Spatial Transcriptomics reveals core resistance niches distinguishing non-MPR from MPR in NSCLC after neoadjuvant chemoimmunotherapy

Background Neoadjuvant chemoimmunotherapy (nCIT) is increasingly used in NSCLC. Major pathologic response (MPR) is a robust prognostic marker, yet bulk or single‑cell assessments of residual tumor do not capture how spatially heterogeneous TMEs yield non‑MPR. Using FFPE Visium CytAssist spatial transcriptomics, we defined tissue‑scale core resistance niches distinguishing MPR from non‑MPR after nCIT and asked whether these niches delineate spatially targetable compartments. Methods FFPE resections from 10 nCIT‑treated patients were profiled; MPR status followed IASLC criteria. Blocks were selected by residual tumor burden (MPR 5-10%; non‑MPR 70-90%). We compared global programs (DEG, GSEA/Reactome, cell‑cycle), inferred cell composition (cell2location), analyzed context‑specific ligand-receptor and metabolic states, and spatially mapped resistance axes (DDR, NRF2/ferroptosis, MDR/ABC) and TACSTD2 (TROP2). Results Non‑MPR activated cell‑cycle/transcription/DNA‑repair programs and showed a proliferative landscape, whereas MPR was ECM/immune‑enriched and quiescent. Deconvolution mapped deep T‑cell/myeloid infiltration into MPR cores/borders, while non‑MPR cores remained epithelial‑dense. Ligand-receptor mapping showed immune‑recruiting ECM-integrin/syndecan and CX3CL1-ITGAV at MPR boundaries but LGALS9-HAVCR2, MIF-CD74, and TIMP1-CD63 within non‑MPR cores, extending into peritumor tissue. Non‑MPR exhibited hyper‑metabolic, antioxidant‑buffered states (glycolysis, OXPHOS/TCA, glutathione), with differences attenuating in cancer‑only analyses, implicating TME contribution; resistance axes were higher in non‑MPR and formed contiguous core hotspots. TROP2 was core‑enriched in a subset and often overlapped NRF2/MDR‑high niches with low signal in adjacent non‑tumor, although TROP2‑independent resistant cores were also observed. Conclusion Spatial transcriptomics defined non‑MPR by a core‑centered, resistance‑rich TME that is proliferative, immune‑suppressive, and metabolically flexible, contrasting with the immune‑permissive, quiescent landscape of MPR. Dismantling core resistance niches, restoring immune access, and tempering metabolic buffering emerge as organizing principles for overcoming residual disease. TROP2‑aligned cores represent a compartment‑selective subset, whereas TROP2‑independent cores argue for complementary strategies.