Clinicogenomic analysis of <i>EGFR</i>-mutant lung tumors identifies Rb pathway inactivation as a hallmark of squamous transformation.

Abstract

Histologic transformation to lung squamous cell carcinoma (LUSC) is an underrecognized mechanism of resistance in epidermal growth factor receptor (<i>EGFR</i>)-mutant lung adenocarcinoma (LUAD). Although AKT and MYC activation have been linked to LUSC features, the clinicogenomic determinants of this transformation remain undefined. In this study, we performed comprehensive clinical and multiomic profiling-including genomic, transcriptomic, methylation, and proteomic analyses-of <i>EGFR</i>-mutant tumors that were transforming, adenosquamous (LUAS), or de novo LUSC. Patients with <i>EGFR</i>-mutant LUSC or LUAS had shorter overall survival on first-line osimertinib compared with those with <i>EGFR</i>-mutant LUAD. Transforming tumors were enriched for alterations in the retinoblastoma (Rb) and AKT pathways, particularly cyclin-dependent kinase inhibitor 2A/B (<i>CDKN2A/B</i>) deletions. These alterations were also frequent in <i>EGFR</i>-wild-type LUSC and associated with shorter time-to-osimertinib discontinuation. In genetically engineered human in vivo models, Rb inactivation, in combination with AKT and MYC activation, enhanced the acquisition of LUSC features. Single-cell RNA profiling of such models recapitulated the molecular changes observed in the transforming clinical specimens and identified MET pathway up-regulation during transformation. Combined EGFR and MET inhibition suppressed tumor growth in patient-derived xenograft models of LUSC transformation. Together, these findings highlight Rb pathway inactivation as a promoter of LUSC transformation in <i>EGFR</i>-mutant lung cancer and identify MET signaling as a therapeutic vulnerability that may suppress plasticity in this setting and extend response to targeted therapy.