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Immunogenetics

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https://www.readbyqxmd.com/read/30039257/comparative-mhc-nomenclature-report-from-the-isag-iuis-vic-committee-2018
#1
Keith T Ballingall, Ronald E Bontrop, Shirley A Ellis, Unni Grimholt, John A Hammond, Chak-Sum Ho, Jim Kaufman, Lorna J Kennedy, Giuseppe Maccari, Donald Miller, James Robinson, Steven G E Marsh
Significant progress has been made over the last decade in defining major histocompatibility complex (MHC) diversity at the nucleotide, allele, haplotype, diplotype, and population levels in many non-human species. Much of this progress has been driven by the increased availability and reduced costs associated with nucleotide sequencing technologies. This report provides an update on the activities of the comparative MHC nomenclature committee which is a standing committee of both the International Society for Animal Genetics (ISAG) and the International Union of Immunological Societies (IUIS) where it operates under the umbrella of the Veterinary Immunology Committee (VIC)...
July 24, 2018: Immunogenetics
https://www.readbyqxmd.com/read/30027299/ipd-mhc-nomenclature-requirements-for-the-non-human-major-histocompatibility-complex-in-the-next-generation-sequencing-era
#2
Giuseppe Maccari, James Robinson, Ronald E Bontrop, Nel Otting, Natasja G de Groot, Chak-Sum Ho, Keith T Ballingall, Steven G E Marsh, John A Hammond
The IPD-MHC Database is the official repository for non-human MHC sequences, overseen and supported by the Comparative MHC Nomenclature Committee, providing access to curated MHC data and associated analysis tools. To address the increasing amount and complexity of data being submitted, an entirely upgraded version of the IPD-MHC Database was recently released to maintain IPD-MHC as the central platform for the comparison of curated MHC data. As a consequence, a new level of nomenclature standardisation is required between the different species to enable data submission and to allow the unambiguous inter- and intra-species comparison of alleles...
July 19, 2018: Immunogenetics
https://www.readbyqxmd.com/read/29998404/cetacea-are-natural-knockouts-for-il20
#3
Mónica Lopes-Marques, André M Machado, Susana Barbosa, Miguel M Fonseca, Raquel Ruivo, L Filipe C Castro
The Cetacea infraorder comprises a very unique group within the mammalian lineage. While sharing common ancestors with terrestrial mammals, their exclusive dependence on aquatic environments makes them attractive models to explore the landscape of molecular shifts in radical habitat transitions. Among their diverse anatomical and physiological solutions, we find detectable genetic remodeling of the immune system. In agreement, here we show that the gene sequence of interleukin-20 (IL20) displays unambiguous signs of inactivation with several disruptive mutations, including stop codons, insertions, and a conserved trans-species mutation abolishing a canonical splice site, in nine analyzed cetacean genomes...
July 12, 2018: Immunogenetics
https://www.readbyqxmd.com/read/29992375/analysis-of-the-affinity-of-influenza-a-virus-protein-epitopes-for-swine-mhc-i-by-a-modified-in-vitro-refolding-method-indicated-cross-reactivity-between-swine-and-human-mhc-i-specificities
#4
Shuhua Fan, Yongli Wang, Xian Wang, Li Huang, Yunxia Zhang, Xiaomeng Liu, Wenshuai Zhu
In vitro refolding assays can be used to investigate the affinity and stability of the binding of epitope peptides to major histocompatibility complex (MHC) class I molecules, which are key factors in the presentation of peptides to cytotoxic T lymphocytes (CTLs). The recognition of peptide epitopes by CTLs is crucial for protection against influenza A virus (IAV) infection. The peptide-binding motif of the swine SLA-3*hs0202 molecule has been previously reported and partly overlaps with the binding motif of the most abundant human MHC allele, HLA-A*0201...
July 10, 2018: Immunogenetics
https://www.readbyqxmd.com/read/29982918/correction-to-two-class-i-genes-of-the-chicken-mhc-have-different-functions-bf1-is-recognized-by-nk-cells-while-bf2-is-recognized-by-ctls
#5
Taejoong Kim, Henry D Hunt, Mark S Parcells, Vicky van Santen, Sandra J Ewald
The Figure 3 in the original version of this article was incorrectly published. In this article the top panel of Figure 3 that describes the amino acid sequence alignment is now added. The original article has been corrected.
July 7, 2018: Immunogenetics
https://www.readbyqxmd.com/read/29931472/the-unique-evolution-of-the-pig-lrc-a-single-kir-but-expansion-of-lilr-and-a-novel-ig-receptor-family
#6
John C Schwartz, John A Hammond
The leukocyte receptor complex (LRC) encodes numerous immunoglobulin (Ig)-like receptors involved in innate immunity. These include the killer-cell Ig-like receptors (KIR) and the leukocyte Ig-like receptors (LILR) which can be polymorphic and vary greatly in number between species. Using the recent long-read genome assembly, Sscrofa11.1, we have characterized the porcine LRC on chromosome 6. We identified a ~ 197-kb region containing numerous LILR genes that were missing in previous assemblies. Out of 17 such LILR genes and fragments, six encode functional proteins, of which three are inhibitory and three are activating, while the majority of pseudogenes had the potential to encode activating receptors...
June 21, 2018: Immunogenetics
https://www.readbyqxmd.com/read/29923028/genomic-convergence-of-locus-based-gwas-meta-analysis-identifies-axin1-as-a-novel-parkinson-s-gene
#7
Mohammad Saeed
Parkinson's disease (PD) is a common, disabling neurodegenerative disorder with significant genetic underpinnings. Multiple genome-wide association studies (GWAS) have been conducted with identification of several PD loci. However, these only explain about 25% of PD genetic risk indicating that additional loci of modest effect remain to be discovered. Association clustering methods such as gene-based tests are more powerful than single-variant analysis for identifying modest genetic effects. Combined with the locus-based algorithm, OASIS, the most significant association signals can be homed in...
June 19, 2018: Immunogenetics
https://www.readbyqxmd.com/read/29947944/two-class-i-genes-of-the-chicken-mhc-have-different-functions-bf1-is-recognized-by-nk-cells-while-bf2-is-recognized-by-ctls
#8
Taejoong Kim, Henry D Hunt, Mark S Parcells, Vicky van Santen, Sandra J Ewald
The function of the chicken's major histocompatibility complex (MHC or B complex) class I major (BF2) and minor (BF1) glycoproteins is compared for their expression, ability to present viral antigens to cytotoxic T lymphocytes (CTLs), and interaction with natural killer (NK) cells. MHC-restricted CTLs recognized virus antigen in the context of the BF2*21 major glycoprotein but not the BF1*21 minor glycoprotein. Marek's disease virus (MDV), a large DNA virus known to reduce the cell surface expression of class I glycoprotein, reduced the expression of BF2 glycoprotein while BF1glycoprotein expressions are remained as no change or slight increase...
June 9, 2018: Immunogenetics
https://www.readbyqxmd.com/read/29947943/identification-and-annotation-of-bovine-granzyme-genes-reveals-a-novel-granzyme-encoded-within-the-trypsin-like-locus
#9
Jie Yang, Christina Vrettou, Tim Connelley, W Ivan Morrison
Granzymes are a family of serine proteases found in the lytic granules of cytotoxic T lymphocytes and natural killer (NK) cells, which are involved in killing of susceptible target cells. Most information on granzymes and their enzymatic specificities derive from studies in humans and mice. Although granzymes shared by both species show a high level of conservation, the complement of granzyme genes differs between the species. The aim of this study was to identify granzyme genes expressed in cattle, determine their genomic locations and analyse their sequences to predict likely functional specificities...
June 8, 2018: Immunogenetics
https://www.readbyqxmd.com/read/29869002/nomenclature-for-the-kir-of-non-human-species
#10
James Robinson, Lisbeth A Guethlein, Giuseppe Maccari, Jeroen Blokhuis, Benjamin N Bimber, Natasja G de Groot, Nicholas D Sanderson, Laurent Abi-Rached, Lutz Walter, Ronald E Bontrop, John A Hammond, Steven G E Marsh, Peter Parham
The increasing number of Killer Immunoglobulin-like Receptor (KIR) sequences available for non-human primate species and cattle has prompted development of a centralized database, guidelines for a standardized nomenclature, and minimum requirements for database submission. The guidelines and nomenclature are based on those used for human KIR and incorporate modifications made for inclusion of non-human species in the companion IPD-NHKIR database. Included in this first release are the rhesus macaque (Macaca mulatta), chimpanzee (Pan troglodytes), orangutan (Pongo abelii and Pongo pygmaeus), and cattle (Bos taurus)...
June 4, 2018: Immunogenetics
https://www.readbyqxmd.com/read/29862454/genome-wide-association-study-identifies-loci-associated-with-milk-leukocyte-phenotypes-following-experimental-challenge-with-streptococcus-uberis
#11
Lydia Siebert, Margaret E Staton, Susan Headrick, Mark Lewis, Barbara Gillespie, Charles Young, Raul A Almeida, Stephen P Oliver, Gina M Pighetti
Mastitis is a detrimental disease in the dairy industry that decreases milk quality and costs upwards of $2 billion annually. Often, mastitis results from bacteria entering the gland through the teat opening. Streptococcus uberis is responsible for a high percentage of subclinical and clinical mastitis. Following an intramammary experimental challenge with S. uberis on Holstein cows (n = 40), milk samples were collected and somatic cell counts (SCC) were determined by the Dairy Herd Improvement Association Laboratory...
June 3, 2018: Immunogenetics
https://www.readbyqxmd.com/read/29808256/cdx-2-polymorphism-in-the-vitamin-d-receptor-gene-vdr-marks-vdr-expression-in-monocyte-macrophages-through-vdr-promoter-methylation
#12
Vanessa Meyer, Liza Bornman
Caudal-type homeobox protein 2 (CDX-2) is an intestine-specific transcription factor (TF), with a polymorphic binding site (Cdx-2, rs11568820, A/G) in the vitamin D receptor gene (VDR). The molecular mechanism underlying Cdx-2 association with conditions like osteoporosis, which depends on intestinal VDR expression and calcium absorption, is believed to be due to higher affinity of CDX-2 for the ancestral A allele compared to the G allele. However, it is unclear why the polymorphism is associated with diseases like tuberculosis, which is dependent on VDR expression in immune cells that do not express CDX-2...
August 2018: Immunogenetics
https://www.readbyqxmd.com/read/29696367/the-distribution-of-hla-haplotypes-in-the-ethnic-groups-that-make-up-the-brazilian-bone-marrow-volunteer-donor-registry-redome
#13
Michael Halagan, Danielli Cristina Oliveira, Martin Maiers, Raquel A Fabreti-Oliveira, Maria Elisa Hue Moraes, Jeane Eliete Laguila Visentainer, Noemi Farah Pereira, Matilde Romero, Juliana Fernandes Cardoso, Luís Cristóvão Porto
The Registries of Bone Marrow Donors around the world include more than 30 million volunteer donors from 57 different countries, and were responsible for over 17,000 hematopoietic stem cell transplants in 2016. The Brazilian Bone Marrow Volunteer Donor Registry (REDOME) was established in 1993 and is the third largest registry in the world with more than 4.3 million donors. We characterized HLA allele and haplotypes frequencies from REDOME comparing them with the donor self-reported race group classification...
August 2018: Immunogenetics
https://www.readbyqxmd.com/read/29696366/genetic-interaction-between-two-insulin-dependent-diabetes-susceptibility-loci-idd2-and-idd13-in-determining-immunoregulatory-dn-t-cell-proportion
#14
Roxanne Collin, Kathy Doyon, Victor Mullins-Dansereau, Martin Karam, Geneviève Chabot-Roy, Erin E Hillhouse, Alexandre Orthwein, Sylvie Lesage
Several immune regulatory cell types participate in the protection against autoimmune diseases such as autoimmune diabetes. Of these immunoregulatory cells, we and others have shown that peripheral CD4- CD8- double negative (DN) T cells can induce antigen-specific immune tolerance. Particularly, we have described that diabetes-prone mice exhibit a lower number of peripheral DN T cells compared to diabetes-resistant mice. Identifying the molecular pathways that influence the size of the DN T cell pool in peripheral lymphoid organs may thus be of interest for maintaining antigen-specific immune tolerance...
August 2018: Immunogenetics
https://www.readbyqxmd.com/read/29602958/hla-g-peptide-preferences-change-in-transformed-cells-impact-on-the-binding-motif
#15
Alexander A Celik, Gwendolin S Simper, Wiebke Hiemisch, Rainer Blasczyk, Christina Bade-Döding
HLA-G is known for its strictly restricted tissue distribution. HLA-G expression could be detected in immune privileged organs and many tumor entities such as leukemia, multiple myeloma, and non-Hodgkin and Hodgkin's lymphoma. This functional variability from mediation of immune tolerance to facilitation of tumor immune evasion strategies might translate to a differential NK cell inhibition between immune-privileged organs and tumor cells. The biophysical invariability of the HLA-G heavy chain and its contrary diversity in immunity implicates a strong influence of the bound peptides on the pHLA-G structure...
August 2018: Immunogenetics
https://www.readbyqxmd.com/read/29397401/absence-of-the-tag-polymorphism-for-the-risk-haplotype-hla-dr2-for-multiple-sclerosis-in-wix%C3%A3-rika-subjects-from-mexico
#16
G V González-Enríquez, B M Torres-Mendoza, J Márquez-Pedroza, M A Macías-Islas, G G Ortiz, J A Cruz-Ramos
The HLA-DRB1*15:01 allele has a demonstrated risk for the development of multiple sclerosis (MS) in most populations around the world. The single nucleotide polymorphism (SNP) rs3129934 is found in linkage disequilibrium with the risk haplotype formed by the HLA-DRB1*15:01 and HLA-DQB1*06:02 alleles, and it is considered a reliable marker of the presence of this haplotype. Native Americans have a null or low prevalence of MS. In this study, we sought to identify the frequency of rs3129934 in the Wixárika ethnic group as well as in Mestizo (mixed race) patients with MS and in controls from western Mexico...
August 2018: Immunogenetics
https://www.readbyqxmd.com/read/29594415/restricted-mhc-class-i-a-locus-diversity-in-olive-and-hybrid-olive-yellow-baboons-from-the-southwest-national-primate-research-center
#17
Rebecca A Morgan, Julie A Karl, Hailey E Bussan, Katelyn E Heimbruch, David H O'Connor, Dawn M Dudley
Baboons are valuable models for complex human diseases due to their genetic and physiologic similarities to humans. Deep sequencing methods to characterize full-length major histocompatibility complex (MHC) class I (MHC-I) alleles in different nonhuman primate populations were used to identify novel MHC-I alleles in baboons. We combined data from Illumina MiSeq sequencing and Roche/454 sequencing to characterize novel full-length MHC-I transcripts in a cohort of olive and hybrid olive/yellow baboons from the Southwest National Primate Research Center (SNPRC)...
July 2018: Immunogenetics
https://www.readbyqxmd.com/read/29508036/the-expression-profile-of-the-ubiquitin-like-modifier-fat10-in-immune-cells-suggests-cell-type-specific-functions
#18
Richard Schregle, Mei Min Mah, Stefanie Mueller, Annette Aichem, Michael Basler, Marcus Groettrup
The TNF and IFN-γ-inducible ubiquitin-like modifier HLA-F adjacent transcript 10 (FAT10) is most prominently expressed in immunological tissues but information regarding basal expression and inducibility of FAT10 in the different types of immune cells is still lacking. Hence, we investigated FAT10 mRNA expression in the major human and murine immune cell subsets, and FAT10 protein expression in human leukocytes. We isolated the different human leukocytes from peripheral blood and the murine immune cell subsets from spleen...
July 2018: Immunogenetics
https://www.readbyqxmd.com/read/29492592/cross-modality-deep-learning-based-prediction-of-tap-binding-and-naturally-processed-peptide
#19
Hanan Besser, Yoram Louzoun
Epitopes presented on MHC class I molecules pass multiple processing stages before their presentation on MHC molecules, the main ones being proteasomal cleavage and TAP binding. Transporter associated with antigen processing (TAP) binding is a necessary stage for most, but not all, MHC-I-binding peptides. The molecular determinants of TAP-binding peptides can be experimentally estimated from binding experiments and from the properties of peptides inducing a CD8 T cell response. We here propose novel optimization formalisms to combine binding and activation experimental results to produce a classifier for TAP binding using dual-output kernel and deep learning approaches...
July 2018: Immunogenetics
https://www.readbyqxmd.com/read/29478145/mhc-class-i-diversity-of-olive-baboons-papio-anubis-unravelled-by-next-generation-sequencing
#20
Marit K H van der Wiel, Gaby G M Doxiadis, N de Groot, N Otting, N G de Groot, N Poirier, G Blancho, R E Bontrop
The olive baboon represents an important model system to study various aspects of human biology and health, including the origin and diversity of the major histocompatibility complex. After screening of a group of related animals for polymorphisms associated with a well-defined microsatellite marker, subsequent MHC class I typing of a selected population of 24 animals was performed on two distinct next-generation sequencing (NGS) platforms. A substantial number of 21 A and 80 B transcripts were discovered, about half of which had not been previously reported...
July 2018: Immunogenetics
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