Lineage transcription factors co-regulate subtype-specific genes providing a roadmap for systematic identification of small cell lung cancer vulnerabilities

Abstract

Lineage-defining transcription factors (LTFs) play key roles in tumor cell growth, making them highly attractive, but currently "undruggable", small cell lung cancer (SCLC) vulnerabilities. Delineating LTF genomic binding sites and associated chromatin features would provide important insights into SCLC dependencies. Here we map super-enhancers (SEs) across multiple patient-derived SCLC preclinical models, and find SE patterns are sufficient to classify the models into the recently defined, LTF-based, SCLC subtypes. 3D-chromatin conformation analysis identified genes associated with SEs that define subtype-specific tumor signatures with genes functioning in diverse processes. Focusing on ASCL1-high SCLC (SCLC-A), we found ASCL1 physically interacts with NKX2-1 and PROX1. These factors bind overlapping genomic regions, and co-regulate a set of genes, including genes encoding cell surface proteins, SCN3A and KCNB2 enriched in SCLC-A. Genetic depletion of NKX2-1 or PROX1 alone, or in combinations with ASCL1, did not inhibit SCLC growth more than that achieved by depleting ASCL1 alone. We demonstrate the SE signature supports the LTF classification of SCLC, identify NKX2-1 and PROX1 as ASCL1 co-factors, and substantiate the central importance of ASCL1 as a key dependency factor in the majority of SCLC. The LTF and SE gene sets provide a molecular roadmap for future ASCL1 therapeutic targeting studies.