Baseline spatial tumor microenvironment states to define response and primary resistance to immune checkpoint inhibition in recurrent/metastatic head and neck squamous cell carcinoma.

Abstract

6068 Background: Despite the clinical impact of immune checkpoint inhibitors (ICIs) in recurrent/metastatic head and neck squamous cell carcinoma (R/M HNSCC), durable benefit is limited to a minority of patients and robust predictive biomarkers are lacking. PD-L1 combined positive score incompletely captures response heterogeneity, likely due to the spatial complexity of the tumor microenvironment (TME). We used spatial transcriptomics to identify baseline TME architectures associated with ICI response. Methods: Pre-treatment primary tumor samples from 12 patients with R/M HNSCC treated with ICIs were profiled using high-resolution spatial transcriptomics (Xenium In Situ, 10x Genomics; 380-gene immuno-oncology panel). Exceptional responders (ER) were defined by progression-free survival (PFS) ≥20 months, while poor responders (PR) had PFS ≤3 months. Differential gene expression and Gene Ontology (GO) enrichment were integrated with cell-type–resolved analyses to map transcriptional programs to cellular compartments. Results: Distinct baseline TME architectures separated ER and PR. ER tumors showed coordinated upregulation of interferon-related and immune activation genes (STAT1, MX1, CD274) together with cell-cycle-associated genes (MKI67, CDK1). Functional enrichment highlighted immune signaling, chemokine-mediated recruitment, and vascular remodeling, consistent with an immune-inflamed and spatially permissive microenvironment. In contrast, PR tumors exhibited dominant fibroblast-driven extracellular matrix and inflammatory programs, with enrichment of FN1, SPARC, LUM, VCAN and IGFBP7. GO enrichment in PR highlighted integrin-mediated processes, PDGFR-centered signaling, TGF-β–related pathways, and platelet-related signaling programs. Cell-type–resolved spatial mapping showed that fibroblast/ECM programs in PR were predominantly localized to fibroblast-enriched stromal compartments, whereas interferon-response programs in ER were distributed across both tumor and immune compartments. Conclusions: Baseline spatially organized TME states are associated with ICI outcomes in R/M HNSCC. ER exhibit an interferon-enriched, immune-permissive architecture, whereas primary resistance is linked to a fibroblast-dominated, ECM-rich and immune-restrictive niche. Proteomic validation of key spatial signals is ongoing to prioritize candidate predictive biomarkers for evaluation in a larger cohort. Enrichment of integrin-mediated processes and PDGFR-centered signaling in PR highlights actionable stromal vulnerabilities warranting translational investigation.