1
|
Genetic factors affect the susceptibility to bacterial infections in diabetes. Sci Rep 2021; 11:9464. [PMID: 33947878 PMCID: PMC8096814 DOI: 10.1038/s41598-021-88273-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 03/23/2021] [Indexed: 11/17/2022] Open
Abstract
Diabetes increases the risk of bacterial infections. We investigated whether common genetic variants associate with infection susceptibility in Finnish diabetic individuals. We performed genome-wide association studies and pathway analysis for bacterial infection frequency in Finnish adult diabetic individuals (FinnDiane Study; N = 5092, Diabetes Registry Vaasa; N = 4247) using national register data on antibiotic prescription purchases. Replication analyses were performed in a Swedish diabetic population (ANDIS; N = 9602) and in a Finnish non-diabetic population (FinnGen; N = 159,166). Genome-wide data indicated moderate but significant narrow-sense heritability for infection susceptibility (h2 = 16%, P = 0.02). Variants on chromosome 2 were associated with reduced infection susceptibility (rs62192851, P = 2.23 × 10–7). Homozygotic carriers of the rs62192851 effect allele (N = 44) had a 37% lower median annual antibiotic purchase rate, compared to homozygotic carriers of the reference allele (N = 4231): 0.38 [IQR 0.22–0.90] and 0.60 [0.30–1.20] respectively, P = 0.01). Variants rs6727834 and rs10188087, in linkage disequilibrium with rs62192851, replicated in the FinnGen-cohort (P < 0.05), but no variants replicated in the ANDIS-cohort. Pathway analysis suggested the IRAK1 mediated NF-κB activation through IKK complex recruitment-pathway to be a mediator of the phenotype. Common genetic variants on chromosome 2 may associate with reduced risk of bacterial infections in Finnish individuals with diabetes.
Collapse
|
2
|
Blackwell JM, Fakiola M, Castellucci LC. Human genetics of leishmania infections. Hum Genet 2020; 139:813-819. [PMID: 32055998 PMCID: PMC7272388 DOI: 10.1007/s00439-020-02130-w] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 02/02/2020] [Indexed: 01/15/2023]
Abstract
Identifying genetic risk factors for parasitic infections such as the leishmaniases could provide important leads for improved therapies and vaccines. Until recently most genetic studies of human leishmaniasis were underpowered and/or not replicated. Here, we focus on recent genome-wide association studies of visceral leishmaniasis (VL) and cutaneous leishmaniasis (CL). For VL, analysis across 2287 cases and 2692 controls from three cohorts identified a single major peak of genome-wide significance (Pcombined = 2.76 × 10–17) at HLA-DRB1–HLA-DQA1. HLA-DRB1*1501 and DRB1*1404/DRB1*1301 were the most significant protective versus risk alleles, respectively, with specific residues at amino acid positions 11 and 13 unique to protective alleles. Epitope-binding studies showed higher frequency of basic AAs in DRB1*1404-/*1301-specific epitopes compared to hydrophobic and polar AAs in DRB1*1501-specific epitopes at anchor residues P4 and P6 which interact with residues at DRB1 positions 11 and 13. For CL, genome-wide significance was not achieved in combined analysis of 2066 cases and 2046 controls across 2 cohorts. Rather, multiple top hits at P < 5 × 10–5 were observed, amongst which IFNG-AS1 was of specific interest as a non-coding anti-sense RNA known to influence responses to pathogens by increasing IFN-γ secretion. Association at LAMP3 encoding dendritic cell lysosomal associated membrane protein 3 was also interesting. LAMP3 increases markedly upon activation of dendritic cells, localizing to the MHC Class II compartment immediately prior to translocation of Class II to the cell surface. Together these GWAS results provide firm confirmation for the importance of antigen presentation and the regulation of IFNγ in determining the outcome of Leishmania infections.
Collapse
Affiliation(s)
- Jenefer M Blackwell
- Telethon Kids Institute, The University of Western Australia, Nedlands, WA, Australia. .,Department of Pathology, University of Cambridge, Cambridge, UK.
| | - Michaela Fakiola
- INGM-National Institute of Molecular Genetics "Romeo Ed Enrica Invernizzi" Milan, Milan, Italy
| | - Léa C Castellucci
- National Institute of Science and Technology in Tropical Diseases, Salvador, Brazil.,Federal University of Bahia, Salvador, Brazil
| |
Collapse
|
3
|
Human Immunology through the Lens of Evolutionary Genetics. Cell 2019; 177:184-199. [DOI: 10.1016/j.cell.2019.02.033] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 02/19/2019] [Accepted: 02/20/2019] [Indexed: 01/04/2023]
|
4
|
Abu Toamih Atamni H, Nashef A, Iraqi FA. The Collaborative Cross mouse model for dissecting genetic susceptibility to infectious diseases. Mamm Genome 2018; 29:471-487. [PMID: 30143822 DOI: 10.1007/s00335-018-9768-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 08/02/2018] [Indexed: 12/18/2022]
Abstract
Infectious diseases, also known as communicable diseases, refer to a full range of maladies caused by pathogen invasion to the host body. Host response towards an infectious pathogen varies between individuals, and can be defined by responses from asymptomatic to lethal. Host response to infectious pathogens is considered as a complex trait controlled by gene-gene (host-pathogen) and gene-environment interactions, leading to the extensive phenotypic variations between individuals. With the advancement of the human genome mapping approaches and tools, various genome-wide association studies (GWAS) were performed, aimed at mapping the genetic basis underlying host susceptibility towards infectious pathogens. In parallel, immense efforts were invested in enhancing the genetic mapping resolution and gene-cloning efficacy, using advanced mouse models including advanced intercross lines; outbred populations; consomic, congenic; and recombinant inbred lines. Notwithstanding the evident advances achieved using these mouse models, the genetic diversity was low and quantitative trait loci (QTL) mapping resolution was inadequate. Consequently, the Collaborative Cross (CC) mouse model was established by full-reciprocal mating of eight divergent founder strains of mice (A/J, C57BL/6J, 129S1/SvImJ, NOD/LtJ, NZO/HiLtJ, CAST/Ei, PWK/PhJ, and WSB/EiJ) generating a next-generation mouse genetic reference population (CC lines). Presently, the CC mouse model population comprises a set of about 200 recombinant inbred CC lines exhibiting a unique high genetic diversity and which are accessible for multidisciplinary studies. The CC mouse model efficacy was validated by various studies in our lab and others, accomplishing high-resolution (< 1 MB) QTL genomic mapping for a variety of complex traits, using about 50 CC lines (3-4 mice per line). Herein, we present a number of studies demonstrating the power of the CC mouse model, which has been utilized in our lab for mapping the genetic basis of host susceptibility to various infectious pathogens. These include Aspergillus fumigatus, Klebsiella pneumoniae, Porphyromonas gingivalis and Fusobacterium nucleatum (causing oral mixed infection), Pseudomonas aeruginosa, and the bacterial toxins Lipopolysaccharide and Lipoteichoic acid.
Collapse
Affiliation(s)
- Hanifa Abu Toamih Atamni
- Department of Clinical Microbiology and Immunology, Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv, Tel Aviv, 69978, Israel
| | - Aysar Nashef
- Department of Prosthodontics, Dental school, The Hebrew University, Hadassah Jerusalem, Israel.,Department of Cranio-maxillofacial Surgery, Poria Medical Centre, The Azrieli School of Medicine, Bar Ilan University, Safed, Israel
| | - Fuad A Iraqi
- Department of Clinical Microbiology and Immunology, Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv, Tel Aviv, 69978, Israel.
| |
Collapse
|
5
|
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]
|
6
|
Graf L, Dick A, Sendker F, Barth E, Marz M, Daumke O, Kochs G. Effects of allelic variations in the human myxovirus resistance protein A on its antiviral activity. J Biol Chem 2018; 293:3056-3072. [PMID: 29330299 DOI: 10.1074/jbc.m117.812784] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Revised: 01/08/2018] [Indexed: 11/06/2022] Open
Abstract
Only a minority of patients infected with seasonal influenza A viruses exhibit a severe or fatal outcome of infection, but the reasons for this inter-individual variability in influenza susceptibility are unclear. To gain further insights into the molecular mechanisms underlying this variability, we investigated naturally occurring allelic variations of the myxovirus resistance 1 (MX1) gene coding for the influenza restriction factor MxA. The interferon-induced dynamin-like GTPase consists of an N-terminal GTPase domain, a bundle signaling element, and a C-terminal stalk responsible for oligomerization and viral target recognition. We used online databases to search for variations in the MX1 gene. Deploying in vitro approaches, we found that non-synonymous variations in the GTPase domain cause the loss of antiviral and enzymatic activities. Furthermore, we showed that these amino acid substitutions disrupt the interface for GTPase domain dimerization required for the stimulation of GTP hydrolysis. Variations in the stalk were neutral or slightly enhanced or abolished MxA antiviral function. Remarkably, two other stalk variants altered MxA's antiviral specificity. Variations causing the loss of antiviral activity were found only in heterozygous carriers. Interestingly, the inactive stalk variants blocked the antiviral activity of WT MxA in a dominant-negative way, suggesting that heterozygotes are phenotypically MxA-negative. In contrast, the GTPase-deficient variants showed no dominant-negative effect, indicating that heterozygous carriers should remain unaffected. Our results demonstrate that naturally occurring mutations in the human MX1 gene can influence MxA function, which may explain individual variations in influenza virus susceptibility in the human population.
Collapse
Affiliation(s)
- Laura Graf
- From the Institute of Virology, Medical Center-University of Freiburg, Hermann-Herder-Strasse 11, 79104 Freiburg, Germany.,the Spemann Graduate School of Biology and Medicine, University of Freiburg, Albertstrasse 19a, 79104 Freiburg, Germany
| | - Alexej Dick
- the Max-Delbrück Centrum for Molecular Medicine, Robert-Rössle-Strasse 10, 13125 Berlin, Germany.,the Institute of Chemistry and Biochemistry, Free University Berlin, Takustrasse 6, 14195 Berlin, Germany
| | - Franziska Sendker
- From the Institute of Virology, Medical Center-University of Freiburg, Hermann-Herder-Strasse 11, 79104 Freiburg, Germany
| | - Emanuel Barth
- the Bioinformatics/High Throughput Analysis, Friedrich Schiller University Jena, Leutragraben 1, 07743 Jena, Germany
| | - Manja Marz
- the Bioinformatics/High Throughput Analysis, Friedrich Schiller University Jena, Leutragraben 1, 07743 Jena, Germany.,the Leibniz Institute for Age Research-Fritz Lipmann Institute (FLI), Beutenbergstrasse 11, 07745 Jena, Germany.,the European Virus Bioinformatics Center, Leutragraben 1, 07743 Jena, Germany, and
| | - Oliver Daumke
- the Max-Delbrück Centrum for Molecular Medicine, Robert-Rössle-Strasse 10, 13125 Berlin, Germany, .,the Institute of Chemistry and Biochemistry, Free University Berlin, Takustrasse 6, 14195 Berlin, Germany
| | - Georg Kochs
- From the Institute of Virology, Medical Center-University of Freiburg, Hermann-Herder-Strasse 11, 79104 Freiburg, Germany, .,the Spemann Graduate School of Biology and Medicine, University of Freiburg, Albertstrasse 19a, 79104 Freiburg, Germany.,the Faculty of Medicine, University of Freiburg, 79085 Freiburg, Germany
| |
Collapse
|
7
|
Mossman K, Nebesio N, Vidal SM. Discovery of Variants Underlying Host Susceptibility to Virus Infection Using Whole-Exome Sequencing. Methods Mol Biol 2017; 1656:209-227. [PMID: 28808973 PMCID: PMC7120756 DOI: 10.1007/978-1-4939-7237-1_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
The clinical course of any viral infection greatly differs in individuals. This variation results from various viral, host, and environmental factors. The identification of host genetic factors influencing inter-individual variation in susceptibility to several pathogenic viruses has tremendously increased our understanding of the mechanisms and pathways required for immunity. Next-generation sequencing of whole exomes represents a powerful tool in biomedical research. In this chapter, we briefly introduce whole-exome sequencing in the context of genetic approaches to identify host susceptibility genes to viral infections. We then describe general aspects of the workflow for whole-exome sequence analysis together with the tools and online resources that can be used to identify and annotate variant calls, and then prioritize them for their potential association to phenotypes of interest.
Collapse
Affiliation(s)
- Karen Mossman
- grid.25073.330000 0004 1936 8227Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON Canada
| | - Nestor Nebesio
- Department of Human Genetics, McGill University, Montreal, QC, Canada.,McGill University Research Center on Complex Traits, Montreal, QC, Canada.,Department of Medicine, McGill University, Montreal, QC, Canada
| | - Silvia M Vidal
- Department of Human Genetics, McGill University, Montreal, QC, Canada. .,McGill University Research Center on Complex Traits, Montreal, QC, Canada. .,Department of Medicine, McGill University, Montreal, QC, Canada.
| |
Collapse
|
8
|
Manry J, Nédélec Y, Fava VM, Cobat A, Orlova M, Thuc NV, Thai VH, Laval G, Barreiro LB, Schurr E. Deciphering the genetic control of gene expression following Mycobacterium leprae antigen stimulation. PLoS Genet 2017; 13:e1006952. [PMID: 28793313 PMCID: PMC5565194 DOI: 10.1371/journal.pgen.1006952] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Revised: 08/21/2017] [Accepted: 08/02/2017] [Indexed: 12/02/2022] Open
Abstract
Leprosy is a human infectious disease caused by Mycobacterium leprae. A strong host genetic contribution to leprosy susceptibility is well established. However, the modulation of the transcriptional response to infection and the mechanism(s) of disease control are poorly understood. To address this gap in knowledge of leprosy pathogenicity, we conducted a genome-wide search for expression quantitative trait loci (eQTL) that are associated with transcript variation before and after stimulation with M. leprae sonicate in whole blood cells. We show that M. leprae antigen stimulation mainly triggered the upregulation of immune related genes and that a substantial proportion of the differential gene expression is genetically controlled. Indeed, using stringent criteria, we identified 318 genes displaying cis-eQTL at an FDR of 0.01, including 66 genes displaying response-eQTL (reQTL), i.e. cis-eQTL that showed significant evidence for interaction with the M. leprae stimulus. Such reQTL correspond to regulatory variations that affect the interaction between human whole blood cells and M. leprae sonicate and, thus, likely between the human host and M. leprae bacilli. We found that reQTL were significantly enriched among binding sites of transcription factors that are activated in response to infection, and that they were enriched among single nucleotide polymorphisms (SNPs) associated with susceptibility to leprosy per se and Type-I Reaction, and seven of them have been targeted by recent positive selection. Our study suggested that natural selection shaped our genomic diversity to face pathogen exposure including M. leprae infection. Each year, 200,000 new leprosy cases are reported worldwide. While there is unambiguous evidence for a role of host genetics in leprosy pathogenesis, the mechanisms by which the human host fights the infection are poorly understood. Here, we highlight the search for naturally occurring genetic variations that modulate gene expression levels following exposure to sonicate of Mycobacterium leprae, the bacterium causing the disease. Because M. leprae is not cultivable and the genuine immune cells involved in the host response during infection are still unknown, we performed a genome-wide search for such genetic variations after stimulation of whole-blood from leprosy patients with M. leprae sonicate. This design allowed to provide a general framework for the genetic control of host responses to M. leprae and outlined the contribution of host genetics to leprosy pathogenesis. Among the M. leprae-dependent genetic regulators of gene expression levels there was an enrichment of variants (i) associated with leprosy, (ii) located in transcription factor binding sites and (iii) targeted by recent positive selection.
Collapse
Affiliation(s)
- Jérémy Manry
- 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
- * E-mail: (ES); (JM)
| | - Yohann Nédélec
- Department of Genetics, CHU Sainte-Justine Research Centre, Montreal, Quebec, Canada
- Department of Biochemistry, Faculty of Medicine, University of Montreal, Montreal, Quebec, Canada
| | - Vinicius M. Fava
- 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
| | - Aurélie Cobat
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Institut National de la Santé et de la Recherche Médicale U.1163, Paris, France
- Paris Descartes University, Imagine Institute, Paris, France
| | - Marianna Orlova
- Program in Infectious Diseases and Immunity in Global Health, The Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
- McGill International TB Centre, McGill University, Montreal, Quebec, Canada
- Departments of Medicine and Human Genetics, McGill University, Montreal, Quebec, Canada
| | | | - Vu Hong Thai
- Hospital for Dermato-Venerology, Ho Chi Minh City, Vietnam
| | - Guillaume Laval
- Institut Pasteur, Unit of Human Evolutionary Genetics, Department of Genomes and Genetics, Paris, France
- Centre National de la Recherche Scientifique, URA3012, Paris, France
- Center of Bioinformatics, Biostatistics and Integrative Biology, Institut Pasteur, Paris, France
| | - Luis B. Barreiro
- Department of Genetics, CHU Sainte-Justine Research Centre, Montreal, Quebec, Canada
- Department of Pediatrics, Faculty of Medicine, University of Montreal, 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
- * E-mail: (ES); (JM)
| |
Collapse
|
9
|
Apt AS, Logunova NN, Kondratieva TK. Host genetics in susceptibility to and severity of mycobacterial diseases. Tuberculosis (Edinb) 2017; 106:1-8. [PMID: 28802396 DOI: 10.1016/j.tube.2017.05.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2017] [Revised: 05/22/2017] [Accepted: 05/24/2017] [Indexed: 01/05/2023]
Abstract
The genetic analysis of susceptibility to infections has proven to be extremely useful for identification of key cells, molecules, pathways, and genes involved in the battle between two genomes - the essence of the infectious process. This is particularly true for tuberculosis and other mycobacterial infections which traditionally attracted much attention from both immunologists and geneticists. In this short review, we observe results of genetic studies performed in human populations and in animal models and compare relative input of forward and reverse genetic approaches in our knowledge about genetic control of and immune responses to mycobacterial infections.
Collapse
Affiliation(s)
- A S Apt
- Laboratory for Immunogenetics, Central Institute for Tuberculosis, Moscow, Russia; Department of Immunology, School of Biology, Moscow State M. V. Lomonosov University, Russia.
| | - N N Logunova
- Laboratory for Immunogenetics, Central Institute for Tuberculosis, Moscow, Russia
| | - T K Kondratieva
- Laboratory for Immunogenetics, Central Institute for Tuberculosis, Moscow, Russia
| |
Collapse
|
10
|
Langlais D, Fodil N, Gros P. Genetics of Infectious and Inflammatory Diseases: Overlapping Discoveries from Association and Exome-Sequencing Studies. Annu Rev Immunol 2017; 35:1-30. [DOI: 10.1146/annurev-immunol-051116-052442] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- David Langlais
- McGill University Research Centre on Complex Traits, McGill University, Montreal, Quebec H3G 0B1, Canada;, ,
- Department of Biochemistry, McGill University, Montreal, Quebec H3G 0B1, Canada
| | - Nassima Fodil
- McGill University Research Centre on Complex Traits, McGill University, Montreal, Quebec H3G 0B1, Canada;, ,
- Department of Biochemistry, McGill University, Montreal, Quebec H3G 0B1, Canada
| | - Philippe Gros
- McGill University Research Centre on Complex Traits, McGill University, Montreal, Quebec H3G 0B1, Canada;, ,
- Department of Biochemistry, McGill University, Montreal, Quebec H3G 0B1, Canada
| |
Collapse
|
11
|
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.
Collapse
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
| |
Collapse
|
12
|
Grant AV, Sabri A, Abid A, Abderrahmani Rhorfi I, Benkirane M, Souhi H, Naji Amrani H, Alaoui-Tahiri K, Gharbaoui Y, Lazrak F, Sentissi I, Manessouri M, Belkheiri S, Zaid S, Bouraqadi A, El Amraoui N, Hakam M, Belkadi A, Orlova M, Boland A, Deswarte C, Amar L, Bustamante J, Boisson-Dupuis S, Casanova JL, Schurr E, El Baghdadi J, Abel L. A genome-wide association study of pulmonary tuberculosis in Morocco. Hum Genet 2016; 135:299-307. [PMID: 26767831 DOI: 10.1007/s00439-016-1633-2] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2015] [Accepted: 01/04/2016] [Indexed: 01/04/2023]
Abstract
Although epidemiological evidence suggests a human genetic basis of pulmonary tuberculosis (PTB) susceptibility, the identification of specific genes and alleles influencing PTB risk has proven to be difficult. Previous genome-wide association (GWA) studies have identified only three novel loci with modest effect sizes in sub-Saharan African and Russian populations. We performed a GWA study of 550,352 autosomal SNPs in a family-based discovery Moroccan sample (on the full population and on the subset with PTB diagnosis at <25 years), which identified 143 SNPs with p < 1 × 10(-4). The replication study in an independent case/control sample identified four SNPs displaying a p < 0.01 implicating the same risk allele. In the combined sample including 556 PTB subjects and 650 controls these four SNPs showed suggestive association (2 × 10(-6) < p < 4 × 10(-5)): rs358793 and rs17590261 were intergenic, while rs6786408 and rs916943 were located in introns of FOXP1 and AGMO, respectively. Both genes are involved in the function of macrophages, which are the site of latency and reactivation of Mycobacterium tuberculosis. The most significant finding (p = 2 × 10(-6)) was obtained for the AGMO SNP in an early (<25 years) age-at-onset subset, confirming the importance of considering age-at-onset to decipher the genetic basis of PTB. Although only suggestive, these findings highlight several avenues for future research in the human genetics of PTB.
Collapse
Affiliation(s)
- A V Grant
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Institut National de la Santé et de la Recherche Médicale U1163, 75015, Paris, France, EU
- Paris Descartes University, Imagine Institute, 75015, Paris, France, EU
| | - A Sabri
- Genetics Unit, Military Hospital Mohammed V, Hay Riad, 10100, Rabat, Morocco
- Faculty of Sciences-Kenitra, Ibn Tofail University, Kenitra, Morocco
| | - A Abid
- Department of Pneumology, Military Hospital Mohammed V, Hay Riad, 10100, Rabat, Morocco
| | - I Abderrahmani Rhorfi
- Department of Pneumology, Military Hospital Mohammed V, Hay Riad, 10100, Rabat, Morocco
| | - M Benkirane
- Blood Transfusion Center, Military Hospital Mohammed V, Hay Riad, 10100, Rabat, Morocco
| | - H Souhi
- Department of Pneumology, Military Hospital Mohammed V, Hay Riad, 10100, Rabat, Morocco
| | - H Naji Amrani
- Department of Pneumology, Military Hospital Mohammed V, Hay Riad, 10100, Rabat, Morocco
| | - K Alaoui-Tahiri
- Department of Pneumology, Military Hospital Mohammed V, Hay Riad, 10100, Rabat, Morocco
| | - Y Gharbaoui
- Department of Pneumology, Military Hospital Mohammed V, Hay Riad, 10100, Rabat, Morocco
| | - F Lazrak
- Centre de Diagnostic de la tuberculose et des Maladies Respiratoires [CDTMR], Salé, Morocco
| | - I Sentissi
- Centre de Diagnostic de la tuberculose et des Maladies Respiratoires [CDTMR], Salé, Morocco
| | - M Manessouri
- Centre de Diagnostic de la tuberculose et des Maladies Respiratoires [CDTMR], Salé, Morocco
| | - S Belkheiri
- Centre de Diagnostic de la tuberculose et des Maladies Respiratoires [CDTMR], Salé, Morocco
| | - S Zaid
- Centre de Diagnostic de la tuberculose et des Maladies Respiratoires [CDTMR], Salé, Morocco
| | - A Bouraqadi
- Centre de Diagnostic de la tuberculose et des Maladies Respiratoires [CDTMR], Salé, Morocco
| | - N El Amraoui
- National Blood Transfusion Center, Rabat, Morocco
| | - M Hakam
- National Blood Transfusion Center, Rabat, Morocco
| | - A Belkadi
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Institut National de la Santé et de la Recherche Médicale U1163, 75015, Paris, France, EU
- Paris Descartes University, Imagine Institute, 75015, Paris, France, EU
| | - M Orlova
- McGill Centre for the Study of Host Resistance, The Research Institute of the McGill University Health Centre, Montreal, PQ H3G 1A4, Canada
| | - A Boland
- CEA, Institut de Génomique, Centre National de Génotypage, 91000, Evry, France, EU
| | - C Deswarte
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Institut National de la Santé et de la Recherche Médicale U1163, 75015, Paris, France, EU
- Paris Descartes University, Imagine Institute, 75015, Paris, France, EU
| | - L Amar
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Institut National de la Santé et de la Recherche Médicale U1163, 75015, Paris, France, EU
- Paris Descartes University, Imagine Institute, 75015, Paris, France, EU
| | - J Bustamante
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Institut National de la Santé et de la Recherche Médicale U1163, 75015, Paris, France, EU
- Paris Descartes University, Imagine Institute, 75015, Paris, France, EU
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, 10065, New York, NY, USA
| | - S Boisson-Dupuis
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Institut National de la Santé et de la Recherche Médicale U1163, 75015, Paris, France, EU
- Paris Descartes University, Imagine Institute, 75015, Paris, France, EU
- Center for the Study of Primary Immunodeficiencies, AP-HP, Necker hospital, 75015, Paris, France, EU
| | - J L Casanova
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Institut National de la Santé et de la Recherche Médicale U1163, 75015, Paris, France, EU
- Paris Descartes University, Imagine Institute, 75015, Paris, France, EU
- Center for the Study of Primary Immunodeficiencies, AP-HP, Necker hospital, 75015, Paris, France, EU
- Howard Hughes Medical Institute, New York, NY, USA
- Pediatric Hematology-Immunology Unit, AP-HP, Necker Hospital, 75015, Paris, France, EU
| | - E Schurr
- McGill Centre for the Study of Host Resistance, The Research Institute of the McGill University Health Centre, Montreal, PQ H3G 1A4, Canada
| | - J El Baghdadi
- Genetics Unit, Military Hospital Mohammed V, Hay Riad, 10100, Rabat, Morocco.
| | - L Abel
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Institut National de la Santé et de la Recherche Médicale U1163, 75015, Paris, France, EU.
- Paris Descartes University, Imagine Institute, 75015, Paris, France, EU.
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, 10065, New York, NY, USA.
- Human Genetics of Infectious Diseases, INSERM, Université Paris Descartes, Unit 1163, Imagine Institute, 24 Bd du Montparnasse, 75105, Paris, France.
| |
Collapse
|
13
|
Fodil N, Langlais D, Gros P. Primary Immunodeficiencies and Inflammatory Disease: A Growing Genetic Intersection. Trends Immunol 2016; 37:126-140. [PMID: 26791050 DOI: 10.1016/j.it.2015.12.006] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Revised: 12/10/2015] [Accepted: 12/13/2015] [Indexed: 02/08/2023]
Abstract
Recent advances in genome analysis have provided important insights into the genetic architecture of infectious and inflammatory diseases. The combined analysis of loci detected by genome-wide association studies (GWAS) in 22 inflammatory diseases has revealed a shared genetic core and associated biochemical pathways that play a central role in pathological inflammation. Parallel whole-exome sequencing studies have identified 265 genes mutated in primary immunodeficiencies (PID). Here, we examine the overlap between these two data sets, and find that it consists of genes essential for protection against infections and in which persistent activation causes pathological inflammation. Based on this intersection, we propose that, although strong or inactivating mutations (rare variants) in these genes may cause severe disease (PIDs), their more subtle modulation potentially by common regulatory/coding variants may contribute to chronic inflammation.
Collapse
Affiliation(s)
- Nassima Fodil
- Department of Biochemistry, Complex Traits Group, McGill University, Montreal, QC, Canada
| | - David Langlais
- Department of Biochemistry, Complex Traits Group, McGill University, Montreal, QC, Canada
| | - Philippe Gros
- Department of Biochemistry, Complex Traits Group, McGill University, Montreal, QC, Canada.
| |
Collapse
|
14
|
Human genetic basis of interindividual variability in the course of infection. Proc Natl Acad Sci U S A 2015; 112:E7118-27. [PMID: 26621739 DOI: 10.1073/pnas.1521644112] [Citation(s) in RCA: 125] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The key problem in human infectious diseases was posed at the turn of the 20th century: their pathogenesis. For almost any given virus, bacterium, fungus, or parasite, life-threatening clinical disease develops in only a small minority of infected individuals. Solving this infection enigma is important clinically, for diagnosis, prognosis, prevention, and treatment. Some microbes will inevitably remain refractory to, or escape vaccination, or chemotherapy, or both. The solution also is important biologically, because the emergence and evolution of eukaryotes alongside more rapidly evolving prokaryotes, archaea, and viruses posed immunological challenges of an ecological and evolutionary nature. We need to study these challenges in natural, as opposed to experimental, conditions, and also at the molecular and cellular levels. According to the human genetic theory of infectious diseases, inborn variants underlie life-threatening infectious diseases. Here I review the history of the field of human genetics of infectious diseases from the turn of the 19th century to the second half of the 20th century. This paper thus sets the scene, providing the background information required to understand and appreciate the more recently described monogenic forms of resistance or predisposition to specific infections discussed in a second paper in this issue.
Collapse
|
15
|
Behr MA, Divangahi M. Freund's adjuvant, NOD2 and mycobacteria. Curr Opin Microbiol 2015; 23:126-32. [DOI: 10.1016/j.mib.2014.11.015] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Revised: 11/18/2014] [Accepted: 11/19/2014] [Indexed: 11/26/2022]
|