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Pires S, Longman RS. Sounding the alarm in the lung with TL1A. J Exp Med 2024; 221:e20240389. [PMID: 38597953 PMCID: PMC11010314 DOI: 10.1084/jem.20240389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/11/2024] Open
Abstract
Environmental airborne antigens are central to the development of allergic asthma, but the cellular processes that trigger disease remain incompletely understood. In this report, Schmitt et al. (https://doi.org/10.1084/jem.20231236) identify TNF-like protein 1A (TL1A) as an epithelial alarmin constitutively expressed by a subset of lung epithelial cells, which is released in response to airborne microbial challenge and synergizes with IL-33 to drive allergic disease.
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Affiliation(s)
- Silvia Pires
- Division of Gastroenterology and Hepatology, Department of Medicine, Jill Roberts Center and Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, New York, NY, USA
| | - Randy S. Longman
- Division of Gastroenterology and Hepatology, Department of Medicine, Jill Roberts Center and Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, New York, NY, USA
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2
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Liman N, Lanasa D, Meylan F, Park JH. The ever-expanding role of cytokine receptor DR3 in T cells. Cytokine 2024; 176:156540. [PMID: 38359559 PMCID: PMC10895922 DOI: 10.1016/j.cyto.2024.156540] [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: 12/21/2023] [Revised: 02/05/2024] [Accepted: 02/06/2024] [Indexed: 02/17/2024]
Abstract
Death Receptor 3 (DR3) is a cytokine receptor of the Tumor Necrosis Factor receptor superfamily that plays a multifaceted role in both innate and adaptive immunity. Based on the death domain motif in its cytosolic tail, DR3 had been proposed and functionally affirmed as a trigger of apoptosis. Further studies, however, also revealed roles of DR3 in other cellular pathways, including inflammation, survival, and proliferation. DR3 is expressed in various cell types, including T cells, B cells, innate lymphocytes, myeloid cells, fibroblasts, and even outside the immune system. Because DR3 is mainly expressed on T cells, DR3-mediated immune perturbations leading to autoimmunity and other diseases were mostly attributed to DR3 activation of T cells. However, which T cell subset and what T effector functions are controlled by DR3 to drive these processes remain incompletely understood. DR3 engagement was previously found to alter CD4 T helper subset differentiation, expand the Foxp3+ Treg cell pool, and maintain intraepithelial γδ T cells in the gut. Recent studies further unveiled a previously unacknowledged aspect of DR3 in regulating innate-like invariant NKT (iNKT) cell activation, expanding the scope of DR3-mediated immunity in T lineage cells. Importantly, in the context of iNKT cells, DR3 ligation exerted costimulatory effects in agonistic TCR signaling, unveiling a new regulatory framework in T cell activation and proliferation. The current review is aimed at summarizing such recent findings on the role of DR3 on conventional T cells and innate-like T cells and discussing them in the context of immunopathogenesis.
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Affiliation(s)
- Nurcin Liman
- Experimental Immunology Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, United States
| | - Dominic Lanasa
- Experimental Immunology Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, United States
| | - Françoise Meylan
- Office of Science and Technology, National Institute of Arthritis, Musculoskeletal, and Skin Diseases, NIH, Bethesda, MD 20892, United States
| | - Jung-Hyun Park
- Experimental Immunology Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, United States.
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3
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O'Brien CL, Summers KM, Martin NM, Carter-Cusack D, Yang Y, Barua R, Dixit OVA, Hume DA, Pavli P. The relationship between extreme inter-individual variation in macrophage gene expression and genetic susceptibility to inflammatory bowel disease. Hum Genet 2024; 143:233-261. [PMID: 38421405 PMCID: PMC11043138 DOI: 10.1007/s00439-024-02642-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 01/14/2024] [Indexed: 03/02/2024]
Abstract
The differentiation of resident intestinal macrophages from blood monocytes depends upon signals from the macrophage colony-stimulating factor receptor (CSF1R). Analysis of genome-wide association studies (GWAS) indicates that dysregulation of macrophage differentiation and response to microorganisms contributes to susceptibility to chronic inflammatory bowel disease (IBD). Here, we analyzed transcriptomic variation in monocyte-derived macrophages (MDM) from affected and unaffected sib pairs/trios from 22 IBD families and 6 healthy controls. Transcriptional network analysis of the data revealed no overall or inter-sib distinction between affected and unaffected individuals in basal gene expression or the temporal response to lipopolysaccharide (LPS). However, the basal or LPS-inducible expression of individual genes varied independently by as much as 100-fold between subjects. Extreme independent variation in the expression of pairs of HLA-associated transcripts (HLA-B/C, HLA-A/F and HLA-DRB1/DRB5) in macrophages was associated with HLA genotype. Correlation analysis indicated the downstream impacts of variation in the immediate early response to LPS. For example, variation in early expression of IL1B was significantly associated with local SNV genotype and with subsequent peak expression of target genes including IL23A, CXCL1, CXCL3, CXCL8 and NLRP3. Similarly, variation in early IFNB1 expression was correlated with subsequent expression of IFN target genes. Our results support the view that gene-specific dysregulation in macrophage adaptation to the intestinal milieu is associated with genetic susceptibility to IBD.
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Affiliation(s)
- Claire L O'Brien
- Centre for Research in Therapeutics Solutions, Faculty of Science and Technology, University of Canberra, Canberra, ACT, Australia
- Inflammatory Bowel Disease Research Group, Canberra Hospital, Canberra, ACT, Australia
| | - Kim M Summers
- Mater Research Institute-University of Queensland, Translational Research Institute, Brisbane, QLD, Australia
| | - Natalia M Martin
- Inflammatory Bowel Disease Research Group, Canberra Hospital, Canberra, ACT, Australia
| | - Dylan Carter-Cusack
- Mater Research Institute-University of Queensland, Translational Research Institute, Brisbane, QLD, Australia
| | - Yuanhao Yang
- Mater Research Institute-University of Queensland, Translational Research Institute, Brisbane, QLD, Australia
| | - Rasel Barua
- Inflammatory Bowel Disease Research Group, Canberra Hospital, Canberra, ACT, Australia
| | - Ojas V A Dixit
- Centre for Research in Therapeutics Solutions, Faculty of Science and Technology, University of Canberra, Canberra, ACT, Australia
| | - David A Hume
- Mater Research Institute-University of Queensland, Translational Research Institute, Brisbane, QLD, Australia.
| | - Paul Pavli
- Inflammatory Bowel Disease Research Group, Canberra Hospital, Canberra, ACT, Australia.
- School of Medicine and Psychology, College of Health and Medicine, Australian National University, Canberra, ACT, Australia.
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4
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Ratajczak F, Joblin M, Hildebrandt M, Ringsquandl M, Falter-Braun P, Heinig M. Speos: an ensemble graph representation learning framework to predict core gene candidates for complex diseases. Nat Commun 2023; 14:7206. [PMID: 37938585 PMCID: PMC10632370 DOI: 10.1038/s41467-023-42975-z] [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: 03/27/2023] [Accepted: 10/27/2023] [Indexed: 11/09/2023] Open
Abstract
Understanding phenotype-to-genotype relationships is a grand challenge of 21st century biology with translational implications. The recently proposed "omnigenic" model postulates that effects of genetic variation on traits are mediated by core-genes and -proteins whose activities mechanistically influence the phenotype, whereas peripheral genes encode a regulatory network that indirectly affects phenotypes via core gene products. Here, we develop a positive-unlabeled graph representation-learning ensemble-approach based on a nested cross-validation to predict core-like genes for diverse diseases using Mendelian disorder genes for training. Employing mouse knockout phenotypes for external validations, we demonstrate that core-like genes display several key properties of core genes: Mouse knockouts of genes corresponding to our most confident predictions give rise to relevant mouse phenotypes at rates on par with the Mendelian disorder genes, and all candidates exhibit core gene properties like transcriptional deregulation in disease and loss-of-function intolerance. Moreover, as predicted for core genes, our candidates are enriched for drug targets and druggable proteins. In contrast to Mendelian disorder genes the new core-like genes are enriched for druggable yet untargeted gene products, which are therefore attractive targets for drug development. Interpretation of the underlying deep learning model suggests plausible explanations for our core gene predictions in form of molecular mechanisms and physical interactions. Our results demonstrate the potential of graph representation learning for the interpretation of biological complexity and pave the way for studying core gene properties and future drug development.
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Affiliation(s)
- Florin Ratajczak
- Institute of Network Biology (INET), Molecular Targets and Therapeutics Center (MTTC), Helmholtz Munich, Neuherberg, Germany
| | | | | | | | - Pascal Falter-Braun
- Institute of Network Biology (INET), Molecular Targets and Therapeutics Center (MTTC), Helmholtz Munich, Neuherberg, Germany.
- Microbe-Host Interactions, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany.
| | - Matthias Heinig
- Institute of Computational Biology (ICB), Helmholtz Munich, Neuherberg, Germany.
- Department of Computer Science, TUM School of Computation, Information and Technology, Technical University of Munich, Garching, Germany.
- German Centre for Cardiovascular Research (DZHK), Munich Heart Association, Partner Site Munich, Berlin, Germany.
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5
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Zhao JH, Stacey D, Eriksson N, Macdonald-Dunlop E, Hedman ÅK, Kalnapenkis A, Enroth S, Cozzetto D, Digby-Bell J, Marten J, Folkersen L, Herder C, Jonsson L, Bergen SE, Gieger C, Needham EJ, Surendran P, Paul DS, Polasek O, Thorand B, Grallert H, Roden M, Võsa U, Esko T, Hayward C, Johansson Å, Gyllensten U, Powell N, Hansson O, Mattsson-Carlgren N, Joshi PK, Danesh J, Padyukov L, Klareskog L, Landén M, Wilson JF, Siegbahn A, Wallentin L, Mälarstig A, Butterworth AS, Peters JE. Genetics of circulating inflammatory proteins identifies drivers of immune-mediated disease risk and therapeutic targets. Nat Immunol 2023; 24:1540-1551. [PMID: 37563310 PMCID: PMC10457199 DOI: 10.1038/s41590-023-01588-w] [Citation(s) in RCA: 87] [Impact Index Per Article: 87.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 07/13/2023] [Indexed: 08/12/2023]
Abstract
Circulating proteins have important functions in inflammation and a broad range of diseases. To identify genetic influences on inflammation-related proteins, we conducted a genome-wide protein quantitative trait locus (pQTL) study of 91 plasma proteins measured using the Olink Target platform in 14,824 participants. We identified 180 pQTLs (59 cis, 121 trans). Integration of pQTL data with eQTL and disease genome-wide association studies provided insight into pathogenesis, implicating lymphotoxin-α in multiple sclerosis. Using Mendelian randomization (MR) to assess causality in disease etiology, we identified both shared and distinct effects of specific proteins across immune-mediated diseases, including directionally discordant effects of CD40 on risk of rheumatoid arthritis versus multiple sclerosis and inflammatory bowel disease. MR implicated CXCL5 in the etiology of ulcerative colitis (UC) and we show elevated gut CXCL5 transcript expression in patients with UC. These results identify targets of existing drugs and provide a powerful resource to facilitate future drug target prioritization.
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Affiliation(s)
- Jing Hua Zhao
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, UK
| | - David Stacey
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, UK
- Australian Centre for Precision Health, Unit of Clinical and Health Sciences, University of South Australia, Adelaide, South Australia, Australia
- South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia
| | - Niclas Eriksson
- Uppsala Clinical Research Center, Uppsala University, Uppsala, Sweden
| | - Erin Macdonald-Dunlop
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Åsa K Hedman
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Development and Medical, Pfizer Worldwide Research, Stockholm, Sweden
| | - Anette Kalnapenkis
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Stefan Enroth
- Department of Immunology, Genetics, and Pathology, Biomedical Center, SciLifeLab Uppsala, Uppsala University, Uppsala, Sweden
| | - Domenico Cozzetto
- Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, UK
| | - Jonathan Digby-Bell
- School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Jonathan Marten
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | | | - Christian Herder
- Institute for Clinical Diabetology, German Diabetes Center, Düsseldorf, Germany
- Department of Endocrinology and Diabetology, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- German Center for Diabetes Research, Munich-Neuherberg, Germany
| | - Lina Jonsson
- Institute of Neuroscience and Physiology, University of Gothenburg, Gothenburg, Sweden
| | - Sarah E Bergen
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Christian Gieger
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Elise J Needham
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, UK
| | - Praveen Surendran
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- British Heart Foundation Centre of Research Excellence, School of Clinical Medicine, Addenbrooke's Hospital, University of Cambridge, Cambridge, UK
- Health Data Research UK, Wellcome Genome Campus and University of Cambridge, Hinxton, UK
| | - Dirk S Paul
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, UK
- British Heart Foundation Centre of Research Excellence, School of Clinical Medicine, Addenbrooke's Hospital, University of Cambridge, Cambridge, UK
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | | | - Barbara Thorand
- German Center for Diabetes Research, Munich-Neuherberg, Germany
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Harald Grallert
- German Center for Diabetes Research, Munich-Neuherberg, Germany
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Michael Roden
- Institute for Clinical Diabetology, German Diabetes Center, Düsseldorf, Germany
- Department of Endocrinology and Diabetology, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- German Center for Diabetes Research, Munich-Neuherberg, Germany
| | - Urmo Võsa
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Tonu Esko
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Caroline Hayward
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Åsa Johansson
- Department of Immunology, Genetics, and Pathology, Biomedical Center, SciLifeLab Uppsala, Uppsala University, Uppsala, Sweden
| | - Ulf Gyllensten
- Department of Immunology, Genetics, and Pathology, Biomedical Center, SciLifeLab Uppsala, Uppsala University, Uppsala, Sweden
| | - Nick Powell
- Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, UK
| | - Oskar Hansson
- Clinical Memory Research Unit, Department of Clinical Sciences Malmö, Lund University, Lund, Sweden
- Skåne University Hospital, Malmö, Sweden
| | - Niklas Mattsson-Carlgren
- Wallenberg Centre for Molecular Medicine, Lund University, Lund, Sweden
- Clinical Memory Research Unit, Faculty of Medicine, Lund University, Lund, Sweden
- Department of Neurology, Skåne University Hospital, Lund University, Lund, Sweden
| | - Peter K Joshi
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh, UK
| | - John Danesh
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, UK
- British Heart Foundation Centre of Research Excellence, School of Clinical Medicine, Addenbrooke's Hospital, University of Cambridge, Cambridge, UK
- Health Data Research UK, Wellcome Genome Campus and University of Cambridge, Hinxton, UK
- NIHR Blood and Transplant Research Unit in Donor Health and Behaviour, University of Cambridge, Cambridge, UK
- Department of Human Genetics, Wellcome Sanger Institute, Hinxton, UK
| | - Leonid Padyukov
- Division of Rheumatology, Department of Medicine (Solna), Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
- Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Lars Klareskog
- Division of Rheumatology, Department of Medicine (Solna), Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
- Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Mikael Landén
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Institute of Neuroscience and Physiology, University of Gothenburg, Gothenburg, Sweden
| | - James F Wilson
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh, UK
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Agneta Siegbahn
- Department of Medical Sciences and Uppsala Clinical Research Center, Uppsala University, Uppsala, Sweden
| | - Lars Wallentin
- Department of Medical Sciences and Uppsala Clinical Research Center, Uppsala University, Uppsala, Sweden
| | - Anders Mälarstig
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Development and Medical, Pfizer Worldwide Research, Stockholm, Sweden
| | - Adam S Butterworth
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK.
- Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, UK.
- British Heart Foundation Centre of Research Excellence, School of Clinical Medicine, Addenbrooke's Hospital, University of Cambridge, Cambridge, UK.
- Health Data Research UK, Wellcome Genome Campus and University of Cambridge, Hinxton, UK.
- NIHR Blood and Transplant Research Unit in Donor Health and Behaviour, University of Cambridge, Cambridge, UK.
| | - James E Peters
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK.
- Health Data Research UK, Wellcome Genome Campus and University of Cambridge, Hinxton, UK.
- Department of Immunology and Inflammation, Imperial College London, London, UK.
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6
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Shimodaira Y, More SK, Hamade H, Blackwood AY, Abraham JP, Thomas LS, Miller JH, Stamps DT, Castanon SL, Jacob N, Ha CWY, Devkota S, Shih DQ, Targan SR, Michelsen KS. DR3 Regulates Intestinal Epithelial Homeostasis and Regeneration After Intestinal Barrier Injury. Cell Mol Gastroenterol Hepatol 2023; 16:83-105. [PMID: 37011811 PMCID: PMC10213104 DOI: 10.1016/j.jcmgh.2023.03.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 03/28/2023] [Accepted: 03/28/2023] [Indexed: 04/05/2023]
Abstract
BACKGROUND & AIMS Tumor necrosis factor (TNF) superfamily member tumor necrosis factor-like protein 1A (TL1A) has been associated with the susceptibility and severity of inflammatory bowel diseases. However, the function of the tumor necrosis factor-like protein 1A and its receptor death receptor 3 (DR3) in the development of intestinal inflammation is incompletely understood. We investigated the role of DR3 expressed by intestinal epithelial cells (IECs) during intestinal homeostasis, tissue injury, and regeneration. METHODS Clinical phenotype and histologic inflammation were assessed in C57BL/6 (wild-type), Tl1a-/- and Dr3-/- mice in dextran sulfate sodium (DSS)-induced colitis. We generated mice with an IEC-specific deletion of DR3 (Dr3ΔIEC) and assessed intestinal inflammation and epithelial barrier repair. In vivo intestinal permeability was assessed by fluorescein isothiocyanate dextran uptake. Proliferation of IECs was analyzed by bromodeoxyuridine incorporation. Expression of DR3 messenger RNA was assessed by fluorescent in situ hybridization. Small intestinal organoids were used to determine ex vivo regenerative potential. RESULTS Dr3-/- mice developed more severe colonic inflammation than wild-type mice in DSS-induced colitis with significantly impaired IEC regeneration. Homeostatic proliferation of IECs was increased in Dr3-/- mice, but blunted during regeneration. Cellular localization and expression of the tight junction proteins Claudin-1 and zonula occludens-1 were altered, leading to increased homeostatic intestinal permeability. Dr3ΔIEC mice recapitulated the phenotype observed in Dr3-/- mice with increased intestinal permeability and IEC proliferation under homeostatic conditions and impaired tissue repair and increased bacterial translocation during DSS-induced colitis. Impaired regenerative potential and altered zonula occludens-1 localization also were observed in Dr3ΔIEC enteroids. CONCLUSIONS Our findings establish a novel function of DR3 in IEC homeostasis and postinjury regeneration independent of its established role in innate lymphoid cells and T-helper cells.
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Affiliation(s)
- Yosuke Shimodaira
- F. Widjaja Foundation Inflammatory Bowel Disease Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California
| | - Shyam K More
- F. Widjaja Foundation Inflammatory Bowel Disease Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California
| | - Hussein Hamade
- F. Widjaja Foundation Inflammatory Bowel Disease Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California
| | - Anna Y Blackwood
- F. Widjaja Foundation Inflammatory Bowel Disease Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California
| | - Jay P Abraham
- F. Widjaja Foundation Inflammatory Bowel Disease Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California
| | - Lisa S Thomas
- F. Widjaja Foundation Inflammatory Bowel Disease Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California
| | - Jordan H Miller
- F. Widjaja Foundation Inflammatory Bowel Disease Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California
| | - Dalton T Stamps
- F. Widjaja Foundation Inflammatory Bowel Disease Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California
| | - Sofi L Castanon
- F. Widjaja Foundation Inflammatory Bowel Disease Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California
| | - Noam Jacob
- F. Widjaja Foundation Inflammatory Bowel Disease Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California; Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California; Division of Gastroenterology, Hepatology and Parenteral Nutrition, Veterans Affairs Greater Los Angeles Healthcare System, Los Angeles, CA
| | - Connie W Y Ha
- F. Widjaja Foundation Inflammatory Bowel Disease Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California
| | - Suzanne Devkota
- F. Widjaja Foundation Inflammatory Bowel Disease Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California
| | - David Q Shih
- F. Widjaja Foundation Inflammatory Bowel Disease Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California
| | - Stephan R Targan
- F. Widjaja Foundation Inflammatory Bowel Disease Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California
| | - Kathrin S Michelsen
- F. Widjaja Foundation Inflammatory Bowel Disease Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California; Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California.
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7
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Genetic and Epigenetic Etiology of Inflammatory Bowel Disease: An Update. Genes (Basel) 2022; 13:genes13122388. [PMID: 36553655 PMCID: PMC9778199 DOI: 10.3390/genes13122388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 12/06/2022] [Accepted: 12/09/2022] [Indexed: 12/23/2022] Open
Abstract
Inflammatory bowel disease (IBD) is a chronic disease with periods of exacerbation and remission of the disease. The etiology of IBD is not fully understood. Many studies point to the presence of genetic, immunological, environmental, and microbiological factors and the interactions between them in the occurrence of IBD. The review looks at genetic factors in the context of both IBD predisposition and pharmacogenetics.
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8
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Xu WD, Li R, Huang AF. Role of TL1A in Inflammatory Autoimmune Diseases: A Comprehensive Review. Front Immunol 2022; 13:891328. [PMID: 35911746 PMCID: PMC9329929 DOI: 10.3389/fimmu.2022.891328] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 05/02/2022] [Indexed: 01/10/2023] Open
Abstract
TL1A, also called TNFSF15, is a member of tumor necrosis factor family. It is expressed in different immune cell, such as monocyte, macrophage, dendritic cell, T cell and non-immune cell, for example, synovial fibroblast, endothelial cell. TL1A competitively binds to death receptor 3 or decoy receptor 3, providing stimulatory signal for downstream signaling pathways, and then regulates proliferation, activation, apoptosis of and cytokine, chemokine production in effector cells. Recent findings showed that TL1A was abnormally expressed in autoimmune diseases, including rheumatoid arthritis, inflammatory bowel disease, psoriasis, primary biliary cirrhosis, systemic lupus erythematosus and ankylosing spondylitis. In vivo and in vitro studies further demonstrated that TL1A was involved in development and pathogenesis of these diseases. In this study, we comprehensively discussed the complex immunological function of TL1A and focused on recent findings of the pleiotropic activity conducted by TL1A in inflammatory autoimmune disease. Finish of the study will provide new ideas for developing therapeutic strategies for these diseases by targeting TL1A.
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Affiliation(s)
- Wang-Dong Xu
- Department of Evidence-Based Medicine, Southwest Medical University, Luzhou, China
| | - Rong Li
- Department of Evidence-Based Medicine, Southwest Medical University, Luzhou, China
| | - An-Fang Huang
- Department of Rheumatology and Immunology, Affiliated Hospital of Southwest Medical University, Luzhou, China
- *Correspondence: An-Fang Huang,
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9
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Plant-Derived Exosomes as A Drug-Delivery Approach for the Treatment of Inflammatory Bowel Disease and Colitis-Associated Cancer. Pharmaceutics 2022; 14:pharmaceutics14040822. [PMID: 35456656 PMCID: PMC9029273 DOI: 10.3390/pharmaceutics14040822] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 04/02/2022] [Accepted: 04/06/2022] [Indexed: 12/10/2022] Open
Abstract
Inflammatory bowel disease (IBD) is a chronic recurrent intestinal disease and includes Crohn’s disease (CD) and ulcerative colitis (UC). Due to the complex etiology of colitis, the current treatments of IBD are quite limited and are mainly concentrated on the remission of the disease. In addition, the side effects of conventional drugs on the body cannot be ignored. IBD also has a certain relationship with colitis-associated cancer (CAC), and inflammatory cells can produce a large number of tumor-promoting cytokines to promote tumor progression. In recent years, exosomes from plants have been found to have the ability to load drugs to target the intestine and have great potential for the treatment of intestinal diseases. This plant-derived exosome-targeting delivery system can load chemical or nucleic acid drugs and deliver them to intestinal inflammatory sites stably and efficiently. This review summarizes the pathophysiological characteristics of IBD and CAC as well as the application and prospect of plant exosomes in the treatment of IBD and CAC.
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10
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Alsheikh AJ, Wollenhaupt S, King EA, Reeb J, Ghosh S, Stolzenburg LR, Tamim S, Lazar J, Davis JW, Jacob HJ. The landscape of GWAS validation; systematic review identifying 309 validated non-coding variants across 130 human diseases. BMC Med Genomics 2022; 15:74. [PMID: 35365203 PMCID: PMC8973751 DOI: 10.1186/s12920-022-01216-w] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 03/17/2022] [Indexed: 02/08/2023] Open
Abstract
Background The remarkable growth of genome-wide association studies (GWAS) has created a critical need to experimentally validate the disease-associated variants, 90% of which involve non-coding variants. Methods To determine how the field is addressing this urgent need, we performed a comprehensive literature review identifying 36,676 articles. These were reduced to 1454 articles through a set of filters using natural language processing and ontology-based text-mining. This was followed by manual curation and cross-referencing against the GWAS catalog, yielding a final set of 286 articles. Results We identified 309 experimentally validated non-coding GWAS variants, regulating 252 genes across 130 human disease traits. These variants covered a variety of regulatory mechanisms. Interestingly, 70% (215/309) acted through cis-regulatory elements, with the remaining through promoters (22%, 70/309) or non-coding RNAs (8%, 24/309). Several validation approaches were utilized in these studies, including gene expression (n = 272), transcription factor binding (n = 175), reporter assays (n = 171), in vivo models (n = 104), genome editing (n = 96) and chromatin interaction (n = 33). Conclusions This review of the literature is the first to systematically evaluate the status and the landscape of experimentation being used to validate non-coding GWAS-identified variants. Our results clearly underscore the multifaceted approach needed for experimental validation, have practical implications on variant prioritization and considerations of target gene nomination. While the field has a long way to go to validate the thousands of GWAS associations, we show that progress is being made and provide exemplars of validation studies covering a wide variety of mechanisms, target genes, and disease areas. Supplementary Information The online version contains supplementary material available at 10.1186/s12920-022-01216-w.
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Affiliation(s)
- Ammar J Alsheikh
- Genomics Research Center, AbbVie Inc, North Chicago, Illinois, 60064, USA.
| | - Sabrina Wollenhaupt
- Information Research, AbbVie Deutschland GmbH & Co. KG, 67061, Knollstrasse, Ludwigshafen, Germany
| | - Emily A King
- Genomics Research Center, AbbVie Inc, North Chicago, Illinois, 60064, USA
| | - Jonas Reeb
- Information Research, AbbVie Deutschland GmbH & Co. KG, 67061, Knollstrasse, Ludwigshafen, Germany
| | - Sujana Ghosh
- Genomics Research Center, AbbVie Inc, North Chicago, Illinois, 60064, USA
| | | | - Saleh Tamim
- Genomics Research Center, AbbVie Inc, North Chicago, Illinois, 60064, USA
| | - Jozef Lazar
- Genomics Research Center, AbbVie Inc, North Chicago, Illinois, 60064, USA
| | - J Wade Davis
- Genomics Research Center, AbbVie Inc, North Chicago, Illinois, 60064, USA
| | - Howard J Jacob
- Genomics Research Center, AbbVie Inc, North Chicago, Illinois, 60064, USA
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11
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Roy R, Soldin SJ, Stolze B, Barbieri M, Tawalbeh SM, Rouhana N, Fronczek AE, Nagaraju K, van den Anker J, Dang UJ, Hoffman EP. Acute serum protein and cytokine response of single dose of prednisone in adult volunteers. Steroids 2022; 178:108953. [PMID: 35026285 DOI: 10.1016/j.steroids.2021.108953] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 12/21/2021] [Accepted: 12/28/2021] [Indexed: 12/28/2022]
Abstract
Pharmacological glucocorticoids are the most prescribed anti-inflammatory medications, and are chemical variants of cortisol, the circadian and stress hormone. Both endogenous and pharmacological glucocorticoids bind the glucocorticoid receptor (NR3C1) with high affinity, and both then bind downstream gene promoter elements (GRE) to drive positive gene transcription of many proteins. Glucocorticoid/GR complexes also bind distinct negative gene promoter elements (nGRE) to inhibit expression of genes involved in NF-κB innate immunity signaling. We sought to define the acute response of a single dose of prednisone (0.2 mg/kg) in young adult volunteers, with blood samples taken at baseline, 2, 3, 4 and 6 h post-oral dose. To control for circadian morning cortisol hitting the same molecular pathways, a day of blood draws was done without oral prednisone (same time of day), one day prior to drug day. Serum samples were processed for steroid hormone profiles (mass spectrometry; 9 steroidal hormones), proteomics (SOMAscan aptamer panels, 1,305 proteins), and inflammatory markers (Meso Scale Discovery; 10 pro-inflammatory cytokines). The pharmacological effect of the prednisone dose was shown by significant declines of adrenal steroids by 3 h after dosing. IL-10 showed drug-related increase to 4 hrs, then decrease to 6 hrs. IL-8 showed drug-related decrease in serum by 4 h, consistent with direct negative action of GR/ligand on IL-8 gene promoter. Proteomics data showed beta-2 microglobulin, TNFSF15, TSH, CST3, NBL1 to show time-related decreases with prednisone, while CXCL13 showed increases, although these require validation. In summary, a single low dose of prednisone leads to broad suppression of the adrenal axis within 3 h, and down-regulation of inflammatory serum proteins by 6 h.
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Affiliation(s)
- Runia Roy
- Department of Biomedical Engineering, Watson School of Engineering, Binghamton University - SUNY, Binghamton, NY, United States
| | - Steven J Soldin
- Department of Laboratory Medicine, NIH Clinical Center, National Institutes of Health, Bethesda, MD, United States
| | - Brian Stolze
- Department of Laboratory Medicine, NIH Clinical Center, National Institutes of Health, Bethesda, MD, United States
| | - Marissa Barbieri
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, Binghamton University - SUNY, Binghamton, NY, United States
| | - Shefa M Tawalbeh
- Department of Biomedical Engineering, Watson School of Engineering, Binghamton University - SUNY, Binghamton, NY, United States
| | - Nicole Rouhana
- Decker College of Nursing and Health Sciences, Binghamton University - SUNY, Binghamton NY, United States
| | - Ann E Fronczek
- Decker College of Nursing and Health Sciences, Binghamton University - SUNY, Binghamton NY, United States
| | - Kanneboyina Nagaraju
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, Binghamton University - SUNY, Binghamton, NY, United States
| | | | - Utkarsh J Dang
- Department of Health Outcomes and Administrative Sciences, School of Pharmacy and Pharmaceutical Sciences, Binghamton University - SUNY, Binghamton, NY, United States
| | - Eric P Hoffman
- Department of Biomedical Engineering, Watson School of Engineering, Binghamton University - SUNY, Binghamton, NY, United States; Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, Binghamton University - SUNY, Binghamton, NY, United States.
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12
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Luu LDW, Popple G, Tsang SPW, Vinasco K, Hilmi I, Ng RT, Chew KS, Wong SY, Riordan S, Lee WS, Mitchell HM, Kaakoush NO, Castaño-Rodríguez N. Genetic variants involved in innate immunity modulate the risk of inflammatory bowel diseases in an understudied Malaysian population. J Gastroenterol Hepatol 2022; 37:342-351. [PMID: 34888949 DOI: 10.1111/jgh.15752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 11/18/2021] [Accepted: 12/01/2021] [Indexed: 12/13/2022]
Abstract
BACKGROUND AND AIM Inflammatory bowel diseases (IBD) are chronic gastrointestinal inflammatory conditions comprising two major subtypes: Crohn's disease (CD) and ulcerative colitis (UC). The incidence of IBD is increasing in Asian countries including Malaysia. The aim of this study was to determine whether 32 single nucleotide polymorphisms (SNPs) strongly associated with IBD from genome-wide association studies, performed mainly in Caucasian populations, are associated with IBD in a Malaysian population, correlating these findings with local and systemic inflammation. METHODS Selected SNPs were investigated in a Malaysian cohort comprising 36 IBD patients and 75 controls using customized matrix-assisted laser desorption ionization time-of-flight genotyping. Local mRNA and/or systemic protein levels of IL-10, IL-12, IL-22, IL-23, and TNF-α were measured in these same subjects. RESULTS ATG16L2 rs11235667 and LINC00824 rs6651252 was significantly associated with increased CD risk while IL12B rs56167332 was a significant protective factor. Three SNPs (SBNO2 rs2024092, CARD9 rs10781499, and rs17085007 between GPR12-USP12) were significantly associated with increased UC risk while NKX2-3 rs4409764 was a significant protective factor. After adjusting for age, gender, and ethnicity, SBNO2 rs2024092, ATG16L2 rs11235667, CARD9 rs10781499, and LINC00824 rs6651252 remained associated with IBD. Interestingly, the risk alleles of IL10 rs3024505, CARD9 rs1078149, and IL12 rs6556412 were associated with higher levels of IL-10, IL-22, and IL-23 in these same subjects, respectively. CONCLUSIONS This study identified eight SNPs associated with IBD and/or its subtypes in the Malaysia population, significantly advancing our understanding of the genetic contribution to IBD in this understudied population. Three of these SNPs modulated relevant cytokine levels and thus, may directly contribute to IBD pathogenesis.
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Affiliation(s)
- Laurence Don Wai Luu
- School of Biotechnology and Biomolecular Sciences, Faculty of Science, University of New South Wales, Sydney, New South Wales, Australia
| | - Georgia Popple
- School of Biotechnology and Biomolecular Sciences, Faculty of Science, University of New South Wales, Sydney, New South Wales, Australia
| | - Samuel Pok Wei Tsang
- School of Biotechnology and Biomolecular Sciences, Faculty of Science, University of New South Wales, Sydney, New South Wales, Australia
| | - Karla Vinasco
- School of Biotechnology and Biomolecular Sciences, Faculty of Science, University of New South Wales, Sydney, New South Wales, Australia
| | - Ida Hilmi
- Department of Medicine, Faculty of Medicine, University Malaya, Kuala Lumpur, Malaysia
| | - Ruey Terng Ng
- Department of Paediatrics, Faculty of Medicine, University Malaya, Kuala Lumpur, Malaysia
| | - Kee Seang Chew
- Department of Paediatrics, Faculty of Medicine, University Malaya, Kuala Lumpur, Malaysia
| | - Shin Yee Wong
- Department of Paediatrics, Faculty of Medicine, University Malaya, Kuala Lumpur, Malaysia
| | - Stephen Riordan
- Gastrointestinal and Liver Unit, Prince of Wales Hospital, University of New South Wales, Sydney, New South Wales, Australia
| | - Way Seah Lee
- Department of Paediatrics, Faculty of Medicine, University Malaya, Kuala Lumpur, Malaysia
| | - Hazel M Mitchell
- School of Biotechnology and Biomolecular Sciences, Faculty of Science, University of New South Wales, Sydney, New South Wales, Australia
| | - Nadeem O Kaakoush
- School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia
| | - Natalia Castaño-Rodríguez
- School of Biotechnology and Biomolecular Sciences, Faculty of Science, University of New South Wales, Sydney, New South Wales, Australia
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13
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Li J, Xie R, Jiang F, Li Y, Zhu Y, Liu Z, Liao M, Liu Y, Meng X, Chen S, Yu J, Du M, Wang X, Chen Y, Yan H. Tumor necrosis factor ligand-related molecule 1A maintains blood-retinal barrier via modulating SHP-1-Src-VE-cadherin signaling in diabetic retinopathy. FASEB J 2021; 35:e22008. [PMID: 34679191 DOI: 10.1096/fj.202100807rr] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 10/03/2021] [Accepted: 10/06/2021] [Indexed: 12/15/2022]
Abstract
An impaired blood-retinal barrier (BRB) leads to diabetic macular edema (DME), which is a major complication of Diabetic retinopathy (DR). Mediators such as inflammation cause BRB breakdown. However, the explicit mechanism of its disruption is largely unknown. In this study, we identified tumor necrosis factor ligand-related molecule 1A (TL1A) as a crucial factor which protect retinal endothelial cells integrity in DR. By providing both human and mouse data, we show that TL1A is significantly decreased in the retinas of DME patients and diabetic rodents. We further demonstrate that the loss of TL1A accelerated diabetes-induced retinal barrier breakdown. TL1A supplementation protects the diabetic retina against BRB breakdown. Mechanistically, TL1A stabilize intracellular junctions and protect vascular integrity by blocking SHP1-Src-regulated VE-cadherin phosphorylation. Collectively, our findings reveal that loss of TL1A in the retina leads to increased vascular permeability in DR, and that TL1A treatment is of potential therapeutic interest for the treatment of DME.
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Affiliation(s)
- Jianan Li
- Department of Ophthalmology, Tianjin Medical University General Hospital, Tianjin, China.,Laboratory of Molecular ophthalmology, Tianjin Medical University, Tianjin, China.,Department of Pharmacology and Tianjin Key Laboratory of Inflammation Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China.,Tianjin Neurological Institute, Key Laboratory of Post-Neuroinjury Neuro-repair and Regeneration in Central Nervous System, Ministry of Education and Tianjin City, Tianjin, China
| | - Ruotian Xie
- Department of Ophthalmology, Tianjin Medical University General Hospital, Tianjin, China
| | - Feng Jiang
- Department of Ophthalmology, Tianjin Medical University General Hospital, Tianjin, China
| | - Yiming Li
- Department of Ophthalmology, Tianjin Medical University General Hospital, Tianjin, China.,Laboratory of Molecular ophthalmology, Tianjin Medical University, Tianjin, China
| | - Yanfang Zhu
- Department of Ophthalmology, Tianjin Medical University General Hospital, Tianjin, China.,Laboratory of Molecular ophthalmology, Tianjin Medical University, Tianjin, China
| | - Zhiheng Liu
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Institute of Urology, Tianjin Medical University, Tianjin, China
| | - Mengyu Liao
- Department of Ophthalmology, Tianjin Medical University General Hospital, Tianjin, China.,Laboratory of Molecular ophthalmology, Tianjin Medical University, Tianjin, China
| | - Yuanyuan Liu
- Department of Ophthalmology, Tianjin Medical University General Hospital, Tianjin, China
| | - Xiangda Meng
- Department of Ophthalmology, Tianjin Medical University General Hospital, Tianjin, China
| | - Song Chen
- Department of Ophthalmology, Tianjin Medical University General Hospital, Tianjin, China
| | - Jinguo Yu
- Department of Ophthalmology, Tianjin Medical University General Hospital, Tianjin, China
| | - Mei Du
- Laboratory of Molecular ophthalmology, Tianjin Medical University, Tianjin, China.,Department of Pharmacology and Tianjin Key Laboratory of Inflammation Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Xiaohong Wang
- Laboratory of Molecular ophthalmology, Tianjin Medical University, Tianjin, China.,Department of Pharmacology and Tianjin Key Laboratory of Inflammation Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Yupeng Chen
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Institute of Urology, Tianjin Medical University, Tianjin, China
| | - Hua Yan
- Department of Ophthalmology, Tianjin Medical University General Hospital, Tianjin, China.,Laboratory of Molecular ophthalmology, Tianjin Medical University, Tianjin, China
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14
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Mascalzoni D, Biasiotto R, Borsche M, Brüggemann N, De Grandi A, Goegele M, Frygner-Holm S, Klein C, Kösters M, Staunton C, Pramstaller PP, Krawczak M, Hicks AA. Balancing scientific interests and the rights of participants in designing a recall by genotype study. Eur J Hum Genet 2021; 29:1146-1157. [PMID: 33981014 PMCID: PMC8298596 DOI: 10.1038/s41431-021-00860-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 12/15/2020] [Accepted: 03/02/2021] [Indexed: 01/14/2023] Open
Abstract
Recall by genotype (RbG) studies aim to better understand the phenotypes that correspond to genetic variants of interest, by recruiting carriers of such variants for further phenotyping. RbG approaches pose major ethical and legal challenges related to the disclosure of possibly unwanted genetic information. The Cooperative Health Research in South Tyrol (CHRIS) study is a longitudinal cohort study based in South Tyrol, Italy. Demand has grown for CHRIS study participants to be enrolled in RbG studies, thus making the design of a suitable ethical framework a pressing need. We here report upon the design of a pilot RbG study conducted with CHRIS study participants. By reviewing the literature and by consulting relevant stakeholders (CHRIS participants, clinical geneticists, ethics board, GPs), we identified key ethical issues in RbG approaches (e.g. complexity of the context, communication of genetic results, measures to further protect participants). The design of the pilot was based on a feasibility assessment, the selection of a suitable test case within the ProtectMove Research Unit on reduced penetrance of hereditary movement disorders, and the development of appropriate recruitment and communication strategies. An empirical study was embedded in the pilot study with the aim of understanding participants' views on RbG. Our experience with the pilot study in CHRIS allowed us to contribute to the development of best practices and policies for RbG studies by drawing recommendations: addressing the possibility of RbG in the original consent, implementing tailored communication strategies, engaging stakeholders, designing embedded empirical studies, and sharing research experiences and methodology.
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Affiliation(s)
- Deborah Mascalzoni
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Bolzano, Italy.
- Department of Public Health and Caring Sciences, Center for Research Ethics and Bioethics, Uppsala University, Uppsala, Sweden.
| | - Roberta Biasiotto
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Bolzano, Italy
| | - Max Borsche
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
- Department of Neurology, University Medical Center Schleswig-Holstein, Lübeck, Germany
| | - Norbert Brüggemann
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
- Department of Neurology, University Medical Center Schleswig-Holstein, Lübeck, Germany
| | - Alessandro De Grandi
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Bolzano, Italy
| | - Martin Goegele
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Bolzano, Italy
| | | | - Christine Klein
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
| | - Maria Kösters
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Bolzano, Italy
| | - Ciara Staunton
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Bolzano, Italy
- School of Law, Middlesex University, London, UK
| | - Peter P Pramstaller
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Bolzano, Italy
| | - Michael Krawczak
- Institute of Medical Informatics and Statistics, Kiel University, Kiel, Germany
| | - Andrew A Hicks
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Bolzano, Italy
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15
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Caliskan M, Brown CD, Maranville JC. A catalog of GWAS fine-mapping efforts in autoimmune disease. Am J Hum Genet 2021; 108:549-563. [PMID: 33798443 PMCID: PMC8059376 DOI: 10.1016/j.ajhg.2021.03.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 03/05/2021] [Indexed: 12/11/2022] Open
Abstract
Genome-wide association studies (GWASs) have enabled unbiased identification of genetic loci contributing to common complex diseases. Because GWAS loci often harbor many variants and genes, it remains a major challenge to move from GWASs’ statistical associations to the identification of causal variants and genes that underlie these association signals. Researchers have applied many statistical and functional fine-mapping strategies to prioritize genetic variants and genes as potential candidates. There is no gold standard in fine-mapping approaches, but consistent results across different approaches can improve confidence in the fine-mapping findings. Here, we combined text mining with a systematic review and formed a catalog of 85 studies with evidence of fine mapping for at least one autoimmune GWAS locus. Across all fine-mapping studies, we compiled 230 GWAS loci with allelic heterogeneity estimates and predictions of causal variants and trait-relevant genes. These 230 loci included 455 combinations of locus-by-disease association signals with 15 autoimmune diseases. Using these estimates, we assessed the probability of mediating disease risk associations across genes in GWAS loci and identified robust signals of causal disease biology. We predict that this comprehensive catalog of GWAS fine-mapping efforts in autoimmune disease will greatly help distill the plethora of information in the field and inform therapeutic strategies.
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Affiliation(s)
- Minal Caliskan
- Department of Informatics and Predictive Sciences, Bristol Myers Squibb, Princeton, NJ 08540, USA.
| | - Christopher D Brown
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Joseph C Maranville
- Department of Informatics and Predictive Sciences, Bristol Myers Squibb, Princeton, NJ 08540, USA
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16
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Lagisetty KH, McEwen DP, Nancarrow DJ, Schiebel JG, Ferrer-Torres D, Ray D, Frankel TL, Lin J, Chang AC, Kresty LA, Beer DG. Immune determinants of Barrett's progression to esophageal adenocarcinoma. JCI Insight 2021; 6:143888. [PMID: 33290281 PMCID: PMC7821593 DOI: 10.1172/jci.insight.143888] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 11/25/2020] [Indexed: 12/14/2022] Open
Abstract
Esophageal adenocarcinoma (EAC) develops from Barrett’s esophagus (BE), a chronic inflammatory state that can progress through a series of transformative dysplastic states before tumor development. While molecular and genetic changes of EAC tumors have been studied, immune microenvironment changes during Barrett’s progression to EAC remain poorly understood. In this study, we identify potential immunologic changes that can occur during BE-to-EAC progression. RNA sequencing (RNA-Seq) analysis on tissue samples from EAC patients undergoing surgical resection demonstrated that a subset of chemokines and cytokines, most notably IL6 and CXCL8, increased during BE progression to EAC. xCell deconvolution analysis investigating immune cell population changes demonstrated that the largest changes in expression during BE progression occurred in M2 macrophages, pro–B cells, and eosinophils. Multiplex immunohistochemical staining of tissue microarrays showed increased immune cell populations during Barrett’s progression to high-grade dysplasia. In contrast, EAC tumor sections were relatively immune poor, with a rise in PD-L1 expression and loss of CD8+ T cells. These data demonstrate that the EAC microenvironment is characterized by poor cytotoxic effector cell infiltration and increased immune inhibitory signaling. These findings suggest an immunosuppressive microenvironment, highlighting the need for further studies to explore immune modulatory therapy in EAC.
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Affiliation(s)
- Kiran H Lagisetty
- Department of Surgery, Section of Thoracic Surgery, University of Michigan, Ann Arbor, Michigan, USA.,VA Ann Arbor Health Care System, Ann Arbor, Michigan, USA
| | - Dyke P McEwen
- Department of Surgery, Section of Thoracic Surgery, University of Michigan, Ann Arbor, Michigan, USA
| | - Derek J Nancarrow
- Department of Surgery, Section of Thoracic Surgery, University of Michigan, Ann Arbor, Michigan, USA
| | - Johnathon G Schiebel
- Department of Surgery, Section of Thoracic Surgery, University of Michigan, Ann Arbor, Michigan, USA
| | | | - Dipankar Ray
- Department of Radiation Oncology, University of Michigan, Ann Arbor, Michigan, USA
| | - Timothy L Frankel
- Department of Surgery, Section of Thoracic Surgery, University of Michigan, Ann Arbor, Michigan, USA
| | - Jules Lin
- Department of Surgery, Section of Thoracic Surgery, University of Michigan, Ann Arbor, Michigan, USA
| | - Andrew C Chang
- Department of Surgery, Section of Thoracic Surgery, University of Michigan, Ann Arbor, Michigan, USA
| | - Laura A Kresty
- Department of Surgery, Section of Thoracic Surgery, University of Michigan, Ann Arbor, Michigan, USA
| | - David G Beer
- Department of Surgery, Section of Thoracic Surgery, University of Michigan, Ann Arbor, Michigan, USA.,Department of Radiation Oncology, University of Michigan, Ann Arbor, Michigan, USA
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17
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Nasef NA, Mehta S. Role of Inflammation in Pathophysiology of Colonic Disease: An Update. Int J Mol Sci 2020; 21:E4748. [PMID: 32635383 PMCID: PMC7370289 DOI: 10.3390/ijms21134748] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 06/28/2020] [Accepted: 07/01/2020] [Indexed: 02/06/2023] Open
Abstract
Diseases of the colon are a big health burden in both men and women worldwide ranging from acute infection to cancer. Environmental and genetic factors influence disease onset and outcome in multiple colonic pathologies. The importance of inflammation in the onset, progression and outcome of multiple colonic pathologies is gaining more traction as the evidence from recent research is considered. In this review, we provide an update on the literature to understand how genetics, diet, and the gut microbiota influence the crosstalk between immune and non‑immune cells resulting in inflammation observed in multiple colonic pathologies. Specifically, we focus on four colonic diseases two of which have a more established association with inflammation (inflammatory bowel disease and colorectal cancer) while the other two have a less understood relationship with inflammation (diverticular disease and irritable bowel syndrome).
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Affiliation(s)
- Noha Ahmed Nasef
- Riddet Institute, Massey University, Private Bag 11222, Palmerston North 4442, New Zealand
| | - Sunali Mehta
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin 9054, New Zealand
- Maurice Wilkins Centre for Biodiscovery, University of Otago, Dunedin 9054, New Zealand
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18
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Jia X, Yamamura T, Gbadegesin R, McNulty MT, Song K, Nagano C, Hitomi Y, Lee D, Aiba Y, Khor SS, Ueno K, Kawai Y, Nagasaki M, Noiri E, Horinouchi T, Kaito H, Hamada R, Okamoto T, Kamei K, Kaku Y, Fujimaru R, Tanaka R, Shima Y, Baek J, Kang HG, Ha IS, Han KH, Yang EM, Abeyagunawardena A, Lane B, Chryst-Stangl M, Esezobor C, Solarin A, Dossier C, Deschênes G, Vivarelli M, Debiec H, Ishikura K, Matsuo M, Nozu K, Ronco P, Cheong HI, Sampson MG, Tokunaga K, Iijima K. Common risk variants in NPHS1 and TNFSF15 are associated with childhood steroid-sensitive nephrotic syndrome. Kidney Int 2020; 98:1308-1322. [PMID: 32554042 DOI: 10.1016/j.kint.2020.05.029] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 04/23/2020] [Accepted: 05/01/2020] [Indexed: 12/16/2022]
Abstract
To understand the genetics of steroid-sensitive nephrotic syndrome (SSNS), we conducted a genome-wide association study in 987 childhood SSNS patients and 3,206 healthy controls with Japanese ancestry. Beyond known associations in the HLA-DR/DQ region, common variants in NPHS1-KIRREL2 (rs56117924, P=4.94E-20, odds ratio (OR) =1.90) and TNFSF15 (rs6478109, P=2.54E-8, OR=0.72) regions achieved genome-wide significance and were replicated in Korean, South Asian and African populations. Trans-ethnic meta-analyses including Japanese, Korean, South Asian, African, European, Hispanic and Maghrebian populations confirmed the significant associations of variants in NPHS1-KIRREL2 (Pmeta=6.71E-28, OR=1.88) and TNFSF15 (Pmeta=5.40E-11, OR=1.33) loci. Analysis of the NPHS1 risk alleles with glomerular NPHS1 mRNA expression from the same person revealed allele specific expression with significantly lower expression of the transcript derived from the risk haplotype (Wilcox test p=9.3E-4). Because rare pathogenic variants in NPHS1 cause congenital nephrotic syndrome of the Finnish type (CNSF), the present study provides further evidence that variation along the allele frequency spectrum in the same gene can cause or contribute to both a rare monogenic disease (CNSF) and a more complex, polygenic disease (SSNS).
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Affiliation(s)
- Xiaoyuan Jia
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Tomohiko Yamamura
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Rasheed Gbadegesin
- Department of Pediatrics, Division of Nephrology, Duke University Medical Center, Durham, North Carolina, USA
| | - Michelle T McNulty
- Department of Medicine-Nephrology, Boston Children's Hospital, Boston, Massachussetts, USA; Medical and Population Genetics, Broad Institute, Cambridge, Massachussetts, USA
| | - Kyuyong Song
- Department of Biochemistry and Molecular Biology, University of Ulsan College of Medicine, Seoul, Korea
| | - China Nagano
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Yuki Hitomi
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Dongwon Lee
- Department of Medicine-Nephrology, Boston Children's Hospital, Boston, Massachussetts, USA; Medical and Population Genetics, Broad Institute, Cambridge, Massachussetts, USA; Harvard Medical School, Boston, Massachussetts, USA
| | - Yoshihiro Aiba
- Clinical Research Center, National Hospital Organization Nagasaki Medical Center, Omura, Japan
| | - Seik-Soon Khor
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Kazuko Ueno
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yosuke Kawai
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Masao Nagasaki
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Eisei Noiri
- Department of Hemodialysis and Apheresis, The University of Tokyo Hospital, Tokyo, Japan
| | - Tomoko Horinouchi
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Hiroshi Kaito
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan; Department of Nephrology, Hyogo Prefectural Kobe Children's Hospital, Kobe, Japan
| | - Riku Hamada
- Department of Nephrology, Tokyo Metropolitan Children's Medical Center, Tokyo, Japan
| | - Takayuki Okamoto
- Department of Pediatrics, Hokkaido University Hospital, Sapporo, Japan
| | - Koichi Kamei
- Division of Nephrology and Rheumatology, National Center for Child Health and Development, Tokyo, Japan
| | - Yoshitsugu Kaku
- Department of Nephrology, Fukuoka Children's Hospital, Fukuoka, Japan
| | - Rika Fujimaru
- Department of Pediatrics, Osaka City General Hospital, Osaka, Japan
| | - Ryojiro Tanaka
- Department of Nephrology, Hyogo Prefectural Kobe Children's Hospital, Kobe, Japan
| | - Yuko Shima
- Department of Pediatrics, Wakayama Medical University, Wakayama, Japan
| | | | - Jiwon Baek
- Department of Biochemistry and Molecular Biology, University of Ulsan College of Medicine, Seoul, Korea
| | - Hee Gyung Kang
- Department of Pediatrics, Seoul National University Children's Hospital, Seoul, Korea
| | - Il-Soo Ha
- Department of Pediatrics, Seoul National University Children's Hospital, Seoul, Korea
| | - Kyoung Hee Han
- Department of Pediatrics, Jeju National University School of Medicine, Jeju, Korea
| | - Eun Mi Yang
- Department of Pediatrics, Chonnam National University Children's Hospital, Gwangju, Korea
| | | | - Asiri Abeyagunawardena
- Department of Pediatrics, Division of Nephrology, Duke University Medical Center, Durham, North Carolina, USA
| | - Brandon Lane
- Department of Pediatrics, Division of Nephrology, Duke University Medical Center, Durham, North Carolina, USA
| | - Megan Chryst-Stangl
- Department of Pediatrics, Division of Nephrology, Duke University Medical Center, Durham, North Carolina, USA
| | - Christopher Esezobor
- Department of Paediatrics, College of Medicine, University of Lagos, Lagos, Nigeria
| | - Adaobi Solarin
- Department of Pediatrics, Lagos State University Teaching Hospital, Ikeja, Nigeria
| | | | - Claire Dossier
- Department of Paediatric Nephrology, Public Assistance Hospital of Paris, Robert-Debré Hospital, Paris, France
| | - Georges Deschênes
- Center of Research on Inflammation, Institut National de la Santé et de la Recherche Médicale UMR 1149, University Sorbonne-Paris, Paris, France
| | | | - Marina Vivarelli
- Division of Nephrology and Dialysis, Bambino Gesù Children's Hospital and Research Institute, Rome, Italy
| | - Hanna Debiec
- Sorbonne University, INSERM UMR_S1155, and Nephrology Day Hospital, Department of Nephrology, Hôpital Tenon, Paris France
| | - Kenji Ishikura
- Division of Nephrology and Rheumatology, National Center for Child Health and Development, Tokyo, Japan
| | - Masafumi Matsuo
- Research Center for Locomotion Biology, Kobe Gakuin University, Kobe, Japan; KNC Department of Nucleic Acid Drug Discovery, Faculty of Rehabilitation, Kobe Gakuin University, Kobe, Japan
| | - Kandai Nozu
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Pierre Ronco
- Sorbonne University, INSERM UMR_S1155, and Nephrology Day Hospital, Department of Nephrology, Hôpital Tenon, Paris France
| | - Hae Il Cheong
- Department of Pediatrics, Seoul National University Children's Hospital, Seoul, Korea
| | - Matthew G Sampson
- Department of Medicine-Nephrology, Boston Children's Hospital, Boston, Massachussetts, USA; Medical and Population Genetics, Broad Institute, Cambridge, Massachussetts, USA; Harvard Medical School, Boston, Massachussetts, USA
| | - Katsushi Tokunaga
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.
| | - Kazumoto Iijima
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan.
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19
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Jung S, Liu W, Baek J, Moon JW, Ye BD, Lee HS, Park SH, Yang SK, Han B, Liu J, Song K. Expression Quantitative Trait Loci (eQTL) Mapping in Korean Patients With Crohn's Disease and Identification of Potential Causal Genes Through Integration With Disease Associations. Front Genet 2020; 11:486. [PMID: 32477412 PMCID: PMC7240107 DOI: 10.3389/fgene.2020.00486] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 04/20/2020] [Indexed: 12/23/2022] Open
Abstract
Background Expression quantitative trait loci (eQTL) datasets have extensively been used to help interpret genome-wide association study signals. Most eQTL analyses have been conducted with populations of European ancestry. Objective To determine the most functionally relevant genes at the Crohn’s disease (CD) loci identified in genome-wide association studies (GWAS) involving Asian populations and to find novel disease-associated genes, we conducted an eQTL analysis. Methods eQTL analysis was performed using whole-blood RNA-sequencing of 101 Korean patients with CD. FastQTL was used for a pair-wise genome analysis of ∼ 6.5 M SNPs and ∼ 22 K transcripts. Results We identified 135,164 cis-eQTL and 3,816 eGenes with a false discovery rate less than 0.05. A significant proportion of the genes identified in our study overlapped with those identified in previous studies. The significantly enriched pathways of these 3,816 eGenes included neutrophil degranulation and small molecule biosynthetic process. Integrated analysis of CD GWAS with Korean eQTL revealed two putative target genes, TNFSF15 and GPR35, at two previously reported loci, whereas TNFSF15 only with the whole blood data from the Genotype-Tissue Expression (GTEx) project, highlighting the utility of building a population-specific data set, even of modest size. The risk alleles of these genes were found to be associated with lower expression levels of TNFSF15 and GPR35, respectively. Our eQTL browser can be accessed at “http://asan.crohneqtl.com/”. Conclusion This resource would be useful for studies that need to employ genome-wide association analyses involving Asian populations.
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Affiliation(s)
- Seulgi Jung
- Department of Biochemistry and Molecular Biology, University of Ulsan College of Medicine, Seoul, South Korea
| | - Wenting Liu
- Human Genetics, Genome Institute of Singapore, Singapore, Singapore
| | - Jiwon Baek
- Department of Biochemistry and Molecular Biology, University of Ulsan College of Medicine, Seoul, South Korea
| | - Jung Won Moon
- Department of Biochemistry and Molecular Biology, University of Ulsan College of Medicine, Seoul, South Korea
| | - Byong Duk Ye
- Department of Gastroenterology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, South Korea
| | - Ho-Su Lee
- Department of Biochemistry and Molecular Biology, University of Ulsan College of Medicine, Seoul, South Korea
| | - Sang Hyoung Park
- Department of Gastroenterology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, South Korea
| | - Suk-Kyun Yang
- Department of Gastroenterology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, South Korea
| | - Buhm Han
- Department of Medicine, Seoul National University College of Medicine, Seoul, South Korea
| | - Jianjun Liu
- Human Genetics, Genome Institute of Singapore, Singapore, Singapore
| | - Kyuyoung Song
- Department of Biochemistry and Molecular Biology, University of Ulsan College of Medicine, Seoul, South Korea
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20
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Hine AM, Loke P. Intestinal Macrophages in Resolving Inflammation. THE JOURNAL OF IMMUNOLOGY 2020; 203:593-599. [PMID: 31332080 DOI: 10.4049/jimmunol.1900345] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 05/22/2019] [Indexed: 12/15/2022]
Abstract
Macrophages not only regulate intestinal homeostasis by recognizing pathogens to control enteric infections but also employ negative feedback mechanisms to prevent chronic inflammation. Hence, macrophages are intriguing targets for immune-mediated therapies, especially when barrier function in the gut is compromised to trigger aberrant inflammatory responses, most notably during inflammatory bowel diseases. Recently, there has been considerable progress in our understanding of human macrophage biology in different tissues, including the intestines. In this review, we discuss some new findings on the properties of distinct populations of intestinal macrophages, how resolution of inflammation and tissue repair by macrophages could be promoted by type 2 cytokines as well as other therapeutic interventions, and highlight some challenges for translating these findings into the future for this exciting area of immunology research.
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Affiliation(s)
- Ashley M Hine
- Department of Microbiology, New York University School of Medicine, New York, NY 10016
| | - P'ng Loke
- Department of Microbiology, New York University School of Medicine, New York, NY 10016
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21
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Wallace C. Eliciting priors and relaxing the single causal variant assumption in colocalisation analyses. PLoS Genet 2020; 16:e1008720. [PMID: 32310995 PMCID: PMC7192519 DOI: 10.1371/journal.pgen.1008720] [Citation(s) in RCA: 142] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 04/30/2020] [Accepted: 03/17/2020] [Indexed: 01/03/2023] Open
Abstract
Horizontal integration of summary statistics from different GWAS traits can be used to evaluate evidence for their shared genetic causality. One popular method to do this is a Bayesian method, coloc, which is attractive in requiring only GWAS summary statistics and no linkage disequilibrium estimates and is now being used routinely to perform thousands of comparisons between traits. Here we show that while most users do not adjust default software values, misspecification of prior parameters can substantially alter posterior inference. We suggest data driven methods to derive sensible prior values, and demonstrate how sensitivity analysis can be used to assess robustness of posterior inference. The flexibility of coloc comes at the expense of an unrealistic assumption of a single causal variant per trait. This assumption can be relaxed by stepwise conditioning, but this requires external software and an LD matrix aligned to study alleles. We have now implemented conditioning within coloc, and propose a new alternative method, masking, that does not require LD and approximates conditioning when causal variants are independent. Importantly, masking can be used in combination with conditioning where allelically aligned LD estimates are available for only a single trait. We have implemented these developments in a new version of coloc which we hope will enable more informed choice of priors and overcome the restriction of the single causal variant assumptions in coloc analysis.
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Affiliation(s)
- Chris Wallace
- Cambridge Institute for Therapeutic Immunology & Infectious Disease, and MRC Biostatistics Unit, University of Cambridge, Cambridge, United Kingdom
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22
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Wang T, Li J, Xie R, Wang J, Zhang W, Jiang F, Du M, Wang X, Huang B, Brant R, Zhang C, Yan H. Intraocular tumour necrosis factor ligand related molecule 1 A links disease progression of proliferative diabetic retinopathy after primary vitrectomy. Clin Exp Pharmacol Physiol 2020; 47:966-976. [PMID: 32064668 DOI: 10.1111/1440-1681.13284] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 01/17/2020] [Accepted: 02/13/2020] [Indexed: 11/30/2022]
Abstract
Tumour necrosis factor ligand related molecule 1 A (TL1A), a member of tumour necrosis factor superfamily, has been identified as a crucial regulator for vascular homeostasis and inflammation. However, the function of TL1A in diabetic retinopathy (DR) is largely unknown. This study aims to examine levels of TL1A in serum and intraocular fluid in patients with proliferative diabetic retinopathy (PDR), and to explore the correlation of intraocular TL1A with the prognosis of PDR progression after primary vitrectomy. Seventy-five patients (75 eyes) with PDR who underwent pars plana vitrectomy (PPV) and 19 patients (19 eyes) who received vitrectomy for idiopathic macular holes (IMH) as non-diabetic control group were enrolled in this prospective study. Serum, aqueous and vitreous fluid samples were collected during cataract and PPV surgery. Protein expressions of TL1A as well as other angiogenic and inflammatory cytokines in serum and intraocular fluid were measured. Correlations of intraocular TL1A concentrations with inflammatory cytokines were analyzed. We found both aqueous and vitreous TL1A levels were significantly higher in the PDR group than in control group (Paqueous = 0.026; Pvitreous <0.001). Angiogenic and inflammatory cytokines such as VEGF, IL-6, IL-8, MCP-1, MIP-1α, and MIP-1β were significantly higher in intraocular fluid in PDR group than in controls, which MCP-1 and MIP-1α showed positive correlation with intraocular TL1A levels. There is no significant difference in the levels of serum TL1A as well as other inflammatory cytokines between PDR patients and controls. Intraocular levels of TL1A were significantly lower in PDR progression group than in the stable group (Paqueous <0.001; Pvitreous <0.001). Multivariate logistic regression analyses revealed that lower levels of intraocular TL1A was an important risk factor for predicting PDR progression after primary PPV (ORaqueous = 0.717, Paqueous = 0.001; ORvitreous = 0.684; Pvitreous = 0.002). In conclusion, TL1A and multiple inflammatory cytokines were highly enriched in the intraocular fluid of PDR patients compared with the controls. Lower levels of intraocular TL1A were associated with development of PDR complications after primary PPV and might be used as prognostic factor in predicting the vitrectomy outcome in PDR patients.
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Affiliation(s)
- Tian Wang
- Department of Ophthalmology, Tianjin Medical University General Hospital, Tianjin, China
| | - Jianan Li
- Department of Ophthalmology, Tianjin Medical University General Hospital, Tianjin, China
| | - Ruotian Xie
- Department of Ophthalmology, Tianjin Medical University General Hospital, Tianjin, China
| | - Jiaxing Wang
- Department of Ophthalmology, Emory University, Atlanta, GA, USA
| | - Wei Zhang
- Tianjin Eye Hospital, Tianjin Key Lab of Ophthalmology and Visual Science, Tianjin Eye Institute, Clinical College of Ophthalmology Tianjin Medical University, Tianjin, China
| | - Feng Jiang
- Department of Ophthalmology, Tianjin Medical University General Hospital, Tianjin, China
| | - Mei Du
- Department of Pharmacology, Tianjin Key Laboratory of Inflammation Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Xiaohong Wang
- Department of Pharmacology, Tianjin Key Laboratory of Inflammation Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Bo Huang
- Department of Ophthalmology, University of Mississippi Medical Center, Jackson, MS, USA
| | - Rodrigo Brant
- Department of Ophthalmology and Visual Sciences, Federal University of São Paulo, São Paulo, Brazil
| | - Cheng Zhang
- Department of Ophthalmology & Visual Sciences, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Hua Yan
- Department of Ophthalmology, Tianjin Medical University General Hospital, Tianjin, China
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23
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A Comprehensive Review and Update on the Pathogenesis of Inflammatory Bowel Disease. J Immunol Res 2019; 2019:7247238. [PMID: 31886308 PMCID: PMC6914932 DOI: 10.1155/2019/7247238] [Citation(s) in RCA: 435] [Impact Index Per Article: 87.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 11/15/2019] [Indexed: 12/13/2022] Open
Abstract
Inflammatory bowel disease (IBD) is a chronic and life-threating inflammatory disease of gastroenteric tissue characterized by episodes of intestinal inflammation. The pathogenesis of IBD is complex. Recent studies have greatly improved our knowledge of the pathophysiology of IBD, leading to great advances in the treatment as well as diagnosis of IBD. In this review, we have systemically reviewed the pathogenesis of IBD and highlighted recent advances in host genetic factors, gut microbiota, and environmental factors and, especially, in abnormal innate and adaptive immune responses and their interactions, which may hold the keys to identify novel predictive or prognostic biomarkers and develop new therapies.
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24
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Zhang W, Yang M, Wang Y, Wu X, Zhang X, Ding Y, Yin Z. Genomic analysis reveals selection signatures of the Wannan Black pig during domestication and breeding. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2019; 33:712-721. [PMID: 31480149 PMCID: PMC7206397 DOI: 10.5713/ajas.19.0289] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2019] [Accepted: 08/01/2019] [Indexed: 12/31/2022]
Abstract
Objective The Wannan Black pig is a typical Chinese indigenous, disease-resistant pig breed with high fertility, and a crude-feed tolerance that has been bred by artificial selection in the south of Anhui province for a long time. However, genome variation, genetic relationships with other pig breeds, and domestication, remain poorly understood. Here, we focus on elucidating the genetic characteristics of the Wannan Black pig and identifying selection signatures during domestication and breeding. Methods We identified the whole-genome variation in the Wannan Black pig and performed population admixture analyses to determine genetic relationships with other domesticated pig breeds and wild boars. Then, we identified the selection signatures between the Wannan Black pig and Asian wild boars in 100-kb windows sliding in 10 kb steps by using two approaches: the fixation index (FST) and π ratios. Results Resequencing the Wannan Black pig genome yielded 501.52 G of raw data. After calling single-nucleotide variants (SNVs) and insertions/deletions (InDels), we identified 21,316,754 SNVs and 5,067,206 InDels (2,898,582 inserts and 2,168,624 deletions). Additionally, we found genes associated with growth, immunity, and digestive functions. Conclusion Our findings help in explaining the unique genetic and phenotypic characteristics of Wannan Black pigs, which in turn can be informative for future breeding programs of Wannan Black pigs.
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Affiliation(s)
- Wei Zhang
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
| | - Min Yang
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
| | - Yuanlang Wang
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
| | - Xudong Wu
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
| | - Xiaodong Zhang
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
| | - Yueyun Ding
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
| | - Zongjun Yin
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
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25
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Valatas V, Kolios G, Bamias G. TL1A (TNFSF15) and DR3 (TNFRSF25): A Co-stimulatory System of Cytokines With Diverse Functions in Gut Mucosal Immunity. Front Immunol 2019; 10:583. [PMID: 30972074 PMCID: PMC6445966 DOI: 10.3389/fimmu.2019.00583] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 03/04/2019] [Indexed: 12/11/2022] Open
Abstract
TL1A and its functional receptor DR3 are members of the TNF/TNFR superfamilies of proteins. Binding of APC-derived TL1A to lymphocytic DR3 provides co-stimulatory signals for activated lymphocytes. DR3 signaling affects the proliferative activity of and cytokine production by effector lymphocytes, but also critically influences the development and suppressive function of regulatory T-cells. DR3 was also found to be highly expressed by innate lymphoid cells (ILCS), which respond to stimulation by TL1A. Several recent studies with transgenic and knockout mice as well as neutralizing or agonistic antibodies for these two proteins, have clearly shown that TL1A/DR3 are important mediators of several chronic immunological disorders, including Inflammatory Bowel Disease (IBD). TL1A and DR3 are abundantly localized at inflamed intestinal areas of patients with IBD and mice with experimental ileitis or colitis and actively participate in the immunological pathways that underlie mucosal homeostasis and intestinal inflammation. DR3 signaling has demonstrated a dichotomous role in mucosal immunity. On the one hand, during acute mucosal injury it exerts protective functions by ameliorating the severity of acute inflammatory responses and facilitating tissue repair. On the other hand, it critically participates in the pro-inflammatory pathways that underlie chronic inflammatory responses, such as those that take place in IBD. These effects are mediated through modulation of the relative mucosal abundance and function of Th1, Th2, Th17, Th9, and Treg lymphocytes, but also of all types of ILCs. Recently, an important role was demonstrated for TL1A/DR3 as potential mediators of intestinal fibrosis that is associated with the presence of gut inflammation. These accumulating data have raised the possibility that TL1A/DR3 pathways may represent a valid therapeutic target for chronic immunological diseases. Nevertheless, applicability of such a therapeutic approach will greatly rely on the net result of TL1A/DR3 manipulation on the various cell populations that will be affected by this approach.
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Affiliation(s)
- Vassilis Valatas
- Gastroenterology and Hepatology Research Laboratory, Medical School, University of Crete, Heraklion, Greece
| | - George Kolios
- Laboratory of Pharmacology, Faculty of Medicine, Democritus University of Thrace, Alexandroupolis, Greece
| | - Giorgos Bamias
- GI-unit, National & Kapodistrian University of Athens, Third Department of Internal Medicine, Sotiria Hospital, Athens, Greece
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