Abstract 3515: LHX9 is a novel oncogene bypassing KRAS addiction

Abstract

Abstract Background Oncogenic mutations of RAS are detected in approximately 30% of human cancers. KRAS is highly mutated in pancreatic, colorectal and lung cancers. Direct therapeutic targeting of Ras and its membrane association has been challenging due to high affinity of GTP to Ras and unexpected mechanism of alternative post-translational modification. While few inhibitors of downstream RAS effectors - MAPK and PI3K pathways - show some clinical efficacy, they are complicated by complex feedback loops, and as single agents are not effective in KRAS-mutant cancers. Combination therapies may be promising yet limited by narrow therapeutic window. Identification of alternative strategies to directly inhibiting RAS and MAPK/PI3K pathways is key to address this unmet need. Methods To this end, we performed a genome-scale open reading frames screen to identify genes capable of restoring viability to KRAS-dependent cells following KRAS suppression. We tested the top 5-standard-deviation hits in low-throughput manner. One of the top hits included LIM homeobox 9 (LHX9), a homeobox family transcription factor essential for mouse gonad, limb, and brain development. While LHX9 is amplified in several cancers, little is known regarding its roles in cancers. We used hypothesis-driven as well as unbiased approaches including RNA-seq, ChIP-seq, and IP-mass spectrometry to investigate the basis of LHX9-mediated bypass of KRAS dependency. Results We showed that LHX9 rescued KRAS suppression in multiple cell lines as well as xenograft. LHX9 overexpression substituted for KRAS in KRAS-driven xenograft. Moreover, in activated-MEK-overexpressing HA1E cells, LHX9 formed tumors as robustly as myristoylated AKT. LHX9 rescued KRAS suppression by both restoring KRAS-dependent pathways and activating KRAS-independent pathways. First, LHX9 reactivated the main KRAS effectors - MAPK and PI3K pathways and conferred resistance to MEK inhibitor Trametinib. Second, using ChIP- and RNA-seq, we observed LHX9 binding to promoters/enhancers of genes whose expression was regulated by KRAS, particularly YAP1. Third, LHX9 increased expression and activation of KRAS-independent genes, including STAT3. Conclusions Here, we identified LHX9 as a novel bypass of KRAS addiction. Multiple unbiased approaches revealed at least three mechanisms by which LHX9 rescued KRAS suppression. Our findings contribute to our understanding of KRAS biology. Further investigation of downstream effectors of LHX9 may highlight potentially novel therapeutic targets for KRAS-dependent cancers. Citation Format: Seav Huong Ly, Chao Dai, Andrew L. Hong, Nina Ilic, Elsa B. Krall, William C. Hahn. LHX9 is a novel oncogene bypassing KRAS addiction [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 3515. doi:10.1158/1538-7445.AM2017-3515