Integrating multi-omics and machine learning systematically deciphers cellular heterogeneity and fibrotic regulatory networks in the progression from MASLD to MASH

Abstract

The progression from metabolic dysfunction-associated steatotic liver disease (MASLD) to metabolic dysfunction-associated steatohepatitis (MASH) is a critical link leading to cirrhosis and hepatocellular carcinoma. Yet the responsible cellular programs remain unclear. We integrated public single-cell, spatial, and bulk transcriptomic datasets to map microenvironmental remodeling and regulatory networks during MASLD-MASH progression. Among the seven major liver cell types identified, monocytes/macrophages and hepatic stellate cells (HSCs) were significantly enriched and demonstrated spatial co-localization within the context of MASH. We identified a DTNA+distinct macrophage subpopulation that was specifically enriched in MASH. This subpopulation exhibited characteristics consistent with M2 polarization, hypoxia, and enhanced inflammatory signaling. Pseudotime trajectory analysis revealed that this state represents a differentiation pathway originating from Kupffer cells to the DTNA+ state. RUNX2 emerged as the key transcriptional regulator. Cell communication analysis demonstrated that DTNA+ macrophages potentially interact with activated HSCs via the RUNX2-PLG-PARD3 axis, contributing to the exacerbation of liver fibrosis. Finally, ensemble machine learning models (mean AUC = 0.839), identified DTNA as the optimal predictive biomarker for distinguishing MASLD from MASH. This study highlight DTNA+ macrophages and the RUNX2-PLG-PARD3 axis as candidate mechanisms and targets for non-invasive diagnosis and therapy in MASH.