Abstract 659: Mechanisms of resistance to SHP2 inhibition

Abstract SHP2 (PTPN11) is required for RAS activation, acting upstream of SOS1/2. Allosteric SHP2 inhibitors (SHP2is) stabilize auto-inhibition mediated by N-SH2/PTP interactions and prevent its activation by upstream stimuli. SHP2is impair the proliferation of oncogenic RTK- or cycling RAS mutant-expressing tumor cells and can overcome adaptive resistance to single agents targeting the RAS-MAPK-ERK pathway (e.g., EGFR, KRASG12C, BRAFV600E, MEK inhibitors). Multiple SHP2is are in clinical trials as single agents or in various combinations. As resistance to targeted therapy is universal, we sought to prospectively identify potential SHP2-extrinsic resistance mechanisms by performing genome-wide CRISPR/Cas9 knockout screens on two SHP2i-sensitive human FLT3-ITD driven AML cell lines, MOLM13 and MV4:11. We identified several expected “hits” based on known signaling pathways, including tumor suppressor (NF1, PTEN,CDKN1B) and “RASopathy” (LZTR1, RASA2) genes, as well as novel targets including INPPL1,MAP4K5, and some epigenetic modifiers. To test the generality of these findings, we built a“mini-CRISPR library of ~30 hits common to MOLM13 and MV4:11 cells and screened 15 SHP2i-sensitive lines. LZTR1 deletion conferred resistance in 14/15, followed by MAP4K5 (9/15),SPRED2 (6/15), STK40 (6/15), INPPL1 (5/15), NCOA6 (4/15), NCOR1 (4/15), and ELAVL1 (4/15). LZTR1 has been reported to regulate RIT or RAS stability. Notably, LZTR1 knockout universally increased RIT1, but in some lines, also increased RAS. INPPL1 encodes SHIP2, a 5’-inositide phosphatase that negatively regulates AKT activation in insulin signaling. However, INPPL1 deletion also increased RAS and ERK activity and activated ERK-dependent genes in FLT3-ITD AML lines. Experiments with INPPL1 mutant showed that SHC binding and an N-terminal region, but not the SH2 domain or phosphatase activity, is required for negative regulation of RAS. Interestingly, INPPL1 deletion also promoted resistance to SHP2 inhibition in several EGFR mutant cell lines. MAP4K5 deletion also increased ERK-dependent gene expression. Kinase activity, but not JNK activation, was required for MAP4K5 action. Our results predict multiple mechanisms of SHP2i resistance, emphasizing the need for detailed understanding of the resistance landscape to arrive a combinations that provide long term disease control. Citation Format: Wei Wei, Mitchell Geer, Xinyi Guo, Neville Sanjana, Benjamin G. Neel. Mechanisms of resistance to SHP2 inhibition [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 659.