Understanding and overcoming innate and acquired MAPK inhibition resistance in anaplastic thyroid cancer.

Anaplastic thyroid cancer (ATC) is highly lethal. Although patients with the BRAFV600E alteration respond to the type I RAF inhibitor (RAFi) dabrafenib with trametinib, most rapidly develop adaptive or acquired resistance. Here, multi-region whole-genome, high-coverage whole-exome, and single-nuclei RNA sequencing of tumors from ATC patients undergoing type I RAFi and MEKi therapy reveals that reactivation of the mitogen-activated protein kinase (MAPK) pathway, along with immunosuppressive macrophage proliferation, may underlie the development of acquired resistance. Screening of several RAFi reveals that ATC cell lines are exquisitely sensitive to the type II RAFi naporafenib, which inhibits EphA2-mediated MAPK signaling. Further, naporafenib and trametinib overcome both innate and acquired treatment resistance to dabrafenib and trametinib in ATC cell lines and patient-derived xenograft models. Finally, we describe a mechanism of acquired resistance to naporafenib through compensatory mutations in MAST1. Taken together, our work rationalizes the clinical investigation of type II RAFi in the setting of thyroid cancer.