MA11.06 Multi-Omic Characterization of Lung Tumors Implicates AKT and MYC Signaling in Adenocarcinoma to Squamous Cell Transdifferentiation

Abstract

Lineage plasticity, the ability to transdifferentiate among distinct phenotypic identities, facilitates therapeutic resistance in multiple cancers. In lung adenocarcinomas (LUADs), this phenomenon includes small cell and squamous cell (LUSC) histologic transdifferentiation in the context of acquired resistance to targeted inhibition of driver mutations. The incidence of transdifferentiation into squamous carcinoma in EGFR mutant tumors, the setting where this histologic shift has been most extensively described, occurs in up to 9% of cases relapsed on osimertinib and has been associated to poor prognosis. The paucity of well annotated pre- and post-transdifferentiation clinical samples has precluded the performance of informative molecular analyses: little is known about the molecular mechanisms leading to this histological transition. We hypothesized that multi-parameter profiling of the components of mixed histology (LUAD/LUSC) tumors, together with pre- and post-transdifferntiation clinical samples, could provide insight into factors licensing lineage plasticity between these histologies and promoting squamous transdifferentiation of LUAD. We performed detailed genomic (whole exome sequencing), epigenomic (bisulfite sequencing), transcriptomic (RNAseq) and proteomic (antibody arrays) characterization. Clinical findings were validated in preclinical models including cell lines and patient-derived xenograft treatments. Our results suggest that LUSC transdifferentiation is primarily driven by transcriptional reprogramming rather than mutational events, and indicate that the resulting squamous tumors retain transcriptomic and methylation profiles of their previous LUAD state. We observed coordinated upregulation of PI3K/AKT, MYC and PRC2 pathway genes in the LUSC component of mixed histology tumors. Concurrent activation of PI3K/AKT and MYC induced squamous features in EGFR-mutant LUAD preclinical models, further augmented under selective pressure of osimertinib. Pharmacologic inhibition of EZH1/2 in combination with osimertinib prevented relapse and squamous transdifferentiation in an EGFR-mutant patient-derived xenograft model, and inhibition of EZH1/2 or PI3K/AKT signaling re-sensitized resistant transdifferentiated LUSC tumors to osimertinib. Our findings provide the first comprehensive molecular characterization of LUSC transdifferentiation, suggesting putative drivers and promising therapeutic targets to constrain or prevent lineage plasticity in this setting.