ArticleHepatology communications2022
Spatial transcriptomics identifies enriched gene expression and cell types in human liver fibrosis.
Article in Hepatology communications, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 43 papers.
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Who cites it
43 citing papers in PubMed, 68 citations in OpenAlex.
- Omics-based Decoding of Metabolic Dysfunction-associated Fatty Liver Disease: From Pathogenesis to Clinical Translation.Journal of clinical and translational hepatology · 2026Review
- SNX3 exacerbates hepatic fibrosis by amplifying TGF-Acta pharmaceutica Sinica. B · 2026Article
- Intrahepatic T cell analysis reveals Th17 and MAIT17 enrichment in primary sclerosing cholangitis.JHEP reports : innovation in hepatology · 2026Article
- The circadian clock controls hepatic stellate cell activation via a BMAL1/CK1ε/REV-ERBα/transgelin signaling pathway.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Revisiting two-stage models of chemically-induced cirrhosis-associated hepatocarcinogenesis in rodents: methodological and histopathological approaches.Journal of molecular histology · 2026Review
- Imaging mass cytometry reveals novel cellular neighborhoods for predicting the prognosis of nonalcoholic fatty liver disease-associated hepatocellular carcinoma.Cancer cell international · 2026Article
- Cholangiocyte biology in primary sclerosing cholangitis and other cholangiopathies: pathogenesis, clinical insights, and experimental tools.Physiological reviews · 2026Review
- The Multifaceted Roles of Gut Microbiota and Their Metabolites in Metabolic Dysfunction-associated Steatotic Liver Disease: A Literature Review.Journal of clinical and translational hepatology · 2026Review
- Review
- Multimodal transcriptomics identifies metallothionein as a novel pathway in primary sclerosing cholangitis.Hepatology (Baltimore, Md.) · 2026Article
- <p>Beyond hepatic stellate cell heterogeneity: Resolving fibrosis, restoring regeneration (Review)</p>.International journal of molecular medicine · 2026Review
- Advances in the application of spatial transcriptomics in understanding development and disease.Molecular and cellular biochemistry · 2026Review
- Mesenchymal Stromal/Stem Cell-Based Therapies for Liver Regeneration: Current Status and Future Directions.International journal of molecular sciences · 2026Review
- Omics landscapes of hepatic echinococcosis: bulk foundations, emerging single-cell studies, and analytical considerations.Frontiers in immunology · 2026Review
- Towards a reference cell atlas of liver diversity over the human lifespan.Nature reviews. Gastroenterology & hepatology · 2026Review
- Conserved Ductular Reaction Mechanisms in Biliary Atresia and Primary Sclerosing Cholangitis Derived From Single-Cell and Spatial Transcriptomics.Cellular and molecular gastroenterology and hepatology · 2026Review
- Exposure-shaped immunometabolic networks in chronic liver disease: translating multi-omics and artificial intelligence into preventive biomarkers.Frontiers in immunology · 2026Review
- Integrated multi-omics, spatial profiling and organoid modeling drive transformative advances in chronic liver disease and hepatocellular carcinoma immunomicroenvironment research.Frontiers in immunology · 2026Review
- Epigenetic reprogramming of hepatic antigen presenting cells in chronic liver disease.Frontiers in immunology · 2026Review
- Digital pathology and spatial omics in steatohepatitis: Clinical applications and discovery potentials.Hepatology (Baltimore, Md.) · 2025Review
Corrections and comments
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Liver fibrosis and cirrhosis have limited therapeutic options and represent a serious unmet patient need. Recent use of single-cell RNA sequencing (scRNAseq) has identified enriched cell types infiltrating cirrhotic livers but without defining the microanatomical location of these lineages thoroughly. To assess whether fibrotic liver regions specifically harbor enriched cell types, we explored whether whole-tissue spatial transcriptomics combined with scRNAseq and gene deconvolution analysis could be used to localize cell types in cirrhotic explants of patients with end-stage liver disease (total n = 8; primary sclerosing cholangitis, n = 4; primary biliary cholangitis, n = 2, alcohol-related liver disease, n = 2). Spatial transcriptomics clearly identified tissue areas of distinct gene expression that strongly correlated with the total area (Spearman r = 0.97, p = 0.0004) and precise location (parenchyma, 87.9% mean congruency; range, 73.1%-97.1%; fibrosis, 68.5% mean congruency; range, 41.0%-91.7%) of liver regions classified as parenchymal or fibrotic by conventional histology. Deconvolution and enumeration of parenchymal and fibrotic gene content as measured by spatial transcriptomics into distinct cell states revealed significantly higher frequencies of ACTA2+ FABP4+ and COL3A1+ mesenchymal cells, IL17RA+ S100A8+ and FCER1G+ tissue monocytes, VCAM1+ SDC3+ Kupffer cells, CCL4+ CCL5+ KLRB1+ and GZMA+ IL17RA+ T cells and HLA-DR+, CD37+ CXCR4+ and IGHM+ IGHG+ B cells in fibrotic liver regions compared with parenchymal areas of cirrhotic explants. Conclusion: Our findings indicate that spatial transcriptomes of parenchymal and fibrotic liver regions express unique gene content within cirrhotic liver and demonstrate proof of concept that spatial transcriptomes combined with additional RNA sequencing methodologies can refine the localization of gene content and cell lineages in the search for antifibrotic targets.
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