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Jabot-Hanin F, Cobat A, Feinberg J, Orlova M, Niay J, Deswarte C, Poirier C, Theodorou I, Bustamante J, Boisson-Dupuis S, Casanova JL, Alcaïs A, Hoal EG, Delacourt C, Schurr E, Abel L. An eQTL variant of ZXDC is associated with IFN-γ production following Mycobacterium tuberculosis antigen-specific stimulation. Sci Rep 2017; 7:12800. [PMID: 28993696 PMCID: PMC5634485 DOI: 10.1038/s41598-017-13017-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Accepted: 09/12/2017] [Indexed: 12/26/2022] Open
Abstract
There is a large inter-individual variability in the response to Mycobacterium tuberculosis infection. In previous linkage analyses, we identified a major locus on chromosome region 8q controlling IFN-γ production after stimulation with live BCG (Bacillus Calmette-Guérin), and a second locus on chromosome region 3q affecting IFN-γ production triggered by the 6-kDa early secretory antigen target (ESAT-6), taking into account the IFN-γ production induced by BCG (IFNγ-ESAT6BCG). High-density genotyping and imputation identified ~100,000 variants within each linkage region, which we tested for association with the corresponding IFN-γ phenotype in families from a tuberculosis household contact study in France. Significant associations were replicated in a South African familial sample. The most convincing association observed was that between the IFNγ-ESAT6BCG phenotype and rs9828868 on chromosome 3q (p = 9.8 × 10−6 in the French sample). This variant made a significant contribution to the linkage signal (p < 0.001), and a trend towards the same association was observed in the South African sample. This variant was reported to be an eQTL of the ZXDC gene, biologically linked to monocyte IL-12 production through CCL2/MCP1. The identification of rs9828868 as a genetic driver of IFNγ production in response to mycobacterial antigens provides new insights into human anti-tuberculosis immunity.
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Affiliation(s)
- Fabienne Jabot-Hanin
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France.,Paris Descartes University, Sorbonne Paris Cité, Imagine Institute, Paris, France
| | - Aurélie Cobat
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France.,Paris Descartes University, Sorbonne Paris Cité, Imagine Institute, Paris, France
| | - Jacqueline Feinberg
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France.,Paris Descartes University, Sorbonne Paris Cité, Imagine Institute, Paris, France
| | - Marianna Orlova
- Program in Infectious Diseases and Immunity in Global Health, The Research Institute of the McGill University Health Centre, Montreal, Canada.,McGill International TB Centre, McGill University, Montreal, Canada.,Department of Human Genetics and Department of Medicine, McGill University, Montreal, Canada
| | - Jonathan Niay
- Université Pierre et Marie Curie, UF d'Histocompatibilité et Immunogénétique, Département d'Immunologie, Groupe Hospitalier Pitié Salpêtrière - Charles Foix, Paris, France
| | - Caroline Deswarte
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France.,Paris Descartes University, Sorbonne Paris Cité, Imagine Institute, Paris, France
| | - Christine Poirier
- Centre de Lutte Anti-Tuberculeuse, Centre Hospitalier Intercommunal de Créteil, Créteil, France
| | - Ioannis Theodorou
- Université Pierre et Marie Curie, UF d'Histocompatibilité et Immunogénétique, Département d'Immunologie, Groupe Hospitalier Pitié Salpêtrière - Charles Foix, Paris, France
| | - Jacinta Bustamante
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France.,Paris Descartes University, Sorbonne Paris Cité, Imagine Institute, Paris, France
| | - Stéphanie Boisson-Dupuis
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France.,Paris Descartes University, Sorbonne Paris Cité, Imagine Institute, Paris, France.,St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY, USA
| | - Jean-Laurent Casanova
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France.,Paris Descartes University, Sorbonne Paris Cité, Imagine Institute, Paris, France.,St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY, USA.,Howard Hughes Medical Institute, New York, NY, USA.,Pediatric Hematology-Immunology Unit, Necker Hospital for Sick Children, AP-HP, Paris, France
| | - Alexandre Alcaïs
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France.,Paris Descartes University, Sorbonne Paris Cité, Imagine Institute, Paris, France
| | - Eileen G Hoal
- Molecular Biology and Human Genetics, MRC Centre for Molecular and Cellular Biology, DST/NRF Centre of Excellence for Biomedical TB Research, Faculty of Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Christophe Delacourt
- Paris Descartes University, Sorbonne Paris Cité, Imagine Institute, Paris, France.,Pediatric Pneumology Unit, Necker Hospital for Sick Children, AP-HP, Paris, France
| | - Erwin Schurr
- Program in Infectious Diseases and Immunity in Global Health, The Research Institute of the McGill University Health Centre, Montreal, Canada.,McGill International TB Centre, McGill University, Montreal, Canada.,Department of Human Genetics and Department of Medicine, McGill University, Montreal, Canada
| | - Laurent Abel
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France. .,Paris Descartes University, Sorbonne Paris Cité, Imagine Institute, Paris, France. .,St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY, USA.
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Jabot-Hanin F, Cobat A, Feinberg J, Grange G, Remus N, Poirier C, Boland-Auge A, Besse C, Bustamante J, Boisson-Dupuis S, Casanova JL, Schurr E, Alcaïs A, Hoal EG, Delacourt C, Abel L. Major Loci on Chromosomes 8q and 3q Control Interferon γ Production Triggered by Bacillus Calmette-Guerin and 6-kDa Early Secretory Antigen Target, Respectively, in Various Populations. J Infect Dis 2015; 213:1173-9. [PMID: 26690346 PMCID: PMC4779307 DOI: 10.1093/infdis/jiv757] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 12/11/2015] [Indexed: 12/31/2022] Open
Abstract
Background. Interferon γ (IFN-γ) release assays (IGRAs) provide an in vitro measurement of antimycobacterial immunity that is widely used as a test for Mycobacterium tuberculosis infection. IGRA outcomes are highly heritable in various populations, but the nature of the involved genetic factors remains unknown. Methods. We conducted a genome-wide linkage analysis of IGRA phenotypes in families from a tuberculosis household contact study in France and a replication study in families from South Africa to confirm the loci identified. Results. We identified a major locus on chromosome 8q controlling IFN-γ production in response to stimulation with live bacillus Calmette-Guerin (BCG; LOD score, 3.81; P = 1.40 × 10−5). We also detected a second locus, on chromosome 3q, that controlled IFN-γ levels in response to stimulation with 6-kDa early secretory antigen target, when accounting for the IFN-γ production shared with that induced by BCG (LOD score, 3.72; P = 1.8 × 10−5). Both loci were replicated in South African families, where tuberculosis is hyperendemic. These loci differ from those previously identified as controlling the response to the tuberculin skin test (TST1 and TST2) and the production of TNF-α (TNF1). Conclusions. The identification of 2 new linkage signals in populations of various ethnic origins living in different M. tuberculosis exposure settings provides new clues about the genetic control of human antimycobacterial immunity.
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Affiliation(s)
- Fabienne Jabot-Hanin
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163 Paris Descartes University, Sorbonne Paris Cité, Imagine Institute
| | - Aurélie Cobat
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163 Paris Descartes University, Sorbonne Paris Cité, Imagine Institute
| | - Jacqueline Feinberg
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163 Paris Descartes University, Sorbonne Paris Cité, Imagine Institute
| | - Ghislain Grange
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163 Paris Descartes University, Sorbonne Paris Cité, Imagine Institute
| | - Natascha Remus
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163 Paris Descartes University, Sorbonne Paris Cité, Imagine Institute
| | - Christine Poirier
- Centre de Lutte Anti-Tuberculeuse, Centre Hospitalier Intercommunal de Créteil
| | - Anne Boland-Auge
- Centre National de Génotypage, Institut de Génomique, CEA, Evry, France
| | - Céline Besse
- Centre National de Génotypage, Institut de Génomique, CEA, Evry, France
| | - Jacinta Bustamante
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163 Paris Descartes University, Sorbonne Paris Cité, Imagine Institute
| | - Stéphanie Boisson-Dupuis
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163 Paris Descartes University, Sorbonne Paris Cité, Imagine Institute St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University
| | - Jean-Laurent Casanova
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163 Paris Descartes University, Sorbonne Paris Cité, Imagine Institute Pediatric Hematology-Immunology Unit, Necker Hospital for Sick Children, AP-HP, Paris St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University Howard Hughes Medical Institute, New York, New York
| | - Erwin Schurr
- McGill International TB Centre, McGill University, Montreal, Canada Department of Human Genetics, McGill University, Montreal, Canada Department of Medicine, McGill University, Montreal, Canada
| | - Alexandre Alcaïs
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163 Paris Descartes University, Sorbonne Paris Cité, Imagine Institute St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University
| | - Eileen G Hoal
- Division of Molecular Biology and Human Genetics, MRC Centre for Molecular and Cellular Biology and DST/NRF Centre of Excellence for Biomedical TB Research, Faculty of Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | | | - Laurent Abel
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163 Paris Descartes University, Sorbonne Paris Cité, Imagine Institute St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University
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Cobat A, Poirier C, Hoal E, Boland-Auge A, de La Rocque F, Corrard F, Grange G, Migaud M, Bustamante J, Boisson-Dupuis S, Casanova JL, Schurr E, Alcaïs A, Delacourt C, Abel L. Tuberculin skin test negativity is under tight genetic control of chromosomal region 11p14-15 in settings with different tuberculosis endemicities. J Infect Dis 2014; 211:317-21. [PMID: 25143445 PMCID: PMC4279780 DOI: 10.1093/infdis/jiu446] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
A substantial proportion of subjects exposed to a contagious tuberculosis case display lack of tuberculin skin test (TST) reactivity. We previously mapped a major locus (TST1) controlling lack of TST reactivity in families from an area in South Africa where tuberculosis is hyperendemic. Here, we conducted a household tuberculosis contact study in a French area where the endemicity of tuberculosis is low. A genome-wide analysis of TST negativity identified a significant linkage signal (P < 3 × 10−5) in close vicinity of TST1. Combined analysis of the 2 samples increased evidence of linkage (P = 2.4 × 10−6), further implicating genetic factors located on 11p14-15. This region overlaps the TNF1 locus controlling mycobacteria-driven tumor necrosis factor α production.
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Affiliation(s)
- Aurélie Cobat
- McGill International TB Centre Department of Human Genetics Department of Medicine, McGill University, Montreal, Canada
| | - Christine Poirier
- Centre de Lutte Anti-Tuberculeuse, Centre Hospitalier Intercommunal de Créteil, Créteil
| | - Eileen Hoal
- Molecular Biology and Human Genetics, MRC Centre for Molecular and Cellular Biology, DST/NRF Centre of Excellence for Biomedical TB Research, Faculty of Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | | | - France de La Rocque
- Association Clinique et Thérapeutique Infantile du Val de Marne, Saint Maur des Fossés
| | - François Corrard
- Association Clinique et Thérapeutique Infantile du Val de Marne, Saint Maur des Fossés
| | - Ghislain Grange
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U.1163
| | - Mélanie Migaud
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U.1163 University Paris Descartes, Sorbonne Paris Cité, Imagine Institute
| | - Jacinta Bustamante
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U.1163 University Paris Descartes, Sorbonne Paris Cité, Imagine Institute
| | - Stéphanie Boisson-Dupuis
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U.1163 University Paris Descartes, Sorbonne Paris Cité, Imagine Institute St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch
| | - Jean-Laurent Casanova
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U.1163 University Paris Descartes, Sorbonne Paris Cité, Imagine Institute St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch Howard Hughes Medical Institute, Rockefeller University, New York, New York
| | - Erwin Schurr
- McGill International TB Centre Department of Human Genetics Department of Medicine, McGill University, Montreal, Canada
| | - Alexandre Alcaïs
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U.1163 University Paris Descartes, Sorbonne Paris Cité, Imagine Institute URC, CIC, Necker, and Cochin Hospitals, Paris, France St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch
| | | | - Laurent Abel
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U.1163 University Paris Descartes, Sorbonne Paris Cité, Imagine Institute St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch
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4
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Pedergnana V, Syx L, Cobat A, Guergnon J, Brice P, Fermé C, Carde P, Hermine O, Pendeven CL, Amiel C, Taoufik Y, Alcaïs A, Theodorou I, Besson C, Abel L. Combined linkage and association studies show that HLA class II variants control levels of antibodies against Epstein-Barr virus antigens. PLoS One 2014; 9:e102501. [PMID: 25025336 PMCID: PMC4099326 DOI: 10.1371/journal.pone.0102501] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Accepted: 06/18/2014] [Indexed: 11/18/2022] Open
Abstract
Over 95% of the adult population worldwide is infected with Epstein-Barr virus (EBV). EBV infection is associated with the development of several cancers, including Hodgkin lymphoma (HL). Elevated levels of anti-EBV antibodies have been associated with increased risk of HL. There is growing evidence that genetic factors control the levels of antibodies against EBV antigens. Here, we conducted linkage and association studies to search for genetic factors influencing either anti-viral capsid antigen (VCA) or anti-Epstein Barr nuclear antigen-1 (EBNA-1) IgG levels in a unique cohort of 424 individuals of European origin from 119 French families recruited through a Hodgkin lymphoma (HL) patient. No major locus controlling anti-VCA antibody levels was identified. However, we found that the HLA region influenced anti-EBNA-1 IgG titers. Refined association studies in this region identified a cluster of HLA class II variants associated with anti-EBNA-1 IgG titers (e.g. p = 5×10–5 for rs9268403). The major allele of rs9268403 conferring a predisposition to high anti-EBNA-1 antibody levels was also associated with an increased risk of HL (p = 0.02). In summary, this study shows that HLA class II variants influenced anti-EBNA-1 IgG titers in a European population. It further shows the role of the same variants in the risk of HL.
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Affiliation(s)
- Vincent Pedergnana
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Institut National de la Santé et de la Recherche Médicale, Paris, France
- University Paris Descartes, Sorbonne Paris Cité, Imagine Institute, Paris, France
| | - Laurène Syx
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Institut National de la Santé et de la Recherche Médicale, Paris, France
- University Paris Descartes, Sorbonne Paris Cité, Imagine Institute, Paris, France
| | - Aurélie Cobat
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Institut National de la Santé et de la Recherche Médicale, Paris, France
- University Paris Descartes, Sorbonne Paris Cité, Imagine Institute, Paris, France
| | - Julien Guergnon
- Laboratory of Immunity and Infection, Institut National de la Santé et de la Recherche Médicale UMR-S 945, Université Pierre et Marie Curie Université Paris 6, Groupe Hospitalier Pitié-Salpêtrière, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Pauline Brice
- Service d’Onco-Hématologie, Hôpital Saint-Louis, Paris, France
| | - Christophe Fermé
- Department of Medicine, Hôpital Gustave Roussy, Villejuif, France
| | - Patrice Carde
- Department of Medicine, Hôpital Gustave Roussy, Villejuif, France
| | - Olivier Hermine
- Service d’Hématologie adultes, Hôpital Necker, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Catherine Le- Pendeven
- Laboratoire de Virologie, Hôpital Tenon, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Corinne Amiel
- Laboratoire de Virologie, Hôpital Tenon, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Yassine Taoufik
- Assistance Publique-Hôpitaux de Paris, CHU Bicetre, Service d’Hématologie et Immunologie Biologiques, Le Kremlin-Bicetre, France, and Université Paris Sud, Faculte de Médecine, Le Kremlin-Bicetre, France, and Institut National de la Santé et de la Recherche Médicale U1012, Le Kremlin-Bicetre, France
| | - Alexandre Alcaïs
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Institut National de la Santé et de la Recherche Médicale, Paris, France
- University Paris Descartes, Sorbonne Paris Cité, Imagine Institute, Paris, France
| | - Ioannis Theodorou
- Laboratory of Immunity and Infection, Institut National de la Santé et de la Recherche Médicale UMR-S 945, Université Pierre et Marie Curie Université Paris 6, Groupe Hospitalier Pitié-Salpêtrière, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Caroline Besson
- Assistance Publique-Hôpitaux de Paris, CHU Bicetre, Service d’Hématologie et Immunologie Biologiques, Le Kremlin-Bicetre, France, and Université Paris Sud, Faculte de Médecine, Le Kremlin-Bicetre, France, and Institut National de la Santé et de la Recherche Médicale U1012, Le Kremlin-Bicetre, France
- * E-mail: (CB); (LA)
| | - Laurent Abel
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Institut National de la Santé et de la Recherche Médicale, Paris, France
- University Paris Descartes, Sorbonne Paris Cité, Imagine Institute, Paris, France
- St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, New York, United States of America
- * E-mail: (CB); (LA)
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Cobat A, Hoal EG, Gallant CJ, Simkin L, Black GF, Stanley K, Jaïs JP, Yu TH, Boland-Auge A, Grange G, Delacourt C, van Helden P, Casanova JL, Abel L, Alcaïs A, Schurr E. Identification of a major locus, TNF1, that controls BCG-triggered tumor necrosis factor production by leukocytes in an area hyperendemic for tuberculosis. Clin Infect Dis 2013; 57:963-70. [PMID: 23800941 DOI: 10.1093/cid/cit438] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Tumor necrosis factor (TNF) is a key immune regulator of tuberculosis resistance, as exemplified by the highly increased risk of tuberculosis disease among individuals receiving TNF-blocker therapy. METHODS We determined the extent of TNF production after stimulation with BCG or BCG plus interferon gamma (IFN-γ) using a whole blood assay in 392 children belonging to 135 nuclear families from an area hyperendemic for tuberculosis in South Africa. We conducted classical univariate and bivariate genome-wide linkage analysis of TNF production using the data from both stimulation protocols by means of an extension of the maximum-likelihood-binomial method for quantitative trait loci to multivariate analysis. RESULTS Stimulation of whole blood by either BCG or BCG plus IFN-γ resulted in a range of TNF release across subjects. Extent of TNF production following both stimulation protocols was highly correlated (r = 0.81). We failed to identify genetic linkage of TNF release when considering each stimulus separately. However, using a multivariate approach, we detected a major pleiotropic locus (P < 10(-5)) on chromosome region 11p15, termed TNF locus 1 (TNF1), that controlled TNF production after stimulation by both BCG alone and BCG plus IFN-γ. CONCLUSIONS The TNF1 locus was mapped in the vicinity of the TST1 locus, previously identified in the same family sample, that controls tuberculin skin test (TST) negativity per se, that is, T-cell-independent resistance to Mycobacterium tuberculosis infection. This suggested that there is a connection between TST negativity per se and TNF production.
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Affiliation(s)
- Aurelie Cobat
- McGill International TB Centre and Departments of Human Genetics and Medicine, McGill University, Montreal, Quebec, Canada
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