Spatial transcriptomics identifies enriched gene expression and cell types in human liver fibrosis

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.

Integrated liver and serum proteomics uncover sexual dimorphism and alteration of several immune response proteins in an aging Werner syndrome mouse model

“…The results are also consistent with the low systemic but chronic inflammation observed in Werner syndrome patients [6,39]. More interestingly, increased expression of the immunoglobulin variants IGKC and IGHM has been associated with NAFLD as well as liver fibrosis and cirrhosis in human subjects [40][41][42][43]. Although analyses on the activation status of the immune cells in Wrn Δhel/Δhel mice compared to age-matched wild type mice are required, the measurements of several serum cytokines in the mouse cohorts have indicated an increase of IL-5 in both females and males at ten months of age compared to four months old groups of mice.…”

Emerging Roles of Spatial Transcriptomics in Liver Research

“…Chung et al confirmed that spatial transcriptome analysis by 10× Visium could discriminate well-defined pathological fibrosis areas from parenchymal areas in fresh-frozen human liver tissues from patients with end-stage liver disease. 100 The cell deconvolution analysis by CIBERSORTx 101 detected a significant enrichment of estimated hepatocytes, cholangiocytes, and cycling cells in parenchymal regions and mesenchymal, endothelial, monocyte, innate lymphoid cells, B cells, and T cells in fibrotic areas, consistent with histological assessment. Among the T cell subtypes, T cells expressing CD63 and CD37 (T cells-1) as well as those expressing LTB , KLRB1 , and IL7R (T cells-2) were predominantly localized in the parenchyma, whereas T cells-3/-4 expressing CCL4 and T cells-5 expressing GZMA and CD53 were identified in the fibrotic regions.…”

Pediatric Cholestatic Diseases: Common and Unique Pathogenic Mechanisms

“…Advanced sequencing techniques have also been used to study pediatric cholestatic liver diseases. Research using single-cell RNA sequencing (Sc-RNA-seq) identified unique tissue-resident T cell populations in human PSC livers (159,160). A new methodology combining Sc-RNAseq with single-nucleus RNA-seq created the first complete transcriptomic map of the human liver (161).…”