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Voorter CEM, Groeneweg M, Olieslagers TI, Fae I, Fischer GF, Andreani M, Troiano M, Vidan-Jeras B, Montanic S, Hepkema BG, Bungener LB, Tilanus MGJ, Wieten L. Resolving unknown nucleotides in the IPD-IMGT/HLA database by extended and full-length sequencing of HLA class I and II alleles. Immunogenetics 2024; 76:109-121. [PMID: 38400869 PMCID: PMC10944811 DOI: 10.1007/s00251-024-01333-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Accepted: 01/16/2024] [Indexed: 02/26/2024]
Abstract
In the past, identification of HLA alleles was limited to sequencing the region of the gene coding for the peptide binding groove, resulting in a lack of sequence information in the HLA database, challenging HLA allele assignment software programs. We investigated full-length sequences of 19 HLA class I and 7 HLA class II alleles, and we extended another 47 HLA class I alleles with sequences of 5' and 3' UTR regions that were all not yet available in the IPD-IMGT/HLA database. We resolved 8638 unknown nucleotides in the coding sequence of HLA class I and 2139 of HLA class II. Furthermore, with full-length sequencing of the 26 alleles, more than 90 kb of sequence information was added to the non-coding sequences, whereas extension of the 47 alleles resulted in the addition of 5.5 kb unknown nucleotides to the 5' UTR and > 31.7 kb to the 3' UTR region. With this information, some interesting features were observed, like possible recombination events and lineage evolutionary origins. The continuing increase in the availability of full-length sequences in the HLA database will enable the identification of the evolutionary origin and will help the community to improve the alignment and assignment accuracy of HLA alleles.
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Affiliation(s)
- Christina E M Voorter
- Department of Transplantation Immunology, Maastricht University Medical Center, P.O. Box 5800, 6202 AZ, Maastricht, The Netherlands.
- GROW School for Oncology and Reproduction, Maastricht University, Maastricht, The Netherlands.
| | - Mathijs Groeneweg
- Department of Transplantation Immunology, Maastricht University Medical Center, P.O. Box 5800, 6202 AZ, Maastricht, The Netherlands
- GROW School for Oncology and Reproduction, Maastricht University, Maastricht, The Netherlands
| | - Timo I Olieslagers
- Department of Transplantation Immunology, Maastricht University Medical Center, P.O. Box 5800, 6202 AZ, Maastricht, The Netherlands
- GROW School for Oncology and Reproduction, Maastricht University, Maastricht, The Netherlands
| | - Ingrid Fae
- Department for Transfusion Medicine and Cell Therapy, Medical University Vienna, Vienna, Austria
| | - Gottfried F Fischer
- Department for Transfusion Medicine and Cell Therapy, Medical University Vienna, Vienna, Austria
| | - Marco Andreani
- Laboratorio di Immunogenetica dei Trapianti, Dipartimento di Oncoematologia, Ospedale Pediatrico Bambino Gesù, Rome, Italy
| | - Maria Troiano
- Laboratorio di Immunogenetica dei Trapianti, Dipartimento di Oncoematologia, Ospedale Pediatrico Bambino Gesù, Rome, Italy
| | - Blanka Vidan-Jeras
- Tissue Typing Center, Blood Transfusion Centre of Slovenia, Ljubljana, Slovenia
| | - Sendi Montanic
- Tissue Typing Center, Blood Transfusion Centre of Slovenia, Ljubljana, Slovenia
| | - Bouke G Hepkema
- Transplantation Immunology, Department of Laboratory Medicine, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Laura B Bungener
- Transplantation Immunology, Department of Laboratory Medicine, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Marcel G J Tilanus
- Department of Transplantation Immunology, Maastricht University Medical Center, P.O. Box 5800, 6202 AZ, Maastricht, The Netherlands
- GROW School for Oncology and Reproduction, Maastricht University, Maastricht, The Netherlands
| | - Lotte Wieten
- Department of Transplantation Immunology, Maastricht University Medical Center, P.O. Box 5800, 6202 AZ, Maastricht, The Netherlands
- GROW School for Oncology and Reproduction, Maastricht University, Maastricht, The Netherlands
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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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Adamek M, Klages C, Bauer M, Kudlek E, Drechsler A, Leuser B, Scherer S, Opelz G, Tran TH. Seven novel HLA alleles reflect different mechanisms involved in the evolution of HLA diversity: description of the new alleles and review of the literature. Hum Immunol 2014; 76:30-5. [PMID: 25500251 DOI: 10.1016/j.humimm.2014.12.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Revised: 05/22/2014] [Accepted: 12/03/2014] [Indexed: 10/24/2022]
Abstract
The human leukocyte antigen (HLA) loci are among the most polymorphic genes in the human genome. The diversity of these genes is thought to be generated by different mechanisms including point mutation, gene conversion and crossing-over. During routine HLA typing, we discovered seven novel HLA alleles which were probably generated by different evolutionary mechanisms. HLA-B*41:21, HLA-DQB1*02:10 and HLA-DQA1*01:12 likely emerged from the common alleles of their groups by point mutations, all of which caused non-synonymous amino acid substitutions. In contrast, a deletion of one nucleotide leading to a frame shift with subsequent generation of a stop codon is responsible for the appearance of a null allele, HLA-A*01:123N. Whereas HLA-B*35:231 and HLA-B*53:31 were probably products of intralocus gene conversion between HLA-B alleles, HLA-C*07:294 presumably evolved by interlocus gene conversion between an HLA-C and an HLA-B allele. Our analysis of these novel alleles illustrates the different mechanisms which may have contributed to the evolution of HLA polymorphism.
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Affiliation(s)
- Martina Adamek
- Department of Transplantation Immunology, Institute of Immunology, University of Heidelberg, Heidelberg, Germany
| | - Cornelia Klages
- Department of Transplantation Immunology, Institute of Immunology, University of Heidelberg, Heidelberg, Germany
| | - Manuela Bauer
- Department of Transplantation Immunology, Institute of Immunology, University of Heidelberg, Heidelberg, Germany
| | - Evelina Kudlek
- Department of Transplantation Immunology, Institute of Immunology, University of Heidelberg, Heidelberg, Germany
| | - Alina Drechsler
- Department of Transplantation Immunology, Institute of Immunology, University of Heidelberg, Heidelberg, Germany
| | - Birte Leuser
- Department of Transplantation Immunology, Institute of Immunology, University of Heidelberg, Heidelberg, Germany
| | - Sabine Scherer
- Department of Transplantation Immunology, Institute of Immunology, University of Heidelberg, Heidelberg, Germany
| | - Gerhard Opelz
- Department of Transplantation Immunology, Institute of Immunology, University of Heidelberg, Heidelberg, Germany
| | - Thuong Hien Tran
- Department of Transplantation Immunology, Institute of Immunology, University of Heidelberg, Heidelberg, Germany.
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Street J, Johnson J, Pepperall J, Darke C. HLA-A*26:92-a further allele possessing a segment of A*02:01:01:01. ACTA ACUST UNITED AC 2014; 82:429-30. [PMID: 24499001 DOI: 10.1111/tan.12220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2013] [Revised: 08/27/2013] [Accepted: 09/13/2013] [Indexed: 10/26/2022]
Affiliation(s)
- J Street
- Welsh Transplantation and Immunogenetics Laboratory, Welsh Blood Service, Pontyclun, UK
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Fabreti-Oliveira RA, Santos MA, Oliveira CKF, Vale EMG, Vilela B, Nascimento E. Description of five novel HLA-B alleles,B*07:184, B*41:27, B*42:19, B*50:32 and B*57:63,identified in Brazilian individuals. Int J Immunogenet 2014; 41:264-6. [DOI: 10.1111/iji.12110] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2013] [Revised: 12/20/2013] [Accepted: 01/05/2014] [Indexed: 12/31/2022]
Affiliation(s)
- R. A. Fabreti-Oliveira
- Departamento de Bioquímica e Imunologia; Instituto de Ciências Biológicas; Universidade Federal de Minas Gerais; Belo Horizonte Brasil
- Departamento da Ciência da Computação; Instituto de Ciências Exatas; Universidade Federal de Minas Gerais; Belo Horizonte Brasil
- IMUNOLAB-Laboratório de Histocompatibilidade; Imunogenética e Imunologia de Transplantes; Belo Horizonte Brasil
| | - M. A. Santos
- Departamento da Ciência da Computação; Instituto de Ciências Exatas; Universidade Federal de Minas Gerais; Belo Horizonte Brasil
| | - C. K. F. Oliveira
- IMUNOLAB-Laboratório de Histocompatibilidade; Imunogenética e Imunologia de Transplantes; Belo Horizonte Brasil
| | - E. M. G. Vale
- IMUNOLAB-Laboratório de Histocompatibilidade; Imunogenética e Imunologia de Transplantes; Belo Horizonte Brasil
| | - B. Vilela
- IMUNOLAB-Laboratório de Histocompatibilidade; Imunogenética e Imunologia de Transplantes; Belo Horizonte Brasil
| | - E. Nascimento
- IMUNOLAB-Laboratório de Histocompatibilidade; Imunogenética e Imunologia de Transplantes; Belo Horizonte Brasil
- Instituto de Ensino; Pesquisas e Clínica de Transplantes do Hospital Santa Casa de Belo Horizonte; Belo Horizonte Brasil
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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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Affiliation(s)
- Steven G E Marsh
- Anthony Nolan Research Institute, Royal Free Hospital, Pond Street, London NW3 2QG, UK.
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Klitz W, Hedrick P, Louis EJ. New reservoirs of HLA alleles: pools of rare variants enhance immune defense. Trends Genet 2012; 28:480-6. [PMID: 22867968 DOI: 10.1016/j.tig.2012.06.007] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2012] [Revised: 06/15/2012] [Accepted: 06/22/2012] [Indexed: 11/16/2022]
Abstract
Highly polymorphic exons of the major histocompatibility complex (MHC, or HLA in humans) encode critical amino acids that bind foreign peptides. Recognition of the peptide-MHC complexes by T cells initiates the adaptive immune response. The particular structure of these exons facilitates gene conversion(GC) events, leading to the generation of new alleles. Estimates for allele creation and loss indicate that more than 10000 such alleles are circulating at low frequencies in human populations. Empirical sampling has affirmed this expectation. This suggests that the MHC loci have a system for moving valuable and often complex variants into adaptive service. Here, we argue that HLA loci carry many new mutant alleles prepared to assume epidemiologically meaningful roles when called on by selection provoked by exposure to new and evolving pathogens. Because new mutant alleles appear in a population at the lowest possible frequency (i.e., a single copy), they have typically been thought of as having little consequence. However, this large population of rare yet potentially valuable new alleles may contribute to pathogen defense.
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Affiliation(s)
- William Klitz
- School of Public Health, University of California, Berkeley, CA, USA.
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Marsh SGE. Nomenclature for factors of the HLA system, update December 2011*. Int J Immunogenet 2012. [DOI: 10.1111/j.1744-313x.2012.01100.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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10
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Marsh SG. Nomenclature for factors of the HLA system, update December 2011. Hum Immunol 2012. [DOI: 10.1016/j.humimm.2012.01.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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