1
|
Jan A, Ali S, Muhammad B, Arshad A, Shah Y, Bahadur H, Khan H, Khuda F, Akbar R, Ijaz K. Decoding type 2 diabetes mellitus genetic risk variants in Pakistani Pashtun ethnic population using the nascent whole exome sequencing and MassARRAY genotyping: A case-control association study. PLoS One 2023; 18:e0281070. [PMID: 36730981 PMCID: PMC9882913 DOI: 10.1371/journal.pone.0281070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 01/14/2023] [Indexed: 02/04/2023] Open
Abstract
Genome-wide association studies have greatly increased the number of T2DM associated risk variants but most of them have focused on populations of European origin. There is scarcity of such studies in developing countries including Pakistan. High prevalence of T2DM in Pakistani population prompted us to design this study. We have devised a two stage (the discovery stage and validation stage) case-control study in Pashtun ethnic population in which 500 T2DM cases and controls each have been recruited to investigate T2DM genetic risk variants. In discovery stage Whole Exome Sequencing (WES) was used to identify and suggest T2DM pathogenic SNPs, based on SIFT and Polyphen scores; whereas in validation stage the selected variants were confirmed for T2DM association using MassARRAY genotyping and appropriate statistical tests. Results of the study showed the target positive association of rs1801282/PPARG (OR = 1.24, 95%Cl = 1.20-1.46, P = 0.010), rs745975/HNF4A (OR = 1.30, 95%Cl = 1.06-1.38, P = 0.004), rs806052/GLIS3 (OR = 1.32, 95%Cl = 1.07-1.66, P = 0.016), rs8192552/MTNR1B (OR = 1.53, 95%Cl = 0.56-1.95, P = 0.012) and rs1805097/IRS-2 (OR = 1.27, 95%Cl = 1.36-1.92, P = 0.045), with T2DM; whereas rs6415788/GLIS3, rs61788900/NOTCH2, rs61788901/NOTCH2 and rs11810554/NOTCH2 (P>0.05) showed no significant association. Identification of genetic risk factors/variants can be used in defining high risk subjects assessment, and disease prevention.
Collapse
Affiliation(s)
- Asif Jan
- Department of Pharmacy, University of Peshawar, Peshawar, Pakistan
- * E-mail: (ZU); (AJ)
| | - Sajid Ali
- Department of Biotechnology, Abdul Wali Khan University, Mardan, Pakistan
| | - Basir Muhammad
- Atomic Energy Cancer Hospital, Swat Institute of Nuclear Medicine, Oncology & Radiotherapy, Swat, Pakistan
| | - Amina Arshad
- Rashid Latif College of Pharmacy, Lahore, Pakistan
| | - Yasar Shah
- Department of Pharmacy, Abdul Wali Khan University, Mardan, Pakistan
| | - Haji Bahadur
- Institute of Pharmaceutical Sciences, Khyber Medical University, Peshawar, Pakistan
| | - Hamayun Khan
- Department of Pharmacy, University of Peshawar, Peshawar, Pakistan
| | - Fazli Khuda
- Department of Pharmacy, University of Peshawar, Peshawar, Pakistan
| | - Rani Akbar
- Department of Pharmacy, Abdul Wali Khan University, Mardan, Pakistan
| | - Kiran Ijaz
- Institute of Pharmaceutical Sciences, Khyber Medical University, Peshawar, Pakistan
| |
Collapse
|
2
|
Wang X, Chen W, Lao W, Chen Y. Silencing LncRNA PVT1 Reverses High Glucose-Induced Regulation of the High Expression of PVT1 in HRMECs by Targeting miR-128-3p. Horm Metab Res 2022; 54:119-125. [PMID: 35130573 DOI: 10.1055/a-1730-5091] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
This paper aims to discuss the possibility of lncRNA PVT1 as a diagnostic biomarker for diabetic retinopathy (DR) and explore the underlying mechanism. Real-time quantitative polymerase chain reaction (RT-qPCR) was selected to determine the expression level of lncRNA PVT1 in the serum of all subjects. The receiver operating characteristic (ROC) curve reflected the diagnostic significance of PVT1 for DR patients. The Cell Counting Kit-8 (CCK-8) and Transwell assays were used to evaluate the effect of PVT1 expression on the proliferation and migration of human retinal microvascular endothelial cells (HRMECs). The luciferase reporter gene was selected to verify the interaction between PVT1 and miR-128-3p. The relative expression level of PVT1 in serum was higher in both the DB and DR group than in the healthy controls group (HC), and it was highest in the DR group. ROC curve indicated that serum PVT1 could distinguish between HC and DB patients, DB patients and DR patients, respectively. In vitro, high glucose induction significantly increased the proliferation and migration capabilities of HRMECs, but silencing PVT1 (si-PVT1) downregulated the proliferation and migration capabilities of HRMECs. The detection of luciferase reporter gene showed that lncRNA PVT1 targeted miR-128-3p, and there was a negative correlation in the serum of DR patients. In conclusion, this study confirmed that lncRNA PVT1 might regulate the process of DR by targeting miR-128-3p, and has the potential as a biomarker for the diagnosis of DR.
Collapse
Affiliation(s)
- Xuyang Wang
- Hainan Eye Hospital and Key Laboratory of Ophthalmology, Zhongshan Opthalmic Center, Sun Yat-sen University, Haikou, 570311, Hainan Province, China
| | - Wangling Chen
- Hainan Eye Hospital and Key Laboratory of Ophthalmology, Zhongshan Opthalmic Center, Sun Yat-sen University, Haikou, 570311, Hainan Province, China
| | - Wei Lao
- Hainan Eye Hospital and Key Laboratory of Ophthalmology, Zhongshan Opthalmic Center, Sun Yat-sen University, Haikou, 570311, Hainan Province, China
| | - Yunxin Chen
- Hainan Eye Hospital and Key Laboratory of Ophthalmology, Zhongshan Opthalmic Center, Sun Yat-sen University, Haikou, 570311, Hainan Province, China
| |
Collapse
|
3
|
Dong Y, Huang G, Wang X, Chu Z, Miao J, Zhou H. Meta-analysis of the association between adiponectin SNP 45, SNP 276, and type 2 diabetes mellitus. PLoS One 2020; 15:e0241078. [PMID: 33091065 PMCID: PMC7580922 DOI: 10.1371/journal.pone.0241078] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 10/07/2020] [Indexed: 02/07/2023] Open
Abstract
Objective The present study aimed to determine whether the polymorphisms at rs2241766 and rs1501299 on the ADIPOQ gene were related to the susceptibility of type 2 diabetes mellitus (T2DM). Methods Eight databases, PubMed, GWAS, Embase, Lochrane, Ebsco, CNKI (Chinese National Knowledge Infrastructure), VIP (Viper Database) and ChinaInfo were searched, and a meta-analysis of susceptibility was conducted between SNP45, SNP276 polymorphisms and T2DM. Furthermore, HWE test was conducted to assess the genetic balance of the study, evaluate the quality of Newcastle–Ottawa quality assessment scale (NOS), and establishing allelic, dominant, recessive, heterozygous, and homozygous gene models. Results This meta-analysis included 53 articles, encompassing 9285 cases with rs2241766 and 14156 controls and 7747 cases with rs1501299 and 10607 controls. For the rs2241766 locus, a significant correlation was found in the three models by the subgroup analysis. Western Asians: dominant gene model (TT + TG vs. GG, P = 0.01); heterozygous gene model (TG vs. GG, P = 0.02); homozygous gene model (TT vs. GG, P = 0.01). South Asians: dominant gene model (TT + TG vs. GG, P = 0.004); heterozygous gene model (TG vs. GG, P = 0.009); homozygous gene model (TT vs. GG, P = 0.005). However, no statistically significant correlation was established among the five genetic models for rs1501299 locus. Conclusion The findings of the present study indicated that the T allele of rs2241766 polymorphism is the susceptibility locus of T2DM in the West Asian population, but has a protective effect in the South Asian population, albeit further studies are needed in other populations. Also, no association was found between the ADIPOQ rs1501299 polymorphism and T2DM.
Collapse
Affiliation(s)
- Yuwei Dong
- College of Food and Biology Engineering, Xuzhou University of Technology, Xuzhou, Jiangsu, China
- * E-mail:
| | - Gongping Huang
- College of Food and Biology Engineering, Xuzhou University of Technology, Xuzhou, Jiangsu, China
| | - Xin Wang
- College of Food and Biology Engineering, Xuzhou University of Technology, Xuzhou, Jiangsu, China
| | - Zhaoming Chu
- College of Food and Biology Engineering, Xuzhou University of Technology, Xuzhou, Jiangsu, China
| | - Jingzhi Miao
- College of Food and Biology Engineering, Xuzhou University of Technology, Xuzhou, Jiangsu, China
| | - Houwen Zhou
- Xuzhou Technology Limited Company of United Gene, Xuzhou, Jiangsu, China
| |
Collapse
|
4
|
Chuluun-Erdene A, Sengeragchaa O, Altangerel TA, Sanjmyatav P, Dagdan B, Battulga S, Enkhbat L, Byambasuren N, Malchinkhuu M, Janlav M. Association of Candidate Gene Polymorphism with Metabolic Syndrome among Mongolian Subjects: A Case-Control Study. Med Sci (Basel) 2020; 8:medsci8030038. [PMID: 32887252 PMCID: PMC7563398 DOI: 10.3390/medsci8030038] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 08/26/2020] [Accepted: 08/31/2020] [Indexed: 12/20/2022] Open
Abstract
Metabolic syndrome (MetS) is complex and determined by the interaction between genetic and environmental factors and their influence on obesity, insulin resistance, and related traits associated with diabetes and cardiovascular disease risk. Some dynamic markers, including adiponectin (ADIPOQ), brain-derived neurotrophic factor (BDNF), and lipoprotein lipase (LPL), are implicated in MetS; however, the influence of their genetic variants on MetS susceptibility varies in racial and ethnic groups. We investigated the association of single nucleotide polymorphism (SNP)-SNP interactions among nine SNPs in six genes with MetS's genetic predisposition in Mongolian subjects. A total of 160 patients with MetS for the case group and 144 healthy individuals for the control group were selected to participate in this study. Regression analysis of individual SNPs showed that the ADIPOQ + 45GG (odds ratio (OR) = 2.09, p = 0.011) and P+P+ of LPL PvuII (OR = 2.10, p = 0.038) carriers had an increased risk of MetS. Conversely, G allele of LPL S447X (OR = 0.45, p = 0.036) and PGC-1α 482Ser (OR = 0.26, p = 0.001) allele were estimated as protective factors, respectively. Moreover, a haplotype containing the G-P+-G combination was related to MetS. Significant loci were also related to body mass index (BMI), systolic blood pressure (SBP), serum high-density lipoprotein cholesterol (HDL-C), triglyceride (TG), and fasting blood glucose (FBG), adipokines, and insulin as well as insulin resistance (p < 0.05). Our results confirm that ADIPOQ + 45T > G, LPL PvII, and PGC-1α Gly482Ser loci are associated with MetS in Mongolian subjects.
Collapse
Affiliation(s)
- Ariunbold Chuluun-Erdene
- Department of Biochemistry, School of Biomedicine, Mongolian National University of Medical Sciences, Ulaanbaatar 14210, Mongolia; (A.C.-E.); (O.S.); (T.-A.A.); (P.S.); (B.D.); (S.B.); (L.E.); (N.B.)
| | - Orgil Sengeragchaa
- Department of Biochemistry, School of Biomedicine, Mongolian National University of Medical Sciences, Ulaanbaatar 14210, Mongolia; (A.C.-E.); (O.S.); (T.-A.A.); (P.S.); (B.D.); (S.B.); (L.E.); (N.B.)
| | - Tsend-Ayush Altangerel
- Department of Biochemistry, School of Biomedicine, Mongolian National University of Medical Sciences, Ulaanbaatar 14210, Mongolia; (A.C.-E.); (O.S.); (T.-A.A.); (P.S.); (B.D.); (S.B.); (L.E.); (N.B.)
| | - Purevjal Sanjmyatav
- Department of Biochemistry, School of Biomedicine, Mongolian National University of Medical Sciences, Ulaanbaatar 14210, Mongolia; (A.C.-E.); (O.S.); (T.-A.A.); (P.S.); (B.D.); (S.B.); (L.E.); (N.B.)
| | - Batnaran Dagdan
- Department of Biochemistry, School of Biomedicine, Mongolian National University of Medical Sciences, Ulaanbaatar 14210, Mongolia; (A.C.-E.); (O.S.); (T.-A.A.); (P.S.); (B.D.); (S.B.); (L.E.); (N.B.)
- Coronary Care Unit, Cardiovascular Center, The Shastin Central Hospital, Ulaanbaatar 16081, Mongolia
| | - Solongo Battulga
- Department of Biochemistry, School of Biomedicine, Mongolian National University of Medical Sciences, Ulaanbaatar 14210, Mongolia; (A.C.-E.); (O.S.); (T.-A.A.); (P.S.); (B.D.); (S.B.); (L.E.); (N.B.)
| | - Lundiamaa Enkhbat
- Department of Biochemistry, School of Biomedicine, Mongolian National University of Medical Sciences, Ulaanbaatar 14210, Mongolia; (A.C.-E.); (O.S.); (T.-A.A.); (P.S.); (B.D.); (S.B.); (L.E.); (N.B.)
| | - Nyamjav Byambasuren
- Department of Biochemistry, School of Biomedicine, Mongolian National University of Medical Sciences, Ulaanbaatar 14210, Mongolia; (A.C.-E.); (O.S.); (T.-A.A.); (P.S.); (B.D.); (S.B.); (L.E.); (N.B.)
| | - Munkhzol Malchinkhuu
- Department of Pathophysiology, School of Biomedicine, Mongolian National University of Medical Sciences, Ulaanbaatar 14210, Mongolia;
| | - Munkhtstetseg Janlav
- Department of Biochemistry, School of Biomedicine, Mongolian National University of Medical Sciences, Ulaanbaatar 14210, Mongolia; (A.C.-E.); (O.S.); (T.-A.A.); (P.S.); (B.D.); (S.B.); (L.E.); (N.B.)
- Correspondence: ; Tel.: +976-9909-2287
| |
Collapse
|
5
|
Association of CAPN10 (SNP-19) genetic polymorphism and obesity with T2DM: a study on Bengali Hindu caste population. Int J Diabetes Dev Ctries 2020. [DOI: 10.1007/s13410-020-00861-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
|
6
|
Association of three SNPs in adiponectin gene with lipid traits of Tianzhu Black Muscovy (Cairina moschata). Mol Biol Rep 2018; 46:325-332. [DOI: 10.1007/s11033-018-4475-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 11/07/2018] [Indexed: 02/06/2023]
|