Spatial profiling of chronic liver disease: a pilot spatial case series

Abstract

Abstract The spatial organization of chronic liver disease across major etiologic contexts remains incompletely understood. Here we present a pilot spatial case series using sequencing-based spatial transcriptomics to examine alcohol-associated liver disease (ALD), metabolic dysfunction–associated steatohepatitis (MASH), and chronic hepatitis C within preserved histological context. Eight liver tissues were profiled using a viral-aware workflow enabling in situ detection of hepatitis viral RNA, histology-guided niche annotation, and cell–cell communication analysis; four cases passed quality control and were included in the core discovery analyses. In HCV case, viral reads localized to immune-enriched microenvironments and extended into adjacent regions enriched for cell-cycle, RNA-processing, and PD-1–axis checkpoint pathways. In ALD and MASH tissues, histology-guided segmentation aligned with transcriptomic clusters, and pseudolobular sub-clustering identified recurrent functional compartments. Across the analyzed cases, immune–mesenchymal signaling hubs associated with extracellular matrix and chemokine programs were observed. Overall, this pilot spatial case series suggests that chronic liver disease tissues may share recurrent pseudolobular functional architecture, upon which etiology-associated immune, metabolic, and viral-response programs are superimposed in a case-dependent manner. Supplementary analyses summarize additional feasibility observations from HBV-profiled sections that did not support inclusion in the core downstream analyses.