1
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Maure A, Lawarée E, Fiorentino F, Pawlik A, Gona S, Giraud-Gatineau A, Eldridge MJG, Danckaert A, Hardy D, Frigui W, Keck C, Gutierrez C, Neyrolles O, Aulner N, Mai A, Hamon M, Barreiro LB, Brodin P, Brosch R, Rotili D, Tailleux L. A host-directed oxadiazole compound potentiates antituberculosis treatment via zinc poisoning in human macrophages and in a mouse model of infection. PLoS Biol 2024; 22:e3002259. [PMID: 38683873 DOI: 10.1371/journal.pbio.3002259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 03/13/2024] [Indexed: 05/02/2024] Open
Abstract
Antituberculosis drugs, mostly developed over 60 years ago, combined with a poorly effective vaccine, have failed to eradicate tuberculosis. More worryingly, multiresistant strains of Mycobacterium tuberculosis (MTB) are constantly emerging. Innovative strategies are thus urgently needed to improve tuberculosis treatment. Recently, host-directed therapy has emerged as a promising strategy to be used in adjunct with existing or future antibiotics, by improving innate immunity or limiting immunopathology. Here, using high-content imaging, we identified novel 1,2,4-oxadiazole-based compounds, which allow human macrophages to control MTB replication. Genome-wide gene expression analysis revealed that these molecules induced zinc remobilization inside cells, resulting in bacterial zinc intoxication. More importantly, we also demonstrated that, upon treatment with these novel compounds, MTB became even more sensitive to antituberculosis drugs, in vitro and in vivo, in a mouse model of tuberculosis. Manipulation of heavy metal homeostasis holds thus great promise to be exploited to develop host-directed therapeutic interventions.
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Affiliation(s)
- Alexandra Maure
- Institut Pasteur, Université Paris Cité, CNRS UMR 6047, Unit for Integrated Mycobacterial Pathogenomics, Paris, France
| | - Emeline Lawarée
- Institut Pasteur, Université Paris Cité, CNRS UMR 6047, Unit for Integrated Mycobacterial Pathogenomics, Paris, France
| | - Francesco Fiorentino
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, Rome, Italy
| | - Alexandre Pawlik
- Institut Pasteur, Université Paris Cité, CNRS UMR 6047, Unit for Integrated Mycobacterial Pathogenomics, Paris, France
| | - Saideep Gona
- Department of Genetic Medicine, University of Chicago, Chicago, Illinois, United States of America
| | | | - Matthew J G Eldridge
- Institut Pasteur, Université Paris Cité, Chromatine et Infection unit, Paris, France
| | - Anne Danckaert
- Institut Pasteur, Université Paris Cité, UTechS BioImaging-C2RT, Paris, France
| | - David Hardy
- Institut Pasteur, Université Paris Cité, Histopathology Platform, Paris, France
| | - Wafa Frigui
- Institut Pasteur, Université Paris Cité, CNRS UMR 6047, Unit for Integrated Mycobacterial Pathogenomics, Paris, France
| | - Camille Keck
- Institut Pasteur, Université Paris Cité, CNRS UMR 6047, Unit for Integrated Mycobacterial Pathogenomics, Paris, France
| | - Claude Gutierrez
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Olivier Neyrolles
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Nathalie Aulner
- Institut Pasteur, Université Paris Cité, UTechS BioImaging-C2RT, Paris, France
| | - Antonello Mai
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, Rome, Italy
- Pasteur Institute, Cenci-bolognetti Foundation, Sapienza University of Rome, Rome, Italy
| | - Mélanie Hamon
- Institut Pasteur, Université Paris Cité, Chromatine et Infection unit, Paris, France
| | - Luis B Barreiro
- Department of Genetic Medicine, University of Chicago, Chicago, Illinois, United States of America
| | - Priscille Brodin
- Université de Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 8204 - CIIL - Center for Infection and Immunity of Lille, Lille, France
| | - Roland Brosch
- Institut Pasteur, Université Paris Cité, CNRS UMR 6047, Unit for Integrated Mycobacterial Pathogenomics, Paris, France
| | - Dante Rotili
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, Rome, Italy
| | - Ludovic Tailleux
- Institut Pasteur, Université Paris Cité, CNRS UMR 6047, Unit for Integrated Mycobacterial Pathogenomics, Paris, France
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2
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Aracena KA, Lin YL, Luo K, Pacis A, Gona S, Mu Z, Yotova V, Sindeaux R, Pramatarova A, Simon MM, Chen X, Groza C, Lougheed D, Gregoire R, Brownlee D, Boye C, Pique-Regi R, Li Y, He X, Bujold D, Pastinen T, Bourque G, Barreiro LB. Epigenetic variation impacts individual differences in the transcriptional response to influenza infection. Nat Genet 2024; 56:408-419. [PMID: 38424460 DOI: 10.1038/s41588-024-01668-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Accepted: 01/16/2024] [Indexed: 03/02/2024]
Abstract
Humans display remarkable interindividual variation in their immune response to identical challenges. Yet, our understanding of the genetic and epigenetic factors contributing to such variation remains limited. Here we performed in-depth genetic, epigenetic and transcriptional profiling on primary macrophages derived from individuals of European and African ancestry before and after infection with influenza A virus. We show that baseline epigenetic profiles are strongly predictive of the transcriptional response to influenza A virus across individuals. Quantitative trait locus (QTL) mapping revealed highly coordinated genetic effects on gene regulation, with many cis-acting genetic variants impacting concomitantly gene expression and multiple epigenetic marks. These data reveal that ancestry-associated differences in the epigenetic landscape can be genetically controlled, even more than gene expression. Lastly, among QTL variants that colocalized with immune-disease loci, only 7% were gene expression QTL, while the remaining genetic variants impact epigenetic marks, stressing the importance of considering molecular phenotypes beyond gene expression in disease-focused studies.
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Affiliation(s)
| | - Yen-Lung Lin
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Kaixuan Luo
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Alain Pacis
- Canadian Centre for Computational Genomics, McGill University, Montreal, Quebec, Canada
| | - Saideep Gona
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Zepeng Mu
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Vania Yotova
- Department of Genetics, CHU Sainte-Justine Research Center, Montreal, Quebec, Canada
| | - Renata Sindeaux
- Department of Genetics, CHU Sainte-Justine Research Center, Montreal, Quebec, Canada
| | | | | | - Xun Chen
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan
| | - Cristian Groza
- Quantitative Life Sciences, McGill University, Montreal, Quebec, Canada
| | - David Lougheed
- Canadian Centre for Computational Genomics, McGill University, Montreal, Quebec, Canada
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Romain Gregoire
- Canadian Centre for Computational Genomics, McGill University, Montreal, Quebec, Canada
| | - David Brownlee
- Canadian Centre for Computational Genomics, McGill University, Montreal, Quebec, Canada
| | - Carly Boye
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, USA
| | - Roger Pique-Regi
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, USA
- Department of Obstetrics and Gynecology, Wayne State University, Detroit, MI, USA
| | - Yang Li
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Xin He
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - David Bujold
- Canadian Centre for Computational Genomics, McGill University, Montreal, Quebec, Canada
- McGill Genome Centre, Montreal, Quebec, Canada
| | - Tomi Pastinen
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
- Genomic Medicine Center, Children's Mercy, Kansas City, MO, USA
| | - Guillaume Bourque
- Canadian Centre for Computational Genomics, McGill University, Montreal, Quebec, Canada.
- McGill Genome Centre, Montreal, Quebec, Canada.
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan.
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada.
| | - Luis B Barreiro
- Department of Human Genetics, University of Chicago, Chicago, IL, USA.
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA.
- Committee on Immunology, University of Chicago, Chicago, IL, USA.
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3
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Shaw DG, Aguirre-Gamboa R, Vieira MC, Gona S, DiNardi N, Wang A, Dumaine A, Gelderloos-Arends J, Earley ZM, Meckel KR, Ciszewski C, Castillo A, Monroe K, Torres J, Shah SC, Colombel JF, Itzkowitz S, Newberry R, Cohen RD, Rubin DT, Quince C, Cobey S, Jonkers IH, Weber CR, Pekow J, Wilson PC, Barreiro LB, Jabri B. Antigen-driven colonic inflammation is associated with development of dysplasia in primary sclerosing cholangitis. Nat Med 2023; 29:1520-1529. [PMID: 37322120 PMCID: PMC10287559 DOI: 10.1038/s41591-023-02372-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 04/26/2023] [Indexed: 06/17/2023]
Abstract
Primary sclerosing cholangitis (PSC) is an immune-mediated disease of the bile ducts that co-occurs with inflammatory bowel disease (IBD) in almost 90% of cases. Colorectal cancer is a major complication of patients with PSC and IBD, and these patients are at a much greater risk compared to patients with IBD without concomitant PSC. Combining flow cytometry, bulk and single-cell transcriptomics, and T and B cell receptor repertoire analysis of right colon tissue from 65 patients with PSC, 108 patients with IBD and 48 healthy individuals we identified a unique adaptive inflammatory transcriptional signature associated with greater risk and shorter time to dysplasia in patients with PSC. This inflammatory signature is characterized by antigen-driven interleukin-17A (IL-17A)+ forkhead box P3 (FOXP3)+ CD4 T cells that express a pathogenic IL-17 signature, as well as an expansion of IgG-secreting plasma cells. These results suggest that the mechanisms that drive the emergence of dysplasia in PSC and IBD are distinct and provide molecular insights that could guide prevention of colorectal cancer in individuals with PSC.
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Affiliation(s)
- Dustin G Shaw
- Committee on Immunology, University of Chicago, Chicago, IL, USA
- Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Raúl Aguirre-Gamboa
- Department of Medicine, University of Chicago, Chicago, IL, USA
- Committee on Genetics, Genomics and Systems Biology, University of Chicago, Chicago, IL, USA
| | - Marcos C Vieira
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
| | - Saideep Gona
- Department of Medicine, University of Chicago, Chicago, IL, USA
- Committee on Genetics, Genomics and Systems Biology, University of Chicago, Chicago, IL, USA
| | - Nicholas DiNardi
- Committee on Immunology, University of Chicago, Chicago, IL, USA
- Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Anni Wang
- Committee on Immunology, University of Chicago, Chicago, IL, USA
- Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Anne Dumaine
- Department of Medicine, University of Chicago, Chicago, IL, USA
- Committee on Genetics, Genomics and Systems Biology, University of Chicago, Chicago, IL, USA
| | - Jody Gelderloos-Arends
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Zachary M Earley
- Committee on Immunology, University of Chicago, Chicago, IL, USA
- Department of Medicine, University of Chicago, Chicago, IL, USA
| | | | - Cezary Ciszewski
- Committee on Immunology, University of Chicago, Chicago, IL, USA
- Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Anabella Castillo
- Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kelly Monroe
- Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Joana Torres
- Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Division of Gastroenterology, Hospital Beatriz Ângelo, Loures, Portugal
- Division of Gastroenterology, Hospital Luz, Lisboa, Portugal
- Faculty of Medicine, Universidade de Lisboa, Lisboa, Portugal
| | - Shailja C Shah
- Division of Gastroenterology, University of California San Diego, San Diego, CA, USA
- Jennifer Moreno VA San Diego Healthcare System, San Diego, CA, USA
| | - Jean-Frédéric Colombel
- Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Steven Itzkowitz
- Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Rodney Newberry
- Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Russell D Cohen
- University of Chicago Inflammatory Bowel Disease Center, Chicago, IL, USA
| | - David T Rubin
- University of Chicago Inflammatory Bowel Disease Center, Chicago, IL, USA
| | - Christopher Quince
- Organisms and Ecosystems, Earlham Institute, Norwich, NR4 7UZ, UK
- Warwick Medical School, University of Warwick, Coventry, CV4 7HL, UK
- Gut Microbes and Health, Quadram Institute, Norwich, NR4 7UQ, UK
| | - Sarah Cobey
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
| | - Iris H Jonkers
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | | | - Joel Pekow
- University of Chicago Inflammatory Bowel Disease Center, Chicago, IL, USA
| | - Patrick C Wilson
- Committee on Immunology, University of Chicago, Chicago, IL, USA
- Department of Medicine, University of Chicago, Chicago, IL, USA
- Section of Rheumatology, University of Chicago, Chicago, IL, USA
| | - Luis B Barreiro
- Committee on Immunology, University of Chicago, Chicago, IL, USA.
- Department of Medicine, University of Chicago, Chicago, IL, USA.
- Committee on Genetics, Genomics and Systems Biology, University of Chicago, Chicago, IL, USA.
| | - Bana Jabri
- Committee on Immunology, University of Chicago, Chicago, IL, USA.
- Department of Medicine, University of Chicago, Chicago, IL, USA.
- Department of Pathology, University of Chicago, Chicago, IL, USA.
- Department of Pediatrics, University of Chicago, Chicago, IL, USA.
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4
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Chen X, Pacis A, Aracena KA, Gona S, Kwan T, Groza C, Lin YL, Sindeaux R, Yotova V, Pramatarova A, Simon MM, Pastinen T, Barreiro LB, Bourque G. Transposable elements are associated with the variable response to influenza infection. Cell Genom 2023; 3:100292. [PMID: 37228757 PMCID: PMC10203045 DOI: 10.1016/j.xgen.2023.100292] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 11/15/2022] [Accepted: 03/06/2023] [Indexed: 05/27/2023]
Abstract
Influenza A virus (IAV) infections are frequent every year and result in a range of disease severity. Here, we wanted to explore the potential contribution of transposable elements (TEs) to the variable human immune response. Transcriptome profiling in monocyte-derived macrophages from 39 individuals following IAV infection revealed significant inter-individual variation in viral load post-infection. Using transposase-accessible chromatin using sequencing (ATAC-seq), we identified a set of TE families with either enhanced or reduced accessibility upon infection. Of the enhanced families, 15 showed high variability between individuals and had distinct epigenetic profiles. Motif analysis showed an association with known immune regulators (e.g., BATFs, FOSs/JUNs, IRFs, STATs, NFkBs, NFYs, and RELs) in stably enriched families and with other factors in variable families, including KRAB-ZNFs. We showed that TEs and host factors regulating TEs were predictive of viral load post-infection. Our findings shed light on the role TEs and KRAB-ZNFs may play in inter-individual variation in immunity.
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Affiliation(s)
- Xun Chen
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto 606-8501, Japan
| | - Alain Pacis
- Canadian Center for Computational Genomics, McGill University, Montréal, QC H3A 0G1, Canada
| | | | - Saideep Gona
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Tony Kwan
- Victor Phillip Dahdaleh Institute of Genomic Medicine at McGill University, Montréal, QC H3A 0G1, Canada
| | - Cristian Groza
- Quantitative Life Science, McGill University, Montréal, QC H3A 1E3, Canada
| | - Yen Lung Lin
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Renata Sindeaux
- Centre de Recherche, CHU Sainte-Justine, Université de Montréal, Montréal, QC H3T 1C5, Canada
| | - Vania Yotova
- Centre de Recherche, CHU Sainte-Justine, Université de Montréal, Montréal, QC H3T 1C5, Canada
| | - Albena Pramatarova
- Victor Phillip Dahdaleh Institute of Genomic Medicine at McGill University, Montréal, QC H3A 0G1, Canada
| | - Marie-Michelle Simon
- Victor Phillip Dahdaleh Institute of Genomic Medicine at McGill University, Montréal, QC H3A 0G1, Canada
| | - Tomi Pastinen
- Genomic Medicine Center, Children’s Mercy Hospital and Research Institute, Kansas City, MO 64108, USA
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada
| | - Luis B. Barreiro
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL 60637, USA
- Committee on Immunology, University of Chicago, Chicago, IL 60637, USA
| | - Guillaume Bourque
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto 606-8501, Japan
- Canadian Center for Computational Genomics, McGill University, Montréal, QC H3A 0G1, Canada
- Victor Phillip Dahdaleh Institute of Genomic Medicine at McGill University, Montréal, QC H3A 0G1, Canada
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada
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5
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Pernet E, Sun S, Sarden N, Gona S, Nguyen A, Khan N, Mawhinney M, Tran KA, Chronopoulos J, Amberkar D, Sadeghi M, Grant A, Wali S, Prevel R, Ding J, Martin JG, Thanabalasuriar A, Yipp BG, Barreiro LB, Divangahi M. Neonatal imprinting of alveolar macrophages via neutrophil-derived 12-HETE. Nature 2023; 614:530-538. [PMID: 36599368 PMCID: PMC9945843 DOI: 10.1038/s41586-022-05660-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 12/14/2022] [Indexed: 01/06/2023]
Abstract
Resident-tissue macrophages (RTMs) arise from embryonic precursors1,2, yet the developmental signals that shape their longevity remain largely unknown. Here we demonstrate in mice genetically deficient in 12-lipoxygenase and 15-lipoxygenase (Alox15-/- mice) that neonatal neutrophil-derived 12-HETE is required for self-renewal and maintenance of alveolar macrophages (AMs) during lung development. Although the seeding and differentiation of AM progenitors remained intact, the absence of 12-HETE led to a significant reduction in AMs in adult lungs and enhanced senescence owing to increased prostaglandin E2 production. A compromised AM compartment resulted in increased susceptibility to acute lung injury induced by lipopolysaccharide and to pulmonary infections with influenza A virus or SARS-CoV-2. Our results highlight the complexity of prenatal RTM programming and reveal their dependency on in trans eicosanoid production by neutrophils for lifelong self-renewal.
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Affiliation(s)
- Erwan Pernet
- McGill University Health Centre, Meakins-Christie Laboratories, McGill University, Montreal, Quebec, Canada.
| | - Sarah Sun
- Department of Medicine, Section of Genetic Medicine, University of Chicago, Chicago, IL, USA
| | - Nicole Sarden
- Calvin, Phoebe and Joan Snyder Institute for Chronic Diseases and Department of Critical Care, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Saideep Gona
- Department of Medicine, Section of Genetic Medicine, University of Chicago, Chicago, IL, USA
| | - Angela Nguyen
- Calvin, Phoebe and Joan Snyder Institute for Chronic Diseases and Department of Critical Care, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Nargis Khan
- McGill University Health Centre, Meakins-Christie Laboratories, McGill University, Montreal, Quebec, Canada
| | - Martin Mawhinney
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Quebec, Canada
| | - Kim A Tran
- McGill University Health Centre, Meakins-Christie Laboratories, McGill University, Montreal, Quebec, Canada
| | - Julia Chronopoulos
- McGill University Health Centre, Meakins-Christie Laboratories, McGill University, Montreal, Quebec, Canada
| | - Dnyandeo Amberkar
- McGill University Health Centre, Meakins-Christie Laboratories, McGill University, Montreal, Quebec, Canada
| | - Mina Sadeghi
- Department of Microbiology and Immunology, McGill University, Montreal, Quebec, Canada
| | - Alexandre Grant
- Department of Microbiology and Immunology, McGill University, Montreal, Quebec, Canada
| | - Shradha Wali
- McGill University Health Centre, Meakins-Christie Laboratories, McGill University, Montreal, Quebec, Canada
| | - Renaud Prevel
- McGill University Health Centre, Meakins-Christie Laboratories, McGill University, Montreal, Quebec, Canada
| | - Jun Ding
- McGill University Health Centre, Meakins-Christie Laboratories, McGill University, Montreal, Quebec, Canada
| | - James G Martin
- McGill University Health Centre, Meakins-Christie Laboratories, McGill University, Montreal, Quebec, Canada
| | - Ajitha Thanabalasuriar
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Quebec, Canada
| | - Bryan G Yipp
- Calvin, Phoebe and Joan Snyder Institute for Chronic Diseases and Department of Critical Care, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Luis B Barreiro
- Department of Medicine, Section of Genetic Medicine, University of Chicago, Chicago, IL, USA
- Department of Genetics, CHU Sainte-Justine Research Center, Montreal, Quebec, Canada
| | - Maziar Divangahi
- McGill University Health Centre, Meakins-Christie Laboratories, McGill University, Montreal, Quebec, Canada.
- Department of Microbiology and Immunology, McGill University, Montreal, Quebec, Canada.
- Department of Pathology, McGill University, Montreal, Quebec, Canada.
- McGill International TB Centre, McGill University, Montreal, Quebec, Canada.
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6
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Earley ZM, Lisicka W, Sifakis JJ, Aguirre-Gamboa R, Kowalczyk A, Barlow JT, Shaw DG, Discepolo V, Tan IL, Gona S, Ernest JD, Matzinger P, Barreiro LB, Morgun A, Bendelac A, Ismagilov RF, Shulzhenko N, Riesenfeld SJ, Jabri B. GATA4 controls regionalization of tissue immunity and commensal-driven immunopathology. Immunity 2023; 56:43-57.e10. [PMID: 36630917 PMCID: PMC10262782 DOI: 10.1016/j.immuni.2022.12.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 11/16/2022] [Accepted: 12/12/2022] [Indexed: 01/12/2023]
Abstract
There is growing recognition that regionalization of bacterial colonization and immunity along the intestinal tract has an important role in health and disease. Yet, the mechanisms underlying intestinal regionalization and its dysregulation in disease are not well understood. This study found that regional epithelial expression of the transcription factor GATA4 controls bacterial colonization and inflammatory tissue immunity in the proximal small intestine by regulating retinol metabolism and luminal IgA. Furthermore, in mice without jejunal GATA4 expression, the commensal segmented filamentous bacteria promoted pathogenic inflammatory immune responses that disrupted barrier function and increased mortality upon Citrobacter rodentium infection. In celiac disease patients, low GATA4 expression was associated with metabolic alterations, mucosal Actinobacillus, and increased IL-17 immunity. Taken together, these results reveal broad impacts of GATA4-regulated intestinal regionalization on bacterial colonization and tissue immunity, highlighting an elaborate interdependence of intestinal metabolism, immunity, and microbiota in homeostasis and disease.
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Affiliation(s)
- Zachary M Earley
- Committee on Immunology, University of Chicago, Chicago, IL, USA; Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Wioletta Lisicka
- Committee on Immunology, University of Chicago, Chicago, IL, USA; Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Joseph J Sifakis
- Department of Chemistry, University of Chicago, Chicago, IL, USA
| | | | - Anita Kowalczyk
- Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Jacob T Barlow
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Dustin G Shaw
- Committee on Immunology, University of Chicago, Chicago, IL, USA; Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Valentina Discepolo
- Department of Medical Translational Sciences and European Laboratory for the Investigation of Food Induced Diseases, University of Federico II, Naples, Italy
| | - Ineke L Tan
- Department of Gastroenterology and Hepatology, University of Groningen and University of Medical Center Groningen, Groningen, the Netherlands
| | - Saideep Gona
- Genetics, Genomics, and Systems Biology, University of Chicago, Chicago, IL, USA
| | - Jordan D Ernest
- Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Polly Matzinger
- Ghost Lab, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Luis B Barreiro
- Committee on Immunology, University of Chicago, Chicago, IL, USA; Department of Medicine, University of Chicago, Chicago, IL, USA; Genetics, Genomics, and Systems Biology, University of Chicago, Chicago, IL, USA
| | - Andrey Morgun
- College of Pharmacy, Oregon State University, Corvallis, OR, USA
| | - Albert Bendelac
- Committee on Immunology, University of Chicago, Chicago, IL, USA; Department of Pathology, University of Chicago, Chicago, IL, USA
| | - Rustem F Ismagilov
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA; Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Natalia Shulzhenko
- Department of Biomedical Sciences, Oregon State University, Corvallis, OR, USA
| | - Samantha J Riesenfeld
- Committee on Immunology, University of Chicago, Chicago, IL, USA; Department of Medicine, University of Chicago, Chicago, IL, USA; Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, USA; Institute for Biophysical Dynamics, University of Chicago, Chicago, IL, USA.
| | - Bana Jabri
- Committee on Immunology, University of Chicago, Chicago, IL, USA; Department of Medicine, University of Chicago, Chicago, IL, USA; Department of Pathology, University of Chicago, Chicago, IL, USA; Department of Pediatrics, University of Chicago, Chicago, IL, USA.
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Labrosse R, Boufaied I, Bourdin B, Gona S, Randolph HE, Logan BR, Bourbonnais S, Berthe C, Chan W, Buckley RH, Parrott RE, Cuvelier GDE, Kapoor N, Chandra S, Dávila Saldaña BJ, Eissa H, Goldman FD, Heimall J, O'Reilly R, Chaudhury S, Kolb EA, Shenoy S, Griffith LM, Pulsipher M, Kohn DB, Notarangelo LD, Pai SY, Cowan MJ, Dvorak CC, Haddad É, Puck JM, Barreiro LB, Decaluwe H. Aberrant T-cell exhaustion in severe combined immunodeficiency survivors with poor T-cell reconstitution after transplantation. J Allergy Clin Immunol 2023; 151:260-271. [PMID: 35987350 PMCID: PMC9924130 DOI: 10.1016/j.jaci.2022.08.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 08/08/2022] [Accepted: 08/10/2022] [Indexed: 02/04/2023]
Abstract
BACKGROUND Severe combined immunodeficiency (SCID) comprises rare inherited disorders of immunity that require definitive treatment through hematopoietic cell transplantation (HCT) or gene therapy for survival. Despite successes of allogeneic HCT, many SCID patients experience incomplete immune reconstitution, persistent T-cell lymphopenia, and poor long-term outcomes. OBJECTIVE We hypothesized that CD4+ T-cell lymphopenia could be associated with a state of T-cell exhaustion in previously transplanted SCID patients. METHODS We analyzed markers of exhaustion in blood samples from 61 SCID patients at a median of 10.4 years after HCT. RESULTS Compared to post-HCT SCID patients with normal CD4+ T-cell counts, those with poor T-cell reconstitution showed lower frequency of naive CD45RA+/CCR7+ T cells, recent thymic emigrants, and TCR excision circles. They also had a restricted TCR repertoire, increased expression of inhibitory receptors (PD-1, 2B4, CD160, BTLA, CTLA-4), and increased activation markers (HLA-DR, perforin) on their total and naive CD8+ T cells, suggesting T-cell exhaustion and aberrant activation, respectively. The exhaustion score of CD8+ T cells was inversely correlated with CD4+ T-cell count, recent thymic emigrants, TCR excision circles, and TCR diversity. Exhaustion scores were higher among recipients of unconditioned HCT, especially when further in time from HCT. Patients with fewer CD4+ T cells showed a transcriptional signature of exhaustion. CONCLUSIONS Recipients of unconditioned HCT for SCID may develop late post-HCT T-cell exhaustion as a result of diminished production of T-lineage cells. Elevated expression of inhibitory receptors on their T cells may be a biomarker of poor long-term T-cell reconstitution.
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Affiliation(s)
- Roxane Labrosse
- Pediatric Immunology and Rheumatology Division, Department of Pediatrics, University of Montreal, Montreal, Quebec, Canada
| | - Ines Boufaied
- Cytokines and Adaptive Immunity Laboratory, Sainte-Justine University Hospital Research Center, Montreal, Quebec, Canada
| | - Benoîte Bourdin
- Cytokines and Adaptive Immunity Laboratory, Sainte-Justine University Hospital Research Center, Montreal, Quebec, Canada
| | - Saideep Gona
- Genetics, Genomics, and Systems Biology, Department of Medicine, Section of Genetic Medicine, University of Chicago, Chicago, Ill
| | - Haley E Randolph
- Genetics, Genomics, and Systems Biology, Department of Medicine, Section of Genetic Medicine, University of Chicago, Chicago, Ill
| | - Brent R Logan
- Division of Biostatistics, Medical College of Wisconsin, Milwaukee, Wis
| | - Sara Bourbonnais
- Cytokines and Adaptive Immunity Laboratory, Sainte-Justine University Hospital Research Center, Montreal, Quebec, Canada
| | - Chloé Berthe
- Cytokines and Adaptive Immunity Laboratory, Sainte-Justine University Hospital Research Center, Montreal, Quebec, Canada
| | - Wendy Chan
- Division of Allergy, Immunology, and Blood and Marrow Transplantation, Department of Pediatrics, University of California, San Francisco, and UCSF Benioff Children's Hospital, San Francisco, Calif
| | | | | | - Geoffrey D E Cuvelier
- Manitoba Blood and Marrow Transplant Program, CancerCare Manitoba, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Neena Kapoor
- Blood and Marrow Transplant Program, Division of Hematology, Oncology, and Blood and Marrow Transplantation, Children's Hospital Los Angeles, Keck School of Medicine, University of Southern California, Los Angeles, Calif
| | - Sharat Chandra
- Division of Bone Marrow Transplantation and Immune Deficiency, Cincinnati Children's Hospital Medical Center, and the Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Blachy J Dávila Saldaña
- Division of Blood and Marrow Transplantation, Children's National Hospital, George Washington University School of Medicine and Health Sciences, Washington, DC
| | - Hesham Eissa
- Children's Hospital of Colorado, University of Colorado School of Medicine, Aurora, Colo
| | - Fred D Goldman
- Department of Pediatrics, The University of Alabama at Birmingham, Birmingham, Ala
| | - Jennifer Heimall
- Allergy and Immunology, The Children's Hospital of Philadelphia, Philadelphia, Pa
| | - Richard O'Reilly
- Department of Pediatrics, Bone Marrow Transplant Service, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Sonali Chaudhury
- Division of Hematology, Oncology, and Stem Cell Transplantation, Ann & Robert H. Lurie Children's Hospital of Chicago, Northwestern University Feinberg School of Medicine, Chicago, Ill
| | - Edward A Kolb
- Nemours Children's Health, Center for Cancer and Blood Disorders, Wilmington, Del
| | - Shalini Shenoy
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Washington University School of Medicine, St Louis, Mo
| | - Linda M Griffith
- Division of Allergy, Immunology, and Transplantation, National Institutes of Health, Bethesda, Md
| | - Michael Pulsipher
- Blood and Marrow Transplant Program, Division of Hematology, Oncology, and Blood and Marrow Transplantation, Children's Hospital Los Angeles, Keck School of Medicine, University of Southern California, Los Angeles, Calif
| | - Donald B Kohn
- Pediatrics, David Geffen School of Medicine at University of California, Los Angeles, Calif
| | - Luigi D Notarangelo
- Laboratory of Clinical Immunology and Microbiology, National Institutes of Health, Bethesda, Md
| | - Sung-Yun Pai
- Immune Deficiency Cellular Therapy Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Md
| | - Morton J Cowan
- Division of Allergy, Immunology, and Blood and Marrow Transplantation, Department of Pediatrics, University of California, San Francisco, and UCSF Benioff Children's Hospital, San Francisco, Calif
| | - Christopher C Dvorak
- Division of Allergy, Immunology, and Blood and Marrow Transplantation, Department of Pediatrics, University of California, San Francisco, and UCSF Benioff Children's Hospital, San Francisco, Calif
| | - Élie Haddad
- Pediatric Immunology and Rheumatology Division, Department of Pediatrics, University of Montreal, Montreal, Quebec, Canada
| | - Jennifer M Puck
- Division of Allergy, Immunology, and Blood and Marrow Transplantation, Department of Pediatrics, University of California, San Francisco, and UCSF Benioff Children's Hospital, San Francisco, Calif
| | - Luis B Barreiro
- Genetics, Genomics, and Systems Biology, Department of Medicine, Section of Genetic Medicine, University of Chicago, Chicago, Ill
| | - Hélène Decaluwe
- Pediatric Immunology and Rheumatology Division, Department of Pediatrics, University of Montreal, Montreal, Quebec, Canada; Cytokines and Adaptive Immunity Laboratory, Sainte-Justine University Hospital Research Center, Montreal, Quebec, Canada.
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Abstract
A precise biological mechanism by which cadmium acts as a developmental toxicant is unknown but is suggested to include an epigenetic basis. In prior work, we analyzed CpG island methylation levels within gene promoters (n = 16,421) in leukocytes collected from mothers and their infants from a pregnancy cohort in Durham County, North Carolina. The CpG methylation levels were examined in relationship to prenatal exposure to cadmium and/or cotinine to identify genes and pathways influenced by in utero exposure. In the present article, we provide an enhanced description of the data collection and processing to facilitate cross-study comparisons. Data are available within the Gene Expression Omnibus database (GSE67976).
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Affiliation(s)
- Saideep Gona
- Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Alison P Sanders
- Department of Preventive Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | | | - Rebecca C Fry
- Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina, USA ; Curriculum in Toxicology, School of Medicine, University of North Carolina, Chapel Hill, North Carolina, USA
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Abstract
PURPOSE To evaluate the epidemiologic characteristics of a large clinical population of patients with recurrent erosions of the cornea. The efficacy of different modalities of treatment was also evaluated. METHODS A retrospective chart review of all patients with the diagnosis of recurrent corneal erosion treated between January 1990 and December 1998 was performed. RESULTS Clinically confirmed recurrent erosions were identified in 104 patients. There were 36 males and 68 females. A history of trauma was present in 47 patients (45%), 30 patients (29%) had epithelial basement membrane dystrophy (EBMD), and 18 patients (17%) had both a history of trauma and evidence of EBMD. More than 87% of all erosions occurred on the inferior third of the cornea. Conservative therapy was used as the primary treatment in 52 patients with a recurrence rate of 6%. Corneal stromal micropuncture was performed on 38 patients with a recurrence rate of 40%. Eleven patients had epithelial debridement with a recurrence rate of 18%. Four patients had a superficial keratectomy with a diamond bur with a recurrence rate of 25%. Only one patient had an excimer phototherapeutic keratectomy, and she had a minor recurrence posttreatment. CONCLUSIONS In our series, the distribution of trauma and EBMD in patients with recurrent erosions of the cornea is roughly equivalent. Conservative therapy was effective in approximately one half of the patients. All surgical treatment modalities were associated with recurrences. Those patients with both EBMD and trauma were more likely to have a recurrence after treatment. More effective treatment modalities for recurrent erosions of the cornea need to be investigated.
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Affiliation(s)
- J J Reidy
- Department of Ophthalmology, The State University of New York, School of Medicine and Biomedical Sciences, Buffalo 14215, USA
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