A Preexisting Rare <i>PIK3CA</i> E545K Subpopulation Confers Clinical Resistance to MEK plus CDK4/6 Inhibition in <i>NRAS</i> Melanoma and Is Dependent on S6K1 Signaling

Abstract

Combined MEK and CDK4/6 inhibition (MEKi + CDK4i) has shown promising clinical outcomes in patients with <i>NRAS</i>-mutant melanoma. Here, we interrogated longitudinal biopsies from a patient who initially responded to MEKi + CDK4i therapy but subsequently developed resistance. Whole-exome sequencing and functional validation identified an acquired <i>PIK3CA</i>^E545K mutation as conferring drug resistance. We demonstrate that <i>PIK3CA</i>^E545K preexisted in a rare subpopulation that was missed by both clinical and research testing, but was revealed upon multiregion sampling due to <i>PIK3CA</i>^E545K being nonuniformly distributed. This resistant population rapidly expanded after the initiation of MEKi + CDK4i therapy and persisted in all successive samples even after immune checkpoint therapy and distant metastasis. Functional studies identified activated S6K1 as both a key marker and specific therapeutic vulnerability downstream of <i>PIK3CA</i>^E545K-induced resistance. These results demonstrate that difficult-to-detect preexisting resistance mutations may exist more often than previously appreciated and also posit S6K1 as a common downstream therapeutic nexus for the MAPK, CDK4/6, and PI3K pathways.<b>Significance:</b> We report the first characterization of clinical acquired resistance to MEKi + CDK4i, identifying a rare preexisting <i>PIK3CA</i>^E545K subpopulation that expands upon therapy and exhibits drug resistance. We suggest that single-region pretreatment biopsy is insufficient to detect rare, spatially segregated drug-resistant subclones. Inhibition of S6K1 is able to resensitize PIK3CA^E545K-expressing NRAS-mutant melanoma cells to MEKi + CDK4i. <i>Cancer Discov; 8(5); 556-67. ©2018 AACR.</i><i>See related commentary by Sullivan, p. 532</i><i>See related article by Teh et al., p. 568</i><i>This article is highlighted in the In This Issue feature, p. 517</i>.