Abstract 2750: Physical and functional landscape of deubiquitinating enzymes (DUBs) in KRAS mutant lung cancer

Abstract

Abstract DUBs are involved in tumorigenesis and are of high interest as potential targets for cancer therapy. However, target discovery is problematic due to the absence of clear DUB activity within subsets of human cancers. Our goal was to profile DUBs and their activity in KRAS-mutated lung cancer cell lines using chemical biology strategies. Approximately 25% of patients with Lung adenocarcinoma have tumor associated KRAS mutations in non-small lung cancers (NSCLC), yet specific RAS inhibitors against KRAS-mutated lung cancer have not yet been successfully developed. We used activity-based protein profiling (ABPP) to profile DUBs in 25 distinct human lung cancer cell lines harboring KRAS mutations. ABPP uses chemical probes that are active-site directed and covalently bind to a class of enzymes in complex proteome. Whole cell lysates were incubated with HA-UB-VME and HA-UB-PA probes and ABPP pull-down was performed. Enriched proteins were trypsin digested and peptides were analyzed using liquid chromatography and tandem mass spectrometry (LC-MS/MS). MAXQUANT software was used to quantify DUBs. We related activity of observed DUBs to effects on cell viability by examining publicly available RNAi (Project DRIVE) and CRISPR (PICKLES) databases. A total of 50 DUBs were identified in our ABPP screen. Each cell line expressed at least 32 different DUBs and 22 DUBs were represented in all cell lines. The identified DUBs include 48% USP, 36% OTU, 8% JAMM and 8% UCH & MJD family. USP5, USP7, USP14, USP15, UCHL5, UCHL3, OTUB1, PRP8, PSMD7 and PSMD14 are the highly expressed DUBs. Functional enrichment approach and protein-protein interaction network reveal that 70% of the active DUBs are involved in cell cycle regulation. DDR, RNA splicing, TGF-beta receptor, NF-kB and Wnt signaling are some other enriched pathways. Of the 35 cell cycle DUBs, CRISPR screens identify 14 DUBs and DRIVE data identified 11 DUBS as having effects on cell viability. Combining the ABPP data, shRNA and CRISPR results, OTUD5, BRCC3, UCHL5, UFD1L, USP5, YY1, USP3, USP39, USP37, OTUB1, USP9X and COPS5 have activity in KRAS mutant lung cancer cell lines and demonstrate reduced cell viability with loss of function through CRISPR or RNAi. We have identified and prioritized DUB targets in KRAS mutant lung cancer. Future studies will further validate DUB as targets and identify mechanisms of activity in KRAS mutant lung cancers, as well as examine DUB activity using ABPP in human lung cancer tumor tissues, including adenocarcinoma (KRAS mutant and wild-type) and squamous cell lung cancer. Citation Format: Emma Adhikari, Shikha Mahajan, Harshani Lawrence, Yan Yang, Bin Fang, Eric Haura. Physical and functional landscape of deubiquitinating enzymes (DUBs) in KRAS mutant lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2750.