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Andrews TS, Nakib D, Perciani CT, Ma XZ, Liu L, Winter E, Camat D, Chung SW, Lumanto P, Manuel J, Mangroo S, Hansen B, Arpinder B, Thoeni C, Sayed B, Feld J, Gehring A, Gulamhusein A, Hirschfield GM, Ricciuto A, Bader GD, McGilvray ID, MacParland S. Single-cell, single-nucleus, and spatial transcriptomics characterization of the immunological landscape in the healthy and PSC human liver. J Hepatol 2024; 80:730-743. [PMID: 38199298 DOI: 10.1016/j.jhep.2023.12.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 12/13/2023] [Accepted: 12/20/2023] [Indexed: 01/12/2024]
Abstract
BACKGROUND & AIMS Primary sclerosing cholangitis (PSC) is an immune-mediated cholestatic liver disease for which there is an unmet need to understand the cellular composition of the affected liver and how it underlies disease pathogenesis. We aimed to generate a comprehensive atlas of the PSC liver using multi-omic modalities and protein-based functional validation. METHODS We employed single-cell and single-nucleus RNA sequencing (47,156 cells and 23,000 nuclei) and spatial transcriptomics (one sample by 10x Visium and five samples with Nanostring GeoMx DSP) to profile the cellular ecosystem in 10 PSC livers. Transcriptomic profiles were compared to 24 neurologically deceased donor livers (107,542 cells) and spatial transcriptomics controls, as well as 18,240 cells and 20,202 nuclei from three PBC livers. Flow cytometry was performed to validate PSC-specific differences in immune cell phenotype and function. RESULTS PSC explants with parenchymal cirrhosis and prominent periductal fibrosis contained a population of cholangiocyte-like hepatocytes that were surrounded by diverse immune cell populations. PSC-associated biliary, mesenchymal, and endothelial populations expressed chemokine and cytokine transcripts involved in immune cell recruitment. Additionally, expanded CD4+ T cells and recruited myeloid populations in the PSC liver expressed the corresponding receptors to these chemokines and cytokines, suggesting potential recruitment. Tissue-resident macrophages, by contrast, were reduced in number and exhibited a dysfunctional and downregulated inflammatory response to lipopolysaccharide and interferon-γ stimulation. CONCLUSIONS We present a comprehensive atlas of the PSC liver and demonstrate an exhaustion-like phenotype of myeloid cells and markers of chronic cytokine expression in late-stage PSC lesions. This atlas expands our understanding of the cellular complexity of PSC and has potential to guide the development of novel treatments. IMPACT AND IMPLICATIONS Primary sclerosing cholangitis (PSC) is a rare liver disease characterized by chronic inflammation and irreparable damage to the bile ducts, which eventually results in liver failure. Due to a limited understanding of the underlying pathogenesis of disease, treatment options are limited. To address this, 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 co-express cholangiocyte markers, whereas immune cells infiltrate the scar lesions. 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 a target for novel therapies.
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Affiliation(s)
- Tallulah S Andrews
- Ajmera Transplant Centre, Toronto General Research Institute, University Health Network, Toronto, ON, M5G 2C4, Canada; Department of Biochemistry, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON, N6A 5C1, Canada; Department of Computer Science, University of Western Ontario, London, ON, N6A 3K7, Canada.
| | - Diana Nakib
- Ajmera Transplant Centre, Toronto General Research Institute, University Health Network, Toronto, ON, M5G 2C4, Canada; Department of Immunology, University of Toronto, Toronto, ON, M5S 1A8, Canada.
| | - Catia T Perciani
- Ajmera Transplant Centre, Toronto General Research Institute, University Health Network, Toronto, ON, M5G 2C4, Canada; Department of Immunology, University of Toronto, Toronto, ON, M5S 1A8, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Xue Zhong Ma
- Ajmera Transplant Centre, Toronto General Research Institute, University Health Network, Toronto, ON, M5G 2C4, Canada
| | - Lewis Liu
- Ajmera Transplant Centre, Toronto General Research Institute, University Health Network, Toronto, ON, M5G 2C4, Canada; Department of Immunology, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Erin Winter
- Ajmera Transplant Centre, Toronto General Research Institute, University Health Network, Toronto, ON, M5G 2C4, Canada
| | - Damra Camat
- Ajmera Transplant Centre, Toronto General Research Institute, University Health Network, Toronto, ON, M5G 2C4, Canada; Department of Immunology, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Sai W Chung
- Ajmera Transplant Centre, Toronto General Research Institute, University Health Network, Toronto, ON, M5G 2C4, Canada; Department of Immunology, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Patricia Lumanto
- Ajmera Transplant Centre, Toronto General Research Institute, University Health Network, Toronto, ON, M5G 2C4, Canada; Department of Immunology, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Justin Manuel
- Ajmera Transplant Centre, Toronto General Research Institute, University Health Network, Toronto, ON, M5G 2C4, Canada
| | - Shantel Mangroo
- Division of Gastroenterology, Hepatology and Nutrition, The Hospital for Sick Children, Toronto, ON, M5G 1X8, Canada
| | - Bettina Hansen
- Toronto Centre for Liver Disease, University Health Network, Toronto, ON, M5G 2C4, Canada; Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON, M5T 3M6, Canada
| | - Bal Arpinder
- Ajmera Transplant Centre, Toronto General Research Institute, University Health Network, Toronto, ON, M5G 2C4, Canada
| | - Cornelia Thoeni
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Blayne Sayed
- Ajmera Transplant Centre, Toronto General Research Institute, University Health Network, Toronto, ON, M5G 2C4, Canada
| | - Jordan Feld
- Toronto Centre for Liver Disease, University Health Network, Toronto, ON, M5G 2C4, Canada
| | - Adam Gehring
- Department of Immunology, University of Toronto, Toronto, ON, M5S 1A8, Canada; Toronto Centre for Liver Disease, University Health Network, Toronto, ON, M5G 2C4, Canada
| | - Aliya Gulamhusein
- Toronto Centre for Liver Disease, University Health Network, Toronto, ON, M5G 2C4, Canada
| | - Gideon M Hirschfield
- Toronto Centre for Liver Disease, University Health Network, Toronto, ON, M5G 2C4, Canada
| | - Amanda Ricciuto
- Division of Gastroenterology, Hepatology and Nutrition, The Hospital for Sick Children, Toronto, ON, M5G 1X8, Canada
| | - Gary D Bader
- The Donnelly Centre, University of Toronto, Toronto, ON, M5S 3E1, Canada.
| | - Ian D McGilvray
- Ajmera Transplant Centre, Toronto General Research Institute, University Health Network, Toronto, ON, M5G 2C4, Canada.
| | - Sonya MacParland
- Ajmera Transplant Centre, Toronto General Research Institute, University Health Network, Toronto, ON, M5G 2C4, Canada; Department of Immunology, University of Toronto, Toronto, ON, M5S 1A8, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, M5G 1L7, Canada.
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Pouyabahar D, Chung SW, Pezzutti OI, Perciani CT, Wang X, Ma XZ, Jiang C, Camat D, Chung T, Sekhon M, Manuel J, Chen XC, McGilvray ID, MacParland SA, Bader GD. A rat liver cell atlas reveals intrahepatic myeloid heterogeneity. iScience 2023; 26:108213. [PMID: 38026201 PMCID: PMC10651689 DOI: 10.1016/j.isci.2023.108213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 08/20/2023] [Accepted: 10/11/2023] [Indexed: 12/01/2023] Open
Abstract
The large size and vascular accessibility of the laboratory rat (Rattus norvegicus) make it an ideal hepatic animal model for diseases that require surgical manipulation. Often, the disease susceptibility and outcomes of inflammatory pathologies vary significantly between strains. This study uses single-cell transcriptomics to better understand the complex cellular network of the rat liver, as well as to unravel the cellular and molecular sources of inter-strain hepatic variation. We generated single-cell and single-nucleus transcriptomic maps of the livers of healthy Dark Agouti and Lewis rat strains and developed a factor analysis-based bioinformatics analysis pipeline to study data covariates, such as strain and batch. Using this approach, we discovered transcriptomic variation within the hepatocyte and myeloid populations that underlie distinct cell states between rat strains. This finding will help provide a reference for future investigations on strain-dependent outcomes of surgical experiment models.
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Affiliation(s)
- Delaram Pouyabahar
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- The Donnelly Centre, University of Toronto, Toronto, ON, Canada
| | - Sai W. Chung
- Ajmera Transplant Centre, Toronto General Hospital Research Institute, Toronto, ON, Canada
- Department of Immunology, University of Toronto, Toronto, ON, Canada
| | - Olivia I. Pezzutti
- Ajmera Transplant Centre, Toronto General Hospital Research Institute, Toronto, ON, Canada
| | - Catia T. Perciani
- Ajmera Transplant Centre, Toronto General Hospital Research Institute, Toronto, ON, Canada
| | - Xinle Wang
- Ajmera Transplant Centre, Toronto General Hospital Research Institute, Toronto, ON, Canada
| | - Xue-Zhong Ma
- Ajmera Transplant Centre, Toronto General Hospital Research Institute, Toronto, ON, Canada
| | - Chao Jiang
- Ajmera Transplant Centre, Toronto General Hospital Research Institute, Toronto, ON, Canada
| | - Damra Camat
- Ajmera Transplant Centre, Toronto General Hospital Research Institute, Toronto, ON, Canada
- Department of Immunology, University of Toronto, Toronto, ON, Canada
| | - Trevor Chung
- Ajmera Transplant Centre, Toronto General Hospital Research Institute, Toronto, ON, Canada
| | - Manmeet Sekhon
- Ajmera Transplant Centre, Toronto General Hospital Research Institute, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Justin Manuel
- Ajmera Transplant Centre, Toronto General Hospital Research Institute, Toronto, ON, Canada
| | - Xu-Chun Chen
- Ajmera Transplant Centre, Toronto General Hospital Research Institute, Toronto, ON, Canada
| | - Ian D. McGilvray
- Ajmera Transplant Centre, Toronto General Hospital Research Institute, Toronto, ON, Canada
| | - Sonya A. MacParland
- Ajmera Transplant Centre, Toronto General Hospital Research Institute, Toronto, ON, Canada
- Department of Immunology, University of Toronto, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Gary D. Bader
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- The Donnelly Centre, University of Toronto, Toronto, ON, Canada
- Department of Computer Science, University of Toronto, Toronto, ON, Canada
- Lunenfeld-Tanenbaum Research Institute, Toronto, ON, Canada
- Princess Margaret Research Institute, University Health Network, Toronto, ON, Canada
- The Multiscale Human Program, Canadian Institute for Advanced Research, Toronto, ON, Canada
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3
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Thoeni C, Perciani CT, Nakib D, Camat D, McGilvray ID, MacParland SA, Fischer S. Analysis of various ATP-binding cassette transporters revealed quantification of ABCB4 as a potential diagnostic tool in primary sclerosing cholangitis (PSC). Histopathology 2023; 83:559-568. [PMID: 37488782 DOI: 10.1111/his.15006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 06/08/2023] [Accepted: 06/26/2023] [Indexed: 07/26/2023]
Abstract
AIMS ATP-binding cassette transporters are important proteins in regulating bile constituent transport between hepatocytes and the bile canalicular system. Dysfunctional transporters lead to accumulation of toxic bile components within hepatocytes or the biliary system, known as cholestasis, resulting in liver damage. It has been previously reported that two particular ATP-binding cassette transporters, ABCB4 and ABCB11, have altered expression in patients with primary sclerosing cholangitis (PSC). Interested in further analysis of expression patterns of ATP-binding cassette transporters in PSC patients, we investigated liver samples from 201 patients, including 43 patients with PSC and 51 patients with primary biliary cholangitis patients (PBC). In addition to ABCB4 and ABCB11, we also included other ATP-binding cassette transporters, to determine if upregulation of ABCB4 and ABCB11 is specifically found in the liver of patients with PSC. METHODS AND RESULTS Retrospectively, formalin-fixed and paraffin-embedded liver biopsies, resections, and explants were selected to investigate the expression of ABCB1, ABCB4, ABCB11, ABCG5/8, and FXR1 using nanoString nCounter and immunohistochemistry for validation of differently expressed transporters seen in PSC liver samples in comparison to non-PSC liver specimens. Strikingly, ABCB4 was the only ATP-binding cassette transporter showing increased gene and protein expression in hepatocytes of PSC livers when compared to non-PSC liver specimens. Furthermore, ABCB4 protein expression also correlated with disease stage in PSC. CONCLUSION Our study concluded that altered ABCB4 expression is specifically seen in liver specimens of PSC patients. Therefore, quantitative ABCB4 analysis may be an additional useful tool for the histopathological diagnosis of PSC to distinguish this entity from other cholangiopathies.
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Affiliation(s)
- Cornelia Thoeni
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Catia T Perciani
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
- Ajmera Transplant Centre, Toronto General Hospital Research Institute, Toronto, ON, Canada
- Department of Immunology, University of Toronto, Medical Sciences Building, Toronto, ON, Canada
| | - Diana Nakib
- Ajmera Transplant Centre, Toronto General Hospital Research Institute, Toronto, ON, Canada
- Department of Immunology, University of Toronto, Medical Sciences Building, Toronto, ON, Canada
| | - Damra Camat
- Ajmera Transplant Centre, Toronto General Hospital Research Institute, Toronto, ON, Canada
- Department of Immunology, University of Toronto, Medical Sciences Building, Toronto, ON, Canada
| | - Ian D McGilvray
- Ajmera Transplant Centre, Toronto General Hospital Research Institute, Toronto, ON, Canada
- Multi-Organ Transplant Program, Toronto General Hospital Research Institute, Toronto, ON, Canada
| | - Sonya A MacParland
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
- Ajmera Transplant Centre, Toronto General Hospital Research Institute, Toronto, ON, Canada
- Department of Immunology, University of Toronto, Medical Sciences Building, Toronto, ON, Canada
| | - Sandra Fischer
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
- Department of Pathology, Laboratory Medicine Program, University Health Network, Toronto, ON, Canada
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4
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Liu LY, Ma XZ, Ouyang B, Ings DP, Marwah S, Liu J, Chen AY, Gupta R, Manuel J, Chen XC, Gage BK, Cirlan I, Khuu N, Chung S, Camat D, Cheng M, Sekhon M, Zagorovsky K, Abdou Mohamed MA, Thoeni C, Atif J, Echeverri J, Kollmann D, Fischer S, Bader GD, Chan WCW, Michalak TI, McGilvray ID, MacParland SA. Nanoparticle Uptake in a Spontaneous and Immunocompetent Woodchuck Liver Cancer Model. ACS Nano 2020; 14:4698-4715. [PMID: 32255624 DOI: 10.1021/acsnano.0c00468] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
There is a tremendous focus on the application of nanomaterials for the treatment of cancer. Nonprimate models are conventionally used to assess the biomedical utility of nanomaterials. However, these animals often lack an intact immunological background, and the tumors in these animals do not develop spontaneously. We introduce a preclinical woodchuck hepatitis virus-induced liver cancer model as a platform for nanoparticle (NP)-based in vivo experiments. Liver cancer development in these out-bred animals occurs as a result of persistent viral infection, mimicking human hepatitis B virus-induced HCC development. We highlight how this model addresses key gaps associated with other commonly used tumor models. We employed this model to (1) track organ biodistribution of gold NPs after intravenous administration, (2) examine their subcellular localization in the liver, (3) determine clearance kinetics, and (4) characterize the identity of hepatic macrophages that take up NPs using RNA-sequencing (RNA-seq). We found that the liver and spleen were the primary sites of NP accumulation. Subcellular analyses revealed accumulation of NPs in the lysosomes of CD14+ cells. Through RNA-seq, we uncovered that immunosuppressive macrophages within the woodchuck liver are the major cell type that take up injected NPs. The woodchuck-HCC model has the potential to be an invaluable tool to examine NP-based immune modifiers that promote host anti-tumor immunity.
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Affiliation(s)
- Lewis Y Liu
- Soham and Shaila Ajmera Family Transplant Centre, Toronto General Research Institute, University Health Network, 200 Elizabeth Street, Toronto, Ontario, Canada M5G 2C4
- Department of Immunology, University of Toronto, 1 King's College Circle, Medical Sciences Building, Room 6271, Toronto, Ontario, Canada M5S 1A8
| | - Xue-Zhong Ma
- Soham and Shaila Ajmera Family Transplant Centre, Toronto General Research Institute, University Health Network, 200 Elizabeth Street, Toronto, Ontario, Canada M5G 2C4
| | - Ben Ouyang
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, 164 College Street, Rosebrugh Building, Room 407, Toronto, Ontario, Canada M5S 3G9
| | - Danielle P Ings
- Molecular Virology and Hepatology Research Group, Faculty of Medicine, Health Sciences Centre, Memorial University, 300 Prince Philip Drive, St. John's, Newfoundland, Canada A1B 3V6
| | - Sagar Marwah
- Soham and Shaila Ajmera Family Transplant Centre, Toronto General Research Institute, University Health Network, 200 Elizabeth Street, Toronto, Ontario, Canada M5G 2C4
| | - Jeff Liu
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Room 230, Toronto, Ontario, Canada M5S 3E1
| | - Annie Y Chen
- Molecular Virology and Hepatology Research Group, Faculty of Medicine, Health Sciences Centre, Memorial University, 300 Prince Philip Drive, St. John's, Newfoundland, Canada A1B 3V6
| | - Rahul Gupta
- Soham and Shaila Ajmera Family Transplant Centre, Toronto General Research Institute, University Health Network, 200 Elizabeth Street, Toronto, Ontario, Canada M5G 2C4
| | - Justin Manuel
- Soham and Shaila Ajmera Family Transplant Centre, Toronto General Research Institute, University Health Network, 200 Elizabeth Street, Toronto, Ontario, Canada M5G 2C4
| | - Xu-Chun Chen
- Soham and Shaila Ajmera Family Transplant Centre, Toronto General Research Institute, University Health Network, 200 Elizabeth Street, Toronto, Ontario, Canada M5G 2C4
| | - Blair K Gage
- Soham and Shaila Ajmera Family Transplant Centre, Toronto General Research Institute, University Health Network, 200 Elizabeth Street, Toronto, Ontario, Canada M5G 2C4
- McEwen Stem Cell Institute, University Health Network, Toronto, Ontario, Canada M5G 1L7
| | - Iulia Cirlan
- Princess Margaret Genomics Centre, University Health Network, Toronto, Ontario, Canada M5G 1L7
| | - Nicholas Khuu
- Princess Margaret Genomics Centre, University Health Network, Toronto, Ontario, Canada M5G 1L7
| | - Sai Chung
- Soham and Shaila Ajmera Family Transplant Centre, Toronto General Research Institute, University Health Network, 200 Elizabeth Street, Toronto, Ontario, Canada M5G 2C4
- Department of Immunology, University of Toronto, 1 King's College Circle, Medical Sciences Building, Room 6271, Toronto, Ontario, Canada M5S 1A8
| | - Damra Camat
- Soham and Shaila Ajmera Family Transplant Centre, Toronto General Research Institute, University Health Network, 200 Elizabeth Street, Toronto, Ontario, Canada M5G 2C4
- Department of Immunology, University of Toronto, 1 King's College Circle, Medical Sciences Building, Room 6271, Toronto, Ontario, Canada M5S 1A8
| | - Michael Cheng
- Soham and Shaila Ajmera Family Transplant Centre, Toronto General Research Institute, University Health Network, 200 Elizabeth Street, Toronto, Ontario, Canada M5G 2C4
- Luna Nanotech, Toronto, Ontario, Canada M5G 1Y8
| | - Manmeet Sekhon
- Soham and Shaila Ajmera Family Transplant Centre, Toronto General Research Institute, University Health Network, 200 Elizabeth Street, Toronto, Ontario, Canada M5G 2C4
| | - Kyryl Zagorovsky
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, 164 College Street, Rosebrugh Building, Room 407, Toronto, Ontario, Canada M5S 3G9
- Luna Nanotech, Toronto, Ontario, Canada M5G 1Y8
| | - Mohamed A Abdou Mohamed
- Luna Nanotech, Toronto, Ontario, Canada M5G 1Y8
- Botany and Microbiology Department, Faculty of Science, Zagazig University, Zagazig, Egypt 44519
| | - Cornelia Thoeni
- Soham and Shaila Ajmera Family Transplant Centre, Toronto General Research Institute, University Health Network, 200 Elizabeth Street, Toronto, Ontario, Canada M5G 2C4
| | - Jawairia Atif
- Soham and Shaila Ajmera Family Transplant Centre, Toronto General Research Institute, University Health Network, 200 Elizabeth Street, Toronto, Ontario, Canada M5G 2C4
- Department of Immunology, University of Toronto, 1 King's College Circle, Medical Sciences Building, Room 6271, Toronto, Ontario, Canada M5S 1A8
| | - Juan Echeverri
- Soham and Shaila Ajmera Family Transplant Centre, Toronto General Research Institute, University Health Network, 200 Elizabeth Street, Toronto, Ontario, Canada M5G 2C4
| | - Dagmar Kollmann
- Soham and Shaila Ajmera Family Transplant Centre, Toronto General Research Institute, University Health Network, 200 Elizabeth Street, Toronto, Ontario, Canada M5G 2C4
| | - Sandra Fischer
- Soham and Shaila Ajmera Family Transplant Centre, Toronto General Research Institute, University Health Network, 200 Elizabeth Street, Toronto, Ontario, Canada M5G 2C4
- Department of Laboratory Medicine and Pathobiology, University of Toronto, 1 King's College Circle, Medical Sciences Building, Room 6271, Toronto, Ontario, Canada M5S 1A8
| | - Gary D Bader
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Room 230, Toronto, Ontario, Canada M5S 3E1
| | - Warren C W Chan
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, 164 College Street, Rosebrugh Building, Room 407, Toronto, Ontario, Canada M5S 3G9
- Department of Materials Science and Engineering, University of Toronto, 160 College Street, Room 450, Toronto, Ontario, Canada M5S 3E1
| | - Tomasz I Michalak
- Molecular Virology and Hepatology Research Group, Faculty of Medicine, Health Sciences Centre, Memorial University, 300 Prince Philip Drive, St. John's, Newfoundland, Canada A1B 3V6
| | - Ian D McGilvray
- Soham and Shaila Ajmera Family Transplant Centre, Toronto General Research Institute, University Health Network, 200 Elizabeth Street, Toronto, Ontario, Canada M5G 2C4
| | - Sonya A MacParland
- Soham and Shaila Ajmera Family Transplant Centre, Toronto General Research Institute, University Health Network, 200 Elizabeth Street, Toronto, Ontario, Canada M5G 2C4
- Department of Immunology, University of Toronto, 1 King's College Circle, Medical Sciences Building, Room 6271, Toronto, Ontario, Canada M5S 1A8
- Department of Laboratory Medicine and Pathobiology, University of Toronto, 1 King's College Circle, Medical Sciences Building, Room 6271, Toronto, Ontario, Canada M5S 1A8
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5
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MacParland SA, Liu JC, Ma XZ, Innes BT, Bartczak AM, Gage BK, Manuel J, Khuu N, Echeverri J, Linares I, Gupta R, Cheng ML, Liu LY, Camat D, Chung SW, Seliga RK, Shao Z, Lee E, Ogawa S, Ogawa M, Wilson MD, Fish JE, Selzner M, Ghanekar A, Grant D, Greig P, Sapisochin G, Selzner N, Winegarden N, Adeyi O, Keller G, Bader GD, McGilvray ID. Single cell RNA sequencing of human liver reveals distinct intrahepatic macrophage populations. Nat Commun 2018; 9:4383. [PMID: 30348985 PMCID: PMC6197289 DOI: 10.1038/s41467-018-06318-7] [Citation(s) in RCA: 767] [Impact Index Per Article: 127.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 08/24/2018] [Indexed: 12/02/2022] Open
Abstract
The liver is the largest solid organ in the body and is critical for metabolic and immune functions. However, little is known about the cells that make up the human liver and its immune microenvironment. Here we report a map of the cellular landscape of the human liver using single-cell RNA sequencing. We provide the transcriptional profiles of 8444 parenchymal and non-parenchymal cells obtained from the fractionation of fresh hepatic tissue from five human livers. Using gene expression patterns, flow cytometry, and immunohistochemical examinations, we identify 20 discrete cell populations of hepatocytes, endothelial cells, cholangiocytes, hepatic stellate cells, B cells, conventional and non-conventional T cells, NK-like cells, and distinct intrahepatic monocyte/macrophage populations. Together, our study presents a comprehensive view of the human liver at single-cell resolution that outlines the characteristics of resident cells in the liver, and in particular provides a map of the human hepatic immune microenvironment. The development of single cell RNA sequencing technologies has been instrumental in advancing our understanding of tissue biology. Here, MacParland et al. performed single cell RNA sequencing of human liver samples, and identify distinct populations of intrahepatic macrophages that may play specific roles in liver disease.
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Affiliation(s)
- Sonya A MacParland
- Multi-Organ Transplant Program, Toronto General Hospital Research Institute, Toronto, ON, M5G 2C4, 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.
| | - Jeff C Liu
- The Donnelly Centre, University of Toronto, Toronto, ON, M5S 3E1, Canada
| | - Xue-Zhong Ma
- Multi-Organ Transplant Program, Toronto General Hospital Research Institute, Toronto, ON, M5G 2C4, Canada
| | - Brendan T Innes
- The Donnelly Centre, University of Toronto, Toronto, ON, M5S 3E1, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, M5G 1A8, Canada
| | - Agata M Bartczak
- Multi-Organ Transplant Program, Toronto General Hospital Research Institute, Toronto, ON, M5G 2C4, Canada
| | - Blair K Gage
- McEwen Centre for Regenerative Medicine, University Health Network, Toronto, ON, M5G 1L7, Canada
| | - Justin Manuel
- Multi-Organ Transplant Program, Toronto General Hospital Research Institute, Toronto, ON, M5G 2C4, Canada
| | - Nicholas Khuu
- Princess Margaret Genomics Centre, University Health Network, Toronto, ON, M5G 1L7, Canada
| | - Juan Echeverri
- Multi-Organ Transplant Program, Toronto General Hospital Research Institute, Toronto, ON, M5G 2C4, Canada
| | - Ivan Linares
- Multi-Organ Transplant Program, Toronto General Hospital Research Institute, Toronto, ON, M5G 2C4, Canada
| | - Rahul Gupta
- Multi-Organ Transplant Program, Toronto General Hospital Research Institute, Toronto, ON, M5G 2C4, Canada
| | - Michael L Cheng
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, M5G 1L7, Canada
| | - Lewis Y Liu
- Department of Immunology, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Damra Camat
- Multi-Organ Transplant Program, Toronto General Hospital Research Institute, Toronto, ON, M5G 2C4, Canada
| | - Sai W Chung
- Department of Immunology, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Rebecca K Seliga
- Multi-Organ Transplant Program, Toronto General Hospital Research Institute, Toronto, ON, M5G 2C4, Canada
| | - Zigong Shao
- Multi-Organ Transplant Program, Toronto General Hospital Research Institute, Toronto, ON, M5G 2C4, Canada
| | - Elizabeth Lee
- Multi-Organ Transplant Program, Toronto General Hospital Research Institute, Toronto, ON, M5G 2C4, Canada
| | - Shinichiro Ogawa
- McEwen Centre for Regenerative Medicine, University Health Network, Toronto, ON, M5G 1L7, Canada
| | - Mina Ogawa
- McEwen Centre for Regenerative Medicine, University Health Network, Toronto, ON, M5G 1L7, Canada
| | - Michael D Wilson
- Department of Molecular Genetics, University of Toronto, Toronto, M5G 1A8, Canada.,Genetics and Genome Biology, Hospital for Sick Children, Toronto, M5G 0A4, Canada
| | - Jason E Fish
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, M5G 1L7, Canada.,Division of Advanced Diagnostics, Toronto General Hospital Research Institute, Toronto, ON, M5G 2C4, Canada
| | - Markus Selzner
- Multi-Organ Transplant Program, Toronto General Hospital Research Institute, Toronto, ON, M5G 2C4, Canada
| | - Anand Ghanekar
- Multi-Organ Transplant Program, Toronto General Hospital Research Institute, Toronto, ON, M5G 2C4, Canada
| | - David Grant
- Multi-Organ Transplant Program, Toronto General Hospital Research Institute, Toronto, ON, M5G 2C4, Canada
| | - Paul Greig
- Multi-Organ Transplant Program, Toronto General Hospital Research Institute, Toronto, ON, M5G 2C4, Canada
| | - Gonzalo Sapisochin
- Multi-Organ Transplant Program, Toronto General Hospital Research Institute, Toronto, ON, M5G 2C4, Canada
| | - Nazia Selzner
- Multi-Organ Transplant Program, Toronto General Hospital Research Institute, Toronto, ON, M5G 2C4, Canada
| | - Neil Winegarden
- Princess Margaret Genomics Centre, University Health Network, Toronto, ON, M5G 1L7, Canada
| | - Oyedele Adeyi
- Multi-Organ Transplant Program, Toronto General Hospital Research Institute, Toronto, ON, M5G 2C4, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, M5G 1L7, Canada.,Laboratory Medicine Program, University Health Network, Toronto, Ontario, M5G 1L7, Canada
| | - Gordon Keller
- McEwen Centre for Regenerative Medicine, University Health Network, Toronto, ON, M5G 1L7, Canada.,Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, M5G 1L7, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Gary D Bader
- The Donnelly Centre, University of Toronto, Toronto, ON, M5S 3E1, Canada. .,Department of Molecular Genetics, University of Toronto, Toronto, M5G 1A8, Canada.
| | - Ian D McGilvray
- Multi-Organ Transplant Program, Toronto General Hospital Research Institute, Toronto, ON, M5G 2C4, Canada.
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