1
|
Giriyappagoudar M, Vastrad B, Horakeri R, Vastrad C. Study on Potential Differentially Expressed Genes in Idiopathic Pulmonary Fibrosis by Bioinformatics and Next-Generation Sequencing Data Analysis. Biomedicines 2023; 11:3109. [PMID: 38137330 PMCID: PMC10740779 DOI: 10.3390/biomedicines11123109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Revised: 10/31/2023] [Accepted: 11/02/2023] [Indexed: 12/24/2023] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is a chronic progressive lung disease with reduced quality of life and earlier mortality, but its pathogenesis and key genes are still unclear. In this investigation, bioinformatics was used to deeply analyze the pathogenesis of IPF and related key genes, so as to investigate the potential molecular pathogenesis of IPF and provide guidance for clinical treatment. Next-generation sequencing dataset GSE213001 was obtained from Gene Expression Omnibus (GEO), and the differentially expressed genes (DEGs) were identified between IPF and normal control group. The DEGs between IPF and normal control group were screened with the DESeq2 package of R language. The Gene Ontology (GO) and REACTOME pathway enrichment analyses of the DEGs were performed. Using the g:Profiler, the function and pathway enrichment analyses of DEGs were performed. Then, a protein-protein interaction (PPI) network was constructed via the Integrated Interactions Database (IID) database. Cytoscape with Network Analyzer was used to identify the hub genes. miRNet and NetworkAnalyst databaseswereused to construct the targeted microRNAs (miRNAs), transcription factors (TFs), and small drug molecules. Finally, receiver operating characteristic (ROC) curve analysis was used to validate the hub genes. A total of 958 DEGs were screened out in this study, including 479 up regulated genes and 479 down regulated genes. Most of the DEGs were significantly enriched in response to stimulus, GPCR ligand binding, microtubule-based process, and defective GALNT3 causes HFTC. In combination with the results of the PPI network, miRNA-hub gene regulatory network and TF-hub gene regulatory network, hub genes including LRRK2, BMI1, EBP, MNDA, KBTBD7, KRT15, OTX1, TEKT4, SPAG8, and EFHC2 were selected. Cyclothiazide and rotigotinethe are predicted small drug molecules for IPF treatment. Our findings will contribute to identification of potential biomarkers and novel strategies for the treatment of IPF, and provide a novel strategy for clinical therapy.
Collapse
Affiliation(s)
- Muttanagouda Giriyappagoudar
- Department of Radiation Oncology, Karnataka Institute of Medical Sciences (KIMS), Hubballi 580022, Karnataka, India;
| | - Basavaraj Vastrad
- Department of Pharmaceutical Chemistry, K.L.E. Socitey’s College of Pharmacy, Gadag 582101, Karnataka, India;
| | - Rajeshwari Horakeri
- Department of Computer Science, Govt First Grade College, Hubballi 580032, Karnataka, India;
| | - Chanabasayya Vastrad
- Biostatistics and Bioinformatics, Chanabasava Nilaya, Bharthinagar, Dharwad 580001, Karnataka, India
| |
Collapse
|
2
|
Genetics and Individual Predispositions in Contact Dermatitis. Contact Dermatitis 2021. [DOI: 10.1007/978-3-030-36335-2_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
|
3
|
Genetics and Individual Predispositions in Contact Dermatitis. Contact Dermatitis 2020. [DOI: 10.1007/978-3-319-72451-5_2-1] [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]
|
4
|
Hoxha M, Zappacosta B. CYP-derived eicosanoids: Implications for rheumatoid arthritis. Prostaglandins Other Lipid Mediat 2019; 146:106405. [PMID: 31838196 DOI: 10.1016/j.prostaglandins.2019.106405] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 11/22/2019] [Accepted: 12/10/2019] [Indexed: 12/18/2022]
Abstract
Today the role of cytochrome P450 metabolites in inflammatory rheumatic disease, such as rheumatoid arthritis (RA) is still poorly understood. In this review we survey the current knowledge on cytochrome P450 metabolites in rheumatoid arthritis. The balance between CYP epoxygenase- and CYP ω- hydroxylase is correlated to the regulation of NF-κB. In RA patients synovial fluid there are higher levels of IL-6, which suppresses activities of CYP enzymes, such as CYP3A, CYP2C19, CYP2C9, and CYP1A2. EETs have anti-inflammatory effects, probably attributed to the PPARγ activation. EETs inhibit bone resorption and osteoclastogenesis, and can be considered as an innovative therapeutic strategy for rheumatoid arthritis. In reference to the CYP ɷ-hydroxylase pathway, 20-HETE is a pro-inflammatory mediator. While there is scarce information on the role of 20-HETE inhibitors and its antagonists in rheumatoid arthritis, the elevation of EETs levels by sEH inhibitors is a promising therapeutic strategy for rheumatoid arthritis patients. In addition, hybrid compounds, such as sEH inhibitors/FLAP inhibitors, or sEHI combined with NSAIDs/COXIBs are also important therapeutic target. However, studies investigating the effects of inflammation and rheumatic disease on CYP-mediated eicosanoid metabolism are necessary. Obtaining a better understanding of the complex role of CYP-derived eicosanoids in inflammatory rheumatic disease, such as rheumatoid arthritis will provide valuable insight for basic and clinical researchers investigation.
Collapse
Affiliation(s)
- Malvina Hoxha
- Catholic University Our Lady of Good Counsel, Department of Chemical-Toxicological and Pharmacological Evaluation of Drugs, Rruga Dritan Hoxha, Tirana, Albania.
| | - Bruno Zappacosta
- Catholic University Our Lady of Good Counsel, Department of Chemical-Toxicological and Pharmacological Evaluation of Drugs, Rruga Dritan Hoxha, Tirana, Albania
| |
Collapse
|
5
|
Taeb M, Jafarzadeh A, Mortazavi-Jahromi SS, Zainodini N, Mirzaei MR, Jafarnezhad-Ansariha F, Aghazadeh Z, Mirshafiey A. Effect of β-D-Mannuronic Acid (M2000) on Oxidative Stress Enzymes' Gene Using Healthy Donor Peripheral Blood Mononuclear Cells for Evaluating the Anti-Aging Property. Curr Drug Discov Technol 2019; 16:265-271. [PMID: 29766814 DOI: 10.2174/1570163815666180515122834] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 05/07/2018] [Accepted: 05/07/2018] [Indexed: 12/14/2022]
Abstract
OBJECTIVE This research aimed to study the anti-aging and anti-inflammatory effects of low and high doses of the β-D-mannuronic (M2000) on gene expression of enzymes involved in oxidative stress (including SOD2, GST, GPX1, CAT, iNOS, and MPO) in peripheral blood mononuclear cells (PBMCs) of healthy donors under in vitro conditions. METHODS The PBMCs were separated and the RNAs were then extracted and the cDNAs synthesized, and expression levels of the mentioned genes were detected by qRT-PCR. RESULTS Our results indicated that the high dose of this drug could significantly reduce the expression level of the SOD2 gene compared to the lipopolysaccharide (LPS) group (p < 0.0001). Moreover, it was found that the high dose of this drug could significantly decrease the expression level of the GST gene compared to the LPS group (p < 0.0001). However, no significant reductions were observed in expression levels of the CAT and GPX1 genes compared to the LPS group. Furthermore, our data revealed that the level of iNOS and MPO gene expression was significantly reduced, in both doses of M2000, respectively, compared to the LPS group (p < 0.0001). CONCLUSION This research showed that M2000 as a novel NSAID with immunosuppressive properties could modify oxidative stress through lowering expression levels of the SOD2, GST, iNOS, and MPO genes compared to the healthy expression levels, with a probable reduction of the risk of developing inflammatory diseases related to age and aging.
Collapse
Affiliation(s)
- Mahsa Taeb
- Department of Immunology, School of Medicine, Rafsanjan University of Medical Sciences, Rafsanjan, Iran
| | - Abdollah Jafarzadeh
- Department of Immunology, School of Medicine, Rafsanjan University of Medical Sciences, Rafsanjan, Iran
| | - Seyed Shahabeddin Mortazavi-Jahromi
- Department of Immunology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran.,Department of Cellular and Molecular Biology, Kish International Campus, University of Tehran, Kish, Iran
| | - Nahid Zainodini
- Immunology of Infectious Diseases Research Center, Rafsanjan University of Medical Sciences, Rafsanjan, Iran
| | - Mohammad Reza Mirzaei
- Molecular Medicine Research Center, Rafsanjan University of Medical Sciences, Rafsanjan, Iran
| | | | - Zahra Aghazadeh
- Department of Immunology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Abbas Mirshafiey
- Department of Immunology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| |
Collapse
|
6
|
Das S, Baruah C, Saikia AK, Tiwari D, Bose S. Genetic and expression changes in
$$\hbox {TNF-}\upalpha $$
TNF-
α
as a risk factor for rheumatoid arthritis pathogenesis in northeast India. J Genet 2019. [DOI: 10.1007/s12041-018-1054-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
|
7
|
Shah AA, Dey-Rao R, Seiffert-Sinha K, Sinha AA. Increased oxidative stress in pemphigus vulgaris is related to disease activity and HLA-association. Autoimmunity 2016; 49:248-57. [PMID: 26911801 DOI: 10.3109/08916934.2016.1145675] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Pemphigus vulgaris (PV) is a rare blistering skin disorder characterized by the disadhesion of keratinocytes due to autoantibody attack against epidermal targets including desmoglein (Dsg) 3, Dsg 1 and possibly other adhesion and non-adhesion molecules. The mechanisms leading to immune-mediated pathology in PV are multifactorial and not fully understood. Recently, oxidative stress (antioxidant/oxidant disequilibrium) has been proposed as a contributory mechanism of autoimmune skin diseases, including PV. In this study, we directly assessed oxidative stress via measurement of total antioxidant capacity (TAC) using ELISA in 47 PV patients, 25 healthy controls and 18 bullous pemphigoid (BP) patients. We also performed microarray gene expression analysis on a separate set of 21 PV patients and 10 healthy controls to evaluate transcriptional dysregulation in oxidative stress-related pathways. Our data indicate that there is a significant reduction in TAC levels in PV patients compared with healthy controls, as well as BP patients. Furthermore, PV patients with active disease have significantly lower TAC levels than PV patients in remission. We also find that HLA allele status has a significant influence on oxidative stress. These findings are corroborated by microarray analysis showing differentially expressed genes involved in oxidative stress between the aforementioned groups. Collectively, our findings provide support for a role of oxidative stress in PV. Whether increased oxidative stress leads to disease manifestation and/or activity, or if disease activity leads to increased oxidative stress remains unknown. Future longitudinal studies may help to further elucidate the relationship between PV and oxidative stress.
Collapse
Affiliation(s)
- Amit Aakash Shah
- a Department of Dermatology , Jacobs School of Medicine and Biomedical Sciences, University at Buffalo , Buffalo , NY , USA
| | - Rama Dey-Rao
- a Department of Dermatology , Jacobs School of Medicine and Biomedical Sciences, University at Buffalo , Buffalo , NY , USA
| | - Kristina Seiffert-Sinha
- a Department of Dermatology , Jacobs School of Medicine and Biomedical Sciences, University at Buffalo , Buffalo , NY , USA
| | - Animesh A Sinha
- a Department of Dermatology , Jacobs School of Medicine and Biomedical Sciences, University at Buffalo , Buffalo , NY , USA
| |
Collapse
|
8
|
Eskafi Sabet E, Salehi Z, Khodayari S, Sabouhi Zarafshan S, Zahiri Z. Spontaneous abortion and functional polymorphism (Val16Ala) in the manganese SOD gene. J OBSTET GYNAECOL 2014; 35:159-62. [PMID: 25140979 DOI: 10.3109/01443615.2014.937330] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Spontaneous abortion is the most common complication of early pregnancy. Genetic factors have been hypothesised to play a role in spontaneous abortion. Since it is possible that the balance of oxidants and antioxidants can be affected by different genetic variants, gene polymorphisms have been proposed as a susceptibility factor that increases the chance of miscarriage. Manganese superoxide dismutase is an important antioxidant enzyme encoded by manganese superoxide dismutase (MnSOD) gene. The aim of this experiment was to assess whether Val16Ala polymorphism of MnSOD gene is associated with miscarriage in northern Iran. Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) was used for genotyping. Statistical analyses were conducted using the χ(2)-test. The genetic distributions did not differ significantly between cases and controls, however slightly more Val/Val genotypes were found among the patients compared with control subjects (p = 0.059). No correlation was observed between susceptibility to abortion and MnSOD Val16Ala polymorphism. Larger population-based studies are needed for clarifying the relationship between abortion and MnSOD genotypes.
Collapse
Affiliation(s)
- E Eskafi Sabet
- Department of Biology, Faculty of Sciences, University of Guilan
| | | | | | | | | |
Collapse
|
9
|
Crawford A, Fassett RG, Geraghty DP, Kunde DA, Ball MJ, Robertson IK, Coombes JS. Relationships between single nucleotide polymorphisms of antioxidant enzymes and disease. Gene 2012; 501:89-103. [PMID: 22525041 DOI: 10.1016/j.gene.2012.04.011] [Citation(s) in RCA: 124] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2012] [Revised: 02/21/2012] [Accepted: 04/05/2012] [Indexed: 12/18/2022]
Abstract
The presence and progression of numerous diseases have been linked to deficiencies in antioxidant systems. The relationships between single nucleotide polymorphisms (SNPs) arising from specific antioxidant enzymes and diseases associated with elevated oxidative stress have been studied with the rationale that they may be useful in screening for diseases. The purpose of this narrative review is to analyse evidence from these studies. The antioxidant enzyme SNPs selected for analysis are based on those most frequently investigated in relation to diseases in humans: superoxide dismutase (SOD2) Ala16Val (80 studies), glutathione peroxidise (GPx1) Pro197Leu (24 studies) and catalase C-262T (22 studies). Although the majority of evidence supports associations between the SOD2 Ala16Val SNP and diseases such as breast, prostate and lung cancers, diabetes and cardiovascular disease, the presence of the SOD2 Ala16Val SNP confers only a small, clinically insignificant reduction (if any) in the risk of these diseases. Other diseases such as bladder cancer, liver disease, nervous system pathologies and asthma have not been consistently related to this SOD SNP genotype. The GPx1 Pro197Leu and catalase C-262T SNP genotypes have been associated with breast cancer, but only in a small number of studies. Thus, currently available evidence suggests antioxidant enzyme SNP genotypes are not useful for screening for diseases in humans.
Collapse
Affiliation(s)
- Amanda Crawford
- School of Human Life Sciences, University of Tasmania, Newnham, Launceston, Tasmania 7248, Australia
| | | | | | | | | | | | | |
Collapse
|
10
|
Zhang W, Zhang WJ, Zhu J, Kong FC, Li YY, Wang HY, Yang YH, Wang C. Genetic polymorphisms are associated with variations in warfarin maintenance dose in Han Chinese patients with venous thromboembolism. Pharmacogenomics 2012; 13:309-21. [PMID: 22248286 DOI: 10.2217/pgs.11.147] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
AIM Warfarin is a clinical anticoagulant that requires periodic monitoring because it is associated with adverse outcomes. Personalized medicine, which is based on pharmacogenetics, holds great promise in solving these types of problems. It aims to provide the tools and knowledge to tailor drug therapy to an individual patient, with the potential of increasing safety and efficacy of medications. MATERIALS & METHODS In the present study we analyzed genotypes of 14 SNPs for seven genes using DNA from 297 Han Chinese venous thromboembolism patients treated with warfarin. RESULTS Multiple regression analyses revealed that CYP2C9 genotype (p = 0.001), VKORC1 genotype (p < 0.001), age (p < 0.01) and weight (p < 0.001) were all associated with warfarin dose requirements, which can explain 37.4% of the variability of warfarin dose among Han Chinese patients. Meanwhile, in the validation cohort, the predicted warfarin daily dose was calculated using the best model with a 64.5% predicted dose being acceptable (-1 mg/day ≤Δwarfarin dose ≤1 mg/day). CONCLUSION We developed a pharmacogenetic dose algorithm for warfarin treatment that uses genotypes from two genes (VKORC1 and CYP2C9) and clinical variables to predict therapeutic maintenance doses in Chinese patients with venous thromboembolism. The validity of the dosing algorithm was confirmed in a cohort of venous thromboembolism patients on warfarin therapy.
Collapse
Affiliation(s)
- Wei Zhang
- Beijing Xiaotangshan Hospital, Xiaotangshan Town, Changping District, Beijing 102211, China
| | | | | | | | | | | | | | | |
Collapse
|
11
|
Kiyohara C, Washio M, Horiuchi T, Asami T, Ide S, Atsumi T, Kobashi G, Takahashi H, Tada Y. Risk modification byCYP1A1andGSTM1polymorphisms in the association of cigarette smoking and systemic lupus erythematosus in a Japanese population. Scand J Rheumatol 2012; 41:103-9. [DOI: 10.3109/03009742.2011.608194] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
|
12
|
Schnuch A, Westphal G, Mössner R, Uter W, Reich K. Genetic factors in contact allergy--review and future goals. Contact Dermatitis 2011; 64:2-23. [PMID: 21166814 DOI: 10.1111/j.1600-0536.2010.01800.x] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The genetics of contact allergy are still only partly understood, despite decades of research; this might be a consequence of inadequately defined phenotypes used in the past. A recommendation is to study an extreme phenotype, namely, polysensitization (sensitization to three or more unrelated allergens). Another approach to unravel the genetics of contact allergy is the study of candidate genes. In this review, we summarize studies on the associations between genetic variation (e.g. single-nucleotide polymorphisms) in certain candidate genes and contact allergy. Polymorphisms and mutations affecting the following proteins were studied: (i) filaggrin; (ii) N-acetyltransferase (NAT) 1 and 2; (iii) glutathione-S-transferase (GST) M and T; (iv) manganese superoxide dismutase; (v) angiotensin-converting enzyme (ACE); (vi) tumour necrosis factor (TNF); and (vii) interleukin-16 (IL-16). The polymorphisms of NAT1, NAT2, GSTM, GSTT, ACE, TNF and IL-16 were shown to be associated with an increased risk of contact allergy. In one of our studies, the increased risk conferred by the TNF and IL-16 polymorphisms was confined to polysensitized individuals. Other relevant candidate genes may be identified by studying diseases related to contact allergy in terms of clinical symptoms, a more general pathology (inflammation), and possibly an overlapping genetic background, such as irritant contact dermatitis.
Collapse
Affiliation(s)
- Axel Schnuch
- Information Network of Departments of Dermatology (IVDK), University of Göttingen, D 37075 Göttingen, Germany.
| | | | | | | | | |
Collapse
|
13
|
de Oliveira Hiragi C, Miranda-Vilela AL, Rocha DMS, de Oliveira SF, Hatagima A, de Nazaré Klautau-Guimarães M. Superoxide dismutase, catalase, glutathione peroxidase and gluthatione S-transferases M1 and T1 gene polymorphisms in three Brazilian population groups. Genet Mol Biol 2011; 34:11-8. [PMID: 21637536 PMCID: PMC3085354 DOI: 10.1590/s1415-47572010005000102] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2010] [Accepted: 08/24/2010] [Indexed: 11/28/2022] Open
Abstract
Antioxidants such as superoxide dismutase (SOD), catalase (CAT) and glutathione peroxidase (GPX1) reduce the oxidation rates in the organism. Gluthatione S-transferases (GSTs) play a vital role in phase 2 of biotransformation of many substances. Variation in the expression of these enzymes suggests individual differences for the degree of antioxidant protection and geographical differences in the distribution of these variants. We described the distribution frequency of CAT (21A/T), SOD2 (Ala9Val), GPX1 (Pro198Leu), GSTM1 and GSTT1 polymorphisms in three Brazilian population groups: Kayabi Amerindians (n = 60), Kalunga Afro-descendants (n = 72), and an urban mixed population from Federal District (n = 162). Frequencies of the variants observed in Kalunga (18% to 58%) and Federal District (33% to 63%) were similar to those observed in Euro and Afro-descendants, while in Kayabi (3% to 68%), depending on the marker, frequencies were similar to the ones found in different ethnic groups. Except for SOD2 in all population groups studied here, and for GPX1 in Kalunga, the genotypic distributions were in accordance with Hardy-Weinberg Equilibrium. These data can clarify the contribution of different ethnicities in the formation of mixed populations, such as that of Brazil. Moreover, outcomes will be valuable resources for future functional studies and for genetic studies in specific populations. If these studies are designed to comprehensively explore the role of these genetic polymorphisms in the etiology of human diseases they may help to prevent inconsistent genotype-phenotype associations in pharmacogenetic studies.
Collapse
Affiliation(s)
- Cássia de Oliveira Hiragi
- Departamento de Genética e Morfologia, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, DF, Brazil
| | | | | | | | | | | |
Collapse
|
14
|
|
15
|
CYP1A2 genotype and rheumatoid arthritis in Koreans. Rheumatol Int 2009; 30:1349-54. [PMID: 19579025 DOI: 10.1007/s00296-009-1050-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2009] [Accepted: 06/21/2009] [Indexed: 02/05/2023]
Abstract
Cytochrome P540 (CYP) 1A2 plays a role in the production of reactive oxygen species (ROS), which have been implicated in the development of rheumatoid arthritis (RA). The objective of this study was to investigate the association between a common polymorphism in the CYP1A2 gene with risk and severity of RA in a Korean population. Cases (n = 1321) with RA and controls (n = 1037) were genotyped for the CYP1A2 -163 A>C polymorphism by real-time PCR. HLA-DRB1 typing and further subtyping of all alleles was performed by PCR, sequence-specific oligonucleotide probe hybridization and direct DNA sequencing analysis. The odds ratio (OR) [(95% confidence interval (CI)] of RA associated with the low inducible C allele was 1.11 (0.80-1.55) among non-shared epitope (SE) carriers, 0.82 (0.56-1.20) among heterozygotes and 0.32 (0.10-1.04) among individuals homozygous for the SE (P = 0.03 for CYP1A2-SE interaction). A protective effect of the low inducibility CYP1A2 C allele among carriers of the SE suggests that a product of CYP1A2-mediated metabolism, such as ROS, may be involved in the development of RA.
Collapse
|
16
|
Horiuchi T, Washio M, Kiyohara C, Tsukamoto H, Tada Y, Asami T, Ide S, Kobashi G, Takahashi H. Combination of TNF-RII, CYP1A1 and GSTM1 polymorphisms and the risk of Japanese SLE: findings from the KYSS study. Rheumatology (Oxford) 2009; 48:1045-9. [PMID: 19561157 DOI: 10.1093/rheumatology/kep166] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
OBJECTIVES Association of the polymorphisms of the genes, TNF receptor type II gene (TNF-RII), cytochrome P4501A1 gene (CYP1A1) and glutathione S-transferase M1 gene (GSTM1), with SLE was investigated. TNF-RII mediates inflammatory and immune response, whereas CYP1A1 and GSTM1 are involved in the metabolism of xenobiotics. These three genes are involved in the generation of reactive oxygen species (ROS), which play a critical role for autoimmune diseases. METHODS A total of 152 SLE patients and 427 healthy individuals in a female Japanese population were enrolled in the study. Case-control studies were performed for the polymorphisms of these three genes. RESULTS The carriers of TNF-RII 196R were at a significantly increased risk for SLE with odds ratio (OR) of 1.59 (95% CI = 1.01, 2.52). CYP1A1 3801C homozygotes had a significantly increased risk of SLE (OR = 2.47, 95% CI = 1.28, 4.78). On the other hand, GSTM1 null genotype was not associated with SLE risk. As for combination action of two loci, CYP1A1 3801C/GSTM1 null combination was more strongly associated with an increased risk of SLE (OR = 4.35; 95% CI = 1.76, 10.73). Moreover, TNF-RII 196M/CYP1A1 3801C/GSTM1 null genotype combination was most significantly associated with SLE (OR = 5.83; 95% CI = 2, 17.04). CONCLUSIONS The individuals carrying two or more 'at-risk' genotypes of TNF-RII, CYP1A1 and GSTM1 had a significantly more increased risk for SLE compared with those having each 'at-risk' genotype. Combination of the risk genotypes will be important to more clearly identify the population at risk for SLE.
Collapse
Affiliation(s)
- Takahiko Horiuchi
- Department of Medicine and Biosystemic Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan.
| | | | | | | | | | | | | | | | | |
Collapse
|
17
|
Abstract
Oxidative stress and mitochondrial damage occur in sepsis. Manganese superoxide dismutase (MnSOD) provides the main defence against oxidative stress within mitochondria. Ala9Val is a single nucleotide polymorphism (SNP) in the MnSOD gene, predicted to affect intra-mitochondrial transport of the enzyme. We found a significant difference in the genotype frequency between healthy subjects (n = 100) and patients with sepsis (n = 40, p = 0.009). For assessment of functionality ten healthy subjects of each homozygous genotype (A/A or V/V) were studied. Peripheral blood mononuclear cells were separated and incubated for 18 h with lipopolysaccharide (LPS), followed by analysis of mitochondrial and cytosolic fractions. There was no difference between genotypes in MnSOD activity and cytochrome c concentration, and minor differences in total antioxidant capacity (TAC) and mitochondrial membrane potential, which did not affect response to LPS. Despite predictions from structural enzyme studies that mitochondrial trafficking would be affected by the Ala9Val polymorphism of the MnSOD gene had little functional effect.
Collapse
Affiliation(s)
- Noha E Elsakka
- Academic Unit of Anaesthesia and Intensive Care, School of Medicine, University of Aberdeen, Aberdeen, UK
| | | | | |
Collapse
|
18
|
Masson LF, Sharp L, Cotton SC, Little J. Cytochrome P-450 1A1 gene polymorphisms and risk of breast cancer: a HuGE review. Am J Epidemiol 2005; 161:901-15. [PMID: 15870154 DOI: 10.1093/aje/kwi121] [Citation(s) in RCA: 85] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Cytochrome P-450 (CYP) 1A1 plays a key role in phase I metabolism of polycyclic aromatic hydrocarbons and in estrogen metabolism. It is expressed predominantly in extrahepatic tissues, including the breast. Four CYP1A1 gene polymorphisms (3801T --> C, Ile462Val, 3205T --> C, and Thr461Asp) have been studied in relation to breast cancer. The 3801C variant is more common than the Val variant. Both variants occur more frequently in Asians than in White populations. The 3205T --> C polymorphism has been observed in African Americans only. Little data are available on the geographic/ethnic distribution of the Thr461Asp polymorphism. The functional significance of the polymorphisms is unclear. In 17 studies, no consistent association between breast cancer and CYP1A1 genotype was found. Meta-analysis found no significant risk for the genotypes 1) 3801C/C (relative risk (RR) = 0.97, 95% confidence interval (CI): 0.52, 1.80) or 3801T/C (RR = 0.91, 95% CI: 0.70, 1.19) versus 3801T/T, 2) Val/Val (RR = 1.04, 95% CI: 0.63, 1.74) or Ile/Val (RR = 0.92, 95% CI: 0.76, 1.10) versus Ile/Ile, or 3) Asp/Asp (RR = 0.95, 95% CI: 0.20, 4.49) or Thr/Asp (RR = 1.12, 95% CI: 0.87, 1.43) versus Thr/Thr. Future studies should explore possible interactions between CYP1A1 and sources of polycyclic aromatic hydrocarbons, markers of estrogen exposure, other lifestyle factors influencing hormonal levels, and other genes involved in polycyclic aromatic hydrocarbon metabolism or hormonal biosynthesis.
Collapse
Affiliation(s)
- L F Masson
- Epidemiology Group, Department of Public Health, University of Aberdeen, Aberdeen, Scotland.
| | | | | | | |
Collapse
|
19
|
Akyol O, Canatan H, Yilmaz HR, Yuce H, Ozyurt H, Sogut S, Gulec M, Elyas H. PCR/RFLP-based cost-effective identification of SOD2 signal (leader) sequence polymorphism (Ala–9Val) using NgoM IV: a detailed methodological approach. Clin Chim Acta 2004; 345:151-9. [PMID: 15193990 DOI: 10.1016/j.cccn.2004.03.021] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2004] [Revised: 03/16/2004] [Accepted: 03/22/2004] [Indexed: 11/29/2022]
Abstract
BACKGROUND Superoxide dismutases (SOD) play an important role in the protection of cells and extracellular space from the products of oxidative stress. Two allelic variants have been described for the SOD2 gene (Ile58Thr involves a C to T substitution at nucleotide residue 339 and Ala-9Val involves a T to C substitution at nucleotide residue 1183). The enzyme proteins encoded by the different alleles have been suggested to have different activity patterns. METHODS The SOD2 polymorphism was determined using a polymerase chain reaction (PCR) and RFLP techniques with restriction endonuclease NgoM IV. RESULTS The most available results were obtained from with 20 pmol primer final concentration in PCR reaction. A total of 20 pmol seems the cost-effective primer concentration with maximum quality. There were no difference between the band quality of 1-5 units of restriction endonucleases. On the other hand, short and long incubation times seem to be similar in order to obtain sharp bands on agarose gel. CONCLUSIONS We have extended a method of SOD2 polymorphism (Ala-9Val) in mitochondrial sequence. This method provides the ability to genotype of SOD2, and it represents a fast, reliable, cost-effective and semi-automated methodology to determine SOD2 polymorphism in order to perform large-scale population studies.
Collapse
Affiliation(s)
- Omer Akyol
- Department of Medical Biology and Genetics, Firat University Medical Faculty, Elazig, Turkey.
| | | | | | | | | | | | | | | |
Collapse
|
20
|
Yen JH, Tsai WC, Chen CJ, Lin CH, Ou TT, Hu CJ, Liu HW. Cytochrome P450 1A1 and manganese superoxide dismutase genes polymorphisms in ankylosing spondylitis. Immunol Lett 2003; 88:113-6. [PMID: 12880680 DOI: 10.1016/s0165-2478(03)00071-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
OBJECTIVES To investigate the associations of cytochrome p450 1A1 (CYP1A1) and manganese superoxide dismutase (MnSOD) genes polymorphisms with the susceptibility to AS in Taiwan. METHODS The polymorphisms of CYP1A1 and MnSOD genes were determined in 70 patients with ankylosing spondylitis (AS) and 93 healthy controls by polymerase chain reaction (PCR)/restriction fragment length polymorphisms (RFLP) methods. RESULTS The genotype frequency of CYP1A1 4887C/A was significantly lower in patients with AS than in controls. The phenotype frequency of CYP1A1 4887A also tended to be decreased in patients with AS. There were no significant differences in the genotype, allele, and phenotype frequencies of MnSOD gene polymorphisms between patients with AS and controls. CONCLUSION CYP1A1 4887A may be a protective factor for the development of AS in Taiwan. However, MnSOD gene polymorphisms are not associated with the susceptibility to AS.
Collapse
Affiliation(s)
- Jeng-Hsien Yen
- Division of Rheumatology, Department of Internal Medicine, Kaohsiung Medical University Hospital, No. 100 Shih-Chuan 1st Road, Kaohsiung 807, Kaohsiung City, Taiwan.
| | | | | | | | | | | | | |
Collapse
|