In this report, HLA polymorphisms (A, B, DRB1 and DQB1 loci) were determined in 149 unrelated Iraqi Arab potential bone marrow and kidney donors. Molecular genotyping was carried out by polymerase chain reaction followed by specific oligonucleotide probe hybridizations. Data were analyzed by Arlequin software. HLA-A, -B and -DRB1 genotype frequencies were significantly deviated from Hardy-Weinberg equilibrium, while HLA-DQB1 frequencies showed no deviation. A*03, B*35, DRB1*11 and DQB1*02 were the most frequent allele groups, while A*02-B*07-DRB1*04-DQB1*03 was the most frequent haplotype. HLA data are available in the Allele Frequencies Net Database (AFND: 3680) under the population name "Iraq Arabs".

The etiology and pathogenesis of Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) are unknown, and autoimmunity is one of many proposed underlying mechanisms. Human Leukocyte Antigen (HLA) associations are hallmarks of autoimmune disease, and have not been thoroughly investigated in a large ME/CFS patient cohort. We performed high resolution HLA -A, -B, -C, -DRB1, -DQB1 and -DPB1 genotyping by next generation sequencing in 426 adult, Norwegian ME/CFS patients, diagnosed according to the Canadian Consensus Criteria. HLA associations were assessed by comparing to 4511 healthy and ethnically matched controls. Clinical information was collected through questionnaires completed by patients or relatives. We discovered two independent HLA associations, tagged by the alleles HLA-C*07:04 (OR 2.1 [95% CI 1.4-3.1]) and HLA-DQB1*03:03 (OR 1.5 [95% CI 1.1-2.0]). These alleles were carried by 7.7% and 12.7% of ME/CFS patients, respectively. The proportion of individuals carrying one or both of these alleles was 19.2% in the patient group and 12.2% in the control group (OR 1.7 [95% CI 1.3-2.2], p_nc = 0.00003). ME/CFS is a complex disease, potentially with a substantial heterogeneity. We report novel HLA associations pointing toward the involvement of the immune system in ME/CFS pathogenesis.

We aimed to compare HLA-DQB1-associations in narcolepsy type 1 (NT1) patients with disease onset before and after the 2009 H1N1 pandemic in a large Dutch cohort. 525 NT1 patients and 1272 HLA-DQB1*06:02-positive healthy controls were included. Because of the discussion that has arisen on the existence of sporadic and post-H1N1 NT1, HLA-DQB1-associations in pre- and post-H1N1 NT1 patients were compared. The associations between HLA-DQB1 alleles and NT1 were not significantly different between pre- and post-H1N1 NT1 patients. Both HLA-DQB1-associations with pre- and -post H1N1 NT1 reported in recent smaller studies were replicated. Our findings combine the results of studies in pre- and post-H1N1 NT1 and argue against considering post-H1N1 NT1 as a different entity.

Colonization of the human gastric mucosa by H. pylori may cause peptic and duodenal ulcers (DUs), gastric lymphomas, and gastric cancers. The cagL gene is a component of cag T4SS and is involved in cagA translocation into host. An association between the risk of gastric cancer and the type of HLA class II (DR and/or DQ) was suggested in different populations. The aim of this study was to investigate, the clinical association of the cagL gene with host HLA alleles in H. pylori strains that were isolated from patients with gastric cancer, DU, and non-ulcer dyspepsia (NUD) and to determine the HLA allele that confers susceptibility or resistance for the risk of gastric cancer and DU development in Turkish patients. A total of 94 patients (44 gastric cancer and 50 DU patients; 58 male, 36 female; mean age, 49.6 years), and 86 individuals (50 NUD patients and 36 persons with normal gastrointestinal system [NGIS]; 30 male, 56 female; mean age, 47.3 years) were included as the patient and the control groups, respectively. CagA and cagL were determined by PCR method. DNA from peripheral blood samples was obtained by EZ-DNA extraction kit. For HLA SSO typing, LIFECODES SSO Typing kits (HLA-A, HLA-B HLA-C, HLA-DRB1 and HLA-DQA1/B1 kits) were used. The CagL/CagA positivity distribution in the groups were as follows: 42 (95.4%) gastric cancer, 46 (92%) DU and, 34 (68%) NUD and no NGIS cases. The HLA-DQA1*01 (OR: 3.82) allele was significantly different, suggesting that these individuals with H. pylori strains harbouring the CagL/CagA positivity are susceptible to the risk of gastric cancer and DU, and the HLA-DQA1*05 (OR, 0.318) allele was suggested as a protective allele for the risk of gastric cancer and DU using univariate analyses. HLA-DQA1*01 (OR, 2.21), HLA-DQB1*06 (OR, 2.67), sex (male, OR, 2.27), and CagL/CagA/(<2) EPIYA C repeats (OR, 5.72) were detected independent risk factors that increased the risk of gastric cancer and DU using multivariate analyses. However, the HLA-DRB1*04 (OR, 0.28) allele was shown to be a protective allele, which decreased the risk of gastric cancer and DU. Gastric pathologies result from an interaction between bacterial virulence factors, host epigenetic and environmental factors, and H. pylori strain heterogeneity, such as genotypic variation among strains and variations in H. pylori populations within an individual host.

This study investigated the diagnostic value of 5-methylcytosine (5-mC) and 5-hydroxymethylcytosine (5-hmC) contents of human leucocyte antigen (HLA)-B and HLA-DQB1 in anti-tuberculosis drug-induced liver injury (ADLI). In total, 110 ADLI patients and 120 patients without ADLI controls were enrolled. Enzyme-linked immunosorbent assay (ELISA) was used to detect the 5-mC and 5-hmC content in DNA from peripheral blood leucocytes. The univariate analysis showed that smoking, drinking, and 5-mC and 5-hmC content of HLA-B and HLA-DQB1 were significantly associated with ADLI. After adjusting for drinking and smoking, we found that 5-mC content of HLA-B and HLA-DQB1 were associated with ADLI (odds ratio [OR] = 0.251 and 0.347, respectively) and 5-hmC contents of HLA-B and HLA-DQB1 were also associated with ADLI (OR = 1.848 and 4.705, respectively). Receiver operating characteristic (ROC) analysis indicated that the 5-hmC contents of both HLA-B and HLA-DQB1 were more clinically significant than the 5-mC contents were. The combined 5-hmC level of HLA-B and HLA-DQB1 was the best diagnostic biomarker for ADLI, with the highest areas under the curve (AUC) for 0.953, sensitivity for 0.900 and specificity for 0.875. Therefore, combined 5-hmC levels of HLA-B and HLA-DQB1 could be significant evidence for diagnosis of ADLI.

HLA-DQB1*03:280 shows a substitution A to G at position 247 when compared to HLA-DQB1*03:03:02. This article is protected by copyright. All rights reserved.

Several prospective studies have shown an association between cow's milk consumption and the risk of islet autoimmunity and/or type 1 diabetes. We wanted to study whether processing of milk plays a role. A population-based birth cohort of 6081 children with HLA-DQB1-conferred risk to type 1 diabetes was followed until the age of 15 years. We included 5545 children in the analyses. Food records were completed at the ages of 3 and 6 months and 1, 2, 3, 4, and 6 years and diabetes-associated autoantibodies were measured at 3-12 month intervals. For milk products in the food composition database we used conventional and processing-based classifications. We analysed the data using a joint model for longitudinal and time-to-event data. By the age of 6 years, islet autoimmunity developed in 246 children. Consumption of all cow's milk products together [energy-adjusted hazard ratio (95% confidence interval) 1.06 (1.02, 1.11), P=0.003], non-fermented milk products [1.06 (1.01, 1.10), P=0.011], and fermented milk products [1.35 (1.10, 1.67), P=0.005] were associated with an increased risk of islet autoimmunity. The early milk consumption was not associated with the risk beyond 6 years. We observed no clear differences based on milk homogenisation and heat treatment. Our results are consistent with the previous studies, which indicate that high milk consumption may cause islet autoimmunity in children at increased genetic risk. The study did not identify any specific type of milk processing that would clearly stand out as a sole risk factor apart from other milk products.

One nucleotide substitution in codon 38 of HLA-DQB1*05:05:01 results in a novel allele, HLA-DQB1*05:05:02. This article is protected by copyright. All rights reserved.

Genetic studies have revealed that autoimmune susceptibility variants are over-represented in memory CD4⁺ T cell regulatory elements^1-3. Understanding how genetic variation affects gene expression in different T cell physiological states is essential for deciphering genetic mechanisms of autoimmunity^4,5. Here, we characterized the dynamics of genetic regulatory effects at eight time points during memory CD4⁺ T cell activation with high-depth RNA-seq in healthy individuals. We discovered widespread, dynamic allele-specific expression across the genome, where the balance of alleles changes over time. These genes were enriched fourfold within autoimmune loci. We found pervasive dynamic regulatory effects within six HLA genes. HLA-DQB1 alleles had one of three distinct transcriptional regulatory programs. Using CRISPR-Cas9 genomic editing we demonstrated that a promoter variant is causal for T cell-specific control of HLA-DQB1 expression. Our study shows that genetic variation in cis-regulatory elements affects gene expression in a manner dependent on lymphocyte activation status, contributing to the interindividual complexity of immune responses.

To optimize strategies that mitigate the risk of graft loss associated with HLA incompatibility, we evaluated whether sequence defined HLA targets (eplets) that result in donor-specific antibodies are associated with transplant outcomes. To define this, we fit multivariable Cox proportional hazard models in a cohort of 118 382 United States first kidney transplant recipients to assess risk of death-censored graft failure by increments of ten antibody-verified eplet mismatches. To verify robustness of our findings, we conducted sensitivity analysis in this United States cohort and assessed the role of antibody-verified eplet mismatches as autonomous predictors of transplant glomerulopathy in an independent Canadian cohort. Antibody-verified eplet mismatches were found to be independent predictors of death-censored graft failure with hazard ratios of 1.231 [95% confidence interval 1.195, 1. 268], 1.268 [1.231, 1.305] and 1.411 [1.331, 1.495] for Class I (HLA-A, B, and C), -DRB1 and -DQB1 loci, respectively. To address linkage disequilibrium between HLA-DRB1 and -DQB1, we fit models in a subcohort without HLA-DQB1 eplet mismatches and found hazard ratios for death-censored graft failure of 1.384 [1.293, 1.480] for each additional antibody-verified HLA-DRB1 eplet mismatch. In a subcohort without HLA-DRB1 mismatches, the hazard ratio was 1.384 [1.072, 1.791] for each additional HLA-DQB1 mismatch. In the Canadian cohort, antibody-verified eplet mismatches were independent predictors of transplant glomerulopathy with hazard ratios of 5.511 [1.442, 21.080] for HLA-DRB1 and 3.640 [1.574, 8.416] for -DRB1/3/4/5. Thus, donor-recipient matching for specific HLA eplets appears to be a feasible and clinically justifiable strategy to mitigate risk of graft loss.

One nucleotide change in position 216 of HLA-DQB1*06:02 result in a novel allele, HLA-DQB1*06:364. This article is protected by copyright. All rights reserved.

HLA-DQB1*06:361 differs from HLA-DQB1*06:04:01:01 by one nucleotide substitution in codon 15 in exon 2. This article is protected by copyright. All rights reserved.

Bullous pemphigoid (BP) is the most common autoimmune subepidermal bullous diseases. Autoantibodies against hemidesmosomal adhesion proteins might be involved in the developing process. BP usually affects the elderly with high mortality whereas the drug-induced BP is often improved and rarely relapses after the withdrawal of the suspected drug. An accumulated evidence suggests that dipeptidyl peptidase-4 inhibitor (DPP-4I), which has been widely used as the antidiabetic drug improves glycemic control with little risk for hypoglycemia, could be an inducer of DPP-4I-associated BP (DPP-4I-BP). While the precise mechanism remains unclear, a unique immunological profile with human leukocyte antigen (HLA)-DQB1*03:01 could be a biomarker of genetic susceptibility to DPP-4I-BP. Here, we encountered an interesting case of DPP-4I-BP with HLA-DQB1*03:01, which was likely triggered by scabies. A 56-year-old Japanese male with type 2 diabetes on hemodialysis was referred to our hospital due to worsened blisters. Prior to his admission, he had been on linagliptin, a DPP-4I, for 5 months. He then suffered from scabies 2 weeks before his admission while the treatment with ivermectin failed to improve his symptom. Based on his clinical symptom, positive for anti-BP180 autoantibody in serum, and the pathological alterations of skin biopsy specimens, he was diagnosed with DPP-4I-BP. Importantly, he also carried an HLA-DQB1*03:01 allele. Oral prednisolone was subsequently administered after the discontinuation of linagliptin, and his symptom gradually disappeared. Given the fact that the DPP-4I-BP could be a life-threating disease, we should be cautious of prescribing DPP-4I in hemodialysis patients, whose immune system could be impaired.

Characterization of two novel HLA-DQB1*06:02:01 variants, HLA-DQB1*06:02:01:05 and -DQB1*06:02:01:06. This article is protected by copyright. All rights reserved.

Two new HLA alleles were characterized in the population of the North Caucasus. This article is protected by copyright. All rights reserved.

Persistent human papillomavirus (HPV) infection is the main causative agent for cervical intraepithelial neoplasia (CIN) and cancer. Variability in host immunogenetic factors is important in determining the overall cellular immune response to the HPV infection. This study was carried out to confirm the association of human leukocyte antigen (HLA) class II DRB1 and DQB1 alleles with CIN and HPV persistent infections in women from Shanghai in a case-controlled study. A total of 170 patients, including 105 HPV positive patients and 65 HPV negative women (control) participated in the study. HybriBio's proprietary flow-through hybridization technique was used to perform HPV genotyping. Low-resolution PCR-sequence specific priming (PCR-SSP) was used to genotype HLA class II for DRB1 and DQB1 loci. Binary and multivariate logistic regression analysis highlighted the association of specific alleles with CIN and HPV persistent infections after adjusting for the confounding factor of age. HLA-DQB1*02 and *06 is significantly associated with increased risk of HPV16 persistent infection (P_c < 0.013). HLA-DRB1*09 is significantly associated with increased risk for CIN, whereas the -DRB1*16 exhibit protective to CIN (P < 0.05). Significant association is found for HLA-DQB1*04 and *06 with increased risk for CIN (P < 0.05). There were possible associations of specific HLA class II alleles either with risk of persistent HPV infection or with developing CIN.

<p><div><b>Background and Aims</b></div>Traditional Chinese medicine (TCM) has been widely applied in chronic hepatitis B (CHB) supplementary treatment in China. Kidney yang deficiency syndrome (KYDS), one of the most common TCM syndromes of CHB, is more likely to progress to liver cirrhosis or hepatocellular carcinoma than other syndromes. Polymorphisms in the human leucocyte antigen- (HLA-) <i>DQB1</i> and <i>-DRB1</i> genes were reported to be associated with hepatitis B virus infection outcomes. Here, we investigated whether <i>HLA-DQB1</i> and <i>HLA-DRB1</i> are associated with the classification of CHB TCM syndromes.</p><p><div><b>Methods</b></div>We genotyped <i>HLA-DQB1</i> and <i>HLA-DRB1</i> alleles in a total of 105 subjects, including 74 CHB patients (28 KYDS and 46 non-KYDS) and 31 healthy individuals from Sichuan Province of Southwest China, by polymerase chain reaction sequence-based typing (PCR-SBT). Moreover, a meta-analysis was carried out for further verification.</p><p><div><b>Results</b></div>The proportion of patients with high HBV DNA load (≥2000 IU/ml) in the KYDS group is higher than that in the non-KYDS group (60.70% [17/28] vs. 28.30% [13/46]); <i>P</i>=0.01). The frequencies of <i>HLA-DQB1∗02</i>:<i>01</i> (<i>P</i>=0.04) and <i>HLA-DRB1∗03</i>:<i>01</i> (<i>P</i>=0.04) in the KYDS group were significantly increased compared to the non-KYDS group. The gene test and meta-analysis showed that <i>HLA-DRB1∗08</i>:<i>03</i> confers susceptibility to CHB (odds ratio = 1.57).</p><p><div><b>Conclusion</b></div>We found an association between <i>HLA-DRB1</i>/<i>DQB1</i> polymorphisms and KYDS of CHB. Moreover, KYDS patients of CHB are characteristic with high HBV DNA loads. These findings help to reveal the biological mechanism of KYDS in high risk of CHB progression and suggest a potential prognostic value for disease outcome evaluation.</p>