Spatial proteomic profiling reveals conserved prognostic immune microenvironment features across molecular subtypes in small cell lung cancer

Small cell lung cancer (SCLC) molecular subtypes, defined by neuroendocrine (NE) status and transcription factor (TF) expression, provide insight into tumor biology but fails to fully capture the spatial complexity of the immune microenvironment (IME) and possess limited prognostic power. In this study, we performed an integrative analysis of targeted bulk transcriptomics, spatial proteomics and immunohistochemistry (IHC) with extensive multiregional sampling across central tumor (CT), invasive margin (IM), and peri-tumoral (PT) compartments in treatment-naïve formalin-fixed, paraffin-embedded SCLC samples to investigate the IME heterogeneity and its clinical significance across molecular subtypes. Targeted bulk transcriptomics of immune gene panel identified two major immune groups, immune-hot group (IHG) and immune-cold group (ICG), which are associated with NE status but independent of TF subtypes and showed limited prognostic value. In contrast, spatial proteomic profiling revealed profound spatial immune heterogeneity within individual tumors, and identified immune activation specifically within the CT as a dominant and independent prognostic biomarker that transcends traditional NE and TF subtypes. IHG-CT tumors, characterized by enriched cytotoxic T cells, activated antigen presentation, and myeloid engagement, were significantly associated with improved survival outcomes, whereas immune heterogeneity in the IM and PT regions did not correlate with survival outcomes, as validated by IHC. Additionally, the IHG status was associated with clinical benefit from immune checkpoint blockade. Collectively, our study highlights the importance of spatial context for understanding clinically relevant IME features, and provides a transformative spatially informed framework for SCLC patient stratification and therapeutic development.