings have led to multiple clinical trials exploiting this vulnerability to PARPi monotherapy and combinatorial therapy. To investigate potential mechanisms by which PARPi resistance might arise, we first modeled PARPi-resistance in IDH1-mutant tumors via serial transplantation of patient-derived xenografts in mice treated with the PARPi talazoparib. An analysis of candidate DNA repair factors in these resistant tumor populations revealed downregulation of end protection factors 53BP1, RIF1 and REV7-which are established negative regulators of HDR. Knockout of these factors by CRISPR/Cas9 in IDH1-mutant cancer cells conferred robust resistance to PARPi and restored HDR capacity, supporting the initial observation that mutations in IDH confer a fundamental HDR defect. To overcome this resistance, we found that treatment with the receptor tyrosine kinase inhibitor, cediranib, previously reported to suppress expression of downstream HDR factors, resensitizes these PARPi-resistant cells to PARPi treatment. As a next step, a genome wide CRISPR-Cas9 knockout screen is underway to uncover undescribed mechanisms PARPi resistance in IDH-mutant tumors. Our findings identify key pathways driving PARPi resistance in IDH1-mutant cancers and highlight potential therapeutic strategies to overcome this resistance.