Abstract

Background Cervical squamous cell carcinoma (CSCC) exhibits profound spatial heterogeneity in evolutionary trajectories across distinct tumour foci, yet the underlying mechanisms remain poorly understood. Methods In this study, we performed an integrated spatial transcriptomic and metabolomic analysis of six CSCC and two normal cervical samples, supported by single-cell RNA sequencing (n = 20) and validated in an independent spatial enhanced resolution omics-sequencing cohort (n = 15), to map the spatial tumour architecture and cellular heterogeneity of CSCC. Findings were functionally confirmed using cell lines, patient-derived organoids, and mouse models. Findings We identified that tumour foci with high spatial continuity demonstrated elevated cancer cell purity and exhibited distinct spatial stratification. The peripheral tumour foci (layer 3) exhibited enhanced proliferative capacity and aggressive traits characterised by elevated epithelial-to-mesenchymal transition (EMT) activity compared to core foci (layer 1), which correlated with advanced evolutionary states. A layer 3-specific gene signature predicted poorer overall survival in both the Cancer Genome Atlas (TCGA) and Tongji Hospital (TJH) cohorts. Spatial multi-omics uncovered progressive metabolic reprogramming along the core-to-periphery axis, with activation of fatty acid degradation emerging as a hallmark of layer 3 aggression. Genetic knockdown ( HADH , HADHA and ECHS1 ) and pharmacological inhibition (mitotane and perhexiline) of fatty acid degradation attenuated malignant phenotypes of layer 3, including proliferation and EMT-driven invasion. Interpretation Our work establishes spatially resolved activation of the fatty acid degradation as a key evolutionary engine fuelling the malignant phenotypes of peripheral tumour foci, and nominates stratification-targeted metabolic disruption as a spatially promising therapeutic strategy for CSCC. Funding Noncommunicable Chronic Diseases-National Scienc