Proteomic characterization of acquired PARP inhibitor resistance in high-grade serous ovarian cancer

High-grade serous ovarian cancer (HGSOC) is the deadliest gynecologic malignancy in women. The incorporation of poly (ADP-ribose) polymerase inhibitors (PARPi) into the HGSOC treatment regimen can increase progression-free survival; however, most patients develop PARPi resistance, limiting the use of this targeted therapy. Therefore, it is imperative to further elucidate the mechanisms driving PARPi resistance in HGSOC. In this project, we sought to elucidate the proteomic alterations that occur with the development of PARPi resistance using patient-derived xenograft (PDX) mouse models of HGSOC.

The PDX models used in this study were homologous recombination deficient (HRD) via a BRCA2 mutation (PH077) or a Rad51C methylation (PH039) and had acquired PARPi resistance through repeated exposure to Niraparib. In the PH077 model, 5,231 proteins were quantified across all tumors (PARPi sensitive (n=3) and resistant (n=2)) based on label-free quantification. Global proteomic analysis resulted in the identification of 32 proteins with significant differences in relative abundance when comparing the sensitive and resistant tumors (fold-change > 2; p < 0.05). Interestingly, Principal Component Analysis revealed that the PARPi sensitive tumors exhibited a higher degree of proteomic similarity, whereas the resistant tumors did not exhibit this characteristic. This suggests that acquired PARPi resistance is tumor-specific and does not occur via common pathways.When carrying out a grouped analysis, we also identified proteins that were unique to only the sensitive or resistant tumors. Significant biological pathways found to be enriched from these unique proteins include: oncogenic MAPK signaling and sumoylation (sensitive), RNA processing and IL-12 signaling (resistant).

To investigate the functional role of HDACi in sensitizing HGSOC tumors to PARPi treatment, next, we explored the differential abundance of HDACs within the PARPi sensitive and resistant groups. Increased HDAC6 expression is associated with poor prognosis and drug resistance in HGSOC. Differential abundances of HDACs 1,2,3,6 and 7 were observed in the HGSOC PDX mice. The relative abundance of HDAC6 was significantly increased in one of the PARPi resistant tumors compared with two of the sensitive tumors, suggesting that decreased levels of lysine acetylation are functionally implicated in refractoriness to PARPi treatment. Ongoing work is includes analysis of the PH039 model and a differential analysis of lysine acetylation modifications between the PARPi sensitive vs. resistant tumors using acetyl-lysine antibody-based peptide enrichment to further elucidate the molecular mechanisms implicated in the responsiveness to PARPi treatment. The results from this study will lead to a more thorough understanding of the mechanisms driving drug response in HGSOC towards an overall goal of establishing therapeutic vulnerabilities to improve patient survival.