Lack of replication of common EXT2 gene variants with susceptibility to type 2 diabetes in Lebanese Arabs

ObjectiveRecent genome-wide association studies and replication analyses have reported the association of variants of the exostosin-2 (EXT2) gene and risk of type 2 diabetes mellitus (T2DM) in some populations, but not in others. This study investigated the associations of EXT2 variants rs1113132, rs3740878 and rs11037909 with T2DM in a Lebanese Arab population.MethodsThis case-control study involved 995 T2DM patients and 1076 control subjects. Genotyping was done by the allelic exclusion method.ResultsWhile minor allele frequencies (MAFs) of rs11037909 (P = 0.028) and rs3740878 (P = 0.048), but not rs1113132 (P = 0.841), were higher in patients, this was lost after correcting for multiple testing. Apart from EXT2 rs1113132, which was marginally associated with T2DM in the additive model (P = 0.054), but not after adjustment for covariates, none of the tested EXT2 SNPs were associated with T2DM in any of the genetic models tested. However, variable associations of EXT2 variants with T2DM were noted according to BMI status. While the three tested EXT2 variants were not associated with T2DM in obese subjects, rs1113132 and rs11037909, but not rs3740878, were associated with T2DM in non-obese subjects. Meta-analysis revealed a significant association of rs11037909 and a marginal association of rs3740878 with T2DM in the fixed model. Using a common (GTA) haplotype as reference, three-locus (rs1113132/rs11037909/rs3740878) haplotype analysis demonstrated no association between any of the EXT2 haplotypes with T2DM, not even before correcting for multiple testing.ConclusionThis study demonstrated no association of rs1113132, rs3740878 and rs11037909 EXT2 variants with T2DM.     

Contribution of common variants of ENPP1, IGF2BP2, KCNJ11, MLXIPL,PPARγ, SLC30A8 and TCF7L2 to the risk of type 2 diabetes in Lebanese and Tunisian Arabs

BackgroundWhile several type 2 diabetes mellitus (T2DM) susceptibility loci identified through genome-wide association studies (GWAS) have been replicated in many populations, their association in Arabs has not been reported. For this reason, the present study looked at the contribution of ENNP1 (rs1044498), IGF2BP2 (rs1470579), KCNJ11 (rs5219), MLXIPL (rs7800944), PPARγ (rs1801282), SLC30A8 (rs13266634) and TCF7L2 (rs7903146) SNPs to the risk of T2DM in Lebanese and Tunisian Arabs.MethodsStudy subjects (case/controls) were Lebanese (751/918) and Tunisians (1470/838). Genotyping was carried out by the allelic discrimination method.ResultsIn Lebanese and Tunisians, neither ENNP1 nor MLXIPL was associated with T2DM, whereas TCF7L2 was significantly associated with an increased risk of T2DM in both the Lebanese [P < 0.001; OR (95% CI): 1.38 (1.20–1.59)] and Tunisians [P < 0.001; OR (95% CI): 1.36 (1.18–1.56)]. Differential associations of IGF2BP2, KCNJ11, PPARγ and SLC30A8 with T2DM were noted in the two populations. IGF2BP2 [P = 1.3 × 10^?5; OR (95% CI): 1.66 (1.42–1.94)] and PPARγ [P = 0.005; OR (95% CI): 1.41 (1.10–1.80)] were associated with T2DM in the Lebanese, but not Tunisians, while KCNJ11 [P = 8.0 × 10^?4; OR (95% CI): 1.27 (1.09–1.47)] and SLC30A8 [P = 1.6 × 10^?5; OR (95% CI): 1.37 (1.15–1.62)] were associated with T2DM in the Tunisians, but not Lebanese, after adjusting for gender and body mass index.ConclusionT2DM susceptibility loci SNPs identified through GWAS showed differential associations with T2DM in two Arab populations, thus further confirming the ethnic contributions of these variants to T2DM susceptibility.     

European genetic variants associated with type 2 diabetes in North African Arabs

AimsRecent genome-wide association studies (GWAS) and previous approaches have identified many genetic variants associated with type 2 diabetes (T2D) in populations of European descent, but their contribution in Arab populations from North Africa is unknown. Our study aimed to validate these markers and to assess their combined effects, using large case-control studies of Moroccan and Tunisian individuals.MethodsOverall, 44 polymorphisms, located at 37 validated European loci, were first analyzed in 1055 normoglycaemic controls and 1193 T2D cases from Morocco. Associations and trends were then assessed in 942 normoglycaemic controls and 1446 T2D cases from Tunisia. Finally, their ability to discriminate cases from controls was evaluated.ResultsCarrying a genetic variant in BCL11A, ADAMTS9, IGF2BP2, WFS1, CDKAL1, TP53INP1, CDKN2A/B, TCF7L2, KCNQ1, HNF1A, FTO, MC4R and GCK increased the risk of T2D when assessing the Moroccan and Tunisian samples together. Each additional risk allele increased the susceptibility for developing the disease by 12% (P = 9.0 × 10^?9). Genotype information for 13 polymorphisms slightly improved the classification of North Africans with and without T2D, as assessed by clinical parameters, with an increase in the area under the receiver operating characteristic curve from 0.64 to 0.67 (P = 0.004).ConclusionIn addition to TCF7L2, 12 additional loci were found to be shared between Europeans and North African Arabs. As for Europeans, the reliability of genetic testing based on these markers to determine the risk for T2D is low. More genome-wide studies, including next-generation sequencing, in North African populations are needed to identify the genetic variants responsible for ethnic disparities in T2D susceptibility.     

Evaluating the association of common LMNA variants with type 2 diabetes and quantitative metabolic phenotypes in French Europids

Aims/hypothesis In the present study, we sought to examine the evidence that LMNA variants are associated with type 2 diabetes and quantitative metabolic traits in French Europid individuals. Methods We genotyped 24 single nucleotide polymorphisms (SNPs) spanning the LMNA gene in 3,093 case–control participants. The association between LMNA SNPs and quantitative metabolic traits was also examined in the 1,674 normoglycaemic adults who made up the control cohort. Results SNP rs505058, a synonymous SNP (D446D) in exon 7, showed nominal evidence of association with type 2 diabetes [p = 0.003, odds ratio (OR) 1.30 (95% CI 1.09–1.56)] in French Europids. A meta-analysis of available rs505058 genotype data from 7,819 participants provided support for a modest association of rs505058 with type 2 diabetes [p = 0.003, OR 1.19 (95% CI 1.06–1.35)]. We found no evidence (p = 0.91) that the tag SNP rs4641 is associated with type 2 diabetes. However, a meta-analysis of all available rs4641 genotype data in a total of 15,591 participants produced borderline evidence of association [p = 0.054, OR 1.05 (95% CI 1.00–1.11)]. SNP rs6669212, in the 3′ untranslated region of LMNA, exhibited suggestive associations with WHR (p = 0.013), fasting serum levels of total cholesterol (p = 0.023) and triacylglycerol (p = 0.015). We emphasise that these quantitative trait associations are not corrected for multiple testing. Conclusions/interpretation The available data do not support a major effect of common LMNA variation on type 2 diabetes susceptibility in northern Europeans. Further large-scale studies are required to conclusively establish the extent to which LMNA variants have an impact on quantitative metabolic traits. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorised users.     

Sleep duration does not mediate or modify association of common genetic variants with type 2 diabetes

Aims/hypothesis

Short and long sleep duration are associated with increased risk of type 2 diabetes. We aimed to investigate whether genetic variants for fasting glucose or type 2 diabetes associate with short or long sleep duration and whether sleep duration modifies the association of genetic variants with these traits.

Methods

We examined the cross-sectional relationship between self-reported habitual sleep duration and prevalence of type 2 diabetes in individuals of European descent participating in five studies included in the Candidate Gene Association Resource (CARe), totalling 1,474 cases and 8,323 controls. We tested for association of 16 fasting glucose-associated variants, 27 type 2 diabetes-associated variants and aggregate genetic risk scores with continuous and dichotomised (≤5 h or ≥9 h) sleep duration using regression models adjusted for age, sex and BMI. Finally, we tested whether a gene × behaviour interaction of variants with sleep duration had an impact on fasting glucose or type 2 diabetes risk.

Results

Short sleep duration was significantly associated with type 2 diabetes in CARe (OR 1.32; 95% CI 1.08, 1.61; p?=?0.008). Variants previously associated with fasting glucose or type 2 diabetes and genetic risk scores were not associated with sleep duration. Furthermore, no study-wide significant interaction was observed between sleep duration and these variants on glycaemic traits. Nominal interactions were observed for sleep duration and PPARG rs1801282, CRY2 rs7943320 and HNF1B rs4430796 in influencing risk of type 2 diabetes (p?<?0.05).

Conclusions/interpretation

Our findings suggest that differences in habitual sleep duration do not mediate or modify the relationship between common variants underlying glycaemic traits (including in circadian rhythm genes) and diabetes.     

脂联素基因变异与2型糖尿病的相关性

聚合酶链反应单链构象多态性和基因测序法观察脂联素基因I164T突变与中国安徽地区汉族人2型糖尿病的关系。受试者中未发现I164T突变,但在糖耐量异常组中,发现该基因的H142P新突变。提示I164T突变可能不是本组2型糖尿病的重要遗传因素,且该基因位点突变具有种族异质性。     

A replication study of 19 GWAS-validated type 2 diabetes at-risk variants in the Lebanese population

Aim

Recent genome-wide association scans (GWAS) and replication studies have expanded the list of validated type 2 diabetes (T2DM) susceptibility loci. We replicated T2DM association of 19 SNPs from 15 candidate loci in Lebanese Arabs.

Methods

Case–control association study, comprising 995 T2DM patients and 1076 control participants. We genotyped by the allelic discrimination method 19 SNPs in/near ADAM30, NOTCH2, THADA, TMEFF2, COL8A1, ADAMTS9-AS2, WFS1, JAZF1, SLC30A8, KCNQ1, LOC387761, ALX4, TSPAN8, FTO, and HNF1.

Results

Allele frequencies of the tested SNPs were comparable with those of Caucasians. COL8A1 rs792837 (P = 2.9 × 10⁻⁹), KCNQ1 rs2237892 (P = 1.8 × 10⁻¹⁸) and rs2237895 (P = 0.002), ALX4 rs729287 (Pc = 7.5 × 10⁻⁵), and HNF1 rs4430796 (P = 0.003) were significantly associated with T2DM, with similar effect sizes to those of Europeans. While FTO rs8050136 and rs17817449, ADAMTS9 rs4607103, and WFS1 rs10010131 were initially associated with T2DM, this was lost upon multiple testing correction. The remaining variants were not associated with T2DM, possibly resulting from insufficient power to detect smaller allele effects.

Conclusion

In addition to previous findings on the association of IGF2BP2, CDKAL1, TCF7L2 variants with T2DM among Lebanese, here we extend these by validating the association of five additional loci with T2DM in Lebanese Arabs.     

IGF2BP2 and IGF2 genetic effects in diabetes and diabetic nephropathy

ObjectiveThe IGF2BP2 gene is located on chromosome 3q27.2 within a region linked to type 1 diabetes (T1D), type 2 diabetes (T2D) and diabetic nephropathy (DN). Its protein functionally binds to 5’-UTR of the imprinting IGF2 gene. The present study aims to evaluate the IGF2BP2-IGF2 genetic effects in diabetes and DN.Materials and MethodsThree cohorts including T1D with and without DN (n = 1139) of European descents from the GoKinD study, Swedish T1D with and without DN (n = 303) and Czech control subjects without diabetes, T1D, T2D with and without DN (n = 1418) were enrolled in TaqMan genotyping experiments for IGF2BP2 rs4402960 and IGF2 rs10770125. Igf2bp2 gene expression in kidney tissues of db/db and control mice at the ages of 5 and 26 weeks was examined with real time RT-PCR and Western blot.ResultsAn association of IGF2BP2 rs4402960 with T2D in the Czech population was replicated. This IGF2BP2 polymorphism (P = 0.037, OR = 0.69 95% CI 0.49–0.98) was found to be associated with DN in male not in female patients with T1D selected from the GoKinD study. In the analyses of combined the GoKinD, Czech and Swedish populations, the association between IGF2BP2 polymorphism and DN in male patients with T1D was still significant (P = 0.030, OR = 0.73, 95% CI 0.54–0.97). IGF2 rs10770125 was also associated with DN in male T1D patients of the GoKinD population (P = 0.038, OR = 0.67 95% CI 0.46–0.98). There might be a genetic interaction between IGF2BP2 and IGF2 (P = 0.05). The Igf2bp2 gene expression levels were increased in the kidneys of db/db mice compared to controls at the age of 5 weeks but not at 26 weeks.ConclusionsThe present study has replicated the association of IGF2BP2 rs4402960 with T2D in the Czech population and provided data suggesting that IGF2BP2 may have genetic interaction with IGF2 with a protective effect against DN in male patients with T1D.     

Strong association of common variants in the miRNA-binding site of NOD2 gene with clinicopathological characteristics and disease activity of systemic lupus erythematosus

Clinical Rheumatology - Systemic lupus erythematosus (SLE) is a multifactorial systemic autoimmune disease, in which genetic susceptibility plays a pivotal role. The nucleotide oligomerization...     

Association testing of common variants in the insulin receptor substrate-1 gene (IRS1) with type 2 diabetes

Aims/hypothesis Activation of the insulin receptor substrate-1 (IRS1) is a key initial step in the insulin signalling pathway. Despite several reports of association of the G972R polymorphism in its gene IRS1 with type 2 diabetes, we and others have not observed this association in well-powered samples. However, other nearby variants might account for the putative association signal. Subjects and methods We characterised the haplotype map of IRS1 and selected 20 markers designed to capture common variations in the region. We genotyped this comprehensive set of markers in several family-based and case-control samples of European descent totalling 12,129 subjects. Results In an initial sample of 2,235 North American and Polish case-control pairs, the minor allele of the rs934167 polymorphism showed nominal evidence of association with type 2 diabetes (odds ratio [OR] 1.25, 95% CI 1.03–1.51, p = 0.03). This association showed a trend in the same direction in 7,659 Scandinavian samples (OR 1.16, 95% CI 0.96–1.39, p = 0.059). The combined OR was 1.20 (p = 0.008), but statistical correction for the number of variants examined yielded a p value of 0.086. We detected no differences across rs934167 genotypes in insulin-related quantitative traits. Conclusions/interpretation Our data do not support an association of common variants in IRS1 with type 2 diabetes in populations of European descent. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorised users. D. Altshuler and L. Groop jointly supervised this project.     

Strong association of common variants in the <Emphasis Type="Italic">CDKN2A/CDKN2B</Emphasis> region with type 2 diabetes in French Europids

Aims/hypothesis Genome-wide association studies (GWASs) recently identified common variants in the CDKN2A/CDKN2B region on chromosome 9p as being strongly associated with type 2 diabetes. Since these association signals were not picked up by the French-Canadian GWAS, we sought to replicate these findings in the French Europid population and to further characterise the susceptibility variants at this novel locus. Methods We genotyped 20 single nucleotide polymorphisms (SNPs) spanning the CDKN2A/CDKN2B locus in our type 2 diabetes case-control cohort. The association between CDKN2A/CDKN2B SNPs and quantitative metabolic traits was also examined in the normoglycaemic participants comprising the control cohort. Results We report replication of the strong association of rs10811661 with type 2 diabetes found in the GWASs (; OR 1.43 [95% CI 1.24–1.64]). The other CDKN2A/CDKN2B susceptibility variant, rs564398, did not attain statistical significance (p = 0.053; OR 1.11 [95% CI 1.00–1.24]) in the present study. We also obtained several additional nominal association signals (p < 0.05) at the CDKN2A/CDKN2B locus; however, only the rs3218018 result (p = 0.002) survived Bonferroni correction for multiple testing (adjusted p = 0.04). Conclusions/interpretation Our comprehensive association study of common variation spanning the CDKN2A/CDKN2B locus confirms the strong association between the distal susceptibility variant rs10811661 and type 2 diabetes in the French population. Further genetic and functional studies are required to identify the aetiological variants at this locus and determine the cellular and physiological mechanisms by which they act to modulate type 2 diabetes susceptibility. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorised users. K. Duesing and G. Fatemifar contributed equally to this work.     

The association of the common fat mass and obesity associated gene polymorphisms with type 2 diabetes in obese Iraqi population

Background & objectivesThis study investigates the association of two potential Fat mass and obesity associated gene (FTO) gene polymorphisms (rs9939609 and rs918031) as potential predictors of type 2 diabetes (T2D) in obese Iraqi population and their metabolic effects on hyperglycemia and insulin sensitivity.Materials & methodsThe study included 400 participants with obesity & T2D, with a matching 400 obese non-diabetic cohort. Venous blood samples were collected for DNA extraction. Using specific primers and restriction enzymes, genotyping was performed to identify the various alleles for each gene. The genotype and allele frequencies determined by multinomial logistic regression analysis for FTO single nucleotide polymorphisms (rs9939609) among all the study groups.ResultsThere is a two-fold increase in the risk of T2D within the homozygous genotype (TT) group (OR = 2.43, CI 95% 3.57–11.2, P ≤ 0.001) as compared to the wild type (TA). In addition, there was a significantly higher level of the minor allele genotype (T) in T2D patients when compared to the control group, (P ≤ 0.001).ConclusionWe conclude that the FTO rs9939609 genotype significantly affect the development of insulin resistance, therefore the future occurrence of T2D, in obese individuals.     

2型糖尿病与簇蛋白基因关联的初步研究

目的探讨2型糖尿病（T2DM）与簇蛋白（Glu）基因多态性的关联。方法聚合酶链式反应-变性梯度凝胶电泳（PCR-DGGE）和DNA测序技术分析62例T2DM患者及60例正常对照者的Glu基因外显子2和外显子5基因多态性。结果Glu基因外显子2发现1个多态位点：1963（＋A）;外显子5发现3个多态位点：（1）7476（-A）,（2）7534（-C）,（3）7521C→T。结论Glu基因外显子2和外显子5多态性在2型糖尿病组和正常对照组多态性位点基因频率分布差异有统计学意义。因此,Clu基因外显子2和外显子5多态性可能与T2DM易感性有关联。     

Association of serine racemase gene variants with type 2 diabetes in the Chinese Han population

A genome‐wide association study in the Chinese Han population has identified several novel genetic variants of the serine racemase (SRR) gene in type 2 diabetes. Our purpose was to systematically evaluate the contribution of SRR variants in the Chinese Han population. rs391300 and rs4523957 in SRR were genotyped respectively in the two independent populations. A meta‐analysis was used to estimate the effects of SRR in 21,305 Chinese Han individuals. Associations between single‐nucleotide polymorphisms and diabetes‐related phenotypes were analyzed among 2,615 newly diagnosed type 2 diabetes patients and 5,029 controls. Neither rs391300 nor rs4523957 were associated with type 2 diabetes in populations. Furthermore, meta‐analysis did not confirm an association between type 2 diabetes and SRR. In the controls, rs391300‐A and rs4523957‐G were associated with higher 30‐min plasma glucose in an oral glucose tolerance test. The present study did not confirm that SRR was associated with type 2 diabetes.     

Genetic variants for type 2 diabetes and new-onset cancer in Chinese with type 2 diabetes

Background

Diabetes is associated with an increased risk of cancer. This study aimed to evaluate associations between recently reported type 2 diabetes (T2D) susceptibility genetic variants and cancer risk in a prospective cohort of Chinese patients with T2D.

Methods

Seven single nucleotide polymorphisms (SNP) in IGF2BP2, CDKAL1, SLC30A8, CDKN2A/B, HHEX and TCF7L2, all identified from genome-wide association studies of T2D, were genotyped in 5900 T2D patients [age mean ± SD = 57 ± 13 years, % males = 46] without any known cancer at baseline. Associations between new-onset of cancer and SNPs were tested by Cox proportional hazard models with adjustment of conventional risk factors.

Results

During the mean follow-up period of 8.5 ± 3.3 years, 429 patients (7.3%) developed cancer. Of the T2D-related SNPs, the G-alleles of HHEX rs7923837 (hazard ratio [HR] (95% C.I.) = 1.34 (1.08–1.65); P = 6.7 × 10⁻³ under dominant model) and TCF7L2 rs290481 (HR (95% C.I.) = 1.16 (1.01–1.33); P = 0.040 under additive model) were positively associated with cancer risk, while the G-allele of CDKAL1 rs7756992 was inversely associated (HR (95% C.I.) = 0.80 (0.65–1.00); P = 0.048 under recessive model). The risk alleles of these significant SNPs exhibited combined effect on increasing cancer risk (per-allele HR (95% C.I.) = 1.25 (1.12–1.39); P = 4.8 × 10⁻⁵). The adjusted cancer risk was 2.41 (95% C.I. 1.23–4.69) for patients with four risk alleles comparing to patients without risk allele.

Conclusions

T2D-related variants HHEX rs7923837, TCF7L2 rs290481 and CDKAL1 rs7756992 increased cancer risk in patients with diabetes.

Impact

Our findings provide novel insights into the pathogenesis of cancer in diabetes.