Association between type 2 diabetes genetic susceptibility loci and visceral and subcutaneous fat area as determined by computed tomography

Visceral fat accumulation has an important role in the development of several metabolic disorders, such as type 2 diabetes, dyslipidemia and hypertension. New genetic loci that contribute to the development of type 2 diabetes have been identified by genome-wide association studies. To examine the association of type 2 diabetes susceptibility loci and visceral fat accumulation, we genotyped 1279 Japanese subjects (556 men and 723 women), who underwent computed tomography for measurements of visceral fat area (VFA) and subcutaneous fat area (SFA) for the following single-nucleotide polymorphisms (SNPs): NOTCH2 rs10923931, THADA rs7578597, PPARG rs1801282, ADAMTS9 rs4607103, IGF2BP2 rs1470579, VEGFA rs9472138, JAZF1 rs864745, CDKN2A/CDKN2B rs564398 and rs10811661, HHEX rs1111875 and rs5015480, TCF7L2 rs7901695, KCNQ1 rs2237892, KCNJ11 rs5215 and rs5219, EXT2 rs1113132, rs11037909, and rs3740878, MTNR1B rs10830963, DCD rs1153188, TSPAN8/LGR5 rs7961581, and FTO rs8050136 and rs9939609. None of the above SNPs were significantly associated with VFA. The FTO rs8050136 and rs9939609 risk alleles exhibited significant associations with body mass index (BMI; P=0.00088 and P=0.0010, respectively) and SFA (P=0.00013 and P=0.00017, respectively). No other SNPs were significantly associated with BMI or SFA. Our results suggest that two SNPs in the FTO gene are associated with subcutaneous fat accumulation. The contributions of other SNPs are inconclusive because of a limitation of the sample power.     

Implication of genetic variants near <Emphasis Type="Italic">SLC30A8, HHEX,CDKAL1, CDKN2A/B,IGF2BP2, FTO,TCF2</Emphasis>, <Emphasis Type="Italic">KCNQ1</Emphasis>, and <Emphasis Type="Italic">WFS1</Emphasis> in Type 2 Diabetes in a Chinese population

Background  

Recently, several genome-wide and candidate gene association studies have identified many novel genetic loci for type 2 diabetes (T2D); among these genes, CDKAL1, IGF2BP2, SLC30A8, CDKN2A/B, HHEX, FTO, TCF2, KCNQ1, and WFS1 are the most important. We aimed to determine the effects of these genetic loci associated with T2D in the Chinese Han population of China.     

中国汉族人群2型糖尿病易感性相关基因多态性

2型糖尿病(type 2 diabetes mellitus,T2DM)的发病与多个基因累加效应及多种环境因素相关.已在中国汉族人群中研究过的与T2DM易感性相关的基因多态性包括:全基因组相关研究中的CDKAL1、CDKN2A/B、SLC30A8、IGF2BP2、HHEX、FTO 以及KCNQ1基因;脂联素基因;核呼吸因子基因;葡萄糖激酶基因;肿瘤坏死因子α基因等.探索这些易感基因可以为人类治疗T2DM起到极大的推动作用.但至今已明确的基因依然很少,国内外的研究结果不尽相同,尚需进一步地深入研究.     

Meta-analysis of the effect of HHEX gene polymorphism on the risk of type 2 diabetes

In the past decade, a number of case-control studies have been carried out to investigate the relationship between the HHEX polymorphism and type 2 diabetes (T2D). However, the results have been inconclusive. To investigate this inconsistency, we performed a meta-analysis of all available studies dealing with the relationship between the HHEX polymorphism and T2D. In total, 22 association studies on two HHEX polymorphisms (rs1111875 and rs7923837) and risk of T2D published before April 2010, including a total of 36?695 T2D cases and 51?800 controls were included. We also explored potential sources of heterogeneity. In a combined analysis, the summary per-allele odds ratio (OR) for T2D of the rs1111875 and rs7923837 polymorphism was 1.17 [95% confidence interval (CI): 1.13-1.21] and 1.23 (95% CI: 1.18-1.28), respectively. The haplotype analysis also showed significant association in the pooled international populations with an OR of 1.19 (95% CI: 1.15-1.22). In the subgroup analysis by ethnicity, significantly increased risks were found in Asians and Caucasians for these polymorphisms in almost all genetic models. Subgroup analysis also showed that ethnicity is the main source of heterogeneity between pooled studies. This meta-analysis demonstrated that the risk allele of HHEX polymorphisms (rs1111875 and rs7923837) is a risk factor for developing T2D. However, additional very large-scale studies are warranted to provide conclusive evidence on the effects of the HHEX gene on risk of T2D.     

Heterogeneity of genetic associations of CDKAL1 and HHEX with susceptibility of type 2 diabetes mellitus by gender

We examined the genetic associations of previously identified sequence variants with type 2 diabetes mellitus (T2DM) and its potentially genetic heterogeneity by gender in a large-scale cohort. A total of 613 T2DM patients and 8221 control subjects from the Korea Association REsource (KARE) cohort were included in the analysis of genetic association of T2DM with 33 nucleotide polymorphic markers identified by previous studies. The association analysis was further conducted with data partitioned by gender. The association analysis resulted in five nucleotide sequence variants associated with the susceptibility of T2DM after Bonferonni correction (P < 0.0015). One was located near the gene of hematopoietically expressed homeobox (HHEX), and the others were all in the gene of cyclin-dependent kinase 5 regulatory subunit-associated protein 1-like 1 (CDKAL1). Further analysis revealed that the sequence variant (rs5015480) near HHEX and two SNPs (rs7756992 and rs9465871) in CDKAL1 were associated with the susceptibility of T2DM in females (P<0.005), but not in males (P>0.005). We suggested heterogeneous genetic associations of the T2DM susceptibility with the CDKAL1 and HHEX genes by gender.     

Genetic variants on chromosome 6p21.1 and 6p22.3 are associated with type 2 diabetes risk: a case-control study in Han Chinese

Recent genome-wide association studies have identified several single nucleotide polymorphisms (SNPs) on chromosome 6p21.1 and 6p22.3 as type 2 diabetes (T2D) susceptibility loci in the European and Japanese populations. However, these SNPs have not been well evaluated in Chinese population. Here, we performed a case-control study with 2925 T2D cases and 3281 controls in a Chinese population. We used TaqMan OpenArray and Sequenom MassARRAY to genotype the four SNPs (rs4712523, rs7756992, rs4712524 and rs6931514) in CDKAL1 (cyclin-dependent kinase 5 regulatory subunit-associated protein 1-like 1) at 6p22.3 and one SNP (rs9472138) near vascular endothelial growth factor A (VEGFA) at 6p21.1. All the five SNPs were significantly associated with T2D risk with overall effects (odds ratio, OR) from 1.19 to 1.29 in the additive genetic model (rs6931514: OR=1.29, 95% confidence intervals (95% CI)=1.19-1.39, P=5.6 × 10(-10); rs7756992: OR=1.23, 95% CI=1.15-1.32, P=1.2 × 10(-8); rs4712523: OR=1.25, 95% CI=1.15-1.35, P=3.8 × 10(-8); rs4712524: OR=1.24, 95% CI=1.15-1.35, P=6.8 × 10(-8); rs9472138: OR=1.19, 95% CI=1.05-1.34, P=006). Conditional analysis identified two independent signals (rs6931514 at 6p22.3 and rs9472138 at 6p21.1) that were significantly associated with T2D. Compared with the wild homozygote of rs6931514 and rs9472138, subjects with variant alleles of the two SNPs had increased risk for T2D susceptibility in a dose-response manner (P(trend)=7.4 × 10(-12)). Our findings indicated that genetic variants of CDKAL1 and VEGFA on chromosome 6 may contribute to T2D risk in Chinese population, especially for rs9472138 at 6p21.1 identified for the first time to significantly increase the T2D risk in Chinese individuals.     

Analysis of novel risk loci for type 2 diabetes in a general French population: the D.E.S.I.R. study

Recently, Genome Wide Association (GWA) studies identified novel single nucleotide polymorphisms (SNPs), highly associated with type 2 diabetes (T2D) in several case-control studies of European descent. However, the impact of these markers on glucose homeostasis in a population-based study remains to be clarified.The French prospective D.E.S.I.R. study (N = 4,707) was genotyped for 22 polymorphisms within 14 loci showing nominal to strong association with T2D in recently published GWA analyses (CDKAL1, IGFBP2, CDKN2A/2B, EXT2, HHEX, LOC646279, SLC30A8, MMP26, KCTD12, LDLR, CAMTA1, LOC38776, NGN3 and CXCR4). We assessed their effects on quantitative traits related to glucose homeostasis in 4,283 normoglycemic middle-aged participants at baseline and their contribution to T2D incidence during 9 years of follow-up.Individuals carrying T2D risk alleles of CDKAL1 or SLC30A8 had lower fasting plasma insulin level (rs7756992 P = 0.003) or lower basal insulin secretion (rs13266634 P = 0.0005), respectively, than non-carriers. Furthermore, NGN3 and MMP26 risk alleles associated with higher fasting plasma glucose levels (rs10823406 P = 0.01 and rs2499953 P = 0.04, respectively). However, for these SNPs, only modest associations were found with a higher incidence of T2D: hazard ratios of 2.03 [1.00-4.11] for MMP26 (rs2499953 P = 0.05) and 1.33 [1.02-1.73] for NGN3 (rs10823406 P = 0.03).We confirmed deleterious effects of SLC30A8, CDKAL1, NGN3 and MMP26 risk alleles on glucose homeostasis in the D.E.S.I.R. prospective cohort. However, in contrast to TCF7L2, the contribution of novel loci to T2D incidence seems only modest in the general middle-aged French population and should be replicated in larger cohorts.     

Variations in/nearby genes coding for JAZF1, TSPAN8/LGR5 and HHEX-IDE and risk of type 2 diabetes in Han Chinese

Several genetic loci (JAZF1, CDC123/CAMK1D, TSPAN8/LGR5, ADAMTS9, VEGFA and HHEX-IDE) were identified to be significantly related to the risk of type 2 diabetes and quantitative metabolic traits in European populations. Here, we aimed to evaluate the impacts of these novel loci on type 2 diabetes risk in a population-based case-control study of Han Chinese (1912 cases and 2041 controls). We genotyped 13 single-nucleotide polymorphisms (SNPs) in/near these genes and examined the differences in allele/genotype frequency between cases and controls. We found that both IDE rs11187007 and HHEX rs1111875 were associated with type 2 diabetes risk (for both variants: odds ratio (OR)=1.15, 95% confidence interval (CI) 1.04-1.28, P=0.009). In a meta-analysis where we pooled our data with the three previous studies conducted in East Asians, we found that the variants of JAZF1 rs864745 (1.09 (1.03-1.16); P=3.49 × 10(-3)) and TSPAN8/LGR5 rs7961581 (1.11(1.05-1.17); P=1.89 × 10(-4)) were significantly associated with type 2 diabetes risk. In addition, the meta-analysis (7207 cases and 8260 controls) also showed that HHEX rs1111875 did have effects on type 2 diabetes in Chinese population (OR=1.15(1.10-1.21); P=1.93 × 10(-8)). This large population-based study and meta-analysis further confirmed the modest effects of the JAZF1, TSPAN8/LGR5 and HHEX-IDE loci on type 2 diabetes in Chinese and other East Asians.     

KCNQl基因多态性与2型糖尿病易感性相关研究

目的探讨KCNQ1基因单核苷酸多态性（SNPs）与2型糖尿病易感性的关系。方法应用基质辅助激光解吸附电离飞行时间质谱（MALDFFOF—Ms）平台以及MassARRARY—iPLEX技术,分别对238例2型糖尿病患者和240例正常对照组KCNQl基因的三个单核苷酸多态性位点（rs231361、rs231359和rs2237892）进行基因分型,并分析KCNQI基因位点在两组间的差异。结果rs2237892存在CC、TC、TT三种基因型多态性,在对照组中的基因型频率分别为45．5％、40．7％、13．8％,在病例组中的基因型频率分别为44．4％、49．6％、6．0％,该位点在对照组和病例组中分布差异有统计学意义（x2=9．334,P=0．009）。相较于cc基因型,TT基因型其OR（95％CI）分别为0．416（0．206-0．840）（P=0．014）。位点rs231361和rs231359均存在三种多态性,但在病例组和对照组间差异无统计学意义。结论KCNQ1基因位点rs2237892与2型糖尿病易感性相关,位点rs231361和rs231359与2型糖尿病易感性不相关。     

Common Variants in KCNQ1 Confer Increased Risk of Type 2 Diabetes and Contribute to the Diabetic Epidemic in East Asians: A Replication and Meta‐Analysis

We aimed to evaluate the effect of four common variants (rs2237892, rs2283228, rs2237895, and rs2237897) in KCNQ1 on susceptibility of type 2 diabetes (T2D) by performing a case‐control study as well as a comprehensive meta‐analysis. We genotyped these four variants in two sets of Chinese Han population, comprising a total of 2533 type 2 diabetic patients and 2643 nondiabetic controls. We also performed a meta‐analysis of our results with published studies in East Asians, meanwhile assessing the population attributable risk (PAR) of these variants. By combining our case‐control sets, a total of 45,204 T2D cases and 42,832 controls were included in the meta‐analyses. The per‐allele ORs ranged from 1.24 to 1.33, and the PARs ranged from 15.8% to 31.8%, with SNP rs2237892 being the most widely studied (16 articles containing a total of 38,338 cases and 35,907 controls), showing strongest association (per‐allele OR: 1.33, 95% CI: 1.28–1.39) and indicating the highest PAR (31.8%). This study confirmed the strong association between common variants in KCNQ1 and risk of T2D. Variants in KCNQ1 were among the leading genetic factors contributing to the overall burden of T2D in East Asians.     

A replication study of the IRS1, CAPN10, TCF7L2, and PPARG gene polymorphisms associated with type 2 diabetes in two different populations of Mexico

Type 2 diabetes (T2D) is a chronic degenerative disease that involves the participation of several genetic and environmental factors. The objective of the study was to determine the association of the IRS1 (rs1801278), CAPN10 (rs3792267), TCF7L2 (rs7903146 and rs12255372), and PPARG (rs1801282) gene polymorphisms with T2D, in two different Mexican populations. We conducted a case-control replication study in the state of Guerrero and in Mexico City, with 400 subjects from Guerrero and 1065 from Mexico City. Data were analyzed by logistic regression, adjusting by ancestry, age, gender, and BMI, to determine the association with T2D. Heterozygosity for the Gly972Arg variant of the IRS1 gene showed the strongest association for T2D in both analyzed samples (OR = 2.43, 95% CI 1.12-5.26 and 2.64, 95% CI 1.37-5.10, respectively). In addition, an association of two SNPs of the TCF7L2 gene with T2D was observed in both cities: rs7903146, (for Guerrero OR = 1.98 CI95% 1.02-3.89 and for Mexico OR = 1.94 CI95% 1.31-2.88) and rs12255372 (OR = 1.79 CI95% 1.08-2.97, OR = 1.78 CI95% 1.17-2.71 respectively). We suggest that our results provide strong evidence that variation in the IRS1 and TCF7L2 genes confers susceptibility to T2D in our studied populations.     

Polymorphisms of the GSTM1, GSTP1, MPO, XRCC1, and NQO1 genes in Chinese patients with non-small cell lung cancers: relationship with aberrant promoter methylation of the CDKN2A and RARB genes

An association between functional polymorphisms of genes resulting in decreased detoxification of carcinogens or DNA repair and aberrant promoter methylation is an attractive hypothesis in lung carcinogenesis. The genotypes at polymorphic sites of the glutathione S-transferase (GST) M1 (null/wildtype) and P1 (nucleotide 2627 A/G), myeloperoxidase (MPO) (nucleotide -463 G/A), X-ray repair cross-complementing group 1 (XRCC1) (nucleotides 26304 C/T; 28152 G/A), and NADPH quinine oxidoreductase (NQO1) (nucleotide 609 C/T) genes in 75 Chinese patients with non-small cell lung cancer (NSCLC) were characterized with polymerase chain reaction-restriction fragment length polymorphism. Results were correlated with aberrant methylation of the CDKN2A (alias p16(INK4A)), retinoic acid receptor beta (RARB), methylguanine-DNA methyltransferase (MGMT), and death-associated-protein (DAP) kinase genes in the tumors. In comparison with an age-matched control, none of the polymorphisms were associated with increased lung cancer risks. In male patients, however, the MPO -463 GG homozygous state was associated with CDKN2A (alias p16(INK4A)) methylation (odds ratio OR=3.63, 95% confidence interval CI=1.26-10.51), and the XRCC1 26304 T allele in the heterozygous/homozygous state was associated with methylation of CDKN2A (OR=6.13, 95% CI=1.55-24.16) and RARB (OR=7.67, 95% CI=1.62-36.18). In female patients, the GSTP1 G allele in the heterozygous/homozygous state was associated with RARB methylation (OR=18.0, 95% CI=0.76-427.29). These results showed that functional deficiencies in metabolic pathways that protect cells from carcinogen induced DNA damage might be linked to aberrant promoter methylation of the CDKN2A and RARB genes during lung carcinogenesis.     

Evidence of association between single-nucleotide polymorphisms in lipid metabolism-related genes and type 2 diabetes mellitus in a Chinese population

Background: Type 2 diabetes mellitus (T2DM) is a complex chronic metabolic disorder triggered by insulin resistance in peripheral tissues. Evidence has shown that lipid metabolism and related genetic factors lead to insulin resistance. Hence, it is meaningful to investigate the association between single-nucleotide polymorphisms (SNPs) in lipid metabolism-related genes and T2DM.Methods: A total of 1,194 subjects with T2DM and 1,274 Non-diabetic subjects (NDM) were enrolled. Five SNPs in three genes (rs864745 in JAZF1, rs35767 in IGF1, and rs4376068, rs4402960, and rs6769511 in IGF2BP2) that contribute to insulin resistance involving lipid metabolism were genotyped using the MassArray method in a Chinese population.Results: The allele and genotypes of rs6769511 in IGF2BP2 were associated with T2DM (P=0.009 and P=0.002, respectively). In inheritance model analysis, compared with the T/T-C/T genotype, the C/C genotype of rs6769511 in IGF2BP2 was a risk factor for the development of T2DM (P<0.001, odds ratio [OR] =1.76; 95% confidence interval [CI]: 1.29-2.42). Haplotype analysis revealed associations of the rs4376068-rs4402960-rs6769511 haplotypes in IGF2BP2 with the development of T2DM (P=0.015). Additionally, rs4376068C-rs4402960T-rs6769511C was a risk haplotype for T2DM (OR=1.179; 95% CI: 1.033-1.346).Conclusion: The rs6769511 in IGF2BP2 was associated with T2DM susceptibility, and the rs4376068-rs4402960-rs6769511 haplotypes in IGF2BP2 was associated with the development of T2DM in a Chinese population.     

CDKN2A/2B基因多态性与妊娠糖尿病相关

目的研究CDKN2A/2B基因rs10811661的单核苷酸多态性(SNP),探讨其与妊娠糖尿病(GDM)的相关性。方法选取鲁西南地区正常糖耐量孕妇(NGT)100例、GDM患者120例、2型糖尿病(T2DM)患者100例作为研究对象,提取基因组DNA,采用PCR-RFLP方法检测CDKN2A/2B基因rs10811661多态性。结果 CDKN2A/2B基因rs10811661的TT、TC、CC 3种基因型分布在NGT组与GDM组间有显著差别(P<0.01),GDM组危险等位基因T分布频率显著高于NGT组(P<0.05)。3种基因型及等位基因分布在NGT组与T2DM组之间亦有显著差别(P<0.05)。结论在鲁西南地区女性人群中,CDKN2A/2B基因rs10811661 T/C多态性可能与妊娠糖尿病有明显相关性。     

Association study of polymorphisms in miRNAs with T2DM in Chinese population

Accumulated evidence indicates that microRNA (miRNA or miR) is involved in the development of type 2 diabetes (T2DM). Several studies have shown that single nucleotide polymorphisms (SNPs) located in miRNAs are associated with T2DM in Caucasian populations. The association studies of miRNA''s SNPs with T2DM in Asian are rarely reported, and there are distinct genetic differences between Caucasian and Asian populations. The focus of this study, therefore, is the association of T2DM with five SNPs (rs895819 in miR-27a, rs531564 in miR-124a, rs11888095 in miR-128a, rs3820455 in miR-194a and rs2910164 in miR-146a) located in five miRNAs in a Han Chinese population. A total of 738 subjects with T2DM and 610 non-diabetic subjects were genotyped using the TaqMan method. Next, the associations between the five SNPs with T2DM and individual metabolic traits were evaluated. Our data showed that the C allele of rs531564 in miR-124a may protect against T2DM (P=0.009, OR=0.758; 95%CI: 0.616-0.933). Conversely, the C allele of rs2910164 in miR-146a may increase the risk of developing T2DM (P<0.001, OR=1.459; 95%CI: 1.244-1.712). However, these five SNPs did not exhibit significant associations with individual metabolic traits in either the T2DM or non-diabetic groups. Our results revealed that genetic variations in miRNAs were associated with T2DM susceptibility in a Han Chinese population, and these results highlight the need to study the functional effects of these variants in miRNAs on the risk of developing T2DM.     

Variants of the MATP/SLC45A2 gene are protective for melanoma in the French population

In this study, we investigated whether variants in three key pigmentation genes-MC1R, MATP/SLC45A2, and OCA2--were involved in melanoma predisposition. A cohort comprising 1,019 melanoma patients (MelanCohort) and 1,466 Caucasian controls without skin cancers were studied. A total of 10 polymorphisms, including five functional MC1R alleles (p.Asp84Glu, p.Arg142His, p.Arg151Cys, p.Arg160Trp, and p.Asp294His), two nonsynonymous SLC45A2 variants (p.Phe374Leu and p.Glu272Lys), and three intronic OCA2 variants previously shown to be strongly associated with eye color (rs7495174 T>C, rs4778241 G>T, and rs4778138 T>C) were genotyped. As expected, MC1R variants were closely associated with melanoma risk (P value <2.20.10(-16); odds ratio [OR]=2.29 [95% confidence interval, CI=1.85-2.82 and OR=3.3 [95% CI=2.00-5.45], for the presence of one or two variants, respectively). Interestingly, the SLC45A2 variant p.Phe374Leu was significantly and strongly protective for melanoma (P-value=2.12.10(-15); OR=0.35 [95% CI=0.26-0.46] and OR=0.32 [95% CI=0.24-0.43], considering the genotypes Phe/Leu and Leu/Leu, respectively). MC1R and SLC45A2 variants had additive effects on melanoma risk, and after adjusting for pigmentation characteristics, the risk was persistent, even though both genes had a strong impact on pigmentation. Future studies may show whether genetic information could provide a useful complement to physical examination in predicting melanoma risk.     

Polymorphic variants of the IL2RA gene and susceptibility to type 1 diabetes in the Polish population

Polymorphic variants of the IL2RA gene, which encodes high-affinity alpha subunit (CD25) of the interleukin-2 receptor, were recently found to affect the risk of several autoimmune disorders. This study was aimed to investigate the association of selected IL2RA polymorphisms (rs11594656, rs3118470, rs2104286 and rs7093069) with type 1 diabetes (T1D) in a Polish cohort comprising 445 patients and 671 healthy control subjects. The minor A allele at rs11594656 was found significantly less frequently among T1D subjects, compared with the control group [P = 0.011; odds ratio (OR) = 0.77; 95% confidence interval (CI) = 0.629-0.942]. In contrast, the minor C allele at rs3118470 appeared to be significantly associated with the occurrence of T1D (P = 0.003; OR = 1.30; 95% CI = 1.094-1.550). Two other IL2RA single nucleotide polymorphisms (SNPs) did not show significant differences among investigated groups. In conclusion, the study confirms the association of the IL2RA locus with T1D in the Polish population.