Spatial single-cell interactome and niche-specific molecular signatures in alcohol-related liver disease

Alcohol-related liver disease (ALD) remains a major global health burden with limited therapeutic options due to an incomplete understanding of its underlying molecular mechanisms and cellular crosstalk. Here, we applied ultra-high resolution (on 2 µm spots) spatial transcriptomics to a cirrhotic liver tissue obtained from an end-stage ALD patient, analyzing >265,000 spatially resolved cells with further validation on single-cell and single-nuclei datasets from patients with ALD cirrhosis. Our analysis delineated distinct cellular sub-populations and molecular landscapes across fibrotic, vascular, and parenchymal niches of ALD cirrhosis. We identified robust zonation of hepatocytes, hepatic stellate cells, and diverse immune subpopulations, including enrichment of pro-inflammatory T cells and dendritic cells in the fibrotic niche and MARCO + tissue-resident macrophages localizing mostly in parenchymal areas. Analysis of spatial metrics assigned expression of WNT4, RCAN3, PPIAL4G, PLA2G5 , and SLC6A9 to the fibrotic environment in ALD. Differential expression and ligand–receptor interactome analyses revealed niche-specific signaling, with marked CCL19 – CCR7 activity in fibrotic regions and DLL4 – NOTCH3 crosstalk in vascular compartments. Notably, WNT4 + fibroblasts emerged as key mediators of extracellular matrix remodeling and chemoattraction, particularly via CCL19-mediated signaling towards CD8 ⁺ T cells, which was validated on single-cell resolution within the ALD cirrhotic liver in external datasets. These spatial and single-cell findings highlight novel potential therapeutic targets for patients with ALD cirrhosis.