Type 1 Diabetes Susceptibility Research Articles

Genetic variants in long noncoding RNA H19 and MEG3 confer risk of type 2 diabetes in an Iranian population

PurposeLong-noncoding RNAs (lncRNAs) have been reported to regulate glucose homeostasis and insulin synthesis and secretion. However, the association of genetic variants of lncRNAs and type 2 diabetes (T2D) has not been evaluated. Therefore, in the present study we investigated the association between H19 rs217727 and H19 rs3741219 variants and MEG3 rs7158663 polymorphism with T2D susceptibility. Materials and methodsThe study population consists of 969 subjects including 496 T2D patients and 473 non-diabetic age and sex-matched controls. The H19 and MEG3 variants genotyping were performed by PCR-RFLP method. ResultsOur results revealed that the T allele of rs217727 was more frequent in T2D group compared with controls (P = 0.007, OR = 1.1, 95% CI:1.02–1.18). Moreover, the rs217727-TT genotype was significantly associated with T2D after adjustment for age, BMI and lipid levels (P = 0.041, OR = 1.53, 95% CI: 1.01–2.32). However, no significant difference was detected for allele or genotype frequencies of H19 rs3741219 between T2D and controls (P = 0.71). Furthermore, the findings showed that the AA genotype of MEG3 rs7158663 was associated with significantly increased risks of T2D compared with the GG genotype (P = 0.026, OR = 1.79, 95% CI: 1.07–2.99). The results remained significance after analysis by logistic regression (P = 0.033, Adjusted OR = 1.72, 95% CI: 1.04–2.84). Finally, bioinformatics analysis showed that these SNPs could alter local RNA folding structure and also the miRNA-lncRNA interactions. ConclusionsOur findings provided the evidence of significant association between H19 rs217727-TT and MEG3 rs7158663-AA genotypes with T2D susceptibility.

Genetic variants of resistin and its plasma levels: Association with obesity and dyslipidemia related to type 2 diabetes susceptibility

Resistin, an adipokine, is involved in obesity and Type 2 Diabetes (T2D). The current study evaluates the association between RETN polymorphisms (−638 G/A, −420C/G & −358 G/A) and the risk towards T2D. Controls and T2D patients were enrolled from Gujarat, India. Polymorphisms of RETN were genotyped by Polymerase Chain Reaction-Restriction Fragment Length Polymorphism. For the genotype-phenotype correlation analysis Fasting Blood Glucose (FBG), Body Mass Index (BMI) and plasma lipid profile were used. Plasma levels of resistin were assayed by ELISA. Our study suggests an association of RETN −420C/G polymorphism with T2D risk. The CC genotype of RETN −420C/G polymorphism was found to be associated with FBG, BMI, and total cholesterol. Plasma resistin levels were found to be significantly increased in diabetic patients as compared to controls. Our findings suggest −420C/G polymorphism of RETN as an important factor which could pose a powerful risk towards T2D susceptibility.

Investigating the Role of CD137 Ligand in the Pathogenesis of Type 1 Diabetes

Pathogenesis of type 1 diabetes (T1D) involves various interactions between genetic and environmental factors. The gene encoding the co-stimulatory molecule CD137 is located within the Idd9.3 T1D susceptibility locus and contributes to diabetes progression in NOD mice. We have previously shown that CD137 expression in T cells has dual functions: CD4+CD137+ T cells negatively regulate T1D development while CD8+CD137+ T cells showed potent diabetogenecity. The protective function of CD137 in CD4+ T cells is likely due to the significant amounts of soluble CD137 (CD137) produced by Foxp3+ Tregs. The interaction between CD137 and its ligand (CD137L) induces two signaling pathways, forward one driven by CD137 and the reverse signaling mediated by CD137L, both of which modulate T cell function. Here, we study the impact of CD137L deficiency on T1D to gain further insight into disease pathogenesis. We successfully generated a mouse strain with the NOD background and knockout of the gene encoding CD137L (Tnfsf9) using CRISPR/Cas9 technology. Relative to wild type NOD, Tnfsf9-/- mice showed significant delay in T1D development, less islet-infiltrating autoreactive CD8 T cells, reduced high-avidity IGRP autoreactive CD8 T cells in the spleen and pancreatic lymph node, and less inflamed islets. Interestingly, we detect significant increase in serum levels of sCD137. Furthermore, we could not detect differences in CD137+ Treg populations between NOD and Tnfsf9-/- mice. In bone marrow transfer experiments, CD137L deficiency in either hosts or donors was able to suppress T1D development. Tnfsf9-/- and wild type T cells showed similar capacity to induce T1D in NOD.Rag1-/- recipients. We are working on identifying the cellular source of increased sCD137 and the mechanism behind this elevation. We direct our efforts to understand how CD137-CD137L interaction can modulate T1D pathogenesis and how to translate the data from NOD mouse to understand the pathogenesis of human diabetes. Disclosure B. Foda: None. M.H. Forsberg: None. A.E. Ciecko: None. K.W. Mueller: None. A. Geurts: None. Y. Chen: None.

Association analysis of copy number variations in type 2 diabetes-related susceptible genes in a Chinese population.

Copy number variations (CNVs) have been implicated as an important genetic marker of common disease. In this study, we explored genetic effects of common CNVs in Type 2 diabetes (T2D) related susceptible genes in Chinese population. Seven common CNV loci were selected from genes enclosing the susceptible single nucleotide polymorphisms (SNPs) of T2D confirmed by genome-wide association studies (GWAS) and replication studies conducted in east Asia population. The CNVs and SNPs were genotyped in 504 T2D patients and 494 non-T2D controls. Cumulative effect of the positive CNV loci was measured using genetic risk score (GRS). Multiplicative and additive interaction between candidate CNV loci and SNPs were assessed. Compared with the common two copies, the deletion of nsv6360 (adjusted OR = 2.28, 95% CI 1.37-3.78, P = 0.001), nsv8414 (adjusted OR = 1.89, 95% CI 1.16-3.08, P = 0.006) and nsv1898 (adjusted OR = 1.84, 95% CI 1.19-2.84, P = 0.005) were significantly associated with increased risk of T2D (P < 0.007). Significant dose-response relationship was observed between GRS and the risk of T2D (χ2 for trend = 19.51, P < 0.001). In addition, significant additive interactions between nsv8414 and rs17584499 in PTPRD (AP = 0.60, 95% CI 0.12-1.07) and nsv1898 and rs16955379 in CMIP (AP = 0.46, 95% CI 0.01-0.91) were observed. There were three CNV loci (nsv6360, nsv8414 and nsv1898) associated with T2D, and a significant cumulative effect of these loci on the risk of T2D. The comprehensive effects of both CNVs and SNPs may provide a more useful tool for the identification of genetic susceptibility for T2D.

MtDNA Haplogroup N9a Increases the Risk of Type 2 Diabetes by Altering Mitochondrial Function and Intracellular Mitochondrial Signals.

Mitochondrial DNA (mtDNA) haplogroups have been associated with the incidence of type 2 diabetes (T2D); however, their underlying role in T2D remains poorly elucidated. Here, we report that mtDNA haplogroup N9a was associated with an increased risk of T2D occurrence in Southern China (odds ratio 1.999 [95% CI 1.229-3.251], P = 0.005). By using transmitochondrial technology, we demonstrated that the activity of respiratory chain complexes was lower in the case of mtDNA haplogroup N9a (N9a1 and N9a10a) than in three non-N9a haplogroups (D4j, G3a2, and Y1) and that this could lead to alterations in mitochondrial function and mitochondrial redox status. Transcriptome analysis revealed that OXPHOS function and metabolic regulation differed markedly between N9a and non-N9a cybrids. Furthermore, in N9a cybrids, insulin-stimulated glucose uptake might be inhibited at least partially through enhanced stimulation of ERK1/2 phosphorylation and subsequent TLR4 activation, which was found to be mediated by the elevated redox status in N9a cybrids. Although it remains unclear whether other signaling pathways (e.g., Wnt pathway) contribute to the T2D susceptibility of haplogroup N9a, our data indicate that in the case of mtDNA haplogroup N9a, T2D is affected, at least partially through ERK1/2 overstimulation and subsequent TLR4 activation.

Selenium and Sex: Competition Between Brain and Testes for Selenium Results in Male‐ Specific Consequences in Mice and Men

Selenium (Se) is essential for normal neurological development and male fertility in mammals, setting the stage for competition between brain and testes when Se is limiting or its distribution is perturbed. Se supplementation studies in humans, and genetic knockout (KO) of selenium transport and recycling proteins in mice, unveiled the surprising finding that males exhibit more severe consequences than females when selenium homeostasis is altered. Se is also critical for thyroid hormone action, with implications for many downstream effects on endocrine and metabolic pathways. In one Se supplementation study in humans, an increased risk of type 2 diabetes (T2D) was reported in men with high baseline Se. However, other studies found no correlation between increased Se and T2D susceptibility, and the discrepancies in these human trials are controversial. The objective of our current studies is to elucidate the mechanisms underlying the sex specific differences in phenotype observed following disruption of the Se transport and recycling pathways in mice, the effects of varying dietary Se in combination with genetic KO, and the implications for human dietary Se requirements. Mice with KO of the Se recycling enzyme, selenocysteine lyase (Scly), exhibit metabolic syndrome that is more pronounced in males. Double KO (DKO) of Scly and the Se transport protein, Selenoprotein P (Sepp1) resulted in low viability and severe neurological deficits, including seizures. These traits are also more pronounced in males. Strikingly, while female DKO mice exhibit milder neurological deficits, they develop hallmarks of metabolic syndrome not seen in male DKO mice. Pre‐pubescent castration of male mice reversed the DKO neurological phenotype and partially attenuated the Scly KO metabolic phenotype. Assessment of brain and testes Se levels in these mice suggests that competition for available Se between these two tissues is a significant contributor to the observed phenotypes. However, preliminary data from testosterone replacement studies indicate that there are also hormone‐dependent mechanisms at play. These studies unveil novel insights into the complex mechanisms involved in Se distribution and utilization, and may be informative regarding sex specific Se requirements in humans.Support or Funding InformationSupported by grants NIH NIMHD G12MD007601, and NIH NIDDK R01DK047320 to MJB.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.

A peripheral blood transcriptomic signature predicts autoantibody development in infants at risk of type 1 diabetes.

Autoimmune-mediated destruction of pancreatic islet β cells results in type 1 diabetes (T1D). Serum islet autoantibodies usually develop in genetically susceptible individuals in early childhood before T1D onset, with multiple islet autoantibodies predicting diabetes development. However, most at-risk children remain islet-antibody negative, and no test currently identifies those likely to seroconvert. We sought a genomic signature predicting seroconversion risk by integrating longitudinal peripheral blood gene expression profiles collected in high-risk children included in the BABYDIET and DIPP cohorts, of whom 50 seroconverted. Subjects were followed for 10 years to determine time of seroconversion. Any cohort effect and the time of seroconversion were corrected to uncover genes differentially expressed (DE) in seroconverting children. Gene expression signatures associated with seroconversion were evident during the first year of life, with 67 DE genes identified in seroconverting children relative to those remaining antibody negative. These genes contribute to T cell-, DC-, and B cell-related immune responses. Near-birth expression of ADCY9, PTCH1, MEX3B, IL15RA, ZNF714, TENM1, and PLEKHA5, along with HLA risk score predicted seroconversion (AUC 0.85). The ubiquitin-proteasome pathway linked DE genes and T1D susceptibility genes. Therefore, a gene expression signature in infancy predicts risk of seroconversion. Ubiquitination may play a mechanistic role in diabetes progression.

Improved Murine MHC-Deficient HLA Transgenic NOD Mouse Models for Type 1 Diabetes Therapy Development.

Improved mouse models for type 1 diabetes (T1D) therapy development are needed. T1D susceptibility is restored to normally resistant NOD.β2m-/- mice transgenically expressing human disease-associated HLA-A*02:01 or HLA-B*39:06 class I molecules in place of their murine counterparts. T1D is dependent on pathogenic CD8+ T-cell responses mediated by these human class I variants. NOD.β2m-/--A2.1 mice were previously used to identify β-cell autoantigens presented by this human class I variant to pathogenic CD8+ T cells and for testing therapies to attenuate such effectors. However, NOD.β2m-/- mice also lack nonclassical MHC I family members, including FcRn, required for antigen presentation, and maintenance of serum IgG and albumin, precluding therapies dependent on these molecules. Hence, we used CRISPR/Cas9 to directly ablate the NOD H2-Kd and H2-Db classical class I variants either individually or in tandem (cMHCI-/-). Ablation of the H2-Ag7 class II variant in the latter stock created NOD mice totally lacking in classical murine MHC expression (cMHCI/II-/-). NOD-cMHCI-/- mice retained nonclassical MHC I molecule expression and FcRn activity. Transgenic expression of HLA-A2 or -B39 restored pathogenic CD8+ T-cell development and T1D susceptibility to NOD-cMHCI-/- mice. These next-generation HLA-humanized NOD models may provide improved platforms for T1D therapy development.

Comprehensive human leukocyte antigen genotyping of patients with type 1 diabetes mellitus in Taiwan.

Type 1 diabetes (T1D) mellitus is an autoimmune disorder involving both complex genetic and environmental factors. The incidence rates are low in Asian countries, and the specific, explanatory genetic factors underlying this have been investigated. The aim of this study was to elucidate the association of human leukocyte antigen (HLA) alleles/haplotypes with T1D in Taiwan. We performed direct comprehensive genotyping of 6 classical HLA loci (HLA-A, -B, -C, -DPB1, -DQB1, and -DRB1) to 4-digit resolution in 104 unrelated T1D patients and 504 controls. Twenty-four of the 104 patients also exhibited thyroid autoimmunity. Three major susceptibility haplotypes were identified: DRB1*03:01-DQB1*02:01 (odds ratio [OR] = 5.39 under the dominant model, P = 2.3 × 10-13 ), DRB1*04:05-DQB1*04:01 (OR = 2.44, P = 5.0 × 10-4 ), and DRB1*09:01-DQB1*03:03 (OR = 2.02, P = 1.4 × 10-3 ); one protective haplotype was identified: DRB1*08:03-DQB1*06:01 (OR = 0.10, P = 1.6 × 10-3 ). DRB1*03:01-DQB1*02:01, the major T1D susceptibility haplotype, was found at a lower frequency in T1D patients with thyroid autoimmunity. The T1D protective allele DRB1*12:02 was shown to be protective against Graves' disease in our previous report. In addition to clarifying the roles of several known T1D HLA alleles and haplotypes, we discovered that the DRB1*08:03-DQB1*06:01 haplotype is protective against T1D. The DRB1*12:02 allele protected against both T1D and Graves' disease.

Replication of MACF1 gene variant rs2296172 with type 2 diabetes susceptibility in the Bania population group of Punjab, India

Microtubule actin cross-linking factor 1 (MACF1) gene variant rs2296172 has recently been associated with type 2 diabetes (T2D). However, this variant has never been evaluated as such in Indian populations. In the present replication study, we genotyped variant rs2296172 by Taqman allele discrimination assay in 432 individuals belonging to the Bania caste group from Punjab, India. The single-nucleotide polymorphism (SNP) was evaluated for association with T2D, in a population based candidate gene case-control association study design, by estimating odds ratio with 95% confidence interval. The SNP rs2296172 of MACF1 was found to be significantly associated with T2D (p = 0.02) and odds ratio (OR) = 1.59 (1.06–2.38) at 95% CI . We further emphasize that the Indian population as such is a conglomeration of various endogamous population groups. It is critical that such replication studies be carried out in various populations to find association of variants to T2D susceptibility and understand genetic heterogeneity. However, it is important to avoid pooling of samples to address the concern of population stratification.

Combination and haplotype effects of protein tyrosine phosphatase receptor type D gene polymorphisms on type 2 diabetes in a sample of Iranian population: A pilot study

PTPRD, or protein tyrosine phosphatase receptor type D, may impact the insulin signaling on its target cells. The function mechanism of PTPRD gene is not exactly clear. However, Genetic threating variants for type 2 diabetes; rs17584499(C/T) and rs649891(A/G) in PTPRD, have been recognized by a genome-wide association. This study sought to investigate whether gene PTPRD polymorphisms were associated with type 2 diabetes (T2D) in Southeast of Iran or not. This case-control study was conducted on a total of 207 individuals with T2D and on 211 controls without any metabolic disease using a random sampling technique. We genotyped the samples using amplification refractory mutation system (ARMS) method, for PTPRD rs17584499(C/T) and Tetra-ARMS, for PTPRD rs649891 (A/G) method. The findings indicated a significant relationship between rs17584499(C/T) in the codominant (CT vs. CC, p=0.0075), dominant (p=0.0044), overdominant (p=0.018), and log-additive (p=0.0021) models and rs649891(A/G) in the codominant1 (AG vs. AA, p=0.012), codominant2 (GG vs. AA, p=0.001), dominant (p=0.0011), recessive (p=0.0002), overdominant (p=0.026), and log-additive (p=0.0001)polymorphisms of PTPRD gene and T2D. The combination effect of CC/GG, CT/AG, CT/GG, and TT/AA genotypes of the rs17584499(C/T) and rs649891 (A/G) polymorphisms were associated with the risk of T2D. In addition, haplotype analysis revealed that TA, CG, and TG haplotype of the rs17584499(C/T) and rs649891(A/G) polymorphisms could increase the T2D risk nearly 1.79-fold, 2.2-fold, and 3.03-fold, respectively. In conclusion, rs17584499(C/T) and rs649891 (A/G) polymorphisms of PTPRD gene were strongly associated with T2D susceptibility in different models, combination, and haplotype.

Linking Metabolic Disease With the PGC-1α Gly482Ser Polymorphism.

Peroxisome proliferator-activated receptor γ coactivator 1-α (PGC-1α) is a highly conserved transcriptional coactivator enriched in metabolically active tissues including liver, adipose, pancreas, and muscle. It plays a role in regulating whole body energy metabolism and its deregulation has been implicated in type 2 diabetes (T2D). A single nucleotide variant of the PPARGC1A gene (rs8192678) is associated with T2D susceptibility, relative risk of obesity and insulin resistance, and lower indices of β cell function. This common polymorphism is within a highly conserved region of the bioactive protein and leads to a single amino acid substitution (glycine 482 to serine). Its prevalence and effects on metabolic parameters appear to vary depending on factors including ethnicity and sex, suggesting important interactions between genetics and cultural/environmental factors and associated disease risk. Interestingly, carriers of the serine allele respond better to some T2D interventions, illustrating the importance of understanding functional impacts of genetic variance on PGC-1α when targeting this pathway for personalized medicine. This review summarizes a growing body of literature surrounding possible links between the PGC-1α Gly482Ser single nucleotide polymorphism and diabetes, with focus on key clinical findings, affected metabolic systems, potential molecular mechanisms, and the influence of geographical or ethnic background on associated risk.

Th17 pathway in recent-onset autoimmune diabetes

AimsEvaluate the participation of IL-17 pathway in T1D pathogenesis. T helper 17 cells are potent, highly inflammatory cells that produce interleukin 17A (IL-17A), considered a mediator of various immune disorders. However, their role in Type 1 diabetes (T1D) pathogenesis in humans is not totally elucidated. MethodsThe expression of IL-17 Receptor A (IL-17RA) in peripheral T lymphocytes and IL-17A serum levels in recent-onset patients with T1D were compared with healthy controls. IL-17A gene variants were evaluated in a greater cohort. ResultsPatients with recent-onset T1D (less than 6 months of diagnosis) exhibited lower expression of IL-17RA in CD3+ T (% of cells = 31.3% × 43.6%; p = .041) and CD4+ T cells (11.1% × 25.2%; p = .0019) and lower number of IL-17RA in CD4+ T cells (MFI = 1.16 × 4.56; p = .03) than controls. IL-17RA expression in CD8+ T cells and IL-17A serum levels were similar in both groups. The coding regions and boundary intron sequences of IL17A were sequenced. Seventeen allelic variants, including three novel variants in exon 3 (3′UTR n) were identified, but no one was associated with T1D susceptibility, as well as the resulting haplotypes and diplotypes. The expression of IL-17RA was not correlated with metabolic variables (glucose and HbA1c levels) or pancreatic autoantibodies titers. ConclusionsThe lower expression of IL-17RA in CD3+ and CD4+ T cells suggests a reduced effect of IL-17A in immune response of recent-onset T1D patients, at least at peripheral tissues. IL-17A allelic variants were not related with T1D susceptibility.

Enrichment of minor allele of SNPs and genetic prediction of type 2 diabetes risk in British population.

Type 2 diabetes (T2D) is a complex disorder characterized by high blood sugar, insulin resistance, and relative lack of insulin. The collective effects of genome wide minor alleles of common SNPs, or the minor allele content (MAC) in an individual, have been linked with quantitative variations of complex traits and diseases. Here we studied MAC in T2D using previously published SNP datasets and found higher MAC in cases relative to matched controls. A set of 357 SNPs was found to have the best predictive accuracy in a British population. A weighted risk score calculated by using this set produced an area under the curve (AUC) score of 0.86, which is comparable to risk models built by phenotypic markers. These results identify a novel genetic risk element in T2D susceptibility and provide a potentially useful genetic method to identify individuals with high risk of T2D.

Human leucocyte antigens class II allele and haplotype association with Type 1 Diabetes in Madeira Island (Portugal).

This study confirms for Madeira Island (Portugal) population the Type 1 Diabetes (T1D) susceptible and protective Human leucocyte antigens (HLA) markers previously reported in other populations and adds some local specificities. Among the strongest T1D HLA associations, stands out, as susceptible, the alleles DRB1*04:05 (OR=7.3), DQB1*03:02 (OR=6.1) and DQA1*03:03 (OR=4.5), as well as the haplotypes DRB1*04:05-DQA1*03:03-DQB1*03:02 (OR=100.9) and DRB1*04:04-DQA1*03:01-DQB1*03:02 (OR=22.1), and DQB1*06:02 (OR=0.07) and DRB1*15:01-DQA1*01:02-DQB1*06:02 (OR=0.04) as protective. HLA-DQA1 positive for Arginine at position 52 (Arg52) (OR=15.2) and HLA-DQB1 negative for Aspartic acid at the position 57 (Asp57) (OR=9.0) alleles appear to be important genetic markers for T1D susceptibility, with higher odds ratio values than any single allele and than most of the haplotypes. Genotypes generated by the association of markers Arg52 DQA1 positive and Asp57 DQB1 negative increase T1D susceptibility much more than one would expected by a simple additive effect of those markers separately (OR=26.9). This study also confirms an increased risk for DRB1*04/DRB1*03 heterozygote genotypes (OR=16.8) and also a DRB1*04-DQA1*03:01-DQB1*03:02 haplotype susceptibility dependent on the DRB1*04 allele (DRB1*04:01, OR=7.9; DRB1*04:02, OR=3.2; DRB1*04:04, OR=22.1).

Immunoglobulin M gene association with autoantibody reactivity and type 1 diabetes

Several lines of evidence show that autoimmune responses evolving in type 1 diabetes (T1D) patients include the generation of multi-reactive autoantibody (AutoAb) repertoires, but their role in T1D pathogenesis remains elusive. We tested the hypothesis that variants at the immunoglobulin heavy chain (IGH) locus are genetic determinants of AutoAbs against pancreatic antigens and contribute to T1D susceptibility. With this aim, two independent study designs were used: a case-control study and a family-based cohort comprising a total of 240 T1D patients, 172 first-degree relatives (mother and/or father), and 130 unrelated healthy controls living in Portugal. We found that three SNPs in the IGH locus show suggestive association with T1D with the highest nominal association at rs1950942 (in the IGHM-IGHJ gene region) in both the case-control study (P = 9.35E−03) and the family-based cohort (P = 3.08E−03). These SNPs were also associated with IgG AutoAbs against pancreatic antigens and with AutoAb multi-reactivity in T1D patients. Notably, we found that the SNP with the highest association with T1D susceptibility and IgG autoantibody reactivity (rs1950942) was also associated with anti-GAD IgM reactivity in T1D patients (P = 5.98E−03) and in non-affected parents (P = 4.17E−03). This finding implies that IGH association with autoreactive IgM is detectable irrespective of disease status.These results suggest that genetic variants at the IgM gene region of the IGH locus contribute to antibody autoreactivity and are associated with T1D. We propose that the control of autoantibody generation by IGH polymorphisms is a component of the complex architecture of T1D genetic susceptibility.

Common and rare exonic MUC5B variants associated with type 2 diabetes in Han Chinese.

Genome-wide association studies have identified over one hundred common genetic risk variants associated with type 2 diabetes (T2D). However, most of the heritability of T2D has not been accounted for. In this study, we investigated the contribution of rare and common variants to T2D susceptibility by analyzing exome array data in 1,908 Han Chinese genotyped with Affymetrix Axiom® Exome Genotyping Arrays. Based on the joint common and rare variants analysis of 57,704 autosomal SNPs within 12,244 genes using Sequence Kernel Association Tests (SKAT), we identified significant associations between T2D and 25 variants (9 rare and 16 common) in MUC5B, p-value 1.01×10−14. This finding was replicated (p = 0.0463) in an independent sample that included 10,401 unrelated individuals. Sixty-six of 1,553 possible haplotypes based on 25 SNPs within MUC5B showed significant association with T2D (Bonferroni corrected p values < 3.2×10−5). The expression level of MUC5B is significantly higher in pancreatic tissues of persons with T2D compared to those without T2D (p-value = 5×10−5). Our findings suggest that dysregulated MUC5B expression may be involved in the pathogenesis of T2D. As a strong candidate gene for T2D, MUC5B may play an important role in the mechanisms underlying T2D etiology and its complications.

Functional annotation of sixty-five type-2 diabetes risk SNPs and its application in risk prediction

Genome-wide association studies (GWAS) have identified more than sixty single nucleotide polymorphisms (SNPs) associated with increased risk for type 2 diabetes (T2D). However, the identification of causal risk SNPs for T2D pathogenesis was complicated by the factor that each risk SNP is a surrogate for the hundreds of SNPs, most of which reside in non-coding regions. Here we provide a comprehensive annotation of 65 known T2D related SNPs and inspect putative functional SNPs probably causing protein dysfunction, response element disruptions of known transcription factors related to T2D genes and regulatory response element disruption of four histone marks in pancreas and pancreas islet. In new identified risk SNPs, some of them were reported as T2D related SNPs in recent studies. Further, we found that accumulation of modest effects of single sites markedly enhanced the risk prediction based on 1989 T2D samples and 3000 healthy controls. The AROC value increased from 0.58 to 0.62 by only using genotype score when putative risk SNPs were added. Besides, the net reclassification improvement is 10.03% on the addition of new risk SNPs. Taken together, functional annotation could provide a list of prioritized potential risk SNPs for the further estimation on the T2D susceptibility of individuals.

Type 1 Diabetes Candidate Genes Linked to Pancreatic Islet Cell Inflammation and Beta-Cell Apoptosis.

Type 1 diabetes (T1D) is a chronic immune-mediated disease resulting from the selective destruction of the insulin-producing pancreatic islet β-cells. Susceptibility to the disease is the result of complex interactions between environmental and genetic risk factors. Genome-wide association studies (GWAS) have identified more than 50 genetic regions that affect the risk of developing T1D. Most of these susceptibility loci, however, harbor several genes, and the causal variant(s) and gene(s) for most of the loci remain to be established. A significant part of the genes located in the T1D susceptibility loci are expressed in human islets and β cells and mounting evidence suggests that some of these genes modulate the β-cell response to the immune system and viral infection and regulate apoptotic β-cell death. Here, we discuss the current status of T1D susceptibility loci and candidate genes with focus on pancreatic islet cell inflammation and β-cell apoptosis.

Type 2 Diabetes Susceptibility in the Greek-Cypriot Population: Replication of Associations with TCF7L2, FTO, HHEX, SLC30A8 and IGF2BP2 Polymorphisms.

Type 2 diabetes (T2D) has been the subject of numerous genetic studies in recent years which revealed associations of the disease with a large number of susceptibility loci. We hereby initiate the evaluation of T2D susceptibility loci in the Greek-Cypriot population by performing a replication case-control study. One thousand and eighteen individuals (528 T2D patients, 490 controls) were genotyped at 21 T2D susceptibility loci, using the allelic discrimination method. Statistically significant associations of T2D with five of the tested single nucleotide polymorphisms (SNPs) (TCF7L2 rs7901695, FTO rs8050136, HHEX rs5015480, SLC30A8 rs13266634 and IGF2BP2 rs4402960) were observed in this study population. Furthermore, 14 of the tested SNPs had odds ratios (ORs) in the same direction as the previously published studies, suggesting that these variants can potentially be used in the Greek-Cypriot population for predictive testing of T2D. In conclusion, our findings expand the genetic assessment of T2D susceptibility loci and reconfirm five of the worldwide established loci in a distinct, relatively small, newly investigated population.