Spatial organization of HPV-associated immune programs across tissue compartments in oropharyngeal cancer

Background Human papillomavirus (HPV)-positive oropharyngeal cancer (OPC) is characterized by a distinct immune microenvironment; however, the biological significance of immune-related transcriptional programs may vary according to their spatial localization. We investigated the spatial organization of HPV-associated transcriptional programs across anatomically distinct tissue compartments in OPC. Methods An oropharynx-restricted The Cancer Genome Atlas (TCGA)-oropharyngeal squamous cell carcinoma (OPSCC) cohort comprising 77 tumors (51 HPV-positive and 26 HPV-negative) was analyzed using single-sample gene set enrichment analysis (ssGSEA). Spatial transcriptomic profiling using GeoMx Digital Spatial Profiling was evaluated in lymphoid follicular regions (LFRs) and tumor tissue regions (TTRs) from six OPC patients (four HPV-positive and two HPV-negative), with the patient treated as the primary experimental unit. Tumor-free surrounding palatine tonsillar tissue (PTT) was analyzed in an independent microarray cohort comprising 23 HPV-positive and four HPV-negative cases. Eight prespecified immune- and metabolism-related transcriptional programs were evaluated, with additional exploratory cell-type deconvolution and overall survival analyses. Results In TCGA-OPSCC, all five immune-related programs were higher in HPV-positive tumors, and Stem-like, Tpex, B-cell activity, and T-cell activity remained significantly associated with HPV-positive status after adjustment for clinicopathological covariates and FDR correction. In paired GeoMx analyses, all five immune-related programs were higher in LFRs than in TTRs in all six patients, whereas Estrogen Response Early and Estrogen Response Late were higher in TTRs in all six patients (BH-FDR = 0.0357 for each program). Bile Acid Metabolism showed no consistent compartment-specific difference. HPV-associated differences within individual GeoMx compartments and HPV-by-compartment interactions were not statistically significant after FDR correction. In PTT, immune-related and metabolic programs showed directional HPV-associated differences, but none remained significant after FDR correction. Higher scores for several immune-related programs were associated with improved overall survival in univariable TCGA-OPSCC analyses, but these associations were attenuated after accounting for HPV status. Conclusions HPV-associated immune transcriptional programs identified in bulk OPC show consistent spatial organization across lymphoid follicular and tumor tissue compartments. The most robust spatial feature was within-patient compartmentalization between LFRs and TTRs, whereas evidence for HPV-associated differences within individual spatial compartments was limited. These findings emphasize the importance of anatomical context when interpreting transcriptional programs in OPC.