HLA and autoimmune diseases: Type 1 diabetes (T1D) as an example

HLA and Nasal Polyposis Susceptibility: A Meta-analysis of Worldwide Studies

OBJECTIVES

Nasal polyposis (NP) is a common and recurrent condition of the sinonasal cavity which has significant impact on patients' quality of life. NP pathophysiology involves a complex interplay of genetic, environmental, and immunological factors. Several studies have explored the association between human leukocyte antigen (HLA) class II alleles and NP, but the results have been conflicting. The aim of this meta-analysis is to investigate the association between HLA class II alleles, specifically HLA-DQA1, HLA-DQB1, and HLA-DRB1and NP risk.

METHODS

A systematic review was conducted using electronic databases, including PubMed, Google Scholar, and Cochrane Library, to identify studies investigating the association between HLA class II alleles and NP. Eligible studies were identified by specific inclusion and exclusion criteria. The odds ratios (ORs) with 95% confidence intervals (CIs) were used to assess the association between HLA class II alleles and NP risk. A random-effects model was used to calculate the pooled OR and corresponding 95% CI, and a study required a heterogeneity assessment value I2 < 25% to be considered for analysis.

STUDY DESIGN

Meta-analysis.

RESULTS

A total of four studies were included in this meta-analysis, involving a total of 258 NP alleles and 802 control alleles. The analysis indicated that DQA1*0201 (OR = 3.08, 95% CI [1.70, 5.59]) and DRB1*7 (OR = 2.04, 95% CI [1.14, 3.66]) were significantly associated with increased risk of NP. The analysis of the NP risk alleles DQA1*0201 and DRB1*7 had an I2 < 0% representing low heterogeneity. Sensitivity analysis with LFK indices showed minor asymmetry in either allele.

CONCLUSIONS

This meta-analysis provides evidence that the HLA-DQA1*0201 and HLA-DRB1*7 alleles are risk factors for the development of NP. These findings could contribute to a better understanding of the genetic predisposition of NP and may have implications for the development of novel approaches for the prevention and treatment of this condition.

Association of HLA Haplotypes with Autoimmune Pathogenesis in Newly Diagnosed Type 1 Romanian Diabetic Children: A Pilot, Single-Center Cross-Sectional Study

BACKGROUND

The increasing incidence of autoimmune diseases in type 1 diabetes mellitus (T1DM) patients highlights the influence of human leukocyte antigen (HLA) haplotypes on their development. This study aims to determine genetic predisposition to autoimmune diseases in T1DM patients, including thyroid disease and celiac diseases, and explore its correlation with vitamin D deficiency.

METHODS

A cross-sectional study involving thirty-six T1DM children was conducted. Typing was performed for the HLA A, B, C, DP, DR, and DQ loci. Regression analysis linked DR-DQ haplotypes to T1DM and the associated conditions.

RESULTS

The most frequent predisposing alleles and haplotypes were HLA-DR3 (70.27%), DQ2 (70.27%), DR3-DQ2 (70.27%), DQB1*02:01 (70.27%), A02 (54.05%), whereas the most prevalent protecting allele was DPB1*04:01 (52.63%). Positive correlations were observed between positive anti-thyroid peroxidase antibodies and the absence of protective alleles (DPB1*04:02, p = 0.036; DPB1*04:01, p = 0.002). Associations were found between the absence of DPB1*04:01 and anti-thyroglobulin antibodies (p = 0.03). HLA allele DPB1*03:01 was linked with vitamin D deficiency (p = 0.021). Positive anti-transglutaminase antibodies correlated with C03:03 (p = 0.026) and DRB1*04:01-DQA1*03-DQB1*03:01 (p < 0.0001) and the lack of DQA1*01:03-DQB1*06:03-DRB1*13:01 (p < 0.0001).

CONCLUSIONS

The predisposing T1DM haplotypes were associated with the presence of anti-transglutaminase and anti-thyroid antibodies, indicating a genetic predisposition to autoimmune diseases.

Autoimmune Disease and Breast Implants: Systematic Review of Outcomes

ABSTRACT

Given that the use of breast implants for both cosmetic and reconstructive purposes is growing in the United States, an evaluation of factors that may affect the outcome of breast implant surgery is needed. A systematic review was conducted to evaluate the question: Does a personal or family history of autoimmune disease affect outcomes in breast implant surgery? The literature search yielded 2425 records, but after removal of duplicates, abstract screening, and full-text assessment, only 2 studies met the inclusion criteria for the final review. Both studies provided level III evidence and the average Methodological Index for Non-Randomized Studies score was 16.5 (range, 15-18 of 24), indicating a fair level of evidence overall. This systematic review found no evidence to support that a diagnosis of an autoimmune disease and/or a family history of autoimmune diseases will lead to poor surgical outcomes in breast implant surgery. Further study is warranted.

G307S DNAM-1 Mutation Exacerbates Autoimmune Encephalomyelitis via Enhancing CD4+ T Cell Activation

Although rs763361, which causes a nonsynonymous glycine-to-serine mutation at residue 307 (G307S mutation) of the DNAX accessory molecule-1 (DNAM-1) immunoreceptor, is a single-nucleotide polymorphism associated with autoimmune disease susceptibility, little is known about how the single-nucleotide polymorphism is involved in pathogenesis. In this study, we established human CD4+ T cell transfectants stably expressing wild-type (WT) or G307S DNAM-1 and showed that the costimulatory signal from G307S DNAM-1 induced greater proinflammatory cytokine production and cell proliferation than that from wild-type DNAM-1. The G307S mutation also enhanced the recruitment of the tyrosine kinase Lck and augmented p-Tyr322 of DNAM-1. We also established a mouse myelin Ag-specific CD4+ T cell transfectant stably expressing the chimeric DNAM-1 (chDNAM-1) consisting of the extracellular, transmembrane, and a part of intracellular regions of mouse DNAM-1 (residues 1-285) fused with the part of the intracellular region (residues 286-336) of human WT or G307S chDNAM-1. Adoptive transfer of the mouse T cell transfectant expressing the G307S chDNAM-1 into mice exacerbated experimental autoimmune encephalomyelitis compared with the transfer of cells expressing the WT chDNAM-1. These findings suggest that rs763361 is a gain-of-function mutation that enhances DNAM-1-mediated costimulatory signaling for proinflammatory responses.

A Mendelian randomization study to assess the genetic liability of type 1 diabetes mellitus for IgA nephropathy

Background

The prevalence of immunoglobulin A nephropathy (IgAN) seems to be higher in patients with type 1 diabetes mellitus (T1DM) than that in the general population. However, whether there exists a causal relationship between T1DM and IgAN remains unknown.

Methods

This study conducted a standard two-sample Mendelian randomization (MR) analysis to assess the causal inference by four MR methods, and the inverse variance-weighted (IVW) approach was selected as the primary method. To further test the independent causal effect of T1DM on IgAN, multivariable MR (MVMR) analysis was undertaken. Sensitivity analyses incorporating multiple complementary MR methods were applied to evaluate how strong the association was and identify potential pleiotropy.

Results

MR analyses utilized 81 single-nucleotide polymorphisms (SNPs) for T1DM. The evidence supports a significant causal relationship between T1DM and increased risk of IgAN [odds ratio (OR): 1.39, 95% confidence interval (CI): 1.10-1.74 for IVW, p < 0.05]. The association still exists after adjusting for triglyceride (TG), fasting insulin (FI), fasting blood glucose (FBG), homeostasis model assessment of beta-cell function (HOMA-B) and insulin resistance (HOMA-IR), and glycated hemoglobin (HbA1c). MVMR analysis indicated that the effect of T1DM on IgAN vanished upon accounting for low-density lipoprotein cholesterol (LDL-c; OR: 0.97, 95% CI: 0.90-1.05, p > 0.05).

Conclusions

This MR study provided evidence that T1DM may be a risk factor for the onset of IgAN, which might be driven by LDL-c. Lipid-lowering strategies targeting LDL-c should be enhanced in patients with T1DM to prevent IgAN.

Reduced Follicular Regulatory T Cells in Spleen and Pancreatic Lymph Nodes of Patients With Type 1 Diabetes

In the attempt to understand the origin of autoantibody (AAb) production in patients with and at risk for type 1 diabetes (T1D), multiple studies have analyzed and reported alterations in T follicular helper (Tfh) cells in presymptomatic AAb⁺ subjects and patients with T1D. Yet, whether the regulatory counterpart of Tfh cells, represented by T follicular regulatory (Tfr) cells, is similarly altered is still unclear. To address this question, we performed analyses in peripheral blood, spleen, and pancreatic lymph nodes (PLN) of organ donor subjects with T1D. Blood analyses were also performed in living AAb^- and AAb⁺ subjects. While negligible differences in the frequency and phenotype of blood Tfr cells were observed among T1D, AAb^-, and AAb⁺ adult subjects, the frequency of Tfr cells was significantly reduced in spleen and PLN of T1D as compared with nondiabetic control subjects. Furthermore, adoptive transfer of Tfr cells delayed disease development in a mouse model of T1D, a finding that could indicate that Tfr cells play an important role in peripheral tolerance and regulation of autoreactive Tfh cells. Together, our findings provide evidence of Tfr cell alterations within disease-relevant tissues in patients with T1D, suggesting a role for Tfr cells in defective humoral tolerance and disease pathogenesis.

New era of therapy for endocrine autoimmune disorders

The new era of immune and reconstitution therapy of autoimmune disorders is ongoing. However, endocrine autoimmune diseases comprise a group of elaborating pathologies where the development of new treatment strategies remains slow. Substitution of the missing hormones is still standard practice, taking care of the devastating symptoms but not the cause of disease. As our knowledge of the genetic contribution to the aetiology of endocrine disorders increases and early diagnostic tools are available, it is now possible to identify persons at risk before they acquire full-blown disease. This review summarizes current knowledge and treatment of endocrine autoimmune disorders, focusing on type 1 diabetes, Addison's disease, autoimmune thyroid diseases and primary ovarian insufficiency. We explore which new therapies might be used in the different stages of the disease, focus on legalized therapy and elaborate on the ongoing clinical studies for these diseases and the research front, before hypothesizing on the way ahead.

Identifying the immune interactions underlying HLA class I disease associations

Variation in the risk and severity of many autoimmune diseases, malignancies and infections is strongly associated with polymorphisms at the HLA class I loci. These genetic associations provide a powerful opportunity for understanding the etiology of human disease. HLA class I associations are often interpreted in the light of 'protective' or 'detrimental' CD8⁺ T cell responses which are restricted by the host HLA class I allotype. However, given the diverse receptors which are bound by HLA class I molecules, alternative interpretations are possible. As well as binding T cell receptors on CD8⁺ T cells, HLA class I molecules are important ligands for inhibitory and activating killer immunoglobulin-like receptors (KIRs) which are found on natural killer cells and some T cells; for the CD94:NKG2 family of receptors also expressed mainly by NK cells and for leukocyte immunoglobulin-like receptors (LILRs) on myeloid cells. The aim of this study is to develop an immunogenetic approach for identifying and quantifying the relative contribution of different receptor-ligand interactions to a given HLA class I disease association and then to use this approach to investigate the immune interactions underlying HLA class I disease associations in three viral infections: Human T cell Leukemia Virus type 1, Human Immunodeficiency Virus type 1 and Hepatitis C Virus as well as in the inflammatory condition Crohn's disease.

Evaluation of the major histocompatibility complex (MHC) class II as a candidate for sudden acquired retinal degeneration syndrome (SARDS) in Dachshunds

Objective

Sudden acquired retinal degeneration syndrome (SARDS) is one of the leading causes of acute blindness in dogs, with an unknown etiology and no effective treatment. Certain breeds such as Dachshunds are overrepresented among SARDS patients, and therefore, the syndrome is suspected to have a genetic component. The objective of this study was to determine if a genetic locus associated with SARDS in Dachshunds could be identified using a genome‐wide association study (GWAS).

Procedures

Genome‐wide association mapping was performed in 15 SARDS‐affected and 16 unaffected Dachshunds. Genotyping of three classical DLA class II genes (DLA‐DRB1, DLA‐DQA1, and DLA‐DQB1) was performed in 34 SARDS‐affected and 66 unaffected Dachshunds to evaluate for an association in this region.

Results

Although no single nucleotide polymorphisms (SNPs) were of genome‐wide statistical significance (P_Bonferroni < 0.05), 5 of the top 9 SNPs were in the major histocompatibility complex (MHC). Using DLA typing, the allele DLA‐DRB1*09401 was identified as a risk factor for the development of SARDS (P = 0.0032, OR = 4.0). The alleles DLA‐DQB1*00101 (P = 0.0050, OR = 0.31), DLA‐DQA1*00901 (P = 0.0087, OR = 0.33), and a previously identified DLA‐DRB1allele described as “DRB1‐T” (P = 0.0284, OR = 0.37) were identified as protective factors.

Conclusions

Although far from definitive, association of SARDS with alleles of immunologic importance further supports the hypothesis that autoimmunity may play a role in the pathogenesis of SARDS.

Contribution of HLA-DQ2/DQ8 haplotypes in type one diabetes patients with/without celiac disease

BACKGROUND

Based on lack of data on the distribution of the related alleles in the T1D population in Iranian population, we assessed the frequency of HLA DQ2 and DQ8 haplotypes in patients with T1D with/without CD compared to healthy population.

MATERIALS AND METHODS

70 patients with T1D without celiac disease, 60 T1D cases with CD were compared to 150 healthy individuals during 2016. Ten mililiter Gheparinized blood samples were collected, genomic DNA was extracted and alleles were genotyped by Real-time PCR using SYBR Green as a low-resolution method.

RESULTS

HLA-DQ2 and/or HLA-DQ8 genotypes was presented in 51% and 23% of T1D patients without CD respectively. Twenty one percent of those patients carried both alleles and 5% were negative for both alleles. T1D patients with CD had much higher DQ2 frequency (72%) and lower DQ8 (11.6%), than T1D patients without CD and controls, 14% carried both alleles and 3% were negative for both. The frequencies of DQ2 and DQ8 alleles in Iranian healthy population were 19 and 5% respectively.

CONCLUSION

According to the same genetic background for CD and T1D we suggest that HLA-typing can be a very useful screening tool for CD in patients with type one diabetes.

High prevalence of humoral autoimmunity in first-degree relatives of Mexican type 1 diabetes patients

AIMS

To assess the prevalence of autoantibodies (Aab) to insulin (IAA), glutamic acid decarboxylase 65 (GADA) and insulinoma antigen 2 (IA-2A), as well as human leukocyte antigen (HLA) class II alleles, in first degree relatives (FDR) of Mexican patients with type 1 diabetes (T1D), and to explore whether these parameters mirror the low incidence of T1D in the Mexican population.

METHODS

Aab titers were determined by ELISA in 425 FDR, 234 siblings, 40 offspring and 151 parents of 197 patients with T1D. Typing of HLA-DR and -DQ alleles was performed in 41 Aab-positive FDR using polymerase chain reaction with allele-specific oligotyping.

RESULTS

Seventy FDR (16.47%) tested positive for Aab. The siblings (19.2%) and the offspring (25%) had significantly higher prevalence of Aab than the parents (9.9%). GADA was the most frequent Aab. Almost half of the Aab-positive FDR had two different Aab (45.7%), and none tested positive for three Aab. The highest prevalence of Aab was found among women in the 15-29 years age group. Moreover, the positivity for two Aab was significantly more frequent among females. A considerable number of FDR (48.8%) carried the susceptible HLA-DR3, -DR4, -DQB1*0201 or -DQB1*0302 alleles, but almost none had the high risk genotype HLA-DR3/DR4.

CONCLUSIONS

FDR of Mexican T1D patients have high prevalence of islet Aab, comparable to countries with the highest incidence of T1D. However, Aab positivity does not seem to be associated with HLA risk genotypes, which may have an impact on the low incidence of T1D in Mexico.

On the pathogenesis of insulin-dependent diabetes mellitus: the role of microbiota

Type 1 diabetes (T1D) is an autoimmune disorder characterized by the selective destruction of insulin-producing β cells as result of a complex interplay between genetic, stochastic and environmental factors in genetically susceptible individuals. An increasing amount of experimental data from animal models and humans has supported the role played by imbalanced gut microbiome in T1D pathogenesis. The commensal intestinal microbiota is fundamental for several physiologic mechanisms, including the establishment of immune homeostasis. Alterations in its composition have been correlated to changes in the gut immune system, including defective tolerance to food antigens, intestinal inflammation and enhanced gut permeability. Early findings reported differences in the intestinal microbiome of subjects affected by prediabetes or overt disease compared to healthy individuals. The present review focuses on microbiota-host homeostasis, its alterations, factors that influence microbiome composition and discusses their putative correlation with T1D development. Further studies are necessary to clarify the role played by microbiota modifications in the processes that cause enhanced permeability and the autoimmune mechanisms responsible for T1D onset.

Understanding Autoimmune Diabetes through the Prism of the Tri-Molecular Complex

The strongest susceptibility allele for Type 1 Diabetes (T1D) is human leukocyte antigen (HLA), which supports a central role for T cells as the drivers of autoimmunity. However, the precise mechanisms that allow thymic escape and peripheral activation of beta cell antigen-specific T cells are still largely unknown. Studies performed with the non-obese diabetic (NOD) mouse have challenged several immunological dogmas, and have made the NOD mouse a key experimental system to study the steps of immunodysregulation that lead to autoimmune diabetes. The structural similarities between the NOD I-A^g7 and HLA-DQ8 have revealed the stability of the T cell receptor (TCR)/HLA/peptide tri-molecular complex as an important parameter in the development of autoimmune T cells, as well as afforded insights into the key antigens targeted in T1D. In this review, we will provide a summary of the current understanding with regard to autoimmune T cell development, the significance of the antigens targeted in T1D, and the relationship between TCR affinity and immune regulation.

Incidence and Mortality Rates and Clinical Characteristics of Type 1 Diabetes among Children and Young Adults in Cochabamba, Bolivia

OBJECTIVES

To determine incidence, mortality, and clinical status of youth with diabetes at the Centro Vivir con Diabetes, Cochabamba, Bolivia, with support from International Diabetes Federation Life for a Child Program.

METHODS

Incidence/mortality data analysis of all cases (<25 year (y)) diagnosed January 2005-February 2017 and cross-sectional data (December 2015).

RESULTS

Over 12.2 years, 144 cases with type 1 diabetes (T1D) were diagnosed; 43.1% were male. Diagnosis age was 0.3-22.2 y; peak was 11-12 y. 11.1% were <5 y; 29.2%, 5-<10 y; 43.1%, 10-<15 y; 13.2%, 15-<20 y; and 3.5%, 20-<25 y. The youngest is being investigated for monogenic diabetes. Measured incidence in Cercado Province (Cochabamba Department) was 2.2/100,000 children < 15 y/y, with ≈80% ascertainment, giving total incidence of 2.7/100,000 children < 15 y/y. Two had died. Crude mortality rate was 2.3/1000 patient years. Clinical data on 141 cases <35 y: mean/median HbA1c was 8.5/8.2% (69/62 mmol/mol), levels higher in adolescents. Three were on renal replacement therapy; four others had substantial renal impairment. Elevated BMI, triglycerides, and cholesterol were common: 19.1%, 18.3%, and 39.1%, respectively.

CONCLUSIONS

Bolivia has low T1D incidence. Reasonable glycemic control is being achieved despite limited resources; however, some have serious complications and adverse cardiovascular risk factor profiles. Further attention is needed for complications.

Peptidomic analysis of type 1 diabetes associated HLA-DQ molecules and the impact of HLA-DM on peptide repertoire editing

HLA-DM and class II associated invariant chain (Ii) are key cofactors in the MHC class II (MHCII) antigen processing pathway. We used tandem mass spectrometry sequencing to directly interrogate the global impact of DM and Ii on the repertoire of MHCII-bound peptides in human embryonic kidney 293T cells expressing HLA-DQ molecules in the absence or presence of these cofactors. We found that Ii and DM have a major impact on the repertoire of peptides presented by DQ1 and DQ6, with the caveat that this technology is not quantitative. The peptide repertoires of type 1 diabetes (T1D) associated DQ8, DQ2, and DQ8/2 are altered to a lesser degree by DM expression, and these molecules share overlapping features in their peptide binding motifs that are distinct from control DQ1 and DQ6 molecules. Peptides were categorized into DM-resistant, DM-dependent, or DM-sensitive groups based on the mass spectrometry data, and representative peptides were tested in competitive binding assays and peptide dissociation rate experiments with soluble DQ6. Our data support the conclusion that high intrinsic stability of DQ-peptide complexes is necessary but not sufficient to confer resistance to DM editing, and provide candidate parameters that may be useful in predicting the sensitivity of T-cell epitopes to DM editing.

Type 1 diabetes associated HLA-DQ2 and DQ8 molecules are relatively resistant to HLA-DM mediated release of invariant chain-derived CLIP peptides

HLA-DM is essential for editing peptides bound to MHC class II, thus influencing the repertoire of peptides mediating selection and activation of CD4(+) T cells. Individuals expressing HLA-DQ2 or DQ8, and DQ2/8 trans-dimers, have elevated risk for type 1 diabetes (T1D). Cells coexpressing DM with these DQ molecules were observed to express elevated levels of CLIP (Class II associated invariant chain peptide). Relative resistance to DM-mediated editing of CLIP was further confirmed by HPLC-MS/MS analysis of eluted peptides, which also demonstrated peptides from known T1D-associated autoantigens, including a shared epitope from ZnT8 that is presented by all four major T1D-susceptible DQ molecules. Assays with purified recombinant soluble proteins confirmed that DQ2-CLIP complexes are highly resistant to DM editing, whereas DQ8-CLIP is partially sensitive to DM, but with an apparent reduction in catalytic potency. DM sensitivity was enhanced in mutant DQ8 molecules with disruption of hydrogen bonds that stabilize DQ8 near the DM-binding region. Our findings show that T1D-susceptible DQ2 and DQ8 share significant resistance to DM editing, compared with control DQ molecules. The relative resistance of the T1D-susceptible DQ molecules to DM editing and preferential presentation of T1D-associated autoantigenic peptides may contribute to the pathogenesis of T1D.

Family-based association study of HLA class II with type 1 diabetes in Moroccans

BACKGROUND

The T1D is a multifactorial disease; with a strong genetic control. The human leukocyte antigen (HLA) system plays a crucial role in the autoimmune process leading to childhood diabetes. About 440,000 of the childhood population of the world (1.8 billion children under 14 years of age), have type 1 diabetes, and each year an additional 70,000 develop this disorder. The objective of this study was to investigate the distribution of HLA class II in Moroccan families of diabetic children to identify susceptibility alleles of the Moroccan population.

SUBJECTS AND METHODS

We included in this study, Moroccan families who have at least one child with T1D. The age of onset of diabetes was less than 15 years. HLA class II (DRB1* and DQB1*) was carried out by molecular biology techniques (PCR-SSP and PCR-SSO). The FBAT test (family-based association test) was used to highlight the association between T1D and the HLA-DRB1* and -DQB1* polymorphism.

RESULTS

The association of HLA class II (DRB1*, DQB1*) in type 1 diabetes was analyzed in fifty-one Moroccan families, including 90 diabetics. The results revealed that the most susceptible haplotypes are the DRB1*03:01-DQB1*02:01, DRB1*04:05-DQB1*03:02 (Z=3.674, P=0.000239; Z=2.828, P=0.004678, respectively). And the most protective haplotype is the DRB1*15-DQB1*06.

CONCLUSION

This is the first family-based association study searching for an association between HLA class II and T1D in a Moroccan population. Despite the different ethnic groups forming Morocco, Moroccan diabetics share the most susceptible and protective HLA haplotypes with other Caucasians populations, specifically the European and Mediterranean populations.

Structural Characteristics of HLA-DQ that May Impact DM Editing and Susceptibility to Type-1 Diabetes

Autoreactive CD4+ T cells initiate the chronic autoimmune disease Type-1 diabetes (T1D), in which multiple environmental and genetic factors are involved. The association of HLA, especially the DR-DQ loci, with risk for T1D is well documented. However, the molecular mechanisms are poorly understood. In this review, we explore the structural characteristics of HLA-DQ and the role of HLA-DM function as they may contribute to an understanding of autoreactive T cell development in T1D.

HLA shared epitope and ACPA: just a marker or an active player?

Autoantibody production is genetically controlled and anti-citrullinated protein/peptide antibodies (ACPA) are not an exception to the rule. ACPA are highly specific markers of rheumatoid arthritis (RA) and are also associated with a more severe disease course. The production of ACPA is almost invariably observed in HLA-shared epitope (SE) positive patients. The DRB1 alleles sharing SE are those conferring susceptibility to RA. SE alleles behave like immune response genes, controlling both the specificity and the amount of ACPA produced. These data suggest a role of SE in the presentation of citrullinated antigens. The ability of SE alleles to bind selectively to citrullinated sequences as compared to the native counterparts has been demonstrated in the case of peptides derived from several joint associated proteins (vimentin, fibrinogen and cartilage intermediate-layer protein). On the contrary, EBV-derived citrullinated peptides do not display a biologically relevant binding to SE alleles even if the immune response to VCPs is under the genetic control of these alleles (namely *0401 and *0404). Thus, the presentation of citrullinated epitopes does not represent the only molecular mechanisms underlying the HLA-DRB1 effect on ACPA production.

Insights on personalized medicine from Ayurveda

The "omics" era of research has provided vital information on the genetic and biochemical diversity of individuals. This has lead to the emergence of "personalized medicine," wherein one aims to design specific drugs for individual patients or subtypes of patients. Indeed, the ongoing patent wars on this matter, suggest that personalized medicine represents a major goal for today's pharmaceutical industries. Although the concept of personalized medicine is new to modern medicine, it is a well-established concept in Ayurveda, the traditional system of Indian medicine that is still being practiced. Therefore, this article discusses topics that are crucial for the advancement of modern personalized medicine. These topics include disease susceptibility, disease subtypes, and Ayurvedic therapeutics. First, we explain how Ayurveda, Traditional Chinese Medicine, and Traditional Korean medicine or Sasang Constitutional medicine; conceptualize disease susceptibility and disease subtypes. Next, we focus on conceptual similarities between molecular medicine and Ayurvedic concepts of disease susceptibility and disease subtypes. For each topic, we explain the relevant experimental evidence reported in the literature. We also propose new hypotheses and suggest experimental approaches for their testing and validation.

Shared HLA Class II in Six Autoimmune Diseases in Latin America: A Meta-Analysis

The prevalence and genetic susceptibility of autoimmune diseases (ADs) may vary depending on latitudinal gradient and ethnicity. The aims of this study were to identify common human leukocyte antigen (HLA) class II alleles that contribute to susceptibility to six ADs in Latin Americans through a meta-analysis and to review additional clinical, immunological, and genetic characteristics of those ADs sharing HLA alleles. DRB1(∗)03:01 (OR: 4.04; 95%CI: 1.41-11.53) was found to be a risk factor for systemic lupus erythematosus (SLE), Sjögren's syndrome (SS), and type 1 diabetes mellitus (T1D). DRB1(∗)04:05 (OR: 4.64; 95%CI: 2.14-10.05) influences autoimmune hepatitis (AIH), rheumatoid arthritis (RA), and T1D; DRB1(∗)04:01 (OR: 3.86; 95%CI: 2.32-6.42) is a susceptibility factor for RA and T1D. Opposite associations were found between multiple sclerosis (MS) and T1D. DQB1(∗)06:02 and DRB1(∗)15 alleles were risk factors for MS but protective factors for T1D. Likewise, DQB1(∗)06:03 allele was a risk factor for AIH but a protective one for T1D. Several common autoantibodies and clinical associations as well as additional shared genes have been reported in these ADs, which are reviewed herein. These results indicate that in Latin Americans ADs share major loci and immune characteristics.

The influence of the HLA-DRB, HLA-DQB and polymorphic positions of the HLA-DRβ1 and HLA-DQβ1 molecules on risk of Iranian type 1 diabetes mellitus patients

Type 1 Diabetes mellitus (T1D) is an autoimmune and multifactorial disease. HLA-DRB1 and DQB1 loci have the strongest association with T1D. This study aimed at investigating (i) susceptibility or protection of alleles, genotypes and haplotypes of HLA-DRB1 and DQB1 loci; and (ii) highly polymorphic amino acid residues of HLA-DRβ1 and DQβ1 in 105 Iranian T1D patients and 100 controls. The results indicated that DRB1*04:01, 03:01, DQB1*03:02, 02:01 alleles, DRB1*03:01/04:01, 03:01/13:03, DQB1*02:01/03:02 genotypes, DRB1*04:01-DQB1*03:02, DRB1*03:01-DQB1*02:01, DRB1*07:01-DQB1*03:03 haplotypes had positive association with T1D. In contrast, HLA-DRB1*15:01, 13:01, DQB1*03:01, 06:01 alleles, DRB1*11:01/15:01, DQB1*03:01/06:01, 03:01/05:01 genotypes and DRB1*15:01-DQB1*06:01, DRB1*11:01-DQB1*03:01 haplotypes had negative association with T1D. Analysis of amino acid sequence of HLA-DRβ1 and DQβ1 revealed that DRβ1(Lys71+) and DQβ1(Asp57-) were significantly more frequent in patients than in controls and had a positive effect in the development of T1D. Haplotype analysis demonstrated that HLA-DRB1(Lys71+) allele provided major susceptibility for T1D, and DQβ1(Asp57-) had an additive effect. We designed an allele-specific primer to develop an easy, quick and cost-benefit method to detect the DRβ1(Lys71+) . This method can identify all 114 DRB1 alleles encoding DRβ1(Lys71+) by three PCR reactions. The PcPPV and PcNPV were also calculated to determine the impact of HLA genotype testing at amino acid positions. It showed that the DRβ1(Lys71+/+) genotype carrier had 1% absolute risk of developing T1D.

Vogt-Koyanagi-Harada disease, diabetes mellitus, and psoriasis in a child

PURPOSE

To report a case of a child with near-simultaneous onset of Vogt Koyanagi Harada disease (VKH) and insulin-dependent diabetes mellitus (IDDM).

DESIGN

Interventional case report.

METHODS

An 11-year-old child with known psoriasis presented with headache and bilateral granulomatous panuveitis. Nine weeks later, he presented with diabetic ketoacidosis and IDDM. Diffuse choroidal depigmentation followed within months. HLA was positive for DRB1*0405. Despite aggressive local and systemic therapy, the ocular disease was complicated by bilateral cataracts, angle closure glaucoma, and choroidal neovascularization.

RESULTS

The patient is currently pseudophakic in one eye and aphakic in the other, with best-corrected visual acuity of 6/24 and 6/5, respectively.

CONCLUSIONS

VKH may present in children with panuveitis in the setting of other autoimmune disorders. Treating such patients is complicated by the need to minimize systemic corticosteroid use. A combination of local therapy and systemic steroid-sparing agents should be the mainstay of treatment.

Expanded dog leukocyte antigen (DLA) single nucleotide polymorphism (SNP) genotyping reveals spurious class II associations

The dog leukocyte antigen (DLA) system contains many of the functional genes of the immune system, thereby making it a candidate region for involvement in immune-mediated disorders. A number of studies have identified associations between specific DLA class II haplotypes and canine immune hemolytic anemia, thyroiditis, immune polyarthritis, type I diabetes mellitus, hypoadrenocorticism, systemic lupus erythematosus-related disease complex, necrotizing meningoencephalitis (NME) and anal furunculosis. These studies have relied on sequencing approximately 300 bases of exon 2 of each of the DLA class II genes: DLA-DRB1, DLA-DQA1 and DLA-DQB1. In the present study, an association (odds ratio=4.29) was identified by this method between Weimaraner dogs with hypertrophic osteodystrophy (HOD) and DLA-DRB1∗01501. To fine map the association with HOD, a genotyping assay of 126 coding single nucleotide polymorphisms (SNPs) from across the entire DLA, spanning a region of 2.5 Mb (3,320,000-5,830,000) on CFA12, was developed and tested on Weimaraners with HOD, as well as two additional breeds with diseases associated with DLA class II: Nova Scotia duck tolling retrievers with hypoadrenocorticism and Pug dogs with NME. No significant associations were found between Weimaraners with HOD or Nova Scotia duck tolling retrievers with hypoadrenocorticism and SNPs spanning the DLA region. In contrast, significant associations were found with NME in Pug dogs, although the associated region extended beyond the class II genes. By including a larger number of genes from a larger genomic region, a SNP genotyping assay was generated that provides coverage of the extended DLA region and may be useful in identifying and fine mapping DLA associations in dogs.

Human leukocyte antigen class II and type 1 diabetes in Latin America: a combined meta-analysis of association and family-based studies

Conclusions from association studies could be spurious because of population stratification; therefore we combined association with family studies seeking to confirm which human leukocyte antigen (HLA) class II alleles/haplotypes were associated with type 1 diabetes (T1D) in the admixed Latin America. By calculating the effect summary odds ratios (OR) and their 95% confidence intervals (95% CI), data up to June 2010 showed that risk associations were observed with DRB1*0301-DQA1*0501-DQB1*0201 (odds ratio [OR]: 7.51; 95% confidence interval [CI]: 3.69-15.25) and DQB1*0302 in presence of DRB1*0405 (OR: 11.64; 95% CI: 3.15-43.01) or DRB1*0401 (OR: 5.85; 95% CI: 3.07-11.14). In contrast, DRB1*0404-DQB1*0302 had a nonsignificant TID risk (OR: 2.23; 95% CI: 0.91-5.43). T1D protective associations were observed with DRB1*11-DQA1*0501-DQB1*0301 (OR: 0.24; 95% CI: 0.1-0.56) and DRB1*15-DQA1*0102-DQB1*0602 (OR: 0.35; 95% CI: 0.17-0.73). These results were similar to those observed in Caucasian and other populations, thus highlighting the primary role of class II HLA in T1D regardless of ethnicity. A DRB1*04 risk hierarchy was confirmed with the DRB1*0405 being in the top. A binding prediction analysis disclosed possible receptor-ligand interactions in the HLA-antigenic peptide complex.

Selected human leukocyte antigen class II polymorphisms and risk of adult glioma

Few studies have examined the relationship between human leukocyte antigen (HLA) polymorphisms and adult glioma, particularly at class II loci. We evaluated the association between selected HLA class II polymorphisms and adult glioma in a large, hospital-based case-control study, using unconditional logistic regression. DQB1 06 (OR=1.67, 95% CI=1.17-2.39) and DRB1 13 (OR=1.69, 95% CI=1.08-2.64) alleles were associated with an increased risk of glioma, while the DQB1 05 allele showed an inverse association (OR=0.63, 95% CI=0.43-0.93). These results, which were of borderline significance once controlled for the false discovery rate, suggest a potential role for the DQB1 06, DQB1 05, and DRB1 13 alleles in glioma susceptibility.

The importance of a genetic component in longitudinal birth cohorts

The risks of most common health and developmental outcomes are contributed to by a combination of genetic and environmental factors. Understanding of ways in which genes influence such outcomes, and especially of how their interaction with environmental factors affects health and development should lead to the identification of causal pathways and thence appropriate intervention strategies.

Impact of HLA on the underlying primary diseases in Turkish patients with end-stage renal disease

The number of patients with end stage renal disease (ESRD) is increasing faster than the number of renal transplantations performed per year worldwide. Of the primary diseases leading to ESRD, diabetic nephropathy is the leading cause. The purpose of the present study is to investigate the association of HLA with the primary diseases leading to ESRD in Turkish patients. A total of 3230 individuals comprising 587 ESRD patients and 2643 healthy controls were enrolled into the study. Class I HLA-A, -B typing was performed by CDC method, while class II HLA-DRB1 typing was performed by low resolution PCR-SSP. We found a significant negative association between almost all A locus antigens and primary disease groups classified as chronic glomerulonephritis and hypertensive nephrosclerosis (p < 0.05). HLA-B58 and HLA-DRB1*03 significantly correlated with amyloidosis and diabetic nephropathy, respectively. Determination of HLAs as risk factors for primary diseases leading to ESRD might be beneficial in preventing progression to ESRD and recurrence of the primary disease post-transplantation.

Association of alleles at polymorphic sites in the Osteopontin encoding gene in young type 1 diabetic patients

The Osteopontin (OPN) encoding gene, SPP1, can be considered as a candidate for genetic susceptibility to type 1 diabetes (T1D) because of its known function in immune response and inflammation. This work aimed to evaluate the role of SPP1 gene in susceptibility to T1D. Patients (238: 130 male, 108 female) and unaffected adult control individuals (137: 68 males and 69 females) have been genotyped for three variants in the SPP1 gene: -156 (G/GG) and -66 (T/G) in the promoter and a biallelic ins/del variant (TG/TGTG) at +245 in the first intron. The G allele at the -66 SNP had significantly higher frequency in controls than T1D patients. Interestingly, case-control comparison in males showed no significant association, whereas the association was confirmed in females. These results suggest that SPP1 can play a role as susceptibility gene, possibly by a sex-specific mechanism acting in the autoimmune process.

The non-inherited maternal HLA haplotype affects the risk for type 1 diabetes

The aim was to test the hypothesis that the human leucocyte antigen (HLA) haplotype that is not inherited from the mother, that is, the non-inherited maternal antigen (NIMA) affects the risk for type 1 diabetes (T1D). A total of 563 children with T1D and 286 non-diabetic control children from Sweden were genotyped for DRB1, DQA1 and DQB1 alleles. The frequency of positively (DR4-DQA1*0301-B1*0302 and DR3-DQA1*0501-B1*0201), negatively (DR15-DQ A1*0102-B1*0602) or neutrally (all other) T1D associated HLA haplotypes were compared between NIMA and non-inherited paternal antigen (NIPA). All comparisons were carried out between HLA-matched patients and controls. The frequency of positively associated NIMA was higher among both DR4/X-positive healthy individuals compared wit DR4/X-positive patients (P < 0.00003) and DR3/X-positive healthy individuals compared with DR3/X-positive patients (P < 0.009). No such difference was observed for NIPA. High-risk NIMA was increased compared to NIPA among healthy DR3/X- and DR4/X-positive children (P < 0.05). There was no difference in frequency of positively associated haplotypes between patient NIMA and NIPA. The NIMA but not the NIPA affects the risk for T1D, suggesting that not only the inherited but also non-inherited maternal HLA haplotypes, perhaps through microchimerism or other mechanisms, may influence the risk for the disease.

Joint genetic susceptibility to type 1 diabetes and autoimmune thyroiditis: from epidemiology to mechanisms

Type 1 diabetes (T1D) and autoimmune thyroid diseases (AITD) frequently occur together within families and in the same individual. The co-occurrence of T1D and AITD in the same patient is one of the variants of the autoimmune polyglandular syndrome type 3 [APS3 variant (APS3v)]. Epidemiological data point to a strong genetic influence on the shared susceptibility to T1D and AITD. Recently, significant progress has been made in our understanding of the genetic association between T1D and AITD. At least three genes have been confirmed as major joint susceptibility genes for T1D and AITD: human leukocyte antigen class II, cytotoxic T-lymphocyte antigen 4 (CTLA-4), and protein tyrosine phosphatase non-receptor type 22. Moreover, the first whole genome linkage study has been recently completed, and additional genes will soon be identified. Not unexpectedly, all the joint genes for T1D and AITD identified so far are involved in immune regulation, specifically in the presentation of antigenic peptides to T cells. One of the lessons learned from the analysis of the joint susceptibility genes for T1D and AITD is that subset analysis is a key to dissecting the etiology of complex diseases. One of the best demonstrations of the power of subset analysis is the CTLA-4 gene in T1D. Although CTLA-4 showed very weak association with T1D, when analyzed in the subset of patients with both T1D and AITD, the genetic effect of CTLA-4 was significantly stronger. Gene-gene and genetic-epigenetic interactions most likely play a role in the shared genetic susceptibility to T1D and AITD. Dissecting these mechanisms will lead to a better understanding of the etiology of T1D and AITD, as well as autoimmunity in general.

Association of narcolepsy-cataplexy with HLA-DRB1 and DQB1 in Mexican patients: a relationship between HLA and gender is suggested

Background

Narcolepsy-cataplexy is characterized by excessive daytime sleepiness with recurrent episodes of irresistible sleep, cataplexy, hallucinations and sleep paralysis. Its aetiology is unknown, but it is positively associated with the human leukocyte antigens (HLA) in all studied populations. The purpose of the present study was to investigate the association of HLA class II DRB1/DQB1 alleles with narcolepsy-cataplexy in Mexican Mestizo patients.

Methods

This is a case-control study of consecutive patients and ethnically matched controls. We included 32 patients diagnosed with typical narcolepsy-cataplexy, of the National Institute of Neurology, of the Institute of Psychiatry and at the Center of Narcolepsy at Stanford University. As healthy controls, 203 Mexican Mestizos were included. DRB1 alleles were identified using sequence based typing. A PCR-SSOP reverse dot blot was used for DQB1 typing. Allele frequency was calculated by direct counting and the significance of the differences was assessed using the Yates Chi square. Odds ratio and confidence intervals were evaluated.

Results

HLA-DRB1*1501 (OR = 8.2; pc < 0.0001) and DQB1*0602 (OR = 8.4; pc < 0.0001) were found positively associated with narcolepsy. When deleting DQB1*0602+ patients from the analysis, DQB1*0301 was also found increased (OR = 2.7; p = 0.035; pc = NS). DQB1*0602/DQB1*0301 genotype was present in 15.6% of the cases (OR = 11.5; p = 0.00035), conferring a high risk. DRB1*0407 (OR = 0.2; p = 0.016 pc = NS) and DQB1*0302(OR = 0.4; p = 0.017, pc = NS) were found decreased in the patients. The gender stratification analysis showed a higher risk in females carrying DRB1*1501 (OR = 15.8, pc < 0.0001) and DQB1*0602 (OR = 19.8, pc < 0.0001) than in males (OR = 5.0 for both alleles; p = 0.012, pc = NS for DRB1 & p = 0.0012, pc = 0.017 for DQB1). The susceptibility alleles found in Mexicans with narcolepsy are also present in Japanese and Caucasians; DRB1*04 linked protection has also been shown in Koreans. A stronger HLA association is suggested in females, in accordance with the sexual dimorphism claimed previously.

Conclusion

This knowledge may contribute to a better understanding of the disease pathogenesis in different populations. The evaluation of the risk to develop narcolepsy-cataplexy in carriers of the described alleles/genotypes may also be possible. A larger sample should be analysed in Mexican and in other Hispanic patients to confirm these results.

The X chromosome in female-predominant autoimmune diseases

Autoimmune diseases affect approximately 5% of the population in Western countries, with high female predominance. Family and twins studies have demonstrated that genetic factors are crucial determinants of susceptibility to autoimmune disease, but no specific genes have yet been identified. Recent studies indicate that X chromosome abnormalities, such as monosomy rates and inactivation patterns, occur in a number of female-predominant autoimmune diseases. We will review herein the most recent evidence on the role of the X chromosome in loss of tolerance and discuss its potential implications. Future studies will identify the X chromosome regions containing candidate genes for autoimmune susceptibility.

Evidence for association between vitamin D receptor BsmI polymorphism and type 1 diabetes in Japanese

Type 1 diabetes is considered to be T-helper 1 (Th1) type autoimmune disease. Because the vitamin D receptor is expressed on CD4+T cells and is known to affect cytokine responses, several groups have investigated the association between the vitamin D receptor gene BsmI polymorphism and type 1 diabetes. However, this issue is still controversial; therefore, we examined this gene polymorphism in a large number of type 1 diabetic patients as a multi-center collaborative study in Japan. A total of 1,373 subjects, including 774 cases and 599 control subjects of Japanese origin, were studied. The frequency of carriers of the BB genotype in type 1 diabetic patients was significantly higher than that in controls (p<0.01, odds ratio 3.65). Moreover, IFN-gamma production upon anti-CD3 stimulation in the BB genotype group was significantly higher than that in the Bb and bb genotype groups (p<0.05), suggesting that the polyclonal T cell response in BB genotype patients is Th1 dominant. Based upon these results, we propose that it may be worthwhile to focus on subjects with the BB genotype of this gene polymorphism as having high risk for type 1 diabetes.

Rotavirus infections and development of type 1 diabetes: an evasive conundrum

Type 1 diabetes (T1D) is an organ-specific autoimmune disease caused by altered immune tolerance to specific proteins leading to a selective destruction of insulin-producing beta cells in genetically predisposed individuals. T1D is likely to be triggered by environmental factors, including virus infections in genetically predisposed individuals. Rotaviruses are the main cause of severe diarrhea among children worldwide, but they seem to have a role also in T1D induction. Epidemiological data may be consistent with a similar hypothesis. Mechanisms hypothesized include molecular mimicry, bystander activation (with or without epitope spreading), and viral persistence. In this review the authors analyze the factors accounting for rotavirus ability to prime islet autoimmunity and cause T1D. A thorough comprehension of their potential pathogenetic mechanisms may allow preventive strategies to be designed.

HLA class II polymorphisms associated with the physiologic characteristics defined by Traditional Chinese Medicine: linking modern genetics with an ancient medicine

OBJECTIVES

The aim of this study was to test whether human leukocyte antigen (HLA) polymorphism contributes to the physical constitutions classified in Traditional Chinese Medicine (TCM).

DESIGN

Seven hundred six (706) individuals of the Han ethnic group inhabiting South China were classified into 7 TCM constitution groups, according to the criteria described in Theories of Physical Constitutions of Traditional Chinese Medicine, and the distributions of HLA-DRB1, DPB1, and DQB1 were investigated using the polymerase chain reaction-sequencing-based typing method.

RESULTS

The allele frequencies of DPB1*0501 in the Yin-deficiency group, DRB1*09012 in the Phlegm-wetness group, and DQB1*03032 in the Qi-deficiency and Phlegm-wetness groups were significantly different from that of the corresponding alleles in the Normality constitution, suggesting those alleles might be group-specific alleles and thus related to a particular constitution. Based on our analysis of serological groups of HLA, the associations of DR*04 with the Blood-stasis group and DQ*09 with the Qi-deficiency and Phlegm-wetness groups were observed.

CONCLUSIONS

This was the first study to systematically investigate the relationship between HLA and TCM constitution using a high-resolution typing technique. The results suggested a genetic basis for the classification of physical constitution in TCM. This study laid the foundation, for the first time ever, toward gaining insight into the theory of traditional medicine using modern biological approaches.

Screening by anti-endomysium antibodies for celiac disease in Tunisian children with type 1 diabetes mellitus

AIM

Celiac disease (CD) and type 1 diabetes mellitus (DM1) can frequently coexist, presumably due to a common genetic predisposition. The present study was designed to evaluate the frequency of CD among Tunisian children with DM1.

PATIENTS AND METHODS

A total of 205 diabetic children (92 girls, 113 boys, age range 6 months-15 years, median 11 years) were screened for CD by determination of IgA anti-endomysium antibodies (EMA).

RESULTS

EMA were positive in 17 out of 205 (8.3%) children with DM1. The median age of DM1 at onset was significantly lower in patients with EMA than those without EMA (P<10(-7)). In 13 of 17 EMA-positive patients, duodenal biopsy could be performed and a destructive type of CD was confirmed in 11 of them: 8 patients showed total villous atrophy, 3 patients showed a partial villous atrophy. The other two patients showed a normal histological picture with normal number of intraepithelial lymphocytes. Parents of the remaining EMA-positive children refused endoscopy. Thus the prevalence of biopsy-proven CD was 5.3% (11/205). It was 7.6% (7/92) in girls and 3.5% (4/113) in boys but the difference was not statistically significant. Seventy three percent of patients with CD were asymptomatic.

CONCLUSIONS

The prevalence of clinically unrecognized CD, found by EMA screening, is high in Tunisian children with DM1. We suggest that children with diabetes should be screened for CD.

Calpains and their multiple roles in diabetes mellitus

Type 2 diabetes mellitus (T2DM) can lead to death without treatment and it has been predicted that the condition will affect 215 million people worldwide by 2010. T2DM is a multifactorial disorder whose precise genetic causes and biochemical defects have not been fully elucidated, but at both levels, calpains appear to play a role. Positional cloning studies mapped T2DM susceptibility to CAPN10, the gene encoding the intracellular cysteine protease, calpain 10. Further studies have shown a number of noncoding polymorphisms in CAPN10 to be functionally associated with T2DM while the identification of coding polymorphisms, suggested that mutant calpain 10 proteins may also contribute to the disease. Here we review recent studies, which in addition to the latter enzyme, have linked calpain 5, calpain 3, and its splice variants, calpain 2 and calpain 1 to T2DM-related metabolic pathways along with T2DM-associated phenotypes, such as obesity and impaired insulin secretion, and T2DM-related complications, such as epithelial dysfunction and diabetic cataract.

A new expression of diabetes: double diabetes

Diabetes is on the increase worldwide. The incidence of both type 1 and type 2 diabetes has shown a rise, in parallel with a notable increase in the incidence of a new expression of the disease in children and adolescents, with the characteristics of a mixture of the two types of diabetes, and referred to as 'double diabetes'. Insulin resistance and obesity, together with the presence of markers of pancreatic autoimmunity - namely, autoantibodies to islet cell antigens - typically define this condition. However, recognition of double diabetes can pose problems. In most cases, a reduction in the 'autoimmune load' and an increase in the 'metabolic load' are helpful for attaining a correct diagnosis in a diabetic child.

Genetic control of alternative splicing in the TAP2 gene: possible implication in the genetics of type 1 diabetes

The transporter 2, ATP-binding cassette, subfamily B (TAP2) is involved in the transport of antigenic peptides to HLA molecules. Coding TAP2 polymorphisms shows a strong association with type 1 diabetes, but it is not clear whether this association may be entirely due to linkage disequilibrium with HLA DR and DQ. Functionally, rat Tap2 nonsynonymous single-nucleotide polymorphisms (nsSNPs) confer differential selectivity for antigenic peptides, but this was not shown to be the case for human TAP2 nsSNPs. In the human, differential peptide selectivity is rather conferred by two splicing isoforms with alternative carboxy terminals. Here, we tested the hypothesis that alleles at the coding SNPs favor different splicing isoforms, thus determining peptide selectivity indirectly. This may be the basis for independent contribution to the type 1 diabetes association. In RNA from heterozygous lymphoblastoid lines, we measured the relative abundance of each SNP haplotype in each isoform. In isoform NM_000544, the G (Ala) allele at 665 Thr>Ala (rs241447) is more than twice as abundant as A (Thr) (GA = 2.2 +/- 0.4, P = 1.5 x 10(-4)), while isoform NM_018833 is derived almost exclusively from chromosomes carrying A (AG = 18.1 +/- 5.6, P = 2.04 x 10(-7)). In 889 Canadian children with type 1 diabetes, differential transmission of parental TAP2 alleles persisted (P = 0.011) when analysis was confined to chromosomes carrying only DQ*02 alleles, which mark a conserved DR-DQ haplotype, thus eliminating most of the variation at DR-DQ. Thus, we present evidence of TAP2 association with type 1 diabetes that is independent of HLA DR-DQ and describe a plausible functional mechanism based on allele dependence of splicing into isoforms known to have differential peptide selectivities.