Major Histocompatibility Complex Associations Research Articles

Common and rare genetic variants predisposing females to unexplained recurrent pregnancy loss

Recurrent pregnancy loss (RPL) is a major reproductive health issue with multifactorial causes, affecting 2.6% of all pregnancies worldwide. Nearly half of the RPL cases lack clinically identifiable causes (e.g., antiphospholipid syndrome, uterine anomalies, and parental chromosomal abnormalities), referred to as unexplained RPL (uRPL). Here, we perform a genome-wide association study focusing on uRPL in 1,728 cases and 24,315 female controls of Japanese ancestry. We detect significant associations in the major histocompatibility complex (MHC) region at 6p21 (lead variant=rs9263738; P = 1.4 × 10−10; odds ratio [OR] = 1.51 [95% CI: 1.33–1.72]; risk allele frequency = 0.871). The MHC associations are fine-mapped to the classical HLA alleles, HLA-C*12:02, HLA-B*52:01, and HLA-DRB1*15:02 (P = 1.1 × 10−10, 1.5 × 10−10, and 1.2 × 10−9, respectively), which constitute a population-specific common long-range haplotype with a protective effect (P = 2.8 × 10−10; OR = 0.65 [95% CI: 0.57–0.75]; haplotype frequency=0.108). Genome-wide copy-number variation (CNV) calling demonstrates rare predicted loss-of-function (pLoF) variants of the cadherin-11 gene (CDH11) conferring the risk of uRPL (P = 1.3 × 10−4; OR = 3.29 [95% CI: 1.78–5.76]). Our study highlights the importance of reproductive immunology and rare variants in the uRPL etiology.

The Interaction of LILRB2 with HLA-B Is Associated with Psoriasis Susceptibility

The strongest signal for genetic susceptibility to psoriasis resides within the major histocompatibility complex near class I loci (Okada et al., 2014). However, the mechanistic basis for how major histocompatibility complex associations confer psoriasis risk has yet to be fully elucidated (Prinz, 2018). Fine-mapping studies have identified specific amino acids in the peptide binding groove of HLA-B and HLA-C as conferring risk (Chen et al., 2012; Okada et al., 2014). This suggests that psoriasis risk may be mediated through HLA presentation of autoantigens.

S01.07 The U19 Plans for Integration of Biomarkers Into Future Lung Cancer Screening

The goal of the U19 Integrative analysis of Lung Cancer Etiology and Risk (INTEGRAL) consortium is to develop biomarkers that characterize individual risk for development and progression from lung cancer. We are using a comprehensive strategy, depicted below in Figure 1, for this analysis and we are drawing on world-wide resources and expertise. There are three projects focusing on i) genetics of smoking behavior and lung cancer risk, ii) biomarker discovery and validation for identifying individuals at highest risk for developing lung cancer and iii) evaluation of these biomarkers in screening cohorts along with radiographic analaysis to evaluate risk for lung cancer development and nodule behavior. There are also administrative and biostatistics cores. We will discuss strategies and novel findings from these projects. For Project 1, to assist in genetic analysis, we have reimputed all the available data from lung cancer cases and controls using the haplotype reference consortium to bring together a data lake comprising data from over 100,000 individuals. The consortium provides data to its members and to collaborators who would like to evaluate hypotheses related to lung cancer by providing access for analyses and we currently are supporting 107 projects evaluating lung cancer risk. Additionally, consortium members from the University of Laval have performed transcriptomic analysis of normal lung tissue from over 500 participants undergoing surgery for lung cancer treatment. We are also studying the role that genetic factors have in influencing smoking behavior by collaborating with other large consortia and by studying multiethnic variation using Hawaiian multiethnic populations. Analyses of the genetic data and further extension to the UK Biobank have identified novel genetic loci that contribute to risk. Interaction analysis of the CHRNA3/A5/B4 cluster with all other genomic regions identifies interactions with the 15q25.1 nicotinic receptors that influence lung cancer risk. Results identified genes in the neuroactive ligand receptor interaction pathway as playing a key role in increasing lung cancer risk. A cross-ethnicity analysis identified genetic factors in the major histocompatibility complex (MHC) that affect risk for lung cancer. We imputed sequence variation for 26,044 cases and 20,836 controls in classical HLA genes, fine-mapped MHC associations for lung cancer risk with major histologies and compared results among ethnicities. Independent and novel associations within HLA genes were identified in Europeans primarily affecting risk for squamous cell histology including amino acids in the HLA-B*0801 peptide binding groove and an independent HLA-DQB1*06 loci group. In Asians, associations are driven by two independent HLA allele sets affecting adenocarcinoma risk primarily that both increase risk in HLA-DQB1*0401 and HLA-DRB1*0701; the latter was better represented by the amino acid Ala-104. These results implicate several HLA-tumor peptide interactions as the major MHC factor modulating lung cancer susceptibility. A rare variant analysis yielded a mutation of the ATM gene that is rare in all populations except individuals of Jewish descent that primarily increase risk for adenocarcinoma and has highest risk in nonsmoking women. Analyses of smoking and genetic data have identified gene-smoking interactions that contribute to lung cancer risk, and particularly several genes that protect at-risk smokers from lung cancer development. Mendelian randomization and mediation analyses are underway to evaluate novel biomarkers that can be further studied in project 2. This effort found a surprising result that elevated levels of vitamin B12 increase risk for lung cancer development. Project 2 has been bringing together an approach to analyzing biomarkers using data from existing cohort consortia, which have collected samples prior to the clinical presentation of lung cancers. Results of an initial study showed that analysis of 4 circulating proteins (CEA125, CEA, CYFRA 21-1 and pro-SFTB) yielded an area under the receiver operator curve accuracy of 83%. This level of accuracy is sufficient to consider the panel for recruitment of individuals for screening studies, but we anticipate that adding additional biomarkers will further improve the accuracy of risk prediction. Biomarkers that are being further considered include additional protein markers along with micoRNA species, the inclusion of polygenic risk scores and additional serum-derived biomarkers like vitamins B-6 and B-12 that have been shown in mendelian randomization studies to help in identifying high risk subjects. Project 3 is focused on the establishment and validation of the models in the LDCT screening programs. In collaboration with National Lung Screening Trial, Canadian LDCT screening programs, NELSON and United Kingdom Lung Study (UKLS), we have begun the data harmonization across LDCT studies, including clinic-epidemiological data as well as nodule characteristics. We have established a pipeline of feature extractions for the radiomics analysis and compared the inter-reader variability. The intraclass correlation coefficients are >0.75 for the majority of the radiomics features extracted. We will conduct cross-study validation for the model building to ensure the maximum generalizability of the model. We will start the work on biomarkers and assess their added values in these models. biomarkers, early detection, genetics

Genetic fine mapping of systemic lupus erythematosus MHC associations in Europeans and African Americans

Genetic variation within the major histocompatibility complex (MHC) contributes substantial risk for systemic lupus erythematosus, but high gene density, extreme polymorphism and extensive linkage disequilibrium (LD) have made fine mapping challenging. To address the problem, we compared two association techniques in two ancestrally diverse populations, African Americans (AAs) and Europeans (EURs). We observed a greater number of Human Leucocyte Antigen (HLA) alleles in AA consistent with the elevated level of recombination in this population. In EUR we observed 50 different A—C—B—DRB1—DQA—DQB multilocus haplotype sequences per hundred individuals; in the AA sample, these multilocus haplotypes were twice as common compared to Europeans. We also observed a strong narrow class II signal in AA as opposed to the long-range LD observed in EUR that includes class I alleles. We performed a Bayesian model choice of the classical HLA alleles and a frequentist analysis that combined both single nucleotide polymorphisms (SNPs) and classical HLA alleles. Both analyses converged on a similar subset of risk HLA alleles: in EUR HLA– B*08:01 + B*18:01 + (DRB1*15:01 frequentist only) + DQA*01:02 + DQB*02:01 + DRB3*02 and in AA HLA–C*17:01 + B*08:01 + DRB1*15:03 + (DQA*01:02 frequentist only) + DQA*02:01 + DQA*05:01+ DQA*05:05 + DQB*03:19 + DQB*02:02. We observed two additional independent SNP associations in both populations: EUR rs146903072 and rs501480; AA rs389883 and rs114118665. The DR2 serotype was best explained by DRB1*15:03 + DQA*01:02 in AA and by DRB1*15:01 + DQA*01:02 in EUR. The DR3 serotype was best explained by DQA*05:01 in AA and by DQB*02:01 in EUR. Despite some differences in underlying HLA allele risk models in EUR and AA, SNP signals across the extended MHC showed remarkable similarity and significant concordance in direction of effect for risk-associated variants.

The Quest for Psoriasis Autoantigens: Genetics Meets Immunology in the Melanocyte

The Quest for Psoriasis Autoantigens: Genetics Meets Immunology in the Melanocyte

Major histocompatibility complex associations of ankylosing spondylitis are complex and involve further epistasis with ERAP1.

Ankylosing spondylitis (AS) is a common, highly heritable, inflammatory arthritis for which HLA-B*27 is the major genetic risk factor, although its role in the aetiology of AS remains elusive. To better understand the genetic basis of the MHC susceptibility loci, we genotyped 7,264 MHC SNPs in 22,647 AS cases and controls of European descent. We impute SNPs, classical HLA alleles and amino-acid residues within HLA proteins, and tested these for association to AS status. Here we show that in addition to effects due to HLA-B*27 alleles, several other HLA-B alleles also affect susceptibility. After controlling for the associated haplotypes in HLA-B, we observe independent associations with variants in the HLA-A, HLA-DPB1 and HLA-DRB1 loci. We also demonstrate that the ERAP1 SNP rs30187 association is not restricted only to carriers of HLA-B*27 but also found in HLA-B*40:01 carriers independently of HLA-B*27 genotype.

Pathogen burden, co-infection and major histocompatibility complex variability in the European badger (Meles meles).

Pathogen-mediated selection is thought to maintain the extreme diversity in the major histocompatibility complex (MHC) genes, operating through the heterozygote advantage, rare-allele advantage and fluctuating selection mechanisms. Heterozygote advantage (i.e. recognizing and binding a wider range of antigens than homozygotes) is expected to be more detectable when multiple pathogens are considered simultaneously. Here, we test whether MHC diversity in a wild population of European badgers (Meles meles) is driven by pathogen-mediated selection. We examined individual prevalence (infected or not), infection intensity and co-infection of 13 pathogens from a range of taxa and examined their relationships with MHC class I and class II variability. This population has a variable, but relatively low, number of MHC alleles and is infected by a variety of naturally occurring pathogens, making it very suitable for the investigation of MHC-pathogen relationships. We found associations between pathogen infections and specific MHC haplotypes and alleles. Co-infection status was not correlated with MHC heterozygosity, but there was evidence of heterozygote advantage against individual pathogen infections. This suggests that rare-allele advantages and/or fluctuating selection, and heterozygote advantage are probably the selective forces shaping MHC diversity in this species. We show stronger evidence for MHC associations with infection intensity than for prevalence and conclude that examining both pathogen prevalence and infection intensity is important. Moreover, examination of a large number and diversity of pathogens, and both MHC class I and II genes (which have different functions), provide an improved understanding of the mechanisms driving MHC diversity.

Fine Mapping Major Histocompatibility Complex Associations in Psoriasis and Its Clinical Subtypes

Psoriasis vulgaris (PsV) risk is strongly associated with variation within the major histocompatibility complex (MHC) region, but its genetic architecture has yet to be fully elucidated. Here, we conducted a large-scale fine-mapping study of PsV risk in the MHC region in 9,247 PsV-affected individuals and 13,589 controls of European descent by imputing class I and II human leukocyte antigen (HLA) genes from SNP genotype data. In addition, we imputed sequence variants for MICA, an MHC HLA-like gene that has been associated with PsV, to evaluate association at that locus as well. We observed that HLA-C∗06:02 demonstrated the lowest p value for overall PsV risk (p = 1.7 × 10−364). Stepwise analysis revealed multiple HLA-C∗06:02-independent risk variants in both class I and class II HLA genes for PsV susceptibility (HLA-C∗12:03, HLA-B amino acid positions 67 and 9, HLA-A amino acid position 95, and HLA-DQα1 amino acid position 53; p < 5.0 × 10−8), but no apparent risk conferred by MICA. We further evaluated risk of two major clinical subtypes of PsV, psoriatic arthritis (PsA; n = 3,038) and cutaneous psoriasis (PsC; n = 3,098). We found that risk heterogeneity between PsA and PsC might be driven by HLA-B amino acid position 45 (pomnibus = 2.2 × 10−11), indicating that different genetic factors underlie the overall risk of PsV and the risk of specific PsV subphenotypes. Our study illustrates the value of high-resolution HLA and MICA imputation for fine mapping causal variants in the MHC.

MHC associations with clinical and autoantibody manifestations in European SLE

Systemic lupus erythematosus (SLE) is a clinically heterogeneous disease affecting multiple organ systems and characterized by autoantibody formation to nuclear components. Although genetic variation within the major histocompatibility complex (MHC) is associated with SLE, its role in the development of clinical manifestations and autoantibody production is not well defined. We conducted a meta-analysis of four independent European SLE case collections for associations between SLE sub-phenotypes and MHC single-nucleotide polymorphism genotypes, human leukocyte antigen (HLA) alleles and variant HLA amino acids. Of the 11 American College of Rheumatology criteria and 7 autoantibody sub-phenotypes examined, anti-Ro/SSA and anti-La/SSB antibody subsets exhibited the highest number and most statistically significant associations. HLA-DRB1*03:01 was significantly associated with both sub-phenotypes. We found evidence of associations independent of MHC class II variants in the anti-Ro subset alone. Conditional analyses showed that anti-Ro and anti-La subsets are independently associated with HLA-DRB1*0301, and that the HLA-DRB1*03:01 association with SLE is largely but not completely driven by the association of this allele with these sub-phenotypes. Our results provide strong evidence for a multilevel risk model for HLA-DRB1*03:01 in SLE, where the association with anti-Ro and anti-La antibody-positive SLE is much stronger than SLE without these autoantibodies.

The non-classical class II genes of the chicken, DMA and DMB, are similar to those of mammals, but a second DMB gene (DMB1) is differentially expressed with unusual regulatory and structural features.

Event Abstract Back to Event The non-classical class II genes of the chicken, DMA and DMB, are similar to those of mammals, but a second DMB gene (DMB1) is differentially expressed with unusual regulatory and structural features. Aimee Parker1*, Karen Staines2, Colin Butter2 and Jim Kaufman1, 3 1 University of Cambridge, Department of Pathology, United Kingdom 2 Institute for Animal Health, Avian Viral Immunology, United Kingdom 3 University of Cambridge, Department of Veterinary Medicine, United Kingdom Although smaller, simpler and rearranged, the chicken major histocompatibility complex (MHC) contains most of the core antigen presentation genes found in the mammalian MHC. Strong associations of chicken MHC haplotypes with resistance to pathogens and response to vaccines are attributed to single dominantly- expressed MHC class I (BF) and class II (BL) molecules. The single dominant class I is the result of co-evolution with the closely-linked antigen processing genes TAP and tapasin, but the situation for class II is less clear. To facilitate investigation of whether single dominant class II expression could result from similar co-evolution with associated antigen presentation molecules, we characterised the chicken class II DM region. We show that chickens have three DM genes in their MHC, a single alpha chain gene DMA, and, unusually, two beta chain genes DMB1 and DMB2, of which DMB2 is dominantly-expressed. The chicken DM genes encode proteins with high structural and sequence homology to those described in mammals. However, the two beta chains differ substantially at the amino acid level and several features of DMB1 suggest an unusual function. We find DMB1 and DMB2 differentially expressed in tissues at the RNA and protein level, with DMB1 strongly expressed in intestinal epithelial cells, suggestive of a role in gut immunity. In pursuing the functional properties of the DMs and their interaction with the classical class II molecules, we aim to enhance our understanding of chicken MHC associations with immune responses and, more generally, illuminate mechanisms underlying class II evolution. Keywords: MHC, DM, antigen processing and presentation, Chickens, intestinal immunity, evolution Conference: 15th International Congress of Immunology (ICI), Milan, Italy, 22 Aug - 27 Aug, 2013. Presentation Type: Abstract Topic: Adaptive Immunity Citation: Parker A, Staines K, Butter C and Kaufman J (2013). The non-classical class II genes of the chicken, DMA and DMB, are similar to those of mammals, but a second DMB gene (DMB1) is differentially expressed with unusual regulatory and structural features.. Front. Immunol. Conference Abstract: 15th International Congress of Immunology (ICI). doi: 10.3389/conf.fimmu.2013.02.01174 Copyright: The abstracts in this collection have not been subject to any Frontiers peer review or checks, and are not endorsed by Frontiers. They are made available through the Frontiers publishing platform as a service to conference organizers and presenters. The copyright in the individual abstracts is owned by the author of each abstract or his/her employer unless otherwise stated. Each abstract, as well as the collection of abstracts, are published under a Creative Commons CC-BY 4.0 (attribution) licence (https://creativecommons.org/licenses/by/4.0/) and may thus be reproduced, translated, adapted and be the subject of derivative works provided the authors and Frontiers are attributed. For Frontiers’ terms and conditions please see https://www.frontiersin.org/legal/terms-and-conditions. Received: 17 Jul 2013; Published Online: 22 Aug 2013. * Correspondence: Dr. Aimee Parker, University of Cambridge, Department of Pathology, Cambridge, Cambridgeshire, CB2 1QP, United Kingdom, ap509@cam.ac.uk Login Required This action requires you to be registered with Frontiers and logged in. To register or login click here. Abstract Info Abstract The Authors in Frontiers Aimee Parker Karen Staines Colin Butter Jim Kaufman Google Aimee Parker Karen Staines Colin Butter Jim Kaufman Google Scholar Aimee Parker Karen Staines Colin Butter Jim Kaufman PubMed Aimee Parker Karen Staines Colin Butter Jim Kaufman Related Article in Frontiers Google Scholar PubMed Abstract Close Back to top Javascript is disabled. Please enable Javascript in your browser settings in order to see all the content on this page.

Class II major histocompatibility complex–associated response to type XI collagen regulates the development of chronic arthritis in rats

Chronic inflammation of the peripheral joints is a hallmark of rheumatoid arthritis (RA). The autoantibody response in RA has been shown to be directed mainly to ubiquitous antigens, whereas the response to cartilage proteins has been less extensively investigated. This study was undertaken to characterize the immune response in pristane-induced arthritis (PIA) in the rat to the cartilage-specific proteins type II collagen (CII) and type XI collagen (CXI) and to genetically fine-map their underlying major histocompatibility complex (MHC) associations. The genetic control of CII and CXI immunity was mapped using intra-MHC-recombinant inbred strains immunized with the respective collagens. Reactivity with CII and CXI was tested in acute and chronic PIA and in 356 HLA-typed patients with recently diagnosed RA. Mapping of arthritis susceptibility within the MHC region revealed a 144-223-kb locus containing <12 genes, including paralogs for HLA-DQ and HLA-DR. Susceptibility to CII and CXI was linked to haplotypes RT1(av1) (DA) and RT1(f) (DA.1F), respectively. After injection of pristane, rats of both strains developed weak T cell and IgG responses to CII, but not to CXI. In chronic arthritis, however, collagen reactivity was stronger, specific for CXI, and restricted to rats with RT1(f) MHC. Among RA patients, 12% exhibited a specific IgG response to CXI, 6% to CII, and 6% to both collagens. These findings demonstrate a shift in cartilage recognition in early and chronic arthritis in the rat, suggesting that CXI autoreactivity contributes to the perpetuation of chronic disease. The results provide evidence of the importance of joint antigens in arthritis development.

Genome-wide association study in a Swedish population yields support for greater CNV and MHC involvement in schizophrenia compared with bipolar disorder.

Schizophrenia (SCZ) and bipolar disorder (BD) are highly heritable psychiatric disorders with overlapping susceptibility loci and symptomatology. We conducted a genome-wide association study (GWAS) of these disorders in a large Swedish sample. We report a new and independent case-control analysis of 1507 SCZ cases, 836 BD cases and 2093 controls. No single-nucleotide polymorphisms (SNPs) achieved significance in these new samples; however, combining new and previously reported SCZ samples (2111 SCZ and 2535 controls) revealed a genome-wide significant association in the major histocompatibility complex (MHC) region (rs886424, P=4.54 × 10(-8)). Imputation using multiple reference panels and meta-analysis with the Psychiatric Genomics Consortium SCZ results underscored the broad, significant association in the MHC region in the full SCZ sample. We evaluated the role of copy number variants (CNVs) in these subjects. As in prior reports, deletions were enriched in SCZ, but not BD cases compared with controls. Singleton deletions were more frequent in both case groups compared with controls (SCZ: P=0.003, BD: P=0.013), whereas the largest CNVs (>500 kb) were significantly enriched only in SCZ cases (P=0.0035). Two CNVs with previously reported SCZ associations were also overrepresented in this SCZ sample: 16p11.2 duplications (P=0.0035) and 22q11 deletions (P=0.03). These results reinforce prior reports of significant MHC and CNV associations in SCZ, but not BD.

MHC class II DRB diversity in raccoons (Procyon lotor) reveals associations with raccoon rabies virus (Lyssavirus)

In North America, the raccoon rabies virus (RRV) is an endemic wildlife disease which causes acute encephalopathies and is a strong selective force on raccoons (Procyon lotor), with estimates of ∼85% of the population succumbing to the disease when epizootic. RRV is regarded as a lethal disease if untreated; therefore, no evolutionary response would be expected of raccoon populations. However, variable immune responses to RRV have been observed in raccoons indicating a potential for evolutionary adaptation. Studies of variation within the immunologically important major histocompatibility complex (MHC) have revealed relationships between MHC alleles and diseases in humans and other wildlife species. This enhances our understanding of how hosts and pathogens adapt and co-evolve. In this study, we used RRV as a model system to study host-pathogen interaction in raccoons from a challenge study and from four wild populations that differ in exposure times and viral lineages. We investigated the potential role of Prlo-DRB polymorphism in relation to susceptibility/resistance to RRV in 113 RRV positive and 143 RRV negative raccoons. Six alleles were found to be associated with RRV negative status and five alleles with RRV positive animals. We found variable patterns of MHC associations given the relative number of selective RRV sweeps in the studied regions and correlations between MHC diversity and RRV lineages. The allelic associations established provide insight into how the genetic variation of raccoons may affect the disease outcome and this can be used to examine similar associations between other rabies variants and their hosts.

TNF block haplotypes associated with conserved MHC haplotypes in European, Asian and Australian Aboriginal donors

Associations between major histocompatibility complex (MHC) ancestral haplotypes (AHs) and immunopathological diseases are traditionally ascribed to human leukocyte antigen (HLA) class I or class II alleles. However, polymorphisms in TNF and nearby genes in the central MHC can influence risk. We have defined TNF block haplotypes in Asian, European and Australian Aboriginal donors and shown conservation of TNF block haplotypes in geographically distinct populations, consistent with a common evolutionary origin. Here we show that most TNF block haplotypes do not align with a single MHC AH and associations often vary with ethnicity. This suggests more recent recombination events between the TNF block and the HLA alleles.

Multiple sclerosis and the major histocompatibility complex

Multiple sclerosis (MS) is the most common neurological disease affecting young adults. The cause is unknown, but detailed epidemiological and genetic studies have shown a clear inherited component. We review here some of the recent findings of MS genetics with a particular focus on genes of the major histocompatibility complex (MHC). Recent studies add further complexity to the role of the MHC in MS. Reported MHC associations are complex, involving haplotypes rather than single alleles and may involve epigenetic mechanisms and other modulators of gene expression. MHC class II haplotypes display a hierarchy of risks, including protective effects and epistatic interactions, which together dwarf any non-MHC genetic effect. Genes in the MHC region have been shown to influence disease severity, display parent-of-origin effects and interact with a major environmental candidate for MS, vitamin D. The MHC class II association with MS is not as straightforward as previously thought. A complete understanding of the epistatic interactions and epigenetic features of this region will be important to understand disease pathogenesis and likely aid the discovery of new therapeutics.

Different patterns of associations with anti–citrullinated protein antibody–positive and anti–citrullinated protein antibody–negative rheumatoid arthritis in the extended major histocompatibility complex region

To identify additional variants in the major histocompatibility complex (MHC) region that independently contribute to risk in 2 disease subsets of rheumatoid arthritis (RA) defined according to the presence or absence of antibodies to citrullinated protein antigens (ACPAs). In a multistep analytical strategy using unmatched as well as matched analyses to adjust for HLA-DRB1 genotype, we analyzed 2,221 single-nucleotide polymorphisms (SNPs) spanning 10.7 Mb, from 6p22.2 to 6p21.31, across the MHC. For ACPA-positive RA, we analyzed samples from the Swedish Epidemiological Investigation of Rheumatoid Arthritis (EIRA) and the North American Rheumatoid Arthritis Consortium (NARAC) studies (totaling 1,255 cases and 1,719 controls). For ACPA-negative RA, we used samples from the EIRA study (640 cases and 670 controls). Plink and SAS statistical packages were used to conduct all statistical analyses. A total of 299 SNPs reached locus-wide significance (P<2.3x10(-5)) for ACPA-positive RA, whereas surprisingly, no SNPs reached this significance for ACPA-negative RA. For ACPA-positive RA, we adjusted for known DRB1 risk alleles and identified additional independent associations with SNPs near HLA-DPB1 (rs3117213; odds ratio 1.42 [95% confidence interval 1.17-1.73], Pcombined=0.0003 for the strongest association). There are distinct genetic patterns of MHC associations in the 2 disease subsets of RA defined according to ACPA status. HLA-DPB1 is an independent risk locus for ACPA-positive RA. We did not identify any associations with SNPs within the MHC for ACPA-negative RA.

MHC haplotype involvement in avian resistance to an ectoparasite

Research on immune function in evolutionary ecology has frequently focused on avian ectoparasites (e.g., mites and lice). However, host immunogenetics involved with bird resistance to ectoparasites has not been determined. The critical role of the major histocompatibility complex (MHC) in adaptive immunity and high genetic variation found within the MHC make this gene complex useful for exploring the immunogenetic basis for bird resistance to ectoparasites. The objective of this study was to determine if the avian MHC influenced resistance to a blood-feeding ectoparasite. Four congenic lines of chickens, differing only at the MHC, were comparatively infested with a cosmopolitan ectoparasite of birds-northern fowl mite (NFM)-which is also a serious pest species of poultry. Mite infestations were monitored over time and mite densities (weekly and maximum) were compared among lines. Chickens with the MHC haplotype B21 were relatively resistant to NFM, compared with birds in the B15 congenic line (P < 0.02). To test for similar effects in an outbred genetic background, a separate experiment was performed with 107 commercial chickens (white leghorn, W-36 strain) infested with NFM. Hens were genotyped using a MHC microsatellite marker (LEI0258) and associations between MHC haplotype and NFM density were tested. The highest peak NFM populations occurred more often on hens with the B15 haplotype versus the B21 haplotype (P = 0.012), which supported the results of the congenic study. These data indicate the avian MHC influences ectoparasite resistance, which is relevant to disease ecology and avian-ectoparasite interaction.

Strong Protective Effect of DR3 Against Ulcerative Colitis in the Spanish Population

Ulcerative colitis (UC) is a chronic inflammatory disease affecting the colon. Major histocompatibility complex (MHC) on the short arm of human chromosome 6 has been thoroughly studied as a susceptibility locus. However, one of the strongest MHC associations found, that of HLA-DR3 with UC protection, has not been observed in all populations. Our aim in the present study was to evaluate this negative association in a large cohort of Spanish UC patients and controls, and to try to elucidate which, if any, of the diverse DR3 haplotypes (identified by TNFa and b microsatellites, located in the MHC class III region) is most tightly associated (negatively) with the disease. A total of 537 UC patients and 748 healthy controls from Spain were included in the present study. Low-resolution DR genotyping was performed by PCR and hybridization with allele-specific oligonucleotide probes. TNFa and b microsatellites were studied in a subset of samples (279 UC patients and 503 healthy controls) by PCR followed by capillary electrophoresis. DR-TNFa-TNFb haplotypes were estimated by the expectation-maximization algorithm and comparisons were performed by a chi2 test. After a stepwise procedure, the only DR alleles significantly associated with the disease were DR3 (very strongly, protection) and DR4 (weakly, protection). The strong protective effect of DR3 was evenly distributed among the haplotypes DR3-TNFa1b5, DR3-TNFa2b3, and DR3-TNFother. Our results confirm the strong protective effect of DR3 in our population, and suggest that the relevant protective gene is located centromeric to TNFa and TNFb markers in the MHC region.

Non-B27 MHC associations of ankylosing spondylitis

Ankylosing spondylitis (AS) has been associated with human leukocyte antigen (HLA)-B27 for over 30 years; however, the mechanism of action has remained elusive. Although many studies have reported associations between AS and other genes in the major histocompatibility complex (MHC) in AS, no conclusive results have emerged. To investigate the contribution of non-B27 MHC genes to AS, a large cohort of AS families and controls were B27 typed and genotyped across the region. Interrogation of the data identified a region of 270 kb, lying from 31 952 649 to 32 221 738 base pairs from the p-telomere of chromosome 6 and containing 23 genes, which is likely to include genes involved with susceptibility to AS.

Individual odortypes: interaction of MHC and background genes

Genes of the major histocompatibility complex (MHC) influence the urinary odors of mice. Behavioral studies have shown (1) that mice differing only at MHC have distinct urinary odors, suggesting an MHC odor phenotype or odortype; (2) that the MHC odortype can be recognized across different background strains; and (3) that the MHC odortype is not an additive trait. Very little is known about the odorants underlying this behavioral phenotype. We compared urinary volatile profiles of two MHC haplotypes (H2(b) and H2(k)) and their heterozygous cross (H2(b) x H2(k)) for two different background strains (C57BL/6J and BALB/c) using solid phase micro-extraction (SPME) headspace analysis and gas chromatography/mass spectrometry (GC/MS). Both MHC and background genes substantially influence the volatile profile. Of 148 compounds screened, 108 of them significantly differ between the six genotypes. Surprisingly, for numerous compounds, their MHC associations are moderated by background genes (i.e., there is a significant MHC x background interaction effect in the statistical model relating genotype to relative compound concentration). These interactions account for nearly 30% of the total genetic effect on the volatile profile. MHC heterozygosity further extends the odortype diversity. For many compounds, the volatile expression for the heterozygote is more extreme than the expression for either homozygote, suggesting a heterozygous-specific odortype. The remarkable breadth of effects of MHC variation on concentrations of metabolites and the interaction between MHC and other genetic variation implies the existence of as yet unknown processes by which variation in MHC genes gives rise to variation in volatile molecules in body fluids.