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Amin USM, Parvez N, Rahman TA, Hasan MR, Das KC, Jahan S, Hasanat MA, Seraj ZI, Salimullah M. CDKAL1 gene rs7756992 A/G and rs7754840 G/C polymorphisms are associated with gestational diabetes mellitus in a sample of Bangladeshi population: implication for future T2DM prophylaxis. Diabetol Metab Syndr 2022; 14:18. [PMID: 35090536 PMCID: PMC8796445 DOI: 10.1186/s13098-021-00782-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 12/30/2021] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Association of single nucleotide polymorphisms (SNP) rs7756992 A/G and rs7754840 G/C of cyclin-dependent kinase 5 regulatory subunit-associated protein 1-like 1 (CDKAL1) gene with the susceptibility of gestational diabetes mellitus (GDM) has been studied in a group of Bangladeshi women. METHODS In this case-control study, 212 GDM patients and 256 control subjects were genotyped for rs7756992 and rs7754840 by PCR-RFLP and TaqMan™ allelic discrimination assay method respectively. Genotyping results were confirmed by DNA sequencing and replicated TaqMan™ assay. The odds ratios and their 95% confidence interval were calculated by logistic regression to determine the associations between genotypes and GDM. RESULTS The genotype frequencies of rs7756992-AA/AG/GG in the GDM group and the control group were 37%/48%, 53%/45%, 10%/7% and those of rs7754840-CC/CG/GG were 51%/55%, 40.1%/39.8%, 9%/5% respectively. Under dominant and log additive models rs7756992 was revealed significantly associated with GDM after being adjusted for family history of diabetes (FHD) and gravidity. Conversely, rs7754840 was significantly associated (P = 0.047) with GDM only under the recessive model after the same adjustment. The risk allele frequency of both SNPs was higher in the GDM group but significantly (P = 0.029) increased prevalence was observed in the rs7756992 G allele. When positive FHD and risk alleles of these SNPs were synergistically present in any pregnant woman, the chance of developing GDM was augmented by many folds. The codominant model revealed 2.5 and 2.1 folds increase in odds by AG (rs7756992) and GC (rs7754840) genotypes and 3.7 and 4.5 folds by GG (rs7756992) and CC (rs7754840) genotypes respectively. A significant 2.7 folds (P = 0.038) increase in odds of GDM resulted from the interaction of rs7756992 and family history of diabetes under the dominant model. The cumulative effect of multigravidity and risk alleles of these SNPs increased the odds of GDM more than 1.5 folds in different genotypes. CONCLUSION This study not only revealed a significant association between rs7756992 and rs7754840 with GDM but also provided the possibility as potential markers for foretelling about GDM and type 2 diabetes mellitus in Bangladeshi women.
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Affiliation(s)
- U S Mahzabin Amin
- Molecular Biotechnology Division, National Institute of Biotechnology (NIB), Ganakbari, Ashulia, Savar, Dhaka, 1349, Bangladesh
| | - Nahid Parvez
- Molecular Biotechnology Division, National Institute of Biotechnology (NIB), Ganakbari, Ashulia, Savar, Dhaka, 1349, Bangladesh
| | - Tahia Anan Rahman
- Molecular Biotechnology Division, National Institute of Biotechnology (NIB), Ganakbari, Ashulia, Savar, Dhaka, 1349, Bangladesh
| | - Md Rakibul Hasan
- Department of Endocrinology and Metabolism, Bangabandhu Sheikh Mujib Medical University (BSMMU), Dhaka, Bangladesh
| | - Keshob Chandra Das
- Molecular Biotechnology Division, National Institute of Biotechnology (NIB), Ganakbari, Ashulia, Savar, Dhaka, 1349, Bangladesh
| | - Sharmin Jahan
- Department of Endocrinology and Metabolism, Bangabandhu Sheikh Mujib Medical University (BSMMU), Dhaka, Bangladesh
| | - Muhammad Abul Hasanat
- Department of Endocrinology and Metabolism, Bangabandhu Sheikh Mujib Medical University (BSMMU), Dhaka, Bangladesh
| | - Zeba I Seraj
- Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
| | - Md Salimullah
- Molecular Biotechnology Division, National Institute of Biotechnology (NIB), Ganakbari, Ashulia, Savar, Dhaka, 1349, Bangladesh.
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Huang G, Liang D, Luo L, Lan C, Luo C, Xu H, Lai J. Significance of the lncRNAs MALAT1 and ANRIL in occurrence and development of glaucoma. J Clin Lab Anal 2022; 36:e24215. [PMID: 35028972 PMCID: PMC8842314 DOI: 10.1002/jcla.24215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 12/06/2021] [Accepted: 12/14/2021] [Indexed: 11/19/2022] Open
Abstract
Background Primary open‐angle glaucoma (POAG) is the commonest form of glaucoma which is estimated to cause bilaterally blind within 11.1 million people by 2020. Therefore, the primary objectives of this study were to investigate the clinical significance of single‐nucleotide polymorphisms (SNPs) in the lncRNAs MALAT1 and ANRIL in a Chinese Han POAG cohort. Methods Three hundred and forty‐six glaucoma patients and 263 healthy controls were recruited, and totally 14 SNPs in MALAT1 and ANRIL were genotyped between the two populations. Results The MALAT1 SNPs rs619586 (A>G), rs3200401 (C>T), and rs664589 (C>G) were associated with POAG risk, and the ANRIL SNPs rs2383207 (A>G), rs564398 (A>G), rs2157719 (A>G), rs7865618 (G>A), and rs4977574 (A>G) were associated with POAG (p < 0.05). The MALAT1 haplotypes ACG and ATC, comprised rs619586, rs3200401, and rs664589, increased POAG risk, and the ANRIL haplotype AAGAA, made up of rs2383207, rs7865618, rs4977574, rs564398, and rs2157719, show a significantly increased risk of POAG. In addition, rs619586 (A>G) of MALAT1 and rs564398/rs2157719 of ANRIL were associated with a smaller vertical cup‐to‐disc ratio, while rs619586 of MALAT1 and rs2383207/rs4977574 of ANRIL were associated with higher intraocular pressure in the POAG population. Conclusion Single‐nucleotide polymorphisms and haplotypes in ANRIL and MALAT1 were associated with POAG onset in our study population, which provide more possibilities to POAG diagnosis and treatment.
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Affiliation(s)
- Guoqiang Huang
- Department of Ophthalmology, Meizhou People's Hospital, Meizhou City, China
| | - Dong Liang
- Department of Ophthalmology, Meizhou People's Hospital, Meizhou City, China
| | - Lidan Luo
- Department of Ophthalmology, Meizhou People's Hospital, Meizhou City, China
| | - Chenghong Lan
- Department of Ophthalmology, Meizhou People's Hospital, Meizhou City, China
| | - Chengfeng Luo
- Department of Ophthalmology, Meizhou People's Hospital, Meizhou City, China
| | - Hongwang Xu
- Department of Ophthalmology, Meizhou People's Hospital, Meizhou City, China
| | - Jiangfeng Lai
- Department of Ophthalmology, Meizhou People's Hospital, Meizhou City, China
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AlRasheed MM. Evaluation of the role of CDKN2B gene in type 2 diabetes mellitus and hypertension in ethnic Saudi Arabs. Saudi Pharm J 2018; 26:1199-1203. [PMID: 30510472 PMCID: PMC6257888 DOI: 10.1016/j.jsps.2018.07.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2018] [Accepted: 07/19/2018] [Indexed: 01/04/2023] Open
Abstract
Background Coronary heart disease (CAD) is a multiple with several contributory risk traits, including type 2 diabetes and hypertension, which may share common genetic risk variants with the disease. Genome-wide association studies (GWASs) have yielded a wealth of information suggesting that CAD, the extent of contributory variants may differ according to genetic locus. The present study aimed at verifying whether the cyclin-dependent kinase 4 inhibitor B (CDKN2B) genomic region strongly associated with coronary artery disease (CAD)/myocardial infarction (MI) may also constitute risk for its risk factors type 2 diabetes mellitus (T2DM) and hypertension (HTN) in ethnic Saudi Arabs. Methodology We genotyped eight CDKN2B SNPs for cardiovascular risk in a total of 4650 Saudi Arabs, (3049 male and 1601 female) by Taqman assay. Of these individuals, 3732 had primary hypertension and 2576 had type 2 diabetes mellitus. Results Out of the eight studied SNPs, two, rs10757274_A [0.915 (0.840-1.00); p = 0.042], rs1333045_T [0.92(0.84-1.00); p = 0.048] were initially associated with type 2 diabetes but lost the association after multivariate adjustments for CAD, hypertension and MI, while rs10757274_A showed borderline association with hypertension. Conclusions Our finding does not support the notion of a critical role for the CDKN2B gene locus as a HTN or T2DM cardiovascular risk in ethnic Arabs. The study also demonstrates the importance of replication studies in ascertaining the role of a genomic sequence in disease.
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Noury AE, Azmy O, Alsharnoubi J, Salama S, Okasha A, Gouda W. Variants of CDKAL1 rs7754840 (G/C) and CDKN2A/2B rs10811661 (C/T) with gestational diabetes: insignificant association. BMC Res Notes 2018; 11:181. [PMID: 29544538 PMCID: PMC5856327 DOI: 10.1186/s13104-018-3288-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 03/09/2018] [Indexed: 12/20/2022] Open
Abstract
Objectives Pathophysiological similarity exists between gestational diabetes mellitus (GDM) and type 2 diabetes mellitus with common genetic origin. Genetic liability for GDM in our population is still not researched. The goal was to reveal the genotypic and allele frequency differences of 2 single nucleotide polymorphisms (SNPs) namely, CDKAL1 (rs7754840) and CDKN2A/2B (rs10811661) between GDM pregnancies and normal pregnancies. We assessed them by real time polymerase chain reaction using Taqman® allelic discrimination assays. We included 47 GDM pregnant subjects and 51 normal glucose tolerance (NGT) pregnant women as controls. Results The genotype frequencies in the GDM group and the NGT group of rs7754840-GG/GC/CC were 6.4/15.7% (3/8), 55.3/45.1% (26/23) and 38.3/39.2% (18/20) respectively. Also, those of rs10811661-CC/CT/TT were 74.5/14.9/4.3% (38/7/2) and 80.9/19.6/5.9% (38/10/3) respectively. The allele frequencies in the GDM group and the NGT group of C/G and T/C were 66/34% (62/32), 61.8/38.2% (63/39) and 11.7/88.3% (11/83), 15.7/84.3% (16/86) respectively. There were no statistical differences between the two groups in allele frequencies and genotype frequencies (all P > 0.05). Non-significant association was seen in the two SNPs of CDKAL1 and CDKN2A/B genes with GDM. Further studies are essential to validate data.
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Affiliation(s)
- Amr El Noury
- National Institute of Laser Enhanced Science, Cairo University, Cairo, Egypt
| | - Osama Azmy
- Reproductive Health Department, National Research Centre, El Buhouth St., Dokki, Giza, 12622, Egypt
| | - Jehan Alsharnoubi
- National Institute of Laser Enhanced Science, Cairo University, Cairo, Egypt
| | - Sameh Salama
- Reproductive Health Department, National Research Centre, El Buhouth St., Dokki, Giza, 12622, Egypt
| | - Ahmed Okasha
- Reproductive Health Department, National Research Centre, El Buhouth St., Dokki, Giza, 12622, Egypt.
| | - Weaam Gouda
- Biochemistry Department, National Research Centre, El Buhouth St., Dokki, Giza, 12622, Egypt
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Sikhayeva N, Iskakova A, Saigi-Morgui N, Zholdybaeva E, Eap CB, Ramanculov E. Association between 28 single nucleotide polymorphisms and type 2 diabetes mellitus in the Kazakh population: a case-control study. BMC MEDICAL GENETICS 2017; 18:76. [PMID: 28738793 PMCID: PMC5525290 DOI: 10.1186/s12881-017-0443-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 07/13/2017] [Indexed: 02/06/2023]
Abstract
Background We evaluated the associations between single nucleotide polymorphisms and different clinical parameters related to type 2 diabetes mellitus (T2DM), obesity risk, and metabolic syndrome (MS) in a Kazakh cohort. Methods A total of 1336 subjects, including 408 T2DM patients and 928 control subjects, were recruited from an outpatient clinic and genotyped for 32 polymorphisms previously associated with T2DM and obesity-related phenotypes in other ethnic groups. For association studies, the chi-squared test or Fisher’s exact test for binomial variables were used. Logistic regression was conducted to explore associations between the studied SNPs and the risk of developing T2DM, obesity, and MS, after adjustments for age and sex. Results After excluding four SNPs due to Hardy-Weinberg disequilibrium, significant associations in age-matched cohorts were found betweenT2DM and the following SNPs: rs9939609 (FTO), rs13266634 (SLC30A8), rs7961581 (TSPAN8/LGR5), and rs1799883 (FABP2). In addition, examination of general unmatched T2DM and control cohorts revealed significant associations between T2DM and SNPsrs1799883 (FABP2) and rs9939609 (FTO). Furthermore, polymorphisms in the FTO gene were associated with increased obesity risk, whereas polymorphisms in the FTO and FABP2 genes were also associated with the risk of developing MS in general unmatched cohorts. Conclusion We confirmed associations between polymorphisms within the SLC30A8, TSPAN8/LGR5, FABP2, and FTO genes and susceptibility to T2DM in a Kazakh cohort, and revealed significant associations with anthropometric and metabolic traits. In particular, FTO and FABP2 gene polymorphisms were significantly associated with susceptibility to MS and obesity in this cohort. Electronic supplementary material The online version of this article (doi:10.1186/s12881-017-0443-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nurgul Sikhayeva
- National Center for Biotechnology, 13/5 Korgalzhyn str, Astana, 010000, Kazakhstan. .,L.N. Gumilyov Eurasian National University, Astana, Kazakhstan.
| | - Aisha Iskakova
- National Center for Biotechnology, 13/5 Korgalzhyn str, Astana, 010000, Kazakhstan
| | - Nuria Saigi-Morgui
- Unit of Pharmacogenetics and Clinical Psychopharmacology, Centre for Psychiatric Neuroscience, Department of Psychiatry, Lausanne University Hospital, 1008, Prilly-Lausanne, Switzerland
| | - Elena Zholdybaeva
- National Center for Biotechnology, 13/5 Korgalzhyn str, Astana, 010000, Kazakhstan
| | - Chin-Bin Eap
- Unit of Pharmacogenetics and Clinical Psychopharmacology, Centre for Psychiatric Neuroscience, Department of Psychiatry, Lausanne University Hospital, 1008, Prilly-Lausanne, Switzerland.,School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, Geneva, Switzerland
| | - Erlan Ramanculov
- National Center for Biotechnology, 13/5 Korgalzhyn str, Astana, 010000, Kazakhstan.,L.N. Gumilyov Eurasian National University, Astana, Kazakhstan.,School of Science and Technology, Nazarbayev University, Astana, Kazakhstan
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Chang W. Non-coding RNAs and Berberine: A new mechanism of its anti-diabetic activities. Eur J Pharmacol 2017; 795:8-12. [DOI: 10.1016/j.ejphar.2016.11.055] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Revised: 11/29/2016] [Accepted: 11/30/2016] [Indexed: 12/20/2022]
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Kong Y, Sharma RB, Nwosu BU, Alonso LC. Islet biology, the CDKN2A/B locus and type 2 diabetes risk. Diabetologia 2016; 59:1579-93. [PMID: 27155872 PMCID: PMC4930689 DOI: 10.1007/s00125-016-3967-7] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 03/29/2016] [Indexed: 02/06/2023]
Abstract
Type 2 diabetes, fuelled by the obesity epidemic, is an escalating worldwide cause of personal hardship and public cost. Diabetes incidence increases with age, and many studies link the classic senescence and ageing protein p16(INK4A) to diabetes pathophysiology via pancreatic islet biology. Genome-wide association studies (GWASs) have unequivocally linked the CDKN2A/B locus, which encodes p16 inhibitor of cyclin-dependent kinase (p16(INK4A)) and three other gene products, p14 alternate reading frame (p14(ARF)), p15(INK4B) and antisense non-coding RNA in the INK4 locus (ANRIL), with human diabetes risk. However, the mechanism by which the CDKN2A/B locus influences diabetes risk remains uncertain. Here, we weigh the evidence that CDKN2A/B polymorphisms impact metabolic health via islet biology vs effects in other tissues. Structured in a bedside-to-bench-to-bedside approach, we begin with a summary of the evidence that the CDKN2A/B locus impacts diabetes risk and a brief review of the basic biology of CDKN2A/B gene products. The main emphasis of this work is an in-depth look at the nuanced roles that CDKN2A/B gene products and related proteins play in the regulation of beta cell mass, proliferation and insulin secretory function, as well as roles in other metabolic tissues. We finish with a synthesis of basic biology and clinical observations, incorporating human physiology data. We conclude that it is likely that the CDKN2A/B locus influences diabetes risk through both islet and non-islet mechanisms.
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Affiliation(s)
- Yahui Kong
- AS7-2047, Division of Diabetes, Department of Medicine, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA, 01605, USA
| | - Rohit B Sharma
- AS7-2047, Division of Diabetes, Department of Medicine, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA, 01605, USA
| | - Benjamin U Nwosu
- Division of Endocrinology, Department of Pediatrics, University of Massachusetts Medical School, Worcester, MA, USA
| | - Laura C Alonso
- AS7-2047, Division of Diabetes, Department of Medicine, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA, 01605, USA.
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Wei F, Cai C, Feng S, Lv J, Li S, Chang B, Zhang H, Shi W, Han H, Ling C, Yu P, Chen Y, Sun N, Tian J, Jiao H, Yang F, Li M, Wang Y, Zou L, Su L, Li J, Li R, Qiu H, Shi J, Liu S, Chang M, Lin J, Chen L, Li WD. TOX and CDKN2A/B Gene Polymorphisms Are Associated with Type 2 Diabetes in Han Chinese. Sci Rep 2015; 5:11900. [PMID: 26139146 PMCID: PMC4650661 DOI: 10.1038/srep11900] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Accepted: 06/08/2015] [Indexed: 12/27/2022] Open
Abstract
To study associations between type 2 diabetes (T2DM) candidate genes and microvascular complications of diabetes (MVCDs), we performed case-control association studies for both T2DM and MVCDs in Han Chinese subjects. We recruited 1,939 unrelated Han Chinese T2DM patients and 918 individuals with normal blood glucose levels as nondiabetic controls. Among T2DM patients, 1116 have MVCDs, 266 have a history of T2DM of >10 years but never developed MVCDs. Eighty-two single-nucleotide polymorphisms (SNPs) in 54 candidate genes were genotyped. Discrete association studies were performed by the PLINK program for T2DM and MVCDs. Significant associations were found among candidate gene SNPs and T2DM, including rs1526167 of the TOX gene (allele A, P = 2.85 × 10−9, OR = 1.44). The SNP rs10811661 of the CDKN2A/B gene was also associated with T2DM (allele T, P = 4.09 × 10−7, OR = 1.36). When we used control patients with >10 years of T2DM history without MVCD, we found that the G allele of SNP rs1526167 of the TOX gene was associated with MVCD (nominal P = 4.33 × 10−4). In our study, significant associations were found between TOX and CDKN2A/B gene SNPs and T2DM. The TOX polymorphism might account for the higher risk of T2DM and the lower risk of MVCDs in the Han Chinese population.
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Affiliation(s)
- Fengjiang Wei
- Research Center of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
| | - Chunyou Cai
- Research Center of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
| | - Shuzhi Feng
- Tianjin General Hospital, Tianjin Medical University, Tianjin, 300052, China
| | - Jia Lv
- Research Center of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
| | - Shen Li
- Research Center of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
| | - Baocheng Chang
- Metabolic Diseases Hospital, Tianjin Medical University, Tianjin, 300070, China
| | - Hong Zhang
- Eye Hospital, Tianjin Medical University, Tianjin, 300384, China
| | - Wentao Shi
- Research Center of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
| | - Hongling Han
- Tianjin General Hospital, Tianjin Medical University, Tianjin, 300052, China
| | - Chao Ling
- Research Center of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
| | - Ping Yu
- Research Center of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
| | - Yongjun Chen
- Eye Hospital, Tianjin Medical University, Tianjin, 300384, China
| | - Ning Sun
- Tianjin General Hospital, Tianjin Medical University, Tianjin, 300052, China
| | - Jianli Tian
- Tianjin General Hospital, Tianjin Medical University, Tianjin, 300052, China
| | - Hongxiao Jiao
- Research Center of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
| | - Fuhua Yang
- Research Center of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
| | - Mingshan Li
- Research Center of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
| | - Yuhua Wang
- Research Center of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
| | - Lei Zou
- Research Center of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
| | - Long Su
- Eye Hospital, Tianjin Medical University, Tianjin, 300384, China
| | - Jingbo Li
- Tianjin People's Hospital, Department of Endocrinology, Tianjin, 300191, China
| | - Ran Li
- Tianjin General Hospital, Tianjin Medical University, Tianjin, 300052, China
| | - Huina Qiu
- Tianjin People's Hospital, Department of Endocrinology, Tianjin, 300191, China
| | - Jingmin Shi
- Research Center of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
| | - Shiying Liu
- Tianjin General Hospital, Tianjin Medical University, Tianjin, 300052, China
| | - Mingqin Chang
- Research Center of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
| | - Jingna Lin
- Tianjin People's Hospital, Department of Endocrinology, Tianjin, 300191, China
| | - Liming Chen
- Metabolic Diseases Hospital, Tianjin Medical University, Tianjin, 300070, China
| | - Wei-Dong Li
- Research Center of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
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Lara-Riegos JC, Ortiz-López MG, Peña-Espinoza BI, Montúfar-Robles I, Peña-Rico MA, Sánchez-Pozos K, Granados-Silvestre MA, Menjivar M. Diabetes susceptibility in Mayas: Evidence for the involvement of polymorphisms in HHEX, HNF4α, KCNJ11, PPARγ, CDKN2A/2B, SLC30A8, CDC123/CAMK1D, TCF7L2, ABCA1 and SLC16A11 genes. Gene 2015; 565:68-75. [PMID: 25839936 DOI: 10.1016/j.gene.2015.03.065] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Revised: 03/13/2015] [Accepted: 03/29/2015] [Indexed: 01/11/2023]
Abstract
Association of type 2 diabetes (T2D) with common variants in HHEX, HNF4α, KCNJ11, PPARγ, CDKN2A/2B, SLC30A8, CDC123/CAMK1D, TCF7L2, ABCA1 and SLC16A11 genes have been reported, mainly in populations of European and Asian ancestry and to a lesser extent in Latin Americans. Thus, we aimed to investigate the contribution of rs1111875 (HHEX), rs1800961 (HNF4α), rs5219 (KCNJ11), rs1801282 (PPARγ), rs10811661 (CDKN2A/2B), rs13266634 (SLC30A8), rs12779790 (CDC123/CAMK1D), rs7903146 (TCF7L2), rs9282541 (ABCA1) and rs13342692 (SLC16A11) polymorphisms in the genetic background of Maya population to associate their susceptibility to develop T2D. This is one of the first studies designed specifically to investigate the inherited component of T2D in the indigenous population of Mexico. SNPs were genotyped by allelic discrimination method in 575 unrelated Maya individuals. Two SNPs rs10811661 and rs928254 were significantly associated with T2D after adjusting for BMI; rs10811661 in a recessive and rs9282541 in a dominant model. Additionally, we found phenotypical alterations associated with genetic variants: HDL to rs9282541 and insulin to rs13342692. In conclusion, these findings support an association of genetic polymorphisms to develop T2D in Maya population.
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Affiliation(s)
- J C Lara-Riegos
- Unidad de Genómica de Poblaciones Aplicada a la Salud, Facultad de Química Universidad Nacional Autónoma de México - Instituto Nacional de Medicina Genómica, Mexico
| | - M G Ortiz-López
- Laboratory of Molecular Endocrinology, Hospital Juárez de México, Mexico
| | - B I Peña-Espinoza
- Unidad de Genómica de Poblaciones Aplicada a la Salud, Facultad de Química Universidad Nacional Autónoma de México - Instituto Nacional de Medicina Genómica, Mexico
| | - I Montúfar-Robles
- Laboratory of Molecular Endocrinology, Hospital Juárez de México, Mexico
| | - M A Peña-Rico
- Unidad de Genómica de Poblaciones Aplicada a la Salud, Facultad de Química Universidad Nacional Autónoma de México - Instituto Nacional de Medicina Genómica, Mexico
| | - K Sánchez-Pozos
- Unidad de Genómica de Poblaciones Aplicada a la Salud, Facultad de Química Universidad Nacional Autónoma de México - Instituto Nacional de Medicina Genómica, Mexico
| | - M A Granados-Silvestre
- Unidad de Genómica de Poblaciones Aplicada a la Salud, Facultad de Química Universidad Nacional Autónoma de México - Instituto Nacional de Medicina Genómica, Mexico
| | - M Menjivar
- Unidad de Genómica de Poblaciones Aplicada a la Salud, Facultad de Química Universidad Nacional Autónoma de México - Instituto Nacional de Medicina Genómica, Mexico.
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Helgeland Ø, Hertel JK, Molven A, Ræder H, Platou CGP, Midthjell K, Hveem K, Nygård O, Njølstad PR, Johansson S. The Chromosome 9p21 CVD- and T2D-Associated Regions in a Norwegian Population (The HUNT2 Survey). Int J Endocrinol 2015; 2015:164652. [PMID: 26089876 PMCID: PMC4451520 DOI: 10.1155/2015/164652] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Accepted: 08/17/2014] [Indexed: 12/21/2022] Open
Abstract
Background. Two adjacent regions upstream CDKN2B on chromosome 9p21 have been associated with type 2 diabetes (T2D) and progression of cardiovascular disease (CVD). The precise location and number of risk variants have not been completely delineated and a possible synergistic relationship between the adjacent regions is not fully addressed. By a population based cross-sectional case-control design, we genotyped 18 SNPs upstream of CDKN2B tagging 138 kb in and around two LD-blocks associated with CVD and T2D and investigated associations with T2D, angina pectoris (AP), myocardial infarction (MI), coronary heart disease (CHD; AP or AMI), and stroke using 5,564 subjects from HUNT2. Results. Single point and haplotype analysis showed evidence for only one common T2D risk haplotype (rs10757282∣rs10811661: OR = 1.19, P = 2.0 × 10(-3)) in the region. We confirmed the strong association between SNPs in the 60 kb CVD region with AP, MI, and CHD (P < 0.01). Conditioning on the lead SNPs in the region, we observed two suggestive independent single SNP association signals for MI, rs2065501 (P = 0.03) and rs3217986 (P = 0.04). Conclusions. We confirmed the association of known variants within the 9p21 interval with T2D and CHD. Our results further suggest that additional CHD susceptibility variants exist in this region.
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Affiliation(s)
- Øyvind Helgeland
- KG Jebsen Center for Diabetes Research, Department of Clinical Science, University of Bergen, 5021 Bergen, Norway
- Department of Pediatrics, Haukeland University Hospital, 5021 Bergen, Norway
- *Øyvind Helgeland:
| | - Jens K. Hertel
- KG Jebsen Center for Diabetes Research, Department of Clinical Science, University of Bergen, 5021 Bergen, Norway
- Department of Pediatrics, Haukeland University Hospital, 5021 Bergen, Norway
- Morbid Obesity Center, Vestfold Hospital Trust, 3116 Tønsberg, Norway
- Department of Heart Disease, Haukeland University Hospital, 5021 Bergen, Norway
| | - Anders Molven
- KG Jebsen Center for Diabetes Research, Department of Clinical Science, University of Bergen, 5021 Bergen, Norway
- Gade Laboratory for Pathology, Department of Clinical Medicine, University of Bergen, 5021 Bergen, Norway
- Department of Pathology, Haukeland University Hospital, 5021 Bergen, Norway
| | - Helge Ræder
- KG Jebsen Center for Diabetes Research, Department of Clinical Science, University of Bergen, 5021 Bergen, Norway
- Department of Pediatrics, Haukeland University Hospital, 5021 Bergen, Norway
| | - Carl G. P. Platou
- HUNT Research Centre, Department of Public Health and General Practice, Norwegian University of Science and Technology, 7600 Levanger, Norway
- Department of Internal Medicine, Levanger Hospital, Nord-Trøndelag Health Trust, 7600 Levanger, Norway
| | - Kristian Midthjell
- HUNT Research Centre, Department of Public Health and General Practice, Norwegian University of Science and Technology, 7600 Levanger, Norway
| | - Kristian Hveem
- HUNT Research Centre, Department of Public Health and General Practice, Norwegian University of Science and Technology, 7600 Levanger, Norway
| | - Ottar Nygård
- KG Jebsen Center for Diabetes Research, Department of Clinical Science, University of Bergen, 5021 Bergen, Norway
- Department of Heart Disease, Haukeland University Hospital, 5021 Bergen, Norway
| | - Pål R. Njølstad
- KG Jebsen Center for Diabetes Research, Department of Clinical Science, University of Bergen, 5021 Bergen, Norway
- Department of Pediatrics, Haukeland University Hospital, 5021 Bergen, Norway
| | - Stefan Johansson
- KG Jebsen Center for Diabetes Research, Department of Clinical Science, University of Bergen, 5021 Bergen, Norway
- Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, 5021 Bergen, Norway
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Bantubungi K, Hannou SA, Caron-Houde S, Vallez E, Baron M, Lucas A, Bouchaert E, Paumelle R, Tailleux A, Staels B. Cdkn2a/p16Ink4a regulates fasting-induced hepatic gluconeogenesis through the PKA-CREB-PGC1α pathway. Diabetes 2014; 63:3199-209. [PMID: 24789920 DOI: 10.2337/db13-1921] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Type 2 diabetes (T2D) is hallmarked by insulin resistance, impaired insulin secretion, and increased hepatic glucose production. The worldwide increasing prevalence of T2D calls for efforts to understand its pathogenesis in order to improve disease prevention and management. Recent genome-wide association studies have revealed strong associations between the CDKN2A/B locus and T2D risk. The CDKN2A/B locus contains genes encoding cell cycle inhibitors, including p16(Ink4a), which have not yet been implicated in the control of hepatic glucose homeostasis. Here, we show that p16(Ink4a) deficiency enhances fasting-induced hepatic glucose production in vivo by increasing the expression of key gluconeogenic genes. p16(Ink4a) downregulation leads to an activation of PKA-CREB-PGC1α signaling through increased phosphorylation of PKA regulatory subunits. Taken together, these results provide evidence that p16(Ink4a) controls fasting glucose homeostasis and could as such be involved in T2D development.
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Affiliation(s)
- Kadiombo Bantubungi
- Université Lille 2, Lille, France INSERM, U1011, Lille, France European Genomic Institute for Diabetes, Lille, France Institut Pasteur de Lille, Lille, France
| | - Sarah-Anissa Hannou
- Université Lille 2, Lille, France INSERM, U1011, Lille, France European Genomic Institute for Diabetes, Lille, France Institut Pasteur de Lille, Lille, France
| | - Sandrine Caron-Houde
- Université Lille 2, Lille, France INSERM, U1011, Lille, France European Genomic Institute for Diabetes, Lille, France Institut Pasteur de Lille, Lille, France
| | - Emmanuelle Vallez
- Université Lille 2, Lille, France INSERM, U1011, Lille, France European Genomic Institute for Diabetes, Lille, France Institut Pasteur de Lille, Lille, France
| | - Morgane Baron
- Université Lille 2, Lille, France INSERM, U1011, Lille, France European Genomic Institute for Diabetes, Lille, France Institut Pasteur de Lille, Lille, France
| | - Anthony Lucas
- Université Lille 2, Lille, France INSERM, U1011, Lille, France European Genomic Institute for Diabetes, Lille, France Institut Pasteur de Lille, Lille, France
| | - Emmanuel Bouchaert
- Université Lille 2, Lille, France INSERM, U1011, Lille, France European Genomic Institute for Diabetes, Lille, France Institut Pasteur de Lille, Lille, France
| | - Réjane Paumelle
- Université Lille 2, Lille, France INSERM, U1011, Lille, France European Genomic Institute for Diabetes, Lille, France Institut Pasteur de Lille, Lille, France
| | - Anne Tailleux
- Université Lille 2, Lille, France INSERM, U1011, Lille, France European Genomic Institute for Diabetes, Lille, France Institut Pasteur de Lille, Lille, France
| | - Bart Staels
- Université Lille 2, Lille, France INSERM, U1011, Lille, France European Genomic Institute for Diabetes, Lille, France Institut Pasteur de Lille, Lille, France
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12
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Salas E, Rabhi N, Froguel P, Annicotte JS. Role of Ink4a/Arf locus in beta cell mass expansion under physiological and pathological conditions. J Diabetes Res 2014; 2014:873679. [PMID: 24672805 PMCID: PMC3941170 DOI: 10.1155/2014/873679] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Accepted: 12/20/2013] [Indexed: 12/11/2022] Open
Abstract
The ARF/INK4A (Cdkn2a) locus includes the linked tumour suppressor genes p16INK4a and p14ARF (p19ARF in mice) that trigger the antiproliferative activities of both RB and p53. With beta cell self-replication being the primary source for new beta cell generation in adult animals, the network by which beta cell replication could be increased to enhance beta cell mass and function is one of the approaches in diabetes research. In this review, we show a general view of the regulation points at transcriptional and posttranslational levels of Cdkn2a locus. We describe the molecular pathways and functions of Cdkn2a in beta cell cycle regulation. Given that aging reveals increased p16Ink4a levels in the pancreas that inhibit the proliferation of beta cells and decrease their ability to respond to injury, we show the state of the art about the role of this locus in beta cell senescence and diabetes development. Additionally, we focus on two approaches in beta cell regeneration strategies that rely on Cdkn2a locus negative regulation: long noncoding RNAs and betatrophin.
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Affiliation(s)
- Elisabet Salas
- European Genomic Institute for Diabetes (EGID), CNRS UMR 8199, Lille 2 University, 59000 Lille, France
| | - Nabil Rabhi
- European Genomic Institute for Diabetes (EGID), CNRS UMR 8199, Lille 2 University, 59000 Lille, France
| | - Philippe Froguel
- European Genomic Institute for Diabetes (EGID), CNRS UMR 8199, Lille 2 University, 59000 Lille, France
- Department of Genomics of Common Disease, Hammersmith Hospital, Imperial College London, London W12 0NN, UK
| | - Jean-Sébastien Annicotte
- European Genomic Institute for Diabetes (EGID), CNRS UMR 8199, Lille 2 University, 59000 Lille, France
- *Jean-Sébastien Annicotte:
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13
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Li H, Tang X, Liu Q, Wang Y. Association between type 2 diabetes and rs10811661 polymorphism upstream of CDKN2A/B: a meta-analysis. Acta Diabetol 2013; 50:657-62. [PMID: 22623142 DOI: 10.1007/s00592-012-0400-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/02/2012] [Accepted: 04/30/2012] [Indexed: 12/12/2022]
Abstract
To assess the association between type 2 diabetes and rs10811661 polymorphism, upstream of CDKN2A/B, a literature-based search was conducted to collect data. The pooled OR (odds ratio) and 95 % confidence intervals (CI) were used to assess the strength of association between rs10811661 polymorphism and type 2 diabetes. OR with 95 % CI were performed for allele contrasts, additive genetic model, dominant genetic model and recessive genetic model, respectively. The effect model was used if there was heterogeneity between studies. Funnel plots were used to predict publication bias. 17 studies with 29,990 cases and 40,977 controls were enrolled in this meta-analysis. Significant association was found in all of the four genetic models: allele contrast (OR = 1.21, 95 % CI 1.18-1.24), additive genetic model (OR = 1.51, 95 % CI 1.40-1.63), dominant genetic model (OR = 1.37, 95 % CI 1.28-1.47) and recessive genetic model (OR = 1.25, 95 % CI 1.21-1.29). The meta-analysis indicated that rs10811661 polymorphism was significantly associated with the risk of type 2 diabetes.
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Affiliation(s)
- Hui Li
- School of Public Health and Management, Chongqing Medical University, Chongqing, China
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14
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Peng F, Hu D, Gu C, Li X, Li Y, Jia N, Chu S, Lin J, Niu W. The relationship between five widely-evaluated variants in CDKN2A/B and CDKAL1 genes and the risk of type 2 diabetes: a meta-analysis. Gene 2013; 531:435-43. [PMID: 24012816 DOI: 10.1016/j.gene.2013.08.075] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2013] [Revised: 08/20/2013] [Accepted: 08/22/2013] [Indexed: 01/12/2023]
Abstract
The genes encoding two cyclin-dependent kinases-inhibitor-2A/B (CDKN2A/B) and 5 regulatory subunit-associated protein-like 1 (CDKAL1) have been investigated extensively in associations with type 2 diabetes; the results, however, are often irreproducible. We therefore sought to evaluate these associations by performing a meta-analysis on five widely-evaluated variants from the two genes. There were 38 studies (patients/controls: 51,940/52,234) for rs10811661, 16 studies (20,029/24,419) for rs564398 in CDKN2A/B gene, and 27 studies (28,383/47,635) for rs7756992, 26 studies (28,816/31,713) for rs7754840, 21 studies (29,260/38,400) for rs10946398 in CDKAL1 gene. Overall risk estimates for type 2 diabetes conferred by rs10811661-T, rs564398-A, rs7754840-C, rs7756992-G, and rs10946398-C alleles were 1.17 (95% CI: 1.10-1.23; P<0.0005; I(2)=83.9%), 1.1 (95% CI: 1.0-1.21; P=0.051; I(2)=88.3%), 1.24 (95% CI: 1.18-1.3; P<0.0005; I(2)=74.3%), 1.2 (95% CI: 1.11-1.3; P<0.0005; I(2)=92.0%), and 1.19 (95% CI: 1.1-1.29; P<0.0005; I(2)=90.8%), respectively. There was evident publication bias for rs564398 and rs7754840. Subgroup analyses by ethnicity showed remarkable divergences in risk estimate for rs564398 between Asians (odds ratio [OR]=1.01; 95% CI: 0.86-1.19; P=0.868) and Caucasians (OR=1.19; 95% CI: 1.03-1.35; P=0.012) (P<0.05). For all variants examined, the results of studies in retrospective design or with population-based controls were comparative with that of overall studies. In meta-regression analyses, age was found to exert a significant influence on the association between rs10811661 and type 2 diabetes (P=0.003), as well as between rs7754840 and gender (P=0.034). Taken together, our findings provide evidence for a significant contribution of CDKN2A/B gene rs10811661 and CDKAL1 gene rs7756992 and rs10946398 to type 2 diabetes.
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Affiliation(s)
- Feng Peng
- Department of Cardiology, the First Affiliated Hospital of Fujian Medical University, Fuzhou, China
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15
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ACE I/D and MTHFR C677T polymorphisms are significantly associated with type 2 diabetes in Arab ethnicity: a meta-analysis. Gene 2013; 520:166-77. [PMID: 23458876 DOI: 10.1016/j.gene.2013.02.017] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2012] [Revised: 01/28/2013] [Accepted: 02/06/2013] [Indexed: 12/14/2022]
Abstract
In this meta-analysis study, SNPs were investigated for their association with type 2 diabetes (T2D) in both Arab and Caucasian ethnicities. A total of 55 SNPs were analyzed, of which 11 fulfilled the selection criteria, and were used for analysis. It was found that TCF7L2 rs7903146 was significantly associated with a pooled OR of 1.155 (95%C.I.=1.059-1.259), p<0.0001 and I(2)=78.30% among the Arab population, whereas among Caucasians, the pooled OR was 1.45 (95%C.I.=1.386-1.516), p<0.0001 and I(2)=77.20%. KCNJ11 rs5219 was significantly associated in both the populations with a pooled OR of 1.176(1.092-1.268), p<0.0001 and I(2)=32.40% in Caucasians and a pooled OR of 1.28(1.111-1.475), p=0.001 among Arabs. The ACE I/D polymorphism was found to be significantly associated with a pooled OR of 1.992 (95%C.I.=1.774-2.236), p<0.0001 and I(2)=83.20% among the Arab population, whereas among Caucasians, the pooled OR was 1.078 (95%C.I.=0.993-1.17), p=0.073 and I(2)=0%. Similarly, MTHFR C677T polymorphism was also found to be significantly associated among Arabs with a pooled OR of 1.924 (95%C.I.=1.606-2.304), p<0.0001 and I(2)=27.20%, whereas among Caucasians, the pooled OR was 0.986 (95%C.I.=0.868-1.122), p=0.835 and I(2)=0%. Meanwhile PPARG-2 Pro12Ala, CDKN2A/2B rs10811661, IGF2BP2 rs4402960, HHEX rs7923837, CDKAL1 rs7754840, EXT2 rs1113132 and SLC30A8 rs13266634 were found to have no significant association with T2D among Arabs. In conclusion, it seems from this study that both Arabs and Caucasians have different SNPs associated with T2D. Moreover, this study sheds light on the profound necessity for further investigations addressing the question of the genetic components of T2D in Arabs.
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JI F, JIN LS, ZENG XM, ZHANG XJ, ZHANG YC, SUN YX, GAO LH, HE H, RAO JH, LIU XM, PENG BL. Comparison of gene expression between naturally occurring and diet-induced T2DM in cynomolgus monkeys. Zool Res 2013; 33:79-84. [DOI: 10.3724/sp.j.1141.2012.01079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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Borglykke A, Grarup N, Sparsø T, Linneberg A, Fenger M, Jeppesen J, Hansen T, Pedersen O, Jørgensen T. Genetic variant SLC2A2 [corrected] Is associated with risk of cardiovascular disease – assessing the individual and cumulative effect of 46 type 2 diabetes related genetic variants. PLoS One 2012. [PMID: 23185617 PMCID: PMC3503928 DOI: 10.1371/journal.pone.0050418] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Aim To assess the individual and combined effect of 46 type 2 diabetes related risk alleles on incidence of a composite CVD endpoint. Methods Data from the first Danish MONICA study (N = 3523) and the Inter99 study (N = 6049) was used. Using Cox proportional hazard regression the individual effect of each risk allele on incident CVD was analyzed. Risk was presented as hazard ratios (HR) per risk allele. Results During 80,859 person years 1441 incident cases of CVD (fatal and non-fatal) occurred in the MONICA study. In Inter99 942 incident cases were observed during 61,239 person years. In the Danish MONICA study four gene variants were significantly associated with incident CVD independently of known diabetes status at baseline; SLC2A2 rs11920090 (HR 1.147, 95% CI 1.027–1.283 , P = 0.0154), C2CD4A rs7172432 (1.112, 1.027–1.205 , P = 0.0089), GCKR rs780094 (1.094, 1.007–1.188 , P = 0.0335) and C2CD4B rs11071657 (1.092, 1.007–1.183 , P = 0.0323). The genetic score was significantly associated with increased risk of CVD (1.025, 1.010–1.041, P = 0.0016). In Inter99 two gene variants were associated with risk of CVD independently of diabetes; SLC2A2 (HR 1.180, 95% CI 1.038–1.341 P = 0.0116) and FTO (0.909, 0.827–0.998, P = 0.0463). Analysing the two populations together we found SLC2A2 rs11920090 (HR 1.164, 95% CI 1.070–1.267, P = 0.0004) meeting the Bonferroni corrected threshold for significance. GCKR rs780094 (1.076, 1.010–1.146, P = 0.0229), C2CD4B rs11071657 (1.067, 1.003–1.135, P = 0.0385) and NOTCH2 rs10923931 (1.104 (1.001 ; 1.217 , P = 0.0481) were found associated with CVD without meeting the corrected threshold. The genetic score was significantly associated with increased risk of CVD (1.018, 1.006–1.031, P = 0.0043). Conclusions This study showed that out of the 46 genetic variants examined only the minor risk allele of SLC2A2 rs11920090 was significantly (P = 0.0005) associated with a composite endpoint of incident CVD below the threshold for statistical significance corrected for multiple testing. This potential pathway needs further exploration.
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Affiliation(s)
- Anders Borglykke
- Research Centre for Prevention and Health, Glostrup University Hospital, Glostrup, Denmark.
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18
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Cugino D, Gianfagna F, Santimone I, de Gaetano G, Donati MB, Iacoviello L, Di Castelnuovo A. Type 2 diabetes and polymorphisms on chromosome 9p21: a meta-analysis. Nutr Metab Cardiovasc Dis 2012; 22:619-625. [PMID: 21315566 DOI: 10.1016/j.numecd.2010.11.010] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/13/2010] [Revised: 11/24/2010] [Accepted: 11/28/2010] [Indexed: 10/18/2022]
Abstract
BACKGROUND AND AIMS Genome-wide association studies found some variants on chromosome 9p21 associated with type 2 diabetes (T2D). We performed a meta-analysis to estimate strength, accuracy and feature of the association of polymorphisms in 9p21 with T2D. METHODS AND RESULTS Articles were retrieved screening electronic databases and cross references. Twenty-two publications were identified, for a total of 38,455 T2D patients and 60,516 controls. Twenty-one studies investigated the role of the SNP rs10811661; in some studies three additional SNPs (rs564398, rs10757278, rs1333040) were genotyped. Population attributable risk (PAR) was computed as: risk allele frequency∗(OR-1)/OR, using the per-allele odds ratio (OR). The risk allele (T) of rs10811661 was associated with T2D in most of the studies. In meta-analysis the overall per-allele OR was 1.24 (95% CI: 1.21-1.27; P < 10(-15)), with no difference according to ethnicity (P = 0.45), and low heterogeneity (P = 0.040) across studies partly explained by sample size. Modeling of inheritance suggested an additive effect of the T allele. PAR of T2D related to this polymorphism was 15% for Caucasians and 13% for Asians. The overall odds ratio for the T allele of the SNP rs564398 was 1.08 (95% CI: 1.05-1.12; PAR = 6%). The other SNPs showed negligible associations. CONCLUSIONS This meta-analysis provides accurate and comprehensive estimates of the association of some genetic variants at chromosome 9p21 and T2D. A relatively small but significant role of the T allele of the rs10811661 SNP in increasing by 21-27% the risk of T2D in an additive way was apparent.
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Affiliation(s)
- D Cugino
- Laboratorio di Epidemiologia Genetica ed Ambientale, Laboratori di Ricerca, Centro di Ricerche e Formazione ad Alta Tecnologia nelle Scienze Biomediche Giovanni Paolo II, Università Cattolica del Sacro Cuore, Campobasso, Italy
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Ohsaka Y, Nishino H. Polymorphisms in the 5′-UTR of PTEN and other gene polymorphisms in normal Japanese individuals. CYTOL GENET+ 2012. [DOI: 10.3103/s0095452712020028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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20
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Pascoe J, Hollern D, Stamateris R, Abbasi M, Romano LC, Zou B, O’Donnell CP, Garcia-Ocana A, Alonso LC. Free fatty acids block glucose-induced β-cell proliferation in mice by inducing cell cycle inhibitors p16 and p18. Diabetes 2012; 61:632-41. [PMID: 22338094 PMCID: PMC3282818 DOI: 10.2337/db11-0991] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Pancreatic β-cell proliferation is infrequent in adult humans and is not increased in type 2 diabetes despite obesity and insulin resistance, suggesting the existence of inhibitory factors. Free fatty acids (FFAs) may influence proliferation. In order to test whether FFAs restrict β-cell proliferation in vivo, mice were intravenously infused with saline, Liposyn II, glucose, or both, continuously for 4 days. Lipid infusion did not alter basal β-cell proliferation, but blocked glucose-stimulated proliferation, without inducing excess β-cell death. In vitro exposure to FFAs inhibited proliferation in both primary mouse β-cells and in rat insulinoma (INS-1) cells, indicating a direct effect on β-cells. Two of the fatty acids present in Liposyn II, linoleic acid and palmitic acid, both reduced proliferation. FFAs did not interfere with cyclin D2 induction or nuclear localization by glucose, but increased expression of inhibitor of cyclin dependent kinase 4 (INK4) family cell cycle inhibitors p16 and p18. Knockdown of either p16 or p18 rescued the antiproliferative effect of FFAs. These data provide evidence for a novel antiproliferative form of β-cell glucolipotoxicity: FFAs restrain glucose-stimulated β-cell proliferation in vivo and in vitro through cell cycle inhibitors p16 and p18. If FFAs reduce proliferation induced by obesity and insulin resistance, targeting this pathway may lead to new treatment approaches to prevent diabetes.
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Affiliation(s)
- Jordan Pascoe
- Division of Endocrinology and Metabolism, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Douglas Hollern
- Division of Endocrinology and Metabolism, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Rachel Stamateris
- Division of Endocrinology and Metabolism, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Munira Abbasi
- Division of Endocrinology and Metabolism, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Lia C. Romano
- Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Baobo Zou
- Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Christopher P. O’Donnell
- Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Adolfo Garcia-Ocana
- Division of Endocrinology and Metabolism, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Laura C. Alonso
- Division of Endocrinology and Metabolism, University of Pittsburgh, Pittsburgh, Pennsylvania
- Corresponding author: Laura C. Alonso,
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Nemr R, Almawi AW, Echtay A, Sater MS, Daher HS, Almawi WY. Replication study of common variants in CDKAL1 and CDKN2A/2B genes associated with type 2 diabetes in Lebanese Arab population. Diabetes Res Clin Pract 2012; 95:e37-40. [PMID: 22119613 DOI: 10.1016/j.diabres.2011.11.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/30/2011] [Accepted: 11/01/2011] [Indexed: 12/16/2022]
Abstract
We investigated the association of CDKAL1 (rs7754840 and rs7756992) and CDKN2A/2B (rs10811661) variants with T2DM. Higher MAF of rs7754840 and rs7756992 were seen in patients, and both were associated with T2DM under additive, dominant, and recessive models. CDKAL1 rs7754840 and rs7756992, but not CDKN2A/2B rs10811661, are associated with T2DM in Lebanese.
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Affiliation(s)
- Rita Nemr
- University Medical Center Rizk Hospital, Beirut, Lebanon
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Polymorphisms associated with type 2 diabetes in familial longevity: The Leiden Longevity Study. Aging (Albany NY) 2011; 3:55-62. [PMID: 21191145 PMCID: PMC3047139 DOI: 10.18632/aging.100250] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Human longevity is in part genetically determined, and the insulin/IGF-1 signal transduction (IIS) pathway has consistently been implicated. In humans, type 2 diabetes is a frequent disease that results from loss of glucose homeostasis and for which new candidate polymorphisms now rapidly emerge from genome wide association studies. In the Leiden Longevity Study (n=2415), the offspring of long lived siblings (“offspring”) who are genetically enriched for longevity were shown to have a more beneficial metabolic profile compared to their environmentally matched partners (“controls”), including better glucose tolerance. We tested whether the “offspring” carry a lower burden of diabetes risk alleles. Fifteen polymorphisms derived from genome wide association (GWA) scans in type 2 diabetes were tested for association with parameters of glucose metabolism in offspring and controls, and burden of risk alleles was compared between offspring and controls. Among all participants, a higher number of type 2 diabetes risk alleles associated with a higher prevalence of diabetes (P=0.011) and higher serum concentration of glucose (P<0.016) but not insulin (P=0.450). None of the polymorphisms differed in frequency between the offspring and controls (all P>0.05), nor did the mean total number of risk alleles (P=0.977). The association between polymorphisms and glucose levels did not differ between controls and offspring (Pinteraction=0.523). The better glucose tolerance of the “offspring” is not explained by a lower burden of type 2 diabetes risk alleles, suggesting that specific mechanisms determining longevity exist.
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Bao XY, Xie C, Yang MS. Association between type 2 diabetes and CDKN2A/B: a meta-analysis study. Mol Biol Rep 2011; 39:1609-16. [PMID: 21625859 DOI: 10.1007/s11033-011-0900-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2011] [Accepted: 05/17/2011] [Indexed: 12/16/2022]
Abstract
Cyclin-dependent kinase inhibitor-2A/B (CDKN2A/B) has been reported as a candidate gene of type 2 diabetes (T2D) based on its chromosomal position and its important role in β-cell function and regeneration. However, studies to date have reported inconsistent findings regarding the association between T2D and CDKN2A/B. To clarify this inconsistence, we conducted a meta-analysis based on alleles and genotypes prevalence of rs10811661 and rs564398 in CDKN2A/B. The PubMed, EMBASE, and Medline databases were systematically reviewed for studies published between January, 2006, and November, 2010. A total of 35 reports were collected, among of them only 16 studies (including 24,407 cases and 33,937 controls) match the inclusion criteria and were selected for the statistical test. In the meta-analysis of published data, our results suggest that the rs10811661 T allele (OR 1.28, 95% CI 1.21-1.36, P < 1 × 10(-5)) and TT genotype (OR 1.32, 95% CI 1.22-1.43, P < 1 × 10(-5)) of CDKN2A/B were associated with type 2 diabetes respectively, but rs564398 was not (for allele only: OR 0.96, 95% CI 0.88-1.05, P = 0.35). The association between rs10811661 T allele and T2D was observed both in Asia (P < 1 × 10(-4)) and Europe ethnicity groups (P = 0.002). This meta-analysis yielded evidence that rs10811661 of CDKN2A/B confers risk for T2D. Larger studies with mixed ethnicity subjects are required to validate our findings.
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Affiliation(s)
- Xiao Yun Bao
- Laboratory of Disorder Genes and Department of Pharmacology, College of Pharmacy, Chongqing Medical University, P.O. 380, 1 Yi Xue Yuan Road, Chongqing 400016, People's Republic of China
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Hribal ML, Presta I, Procopio T, Marini MA, Stančáková A, Kuusisto J, Andreozzi F, Hammarstedt A, Jansson PA, Grarup N, Hansen T, Walker M, Stefan N, Fritsche A, Häring HU, Pedersen O, Smith U, Laakso M, Sesti G. Glucose tolerance, insulin sensitivity and insulin release in European non-diabetic carriers of a polymorphism upstream of CDKN2A and CDKN2B. Diabetologia 2011; 54:795-802. [PMID: 21234743 DOI: 10.1007/s00125-010-2038-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/16/2010] [Accepted: 12/10/2010] [Indexed: 01/09/2023]
Abstract
AIMS/HYPOTHESIS The aim of this study was to investigate the association of the rs10811661 polymorphism near the CDKN2B/CDKN2A genes with glucose tolerance, insulin sensitivity and insulin release in three samples of white people with European ancestry. METHODS Sample 1 comprised 845 non-diabetic offspring of type 2 diabetes patients recruited in five European centres participating in the EUGENE2 study. Samples 2 and 3 comprised, respectively, 864 and 524 Italian non-diabetic participants. All individuals underwent an OGTT. Screening for the rs10811661 polymorphism was performed using a TaqMan allelic discrimination assay. RESULTS The rs10811661 polymorphism did not show a significant association with age, BMI and insulin sensitivity. Participants carrying the TT genotype showed a significant reduction in insulin release, measured by an OGTT-derived index, compared with carriers of the C allele, in the three samples. When these results were pooled with those of three published studies, and meta-analysed with a random-effects model, the T allele was significantly associated with reduced insulin secretion (-35.09 [95% CI 14.68-55.52], p = 0.0008 for CC+CT vs TT; and -29.45 [95% CI 9.51-49.38], p = 0.0038, for the additive model). In addition, in our three samples, participants carrying the TT genotype exhibited an increased risk for impaired glucose tolerance (IGT) compared with carriers of the C allele (OR 1.55 [95% CI 1.20-1.95] for the meta-analysis of the three samples). CONCLUSIONS/INTERPRETATION Our data, together with the meta-analysis of previously published studies, show that the rs10811661 polymorphism is associated with impaired insulin release and IGT, suggesting that this variant may contribute to type 2 diabetes by affecting beta cell function.
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Affiliation(s)
- M L Hribal
- Department of Experimental and Clinical Medicine, Viale Europa, Campus Germaneto, 88100 Catanzaro, Italy
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Fan BJ, Wang DY, Pasquale LR, Haines JL, Wiggs JL. Genetic variants associated with optic nerve vertical cup-to-disc ratio are risk factors for primary open angle glaucoma in a US Caucasian population. Invest Ophthalmol Vis Sci 2011; 52:1788-92. [PMID: 21398277 DOI: 10.1167/iovs.10-6339] [Citation(s) in RCA: 97] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
PURPOSE Genetically complex disorders, such as primary open angle glaucoma (POAG), may include highly heritable quantitative traits as part of the overall phenotype, and mapping genes influencing the related quantitative traits may effectively identify genetic risk factors predisposing to the complex disease. Recent studies have identified SNPs associated with optic nerve area and vertical cup-to-disc ratio (VCDR). The purpose of this study was to evaluate the association between these SNPs and POAG in a US Caucasian case-control sample. METHODS Five SNPs previously associated with optic disc area, or VCDR, were genotyped in 539 POAG cases and 336 controls. Genotype data were analyzed for single SNP associations and SNP interactions with VCDR and POAG. RESULTS SNPs associated with VCDR rs1063192 (CDKN2B) and rs10483727 (SIX1/SIX6) were also associated with POAG (P = 0.0006 and P = 0.0043 for rs1063192 and rs10483727, respectively). rs1063192, associated with smaller VCDR, had a protective effect (odds ratio [OR] = 0.73; 95% confidence interval [CI], 0.58-0.90), whereas rs10483727, associated with larger VCDR, increased POAG risk (OR = 1.33; 95% CI, 1.08-1.65). POAG risk associated with increased VCDR was significantly influenced by the C allele of rs1900004 (ATOH7), associated with increased optic nerve area (P-interaction = 0.025; OR = 1.89; 95% CI, 1.22-2.94). CONCLUSIONS Genetic variants influencing VCDR are associated with POAG in a US Caucasian population. Variants associated with optic nerve area are not independently associated with disease but can influence the effects of VCDR variants suggesting that increased optic disc area can significantly contribute to POAG risk when coupled with risk factors controlling VCDR.
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Affiliation(s)
- Bao Jian Fan
- Department of Ophthalmology, Harvard Medical School, Massachusetts Eye and Ear Infirmary, Boston, Massachusetts, USA
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Cunnington MS, Santibanez Koref M, Mayosi BM, Burn J, Keavney B. Chromosome 9p21 SNPs Associated with Multiple Disease Phenotypes Correlate with ANRIL Expression. PLoS Genet 2010; 6:e1000899. [PMID: 20386740 PMCID: PMC2851566 DOI: 10.1371/journal.pgen.1000899] [Citation(s) in RCA: 297] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2009] [Accepted: 03/08/2010] [Indexed: 12/13/2022] Open
Abstract
Single nucleotide polymorphisms (SNPs) on chromosome 9p21 are associated with coronary artery disease, diabetes, and multiple cancers. Risk SNPs are mainly non-coding, suggesting that they influence expression and may act in cis. We examined the association between 56 SNPs in this region and peripheral blood expression of the three nearest genes CDKN2A, CDKN2B, and ANRIL using total and allelic expression in two populations of healthy volunteers: 177 British Caucasians and 310 mixed-ancestry South Africans. Total expression of the three genes was correlated (P<0.05), suggesting that they are co-regulated. SNP associations mapped by allelic and total expression were similar (r = 0.97, P = 4.8×10−99), but the power to detect effects was greater for allelic expression. The proportion of expression variance attributable to cis-acting effects was 8% for CDKN2A, 5% for CDKN2B, and 20% for ANRIL. SNP associations were similar in the two populations (r = 0.94, P = 10−72). Multiple SNPs were independently associated with expression of each gene (P<0.05 after correction for multiple testing), suggesting that several sites may modulate disease susceptibility. Individual SNPs correlated with changes in expression up to 1.4-fold for CDKN2A, 1.3-fold for CDKN2B, and 2-fold for ANRIL. Risk SNPs for coronary disease, stroke, diabetes, melanoma, and glioma were all associated with allelic expression of ANRIL (all P<0.05 after correction for multiple testing), while association with the other two genes was only detectable for some risk SNPs. SNPs had an inverse effect on ANRIL and CDKN2B expression, supporting a role of antisense transcription in CDKN2B regulation. Our study suggests that modulation of ANRIL expression mediates susceptibility to several important human diseases. Genetic variants on chromosome 9p21 have been associated with several important diseases including coronary artery disease, diabetes, and multiple cancers. Most of the risk variants in this region do not alter any protein sequence and are therefore likely to act by influencing the expression of nearby genes. We investigated whether chromosome 9p21 variants are correlated with expression of the three nearest genes (CDKN2A, CDKN2B, and ANRIL) which might mediate the association with disease. Using two different techniques to study effects on expression in blood from two separate populations of healthy volunteers, we show that variants associated with disease are all correlated with ANRIL expression, but associations with the other two genes are weaker and less consistent. Multiple genetic variants are independently associated with expression of all three genes. Although total expression levels of CDKN2A, CDKN2B, and ANRIL are positively correlated, individual genetic variants influence ANRIL and CDKN2B expression in opposite directions, suggesting a possible role of ANRIL in CDKN2B regulation. Our study suggests that modulation of ANRIL expression mediates susceptibility to several important human diseases.
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Affiliation(s)
- Michael S Cunnington
- Institute of Human Genetics, Newcastle University, Newcastle upon Tyne, United Kingdom
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Abstract
Type 2 diabetes mellitus is a complex metabolic disease that is caused by insulin resistance and beta-cell dysfunction. Furthermore, type 2 diabetes has an evident genetic component and represents a polygenic disease. During the last decade, considerable progress was made in the identification of type 2 diabetes risk genes. This was crucially influenced by the development of affordable high-density single nucleotide polymorphism (SNP) arrays that prompted several successful genome-wide association scans in large case-control cohorts. Subsequent to the identification of type 2 diabetes risk SNPs, cohorts thoroughly phenotyped for prediabetic traits with elaborate in vivo methods allowed an initial characterization of the pathomechanisms of these SNPs. Although the underlying molecular mechanisms are still incompletely understood, a surprising result of these pathomechanistic investigations was that most of the risk SNPs affect beta-cell function. This favors a beta-cell-centric view on the genetics of type 2 diabetes. The aim of this review is to summarize the current knowledge about the type 2 diabetes risk genes and their variants' pathomechanisms.
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Affiliation(s)
- Harald Staiger
- Department of Internal Medicine, Division of Endocrinology, Diabetology, Angiology, Nephrology, and Clinical Chemistry, University Hospital Tübingen, D-72076 Tübingen, Germany
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Hu WL, Li SJ, Liu DT, Wang Y, Niu SQ, Yang XC, Zhang Q, Yu SZ, Jin L, Wang XF. Genetic variants on chromosome 9p21 and ischemic stroke in Chinese. Brain Res Bull 2009; 79:431-5. [PMID: 19559344 DOI: 10.1016/j.brainresbull.2009.04.001] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2009] [Revised: 03/27/2009] [Accepted: 04/07/2009] [Indexed: 12/19/2022]
Abstract
In a hospital based case control study, we investigated the association of cyclin-dependent kinase inhibitor 2A (CDKN2A) gene, cyclin-dependent kinase inhibitor 2B (CDKN2B) gene, and two genetic variants (rs10757274 and rs2383206) on chromosome region 9p21 with ischemic stroke in Chinese Hans. Two polymorphisms in the CDKN2A gene (rs3088440 and rs3731245) and two polymorphisms in the CDKN2B gene (rs3217992 and rs1063192) were selected by using a strategy of tagging single nucleotide polymorphisms (tSNP). We observed significant association of rs2383206 with ischemic stroke. Subjects with the GG/GA genotype of rs2383206 had a 1.51-fold (95%CI 1.11-2.05, p=0.009) increased risk of stroke, compared with those with the AA genotype. In addition, the GG/GA genotypes of rs2383206 and rs3731245 was associated with an increased risk of large vessel subtype and small vessel subtype of ischemic stroke, respectively, with ORs of 2.09 (95%CI 1.30-3.37, p=0.002) and 1.63 (95%CI 1.06-2.51, p=0.026), respectively. In gene-environmental interaction analysis, elevation of ischemic stroke risk was observed among AG+GG genotype carriers who consume alcohol, smoke cigarette, and have hypertension, with adjusted combined ORs of 2.86(1.51-5.41), 4.30(2.38-7.77), and 13.97(7.78-25.07), respectively, compared with low-risk individuals for rs2383206 (GG carriers who did not consume alcohol, smoke cigarette, and without hypertension). We provide evidence that genetic variants on chromosome region 9p21 may implicated in the prevalence of ischemic stroke in Chinese.
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Affiliation(s)
- Wen-li Hu
- Department of Neurology, Beijing Chaoyang Hospital, Capital University of Medical Sciences, Beijing 100020, China
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Staiger H, Machicao F, Schäfer SA, Kirchhoff K, Kantartzis K, Guthoff M, Silbernagel G, Stefan N, Häring HU, Fritsche A. Polymorphisms within the novel type 2 diabetes risk locus MTNR1B determine beta-cell function. PLoS One 2008; 3:e3962. [PMID: 19088850 PMCID: PMC2597741 DOI: 10.1371/journal.pone.0003962] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2008] [Accepted: 11/18/2008] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Very recently, a novel type 2 diabetes risk gene, i.e., MTNR1B, was identified and reported to affect fasting glycemia. Using our thoroughly phenotyped cohort of subjects at an increased risk for type 2 diabetes, we assessed the association of common genetic variation within the MTNR1B locus with obesity and prediabetes traits, namely impaired insulin secretion and insulin resistance. METHODOLOGY/PRINCIPAL FINDINGS We genotyped 1,578 non-diabetic subjects, metabolically characterized by oral glucose tolerance test, for five tagging single nucleotide polymorphisms (SNPs) covering 100% of common genetic variation (minor allele frequency > 0.05) within the MTNR1B locus (rs10830962, rs4753426, rs12804291, rs10830963, rs3781638). In a subgroup (N = 513), insulin sensitivity was assessed by hyperinsulinemic-euglycemic clamp, and in a further subgroup (N = 301), glucose-stimulated insulin secretion was determined by intravenous glucose tolerance test. After appropriate adjustment for confounding variables and Bonferroni correction for multiple comparisons, none of the tagging SNPs was reliably associated with measures of adiposity. SNPs rs10830962, rs4753426, and rs10830963 were significantly associated with higher fasting plasma glucose concentrations (p < 0.0001) and reduced OGTT- and IVGTT-induced insulin release (p < or = 0.0007 and p < or = 0.01, respectively). By contrast, SNP rs3781638 displayed significant association with lower fasting plasma glucose levels and increased OGTT-induced insulin release (p<0.0001 and p < or = 0.0002, respectively). Moreover, SNP rs3781638 revealed significant association with elevated fasting- and OGTT-derived insulin sensitivity (p < or = 0.0021). None of the MTNR1B tagging SNPs altered proinsulin-to-insulin conversion. CONCLUSIONS/SIGNIFICANCE In conclusion, common genetic variation within MTNR1B determines glucose-stimulated insulin secretion and plasma glucose concentrations. Their impact on beta-cell function might represent the prevailing pathomechanism how MTNR1B variants increase the type 2 diabetes risk.
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Affiliation(s)
- Harald Staiger
- Division of Endocrinology, Diabetology, Angiology, Nephrology, and Clinical Chemistry, Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany
| | - Fausto Machicao
- Division of Endocrinology, Diabetology, Angiology, Nephrology, and Clinical Chemistry, Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany
| | - Silke A. Schäfer
- Division of Endocrinology, Diabetology, Angiology, Nephrology, and Clinical Chemistry, Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany
| | - Kerstin Kirchhoff
- Division of Endocrinology, Diabetology, Angiology, Nephrology, and Clinical Chemistry, Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany
| | - Konstantinos Kantartzis
- Division of Endocrinology, Diabetology, Angiology, Nephrology, and Clinical Chemistry, Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany
| | - Martina Guthoff
- Division of Endocrinology, Diabetology, Angiology, Nephrology, and Clinical Chemistry, Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany
| | - Günther Silbernagel
- Division of Endocrinology, Diabetology, Angiology, Nephrology, and Clinical Chemistry, Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany
| | - Norbert Stefan
- Division of Endocrinology, Diabetology, Angiology, Nephrology, and Clinical Chemistry, Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany
| | - Hans-Ulrich Häring
- Division of Endocrinology, Diabetology, Angiology, Nephrology, and Clinical Chemistry, Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany
- * E-mail:
| | - Andreas Fritsche
- Division of Endocrinology, Diabetology, Angiology, Nephrology, and Clinical Chemistry, Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany
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Chen R, Morgan AA, Dudley J, Deshpande T, Li L, Kodama K, Chiang AP, Butte AJ. FitSNPs: highly differentially expressed genes are more likely to have variants associated with disease. Genome Biol 2008; 9:R170. [PMID: 19061490 PMCID: PMC2646274 DOI: 10.1186/gb-2008-9-12-r170] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2008] [Revised: 09/26/2008] [Accepted: 12/05/2008] [Indexed: 12/18/2022] Open
Abstract
Differential expressed genes are more likely to have variants associated with disease. A new tool, fitSNP, prioritizes candidate SNPs from association studies. Background Candidate single nucleotide polymorphisms (SNPs) from genome-wide association studies (GWASs) were often selected for validation based on their functional annotation, which was inadequate and biased. We propose to use the more than 200,000 microarray studies in the Gene Expression Omnibus to systematically prioritize candidate SNPs from GWASs. Results We analyzed all human microarray studies from the Gene Expression Omnibus, and calculated the observed frequency of differential expression, which we called differential expression ratio, for every human gene. Analysis conducted in a comprehensive list of curated disease genes revealed a positive association between differential expression ratio values and the likelihood of harboring disease-associated variants. By considering highly differentially expressed genes, we were able to rediscover disease genes with 79% specificity and 37% sensitivity. We successfully distinguished true disease genes from false positives in multiple GWASs for multiple diseases. We then derived a list of functionally interpolating SNPs (fitSNPs) to analyze the top seven loci of Wellcome Trust Case Control Consortium type 1 diabetes mellitus GWASs, rediscovered all type 1 diabetes mellitus genes, and predicted a novel gene (KIAA1109) for an unexplained locus 4q27. We suggest that fitSNPs would work equally well for both Mendelian and complex diseases (being more effective for cancer) and proposed candidate genes to sequence for their association with 597 syndromes with unknown molecular basis. Conclusions Our study demonstrates that highly differentially expressed genes are more likely to harbor disease-associated DNA variants. FitSNPs can serve as an effective tool to systematically prioritize candidate SNPs from GWASs.
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Affiliation(s)
- Rong Chen
- Stanford Center for Biomedical Informatics Research, 251 Cmpus Drive, Stanford, CA 94305, USA.
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Staiger H, Machicao F, Kantartzis K, Schäfer SA, Kirchhoff K, Guthoff M, Silbernagel G, Stefan N, Fritsche A, Häring HU. Novel meta-analysis-derived type 2 diabetes risk loci do not determine prediabetic phenotypes. PLoS One 2008; 3:e3019. [PMID: 18714373 PMCID: PMC2500187 DOI: 10.1371/journal.pone.0003019] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2008] [Accepted: 08/01/2008] [Indexed: 12/04/2022] Open
Abstract
Background Genome-wide association (GWA) studies identified a series of novel type 2 diabetes risk loci. Most of them were subsequently demonstrated to affect insulin secretion of pancreatic β-cells. Very recently, a meta-analysis of GWA data revealed nine additional risk loci with still undefined roles in the pathogenesis of type 2 diabetes. Using our thoroughly phenotyped cohort of subjects at an increased risk for type 2 diabetes, we assessed the association of the nine latest genetic variants with the predominant prediabetes traits, i.e., obesity, impaired insulin secretion, and insulin resistance. Methodology/Principal Findings One thousand five hundred and seventy-eight metabolically characterized non-diabetic German subjects were genotyped for the reported candidate single nucleotide polymorphisms (SNPs) JAZF1 rs864745, CDC123/CAMK1D rs12779790, TSPAN8/LGR5 rs7961581, THADA rs7578597, ADAMTS9 rs4607103, NOTCH2 rs10923931, DCD rs1153188, VEGFA rs9472138, and BCL11A rs10490072. Insulin sensitivity was derived from fasting glucose and insulin concentrations, oral glucose tolerance test (OGTT), and hyperinsulinemic-euglycemic clamp. Insulin secretion was estimated from OGTT data. After appropriate adjustment for confounding variables and Bonferroni correction for multiple comparisons (corrected α-level: p = 0.0014), none of the SNPs was reliably associated with adiposity, insulin sensitivity, or insulin secretion (all p≥0.0117, dominant inheritance model). The risk alleles of ADAMTS9 SNP rs4607103 and VEGFA SNP rs9472138 tended to associate with more than one measure of insulin sensitivity and insulin secretion, respectively, but did not reach formal statistical significance. The study was sufficiently powered (1-β = 0.8) to detect effect sizes of 0.19≤d≤0.25 (α = 0.0014) and 0.13≤d≤0.16 (α = 0.05). Conclusions/Significance In contrast to the first series of GWA-derived type 2 diabetes candidate SNPs, we could not detect reliable associations of the novel risk loci with prediabetic phenotypes. Possible weak effects of ADAMTS9 SNP rs4607103 and VEGFA SNP rs9472138 on insulin sensitivity and insulin secretion, respectively, await further confirmation by larger studies.
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Affiliation(s)
- Harald Staiger
- Department of Internal Medicine, Division of Endocrinology, Diabetology, Angiology, Nephrology, and Clinical Chemistry, University Hospital Tübingen, Tübingen, Germany.
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