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Glucose-Related Traits and Risk of Migraine—A Potential Mechanism and Treatment Consideration. Genes (Basel) 2022; 13:genes13050730. [PMID: 35627115 PMCID: PMC9141901 DOI: 10.3390/genes13050730] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 04/19/2022] [Accepted: 04/19/2022] [Indexed: 12/16/2022] Open
Abstract
Migraine and glucose-related (glycaemic) traits (fasting glucose, fasting insulin, and type 2 diabetes) are common and complex comorbid disorders that cause major economic and social burdens on patients and their families. Studies on the relationship between migraine and glucose-related traits have yielded inconsistent results. The purpose of this review is to synthesise and discuss the information from the available literature on the relationship between fasting glucose, fasting insulin, and type 2 diabetes (T2D) with migraine. Publications on migraine and fasting glucose, migraine and fasting insulin, and migraine and T2D were identified from a PubMed and Google Scholar database search and reviewed for this article. Multiple publications have suggested that the comorbidity of migraine and glucose-related traits may have a similar complex pathogenic mechanism, including impaired glucose homeostasis, insulin resistance, reduced cerebrovascular reactivity, abnormal brain metabolism, shared genetic factors, neurotransmitters, and sex hormones. Furthermore, several studies have found a bi-directional link between migraine with insulin resistance and T2D. There is strong evidence for a biological association between migraine headache and glucose-related traits, and burgeoning evidence for shared genetic influences. Therefore, genetic research into these comorbid traits has the potential to identify new biomarkers and therapeutic targets and provide biological insight into their relationships. We encourage healthcare professionals to consider the co-occurrence of migraine with glucose-related traits in the evaluation and treatment of their patients.
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Exome sequencing reveals novel rare variants in Iranian familial multiple sclerosis: The importance of POLD2 in the disease pathogenesis. Genomics 2021; 113:2645-2655. [PMID: 34116171 DOI: 10.1016/j.ygeno.2021.06.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 04/20/2021] [Accepted: 06/06/2021] [Indexed: 02/07/2023]
Abstract
The prevalence of familial multiple sclerosis (FMS) is increasing worldwide which endorses the heritability of the disease. Given that many genome variations are ethnicity-specific and consanguineous marriage could affect genetic diseases, hereditary disease gene analysis among FMS patients from Iran, a country with high rates of parental consanguinity, could be highly effective in finding mutations underlying disease pathogenesis. To examine rare genetic mutations, we selected three Iranian FMS cases with ≥3 MS patients in more than one generation and performed whole exome sequencing. We identified a homozygous rare missense variant in POLD2 (p. Arg141Cys; rs372336011). Molecular dynamics analysis showed reduced polar dehydration energy and conformational changes in POLD2 mutant. Further, we found a heterozygote rare missense variant in NBFP1 (p. Gly487Asp; rs778806175). Our study revealed the possible role of novel rare variants in FMS. Molecular dynamic simulation provided the initial evidence of the structural changes behind POLD2 mutant.
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Ereqat S, Cauchi S, Eweidat K, Elqadi M, Nasereddin A. Estrogen receptor 1 gene polymorphisms (PvuII and XbaI) are associated with type 2 diabetes in Palestinian women. PeerJ 2019; 7:e7164. [PMID: 31293826 PMCID: PMC6601601 DOI: 10.7717/peerj.7164] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 05/21/2019] [Indexed: 12/24/2022] Open
Abstract
Background Type 2 diabetes mellitus (T2DM) is a multifactorial disease where both genetic and environmental factors contribute to its pathogenesis. The PvuII and XbaI polymorphisms of the estrogen receptor 1 (ESR1) gene have been variably associated with T2DM in several populations. This association has not been studied in the Palestinian population. Therefore, the aim of this study was to investigate the association between the PvuII and XbaI variants in the ESR1 and T2DM and its related metabolic traits among Palestinian women. Methods This case-control study included 102 T2DM and 112 controls in which PvuII and XbaI variants of the ESR1 gene were genotyped using amplicon based next generation sequencing (NGS). Results Allele frequencies of both PvuII and XbaI variants were not significantly different between patients and control subjects (P > 0.05). In logestic regression analysis adjusted for age and BMI, the ESR1 PvuII variant was associated with risk of T2DM in three genotypic models (P < 0.025) but the strongest association was observed under over-dominant model (TT+CC vs. TC) (OR = 2.32, CI [1.18-4.55] adjusted P = 0.013). A similar but non-significant trend was also observed for the ESR1 XbaI variant under the over-dominant model (AA+GG vs. AG) (OR = 2.03, CI [1.05-3.95]; adjusted P = 0.035). The frequencies of the four haplotypes (TA, CG, CA, TG) were not significantly different in the T2DM patients compared with control group (P > 0.025). Among diabetic group, an inverse trend with risk of cardio vascular diseases was shown in carriers of CG haplotype compared to those with TA haplotype (OR = 0.28, CI [0.09-0.90]; adjusted P = 0.035). Further, stratified analyses based on ESR1 PvuII and XbaI genotypes revealed no evidence for association with lipid levels (TC, TG, HDL, LDL). Conclusions This is the first Palestinian study to conclude that ESR1 PuvII and XbaI variants may contribute to diabetes susceptibility in Palestinian women. Identification of genetic risk markers can be used in defining high risk subjects and in prevention trials.
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Affiliation(s)
- Suheir Ereqat
- Biochemistry and Molecular Biology Department-Faculty of Medicine, Al-Quds University, East Jerusalem, Palestine
| | - Stéphane Cauchi
- CNRS, UMR8204, Lille, France.,INSERM, U1019, Lille, France.,Université de Lille, Lille, France.,Institut Pasteur de Lille, Centre d'Infection et d'Immunité de Lille, Lille, France
| | - Khaled Eweidat
- Biochemistry and Molecular Biology Department-Faculty of Medicine, Al-Quds University, East Jerusalem, Palestine
| | - Muawiyah Elqadi
- Biochemistry and Molecular Biology Department-Faculty of Medicine, Al-Quds University, East Jerusalem, Palestine
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Zhang T, Liu Y, Hu Y, Zhang X, Zhong L, Fan J, Peng Z. Association of donor and recipient SUMO4 rs237025 genetic variant with new-onset diabetes mellitus after liver transplantation in a Chinese population. Gene 2017; 627:428-433. [PMID: 28689037 DOI: 10.1016/j.gene.2017.06.060] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2017] [Revised: 06/28/2017] [Accepted: 06/30/2017] [Indexed: 12/26/2022]
Abstract
BACKGROUNDS & AIMS New-onset diabetes mellitus (NODM) is a common complication after liver transplantation (LT). The small ubiquitin-like modifier 4 (SUMO4) rs237025 polymorphism has been reported to be associated with type 2 diabetes mellitus (T2DM). In this study, we aimed to evaluate the association of donor and recipient SUMO4 rs237025 polymorphisms with NODM and the long-term consequences of NODM after LT. METHODS A total of 126 liver transplant patients were enrolled in the study. One single nucleotide polymorphism, SUMO4 rs237025, was genotyped in both donors and recipients. RESULTS Both donor and recipient SUMO4 rs237025 polymorphisms were found to be significantly associated with NODM after LT. In multivariate analysis, recipient age>50 years, tacrolimus trough concentrations>10ng/mL at 1month after LT, donor and recipient rs237025 genetic variant, and the combined donor and recipient rs237025 genetic variant were independent predictive factors of NODM. Area under the receiver operating characteristic curve (AUROC) analysis indicated the higher predictive ability of the model containing combined donor and recipient rs237025 polymorphisms than the clinical model (p=0.046). Furthermore, Kaplan-Meier survival analysis demonstrated that NODM was related to significantly poorer patient survival in comparison with non-NODM patients (p=0.041). CONCLUSIONS Both donor and recipient SUMO4 rs237025 polymorphisms contribute to the development of NODM after LT and NODM is a frequent complication that negatively affects patient survival.
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Affiliation(s)
- Tao Zhang
- Department of Hepatobiliary Pancreatic Surgery, Shanghai General Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yuan Liu
- Department of Hepatobiliary Pancreatic Surgery, Shanghai General Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yibo Hu
- Department of General Surgery, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Xiaoqing Zhang
- Department of Pharmacy, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Lin Zhong
- Department of Hepatobiliary Pancreatic Surgery, Shanghai General Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Junwei Fan
- Department of Hepatobiliary Pancreatic Surgery, Shanghai General Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
| | - Zhihai Peng
- Department of Hepatobiliary Pancreatic Surgery, Shanghai General Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
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Li YY, Wang H, Yang XX, Geng HY, Gong G, Kim HJ, Zhou YH, Wu JJ. Small Ubiquitin-Like Modifier 4 (SUMO4) Gene M55V Polymorphism and Type 2 Diabetes Mellitus: A Meta-analysis Including 6,823 Subjects. Front Endocrinol (Lausanne) 2017; 8:303. [PMID: 29163370 PMCID: PMC5673665 DOI: 10.3389/fendo.2017.00303] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 10/17/2017] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Many studies suggest that the small ubiquitin-like modifier 4 (SUMO4) M55V gene polymorphism (rs237025) may be associated with an increased risk of type 2 diabetes mellitus (T2DM). However, due to other conflicting results, a clear consensus is lacking in the matter. OBJECTIVE AND METHODS A meta-analysis consisting of 6,823 subjects from 10 studies was conducted to elucidate relationship between the SUMO4 M55V gene polymorphism and T2DM. Depending on the heterogeneity of the data, either a fixed or random-effects model would be used to assess the combined odds ratio (ORs) and their corresponding 95% confidence interval (CI). RESULTS SUMO4 gene M55V polymorphism was significantly associated with T2DM in the whole population under allelic (OR: 1.18, 95% CI: 1.10-1.28, P = 1.63 × 10-5), recessive (OR: 1.59, 95% CI: 1.14-2.23, P = 0.006), dominant (OR: 0.815, 95% CI: 0.737-0.901, P = 6.89 × 10-5), homozygous (OR: 1.415, 95% CI: 1.170-1.710, P = 0.0003), heterozygous (OR: 1.191, 95% CI: 1.072-1.323, P = 0.001), and additive genetic models (OR: 1.184, 95% CI: 1.097-1.279, P = 1.63 × 10-5). In our subgroup analysis, a significant association was found again in the Chinese population, but not in Japanese or Iranian population. CONCLUSION SUMO4 gene M55V polymorphism may correlate with increased T2DM risk. Chinese carriers of the V allele of the SUMO4 gene M55V polymorphism may be predisposed to developing T2DM.
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Affiliation(s)
- Yan-yan Li
- Department of Gerontology, First Affiliated Hospital of Nanjing Medical University, Nanjing, China
- Institute of Clinical Medicine, First Affiliated Hospital of Nanjing Medical University, Nanjing, China
- *Correspondence: Yan-yan Li,
| | - Hui Wang
- Department of Cardiology, First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Xin-xing Yang
- Department of Gerontology, First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Hong-yu Geng
- Department of Gerontology, First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Ge Gong
- Department of Gerontology, First Affiliated Hospital of Nanjing Medical University, Nanjing, China
- Department of Gerontology, Nanjing General Hospital, Nanjing, China
| | - Hyun Jun Kim
- Department of Physiology, University of Cincinnati, Cincinnati, OH, United States
| | - Yan-hong Zhou
- Department of Gerontology, First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Jing-jing Wu
- Department of Nephrology, First Affiliated Hospital of Nanjing Medical University, Nanjing, China
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Motawi TMK, El-Rehany MA, Rizk SM, Ramzy MM, El-Roby DM. Genetic polymorphism of estrogen receptor alpha gene in Egyptian women with type II diabetes mellitus. Meta Gene 2015; 6:36-41. [PMID: 26401488 PMCID: PMC4561236 DOI: 10.1016/j.mgene.2015.08.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Revised: 08/03/2015] [Accepted: 08/05/2015] [Indexed: 12/26/2022] Open
Abstract
Estrogen might play an important role in type 2 diabetes mellitus pathogenesis. A number of polymorphisms have been reported in the estrogen receptor alpha gene including the XbaI and PvuII restriction enzyme polymorphisms. The aim of this study was to determine if ESRα gene polymorphisms are associated with type 2 diabetes mellitus and correlated with lipid profile. Ninety diabetic Egyptian patients were compared with forty healthy controls. ESRα genotyping of PvuII and XbaI was performed using restriction fragment length polymorphism analysis. Our study showed that there is more significant difference in the frequency of C and G polymorphic allele between patients and control groups in PvuII and XbaI respectively. Also carriers of minor C and G alleles of PvuII and XbaI gene polymorphisms were associated with increased fasting blood glucose and disturbance in lipid profile as there is an increase in total cholesterol, triglycerides and Low density lipoprotein. So findings of present study suggest the possibility that PvuII and XbaI polymorphisms in ERα are related to T2DM and with increased serum lipids among Egyptian population.
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Affiliation(s)
- Tarek M K Motawi
- Biochemistry Department, Faculty of Pharmacy, Cairo University, Egypt
| | | | - Sherine M Rizk
- Biochemistry Department, Faculty of Pharmacy, Cairo University, Egypt
| | - Maggie M Ramzy
- Biochemistry Department, Faculty of Medicine, Minia University, Egypt
| | - Doaa M El-Roby
- Biochemistry Department, Faculty of Pharmacy, Cairo University, Egypt
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Translational implications of the β-cell epigenome in diabetes mellitus. Transl Res 2015; 165:91-101. [PMID: 24686035 PMCID: PMC4162854 DOI: 10.1016/j.trsl.2014.03.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Revised: 03/04/2014] [Accepted: 03/06/2014] [Indexed: 12/12/2022]
Abstract
Diabetes mellitus is a disorder of glucose homeostasis that affects more than 24 million Americans and 382 million individuals worldwide. Dysregulated insulin secretion from the pancreatic β cells plays a central role in the pathophysiology of all forms of diabetes mellitus. Therefore, an enhanced understanding of the pathways that contribute to β-cell failure is imperative. Epigenetics refers to heritable changes in DNA transcription that occur in the absence of changes to the linear DNA nucleotide sequence. Recent evidence suggests an expanding role of the β-cell epigenome in the regulation of metabolic health. The goal of this review is to discuss maladaptive changes in β-cell DNA methylation patterns and chromatin architecture, and their contribution to diabetes pathophysiology. Efforts to modulate the β-cell epigenome as a means to prevent, diagnose, and treat diabetes are also discussed.
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Keaton JM, Cooke Bailey JN, Palmer ND, Freedman BI, Langefeld CD, Ng MCY, Bowden DW. A comparison of type 2 diabetes risk allele load between African Americans and European Americans. Hum Genet 2014; 133:1487-95. [PMID: 25273842 DOI: 10.1007/s00439-014-1486-5] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Accepted: 09/08/2014] [Indexed: 12/25/2022]
Abstract
The prevalence of type 2 diabetes (T2D) is greater in populations of African descent compared to European-descent populations. Genetic risk factors may underlie the disparity in disease prevalence. Genome-wide association studies (GWAS) have identified >60 common genetic variants that contribute to T2D risk in populations of European, Asian, African and Hispanic descent. These studies have not comprehensively examined population differences in cumulative risk allele load. To investigate the relationship between risk allele load and T2D risk, 46 T2D single nucleotide polymorphisms (SNPs) in 43 loci from GWAS in European, Asian, and African-derived populations were genotyped in 1,990 African Americans (n = 963 T2D cases, n = 1,027 controls) and 1,644 European Americans (n = 719 T2D cases, n = 925 controls) ascertained and recruited using a common protocol in the southeast United States. A genetic risk score (GRS) was constructed from the cumulative risk alleles for each individual. In African American subjects, risk allele frequencies ranged from 0.024 to 0.964. Risk alleles from 26 SNPs demonstrated directional consistency with previous studies, and 3 SNPs from ADAMTS9, TCF7L2, and ZFAND6 showed nominal evidence of association (p < 0.05). African American individuals carried 38-67 (53.7 ± 4.0, mean ± SD) risk alleles. In European American subjects, risk allele frequencies ranged from 0.084 to 0.996. Risk alleles from 36 SNPs demonstrated directional consistency, and 10 SNPs from BCL11A, PSMD6, ADAMTS9, ZFAND3, ANK1, CDKN2A/B, TCF7L2, PRC1, FTO, and BCAR1 showed evidence of association (p < 0.05). European American individuals carried 38-65 (50.9 ± 4.4) risk alleles. African Americans have a significantly greater burden of 2.8 risk alleles (p = 3.97 × 10(-89)) compared to European Americans. However, GRS modeling showed that cumulative risk allele load was associated with risk of T2D in European Americans, but only marginally in African Americans. This result suggests that there are ethnic-specific differences in genetic architecture underlying T2D, and that these differences complicate our understanding of how risk allele load impacts disease susceptibility.
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Affiliation(s)
- Jacob M Keaton
- Molecular Genetics and Genomics Program, Wake Forest School of Medicine, Winston-Salem, NC, USA
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Wu C, Gong Y, Yuan J, Gong H, Zou Y, Ge J. Identification of shared genetic susceptibility locus for coronary artery disease, type 2 diabetes and obesity: a meta-analysis of genome-wide studies. Cardiovasc Diabetol 2012; 11:68. [PMID: 22697793 PMCID: PMC3481354 DOI: 10.1186/1475-2840-11-68] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/08/2012] [Accepted: 05/28/2012] [Indexed: 01/10/2023] Open
Abstract
Type 2 diabetes (2DM), obesity, and coronary artery disease (CAD) are frequently coexisted being as key components of metabolic syndrome. Whether there is shared genetic background underlying these diseases remained unclear. We performed a meta-analysis of 35 genome screens for 2DM, 36 for obesity or body mass index (BMI)-defined obesity, and 21 for CAD using genome search meta-analysis (GSMA), which combines linkage results to identify regions with only weak evidence and provide genetic interactions among different diseases. For each study, 120 genomic bins of approximately 30 cM were defined and ranked according to the best linkage evidence within each bin. For each disease, bin 6.2 achieved genomic significanct evidence, and bin 9.3, 10.5, 16.3 reached suggestive level for 2DM. Bin 11.2 and 16.3, and bin 10.5 and 9.3, reached suggestive evidence for obesity and CAD respectively. In pooled all three diseases, bin 9.3 and 6.5 reached genomic significant and suggestive evidence respectively, being relatively much weaker for 2DM/CAD or 2DM/obesity or CAD/obesity. Further, genomewide significant evidence was observed of bin 16.3 and 4.5 for 2DM/obesity, which is decreased when CAD was added. These findings indicated that bin 9.3 and 6.5 are most likely to be shared by 2DM, obesity and CAD. And bin 16.3 and 4.5 are potentially common regions to 2DM and obesity only. The observed shared susceptibility regions imply a partly overlapping genetic aspects of disease development. Fine scanning of these regions will definitely identify more susceptibility genes and causal variants.
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Affiliation(s)
- Chaoneng Wu
- Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital, Fudan University, Shanghai 200032, China
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Ganasyam SR, Rao TB, Murthy YSR, Jyothy A, Sujatha M. Association of Estrogen Receptor-α Gene & Metallothionein-1 Gene Polymorphisms in Type 2 Diabetic Women of Andhra Pradesh. Indian J Clin Biochem 2012; 27:69-73. [PMID: 23277715 DOI: 10.1007/s12291-011-0179-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2011] [Accepted: 11/10/2011] [Indexed: 11/26/2022]
Abstract
Type 2 diabetes mellitus (DM) is a multifactorial disease where both genetic and environmental factors contribute to its pathogenesis. Estrogen plays an important role in type 2 DM pathogenesis. A number of polymorphisms have been reported in the estrogen receptor (ESR1), including the XbaI and PvuII restriction enzyme polymorphisms of ESR1,which may be involved in disease pathogenesis. Metallothioneins (MT) act as potent antioxidants against various oxidative damages. Very few studies have indicated the association between Estrogen Receptor-α, MT1 gene polymorphisms with type2 DM. A total of 100 type 2 diabetic women and 100 age, sex matched controls were recruited. Using the PCR based RFLP method, the PvuII and XbaI polymorphisms of ESR1 and in MT1A (rs8052394 and rs11076161) gene polymorphisms were analysed. The genotype distribution and frequency of mutated allele showed no significant differences between diabetic and non-diabetic groups in PvuII (χ2 = 2.443; P = 0.1181) or XbaI (χ2 = 1.789; P = 0.1812) and rs8052394 (χ2 = 1.154; P = 0.2840) or rs11076161 (χ2 = 0.4141; P = 0.5199), polymorphisms. This is the first Indian study to conclude that ESR1 and MT1 gene polymorphisms are not associated with increased susceptibility to type 2 diabetes in Indian women.
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Affiliation(s)
- Shilpa Reddy Ganasyam
- Department of Biochemistry, Institute of Genetics and Hospital for Genetic Diseases, Osmania University, Begumpet, Hyderabad, 500016 Andhra Pradesh India
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Abstract
The risk of type 2 diabetes (T2D) increases with obesity. One possible explanation is that pleiotropic genes affect risk of both T2D and obesity. To identify pleiotropic genes, we performed bivariate analysis of T2D with waist-hip ratio (WHR) and with body mass index (BMI) in the African-American subset of the Genetics of NIDDM (GENNID) sample. Of 12 T2D loci identified through suggestive or higher univariate logarithm of the odds ratio (lod) scores, we inferred pleiotropy with obesity for six (chromosomes 1 at 17-19 Mb, 2 at 237-240 Mb, 7 at 54-73 Mb, 13 at 26-30 Mb, 16 at 26-47 Mb and 20 at 56-59 Mb). These findings provide evidence that at least some of the co-occurrence of obesity with T2D is because of pleiotropic genes. We also inferred four obesity loci through suggestive or higher lod scores for WHR (chromosomes 1 at 24-32 Mb, 2 at 79-88 Mb, 2 at 234-238 Mb and 3 at 148-159 Mb).
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Affiliation(s)
- Sandra J Hasstedt
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112-5330, USA.
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12
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Hellwege JN, Hicks PJ, Palmer ND, Ng MCY, Freedman BI, Bowden DW. Examination of Rare Variants in HNF4 α in European Americans with Type 2 Diabetes. ACTA ACUST UNITED AC 2011; 2. [PMID: 23227446 DOI: 10.4172/2155-6156.1000145] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The hepatocyte nuclear factor 4-α (HNF4α) gene codes for a transcription factor which is responsible for regulating gene transcription in pancreatic beta cells, in addition to its primary role in hepatic gene regulation. Mutations in this gene can lead to maturity-onset diabetes of the young (MODY), an uncommon, autosomal dominant, non-insulin dependent form of diabetes. Mutations in HNF4α have been found in few individuals, and infrequently have they segregated completely with MODY in families. In addition, due to similarity of phenotypes, it is unclear what proportion of type 2 diabetes (T2DM) in the general population is due to MODY or HNF4α mutations specifically. In this study, 27 documented rare and common variants were genotyped in a European American population of 1270 T2DM cases and 1017 controls from review of databases and literature implicating HNF4α variants in MODY and T2DM. Seventeen variants were found to be monomorphic. Two cases and one control subject had one copy of a 6-bp P2 promoter deletion. The intron 1 variant (rs6103716; MAF = 0.31) was not significantly associated with disease status (p>0.8) and the missense variant Thr130Ile (rs1800961; MAF = 0.027) was also not significantly different between cases and controls (p>0.2), but showed a trend consistent with association with T2DM. Four variants were found to be rare as heterozygotes in small numbers of subjects. Since many variants were infrequent, a pooled chi-squared analysis of rare variants was used to assess the overall burden of variants between cases and controls. This analysis revealed no significant difference (P=0.22). We conclude there is little evidence to suggest that HNF4α variants contribute significantly to risk of T2DM in the general population, but a modest contribution cannot be excluded. In addition, the observation of some mutations in controls suggests they are not highly penetrant MODY-causing variants.
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Affiliation(s)
- Jacklyn N Hellwege
- Center for Genomics and Personalized Medicine Research, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA ; Center for Diabetes Research, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA ; Program in Molecular Genetics and Genomics, Wake Forest School of Medicine, Winston-Salem, NC, USA
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Thomas CJ. The confluence of human genomics, environment, and determinants of health-related quality of life among African American hemodialysis patients. SOCIAL WORK IN PUBLIC HEALTH 2011; 26:417-430. [PMID: 21707350 DOI: 10.1080/19371918.2011.579505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The intersection of human genome sequencing, environmental factors that lend to further understanding of the etiology of complex diseases, and components that constitute the health-related quality of life for African American hemodialysis patients are explored in this article. There are many renal diseases that have genetic components. Even though genetic polymorphisms and allelic variations can explain some of the etiology and disparities in disease susceptibility for African Americans, the role of the environment must also be considered. For African American hemodialysis patients, the environmental influences of religiosity and social support, along with genetic factors, affect their health-related quality of life. A study of 176 African American hemodialysis patients revealed that religiosity and social support had a significant impact on patient's health-related quality of life. Implications of the study mandate that social and behavioral researchers, who tend to focus on environmental issues, be given more freedom and latitude, along with genetic researchers, in designing and implementing studies involving genomic sequencing and the influence on health disparities among persons of African descent.
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Affiliation(s)
- Claudie J Thomas
- School of Social Work, Morgan State University, Baltimore, Maryland 21251, USA.
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Fallah S, Jafarzadeh M, Hedayati M. No association of the SUMO4 polymorphism M55V variant in type 2 diabetes in Iranian subjects. Diabetes Res Clin Pract 2010; 90:191-5. [PMID: 20728233 DOI: 10.1016/j.diabres.2010.05.033] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/31/2009] [Revised: 05/02/2010] [Accepted: 05/06/2010] [Indexed: 10/19/2022]
Abstract
INTRODUCTION Diabetes mellitus incidence has an increasing rate and it's genetic aspect is an important approach as a risk factor and predictive value in this disorder. In some population, SUMO4, a regulator of NF-κB, gene polymorphism is associated with diabetes. A single-nucleotide polymorphism was detected in SUMO4; substituting a highly conserved methionine with a valine residue (M55V). We studied the association between M55V polymorphism in the SUMO4 gene insusceptibility of type 2 diabetes in patients with type 2 diabetes. MATERIALS AND METHODS Participants were 50 patients with type 2 diabetes and 50 control Iranian subjects. Genotyping was done using polymorphism chain reaction (PCR) technique and subsequent cleavage by restriction endonuclease (RFLP) for the M55V SUMO4 gene variant. RESULTS The frequency of SUMO4 AA, AG and GG were 13%, 25% and 12% in control group and 20%, 22%, 18% in the type 2 diabetes patients respectively. The SUMO4 M55V variant was not associated with the susceptibility of type 2 diabetes. CONCLUSION The study indicates that the SUMO4 gene M55V variant was not associated with the susceptibility of the type 2 diabetes polymorphism.
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Affiliation(s)
- Soudabeh Fallah
- Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran.
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Lewis JP, Palmer ND, Ellington JB, Divers J, Ng MCY, Lu L, Langefeld CD, Freedman BI, Bowden DW. Analysis of candidate genes on chromosome 20q12-13.1 reveals evidence for BMI mediated association of PREX1 with type 2 diabetes in European Americans. Genomics 2010; 96:211-9. [PMID: 20650312 DOI: 10.1016/j.ygeno.2010.07.006] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2009] [Revised: 07/16/2010] [Accepted: 07/16/2010] [Indexed: 01/02/2023]
Abstract
Chromosome 20q12-q13.1 has been linked to type 2 diabetes (T2D) in multiple populations. We examined the influence of genes in this region on T2D and BMI in two European American case-control populations. SNPs were genotyped in 300 diabetic patients and 310 controls. A subset of 72 SNPs were further genotyped in 470 cases and 442 controls. All genes examined showed evidence of association with T2D in the initial sample (additive P-value [P(a)]=0.00090-0.045). SNPs near PREX1 were also associated in the second case-control population (P(a)=0.017-0.042). The combined analysis resulted in the same SNPs, among others, associated with T2D (P(a)=0.0013-0.041). Stratification analysis by T2D status showed that association with BMI was observed solely in cases (P(a)=0.0018-0.041). Mediation testing revealed that 30-40% of the effects of these SNPs on T2D were significantly mediated by BMI. SNPs near PREX1 may contribute to T2D susceptibility mediated through effects of adiposity in European Americans.
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Affiliation(s)
- Joshua P Lewis
- Center for Human Genomics, Wake Forest University School of Medicine, Winston-Salem, NC 27157, USA
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Czubryt MP, Lamoureux L, Ramjiawan A, Abrenica B, Jangamreddy J, Swan K. Regulation of cardiomyocyte Glut4 expression by ZAC1. J Biol Chem 2010; 285:16942-50. [PMID: 20363751 DOI: 10.1074/jbc.m109.097246] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The transcription factor ZAC1 is expressed in a variety of tissues including the developing heart, but its physiological role is unclear. We examined the role of ZAC1 in regulating expression of the insulin-responsive glucose transporter GLUT4 and whether ZAC1 expression is altered in cardiomyocyte hypertrophy. We demonstrated expression of Zac1 mRNA and protein in rat cardiomyocytes by PCR and Western blotting, respectively. Using a combination of chromatin immunoprecipitation and luciferase assays, we showed that ZAC1 regulates Glut4 expression via a specific binding site in the Glut4 promoter. Overexpression of ZAC1 increased Glut4 mRNA and protein expression and resulted in increased glucose uptake in cardiomyocytes as determined by a fluorescent analog uptake assay. Induction of hypertrophy by phenylephrine or isoproterenol resulted in increased Zac1 expression. We identified a novel putative promoter in the Zac1 gene and demonstrated increased binding of MEF2 to this promoter in response to hypertrophic stimulation. MEF2 regulated transactivation of the Zac1 promoter and ZAC1 protein expression. This work identifies ZAC1 as a novel and previously unknown regulator of cardiomyocyte Glut4 expression and glucose uptake. Our results also implicate MEF2 as a regulator of ZAC1 expression in response to induction of hypertrophy.
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Affiliation(s)
- Michael P Czubryt
- Department of Physiology, University of Manitoba, Institute of Cardiovascular Sciences, St Boniface General Hospital Research Centre, Winnipeg, Manitoba R2H 2A6, Canada
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McKnight AJ, Currie D, Maxwell AP. Unravelling the genetic basis of renal diseases; from single gene to multifactorial disorders. J Pathol 2010; 220:198-216. [PMID: 19882676 DOI: 10.1002/path.2639] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Chronic kidney disease is common with up to 5% of the adult population reported to have an estimated glomerular filtration rate of < 60 ml/min/1.73 m(2). A large number of pathogenic mutations have been identified that are responsible for 'single gene' renal disorders, such as autosomal dominant polycystic kidney disease and X-linked Alport syndrome. These single gene disorders account for < 15% of the burden of end-stage renal disease that requires dialysis or kidney transplantation. It has proved more difficult to identify the genetic susceptibility underlying common, complex, multifactorial kidney conditions, such as diabetic nephropathy and hypertensive nephrosclerosis. This review describes success to date and explores strategies currently employed in defining the genetic basis for a number of renal disorders. The complementary use of linkage studies, candidate gene and genome-wide association analyses are described and a collation of renal genetic resources highlighted.
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Affiliation(s)
- Amy J McKnight
- Nephrology Research Group, Queen's University of Belfast, Belfast BT9 7AB, Northern Ireland, UK
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18
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Leak TS, Langefeld CD, Keene KL, Gallagher CJ, Lu L, Mychaleckyj JC, Rich SS, Freedman BI, Bowden DW, Sale MM. Chromosome 7p linkage and association study for diabetes related traits and type 2 diabetes in an African-American population enriched for nephropathy. BMC MEDICAL GENETICS 2010; 11:22. [PMID: 20144192 PMCID: PMC2829011 DOI: 10.1186/1471-2350-11-22] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2009] [Accepted: 02/08/2010] [Indexed: 12/21/2022]
Abstract
BACKGROUND Previously we performed a linkage scan of 638 African American affected sibling pairs (ASP) with type 2 diabetes (T2D) enriched for end-stage renal disease (ESRD). Ordered subset linkage analysis (OSA) revealed a linkage peak on chromosome 7p in the subset of families with earlier age of T2D diagnosis. METHODS We fine mapped this region by genotyping 11 additional polymorphic markers in the same ASP and investigated a total of 68 single nucleotide polymorphisms (SNPs) in functional candidate genes (GCK1, IL6, IGFBP1 and IGFBP3) for association with age of T2D diagnosis, age of ESRD diagnosis, duration of T2D to onset of ESRD, body mass index (BMI) in African American cases and T2D-ESRD in an African American case-control cohort. OSA of fine mapping markers supported linkage at 28 cM on 7p (near D7S3051) in early-onset T2D families (max. LOD = 3.61, P = 0.002). SNPs in candidate genes and 70 ancestry-informative markers (AIMs) were evaluated in 577 African American T2D-ESRD cases and 596 African American controls. RESULTS The most significant association was observed between ESRD age of diagnosis and SNP rs730497, located in intron 1 of the GCK1 gene (recessive T2D age-adjusted P = 0.0006). Nominal associations were observed with GCK1 SNPs and T2D age of diagnosis (BMI-adjusted P = 0.014 to 0.032). Also, one IGFBP1 and four IGFBP3 SNPs showed nominal genotypic association with T2D-ESRD (P = 0.002-0.049). After correcting for multiple tests, only rs730497 remanined significant. CONCLUSION Variant rs730947 in the GCK1 gene appears to play a role in early ESRD onset in African Americans.
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Affiliation(s)
- Tennille S Leak
- Center for Human Genomics, Wake Forest University School of Medicine, Winston-Salem, NC, USA
- Department of Epidemiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Carl D Langefeld
- Department of Biostatistical Sciences, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Keith L Keene
- Center for Human Genomics, Wake Forest University School of Medicine, Winston-Salem, NC, USA
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA
| | - Carla J Gallagher
- Center for Human Genomics, Wake Forest University School of Medicine, Winston-Salem, NC, USA
- Department of Biochemistry, Wake Forest University School of Medicine, Winston-Salem, NC, USA
- Milton S Hershey Medical Center, Pennsylvania State University, Hershey, PA, USA
| | - Lingyi Lu
- Department of Biostatistical Sciences, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Josyf C Mychaleckyj
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
- Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
- Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA
| | - Barry I Freedman
- Department of Internal Medicine, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Donald W Bowden
- Center for Human Genomics, Wake Forest University School of Medicine, Winston-Salem, NC, USA
- Department of Biochemistry, Wake Forest University School of Medicine, Winston-Salem, NC, USA
- Department of Internal Medicine, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Michèle M Sale
- Center for Human Genomics, Wake Forest University School of Medicine, Winston-Salem, NC, USA
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA
- Department of Medicine, University of Virginia, Charlottesville, VA, USA
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19
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Malhotra A, Igo RP, Thameem F, Kao WL, Abboud HE, Adler SG, Arar NH, Bowden DW, Duggirala R, Freedman BI, Goddard KA, Ipp E, Iyengar SK, Kimmel PL, Knowler WC, Kohn O, Leehey D, Meoni LA, Nelson RG, Nicholas SB, Parekh RS, Rich SS, Chen YDI, Saad MF, Scavini M, Schelling JR, Sedor JR, Shah VO, Taylor KD, Thornley-Brown D, Zager PG, Horvath A, Hanson RL. Genome-wide linkage scans for type 2 diabetes mellitus in four ethnically diverse populations-significant evidence for linkage on chromosome 4q in African Americans: the Family Investigation of Nephropathy and Diabetes Research Group. Diabetes Metab Res Rev 2009; 25:740-7. [PMID: 19795399 PMCID: PMC2783577 DOI: 10.1002/dmrr.1031] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
BACKGROUND Previous studies have shown that in addition to environmental influences, type 2 diabetes mellitus (T2DM) has a strong genetic component. The goal of the current study is to identify regions of linkage for T2DM in ethnically diverse populations. METHODS Phenotypic and genotypic data were obtained from African American (AA; total number of individuals [N] = 1004), American Indian (AI; N = 883), European American (EA; N = 537), and Mexican American (MA; N = 1634) individuals from the Family Investigation of Nephropathy and Diabetes. Non-parametric linkage analysis, using an average of 4404 SNPs, was performed in relative pairs affected with T2DM in each ethnic group. In addition, family-based tests were performed to detect association with T2DM. RESULTS Statistically significant evidence for linkage was observed on chromosome 4q21.1 (LOD = 3.13; genome-wide p = 0.04) in AA. In addition, a total of 11 regions showed suggestive evidence for linkage (estimated at LOD > 1.71), with the highest LOD scores on chromosomes 12q21.31 (LOD = 2.02) and 22q12.3 (LOD = 2.38) in AA, 2p11.1 (LOD = 2.23) in AI, 6p12.3 (LOD = 2.77) in EA, and 13q21.1 (LOD = . 2.24) in MA. While no region overlapped across all ethnic groups, at least five loci showing LOD > 1.71 have been identified in previously published studies. CONCLUSIONS The results from this study provide evidence for the presence of genes affecting T2DM on chromosomes 4q, 12q, and 22q in AA; 6p in EA; 2p in AI; and 13q in MA. The strong evidence for linkage on chromosome 4q in AA provides important information given the paucity of diabetes genetic studies in this population.
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Affiliation(s)
- Alka Malhotra
- National Institute of Diabetes and Digestive and Kidney Diseases, Phoenix, Arizona
| | | | - Farook Thameem
- University of Texas Health Science Center at San Antonio, San Antonio, Texas
| | | | - Hanna E. Abboud
- University of Texas Health Science Center at San Antonio, San Antonio, Texas
| | - Sharon G. Adler
- Harbor-University of California Los Angeles Medical Center, Torrance, California
| | - Nedal H. Arar
- University of Texas Health Science Center at San Antonio, San Antonio, Texas
| | | | | | | | | | - Eli Ipp
- Harbor-University of California Los Angeles Medical Center, Torrance, California
| | | | - Paul L. Kimmel
- National Institute of Diabetes and Digestive and Kidney Diseases Program Office, Bethesda, Maryland
| | - William C. Knowler
- National Institute of Diabetes and Digestive and Kidney Diseases, Phoenix, Arizona
| | - Orly Kohn
- University of Chicago, Chicago, Illinois
| | | | | | - Robert G. Nelson
- National Institute of Diabetes and Digestive and Kidney Diseases, Phoenix, Arizona
| | | | | | | | - Yii-Der I. Chen
- University of California Los Angeles, Los Angeles, California
| | | | - Marina Scavini
- University of New Mexico, Albuquerque, New Mexico
- San Raffaele Scientific Institute, Milan (Italy)
| | | | | | | | - Kent D. Taylor
- University of California Los Angeles, Los Angeles, California
| | | | | | | | - Robert L. Hanson
- National Institute of Diabetes and Digestive and Kidney Diseases, Phoenix, Arizona
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Wongseree W, Assawamakin A, Piroonratana T, Sinsomros S, Limwongse C, Chaiyaratana N. Detecting purely epistatic multi-locus interactions by an omnibus permutation test on ensembles of two-locus analyses. BMC Bioinformatics 2009; 10:294. [PMID: 19761607 PMCID: PMC2759961 DOI: 10.1186/1471-2105-10-294] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2009] [Accepted: 09/17/2009] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND Purely epistatic multi-locus interactions cannot generally be detected via single-locus analysis in case-control studies of complex diseases. Recently, many two-locus and multi-locus analysis techniques have been shown to be promising for the epistasis detection. However, exhaustive multi-locus analysis requires prohibitively large computational efforts when problems involve large-scale or genome-wide data. Furthermore, there is no explicit proof that a combination of multiple two-locus analyses can lead to the correct identification of multi-locus interactions. RESULTS The proposed 2LOmb algorithm performs an omnibus permutation test on ensembles of two-locus analyses. The algorithm consists of four main steps: two-locus analysis, a permutation test, global p-value determination and a progressive search for the best ensemble. 2LOmb is benchmarked against an exhaustive two-locus analysis technique, a set association approach, a correlation-based feature selection (CFS) technique and a tuned ReliefF (TuRF) technique. The simulation results indicate that 2LOmb produces a low false-positive error. Moreover, 2LOmb has the best performance in terms of an ability to identify all causative single nucleotide polymorphisms (SNPs) and a low number of output SNPs in purely epistatic two-, three- and four-locus interaction problems. The interaction models constructed from the 2LOmb outputs via a multifactor dimensionality reduction (MDR) method are also included for the confirmation of epistasis detection. 2LOmb is subsequently applied to a type 2 diabetes mellitus (T2D) data set, which is obtained as a part of the UK genome-wide genetic epidemiology study by the Wellcome Trust Case Control Consortium (WTCCC). After primarily screening for SNPs that locate within or near 372 candidate genes and exhibit no marginal single-locus effects, the T2D data set is reduced to 7,065 SNPs from 370 genes. The 2LOmb search in the reduced T2D data reveals that four intronic SNPs in PGM1 (phosphoglucomutase 1), two intronic SNPs in LMX1A (LIM homeobox transcription factor 1, alpha), two intronic SNPs in PARK2 (Parkinson disease (autosomal recessive, juvenile) 2, parkin) and three intronic SNPs in GYS2 (glycogen synthase 2 (liver)) are associated with the disease. The 2LOmb result suggests that there is no interaction between each pair of the identified genes that can be described by purely epistatic two-locus interaction models. Moreover, there are no interactions between these four genes that can be described by purely epistatic multi-locus interaction models with marginal two-locus effects. The findings provide an alternative explanation for the aetiology of T2D in a UK population. CONCLUSION An omnibus permutation test on ensembles of two-locus analyses can detect purely epistatic multi-locus interactions with marginal two-locus effects. The study also reveals that SNPs from large-scale or genome-wide case-control data which are discarded after single-locus analysis detects no association can still be useful for genetic epidemiology studies.
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Affiliation(s)
- Waranyu Wongseree
- Department of Electrical Engineering, Faculty of Engineering, King Mongkut's University of Technology North Bangkok, 1518 Piboolsongkram Road, Bangsue, Bangkok 10800, Thailand
| | - Anunchai Assawamakin
- Division of Molecular Genetics, Department of Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, 2 Prannok Road, Bangkoknoi, Bangkok 10700, Thailand
| | - Theera Piroonratana
- Department of Electrical Engineering, Faculty of Engineering, King Mongkut's University of Technology North Bangkok, 1518 Piboolsongkram Road, Bangsue, Bangkok 10800, Thailand
| | - Saravudh Sinsomros
- Department of Electrical Engineering, Faculty of Engineering, King Mongkut's University of Technology North Bangkok, 1518 Piboolsongkram Road, Bangsue, Bangkok 10800, Thailand
| | - Chanin Limwongse
- Division of Molecular Genetics, Department of Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, 2 Prannok Road, Bangkoknoi, Bangkok 10700, Thailand
| | - Nachol Chaiyaratana
- Department of Electrical Engineering, Faculty of Engineering, King Mongkut's University of Technology North Bangkok, 1518 Piboolsongkram Road, Bangsue, Bangkok 10800, Thailand
- Division of Molecular Genetics, Department of Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, 2 Prannok Road, Bangkoknoi, Bangkok 10700, Thailand
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A variation in the cerebroside sulfotransferase gene is linked to exercise-modified insulin resistance and to type 2 diabetes. EXPERIMENTAL DIABETES RESEARCH 2009; 2009:429593. [PMID: 19587831 PMCID: PMC2705865 DOI: 10.1155/2009/429593] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 03/09/2009] [Accepted: 05/18/2009] [Indexed: 11/23/2022]
Abstract
Aims. The glycosphingolipid β-galactosylceramide-3-O-sulfate (sulfatide) is present in the secretory granules of the insulin producing β-cells and may act as a molecular chaperone of insulin. The final step in sulfatide synthesis is performed by cerebroside sulfotransferase (CST) (EC 2.8.2.11). The aim of this study was to investigate whether two single nucleotide polymorphisms (SNP), rs2267161 located in an exon or rs42929 located in an intron, in the gene encoding CST are linked to type 2 diabetes (T2D). Methods. As a population survey, 265 male and female patients suffering from T2D and 291 gender matched controls were examined. Results. A higher proportion of T2D patients were heterozygous at SNP rs2267161 with both T (methionine) and C (valine) alleles present (49.8% versus 41.3%, P = .04). The calculated odd risk for T2D was 1.47 (1.01–2.15, P = .047). Among female controls, the homozygous CC individuals displayed lower insulin resistance measured by HOMA-IR (P = .05) than the C/T or TT persons; this was particularly prevalent in individuals who exercise (P = .03). Conclusion. Heterozygosity at SNP rs2267161 in the gene encoding the CST enzyme confers increased risk of T2D. Females with the CC allele showed lower insulin resistance.
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Lillioja S, Wilton A. Agreement among type 2 diabetes linkage studies but a poor correlation with results from genome-wide association studies. Diabetologia 2009; 52:1061-74. [PMID: 19296077 DOI: 10.1007/s00125-009-1324-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/18/2008] [Accepted: 02/13/2009] [Indexed: 12/22/2022]
Abstract
AIMS/HYPOTHESIS Little of the genetic basis for type 2 diabetes has been explained, despite numerous genetic linkage studies and the discovery of multiple genes in genome-wide association (GWA) studies. To begin to resolve the genetic component of this disease, we searched for sites at which genetic results had been corroborated in different studies, in the expectation that replication among studies should direct us to the genomic locations of causative genes with more confidence than the results of individual studies. METHODS We have mapped the physical location of results from 83 linkage reports (for type 2 diabetes and diabetes precursor quantitative traits [QTs, e.g. plasma insulin levels]) and recent large GWA reports (for type 2 diabetes) onto the same human genome sequence to identify replicated results in diabetes genetic 'hot spots'. RESULTS Genetic linkage has been found at least ten times at 18 different locations, and at least five times in 56 locations. All replication clusters contained study populations from more than one ethnic background and most contained results for both diabetes and QTs. There is no close relationship between the GWA results and linkage clusters, and the nine best replication clusters have no nearby GWA result. CONCLUSIONS/INTERPRETATION Many of the genes for type 2 diabetes remain unidentified. This analysis identifies the broad location of yet to be identified genes on 6q, 1q, 18p, 2q, 20q, 17pq, 8p, 19q and 9q. The discrepancy between the linkage and GWA studies may be explained by the presence of multiple, uncommon, mildly deleterious polymorphisms scattered throughout the regulatory and coding regions of genes for type 2 diabetes.
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Affiliation(s)
- S Lillioja
- Illawarra Health and Medical Research Institute, University of Wollongong, Wollongong, NSW, Australia.
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McKnight AJ, O'Donoghue D, Peter Maxwell A. Annotated chromosome maps for renal disease. Hum Mutat 2009; 30:314-20. [PMID: 19085929 DOI: 10.1002/humu.20885] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
A combination of linkage analyses and association studies are currently employed to promote the identification of genetic factors contributing to inherited renal disease. We have standardized and merged complex genetic data from disparate sources, creating unique chromosomal maps to enhance genetic epidemiological investigations. This database and novel renal maps effectively summarize genomic regions of suggested linkage, association, or chromosomal abnormalities implicated in renal disease. Chromosomal regions associated with potential intermediate clinical phenotypes have been integrated, adding support for particular genomic intervals. More than 500 reports from medical databases, published scientific literature, and the World Wide Web were interrogated for relevant renal-related information. Chromosomal regions highlighted for prioritized investigation of renal complications include 3q13-26, 6q22-27, 10p11-15, 16p11-13, and 18q22. Combined genetic and physical maps are effective tools to organize genetic data for complex diseases. These renal chromosome maps provide insights into renal phenotype-genotype relationships and act as a template for future genetic investigations into complex renal diseases. New data from individual researchers and/or future publications can be readily incorporated to this resource via a user-friendly web-form accessed from the website: www.qub.ac.uk/neph-res/CORGI/index.php.
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Affiliation(s)
- Amy Jayne McKnight
- Nephrology Research Group, Queen's University of Belfast, United Kingdom.
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24
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Kenealy SJ, Herrel LA, Bradford Y, Schnetz-Boutaud N, Oksenberg JR, Hauser SL, Barcellos LF, Schmidt S, Gregory SG, Pericak-Vance MA, Haines JL. Examination of seven candidate regions for multiple sclerosis: strong evidence of linkage to chromosome 1q44. Genes Immun 2009; 7:73-6. [PMID: 16341055 DOI: 10.1038/sj.gene.6364275] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Multiple sclerosis (MS) is a debilitating neuroimmunological and neurodegenerative disease with a strong genetic component. Numerous studies have failed to consistently identify genes that confer disease susceptibility except for association with HLA-DR. Seven non-HLA regions (1q, 2q, 9q, 13q, 16q, 18p and 19q) identified in a recent genomic screen were investigated by genotyping approximately 20 single-nucleotide polymorphisms (SNPs) at approximately 1 Mb intervals. Non-parametric multipoint analyses identified a peak LOD* score of 2.99 for the 1q44 region and substantially narrowed the linkage peak to approximately 7 Mb. Ordered subset analyses (OSA) identified significant LOD score increases for 2q35 and 18p11 when ranking families by HLA-DR status and identified a significant LOD score increase in region 2q35 when ranking families by linkage to chromosome 1q44. 1q44 is particularly interesting because of linkage evidence for this region in studies of both rheumatoid arthritis and systemic lupus erythematosus.
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Affiliation(s)
- S J Kenealy
- Center for Human Genetics Research, Vanderbilt University Medical Center, Nashville, TN 37232-0700, USA
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25
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Bostrom MA, Freedman BI, Langefeld CD, Liu L, Hicks PJ, Bowden DW. Association of adiponectin gene polymorphisms with type 2 diabetes in an African American population enriched for nephropathy. Diabetes 2009; 58:499-504. [PMID: 19056609 PMCID: PMC2628626 DOI: 10.2337/db08-0598] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
OBJECTIVE Polymorphisms in the adiponectin gene (ADIPOQ) have been associated with type 2 diabetes and diabetic nephropathy in type 1 diabetes, in mostly European-derived populations. RESEARCH DESIGN AND METHODS A comprehensive association analysis of 24 single-nucleotide polymorphisms (SNPs) in the adiponectin gene was performed for type 2 diabetes and diabetic nephropathy in African Americans. RESULTS The minor allele (A) in a single SNP in intron 1 (rs182052) was associated with diabetic nephropathy (P = 0.0015, odds ratio [OR] 1.37, CI 1.13-1.67, dominant model) in an African American sample of 851 case subjects with diabetic nephropathy and 871 nondiabetic control subjects in analyses incorporating adjustment for varying levels of racial admixture. This association remained significant after adjustment of the data for BMI, age, and sex (P = 0.0013-0.0004). We further tested this SNP for association with longstanding type 2 diabetes without nephropathy (n = 317), and evidence of association was also significant (P = 0.0054, OR 1.46, CI 1.12-1.91, dominant model) when compared with the same set of 871 nondiabetic control subjects. Combining the type 2 diabetes and diabetic nephropathy samples into a single group of case subjects (n = 1,168) resulted in the most significant evidence of association (P = 0.0003, OR 1.40, CI 1.17-1.67, dominant model). Association tests between age at onset of type 2 diabetes and the rs182052 genotypes also revealed significant association between the presence of the minor allele (A/A or A/G) and earlier onset of type 2 diabetes. CONCLUSIONS The SNP rs182052 in intron 1 of the adiponectin gene is associated with type 2 diabetes in African Americans.
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Affiliation(s)
- Meredith A Bostrom
- Department of Biochemistry, Wake Forest University School of Medicine, Winston-Salem, North Carolina, USA
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26
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Elbein SC, Das SK, Hallman DM, Hanis CL, Hasstedt SJ. Genome-wide linkage and admixture mapping of type 2 diabetes in African American families from the American Diabetes Association GENNID (Genetics of NIDDM) Study Cohort. Diabetes 2009; 58:268-74. [PMID: 18840782 PMCID: PMC2606884 DOI: 10.2337/db08-0931] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/10/2008] [Accepted: 09/29/2008] [Indexed: 11/13/2022]
Abstract
OBJECTIVE We used a single nucleotide polymorphism (SNP) map in a large cohort of 580 African American families to identify regions linked to type 2 diabetes, age of type 2 diabetes diagnosis, and BMI. RESEARCH DESIGN AND METHODS After removing outliers and problematic samples, we conducted linkage analysis using 5,914 SNPs in 1,344 individuals from 530 families. Linkage analysis was conducted using variance components for type 2 diabetes, age of type 2 diabetes diagnosis, and BMI and nonparametric linkage analyses. Ordered subset analyses were conducted ranking on age of type 2 diabetes diagnosis, BMI, waist circumference, waist-to-hip ratio, and amount of European admixture. Admixture mapping was conducted using 4,486 markers not in linkage disequilibrium. RESULTS The strongest signal for type 2 diabetes (logarithm of odds [LOD] 4.53) was a broad peak on chromosome 2, with weaker linkage to age of type 2 diabetes diagnosis (LOD 1.82). Type 2 diabetes and age of type 2 diabetes diagnosis were linked to chromosome 13p (3-22 cM; LOD 2.42 and 2.46, respectively). Age of type 2 diabetes diagnosis was linked to 18p (66 cM; LOD 2.96). We replicated previous reports on chromosome 7p (79 cM; LOD 2.93). Ordered subset analysis did not overlap with linkage of unselected families. The best admixture score was on chromosome 12 (90 cM; P = 0.0003). CONCLUSIONS The linkage regions on chromosomes 7 (27-78 cM) and 18p overlap prior reports, whereas regions on 2p and 13p linkage are novel. Among potential candidate genes implicated are TCF7L1, VAMP5, VAMP8, CDK8, INSIG2, IPF1, PAX8, IL18R1, members of the IL1 and IL1 receptor families, and MAP4K4. These studies provide a complementary approach to genome-wide association scans to identify causative genes for African American diabetes.
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Affiliation(s)
- Steven C Elbein
- Division of Endocrinology, Department of Medicine, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA.
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Xu L, Zhang F, Zhang DD, Chen XD, Lu M, Lin RY, Wen H, Jin L, Wang XF. OPRM1 gene is associated with BMI in Uyghur population. Obesity (Silver Spring) 2009; 17:121-5. [PMID: 19008867 DOI: 10.1038/oby.2008.504] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
To test the hypothesis that micro-opioid receptor (OPRM1) gene might be involved in the prevalence of obesity, a population-based association study was carried out in Uyghur population. Overall 10 tagging single-nucleotide polymorphisms (tSNPs) in OPRM1 gene were genotyped. We showed that genotypes of rs1799971 in exon 1, and rs514980 and rs7773995 in intron 1 were significantly associated with the BMI. The BMI significantly decreased by the copy of minor allele carriers of rs1799971 which is a nonsynonymous functional polymorphism, whereas the BMI significantly increased by the copy of minor allele carriers of rs514980 and rs7773995. Subsequently, subjects were subsequently divided into case (BMI >or= 28) and control group (BMI < 24). Significant associations were again observed at rs1799971, rs514980, and rs7773995, regardless of controlling for covariates age and gender or not. The stronger evidence for association was found under the additive model for each of the three SNPs. The per-allele odds ratio of the minor allele for obesity was 0.75 (95% confidence interval 0.58-0.96, P = 0.023) for rs1799971, 1.68 (95% confidence interval 1.14-2.49, P = 0.009) for rs514980, and 1.80 (95% confidence interval 1.14-2.85, P = 0.012) for rs7773995, respectively. Our observations give the evidence that OPRM1 gene is involved in the prevalence of obesity in Uyghurs.
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Affiliation(s)
- Ling Xu
- 1MOE Key Laboratory of Contemporary Anthropology and Center for Evolutionary Biology, School of Life Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
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Sale MM, Lu L, Spruill IJ, Fernandes JK, Lok KH, Divers J, Langefeld CD, Garvey WT. Genome-wide linkage scan in Gullah-speaking African American families with type 2 diabetes: the Sea Islands Genetic African American Registry (Project SuGAR). Diabetes 2009; 58:260-7. [PMID: 18835935 PMCID: PMC2606883 DOI: 10.2337/db08-0198] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
OBJECTIVE The Gullah-speaking African American population from the Sea Islands of South Carolina is characterized by a low degree of European admixture and high rates of type 2 diabetes and diabetic complications. Affected relative pairs with type 2 diabetes were recruited through the Sea Islands Genetic African American Registry (Project SuGAR). RESEARCH DESIGN AND METHODS We conducted a genome-wide linkage scan, genotyping 5,974 single nucleotide polymorphisms in 471 affected subjects and 50 unaffected relatives from 197 pedigrees. Data were analyzed using a multipoint engine for rapid likelihood inference and ordered subsets analyses (OSAs) for age at type 2 diabetes diagnosis, waist circumference, waist-to-hip ratio, and BMI. We searched for heterogeneity and interactions using a conditional logistic regression likelihood approach. RESULTS Linkage peaks on chromosome 14 at 123-124 cM were detected for type 2 diabetes (logarithm of odds [LOD] 2.10) and for the subset with later age at type 2 diabetes diagnosis (maximum LOD 4.05). Two linkage peaks on chromosome 7 were detected at 44-45 cM for type 2 diabetes (LOD 1.18) and at 78 cM for type 2 diabetes (LOD 1.64) and the subset with earlier age at type 2 diabetes diagnosis (maximum LOD 3.93). The chromosome 14 locus and a peak on 7p at 29.5 cM were identified as important in the multilocus model. Other regions that provided modest evidence for linkage included chromosome 1 at 167.5 cM (LOD 1.51) and chromosome 3 at 121.0 cM (LOD 1.61). CONCLUSIONS This study revealed a novel type 2 diabetes locus in an African American population on 14q that appears to reduce age of disease onset and confirmed two loci on chromosome 7.
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Affiliation(s)
- Michèle M Sale
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, USA.
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Anderson-Pompa K, Foster A, Parker L, Wilks L, Cheek DJ. Genetics and Susceptibility to Malignant Hyperthermia. Crit Care Nurse 2008. [DOI: 10.4037/ccn2008.28.6.32] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Affiliation(s)
- Kathryn Anderson-Pompa
- When this article was written, Kathryn Anderson-Pompa, April Foster, Lee Parker, and Lance Wilks were all graduate students in the nurse anesthesia program in the Harris College of Nursing and Health Sciences at Texas Christian University in Fort Worth, Texas. Dennis J. Cheek is the Abell-Hanger Professor of Gerontological Nursing in the School of Nurse Anesthesia and Harris College of Nursing and Health Sciences at Texas Christian University
| | - April Foster
- When this article was written, Kathryn Anderson-Pompa, April Foster, Lee Parker, and Lance Wilks were all graduate students in the nurse anesthesia program in the Harris College of Nursing and Health Sciences at Texas Christian University in Fort Worth, Texas. Dennis J. Cheek is the Abell-Hanger Professor of Gerontological Nursing in the School of Nurse Anesthesia and Harris College of Nursing and Health Sciences at Texas Christian University
| | - Lee Parker
- When this article was written, Kathryn Anderson-Pompa, April Foster, Lee Parker, and Lance Wilks were all graduate students in the nurse anesthesia program in the Harris College of Nursing and Health Sciences at Texas Christian University in Fort Worth, Texas. Dennis J. Cheek is the Abell-Hanger Professor of Gerontological Nursing in the School of Nurse Anesthesia and Harris College of Nursing and Health Sciences at Texas Christian University
| | - Lance Wilks
- When this article was written, Kathryn Anderson-Pompa, April Foster, Lee Parker, and Lance Wilks were all graduate students in the nurse anesthesia program in the Harris College of Nursing and Health Sciences at Texas Christian University in Fort Worth, Texas. Dennis J. Cheek is the Abell-Hanger Professor of Gerontological Nursing in the School of Nurse Anesthesia and Harris College of Nursing and Health Sciences at Texas Christian University
| | - Dennis J. Cheek
- When this article was written, Kathryn Anderson-Pompa, April Foster, Lee Parker, and Lance Wilks were all graduate students in the nurse anesthesia program in the Harris College of Nursing and Health Sciences at Texas Christian University in Fort Worth, Texas. Dennis J. Cheek is the Abell-Hanger Professor of Gerontological Nursing in the School of Nurse Anesthesia and Harris College of Nursing and Health Sciences at Texas Christian University
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Ruchat SM, Girard M, Weisnagel SJ, Bouchard C, Vohl MC, Pérusse L. ASSOCIATION BETWEEN µ-OPIOID RECEPTOR-1 102T>C POLYMORPHISM AND INTERMEDIATE TYPE 2 DIABETES PHENOTYPES: RESULTS FROM THE QUEBEC FAMILY STUDY (QFS). Clin Exp Pharmacol Physiol 2008; 35:1018-22. [DOI: 10.1111/j.1440-1681.2008.04972.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Mottl AK, Vupputuri S, Cole SA, Almasy L, Göring HHH, Diego VP, Laston S, Franceschini N, Shara NM, Lee ET, Best LG, Fabsitz RR, MacCluer JW, Umans JG, North KE. Linkage analysis of glomerular filtration rate in American Indians. Kidney Int 2008; 74:1185-91. [PMID: 18854848 DOI: 10.1038/ki.2008.410] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
American Indians have a disproportionately high rate of kidney disease likely due to a combination of environmental and genetic factors. We performed a genome wide scan of estimated glomerular filtration rate in 3665 participants of the Strong Heart Family Study to localize genes influencing kidney disease risk factors. The participants were men and women from 13 American Indian tribes recruited from 3 centers located in Arizona, the Dakotas and Oklahoma. Multipoint variance component linkage analysis was performed for each center and on the entire cohort after controlling for center effects. Modeling strategies that incorporated age, gender and interaction terms (model 1) and another that also controlled for diabetes mellitus, systolic and diastolic blood pressure, body mass index, low density and high density lipoproteins, triglycerides and smoking status (model 2) were used. Significant evidence for linkage in the Arizona group was found on chromosome 12p12.2 at 39cM (nearest marker D12S310) using model 1. Additional loci with very suggestive evidence for linkage were detected at 1p36.31 for all groups using both models and at 2q33.3 and 9q34.2 for the Dakotas group each using model 1. No significant evidence for additive interaction with diabetes, hypertension or obesity was noted. This evidence for linkage of a quantitative trait locus influencing estimated glomerular filtration rate to a region of chromosome 12p in a large cohort of American Indians will be worth studying in more detail in the future.
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Affiliation(s)
- Amy K Mottl
- UNC Kidney Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7155, USA.
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Degaffe GH, Vander Jagt DL, Bobelu A, Bobelu J, Neha D, Waikaniwa M, Zager P, Shah VO. Distribution of glyoxalase I polymorphism among Zuni Indians: the Zuni Kidney Project. J Diabetes Complications 2008; 22:267-72. [PMID: 18413187 PMCID: PMC2504516 DOI: 10.1016/j.jdiacomp.2007.06.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/03/2006] [Revised: 05/04/2007] [Accepted: 06/01/2007] [Indexed: 12/24/2022]
Abstract
Zuni Indians are experiencing simultaneous epidemics of type 2 diabetes mellitus (T2DM) and renal disease [Scavini, M., Stidley, C. A., Shah, V. O., Narva, A. S., Tentori, F., Kessler, D. S., et al. (2003). Prevalence of diabetes is higher among female than male Zuni Indians: Diabetes among Zuni Indians. Diabetes Care, 26 (1), 55-60; Shah, V. O., Scavini, M., Stidley, C., Tentori, F., Welty, T., Maccluer, J. W., et al. (2003). Epidemic of diabetic and nondiabetic renal disease among the Zuni Indians: The Zuni Kidney Project. Journal of the American Society of Nephrology, 14, 1320-1329]. Methylglyoxal (MG), a highly reactive, cytotoxic, cross-linking endogenous aldehyde involved in the modification of biologic macromolecules, is elevated among patients with T2DM. Glyoxalase I (Glo1) is the initial enzyme involved in the detoxification of MG. Glo1 is a dimeric enzyme with three isoforms Glo1-1, Glo2-1, and Glo2-2, resulting from a point mutation (A-->C) at position 332 of cDNA. The present study was conducted to explore the hypothesis that specific polymorphisms of the Glo1 gene are associated with diabetes and/or albuminuria in Zuni Indians. We studied four groups of Zuni Indians stratified by diabetes status and albuminuria, as assessed by the urinary albumin:creatinine ratio (UACR): Group I--normal controls; Group II--T2DM and UACR<0.03; Group III--T2DM and UACR>or=0.03; and Group IV--nondiabetic participants with UACR>or=0.03. Genomic DNA was used as template for polymerase chain reaction amplification of the Glo1 gene. Products were digested to yield 110-bp bands (homozygous, CC); 54- and 45-bp bands (homozygous, AA); or all three bands (heterozygous CA). Data on age, gender, UACR, serum creatinine, hemoglobin A1(c), serum glucose, systolic and diastolic blood pressures, and the duration of T2DM among participants in Groups II and III were analyzed using analysis of variance. A generalized linear model logistic regression analysis was used to assess the relationships between specific Glo1 polymorphisms to T2DM and UACR. All three Glo1 genotypes were present among Zuni Indians. There were no significant differences in the distributions of Glo1 genotypes among the study groups (chi-square test, P=.5590). The prevalence of Glo1 A allele was higher among diabetic participants (Groups II and III combined) than among nondiabetic participants (Groups I and IV combined) (chi-square test, P=.0233). There was an association (odds ratio=2.9; 95% confidence interval=1.3-7.2) between the Glo1 A allele and T2DM.
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Affiliation(s)
- Guenet H. Degaffe
- Division of Nephrology, Department of Medicine, University of New Mexico School of Medicine, Albuquerque, New Mexico 87131
| | - David L. Vander Jagt
- Department of Biochemistry and Molecular Biology, University of New Mexico School of Medicine, Albuquerque, New Mexico 87131
| | | | - Jeanette Bobelu
- Division of Nephrology, Department of Medicine, University of New Mexico School of Medicine, Albuquerque, New Mexico 87131
| | - Donica Neha
- Division of Nephrology, Department of Medicine, University of New Mexico School of Medicine, Albuquerque, New Mexico 87131
| | - Mildred Waikaniwa
- Division of Nephrology, Department of Medicine, University of New Mexico School of Medicine, Albuquerque, New Mexico 87131
| | - Philip Zager
- Division of Nephrology, Department of Medicine, University of New Mexico School of Medicine, Albuquerque, New Mexico 87131
| | - Vallabh O. Shah
- Division of Nephrology, Department of Medicine, University of New Mexico School of Medicine, Albuquerque, New Mexico 87131
- Department of Biochemistry and Molecular Biology, University of New Mexico School of Medicine, Albuquerque, New Mexico 87131
- * Address correspondence to this author: Vallabh (Raj) Shah, PhD, Department of Internal Medicine, University of New Mexico –HSC, 1 UNM MSC10-5550, Albuquerque, NM 87131-0001, 505 272-4750 –phone, 505-272-2349 –fax,
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Evaluation of a SNP map of 6q24-27 confirms diabetic nephropathy loci and identifies novel associations in type 2 diabetes patients with nephropathy from an African-American population. Hum Genet 2008; 124:63-71. [PMID: 18560894 DOI: 10.1007/s00439-008-0523-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2008] [Accepted: 05/27/2008] [Indexed: 01/29/2023]
Abstract
Previously, we performed a genome scan for type 2 diabetes (T2DM) using 638 African-American (AA) affected sibling pairs from 247 families; non-parametric linkage analysis suggested evidence of linkage at 6q24-27 (LOD 2.26). To comprehensively evaluate this region, we performed a two-stage association study by first constructing a SNP map of 754 SNPs selected from HapMap on the basis of linkage disequilibrium (LD) in 300 AAT2DM end-stage renal disease (ESRD) subjects, 311 AA controls, 43 European American controls and 45 Yoruba Nigerian samples (Set 1). Replication analyses were conducted in an independent population of 283 AA T2DM-ESRD subjects and 282 AA controls (Set 2). In addition, we adjusted for the impact of admixture on association results by using ancestry informative markers (AIMs). In Stage 1, 137 (18.2%) SNPs showed nominal evidence of association (P < 0.05) in one or more of tests of association: allelic (n = 33), dominant (n = 36), additive (n = 29), or recessive (n = 34) genotypic models, and 2- (n = 47) and 3-SNP (n = 43) haplotypic analyses. These SNPs were selected for follow-up genotyping. Stage 2 analyses confirmed association with a predicted 2-SNP "risk" haplotype in the PARK2 gene. Also, two intergenic SNPs showed consistent genotypic association with T2DM-ESRD: rs12197043 and rs4897081. Combined analysis of all subjects from both stages revealed nominal associations with 17 SNPs within genes, including suggestive associations in ESR1 and PARK2. This study confirms known diabetic nephropathy loci and identifies potentially novel susceptibility variants located within 6q24-27 in AA.
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Keene KL, Mychaleckyj JC, Smith SG, Leak TS, Perlegas PS, Langefeld CD, Freedman BI, Rich SS, Bowden DW, Sale MM. Association of the distal region of the ectonucleotide pyrophosphatase/phosphodiesterase 1 gene with type 2 diabetes in an African-American population enriched for nephropathy. Diabetes 2008; 57:1057-62. [PMID: 18184924 DOI: 10.2337/db07-0886] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
OBJECTIVE Variants in the ectonucleotide pyrophosphatase/phosphodiesterase 1 (ENPP1) gene have shown positive associations with diabetes and related phenotypes, including insulin resistance, metabolic syndrome, and type 1 diabetic nephropathy. Additionally, evidence for linkage for type 2 diabetes in African Americans was observed at 6q24-27, with the proximal edge of the peak encompassing the ENPP1 gene. Our objective was to comprehensively evaluate variants in ENPP1 for association with type 2 diabetic end-stage renal disease (ESRD). RESEARCH DESIGN AND METHODS Forty-nine single nucleotide polymorphisms (SNPs) located in the coding and flanking regions of ENPP1 were genotyped in 577 African-American individuals with type 2 diabetic ESRD and 596 African-American control subjects. Haplotypic association and genotypic association for the dominant, additive, and recessive models were tested by calculating a chi(2) statistic and corresponding P value. RESULTS Nine SNPs showed nominal evidence for association (P < 0.05) with type 2 diabetic ESRD in one or more genotypic model. The most significant associations were observed with rs7754586 (P = 0.003 dominant model, P = 0.0005 additive, and P = 0.007 recessive), located in the 3' untranslated region, and an intron 24 SNP (rs1974201: P = 0.004 dominant, P = 0.0005 additive, and P = 0.005 recessive). However, the extensively studied K121Q variant (rs1044498) did not reveal evidence for association with type 2 diabetic ESRD in this African-American population. CONCLUSIONS This study was the first to comprehensively evaluate variants of the ENPP1 gene for association in an African-American population with type 2 diabetes and ESRD and suggests that variants in the distal region of the ENPP1 gene may contribute to diabetes or diabetic nephropathy susceptibility in African Americans.
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Affiliation(s)
- Keith L Keene
- Center for Human Genomics, Wake Forest University School of Medicine, Winston-Salem, North Carolina, USA
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Su Z, Tsaih SW, Szatkiewicz J, Shen Y, Paigen B. Candidate genes for plasma triglyceride, FFA, and glucose revealed from an intercross between inbred mouse strains NZB/B1NJ and NZW/LacJ. J Lipid Res 2008; 49:1500-10. [PMID: 18362393 DOI: 10.1194/jlr.m800053-jlr200] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
To identify the genes controlling plasma concentrations of triglycerides (TGs), FFAs, and glucose, we carried out a quantitative trait loci (QTL) analysis of the closely related mouse strains New Zealand Black (NZB/B1NJ) and New Zealand White (NZW/LacJ), which share 63% of their genomes. The NZB x NZW F(2) progeny were genotyped and phenotyped to detect QTL, and then comparative genomics, bioinformatics, and sequencing were used to narrow the QTL and reduce the number of candidate genes. Triglyceride concentrations were linked to loci on chromosomes (Chr) 4, 7, 8, 10, and 18. FFA concentrations were affected by a significant locus on Chr 4, a suggestive locus on Chr 16, and two interacting loci on Chr 2 and 15. Plasma glucose concentrations were affected by QTL on Chr 2, 4, 7, 8, 10, 15, 17, and 18. Comparative genomics narrowed the QTL by 31% to 86%; haplotype analysis was usually able to further narrow it by 80%. We suggest several candidate genes: Gba2 on Chr 4, Irs2 on Chr 8, and Ppargc1b on Chr 18 for TG; A2bp1 on Chr 16 for FFA; and G6pc2 on Chr 2 and Timp3 on Chr 10 for glucose.
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Affiliation(s)
- Zhiguang Su
- The Jackson Laboratory, Bar Harbor, ME 04609, USA
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Keene KL, Mychaleckyj JC, Smith SG, Leak TS, Perlegas PS, Langefeld CD, Herrington DM, Freedman BI, Rich SS, Bowden DW, Sale MM. Comprehensive evaluation of the estrogen receptor alpha gene reveals further evidence for association with type 2 diabetes enriched for nephropathy in an African American population. Hum Genet 2008; 123:333-41. [PMID: 18305958 DOI: 10.1007/s00439-008-0482-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2007] [Accepted: 02/12/2008] [Indexed: 12/29/2022]
Abstract
We previously investigated the estrogen receptor alpha gene (ESR1) as a positional candidate for type 2 diabetes (T2DM), and found evidence for association between the intron 1-intron 2 region of this gene and T2DM and/or nephropathy in an African American (AA) population. Our objective was to comprehensively evaluate variants across the entire ESR1 gene for association in AA with T2DM and end stage renal disease (T2DM-ESRD). One hundred fifty SNPs in ESR1, spanning 476 kb, were genotyped in 577 AA individuals with T2DM-ESRD and 596 AA controls. Genotypic association tests for dominant, additive, and recessive models, and haplotypic association, were calculated using a chi(2) statistic and corresponding P value. Thirty-one SNPs showed nominal evidence for association (P < 0.05) with T2DM-ESRD in one or more genotypic model. After correcting for multiple tests, promoter SNP rs11964281 (nominal P = 0.000291, adjusted P = 0.0289), and intron 4 SNPs rs1569788 (nominal P = 0.000754, adjusted P = 0.0278) and rs9340969 (nominal P = 0.00109, adjusted P = 0.0467) remained significant at experimentwise error rate (EER) P </= 0.05 for the dominant class of tests. Twenty-three of the thirty-one associated SNPs cluster within the intron 4-intron 6 regions. Gender stratification revealed nominal evidence for association with 35 SNPs in females (352 cases; 306 controls) and seven SNPs in males (225 cases; 290 controls). We have identified a novel region of the ESR1 gene that may contain important functional polymorphisms in relation to susceptibility to T2DM and/or diabetic nephropathy.
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Affiliation(s)
- Keith L Keene
- Center for Human Genomics, Wake Forest University School of Medicine, Winston-Salem, NC, USA
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Schelling JR, Abboud HE, Nicholas SB, Pahl MV, Sedor JR, Adler SG, Arar NH, Bowden DW, Elston RC, Freedman BI, Goddard KAB, Guo X, Hanson RL, Ipp E, Iyengar SK, Jun G, Kao WHL, Kasinath BS, Kimmel PL, Klag MJ, Knowler WC, Nelson RG, Parekh RS, Quade SR, Rich SS, Saad MF, Scavini M, Smith MW, Taylor K, Winkler CA, Zager PG, Shah VO. Genome-wide scan for estimated glomerular filtration rate in multi-ethnic diabetic populations: the Family Investigation of Nephropathy and Diabetes (FIND). Diabetes 2008; 57:235-43. [PMID: 18003762 DOI: 10.2337/db07-0313] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
OBJECTIVE Diabetic nephropathy, the most common cause of end-stage renal disease, aggregates in families and specific ethnic groups. Deconstructing diabetic nephropathy into intermediate, quantitative phenotypes may increase feasibility of detecting susceptibility loci by genetic screens. Glomerular filtration rate (GFR), which characterizes diabetic nephropathy, was employed as a quantitative trait in a preliminary whole-genome scan. RESEARCH DESIGN AND METHODS Estimated GFR (eGFR) was calculated for 882 diabetic sibpairs (mean age 57 years) of African-American (25.6% of total), American Indian (8.6%), European-American (14.2%), and Mexican-American (51.6%) descent enrolled in the initial phase of the Family Investigation of Nephropathy and Diabetes (FIND). A whole-genome scan was performed using 404 microsatellite markers (average spacing 9 cM) and model-free linkage analysis. RESULTS For all ethnicities combined, strong evidence for linkage was observed on chromosomes 1q43 (P = 3.6 x 10(-3)), 7q36.1 (P = 2.1 x 10(-4)), 8q13.3 (P = 4.6 x 10(-4)), and 18q23.3 (P = 2.7 x 10(-3)). Mexican-American families, who comprised the major ethnic subpopulation in FIND, contributed to linkage on chromosomes 1q43, 2p13.3, 7q36.1, 8q13.3, and 18q23.3, whereas African-American and American-Indian families displayed linkage peaks on chromosomes 11p15.1 and 15q22.3, respectively. CONCLUSIONS We have demonstrated multiple chromosomal regions linked to eGFR in a multi-ethnic collection of families ascertained by a proband with diabetic nephropathy. Identification of genetic variants within these loci that are responsible for the linkage signals could lead to predictive tests or novel therapies for subsets of patients at risk for diabetic nephropathy.
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Affiliation(s)
- Jeffrey R Schelling
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Wolstein Research Building, Rm. 1300, 10900 Euclid Ave., Cleveland, OH 44106-7281, USA
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Signorello LB, Schlundt DG, Cohen SS, Steinwandel MD, Buchowski MS, McLaughlin JK, Hargreaves MK, Blot WJ. Comparing diabetes prevalence between African Americans and Whites of similar socioeconomic status. Am J Public Health 2007; 97:2260-7. [PMID: 17971557 DOI: 10.2105/ajph.2006.094482] [Citation(s) in RCA: 134] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
OBJECTIVES We investigated whether racial disparities in the prevalence of type 2 diabetes exist beyond what may be attributable to differences in socioeconomic status (SES) and other modifiable risk factors. METHODS We analyzed data from 34331 African American and 9491 White adults aged 40 to 79 years recruited into the ongoing Southern Community Cohort Study. Participants were enrolled at community health centers and had similar socioeconomic circumstances and risk factor profiles. We used logistic regression to estimate the association between race and prevalence of self-reported diabetes after taking into account age, SES, health insurance coverage, body mass index, physical activity, and hypertension. RESULTS Multivariate analyses accounting for several diabetes risk factors did not provide strong support for higher diabetes prevalence rates among African Americans than among Whites (men: odds ratio [OR]=1.07; 95% confidence interval [CI]=0.95, 1.20); women: OR=1.13, 95% CI=1.04, 1.22). CONCLUSIONS Our findings suggest that major differences in diabetes prevalence between African Americans and Whites may simply reflect differences in established risk factors for the disease, such as SES, that typically vary according to race.
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Affiliation(s)
- Lisa B Signorello
- International Epidemiology Institute, Rockville, MD 20850, USA. lisa.
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Freedman BI, Bostrom M, Daeihagh P, Bowden DW. Genetic Factors in Diabetic Nephropathy. Clin J Am Soc Nephrol 2007; 2:1306-16. [DOI: 10.2215/cjn.02560607] [Citation(s) in RCA: 140] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Leak TS, Keene KL, Langefeld CD, Gallagher CJ, Mychaleckyj JC, Freedman BI, Bowden DW, Rich SS, Sale MM. Association of the proprotein convertase subtilisin/kexin-type 2 (PCSK2) gene with type 2 diabetes in an African American population. Mol Genet Metab 2007; 92:145-50. [PMID: 17618154 PMCID: PMC2752824 DOI: 10.1016/j.ymgme.2007.05.014] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/18/2007] [Accepted: 05/18/2007] [Indexed: 10/23/2022]
Abstract
In a genome-wide scan for type 2 diabetes (T2DM) in African American (AA) families, ordered subsets analysis (OSA) provided evidence for linkage to chromosome 20p in a subset with later age at diagnosis (max LOD 2.57, P=0.008). The proprotein convertase subtilisin/kexin-type 2 (PCSK2) gene is within the LOD-1 interval of this linkage peak. Twenty-nine single nucleotide polymorphisms (SNPs) were genotyped across this gene in 380 unrelated AA individuals with T2DM and end-stage renal disease (T2DM-ESRD), 278 AA controls, 96 European Americans (EA) and 120 Yoruba Nigerian (YRI) controls. In addition, 22 ancestry-informative markers (AIMs) were genotyped in all AA subjects, 120 YRI, and 282 EA controls. ADMIXMAP was used to model the distributions of admixture and generate score tests of allelic and haplotypic association. Association with T2DM was observed among 4 SNPs: rs2021785 (admixture-adjusted Pa=0.00014), rs1609659 (Pa=0.028), rs4814597 (Pa=0.039) and rs2269023 (Pa=0.043). None of the PCSK2 SNPs were associated with age at T2DM diagnosis. A variant in the PCKS2 gene, rs2021785, appears to play a role in susceptibility to T2DM in this AA population.
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Affiliation(s)
- Tennille S. Leak
- Center for Human Genomics, Wake Forest University School of Medicine, Winston-Salem, NC
| | - Keith L. Keene
- Center for Human Genomics, Wake Forest University School of Medicine, Winston-Salem, NC
| | - Carl D. Langefeld
- Division of Public Health Sciences, Wake Forest University School of Medicine, Winston-Salem, NC
| | - Carla J. Gallagher
- Center for Human Genomics, Wake Forest University School of Medicine, Winston-Salem, NC
- Department of Biochemistry, Wake Forest University School of Medicine, Winston-Salem, NC
- Milton S. Hershey Medical Center, Pennsylvania State University, Hershey, PA
| | - Josyf C. Mychaleckyj
- Center for Human Genomics, Wake Forest University School of Medicine, Winston-Salem, NC
- Department of Internal Medicine, Wake Forest University School of Medicine, Winston-Salem, NC
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA
- Department of Public Health Sciences, University of Virginia, Charlottesville, VA
| | - Barry I. Freedman
- Milton S. Hershey Medical Center, Pennsylvania State University, Hershey, PA
| | - Donald W. Bowden
- Center for Human Genomics, Wake Forest University School of Medicine, Winston-Salem, NC
- Department of Biochemistry, Wake Forest University School of Medicine, Winston-Salem, NC
- Department of Internal Medicine, Wake Forest University School of Medicine, Winston-Salem, NC
| | - Stephen S. Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA
- Department of Public Health Sciences, University of Virginia, Charlottesville, VA
- Department of Medicine, University of Virginia, Charlottesville, VA
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA
| | - Michèle M. Sale
- Center for Human Genomics, Wake Forest University School of Medicine, Winston-Salem, NC
- Department of Internal Medicine, Wake Forest University School of Medicine, Winston-Salem, NC
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA
- Department of Medicine, University of Virginia, Charlottesville, VA
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA
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Gallagher CJ, Langefeld CD, Gordon CJ, Campbell JK, Mychaleckyj JC, Mychalecky JC, Bryer-Ash M, Rich SS, Bowden DW, Sale MM. Association of the estrogen receptor-alpha gene with the metabolic syndrome and its component traits in African-American families: the Insulin Resistance Atherosclerosis Family Study. Diabetes 2007; 56:2135-41. [PMID: 17513703 DOI: 10.2337/db06-1017] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
OBJECTIVE We previously detected an association between a region of the estrogen receptor-alpha (ESR1) gene and type 2 diabetes in an African-American case-control study; thus, we investigated this region for associations with the metabolic syndrome and its component traits in African-American families from the Insulin Resistance Atherosclerosis Family Study. RESEARCH DESIGN AND METHODS A total of 17 single nucleotide polymorphisms (SNPs) from a contiguous 41-kb intron 1-intron 2 region of the ESR1 gene were genotyped in 548 individuals from 42 African-American pedigrees. Generalized estimating equations were computed using a sandwich estimator of the variance and exchangeable correlation to account for familial correlation. RESULTS Significant associations were detected between ESR1 SNPs and the metabolic syndrome (P = 0.005 to P = 0.029), type 2 diabetes (P = 0.001), insulin sensitivity (P = 0.0005 to P = 0.023), fasting insulin (P = 0.022 to P = 0.033), triglycerides (P = 0.021), LDL (P = 0.016 to P = 0.034), cholesterol (P = 0.046), BMI (P = 0.016 to P = 0.035), waist circumference (P = 0.012 to P = 0.023), and subcutaneous adipose tissue area (P = 0.016). CONCLUSIONS It appears likely that ESR1 contributes to type 2 diabetes and CVD risk via pleiotropic effects, leading to insulin resistance, a poor lipid profile, and obesity.
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Affiliation(s)
- Carla J Gallagher
- Department of Biochemistry, Wake Forest University School of Medicine, Winston-Salem, North Carolina, USA
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Elbein SC. Evaluation of polymorphisms known to contribute to risk for diabetes in African and African-American populations. Curr Opin Clin Nutr Metab Care 2007; 10:415-9. [PMID: 17563458 DOI: 10.1097/mco.0b013e3281e2c99a] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
PURPOSE OF REVIEW Populations of direct African ancestry have much greater genetic diversity than do other populations. African-American populations exhibit twice the prevalence of type 2 diabetes as compared with their Caucasian counterparts. African-American populations are likely to have unique genetic susceptibility to type 2 diabetes. This review addresses current knowledge of susceptibility genes that are shared with other groups and those that are unique to populations of African descent. RECENT FINDINGS When compared with the plethora of Caucasian studies, relatively few studies have been conducted in African or African-American populations. The most exciting findings have been family-based linkage studies, which point to multiple regions that may harbor susceptibility genes. Recent work suggests that the major Caucasian locus, TCF7L2, plays a role in some African-based populations, whereas unique factors remain to be confirmed. SUMMARY Although progress has been made in finding the genetic cause of type 2 diabetes in African and African-American populations, at this time no variant can be considered unequivocally confirmed as a diabetes susceptibility locus.
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Affiliation(s)
- Steven C Elbein
- Medicine and Research Services, Central Arkansas Veterans Affairs Healthcare System, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA.
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Goodarzi MO, Lehman DM, Taylor KD, Guo X, Cui J, Quiñones MJ, Clee SM, Yandell BS, Blangero J, Hsueh WA, Attie AD, Stern MP, Rotter JI. SORCS1: a novel human type 2 diabetes susceptibility gene suggested by the mouse. Diabetes 2007; 56:1922-9. [PMID: 17426289 DOI: 10.2337/db06-1677] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
OBJECTIVE A small number of susceptibility genes for human type 2 diabetes have been identified by candidate gene analysis or positional cloning. Genes found to influence diabetes or related traits in mice are likely to be susceptibility genes in humans. SorCS1 is the gene identified as responsible for the mouse chromosome 19 T2dm2 quantitative trait locus for fasting insulin levels, acting via impaired insulin secretion and increased islet disruption in obese females. Genes that impair compensatory insulin secretion in response to obesity-induced insulin resistance may be particularly relevant to human diabetes. Thus, we sought to determine whether variation in the human SORCS1 gene was associated with diabetes-related traits. RESEARCH DESIGN AND METHODS We assessed the contribution of variation in SORCS1 to human insulin-related traits in two distinct Mexican-American cohorts. One cohort (the Mexican-American Coronary Artery Disease [MACAD] cohort) consisted of nondiabetic individuals, allowing assessment of genetic association with subclinical intermediate insulin-related traits; the second cohort (the San Antonio Family Diabetes Study [SAFADS]) contained individuals with diabetes, allowing association analyses with overt disease. RESULTS We first found association of SORCS1 single nucleotide polymorphisms and haplotypes with fasting insulin levels and insulin secretion in the MACAD cohort. Similar to our results in the mice, the genetic association was strongest in overweight women. We then observed association with diabetes risk and age at diagnosis in women of the SAFADS cohort. CONCLUSIONS Identification of SORCS1 as a novel gene affecting insulin secretion and diabetes risk is likely to provide important insight into the biology of obesity-induced type 2 diabetes.
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Affiliation(s)
- Mark O Goodarzi
- Cedars-Sinai Medical Center, Division of Endocrinology, Diabetes, and Metabolism, 8700 Beverly Blvd., Becker B-131, Los Angeles, CA 90048, USA.
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Noso S, Fujisawa T, Kawabata Y, Asano K, Hiromine Y, Fukai A, Ogihara T, Ikegami H. Association of small ubiquitin-like modifier 4 (SUMO4) variant, located in IDDM5 locus, with type 2 diabetes in the Japanese population. J Clin Endocrinol Metab 2007; 92:2358-62. [PMID: 17374705 DOI: 10.1210/jc.2007-0031] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
CONTEXT Despite distinct differences in the pathogenesis, epidemiological data have indicated familial clustering of type 1 and type 2 diabetes, suggesting a common genetic basis between these two types of diabetes. Few shared susceptibility genes, however, have been reported to date. OBJECTIVE Small ubiquitin-like modifier 4 (SUMO4) has been identified as a candidate gene for the IDDM5 locus and suggested to have possible involvement in immune responses, such as autoimmunity and inflammation. Recent reports demonstrated that a polymorphism with an amino acid substitution (Met55Val) in SUMO4 was associated with type 1 diabetes in Asian populations, although no association was reproduced in subjects of Caucasian descent. The present study aimed to clarify the contribution of SUMO4 to type 2 diabetes susceptibility in the Japanese population. SUBJECTS The 753 subjects included 355 cases and 398 control subjects. METHODS The SUMO4 Met55Val (rs237025) and 001Msp (rs577001) polymorphisms were genotyped. RESULTS Strong linkage disequilibrium (D': 1.0 in each pair of single-nucleotide polymorphisms) across the MAP3K7IP2/SUMO4 region was shown in the Japanese population. The frequency of genotypes with the G allele of the SUMO4 Met55Val polymorphism was significantly higher in patients with type 2 diabetes [odds ratio, 1.46; 95% confidence interval (CI), 1.08-1.93; P = 0.01, chi(2) test]. The association was concentrated in patients without insulin therapy (odds ratio, 1.56; 95% CI, 1.13-2.15; P = 0.0072), but not in those with insulin (odds ratio, 1.24; 95% CI, 0.81-1.89; not significant). CONCLUSIONS These data, together with previous reports, suggest the contribution of the SUMO4 Met55Val polymorphism to both type 1 and type 2 diabetes susceptibility in the Japanese population.
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Affiliation(s)
- Shinsuke Noso
- Department of Endocrinology, Metabolism, and Diabetes, Kinki University School of Medicine, 377-2 Ohno-Higashi, Osaka-Sayama, Osaka, Japan
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Gallagher CJ, Keene KL, Mychaleckyj JC, Langefeld CD, Hirschhorn JN, Henderson BE, Gordon CJ, Freedman BI, Rich SS, Bowden DW, Sale MM. Investigation of the estrogen receptor-alpha gene with type 2 diabetes and/or nephropathy in African-American and European-American populations. Diabetes 2007; 56:675-84. [PMID: 17327435 DOI: 10.2337/db06-0303] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The estrogen receptor-alpha gene (ESR1) was selected as a positional candidate under a type 2 diabetes linkage peak at 6q24-27. A total of 42 ESR1 single nucleotide polymorphisms (SNPs) were genotyped in 380 African-American type 2 diabetic case subjects with end-stage renal disease (ESRD) and 276 African-American control subjects. A total of 22 ancestry informative markers were also genotyped, and the program Admixmap was used to adjust allelic and haplotypic association tests for individual estimates of admixture. The most significant association with type 2 diabetes-ESRD was with rs1033182 in intron 2 (P = 0.013, admixture-adjusted P(a) = 0.021). Genotyping 17 SNPs across a region of ESR1 intron 1-intron 2 in an expanded population of 851 case and 635 control subjects supported association with rs1033182 (P = 0.004, P(a) = 0.027) and with an independent six-SNP haplotype of high linkage disequilibrium spanning 6.4 kb (P < 0.0001, P(a) < 0.0001). The same 17 ESR1 SNPs were genotyped in 300 European-American type 2 diabetes-ESRD case subjects and 310 European-American control subjects. Two intron 2 SNPs, rs2431260 (P = 0.015) and rs1709183 (P = 0.019), and a four-SNP haplotype containing these SNPs (P = 0.033) were associated with type 2 diabetes and/or ESRD. Results suggest that intron 1 and intron 2 of the ESR1 gene may contain functionally important regions related to type 2 diabetes or ESRD risk.
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Affiliation(s)
- Carla J Gallagher
- Center for Human Genomics, Wake Forest University School of Medicine, Medical Center Blvd., Winston-Salem, NC 27157, USA
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Ehlers CL, Wilhelmsen KC. Genomic screen for substance dependence and body mass index in southwest California Indians. GENES BRAIN AND BEHAVIOR 2007; 6:184-91. [PMID: 16764678 DOI: 10.1111/j.1601-183x.2006.00246.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Substance abuse and obesity are health disparities that may afflict Native Americans more than some other ethnic groups. One theoretical assumption concerning Native people is that the long history of dependence on foraging and subsistence agriculture may have led to selective enrichment of traits that improve genetic fitness, so called 'thrifty' or 'fat sparing' genes. We have speculated that this same selective pressure may have enriched for genetic variants that increase the risk for consumption of alcohol and drugs of abuse. Here, we report the results of a genome scan that compared findings for two consumption phenotypes: 'any drug dependence and/or regular tobacco use' and body mass index (BMI) in southwest California (SWC) Indian families. Variance component analyses from SOLAR were used to generate log of the odds ratio (LOD) scores. Evidence for linkage was found on chromosome 6 for both the 'any drug' (LOD score = 3.3) and BMI (LOD score = 2.3) phenotypes. Bivariate analyses of the two phenotypes revealed a combined LOD score of 4.1 at that location. Additional loci on chromosomes 6, 15, 16 and 21 were found for the 'any drug' phenotype, and on chromosomes 8, 16 and 18 for BMI (LOD scores ranged between 1.2 and 2.3). These results provide suggestive evidence for linkage for substance abuse and BMI in this Mission Indian population and, furthermore, provide preliminary data suggesting that 'consumption phenotypes' may share some genetic determinants.
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Affiliation(s)
- Cindy L Ehlers
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, USA.
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Abstract
Inbred mouse strains provide genetic diversity comparable to that of the human population. Like humans, mice have a wide range of diabetes-related phenotypes. The inbred mouse strains differ in the response of their critical physiological functions, such as insulin sensitivity, insulin secretion, beta-cell proliferation and survival, and fuel partitioning, to diet and obesity. Most of the critical genes underlying these differences have not been identified, although many loci have been mapped. The dramatic improvements in genomic and bioinformatics resources are accelerating the pace of gene discovery. This review describes how mouse genetics can be used to discover diabetes-related genes, summarizes how the mouse strains differ in their diabetes-related phenotypes, and describes several examples of how loci identified in the mouse may directly relate to human diabetes.
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Affiliation(s)
- Susanne M Clee
- Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Drive, Madison, Wisconsin 53706-1544, USA
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Guan W, Pluzhnikov A, Cox NJ, Boehnke M, for the International Type 2 Diabetes Linkage Analysis Consortium. Meta-analysis of 23 type 2 diabetes linkage studies from the International Type 2 Diabetes Linkage Analysis Consortium. Hum Hered 2007; 66:35-49. [PMID: 18223311 PMCID: PMC2855874 DOI: 10.1159/000114164] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2007] [Accepted: 09/05/2007] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND The International Type 2 Diabetes Linkage Analysis Consortium was formed to localize type 2 diabetes predisposing variants based on 23 autosomal linkage scans. METHODS We carried out meta-analysis using the genome scan meta-analysis (GSMA) method which divides the genome into bins of approximately 30 cM, ranks the best linkage results in each bin for each sample, and then sums the ranks across samples. We repeated the meta-analysis using 2 cM bins, and/or replacing bin ranks with measures of linkage evidence: bin maximum LOD score or bin minimum p value for bins with p value <0.05 (truncated p value). We also carried out computer simulations to assess the empirical type I error rates of these meta-analysis methods. RESULTS Our analyses provided modest evidence for type 2 diabetes-predisposing variants on chromosomes 4, 10, and 14 (using LOD scores or truncated p values), or chromosome 10 and 16 (using ranks). Our simulation results suggested that uneven marker density across studies results in substantial variation in empirical type I error rates for all meta-analysis methods, but that 2 cM bins and scores that make more explicit use of linkage evidence, especially the truncated p values, reduce this problem. CONCLUSION We identified regions modestly linked with type 2 diabetes by summarizing results from 23 autosomal genome scans.
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Affiliation(s)
- Weihua Guan
- Department of Biostatistics and Center for Statistical Genetics, School of Public Health, University of Michigan, Ann Arbor, Mich., USA
| | - Anna Pluzhnikov
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, Ill., USA
| | - Nancy J. Cox
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, Ill., USA
| | - Michael Boehnke
- Department of Biostatistics and Center for Statistical Genetics, School of Public Health, University of Michigan, Ann Arbor, Mich., USA
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Elbers CC, Onland-Moret NC, Franke L, Niehoff AG, van der Schouw YT, Wijmenga C. A strategy to search for common obesity and type 2 diabetes genes. Trends Endocrinol Metab 2007; 18:19-26. [PMID: 17126559 DOI: 10.1016/j.tem.2006.11.003] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/28/2006] [Revised: 11/01/2006] [Accepted: 11/14/2006] [Indexed: 12/24/2022]
Abstract
Worldwide, the incidence of type 2 diabetes is rising rapidly, mainly because of the increase in the incidence of obesity, which is an important risk factor for this condition. Both obesity and type 2 diabetes are complex genetic traits but they also share some nongenetic risk factors. Hence, it is tempting to speculate that the susceptibility to type 2 diabetes and obesity might also partly be due to shared genes. By comparing all of the published genome scans for type 2 diabetes and obesity, five overlapping chromosomal regions for both diseases (encompassing 612 candidate genes) have been identified. By analysing these five susceptibility loci for type 2 diabetes and obesity, using six freely available bioinformatics tools for disease gene identification, 27 functional candidate genes have been pinpointed that are involved in eating behaviour, metabolism and inflammation. These genes might reveal a molecular link between the two disorders.
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Affiliation(s)
- Clara C Elbers
- Complex Genetics Section, Department of Biomedical Genetics, University Medical Centre Utrecht, PO Box 85060, 3508 AB Utrecht, the Netherlands
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Estrogen receptor alpha gene polymorphism associated with type 2 diabetes mellitus and the serum lipid concentration in Chinese women in Guangzhou. Chin Med J (Engl) 2006. [DOI: 10.1097/00029330-200611010-00006] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
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