Polyglot and polymorphism. An HLA update.
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Genetic Linkage↗
Biomedical subjects
G T Nepom
Publications and source records attributed to G T Nepom.
Differential transcription elements direct expression of HLA-DQ genes.
Regulation of class II MHC gene expression, including the HLA-DQ genes, is primarily at the level of transcription. Locus-specific control of DQ gene transcription is both tissue-specific and developmentally regulated and relies on complex mechanisms involving specific DNA-protein interactions. Electrophoretic mobility shift and DNase I protection assays demonstrate the presence of unique nuclear protein interactions with the consensus W and Y box elements in the DQB1 promoter region in DQ-negative cell lines. Based on these and other recent studies, a multistage model of DQ gene regulation is outlined to account for specific patterns of DQ gene expression.
Cell Line↗
Differential expression of HLA-DQB1 alleles in a heterozygous cell line.
Regulation of HLA class II transcription is complex, with both locus-specific and allele-specific polymorphisms associated with consensus regulatory region promoter elements. In order to evaluate the potential function of allele-specific elements, HLA-DQB1 transcripts and in vivo footprinting of the DQB1 promoter were studied in human cell lines inducible for HLA class II expression. In the heterozygous melanoma cell line Me9229/18, differential expression was observed for two DQB1 alleles. This variation was reflected in both steady-state and inducible transcripts, although methylation patterns of the promoter elements were similar for both alleles. This in vivo allelic difference expression, which correlates with previous studies of in vitro reporter gene transcription, indicates the potential for functionally important differences in tissue-specific and inducible expression attributable to promoter region polymorphism in HLA genes.
Alleles↗
Ultrastructural allelic variation in HLA-DQB1 promoter elements.
Sequence variation among HLA class II promoter elements may contribute to functional differences in transcriptional regulation of different class II alleles. In addition to influencing the binding sites for nuclear transcription factors, promoter polymorphism may also alter intrinsic structural properties of the DNA strands, such as conformation and curvature, which influence the formation of stable transcription complexes. We used SSCP analysis of PCR-amplified promoter regions from the DQB1 locus to evaluate conformational polymorphism within DQ alleles. Distinct electrophoretic migration patterns of the SSCP products were detected for six DQB1 alleles; analysis of the DQB1*0302 promoter, known to be associated with type 1 diabetes, showed no SSCP differences between IDDM patients and normal controls. Using computer modeling based on a "nearest-neighbor" energy of predicted curvature theory, we examined the effect of allelic promoter region sequence polymorphism on the predicted curvature of double-stranded DNA, and found distinct allelic differences in predicted DNA curvature, both in transcriptional consensus binding sites and in regions located between binding sites. These data are consistent with a model in which intrinsic sequence variation in the promoter region results in ultrastructural differences which may influence DNA bending and interactions with multimeric DNA-protein transcription complexes.
Alleles↗
Glutamic acid decarboxylase and other autoantigens in IDDM.
Autoantigens in insulin-dependent diabetes serve as diagnostic markers and as potential therapeutic immunomodulators. Recent studies have focused particularly on two well studied molecules, glutamic acid decarboxylase and insulin, as well as several new antigens that have been recently identified, recognized by antibody and/or cell-mediated immune responses in diabetic patients. Temporal aspects of antigen exposure, antigen processing of specific peptide antigens, and the interplay between specific antigens, MHC genetics, and host T-cell responses remain to be explored.
Animals↗
Functional effects of a natural polymorphism in the transcriptional regulatory sequence of HLA-DQB1.
DNA sequence polymorphism in the genes encoding HLA class II proteins accounts for allelic diversity in antigen recognition and presentation and, thus, in the role of these cell surface glycoproteins as determinants of the scope of the T-cell repertoire. In addition, sequence polymorphism in the promoter-proximal transcriptional regulatory regions of these genes has been described, particularly for the HLA-DQB1 locus, where these differences may contribute to variation in locus- and allele-specific expression. In this study, we measured the effect of such regulatory sequence polymorphism on the expression of endogenous alleles of DQB1 in heterozygous cells. Quantitative reverse transcriptase-mediated PCR analysis showed that expression of the DQB1*0301 allele responded more rapidly to gamma interferon induction than that of DQB1*0302. We have analyzed functional effects of a prominent allelic polymorphism that consists of a TG dinucleotide present between the W and X1 consensus elements in the DQB1*0302 allele but missing in the DQB1*0301 allele. The dominant effect of this polymorphism was to introduce a variation in the spacing between the W and X1 elements of these two alleles. A secondary compensatory effect was specific for the TG dinucleotide itself, which was essential for the binding of a nuclear protein complex to the *0302 regulatory region immediately 5' of the X1 element. Derivatives of the DQB1 5' regulatory region were used to drive expression of the chloramphenicol acetyltransferase gene in transient transfections of human B-lymphoblastoid and gamma interferon-treated melanoma cell lines, demonstrating that the additional spacing between the W and X1 elements caused by the presence of the TG dinucleotide in the *0302 allele resulted in reduced expression compared with that driven by the *0301 fragment; this difference overshadowed an up-regulating effect on expression which corresponded to the binding of the TG-dependent nuclear protein complex. The presence of this polymorphism in multiple HLA-DQB1 alleles and in several species suggests selection for two alternative transcriptional regulatory mechanisms influencing expression of alleles of the same HLA locus.
Alleles↗
Class II antigens and disease susceptibility.
The role for HLA typing in autoimmune disease is changing with the recognition that HLA markers can identify patients with poor prognosis in some autoimmune disease. Aggressive therapeutic intervention in patients with such HLA prognostic markers has the potential to improve or prevent progressive disease outcomes in a select group of patients.
Arthritis, Rheumatoid↗
Deficient antigen-presenting cell function in multiple genetic complementation groups of type II bare lymphocyte syndrome.
The absence of HLA class II gene expression in type II bare lymphocyte syndrome (BLS) results from defective transcriptional activation of class II histocompatibility genes. Genetic studies have revealed that distinct defects in multiple trans-acting factors result in the immunodeficient BLS phenotype. We studied antigen-presenting cell (APC) function in DR-transfected BLS cells derived from multiple complementation groups. Each BLS cell line displayed the same defective APC phenotype: an inability to mediate class II-restricted presentation of exogenous protein antigens, and structurally altered class II alpha beta dimers. Expression of the HLA class II-like genes DMA and DMB, previously implicated in antigen presentation, was reduced or absent in the BLS cells. Fusion of BLS cells with cell line 721.174, which has a genomic deletion of HLA class II genes, coordinately restores class II structural gene and DM gene expression and a wild-type APC phenotype. Thus each of the molecular defects that silences class II structural gene transcription also results in a defective APC phenotype, providing strong evidence for coregulation of these two functionally linked pathways.
Amino Acid Sequence↗
The prevention of IDDM. Injecting insulin into the cytokine network.
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Animals↗
Genetic and immunological markers of insulin dependent diabetes in Black Americans.
ICA and GAD65 autoantibody profiles and HLA-DR and DQ analysis were performed on 43 Black juvenile onset IDDM patients and 34 unrelated Black controls from Tennessee, USA. 75% of patients were positive for GAD65 autoantibodies but only 53% had ICA; 39% both ICA and GAD65 antibodies. The strongest HLA association was with the DR3 haplotype DRB1*03 DQA1*0501 DQB1*0201 (63% of patients v 12% of controls RR = 13.0, p < 0.00002). DRB1*04 DQA1*0301 DQB1*0302, associated with IDDM in Caucasians but rare in Negroids, occurred in 27% of patients and 6% of controls (RR = 5.9, p < 0.04). All patients carried DQB1*0302 or DQB1*0201. DQB1*0602 was significantly reduced in patients (2.4% v 41%, RR = 0.036, p < 0.008) and DRB1*1501 was absent in patients (0% v 35%). The frequency of GAD65 autoantibodies in Black American IDDM patients is comparable to that in Caucasians; however ICA positivity is reduced. GAD65 antibodies may therefore be a more sensitive serological test to identify individuals in the Black American general population for markers associated with increased risk of developing IDDM. Current screening methods for predicting preclinical IDDM in Caucasians relies on a combination of immune and HLA markers of IDDM; studies of these markers in the Black Americans will make it possible to extend these options to additional genetically diverse populations.
Adolescent↗
Coordinate defects in human histocompatibility leukocyte antigen class II expression and antigen presentation in bare lymphocyte syndrome.
The human immunodeficiency, type II bare lymphocyte syndrome (BLS), has been attributed to a defect in the transcription of class II histocompatibility genes. Immunocompetence, as assessed by functional exogenous antigen presentation, was not restored in immortalized B cells, derived from a BLS patient, after transfection with HLA-DR class II structural genes. Incubation of protein antigens, as well as infectious virus, with DR-transfected BLS cells failed to induce activation of antigen-specific helper T lymphocytes. Peptide antigens were presented by class II molecules displayed on BLS cells, although the conformation of these class II proteins was altered as indicated by epitope mapping. This defect in antigen presentation was independent of the specific class II DR allele transfected into BLS cells. Genetic complementation analysis has been used with BLS cells to demonstrate that the defect in class II gene transcription is linked to the absence of a trans-acting factor. Similarly, functional class II dimers were restored after in vitro fusion of cells derived from two distinct BLS complementation groups, implying that specific transcriptional control elements are shared by a gene critical for antigen presentation and genes encoding HLA class II antigens. Thus, two important functionally linked pathways of class II molecules, structural gene expression and antigen presentation, share a common regulatory pathway defective in BLS.
Alleles↗
Analysis of overlapping T- and B-cell antigenic sites on rubella virus E1 envelope protein. Influence of HLA-DR4 polymorphism on T-cell clonal recognition.
A CTL antigenic site located between residues 273 and 291 of the E1 envelope protein of RV was identified by 51Cr-release assays employing SPs. Two E1-specific CTL clones were examined for immune recognition of RV wild-type and attenuated vaccine strains and recombinant E1 protein. The exact sequence (273-284) recognized by both clones was delineated by using truncated and overlapping SPs covering these residues. The defined T-cell site overlapped almost completely with a virus neutralizing antibody-binding site previously identified with mouse monoclonal and human antibodies. A series of single aa-substituted SP analogues of E1(273-284) was used to define residues critical for T-cell recognition. Using EBV-BL displaying different HLA-DR haplotypes and -DR4 subtypes as targets to determine MHC class II restriction elements, immune recognition by both T-cell clones was shown to be associated with HLA-DR4. Three HLA-DR4 subtypes (DR4Dw13A, DR4Dw13B, and DR4KT2) sharing a common residue, glutamic acid at position 74 in their beta 1 chains, were able to present SP E1(273-284) to the T-cell clones.
Amino Acid Sequence↗
Amino acids in the peptide-binding groove influence an antibody-defined, disease-associated HLA-DR epitope.
A shared amino-acid sequence on the alpha helix of certain DR beta 1 chains is predicted to generate a 'shared epitope' that is implicated in susceptibility to the development of rheumatoid arthritis (RA). Different relative risks (RR) for disease susceptibility and severity conferred by these DR beta 1 chains suggest that their 'shared epitopes' are not equivalent. A set of monoclonal antibodies (MoAb) that map to the critical region, and for which optimal binding depends on DR context and cell lineage, was used to test this idea. Mapping experiments using mutated DR beta 1* molecules showed that the antibody-binding epitopes are overlapping; residue 70Q is pivotal for each, but neighbouring residues on the alpha helix and on the floor of the groove are also involved. Importantly, these epitopes are profoundly modified by peptide loading of DR beta 1*0401 molecules. These data suggest that 'shared epitopes' on DR molecules that are associated with RA are influenced by their context; such structural modifications may be the basis for the varying susceptibilities conferred by these DR molecules for the development of RA.
Amino Acid Sequence↗
High genetic risk for IDDM in the Pacific Northwest. First report from the Washington State Diabetes Prediction Study.
A combination of immune, genetic, and metabolic markers potentially implicated in the development of insulin-dependent diabetes mellitus (IDDM) was studied in the general population. We screened 3,992 healthy schoolchildren, 12-18 years of age with no family history of IDDM, for islet cell antibodies (ICAs). Of the children, 69 (1.7%) were found to be ICA positive (ICA+), of whom 7 (0.17%) also were positive for insulin autoantibodies (IAAs). ICA+ children (group 1) were human leukocyte antigen (HLA) typed at the DQ locus along with 123 matched (group 2) and 235 random (group 3) control subjects (from the original cohort of 3,992). Of the ICA+ children, 28 underwent beta-cell function (beta-CF) studies. High-risk DQ types were surprisingly prevalent in all groups with 35.8% of random control subjects carrying DQB1*0302 and 8.9% carrying the highest risk HLA type for IDDM, DQB1*0302/*0201. Those individuals with higher ICA titer (> 19 Juvenile Diabetes Foundation units [JDF U]) had a significantly higher prevalence of DQB1*0302 than those with lower titer ICA or normal control subjects. Six of 7 individual positive for both ICA and IAA and typed at the DQ locus were DQB1*0302/*0201 heterozygotes or DQB1*0302 or DQB1*0201 homozygotes, representing three of the highest risk genotypes for IDDM. No correlation was observed between ICA titer or DQ type and beta-CF except that all those with beta-CF below the 5th percentile carried either DQB1*0302 or DQB1*0201. Prospective follow-up is underway to determine if any combination of DQ type and immune markers predicts decline in beta-CF and the development of IDDM.
Adolescent↗
Erosive rheumatoid factor negative and positive rheumatoid arthritis are immunogenetically similar.
OBJECTIVE: The relationship between rheumatoid factor positive (RF+) and rheumatoid factor negative (RF-) rheumatoid arthritis (RA) is controversial. We sought to determine whether the HLA genes conferring susceptibility for erosive RF+RA are also prevalent in patients with erosive RF-RA. METHODS: DNA-based HLA typing for DRB1, DQB1, and DPB1 was performed on 16 consistently RF--patients with erosive RA. RESULTS: Thirteen of 16 (81%) RF-RA patients had the HLA susceptibility genes DRB1 *0401, *0404, or *0101, which are associated with RF+RA, as compared to 46% of normal controls (p = 0.017). By contrast, no associations with HLA-DQB1 and HLA-DPB1 alleles were apparent. CONCLUSION: Specific HLA susceptibility alleles are prevalent in patients with erosive RA, regardless of RF status, suggesting a similar immunogenetic basis for RA in these patients.
Adult↗
HLA-DQ allelic polymorphisms constrain patterns of class II heterodimer formation.
HLA-DQ class II molecules are complex heterodimers in which polymorphic alpha- and beta-polypeptides form noncovalent associations leading to cell surface expression. Using gene transfer with retroviral vectors, we demonstrate that surface expression of heterodimers among various DQ alpha and -beta polypeptides is not universal. Two types of allele-specific constraints were found: DQ beta chains that are associated with the DQw1 specificities do not form stable cell surface heterodimers with DQ alpha chains encoded on haplotypes that are associated with DQw2, DQw3, or DQw4. Similarly, surface expression of heterodimers composed of DQw2- or DQw3-associated DQ beta chains and DQw1 DQ alpha chains were not detected. The formation of mixed isotype heterodimers also showed allelic preference: DR alpha/DQw1 beta dimers were detected on the cell surface, but DR alpha/DQw3 beta dimers were not. Failure to express class II heterodimers on the cell surface was apparently due to either inefficient assembly of the alpha- and beta-chains or retention of the mismatched dimers in an intracellular compartment. DQ beta cDNA encoding DQw1- and DQw3-associated beta-polypeptides were modified to create chimeric expression vectors in which portions of the DQ beta polypeptides were exchanged between different alleles. The resulting chimeric DQ beta polypeptides were tested for their ability to form stable heterodimers with different DQ alpha polypeptides. A cluster of polymorphic amino acid residues encoded by the 3' end of the DQB1 second exon, corresponding to residues 60 to 91 in the DQ beta polypeptide, were found to be critical determinants constraining stable cell surface heterodimer formation among preferential alpha- and beta-combinations.
Alleles↗
Analysis of differential HLA-DQB expression in autologous B cell lines.
Class II major histocompatibility complex genes are differentially expressed during cellular activation and differentiation, often in a locus-specific manner. We investigated the differential expression of the HLA-DQB gene, using B cell lines LAZ221 and LAZ388: LAZ221, derived from an early B cell leukemia, expresses HLA-DR but not HLA-DQ: LAZ388, the autologous Epstein-Barr virus-transformed B cell line, expresses both DR and DQ. Transfection experiments demonstrate differential function of class II gene upstream regulatory regions in the two lines, which correlates with differential class II gene expression. Using gel retardation and DNase I footprint assays, we demonstrate that absence of DQB gene expression is associated with characteristic nuclear protein-binding interactions in the proximal DQB gene upstream regulatory region. These interactions are visualized as DNA-protein complexes that are seen with nuclear proteins from the DQ-negative cell line, LAZ221, and involve consensus promoter Y box and W box elements, as well as novel upstream sites. Transcriptional regulatory proteins that differ in these autologous B cell lines may be stage-specific factors involved in the developmental regulation of HLA genes.
Animals↗
Locus- and allele-specific DNA-protein interactions in the HLA-DQB1 X box.
Expression of MHC class II genes is regulated by a complex series of protein-DNA interactions which lead to the initiation of transcription. Although the different MHC class II loci are generally coordinately expressed, important differences in expression can be seen among loci and among individual alleles. The major sites of transcriptional control in the human MHC consist of several highly conserved nucleotide sequence elements located upstream of each MHC class II gene. We have analyzed the interlocus and interallelic variation in one of these key regulatory regions of the HLA-DQB1 promoter, the X box, and identified several sites of protein-DNA interaction. Two protein-DNA complexes were found which differ between the DQ and DR loci as well as two distinct complexes which differed between DQ alleles. These nuclear protein-X box interactions are likely to influence the differential expression of the MHC class II loci and alleles in tissue-specific or developmentally regulated pathways.
Alleles↗