Defining and overcoming lineage plasticity in lung cancer

Icahn School Of Medicine At Mount Sinai, New York NY

Investigators

Abstract

SUMMARY Neuroendocrine (NE) transformation in lung adenocarcinoma (LUAD) is a lethal mechanism of resistance that is without effective treatment or prevention options. Due to a lack of cell-level resolution, preclinical models, and the limited availability of matched clinical specimens, factors underlying this lineage plasticity (LP) from LUAD to more aggressive small cell lung cancer (SCLC) are largely unknown. Our preliminary studies showed that several hallmarks of SCLC appear critical to initiating the process of NE transformation, including RB1 and TP53 loss and downregulation of NOTCH signaling. We further demonstrate the role of NOTCH-driven upregulation of lineage-determining transcription factors (LDTFs) in NE transformation in lung cancer clinical samples. Our objective is to systematically uncover core mechanisms facilitating LP in EGFR-mutant lung cancer. The long- term goal of this application is to develop therapeutic strategies to reverse or prevent LP as a mechanism of acquired resistance. Our overarching hypothesis is that in EGFR-mut LUAD, RB1, and TP53 loss, specific molecular alterations (e.g., EZH2 induction) drive LP through reprogramming of NOTCH signaling and upregulation of LDTFs (such as POU3F2, FOXN4, ONECUT2). In Aim 1, we will assess the epigenetic and transcriptional changes in EGFR-mutant LUAD before, during, and after SCLC transformation in clinical samples. We will assess genetic, transcriptomic, and epigenomic changes in pre-transformed LUAD and transformed SCLC clinical samples (matched and unmatched) at single-cell resolution (scRNAseq, snRNAseq, ATACseq). Furthermore, we will assess the dynamic changes of NOTCH pathway regulators, and LDTFs in EGFR-mutant lung cancer. In Aim 2, we will determine the role of NOTCH signaling and key transcriptional regulators in promoting LP and acquired resistance to EGFR-TKIs in preclinical models. We will establish the functional interplay of NOTCH signaling and LDTFs (POU3F2, FOXN4, ONECUT2) in LP from LUAD to T-SCLC. We will (1) comprehensively assess the genetic, transcriptomic, epigenomic, and proteomic changes driving LP in multiple preclinical models of pre-T LUAD and post-T SCLC at single-cell resolution; (2) model LP in PDX models to investigate the consequences of NOTCH inhibition on TF upregulation and vice versa, and (3) assess the effect on resistance to EGFR-TKIs. In Aim 3, we will establish the therapeutic potential of targeting EZH2 in LUAD to T-SCLC transition. In this aim, we will leverage our established transformation models to assess the role of EZH2 in (1) promoting LP and therapy resistance in EGFR-mutant pre-transformation models; (2) establishing the therapeutic strategy of targeting EZH2 to delay or reverse LP, suppressing neuroendocrine differentiation and therapy resistance in therapy-resistant post transformation models. This proposal will be conducted by a multidisciplinary team and will enhance our understanding of tumor evolution, and cell identity, and identify new therapeutic approaches to target LP. These are critical steps towards improving the detection, treatment, and mortality of patients with lung cancer developing treatment resistance.