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Schurz H, Salie M, Tromp G, Hoal EG, Kinnear CJ, Möller M. The X chromosome and sex-specific effects in infectious disease susceptibility. Hum Genomics 2019; 13:2. [PMID: 30621780 PMCID: PMC6325731 DOI: 10.1186/s40246-018-0185-z] [Citation(s) in RCA: 223] [Impact Index Per Article: 44.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 11/30/2018] [Indexed: 12/18/2022] Open
Abstract
The X chromosome and X-linked variants have largely been ignored in genome-wide and candidate association studies of infectious diseases due to the complexity of statistical analysis of the X chromosome. This exclusion is significant, since the X chromosome contains a high density of immune-related genes and regulatory elements that are extensively involved in both the innate and adaptive immune responses. Many diseases present with a clear sex bias, and apart from the influence of sex hormones and socioeconomic and behavioural factors, the X chromosome, X-linked genes and X chromosome inactivation mechanisms contribute to this difference. Females are functional mosaics for X-linked genes due to X chromosome inactivation and this, combined with other X chromosome inactivation mechanisms such as genes that escape silencing and skewed inactivation, could contribute to an immunological advantage for females in many infections. In this review, we discuss the involvement of the X chromosome and X inactivation in immunity and address its role in sexual dimorphism of infectious diseases using tuberculosis susceptibility as an example, in which male sex bias is clear, yet not fully explored.
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Affiliation(s)
- Haiko Schurz
- DST-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
- South African Tuberculosis Bioinformatics Initiative (SATBBI), Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Muneeb Salie
- Department of Genetics, St. Jude Children’s Research Hospital, Memphis, TN 38105 USA
| | - Gerard Tromp
- DST-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
- South African Tuberculosis Bioinformatics Initiative (SATBBI), Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Eileen G. Hoal
- DST-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Craig J. Kinnear
- DST-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Marlo Möller
- DST-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
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Abstract
ABSTRACT
Familial risk of tuberculosis (TB) has been recognized for centuries. Largely through studies of mono- and dizygotic twin concordance rates, studies of families with Mendelian susceptibility to mycobacterial disease, and candidate gene studies performed in the 20th century, it was recognized that susceptibility to TB disease has a substantial host genetic component. Limitations in candidate gene studies and early linkage studies made the robust identification of specific loci associated with disease challenging, and few loci have been convincingly associated across multiple populations. Genome-wide and transcriptome-wide association studies, based on microarray (commonly known as genechip) technologies, conducted in the past decade have helped shed some light on pathogenesis but only a handful of new pathways have been identified. This apparent paradox, of high heritability but few replicable associations, has spurred a new wave of collaborative global studies. This review aims to comprehensively review the heritability of TB, critically review the host genetic and transcriptomic correlates of disease, and highlight current studies and future prospects in the study of host genomics in TB. An implicit goal of elucidating host genetic correlates of susceptibility to
Mycobacterium tuberculosis
infection or TB disease is to identify pathophysiological features amenable to translation to new preventive, diagnostic, or therapeutic interventions. The translation of genomic insights into new clinical tools is therefore also discussed.
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Hu CY, Zhang XA, Meyer CG, Thye T, Liu W, Cao WC. Polymorphism of X-linked CD40 ligand gene associated with pulmonary tuberculosis in the Han Chinese population. Genes Immun 2015; 16:399-404. [DOI: 10.1038/gene.2015.20] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Revised: 04/15/2015] [Accepted: 04/23/2015] [Indexed: 11/09/2022]
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Qidwai T, Jamal F, Khan MY. DNA Sequence Variation and Regulation of Genes Involved in Pathogenesis of Pulmonary Tuberculosis. Scand J Immunol 2012; 75:568-87. [DOI: 10.1111/j.1365-3083.2012.02696.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Ridruechai C, Mahasirimongkol S, Phromjai J, Yanai H, Nishida N, Matsushita I, Ohashi J, Yamada N, Moolphate S, Summanapan S, Chuchottaworn C, Manosuthi W, Kantipong P, Kanitvittaya S, Sawanpanyalert P, Keicho N, Khusmith S, Tokunaga K. Association analysis of susceptibility candidate region on chromosome 5q31 for tuberculosis. Genes Immun 2010; 11:416-22. [PMID: 20485362 DOI: 10.1038/gene.2010.26] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Chromosome 5q31 spans the T helper (Th) 2-related cytokine gene cluster, which is potentially important in Th1/Th2 immune responses. The chromosome 5q23.2-31.3 has been recently identified as a region with suggestive evidence of linkage to tuberculosis in the Asian population. With the aim of fine-mapping a putative tuberculosis susceptibility locus, we investigated a family-based association test between the dense single nucleotide polymorphism (SNP) markers within chromosome 5q31 and tuberculosis in 205 Thai trio families. Of these, 75 SNPs located within candidate genes covering SLC22A4, SLC22A5, IRF1, IL5, RAD50, IL13, IL4, KIF3A and SEPT8 were genotyped using the DigiTag2 assay. Association analysis revealed the most significant association with tuberculosis in haplotypes comprising SNPs rs274559, rs274554 and rs274553 of SLC22A5 gene (P(Global)=2.02 x 10(-6)), which remained significant after multiple testing correction. In addition, two haplotypes within the SLC22A4 and KIF3A region were associated with tuberculosis. Haplotypes of SLC22A5 were significantly associated with the expression levels of RAD50 and IL13. The results show that the variants carried by the haplotypes of SLC22A4, SLC22A5 and KIF3A region potentially contribute to tuberculosis susceptibility among the Thai population.
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Affiliation(s)
- C Ridruechai
- Department of Microbiology and Immunology, Mahidol University, Bangkok, Thailand
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Sirugo G, Hennig BJ, Adeyemo AA, Matimba A, Newport MJ, Ibrahim ME, Ryckman KK, Tacconelli A, Mariani-Costantini R, Novelli G, Soodyall H, Rotimi CN, Ramesar RS, Tishkoff SA, Williams SM. Genetic studies of African populations: an overview on disease susceptibility and response to vaccines and therapeutics. Hum Genet 2008; 123:557-98. [PMID: 18512079 DOI: 10.1007/s00439-008-0511-y] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2008] [Accepted: 05/07/2008] [Indexed: 01/13/2023]
Abstract
Africa is the ultimate source of modern humans and as such harbors more genetic variation than any other continent. For this reason, studies of the patterns of genetic variation in African populations are crucial to understanding how genes affect phenotypic variation, including disease predisposition. In addition, the patterns of extant genetic variation in Africa are important for understanding how genetic variation affects infectious diseases that are a major problem in Africa, such as malaria, tuberculosis, schistosomiasis, and HIV/AIDS. Therefore, elucidating the role that genetic susceptibility to infectious diseases plays is critical to improving the health of people in Africa. It is also of note that recent and ongoing social and cultural changes in sub-Saharan Africa have increased the prevalence of non-communicable diseases that will also require genetic analyses to improve disease prevention and treatment. In this review we give special attention to many of the past and ongoing studies, emphasizing those in Sub-Saharan Africans that address the role of genetic variation in human disease.
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Affiliation(s)
- Giorgio Sirugo
- Medical Research Council Laboratories, Fajara, The Gambia, West Africa.
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Cooke GS, Campbell SJ, Bennett S, Lienhardt C, McAdam KPWJ, Sirugo G, Sow O, Gustafson P, Mwangulu F, van Helden P, Fine P, Hoal EG, Hill AVS. Mapping of a novel susceptibility locus suggests a role for MC3R and CTSZ in human tuberculosis. Am J Respir Crit Care Med 2008; 178:203-7. [PMID: 18420963 DOI: 10.1164/rccm.200710-1554oc] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
RATIONALE Tuberculosis remains a major cause of morbidity and mortality in the developing world. A better understanding of the mechanisms of disease protection could allow novel strategies to disease management and control. OBJECTIVES To identify human genomic loci with evidence of linkage to tuberculosis susceptibility and, within these loci, to identify individual genes influencing tuberculosis susceptibility. METHODS Affected sibling pair analysis in South African and Malawian populations. Independent case-control study in West Africa. MEASUREMENTS AND MAIN RESULTS Two novel putative loci for tuberculosis susceptibility are identified: chromosome 6p21-q23 and chromosome 20q13.31-33--the latter with the strongest evidence for any locus reported to date in human tuberculosis (single point LOD score of 3.1, P = 10(-4), with a maximum likelihood score [MLS] of 2.8). An independent, multistage genetic association study in West African populations mapped this latter region in detail, finding evidence that variation in the melanocortin 3 receptor (MC3R) and cathepsin Z (CTSZ) genes play a role in the pathogenesis of tuberculosis. CONCLUSIONS These results demonstrate how a genomewide approach to the complex phenotype of human tuberculosis can identify novel targets for further research.
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Affiliation(s)
- Graham S Cooke
- Wellcome Trust Centre for Human Genetics, University of Oxford, Churchill Hospital, Headington, Oxford, United Kingdom.
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Van Hoeyveld E, Zhang PX, De Boeck K, Fuleihan R, Bossuyt X. Hyper-immunoglobulin M syndrome caused by a mutation in the promotor for CD40L. Immunology 2007; 120:497-501. [PMID: 17244160 PMCID: PMC2265910 DOI: 10.1111/j.1365-2567.2006.02520.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Hyper-immunoglobulin M (IgM) syndrome (HIGM) is a rare primary immunodeficiency characterized by elevated or normal IgM and absent or markedly decreased amounts of IgG, IgA and IgE. The X-linked form (HIGM1) is the most common type and is caused by mutations in the gene for CD40L, a T-cell surface molecule required for T-cell driven immunoglobulin class switching by B cells. In the present study we have identified a patient with X-linked hyper-IgM who failed to express CD40L on the cell surface of CD4(+) T lymphocytes. Sequence analysis of CD40L genomic DNA showed no mutations. CD40L mRNA was absent and sequence analysis of the CD40L promotor revealed a mutation at position -123 from the transcription start site. The mutation in the promotor region likely contributed to the decreased transcription as demonstrated by a luciferase reporter assay.
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Affiliation(s)
- Erna Van Hoeyveld
- Laboratory Medicine, Immunology, University Hospital Leuven, Belgium
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Abstract
During tuberculosis (TB) infection, the granuloma provides the microenvironment in which antigen-specific T cells colocate with and activate infected macrophages to inhibit the growth of Mycobacterium tuberculosis. Although the granuloma is the site for mycobacterial killing, virulent mycobacteria have developed a variety of mechanisms to resist this macrophage-mediated killing. These surviving mycobacteria become dormant, however, if host cellular immunity or the signals maintaining granuloma structure wane, or if mycobacteria resume replication, leading to reactivation of TB. This balance of life and death applies not only to the mycobacterium but also to the host macrophages that may undergo apoptosis or necrosis, leading to the characteristic caseous necrosis within the granuloma, and the potential spread of TB infection. The immunological factors controlling the development and maintenance of the granuloma will be reviewed.
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Affiliation(s)
- Bernadette M Saunders
- Mycobacterial Research Programme, Centenary Institute, Newtown, New South Wales, Australia.
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Abstract
Host genetic factors are important in determining susceptibility and resistance to Mycobacterium tuberculosis. The etiology of tuberculosis is complex, and several host genes have been shown to contribute to the development of clinical disease. The success of the strategies used to investigate host genetic susceptibility to mycobacterial infections can serve as a model for the investigation of host susceptibility to other infectious diseases.
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Affiliation(s)
- Richard Bellamy
- James Cook University Hospital, Marton Road, Middlesbrough TS4 3BW, UK.
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Chadha S, Miller K, Farwell L, Lightstone LB, Daly MJ, Rioux JD, Vyse TJ. Haplotype structure of TNFRSF5-TNFSF5 (CD40–CD40L) and association analysis in systemic lupus erythematosus. Eur J Hum Genet 2005; 13:669-76. [PMID: 15657613 DOI: 10.1038/sj.ejhg.5201367] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Systemic lupus erythematosus (SLE) is a prototypic autoimmune disease that is caused by genetic and environmental factors. The tumour necrosis factor (TNF) superfamily of genes play a central role in immune regulation and have been proposed to be involved in the development of SLE. TNFRSF5 (CD40) falls on 20q11-13, a region linked with SLE in three independent genome-wide studies. TNFSF5 (CD40L) falls on Xq26 and is the ligand for TNFRSF5. Seven single-nucleotide polymorphisms (SNPs) in CD40 and eight SNPs in CD40L were looked at for linkage disequilibrium (LD) and haplotype analysis in European-Caucasians. Limited haplotype diversity was observed across CD40 and CD40L, and >97% of the diversity was captured. We also examined the association of SNPs and haplotypes in CD40 and CD40L with SLE in European-Caucasians. There was no evidence of association for CD40 or CD40L in 408 European-Caucasian families with SLE from UK. Haplotype tagging SNPs (htSNPs) are made known, which will facilitate analysis for susceptibility in other autoimmune diseases and risk for infectious disease.
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Affiliation(s)
- Sapna Chadha
- Faculty of Medicine, Imperial College London, Hammersmith Hospital, London, UK
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