Complexity in the major histocompatibility complex

Genetic diversity analysis in Chinese miniature pigs using swine leukocyte antigen complex microsatellites

Objective

The swine leukocyte antigen (SLA) gene group, which is closely linked and highly polymorphic, has important biomedical significance in the protection and utilization of germplasm resources. However, genetic polymorphism analyses of SLA microsatellite markers in Chinese miniature pigs are limited.

Methods

Eighteen pairs of microsatellite primers were used to amplify the SLA regions of seven miniature pig breeds and three wild boar breeds (n = 346) from different regions of China. The indexes of genetic polymorphism, including expected heterozygosity (He), polymorphic information content (PIC), and haplotype, were analyzed. The genetic differentiation coefficient (Fst) and neighbor-joining methods were used for cluster analysis of the breeds.

Results

In miniature pigs, the SLA I region had the highest numbers of polymorphisms, followed by the SLA II and SLA III regions; the region near the centromere had the lowest number of polymorphisms. Among the seven miniature pig breeds, Diannan small-ear pigs had the highest genetic diversity (PIC value = 0.6396), whereas the genetic diversity of the Hebao pig was the lowest (PIC value = 0.4330). The Fst values in the Mingguang small-ear, Diannan small-ear, and Yunnan wild boars were less than 0.05. According to phylogenetic cluster analysis, the South-China-type miniature pigs clustered into one group, among which Mingguang small-ear pigs clustered with Diannan small-ear pigs. Haplotype analysis revealed that the SLA I, II, and III regions could be constructed into 13, 7, and 11 common haplotypes, respectively.

Conclusion

This study validates the high genetic diversity of the Chinese miniature pig. Mingguang small-ear pigs have close kinship with Diannan small-ear pigs, implying that they may have similar genetic backgrounds and originate from the same population. This study also provides a foundation for genetic breeding, genetic resource protection, and classification of Chinese miniature pigs.

Specificity of CD8+ T-Cell Responses Following Vaccination with Conserved Regions of HIV-1 in Nairobi, Kenya

Sub-Saharan Africa carries the biggest burden of the human immunodeficiency virus type 1 (HIV-1)/AIDS epidemic and is in an urgent need of an effective vaccine. CD8+ T cells are an important component of the host immune response to HIV-1 and may need to be harnessed if a vaccine is to be effective. CD8+ T cells recognize human leukocyte antigen (HLA)-associated viral epitopes and the HLA alleles vary significantly among different ethnic groups. It follows that definition of HIV-1-derived peptides recognized by CD8+ T cells in the geographically relevant regions will critically guide vaccine development. Here, we study fine details of CD8+ T-cell responses elicited in HIV-1/2-uninfected individuals in Nairobi, Kenya, who received a candidate vaccine delivering conserved regions of HIV-1 proteins called HIVconsv. Using 10-day cell lines established by in vitro peptide restimulation of cryopreserved PBMC and stably HLA-transfected 721.221/C1R cell lines, we confirm experimentally many already defined epitopes, for a number of epitopes we define the restricting HLA molecule(s) and describe four novel HLA-epitope pairs. We also identify specific dominance patterns, a promiscuous T-cell epitope and a rescue of suboptimal T-cell epitope induction in vivo by its functional variant, which all together inform vaccine design.

HLA and Risk of Diffuse Large B cell Lymphoma After Solid Organ Transplantation

BACKGROUND

Solid organ transplant recipients have heightened risk for diffuse large B cell lymphoma (DLBCL). The role of donor-recipient HLA mismatch and recipient HLA type on DLBCL risk are not well established.

METHODS

We examined 172 231 kidney, heart, pancreas, and lung recipients transplanted in the United States between 1987 and 2010, including 902 with DLBCL. Incidence rate ratios (IRRs) were calculated using Poisson regression for DLBCL risk in relation to HLA mismatch, types, and zygosity, adjusting for sex, age, race/ethnicity, year, organ, and transplant number.

RESULTS

Compared with recipients who had 2 HLA-DR mismatches, those with zero or 1 mismatch had reduced DLBCL risk, (zero: IRR, 0.76, 95% confidence interval [95% CI], 0.61-0.95; one: IRR, 0.83; 95% CI, 0.69-1.00). In stratified analyses, recipients matched at either HLA-A, -B, or -DR had a significantly reduced risk of late-onset (>2 years after transplantation), but not early-onset DLBCL, and there was a trend for decreasing risk with decreasing mismatch across all 3 loci (P = 0.0003). Several individual recipient HLA-A, -B, -C, -DR, and -DQ antigens were also associated with DLBCL risk, including DR13 (IRR, 0.74; 95% CI, 0.57-0.93) and B38 (IRR, 1.48; 95% CI, 1.10-1.93), confirming prior findings that these 2 antigens are associated with risk of infection-associated cancers.

CONCLUSIONS

In conclusion, variation in HLA is related to susceptibility to DLBCL, perhaps reflecting intensity of immunosuppression, control of Epstein-Barr virus infection among transplant recipients or chronic immune stimulation.

Characterization of swine leukocyte antigen (SLA) polymorphism by sequence-based and PCR-SSP methods in Chinese Bama miniature pigs

The highly polymorphic swine leukocyte antigen (SLA) genes have been repeatedly shown to influence swine immune traits, disease resistance, vaccine responsiveness and tumour penetrance. Analysis of the SLA diversity in as many pig breeds as possible is important to clarify the relationships between SLA genes and diseases or traits, and develop these pigs as valuable animal models for biomedical research. The Chinese Bama miniature pig breed is an economically significant breed that is available at several research institutions in China. In this study, we identified a total of 32 alleles at five polymorphic SLA loci (SLA-1, SLA-3, SLA-2, DRB1 and DQB1) representing nine class I and seven class II haplotypes using the reverse transcription polymerase chain reaction (RT-PCR) sequence-based typing (SBT) method. The possible functional sites of the SLA genes were predicted and analyzed by comparison with those of the human and mouse. Based on the sequence information, we subsequently developed a rapid PCR-based typing assay using sequence-specific primers (PCR-SSP) to efficiently follow the SLA types of the progeny. In the studied cohort (2n = 562), the most prevalent Haplotype Hp-35.6 (SLA-1(∗)1201, SLA-1(∗)1301-SLA-3(∗)0502-SLA-2(∗)1001-DRB1(∗)0501-DQB1(∗)0801) was identified in 182 Bama pigs with a frequency of 32.38%. The presence of the duplicated SLA-1 locus was confirmed in five of the class I haplotypes. Moreover, we identified two crossovers within the class I region and one between the class I and class II regions, which corresponded to recombination frequencies of 0.36% and 0.18%, respectively. The information of this study is essential for an understanding of the SLA allelic architecture and diversity, and it will be helpful for studying the adaptive immune response and further developing the more effective vaccines in the context of SLA specificities.

Analyzing the genetic characteristics and function of the swine leukocyte antigen 2 gene in a Chinese inbreed of pigs

To study the genetic characteristics and function of swine leukocyte antigen (SLA) class I from the Hebao pig, a rare inbreed in China, a pair of primers was designed to amplify the SLA-2 gene (SLA-2-HB) and then the genetic characteristics of the gene were analyzed. The 3D homology modeling was used to analyze the structure and function of SLA-2-HB proteins. After cloning, sequencing and computer analysis, four SLA-2-HB alleles were found, all of 1119 bp. Sites 3-1097 were an open reading frame encoding 364 amino acids with two sets of intra-chain disulfide bonds comprising four cysteines situated in sites 125, 188, 227 and 283. By alignment of SLA-2-HB sequences with other SLA-2 alleles in the IPD database, 11 key variable amino acid sites were found in the extracellular domain of the SLA-2-HB alleles at sites 23(F), 24(I), 43(A), 44(K), 50(Q), 73(N), 95(I), 114(R), 155(G), 156(E) and 216(S), which could be used to differentiate other SLA-2 alleles. The 3D homology modeling demonstrated that the eight of 11 key variable amino acid sites were all in antigenic binding groove of SLA-2-HB proteins. The amino acid identities between SLA-2-HB and other SLA-2, SLA-1 and SLA-3 alleles were 86.2-97.0%, 85.0-93.9% and 83.3-88.6%, respectively. The phylogenetic tree of SLA-2-HB showed that it was relatively independent of the other SLA-2 genes. Furthermore, the SLA-2-HB alleles were similar to HLA-B15 and HLA-A2 functional domains and preserved some functional sites of HLA-A2. It was concluded that SLA-2-HB are novel alleles of SLA-2 and that the Hebao pig might have evolved independently in China.

Use of human bronchial epithelial cells (BEAS-2B) to study immunological markers resulting from exposure to PM(2.5) organic extract from Puerto Rico

Fine particulate air pollutants, mainly their organic fraction, have been demonstrated to be associated with cardiovascular and respiratory health problems. Puerto Rico has been reported to have the highest prevalence of pulmonary diseases (e.g., asthma) in the United States. The aim of this study was to assess, for the first time, the immunological response of human bronchial epithelial cells (BEAS-2B) to organic extracts isolated from airborne particulate matter (PM(2.5)) in Puerto Rico. Organic extracts from PM(2.5) collected throughout an 8-month period (2000-2001) were pooled (composite) in order to perform chemical analysis and biological activity testing. BEAS-2B cells were exposed to PM(2.5) organic extract to assess cytotoxicity, levels of cytokines and relative gene expression of MHC-II, hPXR and CYP3A5. Our findings show that organic PM(2.5) consist of toxic as well as bioactive components that can regulate the secretion of cytokines in BEAS-2B, which could modulate inflammatory response in the lung. Trace element analyses confirmed the presence of metals in organic extracts highlighting the relative high abundance of Cu and Zn in polar organic extracts. Polar organic extracts exhibited dose-dependant toxicity and were found to significantly induce the release of interleukin 6 (IL-6), IL-1beta and IL-7 while significantly inhibiting the secretion of IL-8, G-CSF and MCP-1. Moreover, MHC-II transcriptional activity was up-regulated after 24 h of exposure, whereas PXR and CYP3A5 were down-regulated. This research provides a new insight into the effects of PM(2.5) organic fractions on specific effectors and their possible role in the development of respiratory inflammatory diseases in Puerto Rico.

The implications of pharmacogenomics in the treatment of HIV-1-infected patients of African descent

One of the great advances in the treatment of HIV-1 infection was the development of the highly active antiretroviral therapy (HAART). Although this treatment strategy is highly effective in many individuals, interpatient variability of drug response and high incidences of short- and long-term toxicities remain significant problems associated with this treatment. Logically, pharmacogenetic differences among HIV-1-infected individuals are thought to represent important factors contributing to antiretroviral drug response. Studies have identified polymorphisms in drug-metabolizing enzymes, drug transporters, and most recently the human leukocyte antigen locus that appears to have significant effects on the clinical outcomes of antiretroviral therapy. Furthermore, some studies have shown that many of these crucial polymorphisms are more likely or less likely in certain populations. This review investigates the potential role of pharmacogenomics in the management of HIV-1 infection in people of African descent.

Reconfiguration of genomic anchors upon transcriptional activation of the human major histocompatibility complex

The folding of chromatin into topologically constrained loop domains is essential for genomic function. We have identified genomic anchors that define the organization of chromatin loop domains across the human major histocompatibility complex (MHC). This locus contains critical genes for immunity and is associated with more diseases than any other region of the genome. Classical MHC genes are expressed in a cell type-specific pattern and can be induced by cytokines such as interferon-gamma (IFNG). Transcriptional activation of the MHC was associated with a reconfiguration of chromatin architecture resulting from the formation of additional genomic anchors. These findings suggest that the dynamic arrangement of genomic anchors and loops plays a role in transcriptional regulation.

Immunopathogenesis of psoriasis

This paper reviews the pathogenesis of psoriasis, in particular, the immunological cascade in psoriasis. Psoriasis is an immune-mediated skin disease where the T cell plays a pivotal role in the pathogenesis of the disease. The critical steps involved in the pathogenesis include Langerhans cell activation and maturation by antigens in the skin, activation of the T cell by mature Langerhans cells, differentiation and expansion of T cells within the lymph nodes, trafficking of activated T cells from the lymph node to the skin and the subsequent release of cytokines. These cytokines are responsible for epidermal and vascular hyperproliferation and pro-inflammatory effects. Each of these steps provides an opportunity for biological agents designed to block the psoriatic immunological cascade. This paper reviews the immunopathogenesis of psoriasis. Biologic agents in psoriasis, to be published separately, reviews the new biologic therapies that aim to selectively block the immunological steps implicated in the pathogenesis of psoriasis outlined in this paper.

Reconstruction of a swine SLA-I protein complex and determination of binding nonameric peptides derived from the foot-and-mouth disease virus

No experimental system to date is available to identify viral T-cell epitopes in swine. In order to reconstruct the system for identification of short antigenic peptides, the swine SLA-2 gene was linked to the beta(2)m gene via (G4S)3, a linker encoding a 15-amino acid glycine-rich sequence (G4S)3, using splicing overlap extension-PCR (SOE-PCR). The maltose binding protein (MBP)-SLA-2-(G4S)3-beta(2)m fusion protein was expressed and purified in a pMAL-p2X/Escherichia coli TB1 system. The purified MBP-SLA-2-(G4S)3-beta(2)m protein was cleaved by factor Xa protease, and further purified by DEAE-Sepharose chromatography. The conformation of the SLA-2-(G4S)3-beta(2)m protein was determined by circular dichroism (CD) spectrum. In addition, the refolded SLA-2-(G4S)3-beta(2)m protein was used to bind three nonameric peptides derived from the foot-and-mouth disease virus (FMDV) O subtype VP1. The SLA-2-(G4S)3-beta(2)m-associated peptides were detected by mass spectrometry. The molecular weights and amino acid sequences of the peptides were confirmed by primary and secondary spectra, respectively. The results indicate that the SLA-2-(G4S)3-beta(2)m was 41.6kDa, and its alpha-helix, beta-sheet, turn, and random coil by CD estimation were 78 aa, 149 aa, 67 aa, and 93 aa, respectively. SLA-2-(G4S)3-beta(2)m protein was able to bind the nonameric peptides derived from the FMDV VP1 region: 26-34 (RRQHTDVSF) and 157-165 (RTLPTSFNY). The experimental system demonstrated that the reconstructed SLA-2-(G4S)3-beta(2)m protein complex can be used to identify nonameric peptides, including T-cell epitopes in swine.

The immunology of psoriasis and biologic immunotherapy

In this review, we will discuss the immunological basis for psoriasis with special emphasis on the role of effector T cells. With the understanding of this immunologic process, we will present a model for the development of targeted immune response modifiers, termed biologic immunotherapies, and their potential role for the benefit of patients with psoriasis.

Advantage of rare HLA supertype in HIV disease progression

The highly polymorphic human leukocyte antigen (HLA) class I molecules help to determine the specificity and repertoire of the immune response. The great diversity of these antigen-binding molecules confers differential advantages in responding to pathogens, but presents a major obstacle to distinguishing HLA allele-specific effects. HLA class I supertypes provide a functional classification for the many different HLA alleles that overlap in their peptide-binding specificities. We analyzed the association of these discrete HLA supertypes with HIV disease progression rates in a population of HIV-infected men. We found that HLA supertypes alone and in combination conferred a strong differential advantage in responding to HIV infection, independent of the contribution of single HLA alleles that associate with progression of the disease. The correlation of the frequency of the HLA supertypes with viral load suggests that HIV adapts to the most frequent alleles in the population, providing a selective advantage for those individuals who express rare alleles.

The immunologic basis for the treatment of psoriasis with new biologic agents

Psoriasis vulgaris is the most prevalent T-cell-mediated inflammatory disease in humans. The pathogenesis of psoriasis is linked to activation of several types of leukocytes that control cellular immunity and to a T-cell-dependent inflammatory process in skin that accelerates the growth of epidermal and vascular cells in psoriasis lesions. Critical steps in immunologic activation include Langerhans cell maturation (activation), T-cell activation, differentiation and expansion of type 1 T cells, selective trafficking of activated T cells to skin, and induction of an inflammatory cytokine and chemokine cascade in skin lesions. In turn, each of these steps offers an opportunity for intervention with engineered biologic therapeutics.

Narcolepsy and the HLA region

Narcolepsy was first shown to be tightly associated with HLA-DR2 and DQ1 in 1983, suggesting a possible autoimmune mechanism. Early investigations failed to demonstrate this hypothesis, postulating that HLA-DR2 was only a linkage marker for another, unknown narcolepsy-causing gene. The autoimmune hypothesis is now being re-evaluated under the light of recent results. Like many other autoimmune disorders, narcolepsy usually starts during adolescence, is human leukocyte antigen (HLA)-associated, multigenic and environmentally influenced. Furthermore, HLA-association studies indicated a primary HLA-DQ effect with complex HLA class II allele interactions and a partial contribution of HLA to overall genetic susceptibility. Finally, recent result suggests that human narcolepsy is associated with the destruction of a small number of hypothalamic neurons containing the peptide hypocretins (orexins). This data is consistent with an immune destruction of hypocretin-containing cells as the most common etiology for human narcolepsy.

Relationship between HLA-DR antigen and HLA-DRB1 alleles and prostate cancer in Japanese men

PURPOSE

Human leukocyte antigens (HLA) are cell surface glycoproteins playing a key role in the immune system. In some cancers, changes in major histocompatibility complex (MHC) class I and II expression, usually a reduction or loss of these molecules, appear to provide a mechanism whereby tumour cells may escape host immunity. We investigated the relationship between HLA, especially class II, molecules and prostate cancer in Japanese men using molecular techniques.

MATERIALS AND METHODS

HLA class II typing was performed by the polymerase chain reaction-sequence specific primer (PCR-SSP) method of analysis and/or a commercial rapid assay based on the PCR followed by reverse dot-blot hybridization of the PCR products (Inno-LiPA assay). Allele frequencies were calculated. HLA allele frequencies reported in 1216 healthy Japanese individuals were used as the control data. Differences in allele frequency between subjects and the control group were analyzed by the chi-square test. The relationship between HLA antigens/alleles and prostate cancer is expressed in terms of relative risk (RR).

RESULTS

The frequencies of HLA-DR4 were significantly higher in Japanese men with prostate cancer than in the healthy control group (gene frequency 36.2% vs. 26.3% in control, p<0.05), although the relative risk of prostate cancer was less than 2. Furthermore, the frequencies of HLA-DRB1-0406, 0410 and 1405 allele were significantly higher in the prostate cancer group than in the control group (allele frequency was 7.3%, 4.5% and 5.4% vs. 3.03%, 1.79% and 2.22%, p<0.05, respectively). RR of those HLA-DRB1 allele for prostate cancer was 2.6 in each allele.

CONCLUSIONS

HLA molecules may be useful for the early detection of prostate cancer as a risk factor, and also for recognizing cancer activity by using them as a marker helpful in the choice of appropriate treatment by predicting prognosis.

Modulation of class I major histocompatibility complex antigen cell-surface stability by transmembrane domain length variation

Cell surface localization of major histocompatibility complex (MHC) class I proteins is conferred to a large extent by their transmembrane domains (TMs) which exhibit allelic, inter-locus and inter-species variation in both amino acid composition and length. Here, the consequences of TM length variation on trafficking and cell-surface stability were examined using the human MHC class I protein HLA-A2. Transformed B lymphocytes (CIR cells) transfected with an HLA-A2 gene encoding an additional 12 hydrophobic amino acids in the TM exhibited a marked decrease in steady-state cell-surface levels of the HLA-A2 protein relative to cells transfected with the wild-type HLA-A2 gene. Diminished surface expression was observed regardless of the presence or absence of the cytoplasmic domain and could not be accounted for by altered association with beta2-microglobulin. While intracellular trafficking rates were affected by TM length enlargement and/or the absence of cytoplasmic domains, this, as well, could not completely explain the TM length-dependent differential cell-surface levels. Studies using brefeldin A to block transport of HLA-A2 proteins to the cell surface suggested that the diminished cell-surface levels of TM enlarged HLA-A2 proteins was a result of decreased cell-surface stability. A significant negative correlation between cell-surface stability and TM length was observed in a comparison of four HLA-A2 proteins differing only in TM length. Similar studies employing an HLA-A2 protein with the TM of HLA-B27 (which is the same length as the HLA-A2 TM but is only 72% identical) suggested that MHC class I TM length variation, independent of amino acid composition and the cytoplasmic domain, may appreciably affect cell-surface stability.

TNF2, a polymorphism of the tumour necrosis-alpha gene promoter, is a component of the celiac disease major histocompatibility complex haplotype

Celiac disease (CD) is an immune disease triggered by the cereal antigen gliadin, resulting in villous atrophy in the small intestine. Susceptibility to the development of CD is strongly influenced by genes in the major histocompatibility complex, in particular alleles of the DQ genes in the class II region. However recent evidence has suggested that the major histocompatibility complex (MHC) class III region may be linked to celiac disease independently of the class II region. Among the genes located in this area is TNF-alpha, which encodes the cytokine tumor necrosis factor-alpha which has a broad range of pro-inflammatory, immunomodulatory and catabolic activities. Therefore, aberrant expression of TNF-alpha could be important in the pathogenesis of MHC-associated immune disorders. A TNF-alpha variant with a polymorphism in its promoter region has been described and designated TNF2. TNF2 has been associated with a variety of MHC-linked diseases, including systemic lupus erythematosus, dermatitis herpetiformis and insulin-dependent diabetes mellitus (IDDM), as well as parasitic infections. TNF2 has previously been shown to be associated with the MHC haplotype HLA A1-B8-DR3-DQ2, which confers susceptibility to CD. We have analyzed the distribution of TNF2 alleles in a group of celiac patients (n = 52) compared to controls (n = 52) in an effort to evaluate its role, if any, in susceptibility to the condition. TNF2 has a frequency of 0.5000 (SE +/- 0.0490) in CD, compared to 0.1635 (+/- 0.0362) in a control sample (p < 10(-6)). Of 52 patients, 44 carried one or more TNF2 alleles. Analysis indicates that the distribution of TNF2 is best explained by assuming 100% allelic association between it and HLA-DQB1*0201 (frequency = 0.7791 +/- 0.0447). However, the number of TNF2 heterozygotes significantly exceeds expectations and measurements of linkage disequilibrium confirm that allelic associations spanning the DQ and TNF regions are strongly maintained in CD. Taken together, these results indicate that TNF2 may have a role in the pathogenesis of CD; however, since it is not an independent association, the possibility that TNF2 constitutes a passive component of the CD haplotype cannot be excluded.

DNA-based HLA typing for cord blood stem cell transplantation

Molecular analysis of the HLA loci has revealed a pattern of extensive sequence polymorphism. For the class II loci, the polymorphism is localized to the second exon, whereas for the class I loci, both the second and third exons are polymorphic. These polymorphic regions encode the peptide binding groove and appear to be functionally significant in terms of disease susceptibility and transplantation. However, much of this polymorphism cannot be detected by serologic HLA typing methods. DNA typing methods based on PCR amplification and hybridization with sequence-specific oligonucleotide (SSO) probes can distinguish the many allelic sequence variants identified at these loci. The use of arrays of immobilized SSO probes allows genetic typing at many polymorphic sequence motifs in a single PCR and single hybridization reaction, making possible the development of simple, robust, and automated tests. PCR-SSO probe typing of the HLA loci requires very little sample material, is capable of either general or fine discrimination of alleles, and can be used to detect maternal contamination of cord blood. The application of this approach to typing HLA class I and II loci is discussed with regard to hematopoietic transplantation therapy.

Molecular analysis of HLA-DQB1 alleles in childhood common acute lymphoblastic leukaemia

Epidemiological studies suggest that childhood common acute lymphoblastic leukaemia (c-ALL) may be the rare outcome of early post-natal infection with a common infectious agent. One of the factors that may determine whether a child succumbs to c-ALL is how it responds to the candidate infection. Since immune responses to infection are under the partial control of (human leucocyte antigen) HLA genes, an association between an HLA allele and c-ALL could provide support for an infectious aetiology. To define the limit of c-ALL susceptibility within the HLA region, we have compared HLA-DQB1 allele frequencies in a cohort of 62 children with c-ALL with 76 newborn controls, using group-specific polymerase chain reaction (PCR) amplification, and single-strand conformation polymorphism (SSCP) analysis. We find that a significant excess of children with c-ALL type for DQB1*05 [relative risk (RR): 2.54, uncorrected P=0.038], and a marginal excess with DQB1*0501 (RR: 2.18; P=0.095). Only 3 of the 62 children with c-ALL have the other susceptibility allele, DPB1*0201 as well as DQB1*0501, whereas 15 had one or the other allele. This suggests that HLA-associated susceptibility may be determined independently by at least two loci, and is not due to linkage disequilibrium. The combined relative risk of the two groups of children with DPB1*0201 and/or DQB1*0501 is 2.76 (P=0.0076). Analysis of amino acids encoded by exon 2 of DQB1 reveal additional complexity, with significant (P<0.05) or borderline-significant increases in Gly26, His30, Val57, Glu66-Val67 encoding motifs in c-ALL compared with controls. Since these amino acids are not restricted to DQB1*0501, our results suggest that, as with DPB1, the increased risk of c-ALL associated with DQB1 is determined by specific amino acid encoding motifs rather than by an individual allele. These results also suggest that HLA-associated susceptibility to c-ALL may not be restricted to the region bounded by DPB1 and DQB1.

Association of celiac disease with microsatellite polymorphisms close to the tumor necrosis factor genes

Celiac disease is tightly linked to the MHC class II region on chromosome 6. We have studied two highly polymorphic microsatellite loci, TNFa and b, near the TNF genes in the class III region of the MHC, for evidence of their association to CD, as compared to a control population. Our findings show that the microsatellite allele most significantly associated with the disease is TNFb3, which is found in 86.3% of CD patients versus 24.5% of controls, with allele frequencies of 0.5392 and 0.1290, respectively (p < 0.001). The TNFa2 allele had a frequency of 0.6122 in CD patients and 0.2627 in controls (p < 0.001), with phenotype frequencies of 87.8% and 50.0%, respectively. TNFa6 and -a11 and TNFb5 have significantly reduced frequencies in CD patients. TNFb3 shows a maximal level of linkage disequilibrium with HLA-DQB1*0201 in celiac patients. However, while the DQB1*0201/TNFa2 haplotype was strongly associated with CD, DQB1*0201 was not significantly in linkage disequilibrium with TNFa2, suggesting that TNFa2 is independently associated with CD. This association could have functional significance as TNFa2 has been correlated with high TNF production.

The gluten-host interaction

Work continues to progress in the unravelling of the molecular interactions involved in the pathogenesis of coeliac disease. The immunogenetics of the disease implicate certain HLA DQ alleles as necessary for subsequent disease development. These HLA molecules have been shown to be necessary in the binding and presentation of gliadin peptides to antigen-specific T cells. Current work is examining the precise HLA-antigen interaction that may lead to the development of antigen-blocking agents. The isolation of antigen-specific T cells has led to the confirmation of a toxic T-cell epitope of the gliadin protein (residues 31-49) and it would appear likely that additional toxic epitopes may be similarly characterized in the near future. No common TCR motifs have so far been detected, although these may become apparent as this work progresses. The gliadin peptide sequence, residues 31-49, has now been demonstrated to be toxic in vivo. Additional toxic T-cell epitopes may also be present within gliadins, but this identification of a toxic gliadin sequence for the first time raises the possibility of future manipulation of the wheat genome (and other toxic cereals) that could lead to the development of new graminae cereals with the properties of wheat, but which do not induce toxicity in patients with coeliac disease.

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

The genes of the human leukocyte antigen (HLA) region, the major histocompatibility complex (MHC) of humans, control a variety of functions involved in immune response and influence susceptibility to over 40 diseases. Theoretical studies in the development of models to determine the modes of inheritance of the HLA-associated diseases have led to a better understanding of the inheritance patterns in insulin-dependent diabetes mellitus (IDDM), rheumatoid arthritis, multiple sclerosis, ankylosing spondylitis, hemochromatosis, celiac disease, and others. It is now clear that many of the HLA-associated diseases involve heterogeneity in their HLA components, as well as non-HLA genetic factors. This review is presented using HLA-associated diseases, and in particular IDDM, as the example of interest, but the observations and techniques presented have direct relevance to the study of all human diseases with a complex genetic component. Three methods for localizing disease-predisposing genes are presented: (1) association studies, including population, family, and relative predispositional effects, (2) affected sib pair and other affected-relative methods, and (3) lod score analysis. A variety of complementary methods for studying the mode(s) of inheritance of the alleles at the disease-predisposing locus and for identifying the alleles and amino acids directly involved in the disease process also are presented.

Allelic sequence variation in the HLA class II genes and proteins in patients with autoimmune hepatitis

Susceptibility to autoimmune hepatitis in white patients is associated with the human leukocyte antigen class II antigens DR3 and DR4. To analyze the molecular basis of these associations, we used oligonucleotide probes to determine the DRB, DQA and DQB hypervariable nucleotide sequences in 119 patients with autoimmune hepatitis and 177 matched controls. DRB3*0101, which encodes DR52a, predisposed patients most strongly to the disease. It was present in 58% of patients and 25% of controls (corrected P < 0.000005), whereas DQA1*0101 and 0102 conferred protection in males only. The DR4 subtype, DRB1*0401, was raised in the DRB3*0101-negative patients; 81% possessed either DRB3*0101 or DRB1*0401, compared with 42% of controls (corrected P < 0.0000001). These alleles encode the amino acid sequence Leu-Leu-Glu-Gln-Lys-Arg at positions 67 to 72 of the DR beta polypeptide, which was present in 94% of patients and 64% of controls (corrected P < 0.000001) and in all patients who tested positive for autoantibodies to the hepatic asialoglycoprotein receptor. The patients with DRB1*0401 had less severe disease, relapsed less frequently and were first seen significantly later in life than those patients with DRB3*0101; and whereas a single copy of DRB1*0401 predisposed to autoimmune hepatitis, DRB3*0101-associated susceptibility had a dose-related effect. These data provide evidence that specific residues in the DR beta polypeptides predispose to autoimmune hepatitis in white patients and genes linked to DRB3*0101 and DRB1*0401 may determine two clinically distinct disease patterns.

The three-dimensional structure of H-2Db at 2.4 A resolution: implications for antigen-determinant selection

Solution at 2.4 A resolution of the structure of H-2Db with the influenza virus peptide NP366-374 (ASNEN-METM) and comparison with the H-2Kb-VSV (RGY-VYQGL) structure allow description of the molecular details of MHC class I peptide binding interactions for mice of the H-2b haplotype, revealing a strategy that maximizes the repertoire of peptides than can be presented. The H-2Db cleft has a mouse-specific hydrophobic ridge that causes a compensatory arch in the backbone of the peptide, exposing the arch residues to TCR contact and requiring the peptide to be at least 9 residues. This ridge occurs in about 40% of the known murine D and L allelic molecules, classifying them as a structural subgroup.

Human leukocyte antigen subtype analysis in patients with advanced adenocarcinoma of the prostate

Human leukocyte antigens (HLA) are cell surface glycoproteins that have a significant role in the immune system. In some cancers, changes in major histocompatibility complex (MHC) class I and II expression, usually a reduction or loss of these molecules, appear to provide a mechanism whereby tumor cells may escape host immunity. HLA analysis in patients with advanced adenocarcinoma of the prostate revealed the antigens with the highest relative risk factors as DRw52, DRw53, Bw73, DR2, and B5(51). As a result, determination of HLA haplotypes may prove to be useful in determining the men with a higher risk of developing prostate cancer.

Gene mapping of the mammalian genome: the CEPH and Genethon initiative

Over the past four years, the CEPH (Jean Dausset Foundation) has expanded its linkage mapping effort to include physical mapping and, in 1990, co-founded the Genethon to ensure that a combined physical and genetic map of the entire human genome would be achieved. The Genethon has applied methods developed at CEPH on an industrial scale to accomplish the colossal task of constructing an integrated map. It is the role of such an integrated map to accelerate the search for the genes responsible for inherited diseases, and the results of the past 12 months encourage our optimism that this goal will be realized rapidly. These discoveries are providing not only an approach to the diagnosis of genetically based disease but also some of the first breakthroughs in the area of gene therapy.

Particular HLA-DQ molecules play a dominant role in determining susceptibility or resistance to type 1 (insulin-dependent) diabetes mellitus

Genes in the HLA complex are by far the most important in determining genetic predisposition or resistance to Type 1 (insulin-dependent) diabetes mellitus. In this review evidence is presented that the HLA genes mainly involved are those encoding some particular HLA-DQ molecules. Both among Black, Caucasian and Japanese subjects particular cis or trans encoded DQ molecules are significantly associated with susceptibility, while others are associated with resistance. A varying degree of susceptibility or resistance seems to be conferred by these DQ molecules, where those determining resistance are dominant over those determining susceptibility. The degree of genetic predisposition to develop Type 1 diabetes carried by an individual would therefore be the result of his or her particular combination of DQ molecules. A primary association to particular DQ molecules explains previously found associations to other HLA complex genes by linkage disequilibrium. Some mechanisms by which particular DQ molecules may determine susceptibility or resistance are also discussed. Potential islet beta-cell reactive CD4+ T-cells may escape negative selection (deletion) in the thymus, but normally become anergized or remain ignorant extra-thymically. However, under particular circumstances they may be triggered. The DQ molecules associated with Type 1 diabetes susceptibility may preferentially bind and present triggering and/or beta-cell derived peptides to such T cells, causing beta-cell destruction. The finding that particular DQ molecules determine susceptibility may lead to new methods of preventing development of Type 1 diabetes in susceptible individuals.

MHC molecules as peptide receptors

The central unit for regulation of the specific immune system is a trimolecular complex made up of the T cell antigen receptor, the MHC molecule, and the MHC ligand. The third component is a peptide derived as a degradation product from a protein. During recent years there has been some progress in understanding the interaction between MHC molecules and their peptide ligands: MHC molecules are peptide receptors of peculiar specificity, being able to accommodate millions of different peptides provided they share some common features.

Role of HLA genes in predisposition to develop insulin-dependent diabetes mellitus

Insulin-dependent diabetes mellitus (IDDM), or type I diabetes, is the end result mainly of a T-cell mediated autoimmune destruction of pancreatic islet beta cells. Genetical and environmental factors are both of importance in the pathogenesis. Genes in the HLA complex seem to be the most important genetical factors. Among Blacks, Caucasoids and Orientals, IDDM susceptibility is associated with some particular combinations of DQA1 and DQB1 genes in cis or trans position. This strongly argues that susceptibility is primarily associated to the corresponding HLA-DQ molecules themselves. However, weaker contributions by other genes in the HLA complex cannot be excluded. Similarly, a dominant protection is strongly associated with some other DQ molecules, in particular HLA-DQ6, in all three ethnic groups. The function of HLA-DQ (and other class II) molecules is to present peptide-fragments of antigens to CD4+ T cells (mainly helper T cells). Thus, the recognition of certain islet beta cell derived peptides by self-reactive CD4+ T cells, may be an initial event in the pathogenesis. The DQ molecules involved in IDDM susceptibility or protection may exert their function either during thymic development of potential self-reactive CD4+ T cells, or by preferential presentation of certain beta-cell derived peptides to CD4+ T cells, or both. The finding that certain DQ molecules as such confer IDDM susceptibility may lead to new methods to prevent IDDM, for example by using blocking peptide analogues.