Spatial mapping of the lung cancer ecosystem reveals distinct patterns of intratumoral and internodular heterogeneity

The spatial organization of malignant and non-malignant cells within the tumor microenvironment critically influences tumor evolution and therapeutic response. However, the architecture of micro-niches remains incompletely understood. Leveraging Xenium-based spatial transcriptomics, we comprehensively mapped the spatial ecosystem of an orthotopic murine lung cancer model, identifying distinct spatial domains that form unique, organized cellular neighborhoods. These domains cluster into three major communities: (1) non-tumoral regions that recapitulate canonical normal lung structures; (2) a heterogeneous peri-tumoral region composed of spatial domains characterized by mesenchymal remodeling, active immune checkpoint signaling, and immunosuppressive myeloid populations; and (3) intra-tumoral regions that reveal marked tumor nodule heterogeneity, with unique tumor-specific domains exhibiting hallmark cancer pathways. Furthermore, our analytic approach was applicable to human lung cancer tissue. Here, we show that spatial domain analysis resolves tumor nodules into biologically distinct subtypes defined by domain composition, hallmark cancer programs and intercellular communication patterns within the tumor microenvironment.