The complex pattern of genetic associations of leprosy with HLA class I and class II alleles can be reduced to four amino acid positions.

Leprosy is a chronic disease caused by Mycobacterium leprae. Worldwide, more than 200,000 new patients are affected by leprosy annually, making it the second most common mycobacterial disease after tuberculosis. The MHC/HLA region has been consistently identified as carrying major leprosy susceptibility variants in different populations at times with inconsistent results. To establish the unambiguous molecular identity of classical HLA class I and class II leprosy susceptibility factors, we applied next-generation sequencing to genotype with high-resolution 11 HLA class I and class II genes in 1,155 individuals from a Vietnamese leprosy case-control sample. HLA alleles belonging to an extended haplotype from HLA-A to HLA-DPB1 were associated with risk to leprosy. This susceptibility signal could be reduced to the HLA-DRB1*10:01~ HLA-DQA1*01:05 alleles which were in complete linkage disequilibrium (LD). In addition, haplotypes containing HLA-DRB3~ HLA-DRB1*12:02 and HLA-C*07:06~ HLA-B*44:03~ HLA-DRB1*07:01 alleles were found as two independent protective factors for leprosy. Moreover, we replicated the previously associated HLA-DRB1*15:01 as leprosy risk factor and HLA-DRB1*04:05~HLA-DQA1*03:03 as protective alleles. When we narrowed the analysis to the single amino acid level, we found that the associations of the HLA alleles were largely captured by four independent amino acids at HLA-DRß1 positions 57 (D) and 13 (F), HLA-B position 63 (E) and HLA-A position 19 (K). Hence, analyses at the amino acid level circumvented the ambiguity caused by strong LD of leprosy susceptibility HLA alleles and identified four distinct leprosy susceptibility factors.

Family-based genome-wide association study of leprosy in Vietnam.

Leprosy is a chronic infectious disease of the skin and peripheral nerves with a strong genetic predisposition. Recent genome-wide approaches have identified numerous common variants associated with leprosy, almost all in the Chinese population. We conducted the first family-based genome-wide association study of leprosy in 622 affected offspring from Vietnam, followed by replication in an independent sample of 1181 leprosy cases and 668 controls of the same ethnic origin. The most significant results were observed within the HLA region, in which six SNPs displayed genome-wide significant associations, all of which were replicated in the independent case/control sample. We investigated the signal in the HLA region in more detail, by conducting a multivariate analysis on the case/control sample of 319 GWAS-suggestive HLA hits for which evidence for replication was obtained. We identified three independently associated SNPs, two located in the HLA class I region (rs1265048: OR = 0.69 [0.58-0.80], combined p-value = 5.53x10-11; and rs114598080: OR = 1.47 [1.46-1.48], combined p-value = 8.77x10-13), and one located in the HLA class II region (rs3187964 (OR = 1.67 [1.55-1.80], combined p-value = 8.35x10-16). We also validated two previously identified risk factors for leprosy: the missense variant rs3764147 in the LACC1 gene (OR = 1.52 [1.41-1.63], combined p-value = 5.06x10-14), and the intergenic variant rs6871626 located close to the IL12B gene (OR = 0.73 [0.61-0.84], combined p-value = 6.44x10-8). These results shed new light on the genetic control of leprosy, by dissecting the influence of HLA SNPs, and validating the independent role of two additional variants in a large Vietnamese sample.

Excavating the surface-associated and secretory proteome of Mycobacterium leprae for identifying vaccines and diagnostic markers relevant immunodominant epitopes.

For centuries, Mycobacterium leprae, etiological agent of leprosy, has been afflicting mankind regardless of extensive use of live-attenuated vaccines and antibiotics. Surface-associated and secretory proteins (SASPs) are attractive targets against bacteria. We have integrated biological knowledge with computational approaches and present a proteome-wide identification of SASPs. We also performed computational assignment of immunodominant epitopes as coordinates of prospective antigenic candidates in most important class of SASPs, the outer membrane proteins (OMPs). Exploiting the known protein sequence and structural characteristics shared by the SASPs from bacteria, 17 lipoproteins, 11 secretory and 19 novel OMPs (including 4 essential proteins) were identified in M. leprae As OMPs represent the most exposed antigens on the cell surface, their immunoinformatics analysis showed that the identified 19 OMPs harbor T-cell MHC class I epitopes and class II epitopes against HLA-DR alleles (54), while 15 OMPs present potential T-cell class II epitopes against HLA-DQ alleles (6) and 7 OMPs possess T-cell class II epitopes against HLA-DP alleles (5) of humans. Additionally, 11 M. leprae OMPs were found to have B-cell epitopes and these may be considered as prime candidates for the development of new immunotherapeutics against M. leprae.

Differential trafficking of TLR1 I602S underlies host protection against pathogenic mycobacteria.

We recently identified I602S as a frequent single-nucleotide polymorphism of human TLR1 that greatly inhibits cell surface trafficking, confers hyporesponsiveness to TLR1 agonists, and protects against the mycobacterial diseases leprosy and tuberculosis. Because mycobacteria are known to manipulate the TLR system to their advantage, we hypothesize that the hyporesponsive 602S variant may confer protection by enabling the host to overcome this immune subversion. We report that primary human monocytes and macrophages from homozygous TLR1 602S individuals are resistant to mycobacterial-induced downregulation of macrophage MHC class II, CD64, and IFN-γ responses compared with individuals who harbor the TLR1 602I variant. Additionally, when challenged with mycobacterial agonists, macrophages from TLR1 602S/S individuals resist induction of host arginase-1, an enzyme that depletes cellular arginine stores required for the production of antimicrobial reactive nitrogen intermediates. The differences in cell activation mediated by TLR1 602S and TLR1 602I are observed upon stimulation with soluble mycobacterial-derived agonists but not with whole mycobacterial cells. Taken together, these results suggest that the TLR1 602S variant protects against mycobacterial disease by preventing soluble mycobacterial products, perhaps released from granulomas, from disarming myeloid cells prior to their encounter with whole mycobacteria.

Distribution of the HLA class II frequency alleles in patients with leprosy from the mid-west of Brazil.

In an attempt to clarify the issue of genetic predisposition to leprosy, we examined the distribution of class II human leucocyte antigen variants (DR and DQ) in 70 patients from around the city of Goiânia, Brazil. Only two of the patients presented the tuberculoid form of the disease, whereas 17 fell into the lepromatous category; 51 were intermediate. The allele frequencies found were compared with those in a group of 77 healthy controls. We found an increased frequency of the HLA-DRB1*11 allele in patients with lepromatous leprosy compared with healthy controls (P=0.0132; RR=4.130, 95% Cl: 1.338 to 12.747). These results suggest that the DRB1*11 allele could be related with susceptibility to lepromatous leprosy in Brazil.

HLA associations in leprosy patients from Mumbai, India.

Genetic predisposition to both disease susceptibility and to host immune response has been postulated. In India, about 64% of leprosy prevalence and 78% of new case detection of the worlds estimated 719,330 cases occur. Convincing results have been reported from studies on HLA class II association in leprosy. However data on HLA class I association are limited and inconsistent. The HLA A, B and C allele distribution in 103 leprosy patients and 101 normal healthy control individuals were studied by microlymphocytotoxicity assay. Further 32 multibacillary leprosy patients along with the 67 controls were studied by molecular high-resolution PCR-SSOP technique. The significant results from the present study were: 1) serologically, a significant increase in HLA A2, A11, B40 and Cw7, while a decrease of A28, B12, B15 and Cw3 were observed among the leprosy patients when compared with the controls; 2) molecular subtyping in multibacillary leprosy patients revealed a significant increase in frequency of HLA A*0203, A*0206, A*1102, B*1801, B*4016, B*5110, Cw*0407 and Cw*0703 while a decrease in the frequency of HLA A*0101, A*0211, B*4006, Cw*03031, Cw*04011 and Cw*0602 leprosy patients was observed when compared with the controls; 3) further haplotypes A*1102-B*4006-Cw*1502; A*0203-B*4016-Cw*0703; A*11-B*40 was significantly increased among the multibacillary leprosy patients when compared with the controls. It seems that HLA class I alleles play vital roles in disease association/pathogenesis.

Immunogenetics of uveitis in leprosy.

PURPOSE: To identify any possible determinants in the development of uveitis in leprosy patients. METHODS: Human leukocyte antigen (HLA) class I and II antigen, and HLA class II genotypings were analyzed among Japanese leprosy patients. Ninety-three unrelated Japanese leprosy patients (46 patients with a history of uveitis and 47 patients without uveitis) and 114 healthy control subjects were investigated. RESULTS: The occurrence of HLA-DR2 was significantly higher in patients with uveitis (78.3%) than in those without uveitis (57.4%; odds ratio = 2.7, P<.05) and in the controls (33.3%; odds ratio = 7.2, P<.0000005, Pc<.00005). The occurrence of HLA-DR4 was significantly lower in patients with uveitis (15.2%) than in those without it (38.3%; odds ratio = 0.29, P<.05) and in the controls (46.5%; odds ratio = 0.21, P<.0005, Pc<.05). Furthermore, the frequencies of DR2-positive and DR4-negative genotypes were significantly higher in patients with uveitis (69.6%) than in those without it (38.3%; odds ratio = 3.7, P<.005) and in the controls (21.9%; odds ratio = 8.1, P<.00000005). At the genomic level, the occurrence of HLA-DQB1*0302 was significantly lower in the patients with uveitis (8.7%) than in those without it (25.5%; odds ratio = 0.28, P<.05). The distribution of HLA-DRB1 and DQA1 alleles was not significantly different between the patients with and those without uveitis. However, the frequencies of DRB1*1501-positive, as well as DRB1*0405- and DQB1*0302-negative genotypes were significantly higher in the patients with uveitis (47.8%) than in those without it (25.5%; odds ratio = 2.7, P<.05) and in the controls (8.8%; odds ratio = 9.5, P<.00000005). CONCLUSIONS: Our results suggest that HLA Class II genes confer susceptibility to or protection from leprous uveitis.

[HLA class II alleles and leprosy (Hansen's disease) classified by WHO-MDT criteria].

Human leukocyte antigens (HLA) class II alleles were analyzed in Japanese leprosy patients to ascertain whether immunogenetic differences exist among the forms of leprosy in classification of World Health Organization-recommended multidrug therapy (WHO-MDT). The subjects were 86 unrelated Japanese leprosy patients, including 62 multibacillary leprosy (MBL), 24 paucibacillary leprosy (PBL). Controls were 114 unrelated healthy subjects. Genotyping of HLA class II alleles was performed by using the polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) and PCR-restriction fragment length polymorphism (RFLP) methods. The frequencies of HLA-DRB1* 1501, * 1502 and DRB5* 0101,* 0102 and DQA1* 0102 and DQB1* 0602 were significantly increased in the whole patients (44.2%, 34.9%, 44.2%, 34.9%, 53.4% and 41.9%, respectively) as compared with the control subjects (14.0%, 21.1%, 14.0%, 21.1%, 27.2% and 13.2%, respectively). On the other hand, the frequencies of HLA-DRB1* 0405, * 0803, * 0901 and DQA1* 03 and DQB1* 0401 were significantly decreased in the whole patients (10.5%, 5.8%, 16.3%, 41.9% and 9.3%, respectively) as compared with the control subjects (29.8%, 17.5%, 30.7%, 78.1% and 29.8%, respectively). When MBL and PBL patients were compared, the frequencies of HLA-DRB1* 1501, DRB5* 0101 and DQB1* 0602 were significantly increased in the MBL patients (51.6%, 51.6% and 48.4%, respectively) as compared with the PBL patients (25.0%, respectively). Our results suggest that HLA-DRB1* 1501, DRB5* 0101 and DQB1* 0602 contribute to the susceptibility to the Japanese MBL.

The biologic importance of conserved major histocompatibility complex class II motifs in primates.

Phylogenetic comparisons of polymorphic second-exon sequences of MHC class II DRB genes showed that equivalents of the HLA-DRB1*03 alleles are present in various nonhuman primate species such as chimpanzees, gorillas, and rhesus macaques. These alleles must root from ancestral structure(s) that were once present in a progenitor species that lived about 35 million years ago. Due to accumulation of genetic variation, however, sequences that cluster into a lineage are generally unique to a species. To investigate the biologic importance of such conservation and variation, the peptide-binding capacity of various Mhc-DRB1*03 lineage members was studied. Primate Mhc-DRB1*03 lineage members successfully binding the p3-13 peptide of the 65-kD heat-shock protein of Mycobacterium tuberculosis/leprae share a motif that maps to the floor of the peptide-binding site. Apart from that, some rhesus macaque MHC class-II-positive cells were able to present the p3-13 peptide to HLA-DR17-restricted T cells whereas cells obtained from great ape species failed to do so. Therefore, these studies open ways to understand which MHC polymorphisms have been maintained in evolution and which MHC residues are essential for peptide binding and T-cell recognition.

Evidence for an HLA-DR4-associated immune-response gene for Mycobacterium tuberculosis. A clue to the pathogenesis of rheumatoid arthritis?

Antigens of Mycobacterium tuberculosis, M leprae, M scrofulaceum, and M vaccae were injected intradermally in 86 caucasoid leprosy patients, and skin responses (measured in mm of induration at 72 h) were analysed in relation to HLA class II phenotypes. HLA-DR4 was associated with high responsiveness to antigens specific to M tuberculosis but not to antigens shared with other mycobacteria (p = 0.0005). Because DR4 is associated with rheumatoid arthritis (RA) and because a role for M tuberculosis antigens has been suggested both in experimentally induced autoimmune arthritis in rats and in RA, the DR4 associated regulation of the immune response to M tuberculosis may be relevant to the pathogenesis of RA.

Leprosy associated with HLA-DR2 and DQw1 in the population of northern Thailand.

A study of the frequency of HLA-DR2 and DQw1 was performed in leprosy patients and controls in northern Thailand. HLA-DR2 was found in 100% (17/17) of patients with sporadic tuberculoid leprosy and in over 90% (30/32) of all tuberculoid leprosy patients, as compared to 62% (20/32) of controls (p = .02). These strong associations had relative risks of 21.4 for sporadic and 7.4 for all tuberculoid leprosy, and etiologic fractions of 1.0 and 0.84, respectively. There was also a statistically significant and strong association between tuberculoid leprosy and DQw1. These data add to the growing body of evidence that products of HLA class II determinants or closely linked genes may play a role in determining the clinical manifestations of M. leprae infection.

HLA-linked control of predisposition to lepromatous leprosy.

In a study of the relation between HLA and lepromatous leprosy, HLA haplotype segregation was analyzed in 28 families with multiple cases of different types of leprosy. The inheritance of HLA-DR2, HLA-DR3, and HLA-MT1, which had previously been shown to be associated with susceptibility to leprosy or with a leprosy type, was analyzed separately. Segregation occurred in a significantly nonrandom fashion in both polar tuberculoid leprosy and lepromatous leprosy. This finding indicated HLA-encoded control of a predisposition to both of these forms of the disease. In both cases the segregation observed among healthy siblings was random. Thus, susceptibility to leprosy per se is probably not controlled by HLA-linked genes. HLA-DR3 was inherited preferentially by children with polar tuberculoid leprosy rather than lepromatous disease (P = .02), and HLA-MT1 was inherited preferentially by children with lepromatous leprosy (P = .04). The results confirmed the association of these genetic markers with leprosy type.

A study of HLA-DR2 associated HLA-Dw/LD specificities.

HLA-Dw2 and Dw12 are both associated with HLA-DR2; however, these specificities accounts for only 86% (161/188) of the DR2+ haplotypes in our North American Caucasian panel. In an attempt to identify new DR2 associated antigenic clusters, we have generated four primed lymphocyte (LD) typing (PLT) reagents in haploidentical familial combination against DR2+ Dw blank haplotypes. These reagents were positively restimulated by 11 of 16 DR2+ Dw blank cells tested, with good discrimination from Dw2 and Dw12+ cells, thus identifying a new antigenic cluster provisionally termed LD-MN2. We have compared the LD-MN2 specificity with the specificity LD-5a defined by two DR2+ HTCs, BAS and REM, (Layrisse, Caracas) which have been included in the pre-1984 Workshop Cluster DB9. Although none of our DR2+ cells gave typing responses to these two HTCs defining LD-5a, PLT studies did indicate an interrelationship between these specificities and with the specificity tb24 defined with the HTC, FJO (Betuel). The LD-5a HTCs, four LD-5a heterozygous cells, and two additional HTCs (WJR-Hansen, Seattle and FJO/tb24--Betuel, Lyon) significantly restimulated the anti-MN2 PLT reagents, though usually not as strongly as the MN2+ cells. MN2+ cells primed against the LD-5a HTCs were restimulated by only the LD-5a+ cells. Dw2+ cells primed against FJO were restimulated by some, but not all MN2+ cells. These results suggest that MN2, tb24, and LD-5a share some determinants, not shared with most cells which type as Dw2 and Dw12, though differing by other stimulatory determinants. These studies emphasize the necessity of studying new antigenic clusters by both PLT and HTC methodologies as well as testing different ethnic groups.

Association of HLA specificity LB-E12 (MB1, DC1, MT1) with lepromatous leprosy in a Venezuelan population.

To investigate whether an association could be found between HLA and lepromatous leprosy a population study was performed in Tachira, Venezuela. This was done in the same endemic area in which recently both non-random parental HLA-haplotype and preferential segregation of the HLA specificity LB-E12 (MB1, DC1, MT1) was demonstrated in lepromatous leprosy patients from multicase families. In this study 32 lepromatous patients and 32 healthy controls were typed for HLA-A, -B, -C, -DR and the specificities MB and MT. The frequency of LB-E12 (MB1, DC1, MT1) showed a significant increase in lepromatous leprosy patients (p = 0.04). This is the first report concerning HLA and leprosy which confirms in the same endemic area an association observed in families on the population level.

Analysis of the immunogenetic background of Japanese leprosy patients by the HLA system.

295 lepromatous and 74 tuberculoid leprosy patients were typed for HLA-A, -B and -C and compared to 110 healthy controls. It was found that frequency of HLA-B7 was significantly high and that of Bw54 was significantly low in lepromatous leprosy. HLA-DR and MT types were investigated in 84 lepromatous and 28 tuberculoid patients and compared to 55 controls. Both lepromatous and tuberculoid patients showed a marked increase in DR2 frequency. The relative risk is 8.7 and 5.9. Lepromatous leprosy showed an increase in frequency of MT1 and decreases in those of DRw9 and MT3 too.

Studies on the defect in cell-mediated immunity in lepromatous leprosy using HLA-D-identical siblings. Absence of circulating suppressor cells and evidence that the defect is in the T-lymphocyte, rather than the monocyte, population.

Sixteen healthy siblings were identified as HLA-D-identical to 12 borderline lepromatous or polar lepromatous leprosy patients by the absence of a mixed lymphocyte reaction (MLR). The peripheral blood mononuclear cells (PBM) of the healthy siblings showed a lymphoproliferative response (delta cpm) to Mycobacterium leprae antigens which was about fivefold or more greater than that of the lepromatous patients. Lepromatous PBM, with or without mitomycin C treatment, were co-cultured with a constant number of normal PBM. In other experiments the two cell types were co-cultured in various proportions, with the total cell number kept constant. Neither approach revealed suppressor cells in lepromatous PBM capable of suppressing the lymphoproliferative response to M. leprae. On the contrary, we found that lepromatous PBM can respond to M. leprae antigens if the sensitized lymphocyte is provided by mitomycin-C treated normal PBM. Additionally, experiments in which isolated adherent cells and non-adherent cells of sibling pairs were recombined failed to reveal a defect in the M. leprae antigen-presenting function of lepromatous adherent cells. Since we found no evidence that sensitized cells are present in lepromatous PBM with their function unexpressed (due to a monocyte defect) or suppressed (due to suppressor cells), we conclude that lepromatous patients simply lack sufficient numbers of antigen-specific T lymphocytes to initiate a lymphoproliferative response to M. leprae antigens. The reason for their absence remains an important unanswered question.