CDK4/6 and SHP2 mediate BRAF/MEK inhibitor resistance in Class 2 and 3 BRAF mutant cancers

Class 2 and 3 non-V600E BRAF mutations are oncogenic drivers in many cancer types. Currently, there are no established targeted therapies with proven efficacy for cancers with non-V600E BRAF mutations. We developed the investigator-initiated, Phase II BEAVER clinical trial (NCT03839342) to evaluate the efficacy of BRAF and MEK inhibitors in patients with non-V600E BRAF mutations. The best objective response rate was 14% (3/21). By analyzing genomic data from patient tumors, circulating tumor DNA (ctDNA), patient-derived xenograft (PDX) models generated from enrolled patients, and functional genomics of Class 2 & 3 BRAF mutant cell lines, we discovered MAPK-dependent and independent mechanisms of intrinsic and acquired resistance to BRAF/MEK inhibition. These included the acquisition of new mutations in NRAS, MAP2K1, RAF1, and RB in ctDNA at the time of disease progression. We observed an enrichment for alterations in genes that regulate cell cycle progression amongst non-responders and increased expression of genes mediating cell cycle progression in tumors Class 2 BRAF mutant cell lines with acquired resistance to BRAF/MEK inhibitors. In Class 3 BRAF mutant cancers specifically, PTPN11 (SHP2) was an essential gene. CDK4/6 and SHP2 were found to mediate intrinsic resistance to BRAF/MEK inhibition in Class 2 & 3 BRAF mutant tumors. Therapeutic strategies combining CDK4/6 or SHP2 inhibitors with BRAF/MEK inhibitors were more effective than BRAF/MEK inhibitors alone in vitro and in vivo, highlighting the need to explore therapeutic targets outside of the MAPK pathway in these hard-to-treat Class 2 & 3 BRAF mutant cancers.