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Wu P, Xie S, Cai Y, Liu H, Lv Y, Yang Y, He Y, Yin B, Lan T, Wu H. Causality of immune cells on primary sclerosing cholangitis: a bidirectional two-sample Mendelian randomization study. Front Immunol 2024; 15:1395513. [PMID: 39011035 PMCID: PMC11246896 DOI: 10.3389/fimmu.2024.1395513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Accepted: 06/04/2024] [Indexed: 07/17/2024] Open
Abstract
Background Observational studies have indicated that immune dysregulation in primary sclerosing cholangitis (PSC) primarily involves intestinal-derived immune cells. However, the causal relationship between peripheral blood immune cells and PSC remains insufficiently understood. Methods A bidirectional two-sample Mendelian randomization (MR) analysis was implemented to determine the causal effect between PBC and 731 immune cells. All datasets were extracted from a publicly available genetic database. The standard inverse variance weighted (IVW) method was selected as the main method for the causality analysis. Cochran's Q statistics and MR-Egger intercept were performed to evaluate heterogeneity and pleiotropy. Results In forward MR analysis, the expression ratios of CD11c on CD62L+ myeloid DC (OR = 1.136, 95% CI = 1.032-1.250, p = 0.009) and CD62L-myeloid DC AC (OR = 1.267, 95% CI = 1.086-1.477, p = 0.003) were correlated with a higher risk of PSC. Each one standard deviation increase of CD28 on resting regulatory T cells (Treg) (OR = 0.724, 95% CI = 0.630-0.833, p < 0.001) and CD3 on secreting Treg (OR = 0.893, 95% CI = 0.823-0.969, p = 0.007) negatively associated with the risk of PSC. In reverse MR analysis, PSC was identified with a genetic causal effect on EM CD8+ T cell AC, CD8+ T cell AC, CD28- CD127- CD25++ CD8+ T cell AC, CD28- CD25++ CD8+ T cell AC, CD28- CD8+ T cell/CD8+ T cell, CD28- CD8+ T cell AC, and CD45 RA- CD28- CD8+ T cell AC. Conclusion Our study indicated the evidence of causal effects between PSC and immune cells, which may provide a potential foundation for future diagnosis and treatment of PSC.
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Affiliation(s)
- Pu Wu
- Department of General Surgery, West China Hospital, Sichuan University, Chengdu, China
- Liver Transplant Center, Transplant Center, West China Hospital, Sichuan University, Chengdu, China
- Laboratory of Hepatic AI Translation, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Sinan Xie
- Department of General Surgery, West China Hospital, Sichuan University, Chengdu, China
- Liver Transplant Center, Transplant Center, West China Hospital, Sichuan University, Chengdu, China
- Laboratory of Hepatic AI Translation, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Yunshi Cai
- Department of General Surgery, West China Hospital, Sichuan University, Chengdu, China
- Liver Transplant Center, Transplant Center, West China Hospital, Sichuan University, Chengdu, China
- Laboratory of Hepatic AI Translation, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Hu Liu
- Department of General Surgery, West China Hospital, Sichuan University, Chengdu, China
- Liver Transplant Center, Transplant Center, West China Hospital, Sichuan University, Chengdu, China
- Laboratory of Hepatic AI Translation, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Yinghao Lv
- Department of General Surgery, West China Hospital, Sichuan University, Chengdu, China
- Liver Transplant Center, Transplant Center, West China Hospital, Sichuan University, Chengdu, China
- Laboratory of Hepatic AI Translation, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Ying Yang
- Department of General Surgery, West China Hospital, Sichuan University, Chengdu, China
- Liver Transplant Center, Transplant Center, West China Hospital, Sichuan University, Chengdu, China
- Laboratory of Hepatic AI Translation, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Yucheng He
- Department of General Surgery, West China Hospital, Sichuan University, Chengdu, China
- Liver Transplant Center, Transplant Center, West China Hospital, Sichuan University, Chengdu, China
- Laboratory of Hepatic AI Translation, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Bangjie Yin
- Department of General Surgery, West China Hospital, Sichuan University, Chengdu, China
- Liver Transplant Center, Transplant Center, West China Hospital, Sichuan University, Chengdu, China
- Laboratory of Hepatic AI Translation, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Tian Lan
- Department of General Surgery, West China Hospital, Sichuan University, Chengdu, China
- Liver Transplant Center, Transplant Center, West China Hospital, Sichuan University, Chengdu, China
- Laboratory of Hepatic AI Translation, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Hong Wu
- Department of General Surgery, West China Hospital, Sichuan University, Chengdu, China
- Liver Transplant Center, Transplant Center, West China Hospital, Sichuan University, Chengdu, China
- Laboratory of Hepatic AI Translation, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
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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] [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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