Spatial Atlas of Small Cell Lung Carcinoma Reveals Intratumoral Tumor-State Heterogeneity and an MMP12+ Macrophage Niche.

Small-cell lung carcinoma (SCLC) is a highly aggressive tumor with a dismal prognosis among lung cancers. Treatment is failing because of primary or rapidly developing secondary resistance. Recent molecular studies have suggested four SCLC subtypes with unique therapeutic vulnerabilities-ASCL1, NEUROD1, POU2F3, and YAP. These subtypes still distinguish themselves by considerable intra-tumoral heterogeneity and the influence of the microenvironmental context, which are both considered to be responsible for treatment resistance. We integrated in situ hybridization-based spatial transcriptomics with histological and protein-expression analyses of 18 specimens, comprising 16 SCLCs, one atypical carcinoid, and one normal lung specimen. Systematic case-by-case analysis revealed multiple coexisting tumor states, including neuroendocrine and non-neuroendocrine components, regional hypoxic states, and case-specific FABP7-positive and loss-of-chromosome-Y-associated populations. Integrative transcriptome clustering, copy number estimation, and exploratory trajectory analysis revealed transcriptional relationships among spatially coexisting tumor states, including phenotypically distinct tumor components with molecular features consistent with close clonal relationships in selected heterogeneous tumors. Furthermore, we identified immune signatures and uncovered a previously unrecognized MMP12-positive tumor-associated macrophage population, enriched at the tumor interface and spatially associated with necrotic and hypoxic regions. In vitro co-culture experiments further showed that direct contact with SCLC cells increased MMP12 expression in macrophages, with hypoxia further enhancing its expression under specific conditions. Together, our study delineates the complex spatial architecture of SCLC by defining specific cellular programs and adjacent immune phenotypes that provide an organizational framework for understanding its marked intratumoral heterogeneity.