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Mirahmadi M, Salehi A, Golalipour M, Bakhshandeh A, Shahbazi M. Association of rs5051 and rs699 polymorphisms in angiotensinogen with coronary artery disease in Iranian population: A case-control study. Medicine (Baltimore) 2024; 103:e37045. [PMID: 38489704 PMCID: PMC10939567 DOI: 10.1097/md.0000000000037045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Revised: 12/24/2023] [Accepted: 01/03/2024] [Indexed: 03/17/2024] Open
Abstract
Coronary artery disease (CAD) is the third most common cause of mortality globally (with 17.8 million deaths annually). Angiotensinogen (AGT) and polymorphisms in this gene can be considered as susceptibility factors for CAD. We performed a retrospective case-control study to determine the correlation of AGT rs5051 and rs699 polymorphisms with CAD in an Iranian population. We genotyped 310 CAD patients and 310 healthy subjects using polymerase chain reaction-based methods. To confirm the accuracy of the screening approach, 10% of genotyped subjects were validated using gold-standard Sanger Sequencing. To evaluate the effect of the candidate polymorphisms, white blood cells were randomly purified from the subjects and AGT expression was measured by quantitative reverse transcriptase-polymerase chain reaction. Sex stratification indicated a significant correlation between CAD and male sex (P = .0101). We found a significant association between the rs5051 A allele (P = .002) and the rs699 C allele, and CAD (P = .0122) in recessive and dominant models. Moreover, our findings showed a significant association of the haplotype, including the rs5051 A/A and rs699 T/C genotypes, with CAD (P = .0405). Finally, AGT mRNA levels were significantly decreased in patients harboring the candidate polymorphisms (P = .03). According to our findings The AGT rs5051 A and AGT rs699 C alleles are predisposing variants of CAD risk and severity in the Iranian population.
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Affiliation(s)
- Maryam Mirahmadi
- Medical Cellular and Molecular Research Center, Golestan University of Medical Sciences, Gorgan, Iran
- Department of Medical Genetics, Faculty of Medicine, Tarbiat Modares University, Tehran, Iran
- Department of Exomine, PardisGene company, Tehran, Iran
| | - Aref Salehi
- Ischemic Disorders Research Center, Golestan University of Medical Sciences, Gorgan, Iran
| | - Masoud Golalipour
- Medical Cellular and Molecular Research Center, Golestan University of Medical Sciences, Gorgan, Iran
| | - Azam Bakhshandeh
- Medical Cellular and Molecular Research Center, Golestan University of Medical Sciences, Gorgan, Iran
| | - Majid Shahbazi
- Medical Cellular and Molecular Research Center, Golestan University of Medical Sciences, Gorgan, Iran
- AryaTinaGene, Biopharmaceutical Company, Gorgan, Iran
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Vasu M, Ahlawat S, Choudhary V, Kaur R, Arora R, Sharma R, Sharma U, Chhabra P, Mir MA, Kumar Singh M. Identification and validation of stable reference genes for expression profiling of target genes in diverse ovine tissues. Gene 2024; 897:148067. [PMID: 38092161 DOI: 10.1016/j.gene.2023.148067] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Accepted: 12/05/2023] [Indexed: 12/18/2023]
Abstract
Quantitative PCR (qPCR) is a widely-used technique for quantifying the expression of target genes across various tissues, as well as under different pathological and physiological conditions. One of the challenges associated with this method is the need to identify optimal reference genes (RGs) that maintain consistent expression levels under diverse experimental settings, thereby ensuring accurate biological interpretation. In this study, we conducted a thorough analysis of 18 candidate RGs (ACTB, BACH1, B2M, GAPDH, HMBS, HPRT1, PGK1, PPIA, PPIB, RPLP0, RPL19, RPS9, RPS15, RPS28, SDHA, TBP, UXT, and YWHAZ) across 10 ovine tissues (muscle, skin, kidney, liver, intestine, rumen, lung, testis, heart, and spleen) obtained from five individual sheep. We aimed to identify genes with stable expression across these tissues. A literature-based survey helped us shortlist candidate genes representing various functional classes from multiple livestock species. We employed four algorithms: geNorm, NormFinder, BestKeeper, and Delta Ct (ΔCt), to rank these genes based on their stability. A consistent trend in the rankings was observed across these different algorithms. RefFinder was then used for a comprehensive ranking, integrating the outputs from the various methods. ACTB, PPIB, BACH1, and B2M emerged as the most stable RGs, while RPS9, RPS15, and PGK1 displayed variable expression. We validated our findings through qPCR analysis of four target genes (ACTN2, CRYAB, DLK1, and TRIM54) in the skin samples from two different sheep breeds. Based on these results, we recommend ACTB, PPIB, BACH1, and B2M as reliable internal control genes for qPCR experiments involving diverse ovine tissues.
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Affiliation(s)
- Mahanthi Vasu
- ICAR-National Bureau of Animal Genetic Resources, Karnal; ICAR-National Dairy Research Institute, Karnal
| | - Sonika Ahlawat
- ICAR-National Bureau of Animal Genetic Resources, Karnal.
| | - Vikas Choudhary
- District Disease Diagnostic Laboratory, Karnal, Department of Animal Husbandry and Dairying, Haryana
| | - Rashmeet Kaur
- ICAR-National Bureau of Animal Genetic Resources, Karnal
| | - Reena Arora
- ICAR-National Bureau of Animal Genetic Resources, Karnal
| | - Rekha Sharma
- ICAR-National Bureau of Animal Genetic Resources, Karnal
| | - Upasna Sharma
- ICAR-National Bureau of Animal Genetic Resources, Karnal
| | - Pooja Chhabra
- ICAR-National Bureau of Animal Genetic Resources, Karnal
| | - M A Mir
- Mountain Research Centre for Sheep and Goat, Shuhama (Aulestang), SKUAST-Kashmir
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Dong HQ, Hu XY, Liang SJ, Wang RS, Cheng P. Selection of reference genes in liproxstatin-1-treated K562 Leukemia cells via RT-qPCR and RNA sequencing. Mol Biol Rep 2024; 51:55. [PMID: 38165476 DOI: 10.1007/s11033-023-08912-5] [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: 09/15/2023] [Accepted: 11/14/2023] [Indexed: 01/03/2024]
Abstract
BACKGROUND Reverse transcription quantitative polymerase chain reaction (RT-qPCR) can accurately detect relative gene expression levels in biological samples. However, widely used reference genes exhibit unstable expression under certain conditions. METHODS AND RESULTS Here, we compared the expression stability of eight reference genes (RPLP0, RPS18, RPL13, EEF1A1, β-actin, GAPDH, HPRT1, and TUBB) commonly used in liproxstatin-1 (Lip-1)-treated K562 cells using RNA-sequencing and RT-qPCR. The expression of EEF1A1, ACTB, GAPDH, HPRT1, and TUBB was considerably lower in cells treated with 20 μM Lip-1 than in the control, and GAPDH also showed significant downregulation in the 10 μM Lip-1 group. Meanwhile, when we used geNorm, NormFinder, and BestKeeper to compare expression stability, we found that GAPDH and HPRT1 were the most unstable reference genes among all those tested. Stability analysis yielded very similar results when geNorm or BestKeeper was used but not when NormFinder was used. Specifically, geNorm and BestKeeper identified RPL13 and RPLP0 as the most stable genes under 20 μM Lip-1 treatment, whereas RPL13, EEF1A1, and TUBB were the most stable under 10 μM Lip-1 treatment. TUBB and EEF1A1 were the most stable genes in both treatment groups according to the results obtained using NormFinder. An assumed most stable gene was incorporated into each software to validate the accuracy. The results suggest that NormFinder is not an appropriate algorithm for this study. CONCLUSIONS Stable reference genes were recognized using geNorm and BestKeeper but not NormFinder. Overall, RPL13 and RPLP0 were the most stable reference genes under 20 μM Lip-1 treatment, whereas RPL13, EEF1A1, and TUBB were the most stable genes under 10 μM Lip-1 treatment.
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Affiliation(s)
- Hai-Qun Dong
- Department of Radiation Oncology, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, China
| | - Xue-Ying Hu
- Department of Radiation Oncology, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, China
| | - Shi-Jing Liang
- Department of Hematology, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, China
- Key Laboratory of Hematology, Guangxi Medical University, Education Department of Guangxi Zhuang Autonomous Region, Nanning, 530021, China
| | - Ren-Sheng Wang
- Department of Radiation Oncology, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, China.
| | - Peng Cheng
- Department of Hematology, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, China.
- Key Laboratory of Hematology, Guangxi Medical University, Education Department of Guangxi Zhuang Autonomous Region, Nanning, 530021, China.
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Karam-Palos S, Andrés-Blasco I, Campos-Borges C, Zanón-Moreno V, Gallego-Martínez A, Alegre-Ituarte V, García-Medina JJ, Pastor-Idoate S, Sellés-Navarro I, Vila-Arteaga J, Lleó-Perez AV, Pinazo-Durán MD. Oxidative Stress Mediates Epigenetic Modifications and the Expression of miRNAs and Genes Related to Apoptosis in Diabetic Retinopathy Patients. J Clin Med 2023; 13:74. [PMID: 38202081 PMCID: PMC10780047 DOI: 10.3390/jcm13010074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 12/17/2023] [Accepted: 12/19/2023] [Indexed: 01/12/2024] Open
Abstract
Knowledge on the underlying mechanisms and molecular targets for managing the ocular complications of type 2 diabetes mellitus (T2DM) remains incomplete. Diabetic retinopathy (DR) is a major cause of irreversible visual disability worldwide. By using ophthalmological and molecular-genetic approaches, we gathered specific information to build a data network for deciphering the crosslink of oxidative stress (OS) and apoptosis (AP) processes, as well as to identify potential epigenetic modifications related to noncoding RNAs in the eyes of patients with T2DM. A total of 120 participants were recruited, being classified into two groups: individuals with T2MD (T2MDG, n = 67), divided into a group of individuals with (+DR, n = 49) and without (-DR, n = 18) DR, and a control group (CG, n = 53). Analyses of compiled data reflected significantly higher plasma levels of malondialdehyde (MDA), superoxide dismutase (SOD), and glutathione peroxidase (GPx) and significantly lower total antioxidant capacity (TAC) in the +DR patients compared with the -DR and the CG groups. Furthermore, the plasma caspase-3 (CAS3), highly involved in apoptosis (AP), showed significantly higher values in the +DR group than in the -DR patients. The microRNAs (miR) hsa-miR 10a-5p and hsa-miR 15b-5p, as well as the genes BCL2L2 and TP53 involved in these pathways, were identified in relation to DR clinical changes. Our data suggest an interaction between OS and the above players in DR pathogenesis. Furthermore, potential miRNA-regulated target genes were identified in relation to DR. In this concern, we may raise new diagnostic and therapeutic challenges that hold the potential to significantly improve managing the diabetic eye.
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Affiliation(s)
- Sarah Karam-Palos
- Ophthalmic Research Unit “Santiago Grisolía”/FISABIO, 46017 Valencia, Spain; (S.K.-P.); (I.A.-B.); (C.C.-B.); (V.A.-I.); (A.V.L.-P.)
- Cellular and Molecular Ophthalmo-Biology Group, Department of Surgery, University of Valencia, 46010 Valencia, Spain
- Department of Ophthalmology, University Hospital “Arnau de Vilanova”, 25196 Valencia, Spain
| | - Irene Andrés-Blasco
- Ophthalmic Research Unit “Santiago Grisolía”/FISABIO, 46017 Valencia, Spain; (S.K.-P.); (I.A.-B.); (C.C.-B.); (V.A.-I.); (A.V.L.-P.)
- Cellular and Molecular Ophthalmo-Biology Group, Department of Surgery, University of Valencia, 46010 Valencia, Spain
- Net of Research in Inflammatory Diseases and Immunopathology of Organs and Systems “REI-RICORS” RD, Institute of Health Carlos III, 28029 Madrid, Spain; (J.J.G.-M.); (S.P.-I.); (I.S.-N.)
| | - Cristina Campos-Borges
- Ophthalmic Research Unit “Santiago Grisolía”/FISABIO, 46017 Valencia, Spain; (S.K.-P.); (I.A.-B.); (C.C.-B.); (V.A.-I.); (A.V.L.-P.)
- Cellular and Molecular Ophthalmo-Biology Group, Department of Surgery, University of Valencia, 46010 Valencia, Spain
- Institute of Biotechnology, University of Porto, 4169-007 Porto, Portugal
| | - Vicente Zanón-Moreno
- Ophthalmic Research Unit “Santiago Grisolía”/FISABIO, 46017 Valencia, Spain; (S.K.-P.); (I.A.-B.); (C.C.-B.); (V.A.-I.); (A.V.L.-P.)
- Cellular and Molecular Ophthalmo-Biology Group, Department of Surgery, University of Valencia, 46010 Valencia, Spain
- Net of Research in Inflammatory Diseases and Immunopathology of Organs and Systems “REI-RICORS” RD, Institute of Health Carlos III, 28029 Madrid, Spain; (J.J.G.-M.); (S.P.-I.); (I.S.-N.)
- Department of Preventive Medicine and Public Health, University of Valencia, 46010 Valencia, Spain
| | - Alex Gallego-Martínez
- Ophthalmic Research Unit “Santiago Grisolía”/FISABIO, 46017 Valencia, Spain; (S.K.-P.); (I.A.-B.); (C.C.-B.); (V.A.-I.); (A.V.L.-P.)
- Cellular and Molecular Ophthalmo-Biology Group, Department of Surgery, University of Valencia, 46010 Valencia, Spain
| | - Victor Alegre-Ituarte
- Ophthalmic Research Unit “Santiago Grisolía”/FISABIO, 46017 Valencia, Spain; (S.K.-P.); (I.A.-B.); (C.C.-B.); (V.A.-I.); (A.V.L.-P.)
- Cellular and Molecular Ophthalmo-Biology Group, Department of Surgery, University of Valencia, 46010 Valencia, Spain
| | - Jose J. García-Medina
- Net of Research in Inflammatory Diseases and Immunopathology of Organs and Systems “REI-RICORS” RD, Institute of Health Carlos III, 28029 Madrid, Spain; (J.J.G.-M.); (S.P.-I.); (I.S.-N.)
- Department of Ophthalmology, University Hospital “Morales Meseguer”, 30008 Murcia, Spain
- Department of Surgery, Pediatrics, Obstetrics and Ginecology, Faculty of Medicine, University of Murcia, 30100 Murcia, Spain
| | - Salvador Pastor-Idoate
- Net of Research in Inflammatory Diseases and Immunopathology of Organs and Systems “REI-RICORS” RD, Institute of Health Carlos III, 28029 Madrid, Spain; (J.J.G.-M.); (S.P.-I.); (I.S.-N.)
- Institute of Applied Ophthalmobiology “IOBA”, University of Valladolid, 47002 Valladolid, Spain
- Department of Ophthalmology, University Clinic Hospital of Valladolid, 47003 Valladolid, Spain
| | - Inmaculada Sellés-Navarro
- Net of Research in Inflammatory Diseases and Immunopathology of Organs and Systems “REI-RICORS” RD, Institute of Health Carlos III, 28029 Madrid, Spain; (J.J.G.-M.); (S.P.-I.); (I.S.-N.)
- Department of Surgery, Pediatrics, Obstetrics and Ginecology, Faculty of Medicine, University of Murcia, 30100 Murcia, Spain
- Department of Ophthalmology, University Hospital “Reina Sofia”, 30003 Murcia, Spain
| | - Jorge Vila-Arteaga
- Department of Ophthalmology, University and Polyclinic Hospital “La Fé”, 46026 Valencia, Spain;
- Innova Ocular Vila Clinic, 46004 Valencia, Spain
| | - Antonio V. Lleó-Perez
- Ophthalmic Research Unit “Santiago Grisolía”/FISABIO, 46017 Valencia, Spain; (S.K.-P.); (I.A.-B.); (C.C.-B.); (V.A.-I.); (A.V.L.-P.)
- Cellular and Molecular Ophthalmo-Biology Group, Department of Surgery, University of Valencia, 46010 Valencia, Spain
- Department of Ophthalmology, University Hospital “Arnau de Vilanova”, 25196 Valencia, Spain
| | - Maria D. Pinazo-Durán
- Ophthalmic Research Unit “Santiago Grisolía”/FISABIO, 46017 Valencia, Spain; (S.K.-P.); (I.A.-B.); (C.C.-B.); (V.A.-I.); (A.V.L.-P.)
- Cellular and Molecular Ophthalmo-Biology Group, Department of Surgery, University of Valencia, 46010 Valencia, Spain
- Net of Research in Inflammatory Diseases and Immunopathology of Organs and Systems “REI-RICORS” RD, Institute of Health Carlos III, 28029 Madrid, Spain; (J.J.G.-M.); (S.P.-I.); (I.S.-N.)
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