Abstract 6377: Developing combination therapy with SHP2 inhibition for CIN-type gastroesophageal adenocarcinoma with KRAS amplification

Abstract Recent studies from the cancer genome atlas (TCGA. Nature. 2014) (TCGA. Nature. 2017) and other groups showed that a molecular subtype with chromosomal instability (CIN) is the most common subtype of gastroesophageal adenocarcinoma (GEA) and is characterized by aneuploidy without somatic hypermutation. The oncogene KRAS is frequently amplified in CIN type gastric cancer (14.3%) and esophageal adenocarcinoma (10.4%). SHP2 is a phosphatase which is a part of a machinery activating KRAS from GDP-bound inactive status to GTP-bound active status, and our group previously reported that KRAS-amplified gastric tumors are relatively resistant to MEK inhibition but sensitive to MEK/SHP2 co-inhibition. While the combination of MEK and SHP2 inhibitors showed efficacy in pre-clinical models, the translation of this combination has been challenging, in part due to on-target toxicity from inhibitors of the MAPK pathway (Auliac, et al. Cancers. 2020). Therefore, we sought better combination strategy with SHP2 inhibition, using genome-wide CRISPR screen. We conducted primary CRISPR screening with two GEA cell lines (KE-39 and HUG1-N) and CRISPR-KO lentivirus library (Brunello CRISPR knockout pooled library, 77,741 sgRNAs/19,114 genes, Broad Institute Genomic Perturbation Platform) and identified candidate targets both within the MAPK pathway and among upstream tyrosine kinases that may enhance the efficacy of a SHP2 inhibitor in KRAS-amplified GEA. Prior to detailed analyses of potential hits from the screen, we performed the secondary screen with additional KRAS-amplified and -mutant cell lines (CAT12, YCC-1, and GSU) using a custom CRISPR-Cas9 sgRNA library targeting 509 genes of interest including top hits in each cell line data set, and confirmed that knockout of KRAS upstream and downstream genes have additive cytotoxicity to SHP2 inhibition. Given our focus on finding targets that could be readily translated into therapeutics, we focused our analysis on those of most ready translational relevance and specifically chose ERBBs, FAK, SRC, RAFs, ERK1/2, and CDK4/6 as candidate targets. Further analyses showed the potent cytotoxicity of SHP2 inhibition with a pan-ERBB kinase inhibitior (Afatinib) and with a CDK4/6 inhibitor (Ribociclib), with greater efficacy of this combination in KRAS-amplified tumors compared to KRAS-mutant tumors, both in vitro and in vivo experiments. Overall, these results suggest co-inhibition of SHP2 and upstream/downstream of KRAS as a promising treatment strategy against KRAS-amplified CIN-type GEA. Citation Format: Osamu Kikuchi, Tianxia Li, Jin Zhou, Yichen Wang, Klavdija Bastl, Prafulla C. Gokhale, Aine Knott, Yanxi Zhang, John G. Doench, Zandra Ho, Daniel V. Catenacci, Adam J. Bass. Developing combination therapy with SHP2 inhibition for CIN-type gastroesophageal adenocarcinoma with KRAS amplification [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 6377.