DRB1 Alleles Research Articles

HLA-A, -B and -DRB1 allele and haplotype diversity determined by PCR-SSP method in patients and donors at Bach Mai Hospital from 2019 to 2023

HLA-A, -B and -DRB1 allele and haplotype diversity determined by PCR-SSP method in patients and donors at Bach Mai Hospital from 2019 to 2023

Investigating Acute Hepatitis after SARS-CoV-2 Vaccination or Infection: A Genetic Case Series.

(1) Background: Despite the advantages of COVID-19 vaccination, rare cases of acute hepatitis developing after the administration of the COVID-19 vaccine or the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection have been reported. The aim of the study is to describe a case series of patients who experienced the onset of acute hepatitis, with or without autoimmune features, following SARS-CoV-2 vaccination or infection and to hypothesize a genetic susceptibility in the pathogenesis. (2) Methods: A group of patients with acute onset hepatitis following SARS-CoV-2 vaccination or infection were evaluated in our hepatology outpatient clinic, where they underwent biochemical and autoimmune tests. Hepatitis A (HAV), B (HBV), and C virus (HCV), cytomegalovirus (CMV), Epstein-Barr virus (EBV), and human immunodeficiency virus (HIV) infections were excluded. Patients with a diagnosis of autoimmune hepatitis (AIH) or drug-induced liver injury (DILI) underwent HLA typing and histological testing. (3) Results: Five patients experienced new-onset AIH after COVID-19 vaccination, one of which developed mild symptoms after vaccination that strongly worsened during subsequent SARS-CoV-2 infection. One patient had AIH relapse after COVID-19 vaccination while on maintenance immunosuppressive treatment. All of them had HLA DRB1 alleles known to confer susceptibility to AIH (HLA DRB1*03,*07,*13,*14), and in three of them, HLA DRB1*11 was also detected. Two patients developed acute hepatitis without autoimmune hallmarks which resolved spontaneously, both positive for HLA DRB1*11. (4) Conclusions: An association between AIH and COVID-19 vaccine or infection can be hypothesized in individuals with a genetic predisposition. In patients without autoimmune features and spontaneous improvement of hypertransaminasemia, the diagnosis of drug-induced liver injury (DILI) is probable. Further studies are needed to determine the presence of an actual association and identify a possible role of HLA DRB1*11 in the pathogenesis of acute liver injury after SARS-CoV2 vaccination or infection.

SAT056 New-onset Autoimmune Diabetes After COVID-19 mRNA Vaccine: A Systematic Review

Abstract Disclosure: A. Laskova: None. B. Syritsa: None. Background: Vaccination against COVID-19 has become a great tool during the COVID-19 pandemic. Multiple studies have shown that vaccines are safe and effective. However, there have been reports of autoimmune diseases following the vaccination against COVID-19. One of the possible mechanisms is thought to be a reaction to adjuvants in the vaccine (ASIA syndrome). We present a systematic review of the cases of new-onset autoimmune diabetes after the COVID-19 mRNA vaccine. Methods: We included 10 patients from 6 case reports1-6 and 1 case series7 published before December 3, 2022. We analyzed demographics, results, and outcomes using descriptive statistics. Results: 60% were males, and 40% were females. The median age was 51.5 years. 70% received the BNT162b2 vaccine, 20% - the mRNA-1273 vaccine, 10% - an unnamed mRNA vaccine. 70% developed symptoms after the second dose of the vaccine. The onset was distributed from 1 week after the first dose to 8 weeks after the third dose. 30% had either personal or family history of autoimmune diseases. Among other 70%, 57% had HLA DRB1 and/or DQB1 alleles (unknown if HLA was tested in other patients). The disease manifested as diabetic ketoacidosis in 50% of the patients. Anti-GAD antibodies were elevated in 70% of the patients. 30% were weaned off insulin shortly after the diagnosis, meanwhile, the rest required insulin by the time of the articles’ writing. We noted that most of the patients who developed autoimmune diabetes after the COVID-19 vaccine had either personal or family history of autoimmune diseases or tested positive for certain pertinent HLA alleles. However, no causal relationship can be established based on the current cohort, and more research needs to be done.

Individual Immune Response to SARS-CoV-2 Infection-The Role of Seasonal Coronaviruses and Human Leukocyte Antigen.

During the coronavirus pandemic, evidence is growing that the severity, susceptibility and host immune response to SARS-CoV-2 infection can be highly variable. Several influencing factors have been discussed. Here, we investigated the humoral immune response against SARS-CoV-2 spike, S1, S2, the RBD, nucleocapsid moieties and S1 of seasonal coronaviruses: hCoV-229E, hCoV-HKU1, hCoV-NL63 and hCoV-OC43, as well as MERS-CoV and SARS-CoV, in a cohort of 512 individuals. A bead-based multiplex assay allowed simultaneous testing for all the above antigens and the identification of different antibody patterns. Then, we correlated these patterns with 11 HLA loci. Regarding the seasonal coronaviruses, we found a moderate negative correlation between antibody levels against hCoV-229E, hCoV-HKU1 and hCoV-NL63 and the SARS-CoV-2 antigens. This could be an indication of the original immunological imprinting. High and low antibody response patterns were distinguishable, demonstrating the individuality of the humoral response towards the virus. An immunogenetical factor associated with a high antibody response (formation of ≥4 different antibodies) was the presence of HLA A*26:01, C*02:02 and DPB1*04:01 alleles, whereas the HLA alleles DRB3*01:01, DPB1*03:01 and DB1*10:01 were enriched in low responders. A better understanding of this variable immune response could enable more individualized protective measures.

B-253 Performance Characteristics and Validation of Next-Generation Sequencing for Human Leucocyte Antigen Typing

Abstract Background High-resolution human leukocyte antigen (HLA) typing is a crucial process in transplant matching. Sequencing-based typing (SBT) has been the gold standard method used in HLA-based clinical applications. Recently, next-generation sequencing (NGS) has been adopted in clinical laboratories for HLA typing. NGS HLA typing assays cover whole or near-whole target HLA genes, allowing the detection of genetic variants outside of key exons. Multiplex amplicon-based NGS is an efficient high-resolution HLA typing method with minimal ambiguity and a high throughput. Here, we report the performance and validation of NGS for HLA typing and compare the results obtained using NGS with those of SBT to identify any discrepancies between the 2 methods. Methods A total of 237 samples from 2019 to July 2022 were collected from Chang Gung Memorial Hospital, including 42 samples previously subjected to SBT sequencing for 4-digit HLA analysis. NGS was performed for 5 whole genes (HLA-A/B/C/DQA1/DPA1) and 3 near-whole genes (HLA-DRB1/DQB1/DPB1; excluding exon 1 and part of intron 1) by using the AllType NGS kit (One Lambda), Illumina MiSeq platform, and Type Steam Visual NGS analysis software (One Lambda). Results Our validation process comprised 34 NGS runs and 237 samples. In total, 42 samples were analyzed with an overall accuracy and precision of 100% and 100% reproducibility. The overall ambiguity rate was 0% in HLA-A/B/C compared with 56.9% for SBT. Two discrepant alleles of HLA-A and DRB1 were noted in NGS and Sanger sequencing. In accordance with additional SBT exon analyses, one of the results was corrected according to the NGS results. Conclusion NGS HLA typing is a high-throughput approach with high accuracy and precision and a low ambiguity and is promising for use in clinical HLA laboratories.

Biomarkers in Systemic Sclerosis: An Overview.

Systemic sclerosis (SSc) is a complex autoimmune disease characterized by significant fibrosis of the skin and internal organs, with the main involvement of the lungs, kidneys, heart, esophagus, and intestines. SSc is also characterized by macro- and microvascular damage with reduced peripheral blood perfusion. Several studies have reported more than 240 pathways and numerous dysregulation proteins, giving insight into how the field of biomarkers in SSc is still extremely complex and evolving. Antinuclear antibodies (ANA) are present in more than 90% of SSc patients, and anti-centromere and anti-topoisomerase I antibodies are considered classic biomarkers with precise clinical features. Recent studies have reported that trans-forming growth factor β (TGF-β) plays a central role in the fibrotic process. In addition, interferon regulatory factor 5 (IRF5), interleukin receptor-associated kinase-1 (IRAK-1), connective tissue growth factor (CTGF), transducer and activator of transcription signal 4 (STAT4), pyrin-containing domain 1 (NLRP1), as well as genetic factors, including DRB1 alleles, are implicated in SSc damage. Several interleukins (e.g., IL-1, IL-6, IL-10, IL-17, IL-22, and IL-35) and chemokines (e.g., CCL 2, 5, 23, and CXC 9, 10, 16) are elevated in SSc. While adiponectin and maresin 1 are reduced in patients with SSc, biomarkers are important in research but will be increasingly so in the diagnosis and therapeutic approach to SSc. This review aims to present and highlight the various biomarker molecules, pathways, and receptors involved in the pathology of SSc.

Balancing selection shapes population differentiation of major histocompatibility complex genes in wild golden snub-nosed monkeys.

Small and isolated populations face several intrinsic risks, such as genetic drift, inbreeding depression, and reduced gene flow. Thus, patterns of genetic diversity and differentiation have become an important focus of conservation genetics research. The golden snub-nosed monkey Rhinopithecus roxellana, an endangered species endemic to China, has experienced rapid reduction in population size and severe population fragmentation over the past few decades. We measured the patterns of genetic diversity and population differentiation using both neutral microsatellites and adaptive major histocompatibility complex (MHC) genes in 2 R. roxellana populations (DPY and GNG) distributed on the northern and southern slopes of the Qinling Mountains, respectively. Eight MHC-linked haplotypes formed by 5 DQA1 alleles, 5 DQB1 alleles, 5 DRB1 alleles, and 4 DRB2 alleles were detected in the 2 populations. The larger GNG population showed higher genetic variation for both MHC and microsatellites than the smaller DPY population, suggesting an effect of genetic drift on genetic variation. Genetic differentiation index (F ST) outlier analyses, principal coordinate analysis (PCoA), and inferred population genetic structure showed lower genetic differentiation in the MHC variations than microsatellites, suggesting that pathogen-mediated balancing selection, rather than local adaptation, homogenized the MHC genes of both populations. This study indicates that both balancing selection and genetic drift may shape genetic variation and differentiation in small and fragmented populations.

HLA Type Variation Across Populations

Background: Human Leukocyte Antigen (HLA) is highly polymorphic and it is commonly used as a marker for core population genital aspects such as human migration, predisposition to diseases and in tissue transplantation compatibility. Methodology: For our study authors have taken up sample size of 86 for meta- analysis of high-resolution frequency data of the HLA allele. North Indian patients from tertiary centre were analyzed for identification of HLA-A, B, C, DRB1 and DQB1 alleles by sing serological and molecular typing techniques. A plethora of known alleles were identified at different loci e.g., HLA A 18, HLA B 36, HLA C 5, HLA DRB1 28 and HLA DQB1 8. This study focusing on frequencies of HLA alleles and their homozygosity and heterozygosity have been reported, but HLA data in the North Indian population living in Delhi, Haryana, Uttarakhand , Uttar Pradesh, Punjab and Himachal Pradesh, are reported here characterized. Allele frequencies were analyzed by using the Hardy-Weinberg equilibrium. Results: Allele heterozygosity was observed in 96.51% individuals for locus HLA-A, 97.67% individuals for locus HLA-B and 96.51% for HLA-DRB1,overallheterozygosity for all three loci was 89.5% (77/86 individuals). Among individuals showing homozygosity (9 individuals), two showed homozygosity at two loci. Conclusion: The increased heterozygosity for class 1 and class 2 is associated with selective advantage against infectious diseases. The phenotypic frequency of B*35 alleles (B*35:01, B*35:03 and B*35:08) in our study is 31.39%. Comparable B*35 allele phenotypic frequency (27.5%) was reported in north Indian patients.

Effectiveness of integrated bovine leukemia virus eradication strategies utilizing cattle carrying resistant and susceptible major histocompatibility complex class II DRB3 alleles

Bovine leukemia virus (BLV) has spread worldwide and causes serious problems in the cattle industry owing to the lack of effective treatments and vaccines. Bovine leukemia virus is transmitted via horizontal and vertical infection, and cattle with high BLV proviral load (PVL), which is a useful index for estimating disease progression and transmission risk, are considered major infectious sources within herds. The PVL strongly correlates with highly polymorphic bovine lymphocyte antigen (BoLA)-DRB3 alleles. The BoLA-DRB3*015:01 and *012:01 alleles are known susceptibility-associated markers related to high PVL, and cattle with susceptible alleles may be at a high risk of BLV transmission via direct contact with healthy cows. In contrast, the BoLA-DRB3*009:02 and *014:01:01 alleles comprise resistant markers associated with the development of low PVL, and cattle with resistant alleles may be low-risk spreaders for BLV transmission and disrupt the BLV transmission chain. However, whether polymorphisms in BoLA-DRB3 are useful for BLV eradication in farms remains unknown. Here, we conducted a validation trial of the integrated BLV eradication strategy to prevent new infection by resistant cattle and actively eliminate susceptible cattle in addition to conventional BLV eradication strategies to maximally reduce the BLV prevalence and PVL using a total of 342 cattle at 4 stall-barn farms in Japan from 2017 to 2019. First, we placed the resistant milking cattle between the BLV-positive and BLV-negative milking cattle in a stall barn for 3 yr. Interestingly, the resistant cattle proved to be an effective biological barrier to successfully block the new BLV infections in the stall-barn system among all 4 farms. Concomitantly, we actively eliminated cattle with high PVL, especially susceptible cattle. Indeed, 39 of the 60 susceptible cattle (65%), 76 of the 140 neutral cattle (54%), and 20 of the 41 resistant cattle (48.8%) were culled on 4 farms for 3 years. Consequently, BLV prevalence and mean PVL decreased in all 4 farms. In particular, one farm achieved BLV-free status in May 2020. By decreasing the number of BLV-positive animals, the revenue-enhancing effect was estimated to be ¥5,839,262 ($39,292.39) for the 4 farms over 3 yr. Our results suggest that an integrated BLV eradication program utilization of resistant cattle as a biological barrier and the preferential elimination of susceptible cattle are useful for BLV infection control.

Expression patterns of T cells-specific long noncoding RNAs in systemic lupus erythematosus patients carrying HLA risk/nonrisk alleles.

Long noncoding RNAs (LncRNAs) play key roles in the regulation of gene expression and subsequently in the pathogenesis of several autoimmune diseases. This study aimed to explore the peripheral expression levels of T-cells-specific LncRNAs and transcription factors in systemic lupus erythematosus (SLE) patients carrying either human leukocyte antigens (HLA) risk or non-risk alleles. Genotypes of HLA-DRB1 and HLA-DQB1 loci for 106 SLE patients were determined by PCR-SSP. In the next step, patients were stratified based on the presence of HLA-DRB1*03 and/or DRB1*16 allele groups (HLA risk alleles positive or HLA-RPos) or carrying other DRB1 allele groups (HLA-RNeg). Then, transcript levels of LncRNAs (IFNG-AS1, RMRP, Th2LCR, and DQ786243) and mRNAs for transcription factors (Foxp3, Gata3, and Tbx21) were measured using qRT-PCR and compared between two subgroups of patients. Totally, 47 cases were classified as HLA-RPos and 59 cases as HLA-RNeg patients. The HLA-RPos patients showed decreased transcript levels of DQ786243 (p = .001) and elevated expression of IFNG-AS1 (p = .06) and T-bet mRNA (p = .03) compared to the HLA-RNeg group. We observed significantly lower expression of Th2LCR (p < .0001) and DQ786243 (p = .001) and higher expression of Tbx21 (p = .009) and Foxp3 (p = .02) in DR3-positive versus DR3-negative patients. Likewise, decreased transcript levels of DQ786243 (p = .02) and RMRP (p = .003) were observed in DR16-positive versus DR16-negative patients. ROC curve analysis revealed the potential of DQ786243 and RMRP as biomarkers in SLE disease based on the carriage of HLA risk alleles. Our results indicate that the contribution of multiple T cell subsets in SLE disease progression as judged by expression analysis of LncRNAs and transcription factors can be inspired by the inheritance of HLA risk/nonrisk alleles is SLE patients.

The Association of Human Leukocyte Antigen Genotyping Among Sudanese Patients With Rheumatoid Arthritis: Reference to Ethnicity.

Human leukocyte antigens (HLA) account for up to one-half of the total genetic contribution to rheumatoid arthritis (RA) risk. The study investigated the association of HLA class II genotyping with RA susceptibility in Sudanese ethnic groups. The DRB1 and DQB1 alleles and haplotypes were determined in 122 RA patients (i.e., Gaalia = 54, Johayna = 24, Baggara = 17, Nile Nubian = 12, and others = 15) and 120 healthy controls ofethnic groups (i.e., Gaalia = 44, Johayna = 11, Baggara = 15, Nile Nubian = 9, and others = 21) using a polymerase chain reaction with sequence-specific primers method. Susceptibility to RA was associated with a high frequency of DRB1*04(P = 0.04), DRB1*10(P = 0.04), and DQB1*03(P= 2.2 x 10-8/Pc = 6.6 x 10-8) between study ethnic groups, while protective effects were shown with DRB1*07(P= 0.01), DQB1*02(P= 0.02), andDQB1*06(P= 2.2 x 10-6/Pc= 6.6 x 10-6), with an inconsistent frequency between study ethnic groups.The HLA haplotypes that were high in frequency among RA ethnic groups and showed susceptibility associations were DRB1*03-DQB1*03,DRB1*04-DQB1*03,DRB1*08-DQB1*03, DRB1*13-DQB1*02,and DRB1*13-DQB1*03 (P= 0.00003/Pc = 0.0003,P= 0.0001/Pc= 0.0001,P= 0.03, P= 0.004/Pc= 0.03, and P= 3.79x10-8/Pc= 3.3x10-9,respectively). On the contrary, DRB1*03-DQB1*02,DRB1*07-DQB1*02, andDRB1*13-DQB1*06 were lower in frequency in the ethnic groups with RA and may confer protection (P= 0.004/Pc= 0.032,P= 0.002/Pc= 0.02, and P= 0.01, respectively). Our findings indicate an association between HLA-DRB1 and DQB1 genotypes and the susceptibility to RA in the Sudanese population, with a moderate frequency between our ethnic groups.

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.

Primary membranous nephropathy in two siblings with one combined with anti-glomerular basement membrane disease: a case report

BackgroundThe phospholipase A2 receptor (PLA2R) associated with membranous nephropathy (MN) is an organ-specific autoimmune disease associated with PLA2R and human leukocyte antigen (HLA) genes. Familial PLA2R-related MN is rarely reported. The combination of anti-GBM disease and MN has been well documented, though the mechanism behind it remains unclear.Case presentationWe describe two siblings diagnosed with pathology-confirmed PLA2R-related MN 1 year apart. And one of the two siblings developed an anti-GBM disease. The high-resolution HLA typing showed identical alleles in both siblings, specifically heterozygotes of DRB1*15:01/*03:01.ConclusionWe describe a familial case of PLA2R-related MN supporting the role of genetic factors that HLA-DRB1*15:01 and DRB1*03:01 predispose patients in the development of PLA2R-related MN in the Han Chinese population. The combination of MN and anti-GBM disease may also partially be associated with the same susceptible HLA allele DRB1*15:01.

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.

A machine learning approach for identifying variables associated with risk of developing neutralizing antidrug antibodies to factor VIII

A key unmet need in the management of hemophilia A (HA) is the lack of clinically validated markers that are associated with the development of neutralizing antibodies to Factor VIII (FVIII) (commonly referred to as inhibitors). This study aimed to identify relevant biomarkers for FVIII inhibition using Machine Learning (ML) and Explainable AI (XAI) using the My Life Our Future (MLOF) research repository. The dataset includes biologically relevant variables such as age, race, sex, ethnicity, and the variants in the F8 gene. In addition, we previously carried out Human Leukocyte Antigen Class II (HLA-II) typing on samples obtained from the MLOF repository. Using this information, we derived other patient-specific biologically and genetically important variables. These included identifying the number of foreign FVIII derived peptides, based on the alignment of the endogenous FVIII and infused drug sequences, and the foreign-peptide HLA-II molecule binding affinity calculated using NetMHCIIpan. The data were processed and trained with multiple ML classification models to identify the top performing models. The top performing model was then chosen to apply XAI via SHAP, (SHapley Additive exPlanations) to identify the variables critical for the prediction of FVIII inhibitor development in a hemophilia A patient. Using XAI we provide a robust and ranked identification of variables that could be predictive for developing inhibitors to FVIII drugs in hemophilia A patients. These variables could be validated as biomarkers and used in making clinical decisions and during drug development. The top five variables for predicting inhibitor development based on SHAP values are: (i) the baseline activity of the FVIII protein, (ii) mean affinity of all foreign peptides for HLA DRB 3, 4, & 5 alleles, (iii) mean affinity of all foreign peptides for HLA DRB1 alleles), (iv) the minimum affinity among all foreign peptides for HLA DRB1 alleles, and (v) F8 mutation type.

Artificial Intelligence (AI) based approach for identifying biomarkers associated with neutralizing antidrug antibodies to Factor VIII used in Hemophilia A treatment

Abstract Lack of clinically validated markers associated with the development of neutralizing antibodies (inhibitors) to the replacement protein-drug, Factor VIII (FVIII) is a major challenge in managing Hemophilia A (HA). By utilizing Machine Learning (ML) and Explainable AI (XAI) we identified and ranked relevant variables (biomarkers) that could be predictive for developing inhibitors to FVIII drugs in hemophilia A patients. The dataset used for the study was derived from the My Life Our Future (MLOF) repository and included variables such as age, race, ethnicity, mutations in the F8 gene and the Human Leucocyte Antigen Class II (HLA-II) type. We computed the number of foreign FVIII derived peptides, based on the alignment of the endogenous FVIII and infused drug sequences, and the foreign-peptide HLA-II molecule binding affinity (using the NetMHCIIpan algorithm). The complete dataset with the added variables was trained and validated using multiple ML classification models to identify the top performing model, which was chosen for further processing with XAI via SHAP (SHapley Additive exPlanations) to identify the variables critical for the prediction of FVIII inhibitor development in a hemophilia A patients. The top five variables for predicting inhibitor development based on SHAP values are: (i) the baseline activity of the FVIII protein, (ii) mean affinity of all foreign peptides for HLA DRB 3, 4, &amp; 5 alleles, (iii) mean affinity of all foreign peptides for HLA DRB1 alleles, (iv) the maximum affinity among all foreign peptides for HLA DRB1 alleles, and (v) F8 mutation type. This research was supported by funds from the Hemostasis Branch/Division of Plasma Protein 344 Therapeutics/Office of Tissues and Advanced Therapies/Center for Biologics Evaluation and Research 345 of the U.S. Food and Drug Administration and in part by an appointment to the Research Participation 346 Program at the Center for Biologics Evaluation and Research administered by the Oak Ridge Institute 347 for Science and Education through an interagency agreement between the U.S. Department of Energy 348 and the U.S. Food and Drug Administration. The MLOF program was developed as a partnership 349 between NHF, ATHN, Bloodworks Northwest, and Bioverativ and supported financially by 350 Bioverativ, NHF, Bloodworks Northwest, and ATHN.

Association between HLA Class II Alleles/Haplotypes and Genomic Ancestry in Brazilian Patients with Type 1 Diabetes: A Nationwide Exploratory Study.

We aimed to identify HLA-DRB1, -DQA1, and -DQB1 alleles/haplotypes associated with European, African, or Native American genomic ancestry (GA) in admixed Brazilian patients with type 1 diabetes (T1D). This exploratory nationwide study enrolled 1599 participants. GA percentage was inferred using a panel of 46 ancestry informative marker-insertion/deletion. Receiver operating characteristic curve analysis (ROC) was applied to identify HLA class II alleles related to European, African, or Native American GA, and showed significant (p < 0.05) accuracy for identifying HLA risk alleles related to European GA: for DRB1*03:01, the area under the curve was (AUC) 0.533; for DRB1*04:01 AUC = 0.558, for DRB1*04:02 AUC = 0.545. A better accuracy for identifying African GA was observed for the risk allele DRB1*09:01AUC = 0.679 and for the protective alleles DRB1*03:02 AUC = 0.649, DRB1*11:02 AUC = 0.636, and DRB1*15:03 AUC = 0.690. Higher percentage of European GA was observed in patients with risk haplotypes (p < 0.05). African GA percentage was higher in patients with protective haplotypes (p < 0.05). Risk alleles and haplotypes were related to European GA and protective alleles/haplotypes to African GA. Future studies with other ancestry markers are warranted to fill the gap in knowledge regarding the genetic origin of T1D in highly admixed populations such as that found in Brazil.

Comparison of Microsatellite and the MHC Class II DRB Locus Diversity in Raccoon Dogs (Nyctereutes procyonoides) between Finland and Japan

The raccoon dog was introduced from eastern to western Eurasia, and subsequently spread throughout Europe all the way to the middle part of Finland, potentially assisted by its high genetic diversity. To elucidate the genetic diversity of Finnish raccoon dogs and its association with resistance to pathogens, we genotyped 77 individuals for ten neutral and eight MHC-linked microsatellite loci, and sequenced MHC class II DRB alleles for 20 individuals. We compared the results with the data from a Japanese population, and detected no differences in the microsatellite variation between these two populations. By contrast, diversity at DRB loci was lower in the Finnish population as compared with that in the Japanese population. No spatial genetic structure was found in Finland, but our analyses revealed two sympatric genetic clusters. The analysed genetic markers did not show associations with the frequency of infection by pathogens such as Trichinella spp.

The association of HLA-DRB1 alleles and MBL2 gene variant in pediatric acute lymphoblastic leukemia patients

IntroductionEpidemiologic studies on pediatric acute lymphoblastic leukemias (ALL) have been conducted to evaluate the possible risk factors including genetic, infectious and environmental factors with the objective of idenfying the etiology. Mannose-binding lectin 2 (MBL2) plays an important role in first-line immune defense. HLA DRB1 alleles play a role in presentation of peptides to T cells and in activation of the adaptive immune response. ObjectiveIn our study, we aimed to investigate both the MBL2 gene variant and HLA-DRB1 alleles in pediatric ALL patients. MaterialsIn this study, 86 high-risk ALL patients and 100 controls were included. Polymerase Chain Reaction (PCR)-Restriction Fragment Length Polymorphism (PCR-RFLP) and PCR-sequence specific primer (SSP) methods were used for detection of polymorphism of the MBL2 and HLA-DRB1 alleles, respectively. ResultsThe frequency of the MBL2 AB genotype was lower in female ALL patients, compared to male ALL patients (p = 0.034). An association was found between the MBL2 BB genotype and DRB1*07 and among patients with the MBL2 BB genotype; those who also carried the DRB1*07 and *04 alleles were significantly higher than those without the DRB1*07 and *04 alleles. (p = 0.048, p = 0.022, respectively). ConclusionThis is the first study suggesting that the MBL2 BB genotype in association with the DRB1*07 or co-inheritance of the HLA-DRB1*04 and HLA DRB1*07 may have an impact on the etiopathogenesis of the disease.

HLA-DRB1 polymorphism and risk of pediatric-onset and adult-onset multiple sclerosis: a case–control study

The association of predisposition to multiple sclerosis (MS) with HLA-DRB1 gene polymorphisms is the strongest. It is not clear whether the DRB1 alleles associated with the risk of this disease diff er in adult and pediatric populations living in the same environmental conditions.Objective: comparative study of associations of HLA-DRB1 gene polymorphism with the risk of pediatric-onset MS and adult-onset MS in the Altai region.Material and methods. Caucasian with relapsing-remitting MS, born and living in the Altai region of Russia in the southeast of Western Siberia, participated in the case–control study: 200 patients with adult-onset MS, 86 patients with pediatric-onset MS. The control group included 200 volunteers. Genotyping was performed by TaqMan probes. Results. Alleles 03, 13, 15 of the HLA-DRB1 gene are genetic risk factors for both adult-onset MS and pediatric-onset MS in Caucasians in the Altai region. Alleles 01 and 07 of the HLA-DRB1 gene may have a protective eff ect against pediatric-onset MS, alleles 01, 07, 11 and 16 against adult-onset MS.Conclusion. It can be assumed that the diff erence in the age of MS onset is not associated with the diff erent infl uence of risk alleles of the HLA-DRB1 gene in populations under and over 18 years of age.