Abstract A23: Genome-wide discovery of synthetic lethal interactions in PTEN-deficient human mammary epithelial cells

Abstract

Abstract PTEN is one of the most frequently dysregulated tumor suppressor genes in human cancers, and PTEN deficiency is common in breast tumors, particularly those that belong to the aggressive basal-like breast cancer (BLBC) subtype. Because the BLBC subtype is itself very heterogeneous and basal-like tumors lack expression of cancer drug targets like HER2, there is currently no targeted therapy available for effective treatment. To systematically and comprehensively explore potential vulnerabilities in PTEN-deficient BLBC, we sought to discover genes that are synthetic lethal to PTEN loss using a functional genomics approach. We carried out a synthetic lethal siRNA screen in a pair of isogenic cell lines: an untransformed, non-tumorigenic human mammary epithelial cell line with molecular characteristics that closely mimic BLBCs (MCF10A), and a derivative cell line that harbored a targeted deletion of exon 2 in the PTEN gene (MCF10A-PTEN-/-). For greater sensitivity in detecting synthetic lethal effects, we used a high content screening system to determine total cell numbers by direct counting of stained cell nuclei after siRNA knock-down. Through the discovery of synthetic lethal interactions in these PTEN-deficient cell lines, we aim to identify novel components of the PTEN signaling network and uncover vulnerabilities in PTEN-deficient tumors. We first completed a pilot screen of kinase and phosphatase genes and identified synthetic lethal hits which were subsequently confirmed using multiple siRNA sequences for each gene. Our top candidate synthetic lethal genes were not directly involved in the PI3K-Akt signaling pathway, consistent with studies showing that therapeutic targeting of the PI3K pathway in PTEN-deficient cancers is not always effective. Using the strongest hit from the pilot screen as a positive synthetic lethal control, we further completed a whole-genome screen in the same pair of isogenic cell lines. We are currently validating the top candidate synthetic lethal genes and will explore if these putative synthetic lethal interactions are present in other PTEN-deficient breast cancer cell lines belonging to the BLBC subtype. Citation Format: Yew Chung Tang, John McPherson, Elisabeth Tan, Germaine Goh, Frederic Bard, Steve Rozen. Genome-wide discovery of synthetic lethal interactions in PTEN-deficient human mammary epithelial cells. [abstract]. In: Proceedings of the AACR Precision Medicine Series: Synthetic Lethal Approaches to Cancer Vulnerabilities; May 17-20, 2013; Bellevue, WA. Philadelphia (PA): AACR; Mol Cancer Ther 2013;12(5 Suppl):Abstract nr A23.