Transcriptional Profiling Reveals Mesenchymal Subtypes of Small Cell Lung Cancer with Activation of the Epithelial-to-Mesenchymal Transition and Worse Clinical Outcomes

Abstract

Simple Summary The aim of this study is to discover and characterize novel small cell lung cancer (SCLC) subtypes and further identify their relationship with existing SCLC subtypes. We identified SCLC-M (mesenchymal) tumors as SCLC subtypes that are distinctive of SCLC-I (inflamed) tumors. SCLC-M tumors showed elevated epithelial-to-mesenchymal transformation (EMT) activity but a low level of anticancer immune activity also with unfavorable clinical outcomes. Gene expression- and immunohistochemistry-based prediction suggests that SCLC-M tumors comprise approximately 5% of primary SCLC tumors. Given these unique molecular and clinical features, SCLC-M tumors should be taken into account in the clinical settings of SCLC management. While molecular subtypes of small cell lung cancers (SCLC) based on neuroendocrine (NE) and non-NE transcriptional regulators have been established, the association between these molecular subtypes and recently recognized SCLC-inflamed (SCLC-I) tumors is less understood. In this study, we used gene expression profiles of SCLC primary tumors and cell lines to discover and characterize SCLC-M (mesenchymal) tumors distinct from SCLC-I tumors for molecular features, clinical outcomes, and cross-species developmental trajectories. SCLC-M tumors show elevated epithelial-to-mesenchymal transformation (EMT) and YAP1 activity but a low level of anticancer immune activity and worse clinical outcomes than SCLC-I tumors. The prevalence of SCLC-M tumors was 3.2-7.4% in primary SCLC cohorts, which was further confirmed by immunohistochemistry in an independent cohort. Deconvoluted gene expression of tumor epithelial cells showed that EMT and increased immune function are tumor-intrinsic characteristics of SCLC-M and SCLC-I subtypes, respectively. Cross-species analysis revealed that human primary SCLC tumors recapitulate the NE-to-non-NE progression murine model providing insight into the developmental relationships among SCLC subtypes, e.g., early NE (SCLC-A and -N)- vs. late non-NE tumors (SCLC-M and -P). Newly identified SCLC-M tumors are biologically and clinically distinct from SCLC-I tumors which should be taken into account for the diagnosis and treatment of the disease.