Spatial proteomics profiling reveals oncogene-specific immune niches and prognostic markers in NSCLC

Only subset of patients with Non-Small Cell Lung Cancer (NSCLC) benefit from immunotherapy and this is partly due to limited understanding of how oncogenic mutations shape the tumor microenvironment (TME).

To define how EGFR and KRAS mutations influence the spatial organization and immune composition of the NSCLC TME.

We conducted 38-marker high-plex immunofluorescence to 197 NSCLC tumors (>2 million cells) stratified by EGFR and KRAS genotypes. Quantitative phenotyping and spatial analyses, including cellular neighborhoods (CN), nearest neighbors (NNs = 5-20), and spatial proximity profiling (25-100 μm), were performed to assess immune architecture and clinical correlations.

EGFR- and KRAS-mutant tumors showed higher tumor cell density and reduced immune infiltration compared with wild-type tumors. Both mutation types were associated with depletion of cytotoxic T cells, dendritic cells, and granulocytes, while EGFR-mutant tumors showed enrichment of M2-like tumor-associated macrophages (TAMs). CN-analysis identified 14 spatial clusters, with reduced cytotoxic and helper T cell-rich neighborhoods in mutant tumors. NN-analysis revealed shorter distances between M2-like TAMs in EGFR-mutant tumors and greater immune exclusion in non-mutants. Spatial proximity revealed higher densities of T-regs, TAMs near tumor cells in KRAS-mutant tumors. All spatial metrics correlated significantly with prognosis in Cox proportional hazards models, highlighting immune cell positioning as an important predictor of outcome.

EGFR- and KRAS-mutant tumors remodel the NSCLC immune landscape, creating distinct immunosuppressive and immune-excluded niches. Spatial proteomics reveals prognostic immune architectures that may guide mutation-directed immunotherapy strategies.