J-J.Y. is Associate Professor at the Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Seoul National University College of Medicine, Republic of Korea. His main research topic is host immune responses to M. tuberculosis. P.S. is a Senior Scientist at the Department of Immunology, Tuberculosis Research Centre, Indian Council of Medical Research, Chennai, India. His main area of research is the immunology and immunogenetics of tuberculosis.
Genetic susceptibility in tuberculosis
Article first published online: 26 JAN 2010
© 2010 The Authors. Journal compilation © 2010 Asian Pacific Society of Respirology
Volume 15, Issue 2, pages 241–256, February 2010
How to Cite
YIM, J.-J. and SELVARAJ, P. (2010), Genetic susceptibility in tuberculosis. Respirology, 15: 241–256. doi: 10.1111/j.1440-1843.2009.01690.x
SERIES EDITORS: WING WAI YEW, GIOVANNI B. MIGLIORI AND CHRISTOPH LANGE
- Issue published online: 26 JAN 2010
- Article first published online: 26 JAN 2010
- Received 28 August 2009; invited to revise 23 September 2009; revised 19 October 2009; accepted 27 October 2009.
- gene polymorphism;
- human leucocyte antigen;
- solute carrier family 11A member 1;
The importance of host genetic factors in determining susceptibility to tuberculosis (TB) has been studied extensively using various methods, such as case-control, candidate gene and genome-wide linkage studies. Several important candidate genes like human leucocyte antigen/alleles and non-human leucocyte antigen genes, such as cytokines and their receptors, chemokines and their receptors, pattern recognition receptors (including toll-like receptors, mannose binding lectin and the dendritic cell-specific intercellular adhesion molecule-3 grabbing nonintegrin), solute carrier family 11A member 1 (formerly known as natural resistance-associated macrophage protein 1) and purinergic P2X7 receptor gene polymorphisms, have been associated with differential susceptibility to TB in various ethnic populations. This heterogeneity has been explained by host–pathogen and gene–environment interactions and evolutionary selection pressures. Although the achievements of genetics studies might not yet have advanced the prevention and treatment of TB, researchers have begun to widen their scope of investigation to encompass these practical considerations.
Host genetic factors explain, at least in part, why some people resist infection more successfully than others and play a major role in determining differential susceptibility to major infectious diseases. The importance of host genetic factors on genetic susceptibility to various infectious diseases has been reviewed.1–3 The association of host genetic factors with susceptibility or resistance to tuberculosis (TB) has been studied extensively using various methods, such as case–control studies, candidate gene approaches and family-based, genome-wide linkage analyses that have revealed several important candidate genes for susceptibility.3–5 The present review provides information that supplements the existing reviews on human genetic susceptibility to TB.
HOST GENETIC FACTORS AND TUBERCULOSIS SUSCEPTIBILITY/RESISTANCE
Tuberculosis, caused by Mycobacterium tuberculosis infection, remains a major cause of morbidity and mortality around the world.6 It is estimated that one-third of the world's population is infected with M. tuberculosis. Among those putatively infected only around 10% will ever develop clinical disease.7,8 In 1926, the accidental administration of live M. tuberculosis (in place of Bacillus Calmette-Guérin) to babies in Lübeck, Germany left some babies unaffected but led to severe disease and death in others.9 This indicates that the majority of the population has effective innate resistance to TB. On the other hand, twin studies show an increased concordance rate among monozygotes (60%) compared with dizygotes (20%) indicating a genetic component to susceptibility.10
The identification of host genetic factors, such as human leucocyte antigens (HLA) of major histocompatibility complex and other non-major histocompatibility complex genes/gene products that are associated with susceptibility or resistance to TB, may provide genetic markers to predict the development or predisposition to develop TB. Those HLA types that are associated with protection from TB will be useful in the development of a new epitope-based vaccine. Clarification of the role of these markers in the immune mechanisms underlying susceptibility or resistance to TB will be useful in understanding the immunopathogenesis of the disease.
HUMAN LEUCOCYTE ANTIGENS AND TUBERCULOSIS SUSCEPTIBILITY
Human leucocyte antigens, with its ever-increasing allelic diversity (2496 and 1032 class I and II alleles, respectively, as of June 2009),11 is the most polymorphic loci in the human genome. HLA class I molecules present pathogenic peptides to CD8+ T cells, while class II molecules display them to CD4+ T cells. The search for genetic determinants associated with differential susceptibility to TB infection has long been sought in the HLA region, due to its prime role in antigen presentation and the generation of effective immune responses to curtail infection. A large number of HLA association studies12–43 have been carried out and some are summarized in Table 1.
|Population||HLA antigen/allele||Nature of association||Sample size||Reference|
|DRB1*14(DR6), DQB1*0502 and *0503†||Susceptibility||—||114||31|
|Black American‡||B5 and DR5||Susceptibility||54||72||14|
|Korean||DRB1*08032 and DQB1*0601†||Susceptibility||200||53||32|
|Italian||DR4 alone or along with B14||Susceptibility||1089||122||33|
|A2+, B14-, DR4-||Protective||33|
|Indonesian||DR2 and DQw1||Susceptibility||64||101||19|
|Mexican||DRB1*1501, DQA1*0101, and DQB1*0501||Susceptibility||95||50||34|
|DR4, DR8 and DQB1*0402||Protective||34|
|Venda, South African||DRB1*1302, DQB1*0301-0304, DRB1*1101-1121-DQB1*05||Susceptibility||117||95||35|
|DRB1*1601-DQB1*0502, DRB1*04-DQB1*03 and DRB1*14-DQB1*05||Susceptibility||125||61||38|
|Cambodian||DQB1*0503||Susceptibility||49; 39§||78; 48§||39|
|DQ β57 Asp/Asp||Susceptibility||107||436||40|
|Iranian||A26 and B27||Protective||108||44||42|
|B17 and DR14||Susceptibility||42|
|DQA1*0301 and *0501||Protective||43|
|Soviet Union (six ethnic groups)||DR2||Susceptibility||984||643||20|
Racial differences in susceptibility to TB are well known. Several studies have shown an association between various HLA antigens and disease susceptibility in different ethnic populations.12–17 Hypotheses have been proposed to explain this geographic variation. It seems likely that evolutionary selection pressures have given rise to frequent polymorphisms in the genes involved in resisting infectious pathogens and so contributed to marked differences in allele frequency at the same loci. When geographic variation in pathogen polymorphism is superimposed on host genetic heterogeneity, considerable variation may occur in allelic associations. Gene–environment interactions are likely to introduce another layer of complexity. The genes involved in the defence against infectious pathogens evolve more rapidly than others and excessive polymorphism in the human genome may result from selection pressures exerted by infectious diseases. The causative organism, M. tuberculosis, also has genetic variation. All these polymorphic forms might have evolved over time due to host–microbial interaction.3
ASSOCIATION OF HLA-DR2 WITH SUSCEPTIBILITY TO TUBERCULOSIS IN ASIAN POPULATIONS
Earlier studies on the serological determination of HLA-DR antigens in TB reported an association between progressive TB and HLA-DR2 in populations from India, Indonesia and Russia.18–23 The association of HLA-DR2 with susceptibility to TB has been consistently observed across ethnic boundaries. Molecular typing of HLA-DR2 at the allelic level showed that the frequency of the allele DRB1*1501 was higher than that of DRB1*1502 in north Indian patients, and it has been suggested that the DR2 association was stronger in patients with drug failure.22 Studies carried out in south Indian patients revealed the positive association of HLA-DRB1*150124,25 and HLA-DQB1*0601 (a subtype of HLA-DQ1) with susceptibility to pulmonary TB.24 A meta-analysis to estimate the association between TB and HLA antigens based on reported case–control studies that used serological HLA typing indicated a lower risk of thoracic TB in carriers of HLA-B13, DR3 and DR7 antigens and a higher risk for HLA-DR8-positive individuals.26 However, this analysis also suggested an inconsistent positive association between HLA-DR2 and thoracic TB.
Associations with HLA gene polymorphisms appear insufficient to explain the range of variation in immune responses to vaccines and to infections by major pathogens like M. tuberculosis. A model derived from studies of twins in Gambia suggests that the cumulative effect of human non-HLA genes exceeds the contribution of HLA class II genes in immune responses to purified protein derivative of M. tuberculosis antigens.27 In light of this, there has been a surge of interest in non-HLA genes and their role in the immune response against TB bacilli. Genome-wide linkage studies on sib pairs of families affected with TB have identified several candidate genes that are associated with susceptibility to TB.4
CYTOKINES AND RECEPTORS
The immune response to TB is regulated by interactions between lymphocytes with antigen-presenting cells and the cytokines secreted by these cell types. Although cytokines exhibit a low degree of genetic variation, an increasing number of association studies have implicated polymorphisms located on promoter regions or coding regions of cytokine genes as host factors influencing susceptibility to infectious diseases.44,45 Mutations in these genes may result in altered transcription factor recognition sites, affecting transcriptional activation and altering the levels of cytokine production.46,47 Selected association studies of cytokines and their receptors are presented in Table 2.
|Cytokine||Location||SNP db number||Association Status||Sample size||Population||References|
|No association||188||166||South Indian||57|
|−111 (A/T)||No association||151||115||Korean||62|
|IL-2||−330 (T/G)||rs2069762||Susceptibility||188||166||South Indian||57|
|330 G/+160 G||Protective||123||41||Iranian||68|
|No association||188||166||South Indian||57|
|IL-4||−590 (T/C)||rs2243250||No association||123||41||Iranian||68|
|IL-6||−174 (G/C)||rs1800795||No association||188||166||South Indian||57|
|54† + 81‡||140||Colombian||69|
|61¶ + 42†† + 91‡‡||Canadian||70|
|100 + 125 (PPD+)||113||Spanish||52|
|+ 82 (PPD-)|
|TNF-α||−592 (A/C)||rs1800872||No association||111||183||Chinese||58|
|−308 (G/A)||rs1800629||No association||120||210||South Indian||74|
|−238 (G/A) and −376 (G/A)||rs361525||106||358||Cambodian||66|
|−308 A-238 G||Protective||430||135||Colombian||75|
|TGF-β||Codon 10 (+869 T/C)||rs1982073||No association||111||183||Chinese||58|
|54† + 81‡||140||Colombian||69|
|Codon 25 (+915 C/G)||rs1800471||110||101||Japanese||76|
INTERFERON-γ AND ITS RECEPTORS
A874T polymorphism on the intron 1 of interferon (IFN)-γ gene, which is associated with the secretory capacity of IFN-γ, was reported to be associated with the development of TB among Sicilians, South Africans, Hong Kong Chinese and Spanish,49–52 although this association was not found in Malawians54 and in other populations from Houston,55 West Africa,56 South India57 and China.58 However, a recent meta-analysis reported a protective effect of the 874T allele on the development of TB (OR = 0.75; 95% CI: 0.63–0.89).77 Several polymorphisms on the IFN-γ receptor 1 gene have been tested for their association with TB. Three56,78,79 of seven studies80–83 found an association between TB susceptibility and polymorphisms in the gene encoding the IFN-γ receptor 1 protein. Among these, the genotype of 56CC on the promoter region56 and cytosine-adenine repeat polymorphism on intron 184 were reported to be associated with the development of TB. A recent study of 77 TB patients from Japan revealed that the IFNG + 874 AA genotype was strongly and independently predictive of a lower likelihood of sputum conversion. Indeed, four of 56 patients with the IFNG + 874 AA genotype (7.1%) had not achieved culture negativity at 3 months. This study indicates that the presence or absence of this polymorphism could provide useful information on public health decisions, such as the duration of patient isolation as well as the clinical course of treated TB patients.85
IL-12 AND RECEPTORS
IL-12 is a heterodimeric protein (IL-12p70) composed of p40 and p35.86,87 IL-12 is mostly produced by activated phagocytic cells (macrophages, monocytes and neutrophils) with significantly more IL-12p40 than IL-12p35 being secreted. Both the IL-12 receptors β1 and β2 belong to the gp130 cytokine receptor superfamily and are expressed primarily on T and natural killer cells, but they also are found on dendritic cells and B-cell lines. IL-12p40 binds mainly to IL-12Rβ1, while IL-12p35 binds to IL-12Rβ2. Expression of IL-12Rβ2 correlates most closely with IL-12 responsiveness.88
Several polymorphisms in promoter, introns and 3′UTR in the IL-12B gene have been reported to be associated with TB in various populations,89–91 although results have been inconsistent.57,59 Polymorphisms in the coding sequence of the IL-12 receptor β1 gene have been reported to be associated with TB in Moroccan and Japanese populations,60,61,92 but, again, not in Koreans.62
Genes with reported mutations or polymorphisms in the IL-12-dependent IFN-γ pathway that predisposes patients to TB or non-tuberculous mycobacterial infection are summarized in Figure 1.
Several studies on polymorphisms in the IL-1B gene, encoding the beta chain of IL-1, have been carried out. Studies in Gambian and Colombian populations63,64 showed that the IL1B-511 C allele was associated with TB and that the IL1B + 3953 T allele was protective, while studies in Cambodia and a pilot case–control analysis of Gujarati Asians in west London found no association.65–67 A few studies have looked at polymorphisms in the IL-1 receptor, but just one study found an association with pleural TB.67
Polymorphisms in the IL-2 gene (−330 T/G and +160 G/T) are known to influence IL-2 levels. In a south Indian study, an increased frequency of −330 TT genotype was associated with protection against pulmonary TB. In addition, the GG haplotype (−330 G and +160 G) has been associated with susceptibility to pulmonary TB,57 while no association was found with −330 T/G and +160 G/T polymorphisms in an Iranian population.68
A single nucleotide polymorphism (SNP) at position −590 of the IL-4 promoter has been shown to be associated with increased promoter strength.93 In a study conducted in south Indian TB patients, heterozygotes of the IL-4 −590 T polymorphism were found significantly more frequently in the patient group.94 Significant negative associations at position −590 IL-4, the T allele and the T/T genotype were shown in Iranian patients with pulmonary TB and the C allele and T/C genotype were significantly increased, while no significant difference was observed in −1098 G/T and −33 C/T polymorphisms.68 A variable number tandem repeat polymorphism in the IL-4 gene has been shown to be associated with many diseases. However, there was no significant association of this with TB in a south Indian population.57 A Brazilian multicase TB family study found no association in guanine-thymine dinucleotide repeat in intron 3, and a 70-bp repeat in intron 2.95
Analysis of the allele and genotype frequencies of IL-6 −174 (G/C) polymorphism revealed no significant differences between controls and pulmonary TB patients in south Indian and Colombian populations.57,69 In contrast to the above findings a significant positive association with position −174 G/G polymorphism has been shown in Iranian patients, where the G allele was significantly over represented and associated with high production of IL-6.68 A study of Canadian aboriginal Dene and Cree cohorts showed a higher frequency of IL-6 −174G allele, which is associated with enhanced cytokine production,70 compared with that of a Caucasian cohort96 and this contributes to the high rates of TB among the Dene population. The Asian and African American populations studied had a similarly high frequency of the G allele.96
Patients with TB have increased IL-10 production mainly during the anergic state. Polymorphism studies of the IL-10 gene showed that in the −1082 SNP, the G allele was more common in TB patients in Cambodia,66 Sicily71 and Turkey.53 Ates et al.72 found that IL-10 −1082 G/A alleles, or haplotypes containing these alleles, may influence the Th1/Th2 balance and play a role in TB susceptibility in a Turkish population. In Colombian patients, pleural TB was associated with SNP at both −1082 and +874.69 No association with −1082 SNP was found in studies carried out in Gambia,65 Korea,73 Spain52 and south Indian populations.57 In Korea, the C allele at IL-10 −592 and the ht2 haplotype73 were slightly protective; however, no such association was found in IL-10 −592 and −819 polymorphisms in a Chinese population.58 Overall, there is a suggestion of an association of TB with IL-10, especially the −1082 SNP, but the differences in susceptibility are quite modest.
TUMOUR NECROSIS FACTOR-α
Tumour necrosis factor-α (TNF-α) is produced by macrophages, dendritic cells and T cells when stimulated or infected with M. tuberculosis.97,98 In a murine model, the protective role of TNF-α in immunity against M. tuberculosis has been well documented. In mice deficient in TNF-α or the 55-kDa TNF receptor, M. tuberculosis infection resulted in rapid death, with a higher bacterial burden than that observed in control mice.99,100 Furthermore, in the absence of TNF-α or the 55-kDa TNF receptor, the granulomatous response was deficient following acute M. tuberculosis infection in murine models.101,102 However, whether TNF-α is beneficial or detrimental to the clinical course of human TB is still controversial. Although reports of severe disseminated TB in patients treated with anti-TNF agents103,104 underscore the importance of TNF-α in host immunity against the tuberculous bacilli, TNF-α permits the multiplication of M. tuberculosis in human alveolar macrophages.105 Moreover, high levels of TNF-α have been associated with clinical decline in patients with TB.106 Microarray analysis using peripheral blood mononuclear cells from patients with extrapulmonary TB showed increased TNF-α production in peripheral blood mononuclear cells from patients who had recovered from extrapulmonary TB when stimulated with whole lysates of virulent M. tuberculosis, suggesting that higher secretion of TNF-α in humans could be associated with the haematogenous dissemination of M. tuberculosis to other organs.107 The TNF-α−308 G/A polymorphism was found to protect against TB in Sicily;71 and the −308A−238G haplotype was protective in Colombia.75 Studies on TNF-α (–238 G/A, −308 G/A and −376 G/A) and TNF-β gene polymorphisms in Chinese, Cambodian and Indian TB patients revealed no association either with susceptibility or resistance to TB.66,74 A recent meta-analysis including 10 studies found no significant association between −308 G/A on TNF-α gene and the development of TB.77
TRANSFORMING GROWTH FACTOR
Two main SNP have been described for transforming growth factor (TGF)-β1. The first SNP at −509 C-T is in linkage disequilibrium with +29 T-C, encoding leucine 10 to proline at residue 10 and is associated with increased TGF-β1 secretion.108 The second SNP is located at +915 GC, and changes codon 25 arginine to proline. The TGF-β codon 10 polymorphism has been investigated in healthy controls and TB patients, and no significant differences were found in the TGF-β genotypes of the two groups.58,69,76
All these cytokine gene polymorphism studies have had a high degree of heterogeneity in their results, and the modest effects found in most studies make the putative influence of different cytokine SNP on TB susceptibility less credible.
IκB KINASE-γ (NEMO)
Nuclear factor-κB (NF-κB) has attracted scientific attention due to its unusual regulation, the wide variety of stimuli that activate it, and the diverse genes and biological responses that it controls.109–111 Its interaction with the inhibitor of NF-κB (IκB) regulates its cytoplasmic retention and, in turn, NF-κB activities.112,113 The IκB kinase complex (IKK) regulates IκB phosphorylation, leading to its ubiquitination and proteosome degradation, liberating NF-κB to enter the nucleus and initiate its programme of gene transcription. IKK is composed of three subunits: IKKα and IKKβ serve as the catalytic components, while IKKγ (NEMO) is the structural scaffolding that supports the IKK complex.110,114,115 Mutations in IKBKG gene-coding IKKγ (NEMO) protein cause the syndrome of anhidrotic ectodermal dysplasia with immunodeficiency.116 Several reports of mycobacterial diseases including miliary TB in these patients suggest that dysfunction of IKKγ (NEMO) increases ssusceptibility to mycobacteria.117–119
CHEMOKINES AND RECEPTORS
Chemokines are small molecular mass chemotactic cytokines (8–14 kDa) that mediate constitutive recruitment of leucocytes from the blood into tissues. During infection, mycobacteria induce increased expression of CC-chemokine that includes monocyte chemoattractant protein-1 (MCP-1, CCL2), macrophage inflammatory protein-1α (MIP-1α, CCL3), MIP-1β (CCL4), and regulated upon activation normal T cell expressed and secreted (RANTES, CCL5) and CXC chemokine subfamily members, such as IFN-γ-inducible protein-10 (IP-10) (CXCL10) and CXCL8 (IL-8).120–122 The 17q11.2 chromosomal region has been linked to susceptibility to TB and includes genes encoding for several chemokines that may contribute to immunity against TB.123 The associations of selected chemokine and chemokine receptor gene variants with TB are presented in Table 3.
|IL-8||−251 (T/A) (rs4073)||Susceptibility||107||106||Whites||124|
|No association||124||127||South Indian||125|
|CXCR-1 exon2||+2607 G/C||No association||107||106||Whites||124|
|CXCR-2 exon 11||+785 C/T||167||180||African American||124|
|MCP-1 (CCL2)||–2518 (G/A) (rs1024611)||Susceptibility||518†||435||Mexican||131|
|RANTES (CCL5)||−403 G/A (rs2107538), −28 C/G (rs2280788) & In1.1 T/C (rs2280789)||Susceptibility||Chinese||128|
|−403 G/−28 C (haplotype) & GG/CC (diplotype)||Protective||157||76||Caucasian||129|
|MIP-1α (CCL3)||−459 (C/T)||No association||518*||435||Mexican||131|
|MIP-1β (CCL4)||rs1634514 (T/A)||Susceptibility||627||Brazilian||123|
|IP-10 (CXCL10)||−135 (G/A)||Susceptibility||176||240||Chinese||130|
|−1447 (A/G)||No association|
IL-8 (CXCL8) gene polymorphism is associated with susceptibility to human TB, and decreased CXCL8 secretion occurs in HIV-infected patients with miliary TB. In a well-designed study, Ma et al.124 showed an association between the −251 promoter polymorphism of IL-8 and lack of association of its receptor genes +2607 G/C in exon 2 of CXCR-1 and +785C/T in exon 11 of CXCR-2 to human TB susceptibility in two distinct ethnic groups in the USA. However, in south Indian125 and Gambian population no such association was seen with −251 and +781 polymorphisms.126
MONOCYTE CHEMOATTRACTANT PROTEIN–1
Monocyte chemoattractant protein-1, a chemoattractant for monocytes and T lymphocytes, is the central component of the granulomatous response. The G allele of the MCP-1 promoter polymorphism at position −2518 relative to the ATG transcription start codon has been associated with susceptibility to TB in Mexican and Korean populations.131 Persons bearing the GG genotype of MCP-1 −2518 promoter polymorphism produce high concentrations of MCP-1, which inhibits production of IL-12p40 in response to M. tuberculosis and promotes active pulmonary TB. In a group of infected individuals from Mexico, this polymorphism (−2518 G) was five times more prevalent in patients with active TB than in those who remained healthy. However, the same variant was previously reported not to be associated with TB in a Brazilian cohort.123 In the Ghanaian population,127 eight additional MCP-1 polymorphisms were genotyped. Among them MCP-1 −362C was associated with resistance to TB in a case–control study (OR = 0.83, Pcorr = 0.00017) and in affected families (OR = 0.7, Pcorr = 0.004).
MACROPHAGE INFLAMMATORY PROTEIN-1α (CCL3) AND REGULATED UPON ACTIVATION NORMAL T CELL EXPRESSED AND SECRETED (CCL5)
Macrophage inflammatory protein-1 and RANTES are involved in the recruitment of T cells to the site of inflammation, activation of T cells132 and formation of the tuberculous granuloma.133 Functional polymorphisms were studied in the CCL5 gene and TB in a Hong Kong Chinese population.128 This work analysed three SNP in the CCL5 genes (−403 G/A, −28 C/G and In1.1 T/C). Two risk haplotypes of CCL5, A-C-T and G-C-C, at positions −403, −28 and In1.1, respectively, were identified. Furthermore, combining the genotypes of CCL5−403 and In1.1, two diplotypes GA/TT and GG/TC showed strong association with TB. Another study conducted in a Caucasian population129 found that −403 G and −28 C alleles, either separately or combined as G-C haplotype and GG/CC diplotype, may be related to protection against pulmonary TB. By contrast, the −403 A and −28 G alleles, the G-G or A-C haplotypes and the G/G-G/G and A/A-C/C diplotypes may confer susceptibility to pulmonary TB. The study in Mexican and Korean populations did not report significant linkage or association between CCL5 and pulmonary TB. The promoter polymorphism in RANTES −471(A/T), and MIP-1α−459(C/T) alleles or genotypes were not associated with TB.126
INTERFERON GAMMA-INDUCIBLE PROTEIN-10
Interferon gamma-inducible protein, CXCL10, in addition to its chemotactic properties, is also involved in the stimulation of natural killer cells and T cell migration in M. tuberculosis infection.134 A promoter SNP in CXCL-10 (−135 G/A) showed a moderate association with TB, but other SNP (−1447 A/G, −872 G/A) were not associated with TB in a Chinese population.130
SOLUTE CARRIER FAMILY 11A MEMBER 1
Solute carrier family 11A member 1 (SLC11A1), formerly known as natural resistance-associated macrophage protein 1 (NRAMP1), is a human homologue of the mouse gene (Nramp1), in which a single non-conservative amino acid substitution was found to control susceptibility to leishmania, salmonella and mycobacteria in inbred mouse strains.135 SLC11A1 activates microbicidal responses in the infected macrophage, and it is therefore important in the early innate response to mycobacterial infection. Its exact function is unclear, but the fact that it is known to localize to the late endosomal membrane,136 and that it is a bivalent cation antiporter, and has led to speculation that at least part of its role in containing early mycobacterial infection is through the regulation of cytoplasmic cation levels, especially iron.137,138 While iron is an essential mycobacterial nutrient, it is also required by the cell to generate reactive oxygen and nitrogen intermediates. Divalent cations are also essential cofactors for enzymes, such as superoxide dismutase and catalase, which neutralize the cytotoxic effects of the oxidative burst in macrophages.139 The function of SLC11A1 as well as the advantage to host or bacterium of divalent cation transport is therefore in dispute.
The SLC11A1 gene and its association with TB have been extensively studied. The Asn543Asp polymorphism has been reported as a genetic susceptibility factor to TB in Japanese, Korean and Gambian populations.140–142 In addition, the associations between TB and (TGTG) deletion in the 3′ untranslated region (1729 + 55del4) (rs17235416) in Korean, Gambian and South African populations,141–143 between a single nucleotide change in intron 4 (469 + 14 G/C) (rs3731865) and TB in Gambian and Guineans,144 and between a (CA)n repeat polymorphism in the immediate 5′ region and TB among Gambians, Japanese, South Africans and Americans have also been reported.140,142,143,145,146 However, an inverse relationship or lack of the above correlations has also been reported among the various racial groups.66,140,144,147,148 Finally, a recent meta-analysis including 14 case–control studies showed that 3′UTR, D543N (rs17235409) and 5′(GT)n were associated with the development of TB, although racial variation existed (Table 4).
|Polymorphisms||Odds ratio (95% confidence interval)|
|Overall||Asians||African descents||European descents|
|3′UTR||1.33 (1.08–1.63)||1.46 (1.10–1.94)||1.20 (0.86–1.68)||1.81 (0.66–4.93)|
|D543N||1.67 (1.36–2.05)||1.65 (1.29–2.12)||1.69 (1.14–2.50)||1.79 (0.72–4.47)|
|INT4||1.14 (0.96–1.35)||0.91 (0.66–1.25)||1.50 (1.17–1.91)||0.87 (0.61–1.22)|
|5′(GT)n||1.32 (1.03–1.68)||1.86 (1.33–2.62)||1.31 (1.05–1.64)||1.02 (0.35–2.99)|
SLC11A2 (NRAMP2), another member of the SLC11A family of membrane transporters, is an iron transporter,150,151 upregulated by dietary iron deficiency and expressed in many cells and tissues. Although the strong association between TB and iron overload in black South Africans has attracted attention,152 the association between TB and polymorphisms in SCL11A2 was not found in South Africans.143
VITAMIN D RECEPTOR
In the prechemotherapy era, TB was treated with vitamin D supplements, vitamin D-rich diets, and sunlight was the basis of the sanatorium movement.153 Susceptibility to TB has been associated with vitamin D3 deficiency.154,155 Several polymorphisms were found in the gene of the vitamin D receptor (VDR).156 Studies from different populations have determined the differential susceptibility or resistance to TB. A study carried out in 202 pulmonary TB patients and 109 controls from a south Indian population showed a significantly higher frequency of the TaqI tt genotype in female pulmonary TB patients and BsmI (rs1544410) Bb and FF genotypes in male patients.157,158 In a Gujarati Indian population study involving 126 pulmonary TB patients and 116 controls, the FokI (rs10735810) ff genotype was strongly associated with pulmonary TB.155 In a Gambian study carried out in 408 pulmonary TB patients and 414 controls, the TaqI (rs731236) tt genotype was found less frequently in patients, suggesting that this genotype may be associated with resistance to TB.159
A family-based study conducted in a West African population and consisting of 417 TB patients and 722 controls proposed that VDR haplotypes, rather than individual alleles or genotypes, are responsible for the association between TB and VDR variants.160 Moreover, another study of the Venda people in South Africa comprising 95 pulmonary TB patients and 117 controls showed that the F-b-A-T haplotype provided protection against TB.35 In a recent large-scale genetic analysis of native South Americans, the FokI F allele was reported to be associated with protection against infection and TaqI t allele with protection against active disease.161 VDR gene polymorphisms have been associated with the time to sputum culture and auramine stain conversion during anti-TB treatment. In a Peruvian community with a high incidence of TB, the conversions were significantly faster among participants with the FokI FF genotype and TaqI Tt genotype.162 Another similar study involving 249 TB patients and 352 controls from South Africa reported that the ApaI (rs7975232) AA and TaqI T allele containing genotypes were predictive of a faster response to treatment.163
A recent study of 166 pulmonary TB patients and 206 controls from south India showed a significantly decreased frequency of Cdx-2 (rs17883968) G allele and G/G genotype and an increased frequency of A-A haplotype (A allele of Cdx-2 and A allele of A1012G (rs4516035)) in pulmonary TB patients compared with controls. This suggests that the Cdx-2 G/G genotype may be associated with protection and A-A haplotype with susceptibility to TB.164 It emphasizes the need for large family-based studies that will address differential susceptibility. VDR results have confirmed the importance of investigating haplotypes instead of individual SNP.
PATTERN RECOGNITION RECEPTORS
One of the first lines of immune defence is the recognition and uptake of microorganisms by professional phagocytes: macrophages and dendritic cells. On the surface of phagocytic cells are several different pattern recognition receptors, which, in the absence of adaptive immunity, bind to different patterns on microbes to promote phagocytosis and activate signalling that leads to cytokine production, antigen presentation and the development of adaptive immunity. These pattern recognition receptors include toll-like receptors (TLR), scavenger receptors, the complement receptors, mannose-binding lectin (MBL), the dendritic cell-specific intercellular adhesion molecule-3 grabbing nonintegrin, called DC-SIGN, and others. Several of these have been shown to mediate the phagocytosis of M. tuberculosis,165 and have been studied to determine whether different polymorphisms might affect TB susceptibility.166
TOLL LIKE RECEPTORS
The human TLR are pattern recognition molecules that play important roles in early innate immune recognition and inflammatory responses.60,167–170 In addition to their critical roles in innate immunity, TLR are essential in the orientation of the adaptive immune response through the induction of the Th1 immune response.171
Among the 10 human TLR, TLR2 plays a key role in the immune responsiveness to peptidoglycans,172,173 to lipoteichoic acid of Gram-positive bacteria,174 to mycobacterial lipoproteins175 and to leptospiral LPS.176 The fact that TLR2-deficient mice are highly susceptible to M. tuberculosis infection177,178 suggests that TLR2 is one of the indispensable receptors in the immunity against M. tuberculosis infection. In addition, several SNP studies confirmed the crucial roles of TLR2 in the development of TB. Arg753Gln (rs5743708) and Arg677Trp polymorphisms located in the intracellular domain of the TLR2 were reported to be associated with TB in Turkish and Tunisian populations, respectively.179,180 In addition, the genotype of 597CC is associated with susceptibility to TB as a whole (OR = 2.22; 95% CI: 1.23–3.99), with TB meningitis (OR = 3.26; 95% CI: 1.72–6.18), and with miliary TB (OR = 5.28; 95% CI: 2.20–12.65).181 Furthermore, a highly polymorphic guanine-thymine dinucleotide repeat in the 100 bp upstream of the TLR2 translational start site was reported to be associated with TB in Koreans.182,183
TLR4, initially identified as the mediator of LPS inflammatory responses,184 can also interact with both heat-labile soluble mycobacterial factor and whole viable M. tuberculosis to initiate innate responses.185,186 The fact that TLR4 mutant mice, C3H/HeJ, showed a reduced capacity to eliminated M. tuberculosis with lower production of TNF-α, IL-12p40 and MCP-1 suggests a possible role for TLR4 in the human defence system against M. tuberculosis.187 However, the association between clinical TB and the Asp299Gly (rs4986790) polymorphism in the TLR4 gene, which causes hyporesponsiveness to LPS, was excluded in a Gambian population.188 In addition, the small study to test whether Asp299Gly increases chance of developing active TB among HIV-infected individuals in Tanzania failed to reach statistical significance.120
In a large study carried out in Indonesian and Russian populations, four sequence polymorphisms (rs 3764879, rs 3788935, rs 3761624 and rs 3764880) in the TLR8 gene on chromosome X showed evidence of an association with TB susceptibility in men across different populations.189
Mannose-binding lectin belongs to a family of proteins called the collectins, which possess both collagenous regions and lectin domains. This protein consists of multimers of an identical polypeptide chain of 32 kDa. There are two human MBL genes, but MBL1 is a pseudogene and the functional MBL2 gene encodes MBL protein. Inter-individual variations in the serum MBL levels are mainly due to the presence of three common point mutations in exon1 of MBL2 gene at the codons 52 (rs5030737), 54 (rs1800451) and 57 (rs1800450). MBL plays an important role in host defence against pathogens. Upon binding with certain carbohydrate moieties, such as terminal N-acetylglucosamine or mannose on various pathogens, MBL activates complement via specific protease and acts directly as an opsonin using the C1q receptor on macrophages. Mutations at codons 52, 54 and 57 lead to low or near absent serum MBL levels in heterozygotes and homozygotes, respectively.
Several groups have studied MBL genotypes and TB, following a suggestion that MBL deficiency might have had an evolutionary advantage by reducing the capacity of mycobacteria to invade macrophages in the absence of MBL, so leading to resistance to TB.190 A study carried out in South Africa suggested that MBL-54 heterozygotes may have protection against tuberculous meningitis191 and a study carried out in 202 pulmonary TB patients and 109 control subjects of a south Indian population revealed an increased genotype frequency of MBL functional mutant homozygotes (including codons 52, 54 and 57) in pulmonary TB compared with control subjects.192 However, studies in China,193 Poland,194 Turkey,195 Malawi,54 Tanzania196 and Gambia,197 found no association.
DENDRITIC CELL-SPECIFIC INTERCELLULAR ADHESION MOLECULE-3 GRABBING NONINTEGRIN
Dendritic cell-specific intercellular adhesion molecule-3 grabbing non-integrin, is a lectin present on macrophages and monocyte-derived dendritic cells that recognizes many pathogens, including M. tuberculosis through the cell wall lipoglycan, manlam.198 Two variants (−871G (rs735239) and −336A (rs4804803)) have been identified in the promoter region of CD209, the gene for DC-SIGN, and the −336A allele has been shown to increase its expression. In a South African study, consisting of 351 TB patients and 360 controls, these two variants were associated with a lower risk of developing TB, and the alternate nucleotides with an increased risk (−871A OR = 1.85 (95% CI: 1.29–2.66); −336G OR = 1.48 (95% CI: 1.08–2.02)).199 The protective allele, −871G, was present in 21% and 38% of Asians and Europeans, respectively, but was absent in Africans; it has been postulated that this could contribute to the putative increased TB susceptibility in this ethnic group.199 A subsequent study from Colombia found no significant association between TB and the −336 allele, although the frequency of this allele was very low in the population studied.65 A recent study carried out in south India revealed no significant association of −336 allele with TB.200 Although DC-SIGN is an attractive candidate for influencing TB susceptibility, further studies are needed to prove an association.
SURFACTANT PROTEINS AND COMPLEMENT RECEPTOR-1
Lung surfactant proteins (SP), such as SP-A and SP-D, are collagen-containing calcium-dependent lectins called collectins, and are structurally similar to MBL. They recognize many pathogens via their lectin domains and activate immune cells through their collagen region. SP-A is a multichain protein encoded by the SFTP-A1 and SFTB-A2 genes, and several polymorphisms in the SFTP-A2 gene were found to be associated with susceptibility to TB in Ethiopia,201 Mexico202 and India.203 The complement receptor-1 (CR1) present on the surface of the macrophages is associated with phagocytosis of various microorganisms, including M. tuberculosis. A large-scale study in Malawi revealed that homozygotes in one of five CR1 polymorphisms (Q1022H) are associated with increased TB risk. The SNP causes an amino acid change that alters ligand binding, perhaps reducing the phagocytosis of M. tuberculosis.54
THE PURINERGIC P2X7 RECEPTOR
Purinergic P2X7 receptors are cationic channels present on the cells in the blood and immune systems, and are highly expressed on macrophages.204 The P2X7 receptor is activated by extracellular ATP, which causes their cation-selective channel to open, leading to an influx of calcium and induction of the caspase cascade, resulting in apoptosis and mycobacterial killing. A polymorphism with a 1513 A-C (rs3751143) change that causes the glutamic acid at residue 496 to be replaced by alanine, was not associated with pulmonary TB in a case–control study in Gambia;205 however, this study identified five SNP and in one, at −762, the presence of a C showed significant protection against TB. It was suggested that the C at −762 could affect the level of P2X7 expression by altering the binding of a transcription factor. A study of two cohorts of Southeast Asian refugees in Australia found no association of the 1513 SNP with pulmonary TB, but, surprisingly, found a strong association between the C polymorphism and extrapulmonary TB.206 Furthermore, in vitro studies showed that the ATP-mediated killing of mycobacteria was absent in macrophages from patients homozygous for the 1513 C allele, and impaired in macrophages from heterozygous subjects. There was a strong correlation between the capacity for mycobacterial killing and ATP-induced apoptosis.
The development of TB or other mycobacterial diseases is the result of a complex interaction between the host and pathogen influenced by environmental factors. Susceptibility to TB in humans appears to be highly polygenic with many loci implicated but only minority of these convincingly proven. Heterogeneity of genetic and allelic association is frequently observed when comparing results between populations and has many causes, including epistasis, wherein one gene interferes with or prevents the expression of another gene located at a different locus. Although susceptibility to TB is determined by many different genes, each having small effects, and the genes may be different in different populations, the great majority of susceptibility genes are as yet not identified.
Genetic susceptibility or resistance to TB infection is determined by pathogen as well as host factors. In line with this, a west African Ghana population study revealed that autophagy gene variant immunity-related GTPase M (IRGM) 2261T was associated with protection from TB caused by M. tuberculosis but not by M. africanum strains.207 The high prevalence of IRGM 2261TT in the Ghanaian population and the relative protection that it confers from TB caused by M. tuberculosis Euro-American lineage substantiates that lineages have become differentially adapted to different ethnicities with allelic variations conferring traits associated with certain infection phenotypes.208 These studies suggest the potential role of pathogen factors as well as host factors in the immunopathogenesis of TB and investigations in this direction are warranted.
At this point in time, however, we should admit that the achievements of genetics studies might not as yet have advanced the prevention and treatment of TB. So far, the major target of genetic studies on TB patients has been to elucidate the immunopathogenesis of TB through the research focused on the human genes associated with susceptibility to or the clinical manifestation of TB. However, researchers began to widen the scope to more practical fields, such as VDR gene polymorphisms associated with sputum culture and auramine stain conversion during anti-TB treatment,163 association of IFNG + 874 AA genotype with a lower likelihood of sputum conversion,85 as well as genetic trait associated with the response to Bacillus Calmette-Guérin vaccination209 or anti-TB drug-induced hepatitis.210 In fact, IFN-γ treatment or bone marrow transplantation were successfully used in patients with disseminated non-tuberculous mycobacterial infection, based on knowledge of the genetic mutations of specific patients.211 These studies highlight the potential role of immunogenetics in the clinical management of TB and warrant investigations aimed at the replication of significant findings in large cohorts, enabling translation of research findings to the clinical setting. We believe that, in the near future, genetic studies will be no longer just ‘curiosities’ but may well be the leading edge of a major weapon against TB.
The authors thank Mr S. Raghavan, Mr S. Prabhu Anand and Mr M. Hari Shankar (Doctoral students of Dr P.S.), Tuberculosis Research Centre, Chennai, India, for their help in preparing this article.
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