Major Histocompatibility Gene Research Articles

Antibody Sequence and Structure Analyses Using IMGT®: 30 Years of Immunoinformatics.

IMGT®, the international ImMunoGeneTics information system®, http://www.imgt.org , the global reference in immunogenetics and immunoinformatics, was created in 1989 by Marie-Paule Lefranc (Université de Montpellier and CNRS) to manage the huge diversity of the antigen receptors, immunoglobulins (IG) or antibodies, and T cell receptors (TR) of the adaptive immune responses. The founding of IMGT® marked the advent of immunoinformatics, which emerged at the interface between immunogenetics and bioinformatics. IMGT® standardized analysis of the IG, TR, and major histocompatibility (MH) genes and proteins bridges the gap between sequences and three-dimensional (3D) structures, for all jawed vertebrates from fish to humans. This is achieved through the IMGT Scientific chart rules, based on the IMGT-ONTOLOGY axioms, and primarily CLASSIFICATION (IMGT gene and allele nomenclature) and NUMEROTATION (IMGT unique numbering and IMGT Colliers de Perles). IMGT® comprises seven databases (IMGT/LIGM-DB for nucleotide sequences, IMGT/GENE-DB for genes and alleles, etc.), 17 tools (IMGT/V-QUEST, IMGT/JunctionAnalysis, IMGT/HighV-QUEST for NGS, etc.), and more than 20,000 Web resources. In this chapter, the focus is on the tools for amino acid sequences per domain (IMGT/DomainGapAlign and IMGT/Collier-de-Perles), and on the databases for receptors (IMGT/2Dstructure-DB and IMGT/3D-structure-DB) described per receptor, chain, and domain and, for 3D, with contact analysis, paratope, and epitope. The IMGT/mAb-DB is the query interface for monoclonal antibodies (mAb), fusion proteins for immune applications (FPIA), composite proteins for clinical applications (CPCA), and related proteins of interest (RPI) with links to IMGT® 2D and 3D databases and to the World Health Organization (WHO) International Nonproprietary Names (INN) program lists. The chapter includes the human IG allotypes and antibody engineered variants for effector properties used in the description of therapeutical mAb.

A Chromosome-Length Assembly of the Hawaiian Monk Seal (Neomonachus schauinslandi): A History of "Genetic Purging" and Genomic Stability.

The Hawaiian monk seal (HMS) is the single extant species of tropical earless seals of the genus Neomonachus. The species survived a severe bottleneck in the late 19th century and experienced subsequent population declines until becoming the subject of a NOAA-led species recovery effort beginning in 1976 when the population was fewer than 1000 animals. Like other recovering species, the Hawaiian monk seal has been reported to have reduced genetic heterogeneity due to the bottleneck and subsequent inbreeding. Here, we report a chromosomal reference assembly for a male animal produced using a variety of methods. The final assembly consisted of 16 autosomes, an X, and portions of the Y chromosomes. We compared variants in this animal to other HMS and to a frequently sequenced human sample, confirming about 12% of the variation seen in man. To confirm that the reference animal was representative of the HMS, we compared his sequence to that of 10 other individuals and noted similarly low variation in all. Variation in the major histocompatibility (MHC) genes was nearly absent compared to the orthologous human loci. Demographic analysis predicts that Hawaiian monk seals have had a long history of small populations preceding the bottleneck, and their current low levels of heterozygosity may indicate specialization to a stable environment. When we compared our reference assembly to that of other species, we observed significant conservation of chromosomal architecture with other pinnipeds, especially other phocids. This reference should be a useful tool for future evolutionary studies as well as the long-term management of this species.

Bone Marrow-Based Biomarkers for Predicting aGVHD Using Targeted RNA Next Generation Sequencing and Machine Learning

Bone Marrow-Based Biomarkers for Predicting aGVHD Using Targeted RNA Next Generation Sequencing and Machine Learning

Functional genetics for studying the human immune system.

Although small numbers of immune-mediated diseases are inherited due to rare genetic mutations, most are multifactorial diseases caused by multiple elements including genetic and environmental factors. In the case of autoimmune diseases, many disease-susceptibility genes, including several in the major histocompatibility gene complex, have been reported, and over the past 10 years, genome-wide association studies (GWAS) have been used to analyze disease-susceptibility loci in representative diseases. Furthermore, many disease-susceptibility variants have been found to be related to gene expression levels. The expression of genes involved in disease pathogenesis is often cell-type-specific, and this is closely related to epigenome alterations. Genomic information is present even before the onset of a disease and has a clear causal relationship to the disease (i.e. the outcome). Therefore, it is important to establish functional genetics in human immunology to understand the pathogenesis of diseases using these pieces of information. We can then apply these results to drug discovery. Here, we will review these issues, especially focusing on autoimmune diseases, and discuss current and future directions of human immune system research.

Host-parasite co-evolution and its genomic signature.

Studies in diverse biological systems have indicated that host-parasite co-evolution is responsible for the extraordinary genetic diversity seen in some genomic regions, such as major histocompatibility (MHC) genes in jawed vertebrates and resistance genes in plants. This diversity is believed to evolve under balancing selection on hosts by parasites. However, the mechanisms that link the genomic signatures in these regions to the underlying co-evolutionary process are only slowly emerging. We still lack a clear picture of the co-evolutionary concepts and of the genetic basis of the co-evolving phenotypic traits in the interacting antagonists. Emerging genomic tools that provide new options for identifying underlying genes will contribute to a fuller understanding of the co-evolutionary process.

Major Histocompatibility Gene Complex Polymorphism in Gerze Chicken and Some Pure Line Genotypes

Bu çalışmada Gerze tavuğu popülasyonuna ait 43 örnek ile ticari saf hatlardan oluşturulan 50 örneklik Saf hat popülasyonunun majör doku uyumluluğu gen kompleksi (MHC) bakımından moleküler incelenmesi amaçlanmıştır. Allelik çeşitlilik, MHC içerisinde yer alan MCW0371 ve LEI0258 mikrosatellit lokuslarının PCR yöntemi yardımıyla çoğaltılarak elde edilen DNA fragmentlerinin agaroz jel elektroforezi ile ayrımlanması ile hesaplanmıştır. Gerze popülasyonunda LEI0258 lokusunda elde edilen allel sayısı, etkili allel sayısı, gözlenen heterozigotluk ve beklenen heterozigotluk değerleri sırasıyla; 16, 10.82, 0.67, 0.91, Saf hat popülasyonunda ise 19, 11.84, 0.60, 0.92 olarak bulunmuştur. MCW0371 lokusu için sırasıyla; Gerze popülasyonunda 3, 2.68, 0, 0.63 ve Saf hat popülasyonunda 3, 1.96, 0, 0.49 olarak tespit edilmiştir. Popülasyonlar arasında Nei genetik uzaklık ve genetik benzerlik değerleri sırasıyla 0.419 ve 0.658 olarak hesaplanmıştır. Popülasyonlar arasında FST değeri 0.068 olarak bulunmuştur. Elde edilen bulgular, içerdiği allel deseni bakımından Gerze tavuğunun özgün bir genetik kaynak olarak korunmasının ve ıslah programlarına dahil edilmesinin önemli olduğu sonucuna varılmıştır.

Diversity in human major histocompatibility genes among ethnic groups of Nepal

Diversity in human major histocompatibility genes among ethnic groups of Nepal

Kapa Biosystems Library Amplification Kit (KK 2611, KK2612): Developmentof a method for typing the major histocompatibility gene complex in humans (HLA) using a next-generation sequencer (NGS)

Kapa Biosystems Library Amplification Kit (KK 2611, KK2612): Developmentof a method for typing the major histocompatibility gene complex in humans (HLA) using a next-generation sequencer (NGS)

Is granulomatosis with polyangiitis in Asia different from the West?

The incidence and clinical features of antineutrophil cytoplasmic antibody (ANCA) associated vasculitis (AAV) have been shown to vary according to geographical areas, with granulomatosis with polyangiitis (GPA) being more common in northern Europe and microscopic polyangiitis (MPA) being more common in Asian countries. The annual incidence of GPA among Asians varies between 0.37/million to 2.1/million population. The prevalence of GPA has been estimated to be 1.94/100000 in a Chinese population. Polymorphisms in class II major histocompatibility genes and ETS1 proto-oncogene has been shown in Asian patients with GPA. There is a difference in mean age at onset and proteinase 3 (PR3) or myeloperoxidase (MPO) positivity in GPA patients from different Asian countries. Those from India had mean age of 40years and those from Japan had mean age of 65years. Sixty percent of GPA patients from China and Japan were MPO ANCA positive while the majority of patients from India and Korea were PR3 positive. Geographical variation with lower frequency of renal involvement in Indian studies and higher frequency in Chinese patients has also been noted. Treatment outcomes have been similar to those reported from other parts of the world. Remission was achieved in about two-thirds of patients while relapses were noted in one-third to half of the patients. Apart from minor differences in the organ systems involved, MPO-ANCA GPA and PR3-ANCA GPA had similar rates of remission and relapses.

A Scientific Basis for Humanae Vitae and Natural Law

This article will review Humanae Vitae's predictions of the effect of oral contraceptives (the pill) on male-female relationships and societal behaviors. A scientific, biochemical basis underpinning these predictions is made. Evidence of human pheromones will be given. Evidence for the changes in male and female pheromones caused by the pill is given. Observational and experimental evidence of changes in primate and human behaviors by pheromones is detailed. The role these changes have caused in attractiveness and selection of mate by both males and females in preferences concerning major histocompatibility genes is examined. These changes have also resulted in societal changes in sexual behavior and family structure and have led to increased violence against women. Biochemical evidence for the abortifacient properties of the pill is given. The use of natural family planning is given as a needed alternative to the harms of the pill. Summary: The human biological bases of Humanae Vitae's predictions of the effect of the pill on male-female relationships are examined. Evidence of the presence of pheromones in primates and humans is given. The pill changes human pheromones, odors which are subconsciously detected. These pheromones cause humans to change what they find attractive in a mate. Choosing a mate while on the pill can result in unstable and more violent unions. The biological basis for the fact that the pill causes abortion of human embryos is given. A healthy alternative for fertility control is explained.

Sperm competition, but not major histocompatibility divergence, drives differential fertilization success between alternative reproductive tactics in Chinook salmon

Post-copulatory sexual selection processes, including sperm competition and cryptic female choice (CFC), can operate based on major histocompatibility (MH) genes. We investigated sperm competition between male alternative reproductive tactics [jack (sneaker) and hooknose (guard)] of Chinook salmon (Oncorhynchus tshawytscha). Using a full factorial design, we examined invitro competitive fertilization success of paired jack and hooknose males at three time points after sperm activation (0, 15 and 60s) to test for male competition, CFC and time effects on male fertilization success. We also examined egg-mediated CFC at two MH genes by examining both the relationship between competitive fertilization success and MH divergence as well as inheritance patterns of MH alleles in resulting offspring. We found that jacks sired more offspring than hooknose males at 0s post-activation; however, jack fertilization success declined over time post-activation, suggesting a trade-off between sperm speed and longevity. Enhanced fertilization success of jacks (presumably via higher sperm quality) may serve to increase sneaker tactic competitiveness relative to dominant hooknose males. We also found evidence of egg-mediated CFC (i.e. female×male interaction) influencing competitive fertilization success; however, CFC was not acting on the MH genes as we found no relationship between fertilization success and MH II β1 or MH I α1 divergence and we found no deviations from Mendelian inheritance of MH alleles in the offspring. Our study provides insight into evolutionary mechanisms influencing variation in male mating success within alternative reproductive tactics, thus underscoring different strategies that males can adopt to attain success.

MTE10.01 Unique Biologic Aspects of Tobacco-Induced Lung Cancer

MTE10.01 Unique Biologic Aspects of Tobacco-Induced Lung Cancer

MYD88 and functionally related genes are associated with multiple infections in a model population of Kenyan village dogs.

The purpose of this study was to seek associations between immunity-related molecular markers and endemic infections in a model population of African village dogs from Northern Kenya with no veterinary care and no selective breeding. A population of village dogs from Northern Kenya composed of three sub-populations from three different areas (84, 50 and 55 dogs) was studied. Canine distemper virus (CDV), Hepatozoon canis, Microfilariae (Acantocheilonema dracunculoides, Acantocheilonema reconditum) and Neospora caninum were the pathogens studied. The presence of antibodies (CDV, Neospora), light microscopy (Hepatozoon) and diagnostic PCR (Microfilariae) were the methods used for diagnosing infection. Genes involved in innate immune mechanisms, NOS3, IL6, TLR1, TLR2, TLR4, TLR7, TLR9, LY96, MYD88, and three major histocompatibility genes class II genes were selected as candidates. Single nucleotide polymorphism (SNP) markers were detected by Sanger sequencing, next generation sequencing and PCR-RFLP. The Fisher´s exact test for additive and non-additive models was used for association analyses. Three SNPs within the MYD88 gene and one TLR4 SNP marker were associated with more than one infection. Combined genotypes and further markers identified by next generation sequencing confirmed associations observed for individual genes. The genes associated with infection and their combinations in specific genotypes match well our knowledge on their biological role and on the role of the relevant biological pathways, respectively. Associations with multiple infections observed between the MYD88 and TLR4 genes suggest their involvement in the mechanisms of anti-infectious defenses in dogs.

Recent advances in understanding vitiligo

Vitiligo, an acquired depigmentation disorder, manifests as white macules on the skin and can cause significant psychological stress and stigmatization. Recent advances have shed light on key components that drive disease onset and progression as well as therapeutic approaches. Vitiligo can be triggered by stress to the melanin pigment-producing cells of the skin, the melanocytes. The triggers, which range from sunburn to mechanical trauma and chemical exposures, ultimately cause an autoimmune response that targets melanocytes, driving progressive skin depigmentation. The most significant progress in our understanding of disease etiology has been made on three fronts: (1) identifying cellular responses to stress, including antioxidant pathways and the unfolded protein response (UPR), as key players in disease onset, (2) characterizing immune responses that target melanocytes and drive disease progression, and (3) identifying major susceptibility genes. The current model for vitiligo pathogenesis postulates that oxidative stress causes cellular disruptions, including interruption of protein maturation in the endoplasmic reticulum (ER), leading to the activation of the UPR and expression of UPR-regulated chemokines such as interleukin 6 (IL-6) and IL-8. These chemokines recruit immune components to the skin, causing melanocytes to be targeted for destruction. Oxidative stress can further increase melanocyte targeting by promoting antigen presentation. Two key components of the autoimmune response that promote disease progression are the interferon (IFN)-γ/CXCL10 axis and IL-17-mediated responses. Several genome-wide association studies support a role for these pathways, with the antioxidant gene NRF2, UPR gene XBP1, and numerous immune-related genes including class I and class II major histocompatibility genes associated with a risk for developing vitiligo. Novel approaches to promote repigmentation in vitiligo are being investigated and may yield effective, long-lasting therapies.

Maternal microchimerism in health and disease

Circulating maternal cells transfer to the fetus during pregnancy, where they may integrate with the fetal immune and organ systems, creating a state of maternal microchimerism (MMc). MMc can persist throughout the child's life, and it has been implicated in the triggering or perpetuation of chronic inflammatory autoimmune diseases, in the context of specific major histocompatibility genes. Correlative data in humans have now been tested in animal model systems. Results suggest that maternal-fetal tolerance may have health implications far beyond the time of pregnancy and into the child's life.

Association of DLA-DQB1 alleles with exocrine pancreatic insufficiency in Pembroke Welsh Corgis.

Exocrine pancreatic insufficiency (EPI) is a digestive disorder resulting from the insufficient secretion of enzymes from the pancreas. In dogs, this condition is often attributed to pancreatic acinar atrophy, wherein the enzyme-producing acinar cells are believed to be destroyed through an autoimmune process. Although EPI affects many diverse breeds, to date, molecular studies have been limited to the German Shepherd dog. A recent study of major histocompatibility genes in diseased and healthy German Shepherd dogs identified both risk and protective haplotypes. Herein, we genotyped DLA-DQB1 in Pembroke Welsh Corgis to determine whether dog leukocyte antigen alleles contribute to the pathogenesis of EPI across dog breeds. We evaluated 14 affected and 43 control Pembroke Welsh Corgis, which were selected based on an age of onset similar to German Shepherd dogs. We identified one protective allele (odds ratio = 0.13, P-value = 0.044) and one risk allele (odds ratio = 3.8, P-value = 0.047). As in German Shepherd dogs, the risk allele is a duplication of DLA-DQB1 (alleles DQB1*013:03 and 017:01); however, Pembroke Welsh Corgis have acquired a single polymorphism on DQB1*017:01. Thus, the DLA-DQB1 duplication is a risk allele for EPI in at least two breeds.

Immunoglobulin heavy chain variable region and major histocompatibility region genes are linked to induced graves' disease in females from two very large families of recombinant inbred mice.

Graves' hyperthyroidism is caused by antibodies to the TSH receptor (TSHR) that mimic thyroid stimulation by TSH. Stimulating TSHR antibodies and hyperthyroidism can be induced by immunizing mice with adenovirus expressing the human TSHR A-subunit. Prior analysis of induced Graves' disease in small families of recombinant inbred (RI) female mice demonstrated strong genetic control but did not resolve trait loci for TSHR antibodies or elevated serum T4. We investigated the genetic basis for induced Graves' disease in female mice of two large RI families and combined data with earlier findings to provide phenotypes for 178 genotypes. TSHR antibodies measured by inhibition of TSH binding to its receptor were highly significantly linked in the BXD set to the major histocompatibility region (chromosome 17), consistent with observations in 3 other RI families. In the LXS family, we detected linkage between T4 levels after TSHR-adenovirus immunization and the Ig heavy chain variable region (Igvh, chromosome 12). This observation is a key finding because components of the antigen binding region of Igs determine antibody specificity and have been previously linked to induced thyroid-stimulating antibodies. Data from the LXS family provide the first evidence in mice of a direct link between induced hyperthyroidism and Igvh genes. A role for major histocompatibility genes has now been established for genetic susceptibility to Graves' disease in both humans and mice. Future studies using arrays incorporating variation in the complex human Ig gene locus will be necessary to determine whether Igvh genes are also linked to Graves' disease in humans.

Distinct Sets Of Class I Major Histocompatibility Genes In Zebrafish Expressed From Six Divergent Haplotypes

The zebrafish offers unique strengths as an animal model for stem cell biology, cancer, and immunology research. A better understanding of zebrafish histocompatibility genes will further strengthen this foundation. While histocompatibility genes are recognized as the most polymorphic genes in the mammalian genome, by comparison the sequence diversity among Class I genes in teleost species (bony fish) is substantially greater. The functional consequences of this high diversity are not yet well understood. We focused our study on zebrafish Class I major histocompatibility (MH) genes that segregate with specific haplotypes at chromosome 19, as donor-recipient matching at this locus has been shown to improve engraftment after hematopoietic transplantation. Interestingly, these haplotypes display marked differences in genomic sequence at this locus including variable gene copy number and content.We examined six haplotypes that each display unique patterns of single nucleotide polymorphisms (SNPs) in linked genes psmb8 and zbtb22 that flank the Class I major histocompatibility gene locus on chromosome 19. We identified ten full-length Class I genes that are expressed in zebrafish and assigned each of the divergent genes to at least one haplotype. Genomic Southern blot data confirmed the presence of one to three unique Class I MH genes per haplotype. Sequence examination of these ten genes revealed expected motifs for Class I function, including predicted interaction residues for CD8 and beta-2-microglobulin. However, the predicted peptide anchor residues for some of the genes displayed occasional substitutions. This suggests possible flexibility in antigen binding among these genes that may influence their functional repertoire.Using qPCR, we showed non-overlapping and sometimes co-dominant expression patterns of these genes that were specific to fish homozygous for each particular haplotype. For example, mhc1uda, mhc1uea, mhc1ufa were expressed at relatively equivalent levels from haplotype A. In contrast, from haplotype B one of the two genes (mhc1uca) was expressed at levels approximately ten fold lower than the other gene associated with that haplotype (mhc1uba). Similarly, for haplotype C mhc1uka was expressed at levels much lower than mhc1uja. Interestingly, mhc1uca and mhc1uka have relatively atypical sequences among these genes including the presence of additional exons which may indicate that they function in a non-classical capacity. For haplotype D, mhc1uga was the only gene found to be expressed by that haplotype. For haplotype E, only mhc1uia was found to be expressed but genomic Southern blot analysis indicated the presence of an additional gene with unknown sequence within this haplotype. For haplotype F only mhc1uha was expressed.From these data we can predict that most of these unique zebrafish Class I genes function either co-dominantly or as the exclusive classical genes within their respective haplotypes. These predictions will require functional verification, such as via labeled tumor transplantation experiments that are currently underway in our laboratory. Dissecting the function and genetic diversity of zebrafish MHC genes promises to advance future studies with this important animal model including transplantation experiments for disease modeling of cancer, graft versus host disease, and immune response to infectious diseases. Disclosures:No relevant conflicts of interest to declare.

Genetic diversity and conservation in a small endangered horse population

The Old Kladruber horses arose in the 17th century as a breed used for ceremonial purposes. Currently, grey and black coat colour varieties exist as two sub-populations with different recent breeding history. As the population underwent historical bottlenecks and intensive inbreeding, loss of genetic variation is considered as the major threat. Therefore, genetic diversity in neutral and non-neutral molecular markers was examined in the current nucleus population. Fifty microsatellites, 13 single nucleotide polymorphisms (SNPs) in immunity-related genes, three mutations in coat colour genes and one major histocompatibility (MHC-DRA) gene were studied for assessing genetic diversity after 15 years of conservation. The results were compared to values obtained in a similar study 13 years ago. The extent of genetic diversity of the current population was comparable to other breeds, despite its small size and isolation. The comparison between 1997 and 2010 did not show differences in the extent of genetic diversity and no loss of allele richness and/or heterozygosity was observed. Genetic differences identified between the black and grey sub-populations observed 13 years ago persisted. Deviations from the Hardy-Weinberg equilibrium found in 19 microsatellite loci and in five SNP loci are probably due to selective breeding. No differences between neutral and immunity-related markers were found. No changes in the frequencies of markers associated with two diseases, melanoma and insect bite hypersensitivity, were observed, due probably to the short interval of time between comparisons. It, thus, seems that, despite its small size, previous bottlenecks and inbreeding, the molecular variation of Old Kladruber horses is comparable to other horse breeds and that the current breeding policy does not compromise genetic variation of this endangered population.

Regulation of HLA-DR peptide occupancy by histone deacetylase inhibitors

Numerous molecular effects have been attributed to histone deacetylase inhibitors (HDACI’s), including the induction of major histocompatibility (MHC) genes. Here we report that one FDA approved HDACI, Vorinostat, and a second HDACI currently in clinical trials, Entinostat, reduce the ratio of class II associated invariant peptide (CLIP) to the MHC class II molecule, HLA-DR, indicating an increase in the non-CLIP peptides bound to HLA-DR. The HDACI effects are apparent with immortalized B-cells, HLA-DR constitutive melanoma cells and with melanoma cells expressing HLA-DR due to transformation with an expression vector for the HLA-DR gene co-activator, CIITA. Entinostat treatment leads to upregulation of Cathepsin L1, and the HLA-DR peptidome of the Entinostat treated cells is consistent with increased Cathepsin L1 mediated proteolysis. These results indicate that HDACI treatments may alter the HLA-DR peptidome of cells in patients and provide a way to identify novel immunogens for vaccinations and the study of autoantigens.