Polymorphism of HLA-DR2,DQw1 haplotypes in Asian Indians

Associations of HLA-DRB1, DQB1 and DPB1 alleles with pulmonary tuberculosis in south India

SETTING

Tuberculosis is endemic in south India: sputum positive pulmonary tuberculosis is predisposed by HLA-DR2 in south India and few other populations of the world.

OBJECTIVE

To study HLA-DRB1, DQB1, DQA1 and DPB1 allelic polymorphism in pulmonary tuberculosis patients and endemic controls from south India.

DESIGN

One hundred and twenty-six, sputum positive pulmonary tuberculosis patients and 87, endemic controls, from Madurai were studied for MHC class II allelic polymorphism by PCR-SSOP method. XI IHWC primers and probes and non-radioactive probing methods were employed.

RESULTS

HLA DRB1*1501 and DQB1*0601 predisposed for pulmonary tuberculosis (DRB1*1501: odds ratio (OR) = 2.68, 95% confidence interval (CI) = 1.30-5.89, P value (P) = 0.013, aetiological fraction (EF) = 0.17; DQB1*0601: OR = 2.32, CI = 1.29-4.27, P = 0.008, EF = 0.26). Haplotype DRB1*1501-DQB1*0601 was higher in patients (1324 per 10,000, X2 = 27.07) than controls (F = 404/10,000, X2 = 8.84). In a subset of 63 caste matched samples, DPB1*04 was preventive (OR = 0.45, CI = 0.21-0.95, P = 0.036, PF = 0.26): the distributions of DRB1*1501-DQB1*0601-DPB1*04 phenotypes were different between patients and controls (P = 0.0092). These alleles were predominant in patients and controls of T5SU caste.

CONCLUSION

HLA-DRB1*1501 and DQB1*0601 predisposed to sputum positive pulmonary tuberculosis, and DPB1*04 was preventive and epistatic to this risk. Caste T5SU is an ideal model to study immunology of tuberculosis.

Lack of HLA-DR2-associated DRB1 gene in a family

HLA-DR51 haplotypes co-express one DRB1 (B1*15 or B1*16) gene and one DRB5 gene. These haplotypes also carry two pseudogenes (DRB6 and DRB9) During routine HLA typing for transplantation, we observed an unexpected DR51 haplotype in two subjects (mother and daughter) in a family. Serological typing showed that these subjects are positive for DR51 and DQ6 but negative for DR15 and DR16. Investigations of genomic DNA by molecular techniques showed that these individuals carry DRB5*0101, DRB6*02 and DQB1*0602 genes, whereas the DRB1 gene associated with either DR15 (B1*1501 to B1*1504) or DR16 (B1*1601 to B1*1606) was not detected in the mother and daughter. It is possible that the new haplotype, DQB1*0602, DRB6*02, DRB5*0101, arose by deletion of DR2-associated DRB1 gene.

An investigation of HLA-encoded genetic susceptibility to multiple sclerosis in subjects of Asian Indian and Afro-Caribbean ethnic origin

The association of multiple sclerosis (MS) with the HLA class II loci DR and DQ was investigated in populations of Asian Indian and Afro-Caribbean ethnic origin, resident in the United Kingdom. The putative haplotype, DRB1*1501.DQA1*0102.DQB1*0602, was weakly positively associated with MS in both races. The overall contribution to disease susceptibility of this marker was small. Over 80% of the MS patients in both racial groups did not possess this haplotype. The data suggest that other genetic and/or environmental factors may be more important in predisposing to MS in these two races. Our study also raises the possibility that genetically distinct forms of the disease may be expressed in white Caucasian and non-Caucasian populations.

Asian Indian HLA-DR2-, DR4-, and DR52-related DR-DQ genotypes analyzed by polymerase chain reaction based nonradioactive oligonucleotide typing. Unique haplotypes and a novel DR4 subtype

We have employed a PCR-based nonradioactive technique using biotinylated SSOPs to define HLA-DR2-, 4-, DR51-, and DR52-associated DR-DQ genotypes in Asian Indian families. In the DR2 group, most haplotypes described by us in a previous study were confirmed by family analysis. Evidence for one additional haplotype was available in this study. The classic DRB1*1501- and DRB1*1502-associated caucasoid haplotypes occurred with an appreciable frequency in Asian Indians, but two of the DRB1*1601-associated Caucasoid haplotypes were absent. At least six unique and unusual DR2-associated genotypes were encountered. In the DR52 group, the three most common alleles are DRB1*0301, DRB1*1404, and DRB1*1101. The DR6-associated alleles were DRB1*1301, 1302, 1401, and 1404. A few unique haplotypes occurred with low frequency in this group. In the DR4 group, at least three unusual patterns of hybridization were noticed by family analysis. One of these appears to be a novel DR4 subtype upon sequencing. These results demonstrate that, besides HLA-DR2, appreciable complexity occurs in the DR4- and DR52-associated alleles among Asian Indians. The presence of unique DR-DQ haplotypes in addition to those found characteristically among Western Caucasians suggests that the Indian population provides valuable source of many HLA class II haplotypes.

Restriction fragment length polymorphism of HLA-DQ and -DR allogenotypes in normal southern Chinese

We have examined the Taq I restriction fragment length polymorphism (RFLP) of the MHC class II regions of 96 normal Southern Chinese with respect to the HLA-DRB, -DQA, and -DQB genes. The data were compared with the DR and DQ serotyping. RFLP correlates well with the serological typing of the DR types of Chinese. Variants are seen in DR2 and DR12. The variant in DR12 with a 10 kb at the upper band (DR12b) is not found in Caucasoids and is more frequent in Chinese (19.4% of the alleles). With the help of DQA and DQB RFLP the assignment of genotyping of DRB types is facilitated. Some of the linkage disequilibrium patterns among DRB, DQA and DQB are different from Caucasoids. This is particularly obvious in the DR2 and DR5 haplotypes. In the 96 Southern Chinese, the 3 commonest haplotype frequencies are: DR12b, DQ alpha 1b, DQ beta 3b (18.3%); DR9, DQ alpha 3, DQ beta 3a (15.7%); DR4, DQ alpha 3, DQ beta 3a (14.2%). The various DR beta, DQ alpha. DQ beta genes can be accurately defined in Chinese by RFLP. Polymerase chain reactions using sequence-specific primers were performed to confirm the various HLA-DRB and -DQB alleles. The use of RFLP is important in the study of HLA matching and HLA-disease association in Southern Chinese.

Characterization of an HLA-DR15 DQ5 haplotype found in the Spanish caucasoid population

HLA class II typing by RFLP and PCR-SSOP has been performed on HLA-DR2-positive individuals as a part of a study on MHC in a Spanish Caucasoid population. The results of this study reveal that HLA-DR15 (DRB1*1501 DRB5*0101) and DQ5 (DQA1*0102 DQB1*0501/0502) are not uncommonly associated in such a population. Family segregation has been assessed and allogeneic reactivity against some classic DR2 haplotypes has been tested; a stimulatory capability of DQ6 antigen in this situation is shown. It is suggested that the reported association is not uncommon in European Caucasoids as well as in other populations and it should be considered in matching for transplantation and in DR2-associated diseases.

Distribution of HLA antigens in Spanish Gypsies: A comparative study

We have studied the HLA-class I and class II antigen distribution in a sample of 75 Spanish Gypsies and 74 Spanish non-Gypsies by serology, restriction fragment length polymorphism, and protein chain reaction and hybridization with allele-specific oligonucleotide probes. When both population samples are compared, we find that Gypsies have a statistically significantly higher frequency of A1, A11, B61, Cw6, DQ5 and haplotypes DR16 DQ5 Dw21 and DR14 DQ5 Dw9 DR52b. Frequency of A3, A29, B44, DR4, DQ2, DQ8 and haplotypes DR1 DQ5 and DR7 DQ2 DB17 DR53 are significantly lower in this ethnic group. The analysis of the serological data in the two populations demonstrates that Cw6 can be split into long Cw6 (Cw6.1) and short Cw6 (Cw6.2). Haplotype A1-Cw6-B61-DR14-DQ5 is the most characteristic in Gypsies, with a frequency of 13%. Estimation of the genetic distances shows that Spanish Gypsies are closer to Indian Caucasoid populations than to the Spanish non-Gypsy population. HLA data support the proposed historical origin of this ethnic group.

Increasing complexity of HLA-DR2 as detected by serology and oligonucleotide typing

Serological and oligonucleotide typing was performed on a number of HLA-DR2-positive cells from different ethnic origin, including DR2 haplotypes with various DQ associations. Exons 2 of DRB1 and DRB5 of DR2-positive individuals were locus-specific amplified and hybridized with a number of different oligonucleotides capable of discriminating between the various Dw2, Dw12, Dw21, and Dw22 associated sequences. The linkage of DRB with DQA1 and DQB1 in these haplotypes was analyzed. Among the DR2- positive cells we could define 10 different DR DQ haplotypes by serology and 13 by oligonucleotide typing. The DR2.ES specificity is a serological DRw15 variant which could not be discriminated by oligonucleotide typing from a DRw15 DQw5 haplotype. The DR2.JA variant represents a unique DRB1*1602 DRB5*0101 haplotype. The DR1+2s haplotype consists of a DRB1 DQ region from a Dw1 and a DRB5 gene from a Dw2 haplotype. Its short DR2 serum pattern can be explained by the absence of a DR2 DRB1 gene product. DRB5*0101 sequences were found in association with DRB1*1501, *1502, *1602, and *0101 alleles. Since the DRB5 gene is capable of such different associations it is comparable to the DRB3 and DRB4 genes. This may have implications for the definition of the broad DR2 specificity which is predominantly encoded by the DRB5 gene product. New DR2 haplotypes included the following DQ combinations: DQw2-positive DQA1/B1*0301/0201 and DQw6-positive DQA1/B1*0102/0601 and *0102/0603 haplotypes.