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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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2
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Abstract
Immunity to infection has been extensively studied in humans and mice bearing naturally occurring or experimentally introduced germline mutations. Mouse studies are sometimes neglected by human immunologists, on the basis that mice are not humans and the infections studied are experimental and not natural. Conversely, human studies are sometimes neglected by mouse immunologists, on the basis of the uncontrolled conditions of study and small numbers of patients. However, both sides would agree that the infectious phenotypes of patients with inborn errors of immunity often differ from those of the corresponding mutant mice. Why is that? We argue that this important question is best addressed by revisiting and reinterpreting the findings of both mouse and human studies from a genetic perspective. Greater caution is required for reverse-genetics studies than for forward-genetics studies, but genetic analysis is sufficiently strong to define the studies likely to stand the test of time. Genetically robust mouse and human studies can provide invaluable complementary insights into the mechanisms of immunity to infection common and specific to these two species.
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Affiliation(s)
- Philippe Gros
- McGill University Research Center on Complex Traits, Department of Biochemistry, and Department of Human Genetics, McGill University, Montréal, Québec, Canada;
| | - Jean-Laurent Casanova
- Howard Hughes Medical Institute and 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, and University of Paris Cité, Imagine Institute and Necker Hospital for Sick Children, Paris, France
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3
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Lakshmikanth T, Muhammad SA, Olin A, Chen Y, Mikes J, Fagerberg L, Gummesson A, Bergström G, Uhlen M, Brodin P. Human Immune System Variation during 1 Year. Cell Rep 2021; 32:107923. [PMID: 32697987 DOI: 10.1016/j.celrep.2020.107923] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Revised: 03/19/2020] [Accepted: 06/26/2020] [Indexed: 12/22/2022] Open
Abstract
The human immune system varies extensively between individuals, but variation within individuals over time has not been well characterized. Systems-level analyses allow for simultaneous quantification of many interacting immune system components and the inference of global regulatory principles. Here, we present a longitudinal, systems-level analysis in 99 healthy adults 50 to 65 years of age and sampled every third month for 1 year. We describe the structure of interindividual variation and characterize extreme phenotypes along a principal curve. From coordinated measurement fluctuations, we infer relationships between 115 immune cell populations and 750 plasma proteins constituting the blood immune system. While most individuals have stable immune systems, the degree of longitudinal variability is an individual feature. The most variable individuals, in the absence of overt infections, exhibited differences in markers of metabolic health suggestive of a possible link between metabolic and immunologic homeostatic regulation.
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Affiliation(s)
- Tadepally Lakshmikanth
- Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institutet, Karolinska, Sweden
| | - Sayyed Auwn Muhammad
- Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institutet, Karolinska, Sweden
| | - Axel Olin
- Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institutet, Karolinska, Sweden
| | - Yang Chen
- Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institutet, Karolinska, Sweden
| | - Jaromir Mikes
- Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institutet, Karolinska, Sweden
| | - Linn Fagerberg
- Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Anders Gummesson
- Department of Molecular and Clinical Medicine, Wallenberg Laboratory, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden; Department of Physiology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Göran Bergström
- Department of Molecular and Clinical Medicine, Wallenberg Laboratory, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden; Department of Physiology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Mathias Uhlen
- Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Petter Brodin
- Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institutet, Karolinska, Sweden; Department of Pediatric Rheumatology, Karolinska University Hospital, Karolinska, Sweden.
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4
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Duffy D. Understanding immune variation for improved translational medicine. Curr Opin Immunol 2020; 65:83-88. [PMID: 32745736 DOI: 10.1016/j.coi.2020.06.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 06/29/2020] [Accepted: 06/30/2020] [Indexed: 12/19/2022]
Abstract
The goal of translational medicine is to use an improved understanding of human biology to develop new clinical approaches. Immune responses are highly variable from one person to another, with this variability strongly impacting clinical outcome. Variable immunity can determine differential risks for infection, for development of autoimmunity, and for response to therapeutic interventions. Therefore, a better understanding of the causes of such differences has huge potential to improve patient management through precision medicine strategies. Variability in immunity is determined by intrinsic (e.g. age, sex), extrinsic (e.g. environment, diet), and genetic factors. There is a growing consensus that genetics factors account for 20-40% of immune variability between individuals. The remaining unexplained variability is likely due to direct environmental influences, as well as specific gene-environmental interactions, which are more challenging to quantify and study. However, population based cohort studies with systems immunology approaches are now providing new understanding into these associations.
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Affiliation(s)
- Darragh Duffy
- Translational Immunology Lab, Department of Immunology, Institut Pasteur, Paris, France; INSERM U1223, Paris, France
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5
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Brodin P. Technologies for assessing vaccine responses in the very young. Curr Opin Immunol 2020; 65:28-31. [PMID: 32339894 DOI: 10.1016/j.coi.2020.03.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 03/23/2020] [Indexed: 11/16/2022]
Abstract
Many vaccines are administered to young children in order to prevent infectious diseases early in life. At the same time, most of these vaccines are not developed specifically with the immune system of young children in mind and our understanding of how newborn immune systems differ from adult counterparts is incomplete. The main reason for this lack of understanding stems from the ethical and logistical difficulties in obtaining samples from young children as well as the challenges associated with the small volume samples available. Here I review some recent developments made in this field and discuss their implications for studying vaccine responses in young children and developing better vaccines, tailored to this important population of susceptible individuals in the future.
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Affiliation(s)
- Petter Brodin
- Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institutet, SE-17121, Sweden; Unit of Pediatric Rheumatology, Karolinska University Hospital, SE-17176, Sweden.
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6
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Individuation and the Organization in Complex Living Ecosystem: Recursive Integration and Self-assertion by Holon-Lymphocytes. Acta Biotheor 2020; 68:171-199. [PMID: 31541308 DOI: 10.1007/s10441-019-09364-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 09/04/2019] [Indexed: 01/22/2023]
Abstract
Individuation and organization in complex living multi-level ecosystem occurs as dynamical processes from early ontogeny. The notion of living "holon" displaying dynamic self-assertion and integration is used here to explain the ecosystems dynamic processes. The update of the living holon state according to the continuous change of the dynamic system allows for its viability. This is interpreted as adaptation, selection and organization by the human that observes the system a posteriori from its level. Our model concerns the complex dynamics of the adaptive immune system, integrating holon-lymphocytes that collectively preserve the identity and integrity of the organism. Each lymphocyte individualizes as a dynamic holon-lymphocyte, with somatic gene individuation leading to an individual, singular antigen immunoreceptor type, promoting the self-assertion. In turn, the "Immunoception" allows for perception of the environmental antigenic context, thus integration of the holon in its environment. The self-assertion/integration of holon-lymphocyte starts from fetal stages and is influenced by mother Lamarckian acquired historicity transmissions, a requisite for the integrity of the holobiont-organism. We propose a dynamic model of the perception by holon-lymphocyte, and at the supra-clonal level of the immune system functions that sustain the identity and integrity of the holon-holobiont organism.
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7
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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: 65] [Impact Index Per Article: 10.8] [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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8
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Natural variation in the parameters of innate immune cells is preferentially driven by genetic factors. Nat Immunol 2018; 19:302-314. [PMID: 29476184 DOI: 10.1038/s41590-018-0049-7] [Citation(s) in RCA: 174] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2017] [Accepted: 01/12/2018] [Indexed: 12/21/2022]
Abstract
The quantification and characterization of circulating immune cells provide key indicators of human health and disease. To identify the relative effects of environmental and genetic factors on variation in the parameters of innate and adaptive immune cells in homeostatic conditions, we combined standardized flow cytometry of blood leukocytes and genome-wide DNA genotyping of 1,000 healthy, unrelated people of Western European ancestry. We found that smoking, together with age, sex and latent infection with cytomegalovirus, were the main non-genetic factors that affected variation in parameters of human immune cells. Genome-wide association studies of 166 immunophenotypes identified 15 loci that showed enrichment for disease-associated variants. Finally, we demonstrated that the parameters of innate cells were more strongly controlled by genetic variation than were those of adaptive cells, which were driven by mainly environmental exposure. Our data establish a resource that will generate new hypotheses in immunology and highlight the role of innate immunity in susceptibility to common autoimmune diseases.
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9
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Jiang Q, Liu Y, Xu B, Zheng W, Xiang X, Tang X, Dong H, Chen Y, Wang C, Deng G, Mao Q, Shang X, Wu Y. Analysis of T cell receptor repertoire in monozygotic twins concordant and discordant for chronic hepatitis B infection. Biochem Biophys Res Commun 2018; 497:153-159. [PMID: 29438710 DOI: 10.1016/j.bbrc.2018.02.043] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2018] [Accepted: 02/05/2018] [Indexed: 12/12/2022]
Abstract
Due to their identical inheritance and shared surroundings, identical twins have been the recommended group for studying the susceptibility and prognosis of diseases. Here, CD8+ T cell receptor beta (TCRβ) chains were analyzed by high-throughput sequencing in three pairs of healthy identical twins and chronic hepatitis B patients. The data showed a high level of similarity in the TCR repertoire of each pair in terms of average TCR Vβ segment expression and frequency of the complementary determining region 3 (CDR3) pattern and skewed or oligoclonal clonotypes. Notably, the level of similarity in TCR Vβ expression between the twins appeared to be independent of the consistency or inconsistency of chronic HBV infection, although the detailed CDR3 pattern and frequency were related to disease prognosis. There were more immunodominant clonotypes in patients with HBV antigen seroconversion, which showed an increased abundance. These immunodominant clonotypes may be used as favorable prognostic biomarkers and potential targets for immunotherapy. Thus, delineating the CD8+ T cell repertoire of identical twins with concordant chronic viral infections provides a promising means to screen protective TCR genes for immunotherapy.
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Affiliation(s)
- Qiong Jiang
- Institute of Immunology, PLA, Third Military Medical University, Chongqing 400038, PR China
| | - Yao Liu
- Institute of Immunology, PLA, Third Military Medical University, Chongqing 400038, PR China
| | - Baoyan Xu
- Institute of Infectious Diseases, Southwest Hospital, Third Military Medical University, Chongqing 400038, PR China
| | - Wenhong Zheng
- Department of Health, Third Military Medical University, Chongqing 400038, PR China
| | - Xiaomei Xiang
- Institute of Infectious Diseases, Southwest Hospital, Third Military Medical University, Chongqing 400038, PR China
| | - Xiaoqin Tang
- Institute of Immunology, PLA, Third Military Medical University, Chongqing 400038, PR China
| | - Hui Dong
- Institute of Immunology, PLA, Third Military Medical University, Chongqing 400038, PR China
| | - Yongwen Chen
- Institute of Immunology, PLA, Third Military Medical University, Chongqing 400038, PR China
| | - Chenhui Wang
- Institute of Immunology, PLA, Third Military Medical University, Chongqing 400038, PR China
| | - Guohong Deng
- Institute of Infectious Diseases, Southwest Hospital, Third Military Medical University, Chongqing 400038, PR China
| | - Qing Mao
- Institute of Infectious Diseases, Southwest Hospital, Third Military Medical University, Chongqing 400038, PR China
| | - Xiaoyun Shang
- Institute of Immunology, PLA, Third Military Medical University, Chongqing 400038, PR China.
| | - Yuzhang Wu
- Institute of Immunology, PLA, Third Military Medical University, Chongqing 400038, PR China.
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10
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Shah NN, Parta M, Baird K, Rafei H, Cole K, Holland SM, Hickstein DD. Monozygotic twins with GATA2 deficiency: same haploidentical-related donor, different severity of GvHD. Bone Marrow Transplant 2017; 52:1580-1582. [PMID: 28825694 PMCID: PMC7869005 DOI: 10.1038/bmt.2017.180] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- N N Shah
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - M Parta
- Clinical Research Directorate/Clinical Monitoring Research Program, Leidos Biomedical Research, Inc., NCI Campus at Frederick, Frederick, MD, USA
| | - K Baird
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Office of Tissues and Advanced Therapies, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA
| | - H Rafei
- George Washington School of Medicine and Health Sciences, Washington, DC, USA
| | - K Cole
- Office of the Clinical Director, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - S M Holland
- Laboratory of Clinical Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - D D Hickstein
- Experimental Transplantation and Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
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11
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Human Adaptive Immunity Rescues an Inborn Error of Innate Immunity. Cell 2017; 168:789-800.e10. [PMID: 28235196 DOI: 10.1016/j.cell.2017.01.039] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 12/08/2016] [Accepted: 01/25/2017] [Indexed: 11/20/2022]
Abstract
The molecular basis of the incomplete penetrance of monogenic disorders is unclear. We describe here eight related individuals with autosomal recessive TIRAP deficiency. Life-threatening staphylococcal disease occurred during childhood in the proband, but not in the other seven homozygotes. Responses to all Toll-like receptor 1/2 (TLR1/2), TLR2/6, and TLR4 agonists were impaired in the fibroblasts and leukocytes of all TIRAP-deficient individuals. However, the whole-blood response to the TLR2/6 agonist staphylococcal lipoteichoic acid (LTA) was abolished only in the index case individual, the only family member lacking LTA-specific antibodies (Abs). This defective response was reversed in the patient, but not in interleukin-1 receptor-associated kinase 4 (IRAK-4)-deficient individuals, by anti-LTA monoclonal antibody (mAb). Anti-LTA mAb also rescued the macrophage response in mice lacking TIRAP, but not TLR2 or MyD88. Thus, acquired anti-LTA Abs rescue TLR2-dependent immunity to staphylococcal LTA in individuals with inherited TIRAP deficiency, accounting for incomplete penetrance. Combined TIRAP and anti-LTA Ab deficiencies underlie staphylococcal disease in this patient.
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12
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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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13
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Prabhu SB, Rathore DK, Nair D, Chaudhary A, Raza S, Kanodia P, Sopory S, George A, Rath S, Bal V, Tripathi R, Ramji S, Batra A, Aggarwal KC, Chellani HK, Arya S, Agarwal N, Mehta U, Natchu UCM, Wadhwa N, Bhatnagar S. Comparison of Human Neonatal and Adult Blood Leukocyte Subset Composition Phenotypes. PLoS One 2016; 11:e0162242. [PMID: 27610624 PMCID: PMC5017693 DOI: 10.1371/journal.pone.0162242] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 08/21/2016] [Indexed: 12/26/2022] Open
Abstract
The human peripheral leukocyte subset composition depends on genotype variation and pre-natal and post-natal environmental influence diversity. We quantified this composition in adults and neonates, and compared the median values and dispersal ranges of various subsets in them. We confirmed higher frequencies of monocytes and regulatory T cells (Tregs), similar frequencies of neutrophils, and lower frequencies of CD8 T cells, NKT cells, B1 B cells and gamma-delta T cells in neonatal umbilical cord blood. Unlike previous reports, we found higher frequencies of eosinophils and B cells, higher CD4:CD8 ratios, lower frequencies of T cells and iNKT cells, and similar frequencies of CD4 T cells and NK cells in neonates. We characterized monocyte subsets and dendritic cell (DC) subsets in far greater detail than previously reported, using recently described surface markers and gating strategies and observed that neonates had lower frequencies of patrolling monocytes and lower myeloid dendritic cell (mDC):plasmacytoid DC (pDC) ratios. Our data contribute to South Asian reference values for these parameters. We found that dispersal ranges differ between different leukocyte subsets, suggesting differential determination of variation. Further, some subsets were more dispersed in adults than in neonates suggesting influences of postnatal sources of variation, while some show the opposite pattern suggesting influences of developmental process variation. Together, these data and analyses provide interesting biological possibilities for future exploration.
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Affiliation(s)
- Savit B. Prabhu
- Pediatric Biology Center, Translational Health Science and Technology Institute, Faridabad, Haryana, India
- National Institute of Immunology, New Delhi, India
- * E-mail:
| | - Deepak K. Rathore
- Pediatric Biology Center, Translational Health Science and Technology Institute, Faridabad, Haryana, India
| | - Deepa Nair
- Pediatric Biology Center, Translational Health Science and Technology Institute, Faridabad, Haryana, India
| | - Anita Chaudhary
- Pediatric Biology Center, Translational Health Science and Technology Institute, Faridabad, Haryana, India
| | - Saimah Raza
- Pediatric Biology Center, Translational Health Science and Technology Institute, Faridabad, Haryana, India
| | | | - Shailaja Sopory
- Pediatric Biology Center, Translational Health Science and Technology Institute, Faridabad, Haryana, India
| | - Anna George
- National Institute of Immunology, New Delhi, India
| | - Satyajit Rath
- Pediatric Biology Center, Translational Health Science and Technology Institute, Faridabad, Haryana, India
- National Institute of Immunology, New Delhi, India
| | - Vineeta Bal
- Pediatric Biology Center, Translational Health Science and Technology Institute, Faridabad, Haryana, India
- National Institute of Immunology, New Delhi, India
| | - Reva Tripathi
- Department of Obstetrics & Gynecology, Maulana Azad Medical College, New Delhi, India
| | - Siddharth Ramji
- Department of Neonatology, Maulana Azad Medical College, New Delhi, India
| | - Aruna Batra
- Department of Obstetrics & Gynecology, Vardhman Mahavir Medical College and Safdarjung Hospital, New Delhi, India
| | - Kailash C. Aggarwal
- Department of Pediatrics, Vardhman Mahavir Medical College and Safdarjung Hospital, New Delhi, India
| | - Harish K. Chellani
- Department of Pediatrics, Vardhman Mahavir Medical College and Safdarjung Hospital, New Delhi, India
| | - Sugandha Arya
- Department of Pediatrics, Vardhman Mahavir Medical College and Safdarjung Hospital, New Delhi, India
| | - Nidhi Agarwal
- Department of Obstetrics and Gynecology, Gurgaon Civil Hospital, Gurgaon, India
| | - Umesh Mehta
- Department of Pediatrics, Gurgaon Civil Hospital, Gurgaon, India
| | - Uma Chandra Mouli Natchu
- Pediatric Biology Center, Translational Health Science and Technology Institute, Faridabad, Haryana, India
| | - Nitya Wadhwa
- Pediatric Biology Center, Translational Health Science and Technology Institute, Faridabad, Haryana, India
| | - Shinjini Bhatnagar
- Pediatric Biology Center, Translational Health Science and Technology Institute, Faridabad, Haryana, India
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14
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Deschamps M, Laval G, Fagny M, Itan Y, Abel L, Casanova JL, Patin E, Quintana-Murci L. Genomic Signatures of Selective Pressures and Introgression from Archaic Hominins at Human Innate Immunity Genes. Am J Hum Genet 2016; 98:5-21. [PMID: 26748513 DOI: 10.1016/j.ajhg.2015.11.014] [Citation(s) in RCA: 170] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 11/06/2015] [Indexed: 01/25/2023] Open
Abstract
Human genes governing innate immunity provide a valuable tool for the study of the selective pressure imposed by microorganisms on host genomes. A comprehensive, genome-wide study of how selective constraints and adaptations have driven the evolution of innate immunity genes is missing. Using full-genome sequence variation from the 1000 Genomes Project, we first show that innate immunity genes have globally evolved under stronger purifying selection than the remainder of protein-coding genes. We identify a gene set under the strongest selective constraints, mutations in which are likely to predispose individuals to life-threatening disease, as illustrated by STAT1 and TRAF3. We then evaluate the occurrence of local adaptation and detect 57 high-scoring signals of positive selection at innate immunity genes, variation in which has been associated with susceptibility to common infectious or autoimmune diseases. Furthermore, we show that most adaptations targeting coding variation have occurred in the last 6,000-13,000 years, the period at which populations shifted from hunting and gathering to farming. Finally, we show that innate immunity genes present higher Neandertal introgression than the remainder of the coding genome. Notably, among the genes presenting the highest Neandertal ancestry, we find the TLR6-TLR1-TLR10 cluster, which also contains functional adaptive variation in Europeans. This study identifies highly constrained genes that fulfill essential, non-redundant functions in host survival and reveals others that are more permissive to change-containing variation acquired from archaic hominins or adaptive variants in specific populations-improving our understanding of the relative biological importance of innate immunity pathways in natural conditions.
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Affiliation(s)
- Matthieu Deschamps
- Unit of Human Evolutionary Genetics, Institut Pasteur, 75015 Paris, France; CNRS URA3012, 75015 Paris, France; Université Pierre et Marie Curie, Cellule Pasteur UPMC, 75015 Paris, France
| | - Guillaume Laval
- Unit of Human Evolutionary Genetics, Institut Pasteur, 75015 Paris, France; CNRS URA3012, 75015 Paris, France
| | - Maud Fagny
- Unit of Human Evolutionary Genetics, Institut Pasteur, 75015 Paris, France; CNRS URA3012, 75015 Paris, France; Université Pierre et Marie Curie, Cellule Pasteur UPMC, 75015 Paris, France
| | - Yuval Itan
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065, USA
| | - 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 U.1163, 75015 Paris, France; Imagine Institute, Paris Descartes University, 75015 Paris, France
| | - Jean-Laurent Casanova
- 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 U.1163, 75015 Paris, France; Imagine Institute, Paris Descartes University, 75015 Paris, France; Howard Hughes Medical Institute, New York, NY 10065, USA; Pediatric Hematology-Immunology Unit, Necker Hospital for Sick Children, 75015 Paris, France
| | - Etienne Patin
- Unit of Human Evolutionary Genetics, Institut Pasteur, 75015 Paris, France; CNRS URA3012, 75015 Paris, France
| | - Lluis Quintana-Murci
- Unit of Human Evolutionary Genetics, Institut Pasteur, 75015 Paris, France; CNRS URA3012, 75015 Paris, France.
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15
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Casanova JL. Severe infectious diseases of childhood as monogenic inborn errors of immunity. Proc Natl Acad Sci U S A 2015; 112:E7128-37. [PMID: 26621750 PMCID: PMC4697435 DOI: 10.1073/pnas.1521651112] [Citation(s) in RCA: 155] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
This paper reviews the developments that have occurred in the field of human genetics of infectious diseases from the second half of the 20th century onward. In particular, it stresses and explains the importance of the recently described monogenic inborn errors of immunity underlying resistance or susceptibility to specific infections. The monogenic component of the genetic theory provides a plausible explanation for the occurrence of severe infectious diseases during primary infection. Over the last 20 y, increasing numbers of life-threatening infectious diseases striking otherwise healthy children, adolescents, and even young adults have been attributed to single-gene inborn errors of immunity. These studies were inspired by seminal but neglected findings in plant and animal infections. Infectious diseases typically manifest as sporadic traits because human genotypes often display incomplete penetrance (most genetically predisposed individuals remain healthy) and variable expressivity (different infections can be allelic at the same locus). Infectious diseases of childhood, once thought to be archetypal environmental diseases, actually may be among the most genetically determined conditions of mankind. This nascent and testable notion has interesting medical and biological implications.
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MESH Headings
- Adolescent
- Candidiasis, Chronic Mucocutaneous/genetics
- Candidiasis, Chronic Mucocutaneous/immunology
- Child
- Complement System Proteins/genetics
- Encephalitis, Herpes Simplex/genetics
- Encephalitis, Herpes Simplex/immunology
- Epidermodysplasia Verruciformis/genetics
- Epidermodysplasia Verruciformis/immunology
- Genetic Diseases, Inborn/genetics
- Genetic Diseases, Inborn/immunology
- Genetic Predisposition to Disease
- Humans
- Immunologic Deficiency Syndromes/genetics
- Immunologic Deficiency Syndromes/immunology
- Infections/genetics
- Infections/immunology
- Influenza, Human/genetics
- Influenza, Human/immunology
- Interferon-gamma/genetics
- Interferon-gamma/immunology
- Lymphoproliferative Disorders/genetics
- Lymphoproliferative Disorders/immunology
- Malaria/genetics
- Malaria/immunology
- Models, Genetic
- Models, Immunological
- Mycobacterium Infections/genetics
- Mycobacterium Infections/immunology
- Neisseria/immunology
- Neisseria/pathogenicity
- Pneumococcal Infections/genetics
- Pneumococcal Infections/immunology
- Tinea/genetics
- Tinea/immunology
- Young Adult
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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; Howard Hughes Medical Institute, New York, NY 10065; Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Inserm U1163, Necker Hospital for Sick Children, 75015 Paris, France; Imagine Institute, Paris Descartes University, 75015 Paris, France; Pediatric Hematology and Immunology Unit, Assistance Publique-Hôpitaux de Paris, Necker Hospital for Sick Children, 75015 Paris, France
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16
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Bayat A, Burbelo PD, Browne SK, Quinlivan M, Martinez B, Holland SM, Buvanendran A, Kroin JS, Mannes AJ, Breuer J, Cohen JI, Iadarola MJ. Anti-cytokine autoantibodies in postherpetic neuralgia. J Transl Med 2015; 13:333. [PMID: 26482341 PMCID: PMC4617715 DOI: 10.1186/s12967-015-0695-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 10/10/2015] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND The mechanisms by which varicella zoster virus (VZV) reactivation causes postherpetic neuralgia (PHN), a debilitating chronic pain condition, have not been fully elucidated. Based on previous studies identifying a causative role for anti-cytokine autoantibodies in patients with opportunistic infections, we explored this possibility in PHN. METHODS Sera from herpes zoster (HZ) patients without and with PHN (N = 115 and 83, respectively) were examined for the presence of autoantibodies against multiple cytokines, and other known autoantigens. In addition, a cohort of patients with complex regional pain syndrome or neuropathic pain was tested for autoantibodies against selected cytokines. Antibody levels against VZV, Epstein Barr virus, and herpes simplex virus-2 were also measured in the HZ and PHN patients. Patient sera with high levels of anti-cytokine autoantibodies were functionally tested for in vitro neutralizing activity. RESULTS Six PHN subjects demonstrated markedly elevated levels of single, autoantibodies against interferon-α, interferon-γ, GM-CSF, or interleukin-6. In contrast, the HZ and the pain control group showed low or no autoantibodies, respectively, against these four cytokines. Further analysis revealed that one PHN patient with high levels of anti-interleukin-6 autoantibodies had a markedly depressed antibody level to VZV, potentially reflecting poor T cell immunity against VZV. In vitro functional testing revealed that three of the five anti-cytokine autoantibody positive PHN subjects had neutralizing autoantibodies against interferon-α, GM-CSF or interleukin-6. In contrast, none of the HZ patients without PHN had neutralizing autoantibodies. CONCLUSIONS These results suggest the possibility that sporadic anti-cytokine autoantibodies in some subjects may cause an autoimmune immunodeficiency syndrome leading to uncontrolled VZV reactivation, nerve damage and subsequent PHN.
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Affiliation(s)
- Ahmad Bayat
- Department of Perioperative Medicine, Clinical Center, National Institutes of Health, Bethesda, MD, 20892, USA.
| | - Peter D Burbelo
- Dental Clinical Research Core, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, 20892, USA.
| | - Sarah K Browne
- Laboratory of Clinical Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA.
| | - Mark Quinlivan
- Division of Infection and Immunity, University College London, London, WC1E 6BT, UK.
| | - Bianca Martinez
- Laboratory of Clinical Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA.
| | - Steven M Holland
- Laboratory of Clinical Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA.
| | - Asokumar Buvanendran
- Department of Anesthesiology, Rush University Medical Center, Chicago, IL, 60612, USA.
| | - Jeffrey S Kroin
- Department of Anesthesiology, Rush University Medical Center, Chicago, IL, 60612, USA.
| | - Andrew J Mannes
- Department of Perioperative Medicine, Clinical Center, National Institutes of Health, Bethesda, MD, 20892, USA.
| | - Judith Breuer
- Division of Infection and Immunity, University College London, London, WC1E 6BT, UK.
| | - Jeffrey I Cohen
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA.
| | - Michael J Iadarola
- Department of Perioperative Medicine, Clinical Center, National Institutes of Health, Bethesda, MD, 20892, USA.
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