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Qiu ZX, Huang LX, Wang XX, Wang ZL, Li XH, Feng B. Exploring the Pathogenesis of Autoimmune Liver Diseases from the Heterogeneity of Target Cells. J Clin Transl Hepatol 2024; 12:659-666. [PMID: 38993508 PMCID: PMC11233981 DOI: 10.14218/jcth.2023.00531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Revised: 04/28/2024] [Accepted: 04/30/2024] [Indexed: 07/13/2024] Open
Abstract
The incidence of autoimmune liver diseases (ALDs) and research on their pathogenesis are increasing annually. However, except for autoimmune hepatitis, which responds well to immunosuppression, primary biliary cholangitis and primary sclerosing cholangitis are insensitive to immunosuppressive therapy. Besides the known effects of the environment, genetics, and immunity on ALDs, the heterogeneity of target cells provides new insights into their pathogenesis. This review started by exploring the heterogeneity in the development, structures, and functions of hepatocytes and epithelial cells of the small and large bile ducts. For example, cytokeratin (CK) 8 and CK18 are primarily expressed in hepatocytes, while CK7 and CK19 are primarily expressed in intrahepatic cholangiocytes. Additionally, emerging technologies of single-cell RNA sequencing and spatial transcriptomic are being applied to study ALDs. This review offered a new perspective on understanding the pathogenic mechanisms and potential treatment strategies for ALDs.
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Affiliation(s)
| | | | - Xiao-Xiao Wang
- Peking University People’s Hospital, Peking University Hepatology Institute, Beijing Key Laboratory of Hepatitis C and Immunotherapy for Liver Diseases, Beijing International Cooperation Base for Science and Technology on NAFLD Diagnosis, Beijing, China
| | - Zi-Long Wang
- Peking University People’s Hospital, Peking University Hepatology Institute, Beijing Key Laboratory of Hepatitis C and Immunotherapy for Liver Diseases, Beijing International Cooperation Base for Science and Technology on NAFLD Diagnosis, Beijing, China
| | - Xiao-He Li
- Peking University People’s Hospital, Peking University Hepatology Institute, Beijing Key Laboratory of Hepatitis C and Immunotherapy for Liver Diseases, Beijing International Cooperation Base for Science and Technology on NAFLD Diagnosis, Beijing, China
| | - Bo Feng
- Peking University People’s Hospital, Peking University Hepatology Institute, Beijing Key Laboratory of Hepatitis C and Immunotherapy for Liver Diseases, Beijing International Cooperation Base for Science and Technology on NAFLD Diagnosis, Beijing, China
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Poch T, Bahn J, Casar C, Krause J, Evangelakos I, Gilladi H, Kunzmann LK, Laschtowitz A, Iuso N, Schäfer AM, Liebig LA, Steinmann S, Sebode M, Folseraas T, Engesæter LK, Karlsen TH, Franke A, Hubner N, Schlein C, Galun E, Huber S, Lohse AW, Gagliani N, Schwinge D, Schramm C. Intergenic risk variant rs56258221 skews the fate of naive CD4 + T cells via miR4464-BACH2 interplay in primary sclerosing cholangitis. Cell Rep Med 2024; 5:101620. [PMID: 38901430 DOI: 10.1016/j.xcrm.2024.101620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Revised: 04/16/2024] [Accepted: 05/27/2024] [Indexed: 06/22/2024]
Abstract
Primary sclerosing cholangitis (PSC) is an immune-mediated liver disease of unknown pathogenesis, with a high risk to develop cirrhosis and malignancies. Functional dysregulation of T cells and association with genetic polymorphisms in T cell-related genes were previously reported for PSC. Here, we genotyped a representative PSC cohort for several disease-associated risk loci and identified rs56258221 (BACH2/MIR4464) to correlate with not only the peripheral blood T cell immunophenotype but also the functional capacities of naive CD4+ T (CD4+ TN) cells in people with PSC. Mechanistically, rs56258221 leads to an increased expression of miR4464, in turn causing attenuated translation of BACH2, a major gatekeeper of T cell quiescence. Thereby, the fate of CD4+ TN is skewed toward polarization into pro-inflammatory subsets. Clinically, people with PSC carrying rs56258221 show signs of accelerated disease progression. The data presented here highlight the importance of assigning functional outcomes to disease-associated genetic polymorphisms as potential drivers of diseases.
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Affiliation(s)
- Tobias Poch
- I. Department of Medicine, University Medical Centre Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Jonas Bahn
- I. Department of Medicine, University Medical Centre Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Christian Casar
- I. Department of Medicine, University Medical Centre Hamburg-Eppendorf, 20246 Hamburg, Germany; Bioinformatics Core, University Medical Centre Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Jenny Krause
- I. Department of Medicine, University Medical Centre Hamburg-Eppendorf, 20246 Hamburg, Germany; European Reference Network for Hepatological Diseases (ERN RARE-LIVER), 20246 Hamburg, Germany
| | - Ioannis Evangelakos
- Institute of Human Genetics, University Medical Centre Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Hilla Gilladi
- The Goldyne-Savad Institute of Gene Therapy, Hadassah Hebrew University Hospital, Jerusalem 91120, Israel
| | - Lilly K Kunzmann
- I. Department of Medicine, University Medical Centre Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Alena Laschtowitz
- I. Department of Medicine, University Medical Centre Hamburg-Eppendorf, 20246 Hamburg, Germany; Department of Hepatology and Gastroenterology, Charité Universitätsmedizin Berlin, 13353 Berlin, Germany
| | - Nicola Iuso
- I. Department of Medicine, University Medical Centre Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Anne-Marie Schäfer
- I. Department of Medicine, University Medical Centre Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Laura A Liebig
- I. Department of Medicine, University Medical Centre Hamburg-Eppendorf, 20246 Hamburg, Germany; Cardiovascular and Metabolic Sciences, Max Delbrück Centre for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
| | - Silja Steinmann
- I. Department of Medicine, University Medical Centre Hamburg-Eppendorf, 20246 Hamburg, Germany; European Reference Network for Hepatological Diseases (ERN RARE-LIVER), 20246 Hamburg, Germany
| | - Marcial Sebode
- I. Department of Medicine, University Medical Centre Hamburg-Eppendorf, 20246 Hamburg, Germany; European Reference Network for Hepatological Diseases (ERN RARE-LIVER), 20246 Hamburg, Germany
| | - Trine Folseraas
- European Reference Network for Hepatological Diseases (ERN RARE-LIVER), 20246 Hamburg, Germany; Norwegian PSC Research Centre, Department of Transplantation Medicine, Oslo University Hospital Rikshospitalet, 0372 Oslo, Norway; Research Institute of Internal Medicine, Oslo University Hospital Rikshospitalet, 0372 Oslo, Norway
| | - Lise K Engesæter
- European Reference Network for Hepatological Diseases (ERN RARE-LIVER), 20246 Hamburg, Germany; Norwegian PSC Research Centre, Department of Transplantation Medicine, Oslo University Hospital Rikshospitalet, 0372 Oslo, Norway; Research Institute of Internal Medicine, Oslo University Hospital Rikshospitalet, 0372 Oslo, Norway
| | - Tom H Karlsen
- European Reference Network for Hepatological Diseases (ERN RARE-LIVER), 20246 Hamburg, Germany; Norwegian PSC Research Centre, Department of Transplantation Medicine, Oslo University Hospital Rikshospitalet, 0372 Oslo, Norway; Research Institute of Internal Medicine, Oslo University Hospital Rikshospitalet, 0372 Oslo, Norway
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, 24105 Kiel, Germany
| | - Norbert Hubner
- Cardiovascular and Metabolic Sciences, Max Delbrück Centre for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany; DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, 10785 Berlin, Germany; Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Christian Schlein
- Institute of Human Genetics, University Medical Centre Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Eithan Galun
- The Goldyne-Savad Institute of Gene Therapy, Hadassah Hebrew University Hospital, Jerusalem 91120, Israel
| | - Samuel Huber
- I. Department of Medicine, University Medical Centre Hamburg-Eppendorf, 20246 Hamburg, Germany; European Reference Network for Hepatological Diseases (ERN RARE-LIVER), 20246 Hamburg, Germany; Hamburg Centre for Translational Immunology, University Medical Centre Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Ansgar W Lohse
- I. Department of Medicine, University Medical Centre Hamburg-Eppendorf, 20246 Hamburg, Germany; European Reference Network for Hepatological Diseases (ERN RARE-LIVER), 20246 Hamburg, Germany; Hamburg Centre for Translational Immunology, University Medical Centre Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Nicola Gagliani
- I. Department of Medicine, University Medical Centre Hamburg-Eppendorf, 20246 Hamburg, Germany; Hamburg Centre for Translational Immunology, University Medical Centre Hamburg-Eppendorf, 20246 Hamburg, Germany; Department for General, Visceral and Thoracic Surgery, University Medical Centre Hamburg-Eppendorf, 20246 Hamburg, Germany; Immunology and Allergy Unit, Department of Medicine Solna, Karolinska Institute, 17177 Solna, Sweden
| | - Dorothee Schwinge
- I. Department of Medicine, University Medical Centre Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Christoph Schramm
- I. Department of Medicine, University Medical Centre Hamburg-Eppendorf, 20246 Hamburg, Germany; European Reference Network for Hepatological Diseases (ERN RARE-LIVER), 20246 Hamburg, Germany; Hamburg Centre for Translational Immunology, University Medical Centre Hamburg-Eppendorf, 20246 Hamburg, Germany; Martin Zeitz Centre for Rare Diseases, University Medical Centre Hamburg-Eppendorf, 20246 Hamburg, Germany.
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3
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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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Trivedi PJ, Hirschfield GM, Adams DH, Vierling JM. Immunopathogenesis of Primary Biliary Cholangitis, Primary Sclerosing Cholangitis and Autoimmune Hepatitis: Themes and Concepts. Gastroenterology 2024; 166:995-1019. [PMID: 38342195 DOI: 10.1053/j.gastro.2024.01.049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 01/21/2024] [Accepted: 01/28/2024] [Indexed: 02/13/2024]
Abstract
Autoimmune liver diseases include primary biliary cholangitis, primary sclerosing cholangitis, and autoimmune hepatitis, a family of chronic immune-mediated disorders that target hepatocytes and cholangiocytes. Treatments remain nonspecific, variably effective, and noncurative, and the need for liver transplantation is disproportionate to their rarity. Development of effective therapies requires better knowledge of pathogenic mechanisms, including the roles of genetic risk, and how the environment and gut dysbiosis cause immune cell dysfunction and aberrant bile acid signaling. This review summarizes key etiologic and pathogenic concepts and themes relevant for clinical practice and how such learning can guide the development of new therapies for people living with autoimmune liver diseases.
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Affiliation(s)
- Palak J Trivedi
- National Institute for Health Research Birmingham Biomedical Research Centre, Centre for Liver and Gastrointestinal Research, Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, United Kingdom; Liver Unit, University Hospitals Birmingham, Birmingham, United Kingdom; Institute of Translational Medicine, University of Birmingham, Birmingham, United Kingdom.
| | - Gideon M Hirschfield
- Division of Gastroenterology and Hepatology, Toronto Centre for Liver Disease, University of Toronto, Toronto, Ontario, Canada
| | - David H Adams
- National Institute for Health Research Birmingham Biomedical Research Centre, Centre for Liver and Gastrointestinal Research, Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, United Kingdom; Liver Unit, University Hospitals Birmingham, Birmingham, United Kingdom
| | - John M Vierling
- Section of Gastroenterology and Hepatology, Department of Medicine, Baylor College of Medicine, Houston, Texas; Division of Abdominal Transplantation, Department of Surgery, Baylor College of Medicine, Houston, Texas.
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5
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Krause J, Schramm C. Multi-omics characterization of healthy and PSC human liver - what we knew and what we have learned. J Hepatol 2024; 80:681-683. [PMID: 38428642 DOI: 10.1016/j.jhep.2024.02.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 02/15/2024] [Accepted: 02/15/2024] [Indexed: 03/03/2024]
Affiliation(s)
- Jenny Krause
- Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg 20246 Germany
| | - Christoph Schramm
- Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg 20246 Germany; Hamburg Center for Translational Immunology, University Medical Center Hamburg-Eppendorf, Hamburg 20246 Germany; Martin Zeitz Center for Rare Diseases, University Medical Center Hamburg-Eppendorf, Hamburg 20246 Germany.
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6
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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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7
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Padoan B, Casar C, Krause J, Schultheiss C, Baumdick ME, Niehrs A, Zecher BF, Pujantell M, Yuki Y, Martin M, Remmerswaal EBM, Dekker T, van der Bom-Baylon ND, Noble JA, Carrington M, Bemelman FJ, van Lier RAW, Binder M, Gagliani N, Bunders MJ, Altfeld M. NKp44/HLA-DP-dependent regulation of CD8 effector T cells by NK cells. Cell Rep 2024; 43:114089. [PMID: 38615318 DOI: 10.1016/j.celrep.2024.114089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 03/03/2024] [Accepted: 03/26/2024] [Indexed: 04/16/2024] Open
Abstract
Although natural killer (NK) cells are recognized for their modulation of immune responses, the mechanisms by which human NK cells mediate immune regulation are unclear. Here, we report that expression of human leukocyte antigen (HLA)-DP, a ligand for the activating NK cell receptor NKp44, is significantly upregulated on CD8+ effector T cells, in particular in human cytomegalovirus (HCMV)+ individuals. HLA-DP+ CD8+ T cells expressing NKp44-binding HLA-DP antigens activate NKp44+ NK cells, while HLA-DP+ CD8+ T cells not expressing NKp44-binding HLA-DP antigens do not. In line with this, frequencies of HLA-DP+ CD8+ T cells are increased in individuals not encoding for NKp44-binding HLA-DP haplotypes, and contain hyper-expanded CD8+ T cell clones, compared to individuals expressing NKp44-binding HLA-DP molecules. These findings identify a molecular interaction facilitating the HLA-DP haplotype-specific editing of HLA-DP+ CD8+ T cell effector populations by NKp44+ NK cells and preventing the generation of hyper-expanded T cell clones, which have been suggested to have increased potential for autoimmunity.
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Affiliation(s)
- Benedetta Padoan
- Research Department Virus Immunology, Leibniz Institute of Virology, 20251 Hamburg, Germany
| | - Christian Casar
- Bioinformatics Core, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Jenny Krause
- I. Department of Medicine, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; Center for Immunology, University of Minnesota, Minneapolis, MN, USA
| | - Christoph Schultheiss
- Division of Medical Oncology, University Hospital Basel, 4031 Basel, Switzerland; Laboratory of Translational Immuno-Oncology, Department of Biomedicine, University and University Hospital Basel, 4031 Basel, Switzerland
| | - Martin E Baumdick
- Research Department Virus Immunology, Leibniz Institute of Virology, 20251 Hamburg, Germany; III. Department of Medicine, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Annika Niehrs
- Research Department Virus Immunology, Leibniz Institute of Virology, 20251 Hamburg, Germany
| | - Britta F Zecher
- Research Department Virus Immunology, Leibniz Institute of Virology, 20251 Hamburg, Germany; I. Department of Medicine, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Maria Pujantell
- Research Department Virus Immunology, Leibniz Institute of Virology, 20251 Hamburg, Germany
| | - Yuko Yuki
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA; Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Maureen Martin
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA; Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Ester B M Remmerswaal
- Department of Experimental Immunology, Amsterdam Infection and Immunity Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Tamara Dekker
- Department of Experimental Immunology, Amsterdam Infection and Immunity Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Nelly D van der Bom-Baylon
- Department of Experimental Immunology, Amsterdam Infection and Immunity Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Janelle A Noble
- Department of Pediatrics UCSF, Children's Hospital Oakland Research Institute, Oakland, CA 94609, USA
| | - Mary Carrington
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA; Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA; Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Frederike J Bemelman
- Renal Transplant Unit, Division of Internal Medicine, Academic Medical Centre, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | | | - Mascha Binder
- Division of Medical Oncology, University Hospital Basel, 4031 Basel, Switzerland; Laboratory of Translational Immuno-Oncology, Department of Biomedicine, University and University Hospital Basel, 4031 Basel, Switzerland
| | - Nicola Gagliani
- I. Department of Medicine, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; Hamburg Center for Translational Immunology (HCTI), Hamburg, Germany
| | - Madeleine J Bunders
- Research Department Virus Immunology, Leibniz Institute of Virology, 20251 Hamburg, Germany; III. Department of Medicine, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; Hamburg Center for Translational Immunology (HCTI), Hamburg, Germany
| | - Marcus Altfeld
- Research Department Virus Immunology, Leibniz Institute of Virology, 20251 Hamburg, Germany; Hamburg Center for Translational Immunology (HCTI), Hamburg, Germany.
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8
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Dold L, Kalthoff S, Frank L, Zhou T, Esser P, Lutz P, Strassburg CP, Spengler U, Langhans B. STAT activation in regulatory CD4 + T cells of patients with primary sclerosing cholangitis. Immun Inflamm Dis 2024; 12:e1248. [PMID: 38607233 PMCID: PMC11010953 DOI: 10.1002/iid3.1248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 03/25/2024] [Accepted: 03/31/2024] [Indexed: 04/13/2024] Open
Abstract
INTRODUCTION Regulatory CD4+ T cells (Tregs) are pivotal for inhibition of autoimmunity. Primary sclerosing cholangitis (PSC) is an autoimmune cholestatic liver disease of unknown etiology where contribution of Tregs is still unclear. Activation of the JAK-STAT pathway critically modifies functions of Tregs. In PSC, we studied activation of STAT proteins and Treg functions in response to cytokines. METHODS In 51 patients with PSC, 10 disease controls (chronic replicative hepatitis C), and 36 healthy controls we analyzed frequencies of Foxp3+CD25+CD127lowCD4+ Tregs, their expression of ectonucleotidase CD39, and cytokine-induced phosphorylation of STAT1, 3, 5, and 6 using phospho-flow cytometry. In parallel, we measured cytokines IFN-gamma, interleukin (IL)-6, IL-2, and IL-4 in serum via bead-based immunoassays. RESULTS In patients with PSC, ex vivo frequencies of peripheral Tregs and their expression of CD39 were significantly reduced (p < .05 each). Furthermore, serum levels of IFN-gamma, IL-6, IL-2, and IL-4 were markedly higher in PSC (p < .05 each). Unlike activation of STAT1, STAT5, and STAT6, IL-6 induced increased phosphorylation of STAT3 in Tregs of PSC-patients (p = .0434). Finally, STAT3 activation in Tregs correlated with leukocyte counts. CONCLUSIONS In PSC, we observed enhanced STAT3 responsiveness of CD4+ Tregs together with reduced CD39 expression probably reflecting inflammatory activity of the disease.
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Affiliation(s)
- Leona Dold
- Department of Internal Medicine I, University Hospital of Bonn, Bonn, Germany
- German Center for Infection Research (DZIF), Partner Site Cologne-Bonn, Bonn, Germany
| | - Sandra Kalthoff
- Department of Internal Medicine I, University Hospital of Bonn, Bonn, Germany
| | - Leonie Frank
- Department of Internal Medicine I, University Hospital of Bonn, Bonn, Germany
| | - Taotao Zhou
- Department of Internal Medicine I, University Hospital of Bonn, Bonn, Germany
| | - Pia Esser
- Department of Internal Medicine I, University Hospital of Bonn, Bonn, Germany
| | - Philipp Lutz
- Department of Internal Medicine I, University Hospital of Bonn, Bonn, Germany
| | | | - Ulrich Spengler
- Department of Internal Medicine I, University Hospital of Bonn, Bonn, Germany
| | - Bettina Langhans
- Department of Internal Medicine I, University Hospital of Bonn, Bonn, Germany
- German Center for Infection Research (DZIF), Partner Site Cologne-Bonn, Bonn, Germany
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9
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Jiang X, Otterdal K, Chung BK, Maucourant C, Rønneberg JD, Zimmer CL, Øgaard J, Boichuk Y, Holm S, Geanon D, Schneditz G, Bergquist A, Björkström NK, Melum E. Cholangiocytes Modulate CD100 Expression in the Liver and Facilitate Pathogenic T-Helper 17 Cell Differentiation. Gastroenterology 2024; 166:667-679. [PMID: 37995866 DOI: 10.1053/j.gastro.2023.11.283] [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: 02/28/2023] [Revised: 10/18/2023] [Accepted: 11/08/2023] [Indexed: 11/25/2023]
Abstract
BACKGROUND & AIMS Chronic inflammation surrounding bile ducts contributes to the disease pathogenesis of most cholangiopathies. Poor efficacy of immunosuppression in these conditions suggests biliary-specific pathologic principles. Here we performed biliary niche specific functional interpretation of a causal mutation (CD100 K849T) of primary sclerosing cholangitis (PSC) to understand related pathogenic mechanisms. METHODS Biopsy specimens of explanted livers and endoscopy-guided sampling were used to assess the CD100 expression by spatial transcriptomics, immune imaging, and high-dimensional flow cytometry. To model pathogenic cholangiocyte-immune cell interaction, splenocytes from mutation-specific mice were cocultured with cholangiocytes. Pathogenic pathways were pinpointed by RNA sequencing analysis of cocultured cells and cross-validated in patient materials. RESULTS CD100 is mainly expressed by immune cells in the liver and shows a unique pattern around PSC bile ducts with RNA-level colocalization but poor detection at the protein level. This appears to be due to CD100 cleavage as soluble CD100 is increased. Immunophenotyping suggests biliary-infiltrating T cells as the major source of soluble CD100, which is further supported by reduced surface CD100 on T cells and increased metalloproteinases in cholangiocytes after coculturing. Pathogenic T cells that adhered to cholangiocytes up-regulated genes in the T-helper 17 cell differentiation pathway, and the CD100 mutation boosted this process. Consistently, T-helper 17 cells dominate biliary-resident CD4 T cells in patients. CONCLUSIONS CD100 exerts its functional impact through cholangiocyte-immune cell cross talk and underscores an active, proinflammatory role of cholangiocytes that can be relevant to novel treatment approaches.
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Affiliation(s)
- Xiaojun Jiang
- Norwegian PSC Research Center, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital Rikshospitalet, Oslo, Norway; Research Institute of Internal Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital Rikshospitalet, Oslo, Norway
| | - Kari Otterdal
- Research Institute of Internal Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital Rikshospitalet, Oslo, Norway
| | - Brian K Chung
- Norwegian PSC Research Center, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital Rikshospitalet, Oslo, Norway; Research Institute of Internal Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital Rikshospitalet, Oslo, Norway; Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Christopher Maucourant
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Jørgen D Rønneberg
- Norwegian PSC Research Center, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital Rikshospitalet, Oslo, Norway; Research Institute of Internal Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital Rikshospitalet, Oslo, Norway; Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Christine L Zimmer
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Jonas Øgaard
- Norwegian PSC Research Center, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital Rikshospitalet, Oslo, Norway; Research Institute of Internal Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital Rikshospitalet, Oslo, Norway
| | - Yuliia Boichuk
- Norwegian PSC Research Center, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital Rikshospitalet, Oslo, Norway; Research Institute of Internal Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital Rikshospitalet, Oslo, Norway
| | - Sverre Holm
- Research Institute of Internal Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital Rikshospitalet, Oslo, Norway
| | - Daniel Geanon
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Georg Schneditz
- Norwegian PSC Research Center, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital Rikshospitalet, Oslo, Norway; Research Institute of Internal Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital Rikshospitalet, Oslo, Norway
| | - Annika Bergquist
- Department of Gastroenterology and Hepatology, Karolinska University Hospital Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Niklas K Björkström
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Espen Melum
- Norwegian PSC Research Center, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital Rikshospitalet, Oslo, Norway; Research Institute of Internal Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital Rikshospitalet, Oslo, Norway; Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway; Section of Gastroenterology, Department of Transplantation Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital Rikshospitalet, Oslo, Norway; Hybrid Technology Hub-Centre of Excellence, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Oslo, Norway.
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10
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Burtis AEC, DeNicola DMC, Ferguson ME, Santos RG, Pinilla C, Kriss MS, Orlicky DJ, Tamburini BAJ, Gillen AE, Burchill MA. Antigen-driven CD8 + T cell clonal expansion is a prominent feature of MASH in humans and mice. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.20.583964. [PMID: 38562766 PMCID: PMC10983976 DOI: 10.1101/2024.03.20.583964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Background and Aims Chronic liver disease due to metabolic dysfunction-associated steatohepatitis (MASH) is a rapidly increasing global epidemic. MASH progression is a consequence of the complex interplay between inflammatory insults and dysregulated hepatic immune responses. T lymphocytes have been shown to accumulate in the liver during MASH, but the cause and consequence of T cell accumulation in the liver remain unclear. Our study aimed to define the phenotype and T cell receptor diversity of T cells from human cirrhotic livers and an animal model of MASH to begin resolving their function in disease. Approach and Results In these studies, we evaluated differences in T cell phenotype in the context of liver disease we isolated liver resident T cell populations from individuals with cirrhosis and a murine model of MASH. Using both 5' single cell sequencing and flow cytometry we defined the phenotype and T cell receptor repertoire of liver resident T cells during health and disease. Conclusions MASH-induced cirrhosis and diet-induced MASH in mice resulted in the accumulation of activated and clonally expanded T cells in the liver. The clonally expanded T cells in the liver expressed markers of chronic antigenic stimulation, including PD1 , TIGIT and TOX . Overall, this study establishes for the first time that T cells undergo antigen-dependent clonal expansion and functional differentiation during the progression of MASH. These studies could lead to the identification of potential antigenic targets that drive T cell activation, clonal expansion, and recruitment to the liver during MASH.
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11
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Guicciardi ME, Jalan-Sakrikar N. Finding the TRAIL to escape granzyme B-mediated liver injury in PSC. Hepatology 2024:01515467-990000000-00812. [PMID: 38502805 DOI: 10.1097/hep.0000000000000859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 03/06/2024] [Indexed: 03/21/2024]
Affiliation(s)
- Maria Eugenia Guicciardi
- Division of Gastroenterology and Hepatology, Center for Cell Signaling in Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota, USA
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12
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Kellerer M, Javed S, Casar C, Will N, Berkhout LK, Schwinge D, Krebs CF, Schramm C, Neumann K, Tiegs G. Antagonistic effects of the cytotoxic molecules granzyme B and TRAIL in the immunopathogenesis of sclerosing cholangitis. Hepatology 2024:01515467-990000000-00782. [PMID: 38441998 DOI: 10.1097/hep.0000000000000830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 01/23/2024] [Indexed: 03/07/2024]
Abstract
BACKGROUND AND AIMS Primary sclerosing cholangitis (PSC) is a chronic cholestatic liver disease characterized by biliary inflammation and fibrosis. We showed an elevated interferon γ response in patients with primary sclerosing cholangitis and in multidrug resistance protein 2-deficient ( Mdr2-/- ) mice developing sclerosing cholangitis. Interferon γ induced expression of the cytotoxic molecules granzyme B (GzmB) and TRAIL in hepatic lymphocytes and mediated liver fibrosis in sclerosing cholangitis. APPROACH AND RESULTS In patient samples and Mdr2-/- mice, we identified lymphocyte clusters with a cytotoxic gene expression profile using single-cell RNA-seq and cellular indexing of transcriptomes and epitopes by sequencing analyses combined with multi-parameter flow cytometry. CD8 + T cells and NK cells showed increased expression of GzmB and TRAIL in sclerosing cholangitis. Depletion of CD8 + T cells ameliorated disease severity in Mdr2-/- mice. By using Mdr2-/- × Gzmb-/- and Mdr2-/- × Tnfsf10-/- mice, we investigated the significance of GzmB and TRAIL for disease progression in sclerosing cholangitis. Interestingly, the lack of GzmB resulted in reduced cholangiocyte apoptosis, liver injury, and fibrosis. In contrast, sclerosing cholangitis was aggravated in the absence of TRAIL. This correlated with elevated GzmB and interferon γ expression by CD8 + T cells and NK cells enhanced T-cell survival, and increased apoptosis and expansion of cholangiocytes. CONCLUSIONS GzmB induces apoptosis and fibrosis in sclerosing cholangitis, whereas TRAIL regulates inflammatory and cytotoxic immune responses, subsequently leading to reduced liver injury and fibrosis.
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Affiliation(s)
- Mareike Kellerer
- Institute of Experimental Immunology and Hepatology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Hamburg Center for Translational Immunology (HCTI), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Sana Javed
- Institute of Experimental Immunology and Hepatology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Hamburg Center for Translational Immunology (HCTI), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Department of Pharmacy, The University of Faisalabad, Pakistan
| | - Christian Casar
- Hamburg Center for Translational Immunology (HCTI), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Bioinformatics Core, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Nico Will
- Hamburg Center for Translational Immunology (HCTI), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Laura K Berkhout
- Institute of Experimental Immunology and Hepatology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Hamburg Center for Translational Immunology (HCTI), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Dorothee Schwinge
- Hamburg Center for Translational Immunology (HCTI), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Christian F Krebs
- Hamburg Center for Translational Immunology (HCTI), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Christoph Schramm
- Hamburg Center for Translational Immunology (HCTI), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Martin Zeitz Center for Rare Diseases, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Katrin Neumann
- Institute of Experimental Immunology and Hepatology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Hamburg Center for Translational Immunology (HCTI), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Gisa Tiegs
- Institute of Experimental Immunology and Hepatology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Hamburg Center for Translational Immunology (HCTI), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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13
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Dong X, Gong LL, Hong MZ, Pan JS. Investigating the shared genetic architecture between primary sclerosing cholangitis and inflammatory bowel diseases: a Mendelian randomization study. BMC Gastroenterol 2024; 24:77. [PMID: 38373892 PMCID: PMC10875759 DOI: 10.1186/s12876-024-03162-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 02/07/2024] [Indexed: 02/21/2024] Open
Abstract
BACKGROUND Several studies have found that primary sclerosing cholangitis (PSC) and inflammatory bowel disease (IBD) are closely associated. However, the direction and causality of their interactions remain unclear. Thus, this study employs Mendelian Randomization to explore whether there are causal associations of genetically predicted PSC with IBD. METHODS Genetic variants associated with the genome-wide association study (GWAS) of PSC were used as instrumental variables. The statistics for IBD, including ulcerative colitis (UC), and Crohn's disease (CD) were derived from GWAS. Then, five methods were used to estimate the effects of genetically predicted PSC on IBD, including MR Egger, Weighted median (WM), Inverse variance weighted (IVW), Simple mode, and Weighted mode. Last, we also evaluated the pleiotropic effects, heterogeneity, and a leave-one-out sensitivity analysis that drives causal associations to confirm the validity of the analysis. RESULTS Genetically predicted PSC was significantly associated with an increased risk of UC, according to the study (odds ratio [OR] IVW= 1.0014, P<0.05). However, none of the MR methods found significant causal evidence of genetically predicted PSC in CD (All P>0.05). The sensitivity analysis results showed that the causal effect estimations of genetically predicted PSC on IBD were robust, and there was no horizontal pleiotropy or statistical heterogeneity. CONCLUSIONS Our study corroborated a causal association between genetically predicted PSC and UC but did not between genetically predicted PSC and CD. Then, we identification of shared SNPs for PSC and UC, including rs3184504, rs9858213, rs725613, rs10909839, and rs4147359. More animal experiments and clinical observational studies are required to further clarify the underlying mechanisms of PSC and IBD.
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Affiliation(s)
- Xuan Dong
- Department of Hepatology, the First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
- Hepatology Research Institute, Fujian Medical University, Fuzhou, Fujian, China
- Department of Hepatology, National Regional Medical Center, Binhai Campus of the First Affiliated Hosptial, Fujian Medical University, Fuzhou, Fujian, China
- Fujian Clinical Research Center for Hepatopathy and Intestinal Diseases, Fuzhou, Fujian, China
| | - Li-Li Gong
- Department of General Practice, Zhongshan Hospital, Xiamen University, Xiamen, Fujian, China
| | - Mei-Zhu Hong
- Department of Traditional Chinese Medicine, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, Fujian, China.
| | - Jin-Shui Pan
- Department of Hepatology, the First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China.
- Hepatology Research Institute, Fujian Medical University, Fuzhou, Fujian, China.
- Department of Hepatology, National Regional Medical Center, Binhai Campus of the First Affiliated Hosptial, Fujian Medical University, Fuzhou, Fujian, China.
- Fujian Clinical Research Center for Hepatopathy and Intestinal Diseases, Fuzhou, Fujian, China.
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14
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Chen W, Lin F, Feng X, Yao Q, Yu Y, Gao F, Zhou J, Pan Q, Wu J, Yang J, Yu J, Cao H, Li L. MSC-derived exosomes attenuate hepatic fibrosis in primary sclerosing cholangitis through inhibition of Th17 differentiation. Asian J Pharm Sci 2024; 19:100889. [PMID: 38419761 PMCID: PMC10900800 DOI: 10.1016/j.ajps.2024.100889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 12/13/2023] [Accepted: 01/14/2024] [Indexed: 03/02/2024] Open
Abstract
Primary sclerosing cholangitis (PSC) is an autoimmune cholangiopathy characterized by chronic inflammation of the biliary epithelium and periductal fibrosis, with no curative treatment available, and liver transplantation is inevitable for end-stage patients. Human placental mesenchymal stem cell (hpMSC)-derived exosomes have demonstrated the ability to prevent fibrosis, inhibit collagen production and possess immunomodulatory properties in autoimmune liver disease. Here, we prepared hpMSC-derived exosomes (ExoMSC) and further investigated the anti-fibrotic effects and detailed mechanism on PSC based on Mdr2-/- mice and multicellular organoids established from PSC patients. The results showed that ExoMSC ameliorated liver fibrosis in Mdr2-/- mice with significant collagen reduction in the preductal area where Th17 differentiation was inhibited as demonstrated by RNAseq analysis, and the percentage of CD4+IL-17A+T cells was reduced both in ExoMSC-treated Mdr2-/- mice (Mdr2-/--Exo) in vivo and ExoMSC-treated Th17 differentiation progressed in vitro. Furthermore, ExoMSC improved the hypersecretory phenotype and intercellular interactions in the hepatic Th17 microenvironment by regulating PERK/CHOP signaling as supported by multicellular organoids. Thus, our data demonstrate the anti-fibrosis effect of ExoMSC in PSC disease by inhibiting Th17 differentiation, and ameliorating the Th17-induced microenvironment, indicating the promising potential therapeutic role of ExoMSC in liver fibrosis of PSC or Th17-related diseases.
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Affiliation(s)
- Wenyi Chen
- State Key Laboratory for the Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Medical Center for Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China
| | - Feiyan Lin
- State Key Laboratory for the Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Medical Center for Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China
| | - Xudong Feng
- State Key Laboratory for the Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Medical Center for Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China
| | - Qigu Yao
- State Key Laboratory for the Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Medical Center for Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China
| | - Yingduo Yu
- State Key Laboratory for the Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Medical Center for Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China
| | - Feiqiong Gao
- State Key Laboratory for the Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Medical Center for Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China
| | - Jiahang Zhou
- State Key Laboratory for the Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Medical Center for Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China
| | - Qiaoling Pan
- State Key Laboratory for the Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Medical Center for Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China
| | - Jian Wu
- State Key Laboratory for the Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Medical Center for Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China
| | - Jinfeng Yang
- State Key Laboratory for the Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Medical Center for Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China
| | - Jiong Yu
- State Key Laboratory for the Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Medical Center for Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China
| | - Hongcui Cao
- State Key Laboratory for the Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Medical Center for Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China
- Key Laboratory of Diagnosis and Treatment of Aging and Physic-chemical Injury Diseases of Zhejiang Province, Hangzhou 310003, China
| | - Lanjuan Li
- State Key Laboratory for the Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Medical Center for Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan 250117, China
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15
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Singh S, Budiman T, Redmond D, Gupta V. Modulation of canonical Wnt signaling regulates peribiliary mesenchymal identity during homeostasis and injury. Hepatol Commun 2024; 8:e0368. [PMID: 38251878 PMCID: PMC10805418 DOI: 10.1097/hc9.0000000000000368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 12/10/2023] [Indexed: 01/23/2024] Open
Abstract
BACKGROUND The matrix and associated mesenchyme of the extrahepatic bile ducts are distinct, which could drive diseases with a predilection for these ducts, such as primary sclerosing cholangitis. We aimed to understand the molecular drivers of peribiliary mesenchymal cell (PMC) identity in the extrahepatic bile ducts and dissect how this changed in the context of injury using an entirely in vivo approach with transcriptomic analysis. METHODS AND RESULTS Single-cell sequencing with a receptor-ligand analysis showed that PMCs had the most interactions with surrounding cells. Wnt4, Wnt5a, and Wnt7b were identified as the major ligands secreted from PMCs and cholangiocytes that interacted in both paracrine and autocrine fashion. Bile duct ligation caused an increase in all 3 Wingless/Integrated ligands and Axin2 with an associated increase in the transcription factors T-box transcription factor (Tbx)2 and Tbx3. Conversely, Indian hedgehog secretion decreased without an associated decrease in hedgehog signaling effectors. Loss of smoothened within PMCs did not impact hedgehog signaling effectors or cellular identity, whereas smoothened gain of function led to myofibroblast transdifferentiation with upregulation of Tbx2 and Tbx3 without injury. Loss of β-catenin caused a decrease in expression of all 3 Gli transcription factors and associated mesenchymal gene expression, which was phenocopied with compound Gli2 and Gli3 loss in uninjured PMCs. With injury, loss of β-catenin resulted in decreased myofibroblast transdifferentiation with reduced Tbx2 and Tbx3 expression. CONCLUSIONS Our results show how modulation of canonical Wingless/Integrated signaling in PMCs is important for regulating basal mesenchymal gene expression and initiating a myogenic gene transcriptional program during injury. They also highlight reciprocating interactions between the hedgehog and Wingless/Integrated signaling pathways within PMCs.
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Affiliation(s)
- Serrena Singh
- Department of Internal Medicine, Section of Digestive Diseases, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Tifanny Budiman
- Department of Internal Medicine, Section of Digestive Diseases, Yale University School of Medicine, New Haven, Connecticut, USA
| | - David Redmond
- Department of Medicine, Division of Regenerative Medicine, Ansary Stem Cell Institute, Weill Cornell Medicine, New York, New York, USA
| | - Vikas Gupta
- Department of Internal Medicine, Section of Digestive Diseases, Yale University School of Medicine, New Haven, Connecticut, USA
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16
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Cui A, Li B, Wallace MS, Gonye ALK, Oetheimer C, Patel H, Tonnerre P, Holmes JA, Lieb D, Yao BS, Ma A, Roberts K, Damasio M, Chen JH, Piou D, Carlton-Smith C, Brown J, Mylvaganam R, Hon Fung JM, Sade-Feldman M, Aneja J, Gustafson J, Epstein ET, Salloum S, Brisac C, Thabet A, Kim AY, Lauer GM, Hacohen N, Chung RT, Alatrakchi N. Single-cell atlas of the liver myeloid compartment before and after cure of chronic viral hepatitis. J Hepatol 2024; 80:251-267. [PMID: 36972796 DOI: 10.1016/j.jhep.2023.02.040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 01/22/2023] [Accepted: 02/14/2023] [Indexed: 03/29/2023]
Abstract
BACKGROUND & AIMS Chronic viral infections present serious public health challenges; however, direct-acting antivirals (DAAs) are now able to cure nearly all patients infected with hepatitis C virus (HCV), representing the only cure of a human chronic viral infection to date. DAAs provide a valuable opportunity to study immune pathways in the reversal of chronic immune failures in an in vivo human system. METHODS To leverage this opportunity, we used plate-based single-cell RNA-seq to deeply profile myeloid cells from liver fine needle aspirates in patients with HCV before and after DAA treatment. We comprehensively characterised liver neutrophils, eosinophils, mast cells, conventional dendritic cells, plasmacytoid dendritic cells, classical monocytes, non-classical monocytes, and macrophages, and defined fine-grained subpopulations of several cell types. RESULTS We discovered cell type-specific changes post-cure, including an increase in MCM7+STMN1+ proliferating CD1C+ conventional dendritic cells, which may support restoration from chronic exhaustion. We observed an expected downregulation of interferon-stimulated genes (ISGs) post-cure as well as an unexpected inverse relationship between pre-treatment viral load and post-cure ISG expression in each cell type, revealing a link between viral loads and sustained modifications of the host's immune system. We found an upregulation of PD-L1/L2 gene expression in ISG-high neutrophils and IDO1 expression in eosinophils, pinpointing cell subpopulations crucial for immune regulation. We identified three recurring gene programmes shared by multiple cell types, distilling core functions of the myeloid compartment. CONCLUSIONS This comprehensive single-cell RNA-seq atlas of human liver myeloid cells in response to cure of chronic viral infections reveals principles of liver immunity and provides immunotherapeutic insights. CLINICAL TRIAL REGISTRATION This study is registered at ClinicalTrials.gov (NCT02476617). IMPACT AND IMPLICATIONS Chronic viral liver infections continue to be a major public health problem. Single-cell characterisation of liver immune cells during hepatitis C and post-cure provides unique insights into the architecture of liver immunity contributing to the resolution of the first curable chronic viral infection of humans. Multiple layers of innate immune regulation during chronic infections and persistent immune modifications after cure are revealed. Researchers and clinicians may leverage these findings to develop methods to optimise the post-cure environment for HCV and develop novel therapeutic approaches for other chronic viral infections.
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Affiliation(s)
- Ang Cui
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Bo Li
- Broad Institute of MIT and Harvard, Cambridge, MA, USA; Harvard University Virology Program, Harvard Medical School, Boston, MA, USA
| | - Michael S Wallace
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Anna L K Gonye
- Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Christopher Oetheimer
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Hailey Patel
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Pierre Tonnerre
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA; Institut de Recherche Saint-Louis, Université Paris Cité, Inserm U976 (HIPI), Team ATIP-Avenir, Paris, France
| | - Jacinta A Holmes
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA; Department of Gastroenterology, St Vincent's Hospital Melbourne, Melbourne, VIC, Australia
| | - David Lieb
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Brianna S Yao
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Aileen Ma
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Kela Roberts
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Marcos Damasio
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Jonathan H Chen
- Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA; Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - Daphnee Piou
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Charles Carlton-Smith
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Joelle Brown
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Ravi Mylvaganam
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | | | - Moshe Sade-Feldman
- Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Jasneet Aneja
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA; Division of Infectious Diseases, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Jenna Gustafson
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Eliana T Epstein
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Shadi Salloum
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Cynthia Brisac
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Ashraf Thabet
- Department of Interventional Radiology, Massachusetts General Hospital, Boston, MA, USA
| | - Arthur Y Kim
- Division of Infectious Diseases, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Georg M Lauer
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Nir Hacohen
- Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA; Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
| | - Raymond T Chung
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
| | - Nadia Alatrakchi
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
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17
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Sutton H, Karpen SJ, Kamath BM. Pediatric Cholestatic Diseases: Common and Unique Pathogenic Mechanisms. ANNUAL REVIEW OF PATHOLOGY 2024; 19:319-344. [PMID: 38265882 DOI: 10.1146/annurev-pathmechdis-031521-025623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2024]
Abstract
Cholestasis is the predominate feature of many pediatric hepatobiliary diseases. The physiologic flow of bile requires multiple complex processes working in concert. Bile acid (BA) synthesis and excretion, the formation and flow of bile, and the enterohepatic reuptake of BAs all function to maintain the circulation of BAs, a key molecule in lipid digestion, metabolic and cellular signaling, and, as discussed in the review, a crucial mediator in the pathogenesis of cholestasis. Disruption of one or several of these steps can result in the accumulation of toxic BAs in bile ducts and hepatocytes leading to inflammation, fibrosis, and, over time, biliary and hepatic cirrhosis. Biliary atresia, progressive familial intrahepatic cholestasis, primary sclerosing cholangitis, and Alagille syndrome are four of the most common pediatric cholestatic conditions. Through understanding the commonalities and differences in these diseases, the important cellular mechanistic underpinnings of cholestasis can be greater appreciated.
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Affiliation(s)
- Harry Sutton
- The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada;
| | - Saul J Karpen
- Emory University School of Medicine and Children's Healthcare of Atlanta, Atlanta, Georgia, USA
| | - Binita M Kamath
- The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada;
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18
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Santosh Nirmala S, Kayani K, Gliwiński M, Hu Y, Iwaszkiewicz-Grześ D, Piotrowska-Mieczkowska M, Sakowska J, Tomaszewicz M, Marín Morales JM, Lakshmi K, Marek-Trzonkowska NM, Trzonkowski P, Oo YH, Fuchs A. Beyond FOXP3: a 20-year journey unravelling human regulatory T-cell heterogeneity. Front Immunol 2024; 14:1321228. [PMID: 38283365 PMCID: PMC10811018 DOI: 10.3389/fimmu.2023.1321228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 12/19/2023] [Indexed: 01/30/2024] Open
Abstract
The initial idea of a distinct group of T-cells responsible for suppressing immune responses was first postulated half a century ago. However, it is only in the last three decades that we have identified what we now term regulatory T-cells (Tregs), and subsequently elucidated and crystallized our understanding of them. Human Tregs have emerged as essential to immune tolerance and the prevention of autoimmune diseases and are typically contemporaneously characterized by their CD3+CD4+CD25high CD127lowFOXP3+ phenotype. It is important to note that FOXP3+ Tregs exhibit substantial diversity in their origin, phenotypic characteristics, and function. Identifying reliable markers is crucial to the accurate identification, quantification, and assessment of Tregs in health and disease, as well as the enrichment and expansion of viable cells for adoptive cell therapy. In our comprehensive review, we address the contributions of various markers identified in the last two decades since the master transcriptional factor FOXP3 was identified in establishing and enriching purity, lineage stability, tissue homing and suppressive proficiency in CD4+ Tregs. Additionally, our review delves into recent breakthroughs in innovative Treg-based therapies, underscoring the significance of distinct markers in their therapeutic utilization. Understanding Treg subsets holds the key to effectively harnessing human Tregs for immunotherapeutic approaches.
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Affiliation(s)
| | - Kayani Kayani
- Centre for Liver and Gastrointestinal Research and National Institute for Health Research (NIHR) Birmingham Biomedical Research Centre, Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, United Kingdom
- Department of Academic Surgery, Queen Elizabeth Hospital, University of Birmingham, Birmingham, United Kingdom
- Department of Renal Surgery, Queen Elizabeth Hospital Birmingham, University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
| | - Mateusz Gliwiński
- Department of Medical Immunology, Medical University of Gdańsk, Gdańsk, Poland
| | - Yueyuan Hu
- Center for Regenerative Therapies Dresden, Technical University Dresden, Dresden, Germany
| | | | | | - Justyna Sakowska
- Department of Medical Immunology, Medical University of Gdańsk, Gdańsk, Poland
| | - Martyna Tomaszewicz
- Department of Medical Immunology, Medical University of Gdańsk, Gdańsk, Poland
| | | | - Kavitha Lakshmi
- Center for Regenerative Therapies Dresden, Technical University Dresden, Dresden, Germany
| | | | - Piotr Trzonkowski
- Department of Medical Immunology, Medical University of Gdańsk, Gdańsk, Poland
| | - Ye Htun Oo
- Centre for Liver and Gastrointestinal Research and National Institute for Health Research (NIHR) Birmingham Biomedical Research Centre, Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, United Kingdom
- Liver Transplant and Hepatobiliary Unit, University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
- Birmingham Advanced Cellular Therapy Facility, University of Birmingham, Birmingham, United Kingdom
- Centre for Rare Diseases, European Reference Network - Rare Liver Centre, Birmingham, United Kingdom
| | - Anke Fuchs
- Center for Regenerative Therapies Dresden, Technical University Dresden, Dresden, Germany
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19
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Zhu X, Ma S, Wong WH. Genetic effects of sequence-conserved enhancer-like elements on human complex traits. Genome Biol 2024; 25:1. [PMID: 38167462 PMCID: PMC10759394 DOI: 10.1186/s13059-023-03142-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 12/08/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND The vast majority of findings from human genome-wide association studies (GWAS) map to non-coding sequences, complicating their mechanistic interpretations and clinical translations. Non-coding sequences that are evolutionarily conserved and biochemically active could offer clues to the mechanisms underpinning GWAS discoveries. However, genetic effects of such sequences have not been systematically examined across a wide range of human tissues and traits, hampering progress to fully understand regulatory causes of human complex traits. RESULTS Here we develop a simple yet effective strategy to identify functional elements exhibiting high levels of human-mouse sequence conservation and enhancer-like biochemical activity, which scales well to 313 epigenomic datasets across 106 human tissues and cell types. Combined with 468 GWAS of European (EUR) and East Asian (EAS) ancestries, these elements show tissue-specific enrichments of heritability and causal variants for many traits, which are significantly stronger than enrichments based on enhancers without sequence conservation. These elements also help prioritize candidate genes that are functionally relevant to body mass index (BMI) and schizophrenia but were not reported in previous GWAS with large sample sizes. CONCLUSIONS Our findings provide a comprehensive assessment of how sequence-conserved enhancer-like elements affect complex traits in diverse tissues and demonstrate a generalizable strategy of integrating evolutionary and biochemical data to elucidate human disease genetics.
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Affiliation(s)
- Xiang Zhu
- Department of Statistics, The Pennsylvania State University, 326 Thomas Building, University Park, 16802, PA, USA.
- Huck Institutes of the Life Sciences, The Pennsylvania State University, 201 Huck Life Sciences Building, University Park, 16802, PA, USA.
- Department of Statistics, Stanford University, 390 Jane Stanford Way, Stanford, 94305, CA, USA.
| | - Shining Ma
- Department of Statistics, Stanford University, 390 Jane Stanford Way, Stanford, 94305, CA, USA
- Department of Biomedical Data Science, Stanford University School of Medicine, 1265 Welch Road MC5464, Stanford, 94305, CA, USA
| | - Wing Hung Wong
- Department of Statistics, Stanford University, 390 Jane Stanford Way, Stanford, 94305, CA, USA.
- Department of Biomedical Data Science, Stanford University School of Medicine, 1265 Welch Road MC5464, Stanford, 94305, CA, USA.
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20
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Özdirik B, Schnabl B. Microbial Players in Primary Sclerosing Cholangitis: Current Evidence and Concepts. Cell Mol Gastroenterol Hepatol 2023; 17:423-438. [PMID: 38109970 PMCID: PMC10837305 DOI: 10.1016/j.jcmgh.2023.12.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 12/12/2023] [Accepted: 12/12/2023] [Indexed: 12/20/2023]
Abstract
Primary sclerosing cholangitis (PSC) is a rare cholestatic liver disease with progressive biliary inflammation, destruction of the biliary tract, and fibrosis, resulting in liver cirrhosis and end-stage liver disease. To date, liver transplantation is the only definitive treatment option for PSC. The precise etiology of PSC remains elusive, but it is widely accepted to involve a complex interplay between genetic predisposition, immunologic dysfunction, and environmental influence. In recent years, the gut-liver axis has emerged as a crucial pathway contributing to the pathogenesis of PSC, with particular focus on the role of gut microbiota. However, the role of the fungal microbiome or mycobiome has been overlooked for years, resulting in a lack of comprehensive studies on its involvement in PSC. In this review, we clarify the present clinical and mechanistic data and concepts concerning the gut bacterial and fungal microbiota in the context of PSC. This review sheds light on the role of specific microbes and elucidates the dynamics of bacterial and fungal populations. Moreover, we discuss the latest insights into microbe-altering therapeutic approaches involving the gut-liver axis and bile acid metabolism.
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Affiliation(s)
- Burcin Özdirik
- Department of Medicine, University of California San Diego, La Jolla, California
| | - Bernd Schnabl
- Department of Medicine, University of California San Diego, La Jolla, California; Department of Medicine, VA San Diego Healthcare System, San Diego, California.
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21
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Centa M, Thermidor C, Fiel MI, Alexandropoulos K. Profiling of mouse and human liver diseases identifies targets for therapeutic treatment of autoimmune hepatitis. Clin Immunol 2023; 256:109807. [PMID: 37821072 DOI: 10.1016/j.clim.2023.109807] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 10/07/2023] [Indexed: 10/13/2023]
Abstract
Autoimmune hepatitis (AIH), primary sclerosing cholangitis (PSC), and non-alcoholic steatohepatitis (NASH) are chronic liver diseases (CLDs) of distinct etiologies that represent a public health risk with limited therapeutic options. A common feature among CLDs is an aggressive T cell response resulting in destruction of liver tissue and fibrosis. Here, we assessed the presence and nature of T cell inflammation in late-stage human AIH, PSC and NASH and examined whether targeting the T cell response can improve disease pathology in a mouse model (Traf6ΔTEC) of spontaneous AIH. T cell infiltration and ensuing inflammatory pathways were present in human AIH and PSC and to a lesser extent in NASH. However, we observed qualitative differences in infiltrating T cell subsets and upregulation of inflammatory pathways among these diseases, while mouse and human AIH exhibited similar immunogenic signatures. While gene expression profiles differed among diseases, we identified 52 genes commonly upregulated across all diseases that included the JAK3 tyrosine kinase. Therapeutic targeting of chronic AIH with the JAK inhibitor tofacitinib reduced hepatic T cell infiltration, AIH histopathology and associated immune parameters in treated Traf6ΔTEC mice. Our results indicate that targeting T cell responses in established hepatic autoimmune inflammation is a feasible strategy for developing novel therapeutic approaches to treat AIH and possibly other CLDs irrespective of etiology.
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Affiliation(s)
- Monica Centa
- Department of Medicine, Division of Clinical Immunology, Division of Liver Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Christelle Thermidor
- Department of Medicine, Division of Clinical Immunology, Division of Liver Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Maria Isabel Fiel
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Konstantina Alexandropoulos
- Department of Medicine, Division of Clinical Immunology, Division of Liver Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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22
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Pratt HE, Wu T, Elhajjajy S, Zhou J, Fitzgerald K, Fazzio T, Weng Z, Pratt DS. Beyond genome-wide association studies: Investigating the role of noncoding regulatory elements in primary sclerosing cholangitis. Hepatol Commun 2023; 7:e0242. [PMID: 37756045 PMCID: PMC10531193 DOI: 10.1097/hc9.0000000000000242] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 06/13/2023] [Indexed: 09/28/2023] Open
Abstract
BACKGROUND Genome-wide association studies (GWAS) have identified 30 risk loci for primary sclerosing cholangitis (PSC). Variants within these loci are found predominantly in noncoding regions of DNA making their mechanisms of conferring risk hard to define. Epigenomic studies have shown noncoding variants broadly impact regulatory element activity. The possible association of noncoding PSC variants with regulatory element activity has not been studied. We aimed to (1) determine if the noncoding risk variants in PSC impact regulatory element function and (2) if so, assess the role these regulatory elements have in explaining the genetic risk for PSC. METHODS Available epigenomic datasets were integrated to build a comprehensive atlas of cell type-specific regulatory elements, emphasizing PSC-relevant cell types. RNA-seq and ATAC-seq were performed on peripheral CD4+ T cells from 10 PSC patients and 11 healthy controls. Computational techniques were used to (1) study the enrichment of PSC-risk variants within regulatory elements, (2) correlate risk genotype with differences in regulatory element activity, and (3) identify regulatory elements differentially active and genes differentially expressed between PSC patients and controls. RESULTS Noncoding PSC-risk variants are strongly enriched within immune-specific enhancers, particularly ones involved in T-cell response to antigenic stimulation. In total, 250 genes and >10,000 regulatory elements were identified that are differentially active between patients and controls. CONCLUSIONS Mechanistic effects are proposed for variants at 6 PSC-risk loci where genotype was linked with differential T-cell regulatory element activity. Regulatory elements are shown to play a key role in PSC pathophysiology.
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Affiliation(s)
- Henry E. Pratt
- Program in Bioinformatics and Integrative Biology, Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Tong Wu
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Shaimae Elhajjajy
- Program in Bioinformatics and Integrative Biology, Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Jeffrey Zhou
- Program in Innate Immunity, Department of Medicine, University of Massachusetts Chan Medical, School, Worcester, Massachusetts, USA
| | - Kate Fitzgerald
- Program in Innate Immunity, Department of Medicine, University of Massachusetts Chan Medical, School, Worcester, Massachusetts, USA
| | - Tom Fazzio
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Zhiping Weng
- Program in Bioinformatics and Integrative Biology, Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Daniel S. Pratt
- Autoimmune & Cholestatic Liver Center, GI Division, Massachusetts General Hospital, Boston, Massachusetts, USA
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23
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Ji Z, Lu W, Wu S, Zhang Y, Meng D, Zhang X, Dai X, Chen H, Ma L, Sun Y, Jiang L, Kong X. Single-Cell RNA-Sequencing Reveals Peripheral T Helper Cells Promoting the Development of IgG4-Related Disease by Enhancing B Cell Activation and Differentiation. Int J Mol Sci 2023; 24:13735. [PMID: 37762039 PMCID: PMC10530310 DOI: 10.3390/ijms241813735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 08/17/2023] [Accepted: 08/30/2023] [Indexed: 09/29/2023] Open
Abstract
Abnormal B cell differentiation plays a critical role in IgG4-related disease (IgG4-RD), but the underlying mechanism remains largely unknown. We investigated the cell landscape from three IgG4-RD retroperitoneal tissues and three control tissues using single-cell RNA-sequencing. Critical cell type or markers were further validated in the peripheral blood from the patients with IgG4-RD and healthy controls via flow cytometry as well as in the IgG4-RD and control tissue via immunofluorescence staining. The increases in B cells, plasma cells, and CD4+ T cells were found in IgG4-RD retroperitoneal tissue. Importantly, among CD4+ T cells, an increase in CD4+CXCR5-PD1hi peripheral T helper (Tph) cells with a high expression of IL-21 and TIGIT was discovered in IgG4-RD tissue, which was further validated in peripheral blood of the patients with IgG4-RD. The Tph cell and TIGIT+ Tph cell proportion were remarkably higher in active IgG4-RD patients and correlated with disease activity. Moreover, TIGIT+CD4+ cells were able to promote B cell differentiation via IL-21. Our study revealed that Tph cells are increased in IgG4-RD and probably play critical roles in B cell differentiation through TIGIT-IL-21 axis. Peripheral Tph cell and TIGIT+Tph cell are potential markers for IgG4-RD disease activity.
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Affiliation(s)
- Zongfei Ji
- Department of Rheumatology, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai 200032, China; (Z.J.)
| | - Weiqi Lu
- Department of General Surgery, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai 200032, China
| | - Sifan Wu
- Department of Rheumatology, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai 200032, China; (Z.J.)
| | - Yong Zhang
- Department of General Surgery, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai 200032, China
| | - Dan Meng
- Department of Rheumatology, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai 200032, China; (Z.J.)
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Xiao Zhang
- Department of Rheumatology, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai 200032, China; (Z.J.)
| | - Xiaojuan Dai
- Department of Rheumatology, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai 200032, China; (Z.J.)
| | - Huiyong Chen
- Department of Rheumatology, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai 200032, China; (Z.J.)
| | - Lili Ma
- Department of Rheumatology, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai 200032, China; (Z.J.)
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Ying Sun
- Department of Rheumatology, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai 200032, China; (Z.J.)
| | - Lindi Jiang
- Department of Rheumatology, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai 200032, China; (Z.J.)
- Evidence-Based Medicine Center, Fudan University, Shanghai 200032, China
| | - Xiufang Kong
- Department of Rheumatology, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai 200032, China; (Z.J.)
- Evidence-Based Medicine Center, Fudan University, Shanghai 200032, China
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24
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Bhattacharya M, Ramachandran P. Immunology of human fibrosis. Nat Immunol 2023; 24:1423-1433. [PMID: 37474654 DOI: 10.1038/s41590-023-01551-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Accepted: 06/08/2023] [Indexed: 07/22/2023]
Abstract
Fibrosis, defined by the excess deposition of structural and matricellular proteins in the extracellular space, underlies tissue dysfunction in multiple chronic diseases. Approved antifibrotics have proven modest in efficacy, and the immune compartment remains, for the most part, an untapped therapeutic opportunity. Recent single-cell analyses have interrogated human fibrotic tissues, including immune cells. These studies have revealed a conserved profile of scar-associated macrophages, which localize to the fibrotic niche and interact with mesenchymal cells that produce pathological extracellular matrix. Here we review recent advances in the understanding of the fibrotic microenvironment in human diseases, with a focus on immune cell profiles and functional immune-stromal interactions. We also discuss the key role of the immune system in mediating fibrosis regression and highlight avenues for future study to elucidate potential approaches to targeting inflammatory cells in fibrotic disorders.
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Affiliation(s)
- Mallar Bhattacharya
- Division of Pulmonary, Critical Care, Allergy, and Sleep Medicine, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA.
| | - Prakash Ramachandran
- University of Edinburgh Centre for Inflammation Research, Institute for Regeneration and Repair, Edinburgh BioQuarter, Edinburgh, UK.
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25
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Huang Y, Zhang J, Li X, Wu Z, Xie G, Wang Y, Liu Z, Jiao M, Zhang H, Shi B, Wang Y, Zhang Y. Chromatin accessibility memory of donor cells disrupts bovine somatic cell nuclear transfer blastocysts development. FASEB J 2023; 37:e23111. [PMID: 37531300 DOI: 10.1096/fj.202300131rrr] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 06/30/2023] [Accepted: 07/11/2023] [Indexed: 08/04/2023]
Abstract
The post-transfer developmental capacity of bovine somatic cell nuclear transfer (SCNT) blastocysts is reduced, implying that abnormalities in gene expression regulation are present at blastocyst stage. Chromatin accessibility, as an indicator for transcriptional regulatory elements mediating gene transcription activity, has heretofore been largely unexplored in SCNT embryos, especially at blastocyst stage. In the present study, single-cell sequencing assay for transposase-accessible chromatin (scATAC-seq) of in vivo and SCNT blastocysts were conducted to segregate lineages and demonstrate the aberrant chromatin accessibility of transcription factors (TFs) related to inner cell mass (ICM) development in SCNT blastocysts. Pseudotime analysis of lineage segregation further reflected dysregulated chromatin accessibility dynamics of TFs in the ICM of SCNT blastocysts compared to their in vivo counterparts. ATAC- and ChIP-seq results of SCNT donor cells revealed that the aberrant chromatin accessibility in the ICM of SCNT blastocysts was due to the persistence of chromatin accessibility memory at corresponding loci in the donor cells, with strong enrichment of trimethylation of histone H3 at lysine 4 (H3K4me3) at these loci. Correction of the aberrant chromatin accessibility through demethylation of H3K4me3 by KDM5B diminished the expression of related genes (e.g., BCL11B) and significantly improved the ICM proliferation in SCNT blastocysts. This effect was confirmed by knocking down BCL11B in SCNT embryos to down-regulate p21 and alleviate the inhibition of ICM proliferation. These findings expand our understanding of the chromatin accessibility abnormalities in SCNT blastocysts and BCL11B may be a potential target to improve SCNT efficiency.
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Affiliation(s)
- Yuemeng Huang
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, China
- Engineering Center for Animal Embryo Technology, Yangling, China
| | - Jingcheng Zhang
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, China
- Engineering Center for Animal Embryo Technology, Yangling, China
| | - Xinmei Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Zhipei Wu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Guoxiang Xie
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Yong Wang
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, China
- Engineering Center for Animal Embryo Technology, Yangling, China
| | - Zhengqing Liu
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, China
- Engineering Center for Animal Embryo Technology, Yangling, China
| | - Mei Jiao
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, China
- Engineering Center for Animal Embryo Technology, Yangling, China
| | - Hexu Zhang
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, China
- Engineering Center for Animal Embryo Technology, Yangling, China
| | - Binqiang Shi
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, China
- Engineering Center for Animal Embryo Technology, Yangling, China
| | - Yu Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Yong Zhang
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, China
- Engineering Center for Animal Embryo Technology, Yangling, China
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Váncza L, Torok NJ. Primary sclerosing cholangitis and the path to translation. J Clin Invest 2023; 133:e174218. [PMID: 37655665 PMCID: PMC10471165 DOI: 10.1172/jci174218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/02/2023] Open
Affiliation(s)
- Lóránd Váncza
- Gastroenterology and Hepatology, Stanford University, Stanford, California, USA
- VA, Palo Alto, California, USA
| | - Natalie J. Torok
- Gastroenterology and Hepatology, Stanford University, Stanford, California, USA
- VA, Palo Alto, California, USA
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Dold L, Frank L, Lutz P, Kaczmarek DJ, Krämer B, Nattermann J, Weismüller TJ, Branchi V, Toma M, Gonzalez-Carmona M, Strassburg CP, Spengler U, Langhans B. IL-6-Dependent STAT3 Activation and Induction of Proinflammatory Cytokines in Primary Sclerosing Cholangitis. Clin Transl Gastroenterol 2023; 14:e00603. [PMID: 37256725 PMCID: PMC10461951 DOI: 10.14309/ctg.0000000000000603] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 05/04/2023] [Indexed: 06/02/2023] Open
Abstract
INTRODUCTION Primary sclerosing cholangitis (PSC) is a rare cholestatic liver disease with periductal inflammation and fibrosis. Genetic studies suggest inflammatory cytokines and IL-6-dependent activation of transcription factor STAT3 as pivotal steps in PSC pathogenesis. However, details of inflammatory regulation remain unclear. METHODS We recruited 50 patients with PSC (36 with inflammatory bowel disease, 14 without inflammatory bowel disease), 12 patients with autoimmune hepatitis, and 36 healthy controls to measure cytokines in the serum, bile, and immune cell supernatant using bead-based immunoassays and flow cytometry and immunohistochemistry to analyze phosphorylation of STATs in immune cells. Finally, we analyzed cytokines and STAT3 phosphorylation of T cells in the presence of JAK1/2 inhibitors. RESULTS In PSC, IL-6 specifically triggered phosphorylation of STAT3 in CD4 + T cells and lead to enhanced production of interferon (IFN) gamma and interleukin (IL)-17A. Phospho-STAT3-positive CD4 + T cells correlated with systemic inflammation (C-reactive protein serum levels). Combination of immunohistology and flow cytometry indicated that phospho-STAT3-positive cells were enriched in the peribiliary liver stroma and represented CD4 + T cells with prominent production of IFN gamma and IL-17A. JAK1/2 inhibitors blocked STAT3 phosphorylation and production of IFN gamma and IL-6, whereas IL-17A was apparently resistant to this inhibition. DISCUSSION Our results demonstrate systemic and local activation of the IL-6/STAT3 pathway in PSC. Resistance of IL-17A to STAT3-targeted inhibition points to a more complex immune dysregulation beyond STAT3 activation.
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Affiliation(s)
- Leona Dold
- Department of Internal Medicine I, University Hospital of Bonn, Bonn, Germany;
- German Center for Infection Research (DZIF), Partner Site Cologne-Bonn, Bonn, Germany;
| | - Leonie Frank
- Department of Internal Medicine I, University Hospital of Bonn, Bonn, Germany;
| | - Philipp Lutz
- Department of Internal Medicine I, University Hospital of Bonn, Bonn, Germany;
| | | | - Benjamin Krämer
- Department of Internal Medicine I, University Hospital of Bonn, Bonn, Germany;
| | - Jacob Nattermann
- Department of Internal Medicine I, University Hospital of Bonn, Bonn, Germany;
- German Center for Infection Research (DZIF), Partner Site Cologne-Bonn, Bonn, Germany;
| | - Tobias J. Weismüller
- Department of Internal Medicine - Gastroenterology and Oncology, Vivantes Humboldt Hospital, Berlin, Germany;
| | - Vittorio Branchi
- Department of General, Abdominal, Thoracic and Vascular Surgery, University Hospital Bonn, Bonn, Germany;
| | - Marieta Toma
- Institute of Pathology, University Hospital Bonn, Bonn, Germany.
| | | | | | - Ulrich Spengler
- Department of Internal Medicine I, University Hospital of Bonn, Bonn, Germany;
| | - Bettina Langhans
- Department of Internal Medicine I, University Hospital of Bonn, Bonn, Germany;
- German Center for Infection Research (DZIF), Partner Site Cologne-Bonn, Bonn, Germany;
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28
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Zou J, Li J, Zhong X, Tang D, Fan X, Chen R. Liver in infections: a single-cell and spatial transcriptomics perspective. J Biomed Sci 2023; 30:53. [PMID: 37430371 PMCID: PMC10332047 DOI: 10.1186/s12929-023-00945-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 06/27/2023] [Indexed: 07/12/2023] Open
Abstract
The liver is an immune organ that plays a vital role in the detection, capture, and clearance of pathogens and foreign antigens that invade the human body. During acute and chronic infections, the liver transforms from a tolerant to an active immune state. The defence mechanism of the liver mainly depends on a complicated network of intrahepatic and translocated immune cells and non-immune cells. Therefore, a comprehensive liver cell atlas in both healthy and diseased states is needed for new therapeutic target development and disease intervention improvement. With the development of high-throughput single-cell technology, we can now decipher heterogeneity, differentiation, and intercellular communication at the single-cell level in sophisticated organs and complicated diseases. In this concise review, we aimed to summarise the advancement of emerging high-throughput single-cell technologies and re-define our understanding of liver function towards infections, including hepatitis B virus, hepatitis C virus, Plasmodium, schistosomiasis, endotoxemia, and corona virus disease 2019 (COVID-19). We also unravel previously unknown pathogenic pathways and disease mechanisms for the development of new therapeutic targets. As high-throughput single-cell technologies mature, their integration into spatial transcriptomics, multiomics, and clinical data analysis will aid in patient stratification and in developing effective treatment plans for patients with or without liver injury due to infectious diseases.
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Affiliation(s)
- Ju Zou
- Hunan Key Laboratory of Viral Hepatitis, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
- Department of Infectious Diseases, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Jie Li
- Hunan Key Laboratory of Viral Hepatitis, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
- Department of Infectious Diseases, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Xiao Zhong
- Hunan Key Laboratory of Viral Hepatitis, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
- Department of Infectious Diseases, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Daolin Tang
- Department of Surgery, UT Southwestern Medical Center, Dallas, TX, USA
| | - Xuegong Fan
- Hunan Key Laboratory of Viral Hepatitis, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
- Department of Infectious Diseases, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Ruochan Chen
- Hunan Key Laboratory of Viral Hepatitis, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China.
- Department of Infectious Diseases, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China.
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29
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Yang L, Meng Y, Shi Y, Fang H, Zhang L. Maternal hepatic immunology during pregnancy. Front Immunol 2023; 14:1220323. [PMID: 37457700 PMCID: PMC10348424 DOI: 10.3389/fimmu.2023.1220323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 06/20/2023] [Indexed: 07/18/2023] Open
Abstract
The liver plays pivotal roles in immunologic responses, and correct hepatic adaptations in maternal immunology are required during pregnancy. In this review, we focus on anatomical and immunological maternal hepatic adaptations during pregnancy, including our recent reports in this area. Moreover, we summarize maternal pregnancy-associated liver diseases, including hyperemesis gravidarum; intrahepatic cholestasis of pregnancy; preeclampsia, specifically hemolysis, elevated liver enzymes, and low platelet count syndrome; and acute fatty liver of pregnancy. In addition, the latest information about the factors that regulate hepatic immunology during pregnancy are reviewed for the first time, including human chorionic gonadotropin, estrogen, progesterone, growth hormone, insulin like growth factor 1, oxytocin, adrenocorticotropic hormone, adrenal hormone, prolactin, melatonin and prostaglandins. In summary, the latest progress on maternal hepatic anatomy and immunological adaptations, maternal pregnancy-associated diseases and the factors that regulate hepatic immunology during pregnancy are discussed, which may be used to prevent embryo loss and abortion, as well as pregnancy-associated liver diseases.
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30
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Zhang W, Mackay CR, Gershwin ME. Immunomodulatory Effects of Microbiota-Derived Short-Chain Fatty Acids in Autoimmune Liver Diseases. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2023; 210:1629-1639. [PMID: 37186939 PMCID: PMC10188201 DOI: 10.4049/jimmunol.2300016] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 02/01/2023] [Indexed: 05/17/2023]
Abstract
Nonpathogenic commensal microbiota and their metabolites and components are essential to maintain a tolerogenic environment and promote beneficial health effects. The metabolic environment critically impacts the outcome of immune responses and likely impacts autoimmune and allergic responses. Short-chain fatty acids (SCFAs) are the main metabolites produced by microbial fermentation in the gut. Given the high concentration of SCFAs in the gut and portal vein and their broad immune regulatory functions, SCFAs significantly influence immune tolerance and gut-liver immunity. Alterations of SCFA-producing bacteria and SCFAs have been identified in a multitude of inflammatory diseases. These data have particular significance in primary biliary cholangitis, primary sclerosing cholangitis, and autoimmune hepatitis because of the close proximity of the liver to the gut. In this focused review, we provide an update on the immunologic consequences of SCFA-producing microbiota and in particular on three dominant SCFAs in autoimmune liver diseases.
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Affiliation(s)
- Weici Zhang
- Division of Rheumatology, Allergy, and Clinical Immunology, School of Medicine, University of California Davis, CA, USA
| | - Charles R. Mackay
- Department of Microbiology, Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, Melbourne, Australia
| | - M. Eric Gershwin
- Division of Rheumatology, Allergy, and Clinical Immunology, School of Medicine, University of California Davis, CA, USA
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31
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Cai X, Tacke F, Guillot A, Liu H. Cholangiokines: undervalued modulators in the hepatic microenvironment. Front Immunol 2023; 14:1192840. [PMID: 37261338 PMCID: PMC10229055 DOI: 10.3389/fimmu.2023.1192840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 05/02/2023] [Indexed: 06/02/2023] Open
Abstract
The biliary epithelial cells, also known as cholangiocytes, line the intra- and extrahepatic bile ducts, forming a barrier between intra- and extra-ductal environments. Cholangiocytes are mostly known to modulate bile composition and transportation. In hepatobiliary diseases, bile duct injury leads to drastic alterations in cholangiocyte phenotypes and their release of soluble mediators, which can vary depending on the original insult and cellular states (quiescence, senescence, or proliferation). The cholangiocyte-secreted cytokines (also termed cholangiokines) drive ductular cell proliferation, portal inflammation and fibrosis, and carcinogenesis. Hence, despite the previous consensus that cholangiocytes are bystanders in liver diseases, their diverse secretome plays critical roles in modulating the intrahepatic microenvironment. This review summarizes recent insights into the cholangiokines under both physiological and pathological conditions, especially as they occur during liver injury-regeneration, inflammation, fibrosis and malignant transformation processes.
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Affiliation(s)
- Xiurong Cai
- Department of Hematology, Oncology and Tumor Immunology, Charité Universitätsmedizin Berlin, Campus Virchow-Klinikum, Berlin, Germany
| | - Frank Tacke
- Department of Hepatology and Gastroenterology, Charité Universitätsmedizin Berlin, Campus Virchow-Klinikum and Campus Charité Mitte, Berlin, Germany
| | - Adrien Guillot
- Department of Hepatology and Gastroenterology, Charité Universitätsmedizin Berlin, Campus Virchow-Klinikum and Campus Charité Mitte, Berlin, Germany
| | - Hanyang Liu
- Department of Hepatology and Gastroenterology, Charité Universitätsmedizin Berlin, Campus Virchow-Klinikum and Campus Charité Mitte, Berlin, Germany
- Center of Gastrointestinal Diseases, Changzhou Second People's Hospital, Changzhou Medical Center, Nanjing Medical University, Changzhou, China
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32
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Zigmond E, Zecher BF, Bartels AL, Ziv-Baran T, Rösch T, Schachschal G, Lohse AW, Ehlken H, Schramm C. Bile Duct Colonization With Enterococcus sp. Associates With Disease Progression in Primary Sclerosing Cholangitis. Clin Gastroenterol Hepatol 2023; 21:1223-1232.e3. [PMID: 36116754 DOI: 10.1016/j.cgh.2022.09.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Revised: 09/02/2022] [Accepted: 09/07/2022] [Indexed: 02/07/2023]
Abstract
BACKGROUND & AIMS Primary sclerosing cholangitis (PSC) is characterized by chronic inflammation of the biliary mucosa. Bile ducts in PSC are often colonized with bacteria. Although accumulating evidence demonstrates the importance of microbiota for mucosal immunity, little is known about the impact of bile duct colonization with bacteria on the clinical course of PSC. METHODS Bile samples were sent to culture during endoscopic retrograde cholangio-pancreatography before the administration of peri-interventional antibiotics. Procedures during overt bacterial cholangitis or with prior antibiotic treatment were excluded. The primary endpoint was defined as a composite clinical endpoint of decompensated cirrhosis and/or liver transplantation or death. RESULTS A cohort of 189 patients with 591 bile fluid cultures was included. In multivariable Cox regression analysis, the presence of Enterococci (present in 28% of the patients), but not of other bacterial species, conferred risk of disease progression with a hazard ratio of 3.61 (95% confidence interval, 1.6-8.11; P = .002) to reach the composite clinical endpoint. Fungobilia, present in 19.6% of patients, was confirmed to associate with disease progression with a hazard ratio of 3.25 (95% confidence interval, 1.87-5.66; P < .001) to reach the composite clinical endpoint. CONCLUSIONS The novel association of biliary colonization by Enterococci with disease progression underlines the importance of microbiota-mucosal interplay for the pathogenesis of PSC. These results should stimulate further mechanistic studies on the role of microbiota in PSC and highlight potential new therapeutic targets for a disease without effective treatment options.
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Affiliation(s)
- Ehud Zigmond
- Center for Autoimmune Liver Diseases, Department of Gastroenterology, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel; Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.
| | | | - Anna-Lena Bartels
- First Department of Medicine, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - Tomer Ziv-Baran
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Thomas Rösch
- Department for Interdisciplinary Endoscopy, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - Guido Schachschal
- Department for Interdisciplinary Endoscopy, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - Ansgar W Lohse
- First Department of Medicine, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - Hanno Ehlken
- First Department of Medicine, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany; Department for Interdisciplinary Endoscopy, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - Christoph Schramm
- First Department of Medicine, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany; Martin Zeitz Centre for Rare Diseases, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany; Hamburg Centre for Translational Immunology (HCTI), University Medical Centre Hamburg-Eppendorf, Hamburg, Germany.
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Fiorotto R, Mariotti V, Taleb SA, Zehra SA, Nguyen M, Amenduni M, Strazzabosco M. Cell-matrix interactions control biliary organoid polarity, architecture, and differentiation. Hepatol Commun 2023; 7:e0094. [PMID: 36972396 PMCID: PMC10503667 DOI: 10.1097/hc9.0000000000000094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 01/19/2023] [Indexed: 03/29/2023] Open
Abstract
BACKGROUND AND AIMS Cholangiopathies are an important cause of morbidity and mortality. Their pathogenesis and treatment remain unclear in part because of the lack of disease models relevant to humans. Three-dimensional biliary organoids hold great promise; however, the inaccessibility of their apical pole and the presence of extracellular matrix (ECM) limits their application. We hypothesized that signals coming from the extracellular matrix regulate organoids' 3-dimensional architecture and could be manipulated to generate novel organotypic culture systems. APPROACH AND RESULTS Biliary organoids were generated from human livers and grown embedded into Culturex Basement Membrane Extract as spheroids around an internal lumen (EMB). When removed from the EMC, biliary organoids revert their polarity and expose the apical membrane on the outside (AOOs). Functional, immunohistochemical, and transmission electron microscope studies, along with bulk and single-cell transcriptomic, demonstrate that AOOs are less heterogeneous and show increased biliary differentiation and decreased expression of stem cell features. AOOs transport bile acids and have competent tight junctions. When cocultured with liver pathogenic bacteria (Enterococcus spp.), AOOs secrete a range of proinflammatory chemokines (ie, MCP1, IL8, CCL20, and IP-10). Transcriptomic analysis and treatment with a beta-1-integrin blocking antibody identified beta-1-integrin signaling as a sensor of the cell-extracellular matrix interaction and a determinant of organoid polarity. CONCLUSIONS This novel organoid model can be used to study bile transport, interactions with pathobionts, epithelial permeability, cross talk with other liver and immune cell types, and the effect of matrix changes on the biliary epithelium and obtain key insights into the pathobiology of cholangiopathies.
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Affiliation(s)
- Romina Fiorotto
- Department of Internal Medicine, Section of Digestive Diseases, Yale School of Medicine, New Haven, Connecticut, USA
| | - Valeria Mariotti
- Department of Internal Medicine, Section of Digestive Diseases, Yale School of Medicine, New Haven, Connecticut, USA
| | - Shakila Afroz Taleb
- Department of Internal Medicine, Section of Digestive Diseases, Yale School of Medicine, New Haven, Connecticut, USA
| | - Syeda A. Zehra
- Department of Internal Medicine, Section of Digestive Diseases, Yale School of Medicine, New Haven, Connecticut, USA
| | - Mytien Nguyen
- Department of Immunobiology, Yale School of Medicine, New Haven, Connecticut, USA
| | - Mariangela Amenduni
- Department of Internal Medicine, Section of Digestive Diseases, Yale School of Medicine, New Haven, Connecticut, USA
| | - Mario Strazzabosco
- Department of Internal Medicine, Section of Digestive Diseases, Yale School of Medicine, New Haven, Connecticut, USA
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Hov JR, Karlsen TH. The microbiota and the gut-liver axis in primary sclerosing cholangitis. Nat Rev Gastroenterol Hepatol 2023; 20:135-154. [PMID: 36352157 DOI: 10.1038/s41575-022-00690-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/13/2022] [Indexed: 11/11/2022]
Abstract
Primary sclerosing cholangitis (PSC) offers unique opportunities to explore the gut-liver axis owing to the close association between liver disease and colonic inflammation. It is well established that the gut microbiota in people with PSC differs from that of healthy individuals, but details of the microbial factors that demarcate PSC from inflammatory bowel disease (IBD) without PSC are poorly understood. In this Review, we aim to provide an overview of the latest literature on the gut microbiome in PSC and PSC with IBD, critically examining hypotheses on how microorganisms could contribute to the pathogenesis of PSC. A particular emphasis will be put on pathogenic features of the gut microbiota that might explain the occurrence of bile duct inflammation and liver disease in the context of IBD, and we postulate the potential existence of a specific yet unknown factor related to the gut-liver axis as causative in PSC. Available data are scrutinized in the perspective of therapeutic approaches related to the gut-liver axis.
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Affiliation(s)
- Johannes R Hov
- Norwegian PSC Research Center and Section of gastroenterology and Research Institute of Internal Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital, Oslo, Norway.,Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Tom H Karlsen
- Norwegian PSC Research Center and Section of gastroenterology and Research Institute of Internal Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital, Oslo, Norway. .,Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway.
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35
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Han Y, Byun J, Zhu C, Sun R, Roh JY, Cordell HJ, Lee HS, Shaw VR, Kang SW, Razjouyan J, Cooley MA, Hassan MM, Siminovitch KA, Folseraas T, Ellinghaus D, Bergquist A, Rushbrook SM, Franke A, Karlsen TH, Lazaridis KN, McGlynn KA, Roberts LR, Amos CI. Multitrait genome-wide analyses identify new susceptibility loci and candidate drugs to primary sclerosing cholangitis. Nat Commun 2023; 14:1069. [PMID: 36828809 PMCID: PMC9958016 DOI: 10.1038/s41467-023-36678-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 02/10/2023] [Indexed: 02/26/2023] Open
Abstract
Primary sclerosing cholangitis (PSC) is a rare autoimmune bile duct disease that is strongly associated with immune-mediated disorders. In this study, we implemented multitrait joint analyses to genome-wide association summary statistics of PSC and numerous clinical and epidemiological traits to estimate the genetic contribution of each trait and genetic correlations between traits and to identify new lead PSC risk-associated loci. We identified seven new loci that have not been previously reported and one new independent lead variant in the previously reported locus. Functional annotation and fine-mapping nominated several potential susceptibility genes such as MANBA and IRF5. Network-based in silico drug efficacy screening provided candidate agents for further study of pharmacological effect in PSC.
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Affiliation(s)
- Younghun Han
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
- Section of Epidemiology and Population Sciences, Department of Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Jinyoung Byun
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
- Section of Epidemiology and Population Sciences, Department of Medicine, Baylor College of Medicine, Houston, TX, USA
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Catherine Zhu
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
| | - Ryan Sun
- Department of Biostatistics, University of Texas, M.D. Anderson Cancer Center, Houston, TX, USA
| | - Julia Y Roh
- Department of Pharmacy, Ochsner Health, New Orleans, LA, USA
| | - Heather J Cordell
- Population Health Sciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Hyun-Sung Lee
- David J. Sugarbaker Division of Thoracic Surgery, Michael E. DeBakey Department of Surgery, Baylor College of Medicine, Houston, TX, USA
| | - Vikram R Shaw
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
| | - Sung Wook Kang
- David J. Sugarbaker Division of Thoracic Surgery, Michael E. DeBakey Department of Surgery, Baylor College of Medicine, Houston, TX, USA
| | - Javad Razjouyan
- VA HSR&D, Center for Innovations in Quality, Effectiveness and Safety, Michael E. DeBakey VA Medical Center, Houston, TX, USA
- Big Data Scientist Training Enhancement Program (BD-STEP), VA Office of Research and Development, Washington, DC, USA
- Department of Medicine, Baylor College of Medicine, Houston, TX, USA
- VA Quality Scholars Coordinating Center, IQuESt, Michael E. DeBakey VA Medical Center, Houston, TX, USA
| | - Matthew A Cooley
- Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Rochester, MN, USA
| | - Manal M Hassan
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Katherine A Siminovitch
- Departments of Medicine, Immunology and Medical Sciences, University of Toronto, Toronto, Ontario, Canada
- Mount Sinai Hospital, Lunenfeld-Tanenbaum Research Institute and Toronto General Research Institute, Toronto, Ontario, Canada
| | - Trine Folseraas
- Norwegian PSC Research Center, Oslo University Hospital Rikshospitalet, Oslo, Norway
| | - David Ellinghaus
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Annika Bergquist
- Department of Medicine Huddinge, Unit of Gastroenterology and Rheumatology, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Simon M Rushbrook
- Department of Gastroenterology, Norfolk and Norwich University Hospital, Norwich, United Kingdom
- Norwich Medical School, University of East Anglia, Norfolk, United Kingdom
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Tom H Karlsen
- Oslo University Hospital Rikshospitalet and University of Oslo, Oslo, Norway
| | - Konstantinos N Lazaridis
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Mayo Clinic, Rochester, MN, USA
| | - Katherine A McGlynn
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Lewis R Roberts
- Oslo University Hospital Rikshospitalet and University of Oslo, Oslo, Norway
| | - Christopher I Amos
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA.
- Section of Epidemiology and Population Sciences, Department of Medicine, Baylor College of Medicine, Houston, TX, USA.
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA.
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36
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Huang J, Zhao C, Zhang X, Zhao Q, Zhang Y, Chen L, Dai G. Hepatitis B virus pathogenesis relevant immunosignals uncovering amino acids utilization related risk factors guide artificial intelligence-based precision medicine. Front Pharmacol 2022; 13:1079566. [PMID: 36569318 PMCID: PMC9780394 DOI: 10.3389/fphar.2022.1079566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 11/30/2022] [Indexed: 12/14/2022] Open
Abstract
Background: Although immune microenvironment-related chemokines, extracellular matrix (ECM), and intrahepatic immune cells are reported to be highly involved in hepatitis B virus (HBV)-related diseases, their roles in diagnosis, prognosis, and drug sensitivity evaluation remain unclear. Here, we aimed to study their clinical use to provide a basis for precision medicine in hepatocellular carcinoma (HCC) via the amalgamation of artificial intelligence. Methods: High-throughput liver transcriptomes from Gene Expression Omnibus (GEO), NODE (https://www.bio.sino.org/node), the Cancer Genome Atlas (TCGA), and our in-house hepatocellular carcinoma patients were collected in this study. Core immunosignals that participated in the entire diseases course of hepatitis B were explored using the "Gene set variation analysis" R package. Using ROC curve analysis, the impact of core immunosignals and amino acid utilization related gene on hepatocellular carcinoma patient's clinical outcome were calculated. The utility of core immunosignals as a classifier for hepatocellular carcinoma tumor tissue was evaluated using explainable machine-learning methods. A novel deep residual neural network model based on immunosignals was constructed for the long-term overall survival (LS) analysis. In vivo drug sensitivity was calculated by the "oncoPredict" R package. Results: We identified nine genes comprising chemokines and ECM related to hepatitis B virus-induced inflammation and fibrosis as CLST signals. Moreover, CLST was co-enriched with activated CD4+ T cells bearing harmful factors (aCD4) during all stages of hepatitis B virus pathogenesis, which was also verified by our hepatocellular carcinoma data. Unexpectedly, we found that hepatitis B virus-hepatocellular carcinoma patients in the CLSThighaCD4high subgroup had the shortest overall survival (OS) and were characterized by a risk gene signature associated with amino acids utilization. Importantly, characteristic genes specific to CLST/aCD4 showed promising clinical relevance in identifying patients with early-stage hepatocellular carcinoma via explainable machine learning. In addition, the 5-year long-term overall survival of hepatocellular carcinoma patients can be effectively classified by CLST/aCD4 based GeneSet-ResNet model. Subgroups defined by CLST and aCD4 were significantly involved in the sensitivity of hepatitis B virus-hepatocellular carcinoma patients to chemotherapy treatments. Conclusion: CLST and aCD4 are hepatitis B virus pathogenesis-relevant immunosignals that are highly involved in hepatitis B virus-induced inflammation, fibrosis, and hepatocellular carcinoma. Gene set variation analysis derived immunogenomic signatures enabled efficient diagnostic and prognostic model construction. The clinical application of CLST and aCD4 as indicators would be beneficial for the precision management of hepatocellular carcinoma.
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Affiliation(s)
- Jun Huang
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan, China,*Correspondence: Jun Huang, ; Liping Chen, ; Guifu Dai,
| | - Chunbei Zhao
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Xinhe Zhang
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Qiaohui Zhao
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Yanting Zhang
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Liping Chen
- Key Laboratory of Gastroenterology and Hepatology, State Key Laboratory for Oncogenes and Related Genes, Department of Gastroenterology and Hepatology, Ministry of Health, Shanghai Institute of Digestive Disease, Renji Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China,Shanghai Public Health Clinical Center, Fudan University, Shanghai, China,*Correspondence: Jun Huang, ; Liping Chen, ; Guifu Dai,
| | - Guifu Dai
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan, China,*Correspondence: Jun Huang, ; Liping Chen, ; Guifu Dai,
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37
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Zeng L, Yang K, Zhang T, Zhu X, Hao W, Chen H, Ge J. Research progress of single-cell transcriptome sequencing in autoimmune diseases and autoinflammatory disease: A review. J Autoimmun 2022; 133:102919. [PMID: 36242821 DOI: 10.1016/j.jaut.2022.102919] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 09/16/2022] [Accepted: 09/19/2022] [Indexed: 12/07/2022]
Abstract
Autoimmunity refers to the phenomenon that the body's immune system produces antibodies or sensitized lymphocytes to its own tissues to cause an immune response. Immune disorders caused by autoimmunity can mediate autoimmune diseases. Autoimmune diseases have complicated pathogenesis due to the many types of cells involved, and the mechanism is still unclear. The emergence of single-cell research technology can solve the problem that ordinary transcriptome technology cannot be accurate to cell type. It provides unbiased results through independent analysis of cells in tissues and provides more mRNA information for identifying cell subpopulations, which provides a novel approach to study disruption of immune tolerance and disturbance of pro-inflammatory pathways on a cellular basis. It may fundamentally change the understanding of molecular pathways in the pathogenesis of autoimmune diseases and develop targeted drugs. Single-cell transcriptome sequencing (scRNA-seq) has been widely applied in autoimmune diseases, which provides a powerful tool for demonstrating the cellular heterogeneity of tissues involved in various immune inflammations, identifying pathogenic cell populations, and revealing the mechanism of disease occurrence and development. This review describes the principles of scRNA-seq, introduces common sequencing platforms and practical procedures, and focuses on the progress of scRNA-seq in 41 autoimmune diseases, which include 9 systemic autoimmune diseases and autoinflammatory diseases (rheumatoid arthritis, systemic lupus erythematosus, etc.) and 32 organ-specific autoimmune diseases (5 Skin diseases, 3 Nervous system diseases, 4 Eye diseases, 2 Respiratory system diseases, 2 Circulatory system diseases, 6 Liver, Gallbladder and Pancreas diseases, 2 Gastrointestinal system diseases, 3 Muscle, Bones and joint diseases, 3 Urinary system diseases, 2 Reproductive system diseases). This review also prospects the molecular mechanism targets of autoimmune diseases from the multi-molecular level and multi-dimensional analysis combined with single-cell multi-omics sequencing technology (such as scRNA-seq, Single cell ATAC-seq and single cell immune group library sequencing), which provides a reference for further exploring the pathogenesis and marker screening of autoimmune diseases and autoimmune inflammatory diseases in the future.
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Affiliation(s)
- Liuting Zeng
- Department of Rheumatology, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, National Clinical Research Center for Dermatologic and Immunologic Diseases, State Key Laboratory of Complex Severe and Rare Diseases, Beijing, China.
| | - Kailin Yang
- Key Laboratory of Hunan Province for Integrated Traditional Chinese and Western Medicine on Prevention and Treatment of Cardio-Cerebral Diseases, Hunan University of Chinese Medicine, Changsha, China.
| | - Tianqing Zhang
- Key Laboratory of Hunan Province for Integrated Traditional Chinese and Western Medicine on Prevention and Treatment of Cardio-Cerebral Diseases, Hunan University of Chinese Medicine, Changsha, China
| | - Xiaofei Zhu
- Key Laboratory of Hunan Province for Integrated Traditional Chinese and Western Medicine on Prevention and Treatment of Cardio-Cerebral Diseases, Hunan University of Chinese Medicine, Changsha, China.
| | - Wensa Hao
- Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Hua Chen
- Department of Rheumatology, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, National Clinical Research Center for Dermatologic and Immunologic Diseases, State Key Laboratory of Complex Severe and Rare Diseases, Beijing, China.
| | - Jinwen Ge
- Key Laboratory of Hunan Province for Integrated Traditional Chinese and Western Medicine on Prevention and Treatment of Cardio-Cerebral Diseases, Hunan University of Chinese Medicine, Changsha, China; Hunan Academy of Chinese Medicine, Changsha, China.
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38
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Björkström NK. Immunobiology of the biliary tract system. J Hepatol 2022; 77:1657-1669. [PMID: 36116989 PMCID: PMC7615184 DOI: 10.1016/j.jhep.2022.08.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 08/09/2022] [Accepted: 08/17/2022] [Indexed: 12/04/2022]
Abstract
The biliary tract is a complex tubular organ system spanning from the liver to the duodenum. It is the site of numerous acute and chronic disorders, many of unknown origin, that are often associated with cancer development and for which there are limited treatment options. Cholangiocytes with proinflammatory capacities line the lumen and specialised types of immune cells reside in close proximity. Recent technological breakthroughs now permit spatiotemporal assessments of immune cells within distinct niches and have increased our understanding of immune cell tissue residency. In this review, a comprehensive overview of emerging knowledge on the immunobiology of the biliary tract system is provided, with a particular emphasis on the role of distinct immune cells in biliary disorders.
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Affiliation(s)
- Niklas K Björkström
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital Huddinge, Stockholm, Sweden.
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39
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Zheng F, Zhang W, Yang B, Chen M. Multi-omics profiling identifies C1QA/B + macrophages with multiple immune checkpoints associated with esophageal squamous cell carcinoma (ESCC) liver metastasis. ANNALS OF TRANSLATIONAL MEDICINE 2022; 10:1249. [PMID: 36544679 PMCID: PMC9761157 DOI: 10.21037/atm-22-5351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 11/23/2022] [Indexed: 11/30/2022]
Abstract
Background Esophageal squamous cell carcinoma (ESCC) is a highly lethal malignant tumor lacking effective treatments; 20% of ESCC patients develop liver metastasis with an extremely short survival time of ≈5 months. The tumor microenvironment (TME) plays a crucial role in tumor homeostasis, but the relationship between the ESCC TME and liver metastasis is still unknown. Methods To identify potential cell populations contributing to ESCC liver metastasis, single-cell RNA (scRNA) sequencing data were analyzed to identify the major cell populations within the TME. Each of the major cell populations was re-clustered to define detailed cell subsets. Thereafter, the gene set variation analysis (GSVA) score was calculated for the bulk RNA-seq data based on the gene signatures of each cell subset. The relationship between the GSVA score of each cellular subset and clinical outcome was further analyzed to identify the cellular subset associated with ESCC liver metastasis, which was validated by multiplex immunohistochemistry. Results C1QA/B+ tumor-associated macrophages (TAMs) acted as the central regulator of the ESCC TME, closely associated with several key cell subsets. Several immune checkpoints, including CD40, CD47 and LGALS9, were all positively expressed in C1QA/B+ macrophages, which may exert central regulatory control of immune evasion by ESCC via these immune checkpoints expressions. Conclusions Our results comprehensively revealed the landscape of tumor-infiltrating immune cells associated with ESCC prognosis and metastasis, and suggest a novel strategy for developing immunotherapies for ESCC liver metastasis by targeting C1QA/B+ TAMs.
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Affiliation(s)
- Fei Zheng
- Department of Radiation Oncology, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, China
| | - Wei Zhang
- Department of Radiation Oncology, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, China
| | - Baihua Yang
- Department of Radiation Oncology, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, China
| | - Mingqiu Chen
- Department of Radiation Oncology, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, China
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40
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Lazcanoiturburu N, García‐Sáez J, González‐Corralejo C, Roncero C, Sanz J, Martín‐Rodríguez C, Valdecantos MP, Martínez‐Palacián A, Almalé L, Bragado P, Calero‐Pérez S, Fernández A, García‐Bravo M, Guerra C, Montoliu L, Segovia JC, Valverde ÁM, Fabregat I, Herrera B, Sánchez A. Lack of
EGFR
catalytic activity in hepatocytes improves liver regeneration following
DDC
‐induced cholestatic injury by promoting a pro‐restorative inflammatory response. J Pathol 2022; 258:312-324. [DOI: 10.1002/path.6002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 07/22/2022] [Accepted: 08/15/2022] [Indexed: 11/07/2022]
Affiliation(s)
- Nerea Lazcanoiturburu
- Dept. Biochemistry and Molecular Biology, Faculty of Pharmacy Complutense University of Madrid (UCM) Health Research Institute of the “Hospital Clínico San Carlos” (IdISSC), Madrid Spain
| | - Juan García‐Sáez
- Dept. Biochemistry and Molecular Biology, Faculty of Pharmacy Complutense University of Madrid (UCM) Health Research Institute of the “Hospital Clínico San Carlos” (IdISSC), Madrid Spain
| | - Carlos González‐Corralejo
- Dept. Biochemistry and Molecular Biology, Faculty of Pharmacy Complutense University of Madrid (UCM) Health Research Institute of the “Hospital Clínico San Carlos” (IdISSC), Madrid Spain
| | - Cesáreo Roncero
- Dept. Biochemistry and Molecular Biology, Faculty of Pharmacy Complutense University of Madrid (UCM) Health Research Institute of the “Hospital Clínico San Carlos” (IdISSC), Madrid Spain
| | - Julián Sanz
- Anatomical Pathology Service of the “Clínica Universidad de Navarra”, Madrid, Spain, and UCM Madrid Spain
| | - Carlos Martín‐Rodríguez
- Dept. Biochemistry and Molecular Biology, Faculty of Pharmacy Complutense University of Madrid (UCM) Health Research Institute of the “Hospital Clínico San Carlos” (IdISSC), Madrid Spain
| | - M. Pilar Valdecantos
- “Alberto Sols” Biomedical Research Institute, Spanish National Research Council and Autonomous University of Madrid (IIBM, CSIC‐UAM) Biomedical Research Networking Center in Diabetes and Associated Metabolic Disorders of the Carlos III Health Institute (CIBERDEM‐ISCIII) Madrid Spain
| | - Adoración Martínez‐Palacián
- Dept. Biochemistry and Molecular Biology, Faculty of Pharmacy Complutense University of Madrid (UCM) Health Research Institute of the “Hospital Clínico San Carlos” (IdISSC), Madrid Spain
| | - Laura Almalé
- Dept. Biochemistry and Molecular Biology, Faculty of Pharmacy Complutense University of Madrid (UCM) Health Research Institute of the “Hospital Clínico San Carlos” (IdISSC), Madrid Spain
| | - Paloma Bragado
- Dept. Biochemistry and Molecular Biology, Faculty of Pharmacy Complutense University of Madrid (UCM) Health Research Institute of the “Hospital Clínico San Carlos” (IdISSC), Madrid Spain
| | - Silvia Calero‐Pérez
- “Alberto Sols” Biomedical Research Institute, Spanish National Research Council and Autonomous University of Madrid (IIBM, CSIC‐UAM) Biomedical Research Networking Center in Diabetes and Associated Metabolic Disorders of the Carlos III Health Institute (CIBERDEM‐ISCIII) Madrid Spain
| | - Almudena Fernández
- National Center for Biotechnology (CNB‐CSIC), Biomedical Research Networking Center on Rare Diseases (CIBERER‐ISCIII) Madrid Spain
| | - María García‐Bravo
- Cell Technology Division, Research Center for Energy, Environment and Technology (CIEMAT); Biomedical Research Networking Center on Rare Diseases (CIBERER‐ISCIII); Advanced Therapies Mixed Unit, “Fundación Jiménez Díaz” University Hospital Health Research Institute (CIEMAT/IIS‐FJD) Madrid Spain
| | - Carmen Guerra
- Molecular Oncology Programme, Spanish National Cancer Research Center (CNIO), Madrid Spain
| | - Lluis Montoliu
- National Center for Biotechnology (CNB‐CSIC), Biomedical Research Networking Center on Rare Diseases (CIBERER‐ISCIII) Madrid Spain
| | - José Carlos Segovia
- Cell Technology Division, Research Center for Energy, Environment and Technology (CIEMAT); Biomedical Research Networking Center on Rare Diseases (CIBERER‐ISCIII); Advanced Therapies Mixed Unit, “Fundación Jiménez Díaz” University Hospital Health Research Institute (CIEMAT/IIS‐FJD) Madrid Spain
| | - Ángela M. Valverde
- “Alberto Sols” Biomedical Research Institute, Spanish National Research Council and Autonomous University of Madrid (IIBM, CSIC‐UAM) Biomedical Research Networking Center in Diabetes and Associated Metabolic Disorders of the Carlos III Health Institute (CIBERDEM‐ISCIII) Madrid Spain
| | - Isabel Fabregat
- TGF‐β and Cancer Group, Oncobell Program, Bellvitge Biomedical Research Institute (IDIBELL) , Barcelona, Spain; Oncology Program, Biomedical Research Networking Center in Hepatic and Digestive Diseases (CIBEREHD‐ISCIII), Madrid, Spain; Department of Physiological Sciences Faculty of Medicine and Health Sciences, University of Barcelona (UB) Barcelona Spain
| | - Blanca Herrera
- Dept. Biochemistry and Molecular Biology, Faculty of Pharmacy Complutense University of Madrid (UCM) Health Research Institute of the “Hospital Clínico San Carlos” (IdISSC), Madrid Spain
| | - Aránzazu Sánchez
- Dept. Biochemistry and Molecular Biology, Faculty of Pharmacy Complutense University of Madrid (UCM) Health Research Institute of the “Hospital Clínico San Carlos” (IdISSC), Madrid Spain
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41
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Abstract
The human liver is a complex organ made up of multiple specialized cell types that carry out key physiological functions. An incomplete understanding of liver biology limits our ability to develop therapeutics to prevent chronic liver diseases, liver cancers, and death as a result of organ failure. Recently, single-cell modalities have expanded our understanding of the cellular phenotypic heterogeneity and intercellular cross-talk in liver health and disease. This review summarizes these findings and looks forward to highlighting new avenues for the application of single-cell genomics to unravel unknown pathogenic pathways and disease mechanisms for the development of new therapeutics targeting liver pathology. As these technologies mature, their integration into clinical data analysis will aid in patient stratification and in developing treatment plans for patients suffering from liver disease.
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Affiliation(s)
- Jawairia Atif
- Ajmera Transplant Centre, Schwartz Reisman Liver Research Centre, Toronto General Research Institute, University Health Network, Toronto, Ontario, Canada
- Department of Immunology, University of Toronto, Medical Sciences Building, Toronto, Ontario, Canada
| | - Cornelia Thoeni
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Gary D. Bader
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Ian D. McGilvray
- Ajmera Transplant Centre, Schwartz Reisman Liver Research Centre, Toronto General Research Institute, University Health Network, Toronto, Ontario, Canada
| | - Sonya A. MacParland
- Ajmera Transplant Centre, Schwartz Reisman Liver Research Centre, Toronto General Research Institute, University Health Network, Toronto, Ontario, Canada
- Department of Immunology, University of Toronto, Medical Sciences Building, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
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42
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Chung BK, Øgaard J, Reims HM, Karlsen TH, Melum E. Spatial transcriptomics identifies enriched gene expression and cell types in human liver fibrosis. Hepatol Commun 2022; 6:2538-2550. [PMID: 35726350 PMCID: PMC9426406 DOI: 10.1002/hep4.2001] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 03/25/2022] [Accepted: 04/20/2022] [Indexed: 11/30/2022] Open
Abstract
Liver fibrosis and cirrhosis have limited therapeutic options and represent a serious unmet patient need. Recent use of single‐cell RNA sequencing (scRNAseq) has identified enriched cell types infiltrating cirrhotic livers but without defining the microanatomical location of these lineages thoroughly. To assess whether fibrotic liver regions specifically harbor enriched cell types, we explored whether whole‐tissue spatial transcriptomics combined with scRNAseq and gene deconvolution analysis could be used to localize cell types in cirrhotic explants of patients with end‐stage liver disease (total n = 8; primary sclerosing cholangitis, n = 4; primary biliary cholangitis, n = 2, alcohol‐related liver disease, n = 2). Spatial transcriptomics clearly identified tissue areas of distinct gene expression that strongly correlated with the total area (Spearman r = 0.97, p = 0.0004) and precise location (parenchyma, 87.9% mean congruency; range, 73.1%–97.1%; fibrosis, 68.5% mean congruency; range, 41.0%–91.7%) of liver regions classified as parenchymal or fibrotic by conventional histology. Deconvolution and enumeration of parenchymal and fibrotic gene content as measured by spatial transcriptomics into distinct cell states revealed significantly higher frequencies of ACTA2+ FABP4+ and COL3A1+ mesenchymal cells, IL17RA+ S100A8+ and FCER1G+ tissue monocytes, VCAM1+ SDC3+ Kupffer cells, CCL4+ CCL5+ KLRB1+ and GZMA+ IL17RA+ T cells and HLA‐DR+, CD37+ CXCR4+ and IGHM+ IGHG+ B cells in fibrotic liver regions compared with parenchymal areas of cirrhotic explants. Conclusion: Our findings indicate that spatial transcriptomes of parenchymal and fibrotic liver regions express unique gene content within cirrhotic liver and demonstrate proof of concept that spatial transcriptomes combined with additional RNA sequencing methodologies can refine the localization of gene content and cell lineages in the search for antifibrotic targets.
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Affiliation(s)
- Brian K Chung
- Norwegian PSC Research Center, Oslo University Hospital, Rikshospitalet, Oslo, Norway.,Research Institute of Internal Medicine, Oslo University Hospital, Rikshospitalet, Oslo, Norway.,Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Jonas Øgaard
- Norwegian PSC Research Center, Oslo University Hospital, Rikshospitalet, Oslo, Norway.,Research Institute of Internal Medicine, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Henrik Mikael Reims
- Department of Pathology, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Tom H Karlsen
- Norwegian PSC Research Center, Oslo University Hospital, Rikshospitalet, Oslo, Norway.,Research Institute of Internal Medicine, Oslo University Hospital, Rikshospitalet, Oslo, Norway.,Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway.,Section of Gastroenterology, Department of Transplantation Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Espen Melum
- Norwegian PSC Research Center, Oslo University Hospital, Rikshospitalet, Oslo, Norway.,Research Institute of Internal Medicine, Oslo University Hospital, Rikshospitalet, Oslo, Norway.,Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway.,Section of Gastroenterology, Department of Transplantation Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital, Rikshospitalet, Oslo, Norway.,Hybrid Technology Hub-Centre of Excellence, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Oslo, Norway
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43
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How genetic risk contributes to autoimmune liver disease. Semin Immunopathol 2022; 44:397-410. [PMID: 35650446 PMCID: PMC9256578 DOI: 10.1007/s00281-022-00950-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 05/06/2022] [Indexed: 12/16/2022]
Abstract
Genome-wide association studies (GWAS) for autoimmune hepatitis (AIH) and GWAS/genome-wide meta-analyses (GWMA) for primary biliary cholangitis (PBC) and primary sclerosing cholangitis (PSC) have been successful over the past decade, identifying about 100 susceptibility loci in the human genome, with strong associations with the HLA locus and many susceptibility variants outside the HLA locus with relatively low risk. However, identifying causative variants and genes and determining their effects on liver cells and their immunological microenvironment is far from trivial. Polygenic risk scores (PRSs) based on current genome-wide data have limited potential to predict individual disease risk. Interestingly, results of mediated expression score regression analysis provide evidence that a substantial portion of gene expression at susceptibility loci is mediated by genetic risk variants, in contrast to many other complex diseases. Genome- and transcriptome-wide comparisons between AIH, PBC, and PSC could help to better delineate the shared inherited component of autoimmune liver diseases (AILDs), and statistical fine-mapping, chromosome X-wide association testing, and genome-wide in silico drug screening approaches recently applied to GWMA data from PBC could potentially be successfully applied to AIH and PSC. Initial successes through single-cell RNA sequencing (scRNA-seq) experiments in PBC and PSC now raise high hopes for understanding the impact of genetic risk variants in the context of liver-resident immune cells and liver cell subpopulations, and for bridging the gap between genetics and disease.
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44
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Challenges and opportunities in achieving effective regulatory T cell therapy in autoimmune liver disease. Semin Immunopathol 2022; 44:461-474. [PMID: 35641679 PMCID: PMC9256571 DOI: 10.1007/s00281-022-00940-w] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 04/15/2022] [Indexed: 12/29/2022]
Abstract
Autoimmune liver diseases (AILD) include autoimmune hepatitis (AIH), primary biliary cholangitis (PBC) and primary sclerosing cholangitis (PSC). These immune-mediated liver diseases involve a break down in peripheral self-tolerance with largely unknown aetiology. Regulatory T cells (Treg) are crucial in maintaining immunological tolerance. Hence, Treg immunotherapy is an attractive therapeutic option in AILD. Currently, AILD do not have a curative treatment option and patients take life-long immunosuppression or bile acids to control hepatic or biliary inflammation. Clinical investigations using good manufacturing practice (GMP) Treg in autoimmune liver disease have thus far demonstrated that Treg therapy is safe and that Treg migrate to inflamed liver tissue. For Treg immunotherapy to achieve efficacy in AILD, Treg must be retained within the liver and maintain their suppressive phenotype to dampen ongoing immune responses to hepatocytes and biliary epithelium. Therefore, therapeutic Treg subsets should be selected for tissue residency markers and maximal functionality. Optimisation of dosing regime and understanding longevity of Treg in vivo are critical to successful Treg therapy. It is also essential to consider combination therapy options to complement infused Treg, for instance low-dose interleukin-2 (IL-2) to support pre-existing and infused Treg survival and suppressive function. Understanding the hepatic microenvironment in both early- and late-stage AILD presents significant opportunity to better tailor Treg therapy in different patient groups. Modification of a hostile microenvironment to a more favourable one either prior to or during Treg therapy could enhance the efficacy and longevity of infused GMP-Treg. Applying recent technology to discovery of autoantigen responses in AILD, T cell receptor (TCR) sequencing and use of chimeric antigen receptor (CAR) technology represents the next frontier for disease-specific CAR-Treg therapies. Consideration of all these aspects in future trials and discovery research would position GMP Treg immunotherapy as a viable personalised-medicine treatment option for effective control of autoimmune liver diseases.
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45
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Abondio P, De Intinis C, da Silva Gonçalves Vianez Júnior JL, Pace L. SINGLE CELL MULTIOMIC APPROACHES TO DISENTANGLE T CELL HETEROGENEITY. Immunol Lett 2022; 246:37-51. [DOI: 10.1016/j.imlet.2022.04.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 04/16/2022] [Accepted: 04/26/2022] [Indexed: 11/29/2022]
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46
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Lan T, Qian S, Tang C, Gao J. Role of Immune Cells in Biliary Repair. Front Immunol 2022; 13:866040. [PMID: 35432349 PMCID: PMC9005827 DOI: 10.3389/fimmu.2022.866040] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 03/08/2022] [Indexed: 02/06/2023] Open
Abstract
The biliary system is comprised of cholangiocytes and plays an important role in maintaining liver function. Under normal conditions, cholangiocytes remain in the stationary phase and maintain a very low turnover rate. However, the robust biliary repair is initiated in disease conditions, and different repair mechanisms can be activated depending on the pathological changes. During biliary disease, immune cells including monocytes, lymphocytes, neutrophils, and mast cells are recruited to the liver. The cellular interactions between cholangiocytes and these recruited immune cells as well as hepatic resident immune cells, including Kupffer cells, determine disease outcomes. However, the role of immune cells in the initiation, regulation, and suspension of biliary repair remains elusive. The cellular processes of cholangiocyte proliferation, progenitor cell differentiation, and hepatocyte-cholangiocyte transdifferentiation during biliary diseases are reviewed to manifest the underlying mechanism of biliary repair. Furthermore, the potential role of immune cells in crucial biliary repair mechanisms is highlighted. The mechanisms of biliary repair in immune-mediated cholangiopathies, inherited cholangiopathies, obstructive cholangiopathies, and cholangiocarcinoma are also summarized. Additionally, novel techniques that could clarify the underlying mechanisms of biliary repair are displayed. Collectively, this review aims to deepen the understanding of the mechanisms of biliary repair and contributes potential novel therapeutic methods for treating biliary diseases.
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Affiliation(s)
- Tian Lan
- Lab of Gastroenterology and Hepatology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China.,Department of Gastroenterology, West China Hospital, Sichuan University, Chengdu, China
| | - Shuaijie Qian
- Lab of Gastroenterology and Hepatology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China.,Department of Gastroenterology, West China Hospital, Sichuan University, Chengdu, China
| | - Chengwei Tang
- Lab of Gastroenterology and Hepatology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China.,Department of Gastroenterology, West China Hospital, Sichuan University, Chengdu, China
| | - Jinhang Gao
- Lab of Gastroenterology and Hepatology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China.,Department of Gastroenterology, West China Hospital, Sichuan University, Chengdu, China
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Mucosal immunity in primary sclerosing cholangitis: from the bowel to bile ducts and back again. Curr Opin Gastroenterol 2022; 38:104-113. [PMID: 35034083 DOI: 10.1097/mog.0000000000000809] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
PURPOSE OF REVIEW In this article, we provide a contemporary overview on PSC pathogenesis, with a specific focus on the role of mucosal immunity. RECENT FINDINGS The extent of enteric dysbiosis in PSC has been extensively quantified, with evidence of reduced bacterial diversity and enrichment of species capable of driving lymphocyte recruitment from the gut to the liver. Integrative pathway-based analysis and metagenomic sequencing indicate a reduction in butyrate-producing species, near absence of bacteria that activate the nuclear bile acid receptor FXR, and depletion of species that regulate the synthesis of vitamin B6 and branched-chain amino acids. Immunotyping of the cellular inflammatory infiltrate has identified a population of intrahepatic naive T cells, with tendency to acquire a Th17 polarisation state, paralleled by heightened responses to pathogen stimulation. Moreover, the search for antigen specificity has revealed the presence of overlapping nucleotide clonotypes across the gut and liver, highlighting the ability to recognize a common pool of epitopes bearing structural similarities across afflicted sites. SUMMARY Understanding the complex mechanisms that underpin mucosal immune responses between the liver and gut will help identify new druggable targets in PSC, centring on gut microbial manipulation, bile acid therapies, and restoration of immune homeostasis.
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Abstract
PURPOSE OF REVIEW Cholangiopathies are a heterogeneous class of liver diseases where cholangiocytes are the main targets of liver injury. Although available and emerging therapies mainly target bile acids (ursodeoxycholic acid/UDCA, 24-Norursodeoxycholic acid/norUDCA) and related signaling pathways (obeticholic acid, fibrates, FXR, and PPAR agonists), the mechanisms underlying inflammation, ductular reaction and fibrosis in cholestatic liver diseases remain poorly understood. RECENT FINDINGS Data from patients with cholestatic diseases, such as primary biliary cholangitis (PBC) or primary sclerosing cholangitis (PSC) as well as mouse models of biliary injury emphasize the role of immune cells in the pathogenesis of cholestatic disorders and indicate diverse functions of hepatic macrophages. Their versatile polarization phenotypes and their capacity to interact with other cell types (e.g. cholangiocytes, other immune cells) make macrophages central actors in the progression of cholangiopathies. SUMMARY In this review, we summarize recent findings on the response of hepatic macrophages to cholestasis and biliary injury and their involvement in the progression of cholangiopathies. Furthermore, we discuss how recent discoveries may foster the development of innovative therapies to treat patients suffering from cholestatic liver diseases, in particular, treatments targeting macrophages to limit hepatic inflammation.
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Tiegs G, Horst AK. TNF in the liver: targeting a central player in inflammation. Semin Immunopathol 2022; 44:445-459. [PMID: 35122118 PMCID: PMC9256556 DOI: 10.1007/s00281-022-00910-2] [Citation(s) in RCA: 50] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 01/12/2022] [Indexed: 12/11/2022]
Abstract
Tumour necrosis factor-α (TNF) is a multifunctional cytokine. First recognized as an endogenous soluble factor that induces necrosis of solid tumours, TNF became increasingly important as pro-inflammatory cytokine being involved in the immunopathogenesis of several autoimmune diseases. In the liver, TNF induces numerous biological responses such as hepatocyte apoptosis and necroptosis, liver inflammation and regeneration, and autoimmunity, but also progression to hepatocellular carcinoma. Considering these multiple functions of TNF in the liver, we propose anti-TNF therapies that specifically target TNF signalling at the level of its specific receptors.
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Affiliation(s)
- Gisa Tiegs
- Institute of Experimental Immunology and Hepatology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany. .,Hamburg Center for Translational Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
| | - Andrea K Horst
- Institute of Experimental Immunology and Hepatology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,Hamburg Center for Translational Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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50
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Kudira R, Pasula S, Kapil S, Miethke A. Isolation of Liver Mononuclear Cells from a Cholestatic Mice for Single Cell or Single Nuclei Sequencing. Bio Protoc 2022. [DOI: 10.21769/bioprotoc.4400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
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