1MO Multi-omic characterization of lung tumors identify AKT and EZH2 as potential therapeutic targets in adenocarcinoma-to-squamous transdifferentiation

Abstract

Lineage plasticity, the ability to transdifferentiate among distinct phenotypic identities, contributes to therapeutic resistance in cancer. In lung adenocarcinomas (LUADs), this phenomenon drives squamous cell (LUSC) histologic transdifferentiation in the context of acquired resistance to targeted inhibition of driver mutations, with an up to 9% incidence in EGFR-mutant tumors relapsed on osimertinib, and leads to poor prognosis. Limitations on well annotated pre- and post-transdifferentiation clinical samples has hindered the performance of molecular analyses, and thus little is known about the molecular mechanisms leading to this histological transition. We performed multi-parameter profiling of LUAD-to-LUSC transdifferentiating clinical samples, including 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 data suggest that LUSC transdifferentiation is driven by epigenetic, rather than mutational events, and indicate that the transdifferentiated LUSC tumors retain transcriptomic and methylation profiles of their previous LUAD state. We observed coordinated upregulation of PI3K/AKT, MYC and PRC2 pathway genes upon transdifferentiation. Concurrent activation of PI3K/AKT and MYC overexpression induced squamous features in EGFR-mutant LUAD preclinical models, further accentuated by EGFR inhibition. Pharmacologic inhibition of EZH1/2 or PI3K/AKT in combination with osimertinib delayed relapse and squamous transdifferentiation in an EGFR-mutant patient-derived xenograft model, and re-sensitized resistant transdifferentiated LUSC tumors to osimertinib. Here, we provide the first comprehensive molecular characterization of LUSC transdifferentiation and nominate potential therapeutic targets to constrain or prevent lineage plasticity in this setting.