Prediction of the risk of type 1 diabetes from polymorphisms in candidate genes

New Perspectives in Studying Type 1 Diabetes Susceptibility Biomarkers

Type 1 diabetes (T1D) is generally viewed as an etiologic subtype of diabetes caused by the autoimmune destruction of the insulin-secreting β-cells. It has been known that autoreactive T cells unfortunately destroy healthy β-cells. However, there has been a notion of etiologic heterogeneity around the world implicating a varying incidence of a non-autoimmune subgroup of T1D related to insulin deficiency associated with decreased β cell mass, in which the β-cell is the key contributor to the disease. Beta cell dysfunction, reduced mass, and apoptosis may lead to insufficient insulin secretion and ultimately to the development of T1D. Interestingly, Korean as well as other ethnic genetic results have also suggested that genes related with insulin deficiency, let alone those of immune regulation, were associated with the risk of T1D in the young. Genes related with insulin secretion may influence the phenotype of diabetes differentially and different genes may be working on different steps of T1D development. Although we admit the consensus that islet autoimmunity is an essential component in the pathogenesis of T1D, however, dysfunction might occur not only in the immune system but also in the β-cells, the defect of which may induce further dysfunction of the immune system. These arguments stem from the fact that the β-cell might be the trigger of an autoimmune response. This emergent view has many parallels with the fact that by their nature and function, β-cells are prone to biosynthetic stress with limited measures for self-defense. Beta cell stress may induce an immune attack that has considerable negative effects on the production of a vital hormone, insulin. If then, both β-cell stress and islet autoimmunity can be harnessed as targets for intervention strategies. This also may explain why immunotherapy at best delays the progression of T1D and suggests the use of alternative therapies to expand β-cells, in combination with immune intervention strategies, to reverse the disease. Future research should extend to further investigate β-cell biology, in addition to studies of immunologic areas, to find appropriate biomarkers of T1D susceptibility. This will help to decipher β-cell characteristics and the factors regulating their function to develop novel therapeutic approaches.

Precision medicine in diabetes prevention, classification and management

Diabetes has become a major burden of healthcare expenditure. Diabetes management following a uniform treatment algorithm is often associated with progressive treatment failure and development of diabetic complications. Recent advances in our understanding of the genomic architecture of diabetes and its complications have provided the framework for development of precision medicine to personalize diabetes prevention and management. In the present review, we summarized recent advances in the understanding of the genetic basis of diabetes and its complications. From a clinician's perspective, we attempted to provide a balanced perspective on the utility of genomic medicine in the field of diabetes. Using genetic information to guide management of monogenic forms of diabetes represents the best-known examples of genomic medicine for diabetes. Although major strides have been made in genetic research for diabetes, its complications and pharmacogenetics, ongoing efforts are required to translate these findings into practice by incorporating genetic information into a risk prediction model for prioritization of treatment strategies, as well as using multi-omic analyses to discover novel drug targets with companion diagnostics. Further research is also required to ensure the appropriate use of this information to empower individuals and healthcare professionals to make personalized decisions for achieving the optimal outcome.

Vitamin D status and associated factors in recent-onset type 1 diabetic children in Iran

Background

In this study, the prevalence of vitamin D deficiency was assessed in a group of children and adolescent patients with recent-onset type 1 diabetes mellitus (T1DM).

Methods

Fifty-three patients with age 8–18 years and duration of T1DM less than 8 weeks were recruited. A food frequency questionnaire (FFQ) was used to assess dietary vitamin D and calcium intake. Sunshine exposure was measured using a questionnaire to quantify the amount of time children spent in the sun and other sun-related habits, and a sun index score was generated. Serum 25(OH)D < 20 ng/ml was considered as vitamin D deficiency. Logistic regression was used to assess predictors of vitamin D deficiency.

Results

All patients were vitamin D deficient (77%) or insufficient (23%). In a logistic regression model, it was shown that the risk of being vitamin D deficient was significantly decreased by sunlight exposure ≥ 15 minutes during the weekends versus < 15 minutes (OR: 0.06, 95% CI: 0.01–0.75; P=0.029). In addition, vitamin D deficiency in boys was lower than girls in this model (OR: 0.164 [95% CI: 0.02–1.11]; P = 0.063).

Conclusion

Vitamin D deficiency is highly prevalent among children and adolescents with T1DM in Iran. Boys and children with ≥ 15 minutes sunlight exposure in weekends were less likely to be vitamin D deficient than girls and those with < 15 minutes sunlight exposure.

Susceptibility influence of a PTPN22 haplotype with thyroid autoimmunity in Koreans

BACKGROUND

Considerable amount of evidences in the Caucasians have suggested the association of a missense single-nucleotide polymorphism (SNP) in the protein tyrosine phosphatase non-receptor type 22 (PTPN22) gene (rs2476601) with several autoimmune diseases including autoimmune thyroid diseases (AITD) and type 1 diabetes (T1D). As the SNP was reported to be non-polymorphic in Asians, we attempt to explore an association of PTPN22 without restricting to the rs2476601 with AITD or T1D in Korean population.

METHODS

We studied 389 T1D, 212 AITD (84 Graves' disease and 128 Hashimoto's thyroiditis) patients and 225 controls. In addition to the rs2476601, we selected five testing SNPs spanning 58 kb over the PTPN22 gene using the previous resequencing data and International HapMap Project.

RESULTS

We found that neither alleles, genotypes among all five SNPs, nor reconstructed haplotypes of five SNPs were associated with T1D. Interestingly, a minor allele of a SNP (rs12730735) and a haplotype (GGCTT) showed significant association with the susceptibility of AITD, especially with that of Hashimoto's thyroiditis (p<0.01).

CONCLUSIONS

These results indicate that the PTPN22 gene polymorphism independent of the SNP rs2476601 might be a supplementary risk factor to AITD, but not in T1D in Koreans, contradicting a major contributory influence of the PTPN22 gene in explaining common mechanism underlying multiple autoimmune diseases.

T cell cytokine gene polymorphisms in canine diabetes mellitus

Insulin-deficiency diabetes in dogs shares some similarities with human latent autoimmune diabetes of adults (LADA). Canine diabetes is likely to have a complex pathogenesis with multiple genes contributing to overall susceptibility and/or disease progression. An association has previously been shown between canine diabetes and MHC class II genes, although other genes are also likely to contribute to the genetic risk. Potential diabetes susceptibility genes include immuno-regulatory TH1/TH2 cytokines such as IFNgamma, IL-12, IL-4 and IL-10. We screened these candidate genes for single nucleotide polymorphisms (SNPs) in a range of different dog breeds using dHPLC analysis and DNA sequencing. Thirty-eight of the SNPs were genotyped in crossbreed dogs and seven other breed groups (Labrador Retriever, West Highland White Terrier, Collie, Schnauzer, Cairn Terrier, Samoyed and Cavalier King Charles Spaniel), which demonstrated substantial intra-breed differences in allele frequencies. When SNPs were examined for an association with diabetes by case:control analysis significant associations were observed for IL-4 in three breeds, the Collie, Cairn Terrier and Schnauzer and for IL-10 in the Cavalier King Charles Spaniel. These results suggest that canine cytokine genes regulating the TH1/TH2 immune balance might play a contributory role in determining susceptibility to diabetes in some breeds.

[Association between Fok I vitamin D receptor (VDR) gene polymorphism and plasmatic concentrations of transforming growth factor-beta1 and interferon gamma in type 1 diabetes mellitus]

BACKGROUND AND OBJECTIVE

In order to assess whether Fok I vitamin D receptor gene (VDR) polymorphism is involved in the genetic susceptibility of type 1 diabetes, a case-control study was conducted and VDR genotypes were related to serum concentrations of 25(OH) vitamin D and cytokines transforming growth factor beta1 (TGF-beta1) and interferon gamma (INF-gamma).

PATIENTS AND METHOD

151 incident cases of type 1 diabetes and 182 non related healthy controls from Santiago were studied for VDR polymorphisms in peripheral blood DNA. Exon 2 (Fok I) segments were amplified by polimerase chain reaction and analyzed by means of restriction fragment length polymorphism to determine each corresponding genotype. Differences for allele, genotype and serological markers as 25(OH) vitamin D, TGF-beta1 and INF-gamma levels distribution between patients and controls were analyzed.

RESULTS

Fok I polymorphism distribution analysis showed no differences between patients and controls. Among diabetics, higher levels of TGF-beta1 (median, 282.6 pg/ml; range, 131.8-3,031.4) were observed compared with healthy children (median, 232.2 pg/ml; range, 135.7-506.5) (p < 0.0038). Similar results were observed for INF-gamma concentrations (median, 121.1 pg/ml, and range, 5.3-228.8, in cases, and median, 89.6 pg/ml, and range, 10.9-117.2 in controls) (p < 0.0004). The diabetic carriers of the ff genotype showed low levels of 25(OH) vitamin D compared with the carriers of the F allele: mean (standard deviation), 23.1 (5.9) versus 27.9 (10.3) ng/ml (p < 0.03). A similar result was observed for TGF-beta1 concentrations in diabetic carriers of ff genotype and patients carriers of the F allele (298.5 versus 276.6; p < 0.05).

CONCLUSIONS

Fok I polymorphism of VDR could have a marginal role in the immunologic disturbance in type 1 diabetes.

Functional evaluation of the type 1 diabetes (T1D) susceptibility candidate genes

Progress has been made in investigating the genetic factors involved in type 1 diabetes (T1D) development for the past few years. While Linkage disequilibrium (LD) mapping has been useful for both the confirmation and fine-mapping of susceptibility intervals, as well as identification of etiological mutations, identification of specific disease genes has been a challenge and limited to known candidate genes. The overall risk for T1D from the HLA DR and DQ molecules (IDDM1) is determined by combinations of polymorphic alleles. Functional studies indicate that the susceptible and protective HLA-DR and -DQ bind and present non-overlapping peptides. Although consistent linkage evidence was reported for the susceptibility intervals IDDM2, IDDM5 and IDDM12, evidence for most other intervals varies in different data sets. The variable number of tandem repeats at the 5' end of the insulin gene (IDDM2) regulates insulin expression in the thymus. Studies on IDDM5 have led to the discovery of a novel polymorphism 163 A-->G (M55V) in SUMO4 gene, which was found to be associated with T1D patients with Asian origin. Functionally SUMO4 conjugates to IkBalpha and negatively regulates NFkB transcriptional pathway. The M55V substitution reduces the sumoylation activity of the V55 variant, which resulted in higher NFkB dependent transcriptional activity. The polymorphisms of the cytotoxic T lymphocyte antigen 4 gene (CTLA4, IDDM12) encoding a regulatory molecule in the immune system associate with T1D and autoimmune thyroid diseases (ATD). The 3' untranslated region of this gene determines the level of soluble CTLA-4. Genetic mapping of variants conferring a small disease risk can identify pathways in complex disorders, as evidenced by quantitative alterations of candidate genes contributing to autoimmune tissue destruction. Moreover, the identification of two transcription factors that, when mutated, are responsible for severe autoimmune disease is leading to a better understanding of T cell tolerance. Both AIRE and Foxp3, identified initially via their association with genetically manipulated mice, are involved in tolerance induction in humans. Although mutations in these genes may cause rare but serious diseases, it is likely that other transcription factors will contribute to the genetic load that predisposes certain individuals to disease.

VDR polymorphisms influence the immune response in type 1 diabetic children from Santiago, Chile

OBJECTIVE

To evaluate the influence of ApaI, BsmI and TaqI polymorphisms of the VDR gene and HLA-DQB1* alleles in type 1 diabetic children and to assess their possible relationship with circulating levels of 25-hydroxyvitamin D(3), auto-antibodies, and INFgamma/TGFbeta1 cytokines levels in Chilean cases and controls.

METHODS

DNA and serum samples from 216 newly diagnosed type 1 diabetic and 203 unrelated control children were evaluated for IA-2 and GAD(65) auto-antibodies, 25-hydroxyvitamin D(3) levels, HLA-DQB1* alleles, and VDR gene polymorphisms.

RESULTS

The frequency of the b allele and the bb genotype in type 1 diabetic patients was significantly lower compared with the control group (0.635 versus 0.749, p<0.01 and 0.370 versus 0.567, p<0.04). 25-Hydroxyvitamin D(3) levels showed no differences between type 1 diabetic and healthy children. In cases, 25-hydroxyvitamin D(3) levels were not associated with a special auto-antibodies profile according to the presence or absence of GAD(65)(+) or IA-2(+). The haplotype combination BAT was higher in cases (0.062 versus 0.019, p<0.0022) and bAT was more frequent in controls (0.266 versus 0.180, p<0.003). In cases, the aaBbTT genotype showed the most significant increase in TGFbeta1 level across the VDR categories. Finally, when considering the HLA class II risk genotype (DQB1*0302) and the VDR genotypes (AabbTT and aabbTT), higher levels of GAD(65), IA-2 and TGFbeta1 were observed among diabetic children.

CONCLUSION

We found an association between a VDR polymorphism (BsmI) and type 1 diabetes. An association was found of AabbTT and aabbTT genotypes and the HLA-DQB1*0302 allele with high levels of GAD(65), IA-2 and TGFbeta1.

Why is type 1 diabetes uncommon in Asia?

T1D (type 1 diabetes) incidence rates are extremely low in Asian populations. The prevalences of islet-specific autoantibodies are reported to be low compared with Caucasians. Although the clinical and immunologic characteristics of T1D in Asians appear to be different from those of Caucasians, if we apply correct patient definition and standardized methods, the typical T1D patients are very similar, in the immunologic as well as genetic perspectives. Although the association of individual allele seems to be different between populations, if we compare the identical DR-DQ haplotypes, the association and transmission to diabetic offspring were similar for Asians and Caucasians. The high-risk HLA genotypes/haplotypes were found to be independent determinants of diabetes in the first-degree relatives of individuals with T1D, particularly in the presence of autoantibodies. A different genetic susceptibility including a low frequency of high-risk HLA alleles could explain the lower prevalence of islet-specific autoantibodies and the low incidence of T1D, or different genetic and environmental interactions might be involved in the etiology of T1D. It is certain that DR-DQ linkage disequilibrium (LD) is an important factor explaining the difference in T1D incidence in different countries. LD between highly susceptible DRB1 alleles and protective DQB1 alleles, and vice versa, is the major contributing factor to the low incidence of T1D in Asians. We also suggested that different genetic/environmental interactions might operate in the etiology of T1D between Caucasians and Asians. It would be of great help for primary prevention to investigate to what degree genetic determinants influence the well-known regional differences in incidences, since we can identify environmental risk factors that may either initiate the autoimmune process or promote already ongoing beta cell damage in different countries. For this, population-based epidemiological studies are necessary to identify risk determinants that may be useful for primary prevention strategies.

Genetic mapping at 3-kilobase resolution reveals inositol 1,4,5-triphosphate receptor 3 as a risk factor for type 1 diabetes in Sweden

We mapped the genetic influences for type 1 diabetes (T1D), using 2,360 single-nucleotide polymorphism (SNP) markers in the 4.4-Mb human major histocompatibility complex (MHC) locus and the adjacent 493 kb centromeric to the MHC, initially in a survey of 363 Swedish T1D cases and controls. We confirmed prior studies showing association with T1D in the MHC, most significantly near HLA-DR/DQ. In the region centromeric to the MHC, we identified a peak of association within the inositol 1,4,5-triphosphate receptor 3 gene (ITPR3; formerly IP3R3). The most significant single SNP in this region was at the center of the ITPR3 peak of association (P=1.7 x 10(-4) for the survey study). For validation, we typed an additional 761 Swedish individuals. The P value for association computed from all 1,124 individuals was 1.30 x 10(-6) (recessive odds ratio 2.5; 95% confidence interval [CI] 1.7-3.9). The estimated population-attributable risk of 21.6% (95% CI 10.0%-31.0%) suggests that variation within ITPR3 reflects an important contribution to T1D in Sweden. Two-locus regression analysis supports an influence of ITPR3 variation on T1D that is distinct from that of any MHC class II gene.

Genetic influences of the intercellular adhesion molecule 1 (ICAM-1) gene polymorphisms in development of Type 1 diabetes and diabetic nephropathy

AIM

The intercellular adhesion molecule-1 (ICAM-1) gene is located on chromosome 19p13, which is linked to Type 1 diabetes (T1D). ICAM-1 expression is related to development of T1D and diabetic nephropathy. The present study aims to evaluate the genetic influence of ICAM-1 gene polymorphisms on the development of T1D and diabetic nephropathy.

METHODS

Five valid single nucleotide polymorphisms (SNPs) were genotyped in 432 T1D patients (196 patients had diabetic nephropathy) and 187 non-diabetic control subjects by using dynamic allele-specific hybridization (DASH) and pyrosequencing.

RESULTS

SNPs rs281432(C/G) and rs5498 E469K(A/G) had high heterozygous indexes. They were significantly associated with T1D [P = 0.026, OR = 1.644 (95% CI 1.138-2.376) and P < 0.001, OR = 2.456 (1.588-3.8)]. Frequencies of the C allele in SNP rs281432(C/G) and the A allele in SNP rs5498 E469K(A/G) increased stepwise from non-diabetic control subjects to T1D patients without diabetic nephropathy and T1D patients with diabetic nephropathy. Further analysis for these two SNPs indicated that T1D patients had increased frequency of the common haplotype C-A, in comparison with non-diabetic control subjects (38.1 vs. 32.1%, P = 0.035).

CONCLUSION

The present study provided evidence that SNPs rs281432(C/G) and rs5498 E469K(A/G) in the ICAM-1 gene confer susceptibility to the development of T1D and might also be associated with diabetic nephropathy in Swedish Caucasians.

Genetic analysis of HLA, NA and HPA typing in type 2 diabetes and ASO

We examined the genetic status of human leucocyte antigens (HLA), human platelet alloantigens (HPA) and neutrophil-specific antigens (NA) in patients with type 2 diabetes mellitus and diabetic arteriosclerosis obliterans (ASO). To our knowledge, the present study is the first report showing the relationship among three genetic factors in type 2 diabetes mellitus and ASO patients. HLA typing was performed by the polymerase chain reaction (PCR)-restriction fragment length polymorphism method. HPA-typing and NA-typing were by a PCR-sequence-specific primer method. The incidence of HLA-DRB1*1501 was found to be significant in type 2 diabetes and non-diabetic, particularly ASO-positive patients, compared to control subjects. There were no differences in NA1/NA2 between the control and diabetic or non-diabetic ASO groups. However, the frequency of NA2/NA2 in ASO-positive diabetes and non-diabetic ASO patients was significantly higher than controls. The a/b genotype of HPA-5a/5b was significantly lower in type 2 diabetes and non-diabetic ASO-positive patients than in controls. These findings suggest that genetic studies of HLA, NA and HPA could be useful to understand the pathogenesis of type 2 diabetes and ASO.