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Pymm P, Saunders PM, Anand S, MacLachlan BJ, Faoro C, Hitchen C, Rossjohn J, Brooks AG, Vivian JP. The Structural Basis for Recognition of Human Leukocyte Antigen Class I Molecules by the Pan-HLA Antibody W6/32. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2024; 213:876-885. [PMID: 39093013 DOI: 10.4049/jimmunol.2400328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2024] [Accepted: 07/09/2024] [Indexed: 08/04/2024]
Abstract
The central immunological role of HLA class I (HLA-I) in presenting peptide Ags to cellular components of the immune system has been the focus of intense study for >60 y. A confounding factor in the study of HLA-I has been the extreme polymorphism of these molecules. The mAb W6/32 has been a fundamental reagent bypassing the issue of polymorphism by recognizing an epitope that is conserved across diverse HLA-I allotypes. However, despite the widespread use of W6/32, the epitope of this Ab has not been definitively mapped. In this study, we present the crystal structure of the Fab fragment of W6/32 in complex with peptide-HLA-B*27:05. W6/32 bound to HLA-B*27:05 beneath the Ag-binding groove, recognizing a discontinuous epitope comprised of the α1, α2, and α3 domains of HLA-I and β2-microglobulin. The epitope comprises a region of low polymorphism reflecting the pan-HLA-I nature of the binding. Notably, the W6/32 epitope neither overlaps the HLA-I binding sites of either T cell Ag receptors or killer cell Ig-like receptors. However, it does coincide with the binding sites for leukocyte Ig-like receptors and CD8 coreceptors. Consistent with this, the use of W6/32 to block the interaction of NK cells with HLA-I only weakly impaired inhibition mediated by KIR3DL1, but impacted HLA-LILR recognition.
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Affiliation(s)
- Phillip Pymm
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Philippa M Saunders
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, Victoria, Australia
| | - Sushma Anand
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Bruce J MacLachlan
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Camilla Faoro
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Corinne Hitchen
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Jamie Rossjohn
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria, Australia
- Institute of Infection and Immunity, Cardiff University, School of Medicine, Heath Park, Cardiff
| | - Andrew G Brooks
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, Victoria, Australia
| | - Julian P Vivian
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
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Shahbazy M, Ramarathinam SH, Li C, Illing PT, Faridi P, Croft NP, Purcell AW. MHCpLogics: an interactive machine learning-based tool for unsupervised data visualization and cluster analysis of immunopeptidomes. Brief Bioinform 2024; 25:bbae087. [PMID: 38487848 PMCID: PMC10940831 DOI: 10.1093/bib/bbae087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 12/12/2023] [Accepted: 02/15/2024] [Indexed: 03/18/2024] Open
Abstract
The major histocompatibility complex (MHC) encodes a range of immune response genes, including the human leukocyte antigens (HLAs) in humans. These molecules bind peptide antigens and present them on the cell surface for T cell recognition. The repertoires of peptides presented by HLA molecules are termed immunopeptidomes. The highly polymorphic nature of the genres that encode the HLA molecules confers allotype-specific differences in the sequences of bound ligands. Allotype-specific ligand preferences are often defined by peptide-binding motifs. Individuals express up to six classical class I HLA allotypes, which likely present peptides displaying different binding motifs. Such complex datasets make the deconvolution of immunopeptidomic data into allotype-specific contributions and further dissection of binding-specificities challenging. Herein, we developed MHCpLogics as an interactive machine learning-based tool for mining peptide-binding sequence motifs and visualization of immunopeptidome data across complex datasets. We showcase the functionalities of MHCpLogics by analyzing both in-house and published mono- and multi-allelic immunopeptidomics data. The visualization modalities of MHCpLogics allow users to inspect clustered sequences down to individual peptide components and to examine broader sequence patterns within multiple immunopeptidome datasets. MHCpLogics can deconvolute large immunopeptidome datasets enabling the interrogation of clusters for the segregation of allotype-specific peptide sequence motifs, identification of sub-peptidome motifs, and the exportation of clustered peptide sequence lists. The tool facilitates rapid inspection of immunopeptidomes as a resource for the immunology and vaccine communities. MHCpLogics is a standalone application available via an executable installation at: https://github.com/PurcellLab/MHCpLogics.
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Affiliation(s)
- Mohammad Shahbazy
- Department of Biochemistry and Molecular Biology and Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Melbourne, VIC 3800, Australia
| | - Sri H Ramarathinam
- Department of Biochemistry and Molecular Biology and Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Melbourne, VIC 3800, Australia
| | - Chen Li
- Department of Biochemistry and Molecular Biology and Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Melbourne, VIC 3800, Australia
| | - Patricia T Illing
- Department of Biochemistry and Molecular Biology and Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Melbourne, VIC 3800, Australia
| | - Pouya Faridi
- Centre for Cancer Research, Hudson Institute of Medical Research, Clayton, VIC 3168, Australia
- Monash Proteomics and Metabolomics Platform, Department of Medicine, School of Clinical Sciences, Monash University, Clayton, VIC 3800, Australia
| | - Nathan P Croft
- Department of Biochemistry and Molecular Biology and Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Melbourne, VIC 3800, Australia
| | - Anthony W Purcell
- Department of Biochemistry and Molecular Biology and Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Melbourne, VIC 3800, Australia
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Niño Ramírez JE, Gil-Etayo FJ, Jiménez Hernaz I, García Sanz R, Tejeda Velarde A. The novel HLA-DQB1*03:02:01:14 allele was possibly generated by a recombination event. HLA 2023. [PMID: 37127400 DOI: 10.1111/tan.15051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 03/23/2023] [Accepted: 03/24/2023] [Indexed: 05/03/2023]
Abstract
The novel HLA-DQB1*03:02:01:14 was likely generated by a recombination event between DQB1*03:02:01:01 and DQB1*03:03:02:01.
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Affiliation(s)
- Jairo Eduardo Niño Ramírez
- Laboratorio de HLA-Biología Molecular, Servicio de Hematología, Hospital Universitario de Salamanca, Salamanca, Spain
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain
- Universidad de Salamanca (USAL), Salamanca, Spain
| | - Francisco Javier Gil-Etayo
- Laboratorio de HLA-Biología Molecular, Servicio de Hematología, Hospital Universitario de Salamanca, Salamanca, Spain
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain
| | - Isabel Jiménez Hernaz
- Laboratorio de HLA-Biología Molecular, Servicio de Hematología, Hospital Universitario de Salamanca, Salamanca, Spain
| | - Ramón García Sanz
- Laboratorio de HLA-Biología Molecular, Servicio de Hematología, Hospital Universitario de Salamanca, Salamanca, Spain
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain
- Universidad de Salamanca (USAL), Salamanca, Spain
- Centro de Investigación del Cáncer (CIC), Salamanca, Spain
- Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Madrid, Spain
| | - Amalia Tejeda Velarde
- Laboratorio de HLA-Biología Molecular, Servicio de Hematología, Hospital Universitario de Salamanca, Salamanca, Spain
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain
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Uncovering novel MHC alleles from RNA-Seq data: expanding the spectrum of MHC class I alleles in sheep. BMC Genom Data 2023; 24:1. [PMID: 36597020 PMCID: PMC9809118 DOI: 10.1186/s12863-022-01102-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 12/20/2022] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Major histocompatibility complex (MHC) class I glycoproteins present selected peptides or antigens to CD8 + T cells that control the cytotoxic immune response. The MHC class I genes are among the most polymorphic loci in the vertebrate genome, with more than twenty thousand alleles known in humans. In sheep, only a very small number of alleles have been described to date, making the development of genotyping systems or functional studies difficult. A cost-effective way to identify new alleles could be to use already available RNA-Seq data from sheep. Current strategies for aligning RNA-Seq reads against annotated genome sequences or transcriptomes fail to detect the majority of class I alleles. Here, I combine the alignment of RNA-Seq reads against a specific reference database with de novo assembly to identify alleles. The method allows the comprehensive discovery of novel MHC class I alleles from RNA-Seq data (DinoMfRS). RESULTS Using DinoMfRS, virtually all expressed MHC class I alleles could be determined. From 18 animals 75 MHC class I alleles were identified, of which 69 were novel. In addition, it was shown that DinoMfRS can be used to improve the annotation of MHC genes in the sheep genome sequence. CONCLUSIONS DinoMfRS allows for the first time the annotation of unknown, more divergent MHC alleles from RNA-Seq data. Successful application to RNA-Seq data from 16 animals has approximately doubled the number of known alleles in sheep. By using existing data, alleles can now be determined very inexpensively for populations that have not been well studied. In addition, MHC expression studies or evolutionary studies, for example, can be greatly improved in this way, and the method should be applicable to a broader spectrum of other multigene families or highly polymorphic genes.
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Arnaiz-Villena A, Suarez-Trujillo F, Juarez I, Rodríguez-Sainz C, Palacio-Gruber J, Vaquero-Yuste C, Molina-Alejandre M, Fernández-Cruz E, Martin-Villa JM. Evolution and molecular interactions of major histocompatibility complex (MHC)-G, -E and -F genes. Cell Mol Life Sci 2022; 79:464. [PMID: 35925520 PMCID: PMC9352621 DOI: 10.1007/s00018-022-04491-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 07/12/2022] [Accepted: 07/15/2022] [Indexed: 11/30/2022]
Abstract
Classical HLA (Human Leukocyte Antigen) is the Major Histocompatibility Complex (MHC) in man. HLA genes and disease association has been studied at least since 1967 and no firm pathogenic mechanisms have been established yet. HLA-G immune modulation gene (and also -E and -F) are starting the same arduous way: statistics and allele association are the trending subjects with the same few results obtained by HLA classical genes, i.e., no pathogenesis may be discovered after many years of a great amount of researchers’ effort. Thus, we believe that it is necessary to follow different research methodologies: (1) to approach this problem, based on how evolution has worked maintaining together a cluster of immune-related genes (the MHC) in a relatively short chromosome area since amniotes to human at least, i.e., immune regulatory genes (MHC-G, -E and -F), adaptive immune classical class I and II genes, non-adaptive immune genes like (C2, C4 and Bf) (2); in addition to using new in vitro models which explain pathogenetics of HLA and disease associations. In fact, this evolution may be quite reliably studied during about 40 million years by analyzing the evolution of MHC-G, -E, -F, and their receptors (KIR—killer-cell immunoglobulin-like receptor, NKG2—natural killer group 2-, or TCR-T-cell receptor—among others) in the primate evolutionary lineage, where orthology of these molecules is apparently established, although cladistic studies show that MHC-G and MHC-B genes are the ancestral class I genes, and that New World apes MHC-G is paralogous and not orthologous to all other apes and man MHC-G genes. In the present review, we outline past and possible future research topics: co-evolution of adaptive MHC classical (class I and II), non-adaptive (i.e., complement) and modulation (i.e., non-classical class I) immune genes may imply that the study of full or part of MHC haplotypes involving several loci/alleles instead of single alleles is important for uncovering HLA and disease pathogenesis. It would mainly apply to starting research on HLA-G extended haplotypes and disease association and not only using single HLA-G genetic markers.
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Affiliation(s)
- Antonio Arnaiz-Villena
- Departamento de Inmunología, Facultad de Medicina, Universidad Complutense de Madrid, Pabellón 5, planta 4. Avda. Complutense s/n, 28040, Madrid, Spain.
| | - Fabio Suarez-Trujillo
- Departamento de Inmunología, Facultad de Medicina, Universidad Complutense de Madrid, Pabellón 5, planta 4. Avda. Complutense s/n, 28040, Madrid, Spain
| | - Ignacio Juarez
- Departamento de Inmunología, Facultad de Medicina, Universidad Complutense de Madrid, Pabellón 5, planta 4. Avda. Complutense s/n, 28040, Madrid, Spain
| | - Carmen Rodríguez-Sainz
- Instituto de Investigaciones Sanitarias Gregorio Marañón, Hospital Gregorio Marañón, Madrid, Spain
| | - José Palacio-Gruber
- Departamento de Inmunología, Facultad de Medicina, Universidad Complutense de Madrid, Pabellón 5, planta 4. Avda. Complutense s/n, 28040, Madrid, Spain
| | - Christian Vaquero-Yuste
- Departamento de Inmunología, Facultad de Medicina, Universidad Complutense de Madrid, Pabellón 5, planta 4. Avda. Complutense s/n, 28040, Madrid, Spain
| | - Marta Molina-Alejandre
- Departamento de Inmunología, Facultad de Medicina, Universidad Complutense de Madrid, Pabellón 5, planta 4. Avda. Complutense s/n, 28040, Madrid, Spain
| | - Eduardo Fernández-Cruz
- Instituto de Investigaciones Sanitarias Gregorio Marañón, Hospital Gregorio Marañón, Madrid, Spain
| | - José Manuel Martin-Villa
- Departamento de Inmunología, Facultad de Medicina, Universidad Complutense de Madrid, Pabellón 5, planta 4. Avda. Complutense s/n, 28040, Madrid, Spain
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6
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Zhang LQ, Rozemuller E, Wang D, Liu XJ, Cai JP. Characterization of a novel HLA-A*11:335 allele resulting from a rare interlocus recombination involving HLA-A*11:01:01:01/126 and HLA-H*02:07/14/18 alleles with nanopore sequencing, in a volunteer from the China Marrow Donor Program. BMC Med Genomics 2022; 15:58. [PMID: 35296321 PMCID: PMC8925214 DOI: 10.1186/s12920-022-01176-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Accepted: 02/03/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The major histocompatibility complex (MHC) in humans includes three classical class I loci (A, B, and C), which are important biomarkers for the transplantation of organs and hematopoietic stem cells. In the MHC, polymorphism is known to be extremely high while interlocus recombination is rare. We report a rare interlocus recombination between HLA-A and HLA-H, which was analyzed using next generation sequencing and nanopore sequencing. METHODS In the sample, the genotypes of HLA-A, B, C, DRB1, and DQB1 were firstly determined using the methods of sequence-specific primer, sequence-specific oligonucleotide, Sanger's sequencing, and NGS; however, HLA-A could not be phased. Nanopore sequencing was finally utilized to distinguish the sequence of the novel allele. RESULTS Finally, the novel HLA-A*11:335 allele was identified as an interlocus recombination involving HLA-A*11:01:01:01/126 and HLA-H*02:07/14/18 alleles; this was mainly achieved by nanopore sequencing. CONCLUSIONS The identification of the interlocus recombination indicated that nanopore sequencing can be helpful in the characterization of novel alleles with complex rearrangements. Interlocus recombination has been identified as one of the mechanisms involved in the generation of novel HLA alleles.
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Affiliation(s)
- Li-Qun Zhang
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology of National Health Commission, No. 1 DaHua Road, Dong Dan, Beijing, People's Republic of China
| | | | - Dan Wang
- Beijing BoFuRui Gene Diagnostic, LTD, Beijing, People's Republic of China
| | - Xiang-Jun Liu
- Beijing BoFuRui Gene Diagnostic, LTD, Beijing, People's Republic of China
| | - Jian-Ping Cai
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology of National Health Commission, No. 1 DaHua Road, Dong Dan, Beijing, People's Republic of China.
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7
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Miyamae J, Okano M, Nishiya K, Katakura F, Kulski JK, Moritomo T, Shiina T. Haplotype structures and polymorphisms of dog leukocyte antigen (DLA) class I loci shaped by intralocus and interlocus recombination events. Immunogenetics 2022; 74:245-259. [PMID: 34993565 DOI: 10.1007/s00251-021-01234-5] [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: 06/29/2021] [Accepted: 11/10/2021] [Indexed: 11/26/2022]
Abstract
The dog leukocyte antigen (DLA) class I genomic region is located on chromosome 12, and the class I genomic region is composed of at least two distinct haplotypic gene structures, DLA-88-DLA-12 and DLA-88-DLA-88L. However, detailed information of the genomic differences among DLA-88, DLA-12, and DLA-88L are still lacking at the full-length gene level, and therefore, DLA allelic sequences classified for each of these loci are limited in number so far. In this study, we determined the DNA sequence of a 95-kb DLA class I genomic region including DLA-88, DLA-12/88L, and DLA-64 with three DLA homozygous dogs and of 37 full-length allelic gene sequences for DLA-88 and DLA-12/88L loci in 26 DLA class I homozygous dogs. Nucleotide diversity profiles of the 95-kb regions and sequence identity scores of the allelic sequences suggested that DLA-88L is a hybrid gene generated by interlocus and/or intralocus gene conversion between DLA-88 and DLA-12. The putative minimum conversion tract was estimated to be at least an 850-bp segment in length located from the 5´flanking untranslated region to the end of intron 2. In addition, at least one DLA-12 allele (DLA-12*004:01) was newly generated by interlocus gene conversion. In conclusion, the analysis for the occurrence of gene conversion within the dog DLA class I region revealed intralocus gene conversion tracts in 17 of 27 DLA-88 alleles and two of 10 DLA-12 alleles, suggesting that intralocus gene conversion has played an important role in expanding DLA allelic variations.
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Affiliation(s)
- Jiro Miyamae
- Faculty of Veterinary Medicine, Okayama University of Science, 1-3 Ikoino-oka, Imabari, Ehime, 794-8555, Japan.
| | - Masaharu Okano
- Department of Legal Medicine, Nihon University School of Dentistry, 1-8-13 Kanda-Surugadai, Chiyoda-ku, Tokyo, 101-8310, Japan
| | - Kohei Nishiya
- Department of Veterinary Medicine, College of Bioresource Science, Nihon University, 1866 Kameino, Fujisawa, Kanagawa, 252-0880, Japan
| | - Fumihiko Katakura
- Department of Veterinary Medicine, College of Bioresource Science, Nihon University, 1866 Kameino, Fujisawa, Kanagawa, 252-0880, Japan
| | - Jerzy K Kulski
- Discipline of Psychiatry, Medical School, The University of Western Australia, Crawley, WA, Australia
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, 143 Shimokasuya, Isehara, Kanagawa, 259-1143, Japan
| | - Tadaaki Moritomo
- Department of Veterinary Medicine, College of Bioresource Science, Nihon University, 1866 Kameino, Fujisawa, Kanagawa, 252-0880, Japan
| | - Takashi Shiina
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, 143 Shimokasuya, Isehara, Kanagawa, 259-1143, Japan
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Schwartz JC, Maccari G, Heimeier D, Hammond JA. Highly-contiguous bovine genomes underpin accurate functional analyses and updated nomenclature of MHC class I. HLA 2021; 99:167-182. [PMID: 34802191 DOI: 10.1111/tan.14494] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 11/05/2021] [Accepted: 11/17/2021] [Indexed: 11/29/2022]
Abstract
The major histocompatibility complex (MHC) class I region of cattle is both highly polymorphic and, unlike many species, highly variable in gene content between haplotypes. Cattle MHC class I alleles were historically grouped by sequence similarity in the more conserved 3' end of the coding sequence to form phylogenetic allele groups. This has formed the basis of current cattle MHC class I nomenclature. We presently describe and compare five fully assembled MHC class I haplotypes using the latest cattle and yak genome assemblies. Of the five previously described "pseudogenes" in the cattle MHC class I region, Pseudogene 3 is putatively functional in all haplotypes and Pseudogene 6 and Pseudogene 7 are putatively functional in some haplotypes. This was reinforced by evidence of transcription. Based on full gene sequences as well as 3' coding sequence, we identified distinct subgroups of BoLA-3 and BoLA-6 that represent distinct genetic loci. We further examined allele-specific expression using transcriptomic data revealing that certain alleles are consistently weakly expressed compared to others. These observations will help to inform further studies into how MHC class I region variability influences T cell and natural killer cell functions in cattle.
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Affiliation(s)
| | - Giuseppe Maccari
- The Pirbright Institute, Pirbright, UK.,Anthony Nolan Research Institute, London, UK
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9
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Arosa FA, Esgalhado AJ, Reste-Ferreira D, Cardoso EM. Open MHC Class I Conformers: A Look through the Looking Glass. Int J Mol Sci 2021; 22:ijms22189738. [PMID: 34575902 PMCID: PMC8470049 DOI: 10.3390/ijms22189738] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 09/04/2021] [Accepted: 09/08/2021] [Indexed: 12/16/2022] Open
Abstract
Studies carried out during the last few decades have consistently shown that cell surface MHC class I (MHC-I) molecules are endowed with functions unrelated with antigen presentation. These include cis–trans-interactions with inhibitory and activating KIR and LILR, and cis-interactions with receptors for hormones, growth factors, cytokines, and neurotransmitters. The mounting body of evidence indicates that these non-immunological MHC-I functions impact clinical and biomedical settings, including autoimmune responses, tumor escape, transplantation, and neuronal development. Notably, most of these functions appear to rely on the presence in hematopoietic and non-hematopoietic cells of heavy chains not associated with β2m and the peptide at the plasma membrane; these are known as open MHC-I conformers. Nowadays, open conformers are viewed as functional cis-trans structures capable of establishing physical associations with themselves, with other surface receptors, and being shed into the extracellular milieu. We review past and recent developments, strengthening the view that open conformers are multifunctional structures capable of fine-tuning cell signaling, growth, differentiation, and cell communication.
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Affiliation(s)
- Fernando A Arosa
- Health Sciences Research Center (CICS-UBI), University of Beira Interior, 6200-506 Covilhã, Portugal
- Faculty of Health Sciences, University of Beira Interior, 6200-506 Covilhã, Portugal
| | - André J Esgalhado
- Health Sciences Research Center (CICS-UBI), University of Beira Interior, 6200-506 Covilhã, Portugal
| | - Débora Reste-Ferreira
- Health Sciences Research Center (CICS-UBI), University of Beira Interior, 6200-506 Covilhã, Portugal
| | - Elsa M Cardoso
- Health Sciences Research Center (CICS-UBI), University of Beira Interior, 6200-506 Covilhã, Portugal
- Faculty of Health Sciences, University of Beira Interior, 6200-506 Covilhã, Portugal
- Health School, Guarda Polytechnic Institute, 6300-749 Guarda, Portugal
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10
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Steele EJ, Lindley RA. Regulatory T cells and co-evolution of allele-specific MHC recognition by the TCR. Scand J Immunol 2019; 91:e12853. [PMID: 31793005 PMCID: PMC7064991 DOI: 10.1111/sji.12853] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 11/27/2019] [Indexed: 12/13/2022]
Abstract
What is the evolutionary mechanism for the TCR-MHC-conserved interaction? We extend Dembic's model (Dembic Z. In, Scand J Immunol e12806, 2019) of thymus positive selection for high-avidity anti-self-MHC Tregs among double (CD4 + CD8+)-positive (DP) developing thymocytes. This model is based on competition for self-MHC (+ Pep) complexes presented on cortical epithelium. Such T cells exit as CD4 + CD25+FoxP3 + thymic-derived Tregs (tTregs). The other positively selected DP T cells are then negatively selected on medulla epithelium removing high-avidity anti-self-MHC + Pep as T cells commit to CD4 + or CD8 + lineages. The process is likened to the competitive selection and affinity maturation in Germinal Centre for the somatic hypermutation (SHM) of rearranged immunoglobulin (Ig) variable region (V[D]Js) of centrocytes bearing antigen-specific B cell receptors (BCR). We now argue that the same direct SHM processes for TCRs occur in post-antigenic Germinal Centres, but now occurring in peripheral pTregs. This model provides a potential solution to a long-standing problem previously recognized by Cohn and others (Cohn M, Anderson CC, Dembic Z. In, Scand J Immunol e12790, 2019) of how co-evolution occurs of species-specific MHC alleles with the repertoire of their germline TCR V counterparts. We suggest this is not by 'blind', slow, and random Darwinian natural selection events, but a rapid structured somatic selection vertical transmission process. The pTregs bearing somatic TCR V mutant genes then, on arrival in reproductive tissues, can donate their TCR V sequences via soma-to-germline feedback as discussed in this journal earlier. (Steele EJ, Lindley RA. In, Scand J Immunol e12670, 2018) The high-avidity tTregs also participate in the same process to maintain a biased, high-avidity anti-self-MHC germline V repertoire.
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Affiliation(s)
- Edward J Steele
- Melville Analytics Pty Ltd, Melbourne, Vic, Australia.,CYO'Connor ERADE Village Foundation, Perth, WA, Australia
| | - Robyn A Lindley
- GMDxCo Pty Ltd, Melbourne, Vic, Australia.,Department of Clinical Pathology, Faculty of Medicine, Dentistry & Health Sciences, University of Melbourne, Melbourne, Vic, Australia
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Planelles D, Balas A, Rodríguez-Cebriá M, Luis-Hidalgo M, Vicario JL. The new HLA-C*05:199 was generated by intralocus recombination involving C*05:01:01:01 and C*16:01:01:01 alleles. HLA 2019; 93:128-130. [PMID: 30632305 DOI: 10.1111/tan.13467] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Revised: 01/08/2019] [Accepted: 01/08/2019] [Indexed: 11/29/2022]
Abstract
The new HLA allele HLA-C*05:199 was detected and characterized in a Spanish family.
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Affiliation(s)
- Dolores Planelles
- Departamento de Histocompatibilidad, Centro de Transfusión de la Comunidad Valenciana, Valencia, Spain
| | - Antonio Balas
- Departamento de Histocompatibilidad, Centro de Transfusión de la Comunidad de Madrid, Madrid, Spain
| | - Manuel Rodríguez-Cebriá
- Departamento de Histocompatibilidad, Centro de Transfusión de la Comunidad Valenciana, Valencia, Spain
| | - Mar Luis-Hidalgo
- Departamento de Histocompatibilidad, Centro de Transfusión de la Comunidad Valenciana, Valencia, Spain
| | - José L Vicario
- Departamento de Histocompatibilidad, Centro de Transfusión de la Comunidad de Madrid, Madrid, Spain
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12
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Hilton HG, McMurtrey CP, Han AS, Djaoud Z, Guethlein LA, Blokhuis JH, Pugh JL, Goyos A, Horowitz A, Buchli R, Jackson KW, Bardet W, Bushnell DA, Robinson PJ, Mendoza JL, Birnbaum ME, Nielsen M, Garcia KC, Hildebrand WH, Parham P. The Intergenic Recombinant HLA-B∗46:01 Has a Distinctive Peptidome that Includes KIR2DL3 Ligands. Cell Rep 2018; 19:1394-1405. [PMID: 28514659 PMCID: PMC5510751 DOI: 10.1016/j.celrep.2017.04.059] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Revised: 03/07/2017] [Accepted: 04/20/2017] [Indexed: 01/26/2023] Open
Abstract
HLA-B∗46:01 was formed by an intergenic mini-conversion, between HLA-B∗15:01 and HLA-C∗01:02, in Southeast Asia during the last 50,000 years, and it has since become the most common HLA-B allele in the region. A functional effect of the mini-conversion was introduction of the C1 epitope into HLA-B∗46:01, making it an exceptional HLA-B allotype that is recognized by the C1-specific natural killer (NK) cell receptor KIR2DL3. High-resolution mass spectrometry showed that HLA-B∗46:01 has a low-diversity peptidome that is distinct from those of its parents. A minority (21%) of HLA-B∗46:01 peptides, with common C-terminal characteristics, form ligands for KIR2DL3. The HLA-B∗46:01 peptidome is predicted to be enriched for peptide antigens derived from Mycobacterium leprae. Overall, the results indicate that the distinctive peptidome and functions of HLA-B∗46:01 provide carriers with resistance to leprosy, which drove its rapid rise in frequency in Southeast Asia. The interlocus recombinant HLA-B∗46:01 is found at high frequency in Southeast Asia HLA-B∗46:01 has a low-diversity peptidome that is distinct from both its parents A subset of HLA-B∗46:01 peptides provides ligands for the NK cell receptor KIR2DL3 The unique features of HLA-B∗46:01 correlate with protection against leprosy
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Affiliation(s)
- Hugo G Hilton
- Department of Structural Biology, School of Medicine, Stanford University, Stanford, CA 94305, USA; Department of Microbiology & Immunology, School of Medicine, Stanford University, Stanford, CA 94305, USA.
| | - Curtis P McMurtrey
- Department of Microbiology & Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Alex S Han
- Department of Structural Biology, School of Medicine, Stanford University, Stanford, CA 94305, USA; Department of Microbiology & Immunology, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Zakia Djaoud
- Department of Structural Biology, School of Medicine, Stanford University, Stanford, CA 94305, USA; Department of Microbiology & Immunology, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Lisbeth A Guethlein
- Department of Structural Biology, School of Medicine, Stanford University, Stanford, CA 94305, USA; Department of Microbiology & Immunology, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Jeroen H Blokhuis
- Department of Structural Biology, School of Medicine, Stanford University, Stanford, CA 94305, USA; Department of Microbiology & Immunology, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Jason L Pugh
- Department of Structural Biology, School of Medicine, Stanford University, Stanford, CA 94305, USA; Department of Microbiology & Immunology, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Ana Goyos
- Department of Structural Biology, School of Medicine, Stanford University, Stanford, CA 94305, USA; Department of Microbiology & Immunology, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Amir Horowitz
- Department of Structural Biology, School of Medicine, Stanford University, Stanford, CA 94305, USA; Department of Microbiology & Immunology, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Rico Buchli
- Pure Protein LLC, Oklahoma City, OK 73104, USA
| | - Ken W Jackson
- Department of Microbiology & Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Wilfred Bardet
- Department of Microbiology & Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - David A Bushnell
- Department of Structural Biology, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Philip J Robinson
- Department of Structural Biology, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Juan L Mendoza
- Department of Structural Biology, School of Medicine, Stanford University, Stanford, CA 94305, USA; Department of Molecular & Cellular Physiology, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Michael E Birnbaum
- Department of Structural Biology, School of Medicine, Stanford University, Stanford, CA 94305, USA; Department of Molecular & Cellular Physiology, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Morten Nielsen
- Department of Bio and Health Informatics, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark; Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín, Buenos Aires, Argentina
| | - K Christopher Garcia
- Department of Structural Biology, School of Medicine, Stanford University, Stanford, CA 94305, USA; Department of Molecular & Cellular Physiology, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - William H Hildebrand
- Department of Microbiology & Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Peter Parham
- Department of Structural Biology, School of Medicine, Stanford University, Stanford, CA 94305, USA; Department of Microbiology & Immunology, School of Medicine, Stanford University, Stanford, CA 94305, USA
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13
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Chowdhury M, Agrawal N, Kundu D, Biswas N. Association of human leukocyte antigens Class I and Class II antigens with chronic periodontitis in East India. J Indian Soc Periodontol 2017; 21:494-498. [PMID: 29551870 PMCID: PMC5846248 DOI: 10.4103/jisp.jisp_309_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 11/12/2017] [Indexed: 11/19/2022] Open
Abstract
CONTEXT Human leukocyte antigens (HLAs) have an important role in the determination of susceptibility and resistance to periodontal diseases in humans, which may vary from population to population. AIMS The aim of this study was to find out the association of HLA Classes I and II genes with chronic periodontitis in East Indian population. MATERIALS AND METHODS In a cross-sectional study design, a total of sixty participants of chronic periodontitis (CP) (mean age: 44.12 ± 5.85) and sixty subjects of periodontal disease-free controls (NP) Periodontitis free controls (mean age 41.85 ± 7.71) were analyzed for their various HLA combinations using serologic (microlymphocytotoxicity test) method. The results are further compared with the HLA profile of 100 samples of blood donors for which periodontal status was unknown. All the data were statistically analyzed by applying Chi-square test. RESULTS HLA-B7 (P = 0.003), DR7 (P = 0.001), DR53 (P = 0.001), and DQ3 (P = 0.001) were identified as susceptible phenotypes to CP, whereas HLA-A1 (P = 0.010), A3 (P = 0.001), and Cw4 (P = 0.001) phenotypes were identified to be associated with disease resistance. CONCLUSION The HLA-B7, DR7, DR53, and DQ3 alleles may represent as risk factors for CP in Eastern Population of India, whereas HLA-A1, A3, and Cw4 may indicate to protective factors for CP of the same.
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Affiliation(s)
- Mona Chowdhury
- Department of Periodontology, Haldia Institue of Dental Science and Research, Haldia, West Bengal, India
| | - Neeraj Agrawal
- Department of Periodontology, Rishi Raj College of Dental Sciences, Bhopal, Madhya Pradesh, India
| | - Debabrata Kundu
- Department of Periodontology, Dr R Ahmed Dental College and Hospital, Kolkata, West Bengal, India
| | - Nitubroto Biswas
- Department of Periodontology, Buddha Institute of Dental Science and Post Graduate Institute, Patna, Bihar, India
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Mobbs JI, Illing PT, Dudek NL, Brooks AG, Baker DG, Purcell AW, Rossjohn J, Vivian JP. The molecular basis for peptide repertoire selection in the human leucocyte antigen (HLA) C*06:02 molecule. J Biol Chem 2017; 292:17203-17215. [PMID: 28855257 DOI: 10.1074/jbc.m117.806976] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 08/18/2017] [Indexed: 12/31/2022] Open
Abstract
Human leukocyte antigen (HLA)-C*06:02 is identified as the allele associated with the highest risk for the development of the autoimmune skin disease psoriasis. However, the diversity and mode of peptide presentation by the HLA-C*06:02 molecule remains unclear. Here, we describe the endogenous peptide repertoire of ∼3,000 sequences for HLA-C*06:02 that defines the peptide-binding motif for this HLA allomorph. We found that HLA-C*06:02 predominantly presents nonamer peptides with dominant arginine anchors at the P2 and P7 positions and a preference for small hydrophobic residues at the C terminus (PΩ). To determine the structural basis of this selectivity, we determined crystal structures of HLA-C*06:02 in complex with two self-peptides (ARTELYRSL and ARFNDLRFV) and an analogue of a melanocyte autoantigen (ADAMTSL5, VRSRR-abu-LRL) implicated in psoriasis. These structures revealed that HLA-C*06:02 possesses a deep peptide-binding groove comprising two electronegative B- and E-pockets that coincide with the preference for P2 and P7 arginine anchors. The ADAMTSL5 autoantigen possessed a P7-Leu instead of the P7-Arg residue, but nevertheless was accommodated within the HLA-C*06:02 antigen-binding cleft. Collectively, our results provide the structural basis for understanding peptide repertoire selection in HLA-C*06:02.
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Affiliation(s)
- Jesse I Mobbs
- From the Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton 3800, Victoria, Australia
| | - Patricia T Illing
- From the Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton 3800, Victoria, Australia
| | - Nadine L Dudek
- From the Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton 3800, Victoria, Australia
| | - Andrew G Brooks
- the Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne 3000, Australia
| | - Daniel G Baker
- Janssen Research & Development, LLC, Horsham, Philadelphia, Pennsylvania 19044
| | - Anthony W Purcell
- From the Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton 3800, Victoria, Australia,
| | - Jamie Rossjohn
- From the Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton 3800, Victoria, Australia, .,the Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton 3800, Victoria, Australia, and.,the Institute of Infection and Immunity, Cardiff University, School of Medicine, Cardiff CF14 4XN, Wales, United Kingdom
| | - Julian P Vivian
- From the Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton 3800, Victoria, Australia, .,the Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton 3800, Victoria, Australia, and
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15
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Robinson J, Guethlein LA, Cereb N, Yang SY, Norman PJ, Marsh SGE, Parham P. Distinguishing functional polymorphism from random variation in the sequences of >10,000 HLA-A, -B and -C alleles. PLoS Genet 2017. [PMID: 28650991 PMCID: PMC5507469 DOI: 10.1371/journal.pgen.1006862] [Citation(s) in RCA: 114] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
HLA class I glycoproteins contain the functional sites that bind peptide antigens and engage lymphocyte receptors. Recently, clinical application of sequence-based HLA typing has uncovered an unprecedented number of novel HLA class I alleles. Here we define the nature and extent of the variation in 3,489 HLA-A, 4,356 HLA-B and 3,111 HLA-C alleles. This analysis required development of suites of methods, having general applicability, for comparing and analyzing large numbers of homologous sequences. At least three amino-acid substitutions are present at every position in the polymorphic α1 and α2 domains of HLA-A, -B and -C. A minority of positions have an incidence >1% for the 'second' most frequent nucleotide, comprising 70 positions in HLA-A, 85 in HLA-B and 54 in HLA-C. The majority of these positions have three or four alternative nucleotides. These positions were subject to positive selection and correspond to binding sites for peptides and receptors. Most alleles of HLA class I (>80%) are very rare, often identified in one person or family, and they differ by point mutation from older, more common alleles. These alleles with single nucleotide polymorphisms reflect the germ-line mutation rate. Their frequency predicts the human population harbors 8-9 million HLA class I variants. The common alleles of human populations comprise 42 core alleles, which represent all selected polymorphism, and recombinants that have assorted this polymorphism.
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Affiliation(s)
- James Robinson
- Anthony Nolan Research Institute, London, United Kingdom
- UCL Cancer Institute, University College London, London, United Kingdom
| | - Lisbeth A. Guethlein
- Dept. of Structural Biology & Dept. of Microbiology & Immunology, School of Medicine, Stanford University, Stanford, California, United States of America
- * E-mail:
| | - Nezih Cereb
- Histogenetics, Ossining, New York, United States of America
| | - Soo Young Yang
- Histogenetics, Ossining, New York, United States of America
| | - Paul J. Norman
- Dept. of Structural Biology & Dept. of Microbiology & Immunology, School of Medicine, Stanford University, Stanford, California, United States of America
| | - Steven G. E. Marsh
- Anthony Nolan Research Institute, London, United Kingdom
- UCL Cancer Institute, University College London, London, United Kingdom
| | - Peter Parham
- Dept. of Structural Biology & Dept. of Microbiology & Immunology, School of Medicine, Stanford University, Stanford, California, United States of America
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16
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Nie XM, Zhang Y, Qiao WB, Zhu CF, Zhao YR. Identification and characterization a novel HLA-A allele, A*02:355, by sequence-based typing in a Chinese potential donor. Int J Immunogenet 2017; 44:35-37. [PMID: 28044416 DOI: 10.1111/iji.12302] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Revised: 10/20/2016] [Accepted: 12/11/2016] [Indexed: 11/30/2022]
Abstract
The new allele A*02:355 differs from A* 02:03:01 at positions 98 (T→A) and 102(A→C) resulting in an amino acid exchange F9→T. Interallelic sequence exchange is more likely the mechanism of its origination. The amino acid replacement influences the HLA peptide binding cleft and might have significant functional effects.
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Affiliation(s)
- X-M Nie
- Department of Central Laboratory, Shandong Provincial Hospital affiliated to Shandong University, Jinan, China.,HLA Laboratory, Blood Center of Shandong Province, Jinan, China
| | - Y Zhang
- HLA Laboratory, Blood Center of Shandong Province, Jinan, China
| | - W-B Qiao
- HLA Laboratory, Blood Center of Shandong Province, Jinan, China
| | - C-F Zhu
- HLA Laboratory, Blood Center of Shandong Province, Jinan, China
| | - Y-R Zhao
- Department of Central Laboratory, Shandong Provincial Hospital affiliated to Shandong University, Jinan, China
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17
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Santos S, Azkarate M, Eguizabal C, Balas A, Vicario JL. Genomic sequence of HLA-B*41:43, a new HLA-B allele generated by an intralocus recombination mechanism. HLA 2016; 87:111-3. [PMID: 26889907 DOI: 10.1111/tan.12725] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Revised: 11/23/2015] [Accepted: 11/23/2015] [Indexed: 11/29/2022]
Abstract
HLA-B*41:43 has been generated by an intralocus recombination comprising B*41:02:01 and a B*14, 38, or 67 allele.
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Affiliation(s)
- S Santos
- Departamento de Histocompatibilidad, Centro Vasco de Transfusión y Tejidos Humanos, Galdacano, Spain
| | - M Azkarate
- Departamento de Histocompatibilidad, Centro Vasco de Transfusión y Tejidos Humanos, Galdacano, Spain
| | - C Eguizabal
- Departamento de Histocompatibilidad, Centro Vasco de Transfusión y Tejidos Humanos, Galdacano, Spain
| | - A Balas
- Departamento de Histocompatibilidad, Centro de Transfusión de Madrid, Madrid, Spain
| | - J L Vicario
- Departamento de Histocompatibilidad, Centro de Transfusión de Madrid, Madrid, Spain
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18
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Schwartz JC, Hammond JA. The assembly and characterisation of two structurally distinct cattle MHC class I haplotypes point to the mechanisms driving diversity. Immunogenetics 2015; 67:539-44. [PMID: 26227296 PMCID: PMC4539362 DOI: 10.1007/s00251-015-0859-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 07/20/2015] [Indexed: 12/11/2022]
Abstract
In cattle, there are six classical MHC class I genes that are variably present between different haplotypes. Almost all known haplotypes contain between one and three genes, with an allele of Gene 2 present on the vast majority. However, very little is known about the sequence and therefore structure and evolutionary history of this genomic region. To address this, we have refined the MHC class I region in the Hereford cattle genome assembly and sequenced a complete A14 haplotype from a homozygous Holstein. Comparison of the two haplotypes revealed extensive variation within the MHC class Ia region, but not within the flanking regions, with each gene contained within a conserved 63- to 68-kb sequence block. This variable region appears to have undergone block gene duplication and likely deletion at regular breakpoints, suggestive of a site-specific mechanism. Phylogenetic analysis using complete gene sequences provided evidence of allelic diversification via gene conversion, with breakpoints between each of the extracellular domains that were associated with high guanine-cytosine (GC) content. Advancing our knowledge of cattle MHC class I evolution will help inform investigations of cattle genetic diversity and disease resistance.
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Affiliation(s)
- John C Schwartz
- Livestock Viral Diseases Programme, The Pirbright Institute, Ash Road, Pirbright, Woking, Surrey, GU24 0NF, UK
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19
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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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20
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Hernández-Frederick CJ, Giani AS, Cereb N, Sauter J, Silva-González R, Pingel J, Schmidt AH, Ehninger G, Yang SY. Identification of 2127 new HLA class I alleles in potential stem cell donors from Germany, the United States and Poland. ACTA ACUST UNITED AC 2014; 83:184-9. [PMID: 24571476 PMCID: PMC4199310 DOI: 10.1111/tan.12304] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Revised: 01/13/2014] [Accepted: 01/13/2014] [Indexed: 11/28/2022]
Abstract
We describe 2127 new human leukocyte antigen (HLA) class I alleles found in registered stem cell donors. These alleles represent 28.9% of the currently known class I alleles. Comparing new allele sequences to homologous sequences, we found 68.1% nonsynonymous nucleotide substitutions, 28.9% silent mutations and 3.0% nonsense mutations. Many substitutions occurred at positions that have not been known to be polymorphic before. A large number of HLA alleles and nucleotide variations underline the extreme diversity of the HLA system. Strikingly, 156 new alleles were found not only multiple times, but also in carriers of various parentage, suggesting that some new alleles are not necessarily rare. Moreover, new alleles were found especially often in minority donors. This emphasizes the benefits of specifically recruiting such groups of individuals.
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21
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Koutsogiannouli EA, Moutou KA, Stamatis C, Walter L, Mamuris Z. Genetic variation in the major histocompatibility complex of the European brown hare (Lepus europaeus) across distinct phylogeographic areas. Immunogenetics 2014; 66:379-92. [DOI: 10.1007/s00251-014-0772-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Accepted: 03/31/2014] [Indexed: 10/25/2022]
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22
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Sequence-based typing of HLA: an improved group-specific full-length gene sequencing approach. Methods Mol Biol 2014; 1109:101-14. [PMID: 24473781 DOI: 10.1007/978-1-4614-9437-9_7] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Matching for HLA at the allele level is crucial for stem cell transplantation. The golden standard approach for allele definition of full gene polymorphism, the so-called high-resolution HLA typing, is sequence-based typing (SBT). Although the majority of the polymorphism for class I is located in exons 2 and 3 and for class II in exon 2, for allele definition it is necessary to unravel the complete coding and intron sequences leading to an ultrahigh HLA typing resolution at the allele level, i.e., a full-length gene polymorphism identification.This chapter describes our recently developed SBT method for HLA-A, -B, -C, and -DQB1, that is based on full-length hemizygous Sanger sequencing of the alleles, separated by group-specific amplification using the low-resolution typing result as reference starting point. Group-specific amplification has already been established for DRB. This method enables a cost-efficient, user-friendly SBT approach resulting in a timely unambiguous HLA typing to an ultrahigh resolution level with minimal hands-on time.
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23
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Ellis SA, Hammond JA. The functional significance of cattle major histocompatibility complex class I genetic diversity. Annu Rev Anim Biosci 2013; 2:285-306. [PMID: 25384144 DOI: 10.1146/annurev-animal-022513-114234] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Current concerns about food security highlight the importance of maintaining productive and disease-resistant livestock populations. Major histocompatibility complex (MHC) class I genes have a central role in immunity. A high level of diversity in these genes allows populations to survive despite exposure to rapidly evolving pathogens. This review aims to describe the key features of MHC class I genetic diversity in cattle and to discuss their role in disease resistance. Discussion centers on data derived from the cattle genome sequence and studies addressing MHC class I gene expression and function. The impact of intensive selection on MHC diversity is also considered. A high level of complexity in MHC class I genes and functionally related gene families is revealed. This highlights the need for increased efforts to determine key genetic components that govern cattle immune responses to disease, which is increasingly important in the face of changing human and environmental demands.
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Affiliation(s)
- Shirley A Ellis
- The Pirbright Institute, Pirbright, Woking, Surrey GU24 0NF, United Kingdom; ,
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24
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Holmes JC, Holmer SG, Ross P, Buntzman AS, Frelinger JA, Hess PR. Polymorphisms and tissue expression of the feline leukocyte antigen class I loci FLAI-E, FLAI-H, and FLAI-K. Immunogenetics 2013; 65:675-89. [PMID: 23812210 PMCID: PMC3777221 DOI: 10.1007/s00251-013-0711-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Accepted: 05/18/2013] [Indexed: 01/14/2023]
Abstract
Cytotoxic CD8+ T-cell immunosurveillance for intracellular pathogens, such as viruses, is controlled by classical major histocompatibility complex (MHC) class Ia molecules, and ideally, these antiviral T-cell populations are defined by the specific peptide and restricting MHC allele. Surprisingly, despite the utility of the cat in modeling human viral immunity, little is known about the feline leukocyte antigen class I complex (FLAI). Only a few coding sequences with uncertain locus origin and expression patterns have been reported. Of 19 class I genes, three loci--FLAI-E, FLAI-H, and FLAI-K--are predicted to encode classical molecules, and our objective was to evaluate their status by analyzing polymorphisms and tissue expression. Using locus-specific, PCR-based genotyping, we amplified 33 FLAI-E, FLAI-H, and FLAI-K alleles from 12 cats of various breeds, identifying, for the first time, alleles across three distinct loci in a feline species. Alleles shared the expected polymorphic and invariant sites in the α1/α2 domains, and full-length cDNA clones possessed all characteristic class Ia exons. Alleles could be assigned to a specific locus with reasonable confidence, although there was evidence of potentially confounding interlocus recombination between FLAI-E and FLAI-K. Only FLAI-E, FLAI-H, and FLAI-K origin alleles were amplified from cDNAs of multiple tissue types. We also defined hypervariable regions across these genes, which permitted the assignment of names to both novel and established alleles. As predicted, FLAI-E, FLAI-H, and FLAI-K fulfill the major criteria of class Ia genes. These data represent a necessary prerequisite for studying epitope-specific antiviral CD8+ T-cell responses in cats.
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Affiliation(s)
- Jennifer C. Holmes
- Immunology Program, and Department of Clinical Sciences, North Carolina State University College of Veterinary Medicine, Raleigh, North Carolina, United States of America
| | - Savannah G. Holmer
- Immunology Program, and Department of Clinical Sciences, North Carolina State University College of Veterinary Medicine, Raleigh, North Carolina, United States of America
| | - Peter Ross
- Immunology Program, and Department of Clinical Sciences, North Carolina State University College of Veterinary Medicine, Raleigh, North Carolina, United States of America
| | - Adam S. Buntzman
- Department of Immunobiology, University of Arizona, Tucson, Arizona, United States of America
| | - Jeffrey A. Frelinger
- Department of Immunobiology, University of Arizona, Tucson, Arizona, United States of America
| | - Paul R. Hess
- Immunology Program, and Department of Clinical Sciences, North Carolina State University College of Veterinary Medicine, Raleigh, North Carolina, United States of America
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Tseng KC, Tseng CW, Hsieh YH, Chang CK, Lai NS, Hung TH, Chang TT. Effect of human leukocyte antigen class I and II alleles on hepatitis C viral load among chronic hepatitis C patients in Southern Taiwan. Hum Immunol 2013; 74:978-82. [PMID: 23628398 DOI: 10.1016/j.humimm.2013.04.023] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2012] [Revised: 02/03/2013] [Accepted: 04/10/2013] [Indexed: 01/14/2023]
Abstract
The viral load of hepatitis C virus (HCV) in chronic hepatitis C patients affects clinical outcomes and response to interferon treatment. Various factors may be involved in determining the viral load, including host genetic factors. The aim of this study was to investigate the relationship between HCV viral load and human leukocyte antigen (HLA) class I and class II alleles. One hundred and six HCV RNA positive subjects were enrolled, and viral load was measured. HLA-A, -B, -C, -DR, and -DQ loci were determined by sequence-based genotyping. Univariate analysis indicated that HLA-B(*)40 and HLA-C(*)07 alleles had significantly higher HCV RNA levels (P<0.05). Patients with the HLA-C(*)15 allele exhibited a trend toward a lower HCV viral load (P=0.06). After controlling for confounding factors, multivariate analysis revealed that only HLA-C(*)15 allele was identified as a significant determinant for HCV-RNA level (slope=-0.91, 95% CI: -1.58, -0.24; Holm's P<0.01). Patients expressing the HLA-C(*)15 allele had significantly lower HCV RNA levels. HCV genotype 1 was significantly associated with high HCV RNA levels (P<0.05 by Mann-Whitney U test). In conclusion, HLA-C(*)15 is an important host immunogenetic factor with an inverse association to HCV viral load in CHC patients in Taiwan. HCV genotype 1 is the viral factor that associated with high viral load.
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Affiliation(s)
- Kuo-Chih Tseng
- Department of Internal Medicine, Buddhist Dalin Tzu Chi General Hospital, Chia-Yi, Taiwan; School of Medicine, Tzuchi University, Hualien, Taiwan
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Abstract
The strategy of antigenic variation is to present a constantly changing population phenotype that enhances parasite transmission, through evasion of immunity arising within, or existing between, host animals. Trypanosome antigenic variation occurs through spontaneous switching among members of a silent archive of many hundreds of variant surface glycoprotein (VSG) antigen genes. As with such contingency systems in other pathogens, switching appears to be triggered through inherently unstable DNA sequences. The archive occupies subtelomeres, a genome partition that promotes hypermutagenesis and, through telomere position effects, singular expression of VSG. Trypanosome antigenic variation is augmented greatly by the formation of mosaic genes from segments of pseudo-VSG, an example of implicit genetic information. Hypermutation occurs apparently evenly across the whole archive, without direct selection on individual VSG, demonstrating second-order selection of the underlying mechanisms. Coordination of antigenic variation, and thereby transmission, occurs through networking of trypanosome traits expressed at different scales from molecules to host populations.
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Affiliation(s)
- J David Barry
- Wellcome Trust Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary, & Life Sciences, University of Glasgow, Glasgow, United Kingdom.
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Tseng CW, Hsieh YH, Chang CK, Lai NS, Hung TH, Wu SF, Tseng KC. HLA-B*15:02 is associated with anemia in patients with chronic hepatitis C treated with pegylated interferon-α and ribavirin. ACTA ACUST UNITED AC 2012; 80:424-30. [PMID: 22931407 DOI: 10.1111/j.1399-0039.2012.01956.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2012] [Revised: 06/30/2012] [Accepted: 08/06/2012] [Indexed: 01/23/2023]
Abstract
To investigate the relationship between human leukocyte antigen (HLA) class I and II alleles and treatment-induced anemia in chronic hepatitis C (CHC) patients receiving combination therapy with pegylated interferon-α (PEG-IFN-α) and ribavirin (RBV). One hundred six naïve CHC patients (59 females and 47 males; mean age, 53.08 years) who underwent combination treatment were enrolled. The patients were considered positive for hemoglobin (Hb)-related side effects if the Hb concentrations dropped below 10 g/dl during PEG-IFN-α plus RBV treatment. The HLA-A, -B, -C, -DR, and -DQ loci were investigated by sequence-based genotyping. The effects of the clinical characteristics, virologic variables, and the HLA alleles on treatment-induced anemia were evaluated by a logistic regression analysis. Forty patients (37.7%) had Hb levels below 10 g/dl during the treatment course. Low baseline Hb levels and an advanced liver fibrosis stage were associated with decreases in Hb levels to below 10 g/dl. The occurrence of treatment-related anemia (Hb < 10 g/dl) was significantly associated with HLA-B*15:02 as shown by multivariate analysis (adjusted odds ratio, 8.13; 95% confidence interval: 1.19-55.70; P-value after Holm's procedure, 0.03). HLA-B*15:02 is associated with treatment-induced anemia in Taiwanese CHC patients receiving combination therapy with PEG-IFN-α plus RBV.
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Affiliation(s)
- C-W Tseng
- Department of Internal Medicine, Buddhist Dalin Tzu Chi General Hospital, Chia-Yi, Taiwan
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Orysiuk D, Lawrence J, Prashar T, Spangelo L, Pilon R, Fournier J, Rud E, Sandstrom P, Plummer FA, Luo M. Evidence of recombination producing allelic diversity in MHC class I Mafa-B and -A alleles in cynomolgus macaques. ACTA ACUST UNITED AC 2012; 79:351-8. [PMID: 22489944 DOI: 10.1111/j.1399-0039.2012.01867.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The MHC class I-A and -B genes of cynomolgus macaques are highly polymorphic. These genes encode proteins presenting peptides to CD8+ T cells to initiate adaptive immune response. Recombination events are one way the diversity of these alleles can be increased. Such events have been well characterized in humans, but have not been as well characterized in macaques. In order to identify and examine recombinations that create new alleles, it is important to analyze intron sequences. Intron sequences have been shown to be important to understand the evolutionary mechanisms involved in the generation of major histocompatibility complex (MHC) alleles and loci. Thus far, there have been relatively few intron sequences reported for MHC class I alleles in macaques, and this has hampered the understanding of MHC organization and evolution in macaques. In this study, we present evidence of a gene conversion event generating the Mafa-B*099 allele lineage by the combination of Mafa-B*054 and Mafa-B*095 allele lineages. A potential recombination between the Mafa-A3*13 and Mafa-A4:14 lineages was also observed, but it is less clear due to lack of intron 2 sequence. This report stresses the role that recombination can play in MHC class I diversity in cynomologus macaques, and the importance of introns in identifying and analyzing such events.
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Affiliation(s)
- D Orysiuk
- Department of Medical Microbiology, University of Manitoba, Winnipeg, MB, Canada
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Ross P, Buntzman AS, Vincent BG, Grover EN, Gojanovich GS, Collins EJ, Frelinger JA, Hess PR. Allelic diversity at the DLA-88 locus in Golden Retriever and Boxer breeds is limited. TISSUE ANTIGENS 2012; 80:175-83. [PMID: 22571293 PMCID: PMC3407292 DOI: 10.1111/j.1399-0039.2012.01889.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
In the dog, previous analyses of major histocompatibility complex class I genes suggest a single polymorphic locus, dog leukocyte antigen (DLA)-88. While 51 alleles have been reported, estimates of prevalence have not been made. We hypothesized that, within a breed, DLA-88 diversity would be restricted, and one or more dominant alleles could be identified. Accordingly, we determined allele usage in 47 Golden Retrievers and 39 Boxers. In each population, 10 alleles were found; 4 were shared. Seven novel alleles were identified. DLA-88*05101 and *50801 predominated in Golden Retrievers, while most Boxers carried *03401. In these breeds, DLA-88 polymorphisms are limited and largely non-overlapping. The finding of highly prevalent alleles fulfills an important prerequisite for studying canine CD8+ T-cell responses.
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Affiliation(s)
- Peter Ross
- Department of Clinical Sciences, and Immunology Program, North Carolina State University College of Veterinary Medicine, Raleigh, NC, USA
| | - Adam S. Buntzman
- Department of Immunobiology, University of Arizona, Tucson, AZ, USA
| | - Benjamin G. Vincent
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Elise N. Grover
- Department of Clinical Sciences, and Immunology Program, North Carolina State University College of Veterinary Medicine, Raleigh, NC, USA
| | - Gregory S. Gojanovich
- Department of Clinical Sciences, and Immunology Program, North Carolina State University College of Veterinary Medicine, Raleigh, NC, USA
| | - Edward J. Collins
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | | | - Paul R. Hess
- Department of Clinical Sciences, and Immunology Program, North Carolina State University College of Veterinary Medicine, Raleigh, NC, USA
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Andersson E, Villabona L, Bergfeldt K, Carlson JW, Ferrone S, Kiessling R, Seliger B, Masucci GV. Correlation of HLA-A02* genotype and HLA class I antigen down-regulation with the prognosis of epithelial ovarian cancer. Cancer Immunol Immunother 2012; 61:1243-53. [PMID: 22258792 PMCID: PMC8693725 DOI: 10.1007/s00262-012-1201-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2011] [Accepted: 01/07/2012] [Indexed: 10/14/2022]
Abstract
BACKGROUND In recent years, evidence is accumulating that cancer cells develop strategies to escape immune recognition. HLA class I HC down-regulation is one of the most investigated. In addition, different HLA haplotypes are known to correlate to both risk of acquiring diseases and also prognosis in survival of disease or cancer. We have previously shown that patients with serous adenocarcinoma of the ovary in advanced surgical stage disease have a particularly poor prognosis if they carry the HLA-A02* genotype. We aimed to study the relationship between HLA-A02* genotype in these patients and the subsequent HLA class I HC protein product defects in the tumour tissue. MATERIALS AND METHODS One hundred and sixty-two paraffin-embedded tumour lesions obtained from Swedish women with epithelial ovarian cancer were stained with HLA class I heavy chain (HC) and β(2)-microglobulin (β(2)-m)-specific monoclonal antibodies (mAb). Healthy ovary and tonsil tissue served as a control. The HLA genotype of these patients was determined by PCR/sequence-specific primer method. The probability of survival was calculated using the Kaplan-Meier method, and the hazard ratio (HR) was estimated using proportional hazard regression. RESULTS Immunohistochemical staining of ovarian cancer lesions with mAb showed a significantly higher frequency of HLA class I HC and β(2)-m down-regulation in patients with worse prognosis (WP) than in those with better prognosis. In univariate analysis, both HLA class I HC down-regulation in ovarian cancer lesions and WP were associated with poor survival. In multivariate Cox-analysis, the WP group (all with an HLA-A02* genotype) had a significant higher HR to HLA class I HC down-regulation. CONCLUSIONS HLA-A02* is a valuable prognostic biomarker in epithelial ovarian cancer. HLA class I HC loss and/or down-regulation was significantly more frequent in tumour tissues from HLA-A02* positive patients with serous adenocarcinoma surgical stage III-IV. In multivariate analysis, we show that the prognostic impact is reasonably correlated to the HLA genetic rather than to the expression of its protein products.
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Affiliation(s)
- Emilia Andersson
- Department of Oncology-Pathology, Karolinska Institute, Radiumhemmet, Karolinska University Hospital, Stockholm, Sweden
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Gjini E, Haydon DT, Barry JD, Cobbold CA. The impact of mutation and gene conversion on the local diversification of antigen genes in African trypanosomes. Mol Biol Evol 2012; 29:3321-31. [PMID: 22735079 PMCID: PMC3472502 DOI: 10.1093/molbev/mss166] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Patterns of genetic diversity in parasite antigen gene families hold important information about their potential to generate antigenic variation within and between hosts. The evolution of such gene families is typically driven by gene duplication, followed by point mutation and gene conversion. There is great interest in estimating the rates of these processes from molecular sequences for understanding the evolution of the pathogen and its significance for infection processes. In this study, a series of models are constructed to investigate hypotheses about the nucleotide diversity patterns between closely related gene sequences from the antigen gene archive of the African trypanosome, the protozoan parasite causative of human sleeping sickness in Equatorial Africa. We use a hidden Markov model approach to identify two scales of diversification: clustering of sequence mismatches, a putative indicator of gene conversion events with other lower-identity donor genes in the archive, and at a sparser scale, isolated mismatches, likely arising from independent point mutations. In addition to quantifying the respective probabilities of occurrence of these two processes, our approach yields estimates for the gene conversion tract length distribution and the average diversity contributed locally by conversion events. Model fitting is conducted using a Bayesian framework. We find that diversifying gene conversion events with lower-identity partners occur at least five times less frequently than point mutations on variant surface glycoprotein (VSG) pairs, and the average imported conversion tract is between 14 and 25 nucleotides long. However, because of the high diversity introduced by gene conversion, the two processes have almost equal impact on the per-nucleotide rate of sequence diversification between VSG subfamily members. We are able to disentangle the most likely locations of point mutations and conversions on each aligned gene pair.
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Affiliation(s)
- Erida Gjini
- School of Mathematics and Statistics, College of Science and Engineering, University of Glasgow, Glasgow, United Kingdom.
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32
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Zhang P, Kuang YY, Wu HL, Li L, Ge YF, Wan QH, Fang SG. The Père David's deer MHC class I genes show unexpected diversity patterns, with monomorphic classical genes but polymorphic nonclassical genes and pseudogenes. JOURNAL OF EXPERIMENTAL ZOOLOGY. PART B, MOLECULAR AND DEVELOPMENTAL EVOLUTION 2012; 318:294-307. [PMID: 22821865 DOI: 10.1002/jez.b.22445] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Père David's deer (Elaphurus davidianus) is a highly inbred species that arose from 11 founders but now comprises a population of about 3,000 individuals, making it interesting to investigate the adaptive variation of this species from the major histocompatibility complex (MHC) perspective. In this study, we isolated Elda-MHC class I loci using magnetic bead-based cDNA hybridization, and examined the molecular variations of these loci using single-strand conformation polymorphism (SSCP) and sequence analysis. We obtained seven MHC class I genes, which we designated F1, F12, G2, I7, AF, I8, and C1. Our analyses of stop codons, phylogenetic trees, amino acid conservation, and G+C content revealed that F1, F12, G2, and I7 were classical genes, AF was a nonclassical gene, and I8 and C1 were pseudogenes. Our subsequent molecular examinations showed that the diversity pattern in the Père David's deer was unusual. Most mammals have more polymorphic classical class I loci vs. the nonclassical and neutral genes. In contrast, the Père David's deer was found to be monomorphic at classical genes F1, F12, G2, and I7, dimorphic at the nonclassical AF gene, dimorphic at pseudogene I8, and tetramorphic at pseudogene C1. The adverse polymorphism patterns of Elda-I genes might provide evidence for selection too faster deplete MHC variation than drift in the bottlenecked populations, while the postbottleneck tetramorphism of the C1 pseudogene appears to be evidence of strong historical balancing selection.
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Affiliation(s)
- Pei Zhang
- The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, College of Life Sciences, Zhejiang University, Hangzhou, PR China
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Codner GF, Birch J, Hammond JA, Ellis SA. Constraints on haplotype structure and variable gene frequencies suggest a functional hierarchy within cattle MHC class I. Immunogenetics 2012; 64:435-45. [DOI: 10.1007/s00251-012-0612-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2011] [Accepted: 01/13/2012] [Indexed: 12/11/2022]
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Cattle MHC nomenclature: is it possible to assign sequences to discrete class I genes? Immunogenetics 2012; 64:475-80. [PMID: 22419150 DOI: 10.1007/s00251-012-0611-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2012] [Accepted: 03/02/2012] [Indexed: 12/12/2022]
Abstract
The cattle major histocompatibility complex (MHC) region contains a variable number of classical class I genes encoding polymorphic molecules involved in antigen presentation. Six classical class I genes have been described, but assigning sequences to these genes has proved problematic. We propose a refinement of the existing nomenclature, which currently names the 97 known classical class I sequences in a single series. Phylogenetic analysis of the 3' portion of the coding region allows segregation of these into six groups; thus, we have prefixed existing names with the appropriate number. Although it is clear that some of these groups correspond to discrete genes, it is currently not possible to state definitively that all do. However, the main groupings are consistent, and in conjunction with other evidence, we feel it is now appropriate to rename the sequences accordingly. Segregation of sequences into groups in this way will facilitate ongoing research and future use of the cattle MHC section of the Immuno Polymorphism Database.
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Bahr A, Wilson AB. The evolution of MHC diversity: evidence of intralocus gene conversion and recombination in a single-locus system. Gene 2012; 497:52-7. [PMID: 22301266 DOI: 10.1016/j.gene.2012.01.017] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2011] [Revised: 01/16/2012] [Accepted: 01/17/2012] [Indexed: 11/29/2022]
Abstract
Gene conversion, the unidirectional exchange of genetic material between homologous sequences, is thought to strongly influence patterns of genetic diversity. The high diversity of major histocompatibility complex (MHC) genes in many species is thought to reflect a long history of gene conversion events both within and among loci. Theoretical work suggests that intra- and interlocus gene conversion leave characteristic signatures of nucleotide diversity, but empirical studies of MHC variation have rarely been able to analyze the effects of conversion events in isolation, due to the presence of multiple gene copies in most species. The potbellied seahorse (Hippocampus abdominalis), a species with a single copy of the MH class II beta-chain gene (MHIIb), provides an ideal system in which to explore predictions on the effects of intralocus gene conversion on patterns of genetic diversity. The genetic diversity of the MHIIb peptide binding region (PBR) is high in the seahorse, similar to other vertebrate species. In contrast, the remainder of the gene shows a total absence of synonymous variation and low levels of intronic sequence diversity, concentrated in 3 short repetitive regions and 1-12 SNPs per intron. The distribution of substitutions across the gene results in a patchwork pattern of shared polymorphism between otherwise divergent sequences. The pattern of nucleotide diversity observed in the seahorse MHIIb gene is congruent with theoretical expectations for intralocus gene conversion, indicating that this evolutionary mechanism has played an important role in MHC gene evolution, contributing to both the high diversity in the PBR and the low diversity outside this region. Neutral variation at this locus may be further reduced due to biases in nucleotide composition and functional constraints.
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Affiliation(s)
- Angela Bahr
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland.
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36
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Codner GF, Stear MJ, Reeve R, Matthews L, Ellis SA. Selective forces shaping diversity in the class I region of the major histocompatibility complex in dairy cattle. Anim Genet 2011; 43:239-49. [DOI: 10.1111/j.1365-2052.2011.02239.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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37
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Buhler S, Sanchez-Mazas A. HLA DNA sequence variation among human populations: molecular signatures of demographic and selective events. PLoS One 2011; 6:e14643. [PMID: 21408106 PMCID: PMC3051395 DOI: 10.1371/journal.pone.0014643] [Citation(s) in RCA: 101] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2010] [Accepted: 12/21/2010] [Indexed: 12/14/2022] Open
Abstract
Molecular differences between HLA alleles vary up to 57 nucleotides within the peptide binding coding region of human Major Histocompatibility Complex (MHC) genes, but it is still unclear whether this variation results from a stochastic process or from selective constraints related to functional differences among HLA molecules. Although HLA alleles are generally treated as equidistant molecular units in population genetic studies, DNA sequence diversity among populations is also crucial to interpret the observed HLA polymorphism. In this study, we used a large dataset of 2,062 DNA sequences defined for the different HLA alleles to analyze nucleotide diversity of seven HLA genes in 23,500 individuals of about 200 populations spread worldwide. We first analyzed the HLA molecular structure and diversity of these populations in relation to geographic variation and we further investigated possible departures from selective neutrality through Tajima's tests and mismatch distributions. All results were compared to those obtained by classical approaches applied to HLA allele frequencies.Our study shows that the global patterns of HLA nucleotide diversity among populations are significantly correlated to geography, although in some specific cases the molecular information reveals unexpected genetic relationships. At all loci except HLA-DPB1, populations have accumulated a high proportion of very divergent alleles, suggesting an advantage of heterozygotes expressing molecularly distant HLA molecules (asymmetric overdominant selection model). However, both different intensities of selection and unequal levels of gene conversion may explain the heterogeneous mismatch distributions observed among the loci. Also, distinctive patterns of sequence divergence observed at the HLA-DPB1 locus suggest current neutrality but old selective pressures on this gene. We conclude that HLA DNA sequences advantageously complement HLA allele frequencies as a source of data used to explore the genetic history of human populations, and that their analysis allows a more thorough investigation of human MHC molecular evolution.
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Affiliation(s)
- Stéphane Buhler
- Laboratory of Anthropology, Genetics and Peopling History, Department of Anthropology, University of Geneva, Geneva, Switzerland.
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38
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Functional analysis of frequently expressed Chinese rhesus macaque MHC class I molecules Mamu-A1*02601 and Mamu-B*08301 reveals HLA-A2 and HLA-A3 supertypic specificities. Immunogenetics 2011; 63:275-90. [PMID: 21274527 PMCID: PMC3068250 DOI: 10.1007/s00251-010-0502-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2010] [Accepted: 12/07/2010] [Indexed: 01/15/2023]
Abstract
The Simian immunodeficiency virus (SIV)-infected Indian rhesus macaque (Macaca mulatta) is the most established model of HIV infection and AIDS-related research, despite the potential that macaques of Chinese origin is a more relevant model. Ongoing efforts to further characterize the Chinese rhesus macaques' major histocompatibility complex (MHC) for composition and function should facilitate greater utilization of the species. Previous studies have demonstrated that Chinese-origin M. mulatta (Mamu) class I alleles are more polymorphic than their Indian counterparts, perhaps inferring a model more representative of human MHC, human leukocyte antigen (HLA). Furthermore, the Chinese rhesus macaque class I allele Mamu-A1*02201, the most frequent allele thus far identified, has recently been characterized and shown to be an HLA-B7 supertype analog, the most frequent supertype in human populations. In this study, we have characterized two additional alleles expressed with high frequency in Chinese rhesus macaques, Mamu-A1*02601 and Mamu-B*08301. Upon the development of MHC-peptide-binding assays and definition of their associated motifs, we reveal that these Mamu alleles share peptide-binding characteristics with the HLA-A2 and HLA-A3 supertypes, respectively, the next most frequent human supertypes after HLA-B7. These data suggest that Chinese rhesus macaques may indeed be a more representative model of HLA gene diversity and function as compared to the species of Indian origin and therefore a better model for investigating human immune responses.
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Jones DC, Kosmoliaptsis V, Apps R, Lapaque N, Smith I, Kono A, Chang C, Boyle LH, Taylor CJ, Trowsdale J, Allen RL. HLA class I allelic sequence and conformation regulate leukocyte Ig-like receptor binding. THE JOURNAL OF IMMUNOLOGY 2011; 186:2990-7. [PMID: 21270408 DOI: 10.4049/jimmunol.1003078] [Citation(s) in RCA: 100] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Leukocyte Ig-like receptors (LILRs) are a family of innate immune receptors predominantly expressed by myeloid cells that can alter the Ag presentation properties of macrophages and dendritic cells. Several LILRs bind HLA class I. Altered LILR recognition due to HLA allelic variation could be a contributing factor in disease. We comprehensively assessed LILR binding to >90 HLA class I alleles. The inhibitory receptors LILRB1 and LILRB2 varied in their level of binding to different HLA alleles, correlating in some cases with specific amino acid motifs. LILRB2 displayed the weakest binding to HLA-B*2705, an allele genetically associated with several autoimmune conditions and delayed progression of HIV infection. We also assessed the effect of HLA class I conformation on LILR binding. LILRB1 exclusively bound folded β(2)-microglobulin-associated class I, whereas LILRB2 bound both folded and free H chain forms. In contrast, the activating receptor LILRA1 and the soluble LILRA3 protein displayed a preference for binding to HLA-C free H chain. To our knowledge, this is the first study to identify the ligand of LILRA3. These findings support the hypothesis that LILR-mediated detection of unfolded versus folded MHC modulates immune responses during infection or inflammation.
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Affiliation(s)
- Des C Jones
- Immunology Division, Department of Pathology, University of Cambridge, Cambridge CB2 1QP, United Kingdom.
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40
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Shaw BE, Arguello R, Garcia-Sepulveda CA, Madrigal JA. The impact of HLA genotyping on survival following unrelated donor haematopoietic stem cell transplantation. Br J Haematol 2010; 150:251-8. [DOI: 10.1111/j.1365-2141.2010.08224.x] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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41
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Wang D, Zhong L, Wei Q, Gan X, He S. Evolution of MHC class I genes in two ancient fish, paddlefish (Polyodon spathula
) and Chinese sturgeon (Acipenser sinensis
). FEBS Lett 2010; 584:3331-9. [DOI: 10.1016/j.febslet.2010.05.065] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2010] [Revised: 05/13/2010] [Accepted: 05/24/2010] [Indexed: 10/19/2022]
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42
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Tallmadge RL, Campbell JA, Miller DC, Antczak DF. Analysis of MHC class I genes across horse MHC haplotypes. Immunogenetics 2010; 62:159-72. [PMID: 20099063 DOI: 10.1007/s00251-009-0420-9] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2009] [Accepted: 12/12/2009] [Indexed: 11/28/2022]
Abstract
The genomic sequences of 15 horse major histocompatibility complex (MHC) class I genes and a collection of MHC class I homozygous horses of five different haplotypes were used to investigate the genomic structure and polymorphism of the equine MHC. A combination of conserved and locus-specific primers was used to amplify horse MHC class I genes with classical and nonclassical characteristics. Multiple clones from each haplotype identified three to five classical sequences per homozygous animal and two to three nonclassical sequences. Phylogenetic analysis was applied to these sequences, and groups were identified which appear to be allelic series, but some sequences were left ungrouped. Sequences determined from MHC class I heterozygous horses and previously described MHC class I sequences were then added, representing a total of ten horse MHC haplotypes. These results were consistent with those obtained from the MHC homozygous horses alone, and 30 classical sequences were assigned to four previously confirmed loci and three new provisional loci. The nonclassical genes had few alleles and the classical genes had higher levels of allelic polymorphism. Alleles for two classical loci with the expected pattern of polymorphism were found in the majority of haplotypes tested, but alleles at two other commonly detected loci had more variation outside of the hypervariable region than within. Our data indicate that the equine major histocompatibility complex is characterized by variation in the complement of class I genes expressed in different haplotypes in addition to the expected allelic polymorphism within loci.
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Affiliation(s)
- Rebecca L Tallmadge
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
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43
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Zhu F, He Y, Zhang W, He J, He J, Xu X, Yan L. Analysis of the complete genomic sequence of HLA-A alleles in the Chinese Han population. Int J Immunogenet 2009; 36:351-60. [PMID: 19735485 DOI: 10.1111/j.1744-313x.2009.00874.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
To analyse the complete genomic sequences and investigate the intron polymorphism of the human leucocyte antigen (HLA)-A locus, the full-length nucleotide sequences of each major allelic group of HLA-A in the Chinese Han population were determined, including HLA-A*01, A*02, A*03, A*11, A*23, A*24, A*26, A*29, A*30, A*31, A*32, A*33, A*34, A*68, A*69. More than 3.0-kb DNA fragment of HLA-A locus was amplified from 5'-untranslated region to 3'-noncoding region for sequencing. Full-length sequences of the HLA-A alleles were determined using an ABI BigDye((R)) Terminator Cycle Sequencing kit and the HLA-A phylogenetic tree was analysed by dnaman software. Full-length nucleotide sequences of 15 HLA-A alleles (GenBank Accession numbers EU445470-EU445484) were obtained. HLA-A*110101, A*2301, A*300101, A*310102, A*330301, A*340101, A*680102 and A*6901 alleles were firstly reported for complete genomic sequences. Total 247 polymorphism positions were found in the complete genomic sequences of HLA-A alleles and a insertion of 17 nucleotides within intron 3 was observed in several allelic groups. According to the phylogenetic tree of the full-length nucleotide sequences, HLA-A locus was classified into seven major allelic lineages. In this study, complete genomic sequences of common HLA-A alleles were obtained and the data will help us understand the evolution of HLA-A.
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Affiliation(s)
- F Zhu
- HLA Typing Laboratory, Blood Center of Zhejiang Province, Hangzhou, Zhejiang Province 310006, China
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44
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Saakian DB, Kirakosyan Z, Hu CK. Diploid biological evolution models with general smooth fitness landscapes and recombination. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2008; 77:061907. [PMID: 18643300 DOI: 10.1103/physreve.77.061907] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2007] [Revised: 04/02/2008] [Indexed: 05/26/2023]
Abstract
Using a Hamilton-Jacobi equation approach, we obtain analytic equations for steady-state population distributions and mean fitness functions for Crow-Kimura and Eigen-type diploid biological evolution models with general smooth hypergeometric fitness landscapes. Our numerical solutions of diploid biological evolution models confirm the analytic equations obtained. We also study the parallel diploid model for the simple case of recombination and calculate the variance of distribution, which is consistent with numerical results.
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Affiliation(s)
- David B Saakian
- Institute of Physics, Academia Sinica, Nankang, Taipei 11529, Taiwan
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45
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Bodmer J. World distribution of HLA alleles and implications for disease. CIBA FOUNDATION SYMPOSIUM 2007; 197:233-53; discussion 253-8. [PMID: 8827377 DOI: 10.1002/9780470514887.ch13] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The high level of polymorphism of the HLA system makes it useful for the study of diversity in different populations. However, its relationships with disease susceptibility, resistance and progression impose selective pressure on population frequencies that must be taken into consideration. These relationships allow useful studies on the genetic susceptibility to disease, which can be studied further and may provide us with another tool with which to examine the history of populations.
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Affiliation(s)
- J Bodmer
- Imperial Cancer Research Fund, London, UK
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46
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Kamoun M, Israni AK, Joffe MM, Hoy T, Kearns J, Mange KC, Feldman D, Goodman N, Rosas SE, Abrams JD, Brayman KL, Feldman HI. Assessment of differences in HLA-A, -B, and -DRB1 allele mismatches among African-American and non-African-American recipients of deceased kidney transplants. Transplant Proc 2007; 39:55-63. [PMID: 17275474 DOI: 10.1016/j.transproceed.2006.10.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2006] [Indexed: 02/08/2023]
Abstract
Among recipients of deceased donor kidney transplants, African-Americans experience a more rapid rate of kidney allograft loss than non-African-Americans. The purpose of this study was to characterize and quantify the HLA-A, -B, and -DRB1 allele mismatches and amino acid substitutions at antigen recognition sites among African-American and non-African-American recipients of deceased donor kidney transplants matched at the antigen level. In recipients with zero HLA antigen mismatches, the degree of one or two HLA allele mismatches for both racial groups combined was 47%, 29%, and 11% at HLA-DRB1, HLA-B, and HLA-A, respectively. There was a greater number of allele mismatches in African-Americans than non-African-Americans at HLA-A (P < .0001), -B (P = .096), and -DRB1 loci (P < .0001). For both racial groups, the HLA allele mismatches were predominantly at A2 for HLA-A; B35 and B44 for HLA-B; but multiple specificities for HLA-DRB1. The observed amino acid mismatches were concentrated at a few functional positions in the antigen binding site of HLA-A and -B and -DRB1 molecules. Future studies are ongoing to assess the impact of these HLA mismatches on kidney allograft loss.
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Affiliation(s)
- M Kamoun
- Department of Pathology and Laboratory Medicine, Center for Clinical Epidemiology and Biostatistics, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
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47
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Balas A, Alonso-Nieto M, García-Sánchez F, Vicario JL. Characterization of two new human leukocyte antigen class I alleles B*0829 and Cw*0736. ACTA ACUST UNITED AC 2006; 68:267-8. [PMID: 16948653 DOI: 10.1111/j.1399-0039.2006.00644.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- A Balas
- Histocompatibilidad, Centro de Transfusión de la Comunidad de Madrid, Madrid, Spain.
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48
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Birch J, Murphy L, MacHugh ND, Ellis SA. Generation and maintenance of diversity in the cattle MHC class I region. Immunogenetics 2006; 58:670-9. [PMID: 16807744 DOI: 10.1007/s00251-006-0137-y] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2006] [Accepted: 05/31/2006] [Indexed: 10/24/2022]
Abstract
Major histocompatibility complex (MHC) class I genes play a crucial role in the immune defence against intracellular pathogens. An important evolutionary strategy is to generate and maintain a high level of diversity in these genes. Humans express three highly polymorphic classical MHC class I genes (HLA-A, HLA-B and HLA-C). In contrast, some species, for example rat and rhesus macaque, maintain diversity by generation of haplotypes that vary considerably with regard to the number and combination of transcribed genes. Cattle appear to use both strategies. We show that various combinations of six apparently classical genes, three of which are highly polymorphic, are transcribed on different haplotypes. Although additional sequences were identified in both cDNA and gDNA, it was not possible to assign them to any of these defined genes. Most were highly divergent or were non-classical class I genes. Thus, we found little evidence for frequent duplication and deletion of classical class I genes as reported in some other species. However, the maintenance of class I diversity in cattle may involve limited gene shuffling and deletion, possibly as a result of unequal crossing-over within the class I region.
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Affiliation(s)
- James Birch
- Immunology Division, Institute for Animal Health, Compton, RG20 7NN, UK
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49
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Piazza A, Poggi E, Ozzella G, Borrelli L, Monaco PI, Scornajenghi A, Tisone G, Adorno D. Public Epitope Specificity of HLA Class I Antibodies Induced by a Failed Kidney Transplant: Alloantibody Characterization by Flow Cytometric Techniques. Transplantation 2006; 81:1298-305. [PMID: 16699458 DOI: 10.1097/01.tp.0000209654.87584.c5] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND Patients whose kidney grafts fail develop alloantibodies that react with many HLA molecules. We analyzed the epitope specificity of HLA class I alloantibodies in the sera of 55 patients who had been sensitized by kidney grafts, and investigated the immunogenicity of various polymorphic epitopes. METHODS HLA class I alloantibodies were detected and characterized by flow cytometry (FlowPRA beads). Potential "immunizing epitopes" were identified by comparing the amino acid sequences of HLA class I antigens/alleles of the donor, recipient and the antibody-reactivity pattern. RESULTS In the 55 anti-HLA class I-positive patients, 82 different antibody reactivity patterns were identified; all but 5 (94%) were determined by a "public epitope" of donor HLA-A and/or -B molecules. Forty-five of 50 patients who showed HLA-A Res-MMs with their donors produced HLA-A antibodies, but only 31 of 51 subjects with HLA-B Res-MMs produced HLA-B antibodies (P=0.001; O.R.=5.81). The antibody patterns were specific for a "single" epitope of the mismatched donor molecules in 91% of patients. Forty-three of the 120 (36%) mismatched HLA-A and/or -B epitopes were positively correlated with antibody production. The polymorphic determinants of higher immunogenic capacity were b80N (Bw6-associated) and ab82-83LR (Bw4-associated) public epitopes. CONCLUSIONS The humoral immune response against a kidney graft mainly produces HLA class I antibodies specific for "public epitopes" of mismatched donor molecules. A "single" donor-epitope may determine the production of a spread antibody pattern. In renal transplantation, epitope matching is better than HLA antigen matching for avoiding or minimizing development of HLA antibodies.
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Affiliation(s)
- Antonina Piazza
- National Council of Research, Institute of Organ Transplantation and Immunocytology, Rome, Italy.
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50
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Hoelsch K, Lenggeler I, Knabe H, Hartel K, Klein HG, Woelpl A. Identification of a novel HLA-B*44 variant (B*4441) in three unrelated Caucasian individuals. ACTA ACUST UNITED AC 2006; 67:247-9. [PMID: 16573564 DOI: 10.1111/j.1399-0039.2006.00563.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Here, we report the identification of a new human leukocyte antigen (HLA)-B*44 allele found almost simultaneous in three DNA samples which were part of routine bone marrow donor typing by order of the German registry 'Aktion Knochenmarkspende Bayern'. The samples appeared noticeable in different polymerase chain reactions using sequence-specific primers (PCR-SSP) or sequence-specific oligonucleotides (PCR-SSO). Sequence-based typing revealed a novel allele officially designated as B*4441*. This sequence differs from HLA-B*44020101/4427 by two nucleotide positions at the beginning of exon 3: by position 353 (T to C) and by position 355 (A to C). These differences in sequence result in deviant amino acids at codon 94 (Ile94Thr) and codon 95 (Ile95Leu).
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Affiliation(s)
- K Hoelsch
- Laboratory for Medical Genetics, Dr Klein, Martinsried, Munich, Germany
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