Characterisation of the novel HLA-DQA1*04:14N allele by next-generation sequencing.

HLA-DQA1*04:14N differs from HLA-DQA1*04:01:01:03 by a single nucleotide deletion in codon 113 in exon 3.

HLA-DQA1*05 Allele Carriage and Anti-TNF Therapy Persistence in Inflammatory Bowel Disease.

INTRODUCTION: Carriage of the HLA-DQA1*05 allele is associated with development of antidrug antibodies (ADAs) to antitumor necrosis factor (anti-TNF) therapy in patients with Crohn's disease. However, ADA is not uniformly associated with treatment failure. We aimed to determine the impact of carriage of HLA-DQA1*05 allele on outcome of biologic therapy evaluated by drug persistence. METHODS: A multicenter, retrospective study of 877 patients with inflammatory bowel disease (IBD) treated with anti-TNF therapy with HLA-DQA1*05 genotypes were generated by imputation from whole genome sequence using the HIBAG package, in R. Primary end point was anti-TNF therapy persistence, (time to therapy failure), segregated by HLA-DQA1*05 allele genotype and development of a risk score to predict anti-TNF therapy failure, incorporating HLA-DQA1*05 allele genotype status (LORisk score). RESULTS: In all, 877 patients receiving anti-TNF therapy were included in our study; 543 (62%) had no copy, 281 (32%) one copy, and 53 (6%) 2 copies of HLA-DQA1*05 allele. Mean time to anti-TNF therapy failure in patients with 2 copies of HLA-DQA1*05 allele was significantly shorter compared with patients with 0 or 1 copy at 700 days' follow-up: 418 vs 541 vs 513 days, respectively (P = .012). Factors independently associated with time to anti-TNF therapy failure included carriage of HLA-DQA1*05 allele (hazard ratio [HR], 1.2, P = .02; female gender HR, 1.6, P < .001; UC phenotype HR, 1.4, P = .009; and anti-TNF therapy type [infliximab], HR, 1.5, P = .002). The LORisk score was significantly associated with shorter time to anti-TNF therapy failure (P < .001). CONCLUSIONS: Carriage of 2 HLA-DQA1*05 alleles is associated with less favorable outcomes for patients receiving anti-TNF therapy with shorter time to therapy failure. HLA-DQA1*05 genotype status in conjunction with clinical factors may aid in therapy selection in patients with IBD.

Our study found carriage of 2 copies of the HLA-DQA1*05 allele is associated with a less favorable response to anti-TNF therapy with shorter time to therapy failure. HLA-DQA1*05 genotype status in conjunction with clinical factors may aid in therapy selection in IBD patients.

Association of 10 Polymorphisms in PLA2R1 and HLA DQA1 Genes with Primary Membranous Nephropathy Risk: A Meta-Analysis and a Meta-Regression.

Background: Although, several studies have assessed the association of the phospholipase A2 receptor (PLA2R) and HLA-DQA1 SNPs with primary membranous nephropathy (PMN), results were inconsistent and between-studies heterogeneity needs to be investigated. Objectives: The aim of this review was to summarize existing data on the contribution of 10 SNPs in the PLA2R and HLA-DQA1 genes to PMN susceptibility and to investigate the between-studies heterogeneity by subgroup analyses and meta-regressions. Design: This study was performed according to the PRISMA guidelines for systematic reviews and meta-analyses. Data sources and methods: An electronic literature search for eligible studies among all papers published prior to January 10, 2024, was conducted through PubMed, EMBASE, Web of science and Scopus databases. Meta-analyses together with subgroup analyses and meta-regressions were performed for the 10 following SNPs: rs4664308, rs3749117, rs3749119, rs35771982, rs3828323, rs16844715, rs1511223, rs6757188, rs2715918, and rs2187668. Results: Combined analyses revealed a significant increase in PMN risk conferred by the following alleles: rs4664308*A, rs3749117*T, rs3749119*C, rs35771982*G, rs3828323*C, rs16844715*C, rs1511223*A, rs2715918*A, and rs2187668*A, all P-values < .001. Moreover, the PLA2R-rs4664308/HLA-DQA1-rs2187668 interaction was significantly associated with an increased PMN risk, P < .001. However, there was a substantial between-studies heterogeneity for some SNPs. Subgroup analyses by ethnicity for the 9 PLA2R SNPs did not show any cross-ethnic disparity. Inversely, the risk conferred by the HLA-DQA1 rs2187668*A allele was significantly higher in Caucasians (OR [95% CI] = 3.929 [3.251-4.748]) than in Asians (OR [95% CI] = 2.537 [1.94-3.318], P = .007. Besides, meta-regressions revealed for the majority of investigated SNPs significant correlations of the effect size with albumin, 24-hours proteinuria, serum creatinine, and eGFR levels. Hence, the influence on PMN risk conferred by the PLA2R and HLA-DQA1 SNPs was rather noted in patients with a severe disease. Conclusion: This meta-analysis showed that 9 out of the 10 investigated SNPs in PLA2R and HLA-DQA1 genes were associated with increased PMN risk. Heterogeneity could be due to disparate patient groups in terms of disease presentation for almost all SNPs, and ethnicity for the HLA-DQA1 rs2187668 SNP. Registration: This review has been registered on PROSPERO: CRD42024506729. Available from: https://www.crd.york.ac.uk/prospero/display_record.php?ID=CRD42024506729.

Genetic factors in primary membranous nephritis Why was the study done? Primary membranous nephritis (PMN) is the most common etiology of adult-onset nephrotic syndrome. Understanding risk factors, particularly genetic ones, would provide a better understanding of its pathophysiological mechanisms in order to prevent and treat patients more effectively. What did the researchers do? The research team summarized published data on genetic factors associated with PMN including phospholipase A2 receptor (PLA2R) and HLA-DQA1 genes. What did the researchers find? The total number of included studies was 27. Nine out of ten genetic factors were found to be associated with PMN risk. Moreover, we noted significant interaction between PLA2R and HLA-DQA1 in potentializing PMN risk. Nevertheless, there was a significant between-studies heterogeneity which was found to be explained in part by disease severity. What do the findings mean? This study has identified some important some genetic factors associated with PMN together with confounding factors that could influence the aforementioned association.

Identification of the novel HLA-DQA1*02:32 allele by next-generation sequencing.

HLA-DQA1*02:32 differs from DQA1*02:01:01 by one nucleotide substitution in codon 210 in exon 4.

The novel HLA-DQA1*05:05:17:03 allele, identified in a potential organ donor.

HLA-DQA1*05:05:17:03 differs from HLA-DQA1*05:05:01:02 by a single base substitution in exon 1 and HLA-DQA1*05:05:17:01 within introns 1 and 2.

Characterization of the novel HLA-DQA1*01:03:11 allele by sequencing-based typing.

HLA-DQA1*01:03:11 differs from HLA-DQA1*01:03:01:02 by one nucleotide substitution in codon 59 in exon 2.

Identification of the novel HLA-DQA1*05:101 allele by next-generation sequencing in a family.

HLA-DQA1*05:101 differs from HLA-DQA1*05:01:01:02 by one nucleotide substitution at codon 221 (CGT>TGT) in exon 4.

Impact of HLA-DQA1∗05 Genotype in Immunogenicity and Failure to Treatment with Tumor Necrosis Factor-alpha Antagonists in Inflammatory Bowel Disease: A Systematic Review and Meta-analysis.

BACKGROUND: HLA-DQA1*05 carriage has been associated with an increased risk of immunogenicity in patients with immune-mediated inflammatory diseases treated with tumor necrosis factor-alpha (TNF-a) antagonists. Results have shown an inconsistent association with a loss of response (LOR) in patients with inflammatory bowel disease (IBD), which could be modified when using proactive optimization and association with immunomodulatory drugs. AIMS: To define the association of HLA-DQA1*05 on anti-drug antibody development and loss of response (LOR) to anti-TNF-a in IBD. METHODS: We searched MEDLINE, EMBASE and SCOPUS, for the period up to August 2023, to identify studies reporting the risk of immunogenicity and/or LOR in IBD patients with HLA-DQA1*05 genotype. RESULTS: Twenty-four studies comprising 12 papers, 11 abstracts and 1 research letter, with a total of 5,727 IBD patients, were included. In a meta-analysis of 10 studies (2,984 patients; 41.9% with HLA-DQA1*05 genotype), HLA-DQA1*05 carriers had higher risk of immunogenicity compared to non-carriers (risk ratio, 1.54; 95%CI, 1.23-1.94; I2=62%) (low certainty evidence). Lack of therapeutic drug monitoring (TDM) increased immunogenicity in the presence of risk HLA (risk ratio 1.97; 95%CI, 1.35-2.88; I2=66%), while proactive TDM revoked this association (very low certainty of evidence). A meta-analysis of 6 studies (765 patients) found that risk for secondary LOR was higher among HLA-DQA1*05 carriers (hazard ratio 2.21; 95%CI, 1.69-2.88; I2=0%) (very low certainty evidence), although definition and time to assessment varied widely among studies. CONCLUSION: HLA-DQA1*05 carriage may be associated with an increased risk of immunogenicity and secondary LOR in IBD patients treated with TNF-a antagonists.

Identification of the novel HLA-DQA1*01:138 allele by next-generation sequencing.

HLA-DQA1*01:138 is identical to HLA-DQA1*01:03 except for a single nucleotide substitution in exon 3.

Investigating associations between HLA DQA1 ~ DQB1 haplotypes, H. pylori infection, metaplasia, and anti-CagA IgA seropositivity in a Turkish gastritis cohort.

Helicobacter pylori was reported as an important cause of gastritis, and gastric ulcers and CagA oncoprotein-producing H. pylori subgroups were blamed to increase the severity of gastritis. Disparities were reported in that the presence of serum anti-CagA IgA was not parallel with CagA-positive H. pylori cohabitation. We hypothesized that the HLA-DQA1 ~ DQB1 haplotypes in human populations include protective haplotypes that more effectively present immunogenic CagA peptides and susceptible haplotypes with an impaired capacity to present CagA peptides. We recruited patients (n = 201) admitted for gastroendoscopy procedures and performed high-resolution HLA-DQA1 and DQB1 typing. Serum anti-CagA IgA levels were analyzed by ELISA (23.0% positive), and H. pylori was classified as positive or negative in gastric mucosal tissue slides (72.6% positive). The HLA DQA1*05:05 allele (29.1%) and HLA DQB1*03:01 allele (32.8%) were found at the highest frequency among gastritis patients of Turkish descent. In HLA DQA1*05:05 ~ DQB1*03:01 double homozygous (7.3%) and heterozygous (40.7%) haplotype carriers, the presence of anti-CagA IgA decreased dramatically, the presence of H. pylori increased, and the presence of metaplasia followed a decreasing trend. The DQ protein encoded by HLA DQA1*05:05-DQ*03:01 showed a low binding affinity to the CagA peptide when binding capacity was analyzed by the NetMHCIIPan 4.0 prediction method. In conclusion, HLA DQA1 ~ DQB1 polymorphisms are crucial as host defense mechanisms against CagA H. pylori since antigen binding capacity plays a crucial role in anti-CagA IgA production.

Biological treatment interruption in inflammatory bowel disease: Motivation and predictive factors / Interrupción del tratamiento biológico en la enfermedad inflamatoria intestinal: causas y factores predictores

Background: Loss-of-response and adverse events (AE) to biologics have been linked to HLA-DQA1*05 allele. However, the clinical factors or biologic used may influence treatment duration. Our objective was to evaluate the influence of clinical and therapeutic factors, along with HLA, in biological treatment discontinuation. Methods: A retrospective study of consecutive IBD patients treated with biologics between 2007 and 2011 was performed. Main outcome was treatment discontinuation due to primary non-response (PNR), secondary loss of response (SLR) or AE. HLA-DQA1 genotyping was done in all patients. Regression analyses were used to assess risk factors of treatment discontinuation. Results: One hundred fifty patients (61% male) with 312 biologic treatments were included. 147 (47%) were discontinued with a cumulative probability of 30%, 41% and 56% at 1, 2 and 5 years. The use of infliximab (p=0.006) and articular manifestations (p<0.05) were associated with treatment discontinuation. Considering cause of withdrawal, Ulcerative Colitis (UC) had a higher proportion of PNR (HR=4.99; 95% CI=1.71–14.63; p=0.003), SLR was higher if biologics had been indicated due to disease flare (HR=2.32; 95% CI=1.05–5.09; p=0.037) while AE were greater with infliximab (HR=2.46; 95% CI=1.48–4.08; p<0.001) or spondylitis (HR=2.46; 95% CI=1.78–6.89; p<0.001). According to the biological drug, HLA-DQA1*05 with adalimumab showed more SLR in cases with Crohn's disease (HR=3.49; 95% CI=1.39–8,78; p=0.008) or without concomitant immunomodulator (HR=2.8; 95% CI=1.1–6.93; p=0.026). Conclusions: HLA-DQ A1*05 was relevant in SLR of IBD patients treated with adalimumab without immunosupression. In patients treated with other biologics, clinical factors were more important for treatment interruption, mainly extensive UC or extraintestinal manifestations and having indicated the biologic for flare. (AU)

Introducción: Estudios previos han observado una asociación entre el HLA-DQA1*05 y la pérdida de respuesta a biológicos y el desarrollo de efectos adversos (EA). Hay factores clínicos y biológicos que podrían influir en la duración del tratamiento. El objetivo del estudio fue evaluar la influencia del HLA, de factores clínicos y terapéuticos en la interrupción del tratamiento biológico. Métodos: Se realizó un estudio retrospectivo de pacientes con enfermedad inflamatoria intestinal (EII) tratados con biológicos entre 2007 y 2011. Los principales eventos analizados fueron la suspensión del tratamiento por fallo de respuesta primaria (PRP), secundaria (PRS) o EA. Se realizó un tipaje del HLA-DQA1*05 y se evaluaron los factores de riesgo de interrupción del tratamiento mediante un análisis de regresión logística. Resultados: Se incluyeron 150 pacientes y 312 tratamientos, de los cuales se suspendieron 147 (47%) en el seguimiento. El infliximab (p=0,006) y las manifestaciones articulares (p<0,05) se relacionaron con la interrupción del tratamiento. La colitis ulcerosa (CU) presentó mayor PRP (HR: 4,99; IC 95%: 1,71-14,63; p=0,003), el brote como indicación de tratamiento se asoció a más PRS (HR: 2,32; IC 95%: 1,05-5,09; p=0,037); el uso de infliximab (HR: 2,46; IC 95%: 1,48-4,08; p<0,001) y la espondilitis (HR: 2,46; IC 95%: 1,78-6,89; p<0,001) a la suspensión por EA. El HLA-DQA1*05 fue un factor de riesgo de PRS en los pacientes tratados con adalimumab (ADA) con enfermedad de Crohn (HR: 3,49; IC 95%: 1,39-8,78; p=0,008) o con EII sin inmunosupresor asociado (HR: 2,8; IC 95%: 1,1-6,93; p=0,026). Conclusiones: El HLA-DQA1*05 se asoció al cese del tratamiento con ADA por PRS en los pacientes con EII sin inmunosupresor asociado. Respecto a otros biológicos, la suspensión se debió más a factores como la CU, las manifestaciones articulares y la indicación para remisión de brote intestinal. (AU)

The new HLA-DQA1*03:50Q allele discovered by next-generation sequencing in a Korean family.

DQA1*03:50Q differs from DQA1*03:02:01:01 by a three-nucleotide insertion at gDNA position 3968 in exon 2.

The novel HLA-DQA1*03:01:12 allele identified using next-generation sequencing in a Melanesian individual.

HLA-DQA1*03:01:12 differs from HLA-DQA1*03:01:01:01 by one nucleotide substitution in codon 21 in exon 2.

HLA-DQA1*05 Was Not Associated With Primary Nonresponse or Loss of Response to First Anti-TNF in Real-World Inflammatory Bowel Disease Patients.

BACKGROUND: We lack predictors of response to biologics in the management of patients with inflammatory bowel disease (IBD). A recent study has shown a significant association between HLA-DQA1*05 carriers and the development of loss of response to anti-tumor necrosis factor (TNF) mediated by immunogenicity. METHODS: Retrospective single-center cohort study including IBD patients who had received anti-TNF therapy as a first biologic and whose HLA-DQA1*05 had been determined. Primary nonresponse and secondary failure (assessed by survival analysis) have been evaluated as well as safety outcomes. RESULTS: A total of 199 IBD patients (161 [81%] with Crohn's disease and 38 [19%] with ulcerative colitis) were included. A total of 42.4% were HLA-DQA1*05 carriers and 60% received combination therapy at the start of anti-TNF treatment. Median follow-up was 24 (interquartile range, 11-66) months. No statistically significant differences were found in primary nonresponse to anti-TNF (89.3% vs 87.8%; P = .825), depending on HLA carriers and noncarriers. No differences in secondary loss of response according to HLA variant in any of the analyses performed (full cohort, according to IBD or anti-TNF type) were observed. Again, no differences were observed in patients treated with combination therapy. In terms of safety, no significant differences were found in the rate of infusion reactions or serious adverse events. CONCLUSION: In our real-life cohort of IBD patients treated for the first time with anti-TNF, being an HLA-DQA1*05 carrier did not act as a predictor of response failure, either primary or secondary. The safety of anti-TNF treatment has also not been influenced by the variant.

The HLA variant DQA1*05 has been identified as a risk factor for the development of antibodies to anti-tumor necrosis factor drugs. We observed that its presence has no impact on clinical outcomes, such as secondary loss of response. These data suggest that caution is required before making decisions based on this HLA variant.

Bullous Pemphigoid and Human Leukocyte Antigen (HLA)-DQA1: A Systematic Review.

Bullous pemphigoid (BP) is an autoimmune blistering disease that mainly affects the elderly. The human leukocyte antigen (HLA) system is believed to be one of the genetic factors involved in the development of BP. The connection between major histocompatibility complex class II, specifically HLA-DQA1, and BP remains inconclusive. The objective of this review is to find potential associations between BP and HLA-DQA1 alleles, identify the HLA-DQA1 alleles associated with an increased or decreased risk of developing BP, and highlight literature gaps for future research. The Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) guidelines were used to conduct a literature review. Databases used included PubMed/MEDLINE, Google Scholar, Embase, and Cochrane Library. Only studies written in English and conducted after 2000 that investigated the association between HLA-DQA1 and BP in human subjects were included. Odds ratios were calculated from the data provided in the studies, and a meta-analysis was conducted using Review Manager (The Cochrane Collaboration, London, United Kingdom) and MetaXL (EpiGear International Pty Ltd., Queensland, Australia) software. The systematic review found five eligible studies, and all were included in the meta-analysis. Results show an increased odds for BP in the HLA-DQA1*05:05 loci (odds ratio (OR) = 2.25; 95% confidence interval (CI) = 1.80, 2.80) and decreased odds for BP in the HLA-DQA1*02:01 loci (OR = 0.50; 95% CI = 0.36, 0.70). Further research is needed to confirm these findings and explore the potential clinical implications for personalized medicine approaches in BP patients.

Identification of the novel HLA-DQA1*05:75 allele by next-generation sequencing in a Korean cord blood donor.

HLA-DQA1*05:75 differs from DQA1*05:05:01:01 by a single substitution at nucleotide 701 (G/A) in exon 4.

Characterization of the first HLA-DQA1 allele with Aspartic Acid in the transmembrane domain, HLA-DQA1*05:71.

HLA-DQA1*05:71, the first HLA-DQA1 allele with Aspartic Acid at residue 208 in the transmembrane domain.

Characterization of the novel HLA-DQA1*01:64:02 allele by sequencing-based typing.

HLA-DQA1*01:64:02 differs from HLA-DQA1*01:64:01 by one nucleotide substitution in codon 123 in exon 3.

Identification of four novel HLA-DQ alleles, HLA-DQA1*01:106, -DQA1*01:107, -DQA1*05:74 and -DQB1*05:01:48.

Characterization of new alleles, three HLA-DQA1 and one HLA-DQB1, bearing non-synonymous and synonymous mutations, respectively.