Single-cell profiling of tumor lineage plasticity and the immune microenvironment in transformed small cell lung cancer

Background The transformation of non-small cell lung cancer (NSCLC) into small cell lung cancer (SCLC) is a recognized treatment resistance mechanism, most often arising from EGFR-mutant lung adenocarcinoma (LUAD). However, the underlying mechanisms of transformation remain poorly understood. Methods Single-cell RNA sequencing was employed to analyze the tumor cell heterogeneity and to map the intratumoral immune cell landscape of 73,195 cells from five LUAD, three transformed small cell lung cancer (T-SCLC) and four SCLC patients. Multiplex immunofluorescence (mIF) staining and in vitro studies were further conducted to validate the stem-like feature of a malignant cell cluster and the enrichment and the function of interferon-stimulated gene-positive (ISG+) lymphocytes in transformation. Results Although increased intratumoral heterogeneity was observed upon SCLC transformation, a stem-like malignant cell subpopulation was identified to recur across subtypes and groups as the pioneering force of lineage plasticity for SCLC transformation. Further mIF staining and transcription factor analysis validated the stem-like feature. Additionally, tumor immune microenvironment (TIME) analysis revealed that ISG+ T cells and B cells were enriched in T-SCLC. Further cell co-culture analyses disclosed that ISG+ lymphocytes promoted neuroendocrine differentiation in LUAD cells via type I interferons (IFN-Is). Deciphering cell-cell interactions revealed that the stem-like malignant cells might activate and attract ISG+ T cells. Finally, we developed an ISG-associated gene signature that significantly correlates with poor prognosis in LUAD. Conclusion Our findings provide a comprehensive understanding of the lineage plasticity and the immune landscape in T-SCLC, highlighting the crucial role of the stem-like cell cluster and ISG+ lymphocytes in LUAD-to-SCLC transformation. Overall design: Four samples were from treatment-naïve SCLC patients, and three were from T-SCLC patients who had transformed from EGFR-mutant NSCLC following treatments. After resection and biopsy, tumor-tissue samples were immediately transferred for tissue preparation and subjected to single-cell isolation.