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Bassyouni M, Mysara M, Wohlers I, Busch H, Saber-Ayad M, El-Hadidi M. A comprehensive analysis of genetic risk for metabolic syndrome in the Egyptian population via allele frequency investigation and Missense3D predictions. Sci Rep 2023; 13:20517. [PMID: 37993469 PMCID: PMC10665412 DOI: 10.1038/s41598-023-46844-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 11/06/2023] [Indexed: 11/24/2023] Open
Abstract
Diabetes mellitus (DM) represents a major health problem in Egypt and worldwide, with increasing numbers of patients with prediabetes every year. Numerous factors, such as obesity, hyperlipidemia, and hypertension, which have recently become serious concerns, affect the complex pathophysiology of diabetes. These metabolic syndrome diseases are highly linked to genetic variability that drives certain populations, such as Egypt, to be more susceptible to developing DM. Here we conduct a comprehensive analysis to pinpoint the similarities and uniqueness among the Egyptian genome reference and the 1000-genome subpopulations (Europeans, Ad-Mixed Americans, South Asians, East Asians, and Africans), aiming at defining the potential genetic risk of metabolic syndromes. Selected approaches incorporated the analysis of the allele frequency of the different populations' variations, supported by genotypes' principal component analysis. Results show that the Egyptian's reference metabolic genes were clustered together with the Europeans', Ad-Mixed Americans', and South-Asians'. Additionally, 8563 variants were uniquely identified in the Egyptian cohort, from those, two were predicted to cause structural damage, namely, CDKAL1: 6_21065070 (A > T) and PPARG: 3_12351660 (C > T) utilizing the Missense3D database. The former is a protein coding gene associated with Type 2 DM while the latter is a key regulator of adipocyte differentiation and glucose homeostasis. Both variants were detected heterozygous in two different Egyptian individuals from overall 110 sample. This analysis sheds light on the unique genetic traits of the Egyptian population that play a role in the DM high prevalence in Egypt. The proposed analysis pipeline -available through GitHub- could be used to conduct similar analysis for other diseases across populations.
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Affiliation(s)
- Mahmoud Bassyouni
- Bioinformatics Group, Center for Informatics Sciences (CIS), School of Information Technology and Computer Science (ITCS), Nile University, Giza, Egypt
- Bioscience Research Laboratories Department, MARC for Medical Services and Scientific Research, 6th of October, Jiza, Egypt
| | - Mohamed Mysara
- Bioinformatics Group, Center for Informatics Sciences (CIS), School of Information Technology and Computer Science (ITCS), Nile University, Giza, Egypt
- Microbiology unit, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium
| | - Inken Wohlers
- Medical Systems Biology Division, Lübeck Institute of Experimental Dermatology, and Institute for Cardiogenetics, University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany
- Biomolecular Data Science in Pneumology, Research Center Borstel, 23845, Borstel, Germany
| | - Hauke Busch
- Medical Systems Biology Division, Lübeck Institute of Experimental Dermatology, and Institute for Cardiogenetics, University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany
- University Cancer Center Schleswig-Holstein, University Hospital of Schleswig-Holstein, Campus Lübeck, 23538, Lübeck, Germany
| | - Maha Saber-Ayad
- Department of Clinical Sciences, College of Medicine, University of Sharjah, 27272, Sharjah, UAE.
- Pharmacology Department, College of Medicine, Cairo University, Cairo, 12613, Egypt.
| | - Mohamed El-Hadidi
- Bioinformatics Group, Center for Informatics Sciences (CIS), School of Information Technology and Computer Science (ITCS), Nile University, Giza, Egypt.
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham Dubai Campus, Dubai, United Arab Emirates.
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Ereqat S, Cauchi S, Eweidat K, Elqadi M, Ghatass M, Sabarneh A, Nasereddin A. Association of DNA methylation and genetic variations of the APOE gene with the risk of diabetic dyslipidemia. Biomed Rep 2022; 17:61. [PMID: 35719839 PMCID: PMC9198989 DOI: 10.3892/br.2022.1544] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Accepted: 05/05/2022] [Indexed: 11/06/2022] Open
Abstract
Apolipoprotein E (APOE) is a key regulator of lipoprotein metabolism, and consequently, affects the plasma and tissue lipid contents. The aim of the present study was to investigate the parallel effects of APOE genetic variants and promoter methylation levels of six CpGs on the risk of diabetic dyslipidemia. A total of 204 Palestinian type 2 diabetes (T2D) patients (mean age ± SD: 62.7±10.2) were enrolled in the present study (n=96 with dyslipidemia and n=108 without dyslipidemia). Next generation sequencing was performed to analyze five single nucleotide polymorphisms: Two variants rs7412 and rs429358 that determine APOE ε alleles, and three variants in the promoter region (rs769446, rs449647, and rs405509). For all subjects, the most common genotype was ε3/ε3 (79.4%). No statistical differences were observed in the APOE ε polymorphisms and the three promoter variants among T2D patients with and without dyslipidemia (P>0.05). A comparison of lipid parameters between ε3/ε3 subjects and ε4 carriers in both groups revealed no significant differences in the mean values of LDL-C, HDL-C, TG, and TC levels (P>0.05). Six CpG sites in the APOE promoter on chromosome 19:44905755-44906078 were identified, and differential DNA methylation in these CpGs were observed between the study groups. Logistic regression analysis revealed a significant association of DNA methylation level at the six CpGs with an increased risk of diabetic dyslipidemia (odds ratio, 1.038; 95% confidence interval, 1.012-1.064; P=0.004). In conclusion, the present study revealed that DNA methylation levels in six CpGs in the APOE promoter region was associated with the risk of diabetic dyslipidemia independently of the APOE ε4 variant which could be a potential therapeutic target to reverse the methylation of the APOE promoter.
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Affiliation(s)
- Suheir Ereqat
- Biochemistry and Molecular Biology Department, Faculty of Medicine, Al‑Quds University, Abu Dis P144, Palestine
| | - Stéphane Cauchi
- Centre National de la Recherche Scientfique (CNRS), Unité Mixte de Recherche UMR8204 Lille, France
| | - Khaled Eweidat
- Faculty of Medicine, Al‑Quds University, East Jerusalem, Abu Dis P144, Palestine
| | - Muawiyah Elqadi
- Faculty of Medicine, Al‑Quds University, East Jerusalem, Abu Dis P144, Palestine
| | - Manal Ghatass
- Biochemistry and Molecular Biology Department, Faculty of Medicine, Al‑Quds University, Abu Dis P144, Palestine
| | - Anas Sabarneh
- Palestine Medical Complex, Laboratories Division, Ramallah P606, Palestine
| | - Abedelmajeed Nasereddin
- Biochemistry and Molecular Biology Department, Faculty of Medicine, Al‑Quds University, Abu Dis P144, Palestine
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