Multi-omics characterization of cellular state diversity and bidirectional tumor-stroma/immune interactions in cervical squamous cell carcinoma

Abstract Cervical cancer ranks as the fourth leading cause of cancer-related deaths among women, with low response rates to immune-checkpoint blockade (ICB). Here we conducted a multidimensional analysis encompassing single-cell RNA-seq (scRNA-seq), spatial transcriptomics, and spatial proteomics, combined with genetic and pharmacological perturbations to systematically develop a high-resolution and spatially-resolved map of intra-tumoral expression heterogeneity in cervical squamous cell carcinoma (CSCC). Three context-specific tumor states (Epithelial-cytokeratin (Epi-Krt), epithelial-immune (Epi-imm) and epithelial senescence (Epi-Sen)) that recapitulate squamous differentiation substantially alter the tumor immune microenvironment (TIME). Bidirectional interactions between Epi-Krt malignant epithelial cells and MMP11+ CAF form an immune exclusionary microenvironment through TGFβ pathway signaling mediated by FABP5. Epi-Imm malignant epithelial cells and NK/T cells interact bidirectionally through interferon signaling. Notably, preliminary analysis of the NACI clinical trial (NCT04516616) demonstrated neoadjuvant chemotherapy (NACT) induce a state transition to Epi-Imm with the extent of this transition being associated with pathological complete remission (pCR) to subsequent ICB treatment. These findings provide a comprehensive and nuanced understanding of cellular state diversity and have significant implications for developing novel therapeutic strategies in CSCC and potentially other squamous cancers.