Seven new DPB1 alleles and their population distribution

HLA class II peptide-binding-region analysis reveals funneling of polymorphism in action

BACKGROUND

HLA-class II proteins hold important roles in key physiological processes. The purpose of this study was to compile all class II alleles reported in human population and investigate patterns in pocket variants and their combinations, focusing on the peptide-binding region (PBR).

METHODS

For this purpose, all protein sequences of DPA1, DQA1, DPB1, DQB1 and DRB1 were selected and filtered, in order to have full PBR sequences. Proportional representation was used for pocket variants while population data were also used.

RESULTS

All pocket variants and PBR sequences were retrieved and analyzed based on the preference of amino acids and their properties in all pocket positions. The observed number of pocket variants combinations was much lower than the possible inferred, suggesting that PBR formation is under strict funneling. Also, although class II proteins are very polymorphic, in the majority of the reported alleles in all populations, a significantly less polymorphic pocket core was found.

CONCLUSIONS

Pocket variability of five HLA class II proteins was studied revealing favorable properties of each protein. The actual PBR sequences of HLA class II proteins appear to be governed by restrictions that lead to the establishment of only a fraction of the possible combinations and the polymorphism recorded is the result of intense funneling based on function.

HLA class I (A, B, C) and class II (DRB1, DQA1, DQB1, DPB1) alleles and haplotypes in the Han from southern China

In this study, polymerase chain reaction-sequence-specific oligonucleotide prode (SSOP) typing results for the human leukocyte antigen (HLA) class I (A, B, and C) and class II (DRB1, DQA1, DQB1, and DPB1) loci in 264 individuals of the Han ethnic group from the Canton region of southern China are presented. The data are examined at the allele, genotype, and haplotype level. Common alleles at each of the loci are in keeping with those observed in similar populations, while the high-resolution typing methods used give additional details about allele frequency distributions not shown in previous studies. Twenty distinct alleles are seen at HLA-A in this population. The locus is dominated by the A*1101 allele, which is found here at a frequency of 0.266. The next three most common alleles, A*2402, A*3303, and A*0203, are each seen at frequencies of greater than 10%, and together, these four alleles account for roughly two-thirds of the total for HLA-A in this population. Fifty alleles are observed for HLA-B, 21 of which are singleton copies. The most common HLA-B alleles are B*4001 (f= 0.144), B*4601 (f= 0.119), B*5801 (f= 0.089), B*1301 (f= 0.068), B*1502 (f= 0.073), and B*3802 (f= 0.070). At the HLA-C locus, there are a total of 20 alleles. Four alleles (Cw*0702, Cw*0102, Cw*0801, and Cw*0304) are found at frequencies of greater than 10%, and together, these alleles comprise over 60% of the total. Overall, the class II loci are somewhat less diverse than class I. Twenty-eight distinct alleles are seen at DRB1, and the most common three, DRB1*0901, *1202, and *1501, are each seen at frequencies of greater than 10%. The DR4 lineage also shows extensive expansion in this population, with seven subtypes, representing one quarter of the diversity at this locus. Eight alleles are observed at DQA1; DQA1*0301 and 0102 are the most common alleles, with frequencies over 20%. The DQB1 locus is dominated by four alleles of the 03 lineage, which make up nearly half of the total. The two most common DQB1 alleles in this population are DQB1*0301 (f= 0.242) and DQB1*0303 (f= 0.15). Eighteen alleles are observed at DPB1; DPB1*0501 is the most common allele, with a frequency of 37%. The class I allele frequency distributions, expressed in terms of Watterson's (homozygosity) F-statistic, are all within expectations under neutrality, while there is evidence for balancing selection at DRB1, DQA1, and DQB1. Departures from Hardy-Weinberg expectations are observed for HLA-C and DRB1 in this population. Strong individual haplotypic associations are seen for all pairs of loci, and many of these occur at frequencies greater than 5%. In the class I region, several examples of HLA-B and -C loci in complete or near complete linkage disequilibrium (LD) are present, and the two most common, B*4601-Cw*0102 and B*5801-Cw*0302 account for more than 20% of the B-C haplotypes. Similarly, at class II, nearly all of the most common DR-DQ haplotypes are in nearly complete LD. The most common DRB1-DQB1 haplotypes are DRB1*0901-DQB1*0303 (f= 0.144) and DRB1*1202-DQB1*0301 (f= 0.131). The most common four locus class I and class II combined haplotypes are A*3303-B*5801-DRB1*0301-DPB1*0401 (f= 0.028) and A*0207-B*4601-DRB1*0901-DPB1*0501 (f= 0.026). The presentation of complete DNA typing for the class I loci and haplotype analysis in a large sample such as this can provide insights into the population history of the region and give useful data for HLA matching in transplantation and disease association studies in the Chinese population.

HLA Alleles and Risk of Cervical Intraepithelial Neoplasia Among Southwestern American Indian Women

An increase in cervical intraepithelial neoplasia (CIN) has been described in American Indian women in New Mexico. Differences in human leukocyte antigen (HLA) alleles have been reported in cervical intraepithelial neoplasia (CIN) compared with controls in other populations. We investigated HLA alleles and CIN in Southwest American Indian women. The case control study included 89 women with biopsy-proven CIN II/III (diagnosed November 1994 through October 1997) and 271 similar women with normal cervical epithelium from the same clinics. DRB1, DQB1, and DPB1 alleles were determined using DNA typing techniques. DQA1 and HLA-A allele typing was included for some subjects (randomly chosen n = 37 and n = 163 cases and controls, respectively). We found a decreased risk of CIN with DRB1*1402 (OR 0.5, 95% CI 0.3-0.9) and an increased risk with DRB1*1501 (OR 2.7, 95% CI 0.9-7.3). Additionally, DQA1*0102 was associated with increased risk (OR 4.5, 95% CI 1.3-5.3) and HLA-A*02 with decreased risk (OR 0.4, CI 0.2-0.9). Our findings are discussed along with studies in other populations.

HLA diversity, differentiation, and haplotype evolution in Mesoamerican Natives

Genetic variation of the Human Leukocyte Antigen region (HLA) in three Amerindian populations from the Southern Mexican state of Oaxaca, the Zapotec, Mixtec and the Mixe is examined. Individuals were typed using PCR-SSOP for four class II loci (DRB1, DQA1, DQB1, DPB1) and three class I loci (HLA-A, -B, and -C). Based on known HLA distributions, European admixture ranged from 1% to 10%. Individuals with European alleles were excluded from subsequent analysis. New alleles were revealed at each of the class I loci. In general, genotype frequencies were in Hardy-Weinberg equilibrium, although some deviations were detected. Allele frequency distributions at the DRB1, DQA1, DQB1 and HLA-A loci in all populations were more even than expected under neutrality, supporting a model of balancing selection at these loci. A history of directional selection for DPB1 in all three populations was indicated, as homozygosity values were significantly above expected values. Allele frequency distributions at HLA-B and HLA-C did not differ significantly from neutrality expectations. The data also provide evidence from linkage disequilibrium that strong haplotypic associations are present across the entire HLA region in each of the populations. Significant overall linkage disequilibrium exists between all pairs of loci typed in these populations, except those which include the DPB1 locus. These associations exist despite the fact that the recombination fraction between HLA-A, in the class I region, and DQB1, in the class II region, may exceed 0.02. One explanation is that selective pressures are maintaining the relationships between particular alleles at these loci in these populations. These relationships are maintained in general across the entire HLA region in the Oaxacan Amerindians, with the exception of DPB1.

Evidence for HLA-related susceptibility for stroke in children with sickle cell disease

Cerebral infarction occurs in one quarter of all children with sickle cell anemia (SCA). There is an increased risk of stroke in siblings with SCA, suggesting genetic factors may influence risk of stroke. The authors investigated whether HLA type was associated with risk of stroke in children with SCA. Fifty-three patients with SCA underwent complete HLA typing at both HLA class I (HLA-A, B) and HLA class II (HLA-DR, DQ, DP) loci. Of the 53 patients, 22 had magnetic resonance imagining (MRI)–documented evidence of cerebral infarction, and the remaining 31 patients had negative MRI scans. Comparison of the results of HLA typing between the SCA patients with a positive and those with a negative MRI documented that the 2 groups differed with respect to the class I HLA-B (P = .012), and the class II HLA-DRB1 (P = .0008) and DQB1 (P = .029). Susceptibility associations at the HLA-DRB1 locus included both DR3 alleles, where DRB1*0301 and *0302 were both associated with an increased risk of stroke. Protective associations were found in the DR2 group, where DRB1*1501 was protective for stroke. DQB1*0201, which is in linkage disequilibrium with DRB1*0301, was also associated with stroke. Similarly, DQB1*0602, in linkage disequilibrium with DRB1*1501, was protective. Specific HLA alleles may influence the risk of stroke in children with SCA. HLA typing may prove useful in identifying SCA patients at higher risk for stroke.

Evidence for HLA-related susceptibility for stroke in children with sickle cell disease

Cerebral infarction occurs in one quarter of all children with sickle cell anemia (SCA). There is an increased risk of stroke in siblings with SCA, suggesting genetic factors may influence risk of stroke. The authors investigated whether HLA type was associated with risk of stroke in children with SCA. Fifty-three patients with SCA underwent complete HLA typing at both HLA class I (HLA-A, B) and HLA class II (HLA-DR, DQ, DP) loci. Of the 53 patients, 22 had magnetic resonance imagining (MRI)–documented evidence of cerebral infarction, and the remaining 31 patients had negative MRI scans. Comparison of the results of HLA typing between the SCA patients with a positive and those with a negative MRI documented that the 2 groups differed with respect to the class I HLA-B (P = .012), and the class II HLA-DRB1 (P = .0008) and DQB1 (P = .029). Susceptibility associations at the HLA-DRB1 locus included both DR3 alleles, where DRB1*0301 and *0302 were both associated with an increased risk of stroke. Protective associations were found in the DR2 group, where DRB1*1501 was protective for stroke. DQB1*0201, which is in linkage disequilibrium with DRB1*0301, was also associated with stroke. Similarly, DQB1*0602, in linkage disequilibrium with DRB1*1501, was protective. Specific HLA alleles may influence the risk of stroke in children with SCA. HLA typing may prove useful in identifying SCA patients at higher risk for stroke.

HLA class II haplotype associations with inflammatory bowel disease in Jewish (Ashkenazi) and non-Jewish caucasian populations

Ulcerative colitis (UC) and Crohn's disease (CD) are the clinical entities comprising idiopathic inflammatory bowel disease (IBD). Previous studies on the association of IBD and human leukocyte antigen (HLA) class II genes suggested a role for HLA in this disease. Here we present HLA class II (DRB1, DQB1, DQA1, DPB1) allele and haplotype distributions determined using the polymerase chain reaction and sequence-specific oligonucleotide probe methods. A total of 578 UC and CD Caucasian patients and controls from Jewish (Ashkenazi) and non-Jewish populations was examined. Our previously reported association of DR1-DQ5 with CD was attributable to DRB1*0103. A dramatic association with IBD and the highly unusual DRB1*0103-DQA1*0501-DQB1*0301 haplotype (OR = 6.6, p = 0.036) was found. The more common DR1 haplotype, DRB1*0103-DQA1*0101-DQB1*0501, was also associated with IBD (OR = 3.1, p = 0.014), a result suggesting that interaction between DR and DQ may determine the extent of disease risk. Our previously reported association of DR2 with UC was attributable to DRB1*1502 (OR = 2.6, p = 0.006). At the DPB1 locus, a significant association of DPB1*0401 with CD was observed for the combined populations (OR = 1.85, p = 0.007). These observations indicate that some class II alleles and haplotypes confer susceptibility to both UC and CD, implying common immunogenetic mechanisms of pathogenesis, while others confer risk to only one of these diseases, and illustrate the value of DNA HLA typing in disease susceptibility analyses.

Application of RSCA for the typing of HLA-DPB1

We describe the application of RSCA, for the high resolution typing of alleles encoded at the HLA-DPB1 locus. RSCA differs from other sequence based typing methodologies in that the HLA type is assigned on the basis of differences in DNA conformation between different alleles. A total of 251 samples were typed in a blind study, of these 109 samples had been typed previously by conventional techniques. A comparison of the RSCA data with the historical typing results showed a concordance over 93%. Seven samples initially had discordant results, however, when these samples were typed by direct sequencing, the type assigned by RSCA was found to be correct in all but one case, indicating a concordance over 99%. RSCA has proved to be a simple reliable technique for the typing of the HLA-DPB1 locus, and is not limited by the ambiguous combinations of alleles determined in other conventional techniques.

HLA class II polymorphism in the Ticuna of Brazil: evolutionary implications of the DRB1*0807 allele

The alleles at the HLA class II loci HLA-DRB1, DQA1, DQB1 and DPB1 were determined for 49 individuals of the Ticuna, a Native South American population living in Brazil, using PCR/SSO probe hybridization and DNA sequencing. A newly described DRB1*08 variant, DRB1*0807, which has previously been reported only in native Colombians and contemporary Brazilians of African and Caucasian descent, was identified in the Ticuna at a high frequency (f=0.225). Because *0807 has been observed only in South American populations, we propose that it was generated from a parental *0802 allele recently, after the isolation of various Native South American populations, and infer that the DRB1*0807 allele was generated by a C to T change at codon 57 (Asp-->Val, GAT-->GTT) from the ancestral *0802. This inference is supported by the sequence of a complex VNTR in the second intron of the DRB1 gene. The DPB1 alleles *0401, *0402 and *1401 constituted 76% of the observed Ticuna DPB1 alleles (f=0.166, 0.427 and 0.166 respectively). In addition, the DPB1 allele *3501, which has been observed in a few other Native South American groups, was observed at a frequency of 0.053 and may have been generated from the putative ancestral allele *1401 allele in South America. The DRB1 and DPB1 allele frequencies for the Ticuna deviate from expected Hardy-Weinberg equilibrium proportions, while DQA1 and DQB1 allele frequencies do not. When this deviation, which involves an observed excess of DRB1*0807 heterozygotes, is considered with the high frequency of the DRB1*0807 and DPB1*1401 alleles, we infer that native South American populations may have been under selection pressure for increased allele diversity.

Peptide recognition by T-cell clones of an HLA-DRB1*1501/*0901 heterozygous donor is promiscuous only between parental alleles

The HLA class II isotype and allelic restrictions of peptide recognition were analyzed with T cells from a DRB1*1501/DRB1*0901 heterozygous donor. Nineteen T cell clones, all directed against the single mycobacterial epitope p21-40 were tested with HLA homozygous lymphoblastoid cell lines as antigen-presenting cells. The most striking finding has been, that several DR isotype restricted clones recognized the peptide in the context of both parental, but not of unrelated alleles. In contrast, DQ and DP restricted clones responded in the context of one parental allele only. Most DR promiscuous clones produced interferon-gamma but not IL-4, whereas most DQ and DP clones produced IL-4. We postulate that the confinement of DR promiscuity only to the parental alleles was established possibly during thymic maturation of T cells and that the proportions between monogamous and promiscuous T cells may play a role in the MHC mediated influences on host resistance to infections and other immune responses.

Genotype-related fingerprints from HLA-DPB1 exon 2 low-stringency PCR

Techniques based on the formation of heteroduplexes between relevant heterologous amplified HLA loci have proved to be simple and cost-effective screening methods for the detection of DNA sequence diversity. However, the banding patterns produced may not be as complex as required. We used the original procedure of Pena et al. (Proceedings of the National Academy of Sciences USA 91, 1946-1949, 1994) to generate fingerprints from a specific, polymorphic PCR product. HLA-DPB1 exon 2 was amplified, recovered from agarose gel, and used as a template for subsequent low-stringency (30 degrees C) amplification cycles (LS-PCR) in the presence of a single primer. The LS-PCR products were run on 8% PAGE and silver-stained. In total, 22 subjects were characterized by this method. The issues of the reproducibility and specificity of the patterns obtained were addressed by comparing fingerprints from individuals with the same genotype. The results showed that LS-PCR was robust. A further step was the evaluation of the diversity that can be generated, i.e. the sensitivity of the method. Genotype-related fingerprints were produced, and differences as small as a single nucleotide in heterozygous samples could be detected. We then demonstrated the usefulness of LS-PCR in the evaluation of donor/recipient pairs. We believe that LS-PCR may be a valuable adjunct to the battery of tests aimed at the verification of HLA matching before unrelated bone marrow transplantation. We suggest that it could be used to speed up the search process when several candidate donors are retrieved from registries before embarking on SSOP typing or sequencing.

Results of Expedicion Humana. II. Analysis of HLA class II alleles in three African American populations from Colombia using the PCR/SSOP: identification of a novel DQB1*02 (*0203) allele

PCR/SSOP typing methods were used to analyze the HLA Class II DRB1, DQA1, DQB1 and DPB1 loci of samples from three African American populations of Colombia. Forty samples from the Cauca (Pacific), and twenty samples each from the Choco (North Pacific Coast) and the Providencia (Caribbean island) populations, were collected and the Class II loci analyzed under the auspices of the Expedicion Humana. Despite the limited number of samples analyzed, the African Colombian populations exhibit a very high degree of class II polymorphism. A great diversity of DRB1 alleles was found, with representatives from all serological classes, including 19 DRB1 alleles in the Providencia, 16 in the Cauca and 14 in the Choco groups. In addition, a novel DQB1*02 allele (*0203) was found in two individuals from the Cauca population of the Pacific Coast. The sequence of the DQB1*0203 allele, associated with DR3, differs from DQB1*0201 by only one nucleotide substitution (C-->A) in the second position of codon 57, resulting in an Ala to Asp change. The addition of DQB1*0203 brings the total number of DQB1 alleles identified to date to 26. HLA class II diversity is much greater in these African Colombian populations than that seen in nearby Amerindian populations. Analysis of regional Colombian African American HLA population genetics is discussed with respect to the Colombian Amerindian HLA genetics described in an accompanying paper.

Results of Expedicion Humana. I. Analysis of HLA class II (DRB1-DQA1-DPB1) alleles and DR-DQ haplotypes in nine Amerindian populations from Colombia

HLA class II variation was analyzed in nine Native American populations of Colombia using PCR/SSOP typing methods. Under the auspices of the Expedition Humana, approximately 30 unrelated native Colombia Indian samples each from the Tule (NW Pacific Coast), Kogui (Sierra Nevada). Ijka (Sierra Nevada), Ingano (Amazonas), Coreguaje (Amazonas), Nukak (Amazonas), Waunana (Pacific), Embera (Pacific) and Sikuani (Northeastern Plains) were collected and analyzed at the DRBI, DQA1, DQB1 and DPB1 loci. The number of different DRB1, DQA1, DQB1 and DPB1 alleles in the Colombian Indians is markedly reduced in comparison with neighboring African Colombian populations, which exhibit a very high degree of class II variability, as discussed in an accompanying paper. In the Colombian Amerindian groups, DR2 (DRB1*1602), DR4 (DRB1*0407, *0404, *0403 AND *0411), DR6 (DRB1*1402) and DR8 (DRB1*0802) comprise > 95% of all DRB1 alleles. We also found an absence of DR3 in all populations, and DR1, DR7 and DR9 allelic groups were either very rare or absent. Each Colombian Amerindian population has a predominant DRB1 allele (f = approximately 0.22-0.65) and DRB1-DQA1-DQB1 haplotype. Several novel DR-DQ haplotypes were also found. At the DPB1 locus, DPB1*0402 (f = 0.28-0.82), *1401 (f = 0.03-0.45), and *3501 (f = 0.03-0.27), were the three most prevalent alleles, each population maintaining one of these three alleles as the predominant (f > 0.26) DPB1 allele. The reduction of diversity for the HLA class II alleles in the Colombian Indians is suggestive of a population bottleneck during the colonization of the Americans, with little to no subsequent admixture with neighboring African Colombian populations in the last approximately 300 years.

DNA-based HLA typing for cord blood stem cell transplantation

Molecular analysis of the HLA loci has revealed a pattern of extensive sequence polymorphism. For the class II loci, the polymorphism is localized to the second exon, whereas for the class I loci, both the second and third exons are polymorphic. These polymorphic regions encode the peptide binding groove and appear to be functionally significant in terms of disease susceptibility and transplantation. However, much of this polymorphism cannot be detected by serologic HLA typing methods. DNA typing methods based on PCR amplification and hybridization with sequence-specific oligonucleotide (SSO) probes can distinguish the many allelic sequence variants identified at these loci. The use of arrays of immobilized SSO probes allows genetic typing at many polymorphic sequence motifs in a single PCR and single hybridization reaction, making possible the development of simple, robust, and automated tests. PCR-SSO probe typing of the HLA loci requires very little sample material, is capable of either general or fine discrimination of alleles, and can be used to detect maternal contamination of cord blood. The application of this approach to typing HLA class I and II loci is discussed with regard to hematopoietic transplantation therapy.

Three new DPB1 alleles identified in a Bantu-speaking population from central Cameroon

HLA-DPB1 genotyping of 241 individuals from an African Bantu-speaking population in central Cameroon using sequence-specific oligonucleotide probes identified five individuals with novel probe hybridization patterns. DNA sequence analysis of the second exon of the DPB1 alleles from these five individuals identified three new alleles, *6001, *6101N, and *6201. DPB1*6001, found in two individuals, contains a single nucleotide change that results in a polar amino acid, asparagine, at residue 65; this position in the beta 1 domain is occupied by a nonpolar amino acid in all other reported DPB1 alleles. DPB1*6101N, found in one individual, contains a single base mutation that results in a premature termination codon at position 67. DPB1*6201, found in two individuals, is characterized by the apparent motif shuffling that has been hypothesized to be responsible for the majority of DPB1 sequence polymorphism. These new sequences shed additional light on the potential mechanisms by which allelic diversity is generated at the HLA-DPB1 locus.

New HLA-DPB1 alleles generated by interallelic gene conversion detected by analysis of sperm

The rate at which allelic diversity at the HLA loci evolves has been the subject of considerable controversy. The patchwork pattern of sequence polymorphism within the second exon of the HLA class II loci, particularly in the DPB1 locus, may have been generated by segmental exchange (gene conversion). We have analysed the frequency of variant DPB1 sequences that have been created by interallelic gene conversion in the germline by screening pools of sperm using PCR amplification and oligonucleotide probe typing. Our results indicate that about 1/10,000 sperm represents a new DPB1 sequence generated by short tracts of segmental exchange (gene conversion) within the second exon, suggesting that interallelic gene conversion may have an important role in generating the extensive allelic diversity at the HLA loci.

Novel HLA-DPB1 alleles detected in the Ethiopian population

The number of identified HLA-DPB1 alleles increased rapidly by application of DNA-based typing techniques. PCR-SSO typing indicated the presence of possible new HLA-DPB1 variants in the Ethiopian population. The use of the SBT technique, which considers polymorphic as well as constant regions in the second exon of HLA genes, allowed direct identification of two new allelic variants. Moreover, a recently identified HLA-DPA1 variant was also present in this population. The newly defined allelic HLA-DPB1 sequences found in five individuals of the Ethiopian population were confirmed by cloning and subsequent sequencing of the cloned DNA. One of the new alleles was shown to segregate in a family and was also present in unrelated individuals. Both new DPB1 alleles represent new combinations of existing polymorphism in the hypervariable regions. In different populations the frequency of these new HLA-DP variants remains to be determined.

Analysis of mutational changes at the HLA locus in single human sperm

Using a simple and efficient single sperm PCR and direct sequencing method, we screened for HLA-DPB1 gene mutations that may give rise to new alleles at this highly polymorphic locus. More than 800 single sperm were studied from a heterozygous individual whose two alleles carried 16 nucleotide sequence differences clustered in six polymorphic regions. A potential microgene conversion event was detected. Unrepaired heteroduplex DNA similar to that which gives rise to postmeiotic segregation events in yeast was observed in three cases. Control experiments also revealed unusual sperm from DPB1 homozygous individuals. The data may help explain allelic diversity in the MHC and suggest that a possible source of human mosaicism may be incomplete DNA mismatch repair during gametogenesis.