Work

1144 Spatially organized cytokine responses in malignant cells predict immunotherapy response

Year: 2026

Type: conference-abstract

Abstract: Background As malignant cells encounter cytokine-producing immune and stromal cells, they generate adaptive responses to evade immune detection that are partially mediated by expression of cytokine receptors; however, the spatial scale of these receptor-mediated responses and their translational relevance remain poorly defined. We hypothesize that cytokine responses within malignant cells are spatially constrained and associated with immunotherapy resistance in squamous cell carcinomas (SCC).Methods We performed CosMx 1000-plex spatial transcriptomics on a head and neck SCC (HNSCC) dataset containing seven oral and larynx tumors (70,736 malignant cells). Malignant, immune, and stromal cells were annotated using reference datasets. Cytokine source cells were annotated by expression of interferon gamma (IFNG) and TGF-beta (TGFB). Cytokine signaling scores within malignant cells were annotated using gene sets. Malignant cytokine scores were calculated as distance from a source cell and an exponential decay curve was generated. We then validated these cytokine decay curves using a publicly available CosMx dataset of 19 cutaneous SCC (cuSCC) tumors with annotated immunotherapy responses.Results The spatial decay of malignant cytokine programs from their source cells was calculated for ISG + macrophages (λ = 37 µm), T effector cells (λ = 51 µm), and TGFB+ fibroblasts (λ = 36 µm) in HNSCC. Pathway analysis of immune-adjacent malignant cells found they were not transcriptionally different compared to other malignant cells except for their cytokine-driven programs. A tumor-aware neighborhood analysis confirmed IFNG-high malignant cells had greatest enrichment in adjacent CD8+ T cells (3.01-fold, p < 0.001) and ISG+ macrophages (2.49-fold, p < 0.001). The pathway analysis of IFNG high cells and cytokine decay curves were validated within the cuSCC dataset. In cuSCC, immune-adjacent malignant cells had significantly increased IFN and MHC-associated pathways in Responders (n = 10) compared to Nonresponders (n = 9) without other significant transcriptional changes. In particular, MHC class I and II antigen presentation within immune-adjacent malignant cells predicted immunotherapy response (AUC = 0.82, 95% CI 0.61–1.00) more strongly than PD-L1 expression (AUC = 0.54).Conclusions Cytokine-induced transcriptional programs operate over spatially restricted niches and there is heterogeneity in both their length and magnitude between tumors. Additionally, the magnitude of these cytokine-driven transcriptional programs within immune-adjacent cells may help predict immunotherapy responses in SCC patients. These findings support a new framework for studying plasticity of malignant cells to local immune and stromal signaling in the tumor microenvironment.Ethics Approval This study was approved by the Stanford University Institutional Review Board under protocols IRB-59070 and IRB-53304 (for trial participants) and IRB-77725 (for non-trial patient samples). All participants provided written informed consent before any study-related procedures were performed, including the retrieval of archived tissue specimens for research purposes.

Source: Journal for ImmunoTherapy of Cancer

DOI: 10.1136/jitc-2026-sitc2026.1144