Single-cell fixed RNA profiling uncovers SEMA4D and LMCD1 as therapeutic targets in a liver fibrosis model.

Single-cell fixed RNA profiling (FLEX) is a novel technique that captures RNA expression in frozen tissues at a single-cell resolution. We applied FLEX to mouse model of liver fibrosis progression and regression to identify novel antifibrotic targets. Mice were administered intraperitoneal thioacetamide for 10 weeks to induce fibrosis, regression was assessed 2 weeks after cessation. The livers were fixed, dissociated, and analysed using FLEX. Molecular validation included immunoblotting, immunohistochemistry, gene silencing/overexpression, cytokine/phosphokinase arrays, and human liver samples. Approximately 40,000 liver cells were profiled, integrated, and annotated into 10 major cell types using lineage-specific markers. Pericentral signature restoration in hepatocytes, scar-resolving genes (Mmp14 and Ctsl), fenestrae restoration in liver sinusoidal endothelial cells, anti-inflammatory Kupffer cells, reduced fibrogenic cholangiocytes, and recovery-associated immune cell subsets were observed. During fibrosis, monocyte-derived macrophages secrete semaphorin-4D (SEMA4D), which binds to Plexin B2 on hepatic stellate cells (HSCs). SEMA4D+ cells were upregulated in mouse fibrotic livers (n = 6, p <0.05). Recombinant SEMA4D induces type I collagen in HSCs, whereas humanised monoclonal IgG4 SEMA4D blockade (VX15/2503) attenuates fibrosis in vivo (n = 5, p <0.05). LIM and cysteine-rich domains 1 (LMCD1) was enriched in fibrotic HSCs and suppressed during regression. LMCD1 knockdown reduced the expression of fibrotic protein, while LMCD1 overexpression promoted the expression of fibrotic protein via AKT/mTOR signalling. LMCD1 and SEMA4D are localised in the fibrotic septa and are correlated with the fibrotic stage of MASLD (n = 34, p <0.05) and HCV (n = 76, p <0.05) in humans. This FLEX-based single-cell atlas revealed critical transcriptional programs and cell-cell interactions, identifying SEMA4D and LMCD1 as promising therapeutic targets for liver fibrosis. In this study, we applied a novel technique, single-cell fixed RNA profiling, to profile 38,136 cells obtained from control, thioacetamide-induced liver fibrosis, and regression-phase mouse livers, generating a high-resolution atlas of liver fibrosis progression and regression. We identified the transcriptomic patterns of regressed cell subpopulations and uncovered two key therapeutic targets: the macrophage-derived factor semaphorin-4D (SEMA4D) and the hepatic stellate cell-specific transcription factor LIM and cysteine-rich domains 1 (LMCD1). Treatment with a humanised monoclonal IgG4 antibody against SEMA4D significantly alleviated liver fibrosis in the thioacetamide-induced mouse model. SEMA4D and LMCD1 expression correlated with the metabolic dysfunction-associated steatotic liver disease-related fibrosis stage, and the attenuation of SEMA4D and LMCD1 after HCV-sustained virologic response reduced the risk of progression to hepatocellular carcinoma.