1
|
Irgam K, Reddy BS, Hari SG, Banapuram S, Reddy BM. The genetic susceptibility profile of type 2 diabetes and reflection of its possible role related to reproductive dysfunctions in the southern Indian population of Hyderabad. BMC Med Genomics 2021; 14:272. [PMID: 34784930 PMCID: PMC8597259 DOI: 10.1186/s12920-021-01129-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 11/12/2021] [Indexed: 12/25/2022] Open
Abstract
Background The genetic association studies of type 2 diabetes mellitus (T2DM) hitherto undertaken among the Indian populations are grossly inadequate representation of the ethnic and geographic heterogeneity of the country. In view of this and due to the inconsistent nature of the results of genetic association studies, it would be prudent to undertake large scale studies in different regions of India considering wide spectrum of variants from the relevant pathophysiological pathways. Given the reproductive dysfunctions associated with T2DM, it would be also interesting to explore if some of the reproductive pathway genes are associated with T2DM. The present study is an attempt to examine these aspects in the southern Indian population of Hyderabad. Methods A prioritized panel of 92 SNPs from a large number of metabolic and reproductive pathway genes was genotyped on 500 cases and 500 controls, matched for ethnicity, age and BMI, using AGENA MassARRAYiPLEX™ platform. Results The allelic association results suggested 14 SNPs to be significantly associated with T2DM at P ≤ 0.05 and seven of those—rs2241766-G (ADIPOQ), rs6494730-T (FEM1B), rs1799817-A and rs2059806-T (INSR), rs11745088-C (FST), rs9939609-A and rs9940128-A (FTO)—remained highly significant even after correction for multiple testing. A great majority of the significant SNPs were risk in nature. The ROC analysis of the risk scores of the significant SNPs yielded an area under curve of 0.787, suggesting substantial power of our study to confer these genetic variants as predictors of risk for T2DM. Conclusions The associated SNPs of this study are known to be specifically related to insulin signaling, fatty acid metabolism and reproductive pathway genes and possibly suggesting the role of overlapping phenotypic features of insulin resistance, obesity and reproductive dysfunctions inherent in the development of diabetes. Large scale studies involving gender specific approach may be required in order to identify the precise nature of population and gender specific risk profiles for different populations, which might be somewhat distinct. Supplementary Information The online version contains supplementary material available at 10.1186/s12920-021-01129-0.
Collapse
Affiliation(s)
- Kumuda Irgam
- Department of Genetics and Biotechnology, Osmania University, Amberpet, Hyderabad, Telangana, 500007, India
| | - Battini Sriteja Reddy
- Dr Pinnamaneni Siddhartha Institute of Medical Sciences and Research Foundation, Vijayawada, Andhra Pradesh, 521286, India
| | - Sai Gayathri Hari
- Department of Genetics and Biotechnology, Osmania University, Amberpet, Hyderabad, Telangana, 500007, India
| | - Swathi Banapuram
- Department of Genetics and Biotechnology, Osmania University, Amberpet, Hyderabad, Telangana, 500007, India
| | - Battini Mohan Reddy
- Department of Genetics and Biotechnology, Osmania University, Amberpet, Hyderabad, Telangana, 500007, India. .,Molecular Anthropology Laboratory, Indian Statistical Institute, Street No. 8, Habsiguda, Hyderabad, Telangana, 500007, India.
| |
Collapse
|
2
|
Elfaki I, Mir R, Abu-Duhier FM, Jha CK, Ahmad Al-Alawy AI, Babakr AT, Habib SAEH. Analysis of the Potential Association of Drug-Metabolizing Enzymes CYP2C9*3 and CYP2C19*3 Gene Variations With Type 2 Diabetes: A Case-Control Study. Curr Drug Metab 2020; 21:1152-1160. [PMID: 33115391 DOI: 10.2174/1389200221999201027200931] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 08/14/2020] [Accepted: 09/01/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Cytochrome P450s (CYPs) are drug-metabolizing enzymes catalyzing the metabolism of about 75% of drug in clinical use. CYP2C9 represents 20% CYP proteins in liver cells and is a crucial member of CYPs superfamily. CYP2C19 metabolizes very important drugs such as antiulcer drug omeprazole, the antiplatelet drug clopidogrel and anticonvulsant mephenytoin. Single nucleotide polymorphisms (SNPs) of CYP genes have been associated with unexpected drug reactions and diseases in different populations. OBJECTIVE We examined the associations of CYP2C9*3 (rs1057910) and CYP2C19*3 (rs4986893) with T2D in Saudi population. METHODS We used the allele-specific PCR (AS-PCR) and DNA sequencing in 111 cases and 104 controls for rs1057910, and in 119 cases and 110 controls for rs4986893. RESULTS It is indicated that the genotype distribution of rs1057910 in cases and controls were not significantly different (P=0.0001). The genotypes of rs1057910 were not associated with type 2 diabetes (T2D) (P>0.05). Whereas the genotype distribution of rs4986893 in cases and controls was significantly different (P=0.049). The AA genotype of rs4986893 may be associated in increased risk to T2D with OR=17.25 (2.06-143.8), RR=6.14(0.96-39.20), P=0.008. CONCLUSION The CYP2C9*3 (rs1057910) may not be associated with T2D, while CYP2C19*3 (rs4986893) is probably associated with T2D. These findings need to be validated in follow-up studies with larger sample sizes and different populations.
Collapse
Affiliation(s)
- Imadeldin Elfaki
- Department of Biochemistry, Faculty of Science, University of Tabuk, Tabuk, Saudi Arabia
| | - Rashid Mir
- Prince Fahd Ben Sultan Research Chair, Department of Medical Lab Technology, Faculty of Applied Medical Sciences, University of Tabuk, Tabuk, Saudi Arabia
| | - Faisel Mohammed Abu-Duhier
- Prince Fahd Ben Sultan Research Chair, Department of Medical Lab Technology, Faculty of Applied Medical Sciences, University of Tabuk, Tabuk, Saudi Arabia
| | | | | | - Abdullatif Taha Babakr
- Department of Medical Biochemistry, Faculty of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia
| | | |
Collapse
|
3
|
Sabir JSM, Omri AE, Ali Khan I, Banaganapalli B, Hajrah NH, Zrelli H, Omar AMS, Alharbi MG, Alhebshi AM, Jansen RK, Altaf A, Shaik NA, Khan M. ACE insertion/deletion genetic polymorphism, serum ACE levels and high dietary salt intake influence the risk of obesity development among the Saudi adult population. J Renin Angiotensin Aldosterone Syst 2019. [PMCID: PMC6732865 DOI: 10.1177/1470320319870945] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Introduction: Angiotensin-converting enzyme (ACE), which contributes to
adipocyte growth, differentiation and function, has recently been linked
with both salt metabolism and obesity development. Therefore, this study has
aimed to investigate the putative relationship between ACE
genetic polymorphism, serum ACE levels and salt consumption
on the risk of developing obesity in the Saudi population. Materials and methods: ACE genotype status of 267 adult Saudi volunteers (124 obese
and 143 non-obese) was correlated with their serum ACE
activity and dietary salt intake amounts. Results: Obesity was more prevalent in deletion-deletion genotype individuals
(p<0.03), under dominant, co-dominant and
monoallelic conditions (p<0.04). Deletion allele
corresponds to serum ACE activity in obese patients
(p<0.05). The amount of salt intake (<6 g/d) was
significantly associated with obesity and particularly high in
deletion-deletion and insertion-deletion genotype carriers
(p<0.001). STITCH analysis underlined interactions
of the ACE protein with sodium molecule,
REN, ACE2, KNG1 and
AGTR1 in a biological network. Conclusions: Our findings suggest the positive association between ACE
deletion genotype, serum ACE activity and sodium intake
with risk of obesity development in the Saudi population.
Collapse
Affiliation(s)
- Jamal SM Sabir
- Center of Excellence in Bionanoscience Research, King Abdulaziz University, Saudi Arabia
- Genomics and Biotechnology Section and Research Group, Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Saudi Arabia
| | - Abdelfatteh El Omri
- Center of Excellence in Bionanoscience Research, King Abdulaziz University, Saudi Arabia
- Genomics and Biotechnology Section and Research Group, Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Saudi Arabia
| | - Imran Ali Khan
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Babajan Banaganapalli
- Department of Genetic Medicine, Faculty of Medicine, King Abdulaziz University, Saudi Arabia
| | - Nahid H Hajrah
- Center of Excellence in Bionanoscience Research, King Abdulaziz University, Saudi Arabia
- Genomics and Biotechnology Section and Research Group, Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Saudi Arabia
| | - Houda Zrelli
- Center of Excellence in Bionanoscience Research, King Abdulaziz University, Saudi Arabia
- Genomics and Biotechnology Section and Research Group, Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Saudi Arabia
| | - Abdulkader M Shaikh Omar
- Department of Biology, Zoology Division, Faculty of Sciences, King Abdulaziz University, Saudi Arabia
| | - Mona G Alharbi
- Center of Excellence in Bionanoscience Research, King Abdulaziz University, Saudi Arabia
- Genomics and Biotechnology Section and Research Group, Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Saudi Arabia
| | - Alawiah M Alhebshi
- Center of Excellence in Bionanoscience Research, King Abdulaziz University, Saudi Arabia
- Genomics and Biotechnology Section and Research Group, Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Saudi Arabia
| | - Robert K Jansen
- Center of Excellence in Bionanoscience Research, King Abdulaziz University, Saudi Arabia
- Department of Integrative Biology, University of Texas at Austin, Austin, USA
| | - Abdulmalik Altaf
- Department of Surgery, Faculty of Medicine, King Abdulaziz University, Saudi Arabia
| | - Noor Ahmad Shaik
- Department of Genetic Medicine, Faculty of Medicine, King Abdulaziz University, Saudi Arabia
| | - Muhummadh Khan
- Center of Excellence in Bionanoscience Research, King Abdulaziz University, Saudi Arabia
- Genomics and Biotechnology Section and Research Group, Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Saudi Arabia
| |
Collapse
|
4
|
Identification of key genes involved in type 2 diabetic islet dysfunction: a bioinformatics study. Biosci Rep 2019; 39:BSR20182172. [PMID: 31088900 PMCID: PMC6542763 DOI: 10.1042/bsr20182172] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2018] [Revised: 05/03/2019] [Accepted: 05/10/2019] [Indexed: 02/07/2023] Open
Abstract
Aims: To identify the key differentially expressed genes (DEGs) in islet and investigate their potential pathway in the molecular process of type 2 diabetes. Methods: Gene Expression Omnibus (GEO) datasets (GSE20966, GSE25724, GSE38642) of type 2 diabetes patients and normal controls were downloaded from GEO database. DEGs were further assessed by enrichment analysis based on the Database for Annotation, Visualization and Integrated Discovery (DAVID) 6.8. Then, by using Search Tool for the Retrieval Interacting Genes (STRING) 10.0 and gene set enrichment analysis (GSEA), we identified hub gene and associated pathway. At last, we performed quantitative real-time PCR (qPCR) to validate the expression of hub gene. Results: Forty-five DEGs were co-expressed in the three datasets, most of which were down-regulated. DEGs are mostly involved in cell pathway, response to hormone and binding. In protein–protein interaction (PPI) network, we identified ATP-citrate lyase (ACLY) as hub gene. GSEA analysis suggests low expression of ACLY is enriched in glycine serine and threonine metabolism, drug metabolism cytochrome P450 (CYP) and NOD-like receptor (NLR) signaling pathway. qPCR showed the same expression trend of hub gene ACLY as in our bioinformatics analysis. Conclusion: Bioinformatics analysis revealed that ACLY and the pathways involved are possible target in the molecular mechanism of type 2 diabetes.
Collapse
|