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Kafeel S, Bizenjo N, Shivji SS, Keran A, Hashim Z, Nawab SN. DNA Repair Enzyme XRCC4 30 bp Indel Intron 3 Locus Significant Association with Predisposition of Cataract in Senility. Appl Biochem Biotechnol 2024; 196:99-112. [PMID: 37099126 DOI: 10.1007/s12010-023-04533-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/11/2023] [Indexed: 04/27/2023]
Abstract
Impaired DNA damage repair cascade can disrupt the lens transparency due to aging-associated oxidative stress. The aim of study was to assess the association of 30 bp indel mutation (rs28360071) in XRCC4 gene with susceptibility of cataract in senility. The study followed case-control design with a total of n = 200 participants and divided equally into senile cataract patients and control groups. Conventional polymerase chain reaction (PCR) was performed for the genotyping of XRCC4 (rs28360071) mutation. In statistical measures, SPSS ® 20.0 software, MedCal©, and SNPStats© tools were used for data analysis. Distribution of homozygous D/D and mutant D allele was higher in senile cataract patients in comparison to controls. XRCC4 (rs28360071) mutation was significantly associated with predisposition senile cataract (χ2 = 13.96, adjusted OR = 2.29, 95% CI: 1.5-3.4, p < 0.001). Codominant model was suggested to be a best fit model. Mutant D/D genotype described significant association with LDL (adjusted OR = 1.67, 95% CI: 0.14-1.45, p = 0.03),and HDL (adjusted OR = 1.66, 95% CI: 0.92-2.31, p = 0.05) cholesterol with higher risk of senile cataract. XRCC4 (rs28360071) mutation may serve as a potential biomarker for the prognosis of cataract in senility. It can used to measure interruption in NHEJ repair pathway to indicate DNA damage in lens epithelial cells which could accelerate cataractogenesis with aging.
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Affiliation(s)
- Sanober Kafeel
- Faculty of Engineering, Science, Technology and Management, Department of Biomedical Engineering, Ziauddin University (ZUFESTM), F-103, Block B, North Nazimabad, Karachi, 74600, Pakistan.
| | - Neelam Bizenjo
- Faculty of Engineering, Science, Technology and Management, Department of Biomedical Engineering, Ziauddin University (ZUFESTM), F-103, Block B, North Nazimabad, Karachi, 74600, Pakistan
| | - Shams Salman Shivji
- Faculty of Engineering, Science, Technology and Management, Department of Biomedical Engineering, Ziauddin University (ZUFESTM), F-103, Block B, North Nazimabad, Karachi, 74600, Pakistan
| | - Asifa Keran
- Faculty of Engineering, Science, Technology and Management, Department of Biomedical Engineering, Ziauddin University (ZUFESTM), F-103, Block B, North Nazimabad, Karachi, 74600, Pakistan
| | - Zehra Hashim
- Dr. Zafar H. Zaidi Center for Proteomics (ZCP), University of Karachi, Karachi, 75270, Pakistan
| | - Syeda Nuzhat Nawab
- The Karachi Institute of Biotechnology and Genetic Engineering (KIBGE), University of Karachi, Main University Rd, Karachi, 75270, Pakistan
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Association between Genetic Polymorphisms in Superoxide Dismutase Gene Family and Risk of Gastric Cancer. Pathol Oncol Res 2018; 26:335-339. [PMID: 30242560 DOI: 10.1007/s12253-018-0470-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 09/13/2018] [Indexed: 12/14/2022]
Abstract
To determine the association between the SOD1 (Ins/Del), SOD2 (rs2758339, rs5746136), and SOD3 (rs2536512) polymorphisms and the risk of gastric cancer the present study performed. This is a case-control study, including 159 patients with gastric cancer and 242 healthy controls. All subjects were Persian Muslims living in Shiraz (south west Iran). Frequency matching by age and gender was performed. Genomic DNA was extracted from whole blood. Genotypes of the study polymorphism were determined using polymerase chain reaction based methods. The SOD1 Ins/Del and SOD3 rs2536512 polymorphisms did not appear to have relationship with gastric cancer risk. Both SOD2 polymorphisms (rs2758339, rs5746136) showed significant association with the risk of gastric cancer, under assumption that the variant alleles act as dominant alleles. There was significant association between smoking habit and the risk of gastric cancer (OR = 2.54, 95% CI = 1.61-4.02, P < 0.001). Smoker individuals having two putative high-risk genotypes showed elevated risk of gastric cancer compared with nonsmokers without high-risk genotypes, (OR = 5.75, 95% CI = 1.59-20.6, P = 0.007). Assuming that smoking habit and the genotypes are independent risk factors, there was a significant linear trend for the numbers of risk factors and gastric cancer risk (χ2 = 22.9, P < 0.001). This study indicates that the SOD2 polymorphism (rs2758339, rs5746136) is associated with increased risk of gastric cancer, especially in smoker individuals.
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Sani F, Saadat I, Saadat M. Association between genetic polymorphisms of XRCC4 insertion/deletion in intron 3 and G-1394T of XRCC4 and susceptibility to dependency to heroin. GENE REPORTS 2018. [DOI: 10.1016/j.genrep.2018.04.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Boroumand F, Mahmoudinasab H, Saadat M. Association of the SOD2 (rs2758339 and rs5746136) polymorphisms with the risk of heroin dependency and the SOD2 expression levels. Gene 2018; 649:27-31. [DOI: 10.1016/j.gene.2018.01.074] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Revised: 01/07/2018] [Accepted: 01/22/2018] [Indexed: 12/17/2022]
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Lack of association between two genetic polymorphisms of SOD2 (rs2758339 and rs5746136) and the risk of opium dependency. ACTA ACUST UNITED AC 2017. [DOI: 10.1016/j.poamed.2017.03.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Abstract
Several studies have indicated that consanguineous marriages (unions between biologically related persons) are associated with increased risk of autosomal recessive diseases and several multifactorial traits. Mandaeans are a closed ethno-religious community living in areas of southern Iraq and Iran (Khuzestan Province). There are currently no data on the prevalence of consanguineous marriages among Mandaeans. The present study was carried out in 2016 to determine the prevalence of consanguinity among Iranian Mandaeans living in Khuzestan Province, south-west Iran. A total of 137 couples (urban areas: 79 couples; rural areas: 58 couples) were included in the study. Information on the consanguineous marriages of the subjects was collected through direct interviews. Marriages were classified by the degree of relationship between couples as double first cousins, first cousins, first cousin once removed, second cousins and unrelated marriages. The coefficient of inbreeding (F) was calculated for each couple and the mean coefficient of inbreeding (α) estimated for the population, stratified by rural and urban areas. The overall frequency of consanguinity was found to be 50.7% in urban and 86.2% in rural areas. There was a significant difference between rural and urban areas in types of marriages (χ 2=24.8, df=4, p<0.001) and first cousin marriages (51.8%) were the most common type. The overall α-value was estimated to be 0.0363 for the Iranian Mandaean population.
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Saify K, Saadat M. Influence of a 50bp Ins/Del polymorphism at promoter of the superoxide dismutase-1 on gene expression and risk of heroin dependency. Environ Health Prev Med 2017; 22:4. [PMID: 29165112 PMCID: PMC5661911 DOI: 10.1186/s12199-017-0617-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 03/04/2017] [Indexed: 12/14/2022] Open
Abstract
OBJECTIVE Superoxide dismutase-1 (SOD1, OMIM: 147450) is one of the major antioxidant enzymes, which plays a vital role in clearance of reactive oxygen species. A genetic polymorphism of 50 bp insertion/deletion (Ins/Del) in the promoter region of the SOD1 was reported. The aims of the present study are to evaluate the influence of this polymorphism on the SOD1 mRNA levels in human peripheral blood cells and its association with risk of heroin dependency. METHODS The present study consisted of 47 healthy students of Shiraz University (south-west Iran) for investigating the association between the Ins/Del polymorphism on expression level of SOD1, also a total of 442 heroin dependent and 799 healthy controls were included in a case-control study investigating the association between the study polymorphism and risk of dependency to heroin. The quantitative SOD1 mRNA expression levels were investigated using quantitative real-time PCR. RESULTS Statistical analysis revealed a significant difference between the study genotypes (t = 5.17; df = 45; P < 0.001). The Del allele of the study polymorphism decreased approximately 33% of the SOD1 mRNA levels of the gene in the heterozygote individuals. Statistical analysis indicating that in both genders, neither the Ins/Del nor the Del/Del genotypes was associated with the risk of heroin addiction. CONCLUSIONS The present study indicating that although the Ins/Del polymorphism of SOD1 is associated with the SOD1 expression levels, this polymorphism is not associated with the risk of dependency to heroin.
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Affiliation(s)
- Khyber Saify
- Department of Biology, College of Sciences, Shiraz University, Shiraz, 71467-13565, Iran
| | - Mostafa Saadat
- Department of Biology, College of Sciences, Shiraz University, Shiraz, 71467-13565, Iran.
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Aghasadeghi F, Saadat M. Association between ABO and Rh Blood Groups and Risk of Preeclampsia: A Case-Control Study from Iran. Open Access Maced J Med Sci 2017; 5:173-176. [PMID: 28507623 PMCID: PMC5420769 DOI: 10.3889/oamjms.2017.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Revised: 12/05/2016] [Accepted: 12/06/2016] [Indexed: 01/26/2023] Open
Abstract
AIM: Preeclampsia (PE) is a major cause of maternal and neonatal morbidity and mortality. There is a genetic component in the development of PE with estimated heritability around 0.47. Several studies have investigated the association between maternal ABO blood groups (OMIM 110300) and risk of PE, with contradictory results have emerged. Considering that there is no study in this filed from Iranian population, the present case-control study was carried out at Shiraz (south-west Iran). MATERIAL AND METHODS: In this study 331 women; 121 pregnant with PE and 210 normotensive pregnant women were included. Using blood group O (for ABO blood groups) or Rh+ (for Rh blood groups) as a reference, odds ratios (ORs) and its 95% confidence intervals (95% CI) of PE risk were estimated from logistic regression analysis. RESULTS: Although the A (OR = 0.67, 95% CI = 0.39-1.17, P = 0.165), B (OR = 0.86, 95% CI = 0.48-1.53, P = 0.615) and AB (OR = 1.14, 95% CI = 0.37-3.45, P = 0.812) phenotypes showed lower risks compared with the O blood group, statistical analysis indicated that there was no significant association between ABO phenotypes and risk of PE. The frequency of Rh- phenotype was higher among PE patients compared with the control group. However, the association was not significant (OR = 1.79, 95% CI = 0.69-4.65, P = 0.229). Adjusted ORs for age of participants and parity did not change the above-mentioned associations. CONCLUSION: Our present findings indicate that there is no association between ABO and Rh blood groups and risk of PE in Iranian population.
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Affiliation(s)
| | - Mostafa Saadat
- Department of Biology, College of Sciences, Shiraz University, Shiraz 71467-13565, Iran
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DNA repair gene XRCC7 G6721T variant and susceptibility to colorectal cancer. EGYPTIAN JOURNAL OF MEDICAL HUMAN GENETICS 2016. [DOI: 10.1016/j.ejmhg.2016.02.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Saify K, Saadat I, Saadat M. Influence of A-21T and C-262T genetic polymorphisms at the promoter region of the catalase (CAT) on gene expression. Environ Health Prev Med 2016; 21:382-386. [PMID: 27225276 PMCID: PMC5305992 DOI: 10.1007/s12199-016-0540-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2016] [Accepted: 05/14/2016] [Indexed: 01/20/2023] Open
Abstract
OBJECTIVE Catalase (CAT, OMIM: 115500) is one of the major antioxidant enzymes, which plays an important role in the clearance of reactive oxygen species. Three genetic polymorphisms of A-21T (rs7943316), C-262T (rs1001179), and C-844T (rs769214) in the promoter region of the CAT have been reported. It has been suggested that these polymorphisms may alter the recognition sites of transcriptional factors, therefore it might be concluded that these polymorphisms may alter the expression levels of the gene. The aim of the present study is to evaluate the associations between these genetic variations and the CAT mRNA levels in human peripheral blood cells. METHODS The present study consisted of 47 healthy students of Shiraz University (south-west Iran). Genotypes of the CAT polymorphisms were determined by PCR based method. The quantitative CAT mRNA expression levels were investigated using quantitative real-time PCR. RESULTS Analysis of variance revealed significant differences between the study genotypes (For A-21T polymorphism: F = 7.45; df = 2, 44; P = 0.002; For C-262T polymorphism: F = 15.17; df = 2, 44; P < 0.001). The studied polymorphisms showed linkage disequilibrium (D' = 1.0, r 2 = 0.1813, χ 2 = 17.03, P < 0.0001). The mRNA levels of CAT in the AC/TT, TC/TC, TC/TT, and TC/TC diplotypes significantly were higher than the mRNA levels in AC/AC diplotype. There was a significant difference between the study genotypes (F = 9.24; df = 5, 41; P < 0.001). The TC/TC and TT/TT diplotypes showed about 2 and 4 folds CAT mRNA levels compared with the AC/AC diplotype. CONCLUSIONS The present findings indicated that these polymorphisms were significantly associated with the gene expression.
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Affiliation(s)
- Khyber Saify
- Department of Biology, College of Sciences, Shiraz University, Shiraz, 71467-13565 Iran
| | - Iraj Saadat
- Department of Biology, College of Sciences, Shiraz University, Shiraz, 71467-13565 Iran
| | - Mostafa Saadat
- Department of Biology, College of Sciences, Shiraz University, Shiraz, 71467-13565 Iran
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Saify K, Saadat M. Susceptibility to methamphetamine dependence associated with high transcriptional activity alleles of VNTR polymorphism in the promoter region of monoamine oxidase A (MAOA). EGYPTIAN JOURNAL OF MEDICAL HUMAN GENETICS 2016. [DOI: 10.1016/j.ejmhg.2015.08.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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Saify K, Saadat M. Association between VNTR Polymorphism in Promoter Region of Prodynorphin (PDYN) Gene and Methamphetamine Dependence. Open Access Maced J Med Sci 2015; 3:371-3. [PMID: 27275252 PMCID: PMC4877821 DOI: 10.3889/oamjms.2015.079] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Revised: 06/15/2015] [Accepted: 06/16/2015] [Indexed: 12/04/2022] Open
Abstract
AIM: Prodynorphin (PDYN; OMIM: 131340) is the precursor of the dynorphin related peptides which plays an important role in drug abuse. Previous studies have been shown that the expression of PDYN is regulated by a genetic polymorphism of VNTR in the promoter region of the gene. MATERIALS AND METHODS: The present case-control study was performed on 52 (41 males, 11 females) methamphetamine dependence patients and 635 (525 males, 110 females) healthy blood donors frequency matched with the patients according to age and gender, as a control group was participated in the study. RESULTS: The genotypes of VNTR PDYN polymorphism were determined using PCR method. The HL (OR = 1.22, 95%CI: 0.67-2.20, P = 0.500) and LL (OR = 0.86, 95%CI: 0.28-2.57, P = 0.792) genotypes does not alter the risk of methamphetamine dependence, in comparison with the HH genotypes. CONCLUSION: The present study revealed no association between the VNTR polymorphism in the promoter region of the PDYN gene and methamphetamine dependence risk.
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