HLA disease associations: models for the study of complex human genetic disorders

Single-cell sequencing unveils distinct immune microenvironments with CCR6-CCL20 crosstalk in human chronic pancreatitis

OBJECTIVE

Chronic pancreatitis (CP) is a potentially fatal disease of the exocrine pancreas, with no specific or effective approved therapies. Due to difficulty in accessing pancreas tissues, little is known about local immune responses or pathogenesis in human CP. We sought to characterise pancreatic immune responses using tissues derived from patients with different aetiologies of CP and non-CP organ donors in order to identify key signalling molecules associated with human CP.

DESIGN

We performed single-cell level cellular indexing of transcriptomes and epitopes by sequencing and T-cell receptor (TCR) sequencing of pancreatic immune cells isolated from organ donors, hereditary and idiopathic patients with CP who underwent total pancreatectomy. We validated gene expression data by performing flow cytometry and functional assays in a second patient with CP cohort.

RESULTS

Deep single-cell sequencing revealed distinct immune characteristics and significantly enriched CCR6⁺ CD4⁺ T cells in hereditary compared with idiopathic CP. In hereditary CP, a reduction in T-cell clonality was observed due to the increased CD4⁺ T (Th) cells that replaced tissue-resident CD8⁺ T cells. Shared TCR clonotype analysis among T-cell lineages also unveiled unique interactions between CCR6⁺ Th and Th1 subsets, and TCR clustering analysis showed unique common antigen binding motifs in hereditary CP. In addition, we observed a significant upregulation of the CCR6 ligand (CCL20) expression among monocytes in hereditary CP as compared with those in idiopathic CP. The functional significance of CCR6 expression in CD4⁺ T cells was confirmed by flow cytometry and chemotaxis assay.

CONCLUSION

Single-cell sequencing with pancreatic immune cells in human CP highlights pancreas-specific immune crosstalk through the CCR6-CCL20 axis, a signalling pathway that might be leveraged as a potential future target in human hereditary CP.

Association of HLA-DR-DQ alleles, haplotypes, and diplotypes with type 1 diabetes in Saudis

AIMS

Type 1 diabetes (T1D) is an autoimmune disease that affects many children worldwide. Genetic factors and environmental triggers play crucial interacting roles in the aetiology. This study aimed to assess the contribution of HLA-DRB1-DQA1-DQB1 alleles, haplotypes, and genotypes to the risk of T1D among Saudis.

METHODS

A total of 222 children with T1D and 342 controls were genotyped for HLA-DRB1, -DQA1, and -DQB1 using reverse sequence-specific oligonucleotide (rSSO) Lab Type high definition (HD) kits. Alleles, haplotypes, and diplotypes were compared between cases and controls using the SAS statistical package.

RESULTS

DRB1*03:01-DQA1*05:01-DQB1*02:01 (32.4%; OR = 3.68; P_c < .0001), DRB1*04:05-DQA1*03:02-DQB1*03:02 (6.6%; OR = 6.76; P_c < .0001), DRB1*04:02-DQA1*03:01-DQB1*03:02 (6.0%; OR = 3.10; P_c = .0194), DRB1*04:01-DQA1*03:01-DQB1*03:02 (3.7%; OR = 4.22; P_c = .0335), and DRB1*04:05-DQA1*03:02-DQB1*02:02 (2.7%; OR = 6.31; P_c = .0326) haplotypes were significantly increased in cases compared to controls, whereas DRB1*07:01-DQA1*02:01-DQB1*02:02 (OR = 0.41; P_c = .0001), DRB1*13:01-DQA1*01:03-DQB1*06:03 (OR = 0.05; P_c < .0001), DRB1*15:01-DQA1*01:02-DQB1*06:02 (OR = 0.03; P_c < .0001), and DRB1*11:01-DQA1*05:05-DQB1*03:01 (OR = 0.07; P_c = .0291) were significantly decreased. Homozygous DRB1*03:01-DQA1*05:01-DQB1*02:01 genotypes and combinations of DRB1*03:01-DQA1*05:01-DQB1*02:01 with DRB1*04:05-DQA1*03:02-DQB1*03:02, DRB1*04:02-DQA1*03:01-DQB1*03:02, and DRB1*04:01-DQA1*03:01-DQB1*03:02 were significantly increased in cases than controls. Combinations of DRB1*03:01-DQA1*05:01-DQB1*02:01 with DRB1*07:01-DQA1*02:01-DQB1*02:02 and DRB1*13:02-DQA1*01:02-DQB1*06:04 showed low OR values but did not remain significantly decreased after Bonferroni correction.

CONCLUSIONS

HLA-DRB1-DQA1-DQB1 alleles, haplotypes, and diplotypes in Saudis with T1D are not markedly different from those observed in Western and Middle-Eastern populations but are quite different than those of East Asians.

HLA and autoantibodies define scleroderma subtypes and risk in African and European Americans and suggest a role for molecular mimicry

Systemic sclerosis (SSc) is a clinically heterogeneous autoimmune disease characterized by mutually exclusive autoantibodies directed against distinct nuclear antigens. We examined HLA associations in SSc and its autoantibody subsets in a large, newly recruited African American (AA) cohort and among European Americans (EA). In the AA population, the African ancestry-predominant HLA-DRB1*08:04 and HLA-DRB1*11:02 alleles were associated with overall SSc risk, and the HLA-DRB1*08:04 allele was strongly associated with the severe antifibrillarin (AFA) antibody subset of SSc (odds ratio = 7.4). These African ancestry-predominant alleles may help explain the increased frequency and severity of SSc among the AA population. In the EA population, the HLA-DPB1*13:01 and HLA-DRB1*07:01 alleles were more strongly associated with antitopoisomerase (ATA) and anticentromere antibody-positive subsets of SSc, respectively, than with overall SSc risk, emphasizing the importance of HLA in defining autoantibody subtypes. The association of the HLA-DPB1*13:01 allele with the ATA⁺ subset of SSc in both AA and EA patients demonstrated a transancestry effect. A direct correlation between SSc prevalence and HLA-DPB1*13:01 allele frequency in multiple populations was observed (r = 0.98, P = 3 × 10^-6). Conditional analysis in the autoantibody subsets of SSc revealed several associated amino acid residues, mostly in the peptide-binding groove of the class II HLA molecules. Using HLA α/β allelic heterodimers, we bioinformatically predicted immunodominant peptides of topoisomerase 1, fibrillarin, and centromere protein A and discovered that they are homologous to viral protein sequences from the Mimiviridae and Phycodnaviridae families. Taken together, these data suggest a possible link between HLA alleles, autoantibodies, and environmental triggers in the pathogenesis of SSc.

Genetic susceptibility to type 1 diabetes in childhood - estimation of HLA class II associated disease risk and class II effect in various phases of islet autoimmunity

OBJECTIVE

The HLA-DR/DQ region remains the major determinant of susceptibility to type 1 diabetes (T1D) despite the more than 50 risk affecting loci outside human leukocyte antigen (HLA) region that have been identified. We aimed at developing a simple risk estimation based on HLA class II genotyping, which was also tested by analyzing HLA class II effect on the autoantibody seroconversion and further progression to diabetes.

SUBJECTS AND METHODS

A total of 2991 trio families with a diabetic child from the Finnish Pediatric Diabetes Register were genotyped and the risk contributed by each DR-DQ haplotype calculated through transmission analysis. The genotype risk was estimated based on the summary effect of haplotypes. Genotype grouping was further tested in a subcohort of the Finnish Type 1 Diabetes Prediction and Prevention (DIPP) Study

RESULTS

The summary effect of haplotypes was generally seen in genotypes, while the expected synergistic effect of DR3-DQ2 and DR4-DQ8 (DRB1*04:03 excluded) combination was also clear in the T1D risk association analysis. This highest risk DR/DQ genotype was found in 21.6% of patients and 2.0% of controls, odds ratio (OR) = 13.2 (10.1-17.2), whereas the lowest risk genotype contained only 0.8% of patients and 28.0% of controls, OR = 0.02 (0.01-0.03). In the subcohort from the DIPP study the risk grades correlated clearly with seroconversion for islet autoantibodies and T1D development. In contrast, DR/DQ risk groups did not associate with the progression rate from advanced autoimmunity to clinical diabetes.

CONCLUSIONS

Class II HLA genotype groups improve the estimation of T1D risk. Class II effect is limited to the early phase of the disease process characterized by seroconversion for islet autoantibodies.

A survey of disease connections for CD4+ T cell master genes and their directly linked genes

Genome-wide association studies and other genetic analyses have identified a large number of genes and variants implicating a variety of disease etiological mechanisms. It is imperative for the study of human diseases to put these genetic findings into a coherent functional context. Here we use system biology tools to examine disease connections of five master genes for CD4+ T cell subtypes (TBX21, GATA3, RORC, BCL6, and FOXP3). We compiled a list of genes functionally interacting (protein-protein interaction, or by acting in the same pathway) with the master genes, then we surveyed the disease connections, either by experimental evidence or by genetic association. Embryonic lethal genes (also known as essential genes) are over-represented in master genes and their interacting genes (55% versus 40% in other genes). Transcription factors are significantly enriched among genes interacting with the master genes (63% versus 10% in other genes). Predicted haploinsufficiency is a feature of most these genes. Disease-connected genes are enriched in this list of genes: 42% of these genes have a disease connection according to Online Mendelian Inheritance in Man (OMIM) (versus 23% in other genes), and 74% are associated with some diseases or phenotype in a Genome Wide Association Study (GWAS) (versus 43% in other genes). Seemingly, not all of the diseases connected to genes surveyed were immune related, which may indicate pleiotropic functions of the master regulator genes and associated genes.

Association between HLA-DQB1 gene and patients with acute lymphoblastic leukemia (ALL)

Acute lymphoblastic leukemia (ALL) affects both children and adults. Survival in ALL has improved in recent decades due to recognition of its biological heterogeneity. Although children have higher remission and cure rates than adults, both populations have benefited from these improvements. Our aim in this study is to determine the association between HLA-DQB1 genes with childhood and adult ALL patients. To define this association, we compared HLA-DQB1 allele frequencies and allele carrier frequencies in a cohort of 135 adults and children with ALL with 150 controls, using polymerase chain reaction with sequence-specific primers. Allele carrier frequencies in childhood ALL show a deficiency in DQ2 (*0201) (P 0.049 and RR 0.75), but an increase in DQ5 (*0501-*0504) and DQ7 (*0301, *0304) compared to the control group (P 0.001 RR 1.89, P 0.003 RR 1.48, respectively). Allele carrier frequencies in adult ALL indicated an increase in DQ5 (*0501-*0504) (P0.045 RR 2.28). Allelic frequencies in childhood ALL revealed the same increase in DQ5 and DQ7, and a decrease in DQ2. In adult ALL it shows a decrease in DQ7. Therefore, our results in adult ALL were similar to childhood ALL addressing DQ5 allele carriers, which showed an increase in both age groups. We suggest that DQ5 could be more strongly considered as an ALL susceptibility allele, and that this allele may underlie a pathogenic phenotype with a major role in the immunologic process involved in both adults and children with ALL.

Association of polycystic ovarian syndrome with human leukocyte antigen polymorphism in Korean women

Although several studies have demonstrated the genetic contribution to polycystic ovarian syndrome (PCOS), the cause of this syndrome remains unclear. The aim of this study was to elucidate the relationship between human leukocyte antigen (HLA) systems and PCOS in Koreans. We compared the HLA-A, B and DRB1 genotype distribution of 52 PCOS patients and 67 healthy Korean women. In addition, we investigated the association of HLA with free-testosterone level. HLA-A*11, A*31 and B*54 showed increased phenotype frequencies (PFs) in PCOS women compared to controls (p = 0.032, OR 2.79; p = 0.019, OR 6.05; p = 0.002, OR 6.40). HLA-DRB1*15 showed negative correlations with the free-testosterone concentration both in total subjects and PCOS patients (p = 0.024 and p = 0.008). The results of the study suggest mild associations of HLA alleles with pathophysiology of PCOS and/or testosterone production in PCOS. Further investigation in a large number of subjects, including subdivision and multi-population studies, will need to be conducted to prove the consistent or variable association in PCOS.

Evidence for hitchhiking of deleterious mutations within the human genome

Deleterious mutations present a significant obstacle to adaptive evolution. Deleterious mutations can inhibit the spread of linked adaptive mutations through a population; conversely, adaptive substitutions can increase the frequency of linked deleterious mutations and even result in their fixation. To assess the impact of adaptive mutations on linked deleterious mutations, we examined the distribution of deleterious and neutral amino acid polymorphism in the human genome. Within genomic regions that show evidence of recent hitchhiking, we find fewer neutral but a similar number of deleterious SNPs compared to other genomic regions. The higher ratio of deleterious to neutral SNPs is consistent with simulated hitchhiking events and implies that positive selection eliminates some deleterious alleles and increases the frequency of others. The distribution of disease-associated alleles is also altered in hitchhiking regions. Disease alleles within hitchhiking regions have been associated with auto-immune disorders, metabolic diseases, cancers, and mental disorders. Our results suggest that positive selection has had a significant impact on deleterious polymorphism and may be partly responsible for the high frequency of certain human disease alleles.

Speaking the Language of Genetics: A Primer

Genetic research advances will continue to result in clinical applications for genetics in primary care settings. Fluency with the evolving genetic terminology will enable primary care providers to provide better clinical care to their patients, particularly when helping patients understand genetic concepts. This article will help clinicians use genetic terminology with greater precision.

Incidence of antisperm antibodies in males with systemic autoimmune diseases

PROBLEM

To investigate if systemic autoimmune diseases could be one of the risk factors for developing antisperm antibodies (ASA) in males.

METHOD OF STUDY

Antisperm antibodies in the sera of 70 males with systemic autoimmune diseases and 80 healthy controls were examined, by using the indirect-immunobead test (I-IBT). The sperm immobilization test (SIT) was also performed to detect sperm immobilizing antibodies to the patients who were positive in I-IBT.

RESULTS

Among 70 males with systemic autoimmune diseases, five were I-IBT positives, with incidence of 7.1%. However, no positives existed in 80 healthy males. Compared with the healthy controls, the incidence of ASA in males with systemic autoimmune diseases was significantly higher (P = 0.020). None of these five ASA-positive patients had sperm immobilizing antibodies.

CONCLUSION

The incidence of ASA in males with systemic autoimmune diseases was significantly higher than in the healthy controls. Systemic autoimmune diseases may be one of the risk factors for developing ASA in men.

MHC class II exacerbates demyelination in vivo independently of T cells

We have shown previously the importance of MHC class II for central nervous system remyelination; however, the function of MHC class II during cuprizone-induced demyelination has not been examined. Here, we show that I-A(beta)-/- mice exhibit significantly reduced inflammation and demyelination. RAG-1(1/1) mice are indistinguishable from controls, indicating T cells may not play a role. The role of MHC class II depends on an intact cytoplasmic tail that leads to the production of IL-1beta, TNF-alpha, and nitric oxide, and oligodendrocyte apoptosis. Thus, the function of MHC class II cytoplasmic tail appears to increase microglial proliferation and activation that exacerbates demyelination.

Searching for additional disease loci in a genomic region

Our aim is to review methods to optimize detection of all disease genes in a genetic region. As a starting point, we assume there is sufficient evidence from linkage and/or association studies, based on significance levels or replication studies, for the involvement in disease risk of the genetic region under study. For closely linked markers, there will often be multiple associations with disease, and linkage analyses identify a region rather than the specific disease-predisposing gene. Hence, the first task is to identify the primary (major) disease-predisposing gene or genes in a genetic region, and single nucleotide polymorphisms thereof, that is, how to distinguish true associations from those that are just due to linkage disequilibrium with the actual disease-predisposing variants. Then, how do we detect additional disease genes in this genetic region? These two issues are of course very closely interrelated. No existing programs, either individually or in aggregate, can handle the magnitude and complexity of the analyses needed using currently available methods. Further, even with modern computers, one cannot study every possible combination of genetic markers and their haplotypes across the genome, or even within a genetic region. Although we must rely heavily on computers, in the final analysis of multiple effects in a genetic region and/or interaction or independent effects between unlinked genes, manipulation of the data by the individual investigator will play a crucial role. We recommend a multistrategy approach using a variety of complementary methods described below.

HLA-DRB1 alleles control allergic bronchopulmonary aspergillosis-like pulmonary responses in humanized transgenic mice

BACKGROUND

Allergic bronchopulmonary aspergillosis (ABPA) is a lung hypersensitivity disease mediated in part by CD4(+) T(H)2 cells. There is a significant association between ABPA and the HLA-DR2 genotypes DRB1(*)1501 and DRB1(*)1503, whereas resistance might be associated with HLA-DRB1(*)1502.

OBJECTIVE

We sought to elucidate the role of HLA-DR alleles in allergic inflammation in lungs.

METHODS

HLA-DR humanized transgenic mice expressing either the susceptible or resistant alleles were analyzed for the nature and extent of pulmonary inflammation after exposure to Aspergillus species antigens.

RESULTS

Exposed DRB1(*)1501 and DRB1(*)1503 transgenic mice displayed infiltrates made up prominently of eosinophils, which is consistent with the inflammation found in ABPA. The resistant DRB1(*)1502 mice, on the other hand, displayed minimal to moderate inflammation, consisting mainly of T-cell infiltrates. Significantly more mucin was produced in the DRB1(*)1503 and DRB1(*)1501 mice, and their ability to limit the number of Aspergillus species conidia within the lung parenchyma was impaired. Despite their differences, both the DRB1(*)1503 and DRB1(*)1502 strains mounted comparable T cell-proliferative responses to Aspergillus species antigens.

CONCLUSION

The HLA-DR2 alleles DRB1(*)1501 and DRB1(*)1503 play a major role in the development of allergic pulmonary inflammation. In contrast, the HLA-DR2 allele DRB1(*)1502 mediates a nonallergic T(H)1-like response to the organism, possibly explaining an ABPA resistance factor. These results are in support of our published human studies in patients with cystic fibrosis and asthma.

CLINICAL IMPLICATIONS

HLA-DR typing in patients with cystic fibrosis and asthma will aid in the identification of individuals at risk for ABPA.

Role of MHC class II expressing CD4+ T cells in proteolipid protein(91-110)-induced EAE in HLA-DR3 transgenic mice

MHC class II molecules play a central role in the control of adaptive immune responses through selection of the CD4(+) T cell repertoire in the thymus and antigen presentation in the periphery. Inherited susceptibility to autoimmune disorders such as multiple sclerosis, rheumatoid arthritis and IDDM are associated with particular MHC class II alleles. Advent of HLA transgenic mice has helped us in deciphering the role of particular HLA DR and DQ class II molecules in human autoimmune diseases. In mice, the expression of class II is restricted to professional antigen-presenting cells (APC). However, in humans, class II is also expressed on T cells, unlike murine T cells. We have developed new humanized HLA class II transgenic mice expressing class II molecules not only on APC but also on a subset of CD4(+) T cells. The expression of class II on CD4(+) T cells is inducible, and class II(+) CD4(+) T cells can present antigen in the absence of APC. Further, using EAE, a well-established animal model of MS, we tested the functional significance of these class II(+) CD4(+) T cells. DR3.AEo transgenic mice were susceptible to proteolipid protein(91-110)-induced EAE and showed CNS pathology accompanied by widespread inflammation and demyelination seen in human MS patients, suggesting a role for class II(+) CD4(+) T cells in the pathogenesis.

Studies on the human leukocyte antigens in patients with polycystic ovary syndrome in a Japanese population--possible susceptibility of HLA-A11 and -DRB1*0403 to patient population with polycystic ovary syndrome

PROBLEM

The objective of this study was to identify the human leukocyte antigen (HLA) alleles that confer susceptibility or resistance to polycystic ovary syndrome (PCOS) in the Japanese population.

METHOD OF STUDY

HLA-A, -B and -C antigens were determined in 56 patients with PCOS using conventional serological method. HLA-DRB1 genotypes were determined using a polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method in 68 patients with PCOS. As a control population, 237 healthy individuals (males and females) were examined concerning HLA-A, -B and -C antigens, and 292 individuals were examined concerning HLA-DRB1 genotypes. The rate of possession of each antigen was compared between the two populations.

RESULTS

The rate of possession of the HLA-A11 and HLA-DRB1*0403 in the patients with PCOS was significantly higher compared with that in the control group. The rate of possession of HLA-B39 in the patients with PCOS was significantly lower compared with that in the general population group.

CONCLUSION

Human leukocyte antigen systems appear to be linked to PCOS.

Molecular genetic studies on the compatibility of HLA class II alleles in patients with unexplained recurrent miscarriage in the Japanese population

It is hypothesized that patients having unexplained recurrent miscarriage lack an appropriate immune reaction against their partner's antigens, which means possible compatibility of HLA antigens between the patient couples. The conclusion, however, has not yet been achieved, so the purpose was to determine whether significant compatibility of HLA class II exists between the couples. The HLA-DRB1 and -DQB1 genotypes were determined using PCR-RFLP method in 91 patient couples and in 72 normal couples. The number of patient couples with zero-allele mismatch was not significantly different compared with that of control couples regarding HLA-DRB1 genotype and phenotype, as well as regarding HLA-DQB1 genotype and phenotype. While the number of patient couples with zero- and one-allele mismatch was significantly higher compared with that in control as to HLA-DR and -DQ phenotype (P=0.029 by Chi-square test). In conclusion, it is suggested that the compatibility of HLA class II antigens between couples might be involved in the genesis of unexplained recurrent miscarriage.

CAT 53: a protein phosphatase 1 nuclear targeting subunit encoded in the MHC Class I region strongly expressed in regions of the brain involved in memory, learning, and Alzheimer's disease

We identified CAT 53 by cDNA hybridization selection as an expressed sequence tag (EST), located in the vicinity of HLA-C and designated as CAT (for HLA-C associated transcript) 53. CAT 53 encodes a protein described by others and commonly known as phosphatase 1 nuclear targeting subunit (PNUTS). PNUTS is a potent inhibitor of nuclear serine/threonine protein phosphatase 1 (PP1). We present the genomic organization of CAT 53, localize specific sites of mRNA transcription in thin sections of mouse brain by in-situ hybridization, and perform a structural analysis of the peptide domains. We also characterize the protein expression pattern for PNUTS by Western blotting and immunohistochemistry with PNUTS antibody in Alzheimer's disease (AD) brains and age-matched control brains. In-situ hybridization and immunohistochemistry analysis of human and mouse brain show high CAT 53 expression in the olfactory cortex, piriform cortex, and hippocampus. Very high expression of CAT 53 was found mainly in the hippocampus, frontal, and entorhinal cortex of control brains and in the neurofibrillary tangles of AD brain. In the hippocampus, CAT 53 is expressed in CA1 and CA3 cell layers and in the dentate gyrus. The hippocampus is known to play a fundamental role in learning and episodic memories and has been implicated in a number of neurological and psychiatric disorders, including AD, epilepsy, and schizophrenia. Our findings suggest that PNUTS, encoded by CAT 53 on 6p21.3, may have a role in the progression of AD.

Minocycline inhibits antigen processing for presentation to human T cells: additive inhibition with chloroquine at therapeutic concentrations

The ability of minocycline to inhibit processing of tetanus toxoid (TT) for presentation to human T cells was tested. Peripheral blood antigen presenting cells (APC) were incubated with TT before or after addition of test compounds for 4 h. APC were then fixed with paraformaldehyde, and added to autologous TT-responsive T cell lines for a proliferation assay. Minocycline (0.1-0.4 mM) gave significant inhibition of T cell response to TT and was equivalent to chloroquine. Inhibition was not observed when TT was incubated with APC before minocycline, indicating that presentation of preprocessed antigen was not inhibited. Minocycline, doxycycline, and tetracycline all inhibited the proliferation of PBMC to TT. The combination of minocycline and chloroquine resulted in additive inhibition at clinically relevant levels of both drugs (3.7 microM). This study suggests a novel immunosuppressive mechanism for minocycline, as well as possible additive anti-inflammatory effect when combined with chloroquine or hydroxychloroquine.

Polymorphism in transmembrane region of MICA gene and cholelithiasis

AIM: To study the significance of polymorphism of MHC class I chain-related gene A (MICA) gene in patients with cholelithiasis.

METHODS: Subjects included 170 unrelated adults (83 males) with cholelithiasis and 245 randomly selected unrelated adults (130 males) as controls. DNA was extracted from peripheral leukocytes and analyzed for polymorphism of 5 alleles (A4, A5, A5.1, A6 and A9) of the MICA gene.

RESULTS: There was no significant difference in phenotype, allele, and genotype frequencies of any of the 5 alleles between cholelithiasis patients and controls.

CONCLUSION: This study demonstrates that MICA alleles studied bear no relation to cholelithiasis.

HLA class II and TNF genes in African Americans from the Southeastern United States: regional differences in allele frequencies

Knowledge of population major histocompatibility complex gene frequencies is important for construction of organ donor pools and for studies of disease association. Human leukocyte antigen DRB1 (HLA-DRB1), HLA-DQB1, and TNFalpha -308 (G-A) promoter genetic typing was performed in 112 healthy, unrelated African Americans (AAs) from the southeastern United States. Allele frequencies were compared with published frequency data from other AA populations. Our AA population had the highest frequency of HLA- DRB1*09 (6.7%) reported in any AA population. The frequency of the TNF alpha -308A polymorphism was also high (14.4%), when compared with published frequencies in AAs. Significant regional differences in the distribution of most HLA-DRB1 and HLA-DQB1 alleles were observed in all AA populations examined. The AA HLA-DRB1 and -DQB1 frequencies also differed from published Caucasian frequencies. This is the first report describing the distribution of TNF alpha promoter alleles in the Southeastern United States. The high DRB1*09 and TNF alpha -308A allele frequencies of our population most resemble the frequencies of these alleles in certain West African populations. These varying major histocompatibility complex gene frequencies may reflect different regional population structures among AAs in the United States, which may be due to differences in ancestral origins, migration, and racial admixture.

A weak association of HLA-B*2702 with Behçet's disease

This study aimed to analyse the association of HLA-B alleles other than -B51 with Behçet's disease (BD). We also investigated the frequency of HLA-B alleles sharing the same natural killer cell immunoglobulin-like receptor (KIR) binding sequence with HLA-B51. Broad-genotyping of HLA-B locus by PCR-SSOP in 174 Turkish BD patients and 191 healthy controls confirmed the strong association of B*51 with BD (60.9% in BD patients, 24.6% in healthy controls, OR = 4.78). No other HLA-B allele was identified showing an association with BD after adjusting for multiple testing or by using relative predispositional effects (RPE) analysis after the deletion of B*51. HLA-B alleles reacting with the sequence specific oligonucleotide probe 23, which corresponds to the KIR binding site of B*51, were found to be positive in 127 BD patients (73%) and 90 controls (47%) (OR = 3.03, 95% CI 2-4.7). The repeated RPE analysis after separating HLA-B alleles carrying B51-KIR binding sequence as distinct alleles within a broad-type allele group revealed B*2702 allele as the only allele showing an association with BD after the deletion of B*51. Selective increase of B*2702, the only B*27 allele carrying the same KIR binding sequence with B*51, warrants investigation of the possibility of interaction of HLA molecules with KIRs on NK or other T cells in the pathogenesis of BD.

Relative HLA-DRB1*04 allele frequencies in five United States populations found in a hematopoietic stem cell volunteer donor registry and seven new DRB1*04 alleles

The frequencies of 29 HLA-DRB1*04 alleles were determined for five major U.S. populations found within a hematopoietic stem cell volunteer donor registry. One hundred sixty-one DRB1*04 positive individuals from each of the self-described groups, Caucasians, African-Americans, Asian/Pacific Islanders, Hispanics, and Native Americans, were randomly chosen from a database of 82,979 unrelated persons. Subjected to polymerase chain reaction-sequence-specific oligonucleotide probe (PCR-SSOP) typing, these 805 individuals carried a total of ten different DRB1*04 alleles, ranging from DRB1*0401 to DRB1*0411 with DRB1*0409 conspicuously absent from all five groups. The distribution of DRB1*04 alleles varied among the groups, with DRB1*0401 being predominant in Caucasians, African-Americans, and Native Americans. DRB1*0404 and DRB1*0407 were the two most commonly observed alleles in Hispanics, whereas DRB1*0405 and DRB1*04031 were most common in Asian/Pacific Islanders. The remaining 18 DRB1*04 alleles known at the time of the study were not observed. Although not observed in the frequency study, seven previously unreported DRB1*04 alleles are also described.

Inheritance of hypoadrenocorticism in bearded collies

OBJECTIVE

To assess heritability and mode of inheritance for hypoadrenocorticism in Bearded Collies.

ANIMALS

635 Bearded Collies.

PROCEDURES

Dogs were classified as affected by hypoadrenocorticism or unaffected. Phenotypic and pedigree data were analyzed. Heritability was estimated by use of Bayesian statistical methods. Regressive logistic models for complex segregation analyses were used to characterize mode of inheritance.

RESULTS

Hypoadrenocorticism was diagnosed in 60 (9.4%) dogs. Heritability of hypoadrenocorticism was estimated to be 0.76 with both sexes affected with equal probability. Evaluation of the pedigrees did not support a Mendelian autosomal dominant mode of inheritance. Evidence from the complex segregation analysis for a single locus of large effect on hypoadrenocorticism was not convincing.

CONCLUSIONS AND CLINICAL RELEVANCE

Hypoadrenocorticism in Bearded Collies is highly heritable. Although a precise genetic mechanism responsible for inheritance of the disorder remains undetermined, breeding decisions must include consideration of the genetic likelihood of passing on this deleterious disorder to offspring of affected dams and sires.

HLA-class I antigens in patients with unexplained recurrent abortion

In order to clarify the genetic background of recurrent spontaneous abortion, the frequency of HLA-A, -B, and -C alleles was analyzed in eighty-nine patients with a history of unexplained primary recurrent abortion. The frequency of each HLA-A, -B, and -C antigen allele was calculated in patients with recurrent abortion and their husbands, and compared with the frequencies in the general population represented by 207 individuals in the Niigata district of Japan. The incidence of individuals homozygous for the HLA-A, -B, and -C alleles was also compared between the patient group and the control group. The frequency of HLA-B35 in the patient group (5 of 89, 5.6%) was significantly lower than in the general population (40 of 207, 19.3%) (Odds Ratio, 0.25; 95% Confidence Interval, 0.09-0.65; P < 0.005; Pc, not significant). The frequencies of other HLA-A, -B, and -C alleles were not significantly different between the patient group and the general population. No significant difference in the frequency of HLA-A, -B, and -C alleles was observed between the husband group and the general population. The incidence of individuals homozygous for HLA-A, -B, or -C alleles in the patient group was not significantly different from the general population. The significantly lower frequency of HLA-B35 in patients with unexplained recurrent abortion suggests that the Th2-associated immune reactions may be lacking in such patients, as it has been reported that an enhanced Th2 response in conjunction with a decreased T Th1 response is a common immune reaction in HLA-B35-positive individuals.

Family-based association of HLA class II alleles and haplotypes with type I diabetes in Brazilians reveals some characteristics of a highly diversified population

The association of HLA class II haplotypes with type I diabetes was analyzed in 56 Southeastern Brazilian families using affected family-based controls (AFBAC) method. DRB1-DQA1-DQB1 alleles were determined by polymerase chain reaction/sequence-specific primer genotyping. This study first revealed the great haplotype diversity of Brazilians (65 different haplotypes even with incomplete DRB1 subtyping), probably due to the admixture of Africans genes with European and Amerindian genes in this population. The results revealed increased frequencies of the DRB1*03-DQA1*0501-DQB1*02 and DRB1*0401-DQA1*03-DQB1*0302 haplotypes in the patient group The highest risk for type I diabetes was associated with the heterozygote DRB1*03/*04 genotype as largely reported, and DRB1*03/X and DRB1*04/Y genotypes conferred a significant, but much lower disease risk. Protection from type I diabetes revealed some peculiarities in Southeastern Brazilians: a lack of significant protecting effect of the DRB1*1501-DQA1*0102-DQB1*0602 haplotype, and an apparent protection conferred by the DRB1*13-DQB1*0301, DRB1*11-DQB1*0301, and DRB1*01-DQB1*0501 two-locus haplotypes. The risk to type I diabetes in the highly diversified Southeastern Brazilians evidenced specific information to the prediction of the disease in this region of the country.

Microfluidic arrays in genetic analysis

The goal of genetic analysis is to discover genetic markers that are informative for providing high confidence, positive predictive value in managing phenotypic outcomes. Primary consensus sequence data, genetic polymorphism databases and associated phenotype data are rapidly making genetic analysis more useful. Therefore, genetic analysis applications are gradually becoming more mainstream. The diversity and complexity of genetic analysis currently requires an array of analytical techniques, instrument platforms and software to support all the steps from data acquisition to interpretation. As supporting research technologies mature, they are incorporating increasing levels of automation, system integration and miniaturization. Microfluidic arrays are positioned to play a key role in routine genetic analysis, particularly as they begin to appear in more fully integrated analytical platforms.

Genetic and familial considerations of primary biliary cirrhosis

The genetic basis of human autoimmune diseases is receiving increasing attention. Primary biliary cirrhosis (PBC) is a model autoimmune disease reflective of other organ-specific autoimmune pathology. PBC is an enigmatic autoimmune disease that predominantly affects women and leads to destruction of intrahepatic bile ducts. The serological hallmark of this disease is characterized by antimitochondrial antibodies that specifically react with the E2 components of 2-oxodehydrogenase enzymes, including PDC-E2. There are no clear major histocompatibility complex associations with the development of PBC, despite the observation that first-degree relations of index patients with PBC have a 4-6% prevalence of development of PBC. This risk factor is comparable or higher than any other human autoimmune disease and suggests that a genome-wide approach towards dissection of genetic associations would lead to valuable new insights. In this review, we place these concepts in perspective and highlight in particular the genetic associations in PBC and the importance of studying siblings with PBC who are concordant for disease.

Polymorphism in the transmembrane region of the MICA gene and type 1 diabetes

Although MHC class II genes have a stronger association with type 1 diabetes than MHC class I genes, studies have shown that MHC class I molecules play an independent role in the etiology of type 1 diabetes, and the existence of susceptibility genes within a segment of MHC between the HLA-B and TNF genes has been predicted, where MHC class I chain-related gene A (MICA) resides. MICA has a triplet repeat polymorphism in the transmembrane region consisting of five alleles. We analyzed this polymorphism in 162 unrelated children (82 boys) with type 1 diabetes (age at diagnosis 7.01 +/- 3.76 yr) and 154 randomly selected unrelated children (87 boys), age 2.81 +/- 2.12 yr. Phenotype frequency of allele A9 in children with type 1 diabetes was significantly higher than in controls (RR = 2.42, 95% CI = 1.52-3.85, p = 0.000162, pc = 0.00081). Gene frequency of allele A9 was also significantly higher in children with type 1 diabetes when compared with control children (RR = 2.73, 95% CI = 1.85-4.03, p = 2.62 x 10(-7), pc = 1.31 x 10(-6)). This study demonstrates that MICA allele A9 confers risk of type 1 diabetes.

Association of HLA-DQ and -DR alleles with protection from or infection with HIV-1

Infection with human immunodeficiency virus type 1 (HIV-1) and progression to acquired immune deficiency syndrome (AIDS) are controlled by both host genetic factors and viral factors. The HLA (human leukocyte antigen) region in humans controls immune response functions and tissue rejection and influences susceptibility to neoplasia, autoimmune diseases, and infectious diseases including HIV. Twenty-eight African American and 12 Caucasian patients participated in the study. HLA-DQB1 and HLA-DRB1 genotyping was performed using PCR and sequence-specific oligonucleotide probe reverse hybridization and analyzed with the LiPA Key Typing System and LiPA software. DQB1*0603 was found to be positively associated with HIV-1 infection and with HIV-1 infection in Caucasians but not African Americans. DQB1*03032 frequencies indicate a positive association with protection from HIV-1 infection. It was further found to be protective against HIV-1 infection in Caucasians but not in African Amens. DQB1*0201 was observed more frequently in HIV(+) African Americans than HIV(-) African Americans, suggesting a positive association with HIV-1 infection in this ethnic group. HLA-DRB1*04 exhibited a positive association with HIV-1 infection in Caucasians. These data show that there are HLA class II alleles associated with susceptibility to and protection from HIV-1 infection and that these differ between ethnic groups.

Studies on the HLA-DRB1 genotypes in Japanese women with severe pre-eclampsia positive and negative for anticardiolipin antibody using a polymerase chain reaction-restriction fragment length polymorphism method

The human leukocyte antigen (HLA)-DR genotype was determined in 54 Japanese women with severe pre-eclampsia in order to elucidate the relationship between HLA-DR antigen systems and pre-eclampsia. The patients were divided into two groups according to positivity for the anticardiolipin antibody (ACA), i.e. one patient group negative for ACA (n = 41) and the other patient group positive for ACA (n = 13). The frequency of each HLA-DRB1 allele in both groups was compared with that in 81 normally fertile Japanese women who had not experienced pre-eclampsia. The genotypes of HLA-DR antigens were determined using a polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method. The frequency of DRB1*04 and DRB1*0403 in the patient group positive for the ACA was significantly higher compared with that in the group of normal fertile women (P< 0.05). The frequency of each HLA-DRB1 allele was not significantly different between patient group with pre-eclampsia negative for ACA and group of normal fertile women. These results suggest a difference in the immunogenetic background between the patient groups with severe pre-eclampsia positive and negative for the ACA.

Impact of sex on inheritance of ankylosing spondylitis: a cohort study

BACKGROUND

Ankylosing spondylitis is a genetically determined and commonly familial disorder. Men and women differ in their susceptibility to ankylosing spondylitis, with about 2.5 men affected for every woman with the disease. We investigated the influence of the sex of the index case on disease penetrance within families.

METHODS

The ages at which 50% and 75% of patients were diagnosed with ankylosing spondylitis were ascertained from a database of 4400 cases. Index patients with children or siblings who were old enough to have obtained a diagnosis (50% and 75% rates) were assessed for prevalence of disease among relatives. Confirmation of diagnosis for affected relatives was sought for all offspring and a random 25% selection of siblings.

FINDINGS

Ankylosing spondylitis was more prevalent among children (odds ratio 1.9 [95% CI 1.2-3.0], p<0.005) and siblings (1.5 [1.2-1.9], p<0.0001) of female index cases than among those of male cases. Analyses restricted to index cases with a young age at onset (< or = 21 years) indicated that children of women had an even higher incidence of ankylosing spondylitis (7.2 [1.5-34], p=0.013) than did children of men at similar age at onset. 38% of children of female cases had disease compared with 8% of male cases. There was no difference in sex distribution among affected children or siblings of female patients with ankylosing spondylitis. By contrast, the sons and brothers of male patients had a higher prevalence of the disease (odds ratio 2.6 [1.4-5.2], p=0.003) than did daughters and sisters (1.7 [1.3-2.2], p<0.0001).

INTERPRETATION

The influence of female sex is greater than that of male sex in determining increased susceptibility to ankylosing spondylitis in children. The striking maternal effect is greatest for women with young age at onset, which is not seen in men. The sex ratio of affected children depends on the sex of the affected parent.

Corneodesmosin gene polymorphism demonstrates strong linkage disequilibrium with HLA and association with psoriasis vulgaris

Corneodesmosin (CD) is thought to play a key role in corneocyte cohesion, and its proteolysis appears to be a major event in the process of desquamation. Recently it was shown that CD is encoded by the S-gene, which is located approximately 160 kb telomeric of HLA-C. In the present study, the role of CD in the genetics of psoriasis vulgaris was studied in greater detail. The second exon of the CD gene was sequenced in 86 HLA-typed individuals from 13 psoriasis multiplex families. A total of 11 silent dimorphisms and 7 variants resulting in amino acid substitutions were found. Pedigree analysis showed that these variants could be grouped into 7 alleles, encoding 6 different amino acid sequences. These alleles are in strong linkage disequilibrium with HLA-B and -C, indicating that the polymorphism of the CD gene is ancient and well conserved rather than sporadic. One allele at the CD locus, designated CD2, displayed strong linkage disequilibrium with HLA-Cw6, the HLA allele most prominently associated with psoriasis. CD2 demonstrated a greater relative risk than Cw6 (3.4 vs. 2.5, not significant) and higher significant transmission disequilibrium with psoriasis than any of the investigated HLA-alleles. Due to its biologic function, cellular location and disease association, the CD gene appears to be an excellent candidate gene for PSORS1, the HLA-linked determinant of psoriasis vulgaris.

Molecular mechanisms of CD8+ T cell-mediated delayed hypersensitivity: implications for allergies, asthma, and autoimmunity

Delayed-type hypersensitivity (DTH) is defined as the recruitment of T cells into tissues to be activated by antigen-presenting cells to produce cytokines that mediate local inflammation. CD8+ T cells are now known to mediate DTH responses in allergic contact dermatitis, drug eruptions, asthma, and autoimmune diseases. This inflammatory effector capability of CD8+ cytotoxic T cells was previously poorly recognized, but there is now considerable evidence that these diseases may be mediated by CD8+ DTH. The difference between CD8+ T cells and CD4+ T cells mediating DTH relates to the molecular mechanisms by which antigens are processed and presented to the T cells. Antigens external to the cell are phagocytosed and processed for presentation on MHC class II molecules (eg, HLA-DR) to CD4+ T cells. In contrast, internal cytoplasmic antigens are processed by the endogenous pathway for presentation on MHC class I molecules (eg, HLA-A, -B, and -C) to CD8+ T cells. External allergens can also enter the endogenous pathway to be presented to CD8+ T cells. These include many contact sensitizers, chemical and protein respiratory allergens, viral antigens, metabolic products of drugs, and autoantigens. The resulting CD8+ T-cell response explains the role of CD8+ T-cell DTH mechanisms in allergic contact dermatitis, asthma, drug eruptions, and autoimmune diseases.

Linkage disequilibrium analysis of familial psoriasis: identification of multiple disease-associated MHC haplotypes

Although psoriasis vulgaris (PsV) is strongly associated with certain human leukocyte antigens, the pathogenetic nature of these associations remains elusive. The objectives of this study were: (i) to determine whether HLA loci directly determine susceptibility or merely serve as markers for the susceptibility allele; and (ii) to identify additional disease-associated haplotypes. By applying maximum likelihood linkage disequilibrium analysis (LDA) in cases vs. controls, we found the susceptibility gene to be more strongly associated with specific HLA haplotypes than with their component alleles. Stronger linkage disequilibrium between PsV and HLA alleles was detected at HLA-C and HLA-B than at DRB1 and DQB1. Parametric linkage analysis accounting for marker-trait disequilibrium in psoriasis vulgaris pedigrees yielded most significant results for a locus close to HLA-B and -C. Furthermore, we found that susceptibility is linked to at least three different ancestral HLA haplotypes; among them, HLA-Cw7-B8-DRB1*0301-DQB1*02 is linked to PsV for the first time. These results identify a major PsV susceptibility locus in the immediate vicinity of, but distinct from HLA-B or HLA-C, and suggest that multiple disease alleles have arisen during human evolution.

Contribution of T cells to the development of autoimmune diabetes in the NOD mouse model

The nonobese diabetic (NOD) mouse spontaneously develops an autoimmune diabetes that shares many immunogenetic features with human insulin-dependent diabetes mellitus (IDDM), type 1 diabetes. The mononuclear cell infiltrates in the islet, which results in the development of insulitis (a prerequisite step for the development of diabetes) are primarily composed of T cells. It is now well accepted that these T cells play important roles in initiating and propagating an autoimmune process, which in turn destroys insulin-producing islet beta cells in the pancreas. T cells are subdivided into CD4+ helper T cells and CD8+ cytotoxic T cells. CD4+ T cells are further subdivided into Th1 and Th2 cells based on profiles of cytokine production, and these two T-cell populations counterregulate each other. Because many autoimmune diseases are Th1 T-cell mediated, current studies have focused on manipulating the Th1/Th2 imbalance to suppress the autoimmune process in the NOD model. Furthermore, the incidence of disease is much higher in females than that in males, suggesting an involvement of sex-steroid hormones in the development of diabetes. Understanding insights of the mechanism of immune-mediated islet cell destruction and the interaction between the immune and the neuroendocrine system may, therefore, provide new therapeutic means of preventing this chronic debilitating disease.

Response to interferon therapy: influence of human leucocyte antigen alleles in patients with chronic hepatitis C

The response to interferon (IFN) therapy in patients with chronic hepatitis C is characterized by normalization of the serum alanine aminotransferase (ALT) activity during treatment, but relapse within 6 months of cessation of therapy is common. Viral characteristics, such as the genotype and viral load, may influence the patient response to IFN. The aim of this study was to examine host factors, namely the genetically determined human leucocyte antigen (HLA) class II alleles, in patients with chronic hepatitis C, and their relationship to the response to IFN therapy. Seventy white patients with chronic hepatitis C, treated with IFN-alpha for 6 months, were enrolled in the study. Serum ALT was measured at the end of treatment to assess short-term response and again 6 months post-treatment to assess sustained response. Sequence-specific primers were used in the polymerase chain reaction (PCR) to amplify genomic DNA isolated from peripheral mononuclear cells. HLA class II alleles were determined by analysis of the amplicon by gel electrophoresis and hybridization of sequence-specific oligonucleotide probes. At the end of treatment, 25 of the 70 patients (36%) had a normal ALT. By 6 months post-treatment, only six patients (9%) had a sustained normalization of ALT. The frequency of the allele DRB1*0404 was significantly higher in patients with a sustained response as compared to those lacking such a response (25.0% vs 2.3%, with a Bonferonni-corrected P-value of 0.019). There was no difference in the frequency of other class II alleles at the DRB1 and DQB1 loci in responders as compared with non-responders. Therefore, we conclude that the maintenance of a response to IFN in chronic hepatitis C may be, in part, determined by genetic factors in the host.

African-American HLA class II allele and haplotype diversity

Molecular genetic techniques were used to type nine loci in the HLA class II region in 241 unrelated African-Americans from New York City (NYC). Several effects attributable to recent genetic admixture were evident: the number of distinct class II alleles and haplotypes was larger in the African-Americans than in people of African or European origin, the allele frequencies were more consistently even, and linkage disequilibrium was present across the entire class II region. The African-American DRB1 allele frequencies almost always fell between frequencies among samples from northern Europe and the Gambia, two possible founding populations. The exceptions are attributed to the contribution of other genetically dissimilar African groups to the African-American gene pool. DRB1 allele frequencies (specifically DRB1*1501) and some haplotypes of DRB1-DPB1 were different in our NYC and the 11th International Histocompatibility Workshop (IHW) samples of African-Americans. The high level of allele and haplotype diversity found in African-Americans has important implications for the construction of pools of unrelated potential donors for tissue transplantation.

Quantification of the relative contribution of major histocompatibility complex (MHC) and non-MHC genes to human immune responses to foreign antigens

Understanding the extent to which genetic factors influence the immune response is important in the development of subunit vaccines. Associations with HLA gene polymorphisms appear insufficient to explain the range of variation in immune responses to vaccines and to infections by major pathogens. In this study of Gambian twins we report that regulation of the immune response to a variety of antigens from Plasmodium falciparum and Mycobacterium tuberculosis is controlled by factors which are encoded by genes that lie both within and outside the major histocompatibility complex (MHC). We define the relative contribution of these genes, which varies for different antigens. The cumulative genetic contribution of non-MHC genes to the total phenotypic variance exceeds that of the MHC-encoded genes.

African-American HLA class II allele and haplotype diversity

Molecular genetic techniques were used to type nine loci in the HLA class II region in 241 unrelated African-Americans from New York City (NYC). Several effects attributable to recent genetic admixture were evident: the number of distinct class II alleles and haplotypes was larger in the African-Americans than in people of African or European origin, the allele frequencies were more consistently even, and linkage disequilibrium was present across the entire class II region. The African-American DRB1 allele frequencies almost always fell between frequencies among samples from northern Europe and the Gambia, two possible founding populations. The exceptions are attributed to the contribution of other genetically dissimilar African groups to the African-American gene pool. DRB1 allele frequencies (specifically DRB1*1501) and some haplotypes of DRB1-DPB1 were different in our NYC and the 11th International Histocompatibility Workshop (IHW) samples of African-Americans. The high level of allele and haplotype diversity found in African-Americans has important implications for the construction of pools of unrelated potential donors for tissue transplantation.