Abstract C73: A drug-modifier whole-genome shRNA screen identifies novel synthetic lethal interactions with PI3K inhibition in breast cancer

Abstract

Abstract The PI3K pathway is frequently activated in tumors, and was previously shown to be essential for tumorigenesis and tumor cell survival. Never the less, the main response to PI3K inhibition is cytostatic, therefore retaining a significant reservoir of tumor cells with a capability to re-grow and acquire resistance. Our goal is to identify genes that exhibit a synthetic lethal interaction with PI3K inhibition, namely, converting the response to PI3K inhibition from cytostatic to cytotoxic. To this end, we conducted a positive-selection whole-genome shRNA screen in a breast cancer cell line bearing a PI3K activating mutation, also exhibiting a robust cytostatic response to PI3K inhibition. Cells were infected with a pooled shRNA library consisting of 98K shRNAs, targeting ∼17K genes. Following selection, cells were either left untreated, or treated with a PI3K inhibitor (GDC0941) for 2-5 days. Based on cleaved-PARP staining, apoptotic cells were sorted by flow cytometry, and sequenced to identify the shRNAs in the sorted population. We ranked shRNAs according to the significance of their relative occurrence between non-treated and treated samples, thereby identifying shRNAs that induce cell death only upon PI3K inhibition. We validated potential hit genes using an arrayed viability assay, in which we included multiple shRNAs targeting each of the genes. Using seed-control shRNAs and rescue experiments, we confirmed on-target effects of the identified shRNAs, collectively targeting 5 genes. We further confirmed the relevance of the identified genes by testing the shRNAs in additional PI3K-activated breast cancer cell-lines, and in combination with additional PI3K-pathway inhibitors. Interestingly, the effect of the identified genes was specific to inhibition of the PI3K pathway, and was not observed upon unrelated growth inhibition. All together, we identified five genes that exhibit robust synthetic lethal interaction with PI3K inhibition in breast cancer, of which 2 genes are protein kinases, PIM2 and ZAK, thus are potential co-targets with PI3K. Citation Format: Yaara Zwang, Casandra Chen, The Broad Institute Genomic Perturbation Platform, William C. Hahn. A drug-modifier whole-genome shRNA screen identifies novel synthetic lethal interactions with PI3K inhibition in breast cancer. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2015 Nov 5-9; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2015;14(12 Suppl 2):Abstract nr C73.