Differential expression of insulin-dependent diabetes mellitus-associated HLA-DQA1 alleles in vivo

Exploring the HLA complex in autoimmunity: From the risk haplotypes to the modulation of expression

The genes mapping at the HLA region show high density, strong linkage disequilibrium and high polymorphism, which affect the association of HLA class I and class II genes with autoimmunity. We focused on the HLA haplotypes, genomic structures consisting of an array of specific alleles showing some degrees of genetic association with different autoimmune disorders. GWASs in many pathologies have identified variants in either the coding loci or the flanking regulatory regions, both in linkage disequilibrium in haplotypes, that are frequently associated with increased risk and may influence gene expression. We discuss the relevance of the HLA gene expression because the level of surface heterodimers determines the number of complexes presenting self-antigen and, thus, the strength of pathogenic autoreactive T cells immune response.

The effect of type 1 diabetes protection and susceptibility associated HLA class II genotypes on DNA methylation in immune cells

The HLA region, especially HLA class I and II genes, which encode molecules for antigen presentation to T cells, plays a major role in the predisposition to autoimmune disorders. To clarify the mechanisms behind this association, we examined genome-wide DNA methylation by microarrays to cover over 850,000 CpG sites in the CD4+ T cells and CD19+ B cells of healthy subjects homozygous either for DRB1*15-DQA1*01-DQB1*06:02 (DR2-DQ6, n = 14), associated with a strongly decreased T1D risk, DRB1*03-DQA1*05-DQB1*02 (DR3-DQ2, n = 19), or DRB1*04:01-DQA1*03-DQB1*03:02 (DR4-DQ8, n = 17), associated with a moderately increased T1D risk. In total, we discovered 14 differentially methylated CpG probes, of which 10 were located in the HLA region and six in the HLA-DRB1 locus. The main differences were between the protective genotype DR2-DQ6 and the risk genotypes DR3-DQ2 and DR4-DQ8, where the DR2-DQ6 group was hypomethylated compared to the other groups in all but four of the differentially methylated probes. The differences between the risk genotypes DR3-DQ2 and DR4-DQ8 were small. Our results indicate that HLA variants have few systemic effects on methylation and that their effect on autoimmunity is conveyed directly by HLA molecules, possibly by differences in expression levels or function.

Expression of HLA-DQA1 and HLA-DQB1 genes in B lymphocytes, monocytes and whole blood

Differential expression of HLA-DQA1 and HLA-DQB1 gene alleles was analysed in three different cell populations isolated from peripheral blood-B lymphocytes, monocytes and whole-blood cells. Interallelic differences in mRNA levels were observed: DQA1*03 alleles were among the most expressed in all cell types, whereas DQA1*05 alleles were least expressed in whole blood and monocytes and among the most expressed in B cells. For DQB1 gene, DQB1*06 group of alleles were the most expressed, and DQB1*02 group the least expressed within all cell populations examined. In comparison with the rest alleles, DQB1*06 and DQB1*05:02 alleles have higher expression in monocytes than in B cells, professional antigen-presenting cells. Cell type-specific regulation of expression was observed as well, with higher and more balanced expression of alleles in B lymphocytes compared to monocytes.

Expression level of risk genes of MHC class II is a susceptibility factor for autoimmunity: New insights

To date, the study of the impact of major hystocompatibility complex on autoimmunity has been prevalently focused on structural diversity of MHC molecules in binding and presentation of (auto)antigens to cognate T cells. Recently, a number of experimental evidences suggested new points of view to investigate the complex relationships between MHC gene expression and the individual predisposition to autoimmune diseases. Irrespective of the nature of the antigen, a threshold of MHC-peptide complexes needs to be reached, as well as a threshold of T cell receptors engaged is required, for the activation and proliferation of autoantigen-reactive T cells. Moreover, it is well known that increased expression of MHC class II molecules may alter the T cell receptor repertoire during thymic development, and affect the survival and expansion of mature T cells. Many evidences confirmed that the level of both transcriptional and post-transcriptional regulation are involved in the modulation of the expression of MHC class II genes and that both contribute to the predisposition to autoimmune diseases. Here, we aim to focus some of these regulative aspects to better clarify the role of MHC class II genes in predisposition and development of autoimmunity.

HLA-DQ2.5 genes associated with celiac disease risk are preferentially expressed with respect to non-predisposing HLA genes: Implication for anti-gluten T cell response

HLA genes represent the main risk factor in autoimmune disorders. In celiac disease (CD), the great majority of patients carry the HLA DQA1*05 and DQB1*02 alleles, both of which encode the DQ2.5 molecule. The formation of complexes between DQ2.5 and gluten peptides on antigen-presenting cells (APCs) is necessary to activate pathogenic CD4(+) T lymphocytes. It is widely accepted that the DQ2.5 genes establish the different intensities of anti-gluten immunity, depending whether they are in a homozygous or a heterozygous configuration. Here, we demonstrated that HLA DQA1*05 and DQB1*02 gene expression is much higher than expression of non-CD-associated genes. This influences the protein levels and causes a comparable cell surface exposure of DQ2.5 heterodimers between DQ2.5 homozygous and heterozygous celiac patients. As a consequence, the magnitude of the anti-gluten CD4(+) T cell response is strictly dependent on the antigen dose and not on the DQ2.5 gene configuration of APCs. Furthermore, our findings support the concept that the expression of DQ2.5 genes is an important risk factor in celiac disease. The preferential expression of DQ2.5 alleles provides a new functional explanation of why these genes are so frequently associated with celiac disease and with other autoimmune disorders.

DNA methylation and mRNA expression of HLA-DQA1 alleles in type 1 diabetes mellitus

Type 1 diabetes (T1D) belongs among polygenic multifactorial autoimmune diseases. The highest risk is associated with human leucocyte antigen (HLA) class II genes, including HLA-DQA1 gene. Our aim was to investigate DNA methylation of HLA-DQA1 promoter alleles (QAP) and correlate methylation status with individual HLA-DQA1 allele expression of patients with T1D and healthy controls. DNA methylation is one of the epigenetic modifications that regulate gene expression and is known to be shaped by the environment.Sixty one patients with T1D and 39 healthy controls were involved in this study. Isolated DNA was treated with sodium bisulphite and HLA-DQA1 promoter sequence was amplified using nested PCR. After sequencing, DNA methylation of HLA-DQA1 promoter alleles was analysed. Individual mRNA HLA-DQA1 relative allele expression was assessed using two different endogenous controls (PPIA, DRA). We have found statistically significant differences in HLA-DQA1 allele 02:01 expression (PPIA normalization, Pcorr = 0·041; DRA normalization, Pcorr = 0·052) between healthy controls and patients with T1D. The complete methylation profile of the HLA-DQA1 promoter was gained with the most methylated allele DQA1*02:01 and the least methylated DQA1*05:01 in both studied groups. Methylation profile observed in patients with T1D and healthy controls was similar, and no correlation between HLA-DQA1 allele expression and DNA methylation was found. Although we have not proved significant methylation differences between the two groups, detailed DNA methylation status and its correlation with expression of each HLA-DQA1 allele in patients with T1D have been described for the first time.

EBP1 and DRBP76/NF90 binding proteins are included in the major histocompatibility complex class II RNA operon

Major histocompatibility complex class II mRNAs encode heterodimeric proteins involved in the presentation of exogenous antigens during an immune response. Their 3'UTRs bind a protein complex in which we identified two factors: EBP1, an ErbB3 receptor-binding protein and DRBP76, a double-stranded RNA binding nuclear protein, also known as nuclear factor 90 (NF90). Both are well-characterized regulatory factors of several mRNA molecules processing. Using either EBP1 or DRBP76/NF90-specific knockdown experiments, we established that the two proteins play a role in regulating the expression of HLA-DRA, HLA-DRB1 and HLA-DQA1 mRNAs levels. Our study represents the first indication of the existence of a functional unit that includes different transcripts involved in the adaptive immune response. We propose that the concept of 'RNA operon' may be suitable for our system in which MHCII mRNAs are modulated via interaction of their 3'UTR with same proteins.

Differential expression of HLA-DQ alleles in peripheral blood mononuclear cells: alleles associated with susceptibility to and protection from autoimmune type 1 diabetes

Differential expression of human leucocyte antigen (HLA) class II genes has been postulated to influence the risk of developing autoimmune disease. In this study, we investigated the relationship between the level of mRNA expression of DQA1 and DQB1 alleles in peripheral blood mononuclear cells and the influence of the alleles on susceptibility to type 1 diabetes (T1D). Transcripts from pairs of DQA1 and DQB1 alleles were quantified in 59 DQ-heterozygous individuals (29 patients with T1D and 30 healthy control subjects). Luciferase reporter gene assays were used to investigate the relative promoter activities of the alleles associated with high and low risk of disease. DQA1*0301 and the DQB1*06 group of alleles (*0601, *0602, *0603 and *0604) were generally overexpressed in comparison to other alleles. In contrast, mRNA for DQB1*0201/*0202 was generally less abundant than other DQB1 transcripts. These data correlated well with the relative promoter activities observed for the diabetes-associated alleles; the strongest promoters were those derived from DQA1*0301 and DQB1*0602, while a 700-bp fragment derived from the DQB1*0201 promoter showed the lowest activity of the DQB1 constructs. There was no simple correlation between the level of expression of specific DQ alleles and their influence on the risk of diabetes. The functional relevance of our findings and their implications for the pathogenesis of autoimmunity remain to be determined.

VMAT2 gene expression and function as it applies to imaging beta-cell mass

Diabetes mellitus is a metabolic disorder characterized by hyperglycemia. The two main forms of the disease are distinguished by different pathogenesis, natural histories, and population distributions and indicated as either type 1 (T1DM) or type 2 diabetes mellitus (T2DM). It is well established that T1DM is an autoimmune disease whereby beta-cells of pancreatic islets are destroyed leading to loss of endogenous insulin production. Albeit less dramatic, beta-cell mass (BCM) also drops in T2DM. Therefore, it is realistic to expect that noninvasive measures of BCM might provide useful information in the diabetes-care field. Preclinical studies have demonstrated that BCM measurements by positron emission tomography scanning, using the vesicular monoamine transporter type 2 (VMAT2) as a tissue-specific surrogate marker of insulin production and [11C] Dihydrotetrabenazine (DTBZ) as the radioligand specific for this molecule, is feasible in animal models. Unfortunately, the mechanisms underlying beta-cell-specific expression of VMAT2 are still largely unexplored, and a much better understanding of the regulation of VMAT2 gene expression and of its function in beta-cells will be required before the full utility of this technique in the prediction and treatment of individuals with diabetes can be understood. In this review, we summarize much of what is understood about the regulation of VMAT2 and identify questions whose answers may help in understanding what measurements of VMAT2 density mean in the context of diabetes.

Effect of interferon alpha on MHC class II gene expression in ex vivo human islet tissue

Type 1 diabetes (T1D) is caused by autoimmune destruction of the insulin-producing beta-cells of the islets of Langerhans. One still open question is where naive islet-reactive T cells encounter antigens and become stimulated. In this report we have re-examined the expression of MHC class II (MHCII) genes in human islets to further explore the possibility that non-professional antigen presenting cells (APCs) within islets contribute to autoimmunity. Since development of T1D has been linked to viral infections, we also studied ex-vivo MHCII expression in response to interferon-alpha (IFNalpha) in islet tissue and in different APCs. The findings are: first, MHCII genes expression in human islets is linked with the expression of the class II transactivator isoform transcribed from the promoter IV, similar to that described in non-professional APCs. Second, there is IFNalpha-mediated lineage-specific regulation of MHCII genes expression, seen as a decrease in the accumulation of MHCII transcripts in pancreatic islets opposite to an increase in dendritic cells and B-lymphoblastoid cell lines. Third, there is allele-specific regulation of the HLA-DQA1 gene by IFNalpha in islet tissue. These findings may begin to explain the molecular events that create favorable conditions for organ-specific autoimmunity and explain the incomplete penetrance of T1D susceptibility alleles.

HLA DQA1 genes generate multiple transcripts by alternative splicing and polyadenylation of the 3' untranslated region

Regulation of the human leucocyte antigen (HLA) class II genes expression is an important field in immunology, because these molecules play a crucial role in the function of the immune system. HLA DQ genes expression is a complex phenomenon regulated at both transcriptional and post-transcriptional levels. In this study, we have investigated the post-transcriptional mechanisms accounting for alleles-dependent length polymorphism of DQA1 mRNA. We have first sequenced the genomic DNA encoding the 3' untranslated region (UTR) of DQA1 *0101, *0102, *0103, *0201, *0301, *0401, and *0501 alleles. We have identified two competing splicing sites: a unique splicing donor site AG/GTA located 20 nucleotides downstream from the stop codon associated to two spliced acceptor sequences, approximately 165 and approximately 370 nucleotides downstream. In addition, three polyadenylation signals have been identified, respectively, at approximately 475, approximately 795, and approximately 855 nucleotides downstream from the stop codon. Subsequently, we have analyzed mRNAs derived from DQA1 alleles in homozygous B lymphoblastoid cell lines by reverse transcriptase-polymerase chain reaction. We show that allele-dependent length polymorphism of DQA1 mRNA-3' UTR results from a combination of differential splicing and alternative polyadenylations. Four mRNA isoforms (two spliced variant cleaved at two distinct polyadenylation sites) were detected in DQA1 *0101, *0102, and *0103 homozygous cell lines, and six mRNA species (three spliced variant cleaved at two polyadenylation-sequence signal) were generated by the other four alleles. Possible advantages for cells to generate multiple transcripts previously undetected are discussed.

HLA class II antigens associated with lupus nephritis in Italian SLE patients

Human leukocyte antigen DR2 (HLA-DR2), namely the allelic variant HLA-DR15, have been associated with lupus nephritis (LN) in Caucasians. The study investigated the relationships between HLA class II alleles and lupus nephritis in Italian patients. Two hundred forty-four patients fulfilling the American Rheumatism Association criteria for systemic lupus erythematosus (SLE) were typed for HLA-DRB1*, -DQA1*, -DQB1*, and -DPB1* alleles by polymerase chain reaction-sequence-specific oligonucleotide and polymears chain reaction-single-strand polymorphism; 71 patients had renal damage assessed by renal biopsy. Glomerulonephritis was classified using WHO criteria. Significance was tested by X(2) on 2x2 tables. HLA-DQA1*0101 was strongly associated with LN (OR = 2.72 [1.43-5.19]; p = 0.002), whereas HLA-DRB1*1501 was only marginally associated (OR = 1.94 [0.88-4.26]; p = not significant). HLA-DQA1*0102 demonstrated a significant protective effect (OR = 0.31 [0.14-0.86]; p = 0.002). On analyzing the distribution of HLA-DRB1*1501 bearing haplotypes in our SLE patients we found that the HLA-DRB1*1501 greatly enhanced the risk of developing LN conferred by the DQA1*0101 allele (OR = 65.96 [9.35-1326.25]), whereas DQA1*0102 suppressed the nephritogenic effect of DRB1*1501. At renal biopsy, 80% of DRB1*15 positive patients were classified as having class IV LN with the remaining 20% having class III LN. The figures were 19% and 21%, respectively, among the HLA-DR15 negative patients. In the Italian population HLA-DQA and HLA-DR alleles interact in conferring susceptibility to or protection against lupus nephritis, the diffuse proliferative glomerulonephritis (i.e., the most severe form of nephritis) is associated with the HLA-DR15 bearing haplotypes.

Unbalanced amounts of HLA-DQA1 allele mRNA: DQA1*03 shows high and DQA1*0501 low amounts of mRNA in heterozygous individuals

Genes of the HLA-DR, DQ region confer strong susceptibility to type 1 diabetes mellitus (IDDM). A possible mechanism of susceptibility is a difference in the amounts of transcripts of predisposing and neutral or protective haplotypes. In this study we developed an assay to compare the amounts of mRNA of two distinct HLA-DQA1 alleles in peripheral blood lymphocytes (PBLs) of heterozygous individuals, using a quantitative RT-PCR with an internal standard covering all HLA-DQA1 specifities. We also developed an algorithm to calculate the amounts of mRNA for two distinct alleles in heterozygous individuals based on the comparison to the same internal standard. In total, 37 HLA-DQA1 heterozygous individuals were analysed, including patients with IDDM (n = 14) and healthy controls (n = 23). Intra-individually, we observed different amounts of mRNA for different HLA-DQA1 alleles in the order: HLA-DQA1*03 > *01 > *0201 > *05. This order was observed in all individuals. We also observed a variation in the ratio of these unbalanced amounts of mRNA in individuals with the same HLA-DQA1 allele combinations. In all allele combinations the average ratio was increased in patients with IDDM compared to the control samples. HLA-DQA1*03 positive and DQA1*03, *05 heterozygous patients had the highest average ratios. Nevertheless, based on limited sample numbers, these differences did not reach significance. We therefore conclude that variations between HLA-DQA1 alleles are not limited to the nucleotide sequence but are also found at the level of amounts of mRNA.

Rheumatoid arthritis in southern Spain: toward elucidation of a unifying role of the HLA class II region in disease predisposition

OBJECTIVE

To evaluate the contributions of HLA-DQ and -DR polymorphisms to susceptibility to rheumatoid arthritis (RA) in a population in southern Spain, and to compare the value of the shared epitope (SE) and RA protection (RAP) models in accounting for the HLA class II region's contribution to RA predisposition.

METHODS

One hundred sixty RA patients and 153 healthy controls were typed for HLA-DRB1 and -DQB1 using high-resolution DNA techniques. Distributions of predisposing DRB1 alleles in patients and control subjects according to the SE model were compared with distributions of predisposing DQ and protective DERAA-positive DRBI alleles according to the RAP model.

RESULTS

DQ3 (DQBI*03 and *04 combined with DQA1*03) and DQ5 (DQB1*0501/DQA1*0101) alleles predisposed individuals to RA independently of SE-positive DRB1 alleles. DQ3/3-homozygous individuals had the strongest risk of developing RA. DQ3 molecules predisposed to RA more than did DQ5 molecules. The weaker predisposition mediated by DQ5 included the DRB1*1001-carrying haplotype; no DRB1*1001-homozygous patients were observed. DRBI*0401 played a unique role in the contribution of DQ3-DR4 haplotypes to RA, in spite of its low frequency in southern Spain.

CONCLUSION

The low prevalences of RA and of mild disease observed in Spain, and in southern Europe in general, can be explained in great part by the low frequency of DQ3-DR4 haplotypes, especially those carrying DRB1*0401. However, the overall distribution of HLA-DQ and -DR alleles in RA patients compared with control subjects is similar to that in other European and North American populations. A model involving both DQ and DR can best account for the contribution of HLA to RA.

HLA association with autoimmune disease: a failure to protect?

That certain HLA specificities are associated with predisposition to autoimmune disease does not necessarily imply that self-reactive T cells restricted to particular HLA alleles are eliciting the disease. In the present essay, we argue that HLA can be a major genetic factor in the development of autoimmune diseases without T cells being primarily involved in its initiation or perpetuation. There is now ample evidence that self-reactive, regulatory T cells can protect against pernicious autoimmunity. Hereafter, we propose that extended HLA haplotypes, such as DQ3-DR4, DQ3-DR9, DQ5-DR1 and DQ5-DR10 in the case of rheumatoid arthritis, predispose to impaired T-cell-mediated immune regulation. The haplotypes associated with impaired regulation are the combination of certain class II alleles and a yet unknown 'amplifier'. In this model, products of the HLA class II region are not involved in the presentation of particular organ-specific autoantigens. Therefore, HLA does not predispose to autoimmune disease per se, but rather fails to provide efficient protection.