Association between HLA-DR4 haplotypes and tuberculin skin test response in the Aché population.

The human leukocyte antigen (HLA) system has a major role in the regulation of the immune response as it is involved in the defense against pathogens. Evidence for association with tuberculosis (TB) is more consistent for class II than for class I HLA genes. TB is important among indigenous peoples in South America, not only because of its historical role in regional depopulation, but also because it is still widespread. The aim of this study was to evaluate the association of HLA class II alleles, haplotypes and genotypes and tuberculin skin test response (TST) in 76 individuals of the Aché population. Poisson Regression was employed to assess risk genotypes. DRB1*04, DQA1*03 and DQB1*03:02 were associated with TST response in this population.

Distribution patterns of variability for 18 immune system genes in Amerindians--relationship with history and epidemiology.

Native American populations generally have a higher prevalence of infectious diseases than non-Native populations and this fact can induce different pressures in their immune system. We investigated the patterns of population differentiation (FST ) of 32 polymorphisms related to adaptive immune response in four Native American populations (Aché, Guarani-Kaiowá, Guarani-Ñandeva and Kaingang), and the results were compared with the three major world population data [Yoruba of Ibadan, Nigeria (YRI), Utah residents with northern and Western Europe ancestry (CEU) and Han Chinese of Beijing, China (CHB)] available in the HapMap database. The Aché clearly differentiated from the other Amerindians, but when all Native Americans were compared with the samples of other ethnic groups the lowest difference (0.08) was found with CHB (Asians), the second lowest (0.15) with YRI (Africans) and the most marked with CEU (European-derived). The considerable intra and interethnic differences found can be explained both in terms of diverse evolutionary distances and more recent environmental pathogen exposures; and they should be appropriately considered prior to any specific public health action.

HLA and MICA genes in patients with tuberculosis in Brazil.

Major histocompatibility complex (MHC) genes have been investigated because of their crucial role in the defense against pathogens and their high degree of polymorphism. We performed a case-control study to assess a genetic association of MHC genes with susceptibility to tuberculosis (TB). The allelic lineages HLA-A*02 and B*18 were significantly less frequent in TB patients (n = 112, 44.6% women) than in controls (n = 224, 51.5% women): 18.8% vs 26.5%; odds ratio (OR) = 0.64; P = 0.037 and 2.7% vs 6.9%; OR = 0.37; P = 0.041. The negative association with haplotype HLA-B*18-MICA*018 (2.3% patients vs 6.4% controls; OR = 0.34; P = 0.035) was significant as a consequence of strong linkage disequilibrium (D' = 0.827 for patients and 0.923 for controls). These findings suggest a trend toward protection of the HLA-A*02 and HLA-B*18 alleles.

Frequencies of MICA alleles in patients from southern Brazil with multibacillary and paucibacillary leprosy.

Leprosy is a chronic infectious disease caused by Mycobacterium leprae, which mainly affects the skin and nervous system. The disease has several clinical forms. This study investigated the MICA and HLA-B genes in 223 samples from leprosy patients and 201 samples from healthy individuals matched for age, gender and ethnical background. Of the patients, 153 had multibacillary, 45 paucibacillary and 25 indeterminate leprosy. The aim of this case-control study was to assess whether the MICA alleles influence susceptibility for leprosy or affect the subtype of the disease in a population of southern Brazil. There were significant differences in frequencies of the MICA*027 allele (4.7% vs 1.8%, P-value = 0.01, OR = 0.37; 95% CI = 0.16-0.85) between leprosy patients and controls, and of the MICA*010 (4.5% vs 1.6%, P-value = 0.05, OR = 0.35, 95% CI = 0.13-0.97) and MICA*027 alleles (4.7% vs 1.3%, P-value = 0.01; OR = 0.27; 95% CI = 0.09-0.79) between multibacillary leprosy patients and the control group. There were no significant differences in the frequency of MICA alleles between paucibacillary leprosy patients and controls. Thus, the MICA*027 allele is associated with a protective effect for leprosy per se, while the MICA*010 and MICA*027 alleles are associated with protection against multibacillary leprosy, the most severe clinical subtype.

High frequencies of alleles MICA*020 and MICA*027 in Amerindians and evidence of positive selection on exon 3.

MICA is a nonclassical polymorphic MHC molecule. We investigated MICA allelic frequencies and MICA-HLA-B-HLA-C haplotypes in Brazilian Amerindians to describe the polymorphism and to extract information about the evolution of MICA gene. Kaingang is the first population described to have a high frequency of MICA*020, found associated with HLA-B*3505-HLA-Cw*0401. Allele MICA*020 probably originated de novo in South America. The Guarani population had high frequencies of MICA*027. Allele MICA*00801 is common worldwide but rare among Amerindians, occurring only because of gene flow. The analysis of the 64 described MICA alleles revealed that in exons 2 and 4, synonymous substitutions are in excess, a result compatible with purifying selection. The opposite was observed for exons 3 and 6 and the excess of nonsynonymous substitutions was significant for exon 3, indicating positive selection. Few of the alleles described so far had exon 6 sequenced, impeding conclusions for the corresponding portion of the molecule. The analysis of the entire gene is required for a better understanding of the evolution of MICA's polymorphism and its functional consequences. This knowledge is of prime importance in view of the increasing awareness of the functional and medical implications of MICA gene variability.

Association between killer-cell immunoglobulin-like receptor genotypes and leprosy in Brazil.

The aim of this study was to investigate the role of killer cell immunoglobulin-like receptor (KIR) genes in leprosy immunopathogenesis. Genotyping of KIR and human leukocyte antigen (HLA) genes was performed by polymerase chain reaction with sequence-specific oligonucleotide probes in 165 leprosy patients. Both activating KIR2DS2 and KIR2DS3 frequencies were higher in tuberculoid leprosy (TT) patients than in lepromatous leprosy (LL) patients, and the inhibitory KIR with its ligand, KIR2DL1-C2/C2, was elevated in TT patients in comparison to all other leprosy subgroups and controls. However, a negative association between KIR2DL3-C1 and KIR2DL3-C1/C1 and the TT group was identified. Borderline patients exhibited a higher frequency of KIR3DL2-A3/11 than the controls and LL patients, and a lower frequency of KIR2DL1-C2 than the controls and TT subgroup. Some KIR-HLA genotypes could be associated to the development of clinical forms of leprosy and should be investigated further.

IL2 and TNFA gene polymorphisms and the risk of graft-versus-host disease after allogeneic haematopoietic stem cell transplantation.

This study aimed to analyse the association of gene polymorphisms with the outcome of allogeneic haematopoietic stem cell transplantation. We studied 122 donor/recipient pairs who received HLA-identical transplants from siblings at the Universidade Estadual de Campinas, Brazil, between June 1996 and June 2006. Donor/recipient alleles for TNFA-238 and IL2-330/+166 single-nucleotide polymorphisms (SNP) were analysed by PCR-SSP. No association was observed between the risk of acute graft-versus-host disease (GVHD) and these SNP. However, our findings suggest that the polymorphism of promoter gene TNFA-238GA is associated with the occurrence and severity of chronic GVHD. The probability of chronic GVHD in patients with GA genotype at position -238 of TNFA gene is 91.7% in contrast to 59.4% in patients with GG genotype (P = 0.038). In patients with donor GA genotype the probability of chronic GVHD is 90.8%, and 57.9% in patients with donor GG genotype (P = 0.038). The probability of extensive chronic GVHD in patients with TNFA-238GA is 91.7% compared with 46.3% in patients with TNFA-238GG (P = 0.0046). In patients with donor GA genotype at position -238 of the TNFA gene, it is 81.7%, compared with 44.5% in patients with donor GG genotype (P = 0.016). However, further studies with more patients are required to identify cytokine gene polymorphisms and their association with transplant-related complication in Brazil, particularly due to ethnic background, the relatively low power of detection of genetic markers of this study, and the complexity of the MHC region.

Diversity of the MBL2 gene in various Brazilian populations and the case of selection at the mannose-binding lectin locus.

The mannose binding lectin (MBL2) polymorphism is responsible for a common immunodeficiency in the human species. There were suggestions that the MBL2 polymorphism has been under balancing selection, based on the high global frequency of alleles generating MBL deficiency and on the worldwide distribution of diseases negatively associated with them. To describe the distribution of MBL2 allelic haplotypes in Brazilian populations and to discuss the evolution of this polymorphism, we analyzed six South Brazilian populations (152 Guarani Amerindian, 239 Kaingang Amerindian, 107 admixed, Brazilian 32 Afro-Brazilian, 202 Euro-Brazilian and 16 Oriental-Brazilian). Eight haplotypes were observed: MBL2*HYPA, LYQA, LYPA, LXPA, LYPB, LYQC, HYPD, and LYPD. In addition, through sequencing of the promoter and exon 1 from Amerindian and Oriental individuals, three new single-nucleotide polymorphisms (SNPs) were found in the MBL2 promoter region in the Kaingang. Analysis of the sequencing data by neutrality tests (Tajima's D and Fu and Li's D* and F*) revealed no deviation from selective neutrality equilibrium in the Guarani and Kaingang. Significant Fay and Wu's H results are explained by the recent gene flow in these populations. Contrarily to previous thoughts, stochastic evolutionary factors seem therefore to have had a predominant role in shaping the MBL2 polymorphism, at least in the Amerindians.

Association of leprosy with HLA-DR2 in a Southern Brazilian population.

The association between HLA specificities and leprosy was investigated in a southern Brazilian population. One hundred and twenty-one patients and 147 controls were typed for HLA-A, B, Cw, DR and DQ. Patients were subdivided into the following subgroups, according to clinical, histological and immunological criteria: lepromatous (N = 55), tuberculoid (N = 32), dimorphous (N = 20), and indeterminate (N = 14). The frequencies of HLA specificities were compared between the total group of patients and controls, and between the same controls and each subgroup of patients. After correction of the probabilities, deviations, were not significant, except for the DR2 specificity, which presented a frequency of 44.2% in the total group of patients and 56.3% in the subgroup of individuals with the tuberculoid form of the disease, compared to 23.3% in the controls. Stratified analysis showed that the increased DR2 frequency in the total group of patients was due to the subgroups with tuberculoid and dimorphous forms. The relative risk of tuberculoid leprosy for DR2-positive individuals was 4.2, and the etiologic fraction of DR2 was 0.429. In conclusion, a positive association of the DR2 specificity with the tuberculoid form of leprosy, but not with the lepromatous, dimorphous, or indeterminate forms, was demonstrated in this Southern Brazilian population.

HLA-A, HLA-B and HLA-DRB1 haplotype frequencies in Piauí's volunteer bone marrow donors enrolled at the Brazilian registry.

This study aimed to report the antigen and haplotype frequencies (HFs) of volunteer bone marrow donors (VBMDs) from the state of Piauí who were enrolled in the National Volunteer Bone Marrow Donor Registry (REDOME). The research subjects were 21,943 volunteer bone marrow donors, predominantly young adult women (53.3%). The most frequent allelic group was HLA-A2, followed by -DRB1*13, -DRB1*04, -DRB1*07, -B*15, -B∗35, -B*44, -A*24 and -A*03. Of the 2,704 haplotypes observed, the three most frequent haplotypes were A*29 B*44 DRB1*07 (1.45%), A*01 B*08 DRB1*03 (1.4%) and A*03 B*07 DRB1*15 (0.92%). These three haplotypes were in linkage disequilibrium. PCA showed that 98% of the VBMDs have HLA allele frequencies that are very similar to those from Teresina, the capital city of Piauí. According to the PCA results, these municipalities are distributed with a close proximity to Teresina, which in turn has a close genetic proximity to the Hispanic ethnicity, intermediate proximity to Caucasians and Africans and a distant kinship to Amerindians. The hierarchical proximity of the population of Piauí to the Portuguese and Hispanic populations to shows the strong influence of the latter on the former.

HLA-A29 and genetic susceptibility to chromoblastomycosis.

The distribution of 12 HLA-A, 14 HLA-B, seven HLA-C, seven HLA-DR and three HLA-DQ antigens was determined in 32 non-consanguineous white Brazilians suffering from chromoblastomycosis and 77 healthy controls, matched for ethnic background, sex and age and living in the same geographical area. A significant difference between the two groups was seen only in respect to one HLA-A antigen: A29 was present in 28% of patients as opposed to 4% of the controls (P corrected = 0.03). This finding indicates that susceptibility to chromoblastomycosis may be influenced by a gene located on chromosome 6, in the region of the major histocompatibility complex. The relative risk for an HLA-A29 carrier to develop chromoblastomycosis was estimated as 10.

Association of HLA-DR7 with rheumatic fever in the Brazilian population.

OBJECTIVE: Rheumatic fever (RF) is a multisystem inflammatory disease that develops as a sequel of untreated throat infection by the group A beta-hemolytic streptococcus. As HLA antigens are known to be important in controlling immunological responsiveness, studies have investigated HLA antigen association with RF. Studies with Caucasians, Black Americans, and Indians showed associations with HLA-DR4, DR2, and DR3, respectively. One study on a Brazilian population suggested an association with HLA-DR7 and HLA-DR53. We investigated the association between RF and antigens HLA-DR7 and DR53 in the white Brazilian population. METHODS: Thirty-five patients and 209 healthy individuals living in the northern region of the state of Parana, Brazil, were used as test and control groups, respectively. Classical statistical methods were used to compare HLA frequencies between these groups. Results. Data confirmed positive association with HLA-DR7 (46.7 vs. 25.7%; p = 0.015), but not with HLA-DR53 (54.3 vs. 44.5%; p = 0.28). The relative risk and etiologic fractions were 2.4 and 0.27%, respectively. CONCLUSION: Positive association between HLA-DR7 specificity and RF was observed in the white Brazilian population by 2 independent studies, supporting the hypothesis of the involvement of genetic factors in susceptibility of rheumatic fever.

HLA polymorphism and evaluation of European, African, and Amerindian contribution to the white and mulatto populations from Paraná, Brazil.

Polymorphism of classical HLA-A, HLA-B, HLA-C, HLA-DR, and HLA-DQ genes differs greatly among populations, both in frequencies and in the presence of alleles and haplotypes particular to population groups, making these genes powerful tools for the study of origins of populations and their degree of admixture. Antigen, allele, and haplotype frequencies, together with linkage disequilibrium patterns, are reported for 2 populations in the southern Brazilian state of Paraná, one of predominantly European ancestry (white), the other of predominantly African and European ancestry (mulatto). Genetic distance estimates between the 2 groups and other populations studied previously, and of degree of admixture, were performed. In accordance with phenotypic classification, the white population is of predominantly European origin (80.6%), with a smaller contribution of African (12.5%) and Amerindian (7.0%) genes. The mulatto population consists of African (49.5%) and European (41.8%) ancestry, with a smaller but significant contribution of Amerindian (8.7%) ancestry. On the basis of history and population genetics, there is controversy regarding the Amerindian contribution to Paraná's gene pool. These results provide a better picture of Paraná's ethnic constitution and on the Amerindian contribution to the white and mulatto populations.

Alu insertions versus blood group plus protein genetic variability in four Amerindian populations.

BACKGROUND: Do the population relationships obtained using DNA or blood group plus protein markers remain the same or do they reveal different patterns, indicating that the factors which influence genetic variation at these two levels of analysis are diverse? Can these markers shed light on the biological classification of the Aché, a Paraguayan tribe which only recently established more permanent contacts with non-Indians? SUBJECTS AND METHODS: To consider these questions we typed 193 individuals from four Amerindian tribes in relation to 12 Alu polymorphisms (five of them never studied in these populations), while 22 blood group plus protein systems were studied among the Aché. These data were then integrated with those previously available (blood groups plus proteins) for the three other populations. DNA extraction and amplification, as well as the other laboratory procedures, were performed using standard methods currently in use in our laboratory. The genetic relationships were obtained using the D(A) distance, and the trees were constructed by the neighbour-joining method, both developed by M. Nei and collaborators. Reliability of the trees was tested by bootstrap replications. Other population variability values were also determined using Nei's methods. RESULTS: Alu polymorphism was observed in all populations and for most of the loci; in the seven systems from which we could compare our results with those of other Amerindian groups agreement was satisfactory. Unusual findings on the blood group plus protein systems of the Aché were a very low (5%) HP*1 frequency and the presence of the C(W) phenotype in the Rh blood group. The intertribal patterns of relationship and other aspects of their variation were remarkably congruent in the two sets (Alu; blood group plus protein) of systems. CONCLUSIONS: The answer to the first question posed above is affirmative. However, the problem of whether the Aché derived from a Gê group that preceded the Guarani colonization of Paraguay, or are just a differentiated Guarani group, could not be answered with the genetic information available; the second hypothesis seems more likely at present, but the point to be emphasized is the striking genetic distinctiveness of the Aché as compared to other Amerindians.

Y-chromosome biallelic polymorphisms and Native American population structure.

It has been proposed that women had a higher migration rate than men throughout human evolutionary history. However, in a recent study of South American natives using mtDNA restriction fragment polymorphisms and Y-chromosome microsatellites we failed to detect a significant difference in estimates of migration rates between the sexes. As the high mutation rate of microsatellites might affect estimates of population structure, we now examine biallelic polymorphisms in both mtDNA and the Y-chromosome. Analyses of these markers in Amerinds from North, Central and South America agree with our previous findings in not supporting a higher migration rate for women in these populations. Furthermore, they underline the importance of genetic drift in the evolution of Amerinds and suggest the existence of a North to South gradient of increasing drift in the Americas.

HLA class II diversity in seven Amerindian populations. Clues about the origins of the Aché.

The study of the HLA variability of Native American populations revealed several alleles specific to one or more of the Latin American indigenous populations. The analysis of Amerindian groups distributed all over the continent might inform about the area of origin and the dispersal of these alleles and shed light on the evolution of this remarkable polymorphism. Moreover, HLA alleles and haplotypes are excellent markers to understand the genetic relationships between populations. For these reasons, we characterized the HLA class II polymorphism in seven South American Amerindian populations and compared the results with those previously reported for other Amerindian groups. The Guarani-Kaiowá (n = 160) and Guarani-Nandeva (n = 87) were from the Brazilian state of Mato Grosso do Sul, the Guarani-M'byá (n = 93) and Kaingang (n = 235) from Paraná state, the Aché (n = 89) from eastern Paraguay, the Quechua (n = 44) from Andean Peru. From Amazonia, a heterogeneous group was analyzed (n = 45). The most frequent alleles and haplotypes are common also in other Amerindian populations. Each HLA-DRB1 allele was typically found in combination with just one DQA1-DQB1 haplotype, most likely as a result of some form of random genetic drift and reduced gene flow from non-Amerindians. The frequency distribution differed significantly among all populations, although differences were less pronounced between the Guarani subgroups. Marker alleles allowed an estimate of European and sub-Saharan African gene flow into these populations: Quechua 23%, Guarani-Nandeva 14%, Kaingang 7%, Guarani-M'byá 4%, Guarani-Kaiowá, Amazonia, and Aché 0%. Interestingly, the DRB1*1413 allele, previously found only among the Guarani-M'byá (frequency 15%), appeared in the Aché (8%). The relationship of the Aché to other Amerindian populations is unclear, and this finding reveals a link with the Guarani. On the basis of genetic distance and the HLA allele/haplotype set, we propose that the Aché are differentiated Tupi-Guarani group, most closely related to the Guarani-M'byá.

Association of leprosy with HLA-DR2 in a Southern Brazilian population

The association between HLA specificities and leprosy was investigated in a Southern Brazilian population. One hundred and twenty- one patients and 147 controls were typed for HLA-A, B, Cw, DR and DQ. Patients were subdivided into the following subgroups, according to clinical, histological and immunological criteria: lepromatous (N = 55), tuberculoid (N = 32), dimorphous (N = 20), and indeterminate (N = 14). The frequencies of HLA specificities were compared between the total group of patients and controls, and between the same controls and each subgroup of patients. After correction of the probabilities, deviations were not significant, except for the DR2 specificity, which presented a frequency of 44.2 per cent in the total group of patients and 56.3 per cent in the subgroup of individuals with the tuberculoid form of the disease, compared to 23.3 per cent in the controls. Stratified analysis showed that the increased DR2 frequency in the total group of patients was due to the subgroups with the tuberculoid and dimorphous forms. The relative risk of tuberculoid leprosy for DR2-positive individuals was 4.2, and the etiologic fraction of DR2 was 0.429. In conclusion, a positive association of the DR2 specificity with the tuberculoid form of leprosy, but not with the lepromatous, dimorphous, or indeteterminate forms, was demonstrated in this Southern Brazilian population.