HLA-A locus alleles identified by sequence specific PCR

Self-referent MHC type matching in frog tadpoles

Self/non-self recognition mechanisms underlie the development, immunology and social behaviour of virtually all living organisms, from bacteria to humans. Indeed, recognition processes lie at the core of how social cooperation evolved. Much evidence suggests that the major histocompatibility complex (MHC) both facilitates nepotistic interactions and promotes inbreeding avoidance. Social discrimination based on MHC differences has been demonstrated in many vertebrates but whether the labels used in discrimination are directly associated with the MHC, rather than with other genes with which it covaries, has remained problematic. Furthermore, effects of familiarity on natural preferences have not been controlled in most previous studies. Here we show that African clawed frog (Xenopus laevis) tadpoles discriminate among familiar full siblings based on MHC haplotype differences. Subjects (N=261) from four parental crosses preferred siblings with which they shared MHC haplotypes to those with no MHC haplotypes in common. Using only full siblings in experimental tests, we controlled for genetic variation elsewhere in the genome that might influence schooling preferences. As test subjects were equally familiar with stimulus groups, we conclude that tadpole discrimination involves a self-referent genetic recognition mechanism whereby individuals compare their own MHC type with those of conspecifics.

Polymorphisms of human leukocyte antigen genes in korean children with Kawasaki disease

BACKGROUND

Kawasaki disease is a leading cause of acquired heart disease in children. The prevalence rate varies in different ethnic groups. Recently, with the clinical application of molecular genetic technology, human leukocyte antigen (HLA) polymorphisms associated with several diseases have been identified by DNA analysis. This study aimed to assess the association of HLA alleles with susceptibility and complications of Kawasaki disease in Korean children.

METHODS

In this study, DNA was extracted from 74 children with a diagnosis of Kawasaki disease. The polymorphisms of the HLA-A, -B, -C, and -DRB1 alleles of patients with Kawasaki disease were determined by polymerase chain reaction (PCR)-amplification refractory mutation system (ARMS) and PCR-sequence-specific primer (SSP) analysis. The polymorphisms identified were compared with those of 159 normal healthy control subjects.

RESULTS

There was a significant increase in the frequencies of the HLA-B35, -B75, and -Cw09 alleles in patients with Kawasaki disease compared with the healthy control group. There was no increase in the frequency of HLA-DRB1 alleles among the Kawasaki disease patients compared with a healthy control group. When the patients with Kawasaki disease were divided into two subgroups, with or without coronary complications, the Kawasaki disease patients with coronary complications showed a significantly increased frequency of the HLA-DRB1*11 allele compared with the healthy control group and increased frequency of HLA-DRB1*09 in a comparison of the subgroups.

CONCLUSIONS

This study suggests that polymorphisms in some alleles of B and C in HLA class I genes are associated with Kawasaki disease in Korean children.

Association of HLA alleles with non-Hodgkin's lymphoma in Korean population

Several studies have been performed on the association between non-Hodgkin's lymphoma (NHL) and the presence of certain human leukocyte antigens (HLA) class II alleles in Asian countries, and these studies have shown different results, according to the ethnicity, for the frequencies of the HLA class II alleles, and especially for HLA-DRB1. Therefore, the distribution of the HLA-A, B, C, DRB1, and DQB1 alleles in 89 Korean patients with NHL and also in 200 healthy Korean controls was investigated in this study. For the class I alleles, the frequencies of HLA-B51 was increased in patients with NHL and diffuse large B cell (DLBC) lymphoma compared with the normal control. For the class II alleles, the frequencies of the HLA-DRB1*09 and DQB1*03 alleles were increased in patients with NHL and DLBC lymphoma compared with the normal controls. Also, the B51-DRB1*09-DQB1*03 haplotype was significantly increased in the patients with NHL. These results suggest that some genes in HLA-B*51-DRB1*09-DQB1*03 haplotype may contribute to NHL susceptibility in the Korean population.

Analysis of T cell receptor alpha-chain variable region (Valpha) usage and CDR3alpha of T cells infiltrated into lesions of psoriasis patients

Psoriasis is a common inflammatory skin disease and is considered as T cell-mediated immune response. In this study, we analyzed T cell receptor alpha-chain variable region (TCR Valpha) usage in the lesions of psoriasis patients using 5'-RACE. As the results, Valpha1, -2, -7, -8, -10, -11, -12, and -23 were commonly detected in psoriatic lesions and comparison of expressions of these Valpha types between psoriasis patients and healthy individuals showed that Valpha1, -7, -11, and -12 were highly increased in psoriasis patients than in healthy individuals. Compared with atopy dermatitis patients, the expressions of Valpha1 and Valpha7 were increased in psoriasis patients. Then, to identify CDR3alpha of T cells infiltrated in psoriatic lesions, we examined which type of J gene segment was rearranged with Valpha1 or Valpha7, which the expressions was specifically increased in psoriatic lesions. The result showed that the V-J rearrangements between the examined patients were not equivalent and their frequencies were diverse, however, several common rearrangements such as Valpha1-Jalpha13, -23, -27, or -34 and Valpha7-Jalpha12, -33 were detected. The results in this study might provide the clue to define the characteristics of T cells associated with the pathogenesis of psoriasis.

Roles of HLA-B, HLA-C and HLA-DPA1 incompatibilities in the outcome of unrelated stem-cell transplantation

In unrelated stem-cell transplantation, the value of matching at the HLA-A, -B and -DR loci between donor and recipient is well documented. The effect of HLA-C, DPB1 and DPA1 mismatches on transplantation outcome is unclear. In this study, 104 donor recipient-pairs, transplanted at Huddinge University Hospital between 1988 and 1999, were retrospectively HLA class I- and class II-typed by PCR-SSP. The samples were typed for HLA-A, -B and -C and HLA-DRB1, -DRB3, -DRB4, -DRB5, -DQA1, -DQB1, -DPB1 and -DPA1 with allele level resolution. Isolated HLA-B allele level mismatches were associated with an increased incidence of acute graft versus host disease grades II-IV and grades III-IV. HLA-C-mismatched, but killer cell immunoglobulin-like receptor (KIR) ligand motif-matched stem-cell grafts were significantly associated with improved survival rates and relapse-free survival (RFS). In patients receiving HLA-DPA1-mismatched stem cell grafts, reduced survival and shorter RFS were seen. These patients also had an increased frequency of relapses (64%vs 26%). We conclude that genomic HLA class I- and class II-typing may improve the outcome after unrelated stem-cell transplantation. The awareness of HLA class I- and II-mismatches in a recipient-donor pair makes it possible to give appropriate pre- and post-transplantation treatment.

HLA-DPB1 typing by polymerase chain reaction amplification with sequence-specific primers

DPB1 is the second most polymorphic class II locus with currently 84 recognized alleles, i.e. DPB1*0101 to DPB1*8101. Most of the alleles have been described during the last few years using oligonucleotide and sequencing techniques and relatively little is known about the role and importance of the polymorphic residues as regards to the function of DP molecules. In the present study, polymerase chain reaction (PCR) primers were designed for identification of all the phenotypically different DPB1 alleles by PCR amplification with sequence-specific primers. Forty-eight standard genomic PCR reactions per sample were performed in order to achieve this resolution. Unique amplification patterns were obtained in 2983 of 3160 (94.4%) possible genotypes. The primers were combined so that only very rare genotypes gave rise to ambiguous patterns. Sixty-four Histocompatibility Workshop cell lines and 150 DNAs provided by the UCLA DNA exchange were investigated by the DPB1 primer set. All typing results were conclusive. Analysis of the distribution of DPB1 alleles was performed in 200 Caucasian samples, 100 African samples and 40 Oriental samples. The population study by the DPB1 PCR-SSP method showed a characteristic distribution of HLA-DPB1 alleles. Each ethnic group had one, or two, frequent DPB1 allele(s) and the frequency of homozygotes was high, suggesting that balancing selection does not appear to be affecting the evolution of the DPB1 locus.

Going back to the roots: effective utilisation of HLA typing information for bone marrow registries requires full knowledge of the DNA sequences of the oligonucleotide reagents used in the testing

Information obtained by DNA-based HLA typing assays is more detailed and of higher quality than that obtained by conventional serological techniques. Nevertheless, it is common for data acquired in this way to be presented in the more familiar serological format. In many cases this representation can lead to significant loss of information, which may only become apparent at a later time, with the discovery of novel allele sequences. DNA-based typing methods, such as sequence-specific oligonucleotide probing (SSOP) or sequence-specific priming (SSP) generate fragmentary sequence data which is information rich. An alternative to assigning allele names to these fragments is to simply store the sequence data itself without interpretation. Bone marrow donor repositories can then be searched directly with sequence information, which though complex is more complete, rather than searching by derivative allele names.

Pediatric and adult forms of type I autoimmune hepatitis in Argentina: evidence for differential genetic predisposition

The aim of this study was to compare major histocompatibility complex (MHC) class II susceptibility to type 1 autoimmune hepatitis (AH) between children and adults of the same ethnic group. HLA-DRB1, HLA-DRB3, HLA-DQA1, and HLA-DQB1 gene subtypes were examined by high resolution oligonucleotide typing in 122 pediatric (PAH) and 84 adult (AAH) patients and in 208 controls. In children, HLA-DRB1*1301 was the primary susceptibility allele (66.4% patients vs. 10.6% controls, relative risk [RR] = 16.3, Pc < 10(-24)) whereas HLA-DRB1*1302, which differs from HLA-DRB1*1301 by only 1 amino acid, appeared to be protective. The exclusion of individuals with HLA-DRB1*1301 from control and pediatric patients allowed us to find a secondary association of PAH with HLA-DRB1*0301. Possession of HLA-DRB1*1301, however, was associated with a lower therapeutic response rate. Analysis of peptide binding pocket residues indicated that Tyr 10, Ser 11, Ser 13, and Val 86 in the class II beta chain were present in 85% of patients compared with 37% of controls, suggesting that a high proportion of AH susceptibility is attributable to these residues (etiologic fraction [EF] = 76%). In contrast to the class II associations in children, AAH was associated with HLA-DRB1*0405 (RR = 10.4, Pc <.005) but not with HLA-DRB1*1301 or HLA-DRB1*0301. In addition, HLA-DR4 with the class I gene, HLA-A11, appeared synergistic in predisposing AAH patients to develop extra-hepatic autoimmune (AI) manifestations (odds ratio [OR] = 104.9, Pc < 10(-4)). Concomitant differences in autoantibody profiles were also observed in PAH versus AAH: smooth muscle antibodies (SMA) were most prevalent in PAH but antinuclear antibodies were most prevalent in AAH (P =.003). This study therefore reveals that different HLA-DRB1 allotypes confer susceptibility to AH in children and adults and raises the possibility that PAH and AAH may be triggered by different factors.

New high resolution typing strategy for HLA-A locus alleles based on dye terminator sequencing of haplotypic group-specific PCR-amplicons of exon 2 and exon 3

In this study, a new sequencing-based typing strategy for the HLA-A locus is presented which involves group-specific separate amplification of exon 2 and 3 of HLA-A alleles in a first step. Conserved HLA-A locus-specific primers of intron 1 or 3 were combined in 10 primer-mixes with group-specific primers hybridizing to the 5'- or 3'-end of exon 3 or 2 for pre-typing of the HLA-A alleles in 14 allelic groups. Maximally four overlapping short amplicons are produced under identical polymerase chain reaction (PCR) conditions with individual separate amplification of exon 2 and exon 3 of the haplotypic alleles in most heterozygous combinations. Time- and money-saving one-directional Big Dye Terminator cycle sequencing is shown to provide reliable high resolution typing of the HLA-A alleles, even in a few cases of two amplicons in one primer reaction mixture. In comparison, to other sequencing-based typing (SBT) techniques the applied typing strategy minimizes the risk of unequal amplification or of drop-outs of one of the haplotypic alleles and allows unequivocal definition of the cis/ trans linkage of polymorphic positions of the complete exon 2 and exon 3 in most heterozygous cells. This also includes detection of new alleles differing in the polymorphic template generating primer annealing sites as well as in unusual combinations of known exon 2 and 3 sequences. With 10 primer sets working under identical conditions for pre-grouping and separate amplification of the haplotypic alleles our SBT procedure also could be implemented in clinical settings of large-scale stem cell donor histocompatibility testing for fast molecular HLA-A matching.

Molecular, serological and population studies on a novel HLA-B allele--HLA-B*5002

A novel HLA-B allele (B*5002), detected as a discrepancy between serological and PCR-SSP HLA-A and B phenotyping of bone marrow panel donors, was identified by nucleotide sequencing of exons 2 and 3. Titration studies on 39 HLA-B12/B21 cross-reactive antisera showed that the serological specificity of HLA-B*5002 was HLA-B45. PCR-SSP testing of 287 serologically defined HLA-B45-positive subjects from a panel of 12,411 donors, together with HLA-B*45 and B*5002 frequency data on 4,342 PCR-SSP typed subjects, indicated that 4.53% of serologically defined HLA-B45-positive subjects possess HLA-B*5002 and not HLA-B*4501. The phenotype frequency of HLA-B*5002 was 0.08954%; gene frequency was 0.00045 (n=16,753). In 73.3% of instances B*5002 appeared to be present on a haplotype with DRB1*0406 and DQB1*0402, 54.6% of which possessed A*2301. The B*5002, DRB1*0406, DQB1*0402 haplotype represents 52.4% of all haplotypes with DRB1*04 and DQB1*04 and 78.6% of haplotypes possessing DRB1*0406 and DQB1*0402.

HLA-A towards a high-resolution DNA typing

Sequencing-based typing (SBT) and sequence-specific oligonucleotide probing (PCR-SSOP) are DNA-based typing approaches to identify HLA-A alleles. In this study PCR-SSOP SBT have been evaluated and considered to reach a high-resolution typing. Based upon serological typing, 32 genomic samples were typed by SBT and PCR-SSOP Three main clusters of resolution could be defined. The advantage of the PCR-SSOP approach is the possibility to type numerous samples in a short time. SBT minimizes the number of ambiguous heterozygous combinations and often allows direct detection and identification of new alleles.

HLA-B14 subtyping by semi-nested PCR-SSP and haplotype distribution in a Spanish population

HLA-B14 serological subtyping is very limited probably due to the internal position of the unique amino acid residue that differentiates B64 and B65 molecules. In order to carry out an accurate B14 subtyping we have designed a semi-nested PCR-SSP procedure that can differentiate B*1401 and B*1402 in any HLA-A, -B or -C antigen combination. A panel of 133 B14-positive and 31 B14-negative healthy and unrelated Spanish individuals were studied. Additionally, 45 B14-bearing haplotypes (-A,-B,-C,-DRB1,-DRB3/DRB4/DRB5,-DQA1,- DQB1) were available through family studies. The relative frequencies of HLA-B14 subtypes were 74% for B*1402 and 26% for B*1401, in agreement with those found in other Central European populations, but differing from those in Wales, where the relative presence of B64 goes to 41%. A total of 11/17 and 18/28 different haplotypes for B*1401 and B*1402, respectively, were identified. Both alleles showed the strongest association to Cw8 (43/45), indicating a primary ancestral B14-Cw8 association. However, B14 subtypes evidenced very distinguishable haplotype distributions. B*1401 is strongly associated with the common HLA class II haplotype DRB1*0701-DQA1*0201-DQB1*02 (13/17), while B*1402 is mainly associated to DRB1*0102 (16/28). Three major haplotypes were identified: A32-Cw8-B*1401-DR7-DQ2 (5/17), A33-Cw8-B*1402-DRB1*0102-DQ5 (5/28) and A2-Cw8-B*1402-DRB1*0102-DQ5 (5/28).

Complete HLA-A DNA typing using the PCR-RFLP method combined with allele group- and sequence-specific amplification

We have established a practical method of complete high-resolution typing for all HLA-A alleles using the polymerase chain reaction (PCR)-restriction fragment-length polymorphism (RFLP) technique combined with allele group- and sequence-specific amplification. The second and third exons of the HLA-A gene, in which most allelic variations are observed, were separately amplified by PCRs with 3 and 4 group-specific primer pairs, respectively. Each PCR-amplified product was digested by allele-specific restriction endonucleases and then subjected to electrophoresis on a 10% polyacrylamide gel. In this way, 62 out of 79 HLA-A alleles could be discriminated by the RFLP patterns derived from the genetic polymorphism in the exon 2 and 3 domains. The remaining 17 alleles could be defined unequivocally by either PCR-RFLP analysis after exon 4 amplification or PCR analysis with sequence-specific primers (SSP). By this method, complete HELA-A genotyping for all homozygous and heterozygous combinations can be accomplished, establishing technically simple, economical and practical routine typing of the HLA-A gene, especially for small samples.

HLA-A typing: comparison between serology, the amplification refractory mutation system with polymerase chain reaction and sequencing

In this study we typed HLA-A polymorphisms by a new sequence-based typing (SBT) method, which involved one PCR reaction and four sequencing reactions covering exon 2 and exon 3. This method allowed complete identification of all known HLA-A alleles and revealed the presence of a new allele, named HLA-A*2608. We also introduced sequencing of exon 4 for some samples in order to discriminate the allelic pairs that are identical in exon 2 and 3, thus improving SBT resolution. Finally, we compared the results obtained by SBT with data obtained by serological typing and the amplification refractory mutation system (ARMS-PCR). Together, our results suggest that the SBT here described provides an optimal HLA-A typing technique that may be useful in selecting donor-recipient pairs in bone marrow transplantation between unrelated individuals.

A generic sequencing based typing approach for the identification of HLA-A diversity

Sequencing Based Typing (SBT) is a generic approach for the identification of HLA-A polymorphism. This approach includes the high resolution typing of the HLA-A broad reacting groups, HLA-A subtypes and will identify new alleles directly. The SBT approach described here uses a locus specific amplification of DNA from exon 1 to exon 5. The resulting 2,022 bp PCR product serves as a template for the subsequent sequencing reactions. Amplification is followed by direct sequencing of exons 2, 3 and 4 in both orientations with fluorescently labeled primers to define all polymorphic positions leading to a high resolution typing result. In this study the sequence of exons 2 and 3 of a panel of 49 cell lines was determined. In addition, the exon 4 region of 35 cell lines was also sequenced to evaluate the exon 4 polymorphism. The HLA-A type of most of the cells could be identified by sequencing only exons 2 and 3. However, the sequence of exon 4 was required to discriminate A*0201 from A*0209 and A*0207 from A*0215N. In this panel, an identical new "HLA-A*0103" was identified in two Caucasian samples.

Determination of HLA-A*02 antigen status in Hodgkin's disease and analysis of an HLA-A*02-restricted epitope of the Epstein-Barr virus LMP-2 protein

There is good evidence for an association between Epstein-Barr virus (EBV) and Hodgkin's disease (HD). In approximately one-third of cases, the EBV genome is detectable in Reed-Sternberg (RS) cells and there is expression of the viral nuclear antigen EBNA-1 and the latent membrane protein LMP-1. Expression of LMP-2 has been demonstrated at the mRNA level, and it is presumed that the protein is expressed alongside LMP-1. The LMP-2 protein is known to contain an epitope presented to cytotoxic T-cells which is restricted through the HLA class I antigen A*0201 in healthy seropositive individuals. Since most HLA-A*02-positive Caucasians are HLA-A*0201-positive, it was hypothesized that HLA-A*02-positive individuals would be under-represented among Caucasians with EBV-associated HD. HLA-A*02 status was determined, using flow cytometry and/or the polymerase chain reaction, for 276 individuals including 176 cases of HD. There was no significant difference between the frequency of HLA-A*02 positivity in HD cases and controls, and between EBV-associated and non-associated cases of HD. The A*02 alleles of 14 cases of EBV-associated HD were further subtyped using nested PCR; all except one case were found to be A*0201-positive. We therefore investigated whether there was any evidence for mutation of the epitope representing amino acids 426-434 of LMP-2a which is restricted through HLA-A*0201. In 10/11 cases the nucleotide sequence encoding this epitope was identical to the published sequence; in the remaining case there was a mutation which would not be expected to alter the conformation of the epitope. Overall, our data suggest that other mechanisms of immune escape must be operative in EBV-associated HD.

Allele typing of HLA-A10 group by nested-PCR-low ionic strength single stranded conformation polymorphism and a novel A26 allele (A26KY, A*2605)

HLA-A26 is one of the most polymorphic HLA-A locus antigens among the Japanese population. Four HLA-A26 subtypes have so far been defined: A*2601-2604 [1]. We developed a means of typing alleles of the HLA-A10 group by nested PCR low ionic strength single-stranded conformation polymorphism (NPCR-LIS-SSCP) that is simple and cost effective. We used it to type 200 DNA samples from unrelated Japanese individuals who were serologically HLA-A26 positive. We found a novel A26 allele that had been suggested by PCR-SSO. Sequence analysis of A26KY (officially assigned A*2605, Accession No. D50068) revealed that the allele differs from A*2601 by a single nucleotide substitution at position 299, which leads to an amino acid substitution Ala-->Glu at position 76 in the alpha helix loop of the alpha 1 domain. From our results, A*2605 is likely to originate from A*2601 by a single point mutation. HLA-A*2601 showed the highest frequency (61.9%), followed by A*2603 (19.5%), A*2602 (17.6%), A*2604 (0.5%), and A*2605 (0.5%) in Japanese.

HLA-DPA1 typing by PCR amplification with sequence-specific primers (PCR-SSP) and distribution of DPA1 alleles in Caucasian, African and Oriental populations

In the present study PCR primers were designed for detecting all known DPA1 variability, i.e., the presently recognized six DPA1 alleles 0103 to 0401, and also for separation of the four DPA1*02 alleles, by PCR amplification with sequence-specific primers (PCR-SSP). For each sample seven different PCR reactions were performed which allowed the identification of all DPA1 alleles and the resolution of all DPA1 genotypes. Forty-eight cell lines and 100 donor spleen cells were investigated by the DPA1 PCR-SSP technique. In the forty-eight known workshop cell-lines no false positive or false negative results were obtained. The 100 donor spleen cells were only typed by the PCR-SSP technique and in their DNAs only one or two DPA1 alleles were found. Twenty cell lines and twenty donor spleen cells were typed on two separate occasions and interpreted blindly. The reproducibility between the repeated typings was 100%. The length of the specific products ranged from 103 to 258 base pairs and the amplification patterns obtained were easy to interpret. In conclusion, DPA1 typing by the PCR-SSP method is an accurate typing technique with high sensitivity, specificity and reproducibility. Analysis of the distribution of DPA1 alleles was performed in 100 Caucasian samples, 100 African samples and 80 Oriental samples, including separation of the four of HLA-DPA1 alleles. Each ethnic group appeared to have one (Caucasians), or two (Africans and Orientals), frequent DPA1 allele(s) and a high frequency of DPA1 homozygotes, suggesting that, like for the DPB1 locus, balancing selection does not appear to be affecting the evolution of the DPA1 locus.

HLA-A and -B genotyping in living related one haploidentical kidney

Sixty-five haplo-identical living-related renal transplant pairs were subjected to comparative studies for HLA class-I typing suitability between the DNA and serological methods. Our HLA-A genotyping method was highly resolutive and allowed assigning 33 serologically blank specificities and subdividing some HLA-A serological specificities, of which A2 discrimination was considered to be indispensable for the matching analysis because of its high frequency among Japanese. Our HLA-B genotyping method made it possible to identify the 17 serologically blank specificities despite their "low resolutive" capacities. Analysis of 14 DRB1-compatible pairs suggested that HLA-A and -B compatibilities had beneficial effects on the long term graft survival. It was concluded that HLA-A and -B should be genotyped for the matching analysis of the kidney transplant pairs to obtain satisfactory graft outcome.

Comparison of HLA-A antigen typing by serology with two polymerase chain reaction based DNA typing methods: implications for proficiency testing

Serology has been routinely used for class I HLA typing for the selection of donors for allotransplantation. However, serology is not adequate for the assignment of all class I specificities especially when testing non-Caucasians subjects and it is necessary to adopt new strategies for routine testing. At the present time the extent of incorrect serologic HLA-A assignments in clinical testing is not known. The polymerase chain reaction (PCR) based techniques have become useful standard clinical typing methods of HLA class II alleles but most laboratories still use serology for class I typing. In this report we have compared two PCR based techniques, PCR amplification with sequence-specific primers (PCR-SSP) and PCR amplification and subsequent hybridization with sequence-specific oligonucleotide probes (PCR-SSOP), for the assignment of HLA-A specificities in 56 blood samples from patients and families serologically typed for HLA-A. This side-by-side comparison of PCR methods showed 100% correlation between them. However, serology showed 7.1% misassignments and, in an additional panel of 19 cells where serology produced equivocal results, the PCR-SSP and SSOP methods identified the correct HLA-A specificity. Our results emphasize the need to complement routine serologic testing of HLA specificities with a small number of primers designed to test HLA-A34, A36, A43, A66, A74 and A80, that are not detected with high precision by serology. We concluded that the PCR-SSP and -SSOP methods can be used in routine HLA-A typing of patients and donors for transplantation with a greater precision than serology.

Defining the allelic variants of HLA-A30 in the Sardinian population using amplification refractory mutation system--polymerase chain reaction

HLA-A30 is present in the Sardinian population at a frequency of 23%. We have designed a system using nested ARMS-PCR to determine the relative frequencies of the HLA-A*30 allelic variants (A*3001, A*3002, and A*3003) within this population. The use of a nested PCR approach, in which the first-round reaction provides HLA-A*30 specificity and template DNA for the subsequent nested reactions, is a powerful means of discriminating between alleles of very similar sequence. Using this method, we performed subtyping of 35 serologically defined HLA-A30 Sardinian individuals, and taking into account homozygotes, identified 38 A*30 alleles. Of these, 33 typed as A*3002, four typed as A*3001, and one sample did not conform to the patterns of reactivity of any of the published A*30 alleles. Haplotype information showed strong linkage disequilibrium between A*3002 and B18. This study underlines the potential of DNA-based methods for typing HLA class I in terms of adding further levels of definition to studies of population structure and also as a means of identifying new alleles.

The HLA-A,B,C genotype of the class I negative cell line Daudi reveals novel HLA-A and -B alleles

Daudi, a lymphoblastoid B cell line derived from an African Burkitt lymphoma does not express HLA-A,B,C antigens at the cell surface. Although HLA-A,B,C heavy chains are made normally they do not assemble into functional molecules because beta 2-microglobulin is absent. Previous serological analysis of somatic cell hybrids indicated that the HLA haplotypes of Daudi encoded HLA-A1, A10(A26), B17, and B16(38) antigens. Here we describe the application of molecular methods: ARMS-PCR, cDNA cloning and sequencing, immunoprecipitation and gel electrophoresis, to define the class I genotype of the Daudi cell line which is HLA-A*0102, A*6601, B*5801, B*5802, Cw*0302 and Cw*0602. With the exception of the B38 antigen, which is not a product of the alleles defined, the genotype is consistent with the serological description. Two previously undiscovered alleles emerged from this analysis: A*0102 and B*5802. The A*0102 allele differs from A*0101 by 5 nucleotide substitutions within exon 2 where it has a motif shared with A*30 alleles; the B*5802 allele differs from B*5801 by 3 substitutions in exon 3 where it has a motif shared with B*14 alleles. Subtyping HLA-A1 alleles showed A*0102 was well represented amongst individuals typed serologically as A1 in an African population but was absent from caucasoids. B*5802 has been found in a second individual. Thus the novel A and B alleles are not specific to the Daudi tumor. Overall, this analysis of a single East African cell illustrates the power of molecular methods to define new class I HLA alleles in non-caucasoid populations.

Population diversity of B-locus alleles observed by high-resolution DNA typing

HLA B-locus typing by group-specific PCR and hybridization with SSOP was performed in 81 10th IHWS B cell lines and 334 selected subjects of our local panel, from four ethnic groups. Most of the B-locus serological specificities were well defined. However, some antigens like B41, B58, B56, the splits of B14, and some subtypes of B5, were not accurately assigned by serology. In the panel studied, we found 17 hybridization patterns that corresponded to probable new alleles. New patterns occurred in the four ethnic groups examined. Multiple subtypes of B35, B5, B15, B41, B44, B57, B58, B70, B14, B40, B22 were found in subjects of the same ethnic group. In view of the poor serological definition of some alleles, and the occurrence of multiple subtypes in the same ethnic population, it appears that high resolution B-locus typing may be an important addition for detection of potentially relevant HLA incompatibilities in transplantation. It should also be valuable for population studies and for the investigation of HLA associations with diseases.

Comprehensive, serologically equivalent DNA typing for HLA-B by PCR using sequence-specific primers (PCR-SSP)

Polymorphic products of HLA class I genes from the human major histocompatibility complex (MHC) are traditionally assigned by serology with additional heterogeneity detectable using one-dimensional isoelectric focusing (1D-IEF). With the increased availability of HLA class I DNA sequence information it has become feasible to genotype for class I by polymerase chain reaction utilising sequence-specific primers (PCR-SSP). We describe here a comprehensive HLA-B PCR-SSP typing system based on available HLA nucleotide sequences which can detect all serologically defined antigens in most heterozygous combination in 48 one-step PCR reactions. In addition, four new unsequenced variants have been identified. DNA samples from 57 International Histocompatibility Workshop reference cell lines and 160 control individuals have been typed by the HLA-B PCR-SSP technique. 3/57 cell line types and 12/160 normal control individuals types were discrepant with the reported serological types. The SSP system has been designed to be higher resolution than serology but is not a complete allele-specific PCR although many single alleles can be identified. The system is entirely complementary to previous published PCR-SSP systems for HLA-Class II and HLA-Class I in that the same PCR conditions and controls are used which allows us to do one step PCR-SSP for all relevant HLA loci in under 3 hours in a system suitable for the typing of cadaver donors.

Low resolution DNA typing of the HLA-B5 cross-reactive group by nested PCR-SSP

We have established a DNA typing system for the HLA-B5 serologically cross-reactive group (CREG) by means of a two-step PCR amplification with nested sequence-specific primers (nPCR-SSP). The present study provides a low resolution definition of the HLA-B5 CREG, i.e. identifying polymorphism equivalent to serology. Two different primer combinations allow group-specific amplification of all HLA-B5 CREG alleles and other related HLA class I alleles from genomic DNA. The amplified DNA is subjected to a second amplification step using eleven nested primer pairs. This assay permits the detection of the HLA-B5 CREG specificities B35, B51, B52, B53, and B7801 in all homozygous and heterozygous combinations. Sensitivity and specificity as judged by a blind quality control study investigating a reference panel (n = 50) is 100%. Extension of this approach should allow rapid DNA typing of all serologically defined HLA-B specificities by nPCR-SSP.

Locus-specific amplification of HLA class I genes from genomic DNA: locus-specific sequences in the first and third introns of HLA-A, -B, and -C alleles

We have identified locus-specific sequences in the first and third introns flanking the polymorphic second and third exons of HLA class I genes. PCR primers derived from these conserved sequences produced DNA fragments of the expected sizes for each of the HLA-A, -B, and -C loci in the amplification of genomic DNA. PCR products generated using each of the locus-specific sets of primers displayed exquisite locus specificity, as assessed by hybridization with oligonucleotide probes specific for ten classical and non-classical HLA class I genes. Amplification with these primer sets was effective and specific for the HLA alleles tested under the given PCR conditions. When hybridized with oligonucleotides derived from shared polymorphic sequence motifs, reaction patterns of PCR products from each locus were precisely as expected from published or database sequences. Chemiluminescent signals generated from digoxygenin-ddUTP-labeled probes were even for all samples and as strong as those obtained in MHC class II typing. These locus-specific primer sets derived from intron sequences provide an effective means to amplify genomic DNA which will facilitate PCR-based HLA class I typing methods. This will also allow HLA class I typing to be conducted with greater precision, at lower cost, and faster than previously described class I typing methodologies.

Low-resolution DNA typing for HLA-B using sequence-specific primers in allele- or group-specific ARMS/PCR

The products of the human major histocompatibility complex (HLA Class I and II) have historically been detected using serological or cellular assays. With the availability of DNA sequence information for alleles of the HLA system, and with the development of molecular biological techniques it has become possible to tissue type for allelic differences in the HLA genes themselves. We describe here a polymerase chain reaction (PCR) system, based on the principle of the amplification refractory mutation system (ARMS), for low-resolution DNA typing of the HLA-B gene. The technique involves a one-step PCR from genomic DNA using sequence-specific primers in particular combinations that determine the specificity of each reaction. A low-resolution primer panel has been designed, based on published HLA-B gene nucleotide sequences, consisting of 34 sequence-specific primers (SSP) in 24 PCR reactions which cover all known HLA-B alleles, to give allele-specific or group-specific amplification of DNA fragments of defined size (344-784bp). Advantages of the system are that it can be performed in under 4 hours including DNA extraction, results are easy to interpret and it does not require viable cells.

Advances in DNA-based HLA-typing methods

The last five years has witnessed spectacular progress in the developments of PCR-based HLA-typing methods. Here, Jeffrey Bidwell charts a course through the huge array of methodologies now available both for MHC class I and class II analysis.

HLA-A locus DNA typing of the 4AOH cell panel by arms PCR

As part of the Fourth Asia-Oceania Histocompatibility (4AOH) Workshop, the authors have demonstrated a method of DNA-based tissue typing of the HLA-A locus using ARMS-designed primers in a panel of specific PCR reactions. The study was carried out blind under Workshop conditions and the results confirm the method as an accurate means of determining HLA-A locus tissue types.

A comprehensive polymerase chain reaction-oligonucleotide typing system for the HLA class I A locus

A comprehensive system for genetic typing of the HLA class I A locus is described, based on PCR amplification and typing with nonradioactively labeled SSO probes. Exons 1-3 of the A locus are amplified and typing is performed with a set of 30 nonradioactively labeled oligonucleotide probes. This system resolves 34 of 39 known alleles and 561 (94%) of 595 possible genotypes. Among a sample of 354 individuals from Sweden and China, 97.5% of the genotypes were resolved. Probes were directed preferentially at replacement substitutions in foreign antigen-binding sites, in order to detect not only the known alleles but also new combinations of polymorphic motifs, indicative of previously unrecognized alleles. Three individuals were found with a new combination of polymorphic motifs, suggesting the presence of at least one previously undescribed allele in the populations sampled. This typing system is useful for disease association studies, tissue typing, and in forensic medicine.

HLA-B locus DNA typing: detection of B*7801 and seven additional alleles by BW6-specific exon 2 amplification

A molecular approach to type a new HLA-B5 antigen, HLA-BSNA, characterized by its unusual association with the public determinant BW6, referred to as B*7801, has been designed. Antigens disclosing serological identity with SNA, BX1 and Te76 were also investigated. Based upon HLA-B exon 2 group-specific PCR, the following procedure was established: 5' and 3' primers were designed by targetting the codons 11-12 (AM) and 81-83 (LRG), respectively, in exon 2 (alpha 1 domain). The 5' primer discriminates with HLA-A, -C genes and pseudogenes, while the 3' primer detects the sequence encoding the BW6 epitope (NLRG) and discriminates it from the BW4 epitope. The combination of this pair of primers specifically amplifies 26 HLA-B alleles. Oligotyping for B*7801 was performed using a combination of two non-radioactively labeled SSO probes identifying positions T45 and D74 in exon 2. To resolve ambiguous hybridization patterns, an additional set of probes was used. The specificity of this BW6-group-specific amplification procedure was investigated on 150 genomic DNA samples. Among them, we obtained 94 amplified DNA products which were tested with eight SSOs. Beside B*7801, the following B alleles could be defined: B*0801, B*35, B*5401, B*5501-2, B*5601-2, B*1501-7 (including B62, B75 and B72) and B*4601. SNA, BX1 and Te76 DNA samples gave similar hybridization pattern providing a clue to the identity of these antigens. This "one PCR and two probes" procedure represents a simple oligotyping strategy which can also be applied to type many other HLA-B specificities.

Defining the common subtypes of HLA A9, A10, A28 and A19 by use of ARMS/PCR

We describe sequence-specific primer (SSP) combinations for use in a one-step polymerase chain reaction (PCR) typing system to determine HLA-A locus subtypes of A9 (A23, A24), A10 (A25, A26, A43), A28 (A*6801, A*6802, A*6901) and A19 (A*2901, A*2902, A*3001, A*3002, A31, A32, A33) from genomic DNA. SSP's were designed on the basis of the amplification refractory mutation system (ARMS) in which a mismatch at the 3' residue inhibits non-specific amplification. The SSP combinations described extend our low-resolution typing system, to provide a high-definition typing of the HLA-A locus.

Highly lytic CD8+, alpha beta T-cell receptor cytotoxic T cells with major histocompatibility complex (MHC) class I antigen-directed cytotoxicity in beta 2-microglobulin, MHC class I-deficient mice

Targeted disruption of the beta 2-microglobulin (beta 2m) gene results in major histocompatibility complex (MHC) class I deficiency and virtual disappearance of functional CD8+ cytotoxic T lymphocytes (CTLs) in beta 2m-deficient (beta 2m-/-) mice. We asked whether the beta 2m-/- mice are able to reject tumor cells injected i.p. and what is the cellular composition of peritoneal exudate leukocytes (PELs) from such mice. We found that beta 2m-/- mice do reject MHC class I-bearing tumor cells injected i.p. Surprisingly, analysis of PEL CTLs obtained from i.p. tumor-injected beta 2m -/- mice revealed the presence of a large proportion of functional, tumor-destroying CD8+, CD4-, alpha beta T-cell receptor-positive, CD3+, Thy-1+, MHC class I-negative CTLs with strong MHC class I-directed cytotoxic activity. These results call for careful studies of local accumulation of CD8+ CTLs in beta 2m -/- mouse models and suggest that the dramatic decrease in MHC class I expression caused by beta 2m gene disruption does not prevent CD8+/CD4- cell selection and expansion.

Tissue typing the HLA-A locus from genomic DNA by sequence-specific PCR: comparison of HLA genotype and surface expression on colorectal tumor cell lines

A system devised for tissue typing the HLA-A locus by PCR from genomic DNA has been used to investigate abnormalities of HLA expression in a panel of 30 colorectal tumor cell lines, by comparing the HLA-A locus genotype with surface expression of HLA. Three cell lines showed complete lack of HLA expression associated with failure to express beta 2-microglobulin. In two other cell lines, loss of expression of HLA-A2 was observed, in spite of the presence of the gene in genomic DNA. Eleven cell lines gave a single HLA-A locus specificity on PCR typing. In one of these cell lines we have demonstrated the loss of an HLA-A locus gene in the tumor cell by comparison with DNA from a lymphoblastoid B-cell line derived from the same patient. These data indicate that at least three independent mechanisms were involved in the loss of HLA expression on the colorectal tumor cell lines.