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Sarri CA, Giannoulis T, Moutou KA, Mamuris Z. HLA class II peptide-binding-region analysis reveals funneling of polymorphism in action. Immunol Lett 2021; 238:75-95. [PMID: 34329645 DOI: 10.1016/j.imlet.2021.07.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 07/05/2021] [Accepted: 07/17/2021] [Indexed: 01/24/2023]
Abstract
BACKGROUND HLA-class II proteins hold important roles in key physiological processes. The purpose of this study was to compile all class II alleles reported in human population and investigate patterns in pocket variants and their combinations, focusing on the peptide-binding region (PBR). METHODS For this purpose, all protein sequences of DPA1, DQA1, DPB1, DQB1 and DRB1 were selected and filtered, in order to have full PBR sequences. Proportional representation was used for pocket variants while population data were also used. RESULTS All pocket variants and PBR sequences were retrieved and analyzed based on the preference of amino acids and their properties in all pocket positions. The observed number of pocket variants combinations was much lower than the possible inferred, suggesting that PBR formation is under strict funneling. Also, although class II proteins are very polymorphic, in the majority of the reported alleles in all populations, a significantly less polymorphic pocket core was found. CONCLUSIONS Pocket variability of five HLA class II proteins was studied revealing favorable properties of each protein. The actual PBR sequences of HLA class II proteins appear to be governed by restrictions that lead to the establishment of only a fraction of the possible combinations and the polymorphism recorded is the result of intense funneling based on function.
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Affiliation(s)
- Constantina A Sarri
- Department of Biochemistry and Biotechnology, Laboratory of Genetics, Comparative and Evolutionary Biology, University of Thessaly, Viopolis, Mezourlo, 41500, Larisa, Greece
| | - Themistoklis Giannoulis
- Department of Biochemistry and Biotechnology, Laboratory of Genetics, Comparative and Evolutionary Biology, University of Thessaly, Viopolis, Mezourlo, 41500, Larisa, Greece; Department of Animal Science, University of Thessaly, Trikallon 224, 43100 Karditsa, Greece
| | - Katerina A Moutou
- Department of Biochemistry and Biotechnology, Laboratory of Genetics, Comparative and Evolutionary Biology, University of Thessaly, Viopolis, Mezourlo, 41500, Larisa, Greece
| | - Zissis Mamuris
- Department of Biochemistry and Biotechnology, Laboratory of Genetics, Comparative and Evolutionary Biology, University of Thessaly, Viopolis, Mezourlo, 41500, Larisa, Greece.
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Street J, Darke C. Epitopes and motifs of the HLA-B*14 allele family products and related HLA-B14 cross-reactive specificities. Int J Immunogenet 2017; 44:225-233. [PMID: 28691368 DOI: 10.1111/iji.12328] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 03/29/2017] [Accepted: 05/31/2017] [Indexed: 11/29/2022]
Abstract
The split specificities of HLA-B14 (B64, B65) are assigned to the B*14:01 (B64) and B*14:02 (B65) products only. Of the further 50 B*14 expressed products, only B*14:03 and B*14:06 are officially designated as HLA-B14. The B*14:08 product differs from B64 by a single amino acid substitution of W97R, while the B*14:53 specificity (which is a "short" B14 and neither B64 nor B65) differs from B64 by three residues (W97S, Y113H and F116Y). Comprehensive testing of B*14:08:01 cells (using 49 alloantisera with B64 or B64, B65 specificities, and five monoclonal antibodies with B65 or B64, B65 activity) showed that the B*14:08 specificity is, like the B*14:53 product, neither B64 nor B65 and appears as a "short" B14 specificity. To help understand the serological reactivity of the B*14:08 and B*14:53 products, and B64 and B65, we identified seven published epitopes (11AV, 97W, 61ICT, 116F, 131S+163T, 170RH and 420) and, by inspection, 29 motifs, that encompass one or more of B64, B65 and various HLA-B14 cross-reactive group specificities. We then considered the possession of these epitopes and motifs by the products of B*14:01 to B*14:06, B*14:08 and B*14:53. Seventeen of the 29 motifs fully complied with the one-/two-patch functional epitope concept for amino acid proximity, as determined by Cn3D software, the remainder partially complied. The nature and patterns of epitopes and motifs possessed by both B*14:08 and B*14:53 specificities supported their designation as HLA-B14 but non-B64/B65. Also that epitope 97W, with 11S or 11A, is critical for serological B64 and B65 reactivity. And conversely, that epitope 116F, and several identified motifs, are probably unimportant for HLA-B14 antibody reactivity. The previous submission that the B*14:03 specificity is HLA-B65 was compatible with its epitope/motif pattern. B*14:04 cells would also be expected to react as B65, based on its epitope/motif pattern, and not as B64 as previously implied. Also, from their epitope/motif patterns, and external serological information, it is probable that the B*14:05 and B*14:06 specificities will both appear as "short" HLA-B14, non-B64/B65. Several epitopes and motifs encompassed a range of HLA-B specificities included in the serological HLA-B14 cross-reactive group, thus supporting these original serological findings.
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Affiliation(s)
- J Street
- Welsh Transplantation and Immunogenetics, Laboratory Welsh Blood Service, Pontyclun, Wales, UK
| | - C Darke
- Welsh Transplantation and Immunogenetics, Laboratory Welsh Blood Service, Pontyclun, Wales, UK
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Zhang C, Wang Y, Huang C, Zhang M, Chen C, Cao H, Chai X, Li J. Characterization of 27 novel HLA class II alleles from China Marrow Donor Program. ACTA ACUST UNITED AC 2013; 82:201-2. [DOI: 10.1111/tan.12167] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Revised: 05/23/2013] [Accepted: 06/18/2013] [Indexed: 11/28/2022]
Affiliation(s)
| | | | | | | | | | | | | | - Jian Li
- BGI-Shenzhen; Shenzhen; China
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Yang KL, Lee SK, Kao RH, Lin PY. Discovery of the novel HLA-DRB1*10:04 allele in a Taiwanese volunteer bone marrow donor and identification of the probable HLA-A, -B, -C and -DRB1 haplotype in association with DRB1*10:04. Int J Immunogenet 2013; 39:448-50. [PMID: 23115788 DOI: 10.1111/j.1744-313x.2012.01106.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
We report here a novel variant of HLA-DRB1*10, DRB1*10:04, discovered in a Taiwanese volunteer bone marrow donor by a sequence-based typing (SBT) method. The DNA sequence of DRB1*10:04 differs from DRB1*10:01:01, in exon 2, at nucleotide positions 296 (G fi A) and 303 (T fi G). The nucleotide changes caused an amino acid substitution at amino acid residue 70 (R fi Q). We hypothesize that the formation of DRB1*10:04 was probably the result of a gene recombination event where DRB1*10:01:01 received a minimum length of DNA sequence from DRB1*04:05:01, as the sequence of DRB1*10:04 is identical to DRB1*10:01:01 in exon 2 except the sequence from nucleotide 296 to nucleotide 303, which is identical to DRB1*04:05:01. The plausible HLA-A, -B, -C and - DRB1 haplotypes in association with DRB1*10:04 was deduced as A*01:01-B*37:01-C*06:02-DRB1*10:04.
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Affiliation(s)
- K L Yang
- Laboratory of Immunogenetics and Cord Blood Bank, Buddhist Tzu Chi Stem Cells Centre and Marrow Donor Registry, Buddhist Tzu Chi General Hospital, Buddhist Compassion Relief Tzu Chi Foundation, Hualien, Taiwan.
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Li J, Qu J, Zhang X, Zhang C, Liu Y, Cao H, Zhang W, Wang Y, Chen H, Chen G, Zheng Z, Shen M, Cheng Z, Tang J, Zhen H, Liao K, Chen C, Yang H, Tian Z, Zhang H, Hua S, Rao B, Wang N, Zhang Q, Liu T, Chen S, Wang L, Yi X. Characterization of 236 novel alleles at the HLA-A, -B, -C, -DRB1, -DQB1 and -DPB1 loci from China Marrow Donor Program. ACTA ACUST UNITED AC 2011; 78:267-70. [PMID: 21732917 DOI: 10.1111/j.1399-0039.2011.01731.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Two hundred and thirty-six novel human leukocyte antigen (HLA) alleles are described from volunteer donors of the China Marrow Donor Program: 71 HLA-A alleles, 79 HLA-B alleles, 43 HLA-C, 16 HLA-DRB1 alleles, 26 HLA-DQB1 and 1 HLA-DPB1. Two hundred and thirteen (90.3%) of the 236 novel alleles are single nucleotide substitution variants when compared with their most homologous allele. Seventy-eight of these single nucleotide variants are silent substitutions. The remaining novel alleles differ from their most similar allele by two to four nucleotide substitutions. Some of the novel alleles encode amino acid changes at positions not previously reported to be polymorphic, such as codons 57, 62, 67, 41 and 52 in HLA-A alleles; codons 133, 156, 201 and 215 in HLA-B alleles; codons 74, 208 and 225 in HLA-C; codons 25, 32 and 72 in HLA-DRB1; codons 20, 39 and 77 in HLA-DQB1.
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Affiliation(s)
- J Li
- Beijing Genomics Institute at Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen, China.
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Marsh SGE, Albert ED, Bodmer WF, Bontrop RE, Dupont B, Erlich HA, Fernández-Viña M, Geraghty DE, Holdsworth R, Hurley CK, Lau M, Lee KW, Mach B, Maiers M, Mayr WR, Müller CR, Parham P, Petersdorf EW, Sasazuki T, Strominger JL, Svejgaard A, Terasaki PI, Tiercy JM, Trowsdale J. Nomenclature for factors of the HLA system, 2010. TISSUE ANTIGENS 2010. [PMID: 20356336 DOI: 10.1111/j.1399‐0039.2010.01466.x] [Citation(s) in RCA: 144] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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Marsh SGE, Albert ED, Bodmer WF, Bontrop RE, Dupont B, Erlich HA, Fernández-Viña M, Geraghty DE, Holdsworth R, Hurley CK, Lau M, Lee KW, Mach B, Maiers M, Mayr WR, Müller CR, Parham P, Petersdorf EW, Sasazuki T, Strominger JL, Svejgaard A, Terasaki PI, Tiercy JM, Trowsdale J. Nomenclature for factors of the HLA system, 2010. TISSUE ANTIGENS 2010; 75:291-455. [PMID: 20356336 PMCID: PMC2848993 DOI: 10.1111/j.1399-0039.2010.01466.x] [Citation(s) in RCA: 2933] [Impact Index Per Article: 209.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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Marsh SGE. Nomenclature for factors of the HLA system, March 2009 update. Int J Immunogenet 2009. [DOI: 10.1111/j.1744-313x.2009.00852.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Skrablin PS, Brixner V, Richter R, Boehme A, Seifried E, Seidl C. Confirmation of allele HLA-A*3116 found in a family of a leukaemia patient with Caucasian and Caribbean origin. Int J Immunogenet 2009; 36:383-4. [PMID: 19703232 DOI: 10.1111/j.1744-313x.2009.00872.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We confirm allele HLA-A*3116 that we found in the family of a leukaemia patient of mixed Caucasian and Caribbean origin by sequence based typing. This allele is closest related to HLA-A*310102 with one nucleotide replacement at position 221 (C>T) leading to an amino acid substitution at position 50 of the mature protein from proline to leucine. As the amino acid at position 50 in the alpha 1 domain is part of the peptide-binding region, this change could be relevant for the functionality in peptide presentation.
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Affiliation(s)
- P S Skrablin
- German Red Cross Donor Service Baden-Wuerttemberg-Hessen, Institute for Transfusion Medicine and Immunohaematology, Frankfurt, Germany
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Marsh SGE. Nomenclature for factors of the HLA system, update March 2009. TISSUE ANTIGENS 2009; 74:183-186. [PMID: 19500312 DOI: 10.1111/j.1399-0039.2009.01288.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Affiliation(s)
- Steven G E Marsh
- Anthony Nolan Research Institute, Royal Free Hospital, Pond Street, London NW32QG, UK.
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Marsh SG. Nomenclature for factors of the HLA system, update March 2009. Hum Immunol 2009. [DOI: 10.1016/j.humimm.2009.04.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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