Comparison of transcriptomes of PARP inhibitor-treated and -untreated isogenic human BRCA-wildtype ovarian cancer PDX

Background: PARP inhibitors (PARPi) kill cancer cells by stalling DNA replication and preventing DNA repair, resulting in a critical accumulation of DNA damage. Resistance to PARPi is a growing clinical problem in the treatment of high grade serous ovarian carcinoma (HGSOC). Acetylation of histone H3 lysine 14 (H3K14ac) and associated histone acetyltransferases (HATs) have known functions in DNA repair and replication, but their expression and activities have not been examined in the context of PARPi-resistant HGSOC. Results: Using mass spectrometry profiling of histone modifications, we observed altered H3K14ac enrichment in PARPi-resistant HGSOC cells relative to isogenic PARPi-sensitive lines. By RT-qPCR and RNA-Seq, we also observed altered expression of numerous HATs in PARPi-resistant HGSOC cells and a PARPi-resistant PDX model. Knockdown of HATs only modestly altered PARPi response, although knockdown and inhibition of PCAF significantly increased resistance. Pharmacologic inhibition of HBO1 severely depleted H3K14ac but did not affect PARPi response. However, knockdown and inhibition of BRPF3, which is known to interact in a complex with HBO1, did reduce PARPi resistance. Conclusions: This study demonstrates that severe depletion of H3K14ac does not affect PARPi response in HGSOC. Our data suggest that bromodomain functions of HAT proteins such as PCAF, or accessory proteins such as BRPF3, may play a greater role in PARPi response than acetyltransferase functions. Overall design: GTFB-PDX1009 is a BRCA-wildtype human HGSOC that develops significant ascites disease burden. Patient ascites cells were injected via intraperitoneal route into NSG mice and allowed to develop for 7 days. Mice were then treated once daily for 21 days by IP injection of vehicle control or 50 mg/kg olaparib. After the treatment regimen, disease burden was allowed to develop/recur for 2 months. At this point, mice were sacrificed and necropsied. Solid tumors and ascites were collected. The ascites cells were used for RNA-seq analysis. We hypothesized that olaparib treatment would select for a PARP inhibitor-resistant population of cells. We then used RNA-seq to compare the transcriptomes of the treated/selected cells vs. the untreated/unselected groups.