Single-cell and spatial transcriptomics characterisation of the immunological landscape in the healthy and PSC human liver.

Journal

Journal of hepatology
ISSN: 1600-0641
Titre abrégé: J Hepatol
Pays: Netherlands
ID NLM: 8503886

Informations de publication

Date de publication:
04 Jan 2024
Historique:
received: 01 02 2023
revised: 13 12 2023
accepted: 20 12 2023
medline: 11 1 2024
pubmed: 11 1 2024
entrez: 10 1 2024
Statut: aheadofprint

Résumé

Primary sclerosing cholangitis (PSC) is an immune-mediated cholestatic liver disease characterized by bile retention, biliary tree destruction, and progressive fibrosis leading to end stage liver disease and transplantation. There is an unmet need to understand the cellular composition of the PSC liver and how it underlies disease pathogenesis. We generated a comprehensive atlas of the PSC liver in comparison to a primary biliary cholangitis (PBC) and reference healthy liver dataset using multiple multi-omic modalities and functional validation. We employed single-cell (sc) RNA-seq (47,156 cells), single-nucleus (sn) RNA-seq (23,000 nuclei) and spatial transcriptomics (1 sample by 10x Visium and 5 samples with multi-region profiling by Nanostring GeoMx Digital Spatial Profiler) to profile the cellular ecosystem in 10 patients with PSC. Transcriptomic profiles were compared to 24 neurologically deceased donor livers (107,542 cells) and spatial transcriptomics controls, 18,240 cells and 20,202 nuclei from 3 patients with PBC, and publicly available scRNA-seq data from 5 uninjured, 2 NAFLD, 2 ALD, and 1 PBC liver samples. Flow cytometry and intracellular cytokine staining was performed to validate PSC-specific differences in immune cell phenotype and function. PSC explants with cirrhosis of the liver parenchyma and prominent periductal fibrosis contained a population of hepatocytes expressing a cholangiocyte-like phenotype. These hepatocytes were surrounded by diverse immune cell populations, including monocyte-like macrophages, liver-resident and circulating natural killer cells. PSC-associated cholangiocytes, hepatic stellate cells, and endothelial cells expressed chemokine and cytokine transcripts typically involved in immune cell recruitment. As well, expanded CD4 We present a comprehensive atlas of the PSC liver and demonstrate hyper-activation and exhaustion-like phenotypes of myeloid cells and markers of chronic cytokine expression in late-stage PSC lesions. This atlas has the potential to expand our understanding of the cellular complexity of PSC and to inform novel treatment development. Primary sclerosing cholangitis (PSC) is a rare liver disease characterized by chronic inflammation and irreparable damage to the bile ducts resulting in liver failure. Due to a limited understanding of the underlying pathogenesis of disease, there remains a paucity of treatment options. We sequenced healthy and diseased livers to compare the activity, interactions, and localization of immune and non-immune cells. This revealed that hepatocytes lining PSC scar regions are transforming into cholangiocytes, whereas immune cells are accumulating within the scars. Of these cells, macrophages, which typically contribute to tissue repair, were enriched in immunoregulatory genes and demonstrated a lack of responsiveness to stimulation. These cells may be involved in maintaining hepatic inflammation and could be targeted in novel therapeutic drug development.

Sections du résumé

BACKGROUND BACKGROUND
Primary sclerosing cholangitis (PSC) is an immune-mediated cholestatic liver disease characterized by bile retention, biliary tree destruction, and progressive fibrosis leading to end stage liver disease and transplantation. There is an unmet need to understand the cellular composition of the PSC liver and how it underlies disease pathogenesis. We generated a comprehensive atlas of the PSC liver in comparison to a primary biliary cholangitis (PBC) and reference healthy liver dataset using multiple multi-omic modalities and functional validation.
METHODS METHODS
We employed single-cell (sc) RNA-seq (47,156 cells), single-nucleus (sn) RNA-seq (23,000 nuclei) and spatial transcriptomics (1 sample by 10x Visium and 5 samples with multi-region profiling by Nanostring GeoMx Digital Spatial Profiler) to profile the cellular ecosystem in 10 patients with PSC. Transcriptomic profiles were compared to 24 neurologically deceased donor livers (107,542 cells) and spatial transcriptomics controls, 18,240 cells and 20,202 nuclei from 3 patients with PBC, and publicly available scRNA-seq data from 5 uninjured, 2 NAFLD, 2 ALD, and 1 PBC liver samples. Flow cytometry and intracellular cytokine staining was performed to validate PSC-specific differences in immune cell phenotype and function.
RESULTS RESULTS
PSC explants with cirrhosis of the liver parenchyma and prominent periductal fibrosis contained a population of hepatocytes expressing a cholangiocyte-like phenotype. These hepatocytes were surrounded by diverse immune cell populations, including monocyte-like macrophages, liver-resident and circulating natural killer cells. PSC-associated cholangiocytes, hepatic stellate cells, and endothelial cells expressed chemokine and cytokine transcripts typically involved in immune cell recruitment. As well, expanded CD4
CONCLUSIONS CONCLUSIONS
We present a comprehensive atlas of the PSC liver and demonstrate hyper-activation and exhaustion-like phenotypes of myeloid cells and markers of chronic cytokine expression in late-stage PSC lesions. This atlas has the potential to expand our understanding of the cellular complexity of PSC and to inform novel treatment development.
IMPACT AND IMPLICATIONS UNASSIGNED
Primary sclerosing cholangitis (PSC) is a rare liver disease characterized by chronic inflammation and irreparable damage to the bile ducts resulting in liver failure. Due to a limited understanding of the underlying pathogenesis of disease, there remains a paucity of treatment options. We sequenced healthy and diseased livers to compare the activity, interactions, and localization of immune and non-immune cells. This revealed that hepatocytes lining PSC scar regions are transforming into cholangiocytes, whereas immune cells are accumulating within the scars. Of these cells, macrophages, which typically contribute to tissue repair, were enriched in immunoregulatory genes and demonstrated a lack of responsiveness to stimulation. These cells may be involved in maintaining hepatic inflammation and could be targeted in novel therapeutic drug development.

Identifiants

DOI: 10.1016/j.jhep.2023.12.023 PMID: 38199298
pubmed: 38199298
pii: S0168-8278(24)00003-5
doi: 10.1016/j.jhep.2023.12.023
pii:
doi:

Types de publication

Journal Article

Langues

eng

Sous-ensembles de citation

IM

Informations de copyright

Copyright © 2024 The Author(s). Published by Elsevier B.V. All rights reserved.

Auteurs

Tallulah S Andrews (TS)

Ajmera Transplant Centre, Toronto General Research Institute, University Health Network, Toronto, ON, Canada; Department of Biochemistry, Schulich School of Medicine and Dentistry, University of Western Ontario, N6A 5C1; Department of Computer Science, University of Western Ontario, N6A 3K7. Electronic address: tandrew6@uwo.ca.

Diana Nakib (D)

Ajmera Transplant Centre, Toronto General Research Institute, University Health Network, Toronto, ON, Canada; Department of Immunology, University of Toronto, Toronto, ON, M5S 1A8, Canada. Electronic address: diana.nakib@mail.utoronto.ca.

Catia T Perciani (CT)

Ajmera Transplant Centre, Toronto General Research Institute, University Health Network, Toronto, ON, Canada; Department of Immunology, University of Toronto, Toronto, ON, M5S 1A8, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, M5G 1L7, Canada.

Xue Zhong Ma (XZ)

Ajmera Transplant Centre, Toronto General Research Institute, University Health Network, Toronto, ON, Canada.

Lewis Liu (L)

Ajmera Transplant Centre, Toronto General Research Institute, University Health Network, Toronto, ON, Canada; Department of Immunology, University of Toronto, Toronto, ON, M5S 1A8, Canada.

Erin Winter (E)

Ajmera Transplant Centre, Toronto General Research Institute, University Health Network, Toronto, ON, Canada.

Damra Camat (D)

Ajmera Transplant Centre, Toronto General Research Institute, University Health Network, Toronto, ON, Canada; Department of Immunology, University of Toronto, Toronto, ON, M5S 1A8, Canada.

Sai W Chung (SW)

Ajmera Transplant Centre, Toronto General Research Institute, University Health Network, Toronto, ON, Canada; Department of Immunology, University of Toronto, Toronto, ON, M5S 1A8, Canada.

Patricia Lumanto (P)

Ajmera Transplant Centre, Toronto General Research Institute, University Health Network, Toronto, ON, Canada; Department of Immunology, University of Toronto, Toronto, ON, M5S 1A8, Canada.

Justin Manuel (J)

Ajmera Transplant Centre, Toronto General Research Institute, University Health Network, Toronto, ON, Canada.

Shantel Mangroo (S)

Division of Gastroenterology, Hepatology and Nutrition, The Hospital for Sick Children, Toronto, M5G 1X8, Canada.

Bettina Hansen (B)

Toronto Centre for Liver Disease, University Health Network, Toronto, Ontario, Canada; Institute of Health Policy, Management and Evaluation, University of Toronto, M5T 3M6, Toronto, Canada.

Bal Arpinder (B)

Ajmera Transplant Centre, Toronto General Research Institute, University Health Network, Toronto, ON, Canada.

Cornelia Thoeni (C)

Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, M5G 1L7, Canada.

Blayne Sayed (B)

Ajmera Transplant Centre, Toronto General Research Institute, University Health Network, Toronto, ON, Canada.

Jordan Feld (J)

Toronto Centre for Liver Disease, University Health Network, Toronto, Ontario, Canada.

Adam Gehring (A)

Department of Immunology, University of Toronto, Toronto, ON, M5S 1A8, Canada; Toronto Centre for Liver Disease, University Health Network, Toronto, Ontario, Canada.

Aliya Gulamhusein (A)

Toronto Centre for Liver Disease, University Health Network, Toronto, Ontario, Canada.

Gideon M Hirschfield (GM)

Toronto Centre for Liver Disease, University Health Network, Toronto, Ontario, Canada.

Amanda Ricciuto (A)

Division of Gastroenterology, Hepatology and Nutrition, The Hospital for Sick Children, Toronto, M5G 1X8, Canada.

Gary D Bader (GD)

The Donnelly Centre, University of Toronto, Toronto, ON, M5S 3E1, Canada. Electronic address: gary.bader@utoronto.ca.

Ian D McGilvray (ID)

Ajmera Transplant Centre, Toronto General Research Institute, University Health Network, Toronto, ON, Canada. Electronic address: Ian.Mcgilvray@uhn.ca.

Sonya MacParland (S)

Ajmera Transplant Centre, Toronto General Research Institute, University Health Network, Toronto, ON, Canada; Department of Immunology, University of Toronto, Toronto, ON, M5S 1A8, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, M5G 1L7, Canada. Electronic address: s.macparland@utoronto.ca.

Classifications MeSH