Abstract 5265: Single cell and spatial analysis unravels the immunosuppressive tumor microenvironment, HPV-associated features, and potential immunotherapy response in vulvar squamous cell carcinoma

Abstract Vulvar squamous cell carcinoma (VSCC) is a rare gynecological cancer with a projection of a 35% increase in the next 20 years in North America. HPV is a known risk factor in VSCC, but HPV+ and HPV- subtypes of VSCC have previously been reported to be biologically but not clinically distinct. In addition, VSCC could be categorized by HPV and TP53 status with different prognoses. However, the VSCC tumor microenvironment (TME) and its contributions to patient clinical outcomes are not well understood. Here, we use single-cell and spatial omics to interrogate VSCC TME transcriptional and cellular heterogeneity as a foundation for understanding the tumor, stromal, and immune cell compartments of HPV+ and HPV-VSCC. Our integrated bioinformatics analysis of 8 scRNA-seq samples (5 HPV+ and 3 HPV-) from vulvar cancer patients identified diverse stromal and immune compartments with immunosuppressive features (high presence of Tregs, pro-tumoral macrophages and myofibroblasts) presenting “immunologically cold” tumor phenotypes. In addition, we identified HPV+ epithelial cells and analyzed HPV-associated cell-cell interactions. Furthermore, we used scRNA-Seq gene signature to deconvolute a bulk 800-gene dataset from an independent patient cohort of 48 samples with different HPV subtypes, including integrated and beta-HPV, to identify TME features associated with different HPV risk subtypes. Bioinformatics deconvolution results showed a new way to subtype VSCC, including a subset of “immunologically hot tumors” (increased CD8 T cells and dendritic cells) with high expression of known and emerging immunotherapy response markers (PD-L1 high, CXCL9 high). Lastly, we integrate scRNA-Seq with patient-matched spatial transcriptomics to identify cellular neighborhood and Ligand-Receptor interactions that may be associated with HPV, subtypes, and clinical outcomes. This study reports a comprehensive single-cell and spatial VSCC TME atlas, highlighting the immunosuppressive features of the TME, differences between HPV+ and HPV- samples, and identification of a subset of patients with “immunologically hot” tumors that may respond favorably to immunotherapy. These findings provide a foundation and resource to further study VSCC TME in both HPV+ and HPV- subtypes. Future studies include validating and studying potential biomarkers of clinical outcomes and immunotherapeutic targets of VSCC treatment. Citation Format: Athena Golfinos-Owens, Taja Lozar, Evie Carchman, Paul F. Lambert, Megan Fitzpatrick, Huy Q. Dinh. Single cell and spatial analysis unravels the immunosuppressive tumor microenvironment, HPV-associated features, and potential immunotherapy response in vulvar squamous cell carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 5265.