Transcriptional Circuitry of NKX2-1 and SOX1 Defines an Unrecognized Lineage Subtype of Small Cell Lung Cancer.

Rationale : The current molecular classification of small cell lung cancer (SCLC) based on expression of four lineage transcription factors still leaves its major subtype SCLC-A as a heterogeneous group, necessitating more precise characterization of lineage subclasses. Objectives : To refine the current SCLC classification with epigenomic profiles and to identify features of the re-defined SCLC subtypes. Methods : We performed unsupervised clustering of epigenomic profiles on 25 SCLC cell lines. Functional significance of NKX2-1 was evaluated by cell growth, apoptosis and xenograft using CRISPR-Cas9-mediated deletion. NKX2-1 specific cistromic profiles were determined by ChIP-seq and its functional transcriptional partners were determined using co-immunoprecipitation followed by mass-spectrometry. Rb1 fl/fl Trp53 fl/fl and Rb1 fl/fl Trp53 fl/fl Nkx2-1 fl/fl mouse models were engineered to explore the function of Nkx2-1 in SCLC tumorigenesis. Epigenomic landscapes of 6 human SCLC specimens and 20 tumors from 2 mouse models were characterized. Measurements and Main Results : We identified an epigenomic subcluster of the major SCLC-A subtype: SCLC-Aα and SCLC-Aσ. SCLC-Aα was characterized by the presence of a super-enhancer at the NKX2-1 locus, which was observed in human SCLC specimens and a murine SCLC model. We found NKX2-1, a dual lung and neural lineage factor, is uniquely relevant in SCLC-Aα. Additionally, we found maintenance of this neural identity in SCLC-Aα is mediated by collaborative transcriptional activity with another neuronal transcriptional factor SOX1. Conclusions : We comprehensively describe additional epigenomic heterogeneity of the major SCLC-A subtype, and define SCLC-Aα subtype by the core regulatory circuitry of NKX2-1 and SOX1 super-enhancers and their functional collaborations to maintain neuronal linage state.