Uncovering Epigenetic and Transcriptional Drivers of Neuroendocrine Plasticity at Single-Cell Level in Patients with Small Cell Lung Cancer Transformation

PROJECT SUMMARY/ABSTRACT Research: In lung adenocarcinoma (LUAD), neuroendocrine (NE) transformation to small cell lung cancer (SCLC) is associated with metastasis and resistance to targeted therapies. This lineage plasticity often leads to LUAD and SCLC admixed in the same tumor. We demonstrated that laser-microdissected LUAD and SCLC

intratumoral components share truncal mutations, confirming NE transformation. SCLC itself is classified as classical, variant, and non-NE subtypes. Preclinical studies demonstrate that variant and non-NE subtypes have increased risk for metastasis and chemoresistance. It is poorly understood what gene regulatory mechanism

drives SCLC transformation and SCLC subtype switching. Single-cell RNA and ATAC sequencing (scRNA-seq, snATAC-seq) in samples of combined LUAD/SCLC histology present an ideal platform to characterize the intratumoral heterogeneity of NE plasticity. As a control reference, we completed scRNA-seq in a cohort of de

novo SCLC (Chan, et al. bioRxiv, under review at Cancer Cell). We performed scRNA-seq in an initial cohort of combined LUAD/SCLC and found significantly increased intratumoral subtype diversity in transformed SCLC (T- SCLC). We found Notch suppression in T-SCLC and reactivation with subsequent SCLC subtype diversification.

We observed overexpressed SOX2 and ELF3 in pre-transformed vs classical LUAD, and PHOX2B and ELF3 in T-SCLC vs de novo SCLC. We hypothesize that under RB1 and TP53 loss, key transcription factors (SOX2, PHOX2B, ELF3), epigenetic regulators, and modulation of Notch signaling all contribute to NE transformation

and subtype diversification. We will leverage scRNA-seq and snATAC-seq in samples of combined LUAD/SCLC histology to 1) identify molecular markers of subclonal populations, 2) reconstruct the regulatory network, and 3) validate transcriptomic and epigenetic drivers of NE plasticity in preclinical in vitro and in vivo models, including

an EGFR+ LUAD patient-derived xenograft undergoing NE transformation after osimertinib treatment. Candidate: Dr. Joseph Chan, MD, PhD is a Medical Oncology Fellow at MSKCC. He aims to become an independent, tenure-track physician-scientist investigating lineage plasticity in metastasis and treatment

resistance in cancer. His mentors Drs. Charles Rudin and Dana Pe’er are leading experts in lung cancer and single-cell sequencing, respectively. Dr. Chan proposes a five-year period of mentored training to acquire wet lab and advanced computational skills. His wet lab training will include 1) single-cell library preparation and 2)

genetic manipulation of preclinical models for functional validation. His computational training will include 1) snATAC-seq analysis and 2) advanced machine learning. His advisory committee—Drs. Charles Sawyers, Helena Yu, Ronan Chaligné, and Christina Leslie—will guide his training and research.

Environment: MSKCC is a cancer center renowned for patient care, innovative research, and training for junior faculty seeking careers as independent physician-scientists. MSKCC houses the Single Cell Research Initiative that advances single-cell sequencing, which will support this proposal for research and career development.