From a Multi-Omics Signature to a Therapeutic Candidate: Computational Prediction and Experimental Validation in...

Background: Advanced liver fibrosis (LF) is a major determinant of prognosis across chronic liver diseases. Current biomarkers are often etiology-specific and lack cross-cohort robustness. Shared molecular drivers across etiologies remain incompletely defined, and effective anti-fibrotic therapies are limited. Methods: We developed a multi-algorithm consensus machine-learning framework to derive a robust LF progression signature. In the training non-alcoholic fatty liver disease (NAFLD) cohort GSE213621 (n = 368), samples were formulated as a binary classification task (mild fibrosis, F0-F2; advanced fibrosis, F3-F4). Candidate genes were screened in parallel using Boruta, Least Absolute Shrinkage and Selection Operator (LASSO), random forest, and eXtreme Gradient Boosting (XGBoost). Genes selected by at least two algorithms were defined as a high-consensus pool, and genes consistently selected by all four algorithms were prioritized to construct a core signature. Model performance was evaluated by stratified cross-validation in the training cohort and externally validated in four independent cohorts of different etiologies (GSE49541, GSE84044, GSE130970, and GSE276114). Cellular sources of signature genes were characterized using single-cell RNA sequencing (scRNA-seq) datasets GSE136103 (human) and GSE172492 (mouse). For therapeutic discovery, the high-consensus expression profile was queried against the Connectivity Map (CMap) to prioritize compounds predicted to reverse the fibrotic transcriptional program. Withaferin A (WFA) was selected for experimental validation in a carbon tetrachloride (CCl₄)-induced mouse LF model and in the transforming growth factor-β1 (TGF-β1)-stimulated human hepatic stellate cell line LX-2. Bulk liver RNA-seq profiling was performed to interrogate WFA-associated molecular changes in vivo. Results: We identified a six-gene signature (CLEC4M, COL25A1, ITGBL1, NALCN, PAPPA, and PEG3) that discriminated advanced from mild fibrosis, achieving a mean AUC of 0.890 in internal cross-validation and an average AUC of 0.864 across external validation cohorts. scRNA-seq analysis revealed cell-type-specific expression with prominent enrichment in fibroblast populations. In vivo, WFA markedly attenuated CCl₄-induced fibrosis (p < 0.05) and reversed 1314 fibrosis-associated differentially expressed genes (adjusted p < 0.05), which were enriched in fatty acid metabolism and PPAR signaling, as well as extracellular matrix (ECM)-receptor interaction and focal adhesion (adjusted p < 0.05). In vitro, WFA suppressed TGF-β1-induced LX-2 activation, reducing α-SMA and Fibronectin expression (p < 0.05). Conclusions: We report a six-gene signature that robustly predicts advanced LF across etiologies, define its cellular context using single-cell atlases, and validate the anti-fibrotic activity of WFA in both in vivo and in vitro models. Bulk liver RNA-seq and cellular evidence further suggest that WFA-associated effects are linked to lipid metabolic programs, ECM remodeling, and attenuation of hepatic stellate cell activation.