Genetic complexity and expression of human class II histocompatibility antigens

DNA structural features and variability of complete MHC locus sequences

The major histocompatibility (MHC) locus, also known as the Human Leukocyte Antigen (HLA) genes, is located on the short arm of chromosome 6, and contains three regions (Class I, Class II and Class III). This 5 Mbp locus is one of the most variable regions of the human genome, yet it also encodes a set of highly conserved and important proteins related to immunological response. Genetic variations in this region are responsible for more diseases than in the entire rest of the human genome. However, information on local structural features of the DNA is largely ignored. With recent advances in long-read sequencing technology, it is now becoming possible to sequence the entire 5 Mbp MHC locus, producing complete diploid haplotypes of the whole region. Here, we describe structural maps based on the complete sequences from six different homozygous HLA cell lines. We find long-range structural variability in the different sequences for DNA stacking energy, position preference and curvature, variation in repeats, as well as more local changes in regions forming open chromatin structures, likely to influence gene expression levels. These structural maps can be useful in visualizing large scale structural variation across HLA types, in particular when this can be complemented with epigenetic signals.

The Regulation of Immunity

In their AAI President's Addresses reproduced in this issue, Jeremy M. Boss, Ph.D. (AAI '94; AAI president 2019–2020), and Jenny P.-Y. Ting, Ph.D. (AAI '97; AAI president 2020–2021), welcomed attendees to the AAI annual meeting, Virtual IMMUNOLOGY2021™. Due to the SARS-CoV-2 pandemic and the cancellation of IMMUNOLOGY2020™, Dr. Boss and Dr. Ting each presented their respective president's address to open the meeting.

Therapeutic IGF-I receptor inhibition alters fibrocyte immune phenotype in thyroid-associated ophthalmopathy

Thyroid-associated ophthalmopathy (TAO) represents a disfiguring and potentially blinding autoimmune component of Graves' disease. It appears to be driven, at least in part, by autoantibodies targeting the thyrotropin receptor (TSHR)/insulin-like growth factor I receptor (IGF-IR) complex. Actions mediated through either TSHR or IGF-IR are dependent on IGF-IR activity. CD34+ fibrocytes, monocyte lineage cells, reside uniquely in the TAO orbit, where they masquerade as CD34+ orbital fibroblasts. Fibrocytes present antigens to T cells through their display of the major histocompatibility complex class II (MHC II) while providing costimulation through B7 proteins (CD80, CD86, and programmed death-ligand 1 [PD-L1]). Here, we demonstrate that teprotumumab, an anti-IGF-IR inhibitor, attenuates constitutive expression and induction by the thyroid-stimulating hormone of MHC II and these B7 members in CD34+ fibrocytes. These actions are mediated through reduction of respective gene transcriptional activity. Other IGF-IR inhibitors (1H7 and linsitinib) and knocking down IGF-IR gene expression had similar effects. Interrogation of circulating fibrocytes collected from patients with TAO, prior to and following teprotumumab treatment in vivo during a phase 2 clinical trial, demonstrated reductions in cell-surface MHC II and B7 proteins similar to those found following IGF-IR inhibitor treatment in vitro. Teprotumumab therapy reduces levels of interferon-γ and IL-17A expression in circulating CD4+ T cells, effects that may be indirect and mediated through actions of the drug on fibrocytes. Teprotumumab was approved by the US Food and Drug Administration for TAO. Our current findings identify potential mechanisms through which teprotumumab might be eliciting its clinical response systemically in patients with TAO, potentially by restoring immune tolerance.

LAG3 and Its Ligands Show Increased Expression in High-Risk Uveal Melanoma

Uveal melanoma (UM) is a rare ocular malignancy which originates in the uveal tract, and often gives rise to metastases. Potential targets for immune checkpoint inhibition are lymphocyte-activation gene 3 (LAG3) and its ligands. We set out to analyse the distribution of these molecules in UM. The expression of mRNA was determined using an Illumina array in 64 primary UM from Leiden. The T lymphocyte fraction was determined by digital droplet PCR. In a second cohort of 15 cases from Leiden, mRNA expression was studied by Fluidigm qPCR, while a third cohort consisted of 80 UM from TCGA. In the first Leiden cohort, LAG3 expression was associated with the presence of epithelioid cells (p = 0.002), monosomy of chromosome 3 (p = 0.004), and loss of BAP1 staining (p = 0.001). In this Leiden cohort as well as in the TCGA cohort, LAG3 expression correlated positively with the expression of its ligands: LSECtin, Galectin-3, and the HLA class II molecules HLA-DR, HLA-DQ, and HLA-DP (all p < 0.001). Furthermore, ligands Galectin-3 and HLA class II were increased in monosomy 3 tumours and the expression of LAG3 correlated with the presence of an inflammatory phenotype (T cell fraction, macrophages, HLA-A and HLA-B expression: all p < 0.001). High expression levels of LAG3 (p = 0.01), Galectin-3 (p = 0.001), HLA-DRA1 (p = 0.002), HLA-DQA1 (p = 0.04), HLA-DQB2 (p = 0.03), and HLA-DPA1 (p = 0.007) were associated with bad survival. We conclude that expression of the LAG ligands Galectin-3 and HLA class II strongly correlates with LAG3 expression and all are increased in UM with Monosomy 3/BAP1 loss. The distribution suggests a potential benefit of monoclonal antibodies against LAG3 or Galectin-3 as adjuvant treatment in patients with high-risk UM.

Genome-wide CNV investigation suggests a role for cadherin, Wnt, and p53 pathways in primary open-angle glaucoma

BACKGROUND

To investigate whether copy number variations (CNVs) are implicated in molecular mechanisms underlying primary open-angle glaucoma (POAG), we used genotype data of POAG individuals and healthy controls from two case-control studies, AGS (n = 278) and GLGS-UGLI (n = 1292). PennCNV, QuantiSNP, and cnvPartition programs were used to detect CNV. Stringent quality controls at both sample and marker levels were applied. The identified CNVs were intersected in CNV region (CNVR). After, we performed burden analysis, CNV-genome-wide association analysis, gene set overrepresentation and pathway analysis. In addition, in human eye tissues we assessed the expression of the genes lying within significant CNVRs.

RESULTS

We reported a statistically significant greater burden of CNVs in POAG cases compared to controls (p-value = 0,007). In common between the two cohorts, CNV-association analysis identified statistically significant CNVRs associated with POAG that span 11 genes (APC, BRCA2, COL3A1, HLA-DRB1, HLA-DRB5, HLA-DRB6, MFSD8, NIPBL, SCN1A, SDHB, and ZDHHC11). Functional annotation and pathway analysis suggested the involvement of cadherin, Wnt signalling, and p53 pathways.

CONCLUSIONS

Our data suggest that CNVs may have a role in the susceptibility of POAG and they can reveal more information on the mechanism behind this disease. Additional genetic and functional studies are warranted to ascertain the contribution of CNVs in POAG.

Association of human leukocyte antigen (HLA)-DQ and HLA-DQA1/DQB1 alleles with Vogt-Koyanagi-Harada disease: A systematic review and meta-analysis

OBJECTIVE

The aim of this study was to evaluate the association of human leukocyte antigen (HLA)-DQ and HLA-DQA1/DQB1 alleles with Vogt-Koyanagi-Harada (VKH), providing further evidences on the genetic background of this disease.

METHODS

A comprehensive literature search was conducted on the relationship of HLA-DQ and/or HLA-DQA1/DQB1 alleles with VKH through PubMed, Embase, Cochrane Library, China National Knowledge Infrastructure, VIP, and databases for grey literature. The last search was in October 2017. Pooled odds ratio (OR) with 95% confidence interval (95% CI) was calculated from extracted data to access the strength of the association between a genotype and VKH.

RESULTS

HLA-DQ4 was confirmed to increase the risk of VKH significantly (OR = 4.63, 95% CI: 1.74-12.31, P = .002), while HLA-DQ1 seemed to reduce VKH occurrence with OR = 0.32 (95% CI: 0.22-0.47, P < .00001). HLA-DQA1*0301-(OR = 4.52, 95% CI: 1.42-14.35, P = .01) and HLA-DQB1*0401-(OR = 23.12, 95% CI: 11.54-46.31, P < .00001) positive patients probably had a rising tendency to suffer from VKH. Alleles including HLA-DQA1*0103, 0401, 0501 and HLA-DQB1*0301, 0402, 0601, 0603 were significant protective genetic factors.

CONCLUSION

We concluded that HLA-DQ4 carriers had a higher risk of VKH and HLA-DQ1 seemed to be protective. People with positive HLA-DQA1*0301 and HLA-DQB1*0401 demonstrated to be more susceptible to VKH. HLA-DQA1*0103, 0401, 0501 and HLA-DQB1*0301, 0402, 0601, 0603 could be potential protectors.

Use of complement binding assays to assess the efficacy of antibody mediated rejection therapy and prediction of graft survival in kidney transplantation

BACKGROUND

The Luminex® single antigen bead assay (SAB) is the method of choice for monitoring the treatment for antibody-mediated rejection (AMR). A ⩾50% reduction of the dominant donor-specific antibody (IgG-DSA) mean fluorescence intensity (MFI) has been associated with improved kidney allograft survival, and C1q-fixing DSA activity is associated with poor outcomes in patients with AMR. We aimed to investigate if C1q-DSA can be used as a reliable predictor of response to therapy and allograft survival in patients with biopsy-proven AMR.

METHODS

We tested pre- and post-treatment sera of 30 kidney transplant patients receiving plasmapheresis and low-dose IVIG for biopsy-proven AMR. IgG-DSA and C1q-DSA MFI were measured and correlated with graft loss or survival. Patients were classified as nonresponders (NR) when treatment resulted in <50% reduction in MFI of IgG-DSA and/or C1q-DSA was detectable following therapy.

RESULTS

Differences in the percentage of patients deemed NR depended upon the end-point criterion (73% by reduction in IgG-DSA MFI vs. 50% by persistent C1q-DSA activity). None of the seven patients with <50% reduction of IgG-DSA but non-detectable C1q-DSA-fixing activity after therapy experienced graft loss, suggesting that C1q-DSA activity may better correlate with response. Reduction of C1q-DSA activity predicted graft survival better than IgG-DSA in the univariate Cox analysis (20.1% vs. 5.9% in NR; log-rank P-value=0.0147).

CONCLUSIONS

A rapid reduction of DSA concentration below the threshold required for complement activation is associated with better graft survival, and C1q-DSA is a better predictor of outcomes than IgG-DSA MFI reduction.

CTCF controls expression and chromatin architecture of the human major histocompatibility complex class II locus

The major histocompatibility complex class II (MHC-II) locus includes a dense cluster of genes that function to initiate immune responses. Expression of insulator CCCTC binding factor (CTCF) was found to be required for expression of all MHC class II genes associated with antigen presentation. Ten CTCF sites that divide the MHC-II locus into apparent evolutionary domains were identified. To define the role of CTCF in mediating regulation of the MHC II genes, chromatin conformation capture assays, which provide an architectural assessment of a locus, were conducted across the MHC-II region. Depending on whether MHC-II genes and the class II transactivator (CIITA) were being expressed, two CTCF-dependent chromatin architectural states, each with multiple configurations and interactions, were observed. These states included the ability to express MHC-II gene promoter regions to interact with nearby CTCF sites and CTCF sites to interact with each other. Thus, CTCF organizes the MHC-II locus into a novel basal architecture of interacting foci and loop structures that rearranges in the presence of CIITA. Disruption of the rearranged states eradicated expression, suggesting that the formation of these structures is key to coregulation of MHC-II genes and the locus.

Toxoplasma gondii infection and cerebral toxoplasmosis in HIV-infected patients

Cerebral toxoplasmosis is a major cause of morbidity and mortality among HIV-infected patients, particularly from developing countries. This article summarizes current literature on cerebral toxoplasmosis. It focuses on: Toxoplasma gondii genetic diversity and its possible relationship with disease presentation; host responses to the parasite antigens; host immunosupression in HIV and cerebral toxoplasmosis as well as different diagnostic methods; clinical and radiological features; treatment; and the direction that studies on cerebral toxoplasmosis will likely take in the future.

Identification of genetic variation in the bovine major histocompatibility complex DR beta-like genes using sequenced bovine genomic probes

Two bovine genomic clones that crosshybridize with HLA-DR beta cDNA have been isolated. Nucleotide sequence analysis of the beta 1, beta 2 and transmembrane (TM) exon regions for one of these clones revealed 70, 89 and 86% identity with the corresponding HLA-DR beta exons. Stop codons are present in the beta 1 and TM exons and a single base deletion toward the 3' end of the TM exon negates the consensus sequence for exon/intron splicing. Therefore, we conclude this is a bovine DR beta-like pseudogene, BoDR beta I. Exon-containing regions have been used as probes in Southern blot analyses of bovine genomic DNA digested with EcoRI. The beta 2 exon of BoDR beta I results in prominent bands of 18.9, 7.8, 7.2, 6.4, 5.6, 3.6, 3.0 and 2.7 kb. Polymorphisms were observed for all but the 18.9 kb band and at least three of these bands were identified in each of the 185 animals sampled. A probe containing the TM exon of BoDR beta I hybridizes only to the 5.6- and 3.6-kb bands, suggesting that these are allelic bands corresponding to this pseudogene. Results from hybridizations of a TM exon-containing probe of the second bovine DR beta-like clone (BoDR beta II) suggest that the 6.4- and 2.7-kb bands correspond to this second bovine gene. A nonpolymorphic 8.1-kb band results from a probe containing the BoDR beta I beta 1 exon. Major differences in frequency for the 6.4/2.7 alleles were found for the four breeds sampled.

Nucleotide sequence and northern analysis of a bovine major histocompatibility class II DR beta-like cDNA

A 1.2-kb bovine DR beta-like cDNA clone (BoLA-DRB3) was isolated from a peripheral blood lymphocyte cDNA library utilizing a human DR beta cDNA as a probe. BoLA-DRB3 was found to have a high degree of nucleotide sequence similarity (96.8%) with a previously sequenced bovine DR beta-like gene (A1). It is believed that BoLA-DRB3 and A1 represent distinct alleles of one of the three bovine DR beta-like loci. Sequence comparison of BoLA-DRB3 with genes representing the other two bovine DR beta-like loci resulted in moderate degrees of sequence similarities (83.1% and 86.3%, respectively). Comparison of the relative abundance of RNA transcripts of the three bovine DR beta-like loci by Northern analysis of lymphocyte RNA indicated that BoLA-DRB3 is the most actively transcribed of the three bovine DR beta-like genes. Based on these results we suggest that of the three DR beta-like loci thus far identified in the bovine, only one is actively transcribed.

Partial nucleotide sequence of a bovine major histocompatibility class II DR beta-like gene

A genomic clone containing a bovine DR beta-like gene, BoDR beta II, was isolated from a bovine genomic library and characterized by restriction enzyme mapping and nucleotide sequencing of exon regions. Alignment of this sequence with the human DR beta cDNA sequence allowed identification of exon/intron boundaries. The clone contains a 13.3-kilobase (kb) insert, and includes 1.3 kb 5' of the beta 1 exon and 6.7 kb 3' of the transmembrane (TM) exon. Open reading frames were present in the BoDR beta exons sequenced. Nucleotide identities of the bovine beta 1, beta 2 and TM exons with the corresponding human DR beta exons were 73, 91 and 83%, respectively. Nucleotide identities of these exons with those of a previously described bovine DR beta-like pseudogene, BoDR beta I, were 69, 95 and 81%, respectively. Although a limited amount of sequence data was obtained for the intron regions, a 71% identity was found within a 514-nucleotide region immediately 3' to the beta 2 exons in BoDR beta I and BoDR beta II. A series of GT residues followed by a longer series of GA residues began about 35 nucleotides 3' of the beta 1 exon in both BoDR beta I and BoDR beta II.

Sequence analysis of the MHC class II DPB1 gene in chimpanzees (Pan troglodytes)

The diversity of the MHC class II region in non-human primates is a focus of biomedical research because this region plays a crucial role in the recognition of antigens in the immune system. In particular, the chimpanzee [Pan troglodytes (Patr)], which belongs to the superfamily Hominoidea, has been used as a human model for the study of diseases such as human hepatitis C virus (HCV), human hepatitis B virus (HBV) and human immunodeficiency virus (HIV) infections, to which only humans and chimpanzees are susceptible. In the present study, polymorphisms of the MHC-DPB1 gene (Patr-DPB1) in a chimpanzee colony in Japan were examined using a stepwise polymerase chain reaction (PCR) technique. In order to design a suitable primer pair which would amplify exon 2 of the Patr-DPB1 gene, a fragment of approximately 8 kb from exon 1 to exon 3 was amplified from chimpanzee genomic DNA. After designing a 500-bp primer pair at the 3' region of intron 1 and the 5' region of intron 2, analysis of DPB1 exon 2 alleles of each chimpanzee was carried out. Twenty-two chimpanzees were used in our study, and we identified seven alleles by sequence analysis on the Patr-DPB1 gene, including one new allele. The obtained nucleotide sequence patterns suggest that Patr-DPB1 alleles emerge by genetic variations such as the exchange of sequence motifs and the accumulation of point mutations.

HLA class II involvement in HIV-associated Toxoplasmic encephalitis development

A total of 220 individuals were included in this study, 112 HIV-seronegative healthy individuals and 108 HIV-1-infected patients involving: 18 AIDS patients with Toxoplasmic encephalitis (AIDS-TE), 49 AIDS patients without TE, and 41 asymptomatic patients, were genotyping for DR and DQ loci by molecular biology techniques. Fisher's Exact test was used for statistical analysis. HLA-DQB*0402 and DRB1*08 alleles were associated with a high risk to develop opportunistic infections with neurological involvement, mainly Toxoplasma encephalitis in relationship with subjects healthy (OR = 20.43; Pc = 7.0 x 10(-6) and OR = 11; Pc = 2.6 x 10(-4), respectively); in relationship with AIDS no TE (OR = 6.98; Pc = 0.028 and OR = 4.85; P = 0.012, Pc = 0.14) and with patients in asymptomatic stage (OR = 61.50, Pc = 8.4 x 10(-6) and OR = 19.38; Pc = 3.9 x 10(-4)), respectively.

CONCLUSIONS

It was concluded that the presence of HLA-DQB*0402 and DRB1*08 alleles in HIV-1-positive patients could be considered risk factors for developing neurological opportunistic infections, mainly Toxoplasmic encephalitis.

Coeliac disease, epilepsy and cerebral calcifications

Coeliac disease, epilepsy and cerebral calcifications (CEC) syndrome is a rare clinical condition. One hundred and seventy-one patients have been reported in the literature. Patients are mostly from Italy, Spain, and Argentina, suggesting a geographically restricted condition. Epilepsy is more frequently characterized by occipital seizures. It may be benign or drug-resistant, sometime evolving into severe epileptic encephalopathy. Gluten free diet (GFD) efficacy seems to be inversely related to the duration of epilepsy and the young age of the patient. Patients with cerebral calcifications (CC) and coeliac disease (CD) without epilepsy are considered as having an incomplete form of CEC syndrome. Some patients with epilepsy and CC without CD are supposed to have a CEC syndrome with silent or latent CD. Whether CEC syndrome is a genetic condition, or whether epilepsy and/or CC are a consequence of an untreated CD is unknown yet. Since histopathological findings seem to be the expression of vascular calcified malformation, CEC syndrome may be considered a genetically determined entity, such as a type of Sturge-Weber-like phacomatosis. Moreover, CEC, as well as CD, is associated with HLA-DQ2 and HLA-DQ8 phenotype and genotype. The progressive growth and late occurrence of CC before beginning a GFD, the demonstration of anti-gliadin antibodies in the cerebro-spinal fluid and the association with HLA class II genes, suggest that an immune reaction originating from the jejunal mucosa, triggered by gliadin in gluten intolerance predisposed subjects (HLA phenotype) may be responsible for seizures and CC. Moreover, a long-lasting untreated CD folic acid deficiency may cause calcifications. Probably, CEC is considered a genetic, non-inherited, ethnically and geographically restricted syndrome associated with environmental factors.

Identification of a phorbol ester-responsive element in the interferon-gamma receptor 1 chain gene

Human monocytic leukemia THP-1 cells differentiate into macrophage-like cells when treated with 12-O-tetradecanoylphorbol-13-acetate (TPA). During this process, interferon-gamma (IFN-gamma)-inducible expression of human leukocyte antigen-DR alpha is markedly enhanced. The enhancement of human leukocyte antigen-DR alpha expression is at least due to the TPA-dependent induction of the IFN-gamma receptor 1 chain and IFN-gamma receptor 2 chain genes. Here we have studied the mechanism of TPA-induced up-regulation of the IFN-gamma receptor 1 chain gene. Reporter gene analyses of 5'-deletion constructs of the IFN-gamma receptor 1 gene (IFNGR1) promoter indicated that the critical region for control of transcription and the TPA-responsive element (TRE) were present in the -128 to -109 base pair (bp) region. We confirmed that this region of the IFNGR1 promoter was responsive to TPA-induced signals by using a reporter construct whose promoter consisted of the -128 to -109 bp fragment and the minimal herpes simplex virus thymidine kinase promoter. Moreover, a supershift assay indicated that Sp1 bound to this TRE in TPA-treated THP-1 cells. These results suggest that in TPA-treated cells the binding of Sp1 to the TRE of the IFNGR1 promoter causes the up-regulation of this gene.

Sequence-based typing of HLA class II DQB1

Due to the expanding number of known HLA class II DQB1 alleles, high-resolution oligotyping is becoming ineffective, therefore a sequence-based typing (SBT) strategy was developed to provide rapid and definitive typing of HLA-DQB1. HLA-DQB1*02, *03, *04, *05, and *06 alleles were individually amplified by polymerase chain reaction (PCR) using exon 2 group-specific primers. Forward and reverse PCR primers were tailed with M13 universal and M13 reverse sequences, respectively. Subsequent bi-directional cycle-sequencing was carried out using Cy5.5-labeled M13 universal primer and Cy5.0-labeled M13 reverse primer. Automated sequencing was performed in 30 min using a Visible Genetics, Inc. (VGI) MicroGene Clipper Sequencer. Full concordance was observed between this SBT method and oligotyping among 151 individuals.

HLA class II restriction of autoreactive T cell responses in pemphigus vulgaris: review of the literature and potential applications for the development of a specific immunotherapy

Pemphigus vulgaris (PV) is a life-threatening autoimmune bullous disease of the skin and mucous membranes which requires immunosuppressive therapy, most commonly a combination of glucocorticoids and additional immunosuppressive agents. Since the side effects of long-term immunosuppressive therapy contribute to the poor prognosis of this disorder, there is considerable interest in a more specific treatment of this severe skin disease. PV may serve as a model disease for the development of a specific immunotherapy, because its pathogenesis as well as involved immunogenetic factors are well-characterized. This review focuses on the characterization of autoreactive T cell responses to desmoglein 3 (Dsg3), the autoantigen of PV, that presumably regulate the production of autoantibodies by providing help to the autoreactive B cells. Current knowledge on T cell epitopes of Dsg3 and the HLA class II alleles that restrict Dsg3-specific autoreactive T cell responses, as well as potential applications for a specific immunotherapy of PV, are described.

Possible susceptibility of the HLA-DPB1*0402 and HLA-DPB1*04 alleles to unexplained recurrent abortion: analysis by means of polymerase chain reaction-restricted fragment length polymorphism method

PROBLEM

To clarify whether HLA-DP antigens are associated with patient population of unexplained recurrent abortion.

METHOD OF STUDY

The frequency of HLA-DPB1 alleles in patients with unexplained recurrent abortion, and the compatibility of HLA-DPB1 alleles between patient couples, were studied using a polymerase chain reaction (PCR)-restricted fragment length polymorphism (RFLP) method. Thirty patients who had a history of unexplained primary recurrent abortion, and their husbands, were typed for HLA-DPB1 genotype. Two hundred and ninety-nine base pair fragments from the second exon of HLA-DPB1 genes were selectively amplified using the PCR-primers. After amplification, the DNAs were digested with restriction endonucleases, and subjected to electrophoresis in a 12% polyacrilamide gel to determine HLA-DPB1 genotype.

RESULTS

The frequency of HLA-DPB1*0402 and DPB1*04 alleles in the patient group (n = 30) was significantly increased, as compared to that in the normal fertile women (n = 30). The frequency of HLA-DPB1*04 allele in the patient group was significantly increased, as compared to that in the general population (n = 112). No significant compatibility of HLA-DPB1 alleles could be observed between patient couples and normal fertile couples.

CONCLUSION

These findings suggest a possible new class II association with patient population of unexplained recurrent abortion.

Cutting Edge: Phorbol Ester Induction of IFN-γ Receptors Leads to Enhanced DRα Gene Expression

We observed that IFN-γ-inducible expression of the DRα gene was enhanced when THP-1 cells are differentiated into macrophage-like cells by phorbol ester treatment. Here, we observed that class II MHC trans-activator and STAT1α mRNA, mediators of the signaling cascade from the IFN-γ receptor to the DRα induction, were markedly increased by IFN-γ stimulation in phorbol ester-activated THP-1 cells; however, both mRNAs were not increased by phorbol ester treatment alone. Then, we demonstrated that the mRNA and proteins of the IFN-γ receptor α- and β-chains were amplified by phorbol ester treatment in THP-1 cells. Consequently, these results indicate that the enhancement of DRα gene expression by IFN-γ treatment in phorbol ester-activated THP-1 cells is due to the phorbol ester-induced up-regulation of IFN-γ receptor α- and β-chains. As a result, the amplification of STAT1α and the increment of class II MHC trans-activator results in enhancement of DRα expression.

Analysis of the human HLA-DRA gene upstream region: evidence for a stem-loop array directed by nuclear factors

Sequence analysis of the far-upstream region of the human HLA-DRA gene has revealed the presence of Y' and X' boxes, highly homologous to the well characterized Y and X boxes present within the proximal-promoter region. Comparison of Y, Y', X, and X' box sequences present within different class II MHC genes of different species demonstrates that these boxes are conserved during evolution, suggesting an important role in regulation of gene expression. The far-upstream region and the proximal promoter region of the class II MHC genes could be organized in secondary structures, as suggested for the EA gene, the murine counterpart of the human HLA-DRA gene. The essential feature of this model is a dimerization of the proteins binding to X and X' and/or Y and Y' boxes resulting in a loop-out of the intervening DNA and a rapprochement of the far-upstream and proximal-promoter regions, and consequently of any proteins binding to them. We set up an in vitro approach in order to determine whether proteins bound to sequences present within far-upstream and proximal-promoter regions of the human HLA-DRA gene could direct a secondary structure assembly of regulative regions. Moreover, by gel retardation and DNase I footprinting assays, we demonstrate that similar proteins bind to Y and Y' boxes and, among these proteins, NF-Y was unambiguously identified by antibody-super shift experiments. Taken together, the data presented in this paper provide evidence supporting the hypothesis that a stem-loop array of the 5'-upstream region of the human HLA-DRA gene could be directed by nuclear factors. In this manner, additional nuclear factors bound to the far region could be driven in close proximity of the transcription initiation site.

Engineering protein for X-ray crystallography: the murine Major Histocompatibility Complex class II molecule I-Ad

Class II Major Histocompatibility (MHC) molecules are cell surface heterodimeric glycoproteins that play a central role in the immune response by presenting peptide antigens for surveillance by T cells. Due to the inherent instability of the class II MHC heterodimer, and its dependence on bound peptide for proper assembly, the production of electrophoretically pure samples of class II MHC proteins in complex with specific peptides has been problematic. A soluble form of the murine class II MHC molecule, I-Ad, with a leucine zipper tail added to each chain to enhance dimer assembly and secretion, has been produced in Drosophila melanogaster SC2 cells. To facilitate peptide loading, a high affinity ovalbumin peptide was covalently engineered to be attached by a six-residue linker to the amino terminus of the I-Adbeta chain. This modified I-Ad molecule was purified using preparative IEF and one fraction, after removal of the leucine zipper tails, produced crystals suitable for X-ray crystallographic analysis. The protein engineering and purification methods described here should be of general value for the expression of I-A and other class II MHC-peptide complexes.

High-resolution HLA typing for the DQB1 gene by sequence-based typing

The ideal high-resolution typing strategy for polymorphic genes is sequence-based typing. SBT of genomic DNA has been developed for the HLA class II genes DRB1, DRB3/4/5 and DPB1. For the DQB1 gene the sequence-based typing method was shown to cause a number of problems. To resolve those problems, different primers to amplify and sequence exon 2 of DQB1 were designed and tested. With several primer combinations, preferential amplification was observed in individuals heterozygous for DQB1*02/*03 and DQB1*02/*04. The preference was for DQB1*02 in many instances but could also be demonstrated for DQB1*03 or *04 and resulted occasionally in allelic drop-out. The best primer combination was selected and successfully used to type individuals heterozygous for DQB1*02, *03 and *04. To distinguish DQB1*0201 and *0202, primers for amplification and sequencing of exon 3 were developed and correct subtyping was obtained. The ambiguous typing DQB1*0301/*0302 and DQB1*0303/*0304 was resolved by allele-specific amplification and sequencing. A total of 258 individuals were fully typed for their DQB1 subtypes. All samples had been previously typed by PCR-SSP and serology. Concordant typing results were obtained for all individuals tested. The DQB1 alleles detected included *0501, *0502, *0503, *0601, *0602, *0603, *0604, *0609, *0201, *0202, *0301, *0302, *0303, *0304, *0401 and *0402. Sequence-based typing of the DQB1 gene proved a reliable typing strategy for assignment of the different DQB1 alleles after intensive selection of primers and test conditions.

Major histocompatibility complex class II deficiency: a clinical review

Major histocompatibility complex Class II deficiency or bare lymphocyte syndrome is a rare combined immunodeficiency that accounts for 5% of all cases of severe combined immunodeficiency. The syndrome is characterized by a lack of human leucocyte antigen Class II gene expression, absence of cellular and humoral T-cell immune response to foreign antigens, and impaired antibody productions, resulting in extreme susceptibility to viral, bacterial and fungal infections. In some patients, there is a reduced cell surface expression of human leucocyte antigen Class I molecules also. Major histocompatibility complex Class II deficiency is an autosomal recessive disease, most frequent in the Mediterranean area. The disease is caused by impaired gene regulation involving trans-acting proteins. Somatic cell genetics using cell fusion experiments identified four complementation groups, all resulting in the same clinical manifestation. Two regulatory genes have been identified so far: Class II trans activator and regulatory factor X5. Supportive treatment includes intravenous gammaglobulin and prophylaxis against Pneumocystis carinii. The only curative treatment is bone-marrow transplantation.

A new HLA-DQB1*0306 allele sharing motifs from DQB1*03032 and DQB1*04 sequences

We have discovered a new HLA-DQB1 allele in a Japanese family, MAT. In the family the new allele segregates in three generations and demonstrates the positive association with DRB1*0901. We observed a novel RFLP pattern in the course of examining the modified PCR-RFLP method for HLA-DQB1 genotyping. The PCR-SSOP analysis also showed a new hybridized pattern. Sequence analysis of the allele indicates that it was generated by a gene conversion-like event between the HLADQB1*03032 and one of DQB1*04 contemporary alleles. This new allelic product did not react with all of allosera and monoclonal antibodies against DQ1, DQ2, DQ3, DQ4 and DQ7. The HLA molecule encoded by the allele is not defined by serology. This new allele was officially recognized and named DQB1*0306 by the WHO Nomenclature Committee in November 1995.

ΔIK17 Antigen: A Possible Early Marker of Cancer Development

ΔIK17 is a 44 kD molecule located on the surface of T, B and NK cells in normal peripheral blood mononuclear cells (PBMC) (1). The portion of PBMC expressing ΔIK17 was determined in 52 patients with benign breast diseases, 182 patients with breast malignancies and 132 healthy individuals. The percentage of ΔIK17'-positive cells was significantly lower in the early stages (I-IIA) of malignancy compared to that of healthy donors. However, the percentage of PBMC expressing ΔIK17 tended to increase as the stage of the disease advanced. ΔIK17 seems to be the only antigen among the other cellular markers tested (CD2, CD4, CD8, HLA-DR) with a statistically significant correlation between a low percentage of positive cells and the early stages of malignancy and between a high expression and advanced disease. Its potential use as a tumor marker in breast cancer is discussed here.

Allogeneic recognition of HLA-DRB1*0406 by T cells with HLA-DRB1*0403: role of amino acid residue 37 on the beta sheet in T cell recognition

Five T cell clones reactive with allogeneic HLA-DR molecules were obtained by stimulating CD4+ T cells (DRB1*0403) with DRB1*0406-homozygous KT13 cells whose DR beta chain differed by a single amino acid residue (37) on the beta sheet from the DRB1*0403 product. Except for one T cell clone which had both auto- and alloreactivities, these clones proliferated by stimulation with KT13 but not with autologous cells, indicating that the single substitution at position 37 on the HLA-DR molecule was sufficient to alter the alloantigenicity of the DR molecule and to elicit an allogeneic T cell response. Two clones reacted with some but not all B cell lines with DRB1*0406, suggesting the possible involvement of a certain peptide whose distribution is restricted to some cells which form the alloantigenic structure recognized by these clones. The two remaining clones showed broad but distinct anti-DR specificity in addition to anti-DRB1*0406 reactivity, suggesting that they recognize the DRB1*0406-peptide complex whose antigenic structures also occur in some combinations of other DRB1 alleles with certain peptides bound to these alleles. The T cell clone with both auto- and alloreactivity was found to react with autologous monocytes but not with autologous B or T cells and to express lower TCR alpha beta than other T cell clones which showed no autoreactivity. The possible recognition molecule for this autoreactive T cell clone is discussed.

Coordinate regulation of HLA class II genes: a novel DNA binding complex

We have characterized a nuclear protein complex from B lymphoblastoid cell lines that binds to HLA class II promoters as detected by electrophoretic gel mobility shift assays (EMSA). This complex (C1) binds to three independent sites in the proximal DRA promoter which have not been identified previously as cis-acting elements. C1 is very abundant in Burkitt's lymphoma cell lines, but less abundant in "normal" B lymphoblastoid cell lines. The binding specificity of the C1 complex was analysed using competition experiments and chemical footprinting methods. Complexes with specificity similar to C1 also bind the DPA and DQA promoters. Though mutation of the sequences in the DRA promoter that severely reduced binding of the C1 complex had no effect on the ability of the DRA fragment to drive transcription of the reporter gene in transient expression or in vitro transcription assays, this conservation of binding sites among all class II promoters tested suggests functional relevance in transcription. In addition, complexes similar to C1 were observed in nuclear extracts from all cell lines examined, but minor differences in mobility appeared to correlate with class II expression. Thus, the C1 complex may act as a trans-acting factor in MHC class II expression.

Sequencing of an upstream region of the human HLA-DRA gene containing X' and Y' boxes

In this paper we report the characterization of a newly sequenced 5' upstream region of the human HLA-DRA gene. We performed (i) search for transcription factor motifs, (ii) analysis of CpG display and observed/expected frequency ratios, (iii) search for regions homologous to the 5' upstream sequences of the murine EA gene, (iv) DNase I footprinting experiments and (v) electrophoretic mobility shift assays. Our results demonstrate the existence, in the HLA-DRA gene, of Y' and X' boxes highly homologous to the Y and X boxes present in MHC class II genes, but oriented in the opposite direction. These Y' and X' boxes have been conserved during the molecular evolution of both human HLA-DRA and murine EA genes. DNase I footprinting and gel retardation experiments suggest that the X' and Y' boxes of the HLA-DRA upstream gene region are specifically recognized by nuclear proteins that also bind to the X and Y boxes of the HLA-DRA proximal promoter, respectively.

A factor that regulates the class II major histocompatibility complex gene DPA is a member of a subfamily of zinc finger proteins that includes a Drosophila developmental control protein

A novel DNA sequence element termed the J element involved in the regulated expression of class II major histocompatibility complex genes was recently described. To study this element and its role in class II gene regulation further, a cDNA library was screened with oligonucleotide probes containing both the S element and the nearby J element of the human DPA gene. Several DNA clones were obtained by this procedure, one of which, clone 18, is reported and characterized here. It encodes a protein predicted to contain 688 amino acid residues, including 11 zinc finger motifs of the C2H2 type in the C-terminal region, that are Krüppel-like in the conservation of the H/C link sequence connecting them. The 160 N-terminal amino acids in the nonfinger region of clone 18 are highly homologous with similar regions of several other human, mouse, and Drosophila sequences, defining a subfamily of Krüppel-like zinc finger proteins termed TAB (tramtrack [ttk]-associated box) here. One of the Drosophila sequences, ttk, is a developmental control gene, while a second does not contain a zinc finger region but encodes a structure important in oocyte development. An acidic activation domain is located between the N-terminal conserved region of clone 18 and its zinc fingers. This protein appears to require both the S and J elements, which are separated by 10 bp for optimal binding. Antisense cDNA to clone 18 inhibited the expression of a reporter construct containing the DPA promoter, indicating its functional importance in the expression of this class II gene.

In cutaneous T-cell lymphoma, class II MHC molecules on CD1+ antigen-presenting cells are upregulated in involved compared with uninvolved epidermis

CD1+ antigen-presenting cells in involved epidermis of patients with cutaneous T-cell lymphoma exhibit and enhanced functional capacity to activate autologous CD4+ T cells compared with CD1+ antigen-presenting cells from uninvolved and normal epidermis. Class II major histocompatibility complex molecules are involved in antigen presentation, and their expression on CD1+ Langerhans cells is known to vary. The expression of all three class II (HLA-DR, -DQ, -DP) molecules was therefore determined on CD1+ epidermal cells from both involved and uninvolved epidermis, using flow cytometry. The involved CD1+ epidermal cells exhibited a 1.5-1.6-fold, statistically significant increase in fluorescence intensity after staining of the class II molecules (HLA-DR, -DQ, -DP) compared with CD1+ epidermal cells from uninvolved epidermis. The autologous CD4+ T cells, activation was almost completely blocked by anti-HLA-DR, and partly by anti-HLA-DQ and anti-HLA-DP. In contrast, an antibody against class I, and an irrelevant control antibody, had no blocking effect. In a pokeweed mitogen assay it was demonstrated that autologous CD4+ T cells, activated by involved epidermal cells, demonstrated suppressor activity rather than helper activity. The suppressor activity was dependent on the presence of HLA-DR-positive epidermal cells. Thus, in cutaneous T-cell lymphoma, class II molecules on the individual CD1+ antigen-presenting cell are upregulated in clinically involved compared with uninvolved epidermis, and these molecules are crucially involved in activation of CD4+ T cells.

A factor that regulates the class II major histocompatibility complex gene DPA is a member of a subfamily of zinc finger proteins that includes a Drosophila developmental control protein

A novel DNA sequence element termed the J element involved in the regulated expression of class II major histocompatibility complex genes was recently described. To study this element and its role in class II gene regulation further, a cDNA library was screened with oligonucleotide probes containing both the S element and the nearby J element of the human DPA gene. Several DNA clones were obtained by this procedure, one of which, clone 18, is reported and characterized here. It encodes a protein predicted to contain 688 amino acid residues, including 11 zinc finger motifs of the C2H2 type in the C-terminal region, that are Krüppel-like in the conservation of the H/C link sequence connecting them. The 160 N-terminal amino acids in the nonfinger region of clone 18 are highly homologous with similar regions of several other human, mouse, and Drosophila sequences, defining a subfamily of Krüppel-like zinc finger proteins termed TAB (tramtrack [ttk]-associated box) here. One of the Drosophila sequences, ttk, is a developmental control gene, while a second does not contain a zinc finger region but encodes a structure important in oocyte development. An acidic activation domain is located between the N-terminal conserved region of clone 18 and its zinc fingers. This protein appears to require both the S and J elements, which are separated by 10 bp for optimal binding. Antisense cDNA to clone 18 inhibited the expression of a reporter construct containing the DPA promoter, indicating its functional importance in the expression of this class II gene.

Immunogenetics of chronic liver diseases

The genetic background of autoimmune diseases becomes more and more evident. Immunogenetics comprises the analysis of genes and their products located at the region 6p21 on the short arm of chromosome 6, which is also known as the major histocompatibility complex (MHC). MHC class I and II genes are highly polymorphic. The complement genes C2, C4A, C4B, and BF, which are also polymorphic, became known as MHC class III genes. In autoimmune hepatitis type 1, there is a dual association for white persons with either HLA-A1-B8-DR3 or HLA-DR4. In patients from Japan, autoimmune hepatitis type 1 is predominantly associated with HLA-DR4. This dual association is confirmed at the DNA level. Whereas only limited data are available for autoimmune hepatitis type 2, the association of primary biliary cirrhosis with HLA-DR8 is based on several studies. Primary sclerosing cholangitis is associated with HLA-B8-DR3 and -DR52a. This association was confirmed at the DNA level because of a significant increase of the DRB3*0101 allele. For DRB3*0101-negative individuals, a second association with DRB5*0101 (= DR2) was described. Further analysis of the hypervariable region of the HLA class II molecule indicates that lysine at position 71 is crucial for autoimmune hepatitis type 1 in white persons, whereas position 13 is important for people from Japan. In contrast, leucine at position 35 is important for patients with primary biliary cirrhosis, whereas leucine at position 38 is an important risk factor for primary sclerosing cholangitis. The MHC class III allele C4A-QO is significantly increased in autoimmune hepatitis type 1 and 2 and in primary biliary cirrhosis. Advances in immunogenetics will certainly increase our knowledge of the etiology and pathogenesis of immune-mediated liver diseases, which hopefully will lead to more specific therapeutic interventions.

First-trimester human trophoblast is class II major histocompatibility complex mRNA+/antigen

Lack of expression of the polymorphic class I and class II MHC antigens in the cytotrophoblast is one of the major factors determining the privileged immunologic status of the placenta. In this report, we show that first-trimester human placental cytotrophoblast cells display moderate to strong expression of class II MHC (HLA-DR alpha and -DR beta) and Ii chain transcripts, apparently in absence of detectable class II antigens and Ii chain. In addition, DR alpha, DR beta, and Ii mRNAs, but not antigens, are consistently upregulated by IFN-gamma. Constitutive expression and upregulation of mRNAs are detectable in trophoblast cells kept in short term as well as prolonged (2-3 weeks) culture. These results are reminiscent of an analogous mRNA+/antigen- dissociation occurring, in the case of class I MHC gene products, in a subpopulation of first-trimester cytotrophoblast cells. Thus, analogous mechanisms prevent the expression of potentially hazardous class I and II allodeterminants at early stages of semiallogeneic pregnancy.

HLA-DRB1 typing of Vogt-Koyanagi-Harada's disease by PCR-RFLP and the strong association with DRB1*0405 and DRB1*0410

Vogt-Koyanagi-Harada's (VKH) disease is reported to be closely associated with the HLA class II antigen, HLA-DR4. Serologically defined DR4 is further divided into 11 alleles by molecular HLA genotyping. However, no study of HLA-DNA typing of VKH patients has been reported. To clarify molecular genetic mechanism underlying the susceptibility/resistance to VKH disease, HLA-DNA typing of DR antigens (DRB1 genotyping) by the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method was performed. It was found that DRB1*0405 showed a significant association with VKH disease compared with the healthy controls (corrected p value < 1 x 10(-5)) and that all the patients had DRB1*0405 and/or DRB1*0410. The specific amino acid residue shared only by these two alleles is Ser at position 57 which is located in the antigen binding groove and may influence the immunological function as an antigen-presenting molecule, suggesting that Ser at position 57 plays an important role in the susceptibility to VKH disease, although the possibility that the involvement of the HLA-DQ molecule, DQ4, in strong linkage disequilibrium with DRB1*0405 and DRB1*0410, cannot be excluded.

Complete association of the HLA-DRB1*04 and -DQB1*04 alleles with Vogt-Koyanagi-Harada's disease

VKH disease is a bilateral panuveitis and has been known to be closely associated with the particular HLA class II antigens HLA-DR4 and -DQ4, defined by serologic typing. In this study, 63 Japanese VKH patients were analyzed for HLA class II alleles at the DNA level using the PCR-RFLP method. The DRB1*04 alleles encoding the serologic specificity DR4 were found in 100% of the VKH patients carrying DRB1*0405 or DRB1*0410. By statistical analysis, only DRB1*0405 was found to be significantly increased as compared to the healthy controls (RR = 46.7 and pc < 1 x 10(-5)). As to the DQB1 locus, all the patients carried DQB1*0401 or DQB1*0402 expressing the serologic DQ4 specificity, which is in a strong linkage disequilibrium with DRB1*0405 or DRB1*0410 in a Japanese population, respectively. Only DQB1*0401 showed a statistically significant increase as compared to the healthy controls (RR = 41.3 and pc < 1 x 10(-5)). Comparison of the amino acid sequences of these DRB1 and DQB1 alleles indicates that Ser at position 57 of DRB1 and/or Glu at position 70 and Asp at position 71 of DQB1 plays a crucial role in determining the susceptibility to VKH disease.

Methylation state of the human HLA-DRA gene in T-lymphocytes and B-lymphocytes of transgenic mice. Lack of methylation at one 5'-GCGC site is not required for gene expression

A consistent lack of DNA methylation at one or both of two GCGC (Hha I) restriction sites in the 5' region of the HLA-DRA gene has been previously documented by the use of methyl-sensitive restriction enzymes in human cells and tissues, irrespectively of their expression of DR alpha products. Evidence presently available, however, does not exclude that a lack of methylation in this region, although not sufficient, might be necessary for gene expression. In this report, we show that only one of the 5'-GCGC sites is protected, although less efficiently than in man, from CG-->mCG modifications in tissues and cells of transgenic mice carrying an expressed single copy of the HLA-DRA gene/diploid genome. We demonstrate that the two 5' GCGC sites of the HLA-DRA transgene are fully methylated in DR alpha- splenocytes (more than 80% T-lymphocytes), while one of them (the most 5' site) is not methylated in a fraction of DR alpha+ splenocytes (more than 95% B-lymphocytes). These results provide evidence that absence of DNA methylation in the 5' region is not necessary for, but might be associated with and possibly secondary to the expression of the DRA gene.

Oligonucleotide typing reveals association of type I psoriasis with the HLA-DRB1*0701/2, -DQA1*0201, -DQB1*0303 extended haplotype

Although the pathogenesis of psoriasis is still a matter of debate, there are several lines of evidence supporting the concept of this disease being immunologically mediated with T cells playing a crucial role. Because a considerable portion of the cellular infiltrate in psoriasis consists of activated T-helper cells, expression of HLA class II antigens might be of particular importance for the understanding of its pathogenesis. Therefore, we investigated the HLA type of patients with type I (early onset, positive family history) and type II (late onset, no family history) psoriasis by means of serology (n = 89) and genotyping using sequence-specific oligonucleotide probes (n = 64). Serologic analysis of class I documented the association of type I psoriasis with HLA-Cw6, -B13, and -B57, whereas type II psoriasis showed a weaker correlation with HLA-Cw2 and -B27. Genotyping using SSO for class II detected the elevation of the HLA-DRB1*0701/2 allele frequency from 13% in normal population to 36% in type I, but only to 15% in type II psoriatics. Moreover, positive correlations with type I psoriasis were detected for HLA-DQA1*0201 and HLA-DQB1*0303. The HLA-DRB1*0701/2, -DQA1*0201, -DQB1*0303 extended haplotype was found exclusively in type I psoriasis. This is the first report documenting the association of distinct HLA class II alleles with type I psoriasis as detected on the DNA level, an approach both more specific and more sensitive when compared to serology.

HLA-DRB1 gene sequences in HLA-DR4 positive and negative patients with rheumatoid arthritis

The second exon of the DRB1 gene encoding for the first domain of the HLA-DR beta 1-chain was sequenced in 16 patients (10 DR4/DR1 positive, 6 DR4/DR1 negative) with seropositive rheumatoid arthritis (RA). We could confirm the strong association of susceptibility to RA with functionally equivalent conformations on otherwise distinct MHC molecules. At least one HLA-DR allele in all of the analysed DR4 or DR1 positive patients showed such an epitope with a minimal variability limited to residue 71. However, in HLA-DR4 and -DR1 negative patients such a similar epitope could not be detected.

Isoelectric focusing subtypes of HLA-A can be defined by oligonucleotide typing

This study describes a simple and direct method for sequence-specific oligonucleotide probe (SSOP) typing of the A locus of HLA class I genes. Genomic DNA from a panel of over 200 cells which have been characterized by the methods of serology and isoelectric focusing (IEF) for the HLA class I antigens was used for locus-specific PCR amplification of HLA-A sequences. Dot blot hybridization of the amplified products was performed with 28 SSOPs derived from hypervariable regions in exon 2 and 3. Co-amplification of three alleles of HLA-H pseudogene in apparent linkage disequilibrium with HLA-A2 and A10 was observed but did not interfere with the typing of HLA-A alleles. Using short SSOPs (15 nucleotides each) in single temperature tetramethylammonium chloride (TMAC) hybridization and washing steps, 30 IEF-definable isotypes of HLA-A antigens could be unambiguously defined by their hybridization patterns. Moreover, comparison of the typing results with available nucleotide sequences of HLA-A alleles showed that the conditions used allowed faithful detection of single codon mismatches between probe and template. Thus, these alleles can be identified by their unique hybridization patterns generated by the SSOPs. Nucleotide sequence analysis of any new HLA-A allele will further permit its rapid and unambiguous characterization by SSOP typing.

Polymorphism in the promoter region of HLA-DRB genes

Polymorphism is a hallmark of the molecules encoded within the MHC of humans and other mammals. Recently, evidence of polymorphism has also been shown to exist in the transcriptional regulatory regions of HLA-DQB genes. In this article, we report that polymorphism exists also in the promoter region of HLA-DRB genes. The sequence of the regulatory region of DRB genes from five homozygous DR B-cell lines, each of a distinct DR haplotype, revealed a number of differences, some of which are in the critical class II boxes that are generally conserved in class II promoters. The major differences occurred in a comparison of DR4 to the other DR haplotypes. These data suggest the existence of another important source of HLA class II polymorphism that may play a role in susceptibility to HLA-associated autoimmune disease.

Asp57-negative HLA DQ beta chain and DQA1*0501 allele are essential for the onset of DQw2-positive and DQw2-negative coeliac disease

The genetic predisposition to coeliac disease is associated with the HLA DQw2 allele. Coeliac patients lacking the DQw2 allele are very rare and always exhibit the DR4-DQw3 haplotype. We performed oligotyping of polymerase chain reaction (PCR)-amplified DQA1 and DQB1 genes in six DQw2-negative and 30 DQw2-positive coeliac patients. The DQB analysis showed that all six DQw2-negative patients possessed the DQB1*0302 allele. The other DQB alleles found in five of these patients were DQB1*0501, DQB1*0604 and DQB1*0302. The DQ beta chains encoded from all these alleles have the replacement of aspartic acid residue at position 57 (Asp57), as well as the DQB1*0201 allele which was found in all 30 DQw2-positive coeliac patients. The DQw2-negative proband who lacked the homozygous Asp57 replacement exhibited the DQA1*0501 allele in the DQA1 gene. The DQA1*0501 allele was also found in 27 of the 30 DQw2-positive coeliac patients. Among this group of coeliacs, the four cases lacking the DQA1*0501 allele exhibited the homozygous Asp57 replacement in the DQ beta chain. Our results indicate that Asp57-negative DQ beta alleles are involved in both DQw2-positive and -negative coeliac patients. Moreover, when the Asp57-negative DQ beta chain is encoded from only one of the two DQB1 genes the DQA1*0501 allele is always present.

Interferon-γ response region in the promoter of the class II MHC gene, DPA

The class II MHC gene DPA is inducible by interferon-gamma (IFN-gamma), whereas the DQB gene is not inducible in most cell types. To investigate the DNA region specifically responsible for inducibility or its lack that may be required (in addition to the elements required for constitutive expression of class II genes), hybrid promoters were constructed between the proximal 5' regions of the DPA promoter up to -148 bp, which is IFN-gamma inducible, and of the DQB promoter up to -160 bp, which is not inducible. As a result of these and previous studies [9, 10], the region of the DPA gene required for its IFN-gamma inducibility was localized to 27 bp between -55 and -81, including the Y-box element and its flanking nucleotides.

HLA-DP polymorphism in northern Italian celiac patients

The contribution of HLA-DP genes to celiac disease susceptibility has been investigated in 95 Italian patients, 41 with childhood and 54 with adult disease onset. Polymerase chain reaction amplification, sequence-specific oligonucleotide probe hybridization and restriction fragment length polymorphism analyses have been carried out. All celiac patients and 56 out of 128 random healthy controls were DQw2-positive. The frequency of the DPB1*0101 allele was significantly increased (pc = 0.002, relative risk 5.21) in patients with celiac disease (23.2%) compared to the whole panel of controls (5.5%), but not to the 56 controls bearing DQw2 (10.7%). No significant difference in the frequency of DPB1*0101 was found between celiac patients with pediatric (24.4%) or adult (22.2%) onset. The DPB1*0101 allele was associated with both the DR3-DQw2 and DR7-DQw2 haplotypes. Moreover, our study has not confirmed the association with DPB1*0402 and DPB1*0301 previously reported in celiac children from southern Italy. The linkage of the DPB1*0101 allele with the DQ locus and the observation that the DP but not the DQ association appears to be ethnically dependent strongly support a secondary role of DP molecules in celiac disease susceptibility.

Comparative anatomy of the primate major histocompatibility complex DR subregion: evidence for combinations of DRB genes conserved across species

The class II region of the human major histocompatibility complex (HLA) is made up of three major subregions designated DR, DQ, and DP. With the aim of gaining an insight into the evolution and stability of DR haplotypes, a total of 63 cosmid clones were isolated from the DR subregion (Gogo-DR) of a western lowland gorilla. All but one of these cosmid clones were found to fall into two clusters. The larger cluster, A, was defined by 41 overlapping cosmid clones and contained a DRB gene segment made up of exons 4 through 6 and four DRB genes, designated Gogo-DRB6, Gogo-DRB5*01, Gogo-DRB8, and Gogo-DRB3*01. The total length of this cluster was approximately 180 kb. The second cluster, B, encompassed a contiguous DNA stretch of approximately 145 kb and was composed of 21 overlapping cosmid clones. Cluster B contained three DRB genes, designated Gogo-DRB1*08, Gogo-DRB2, and Gogo-DRB3*02. One cosmid clone (WP1-9) containing a DRB pseudogene could not be linked to either cluster A or B. Neither the organization of cluster A nor that of cluster B was identical to that of known HLA-DR haplotypes. However, two gorilla DRB genes, Gogo-DRB6 and Gogo-DRB5*01, the human counterparts of which are linked in the HLA-DR2 haplotype, were found to be located next to each other in cluster A. The arrangement of the Gogo-DRB genes in cluster B, which is presumed to be the gorilla DR8 haplotype, was similar to that of HLA-DR3/DR5/DR6 haplotypes and to that of the presumed ancestral HLA-DR8 haplotype.(ABSTRACT TRUNCATED AT 250 WORDS)

HLA-DP polymorphism in Sudanese controls and patients with insulin-dependent diabetes mellitus

Human leukocyte antigen (HLA) genes are candidates for susceptibility to insulin-dependent diabetes mellitus (IDDM). The association of IDDM with particular DR and DQ alleles has been reported in all populations studied, but its association with HLA-DP alleles has been controversial. To address this question we analyzed 19 DPB1 and 2 DPA1 alleles and their associations in well-characterized Sudanese (an admixture of Arab and Black) IDDM patients (n = 71) and ethnically matched controls (n = 86) using polymerase chain reaction-sequence specific oligonucleotide (PCR-SSO) typing. There were no significant differences between the patient and control groups in the DPB1 frequencies. DPB1*0201, *0401 and DPA1*01 were the most frequent alleles in both IDDM patients and control subjects. Significant positive and negative associations between DPB1 and DPA1 alleles were detected in both groups. A novel DPB1 allele included in DPB1*1701 was identified.