Project 2 - Epigenetic Drivers of Lineage Plasticity in Lung Cancer

Dana-Farber Cancer Inst, Boston MA

Investigators

Abstract

PROJECT SUMMARY (Project 2) Lung cancer remains the leading cause of cancer death worldwide and can be divided into distinct histological subtypes including lung adenocarcinoma (LUAD) and small cell lung cancer (SCLC). Lineage plasticity is an emerging mechanism of resistance to targeted therapies in lung cancer, yet the mechanisms that drive this are largely unknown. It is thus fundamentally important to understand how SCLC/LUAD lineage plasticity is regulated within the autochthonous lung tumor immune microenvironment. To study the role of the epigenetic modifier EED in SCLC tumorigenesis, we used a CRISPR/Cas9-based approach to develop SCLC genetically engineered mouse models (GEMMs), where EED was simultaneously inactivated at tumor initiation in the lung. Strikingly, EED deletion results in complete histological transformation from SCLC to LUAD in nearly all mice, with only a small percentage of mice retaining some degree of SCLC histology. Moreover, EED inactivation in SCLC cell lines in vitro was not sufficient to induce complete SCLC to LUAD lineage plasticity, suggesting that non-cell autonomous mechanisms contribute to this phenotype in vivo. Based on these data, we hypothesize that SCLC to LUAD histological transformation after EED inactivation requires both tumor cell intrinsic de-repression of EED target genes and selection by tumor cell extrinsic mechanisms. Specifically, we hypothesize that EED normally binds and directly represses key LUAD lineage oncogenes, and that EED inactivation primes for SCLC to LUAD lineage plasticity by de-repressing these key LUAD lineage oncogenes. We will interrogate this hypothesis in aim 1 by combining ChIP-seq, RNA-seq, and functional genomics experiments, aided by the deep expertise in these methods and analyses of our wider P01 team. Since de-repression of this epigenetic program alone is not sufficient for full SCLC to LUAD histological transformation, we hypothesize that full histological transformation requires further selection by extrinsic stimuli from the tumor microenvironment (TME). We hypothesize that the TME provides ligands to stimulate receptor tyrosine kinases that drive LUAD oncogenic signaling. Moreover, EED inactivation promotes MHC-I antigen presentation that normally causes immunological rejection and thus we also hypothesize that LUAD lineage oncogenic signaling creates an immunosuppressive TME that permits the development of LUAD in the presence of restored MHC-I antigen presentation after EED inactivation. We will test whether growth factor ligands from the TME and restored tumor cell MHC-I help drive SCLC to LUAD lineage plasticity in aim 2. Together, these studies will deeply dissect how EED restricts the SCLC lung cancer lineage in the contexture of the native tumor immune microenvironment and could inform new therapeutic strategies to intercept this treatment refractory resistance mechanism in lung and other cancer types.