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Abstract
Compared to the major histocompatibility complex (MHC) of typical mammals, the chicken BF/BL region is small and simple, with most of the genes playing central roles in the adaptive immune response. However, some genes of the chicken MHC are almost certainly involved in innate immunity, such as the complement component C4 and the lectin-like receptor/ligand gene pair BNK and Blec. The poorly expressed classical class I molecule BF1 is known to be recognised by natural killer (NK) cells and, analogous to mammalian immune responses, the classical class I molecules BF1 and BF2, the CD1 homologs and the butyrophilin homologs called BG may be recognised by adaptive immune lymphocytes with semi-invariant receptors in a so-called adaptate manner. Moreover, the TRIM and BG regions next to the chicken MHC, along with the genetically unlinked Y and olfactory/scavenger receptor regions on the same chromosome, have multigene families almost certainly involved in innate and adaptate responses. On this chicken microchromosome, the simplicity of the adaptive immune gene systems contrasts with the complexity of the gene systems potentially involved in innate immunity.
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Potts ND, Bichet C, Merat L, Guitton E, Krupa AP, Burke TA, Kennedy LJ, Sorci G, Kaufman J. Development and optimization of a hybridization technique to type the classical class I and class II B genes of the chicken MHC. Immunogenetics 2019; 71:647-663. [PMID: 31761978 PMCID: PMC6900278 DOI: 10.1007/s00251-019-01149-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2019] [Accepted: 11/17/2019] [Indexed: 01/02/2023]
Abstract
The classical class I and class II molecules of the major histocompatibility complex (MHC) play crucial roles in immune responses to infectious pathogens and vaccines as well as being important for autoimmunity, allergy, cancer and reproduction. These classical MHC genes are the most polymorphic known, with roughly 10,000 alleles in humans. In chickens, the MHC (also known as the BF-BL region) determines decisive resistance and susceptibility to infectious pathogens, but relatively few MHC alleles and haplotypes have been described in any detail. We describe a typing protocol for classical chicken class I (BF) and class II B (BLB) genes based on a hybridization method called reference strand-mediated conformational analysis (RSCA). We optimize the various steps, validate the analysis using well-characterized chicken MHC haplotypes, apply the system to type some experimental lines and discover a new chicken class I allele. This work establishes a basis for typing the MHC genes of chickens worldwide and provides an opportunity to correlate with microsatellite and with single nucleotide polymorphism (SNP) typing for approaches involving imputation.
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Affiliation(s)
- Nicola D Potts
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QP, UK.,LGC Ltd., Newmarket Road, Fordham, Ely, CB7 5WW, UK
| | - Coraline Bichet
- BioGéoSciences, CNRS UMR 5561, Université de Bourgogne Franche-Comté, 6 Boulevard Gabriel, 21000, Dijon, France.,Institute of Avian Research, An der Vogelwarte 21, 26386, Wilhelmshaven, Germany
| | - Laurence Merat
- Plate-Forme d'Infectiologie Expérimentale (PFIE), UE-1277, INRA Centre Val de Loire, 37380, Nouzilly, France
| | - Edouard Guitton
- Plate-Forme d'Infectiologie Expérimentale (PFIE), UE-1277, INRA Centre Val de Loire, 37380, Nouzilly, France
| | - Andrew P Krupa
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, S10 2TN, Sheffield, UK
| | - Terry A Burke
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, S10 2TN, Sheffield, UK
| | - Lorna J Kennedy
- Division of Population Health, Health Services Research & Primary Care, University of Manchester, Oxford Road, M13 9PL, Manchester, UK
| | - Gabriele Sorci
- BioGéoSciences, CNRS UMR 5561, Université de Bourgogne Franche-Comté, 6 Boulevard Gabriel, 21000, Dijon, France
| | - Jim Kaufman
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QP, UK. .,Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, CB3 0ES, UK.
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Afrache H, Tregaskes CA, Kaufman J. A potential nomenclature for the Immuno Polymorphism Database (IPD) of chicken MHC genes: progress and problems. Immunogenetics 2019; 72:9-24. [PMID: 31741010 PMCID: PMC6971145 DOI: 10.1007/s00251-019-01145-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 10/20/2019] [Indexed: 12/25/2022]
Abstract
Among the genes with the highest allelic polymorphism and sequence diversity are those encoding the classical class I and class II molecules of the major histocompatibility complex (MHC). Although many thousands of MHC sequences have been deposited in general sequence databases like GenBank, the availability of curated MHC sequences with agreed nomenclature has been enormously beneficial. Along with the Immuno Polymorphism Database-IMunoGeneTics/human leukocyte antigen (IPD-IMGT/HLA) database, a collection of databases for curated sequences of immune importance has been developed. A recent addition is an IPD-MHC database for chickens. For many years, the nomenclature system for chicken MHC genes has been based on a list of standard, presumed to be stable, haplotypes. However, these standard haplotypes give different names to identical sequences. Moreover, the discovery of new recombinants between haplotypes and a rapid increase in newly discovered alleles leaves the old system untenable. In this review, a new nomenclature is considered, for which alleles of different loci are given names based on the system used for other MHCs, and then haplotypes are named according to the alleles present. The new nomenclature system is trialled, first with standard haplotypes and then with validated sequences from the scientific literature. In the trial, some class II B sequences were found in both class II loci, presumably by gene conversion or inversion, so that identical sequences would receive different names. This situation prompts further suggestions to the new nomenclature system. In summary, there has been progress, but also problems, with the new IPD-MHC system for chickens.
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Affiliation(s)
- Hassnae Afrache
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QP, UK
| | - Clive A Tregaskes
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QP, UK
| | - Jim Kaufman
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QP, UK. .,Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, CB2 0ES, UK.
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Chen L, Fakiola M, Staines K, Butter C, Kaufman J. Functional Alleles of Chicken BG Genes, Members of the Butyrophilin Gene Family, in Peripheral T Cells. Front Immunol 2018; 9:930. [PMID: 29765375 PMCID: PMC5938342 DOI: 10.3389/fimmu.2018.00930] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 04/16/2018] [Indexed: 11/16/2022] Open
Abstract
γδ T cells recognize a wide variety of ligands in mammals, among them members of the butyrophilin (BTN) family. Nothing is known about γδ T cell ligands in chickens, despite there being many such cells in blood and lymphoid tissues, as well as in mucosal surfaces. The major histocompatibility complex (MHC) of chickens was discovered because of polymorphic BG genes, part of the BTN family. All but two BG genes are located in the BG region, oriented head-to-tail so that unequal crossing-over has led to copy number variation (CNV) as well as hybrid (chimeric) genes, making it difficult to identify true alleles. One approach is to examine BG genes expressed in particular cell types, which likely have the same functions in different BG haplotypes and thus can be considered “functional alleles.” We cloned nearly full-length BG transcripts from peripheral T cells of four haplotypes (B2, B15, B19, and B21), and compared them to the BG genes of the B12 haplotype that previously were studied in detail. A dominant BG gene was found in each haplotype, but with significant levels of subdominant transcripts in three haplotypes (B2, B15, and B19). For three haplotypes (B15, B19, and B21), most sequences are closely-related to BG8, BG9, and BG12 from the B12 haplotype. We found that variation in the extracellular immunoglobulin-variable-like (Ig-V) domain is mostly localized to the membrane distal loops but without evidence for selection. However, variation in the cytoplasmic tail composed of many amino acid heptad repeats does appear to be selected (although not obviously localized), consistent with an intriguing clustering of charged and polar residues in an apparent α-helical coiled-coil. By contrast, the dominantly-expressed BG gene in the B2 haplotype is identical to BG13 from the B12 haplotype, and most of the subdominant sequences are from the BG5-BG7-BG11 clade. Moreover, alternative splicing leading to intron read-through results in dramatically truncated cytoplasmic tails, particularly for the dominantly-expressed BG gene of the B2 haplotype. The approach of examining “functional alleles” has yielded interesting data for closely-related genes, but also thrown up unexpected findings for at least one haplotype.
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Affiliation(s)
- Lei Chen
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Michaela Fakiola
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Karen Staines
- Pirbright Institute, Compton, United Kingdom.,School of Life Sciences, University of Lincoln, Lincoln, United Kingdom
| | - Colin Butter
- Pirbright Institute, Compton, United Kingdom.,School of Life Sciences, University of Lincoln, Lincoln, United Kingdom
| | - Jim Kaufman
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom.,Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
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