Multimodal single-cell network analysis uncovers BSG/CD147 as an early biomarker and signaling hub in hepatocellular carcinoma

Background Hepatocellular carcinoma (HCC) is a leading cause of cancer-related mortality worldwide, largely due to late-stage diagnosis and the limited sensitivity of current biomarkers such as α-fetoprotein (AFP). Early detection requires molecularly defined targets that capture the initial steps of malignant transformation. Single-cell RNA sequencing (scRNA-seq) offers high-resolution insight into tumor heterogeneity and lineage progression to enable the identification of early biomarkers. This study aimed apply scRNA-seq analysis to detect clinically important molecular patterns that define the early stages of malignant transformation in HCC and facilitate the diagnosis of small or ambiguous lesions. Methods Two independent scRNA-seq datasets (GSE149614 and GSE189903) comprising non-tumor and HCC tissues were analyzed. Following batch correction and clustering, hepatocyte subpopulations were characterized by differential expression, pseudotime, and CytoTRACE analyses to reconstruct the trajectory from normal to malignant states. High-dimensional weighted gene co-expression network analysis (hdWGCNA) was used to identify stage-associated modules, while CellChat and protein-protein interaction analyses delineated intercellular signaling networks. Target expression was validated in paired human liver specimens using quantitative immunofluorescence. Results scRNA-seq revealed a continuum of hepatocyte states characterized by progressive stemness and oncogenic pathway activation (MYC, E2F, G2M). Module Hep-M20 exhibited the strongest correlation with tumor stage and identified BSG/CD147 as a central hub gene with monotonic upregulation along pseudotime and strong correlation with stemness potential. CellChat analysis uncovered a cyclophilin (PPIA/PPIB)-dependent tumor-stroma signaling axis that positions BSG/CD147 as the key mediator for intercellular communication between tumor hepatocytes, fibroblasts and T cells. Ex vivo validation confirmed significantly higher BSG/CD147 protein expression in HCC versus background liver (P = 2.9×10⁻ ¹¹ ) with excellent diagnostic accuracy (AUC = 0.93–0.96; sensitivity 86–87%; specificity 93–97%) including in lesions < 2 cm that are frequently indeterminate on conventional imaging. Conclusions This study establishes BSG/CD147 upregulation as an early molecular event in hepatocarcinogenesis that integrates hepatocyte dedifferentiation, microenvironmental signaling, and tumor progression. Strong and specific expression in small lesions < 2 cm underscores potential as a precision biomarker and imaging target for early HCC detection, risk stratification, and therapeutic development.