71 Spatial analysis of tumor microenvironment remodeling during non-small cell lung cancer progression
Year: 2026
Type: conference-abstract
Abstract: Background Spatial organization of the tumor microenvironment (TME) plays a critical role in shaping anti-tumor immunity in non-small cell lung cancer (NSCLC). Here, we performed spatial transcriptomic profiling and multiplex immunofluorescence of early- to late-stage NSCLC to characterize stage-dependent remodeling of the TME. We also show how cellular composition, spatial niches and immune function evolve across disease stages.Methods Visium spatial transcriptomics and COMET multiplex immunofluorescence was applied to NSCLC specimens spanning Stage I, II, and III disease. On BioTuring platform cell type composition was inferred using a Bayesian deconvolution approach (cell2location) with reference single-cell RNA-seq datasets from human NSCLC tumors and adjacent normal tissue. Spatial neighborhoods were defined and clustered into niches using hoodscanR and scNiche based on local cellular composition. Differential gene expression and pathway enrichment analyses were performed to characterize functional changes across stages. Using HORIZON® we analyzed the multiplex IF datasets, performed cellular phenotyping, neighborhood analysis and unbiased cell marker clustering.Results Progression from early to advanced disease was marked by substantial remodeling of cellular composition and spatial organization. Malignant cell fraction increased markedly in late-stage tumors (up to ~46%), accompanied by a loss of normal epithelial populations and disruption of tissue architecture. Immune composition exhibited stage-dependent dynamics: Stage II tumors displayed transient enrichment, whereas Stage III tumors showed a pronounced decline of adaptive immune populations consistent with reduced anti-tumor immunity. No tertiary lymphoid structures (TLS) were observed in Stage III tumor.Spatial niche analysis identified tumor-centric, stromal, immune, and normal epithelial niches. Early-stage tumors exhibited structurally and immunologically complex microenvironments with active tumor–stroma and tumor–immune interfaces. Stage II tumors represented a transitional state with strong but functionally constrained immune engagement. In contrast, Stage III tumors were dominated by tumor-core niches, with collapse of stromal structure. While immune cells were present, these cells lacked activation and effector function. Functional analysis further demonstrated that Stage II tumor-immune niches were characterized by inflammatory signaling and antigen presentation uncoupled from effective immune clearance, whereas Stage III tumors exhibited global suppression of immune recruitment and activation alongside metabolic and mitochondrial adaptations supporting tumor survival.Conclusions Our study reveals a continuum of TME remodeling during NSCLC progression, transitioning from immune-interacting early-stage tumors to immuno-suppressed tumor-dominant late-stage disease. These findings highlight spatial immune suppression and niche reorganization as key features of advanced NSCLC suggestive of strategizing therapies to stage-specific TME states to improve immunotherapy responses.Ethics Approval FFPE blocks with non-small cell lung cancer at various stages were purchased from Avaden biosciences and iSpecimen.
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: gold
Estimated APC paid: $2,490
OpenAlex ID: W7225329808