pHLA3D: Updating the database of predicted three-dimensional structures of HLA with HLA-DR, HLA-DQ and HLA-DP molecules

Characterization of the novel HLA-B*14:121 allele by sequencing-based typing

HLA-B*14:121 differs from HLA-B*14:01:01:01 by one nucleotide substitution in codon 319 in exon 6.

Characterization of the novel HLA-C*01:263 allele by sequencing-based typing

HLA-C*01:263 differs from HLA-C*01:02:01:01 by one nucleotide substitution in codon 98 in exon 3.

Characterization of the novel HLA-C*05:286 allele by sequencing-based typing

HLA-C*05:286 differs from HLA-C*05:01:01:02 by one nucleotide substitution in codon 283 in exon 5.

HLA class I peptide polymorphisms contribute to class II DQβ0603:DQα0103 antibody specificity

Antibodies reactive to human leukocyte antigens (HLA) represent a barrier for patients awaiting transplantation. Based on reactivity patterns in single-antigen bead (SAB) assays, various epitope matching algorithms have been proposed to improve transplant outcomes. However, some antibody reactivities cannot be explained by amino acid motifs, leading to uncertainty about their clinical relevance. Antibodies against the HLA class II molecule, DQβ0603:DQα0103, present in some candidates, represent one such example. Here, we show that peptides derived from amino acids 119-148 of the HLA class I heavy chain are bound to DQβ0603:DQα0103 proteins and contribute to antibody reactivity through an HLA-DM-dependent process. Moreover, antibody reactivity is impacted by the specific amino acid sequence presented. In summary, we demonstrate that polymorphic HLA class I peptides, bound to HLA class II proteins, can directly or indirectly be part of the antibody binding epitope. Our findings have potential important implications for the field of transplant immunology and for our understanding of adaptive immunity.

MHCSeqNet2-improved peptide-class I MHC binding prediction for alleles with low data

MOTIVATION

The binding of a peptide antigen to a Class I major histocompatibility complex (MHC) protein is part of a key process that lets the immune system recognize an infected cell or a cancer cell. This mechanism enabled the development of peptide-based vaccines that can activate the patient's immune response to treat cancers. Hence, the ability of accurately predict peptide-MHC binding is an essential component for prioritizing the best peptides for each patient. However, peptide-MHC binding experimental data for many MHC alleles are still lacking, which limited the accuracy of existing prediction models.

RESULTS

In this study, we presented an improved version of MHCSeqNet that utilized sub-word-level peptide features, a 3D structure embedding for MHC alleles, and an expanded training dataset to achieve better generalizability on MHC alleles with small amounts of data. Visualization of MHC allele embeddings confirms that the model was able to group alleles with similar binding specificity, including those with no peptide ligand in the training dataset. Furthermore, an external evaluation suggests that MHCSeqNet2 can improve the prioritization of T cell epitopes for MHC alleles with small amount of training data.

AVAILABILITY AND IMPLEMENTATION

The source code and installation instruction for MHCSeqNet2 are available at https://github.com/cmb-chula/MHCSeqNet2.

Characterization of the novel HLA-DPA1*01:159 allele by sequencing-based typing

HLA-DPA1*01:159 differs from HLA-DPA1*01:03:01:03 by one nucleotide substitution in codon 120 in exon 3.

Characterization of the novel HLA-DRB3*02:192 allele by sequencing-based typing

HLA-DRB3*02:192 differs from DRB3*02:02:01:02 by one nucleotide substitution in codon 204 in exon 4.

HLA3DB: comprehensive annotation of peptide/HLA complexes enables blind structure prediction of T cell epitopes

The class I proteins of the major histocompatibility complex (MHC-I) display epitopic peptides derived from endogenous proteins on the cell surface for immune surveillance. Accurate modeling of peptides bound to the human MHC, HLA, has been mired by conformational diversity of the central peptide residues, which are critical for recognition by T cell receptors. Here, analysis of X-ray crystal structures within our curated database (HLA3DB) shows that pHLA complexes encompassing multiple HLA allotypes present a discrete set of peptide backbone conformations. Leveraging these backbones, we employ a regression model trained on terms of a physically relevant energy function to develop a comparative modeling approach for nonamer pHLA structures named RepPred. Our method outperforms the top pHLA modeling approach by up to 19% in structural accuracy, and consistently predicts blind targets not included in our training set. Insights from our work may be applied towards predicting antigen immunogenicity, and receptor cross-reactivity.

Characterization of the novel HLA-DPA1*01:150 allele by sequencing-based typing

HLA-DPA1*01:150 differs from HLA-DPA1*01:03:01:05 by one nucleotide substitution in codon 190 in exon 4.

Characterization of the novel HLA-C*12:384 allele by sequencing-based typing

HLA-C*12:384 differs from HLA-C*12:03:01:02 by one nucleotide substitution in codon 42 in exon 2.

Characterization of the novel HLA-B*51:370 allele by sequencing-based typing

HLA-B*51:370 differs from HLA-B*51:01:01:04 by one nucleotide substitution in codon 276 in exon 5.

Characterization of the novel HLA-A*24:587 allele by sequencing-based typing

HLA-A*24:587 differs from HLA-A*24:02:01:01 by one nucleotide substitution in codon 220 in exon 4.

Characterization of the novel HLA-DPB1*1348:01 allele by sequencing-based typing

HLA-DPB1*1348:01 differs from HLA-DPB1*14:01:01:01 by one nucleotide substitution in codon 147 in exon 3.

Characterization of the novel HLA-B*08:302 allele by sequencing-based typing

HLA-B*08:302 differs from HLA-B*08:01:01:01 by one nucleotide substitution in codon 116 in exon 3.

Characterization of the novel HLA-DRB1*01:140 allele by sequencing-based typing

HLA-DRB1*01:140 differs from HLA-DRB1*01:02:01:01 by one nucleotide substitution in codon 147 in exon 3.

Characterization of the novel HLA-DQB1*02:197 allele by sequencing-based typing

HLA-DQB1*02:197 differs from HLA-DQB1*02:01:01:01 by one nucleotide substitution in codon 18 in exon 2. This article is protected by copyright. All rights reserved.

Characterization of the novel HLA-C*12:354 allele by sequencing-based typing

HLA-C*12:354 differs from HLA-C*12:03:01:01 by one nucleotide substitution in codon 240 in exon 4. This article is protected by copyright. All rights reserved.

Characterization of the novel HLA-A*24:564 allele by sequencing-based typing

HLA-A*24:564 differs from HLA-A*24:02:01:01 by one nucleotide substitution in codon 240 in exon 4. This article is protected by copyright. All rights reserved.

Characterization of the novel HLA-A*03:436 allele by sequencing-based typing

HLA-A*03:436 differs from HLA-A*03:01:01:05 by one nucleotide substitution in codon 26 in exon 2. This article is protected by copyright. All rights reserved.

Characterization of the novel HLA-DQA1*05:49 allele by sequencing-based typing

HLA-DQA1*05:49 differs from HLA-DQA1*05:01:01:02 by one nucleotide substitution in codon 78 in exon 2.

Characterization of the novel HLA-DRB4*01:151 allele by sequencing-based typing

HLA-DRB4*01:151 differs from DRB4*01:01:01:01 by one nucleotide substitution in codon 178 in exon 3.

Characterization of the novel HLA-B*57:146 allele by sequencing-based typing

HLA-B*57:146 differs from HLA-B*57:01:01:01 by one nucleotide substitution in codon 103 in exon 3.

Contribution of HLA class II genes, DRB4*01:01, DRB1*07:01, and DQB1*03:03:2 to clinical features of Vitiligo disease in Iranian population

BACKGROUND

Vitiligo is a multifactorial depigmentation condition, which is due to skin melanocyte destruction. Increased expression of HLA class II genes in patients with pre-lesions of Vitiligo suggests a crucial role for the participation of immune response in Vitiligo development. Recent studies progressively focused on HLA-DRB1 and DQB1 genes. In this study, we have evaluated the association and role of HLA-DRB4*01:01, -DRB1*07:01, and -DQB1*03:03:2 genes in different clinical subtypes of Vitiligo in the Iranian population.

METHODS

First, Genomic DNA from peripheral blood of 125 unrelated Vitiligo patients and 100 unrelated healthy controls were extracted through the salting-out method. Then, HLA class II genotyping was performed using the sequence-specific primer PCR method. Finally, the clinical relevance of the testing for these genotypes was evaluated by applying the PcPPV (prevalence-corrected positive predictive value) formula.

RESULTS

Our results indicated the positive associations of DRB4*01:01 and DRB1*07:01 allelic genes with early-onset Vitiligo (p = 0.024 and 0.022, respectively). DRB4*01:01 also showed strong protection against late-onset Vitiligo (p = 0.0016, RR = 0.360). Moreover, our data revealed that the DRB1*07:01 increases the susceptibility to Sporadic Vitiligo (p = 0.030, RR = 1.702). Furthermore, our findings proposed that elevated vulnerability of Vitiligo patients due to DRB4*01:01 and DRB1*07:01 alleles maybe is correlated with the presence of amino acid Arginine at position 71 at pocket 4 on the antigen-binding site of the HLA-DRB1 receptor.

CONCLUSION

Our findings on different subtypes of Vitiligo suggest that, despite a more apparent autoimmune involvement, a non-autoimmune nature for the etiology of Vitiligo should also be considered.

Characterization of the novel HLA-DPA1*01:61 allele by sequencing-based typing

HLA-DPA1*01:61 differs from HLA-DPA1*01:03:01:22 by one nucleotide substitution in codon 96 in exon 3.

Characterization of the novel HLA-C*15:241 allele by sequencing-based typing

HLA-C*15:241 differs from HLA-C*15:02:01:01 by one nucleotide substitution in codon 48 in exon 2.

Characterization of the novel HLA-A*36:12 allele by sequencing-based typing

HLA-A*36:12 differs from HLA-A*36:01:01:01 by one nucleotide substitution in codon 211 in exon 4.

Characterization of the novel HLA-DPA1*01:57 allele by sequencing-based typing

HLA-DPA1*01:57 differs from DPA1*01:03:01:01 by one nucleotide substitution in codon 13 in exon 2.

Characterization of the novel HLA-DRB1*11:282 allele by sequencing-based typing

HLA-DRB1*11:282 differs from HLA-DRB1*11:04:01:01 by one nucleotide substitution in codon 41 in exon 2.

Characterization of the novel HLA-A*01:367 allele by sequencing-based typing

HLA-A*01:367 differs from HLA-A*01:01:01:01 by one nucleotide substitution in codon 271 in exon 4.

Characterization of the novel HLA-DQA1*03:20 allele by sequencing-based typing

HLA-DQA1*03:20 differs from HLA-DQA1*03:03:01:01 by one nucleotide substitution in codon 33 in exon 2.

Characterization of the novel HLA-DQB1*06:385 allele by sequencing-based typing

HLA-DQB1*06:385 differs from HLA-DQB1*06:07:01 by one nucleotide substitution in codon 70 in exon 2.

Characterization of the novel HLA-DPA1*01:44 allele by sequencing-based typing

HLA-DPA1*01:44 differs from DPA1*01:03:01:04 by one nucleotide substitution in codon 175 in exon 3.