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Borghesi A. Life-threatening infections in human newborns: Reconciling age-specific vulnerability and interindividual variability. Cell Immunol 2024; 397-398:104807. [PMID: 38232634 DOI: 10.1016/j.cellimm.2024.104807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Revised: 01/05/2024] [Accepted: 01/10/2024] [Indexed: 01/19/2024]
Abstract
In humans, the interindividual variability of clinical outcome following exposure to a microorganism is immense, ranging from silent infection to life-threatening disease. Age-specific immune responses partially account for the high incidence of infection during the first 28 days of life and the related high mortality at population level. However, the occurrence of life-threatening disease in individual newborns remains unexplained. By contrast, inborn errors of immunity and their immune phenocopies are increasingly being discovered in children and adults with life-threatening viral, bacterial, mycobacterial and fungal infections. There is a need for convergence between the fields of neonatal immunology, with its in-depth population-wide characterization of newborn-specific immune responses, and clinical immunology, with its investigations of infections in patients at the cellular and molecular levels, to facilitate identification of the mechanisms of susceptibility to infection in individual newborns and the design of novel preventive and therapeutic strategies.
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Affiliation(s)
- Alessandro Borghesi
- Neonatal Intensive Care Unit, San Matteo Research Hospital, Pavia, EU, Italy; School of Life Sciences, Swiss Federal Institute of Technology, Lausanne, Switzerland.
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2
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Sharma M, Suratannon N, Leung D, Baris S, Takeuchi I, Samra S, Yanagi K, Rosa Duque JS, Benamar M, Del Bel KL, Momenilandi M, Béziat V, Casanova JL, van Hagen PM, Arai K, Nomura I, Kaname T, Chatchatee P, Morita H, Chatila TA, Lau YL, Turvey SE. Human germline gain-of-function in STAT6: from severe allergic disease to lymphoma and beyond. Trends Immunol 2024; 45:138-153. [PMID: 38238227 DOI: 10.1016/j.it.2023.12.003] [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: 12/07/2023] [Revised: 12/18/2023] [Accepted: 12/20/2023] [Indexed: 02/12/2024]
Abstract
Signal transducer and activator of transcription (STAT)-6 is a transcription factor central to pro-allergic immune responses, although the function of human STAT6 at the whole-organism level has long remained unknown. Germline heterozygous gain-of-function (GOF) rare variants in STAT6 have been recently recognized to cause a broad and severe clinical phenotype of early-onset, multi-system allergic disease. Here, we provide an overview of the clinical presentation of STAT6-GOF disease, discussing how dysregulation of the STAT6 pathway causes severe allergic disease, and identifying possible targeted treatment approaches. Finally, we explore the mechanistic overlap between STAT6-GOF disease and other monogenic atopic disorders, and how this group of inborn errors of immunity (IEIs) powerfully inform our fundamental understanding of common human allergic disease.
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3
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Cobat A, Zhang Q, Abel L, Casanova JL, Fellay J. Human Genomics of COVID-19 Pneumonia: Contributions of Rare and Common Variants. Annu Rev Biomed Data Sci 2023; 6:465-486. [PMID: 37196358 PMCID: PMC10879986 DOI: 10.1146/annurev-biodatasci-020222-021705] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) infection is silent or benign in most infected individuals, but causes hypoxemic COVID-19 pneumonia in about 10% of cases. We review studies of the human genetics of life-threatening COVID-19 pneumonia, focusing on both rare and common variants. Large-scale genome-wide association studies have identified more than 20 common loci robustly associated with COVID-19 pneumonia with modest effect sizes, some implicating genes expressed in the lungs or leukocytes. The most robust association, on chromosome 3, concerns a haplotype inherited from Neanderthals. Sequencing studies focusing on rare variants with a strong effect have been particularly successful, identifying inborn errors of type I interferon (IFN) immunity in 1-5% of unvaccinated patients with critical pneumonia, and their autoimmune phenocopy, autoantibodies against type I IFN, in another 15-20% of cases. Our growing understanding of the impact of human genetic variation on immunity to SARS-CoV-2 is enabling health systems to improve protection for individuals and populations.
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Affiliation(s)
- Aurélie Cobat
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France;
- Imagine Institute, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA;
| | - Qian Zhang
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France;
- Imagine Institute, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA;
| | - Laurent Abel
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France;
- Imagine Institute, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA;
| | - Jean-Laurent Casanova
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France;
- Imagine Institute, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA;
- Howard Hughes Medical Institute, New York, NY, USA
- Department of Pediatrics, Necker Hospital for Sick Children, Paris, France
| | - Jacques Fellay
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland;
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Precision Medicine Unit, Biomedical Data Science Center, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
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4
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Gelemanović A, Ćatipović Ardalić T, Pribisalić A, Hayward C, Kolčić I, Polašek O. Genome-Wide Meta-Analysis Identifies Multiple Novel Rare Variants to Predict Common Human Infectious Diseases Risk. Int J Mol Sci 2023; 24:7006. [PMID: 37108169 PMCID: PMC10138356 DOI: 10.3390/ijms24087006] [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: 03/20/2023] [Revised: 04/02/2023] [Accepted: 04/05/2023] [Indexed: 04/29/2023] Open
Abstract
Infectious diseases still threaten global human health, and host genetic factors have been indicated as determining risk factors for observed variations in disease susceptibility, severity, and outcome. We performed a genome-wide meta-analysis on 4624 subjects from the 10,001 Dalmatians cohort, with 14 infection-related traits. Despite a rather small number of cases in some instances, we detected 29 infection-related genetic associations, mostly belonging to rare variants. Notably, the list included the genes CD28, INPP5D, ITPKB, MACROD2, and RSF1, all of which have known roles in the immune response. Expanding our knowledge on rare variants could contribute to the development of genetic panels that could assist in predicting an individual's life-long susceptibility to major infectious diseases. In addition, longitudinal biobanks are an interesting source of information for identifying the host genetic variants involved in infectious disease susceptibility and severity. Since infectious diseases continue to act as a selective pressure on our genomes, there is a constant need for a large consortium of biobanks with access to genetic and environmental data to further elucidate the complex mechanisms behind host-pathogen interactions and infectious disease susceptibility.
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Affiliation(s)
- Andrea Gelemanović
- Department of Public Health, University of Split School of Medicine, 21000 Split, Croatia
| | | | - Ajka Pribisalić
- Department of Public Health, University of Split School of Medicine, 21000 Split, Croatia
| | - Caroline Hayward
- Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, UK
| | - Ivana Kolčić
- Department of Public Health, University of Split School of Medicine, 21000 Split, Croatia
- Department of General Courses, Algebra University College, 10000 Zagreb, Croatia
| | - Ozren Polašek
- Department of Public Health, University of Split School of Medicine, 21000 Split, Croatia
- Department of General Courses, Algebra University College, 10000 Zagreb, Croatia
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5
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Hu W, Xu K. Research progress on genetic control of host susceptibility to tuberculosis. Zhejiang Da Xue Xue Bao Yi Xue Ban 2022; 51:679-690. [PMID: 36915969 PMCID: PMC10262011 DOI: 10.3724/zdxbyxb-2022-0484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 10/11/2022] [Indexed: 02/16/2023]
Abstract
The "Lübeck disaster", twins studies, adoptees studies, and other epidemiological observational studies have shown that host genetic factors play a significant role in determining the host susceptibility to Mycobacterium tuberculosis infection and pathogenesis of tuberculosis. From linkage analyses to genome-wide association studies, it has been discovered that human leucocyte antigen (HLA) genes as well as non-HLA genes (such as SLC11A1, VDR, ASAP1 as well as genes encoding cytokines and pattern recognition receptors) are associated with tuberculosis susceptibility. To provide ideas for subsequent studies about risk prediction of MTB infection and the diagnosis and treatment of tuberculosis, we review the research progress on tuberculosis susceptibility related genes in recent years, focusing on the correlation of HLA genes and non-HLA genes with the pathogenesis of tuberculosis. We also report the results of an enrichment analysis of the genes mentioned in the article. Most of these genes appear to be involved in the regulation of immune system and inflammation, and are also closely related to autoimmune diseases.
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Host Defenses to Viruses: Lessons from Inborn Errors of Immunity. Medicina (B Aires) 2022; 58:medicina58020248. [PMID: 35208572 PMCID: PMC8879264 DOI: 10.3390/medicina58020248] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 01/27/2022] [Accepted: 01/29/2022] [Indexed: 01/03/2023] Open
Abstract
The constant battle between viruses and their hosts leads to their reciprocal evolution. Viruses regularly develop survival strategies against host immunity, while their ability to replicate and disseminate is countered by the antiviral defense mechanisms that host mount. Although most viral infections are generally controlled by the host’s immune system, some viruses do cause overt damage to the host. The outcome can vary widely depending on the properties of the infecting virus and the circumstances of infection but also depends on several factors controlled by the host, including host genetic susceptibility to viral infections. In this narrative review, we provide a brief overview of host immunity to viruses and immune-evasion strategies developed by viruses. Moreover, we focus on inborn errors of immunity, these being considered a model for studying host response mechanisms to viruses. We finally report exemplary inborn errors of both the innate and adaptive immune systems that highlight the role of proteins involved in the control of viral infections.
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7
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Borghesi A, Trück J, Asgari S, Sancho-Shimizu V, Agyeman PKA, Bellos E, Giannoni E, Stocker M, Posfay-Barbe KM, Heininger U, Bernhard-Stirnemann S, Niederer-Loher A, Kahlert CR, Natalucci G, Relly C, Riedel T, Kuehni CE, Thorball CW, Chaturvedi N, Martinon-Torres F, Kuijpers TW, Coin L, Wright V, Herberg J, Levin M, Aebi C, Berger C, Fellay J, Schlapbach LJ. Whole-exome Sequencing for the Identification of Rare Variants in Primary Immunodeficiency Genes in Children With Sepsis: A Prospective, Population-based Cohort Study. Clin Infect Dis 2021; 71:e614-e623. [PMID: 32185379 PMCID: PMC7744985 DOI: 10.1093/cid/ciaa290] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 03/15/2020] [Indexed: 11/15/2022] Open
Abstract
Background The role of primary immunodeficiencies (PID) in susceptibility to sepsis remains unknown. It is unclear whether children with sepsis benefit from genetic investigations. We hypothesized that sepsis may represent the first manifestation of underlying PID. We applied whole-exome sequencing (WES) to a national cohort of children with sepsis to identify rare, predicted pathogenic variants in PID genes. Methods We conducted a multicenter, population-based, prospective study including previously healthy children aged ≥28 days and <17 years admitted with blood culture-proven sepsis. Using a stringent variant filtering procedure, analysis of WES data was restricted to rare, predicted pathogenic variants in 240 PID genes for which increased susceptibility to bacterial infection has been reported. Results There were 176 children presenting with 185 sepsis episodes who underwent WES (median age, 52 months; interquartile range, 15.4–126.4). There were 41 unique predicted pathogenic PID variants (1 homozygous, 5 hemizygous, and 35 heterozygous) found in 35/176 (20%) patients, including 3/176 (2%) patients carrying variants that were previously reported to lead to PID. The variants occurred in PID genes across all 8 PID categories, as defined by the International Union of Immunological Societies. We did not observe a significant correlation between clinical or laboratory characteristics of patients and the presence or absence of PID variants. Conclusions Applying WES to a population-based cohort of previously healthy children with bacterial sepsis detected variants of uncertain significance in PID genes in 1 out of 5 children. Future studies need to investigate the functional relevance of these variants to determine whether variants in PID genes contribute to pediatric sepsis susceptibility.
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Affiliation(s)
- Alessandro Borghesi
- Swiss Institute of Bioinformatics, Lausanne, Switzerland.,Global Health Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.,Neonatal Intensive Care Unit, Fondazione Institute for Research, Hospitalization and Health Care (IRCCS) Policlinico San Matteo, Pavia, Italy
| | - Johannes Trück
- University Children's Hospital Zurich and the Children's Research Center, Zurich, Switzerland.,University of Zurich, Zurich, Switzerland
| | - Samira Asgari
- Swiss Institute of Bioinformatics, Lausanne, Switzerland.,Global Health Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.,Division of Genetics and Rheumatology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA.,Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - Vanessa Sancho-Shimizu
- Section of Paediatrics, Imperial College London, London, United Kingdom.,Section of Virology, Imperial College London, London, United Kingdom
| | - Philipp K A Agyeman
- Department of Paediatrics, Bern University Hospital, Inselspital, University of Bern, Bern, Switzerland
| | - Evangelos Bellos
- Section of Paediatrics, Imperial College London, London, United Kingdom
| | - Eric Giannoni
- Service of Neonatology, Department Woman-Mother-Child, and Infectious Diseases Service, Department of Medicine, Lausanne University Hospital, Lausanne, Switzerland
| | - Martin Stocker
- Department of Paediatrics, Children's Hospital Lucerne, Lucerne, Switzerland
| | - Klara M Posfay-Barbe
- Paediatric Infectious Diseases Unit, Children's Hospital of Geneva, University Hospitals of Geneva, Geneva, Switzerland
| | - Ulrich Heininger
- Infectious Diseases and Vaccinology, University of Basel Children's Hospital, Basel, Switzerland
| | | | | | | | | | - Christa Relly
- University Children's Hospital Zurich and the Children's Research Center, Zurich, Switzerland
| | - Thomas Riedel
- Department of Paediatrics, Cantonal Hospital Graubuenden, Chur, Switzerland
| | - Claudia E Kuehni
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | - Christian W Thorball
- Swiss Institute of Bioinformatics, Lausanne, Switzerland.,Global Health Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Nimisha Chaturvedi
- Swiss Institute of Bioinformatics, Lausanne, Switzerland.,Global Health Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Federico Martinon-Torres
- Translational Paediatrics and Infectious Diseases Section, Paediatrics Department, Santiago de Compostela, Spain.,Instituto de Investigación Sanitaria de Santiago, Genetics, Vaccines, Infectious Diseases and Paediatrics Research Group, Santiago de Compostela, Spain
| | - Taco W Kuijpers
- Academic Medical Center, Emma Children's Hospital, University of Amsterdam, Amsterdam, The Netherlands
| | - Lachlan Coin
- Institute of Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Victoria Wright
- Section of Paediatrics, Imperial College London, London, United Kingdom
| | - Jethro Herberg
- Section of Paediatrics, Imperial College London, London, United Kingdom
| | - Michael Levin
- Section of Paediatrics, Imperial College London, London, United Kingdom
| | - Christoph Aebi
- Department of Paediatrics, Bern University Hospital, Inselspital, University of Bern, Bern, Switzerland
| | - Christoph Berger
- University Children's Hospital Zurich and the Children's Research Center, Zurich, Switzerland
| | - Jacques Fellay
- Swiss Institute of Bioinformatics, Lausanne, Switzerland.,Global Health Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.,Precision Medicine Unit, Lausanne University Hospital, Lausanne, Switzerland
| | - Luregn J Schlapbach
- University Children's Hospital Zurich and the Children's Research Center, Zurich, Switzerland.,Paediatric Critical Care Research Group, Child Health Research Centre, The University of Queensland, Brisbane, Australia.,Paediatric Intensive Care Unit, Queensland Children's Hospital, Children's Health Queensland, Brisbane, Australia
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8
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Meyts I, Casanova JL. Viral infections in humans and mice with genetic deficiencies of the type I IFN response pathway. Eur J Immunol 2021; 51:1039-1061. [PMID: 33729549 DOI: 10.1002/eji.202048793] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 01/31/2021] [Accepted: 03/04/2021] [Indexed: 12/11/2022]
Abstract
Type I IFNs are so-named because they interfere with viral infection in vertebrate cells. The study of cellular responses to type I IFNs led to the discovery of the JAK-STAT signaling pathway, which also governs the response to other cytokine families. We review here the outcome of viral infections in mice and humans with engineered and inborn deficiencies, respectively, of (i) IFNAR1 or IFNAR2, selectively disrupting responses to type I IFNs, (ii) STAT1, STAT2, and IRF9, also impairing cellular responses to type II (for STAT1) and/or III (for STAT1, STAT2, IRF9) IFNs, and (iii) JAK1 and TYK2, also impairing cellular responses to cytokines other than IFNs. A picture is emerging of greater redundancy of human type I IFNs for protective immunity to viruses in natural conditions than was initially anticipated. Mouse type I IFNs are essential for protection against a broad range of viruses in experimental conditions. These findings suggest that various type I IFN-independent mechanisms of human cell-intrinsic immunity to viruses have yet to be discovered.
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Affiliation(s)
- Isabelle Meyts
- Department of Immunology, Microbiology and Transplantation, Laboratory of Inborn Errors of Immunity, Leuven, Belgium.,Department of Pediatrics, University Hospitals Leuven, Leuven, Belgium
| | - Jean-Laurent Casanova
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY, USA.,Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR 1163, Necker Hospital for Sick Children, Paris, France.,Imagine Institute, University of Paris, Paris, France.,Howard Hughes Medical Institute, New York, NY, USA
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9
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Casanova JL, Abel L. Lethal Infectious Diseases as Inborn Errors of Immunity: Toward a Synthesis of the Germ and Genetic Theories. ANNUAL REVIEW OF PATHOLOGY 2021; 16:23-50. [PMID: 32289233 PMCID: PMC7923385 DOI: 10.1146/annurev-pathol-031920-101429] [Citation(s) in RCA: 67] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
It was first demonstrated in the late nineteenth century that human deaths from fever were typically due to infections. As the germ theory gained ground, it replaced the old, unproven theory that deaths from fever reflected a weak personal or even familial constitution. A new enigma emerged at the turn of the twentieth century, when it became apparent that only a small proportion of infected individuals die from primary infections with almost any given microbe. Classical genetics studies gradually revealed that severe infectious diseases could be driven by human genetic predisposition. This idea gained ground with the support of molecular genetics, in three successive, overlapping steps. First, many rare inborn errors of immunity were shown, from 1985 onward, to underlie multiple, recurrent infections with Mendelian inheritance. Second, a handful of rare and familial infections, also segregating as Mendelian traits but striking humans resistant to other infections, were deciphered molecularly beginning in 1996. Third, from 2007 onward, a growing number of rare or common sporadicinfections were shown to result from monogenic, but not Mendelian, inborn errors. A synthesis of the hitherto mutually exclusive germ and genetic theories is now in view.
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Affiliation(s)
- Jean-Laurent Casanova
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065, USA;
- Howard Hughes Medical Institute, New York, NY 10065, USA
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, 75015 Paris, France
- Paris University, Imagine Institute, 75015 Paris, France
- Pediatric Hematology-Immunology Unit, Necker Hospital for Sick Children, 75015 Paris, France
| | - Laurent Abel
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065, USA;
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, 75015 Paris, France
- Paris University, Imagine Institute, 75015 Paris, France
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10
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Immunological Evaluation for Personalized Interventions in Children with Tuberculosis: Should It Be Routinely Performed? J Immunol Res 2020; 2020:8235149. [PMID: 33005692 PMCID: PMC7509549 DOI: 10.1155/2020/8235149] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 07/03/2020] [Accepted: 08/18/2020] [Indexed: 12/14/2022] Open
Abstract
Childhood tuberculosis (TB) is a significant public health problem and the ninth leading cause of death worldwide. Progression of Mycobacterium tuberculosis infection to active disease depends on mycobacterial virulence, environmental diversity, and host susceptibility and immune response. In children, malnutrition and immaturity of the immune system contribute to an inadequate immune response. Coinfections, though rarely described in TB, might be associated with host immune deficiencies. Here, we describe the immunological evaluation of eight pediatric patients infected with a member of the M. tuberculosis complex, most of them with concomitant pulmonary infections (bacteria, viruses, or fungi). We assessed the functionality of several innate immunity receptors, IL-12 receptor, and IFN-γ receptor, as well as the antioxidant levels (glutathione), which are essential mechanisms for fighting intracellular pathogens such as M. tuberculosis. This study is aimed at developing a thorough immunological evaluation of patients with TB and a coinfection.
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11
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Abstract
PURPOSE OF REVIEW Sepsis remains among the leading causes of childhood mortality worldwide. This review serves to highlight key areas of knowledge gain and ongoing controversies pertinent to sepsis in children. RECENT FINDINGS Several recent publications describe the epidemiology of paediatric sepsis, demonstrating the impact on child health in terms of mortality and morbidity, and the shortcomings of current paediatric sepsis definitions. Although emerging data support the importance of organ dysfunction as a hallmark of paediatric sepsis, the understanding of host susceptibility to sepsis and to sepsis severity remains very limited. Next-generation sequencing and host transcriptomics have the potential to provide new insights into the pathogenesis of sepsis and may enable personalized medicine approaches. Despite good observational data indicating benefit of sepsis recognition and treatment bundles, the evidence for the individual bundle components remains scarce, implying an urgent need for large trials. SUMMARY Recent studies have demonstrated distinct epidemiological patterns pertinent to age groups, healthcare settings, and comorbidities in the era post meningococcal epidemics. Although sepsis quality improvement initiatives have led to substantial outcome improvements, there is urgency for innovative trials to reduce uncertainty around the optimal approach for the recognition and treatment of sepsis in children.
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12
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The human genetic determinism of life-threatening infectious diseases: genetic heterogeneity and physiological homogeneity? Hum Genet 2020; 139:681-694. [PMID: 32462426 PMCID: PMC7251220 DOI: 10.1007/s00439-020-02184-w] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Multicellular eukaryotes emerged late in evolution from an ocean of viruses, bacteria, archaea, and unicellular eukaryotes. These macroorganisms are exposed to and infected by a tremendous diversity of microorganisms. Those that are large enough can even be infected by multicellular fungi and parasites. Each interaction is unique, if only because it operates between two unique living organisms, in an infinite diversity of circumstances. This is neatly illustrated by the extraordinarily high level of interindividual clinical variability in human infections, even for a given pathogen, ranging from a total absence of clinical manifestations to death. We discuss here the idea that the determinism of human life-threatening infectious diseases can be governed by single-gene inborn errors of immunity, which are rarely Mendelian and frequently display incomplete penetrance. We briefly review the evidence in support of this notion obtained over the last two decades, referring to a number of focused and thorough reviews published by eminent colleagues in this issue of Human Genetics. It seems that almost any life-threatening infectious disease can be driven by at least one, and, perhaps, a great many diverse monogenic inborn errors, which may nonetheless be immunologically related. While the proportions of monogenic cases remain unknown, a picture in which genetic heterogeneity is combined with physiological homogeneity is emerging from these studies. A preliminary sketch of the human genetic architecture of severe infectious diseases is perhaps in sight.
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13
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Manry J, Vincent QB, Johnson C, Chrabieh M, Lorenzo L, Theodorou I, Ardant MF, Marion E, Chauty A, Marsollier L, Abel L, Alcaïs A. Genome-wide association study of Buruli ulcer in rural Benin highlights role of two LncRNAs and the autophagy pathway. Commun Biol 2020; 3:177. [PMID: 32313116 PMCID: PMC7171125 DOI: 10.1038/s42003-020-0920-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 03/24/2020] [Indexed: 02/07/2023] Open
Abstract
Buruli ulcer, caused by Mycobacterium ulcerans and characterized by devastating necrotizing skin lesions, is the third mycobacterial disease worldwide. The role of host genetics in susceptibility to Buruli ulcer has long been suggested. We conduct the first genome-wide association study of Buruli ulcer on a sample of 1524 well characterized patients and controls from rural Benin. Two-stage analyses identify two variants located within LncRNA genes: rs9814705 in ENSG00000240095.1 (P = 2.85 × 10−7; odds ratio = 1.80 [1.43–2.27]), and rs76647377 in LINC01622 (P = 9.85 × 10−8; hazard ratio = 0.41 [0.28–0.60]). Furthermore, we replicate the protective effect of allele G of a missense variant located in ATG16L1, previously shown to decrease bacterial autophagy (rs2241880, P = 0.003; odds ratio = 0.31 [0.14–0.68]). Our results suggest LncRNAs and the autophagy pathway as critical factors in the development of Buruli ulcer. Jeremy Manry, Quentin Vincent et al. report a genome-wide association study for susceptibility to Buruli ulcer in a rural population from the West African country of Benin. They identify two independently associated variants within LncRNA genes and confirm the protective effect of a missense variant in the bacterial autophagy gene ATG16L1.
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Affiliation(s)
- Jeremy Manry
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Institut National de la Santé et de la Recherche Médicale (INSERM) UMR 1163, Paris, France. .,Université de Paris, Imagine Institute, Paris, France.
| | - Quentin B Vincent
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Institut National de la Santé et de la Recherche Médicale (INSERM) UMR 1163, Paris, France.,Université de Paris, Imagine Institute, Paris, France
| | - Christian Johnson
- Fondation Raoul Follereau, Paris, France.,Centre Interfacultaire de Formation et de Recherche en Environnement pour le Développement Durable. Université d'Abomey, Calavi, Benin
| | - Maya Chrabieh
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Institut National de la Santé et de la Recherche Médicale (INSERM) UMR 1163, Paris, France.,Université de Paris, Imagine Institute, Paris, France
| | - Lazaro Lorenzo
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Institut National de la Santé et de la Recherche Médicale (INSERM) UMR 1163, Paris, France.,Université de Paris, Imagine Institute, Paris, France
| | - Ioannis Theodorou
- Center for Immunology and Infectious Diseases, INSERM UMR S 1135, Pierre and Marie Curie University, and AP-HP Laboratoire d'Immunologie et Histocompatibilité Hôpital Saint-Louis, Paris, France
| | - Marie-Françoise Ardant
- Fondation Raoul Follereau, Paris, France.,Centre de Dépistage et de Traitement de la Lèpre et de l'Ulcère de Buruli (CDTLUB), Pobè, Benin
| | - Estelle Marion
- INSERM UMR-U892 and CNRS U6299, team 7, Angers University, Angers University Hospital, Angers, France
| | - Annick Chauty
- Fondation Raoul Follereau, Paris, France.,Centre de Dépistage et de Traitement de la Lèpre et de l'Ulcère de Buruli (CDTLUB), Pobè, Benin
| | - Laurent Marsollier
- INSERM UMR-U892 and CNRS U6299, team 7, Angers University, Angers University Hospital, Angers, France
| | - Laurent Abel
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Institut National de la Santé et de la Recherche Médicale (INSERM) UMR 1163, Paris, France.,Université de Paris, Imagine Institute, Paris, France.,St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY, USA
| | - Alexandre Alcaïs
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Institut National de la Santé et de la Recherche Médicale (INSERM) UMR 1163, Paris, France. .,Université de Paris, Imagine Institute, Paris, France.
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14
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Herpes simplex virus encephalitis of childhood: inborn errors of central nervous system cell-intrinsic immunity. Hum Genet 2020; 139:911-918. [PMID: 32040615 DOI: 10.1007/s00439-020-02127-5] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 02/02/2020] [Indexed: 12/23/2022]
Abstract
Herpes simplex virus 1 (HSV-1) encephalitis (HSE) is the most common sporadic viral encephalitis in Western countries. Over the last 15 years, human genetic and immunological studies have provided proof-of-principle that childhood HSE can result from inborn errors of central nervous system (CNS)-specific, cell-intrinsic immunity to HSV-1. HSE-causing mutations of eight genes disrupt known (TLR3-dependent IFN-α/β immunity) and novel (dependent on DBR1 or snoRNA31) antiviral mechanisms. Monogenic inborn errors confer susceptibility to forebrain (TLR3-IFN or snoRNA31) or brainstem (DBR1) HSE. Most of these disorders display incomplete clinical penetrance, with the possible exception of DBR1 deficiency. They account for a small, but non-negligible proportion of cases (about 7%). These findings pave the way for the gradual definition of the genetic and immunological architecture of childhood HSE, with both biological and clinical implications.
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15
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Riggle BA, Miller LH, Pierce SK. Desperately Seeking Therapies for Cerebral Malaria. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2020; 204:327-334. [PMID: 31907275 PMCID: PMC6951433 DOI: 10.4049/jimmunol.1900829] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 09/10/2019] [Indexed: 02/07/2023]
Abstract
Malaria is a deadly infectious disease caused by parasites of the Plasmodium spp. that takes an estimated 435,000 lives each year, primarily among young African children. For most children, malaria is a febrile illness that resolves with time, but in ∼1% of cases, for reasons we do not understand, malaria becomes severe and life threatening. Cerebral malaria (CM) is the most common form of severe malaria, accounting for the vast majority of childhood deaths from malaria despite highly effective antiparasite chemotherapy. Thus, CM is one of the most prevalent lethal brain diseases, and one for which we have no effective therapy. CM is, in part, an immune-mediated disease, and to fully understand CM, it is essential to appreciate the complex relationship between the malarial parasite and the human immune system. In this study, we provide a primer on malaria for immunologists and, in this context, review progress identifying targets for therapeutic intervention.
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Affiliation(s)
- Brittany A Riggle
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852; and
| | - Louis H Miller
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852
| | - Susan K Pierce
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852; and
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16
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Borghesi A, Marzollo A, Michev A, Fellay J. Susceptibility to infection in early life: a growing role for human genetics. Hum Genet 2020; 139:733-743. [PMID: 31932884 DOI: 10.1007/s00439-019-02109-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 12/30/2019] [Indexed: 12/23/2022]
Abstract
The unique vulnerability to infection of newborns and young infants is generally explained by a constellation of differences between early-life immune responses and immune responses at later ages, often referred to as neonatal immune immaturity. This developmental view, corroborated by robust evidence, offers a plausible, population-level description of the pathogenesis of life-threatening infectious diseases during the early-life period, but provides little explanation on the wide inter-individual differences in susceptibility and resistance to specific infections during the first months of life. In this context, the role of individual human genetic variation is increasingly recognized. A life-threatening infection caused by an opportunistic pathogen in an otherwise healthy infant likely represents the first manifestation of an inborn error of immunity. Single-gene disorders may also underlie common infections in full-term infants with no comorbidities or in preterm infants. In addition, there is increasing evidence of a possible role for common genetic variation in the pathogenesis of infection in preterm infants. Over the past years, a unified theory of infectious diseases emerged, supporting a hypothetical, age-dependent general model of genetic architecture of human infectious diseases. We discuss here how the proposed genetic model can be reconciled with the widely accepted developmental view of early-life infections in humans.
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Affiliation(s)
- Alessandro Borghesi
- Neonatal Intensive Care Unit, Fondazione IRCCS Policlinico "San Matteo", Pavia, Italy. .,School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.
| | - Antonio Marzollo
- Pediatric Hematology-Oncology Unit, Department of Women's and Children's Health, Azienda Ospedaliera-University of Padova, Padua, Italy
| | - Alexandre Michev
- Department of Pediatrics, Fondazione IRCCS Policlinico "San Matteo", University of Pavia, Pavia, Italy
| | - Jacques Fellay
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.,Precision Medicine Unit, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
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17
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Complete clinical remission of invasive Candida infection with CARD9 deficiency after G-CSF treatment. Comp Immunol Microbiol Infect Dis 2020; 70:101417. [PMID: 32113042 DOI: 10.1016/j.cimid.2020.101417] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Revised: 12/19/2019] [Accepted: 01/03/2020] [Indexed: 01/09/2023]
Abstract
Caspase-associated recruitment domain-containing protein 9 (CARD9) deficiency is an autosomal-recessive primary immunodeficiency characterized by susceptibility to recurrent Candida infections, and its diagnosis and treatment is challenging. The present study aims to investigate the genetic characteristic and treatment strategy of a Chinese pediatric patient with CARD9 deficiency. In the present study, whole-exome sequencing (WES) was performed to screen the causal variants in a Chinese pediatric patient who exhibited an invasive Candida infection in the abdominal cavity and central nervous system. After the disease-causing gene being confirmed, the patient was treated with a combination of G-CSF and antifungal agents. DNA sequencing revealed a homozygous insertion mutation (c.819-820insG) in exon 6 of the CARD9 gene, which led to downstream amino acids conversion on codon 274 (p.D274fsX60). Th17 cell populations and cytokine levels showed decreased levels. The treatment regimen successfully resolved the patient's symptoms, and he remained symptom-free after more than 1 year of follow-up. This study described an invasive Candida infection in a pediatric patient and WES identified an insertion variant of the CARD9 gene. A combination of G-CSF and antifungal agents was highly effective in treating the invasive fungal infection accompanied by CARD9-induced immunodeficiency.
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18
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Cabral-Marques O, Schimke LF, de Oliveira EB, El Khawanky N, Ramos RN, Al-Ramadi BK, Segundo GRS, Ochs HD, Condino-Neto A. Flow Cytometry Contributions for the Diagnosis and Immunopathological Characterization of Primary Immunodeficiency Diseases With Immune Dysregulation. Front Immunol 2019; 10:2742. [PMID: 31849949 PMCID: PMC6889851 DOI: 10.3389/fimmu.2019.02742] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 11/08/2019] [Indexed: 12/24/2022] Open
Abstract
Almost 70 years after establishing the concept of primary immunodeficiency disorders (PIDs), more than 320 monogenic inborn errors of immunity have been identified thanks to the remarkable contribution of high-throughput genetic screening in the last decade. Approximately 40 of these PIDs present with autoimmune or auto-inflammatory symptoms as the primary clinical manifestation instead of infections. These PIDs are now recognized as diseases of immune dysregulation. Loss-of function mutations in genes such as FOXP3, CD25, LRBA, IL-10, IL10RA, and IL10RB, as well as heterozygous gain-of-function mutations in JAK1 and STAT3 have been reported as causative of these disorders. Identifying these syndromes has considerably contributed to expanding our knowledge on the mechanisms of immune regulation and tolerance. Although whole exome and whole genome sequencing have been extremely useful in identifying novel causative genes underlying new phenotypes, these approaches are time-consuming and expensive. Patients with monogenic syndromes associated with autoimmunity require faster diagnostic tools to delineate therapeutic strategies and avoid organ damage. Since these PIDs present with severe life-threatening phenotypes, the need for a precise diagnosis in order to initiate appropriate patient management is necessary. More traditional approaches such as flow cytometry are therefore a valid option. Here, we review the application of flow cytometry and discuss the relevance of this powerful technique in diagnosing patients with PIDs presenting with immune dysregulation. In addition, flow cytometry represents a fast, robust, and sensitive approach that efficiently uncovers new immunopathological mechanisms underlying monogenic PIDs.
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Affiliation(s)
- Otavio Cabral-Marques
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Lena F Schimke
- Department of Rheumatology and Clinical Immunology, Faculty of Medicine, Center for Chronic Immunodeficiency (CCI), Medical Center-University of Freiburg, University of Freiburg, Freiburg im Breisgau, Germany
| | | | - Nadia El Khawanky
- Department of Hematology, Oncology and Stem Cell Transplantation, Freiburg University Medical Center, Freiburg im Breisgau, Germany.,Precision Medicine Theme, The South Australian Health and Medical Research Institute (SAHMRI), Adelaide, SA, Australia
| | - Rodrigo Nalio Ramos
- INSERM U932, SiRIC Translational Immunotherapy Team, Institut Curie, Paris Sciences et Lettres Research University, Paris, France
| | - Basel K Al-Ramadi
- Department of Medical Microbiology and Immunology, College of Medicine and Health Sciences, UAE University, Al Ain, United Arab Emirates
| | | | - Hans D Ochs
- Department of Pediatrics, University of Washington School of Medicine, and Seattle Children's Research Institute, Seattle, WA, United States
| | - Antonio Condino-Neto
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
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19
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Wu S, Wang Y, Zhang M, Wang M, He JQ. Genetic variants in IFNG and IFNGR1 and tuberculosis susceptibility. Cytokine 2019; 123:154775. [PMID: 31310896 DOI: 10.1016/j.cyto.2019.154775] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 07/06/2019] [Accepted: 07/08/2019] [Indexed: 02/05/2023]
Abstract
BACKGROUND Tuberculosis (TB) is the type of chronic infectious disease which majorly caused by Mycobacterium tuberculosis (M. TB). Emerging data suggest that interferon gamma (IFNG) and its receptor IFNGR1 may be involved in the risk of TB. METHODS A total of 636 TB patients and 608 healthy controls were selected. The association between single nucleotide polymorphisms (SNPs) and TB was estimated by logistic analyses adjusting for age, gender and smoking status. SNPs genotyping was done by using the improved multiplex ligase detection reaction (iMLDR). RESULTS The IFNG rs1861494 allele C was related to an increased risk for TB (OR = 1.25, 95%CI: 1.06-1.48; P = 0.009). Compared with TT genotype, CT (OR = 1.28, 95%CI: 1.01-1.63; P = 0.040) and CC (OR = 1.51, 95%CI: 1.04-2.19; P = 0.031) were also risk factors for TB. In the subgroup analysis, the association was stronger among participants < 25 years (OR = 2.40, 95%CI: 1.70-3.38; P < 0.001) and male groups (OR = 1.31, 95%CI: 1.03-1.66; P = 0.030). In addition, IFNG rs1861494 was associated with anti-TB treatment outcome (OR = 0.70, 95%CI: 0.52-0.94; P = 0.017). We also detected that IFNGR1 rs2234711 influenced the IFNG production. CONCLUSION IFNG rs1861494 polymorphism was associated with TB, particularly in the younger and male subgroups.
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Affiliation(s)
- Shouquan Wu
- Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yu Wang
- Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, China.
| | - Miaomiao Zhang
- Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, China.
| | - Minggui Wang
- Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Jian-Qing He
- Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, China.
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20
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Biological Network Approaches and Applications in Rare Disease Studies. Genes (Basel) 2019; 10:genes10100797. [PMID: 31614842 PMCID: PMC6827097 DOI: 10.3390/genes10100797] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 09/30/2019] [Accepted: 10/10/2019] [Indexed: 12/26/2022] Open
Abstract
Network biology has the capability to integrate, represent, interpret, and model complex biological systems by collectively accommodating biological omics data, biological interactions and associations, graph theory, statistical measures, and visualizations. Biological networks have recently been shown to be very useful for studies that decipher biological mechanisms and disease etiologies and for studies that predict therapeutic responses, at both the molecular and system levels. In this review, we briefly summarize the general framework of biological network studies, including data resources, network construction methods, statistical measures, network topological properties, and visualization tools. We also introduce several recent biological network applications and methods for the studies of rare diseases.
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21
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Lim HK, Huang SXL, Chen J, Kerner G, Gilliaux O, Bastard P, Dobbs K, Hernandez N, Goudin N, Hasek ML, García Reino EJ, Lafaille FG, Lorenzo L, Luthra P, Kochetkov T, Bigio B, Boucherit S, Rozenberg F, Vedrinne C, Keller MD, Itan Y, García-Sastre A, Celard M, Orange JS, Ciancanelli MJ, Meyts I, Zhang Q, Abel L, Notarangelo LD, Snoeck HW, Casanova JL, Zhang SY. Severe influenza pneumonitis in children with inherited TLR3 deficiency. J Exp Med 2019; 216:2038-2056. [PMID: 31217193 PMCID: PMC6719423 DOI: 10.1084/jem.20181621] [Citation(s) in RCA: 120] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Revised: 04/10/2019] [Accepted: 05/09/2019] [Indexed: 12/20/2022] Open
Abstract
Autosomal recessive IRF7 and IRF9 deficiencies impair type I and III IFN immunity and underlie severe influenza pneumonitis. We report three unrelated children with influenza A virus (IAV) infection manifesting as acute respiratory distress syndrome (IAV-ARDS), heterozygous for rare TLR3 variants (P554S in two patients and P680L in the third) causing autosomal dominant (AD) TLR3 deficiency. AD TLR3 deficiency can underlie herpes simplex virus-1 (HSV-1) encephalitis (HSE) by impairing cortical neuron-intrinsic type I IFN immunity to HSV-1. TLR3-mutated leukocytes produce normal levels of IFNs in response to IAV. In contrast, TLR3-mutated fibroblasts produce lower levels of IFN-β and -λ, and display enhanced viral susceptibility, upon IAV infection. Moreover, the patients' iPSC-derived pulmonary epithelial cells (PECs) are susceptible to IAV. Treatment with IFN-α2b or IFN-λ1 rescues this phenotype. AD TLR3 deficiency may thus underlie IAV-ARDS by impairing TLR3-dependent, type I and/or III IFN-mediated, PEC-intrinsic immunity. Its clinical penetrance is incomplete for both IAV-ARDS and HSE, consistent with their typically sporadic nature.
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Affiliation(s)
- Hye Kyung Lim
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY.,Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Institut National de la Santé et de la Recherche Médicale UMR 1163, Paris, France.,Paris Descartes University, Imagine Institute, Paris, France
| | - Sarah X L Huang
- Columbia Center for Translational Immunology, Columbia University Medical Center, New York, NY.,Department of Medicine, Columbia University Medical Center, New York, NY.,Center for Stem Cell and Regenerative Medicine, University of Texas Health Science Center at Texas, Houston, TX
| | - Jie Chen
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY.,Department of Infectious Diseases, Shanghai Sixth Hospital, Shanghai Jiaotong University, Shanghai, China
| | - Gaspard Kerner
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Institut National de la Santé et de la Recherche Médicale UMR 1163, Paris, France.,Paris Descartes University, Imagine Institute, Paris, France
| | - Olivier Gilliaux
- Laboratory of Experimental Medicine (ULB222), Medicine Faculty, Libre de Bruxelles University, Brussels, Belgium.,Department of Pediatrics, University Hospital Center of Charleroi, Charleroi, Belgium
| | - Paul Bastard
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Institut National de la Santé et de la Recherche Médicale UMR 1163, Paris, France.,Paris Descartes University, Imagine Institute, Paris, France
| | - Kerry Dobbs
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Nicholas Hernandez
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY
| | - Nicolas Goudin
- Cell Imaging Platform Structure Fédérative de Recherche Necker, Institut National de la Santé et de la Recherche Médicale US 24, Paris, France
| | - Mary L Hasek
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY
| | - Eduardo Javier García Reino
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY
| | - Fabien G Lafaille
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY
| | - Lazaro Lorenzo
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Institut National de la Santé et de la Recherche Médicale UMR 1163, Paris, France.,Paris Descartes University, Imagine Institute, Paris, France
| | - Priya Luthra
- Department of Microbiology, Global Health and Emerging Pathogens Institute, The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY.,Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Tatiana Kochetkov
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY
| | - Benedetta Bigio
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY
| | - Soraya Boucherit
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Institut National de la Santé et de la Recherche Médicale UMR 1163, Paris, France.,Paris Descartes University, Imagine Institute, Paris, France
| | - Flore Rozenberg
- Virology, Cochin-Saint-Vincent de Paul Hospital, Paris Descartes University, Paris, France
| | - Catherine Vedrinne
- Department of Anesthesia and Intensive Care Medicine in Cardiovascular Surgery, Louis Pradel Cardiological Hospital, Lyon, France
| | - Michael D Keller
- Division of Allergy and Immunology, Center for Cancer and Immunology Research, Children's National Health System, Washington, DC
| | - Yuval Itan
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY.,The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Adolfo García-Sastre
- Department of Microbiology, Global Health and Emerging Pathogens Institute, The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY.,Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Marie Celard
- National Center for Staphylococcus, Lyon Civil Hospital, Lyon, France
| | - Jordan S Orange
- Texas Children's Hospital, Baylor College of Medicine, Houston, TX
| | - Michael J Ciancanelli
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY
| | - Isabelle Meyts
- Laboratory for Inborn Errors of Immunity, Department of Immunology, Microbiology, and Transplantation, Katholieke Universiteit Leuven, Leuven, Belgium.,Department of Pediatrics, University Hospitals Leuven, Leuven, Belgium.,Precision Immunology Institute and Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Qian Zhang
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY
| | - Laurent Abel
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY.,Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Institut National de la Santé et de la Recherche Médicale UMR 1163, Paris, France.,Paris Descartes University, Imagine Institute, Paris, France
| | - Luigi D Notarangelo
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Hans-Willem Snoeck
- Columbia Center for Translational Immunology, Columbia University Medical Center, New York, NY.,Department of Medicine, Columbia University Medical Center, New York, NY
| | - Jean-Laurent Casanova
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY.,Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Institut National de la Santé et de la Recherche Médicale UMR 1163, Paris, France.,Paris Descartes University, Imagine Institute, Paris, France.,Pediatric Immuno-Hematology Unit, Necker Hospital for Sick Children, Assistance Publique-Hôpitaux de Paris, Paris, France.,Howard Hughes Medical Institute, New York, NY
| | - Shen-Ying Zhang
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY .,Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Institut National de la Santé et de la Recherche Médicale UMR 1163, Paris, France.,Paris Descartes University, Imagine Institute, Paris, France
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22
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Stereotypic Immune System Development in Newborn Children. Cell 2019; 174:1277-1292.e14. [PMID: 30142345 PMCID: PMC6108833 DOI: 10.1016/j.cell.2018.06.045] [Citation(s) in RCA: 390] [Impact Index Per Article: 78.0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Revised: 05/18/2018] [Accepted: 06/22/2018] [Indexed: 02/07/2023]
Abstract
Epidemiological data suggest that early life exposures are key determinants of immune-mediated disease later in life. Young children are also particularly susceptible to infections, warranting more analyses of immune system development early in life. Such analyses mostly have been performed in mouse models or human cord blood samples, but these cannot account for the complex environmental exposures influencing human newborns after birth. Here, we performed longitudinal analyses in 100 newborn children, sampled up to 4 times during their first 3 months of life. From 100 μL of blood, we analyze the development of 58 immune cell populations by mass cytometry and 267 plasma proteins by immunoassays, uncovering drastic changes not predictable from cord blood measurements but following a stereotypic pattern. Preterm and term children differ at birth but converge onto a shared trajectory, seemingly driven by microbial interactions and hampered by early gut bacterial dysbiosis. Cord blood is not representative of postnatal immunity Preterm and term children differ at birth but rapidly converge thereafter Immune system development follows a stereotypic pattern early in life Dynamic parameters imply microbial interactions during early immune development
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23
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Fayez EA, Koohini Z, Koohini Z, Zamanzadeh H, de Boer M, Roos D, Teimourian S. Characterization of two novel mutations in IL-12R signaling in MSMD patients. Pathog Dis 2019; 77:ftz030. [PMID: 31158284 DOI: 10.1093/femspd/ftz030] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 05/31/2019] [Indexed: 12/17/2023] Open
Abstract
Mendelian Susceptibility to Mycobacterial Disease (MSMD) is a rare syndrome with infections-among other complications-after Bacillus Calmette-Guerin (BCG) vaccination in children. We focused on the IL-12/IFN-γ pathway to identify new mutations in our patients. This study included 20 patients by vulnerability to mycobacteria and clinical manifestations of severe, recurrent infections. Blood samples were activated with BCG, BCG + IL-12 and BCG + IFN-γ. Cytokine levels were analyzed by ELISA. Measurements of IL-12Rβ1 and IL-12Rβ2 on the surface of peripheral blood mononuclear cells were performed by flow cytometry. To detect genetic defects, next-generation sequencing was performed by Thermo Fisher immunodeficiency panel. Flow cytometry analysis of 20 patients indicated reduction in IL-12R (β1/β2) expression in seven patients who showed incomplete production of IFN-γ by ELISA. In the patient with reduced IL-12 production, IFN-γR and IL-12R (β1/β2) expression levels were normal. Mutation analysis showed three previously reported mutations, two novel mutations in IL-12 R (β1/β2), and one previously reported mutation in IL-12.
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Affiliation(s)
- Elham Alipour Fayez
- Department of Immunology, School of Medicine, Iran University of Medical Sciences Tehran, Iran
| | - Zahra Koohini
- Department of Medical Genetics, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Zohreh Koohini
- Department of Immunology, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Hossein Zamanzadeh
- Department of biology, School of basic sciences, University of Sistan and Balouchestan, Zahedan, Iran
| | - Martin de Boer
- Sanquin Research, and Landsteiner Laboratory, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Dirk Roos
- Sanquin Research, and Landsteiner Laboratory, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Shahram Teimourian
- Department of Medical Genetics, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
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24
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Thaler DS, Head MG, Horsley A. Precision public health to inhibit the contagion of disease and move toward a future in which microbes spread health. BMC Infect Dis 2019; 19:120. [PMID: 30727964 PMCID: PMC6364421 DOI: 10.1186/s12879-019-3715-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2018] [Accepted: 01/10/2019] [Indexed: 12/15/2022] Open
Abstract
Antimicrobial resistance continues to outpace the development of new chemotherapeutics. Novel pathogens continue to evolve and emerge. Public health innovation has the potential to open a new front in the war of "our wits against their genes" (Joshua Lederberg). Dense sampling coupled to next generation sequencing can increase the spatial and temporal resolution of microbial characterization while sensor technologies precisely map physical parameters relevant to microbial survival and spread. Microbial, physical, and epidemiological big data could be combined to improve prospective risk identification. However, applied in the wrong way, these approaches may not realize their maximum potential benefits and could even do harm. Minimizing microbial-human interactions would be a mistake. There is evidence that microbes previously thought of at best "benign" may actually enhance human health. Benign and health-promoting microbiomes may, or may not, spread via mechanisms similar to pathogens. Infectious vaccines are approaching readiness to make enhanced contributions to herd immunity. The rigorously defined nature of infectious vaccines contrasts with indigenous "benign or health-promoting microbiomes" but they may converge. A "microbial Neolithic revolution" is a possible future in which human microbial-associations are understood and managed analogously to the macro-agriculture of plants and animals. Tradeoffs need to be framed in order to understand health-promoting potentials of benign, and/or health-promoting microbiomes and infectious vaccines while also discouraging pathogens. Super-spreaders are currently defined as individuals who play an outsized role in the contagion of infectious disease. A key unanswered question is whether the super-spreader concept may apply similarly to health-promoting microbes. The complex interactions of individual rights, community health, pathogen contagion, the spread of benign, and of health-promoting microbiomes including infectious vaccines require study. Advancing the detailed understanding of heterogeneity in microbial spread is very likely to yield important insights relevant to public health.
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Affiliation(s)
- David S. Thaler
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, CH-4056 Basel, Switzerland
| | - Michael G. Head
- Clinical Informatics Research Unit, Faculty of Medicine, University of Southampton, University Hospital Southampton, Coxford Road, Southampton, SO16 6YD UK
| | - Andrew Horsley
- Research School of Physics and Engineering, The Australian National University, Mills Rd., Canberra, ACT 2601 Australia
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25
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Blacklisting variants common in private cohorts but not in public databases optimizes human exome analysis. Proc Natl Acad Sci U S A 2018; 116:950-959. [PMID: 30591557 DOI: 10.1073/pnas.1808403116] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Computational analyses of human patient exomes aim to filter out as many nonpathogenic genetic variants (NPVs) as possible, without removing the true disease-causing mutations. This involves comparing the patient's exome with public databases to remove reported variants inconsistent with disease prevalence, mode of inheritance, or clinical penetrance. However, variants frequent in a given exome cohort, but absent or rare in public databases, have also been reported and treated as NPVs, without rigorous exploration. We report the generation of a blacklist of variants frequent within an in-house cohort of 3,104 exomes. This blacklist did not remove known pathogenic mutations from the exomes of 129 patients and decreased the number of NPVs remaining in the 3,104 individual exomes by a median of 62%. We validated this approach by testing three other independent cohorts of 400, 902, and 3,869 exomes. The blacklist generated from any given cohort removed a substantial proportion of NPVs (11-65%). We analyzed the blacklisted variants computationally and experimentally. Most of the blacklisted variants corresponded to false signals generated by incomplete reference genome assembly, location in low-complexity regions, bioinformatic misprocessing, or limitations inherent to cohort-specific private alleles (e.g., due to sequencing kits, and genetic ancestries). Finally, we provide our precalculated blacklists, together with ReFiNE, a program for generating customized blacklists from any medium-sized or large in-house cohort of exome (or other next-generation sequencing) data via a user-friendly public web server. This work demonstrates the power of extracting variant blacklists from private databases as a specific in-house but broadly applicable tool for optimizing exome analysis.
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26
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Primary immunodeficiency diseases in a tuberculosis endemic region: challenges and opportunities. Genes Immun 2018; 20:447-454. [PMID: 30185814 DOI: 10.1038/s41435-018-0041-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 06/26/2018] [Accepted: 06/29/2018] [Indexed: 12/11/2022]
Abstract
While individual primary immunodeficiency diseases (PIDs) are rare, collectively they represent a significant burden of disease. Recent estimates show that about one million people in Africa suffer from a PID. However, data from African PID registries reflect only a small percentage of the estimated prevalence. This disparity is partly due to the lack of PID awareness and the masking of PIDs by the endemic pathogens. Over three million tuberculosis (TB) cases were reported in Africa in 2016, with many of these from southern Africa. Despite concerted efforts to address this high burden of disease, the underlying genetic correlates of susceptibility to TB remain poorly understood. High penetrance mutations in immune system genes can cause PIDs that selectively predispose individuals to TB and other mycobacterial diseases. Additionally, the identification of individuals at a heightened risk of developing TB or of presenting with severe or disseminated TB due to their genetic ancestry is crucial to promote a positive treatment outcome. The screening for and identification of PID mutations in TB-endemic regions by next-generation sequencing (NGS) represents a promising approach to improve the understanding of what constitutes an effective immune response to TB, as well as the range of associated PIDs and phenotypes.
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27
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Dallmann-Sauer M, Correa-Macedo W, Schurr E. Human genetics of mycobacterial disease. Mamm Genome 2018; 29:523-538. [PMID: 30116885 PMCID: PMC6132723 DOI: 10.1007/s00335-018-9765-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Accepted: 07/23/2018] [Indexed: 12/18/2022]
Abstract
Mycobacterial diseases are caused by members of the genus Mycobacterium, acid-fast bacteria characterized by the presence of mycolic acids within their cell walls. Claiming almost 2 million lives every year, tuberculosis (TB) is the most common mycobacterial disease and is caused by infection with M. tuberculosis and, in rare cases, by M. bovis or M. africanum. The second and third most common mycobacterial diseases are leprosy and buruli ulcer (BU), respectively. Both diseases affect the skin and can lead to permanent sequelae and deformities. Leprosy is caused by the uncultivable M. leprae while the etiological agent of BU is the environmental bacterium M. ulcerans. After exposure to these mycobacterial species, a majority of individuals will not progress to clinical disease and, among those who do, inter-individual variability in disease manifestation and outcome can be observed. Susceptibility to mycobacterial diseases carries a human genetic component and intense efforts have been applied over the past decades to decipher the exact nature of the genetic factors controlling disease susceptibility. While for BU this search was mostly conducted on the basis of candidate genes association studies, genome-wide approaches have been widely applied for TB and leprosy. In this review, we summarize some of the findings achieved by genome-wide linkage, association and transcriptome analyses in TB disease and leprosy and the recent genetic findings for BU susceptibility.
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Affiliation(s)
- Monica Dallmann-Sauer
- Program in Infectious Diseases and Immunity in Global Health, Research Institute, McGill University Health Centre, Montreal, QC, Canada.,The McGill International TB Centre, McGill University, Montreal, QC, Canada.,Departments of Human Genetics and Medicine, Faculty of Medicine, McGill University, Montreal, QC, Canada
| | - Wilian Correa-Macedo
- Program in Infectious Diseases and Immunity in Global Health, Research Institute, McGill University Health Centre, Montreal, QC, Canada.,The McGill International TB Centre, McGill University, Montreal, QC, Canada.,Department of Biochemistry, Faculty of Medicine, McGill University, Montreal, QC, Canada
| | - Erwin Schurr
- Program in Infectious Diseases and Immunity in Global Health, Research Institute, McGill University Health Centre, Montreal, QC, Canada. .,The McGill International TB Centre, McGill University, Montreal, QC, Canada. .,Departments of Human Genetics and Medicine, Faculty of Medicine, McGill University, Montreal, QC, Canada. .,Department of Biochemistry, Faculty of Medicine, McGill University, Montreal, QC, Canada.
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28
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de Valles-Ibáñez G, Esteve-Solé A, Piquer M, González-Navarro EA, Hernandez-Rodriguez J, Laayouni H, González-Roca E, Plaza-Martin AM, Deyà-Martínez Á, Martín-Nalda A, Martínez-Gallo M, García-Prat M, Del Pino-Molina L, Cuscó I, Codina-Solà M, Batlle-Masó L, Solís-Moruno M, Marquès-Bonet T, Bosch E, López-Granados E, Aróstegui JI, Soler-Palacín P, Colobran R, Yagüe J, Alsina L, Juan M, Casals F. Evaluating the Genetics of Common Variable Immunodeficiency: Monogenetic Model and Beyond. Front Immunol 2018; 9:636. [PMID: 29867916 PMCID: PMC5960686 DOI: 10.3389/fimmu.2018.00636] [Citation(s) in RCA: 106] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 03/14/2018] [Indexed: 12/16/2022] Open
Abstract
Common variable immunodeficiency (CVID) is the most frequent symptomatic primary immunodeficiency characterized by recurrent infections, hypogammaglobulinemia and poor response to vaccines. Its diagnosis is made based on clinical and immunological criteria, after exclusion of other diseases that can cause similar phenotypes. Currently, less than 20% of cases of CVID have a known underlying genetic cause. We have analyzed whole-exome sequencing and copy number variants data of 36 children and adolescents diagnosed with CVID and healthy relatives to estimate the proportion of monogenic cases. We have replicated an association of CVID to p.C104R in TNFRSF13B and reported the second case of homozygous patient to date. Our results also identify five causative genetic variants in LRBA, CTLA4, NFKB1, and PIK3R1, as well as other very likely causative variants in PRKCD, MAPK8, or DOCK8 among others. We experimentally validate the effect of the LRBA stop-gain mutation which abolishes protein production and downregulates the expression of CTLA4, and of the frameshift indel in CTLA4 producing expression downregulation of the protein. Our results indicate a monogenic origin of at least 15–24% of the CVID cases included in the study. The proportion of monogenic patients seems to be lower in CVID than in other PID that have also been analyzed by whole exome or targeted gene panels sequencing. Regardless of the exact proportion of CVID monogenic cases, other genetic models have to be considered for CVID. We propose that because of its prevalence and other features as intermediate penetrancies and phenotypic variation within families, CVID could fit with other more complex genetic scenarios. In particular, in this work, we explore the possibility of CVID being originated by an oligogenic model with the presence of heterozygous mutations in interacting proteins or by the accumulation of detrimental variants in particular immunological pathways, as well as perform association tests to detect association with rare genetic functional variation in the CVID cohort compared to healthy controls.
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Affiliation(s)
- Guillem de Valles-Ibáñez
- Institut de Biologia Evolutiva (UPF-CSIC), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona, Spain
| | - Ana Esteve-Solé
- Allergy and Clinical Immunology Department, Hospital Sant Joan de Déu, Institut de Recerca Pediàtrica Hospital Sant Joan de Déu, Barcelona, Spain.,Functional Unit of Clinical Immunology Hospital Sant Joan de Déu-Hospital Clinic, Barcelona, Spain
| | - Mònica Piquer
- Allergy and Clinical Immunology Department, Hospital Sant Joan de Déu, Institut de Recerca Pediàtrica Hospital Sant Joan de Déu, Barcelona, Spain.,Functional Unit of Clinical Immunology Hospital Sant Joan de Déu-Hospital Clinic, Barcelona, Spain
| | - E Azucena González-Navarro
- Functional Unit of Clinical Immunology Hospital Sant Joan de Déu-Hospital Clinic, Barcelona, Spain.,Servei d'Immunologia, Centre de Diagnòstic Biomèdic, Hospital Clinic-IDIBAPS, Barcelona, Spain
| | - Jessica Hernandez-Rodriguez
- Institut de Biologia Evolutiva (UPF-CSIC), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona, Spain
| | - Hafid Laayouni
- Institut de Biologia Evolutiva (UPF-CSIC), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona, Spain.,Bioinformatics Studies, ESCI-UPF, Barcelona, Spain
| | - Eva González-Roca
- Functional Unit of Clinical Immunology Hospital Sant Joan de Déu-Hospital Clinic, Barcelona, Spain.,Servei d'Immunologia, Centre de Diagnòstic Biomèdic, Hospital Clinic-IDIBAPS, Barcelona, Spain
| | - Ana María Plaza-Martin
- Allergy and Clinical Immunology Department, Hospital Sant Joan de Déu, Institut de Recerca Pediàtrica Hospital Sant Joan de Déu, Barcelona, Spain.,Functional Unit of Clinical Immunology Hospital Sant Joan de Déu-Hospital Clinic, Barcelona, Spain
| | - Ángela Deyà-Martínez
- Allergy and Clinical Immunology Department, Hospital Sant Joan de Déu, Institut de Recerca Pediàtrica Hospital Sant Joan de Déu, Barcelona, Spain.,Functional Unit of Clinical Immunology Hospital Sant Joan de Déu-Hospital Clinic, Barcelona, Spain
| | - Andrea Martín-Nalda
- Pediatric Infectious Diseases and Immunodeficiencies Unit, Hospital Universitari Vall d'Hebron (HUVH), Vall d'Hebron Institut de Recerca (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain.,Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Barcelona, Spain
| | - Mónica Martínez-Gallo
- Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Barcelona, Spain.,Immunology Division, Department of Clinical and Molecular Genetics, Hospital Universitari Vall d'Hebron (HUVH), Vall d'Hebron Research Institute (VHIR), Barcelona, Spain.,Department of Cell Biology, Physiology and Immunology, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Marina García-Prat
- Pediatric Infectious Diseases and Immunodeficiencies Unit, Hospital Universitari Vall d'Hebron (HUVH), Vall d'Hebron Institut de Recerca (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain.,Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Barcelona, Spain
| | - Lucía Del Pino-Molina
- Clinical Immunology Department, University Hospital La Paz and Physiopathology of Lymphocytes in Immunodeficiencies Group, IdiPAZ Institute for Health Research, Madrid, Spain
| | - Ivón Cuscó
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBER-ER), Madrid, Spain
| | - Marta Codina-Solà
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBER-ER), Madrid, Spain
| | - Laura Batlle-Masó
- Institut de Biologia Evolutiva (UPF-CSIC), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona, Spain.,Servei de Genòmica, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona, Spain
| | - Manuel Solís-Moruno
- Institut de Biologia Evolutiva (UPF-CSIC), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona, Spain.,Servei de Genòmica, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona, Spain
| | - Tomàs Marquès-Bonet
- Institut de Biologia Evolutiva (UPF-CSIC), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona, Spain.,Catalan Institution of Research and Advanced Studies (ICREA), Barcelona, Spain.,CNAG-CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Elena Bosch
- Institut de Biologia Evolutiva (UPF-CSIC), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona, Spain
| | - Eduardo López-Granados
- Clinical Immunology Department, University Hospital La Paz and Physiopathology of Lymphocytes in Immunodeficiencies Group, IdiPAZ Institute for Health Research, Madrid, Spain
| | - Juan Ignacio Aróstegui
- Functional Unit of Clinical Immunology Hospital Sant Joan de Déu-Hospital Clinic, Barcelona, Spain.,Servei d'Immunologia, Centre de Diagnòstic Biomèdic, Hospital Clinic-IDIBAPS, Barcelona, Spain
| | - Pere Soler-Palacín
- Pediatric Infectious Diseases and Immunodeficiencies Unit, Hospital Universitari Vall d'Hebron (HUVH), Vall d'Hebron Institut de Recerca (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain.,Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Barcelona, Spain
| | - Roger Colobran
- Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Barcelona, Spain.,Immunology Division, Department of Clinical and Molecular Genetics, Hospital Universitari Vall d'Hebron (HUVH), Vall d'Hebron Research Institute (VHIR), Barcelona, Spain.,Department of Cell Biology, Physiology and Immunology, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Jordi Yagüe
- Functional Unit of Clinical Immunology Hospital Sant Joan de Déu-Hospital Clinic, Barcelona, Spain.,Servei d'Immunologia, Centre de Diagnòstic Biomèdic, Hospital Clinic-IDIBAPS, Barcelona, Spain
| | - Laia Alsina
- Allergy and Clinical Immunology Department, Hospital Sant Joan de Déu, Institut de Recerca Pediàtrica Hospital Sant Joan de Déu, Barcelona, Spain.,Functional Unit of Clinical Immunology Hospital Sant Joan de Déu-Hospital Clinic, Barcelona, Spain
| | - Manel Juan
- Functional Unit of Clinical Immunology Hospital Sant Joan de Déu-Hospital Clinic, Barcelona, Spain.,Servei d'Immunologia, Centre de Diagnòstic Biomèdic, Hospital Clinic-IDIBAPS, Barcelona, Spain
| | - Ferran Casals
- Servei de Genòmica, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona, Spain
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29
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Sologuren I, Martínez-Saavedra MT, Solé-Violán J, de Borges de Oliveira E, Betancor E, Casas I, Oleaga-Quintas C, Martínez-Gallo M, Zhang SY, Pestano J, Colobran R, Herrera-Ramos E, Pérez C, López-Rodríguez M, Ruiz-Hernández JJ, Franco N, Ferrer JM, Bilbao C, Andújar-Sánchez M, Álvarez Fernández M, Ciancanelli MJ, Rodríguez de Castro F, Casanova JL, Bustamante J, Rodríguez-Gallego C. Lethal Influenza in Two Related Adults with Inherited GATA2 Deficiency. J Clin Immunol 2018; 38:513-526. [PMID: 29882021 PMCID: PMC6429553 DOI: 10.1007/s10875-018-0512-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 03/28/2018] [Indexed: 11/18/2022]
Abstract
The pathogenesis of life-threatening influenza A virus (IAV) disease remains elusive, as infection is benign in most individuals. We studied two relatives who died from influenza. We Sanger sequenced GATA2 and evaluated the mutation by gene transfer, measured serum cytokine levels, and analyzed circulating T- and B-cells. Both patients (father and son, P1 and P2) died in 2011 of H1N1pdm IAV infection at the ages of 54 and 31 years, respectively. They had not suffered from severe or moderately severe infections in the last 17 (P1) and 15 years (P2). A daughter of P1 had died at 20 years from infectious complications. Low B-cell, NK- cell, and monocyte numbers and myelodysplastic syndrome led to sequence GATA2. Patients were heterozygous for a novel, hypomorphic, R396L mutation leading to haplo-insufficiency. B- and T-cell rearrangement in peripheral blood from P1 during the influenza episode showed expansion of one major clone. No T-cell receptor excision circles were detected in P1 and P3 since they were 35 and 18 years, respectively. Both patients presented an exuberant, interferon (IFN)-γ-mediated hypercytokinemia during H1N1pdm infection. No data about patients with viremia was available. Two previously reported adult GATA2-deficient patients died from severe H1N1 IAV infection; GATA2 deficiency may predispose to life-threatening influenza in adulthood. However, a role of other genetic variants involved in immune responses cannot be ruled out. Patients with GATA2 deficiency can reach young adulthood without severe infections, including influenza, despite long-lasting complete B-cell and natural killer (NK) cell deficiency, as well as profoundly diminished T-cell thymic output.
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Affiliation(s)
- Ithaisa Sologuren
- Department of Immunology, Gran Canaria Dr. Negrín University Hospital, Las Palmas de Gran Canaria, Spain
| | | | - Jordi Solé-Violán
- Intensive Care Unit, Gran Canaria Dr. Negrín University Hospital, Las Palmas de Gran Canaria, Spain
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Edgar de Borges de Oliveira
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Imagine Institute, Necker Hospital for Sick Children, Paris, France
- Paris Descartes University, Paris, France
| | - Eva Betancor
- Department of Biochemistry, Molecular Biology, Physiology, Genetics and Immunology, School of Medicine, University of Las Palmas de Gran Canaria, Las Palmas de Gran Canaria, Spain
| | - Inmaculada Casas
- National Influenza Center-Madrid, National Center of Microbiology, Instituto de Salud Carlos III, Madrid, Spain
| | - Carmen Oleaga-Quintas
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Imagine Institute, Necker Hospital for Sick Children, Paris, France
- Paris Descartes University, Paris, France
| | | | - Shen-Ying Zhang
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Imagine Institute, Necker Hospital for Sick Children, Paris, France
- Paris Descartes University, Paris, France
- St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, 10065, USA
| | - Jose Pestano
- Department of Biochemistry, Molecular Biology, Physiology, Genetics and Immunology, School of Medicine, University of Las Palmas de Gran Canaria, Las Palmas de Gran Canaria, Spain
| | - Roger Colobran
- Department of Immunology, Vall d'Hebrón University Hospital, Barcelona, Spain
- Department of Cell Biology, Physiology and Immunology, Universitat Autónoma de Barcelona (UAB), Barcelona, Spain
| | - Estefanía Herrera-Ramos
- Department of Immunology, Gran Canaria Dr. Negrín University Hospital, Las Palmas de Gran Canaria, Spain
| | - Carmen Pérez
- Department of Microbiology, Gran Canaria Dr. Negrín University Hospital, Las Palmas de Gran Canaria, Spain
| | - Marta López-Rodríguez
- Department of Immunology, Gran Canaria Dr. Negrín University Hospital, Las Palmas de Gran Canaria, Spain
| | - José Juan Ruiz-Hernández
- Department of Internal Medicine, Gran Canaria Dr. Negrín University Hospital, Las Palmas de Gran Canaria, Spain
| | - Nieves Franco
- Intensive Care Unit, Mostoles University Hospital, Madrid, Spain
| | - José María Ferrer
- Intensive Care Unit, Gran Canaria Dr. Negrín University Hospital, Las Palmas de Gran Canaria, Spain
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Cristina Bilbao
- Department of Hematology, Gran Canaria Dr. Negrín University Hospital, Las Palmas de Gran Canaria, Spain
| | - Miguel Andújar-Sánchez
- Department of Pathology, Complejo Hospitalario Universitario Insular Materno Infantil, Las Palmas de Gran Canaria, Spain
| | | | - Michael J Ciancanelli
- St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, 10065, USA
| | - Felipe Rodríguez de Castro
- Department of Respiratory Diseases, Gran Canaria Dr. Negrín University Hospital, Las Palmas de Gran Canaria, Spain
| | - Jean-Laurent Casanova
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Imagine Institute, Necker Hospital for Sick Children, Paris, France
- Paris Descartes University, Paris, France
- St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, 10065, USA
- Howard Hughes Medical Institute, New York, NY, USA
- Pediatric Hematology-Immunology Unit, Necker Hospital for Sick Children, Paris, France
| | - Jacinta Bustamante
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Imagine Institute, Necker Hospital for Sick Children, Paris, France
- Paris Descartes University, Paris, France
- St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, 10065, USA
- Center for the Study of Primary Immunodeficiencies, Necker Hospital for Sick Children, Paris, France
- Department of Immunology, Hospital Universitario de Gran Canaria Dr. Negrín, Calle Barranco de la Ballena s/n, 35019, Las Palmas de Gran Canaria, Spain
| | - Carlos Rodríguez-Gallego
- Department of Immunology, Gran Canaria Dr. Negrín University Hospital, Las Palmas de Gran Canaria, Spain.
- Department of Immunology, Hospital Universitario de Gran Canaria Dr. Negrín, Calle Barranco de la Ballena s/n, 35019, Las Palmas de Gran Canaria, Spain.
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30
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Zhang X, Huo Q, Sun W, Zhang C, Wu Z, Xing B, Li Q. Rs2910164 in microRNA‑146a confers an elevated risk of depression in patients with coronary artery disease by modulating the expression of NOS1. Mol Med Rep 2018; 18:603-609. [PMID: 29749487 DOI: 10.3892/mmr.2018.8929] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 01/13/2017] [Indexed: 11/06/2022] Open
Abstract
Depression has been well established as an independent predictor of mortality and cardiac morbidity rates in patients with coronary artery disease (CAD). Evidence has shown that single nucleotide polymorphisms located in pre‑microRNA (miRNA) or mature miRNA may modify various biological processes and affect the process of carcinogenesis, and the downregulation of neuronal nitric oxide synthase 1 (NOS1) can induce depression. It has been shown that NOS1 is the target gene of miR‑146a, and that the rs2910164 G/C polymorphism can downregulate the expression of miR‑146a. In the present study, computational analysis was used to identify the target of miR‑146a, and a luciferase reporter assay system was used to validate NOS1 as a target gene of miR‑146a. In addition, U251 cells were treated with miR‑146a mimics/inhibitors to verify the negative regulatory association between miR‑146a and NOS1. Reverse transcription‑quantitative polymerase chain reaction analysis and western blot analysis were used to estimate the mRNA expression of NOS1 and the expression of miR‑146a. The results showed that the 'seed sequence' was located within the 3'‑untranslated region of NOS1 by searching an online miRNA database (www.mirdb.org), and the luciferase reporter assay confirmed that NOS1 was a direct target gene of miR‑146a. It was also found that the mRNA and protein expression levels of NOS1 in U251 cells treated with miR‑146a mimics and NOS1 small interfering RNA were substantially downregulated, compared with cells treated with the scramble control. The cells treated with miR‑146a inhibitors showed increased expression of NOS1. In addition, the presence of a minor allele of the rs2910164 polymorphism was significantly associated with risk of depression in patients with CAD. Taken together, the findings indicated a decreased risk of depression in the patients with CAD who were carriers of the miR‑146a rs2910164 C allele, and this association may be attributed to its ability to compromise the expression of miR‑146a, and thereby increase the expression of its target gene, NOS1.
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Affiliation(s)
- Xinling Zhang
- Department of Cardiology, The First People's Hospital, Jining, Shandong 272011, P.R. China
| | - Qianqian Huo
- Department of Cardiology, The First People's Hospital, Jining, Shandong 272011, P.R. China
| | - Wei Sun
- Department of Cardiology, The First People's Hospital, Jining, Shandong 272011, P.R. China
| | - Chunxiang Zhang
- Department of Cardiology, The First People's Hospital, Jining, Shandong 272011, P.R. China
| | - Zongyin Wu
- Department of Cardiology, The First People's Hospital, Jining, Shandong 272011, P.R. China
| | - Bing Xing
- Department of Cardiology, The First People's Hospital, Jining, Shandong 272011, P.R. China
| | - Qiang Li
- Department of Cardiology, The First People's Hospital, Jining, Shandong 272011, P.R. China
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31
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Casanova JL, Abel L. Human genetics of infectious diseases: Unique insights into immunological redundancy. Semin Immunol 2018; 36:1-12. [PMID: 29254755 PMCID: PMC5910248 DOI: 10.1016/j.smim.2017.12.008] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 12/13/2017] [Indexed: 01/18/2023]
Abstract
For almost any given human-tropic virus, bacterium, fungus, or parasite, the clinical outcome of primary infection is enormously variable, ranging from asymptomatic to lethal infection. This variability has long been thought to be largely determined by the germline genetics of the human host, and this is increasingly being demonstrated to be the case. The number and diversity of known inborn errors of immunity is continually increasing, and we focus here on autosomal and X-linked recessive traits underlying complete deficiencies of the encoded protein. Schematically, four types of infectious phenotype have been observed in individuals with such deficiencies, each providing information about the redundancy of the corresponding human gene, in terms of host defense in natural conditions. The lack of a protein can confer vulnerability to a broad range of microbes in most, if not all patients, through the disruption of a key immunological component. In such cases, the gene concerned is of low redundancy. However, the lack of a protein may also confer vulnerability to a narrow range of microbes, sometimes a single pathogen, and not necessarily in all patients. In such cases, the gene concerned is highly redundant. Conversely, the deficiency may be apparently neutral, conferring no detectable predisposition to infection in any individual. In such cases, the gene concerned is completely redundant. Finally, the lack of a protein may, paradoxically, be advantageous to the host, conferring resistance to one or more infections. In such cases, the gene is considered to display beneficial redundancy. These findings reflect the current state of evolution of humans and microbes, and should not be considered predictive of redundancy, or of a lack of redundancy, in the distant future. Nevertheless, these observations are of potential interest to present-day biologists testing immunological hypotheses experimentally and physicians managing patients with immunological or infectious conditions.
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Affiliation(s)
- Jean-Laurent Casanova
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA; Howard Hughes Medical Institute, New York, NY, USA; Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Inserm U1163, Necker Hospital for Sick Children, Paris, France, EU; Paris Descartes University, Imagine Institute, Paris, France, EU; Pediatric Hematology and Immunology Unit, Necker Hospital for Sick Children, Paris, France, EU.
| | - Laurent Abel
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA; Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Inserm U1163, Necker Hospital for Sick Children, Paris, France, EU; Paris Descartes University, Imagine Institute, Paris, France, EU.
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32
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Abel L, Fellay J, Haas DW, Schurr E, Srikrishna G, Urbanowski M, Chaturvedi N, Srinivasan S, Johnson DH, Bishai WR. Genetics of human susceptibility to active and latent tuberculosis: present knowledge and future perspectives. THE LANCET. INFECTIOUS DISEASES 2018; 18:e64-e75. [DOI: 10.1016/s1473-3099(17)30623-0] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Revised: 01/18/2017] [Accepted: 01/27/2017] [Indexed: 02/07/2023]
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33
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Song Y, Laureijssen-van de Sande WWJ, Moreno LF, Gerrits van den Ende B, Li R, de Hoog S. Comparative Ecology of Capsular Exophiala Species Causing Disseminated Infection in Humans. Front Microbiol 2017; 8:2514. [PMID: 29312215 PMCID: PMC5742258 DOI: 10.3389/fmicb.2017.02514] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 12/04/2017] [Indexed: 12/15/2022] Open
Abstract
Exophiala spinifera and Exophiala dermatitidis (Fungi: Chaetothyriales) are black yeast agents potentially causing disseminated infection in apparently healthy humans. They are the only Exophiala species producing extracellular polysaccharides around yeast cells. In order to gain understanding of eventual differences in intrinsic virulence of the species, their clinical profiles were compared and found to be different, suggesting pathogenic strategies rather than coincidental opportunism. Ecologically relevant factors were compared in a model set of strains of both species, and significant differences were found in clinical and environmental preferences, but virulence, tested in Galleria mellonella larvae, yielded nearly identical results. Virulence factors, i.e., melanin, capsule and muriform cells responded in opposite direction under hydrogen peroxide and temperature stress and thus were inconsistent with their hypothesized role in survival of phagocytosis. On the basis of physiological profiles, possible natural habitats of both species were extrapolated, which proved to be environmental rather than animal-associated. Using comparative genomic analyses we found differences in gene content related to lipid metabolism, cell wall modification and polysaccharide capsule production. Despite the fact that both species cause disseminated infections in apparently healthy humans, it is concluded that they are opportunists rather than pathogens.
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Affiliation(s)
- Yinggai Song
- Department of Dermatology, Peking University First Hospital, Beijing, China.,Research Center for Medical Mycology, Peking University, Beijing, China.,Beijing Key Laboratory of Molecular Diagnosis of Dermatoses, Peking University First Hospital, Beijing, China.,Westerdijk Fungal Biodiversity Institute, Utrecht, Netherlands
| | | | | | | | - Ruoyu Li
- Department of Dermatology, Peking University First Hospital, Beijing, China.,Research Center for Medical Mycology, Peking University, Beijing, China.,Beijing Key Laboratory of Molecular Diagnosis of Dermatoses, Peking University First Hospital, Beijing, China
| | - Sybren de Hoog
- Westerdijk Fungal Biodiversity Institute, Utrecht, Netherlands.,Center of Expertise in Mycology Radboudumc/CWZ, Radboud University Nijmegen Medical Center, Nijmegen, Netherlands
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34
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Inborn errors of immunity underlying fungal diseases in otherwise healthy individuals. Curr Opin Microbiol 2017; 40:46-57. [PMID: 29128761 DOI: 10.1016/j.mib.2017.10.016] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 10/20/2017] [Indexed: 01/02/2023]
Abstract
It has been estimated that there are at least 1.5 million fungal species, mostly present in the environment, but only a few of these fungi cause human disease. Most fungal diseases are self-healing and benign, but some are chronic or life-threatening. Acquired and inherited defects of immunity, including breaches of mucocutaneous barriers and circulating leukocyte deficiencies, account for most severe modern-day mycoses. Other types of infection typically accompany these fungal infections. More rarely, severe fungal diseases can strike otherwise healthy individuals. Historical reports of fungi causing chronic peripheral infections (e.g. affecting the nails, skin, hair), and invasive diseases (e.g. brain, lungs, liver), in otherwise healthy patients, can be traced back to the mid-20th century. These fungi typically cause endemic, but not epidemic diseases, are more likely to underlie sporadic than familial cases, and only threaten a small proportion of infected individuals. The basis of this 'idiosyncratic' susceptibility has long remained unexplained, but it has recently become apparent that 'idiopathic' fungal diseases, in children, teenagers, and even adults, may be caused by single-gene inborn errors of immunity. The study of these unusual primary immunodeficiencies (PIDs) has led to the identification of molecules and cells playing a crucial role in human host defenses against certain fungi at particular anatomic sites. A picture is emerging of inborn errors of IL-17 immunity selectively underlying chronic mucocutaneous candidiasis, with little inter-individual variability, and of inborn errors of CARD9 immunity underlying various life-threatening invasive fungal diseases, differing between patients.
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35
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Pathogenesis of infections in HIV-infected individuals: insights from primary immunodeficiencies. Curr Opin Immunol 2017; 48:122-133. [PMID: 28992464 PMCID: PMC5682227 DOI: 10.1016/j.coi.2017.09.002] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Revised: 09/14/2017] [Accepted: 09/17/2017] [Indexed: 12/12/2022]
Abstract
Following infection with almost any given microorganism other than an emerging pathogen, only a minority of individuals develop life-threatening clinical disease, implying that these individuals have some form of immunodeficiency. A growing number of inherited and acquired immunodeficiencies have been deciphered over the last 50 years. HIV infection is probably the best-known acquired immunodeficiency. It emerged about 40 years ago and precipitates various severe infections, the occurrence of which is associated with a fall in circulating CD4+ T cells. However, despite the strength of this correlation, infection rates differ between patients with similar levels and durations of CD4+ T lymphopenia in the presence or absence of antiretroviral treatment. Moreover, a few infections seem to be less dependent on total CD4+ T-cell levels. The fine detail of the mechanisms underlying these infections is unknown. We discuss here how studies of the human genetics and immunology of some of these infections in patients with primary immunodeficiencies (PIDs) have provided unique insights into their molecular and cellular basis. Defects of specific CD4+ Th-cell subsets account for some of these infections, as best exemplified by Th1* for mycobacteriosis and Th17 for candidiasis. PIDs are individually rare, but collectively much more common than initially thought, with new disorders being discovered at an ever-increasing pace and a global prevalence worldwide approaching that of HIV infection. Studies of known and new PIDs should make it possible to dissect the pathogenesis of most human infections at an unprecedented level of molecular and cellular precision. The predictive, preventive, and therapeutic implications of studies of immunity to infection in PIDs may extend to HIV-infected patients and patients with infectious diseases in other settings.
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36
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Orlova M, Schurr E. Human Genomics of Mycobacterium tuberculosis Infection and Disease. CURRENT GENETIC MEDICINE REPORTS 2017; 5:125-131. [PMID: 29201558 DOI: 10.1007/s40142-017-0124-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Purpose of review The study of the genetic basis of tuberculosis pathogenesis has benefited from powerful technological innovations, a more structured definition of latent and clinical manifestations of the disease, and the application of functional genomics approaches. This short review aims to summarize recent advances and to provide a link with results of previous human genetic studies of tuberculosis susceptibility. Recent findings Transcriptomics has been shown to be a useful tool to predict progression from latency to clinical disease while functional genomics has traced the molecular events that link pathogen-triggered gene expression and host genetics. Resistance to infection with Mycobacterium tuberculosis has been revealed to be strongly impacted by host genetics. Host genomics of clinical disease has been shown to be most powerful when focusing on carefully selected clinical entities and possibly by considering host pathogen combinations. Summary Future studies need to build on the latest molecular findings to define disease subtypes to successfully elucidate the human genetic component in tuberculosis pathogenesis.
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Affiliation(s)
- Marianna Orlova
- Program in Infectious Diseases and Immunity in Global Health, The Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada.,McGill International TB Centre, McGill University, Montreal, Quebec, Canada.,Departments of Medicine and Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Erwin Schurr
- Program in Infectious Diseases and Immunity in Global Health, The Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada.,McGill International TB Centre, McGill University, Montreal, Quebec, Canada.,Departments of Medicine and Human Genetics, McGill University, Montreal, Quebec, Canada
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37
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Thaler DS, Stoeckle MY. Bridging two scholarly islands enriches both: COI DNA barcodes for species identification versus human mitochondrial variation for the study of migrations and pathologies. Ecol Evol 2017; 6:6824-6835. [PMID: 28725363 PMCID: PMC5513234 DOI: 10.1002/ece3.2394] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Revised: 07/19/2016] [Accepted: 08/01/2016] [Indexed: 11/08/2022] Open
Abstract
DNA barcodes for species identification and the analysis of human mitochondrial variation have developed as independent fields even though both are based on sequences from animal mitochondria. This study finds questions within each field that can be addressed by reference to the other. DNA barcodes are based on a 648-bp segment of the mitochondrially encoded cytochrome oxidase I. From most species, this segment is the only sequence available. It is impossible to know whether it fairly represents overall mitochondrial variation. For modern humans, the entire mitochondrial genome is available from thousands of healthy individuals. SNPs in the human mitochondrial genome are evenly distributed across all protein-encoding regions arguing that COI DNA barcode is representative. Barcode variation among related species is largely based on synonymous codons. Data on human mitochondrial variation support the interpretation that most - possibly all - synonymous substitutions in mitochondria are selectively neutral. DNA barcodes confirm reports of a low variance in modern humans compared to nonhuman primates. In addition, DNA barcodes allow the comparison of modern human variance to many other extant animal species. Birds are a well-curated group in which DNA barcodes are coupled with census and geographic data. Putting modern human variation in the context of intraspecies variation among birds shows humans to be a single breeding population of average variance.
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Affiliation(s)
- David S Thaler
- Biozentrum University of Basel CH 4056 Basel Switzerland
| | - Mark Y Stoeckle
- Program for the Human Environment The Rockefeller University New York New York 10065
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38
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Quach H, Quintana-Murci L. Living in an adaptive world: Genomic dissection of the genus Homo and its immune response. J Exp Med 2017; 214:877-894. [PMID: 28351985 PMCID: PMC5379985 DOI: 10.1084/jem.20161942] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2016] [Revised: 02/14/2017] [Accepted: 03/06/2017] [Indexed: 12/14/2022] Open
Abstract
More than a decade after the sequencing of the human genome, a deluge of genome-wide population data are generating a portrait of human genetic diversity at an unprecedented level of resolution. Genomic studies have provided new insight into the demographic and adaptive history of our species, Homo sapiens, including its interbreeding with other hominins, such as Neanderthals, and the ways in which natural selection, in its various guises, has shaped genome diversity. These studies, combined with functional genomic approaches, such as the mapping of expression quantitative trait loci, have helped to identify genes, functions, and mechanisms of prime importance for host survival and involved in phenotypic variation and differences in disease risk. This review summarizes new findings in this rapidly developing field, focusing on the human immune response. We discuss the importance of defining the genetic and evolutionary determinants driving immune response variation, and highlight the added value of population genomic approaches in settings relevant to immunity and infection.
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Affiliation(s)
- Hélène Quach
- Human Evolutionary Genetics Unit, Department of Genomes and Genetics, Institut Pasteur, 75015 Paris, France.,Center of Bioinformatics, Biostatistics and Integrative Biology, Institut Pasteur, 75015 Paris, France.,Centre National de la Recherche Scientifique, URA3012, 75015 Paris, France
| | - Lluis Quintana-Murci
- Human Evolutionary Genetics Unit, Department of Genomes and Genetics, Institut Pasteur, 75015 Paris, France .,Center of Bioinformatics, Biostatistics and Integrative Biology, Institut Pasteur, 75015 Paris, France.,Centre National de la Recherche Scientifique, URA3012, 75015 Paris, France
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39
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Borghesi A, Stronati M, Fellay J. Neonatal Group B Streptococcal Disease in Otherwise Healthy Infants: Failure of Specific Neonatal Immune Responses. Front Immunol 2017; 8:215. [PMID: 28326082 PMCID: PMC5339282 DOI: 10.3389/fimmu.2017.00215] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 02/15/2017] [Indexed: 12/26/2022] Open
Abstract
Only a small proportion of newborn infants exposed to a pathogenic microorganism develop overt infection. Susceptibility to infection in preterm infants and infants with known comorbidities has a likely multifactorial origin and can be often attributed to the concurrence of iatrogenic factors, environmental determinants, underlying pathogenic processes, and probably genetic predisposition. Conversely, infection occurring in otherwise healthy full-term newborn infants is unexplained in most cases. Microbial virulence factors and the unique characteristics of the neonatal immune system only partially account for the interindividual variability in the neonatal immune responses to pathogens. We here suggest that neonatal infection occurring in otherwise healthy infants is caused by a failure of the specific protective immunity to the microorganism. To explain infection in term and preterm infants, we propose an extension of the previously proposed model of the genetic architecture of infectious diseases in humans. We then focus on group B streptococcus (GBS) disease, the best characterized neonatal infection, and outline the potential molecular mechanisms underlying the selective failure of the immune responses against GBS. In light of the recent discoveries of pathogen-specific primary immunodeficiencies and of the role of anticytokine autoantibodies in increasing susceptibility to specific infections, we hypothesize that GBS disease occurring in otherwise healthy infants could reflect an immunodeficiency caused either by rare genetic defects in the infant or by transmitted maternal neutralizing antibodies. These hypotheses are consistent with available epidemiological data, with clinical and epidemiological observations, and with the state of the art of neonatal physiology and disease. Studies should now be designed to comprehensively search for genetic or immunological factors involved in susceptibility to severe neonatal infections.
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Affiliation(s)
- Alessandro Borghesi
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Neonatal Intensive Care Unit, San Matteo Hospital, Pavia, Italy
| | - Mauro Stronati
- Neonatal Intensive Care Unit, San Matteo Hospital, Pavia, Italy
| | - Jacques Fellay
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
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40
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Gelemanović A, Dobberpuhl K, Krakar G, Patarčić I, Kolčić I, Polašek O. Host genetics and susceptibility to congenital and childhood cytomegalovirus infection: a systematic review. Croat Med J 2017; 57:321-30. [PMID: 27586547 PMCID: PMC5048223 DOI: 10.3325/cmj.2016.57.321] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Aim To summarize available evidence on the role of host genetics in the susceptibility to congenital and childhood cytomegalovirus (CMV) infections by conducting a systematic review of published studies. Methods We searched online databases (PubMed, Web of Science, Scopus and HuGe Navigator) for relevant studies with well-defined inclusion and exclusion criteria and assessed the risk of bias using novel Confounding-Selection-Information bias score (CSI). Results 5105 studies were initially identified, but only 5 met all the inclusion criteria and were analyzed in detail. Polymorphisms of the toll-like receptors (TLRs) and mannose-binding lectin (MBL) genes were shown to have an impact on the CMV infection in infants. Polymorphisms of the TLR2 (rs3804100, rs1898830), TLR4 (rs4986791), and TLR9 (rs352140) were shown to have a role in congenital CMV infection. Low MBL levels were associated with CMV infection in Chinese individuals, a finding that was not replicated in Caucasians. The overall credibility of evidence was weak. Conclusions Based on currently available very limited amount of evidence, it is uncertain whether congenital and childhood CMV infections are under host genetic control. Additional primary studies are needed with more specific research hypotheses that will enable gradual understanding of specific mechanisms of the CMV pathogenesis. More genetic studies in the future will facilitate better understanding of host susceptibility and likely enable novel preventative and curative measures.
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Affiliation(s)
| | | | | | | | | | - Ozren Polašek
- Ozren Polašek, School of Medicine, University of Split, Šoltanska 2, 21000 Split, Croatia,
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41
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Fava VM, Sales-Marques C, Alcaïs A, Moraes MO, Schurr E. Age-Dependent Association of TNFSF15/ TNFSF8 Variants and Leprosy Type 1 Reaction. Front Immunol 2017; 8:155. [PMID: 28261213 PMCID: PMC5306391 DOI: 10.3389/fimmu.2017.00155] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 01/30/2017] [Indexed: 11/21/2022] Open
Abstract
A current major challenge in leprosy control is the prevention of permanent disabilities. Host pathological inflammatory responses termed type 1 reaction (T1R) are a leading cause of nerve damage for leprosy patients. The environmental or inherited factors that predispose leprosy cases to undergo T1R are not known. However, studies have shown an important contribution of host genetics for susceptibility to T1R. We have previously identified variants encompassing the TNFSF15/TNFSF8 genes as T1R risk factors in a Vietnamese sample and replicated this association in a Brazilian sample. However, we failed to validate in Brazilian patients the strong association of TNFSF15/TNFSF8 markers rs6478108 and rs7863183 with T1R that we had observed in Vietnamese patients. Here, we investigated if the lack of validation of these variants was due to age-dependent effects on association using four independent population samples, two from Brazil and two from Vietnam. In the combined analysis across the four samples, we observed a strong association of the TNFSF15/TNFSF8 variants rs6478108, rs7863183, and rs3181348 with T1R (pcombined = 1.5E−05, pcombined = 1.8E−05, and pcombined = 6.5E−06, respectively). However, the association of rs6478108 with T1R was more pronounced in leprosy cases under 30 years of age compared to the global sample [odds ratio (OR) = 1.95, 95% confidence interval (CI) = 1.54–2.46, pcombined = 2.5E−08 versus OR = 1.46, 95% CI = 1.23–1.73, pcombined = 1.5E−05]. A multivariable analysis indicated that the association of rs6478108 with T1R was independent of either rs7863183 or rs3181348. These three variants are known regulators of the TNFSF8 gene transcription level in multiple tissues. The age dependency of association of rs6478108 and T1R suggests that the genetic control of gene expression varies across the human life span.
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Affiliation(s)
- Vinicius M Fava
- Program in Infectious Diseases and Immunity in Global Health, Research Institute of the McGill University Health Centre, Montreal, QC, Canada; The McGill International TB Centre, Department of Human Genetics, McGill University, Montreal, QC, Canada
| | | | - Alexandre Alcaïs
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Institut National de la Santé et de la Recherche Médicale U1163, Paris, France; Imagine Institute, University Paris Descartes, Paris, France; Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY, USA
| | - Milton O Moraes
- Laboratório de Hanseníase, Instituto Oswaldo Cruz, FIOCRUZ , Rio de Janeiro , Brazil
| | - Erwin Schurr
- Program in Infectious Diseases and Immunity in Global Health, Research Institute of the McGill University Health Centre, Montreal, QC, Canada; The McGill International TB Centre, Department of Human Genetics, McGill University, Montreal, QC, Canada; Department of Medicine, McGill University, Montreal, QC, Canada
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42
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Garaeva AF, Babushkina NP, Rudko AA, Goncharova IA, Bragina EY, Freidin MB. Differential genetic background of primary and secondary tuberculosis in Russians. Meta Gene 2017. [DOI: 10.1016/j.mgene.2016.10.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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43
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Abstract
The human immune system is highly variable between individuals but relatively stable over time within a given person. Recent conceptual and technological advances have enabled systems immunology analyses, which reveal the composition of immune cells and proteins in populations of healthy individuals. The range of variation and some specific influences that shape an individual's immune system is now becoming clearer. Human immune systems vary as a consequence of heritable and non-heritable influences, but symbiotic and pathogenic microbes and other non-heritable influences explain most of this variation. Understanding when and how such influences shape the human immune system is key for defining metrics of immunological health and understanding the risk of immune-mediated and infectious diseases.
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Affiliation(s)
- Petter Brodin
- Science for Life Laboratory, Department of Medicine, Solna, Karolinska Institutet, Stockholm 17165, Sweden.,Department of Neonatology, Karolinska University Hospital, Stockholm 14186, Sweden
| | - Mark M Davis
- Department of Microbiology and Immunology, Stanford University School of Medicine.,Institute of Immunity, Transplantation and Infection, Stanford University School of Medicine.,Howard Hughes Medical Institute, Stanford University School of Medicine, California 94304, USA
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44
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Abstract
The wealth of available genetic information is allowing the reconstruction of human demographic and adaptive history. Demography and purifying selection affect the purge of rare, deleterious mutations from the human population, whereas positive and balancing selection can increase the frequency of advantageous variants, improving survival and reproduction in specific environmental conditions. In this review, I discuss how theoretical and empirical population genetics studies, using both modern and ancient DNA data, are a powerful tool for obtaining new insight into the genetic basis of severe disorders and complex disease phenotypes, rare and common, focusing particularly on infectious disease risk.
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Affiliation(s)
- Lluis Quintana-Murci
- Human Evolutionary Genetics Unit, Department of Genomes & Genetics, Institut Pasteur, Paris, 75015, France.
- Centre National de la Recherche Scientifique, URA3012, Paris, 75015, France.
- Center of Bioinformatics, Biostatistics and Integrative Biology, Institut Pasteur, Paris, 75015, France.
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45
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Meyts I, Bosch B, Bolze A, Boisson B, Itan Y, Belkadi A, Pedergnana V, Moens L, Picard C, Cobat A, Bossuyt X, Abel L, Casanova JL. Exome and genome sequencing for inborn errors of immunity. J Allergy Clin Immunol 2016; 138:957-969. [PMID: 27720020 PMCID: PMC5074686 DOI: 10.1016/j.jaci.2016.08.003] [Citation(s) in RCA: 138] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 08/22/2016] [Accepted: 08/23/2016] [Indexed: 01/03/2023]
Abstract
The advent of next-generation sequencing (NGS) in 2010 has transformed medicine, particularly the growing field of inborn errors of immunity. NGS has facilitated the discovery of novel disease-causing genes and the genetic diagnosis of patients with monogenic inborn errors of immunity. Whole-exome sequencing (WES) is presently the most cost-effective approach for research and diagnostics, although whole-genome sequencing offers several advantages. The scientific or diagnostic challenge consists in selecting 1 or 2 candidate variants among thousands of NGS calls. Variant- and gene-level computational methods, as well as immunologic hypotheses, can help narrow down this genome-wide search. The key to success is a well-informed genetic hypothesis on 3 key aspects: mode of inheritance, clinical penetrance, and genetic heterogeneity of the condition. This determines the search strategy and selection criteria for candidate alleles. Subsequent functional validation of the disease-causing effect of the candidate variant is critical. Even the most up-to-date dry lab cannot clinch this validation without a seasoned wet lab. The multifariousness of variations entails an experimental rigor even greater than traditional Sanger sequencing-based approaches in order not to assign a condition to an irrelevant variant. Finding the needle in the haystack takes patience, prudence, and discernment.
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Affiliation(s)
- Isabelle Meyts
- Department of Immunology and Microbiology, Childhood Immunology, Department of Pediatrics, University Hospitals Leuven and KU Leuven, Leuven, Belgium.
| | - Barbara Bosch
- Department of Pediatrics, University Hospitals Leuven and KU Leuven, Leuven, Belgium; St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY
| | - Alexandre Bolze
- St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY; Helix, San Carlos, Calif
| | - Bertrand Boisson
- St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY; Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France; Paris Descartes University, Imagine Institute, Paris, France
| | - Yuval Itan
- St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY
| | - Aziz Belkadi
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France; Paris Descartes University, Imagine Institute, Paris, France
| | - Vincent Pedergnana
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France; Paris Descartes University, Imagine Institute, Paris, France; Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Leen Moens
- Laboratory Medicine, Experimental Laboratory Immunology, Department of Laboratory Medicine, University Hospitals Leuven and KU Leuven, Leuven, Belgium
| | - Capucine Picard
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France; Paris Descartes University, Imagine Institute, Paris, France; Paris Descartes University-Sorbonne Paris Cité, Paris, France; Study Center for Immunodeficiency, Necker-Enfants Malades Hospital, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Aurélie Cobat
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France; Paris Descartes University, Imagine Institute, Paris, France
| | - Xavier Bossuyt
- Laboratory Medicine, Experimental Laboratory Immunology, Department of Laboratory Medicine, University Hospitals Leuven and KU Leuven, Leuven, Belgium
| | - Laurent Abel
- St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY; Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France; Paris Descartes University, Imagine Institute, Paris, France
| | - Jean-Laurent Casanova
- St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY; Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France; Paris Descartes University, Imagine Institute, Paris, France; Howard Hughes Medical Institute, New York, NY; Pediatric Hematology and Immunology Unit, Assistance Publique-Hôpitaux de Paris, Necker Hospital for Sick Children, Paris, France
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46
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Kumar P. Adult pulmonary tuberculosis as a pathological manifestation of hyperactive antimycobacterial immune response. Clin Transl Med 2016; 5:38. [PMID: 27709522 PMCID: PMC5052244 DOI: 10.1186/s40169-016-0119-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 09/09/2016] [Indexed: 12/21/2022] Open
Abstract
The intricate relationship between tuberculosis (TB) and immune system remains poorly understood. It is generally believed that weakening of the immune response against Mycobacterium tuberculosis leads to reactivation of latent infection into the active pulmonary disease. However, heterogeneous nature of TB and failure of rationally designed vaccines in clinical trials raises serious questions against the simplistic view of TB as an outcome of weakened immunity. In the wake of accumulating human TB data, it is argued here that a hyperactive antimycobacterial immune response is to blame for the pathogenesis of pulmonary TB in immunocompetent adults. Direct and indirect evidence supporting this notion is presented in this article. Revisiting the role of immune system in TB pathogenesis will pave the way for effective anti-TB vaccines.
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Affiliation(s)
- Pawan Kumar
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Mehrauli Road, New Delhi, 110067, India.
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47
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Interferon-Gamma Improves Macrophages Function against M. tuberculosis in Multidrug-Resistant Tuberculosis Patients. CHEMOTHERAPY RESEARCH AND PRACTICE 2016; 2016:7295390. [PMID: 27478636 PMCID: PMC4960331 DOI: 10.1155/2016/7295390] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2016] [Accepted: 06/14/2016] [Indexed: 01/04/2023]
Abstract
Background. Mycobacterium tuberculosis (M. tuberculosis) that causes tuberculosis (TB) kills millions of infected people annually especially multidrug-resistant tuberculosis (MDR-TB). On infection, macrophages recognize the mycobacteria by toll-like receptor (TLR) followed by phagocytosis and control of mycobacteria. In addition, macrophages also secrete IL-12 to induce IFN-γ production by T, which, in turn, increases the phagocytosis and oxidative burst. Individuals with defects in innate or adaptive immunity exhibit increased susceptibility to M. tuberculosis. Understanding these immunologic mechanisms will help in TB control. We aimed to investigate the immunopathologic mechanisms in MDR-TB and role of recombinant human interferon-gamma (rhIFN-γ). Study Design and Methods. Monocyte-derived macrophages (MDMs) were generated from peripheral blood mononuclear cells of MDR-TB patients and healthy subjects and were investigated for immunologic response by ELISA and flow cytometry. Results. Different functional and molecular anomalies were observed in macrophages. In addition, a defective immune response to M. tuberculosis from the patient's MDMs was characterized, which in turn improved by pretreatment with rhIFN-γ. Conclusion. This work highlights the fact that rhIFN-γ improves macrophages function against M. tuberculosis and treatment of patients with poor responsiveness to TB therapy may be needed in future to include IFN-γ as adjuvant therapy after the full characterization of pathological and molecular mechanisms in these and in other more multidrug-resistant TB patients.
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48
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Quintana-Murci L. Genetic and epigenetic variation of human populations: An adaptive tale. C R Biol 2016; 339:278-83. [PMID: 27185590 DOI: 10.1016/j.crvi.2016.04.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Accepted: 04/12/2016] [Indexed: 01/27/2023]
Abstract
The evolutionary history of modern humans means much more than their demographic past. It includes the way in which humans have had to genetically adapt to the different environments they have encountered-nutritional, climatic or pathogenic-as well as the different epigenetic responses elicited by such environmental cues. Detecting how natural selection has affected human genome variability has proven to be a powerful tool to delineate genes and biological functions having played a key role in human adaptation, a variation which can also be involved in phenotypes of medical relevance. This article reviews several examples that illustrate well how different environmental pressures, particularly those imposed by pathogens and infectious diseases, have shaped the patterns of genetic and epigenetic variability currently observed in human populations.
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Affiliation(s)
- Lluis Quintana-Murci
- Unit of Human Evolutionary Genetics, CNRS URA3012, Institut Pasteur, 25-28, rue du Docteur-Roux, 75015 Paris, France.
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49
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Nakauchi A, Wong JH, Mahasirimongkol S, Yanai H, Yuliwulandari R, Mabuchi A, Liu X, Mushiroda T, Wattanapokayakit S, Miyagawa T, Keicho N, Tokunaga K. Identification of ITPA on chromosome 20 as a susceptibility gene for young-onset tuberculosis. Hum Genome Var 2016; 3:15067. [PMID: 27081565 PMCID: PMC4760120 DOI: 10.1038/hgv.2015.67] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Revised: 10/30/2015] [Accepted: 11/04/2015] [Indexed: 01/31/2023] Open
Abstract
Tuberculosis (TB) is a complex disease, and both genetic and environmental factors contribute to disease progression. A previous genome-wide linkage study in Thailand determined that chromosome 20p13-12.3 may contain risk factors for young-onset disease. The present study aimed to identify novel susceptibility genes for young-onset TB within a 1-Mbp target region adjacent to the top-ranking risk marker in Chr.20p13-12.3. We performed next-generation sequencing (NGS) of the region in 13 young patients from multi-case families in Thailand. We then selected the functionally interesting single-nucleotide polymorphisms as candidates for subsequent analyses. The detected candidates rs13830 and rs1127354 in ITPA showed an association with young (<45 years old) TB patients. However, there was no association in old (⩾45 years old) patients. These findings confirm that stratifying patients based on age of TB onset can be important for identifying genetic risk factors for TB susceptibility. In addition, in silico expression quantitative trait loci analyses indicated that ITPA expression was associated with rs13830 genotype. This is the first study to use NGS resequencing to gain insight into host genetic factors associated with TB and to report a significant association for ITPA with host susceptibility in young-onset TB. The study also demonstrated the effectiveness of NGS in identifying susceptibility genes in common diseases.
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Affiliation(s)
- Ayaka Nakauchi
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo , Tokyo, Japan
| | - Jing Hao Wong
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo , Tokyo, Japan
| | - Surakameth Mahasirimongkol
- Medical Genetics Center, Medical Life Sciences Institute, Department of Medical Sciences, Ministry of Public Health , Nonthaburi, Thailand
| | - Hideki Yanai
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan; Fukujuji Hospital, Japan Anti-Tuberculosis Association (JATA), Tokyo, Japan
| | - Rika Yuliwulandari
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan; Genomic Medicine Research Group, YARSI Research Institute, YARSI University, Jakarta, Indonesia
| | - Akihiko Mabuchi
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo , Tokyo, Japan
| | - Xiaoxi Liu
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan; RIKEN Brain Science Institute, Saitama, Japan
| | - Taisei Mushiroda
- Research Group for Pharmacogenomics, RIKEN Center for Integrative Medical Sciences , Kanagawa, Japan
| | - Sukanya Wattanapokayakit
- Medical Genetics Center, Medical Life Sciences Institute, Department of Medical Sciences, Ministry of Public Health , Nonthaburi, Thailand
| | - Taku Miyagawa
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo , Tokyo, Japan
| | - Naoto Keicho
- Department of Pathophysiology and Host Defense, The Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association (JATA) , Tokyo, Japan
| | - Katsushi Tokunaga
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo , Tokyo, Japan
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50
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Milano M, Moraes MO, Rodenbusch R, Carvalho CX, Delcroix M, Mousquer G, Laux da Costa L, Unis G, Dalla Costa ER, Rossetti MLR. Single Nucleotide Polymorphisms in IL17A and IL6 Are Associated with Decreased Risk for Pulmonary Tuberculosis in Southern Brazilian Population. PLoS One 2016; 11:e0147814. [PMID: 26840977 PMCID: PMC4740512 DOI: 10.1371/journal.pone.0147814] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Accepted: 01/08/2016] [Indexed: 12/12/2022] Open
Abstract
In Mycobacterium tuberculosis (MTB) infection, the complex interaction of host immune system and the mycobacteria is associated with levels of cytokines production that play a major role in determining the outcome of the disease. Several single-nucleotide polymorphisms (SNPs) in cytokine genes have been associated with tuberculosis (TB) outcome. The aim of this study was to evaluate the association between previously reported SNPs IL2–330 T>G (rs2069762); IL4–590 C>T (rs2243250); IL6–174 G>C (rs1800795); IL10–592 A>C (rs1800872); IL10–1082 G>A (rs1800896); IL17A -692 C>T (rs8193036); IL17A -197 G>A (rs2275913); TNF -238 G>A (rs361525); TNF -308 G>A (rs1800629) and IFNG +874 T>A (rs2430561) and pulmonary TB (PTB) susceptibility. We conducted a case-control study in individuals from Southern Brazil who were recruited between February 2012 and October 2013 in a high incidence TB city. We performed a multiplex genotyping assay in 191 patients with PTB and 175 healthy subjects. Our results suggest a decreased risk for PTB development associated with the IL17A -197A allele (OR = 0.29; p = 0.04), AA genotype (OR = 0.12; p = 0.04) and A carrier (AG/AA) (OR = 0.29; p = 0.004) and IL6 -174C carrier (CC/CG) (OR = 0.46; p = 0.04). We could not properly analyze IL17A -692 C>T (rs8193036) and IFNG +874T>A due to genotypic inconsistencies and found no evidence of association for the IL2, IL4, IL10 and TNF polymorphisms and PTB. In conclusion, our results show a protective effect of IL17 and IL6 polymorphisms on PTB outcome in Southern Brazilian population.
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Affiliation(s)
- Mariana Milano
- Programa de Pós-Graduação em Biologia Celular e Molecular, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
- Centro de Desenvolvimento Científico e Tecnológico, Fundação Estadual de Produção e Pesquisa em Saúde, Porto Alegre, Rio Grande do Sul, Brazil
- * E-mail: (MM); (MOM)
| | - Milton Ozório Moraes
- Laboratório de Hanseníase, Instituto Oswaldo Cruz Fundação Oswaldo Cruz, Rio de Janeiro, Rio de Janeiro, Brazil
- * E-mail: (MM); (MOM)
| | - Rodrigo Rodenbusch
- Centro de Desenvolvimento Científico e Tecnológico, Fundação Estadual de Produção e Pesquisa em Saúde, Porto Alegre, Rio Grande do Sul, Brazil
| | - Caroline Xavier Carvalho
- Laboratório de Hanseníase, Instituto Oswaldo Cruz Fundação Oswaldo Cruz, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Melaine Delcroix
- Division of Infectious Disease and Vaccinology, University of California, Berkeley, United States of America
| | - Gabriel Mousquer
- Universidade Federal de Ciências da Saúde de Porto Alegre, Porto Alegre, Rio Grande do Sul, Brazil
| | - Lucas Laux da Costa
- Centro de Desenvolvimento Científico e Tecnológico, Fundação Estadual de Produção e Pesquisa em Saúde, Porto Alegre, Rio Grande do Sul, Brazil
- Programa de Pós-Graduação em Clínica Médica, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Gisela Unis
- Hospital Sanatório Partenon, Porto Alegre, Rio Grande do Sul, Brazil
| | - Elis Regina Dalla Costa
- Centro de Desenvolvimento Científico e Tecnológico, Fundação Estadual de Produção e Pesquisa em Saúde, Porto Alegre, Rio Grande do Sul, Brazil
| | - Maria Lucia Rosa Rossetti
- Programa de Pós-Graduação em Biologia Celular e Molecular, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
- Centro de Desenvolvimento Científico e Tecnológico, Fundação Estadual de Produção e Pesquisa em Saúde, Porto Alegre, Rio Grande do Sul, Brazil
- Universidade Luterana do Brazil, Canoas, Rio Grande do Sul, Brazil
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