Spatial Transcriptomics of Primary and Metastatic ALK-Rearranged NSCLC Reveals Site-Specific Adaptations and Prognostic Signatures Authors

We used spatial transcriptomics to analyze tumor and stromal compartments from 16 archival tumor samples: primary lung (LT, n=3), lymph node (LNT, n=10), and brain metastases (BT, n=3), alongside 3 site-matched non-tumor controls. Result Gene expression varied significantly by anatomical site and compartment. The LNT microenvironment was enriched with fibroblasts and macrophages, while its tumor compartment showed significant neutrophil enrichment.

Concurrently, BT had higher stromal M2-macrophage markers. Functionally, tumor cells universally centered on 'Translation' and the TME on 'Extracellular Matrix Organization. Tumor cells evolved distinctly during metastasis; LT cells focused on protein synthesis, while those in LNT shifted to senescence and epigenetic remodeling, and those in the BT uniquely activated GPCR, chemokine, and drug metabolism pathways.

Prognostic signatures were site-dependent: survival in LNT correlated with a protective TME marked by B-cell signatures (CD79A), TCR/BCR signaling, and immune response, while high risk was linked to olfactory signaling and stromal MET activation. In contrast, poor outcomes in the BT were associated with complement activation and stress response pathways, while survival was linked to tumoral FGFR1/FGFR2 signaling. Conclusion This study delineates the site-specific molecular evolution of ALK+ NSCLC, demonstrating that therapeutic strategies must account for the unique biology of each metastatic niche.