Single-cell atlas of hepatic cellular plasticity and immune niche reprogramming in liver cirrhosis

Cirrhosis is a severe liver disease characterized by inflammation, fibrosis, and immune dysregulation. This study exploits publicly available single-cell sequencing datasets to decipher disease-relevant specific immune cell subtypes, their gene expression profiles and altered transcription factor activity in cirrhosis, aiming to understand their roles in disease onset and progression.

To investigate the dynamic changes and underlying mechanisms of immune cells in cirrhosis, we employed a comprehensive bioinformatics approach integrating several advanced tools and analytical methods. Single-cell RNA sequencing data were processed and analyzed using Seurat for cell clustering and annotation. Monocle was used for pseudotime trajectory analysis to explore cellular differentiation pathways. CellChat enabled the assessment of cell‒cell communication networks among immune populations. Additionally, we conducted single-cell regulatory network inference to identify key transcriptional regulators. Immune response enrichment analysis (IREA) was performed to evaluate immune-related functional pathways, providing deeper insights into the immune landscape and disease progression in cirrhosis.

We analyzed 35,017 cells, identifying 21 clusters and 12 major immune cell types. Macrophages, CD4⁺ T cells, and NK cells showed notable shifts in proportion in cirrhosis, suggesting key roles in disease progression. Pseudotime analysis revealed core macrophage and CD4⁺ T-cell subpopulations linked to cirrhosis. Functional analysis showed enrichment of IFN-α, IFN-β, and IL-1β in cirrhotic immune cells, primarily regulated by ETS2 and THRA. Fibroblast-mediated intercellular communication was enhanced, especially via increased macrophage migration inhibitory factor (MIF) signaling with B cells, indicating potential therapeutic targets in cytokine pathways and transcriptional regulation.

The analysis revealed three key axes influencing disease-related immune regulation: TNF-α/ETS2-driven polarization of macrophages toward a Mac-d phenotype, IL-1α/β/THRA-associated polarization of CD4⁺ T cells toward a T4-c phenotype, and enhancement of the fibroblast-to-B-cell MIF signaling axis. This network offers valuable insights and potential therapeutic targets for advancing cirrhosis research and clinical treatment.