Abstract A051: Integrative Single-Cell and Spatial Transcriptomics Reveal Metabolic Reprogramming and Spatiotemporal Transition of Macrophages Driving Immune Suppression in Head and Neck Cancer

Abstract Introduction: Metabolic heterogeneity in head and neck squamous cell carcinoma (HNSCC) remains poorly characterized, limiting our understanding of how metabolic reprogramming shapes tumor progression and the tumor microenvironment (TME). Here, we aimed to elucidate the interplay between metabolic programs and immune evasion mechanisms in HNSCC. Methods: We performed an integrative analysis of transcriptomic data from nine independent HNSCC cohorts using pathway-level metabolic profiling. Findings were validated and expanded using single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics to map cellular trajectories and cell-to-cell interactions within the TME. Results: Consensus clustering identified three distinct metabolic subtypes (MS1–3), with MS3 characterized by the selective activation of glycan-related pathways and significantly poorer clinical outcomes. scRNA-seq analysis revealed that these glycan-related pathways were predominantly activated in tumor-infiltrating macrophages, which exhibited enhanced lysosomal and phagocytic activities. Trajectory analysis uncovered a spatiotemporal transition of monocyte-driven macrophages during HNSCC progression: initiating from FCN1+ monocyte-like cells, passing through intermediate states, and culminating in APOE+ lipid-associated macrophages (LAMs). Notably, this macrophage evolution closely mirrored stepwise tumor progression, where transitional precursors exhibiting glycan degradation activity emerged from early stages. Spatially, distinct architectures were observed: while monocyte-like cells resided near epithelial-like tumor cells, the evolved LAMs preferentially infiltrated the niche surrounding tumor cells exhibiting mesenchymal-like features. Within this niche, ligand-receptor interaction analysis demonstrated that these metabolically reprogrammed macrophages establish an immune-suppressive and pro-metastatic microenvironment through intercellular crosstalk with adjacent tumor fibroblasts and T cells. Conclusion: Collectively, our findings elucidate the metabolic reprogramming and spatiotemporal transition of tumor-associated macrophages, where the differentiation toward a lipid-associated phenotype promotes an immune-suppressive microenvironment enriched with mesenchymal-like tumor cells. These results suggest that targeting the metabolic vulnerabilities and specific interactions of these macrophages offers a novel therapeutic strategy to halt HNSCC progression. Citation Format: Ji-Hye Choi, Hyo Jung Kim, Bok-Soon Lee, Jin Roh, Hyun Goo Woo, Chul-Ho Kim. Integrative Single-Cell and Spatial Transcriptomics Reveal Metabolic Reprogramming and Spatiotemporal Transition of Macrophages Driving Immune Suppression in Head and Neck Cancer abstract. In: Proceedings of the AACR Immuno-Oncology Conference (AACR IO): Discovery and Innovation in Cancer Immunology: Revolutionizing Treatment through Immunotherapy; 2026 Feb 18-21; Los Angeles, CA. Philadelphia (PA): AACR; Cancer Immunol Res 2026;14(2 Suppl):Abstract nr A051.