In-depth bioinformatics analysis of the phosphoproteome of triple negative breast cancer treated with a tumor selective NQO1 bioactivatable drug

Abstract

The main focus of this study is to elucidate changes in the proteome of triple negative breast cancer cells in response to a novel bioactivated anti-cancer agent IB-DNQ (isobutyl-deoxyniboquinone). NQO1 or NADPH:quinone oxidoreductase-1 is a detoxifying enzyme overexpressed in many solid tumors and low expression in normal cells. IB-DNQ is bio-activated by NQO1 enzyme via a futile redox cycling, producing large amounts of reactive oxygen species (ROS) in the process, which causes DNA lesions in cancer cells. The status of NQO1 is important for the IB-DNQ mediated cancer cell death. IB-DNQ mediated therapy has great potency in killing breast cancer cells compared to PARP inhibitor Rucaparib. From this proteomics study, large changes in phosphorylation are observed in utilizing a combination therapy with low dose of IB-DNQ and PARP inhibitor Rucaparib. Protein phosphorylation events within the transcription machinery and DNA damage repair pathways are changed upon drug treatment. Computational and bioinformatic analysis of kinases involved through kinase substrate enrichment analysis revealed changes in downstream signaling of cell cycle checkpoint proteins. CDK1 and CDK2 substrate phosphorylation was decreased in response to combination drug therapy. Based on the differential kinase activity as determined by substrate abundance, we hypothesize that since CDK1/2 plays an important role in DNA damage repair via the homologous recombination pathway, its downregulation further abrogated double stranded break repair in BRCA deficient cells creating a state of “BRCAness”, leading to heightened sensitivity to the PARP inhibitor Rucaparib. These studies give insight into the mechanism of IB-DNQ action as an anticancer agent.