Chemical proteomics identifies a transcription-related network of proteins that interact with the next-generation poly(ADP-ribose) polymerase inhibitor saruparib

Introduction: Ovarian cancer is one of the leading causes of gynecological-related mortality rates, often due to late-stage diagnosis. Poly(ADP-ribose) polymerase 1 inhibitors (PARPi) have been FDA approved for treatment in ovarian, breast, pancreatic, and prostate cancers. PARPi's lead to synthetic lethality in cells deficient in homologous recombination repair. Although PARPi's are a promising cancer therapeutic, drug resistance as well as side effects like hematological toxicity remain unmet clinical challenges. Methods: In this study we utilized PARP1 -proficient and generated CRISPR PARP1 -deficient isogenic HEYA8 and HAP1 cell lines to perform chemical proteomics using derivatized Olaparib and a next-generation PARPi, Saruparib. Proteins and protein complexes engaged with the drug were pulled down after click chemistry in cell lysates, followed by LC-MS/MS to identify new targets of Saruparib. Results: The subsequent analysis revealed a statistically significant set (p-value ≤ 0.03) of 247 unique proteins that were ≥2-fold enriched when compared to the unmodified PARPi competition. Within those 247 proteins, we compared the different conditions in both cell lines to identify proteins that interacted with Saruparib as well as its canonical target, PARP1. 182 were found exclusively in the Saruparib pulldown, 192 were found only in PARP1-proficient conditions regardless of drug, and 159 were found in both the Saruparib pulldown and PARP1-proficient conditions. Several proteins associated with the TFIID complex, composed of pre-initiation transcription factors, were shown to be enriched only in the Saruparib pulldown regardless of PARP1-proficiency, indicating a potential deregulation of the transcriptional machinery. However, one protein of the TFIID complex, BRD2, was shown to have enrichment dependent on PARP1-proficiency, indicating both potential drug and PARP specificity. BRD2 is a member of the BET family of proteins, which plays a role in transcriptional regulation and gene expression. We further validated the interaction between endogenous BRD2 and PARP1 through co-immunoprecipitation experiments with HEK293T whole cell lysates. Conclusions: Our findings have uncovered a novel landscape of transcription-related proteins, including BRD2, that might provide targets for combination therapy with the PARPi Saruparib.