HLA-DRB1 and -DRB3 allele frequencies and haplotypic associations in Koreans

Plausible Influence of HLA Class I and Class II Diversity on SARS-CoV-2 Vulnerability

Severe acute respiratory syndrome CoV-2 (SARS-CoV-2) caused the global coronavirus disease 2019 (COVID-19) pandemic, which adversely affected almost all aspects of human life and resulted in the loss of millions of lives, while affecting nearly 0.67 billion people worldwide. SARS-CoV-2 still poses a challenge to the healthcare system as there are more than 200,000 active cases of COVID-19 around the globe. Epidemiological data suggests that the magnitude of morbidity and mortality due to COVID-19 was low in a few geographical regions and was unpredictably higher in a few regions. The genetic diversity of different geographical regions might explain the sporadic prevalence of the disease. In this context, human leukocyte antigens (HLA) represent the most polymorphic gene-dense region of the human genome and serve as an excellent mini-genome model for evaluating population genetic diversity in the context of susceptibility and progression of various diseases. In this review, we highlight the plausible influence of HLA in susceptibility, severity, immune response, and designing of epitope-based vaccines for COVID-19. Further, there is a need for extensive investigations for illustration and clarification of the functional impact of HLA class I and II alleles in the pathogenesis and progression of SARS-CoV-2.

Distributions of 11-loci HLA alleles typed by amplicon-based next-generation sequencing in South Koreans

The range of HLA typing for successful hematopoietic stem cell transplantation (HSCT) is gradually expanding with the next-generation sequencing (NGS)-based improvement in its quality. However, it is influenced by the allocation of finances and laboratory conditions. HLA-A, -B, -C, -DRB1/3/4/5, -DQA1, -DQB1, -DPA1, and -DPB1 alleles were genotyped at the 3-field level by amplicon-based NGS using MiSeqDx system and compared to our previous study employing long-range PCR and NGS using TruSight HLA v2 kit, in healthy donors from South Korea. Exon 2, exons 2/3, exons 2/3/4 or 5 of 11-loci were amplified by multiplex PCR. The sequence reads of over 53 depth counts were consistently obtained in each sample exon, depending on the target exon determined to match the reference sequence contained in the IPD-IMGT/HLA Database. HLA alleles were investigated by combinations of the determined exons. A total of 18 alleles with a frequency over 10% were found at the 11 HLA loci. Three ambiguities of HLA-A, -C, and -DRB1 were resolved. We observed a total of 26 HLA-A ~ C ~ B and 6 HLA-DRB1 ~ DQA1 ~ DQB1 ~ DPA1 ~ DPB1 haplotypes having significant linkage disequilibrium between alleles at all neighboring HLA loci. This result was compatible with the previous one, using TruSight HLA v2 kit. Advantages are simple and short progress time because one plate is used for each PCR step in one PCR machine and 11-loci HLA typing is possible even if only eight samples. These data suggested that expanded 11-loci HLA typing data by amplicon-based NGS might help perform HSCT.

Allele and haplotype frequencies of human leukocyte antigen-A, -B, -C, -DRB1, -DRB3/4/5, -DQA1, -DQB1, -DPA1, and -DPB1 by next generation sequencing-based typing in Koreans in South Korea

Allele frequencies and haplotype frequencies of HLA-A, -B, -C, -DRB1, -DRB3/4/5, -DQA1, -DQB1, -DPA1, and -DPB1 have been rarely reported in South Koreans using unambiguous, phase-resolved next generation DNA sequencing. In this study, HLA typing of 11 loci in 173 healthy South Koreans were performed using next generation DNA sequencing with long-range PCR, TruSight^® HLA v2 kit, Illumina MiSeqDx platform system, and Assign^™ for TruSight^™ HLA software. Haplotype frequencies were calculated using the PyPop software. Direct counting methods were used to investigate the association with DRB1 for samples with only one copy of a particular secondary DRB locus. We compared these allele types with the ambiguous allele combinations of the IPD-IMGT/HLA database. We identified 20, 40, 26, 31, 19, 16, 4, and 16 alleles of HLA-A, HLA-B, HLA-C, HLA-DRB1, HLA-DQA1, HLA-DQB1, HLA-DPA1, and HLA-DPB1, respectively. The number of HLA-DRB3/4/5 alleles was 4, 5, and 3, respectively. The haplotype frequencies of most common haplotypes were as follows: A*33:03:01-B*44:03:01-C*14:03-DRB1*13:02:01-DQB1*06:04:01-DPB1*04:01:01 (2.89%), A*33:03:01-B*44:03:01-C*14:03 (4.91%), DRB1*08:03:02-DQA1*01:03:01-DQB1*06:01:01-DPA1*02:02:02-DPB1*05:01:01 (5.41%), DRB1*04:05:01-DRB4*01:03:01 (12.72%), DQA1*01:03:01-DQB1*06:01:01 (13.01%), and DPA1*02:02:02-DPB1*05:01:01 (30.83%). In samples with only one copy of a specific secondary DRB locus, we examined its association with DRB1. We, thus, resolved 10 allele ambiguities in HLA-B, -C (each exon 2+3), -DRB1, -DQB1, -DQA1, and -DPB1 (each exon 2) of the IPD-IMGT/HLA database. Korean population was geographically close to Japanese and Han Chinese populations in the genetic distances by multidimensional scaling (MDS) plots. The information obtained by HLA typing of the 11 extended loci by next generation sequencing may be useful for more exact diagnostic tests on various transplantations and the genetic population relationship studies in South Koreans.

Distributions of HLA-A, -B, and -DRB1 alleles typed by amplicon-based next generation sequencing in Korean volunteer donors for unrelated hematopoietic stem cell transplantation

HLA genes play a pivotal role for successful hematopoietic stem cell transplantation (HSCT). There is an increasing need for sophisticated screening of donor HLA genotypes for unrelated HSCT. Next generation sequencing (NGS) has emerged as an alternative for classical Sanger sequence for HLA typing. In this study, HLA-A, -B, and -DRB1 alleles were genotyped at the allelic (6-digit) level using MiSeqDx in 26,202 volunteers from the Korean Network for Organ Sharing. Exon 2 and 3 of HLA-A and -B and exon 2 of HLA-DRB1 were amplified by polymerase chain reaction (PCR) and each allele was determined by matching the targeted exons and the reference sequence consisting of the IPD-IMGT/HLA Database. Seventy alleles of HLA-A, 102 alleles of HLA-B, and 69 alleles of HLA-DRB1 were identified. According to common and well-documented catalogs, 34 alleles in HLA-A, 61 in HLA-B, and 45 in HLA-DRB1 locus were common alleles, and 12, 14, and 11 kinds, were well-documented alleles, respectively. Thirteen novel alleles including 3 alleles in HLA-A, 8 alleles in HLA-B, and 2 alleles in HLA-DRB1 loci were found. Ten haplotypes with a frequency of more than 1.0% accounted for 22.4% of the total haplotype frequencies. Cis/trans ambiguities of HLA-A and -B loci by combination of exons 2 and 3 were analyzed to be 0.17% of 3 and 3.95% of 22 genotypes, respectively. This information on rare and novel alleles found by accurate HLA typing with NGS may be helpful for unrelated HSCT among Koreans.

Novel susceptibility alleles in HLA region for myositis and myositis specific autoantibodies in Korean patients

OBJECTIVES

HLA genes are a major genetic risk factor for myositis and myositis specific antibodies (MSAs), exhibiting unique HLA backgrounds for myositis in different ethnic groups. This is the first large scale Korean study to genotype the HLA-DRB1 and -DPB1 alleles and to examine their association with myositis and MSAs.

METHODS

HLA-DRB1 and HLA-DPB1 alleles and MSAs were examined in 179 patients with dermatomyositis (DM, n = 129) or polymyositis (PM, n = 50) and healthy controls (n = 800 for HLA-DRB1, n = 548 for HLA-DPB1). Associations between individual HLA alleles and myositis/MSA were examined. Bonferroni correction was applied for multiple testing comparing patients and controls.

RESULTS

A total of 33 HLA-DRB1 and 24 HLA-DPB1 alleles were genotyped in patients and controls. MSAs were found in 67.0% of patients. Anti-MDA5 (26.8%) and anti-aminoacyl-tRNA synthetase antibodies (15.6%) were most common, followed by anti-Mi2 (9.5%) and anti-TIF1γ antibodies (8.9%). HLA-DRB1*12:02 and HLA-DRB1*14:03 were associated with DM and PM, respectively. HLA-DRB1*12:02 was associated with anti-MDA5, HLA-DRB1*08:03 with anti-ARS, HLA-DRB1*14:03 with anti-SRP, and HLA-DRB1*07:01 with anti-Mi2 antibodies. Although HLA-DRB1*13:01 was associated with anti-TIF1γ antibodies, the frequency of HLA-DRB1*13:01 was rare. HLA-DPB1*02:01 was negatively associated with myositis and PM while HLA-DPB1*17:01 was associated with anti-Mi2 positive DM.

CONCLUSIONS

Unique immunogenetic background was observed for Korean patients with myositis. Novel myositis susceptibility alleles, HLA-DRB1*12:02 and HLA-DRB1*14:03, were identified, together with MSA-associated HLA alleles unique to Korean patients with myositis.

Identification of a novel DRB1 allele through intergenic recombination between HLA-DRB1 and HLA-DRB3∗02 in a Chinese family

In this study, a novel DRB1 allele was revealed by routine HLA-SBT typing noted for its extensive mismatches to any known DRB1 alleles within the exon 2. Sequences containing the exons 2, 3 of HLA-DRB1, their surrounding introns, and the full-length cDNA of DRB1 were analyzed to determine a possible recombination event. Interestingly, the sequences of entire exon 2 were characterized as DRB3(∗)02:02:01:01/02; while exon 3 were characterized as DRB1(∗)14 like alleles. Further analysis of the sequences using Simplot software suggested that an intergenic recombinant event (i.e. exchange of sequence between non-allelic genes) may have occurred between DRB3(∗)02 allele and DRB1(∗)14 like allele, and the recombination sites are located at intron 1 and the boundary of exon 2 and intron 2 of DRB1. There are 5 CGGGG sequences flanking each side of exon 2 could serve as potential recombination site. Moreover, the full-length cDNA of the novel allele has been identified. The exon 1 and exon 3 to exon 6 share the same sequence as DRB1(∗)14 like alleles. At the mRNA level, the new allele has no significant difference when compared with the other DRB1 allele. This novel recombinant allele is also found to be paternally inherited. In conclusion, this is the first report of a DRB1 and DRB3 intergenic recombination event involving whole exon 2, which generate a new DRB1(∗)14:141.

HLA-DRB1 alleles are associated with the susceptibility to sporadic Parkinson's disease in Chinese Han population

Immune disorders may play an important role in the pathogenesis of Parkinson's disease (PD). Recently, polymorphisms in the HLA-DR region have been found to be associated with sporadic PD in European ancestry populations. However, polymorphisms in the HLA complex are highly variable with ethnic and geographic origin. To explore the relationships between polymorphisms of the HLA-DR region and sporadic PD in Chinese Han population, we genotyped 567 sporadic PD patients and 746 healthy controls in two independent series for the HLA-DRB1 locus with Polymerase chain reaction-sequence based typing(PCR-SBT). The χ(2) test was used to evaluate the distribution of allele frequencies between the patients and healthy controls. The impact of HLA-DRB1 alleles on PD risk was estimated by unconditional logistic regression. We found a significant higher frequency of HLA-DRB1*0301 in sporadic PD patients than in healthy controls and a positive association, which was independent of onset age, between HLA-DRB1*0301 and PD risk. Conversely, a lower frequency of HLA-DRB1*0406 was found in sporadic PD patients than in healthy controls, with a negative association between HLA-DRB1*0406 and PD risk. Furthermore, a meta-analysis involving 195205 individuals was conducted to summarize the frequencies of these two alleles in populations from various ethnic regions, we found a higher frequency of HLA-DRB1*0301, but a lower frequency of HLA-DRB1*0406 in European ancestry populations than that in Asians, this was consistent with the higher prevalence of sporadic PD in European ancestry populations. Based on these results, we speculate that HLA-DRB1 alleles are associated with the susceptibility to sporadic PD in Chinese Han population, among them HLA-DRB1*0301 is a risk allele while the effect of HLA-DRB1*0406 deserves debate.

Detection of HLA-DRB1 microchimerism using nested polymerase chain reaction and single-strand conformation polymorphism analysis

For the detection of microchimerism, molecular methods detecting donor-specific HLA-DRB1 alleles in the recipient are most commonly used. Nested polymerase chain reaction sequence specific primer (nested PCR-SSP) methods widely used to increase the sensitivity of detection have been reported to give frequent false-positive reactions. We have developed a new method combining nested PCR with single-strand conformation polymorphism analysis (nested PCR-SSCP) and tested the 1 to 0.00001% level of microchimerism for 27 different HLA-DRB1 alleles. For most (26/27) of the HLA-DRB1 alleles tested, this method could detect 0.01 to 0.001% of microchimerism and its sensitivity was equal to or better than that of nested PCR-SSP tested in parallel. Its specificity was verified by visualizing particular DRB1-specific SSCP bands under test. Nested PCR-SSP indicated frequent false-positive reactions, mainly caused by nonspecific amplification of DRB3/B4/B5 alleles present in the major (recipient) DNAs. We have compared a real-time quantitative PCR for non-human leukocyte antigen (HLA) target (insertion/deletion marker) using a commercial kit (AlleleSEQR Chimerism assay), and its microchimerism detection sensitivity (around 0.1%) was 1 step (10 times) lower than that of nested PCR-SSP or -SSCP methods for HLA-DRB1 alleles. We validated that the newly designed nested PCR-SSCP affords good sensitivity and specificity and may be useful for studying microchimerism in clinical settings.

[Allelic and haplotypic diversity of HLA-A, -B, -C, and -DRB1 genes in Koreans defined by high-resolution DNA typing]

BACKGROUND

In this study, we used high-resolution DNA typing to investigate the distribution of HLA alleles and haplotypes in Koreans.

METHODS

HLA-A, -B, -C, and -DRB1 alleles were genotyped at the allelic (4-digit) level in 474 healthy Koreans. HLA genotyping was performed in two steps. Initially, serologic typing or generic-level DNA typing was performed using the PCR-sequence-specific oligonucleotide method, and then allelic DNA typing (exons 2 and 3 for class I, and exon 2 for DRB1) was carried out using the PCR-single-strand conformation polymorphism method or sequence-based typing. HLA allele and haplotype frequencies and linkage disequilibrium values were calculated by the maximum likelihood method using a computer program developed for the 11th International Histocompatibility Workshop.

RESULTS

A total of 21 HLA-A, 40 HLA-B, 22 HLA-C, and 29 HLA-DRB1 alleles were found in Koreans. The most frequent alleles in each locus with frequencies of ≥ 10% were, in decreasing order of frequency, as follows: A*24:02, A*02:01, A*33:03; B*51:01; C*01:02, C*03:03; and DRB1*09:01. The numbers of two- and three-locus haplotypes with frequencies of >0.5% were as follows: 44 A-C, 42 B-C, 51 A-B, 52 B-DRB1, 42 A-C-B, and 34 A-B-DRB1. Thirteen A-B-DRB1 haplotypes with frequencies of ≥ 1.0% comprised 26.0% of the total haplotypes. The six most common haplotypes were as follows: A*33:03-B*44:03-DRB1*13:02 (3.7%), A*33:03-B*44:03-DRB1*07:01 (3.0%), A*33:03-B*58:01-DRB1*13:02 (3.0%), A*24:02-B*07:02-DRB1*01:01 (2.8%), A*30:01-B*13:02-DRB1*07:01 (2.3%), and A*11:01-B*15:01-DRB1*04:06 (2.2%).

CONCLUSIONS

The information obtained in this study can be used as basic data for Koreans in the fields of organ transplantation, disease association, and anthropologic studies.

Association of human leukocyte antigen class II alleles with response to immunosuppressive therapy in Korean aplastic anemia patients

HLA-DR15 (DR2) is overrepresented in aplastic anemia (AA) patients, and its presence is associated with a better response to cyclosporine-based immunosuppressive therapy (IST). However, little is known about other human leukocyte antigen (HLA) alleles affecting therapy response. We investigated 37 Korean patients with severe AA for the association of HLA class II alleles with response to IST: cyclosporine A combined with antithymocyte globulin or antilymphocyte globulin. Molecular or serologic typing of HLA-DR and HLA-DQ alleles was performed. In responders (13/37, 35.1%), the frequency of HLA-DR15 was increased (69.2% vs 8.3%, p = 0.0002) and that of DR4 was decreased (7.7% vs 66.7%, p = 0.0007) compared with nonresponders. The response rate was significantly higher in DR15(+) than in DR15(-) (81.8% vs 15.4%, p = 0.0002) and in DR4(-) than in DR4(+) patients (60.0% vs 5.9%, p = 0.0007). The response rates in the best (DR15(+)/DR4(-)), intermediate, and poor response groups (DR15(-)/DR4(+)) were 88.9, 38.5, and 0%, respectively (p = 0.00001). At the allelic level, DRB1*1501 and closely linked DQB1*0602 were associated with a good response and DRB1*0405 and closely linked DQB1*0401 with a poor response to IST. HLA-DR typing may be useful for predicting a response to IST in AA patients.

Description of three novel HLA-DRB3 alleles: DRB3*010105, DRB3*0112 and DRB3*0113

This communication describes three novel DRB3 alleles whose exon 2 sequences are identical to that of DRB3*010102 except for a single nucleotide substitutions. Comparing with DRB3*010102, the sequence of DRB3*010105, DRB3*0112, and DRB3*0113 differ at codon 31 (TTC -> TTT), codon 84 (GGG -> CGG; Gly -> Arg), and codon 37 (TTC -> CTC; Phe -> Leu), respectively.

The structure of HLA-DR52c: comparison to other HLA-DRB3 alleles

Class II major histocompatibility complex (MHCII) molecules present antigens to CD4(+) T cells. In addition to the most commonly studied human MHCII isotype, HLA-DR, whose beta chain is encoded by the HLA-DRB1 locus, several other isotypes that use the same alpha chain but have beta chains encoded by other genes. These other DR molecules also are expressed in antigen-presenting cells and are known to participate in peptide presentation to T cells and to be recognized as alloantigens by other T cells. Like some of the HLA-DRB1 alleles, several of these alternate DR molecules have been associated with specific autoimmune diseases and T cell hypersensitivity. Here we present the structure of an HLA-DR molecule (DR52c) containing one of these alternate beta chains (HLA-DRB3*0301) bound to a self-peptide derived from the Tu elongation factor. The molecule shares structurally conserved elements with other MHC class II molecules but has some unique features in the peptide-binding groove. Comparison of the three major HLA-DBR3 alleles (DR52a, b, and c) suggests that they were derived from one another by recombination events that scrambled the four major peptide-binding pockets at peptide positions 1, 4, 6, and 9 but left virtually no polymorphisms elsewhere in the molecules.

Balancing selection and heterogeneity across the classical human leukocyte antigen loci: a meta-analytic review of 497 population studies

This paper presents a meta-analysis of high-resolution human leukocyte antigen (HLA) allele frequency data describing 497 population samples. Most of the datasets were compiled from studies published in eight journals from 1990 to 2007; additional datasets came from the International Histocompatibility Workshops and from the AlleleFrequencies.net database. In all, these data represent approximately 66,800 individuals from throughout the world, providing an opportunity to observe trends that may not have been evident at the time the data were originally analyzed, especially with regard to the relative importance of balancing selection among the HLA loci. Population genetic measures of allele frequency distributions were summarized across populations by locus and geographic region. A role for balancing selection maintaining much of HLA variation was confirmed. Further, the breadth of this meta-analysis allowed the ranking of the HLA loci, with DQA1 and HLA-C showing the strongest balancing selection and DPB1 being compatible with neutrality. Comparisons of the allelic spectra reported by studies since 1990 indicate that most of the HLA alleles identified since 2000 are very-low-frequency alleles. The literature-based allele-count data, as well as maps summarizing the geographic distributions for each allele, are available online.

Association of human leukocyte antigen-DRB1 alleles with disease susceptibility and severity of aplastic anemia in Korean patients

Although association of human leukocyte antigen (HLA)-DR2 (DRB1*1501) with susceptibility to aplastic anemia (AA) has been well documented in several different ethnic groups, little is known about the protective role of HLA in this disease. HLA-DRB1 alleles were analyzed in 109 Korean AA patients (26 nonsevere and 83 severe) and 800 healthy controls. The frequency of DRB1*1501 was significantly higher in AA patients compared with controls [33.0% vs 15.3%, p=0.000004, p(c)=0.0001, odds ratio (OR)=2.74]. Nonsevere AA (30.8%, OR=2.47) and severe AA patients (33.7%, OR=2.83) showed similar changes, and DRB1*1501 was considered a susceptibility factor to AA in both forms of the disease. The frequency of DRB1*1302 in total AA patients was not different from controls (12.8% vs 17.9%), but it was significantly lower in severe AA compared with nonsevere AA patients (6.0% vs 34.6%, p=0.0006, p(c)=0.02, OR=0.12). DRB1*1302 was considered a protective factor against severe AA. In Koreans, DRB1*1501 was associated with disease susceptibility to AA and DRB1*1302 with protection against the severe form of the disease.

Characterization of HLA-B*5516, -B*1313, -B*9512, and -DRB1*1457 alleles identified in a southwest Chinese population

The human leukocyte antigen (HLA)-B*5516 allele differs from the B*5502 by a single 97 T --> C substitution (His to Tyr at position 33) in exon 2. The B*1313 allele results from 419 T --> A and 420 A --> C substitutions, encoding a Leu to Tyr substitution at 140 in exon 2 of the B*1301 allele. The B*9512 allele differs from B*1502 by a single 360 G --> C substitution (Gln to His at 120) in exon 3. The DRB1*1457 allele appears to be a hybrid molecule generated by recombination between the DRB1*13 and DRB1*14 alleles. The serological equivalents of these new alleles are HLA-B22, -B13, -B15, and DR13, respectively. Family studies detected two rare haplotypes: A*11, B*9512, DRB1*14 and A*24, B*52, Cw*07, DRB1*1457, DRB3*020201, DQB1*050301. The gene frequencies of these alleles in the Chinese population are less than 0.0001.

Association of HLA-DR and -DQ genes with narcolepsy in Koreans: comparison with two control groups, randomly selected subjects and DRB1*1501-DQB1*0602--positive subjects

The purpose of this study was to investigate the association of human leukocyte antigen (HLA) class II alleles with narcolepsy-cataplexy susceptibility in Koreans. The distribution of HLA-DRB1 and -DQB1 alleles and presence or absence of DRB3/4/5 alleles were examined in 60 narcoleptic patients with clear-cut cataplexy, and the results were compared with two groups of healthy controls: 200 randomly selected controls and 144 DRB1*1501-DQB1*0602 positive controls. All of the narcoleptic patients were DRB1*1501 and DQB1*0602 positive, and their frequencies were significantly higher in patients than in random controls (100% vs 17.0%, p(c) = 2.3 x 10(-30), OR = 583.96; 100% vs 16.5%, p(c) = 3.9 x 10(-31), OR = 605.00). The HLA association in Koreans was as tight as that reported in Japanese. Several DRB1 (*0101, *0405, *0901) and DQB1 alleles (*0303, *0401, *0501, *0601, *0604) were found to have weak protective effects against narcolepsy. DRB4 showed strong protective effect, and this was also significant when compared with DRB1*1501-DQB1*0602 positive controls (18.3% vs 44.4%, p(c) = 0.001, OR = 0.28). DRB3 (OR = 1.86) and DQB1*0301 (OR = 2.45) were found to have weak predisposing effect, when compared with DRB1*1501-DQB1*0602 positive controls. The protective effect of DRB4 has to be further studied in other populations.