Leanne G Ahronian 1 , Erin M Sennott 1 , Eliezer M Van Allen 2 , Nikhil Wagle 2 , Eunice L Kwak 1 , Jason E Faris 1 , Jason T Godfrey 3 , Koki Nishimura 3 , Kerry D Lynch 4 , Craig H Mermel 5 , Elizabeth L Lockerman 3 , Anuj Kalsy 3 , Joseph M Gurski 1 , Samira Bahl 6 , Kristin Anderka 6 , Lisa M Green 6 , Niall J Lennon 6 , Tiffany G Huynh 4 , Mari Mino-Kenudson 4 , Gad Getz 5 , Dora Dias-Santagata 4 , A John Iafrate 4 , Jeffrey A Engelman 1 , Levi A Garraway 2 , Ryan B Corcoran 7
BRAF mutations occur in approximately 10% of colorectal cancers. Although RAF inhibitor monotherapy is highly effective in BRAF-mutant melanoma, response rates in BRAF-mutant colorectal cancer are poor. Recent clinical trials of combined RAF/EGFR or RAF/MEK inhibition have produced improved efficacy, but patients ultimately develop resistance. To identify molecular alterations driving clinical acquired resistance, we performed whole-exome sequencing on paired pretreatment and postprogression tumor biopsies from patients with BRAF-mutant colorectal cancer treated with RAF inhibitor combinations. We identified alterations in MAPK pathway genes in resistant tumors not present in matched pretreatment tumors, including KRAS amplification, BRAF amplification, and a MEK1 mutation. These alterations conferred resistance to RAF/EGFR or RAF/MEK combinations through sustained MAPK pathway activity, but an ERK inhibitor could suppress MAPK activity and overcome resistance. Identification of MAPK pathway reactivating alterations upon clinical acquired resistance underscores the MAPK pathway as a critical target in BRAF-mutant colorectal cancer and suggests therapeutic options to overcome resistance.