Visium spatial transcriptomics and proteomics identifies novel hepatic cell populations and transcriptomic signatures of alcohol-associated hepatitis

Tyler C Gripshover; Rui S Treves; Eric C Rouchka; Julia H Chariker; Shirong Zheng; Elizabeth Hudson; Melissa L Smith; Ashwani K Singal; Craig J McClain; Josiah E Hardesty

doi:10.1111/acer.15494

Visium spatial transcriptomics and proteomics identifies novel hepatic cell populations and transcriptomic signatures of alcohol-associated hepatitis

Alcohol Clin Exp Res (Hoboken). 2024 Nov 26. doi: 10.1111/acer.15494. Online ahead of print.

Authors

Tyler C Gripshover¹, Rui S Treves¹, Eric C Rouchka^{2

3}, Julia H Chariker³, Shirong Zheng⁴, Elizabeth Hudson⁴, Melissa L Smith^{2

4}, Ashwani K Singal^{5

6

7}, Craig J McClain^{1

5

6

7

8}, Josiah E Hardesty^{1

5}

Affiliations

¹ Department of Pharmacology and Toxicology, University of Louisville School of Medicine, Louisville, Kentucky, USA.
² Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, Kentucky, USA.
³ Kentucky INBRE Bioinformatics Core, University of Louisville School of Medicine, Louisville, Kentucky, USA.
⁴ Sequencing Technology Center, University of Louisville School of Medicine, Louisville, Kentucky, USA.
⁵ Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, University of Louisville, Louisville, Kentucky, USA.
⁶ Robley Rex Veterans Medical Center, Louisville, Kentucky, USA.
⁷ University of Louisville Alcohol Research Center, University of Louisville School of Medicine, Louisville, Kentucky, USA.
⁸ University of Louisville Hepatobiology and Toxicology Center, University of Louisville School of Medicine, Louisville, Kentucky, USA.

PMID: 39592394
DOI: 10.1111/acer.15494

Abstract

Background: Alcohol-associated hepatitis (AH) is the clinical manifestation of alcohol-associated liver disease (ALD). AH is a complex disease encompassing the dysregulation of many cells and cell subpopulations. This study used a hepatic spatial transcriptomic and proteomic approach (10X Genomics Visium) to identify hepatic cell populations and their associated transcriptomic and proteomic alterations in human AH.

Methods: Formalin-fixed paraffin-embedded liver tissue from AH patients (n = 2) and non-ALD controls (donors) (n = 2) were used for Visium spatial transcriptomic and proteomic analysis.

Results: AH cell clusters and cell markers were drastically different in regard to tissue pattern and number of cell types compared to non-ALD controls. Cholangiocytes, endothelial cells, macrophages, and stellate cells were more profuse in AH relative to non-ALD controls. Transcriptionally, proliferating cell nuclear antigen-positive (PCNA⁺) hepatocytes in AH more closely resembled cholangiocytes suggesting they were non-functional hepatocytes derived from cholangiocytes. Furthermore, mitochondria protein-coding genes were reduced in AH versus non-ALD control hepatocytes, suggesting reduced functionality and loss of regenerative mechanisms. Macrophages in AH exhibited elevated gene expression involved in exosomes as compared to non-ALD controls. The most upregulated macrophage genes observed in AH were those involved in exosome trafficking. Gene and protein signatures of disease-associated hepatocytes (ANXA2⁺/CXCL1⁺/CEACAM8⁺) were elevated in AH and could visually identify a pre-malignant lesion.

Conclusions: This study identified global cell type alterations in AH and distinct transcriptomic changes between AH and non-ALD controls. These findings characterize cellular plasticity and profuse transcriptomic and proteomic changes that are apparent in AH and contribute to the identification of novel therapeutics.

Keywords: Visium spatial transcriptomics; alcohol‐associated hepatitis; proliferating cell nuclear antigen‐positive (PCNA+) hepatocytes.

Abstract

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