DRB Genes Research Articles

HLA Genetic Variants in COVID-19 Susceptibility: Assessing Diversity in Indian and Global Populations

Background: The rapid spread of the SARS-CoV-2 virus has had a global impact on various ethnic groups. In order to assess the genetic predisposition of the Indian population towards COVID-19, a comparative analysis was conducted using the Human Leukocyte Antigen (HLA) to investigate the frequencies of polymorphisms directly or potentially associated with COVID-19 susceptibility, severity, immune response, and fatal outcomes in comparison to other major populations. Objectives: The objective of this study is to evaluate the genetic predisposition of the Indian population to COVID-19 by analyzing the frequencies and associations of Human Leukocyte Antigen (HLA) polymorphisms. In addition, by delineating the role of specific HLA variants in the Indian context, the study seeks to enhance our understanding of genetic factors influencing COVID-19 impact and contribute to personalized approaches for disease management and prevention across diverse ethnic groups. Methods: We collected allelic information for DRB1 gene from 653 populations globally, as documented in The Allele Frequency Net Database (AFND). Data on COVID-19 susceptibility, severity, mortality, and protective factors were obtained from a previous global study. This study aimed to compare the specific frequencies of HLA-DRB1* in different ethnic groups, including other Indian populations with COVID-19-associated alleles and protective factors. Results: HLA-DRB1*01 was identified as a significant determinant of COVID-19 susceptibility among patients in 28 states of Mexico, whereas DRB1*08 in Saudi Arabian populations, DRB1*09:01 in Japanese populations, and DRB1*15:01 in Italian populations also showed this association. Likewise, DRB1*04 in the Iranian population played a role in disease severity, and DRB1*08 in the Italian population was associated with mortality in COVID-19 patients. In addition, alleles DRB1*01:01 and DRB1*04:01 were found to exhibit a protective role in Northeast England, whereas DRB1*04 demonstrated protective effects in Saudi Arabian populations. Conclusion: The involvement of HLA in COVID-19 requires further investigation, and epidemiological studies should focus on HLA profiles as determinants of the host immune system. Prolonged homozygosity in particular genomic regions could potentially increase susceptibility to COVID-19 infection. Therefore, prudent management strategies are recommended for this pandemic in isolated communities in India and worldwide.

Genetic diversity and evolutionary significance of Cahi-DRB1 gene in Indian goat from semi-arid regions

Unlocking the genetic diversity of the Cahi-DRB1 gene in Indian goat breeds sheds light on their immune system's resilience. While extensive studies have elucidated MHC diversity in cattle and sheep, research on goats remains limited. Thus, this study aimed to investigate the genetic diversity of cahi-DRB1 across five goat breeds in India, encompassing a total of 233 individual goats. Using a PCR sequence-based typing approach, DRB1 fragments (285 bp) were amplified and sequenced. The PCR products were purified and sequenced. Amino acid variability within breeds was evaluated using the Wu-Kabat index at peptide-binding pockets. Selection analysis included assessing positive selection through relative rates of nonsynonymous and synonymous mutations, Z-test, and Tajima's test of neutrality. The findings revealed notable heterozygosity across breeds (mean: 100 %), with nucleotide content averaging 22.51 % for A, 18.62 % for T, 24.33 % for C, and 34.35 % for G. The GC content was rich (59.26 %) across breeds for the DRB1 region. The mean distance for DRB1 was highest in Barbari (0.20) and lowest in Osmanabadi goat (0.12), with a higher rate of transversions observed. The Wu-Kabat index assessments underscored substantial genetic variation within the peptide binding sites (PBS) of DRB1, with specific residues (12, 14, 33, 58, and 87) showing polymorphism relevant to antigen presentation. Positive selection pressure was evident across all breeds for the DRB1 locus (dN>dS), highlighting its evolutionary significance. The rich diversity of the DRB1 gene underscores the fitness of the population and the significance of this locus for future selection programs. These results highlight the highly polymorphic nature of the DRB1 locus in Indian goat breeds, emphasizing its crucial role in modulating immune responses. Consequently, our study offers valuable insights for developing targeted breeding strategies to enhance disease resistance in goats, thereby providing practical implications for sustainable livestock management.

Moderate Genetic Diversity of MHC Genes in an Isolated Small Population of Black-and-White Snub-Nosed Monkeys (Rhinopithecus bieti).

Genetic diversity is an essential indicator that echoes the natural selection and environmental adaptation of a species. Isolated small populations are vulnerable to genetic drift, inbreeding, and limited gene flow; thus, assessing their genetic diversity is critical in conservation. In this study, we studied the genetic diversity of black-and-white snub-nosed monkeys (Rhinopithecus bieti) using neutral microsatellites and five adaptive major histocompatibility complex (MHC) genes. Two DQA1 alleles, two DQB1 alleles, two DRB1 alleles, two DRB5 alleles, and three DPB1 alleles were isolated from a population. The results indicate that neutral microsatellites demonstrate a high degree of heterozygosity and polymorphism, while adaptive MHC genes display a high degree of heterozygosity and moderate polymorphism. The results also show that balancing selection has prominently influenced the MHC diversity of the species during evolution: (1) significant positive selection is identified at several amino acid sites (primarily at and near antigen-binding sites) of the DRB1, DRB5, and DQB1 genes; (2) phylogenetic analyses display the patterns of trans-species evolution for all MHC loci. This study provides valuable genetic diversity insights into black-and-white snub-nosed monkeys, which dwell at the highest altitude and have experienced the harshest environmental selection of all primates globally since the Pleistocene. Such results provide valuable scientific evidence and a reference for making or amending conservation strategies for this endangered primate species.

Molecular Characterization and Gene Expression of MHC II DRB3 Gene Associated with Subclinical Mastitis in Goats

The Major Histocompatibility Complex (MHC) genes have a vital role in the immune response of vertebrates by encoding molecules involved in self/non-self-discrimination and antigen presentation. This study focused on the MHC II DRB3 gene in goats, specifically comparing its nucleotide and amino acid sequences with those of other ruminant species. Four different goat breeds (Native, Upgraded, Anglo-Nubian, and Saanen) were analyzed, and their MHC II DRB3 sequences were aligned with sequences from NCBI GenBank. The nucleotide sequences exhibited high similarity between the different goat breeds and other ruminant species, indicating a conserved structure across mammalian species. Results from sequence comparisons revealed varying degrees of similarity between goat MHC II DRB3 sequences and those of Capra hircus, Ovis aries, Bos taurus, Bos grunniens, and Bubalus bubalis. Phylogenetic analysis further supported the close relationship between goats and other ruminants. Functional domain analysis identified conserved regions in the MHC II DRB3 gene across different breeds of goats and other ruminants. Moreover, polymorphism analysis using the HaeIII restriction enzyme highlighted genetic variability within the MHC II DRB3 gene in goats. This study enhances our understanding of the MHC II DRB3 gene in goats, its similarities to other ruminant species, and its potential role in immune responsiveness.

Genomic variability of the MHC region: Empirical evidence from five horse breeds

The purpose of this study was to analyse the level of variability in the autosomal genome, especially in the equine major histocompatibility complex region, in five horse breeds and identify heterozygosity-rich regions and potential footprints of balancing selection. Depending on data quality control, the dataset consisted of 51,168 or 53,874 single nucleotide polymorphism markers, available for 514 individuals (89 Lipizzan, 238 Old Kladruber, 47 Shagya Arabian, 61 Czech Warmblood and 81 Slovak Warmblood horses). Genomic variability within and between breeds was examined based on levels of heterozygosity (observed and expected), genomic inbreeding, Wright's FIS index and linkage disequilibrium. Subsequently, the screening of heterozygosity-rich regions and balancing selection signals derived from Tajima's D positive values was performed. As expected, due to the polymorphic nature of the major histocompatibility complex, the genomic variability level was generally higher when analysing only markers located in this area (mainly around genes belonging to class I). The Slovak and Czech Warmblood horses, as breeds with open herdbook, showed higher average values of heterozygosity indices than Lipizzan, Old Kladruber or Shagya Arabian breeds. Concerning only markers in the major histocompatibility complex region in complete or very high linkage disequilibrium, common patterns were found close to EQMHCB2, MHCB3 and EQMHCC1 genes belonging to class I and DQA1, DRB2, DRB3 and HLA-DOB genes from class II. Genome-wide, the number of heterozygosity-rich regions per animal ranged from 345.25 (Old Kladruber) to 603.33 (Czech Warmblood). Across all breeds, 254 heterozygosity-rich regions were detected directly in the major histocompatibility complex region (194 in class I and 60 in class II). Among them, the highest overlap showed regions found in the genomes of historically connected Czech and Slovak Warmblood breeds. The results suggested that the frequency of markers in heterozygosity-rich regions increased in Lipizzan, Old Kladruber and Shagya Arabian breeds in the genomic region of EQMCE1 gene (class I) and in Czech and Slovak Warmblood horses in DQB1, DQA2, DQB2, DQA3 and DRB2 genes (class II). Although the identified heterozygosity-rich regions formed 330 islands across the genomes of tested breeds, these islands were outside the major histocompatibility complex region. On the other hand, four of 425 balancing selection signals detected across breeds were located directly in the major histocompatibility complex region, close to DRA, DRB1, DQA1, DQB1 and DQB2 genes (class II). Shared islands and balancing selection footprints among breeds were found mainly on chromosomes 7 and 11.

Ophthalmological and Neurological Findings in Patients with Idiopathic Uveitis Associated with Retinal Vasculitis and the Relation with the HLA DR15 Allele

ABSTRACT Purpose In 15 patients with idiopathic uveitis associated with retinal vasculitis, HLA DRB1 gene testing was performed to detect a possible association. 11 patients tested positive and 4 negative for the HLA DRB1 × 15 allele. The presence of the HLA DRB1 × 15 haplotype might be associated with a higher susceptibility to develop Multiple Sclerosis (MS). Methods In this case series, we describe the ophthalmological and neurological findings in 10 HLA DR15-positive patients and 4 HLA DR15-negative patients that had neurological workup, including Magnetic Resonance Imaging (MRI) of the brain. Results All patients had granulomatous ocular inflammation with either panuveitis or intermediate uveitis. MRI of the brain showed white matter lesions in 13 patients (9/10 and 4/4 respectively) of which 4 patients were eventually diagnosed with MS (3/10 and 1/4 respectively). Conclusion Although the majority of tested patients was carrying at least one HLA DRB1–15 allele, there was no difference in ophthalmological and neurological findings in both groups.

Human Leukocyte Antigen Markers for Distinguishing Pustular Psoriasis and Adult-Onset Immunodeficiency with Pustular Reaction.

Pustular skin diseases, with pustular psoriasis (PP) being the prototype, are immune-mediated diseases characterized by the presence of multiple pustules, resulting from neutrophil accumulation in the layer of epidermis. Sterile skin pustular eruption, like PP, is also observed in 20-30% of patients with adult-onset immunodeficiency syndrome (AOID) and anti-interferon γ autoantibodies (IFN-γ), leading to challenges in classification and diagnosis. While the mechanism underlying this similar phenotype remains unknown, genetic factors in relation to the immune system are suspected of playing an important role. Here, the association between human leukocyte antigen (HLA) genes, which play essential roles in antigen presentation, contributing to immune response, and the presence of skin pustules in AOID and PP was revealed. HLA genotyping of 41 patients from multiple centers in Thailand who presented with multiple sterile skin pustules (17 AOID patients and 24 PP patients) was conducted using a next-generation-sequencing-based approach. In comparison to healthy controls, HLA-B*13:01 (OR = 3.825, 95%CI: 2.08-7.035), C*03:04 (OR = 3.665, 95%CI: 2.102-6.39), and DQB1*05:02 (OR = 2.134, 95%CI: 1.326-3.434) were significantly associated with the group of aforementioned conditions having sterile cutaneous pustules, suggesting a common genetic-related mechanism. We found that DPB1*05:01 (OR = 3.851, p = 0.008) and DRB1*15:02 (OR = 3.195, p = 0.033) have a significant association with pustular reaction in AOID patients, with PP patients used as a control. A variant in the DRB1 gene, rs17885482 (OR = 9.073, p = 0.005), was observed to be a risk factor for PP when using AOID patients who had pustular reactions as a control group. DPB1*05:01 and DRB1*15:02 alleles, as well as the rs17885482 variant in the DRB1 gene, were proposed as novel biomarkers to differentiate PP and AOID patients who first present with multiple sterile skin pustules without known documented underlying conditions.

Putative SNPs in Ovar-DRB1 and GALNTL6 Genes Conferring Susceptibility to Natural Infection of Haemonchus Contortus in Southern Indian Sheep.

To explore associations between phenotypic traits and polymorphisms in the DRB1 and GALNT6 gene in Nellore, Deccani and Kenguri sheep naturally infected with Haemonchus contortus. Blood and faecal samples were collected to evaluate fecal worm egg counts (FEC), packed cell volume (PCV), hemoglobin (Hb), eosinophilia and for DNA isolation. Animals were grouped into susceptible and resistant groups based on EPG counts. FEC and circulating eosinophilia were higher in a susceptible group. Log FEC was negatively correlated (P < 0.01) with PCV, and Hb estimates. The second exon of DRB1 and intron variant of GALNTL6 genes were amplified from DNA samples of resistant and susceptible sheep. Characterization of Ovar-DRB1 amplicon by RFLP revealed two genotypes ('bb' and 'ab'). The genotype frequencies differed significantly between both groups (P < 0.05). The 'bb' genotypes had higher (P < 0.05) log FEC value than 'ab' genotypes and 'b' allele was linked with susceptibility to haemonchosis in sheep. The mean FEC of Nellore sheep was high indicating susceptibility of the breed and also in which the frequency of 'b' allele was more compared to the other two breeds. OVAR-DRB1 genotypes associated with FEC did not affect PCV and Hb. PCR-RFLP assay developed to determine the genotypes with respect to SNP rs424521894 of GALNTL6 revealed monomorphic nature at the locus in the breeds studied. MHC polymorphism could be used as a genetic marker for the selection of sheep resistant to H. contortus. However, a more intensive study, involving controlled infections and other GALNTL6 SNPs may be enforced to make any decisive assertion.

Influence of HLA-A, [sbnd]B, and -DRB1 genes and panel-reactive antibodies on the waitlist time for kidney transplantation in the state of Sao Paulo-Brazil

BackgroundBrazil ranks second in the absolute number of transplants. However, the supply remains insufficient to meet the demands, resulting in a lengthy waitlist. This study aimed to analyze whether the frequency of human leukocyte antigen (HLA) and the value of calculated panel reactive antibody (cPRA) would influence the waiting time for kidney transplantation. MethodsThe HLA-A, B, and -DRB1 frequencies and the cPRA value were analyzed in 11,186 kidney transplant candidates included in the waitlist from 2006 to 2016. ResultsThe most frequent alleles were HLA-A*02, HLA-B*35, and HLA-DRB1*13. The overall mean length of stay on the list was 986 ± 1001 days. The mean waiting time for the three most frequent alleles of the HLA-A and B loci showed no significant difference when compared with the least frequent alleles; however, for the HLA-DRB1 locus, the most frequent alleles showed a shorter waiting time. In the association between HLA and PRA, the average length of stay on the list increased according to the candidate's degree of sensitization, regardless of the analyzed HLA frequency. ConclusionThe length of stay on the waitlist is influenced by the frequency of the HLA alleles of the DRB1 locus and the degree of sensitization.

The rare DRB1*04:08-DQ8 haplotype is the main HLA class II genetic driver and discriminative factor of Early-onset Type 1 diabetes in the Portuguese population.

Early-onset Type 1 diabetes (EOT1D) is considered a disease subtype with distinctive immunological and clinical features. While both Human Leukocyte Antigen (HLA) and non-HLA variants contribute to age at T1D diagnosis, detailed analyses of EOT1D-specific genetic determinants are still lacking. This study scrutinized the involvement of the HLA class II locus in EOT1D genetic control. We conducted genetic association and regularized logistic regression analyses to evaluate genotypic, haplotypic and allelic variants in DRB1, DQA1 and DQB1 genes in children with EOT1D (diagnosed at ≤5 years of age; n=97), individuals with later-onset disease (LaOT1D; diagnosed 8-30 years of age; n=96) and nondiabetic control subjects (n=169), in the Portuguese population. Allelic association analysis of EOT1D and LaOT1D unrelated patients in comparison with controls, revealed that the rare DRB1*04:08 allele is a distinctive EOT1D susceptibility factor (corrected p-value=7.0x10-7). Conversely, the classical T1D risk allele DRB1*04:05 was absent in EOT1D children while was associated with LaOT1D (corrected p-value=1.4x10-2). In corroboration, HLA class II haplotype analysis showed that the rare DRB1*04:08-DQ8 haplotype is specifically associated with EOT1D (corrected p-value=1.4x10-5) and represents the major HLA class II genetic driver and discriminative factor in the development of early onset disease. This study uncovered that EOT1D holds a distinctive spectrum of HLA class II susceptibility loci, which includes risk factors overlapping with LaOT1D and discriminative genetic configurations. These findings warrant replication studies in larger multicentric settings encompassing other ethnicities and may impact target screening strategies and follow-up of young children with high T1D genetic risk as well as personalized therapeutic approaches.

The Relationship Between Genotype of DRB1 Gene and some Performance Traits of Iraqi Sheep

The experiment was conducted at the Sheep and Goat Research Station in Al-Shatrah district located in the north of Thi Qar Governorate, Thi Qar Agriculture Directorate, Ministry of Agriculture, Marshlands Research Center, Thi Qar University. It included 59 animals from the ewes of Iraqi sheep (Awassi), to study the relationship between the genotype of the DRB1 gene and some performance traits in Iraqi sheep, where the study included taking some measurements of body dimensions, taking blood samples for the purpose of laboratory examination of the study, included extraction of genetic material and genetic analysis, using PCR technology at the Marshes Research Center at Thi Qar University. The results of the analysis of the nucleotide sequence sequence of the studied genetic segment of the DRB1 gene showed that the mutation T>G.245 was present in the coding regions of the DRB1 gene, occurred in GTT coding for Valine (V) and changed to GGT coding for the amino acid Glycine (G), located at position (82) in the amino acid sequence of the DRB1 gene, this mutation was located in the region of the second exon, where this mutation was considered a missense mutation. It has three genotypes: TT, TG, and GG, by calculating the allelic frequency, there was a highly significant superiority of the T allele (0.53) over the G allele (0.47) in the T>G mutation.245, the genotypes of the mutation T>G.245 of the DRB1 gene, it was found that there were highly significant differences (P≤0.01) in all characteristics under study, such as birth weight and body dimensions, it was found that the effect of some non-genetic factors on the studied traits, namely, the state of pregnancy, the age of the ewes, and the sequence of childbirth, was highly significant (P≤0.01) in all characteristics of the animal’s body dimensions, except for the width of the breast, it was observed that ewes aged 3-4 years outperformed the rest of the ewes compared to other age groups, was the lowest in sheep less than a year old in all traits under study, the regression coefficient of the characteristics of body dimensions on the weight of the animal were not significant except for the regression coefficient of the rear height of the animal on the weight of the animal. All characteristics of body dimensions (body length, frontal height, posterior height, chest width, and chest circumference) showed a highly significant correlation (P≤0.01), positive and high.

Diversity and evolution of the MHC class II DRB gene in the Capra sibirica experienced a demographic fluctuation in China

The major histocompatibility complex (MHC) genes are the most polymorphic genes in vertebrates, and their proteins play a critical role in adaptive immunity for defense against a variety of pathogens. MHC diversity was lost in many species after experiencing a decline in size. To understand the variation and evolution of MHC genes in the Siberian ibex, Capra sibirica, which has undergone a population decline, we analyzed the variation of the second exon of MHC class II DRB genes in samples collected from five geographic localities in Xinjiang, China, that belong to three diverged mitochondrial clades. Consequently, we identified a total of 26 putative functional alleles (PFAs) with 260 bp in length from 43 individuals, and found one (for 27 individuals) to three (for 5 individuals) PFAs per individual, indicating the presence of one or two DRB loci per haploid genome. The Casi-DRB1*16 was the most frequently occurring PFA, Casi-DRB1*22 was found in only seven individuals, 14 PFAs occurred once, 7 PFAs twice, implying high frequency of rare PFAs. Interestingly, more than half (15) of the PFAs were specific to clade I, only two and three PFAs were specific to clades II and III, respectively. So, we assume that the polygamy and sexual segregation nature of this species likely contributed to the allelic diversity of DRB genes. Genetic diversity indices showed that PFAs of clade II were lower in nucleotide, amino acid, and supertype diversity compared to those of the other two clades. The pattern of allele sharing and FST values between the three clades was to some extent in agreement with the pattern observed in mitochondrial DNA divergence. In addition, recombination analyses revealed no evidence for significant signatures of recombination events. Alleles shared by clades III and the other two clades diverged 6 million years ago, and systematic neighbor grids showed Trans-species polymorphism. Together with the PAML and MEME analyses, the results indicated that the DRB gene in C. sibirica evolved under balancing and positive selection. However, by comparison, it can be clearly seen that different populations were under different selective pressures. Our results are valuable in understanding the diversity and evolution of the DRB gene in a mountain living C. sibirica and in making decisions on future long-term protection strategies.

Interindividual HLA Evolutionary Divergence in Single HLA-Mismatched Unrelated Donor Hematopoietic Cell Transplantation for Malignant Hematological Disorders: A Report on Behalf of the Cellular Therapy and Immunobiology Working Party of the EBMT

In allogeneic hematopoietic cell transplantation (allo-HCT), alloreactive T-cell responses (graft versus leukemia - GvL and graft versus host disease - GvHD) are mediated by the interaction between recipient antigens and donor lymphocytes via human leukocyte antigen (HLA) molecules. HLA evolutionary divergence (HED) is a metric recently implemented as a functional proxy for the structural variability between two homologous HLA alleles at their peptide binding sites, mirroring quantitative differences in pathogen and cancer-related immunopeptidomes ( A). 1 Here, we hypothesize that differences in and between donor and recipient HEDs at given loci may modulate the direction and the intensity of alloreactivity, informing on post-transplant outcomes. We tested this hypothesis in onco-hematologic patients undergoing allo-HCT from a single HLA-A, -B, -C, -DRB1, or -DQB1 (9/10) mismatched unrelated donor (MMUD) at EBMT centers. We included patients with selected hematological malignancies, receiving a thymoglobulin-based T cell depletion, for whom complete clinical and HLA information was available in the EBMT database. We deployed individual locus-specific recipient/donor HED (HED-R, HED-D) metrics as previously described 1, and conceptualized two novel interindividual HED scores accounting for functional differences at the mismatched HLA loci ( A). The latter were considered as: 1) DeltaHED, quantifying the relative directional difference between HED-D and HED-R and informing on differences in immunopeptidome sizes, potentially capturing the direction and the intensity of the alloreactive response (GvH or HvG); 2) HEDmismatch, describing the HED of the mismatched locus as a proxy for the qualitative differences in immunopeptidomes between donor and recipient ( B). Using multivariable Cox regression (cause-specific) models adjusted for relevant clinical variables, we investigated the associations of HED-R, DeltaHED and HEDmismatch, analyzed as continuous variables, with relapse free survival (RFS), overall survival (OS), non-relapse mortality (NRM), relapse and grade II-IV acute and chronic GvHD. For each outcome and in each mismatched subgroup, we built separate models for these immunogenetic parameters and checked for proportional hazards assumption (PHA). To account for multiple comparisons, only p-values &amp;lt;0.01 were considered significant. Overall, 4639 adult patients, with available HLA data, received a 9/10 MMUD allo-HCT between 2010 and 2019 for acute leukemia (N=3853, 83%), myelodysplastic syndromes or myeloproliferative neoplasms (N=786, 17%). Median recipient age was 53.5 (IQR 40.2-61.9) with a male/female ratio of 1.28, whilst median donor age was 33.1 (IQR 24.5-40). Majority of patients (90%) received peripheral blood stem cells and were mismatched with their donors for locus A (33%), followed by C (21%), B (15%), DQB1 (14%) and DRB1 (6%). When analyzing the impact of HED-related parameters in each model, we observed that most recurrent associations with outcomes occurred with DRB1-related metrics. In the DRB1-mismatched subgroup (N=276), a time-varying association was found for HEDmismatch of DRB1 locus with higher HEDmismatch leading to worse RFS [HR:1.25 at t=0, (95% CI 1.1-1.42), p&amp;lt;0.001] and lower OS [HR:1.23 at t=0, (95%CI 1.08-1.41), p=0.002]. The strength of this associations declined over time for both endpoints (respectively RFS: HR:0.91, 95% CI 0.86-0.97, p=0.005 and OS: HR:0.93, 95% CI 0.88-0.98, p=0.013). The (directional) DeltaHED DRB1 measure instead did not display any impact on outcomes. In the same subgroup, higher HED-R in the locus C showed also a time-varying association with NRM at transplant [HR:1.89, (95% CI 1.29-2.85), p=0.002], progressively declining over time (HR:0.77, 95% CI 0.65-0.92, p=0.003). Furthermore, DRB1 HED-R modulated the probability of survival in B-mismatched subgroup, being higher scores associated with reduced OS [HR:1.03, (95%CI 1.01-1.06), p=0.009]. Here, we provide an immunogenetic benchmark to explore donor-recipient interactions in MMUD allo-HCT, demonstrating how different HLA configurations within the mismatched loci, in particular for DRB1 genes, can influence post-transplant outcomes. Given the peculiar associations observed, HED may have a role in driving early GvL effects, informing on future donor selection strategies in high-risk patients.

Low proviral load in the Kumamoto strain of Japanese Brown cattle infected with the bovine leukemia virus

BackgroundThe Kumamoto strain of Japanese Brown (JBRK) cattle is a sub-breed of Wagyu and has a different genetic background than that of Japanese Black (JB) cattle. Bovine leukemia virus (BLV) is the pathogen causing enzootic bovine leukosis (EBL), the predominant type of bovine leukosis (BL). EBL is one of the most common bovine infectious diseases in dairy countries, including Japan. Some host genetic factors, including the bovine leukocyte antigen (BoLA)-DRB3 gene, have been associated with the proviral load (PVL) of BLV and/or onset of EBL. Here, we determined the number of BL cases by analyzing prefectural case records in detail. We measured the PVL of BLV-infected JBRK cattle and compared it with that obtained for other major breeds, JB and Holstein-Friesian (HF) cattle. Finally, the relationship between PVL levels and BoLA-DRB3 haplotypes was investigated in BLV-infected JBRK cattle.ResultsWe determined the number of BL cases recorded over the past ten years in Kumamoto Prefecture by cattle breed. A limited number of BL cases was observed in JBRK cattle. The proportion of BL cases in the JBRK was lower than that in JB and HF. The PVL was significantly lower in BLV-infected JBRK cattle than that in the JB and HF breeds. Finally, in BLV-infected JBRK cattle, the PVL was not significantly affected by BoLA-DRB3 alleles and haplotypes. BoLA-DRB3 allelic frequency did not differ between BLV-infected JBRK cattle with low PVL and high PVL.ConclusionsTo our knowledge, this is the first report showing that BL occurred less in the JBRK population of Kumamoto Prefecture. After BLV-infection, the PVL was significantly lower in JBRK cattle than that in JB and HF breeds. The genetic factors implicated in maintaining a low PVL have yet to be elucidated, but the BoLA-DRB3 haplotypes are likely not involved.

ALLELE DIVERSITY OF THE MAJOR HISTOCOMPATIBILITY COMPLEX GENE DRB1 IN TWO SPECIES OF HAMSTER OF THE GENUS &lt;i&gt;ALLOCRICETULUS&lt;/i&gt; Argyropulo 1932

For the first time, the allelic diversity of exon 2 of the DRB1 gene (class II of the major histocompatibility complex, MHC) was determined by NGS sequencing in natural populations of two species of the genus Allocricetulus: Eversmann’s hamster (A. eversmanni) and the Mongolian hamster (A. curtatus). These species are genetically close, but allopatric and demonstrate different habitat preferences. Eversmann’s hamster inhabits the steppes and is often associated with agrocenosis, while the Mongolian hamster occures semi-deserts and deserts, where anthropogenic pressure is practically absent. Our analysis revealed a significant effect of positive selection on the diversity of alleles of the DRB1 gene in both study species. However, Eversmann's hamster is characterized by a large average distance between alleles, but a smaller proportion of heterozygous individuals, while the Mongolian hamster is characterized by a larger individual variety of alleles. Thus, despite the extensive range of Eversmann’s hamster, we noted significantly less functional diversity of adaptive genes, which may be due to an increased anthropogenic exposure.

Genome-wide association study identifies multiple HLA loci for sarcoidosis susceptibility.

Sarcoidosis is a complex systemic disease. Our study aimed to (1) identify novel alleles associated with sarcoidosis susceptibility; (2) provide an in-depth evaluation of HLA alleles and sarcoidosis susceptibility and (3) integrate genetic and transcription data to identify risk loci that may more directly impact disease pathogenesis. We report a genome-wide association study of 1335 sarcoidosis cases and 1264 controls of European descent (EA) and investigate associated alleles in a study of African Americans (AA: 1487 cases and 1504 controls). The EA and AA cohort was recruited from multiple United States sites. HLA alleles were imputed and tested for association with sarcoidosis susceptibility. Expression quantitative locus and colocalization analysis were performed using a subset of subjects with transcriptome data. Forty-nine SNPs in the HLA region in HLA-DRA, -DRB9, -DRB5, -DQA1 and BRD2 genes were significantly associated with sarcoidosis susceptibility in EA, rs3129888 was also a risk variant for sarcoidosis in AA. Classical HLA alleles DRB1*0101, DQA1*0101 and DQB1*0501, which are highly correlated, were also associated with sarcoidosis. rs3135287 near HLA-DRA was associated with HLA-DRA expression in peripheral blood mononuclear cells and bronchoalveolar lavage from subjects and lung tissue and whole blood from GTEx. We identified six novel SNPs (out of the seven SNPs representing the 49 significant SNPs) and nine HLA alleles associated with sarcoidosis susceptibility in the largest EA population. We also replicated our findings in an AA population. Our study reiterates the potential role of antigen recognition and/or presentation HLA class II genes in sarcoidosis pathogenesis.

Expression profile of HLA-DRB1, RFX5, and CIITA promoters in chronic kidney disease patients from South India

Background The present study elucidated HLA-DRB1 allele frequency, the gene expression profile of HLA-DRB1, CIITA promoters PI, PIV, and RFX5 and their association in chronic kidney disease (CKD). Patients and methods In all, 133 CKD patients and 144 healthy controls were enrolled, and qRT-PCR based expression analysis of HLA-DRB1, CIITA-PI, PIV, and RFX5 promoters was carried out. The typing of HLA-DRB1* alleles was performed by the PCR-SSP method. The immune cell profiling was performed by flow cytometry. Results Out of the 13 HLA-DRB1 alleles genotyped, increased frequencies for DRB1*07 [odds ratio (OR)=2.103] and DRB1*12 (OR=2.50) and decreased frequency for DRB1*10 (OR=0.455) in CKD patients were observed. HLA-DRB1 expression was significantly upregulated in pooled-CKD (Fc: 1.49 ± 0.21; P&lt;0.0001), DRB1*07 (Fc: 3.10 ± 0.70; P&lt;0.057), and DRB1*12 (Fc: 3.62 ± 0.74; P&lt;0.0001) positive CKD patients. Significantly higher levels of expressions were observed for CIITA-PI (Fc: 2.35 ± 0.23; P&lt;0.0005) and PIV (Fc: 1.76 ± 0.23; P&lt;0.0009) in pooled-CKD patients. With HLA-DRB1 alleles, a higher level of expressions of CIITA-PIV was observed in patients with DRB1*12 (Fc: 1.45 ± 0.38; P&lt;0.007). Interestingly, a significantly downregulated expression was observed for CIITA-PIV in patients heterozygous for DRB1*12 (2.15 ± 0.24 vs. 0.16 ± 0.82; P&lt;0.017). An upregulated RFX5 expression was observed for pooled-CKD (Fc: 1.37 ± 0.17; P&lt;0.0001) and DRB1*12 (1.40 ± 0.34; P&lt;0.045) positive patients. Immunophenotyping analysis showed an increased CD3+ and decreased CD19+, CD4+,and CD8+ cell populations in CKD patients compared with controls. Conclusion The study confirmed the increased expression of CIITA-PI, PIV promoters, and RFX5 that in turn led to the upregulation of the DRB1 gene resulting in CKD. Thus, the study concluded the positive association of HLA-DRB1*07 and DRB1*12 alleles, with a differential expression of DRB1 genes as a consequence of upregulation of respective promoters in CKD pathogenesis in South India.

Multilocus HLA haplotypes &lt;i&gt;(A-B-C-DRB1-DRB3/DRB4/DRB5-DQA1-DQB1-DPA1-DPB1)&lt;/i&gt; in families of patients scheduled for allogeneic hematopoietic stem cell transplantation

HLA haplotype is a block of HLA genes located on the same chromosome. Highly polymorphic HLA genes display strong linkage disequilibrium, which results in conserved multilocus HLA haplotypes. Assessment of HLA haplotypic diversity of a specific population is important, particularly for allogeneic hematopoietic stem cell transplantation. Family pedigrees remain the gold standard for studying HLA haplotype segregation. HLA haplotypes, obtained by observations of the segregation of HLA alleles within the family, really exist in the human population. The aim of this work has been to establish the frequencies of HLA haplotypes A-B-C-DRB1-DRB3/DRB4/DRB5-DQA1-DQB1-DPA1-DPB1 in families of patients with assignment to HLA-typing for allogeneic hematopoietic stem cell transplantation. The study included 109 families of patients, in which patients and their potential relative donors of allogeneic hematopoietic stem cell were subjected to HLA-typing. Patients and members of their families were typed by the NGS method in the Laboratory of Tissue Typing at the National Medical Research Center for Hematology for 11 HLA genes – A, B, C, DRB1, DRB3, DRB4, DRB5, DQA1, DQB1, DPA1 and DPB1. The genotyping was performed by the NGS method using the AllType NGS 11 Loci Amplification Kits (One Lambda, USA) on the MiSeq sequencing platform (Illumina, USA). The sequences were analyzed using the TypeStream Visual Software (TSV) (One Lambda, USA) and the IPD-IMGT/HLA database 3.44. 360 copies of HLA-haplotypes were found in the studied families. The frequencies of HLA haplotypes were determined by direct counting. The most common 7-locus haplotype was A*01:01-B*08:01-C*07:01-DRB1*03:01-(DRB3*01:01-DQA1*05:01)-DQB1*02:01/163N, the most common 9-locus haplotype was A*03:01-B*07:02-C*07:02-DRB1*15:01-DRB5*01:01-DQA1*01:02-DQB1*06:02-DPA1*01:03-DPB1*04:01P. These HLA haplotypes (in brief, A-B-C-DRB1-DQB1) are the first and second most common HLA haplotypes in most Russian registries of bone marrow donors. Despite several differences, the distribution of HLA haplotypes in families of the patients and in donor registries is similar, and the probability of finding a compatible donor for patients with common HLA-haplotypes in Russian registries is quite high. Most of 7-locus haplotypes are associated with different alleles of the HLA-DP locus in the 9-locus haplotypes, due to presence of a recombination hot spot. The study revealed strong linkage disequilibrium between the HLA alleles DRB1*03:01 and DPB1*01:01P (D’ = 0.579), DRB1*07:01, and DPB1*17:01 (D’ = 0.808), DRB1*09:01 and DPB1*04:02P (D’ = 0.502). The information obtained about real 7- and 9-locus HLA-haplotypes in families may be used in clinical practice as a reference for analyzing the results of HLA-typing and predicting the expected HLA-haplotypes. It has been shown that, despite recombination hot spot between the HLA-DP locus and the rest of the HLA complex, there is strong linkage disequilibrium between some alleles of the DRB1 and DPB1 genes.

Characterization and genetic diversity of MHC class II DRB genes in the Arabian camel (Camelus dromedarius).

This study investigated the MHC DRB genes in the Arabian camel (Camelus dromedarius). The results revealed the presence of - at least - two transcribed DRB-like genes in chromosome 20, designated MhcCadr-DRB1 and MhcCadr-DRB2. These genes are 155Kb apart, have similar gene structure, and are transcribed in opposite directions. Compared to DRB1, the DRB2 locus contains a deletion of 12 nucleotides in the second exon (270bp), exhibits lower transcript abundance, and is expressed as two splice variants differing by exon 2 skipping. This gene seems to be of minor functional relevance in the dromedary camel. Conversely, the DRB1 is thought to be the main gene in this species showing higher transcript abundance and polymorphism levels. A total of seven DRB1 exon 2 alleles were identified in the Tunisian dromedary camel resulting from 18 amino acid substitutions. Six full length alleles were characterized at the mRNA level. Although there is no clear evidence for balancing selection (i.e., heterozygote advantage), signals of weak historical positive selection acting on the DRB1 gene were detected, as indicated by the limited number of the sites being positively selected. This trend might be related to the low exposure to pathogens and to the demographic history of the species. Comparative analysis with Bactrian and wild camel genomes suggested occurrence of trans species polymorphism (TSP) in the Camelus genus. The results lay the foundation for the MHC DRB1 genetic diversity analysis in this genus since the developed genotyping protocols are fully applicable in the three Camelus species.

Human papillomavirus infection and its relationship with common polymorphism of HLA gene by PCR method

Studies have shown that human papillomavirus (HPV) causes cervical cancer, but investigations on the relationship between HPV and HLA gene polymorphism are limited.Objective: The purpose of this study is to investigate the prevalence of HPV infection and its relationship with common HLA gene polymorphisms in cervical cancer patients using the PCR method. This study used 52 fixed samples from the laboratory of Khatam al-Anbia Hospital in Tehran. DNA was isolated using proteinase K and a DNPTM commercial extraction kit. The PCR technique was used to identify L1, HPV-16, HPV-18, HPV-31, HPV-11, HPV-33, and HPV-35 genes. The ARMS-PCR method was used to determine the genotypes of common HLA polymorphisms. The data were analyzed using one-way analysis of variance. The ARMS-PCR results showed that 10 polymorphisms were observed in the HLA gene in the samples, with 7 related to DRB1, 2 related to DQB1, and 1 related to DQA1. However, the desired polymorphisms were not observed in 42 of the studied samples. Polymorphism of DRB1 genes in 7 samples showed that 6 of these 7 samples were infected with HPV16 and one with HPV18. The study results suggest that HPV16 and HPV18 are the most common HPV types isolated from cervical cancer patients. HLA gene polymorphism may predispose people to these infections. Understanding these relationships in different populations and races is essential for understanding the role of HLA gene polymorphism in cervical cancer and its relationship with HPV infection.