Distinct gene pathways and cell types define peribiliary disease states in PSC

Background and Aims: Primary sclerosing cholangitis (PSC) is a cholangiopathy of unknown etiology featuring peribiliary infiltration and fibrosis. To identify novel PSC pathways, we analyzed liver explants using spatial and single-nuclei transcriptomics (snRNA-seq) and compared differential expressed genes (DEGs) across biliary regions in early and advanced PSC.

Methods: Fresh-frozen liver explants from PSC patients (4 recurrent cholangitis, 7 dysplasia,12 cirrhotic) and cirrhotic controls (4 ALD, 3 MASH) were analyzed by spatial transcriptomics (Visium,10X Genomics). Sixteen of the same explants (12 PSC, 4 controls) were assessed by snRNA-seq (Chromium 3’, 10X Genomics). Spatial and snRNA-seq transcripts were clustered using Seurat v5.0.0 (Satija Lab, Broad Institute/MIT) and all DEGs reported reached statistical significance (P-adj<0.001).

Results: To identify unique PSC pathways, we first classified liver regions as early or advanced disease using histology features and fibrosis markers detected by spatial transcriptomics (COL1A1/2+COL3A1, COL6A2). Local profiling of biliary regions (KRT19+FXYD2+) by spatial transcriptomics revealed robust expression of metallothionein genes MT1E, MT1G and MT1H (14.9-fold) and inflammatory SAA1 and SAA2 (8.4-fold) by peribiliary hepatocytes at the interface between early and advanced PSC compared to controls. snRNA-seq identified 9 distinct liver cell types and showed highest metallothionein expression in PSC hepatocytes. Moreover, elevated metallothionein correlated with features of liver decompensation and cholestasis, including decreased serum sodium and elevated serum bilirubin.

Conclusions: Metallothionein is highly overrepresented in peribiliary regions at all stages of PSC suggesting that metallothionein may be triggered by early cholangiopathy in PSC livers.

Publication History

Article published online:
20 January 2025