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Abdelrahman RE, Hassan MS, Morgan AM, Ibrahim MA, Hassanen EI. Acetamiprid Induces Cardiotoxicity in Rats by Dysregulating α7 nAChR and its Downstream Targets: the Ameliorative Role of Resveratrol. Food Chem Toxicol 2024:114892. [PMID: 39067744 DOI: 10.1016/j.fct.2024.114892] [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: 06/01/2024] [Revised: 07/11/2024] [Accepted: 07/24/2024] [Indexed: 07/30/2024]
Abstract
Acetamiprid (ACP) is a novel neonicotinoid insecticide used for controlling insect pests. Resveratrol (RSV) is a natural polyphenol that possesses anti-oxidant, anti-inflammatory and anti-apoptotic actions. The current research explores the mechanism of ACP-induced cardiotoxicity and the alleviative effects of RSV. Male rats were allocated to four groups of ten each. Rats were treated daily for 90 days via oral route. Control rats received distilled water, ACP rats received 25 mg acetamiprid/kg, RSV rats received 20 mg resveratrol/kg and ACP + RSV rats received both ACP and RSV. ACP exposure increased serum creatine phosphokinase activity and cardiac troponin level. It also induced oxidative stress, as evidenced by the glutathione reduction, and malondialdehyde elevation, as well as the detrimental histopathological and immunohistochemical changes in the myocardium. Gene expression analysis revealed down-regulation in the mRNA expression of the survival-related genes α7 nAChR, Erk and Bcl-2, and up-regulation in the apoptosis-related genes Jnk, Bax and Caspase-3. Conversely, the concomitant administration of ACP with RSV alleviated most of the aforementioned toxic impacts. It can be concluded that ACP induces cardiotoxicity by dysregulating the mRNA expression of α7 nAChR and its downstream targets. Additionally, RSV is proved to be a promising ameliorative agent against ACP-induced cardiotoxicity.
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Affiliation(s)
- Rehab E Abdelrahman
- Department of Toxicology and Forensic Medicine, Faculty of Veterinary Medicine, Cairo University, Giza, Egypt
| | - Mohamed S Hassan
- Department of Toxicology and Forensic Medicine, Faculty of Veterinary Medicine, Cairo University, Giza, Egypt
| | - Ashraf M Morgan
- Department of Toxicology and Forensic Medicine, Faculty of Veterinary Medicine, Cairo University, Giza, Egypt.
| | - Marwa A Ibrahim
- Department of Biochemistry and Molecular Biology, Faculty of Veterinary Medicine, Cairo University, Giza, Egypt
| | - Eman I Hassanen
- Department of Pathology, Faculty of Veterinary Medicine, Cairo University, Giza, Egypt
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2
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Wang S, Zhang Z, Liang J, Li K, Bo L, Zhan H, Hong X, Hu J, Yang Qian L, Liu X, Zhang B. Identification of several inflammation-related genes based on bioinformatics and experiments. Int Immunopharmacol 2023; 121:110409. [PMID: 37301122 DOI: 10.1016/j.intimp.2023.110409] [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] [Received: 11/28/2022] [Revised: 04/16/2023] [Accepted: 05/28/2023] [Indexed: 06/12/2023]
Abstract
BACKGROUND Osteoarthritis (OA) is a common disease of elderly individuals, with an unclear pathogenesis and limited treatment options to date. Inflammation occurs prominently in osteoarthritis, thereby making anti-inflammatory treatments promising in clinical outcomes. Therefore, it is of diagnostic and therapeutic significance to explore more inflammatory genes. METHOD In this study, appropriate datasets were first acquired through gene set enrichment analysis (GSEA), followed by inflammation-related genes through weighted gene coexpression network analysis (WGCNA). Two machine learning algorithms (random forest-RF and support vector machine-recursive feature elimination, SVM-RFE) were used to capture the hub genes. In addition, two genes negatively associated with inflammation and osteoarthritis were identified. Afterwards, these genes were verified through experiments and network pharmacology. Due to the association between inflammation and many diseases, the expression levels of the above genes in various inflammatory diseases were determined through literature and experiments. RESULT Two hub genes closely related to osteoarthritis and inflammation were obtained, namely, lysyl oxidase-like 1 (LOXL1) and pituitary tumour-transforming gene (PTTG1), which were shown to be highly expressed in osteoarthritis according to the literature and experiments. However, the expression levels of receptor expression-enhancing protein (REEP5) and cell division cycle protein 14B (CDC14B) remained unchanged in osteoarthritis. This finding was consistent with our verification from the literature and experiments that some genes were highly expressed in numerous inflammation-related diseases, while REEP5 and CDC14B were almost unchanged. Meanwhile, taking PTTG1 as an example, we found that inhibition of PTTG1 expression could suppress the expression of inflammatory factors and protect the extracellular matrix through the microtubule-associated protein kinase (MAPK) signalling pathway. CONCLUSIONS LOXL1 and PTTG1 were highly expressed in some inflammation-related diseases, while that of REEP5 and CDC14B were almost unchanged. PTTG1 may be a potential target for the treatment of osteoarthritis.
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Affiliation(s)
- Song Wang
- Department of Orthopedics, The First Affiliated Hospital of Nanchang University, Artificial Joints Engineering and Technology Research Center of Jiangxi Province, Nanchang, China
| | - Zhiwei Zhang
- Department of Orthopedics, The First Affiliated Hospital of Nanchang University, Artificial Joints Engineering and Technology Research Center of Jiangxi Province, Nanchang, China.
| | - Jianhui Liang
- Department of Orthopedics, The First Affiliated Hospital of Nanchang University, Artificial Joints Engineering and Technology Research Center of Jiangxi Province, Nanchang, China
| | - Kaihuang Li
- Department of Orthopedics, The First Affiliated Hospital of Nanchang University, Artificial Joints Engineering and Technology Research Center of Jiangxi Province, Nanchang, China
| | - Li Bo
- Department of Orthopedics, The First Affiliated Hospital of Nanchang University, Artificial Joints Engineering and Technology Research Center of Jiangxi Province, Nanchang, China
| | - Haibo Zhan
- Department of Orthopedics, The First Affiliated Hospital of Nanchang University, Artificial Joints Engineering and Technology Research Center of Jiangxi Province, Nanchang, China
| | - Xin Hong
- Department of Orthopedics, The First Affiliated Hospital of Nanchang University, Artificial Joints Engineering and Technology Research Center of Jiangxi Province, Nanchang, China
| | - Jiawei Hu
- Department of Orthopedics, The First Affiliated Hospital of Nanchang University, Artificial Joints Engineering and Technology Research Center of Jiangxi Province, Nanchang, China
| | - Lu Yang Qian
- Department of Orthopedics, The First Affiliated Hospital of Nanchang University, Artificial Joints Engineering and Technology Research Center of Jiangxi Province, Nanchang, China
| | - Xuqiang Liu
- Department of Orthopedics, The First Affiliated Hospital of Nanchang University, Artificial Joints Engineering and Technology Research Center of Jiangxi Province, Nanchang, China.
| | - Bin Zhang
- Department of Orthopedics, The First Affiliated Hospital of Nanchang University, Artificial Joints Engineering and Technology Research Center of Jiangxi Province, Nanchang, China.
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3
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Muslimova E, Rebrova T, Kondratieva D, Korepanov V, Sonduev E, Kozlov B, Afanasiev S. Expression of the β1-adrenergic receptor (ADRB1) gene in the myocardium and β-adrenergic reactivity of the body in patients with a history of myocardium infraction. Gene 2022; 844:146820. [PMID: 35987510 DOI: 10.1016/j.gene.2022.146820] [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] [Received: 05/12/2022] [Revised: 08/08/2022] [Accepted: 08/12/2022] [Indexed: 11/18/2022]
Abstract
β1-adrenergic receptors (β1-AR) directly affect on intracardiac hemodynamic and the ability of the heart to tolerate physical activity by regulating its inotropic and chronotropic functions. Severe hypersympathicotonia, specific to coronary artery disease (CAD) and chronic heart failure (HF), leads to impaired functioning of β1-AR. The aim of this research was to assess the expression level of the β1-AR ADRB1 gene in the myocardium, to evaluate the β-adrenergic reactivity of the membrane (β-ARM) of erythrocytes, and to analyze the association of these parameters with myocardial contractile dysfunction in patients with a myocardial infarction (MI) in the past and without it. The study included 126 patients with chronic CAD. Among the patients, 55.6 % had a history of MI at least 6 months ago. The expression of the ADRB1 gene was assessed using real-time polymerase chain reaction. With this purpose, we isolated RNA from the right atrial appendage, which was excised when a heart-lung machine was connected during a planned coronary bypass surgery. β-ARM was evaluated in 57 patients. This method is based on the fact of inhibition of hemolysis of erythrocytes, placed in a hyposmotic medium, in the presence of a β-blocker. Within the whole sample of patients, the expression of the ADRB1 gene is comparable in different functional classes of HF. There was no linear correlation between the expression of the ADRB1 gene and left ventricle ejection fraction (LVEF). In patients with a history of MI, the expression of the ADRB1 gene was elevated when compared to a group of patients without MI (p = 0.017). Patients with a history of MI had higher values of β-ARM than those without MI (p = 0.017). The reverse correlation between β-ARM and LVEF (r = -0,570, p = 0,002) was revealed in the group of patients without MI but not in the group of patients with a history of MI (r = -0,137, p = 0,479). In the sample of patients with chronic CAD, in the myocardium of subjects with a history of MI, the relative expression of ADRB1 gene was higher compared to the group of patients without MI. In patients with different functional classes (FC) of HF and with different ejection fraction, both with MI and without it, ADRB1 gene expression was comparable. In the group of patients with a history of MI, an increase in β-ARM was observed, i.e. decrease in the number or sensitivity of β-AR. Among patients without MI, an inverse correlation was found between β-ARM and LVEF.
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Affiliation(s)
- Elvira Muslimova
- Laboratory of Molecular and Cellular Pathology and Gene Diagnostics, Cardiology Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk, Russia.
| | - Tatiana Rebrova
- Laboratory of Molecular and Cellular Pathology and Gene Diagnostics, Cardiology Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk, Russia
| | - Dina Kondratieva
- Laboratory of Molecular and Cellular Pathology and Gene Diagnostics, Cardiology Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk, Russia
| | - Viacheslav Korepanov
- Laboratory of Molecular and Cellular Pathology and Gene Diagnostics, Cardiology Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk, Russia
| | - Erdeni Sonduev
- Department of Cardiovascular Surgery, Cardiology Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk, Russia
| | - Boris Kozlov
- Department of Cardiovascular Surgery, Cardiology Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk, Russia
| | - Sergey Afanasiev
- Laboratory of Molecular and Cellular Pathology and Gene Diagnostics, Cardiology Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk, Russia
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Normalization strategy for selection of reference genes for RT-qPCR analysis in left ventricles of failing human hearts. BMC Cardiovasc Disord 2022; 22:180. [PMID: 35439923 PMCID: PMC9019989 DOI: 10.1186/s12872-022-02614-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 03/11/2022] [Indexed: 11/10/2022] Open
Abstract
Background Quantitative RT-PCR is a valuable tool for assessing the gene expression in different human tissues, particularly due to its exceptional sensitivity, accuracy and reliability. However, the choice of adequate control for normalization is a crucial step, greatly affecting the results of all subsequent analyses. So far, only a few studies were focused on the selection of optimal reference genes in left ventricles of failing human hearts, leading to several disparities in experimental results focused on differential gene expression in this area. Therefore, the main objective of this study was to identify a set of suitable reference genes in normal and failing left ventricle tissues, which could increase the reliability of RT-qPCR-based studies in the future. Methods We analyzed the expression of 15 commonly used housekeeping genes (ACTB, B2M, GAPDH, GUSB, HMBS, HPRT1, IPO8, PGK1, POLR2A, PPIA, RPLP0, TBP, TFRC, UBC and YWHAZ) in left ventricles of normal and failed hearts with two-step approach. In the first step, we excluded genes which are variantly expressed using ANOVA-based statistical method. Afterwards, the remaining genes were analyzed using geNorm, NormFinder and BestKeeper algorithms, together with delta Cq method. Finally, the geometric mean of gene rankings across all methods was calculated. Results Our analysis identified IPO8 and POLR2A as the most stably expressed genes, whereas ACTB and B2M were found to be expressed variantly, suggesting a potential role of these genes in the pathophysiological processes in failing human hearts. Discussion/conclusion Using our two-step approach, we identified and validated two reference genes expressed invariantly in left ventricles of both healthy and failing human hearts, as well as provided a guideline for the selection of reference genes in studies comparing gene expression in these types of tissues. Supplementary Information The online version contains supplementary material available at 10.1186/s12872-022-02614-9.
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Chen J, Wu X, Wang Y, Pan Y, Ren Y, Nakabeppu Y, Fan Y, Wang Y. Mutyh deficiency downregulates mitochondrial fusion proteins and causes cardiac dysfunction via α-ketoglutaric acid reduction with oxidative stress. Free Radic Res 2022; 56:129-142. [DOI: 10.1080/10715762.2022.2036336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Affiliation(s)
- Jingwen Chen
- Department of Medical Genetics, Nanjing University School of Medicine, Nanjing 210093, China
- Jiangsu Key Laboratory of Molecular Medicine, Nanjing University, Nanjing 210093, China
| | - Xin Wu
- Department of Medical Genetics, Nanjing University School of Medicine, Nanjing 210093, China
- Jiangsu Key Laboratory of Molecular Medicine, Nanjing University, Nanjing 210093, China
| | - Yanyi Wang
- Department of Medical Genetics, Nanjing University School of Medicine, Nanjing 210093, China
- Jiangsu Key Laboratory of Molecular Medicine, Nanjing University, Nanjing 210093, China
| | - Yunfeng Pan
- Department of Medical Genetics, Nanjing University School of Medicine, Nanjing 210093, China
- Jiangsu Key Laboratory of Molecular Medicine, Nanjing University, Nanjing 210093, China
| | - Yan Ren
- Department of Medical Genetics, Nanjing University School of Medicine, Nanjing 210093, China
- Jiangsu Key Laboratory of Molecular Medicine, Nanjing University, Nanjing 210093, China
| | - Yusaku Nakabeppu
- Division of Neurofunctional Genomics, Department of Immunobiology and Neuroscience, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Yimei Fan
- Department of Medical Genetics, Nanjing University School of Medicine, Nanjing 210093, China
- Jiangsu Key Laboratory of Molecular Medicine, Nanjing University, Nanjing 210093, China
| | - Yaping Wang
- Department of Medical Genetics, Nanjing University School of Medicine, Nanjing 210093, China
- Jiangsu Key Laboratory of Molecular Medicine, Nanjing University, Nanjing 210093, China
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Hotz PW, Müller S, Mendler L. SUMO-specific Isopeptidases Tuning Cardiac SUMOylation in Health and Disease. Front Mol Biosci 2021; 8:786136. [PMID: 34869605 PMCID: PMC8641784 DOI: 10.3389/fmolb.2021.786136] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 10/26/2021] [Indexed: 12/28/2022] Open
Abstract
SUMOylation is a transient posttranslational modification with small-ubiquitin like modifiers (SUMO1, SUMO2 and SUMO3) covalently attached to their target-proteins via a multi-step enzymatic cascade. SUMOylation modifies protein-protein interactions, enzymatic-activity or chromatin binding in a multitude of key cellular processes, acting as a highly dynamic molecular switch. To guarantee the rapid kinetics, SUMO target-proteins are kept in a tightly controlled equilibrium of SUMOylation and deSUMOylation. DeSUMOylation is maintained by the SUMO-specific proteases, predominantly of the SENP family. SENP1 and SENP2 represent family members tuning SUMOylation status of all three SUMO isoforms, while SENP3 and SENP5 are dedicated to detach mainly SUMO2/3 from its substrates. SENP6 and SENP7 cleave polySUMO2/3 chains thereby countering the SUMO-targeted-Ubiquitin-Ligase (StUbL) pathway. Several biochemical studies pinpoint towards the SENPs as critical enzymes to control balanced SUMOylation/deSUMOylation in cardiovascular health and disease. This study aims to review the current knowledge about the SUMO-specific proteases in the heart and provides an integrated view of cardiac functions of the deSUMOylating enzymes under physiological and pathological conditions.
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Affiliation(s)
- Paul W Hotz
- Institute of Biochemistry II, Gustav Embden Zentrum, Faculty of Medicine, Goethe University Frankfurt, Frankfurt, Germany
| | - Stefan Müller
- Institute of Biochemistry II, Gustav Embden Zentrum, Faculty of Medicine, Goethe University Frankfurt, Frankfurt, Germany
| | - Luca Mendler
- Institute of Biochemistry II, Gustav Embden Zentrum, Faculty of Medicine, Goethe University Frankfurt, Frankfurt, Germany
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7
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Afanas'ev SA, Kondrat'eva DS, Muslimova EF, Budnikova ОV, Akhmedov SD, Kozlov BN. Expression of Genes and Proteins of the Sarcoplasmic Reticulum Са 2+-Transport Systems in Cardiomyocytes in Concomitant Coronary Heart Disease and Type 2 Diabetes Mellitus. Bull Exp Biol Med 2021; 172:117-120. [PMID: 34855078 DOI: 10.1007/s10517-021-05346-6] [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: 05/28/2021] [Indexed: 11/28/2022]
Abstract
We compared the expression of Са2+-ATPase (SERCA2a), calsequestrin (CASQ2), ryanodine receptors (RyR2) proteins and their genes (ATP2A2, CASQ2, and RYR2) in coronary heart disease (CHD) patients with and without comorbid type 2 diabetes mellitus. All studies were performed on the right atrial appendages resected during coronary bypass surgeries. Expression of SERCA2a and RyR2 proteins and their ATP2A2 (p=0.046) and RYR2 genes in comorbid pathology was significantly (p=0.042) higher (by 1.2 and 2 times; p=0.025). The expression of CASQ2 protein and its gene did not differ significantly between the groups (p=0.82 and p=0.066, respectively). It was concluded that the expression of SERCA2a and RyR2 proteins and their genes (but not CASQ2 and its gene) is elevated in CHD associated with type 2 diabetes mellitus. Expression of the studied proteins correlated with the expression of their genes. Increased expression of CASQ2 protein and its gene can probably prevent imbalance of the Ca2+-transporting systems in cardiomyocytes and contractile dysfunction of the myocardium, even in CHD associated with type 2 diabetes mellitus.
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Affiliation(s)
- S A Afanas'ev
- Cardiology Research Institute, Tomsk National Research Medical Center, Tomsk, Russia.
| | - D S Kondrat'eva
- Cardiology Research Institute, Tomsk National Research Medical Center, Tomsk, Russia
| | - E F Muslimova
- Cardiology Research Institute, Tomsk National Research Medical Center, Tomsk, Russia
| | - О V Budnikova
- Cardiology Research Institute, Tomsk National Research Medical Center, Tomsk, Russia
| | - Sh D Akhmedov
- Cardiology Research Institute, Tomsk National Research Medical Center, Tomsk, Russia
| | - B N Kozlov
- Cardiology Research Institute, Tomsk National Research Medical Center, Tomsk, Russia
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8
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Muslimova EF, Rebrova TY, Kondratieva DS, Sonduev EL, Kozlov BN, Afanasiev SA. Expression of the β1 Adrenergic Receptor Gene (ADRB1) in the Myocardium of Patients with Chronic Heart Failure. RUSS J GENET+ 2021. [DOI: 10.1134/s1022795421110089] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Ren J, Zhang N, Li X, Sun X, Song J. Identification of reference genes for gene expression studies among different developmental stages of murine hearts. BMC DEVELOPMENTAL BIOLOGY 2021; 21:13. [PMID: 34496746 PMCID: PMC8425138 DOI: 10.1186/s12861-021-00244-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 08/24/2021] [Indexed: 02/01/2023]
Abstract
Background Real-time quantitative polymerase chain reaction (RT-qPCR) is a widely-used standard assay for assessing gene expression. RT-qPCR data requires reference genes for normalization to make the results comparable. Therefore, the selected reference gene should be highly stable in its expression throughout the experimental datasets. So far, reports about the optimal set of reference genes in murine left ventricle (LV) across embryonic and postnatal stages are few. The objective of our research was to identify the appropriate reference genes in murine LV among different developmental stages. Methods We investigated the gene expression profiles of 21 widely used housekeeping genes in murine LV from 7 different developmental stages (almost throughout the whole period of the mouse lifespan). The stabilities of the potential reference genes were evaluated by five methods: GeNorm, NormFinder, BestKeeper, Delta-Ct and RefFinder. Results We proposed a set of reliable reference genes for normalization of RT-qPCR experimental data in different conditions. Furthermore, our results showed that 6 genes (18S, Hmbs, Ubc, Psmb4, Tfrc and Actb) are not recommended to be used as reference genes in murine LV development studies. The data also suggested that the Rplp0 gene might serve as an optimal reference gene in gene expression analysis. Conclusions Our study investigated the expression stability of the commonly used reference genes in process of LV development and maturation. We proposed a set of optimal reference genes that are suitable for accurate normalization of RT-qPCR data in specific conditions. Our findings may be helpful in future studies for investigating the gene expression patterns and mechanism of mammalian heart development. Supplementary Information The online version contains supplementary material available at 10.1186/s12861-021-00244-6.
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Affiliation(s)
- Jie Ren
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, 167A Beilishi Road, Xi Cheng District, Beijing, 100037, People's Republic of China.
| | - Ningning Zhang
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, 167A Beilishi Road, Xi Cheng District, Beijing, 100037, People's Republic of China
| | - Xiangjie Li
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, 167A Beilishi Road, Xi Cheng District, Beijing, 100037, People's Republic of China
| | - Xiaogang Sun
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, 167A Beilishi Road, Xi Cheng District, Beijing, 100037, People's Republic of China
| | - Jiangping Song
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, 167A Beilishi Road, Xi Cheng District, Beijing, 100037, People's Republic of China.
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Liu L, Han H, Li Q, Chen M, Zhou S, Wang H, Chen L. Selection and Validation of the Optimal Panel of Reference Genes for RT-qPCR Analysis in the Developing Rat Cartilage. Front Genet 2020; 11:590124. [PMID: 33391345 PMCID: PMC7772434 DOI: 10.3389/fgene.2020.590124] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 11/24/2020] [Indexed: 11/20/2022] Open
Abstract
Real-time fluorescence quantitative PCR (RT-qPCR) is widely used to detect gene expression levels, and selection of reference genes is crucial to the accuracy of RT-qPCR results. Minimum Information for Publication of RT-qPCR Experiments (MIQE) proposes that using the panel of reference genes for RT-qPCR is conducive to obtaining accurate experimental results. However, the selection of the panel of reference genes for RT-qPCR in rat developing cartilage has not been well documented. In this study, we selected eight reference genes commonly used in rat cartilage from literature (GAPDH, ACTB, 18S, GUSB, HPRT1, RPL4, RPL5, and SDHA) as candidates. Then, we screened out the optimal panel of reference genes in female and male rat cartilage of fetus (GD20), juvenile (PW6), and puberty (PW12) in physiology with stability analysis software of genes expression. Finally, we verified the reliability of the selected panel of reference genes with the rat model of intrauterine growth retardation (IUGR) induced by prenatal dexamethasone exposure (PDE). The results showed that the optimal panel of reference genes in cartilage at GD20, PW6, and PW12 in physiology was RPL4 + RPL5, which was consistent with the IUGR model, and there was no significant gender difference. Further, the results of standardizing the target genes showed that RPL4 + RPL5 performed smaller intragroup differences than other panels of reference genes or single reference genes. In conclusion, we found that the optimal panel of reference genes in female and male rat developing cartilage was RPL4 + RPL5, and there was no noticeable difference before and after birth.
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Affiliation(s)
- Liang Liu
- Department of Orthopedic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Hui Han
- Department of Orthopedic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Qingxian Li
- Department of Orthopedic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Ming Chen
- Department of Orthopedic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Siqi Zhou
- Department of Orthopedic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Hui Wang
- Department of Pharmacology, Wuhan University School of Basic Medical Sciences, Wuhan, China.,Hubei Provincial Key Laboratory of Developmentally Originated Disease, Wuhan, China
| | - Liaobin Chen
- Department of Orthopedic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, China.,Hubei Provincial Key Laboratory of Developmentally Originated Disease, Wuhan, China
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11
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Liu H, Zhang CH, Ammanamanchi N, Suresh S, Lewarchik C, Rao K, Uys GM, Han L, Abrial M, Yimlamai D, Ganapathy B, Guillermier C, Chen N, Khaladkar M, Spaethling J, Eberwine JH, Kim J, Walsh S, Choudhury S, Little K, Francis K, Sharma M, Viegas M, Bais A, Kostka D, Ding J, Bar-Joseph Z, Wu Y, Yechoor V, Moulik M, Johnson J, Weinberg J, Reyes-Múgica M, Steinhauser ML, Kühn B. Control of cytokinesis by β-adrenergic receptors indicates an approach for regulating cardiomyocyte endowment. Sci Transl Med 2020; 11:11/513/eaaw6419. [PMID: 31597755 PMCID: PMC8132604 DOI: 10.1126/scitranslmed.aaw6419] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 06/10/2019] [Accepted: 08/30/2019] [Indexed: 12/28/2022]
Abstract
One million patients with congenital heart disease (CHD) live in the United States. They have a lifelong risk of developing heart failure. Current concepts do not sufficiently address mechanisms of heart failure development specifically for these patients. Here, analysis of heart tissue from an infant with tetralogy of Fallot with pulmonary stenosis (ToF/PS) labeled with isotope-tagged thymidine demonstrated that cardiomyocyte cytokinesis failure is increased in this common form of CHD. We used single-cell transcriptional profiling to discover that the underlying mechanism of cytokinesis failure is repression of the cytokinesis gene ECT2, downstream of β-adrenergic receptors (β-ARs). Inactivation of the β-AR genes and administration of the β-blocker propranolol increased cardiomyocyte division in neonatal mice, which increased the number of cardiomyocytes (endowment) and conferred benefit after myocardial infarction in adults. Propranolol enabled the division of ToF/PS cardiomyocytes in vitro. These results suggest that β-blockers could be evaluated for increasing cardiomyocyte division in patients with ToF/PS and other types of CHD.
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Affiliation(s)
- Honghai Liu
- Richard King Mellon Foundation Institute for Pediatric Research and Division of Cardiology, UPMC Children's Hospital of Pittsburgh and Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Cheng-Hai Zhang
- Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA.,Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Niyatie Ammanamanchi
- Richard King Mellon Foundation Institute for Pediatric Research and Division of Cardiology, UPMC Children's Hospital of Pittsburgh and Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Sangita Suresh
- Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA.,Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Christopher Lewarchik
- Richard King Mellon Foundation Institute for Pediatric Research and Division of Cardiology, UPMC Children's Hospital of Pittsburgh and Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Krithika Rao
- Richard King Mellon Foundation Institute for Pediatric Research and Division of Cardiology, UPMC Children's Hospital of Pittsburgh and Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Gerrida M Uys
- Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA.,Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Lu Han
- Richard King Mellon Foundation Institute for Pediatric Research and Division of Cardiology, UPMC Children's Hospital of Pittsburgh and Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Maryline Abrial
- Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA.,Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Dean Yimlamai
- Department of Pediatric Gastroenterology, Hepatology and Nutrition, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Balakrishnan Ganapathy
- Richard King Mellon Foundation Institute for Pediatric Research and Division of Cardiology, UPMC Children's Hospital of Pittsburgh and Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Christelle Guillermier
- Division of Genetics and Harvard Medical School, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Nathalie Chen
- Richard King Mellon Foundation Institute for Pediatric Research and Division of Cardiology, UPMC Children's Hospital of Pittsburgh and Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Mugdha Khaladkar
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, 301A/B Lynch Laboratory, 433 S University Avenue, Philadelphia, PA 19104, USA
| | - Jennifer Spaethling
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - James H Eberwine
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Junhyong Kim
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, 301A/B Lynch Laboratory, 433 S University Avenue, Philadelphia, PA 19104, USA
| | - Stuart Walsh
- Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA.,Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Sangita Choudhury
- Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA.,Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Kathryn Little
- Richard King Mellon Foundation Institute for Pediatric Research and Division of Cardiology, UPMC Children's Hospital of Pittsburgh and Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Kimberly Francis
- Richard King Mellon Foundation Institute for Pediatric Research and Division of Cardiology, UPMC Children's Hospital of Pittsburgh and Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Mahesh Sharma
- Division of Cardiothoracic Surgery, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Melita Viegas
- Pediatric Cardiothoracic Surgery, UPMC Children's Hospital of Pittsburgh and Department of Cardiothoracic Surgery, University of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Abha Bais
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15201, USA
| | - Dennis Kostka
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15201, USA.,Department of Computational & Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA.,Pittsburgh Center for Evolutionary Biology and Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Jun Ding
- Computational Biology Department and Machine Learning Department, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Ziv Bar-Joseph
- Computational Biology Department and Machine Learning Department, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Yijen Wu
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15201, USA.,Rangos Research Center Animal Imaging Core, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Vijay Yechoor
- Diabetes and Beta Cell Biology Center, Division of Endocrinology, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15238, USA
| | - Mousumi Moulik
- Division of Cardiology, Department of Pediatrics, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh School of Medicine, Pittsburgh, PA 15224, USA
| | - Jennifer Johnson
- Division of Cardiology, Department of Pediatrics, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh School of Medicine, Pittsburgh, PA 15224, USA.,Neonatal-Perinatal Medicine, UPMC Magee-Womens Hospital, Pittsburgh, PA 15213, USA
| | - Jacqueline Weinberg
- Division of Cardiology, Department of Pediatrics, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh School of Medicine, Pittsburgh, PA 15224, USA
| | - Miguel Reyes-Múgica
- Division of Pediatric Pathology, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh School of Medicine, Pittsburgh, PA 15224, USA
| | - Matthew L Steinhauser
- Division of Genetics and Harvard Medical School, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Bernhard Kühn
- Richard King Mellon Foundation Institute for Pediatric Research and Division of Cardiology, UPMC Children's Hospital of Pittsburgh and Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA 15224, USA. .,McGowan Institute of Regenerative Medicine, Pittsburgh, PA 15219, USA.,Pediatric Institute for Heart Regeneration and Therapeutics, Pittsburgh, PA 15224, USA
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12
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Hul LM, Ibelli AMG, Peixoto JDO, Souza MR, Savoldi IR, Marcelino DEP, Tremea M, Ledur MC. Reference genes for proximal femoral epiphysiolysis expression studies in broilers cartilage. PLoS One 2020; 15:e0238189. [PMID: 32841273 PMCID: PMC7447007 DOI: 10.1371/journal.pone.0238189] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 08/11/2020] [Indexed: 12/18/2022] Open
Abstract
The use of reference genes is required for relative quantification in gene expression analysis and the stability of these genes can be variable depending on the experimental design. Therefore, it is indispensable to test the reliability of endogenous genes previously to their use. This study evaluated nine candidate reference genes to select the most stable genes to be used as reference in gene expression studies with the femoral cartilage of normal and epiphysiolysis-affected broilers. The femur articular cartilage of 29 male broilers with 35 days of age was collected, frozen and further submitted to RNA extraction and quantitative PCR (qPCR) analysis. The candidate reference genes evaluated were GAPDH, HMBS, HPRT1, MRPS27, MRPS30, RPL30, RPL4, RPL5, and RPLP1. For the gene stability evaluation, three software were used: GeNorm, BestKeeper and NormFinder, and a global ranking was generated using the function RankAggreg. In this study, the RPLP1 and RPL5 were the most reliable endogenous genes being recommended for expression studies with femur cartilage in broilers with epiphysiolysis and possible other femur anomalies.
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Affiliation(s)
- Ludmila Mudri Hul
- Programa de Pós-Graduação em Ciências Veterinárias, Universidade Estadual do Centro-Oeste, Guarapuava, Paraná, Brazil
| | - Adriana Mércia Guaratini Ibelli
- Programa de Pós-Graduação em Ciências Veterinárias, Universidade Estadual do Centro-Oeste, Guarapuava, Paraná, Brazil
- Embrapa Suínos e Aves, Concórdia, Santa Catarina, Brazil
| | - Jane de Oliveira Peixoto
- Programa de Pós-Graduação em Ciências Veterinárias, Universidade Estadual do Centro-Oeste, Guarapuava, Paraná, Brazil
- Embrapa Suínos e Aves, Concórdia, Santa Catarina, Brazil
| | - Mayla Regina Souza
- Programa de Pós-Graduação em Zootecnia, UDESC-Oeste, Chapecó, Santa Catarina, Brazil
| | - Igor Ricardo Savoldi
- Programa de Pós-Graduação em Zootecnia, UDESC-Oeste, Chapecó, Santa Catarina, Brazil
| | | | - Mateus Tremea
- Universidade Federal de Santa Maria, campus Palmeira das Missões, Rio Grande do Sul, Brazil
| | - Mônica Corrêa Ledur
- Embrapa Suínos e Aves, Concórdia, Santa Catarina, Brazil
- Programa de Pós-Graduação em Zootecnia, UDESC-Oeste, Chapecó, Santa Catarina, Brazil
- * E-mail:
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13
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Tian Z, He W, Tang J, Liao X, Yang Q, Wu Y, Wu G. Identification of Important Modules and Biomarkers in Breast Cancer Based on WGCNA. Onco Targets Ther 2020; 13:6805-6817. [PMID: 32764968 PMCID: PMC7367932 DOI: 10.2147/ott.s258439] [Citation(s) in RCA: 92] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 06/17/2020] [Indexed: 12/12/2022] Open
Abstract
Introduction Breast cancer (BRCA) has the highest incidence among female malignancies, and the prognosis for these patients remains poor. Materials and Methods In this study, core modules and central genes related to BRCA were identified through a weighted gene co-expression network analysis (WGCNA). Gene expression profiles and clinical data of GSE25066 were obtained from the Gene Expression Omnibus (GEO) database. The result was validated with RNA-seq data from The Cancer Genome Atlas (TCGA) and Oncomine database. The top 30 key module genes with the highest intramodule connectivity were selected as the core genes (R2 = 0.40). Results According to TCGA and Oncomine datasets, seven genes were selected as candidate hub genes. Following further experimental verification, four hub genes (FAM171A1, NDFIP1, SKP1, and REEP5) were retained. Conclusion We identified four hub genes as candidate biomarkers for BRCA. These hub genes may provide a theoretical basis for targeted therapy against BRCA.
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Affiliation(s)
- Zelin Tian
- Department of Thyroid and Breast Surgery, Zhongnan Hospital of Wuhan University, Wuhan, People's Republic of China
| | - Weixiang He
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, People's Republic of China
| | - Jianing Tang
- Department of Thyroid and Breast Surgery, Zhongnan Hospital of Wuhan University, Wuhan, People's Republic of China
| | - Xing Liao
- Department of Thyroid and Breast Surgery, Zhongnan Hospital of Wuhan University, Wuhan, People's Republic of China
| | - Qian Yang
- Department of Thyroid and Breast Surgery, Zhongnan Hospital of Wuhan University, Wuhan, People's Republic of China
| | - Yumin Wu
- Department of Thyroid and Breast Surgery, Zhongnan Hospital of Wuhan University, Wuhan, People's Republic of China
| | - Gaosong Wu
- Department of Thyroid and Breast Surgery, Zhongnan Hospital of Wuhan University, Wuhan, People's Republic of China
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14
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Gromboni JGG, Cedraz de Oliveira H, Botelho Diniz Marques D, Amândio Pinto Garcia Junior A, Vasconcelos Farias Filho R, Fernando Gromboni C, Machado Souza T, Arias Wenceslau A. Influence of heat stress on reference genes stability in heart and liver of two chickens genotypes. PLoS One 2020; 15:e0228314. [PMID: 32027666 PMCID: PMC7004300 DOI: 10.1371/journal.pone.0228314] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 01/13/2020] [Indexed: 12/02/2022] Open
Abstract
Introduction Real-time polymerase chain reaction (RT-qPCR) is an important tool for analyzing gene expression. However, before analyzing the expression of target genes, it is crucial to normalize the reference genes, in order to find the most stable gene to be used as an endogenous control. A gene that remains stable in all samples under different treatments is considered a suitable normalizer. In this sense, we aimed to identify stable reference genes for normalization of target genes in the heart and liver tissues from two genetically divergent groups of chickens (Cobb 500® commercial line and Peloco backyard chickens) under comfort and acute heat stress environmental conditions. Eight reference genes (ACTB, HPRT1, RPL5, EEF1, MRPS27, MRPS30, TFRC and LDHA) were analyzed for expression stability. The samples were obtained from 24 chickens, 12 from the backyard Peloco and 12 from the Cobb 500® line, exposed to two environmental conditions (comfort and heat stress). Comfort temperature was 23°C and heat stress temperature was 39.5°C for one hour. Subsequently, the animals were euthanized, and heart and liver tissue fragments were collected for RNA extraction and amplification. To determine the stability rate of gene expression, three different statistical algorithms were applied: BestKeeper, geNorm and NormFinder, and to obtain an aggregated stability list, the RankAgregg package of R software was used. Results The most stable genes using BestKeeper tool, including the two factors (genetic group and environmental condition), were LDHA, RPL5 and MRPS27 for heart tissue, and TFRC, RPL5 and EEF1 for liver tissue. Applying geNorm algorithm, the best reference genes were RPL5, EEF1 and MRPS30 for heart tissue and LDHA, EEF1 and RPL5 for liver. Using the NormFinder algorithm, the best normalizer genes were EEF1, RPL5 and LDHA in heart, and EEF1, RPL5 and ACTB in liver tissue. In the overall ranking obtained by RankAggreg package, considering the three algorithms, the RPL5, EEF1 and LDHA genes were the most stable for heart tissue, whereas RPL5, EEF1 and ACTB were the most stable for liver tissue. Conclusion According to the RankAggreg tool classification based on the three different algorithms (BestKeeper, geNorm and NormFinder), the most stable genes were RPL5, EEF1 and LDHA for heart tissue and RPL5, EEF1 and ACTB for liver tissue of chickens subjected to comfort and acute heat stress environmental conditions. However, the best reference genes may vary depending on the experimental conditions of each study, such as different breeds, environmental stressors, and tissues analyzed. Therefore, the need to perform priori studies to assay the best reference genes at the outset of each study is emphasized.
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Affiliation(s)
| | | | | | | | | | | | - Teillor Machado Souza
- Bachelor student of Veterinary Medicine, Universidade Estadual de Santa Cruz—UESC, Ilhéus, BA, Brazil
| | - Amauri Arias Wenceslau
- Department of Agricultural and Environmental Sciences, Universidade Estadual de Santa Cruz—UESC, Ilhéus, BA, Brazil
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15
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Kodama M, Furutani K, Kimura R, Ando T, Sakamoto K, Nagamori S, Ashihara T, Kurachi Y, Sekino Y, Furukawa T, Kanda Y, Kurokawa J. Systematic expression analysis of genes related to generation of action potentials in human iPS cell-derived cardiomyocytes. J Pharmacol Sci 2019; 140:325-330. [DOI: 10.1016/j.jphs.2019.06.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 06/04/2019] [Accepted: 06/12/2019] [Indexed: 01/25/2023] Open
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16
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Selection of optimal reference genes for gene expression studies in chronically hypoxic rat heart. Mol Cell Biochem 2019; 461:15-22. [PMID: 31300984 DOI: 10.1007/s11010-019-03584-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 06/30/2019] [Indexed: 10/26/2022]
Abstract
Adaptation to chronic hypoxia renders the heart more tolerant to ischemia/reperfusion injury. To evaluate changes in gene expression after adaptation to chronic hypoxia by RT-qPCR, it is essential to select suitable reference genes. In a chronically hypoxic rat model, no specific reference genes have been identified in the myocardium. This study aimed to select the best reference genes in the left (LV) and right (RV) ventricles of chronically hypoxic and normoxic rats. Sprague-Dawley rats were adapted to continuous normobaric hypoxia (CNH; 12% O2 or 10% O2) for 3 weeks. The expression levels of candidate genes were assessed by RT-qPCR. The stability of genes was evaluated by NormFinder, geNorm and BestKeeper algorithms. The best five reference genes in the LV were Top1, Nupl2, Rplp1, Ywhaz, Hprt1 for the milder CNH and Top1, Ywhaz, Sdha, Nupl2, Tomm22 for the stronger CNH. In the RV, the top five genes were Hprt1, Nupl2, Gapdh, Top1, Rplp1 for the milder CNH and Tomm22, Gapdh, Hprt1, Nupl2, Top1 for the stronger CNH. This study provides validation of reference genes in LV and RV of CNH rats and shows that suitable reference genes differ in the two ventricles and depend on experimental protocol.
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17
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Molina CE, Jacquet E, Ponien P, Muñoz-Guijosa C, Baczkó I, Maier LS, Donzeau-Gouge P, Dobrev D, Fischmeister R, Garnier A. Identification of optimal reference genes for transcriptomic analyses in normal and diseased human heart. Cardiovasc Res 2019; 114:247-258. [PMID: 29036603 DOI: 10.1093/cvr/cvx182] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 09/20/2017] [Indexed: 11/13/2022] Open
Abstract
Aims Quantitative real-time RT-PCR (RT-qPCR) has become the method of choice for mRNA quantification, but requires an accurate normalization based on the use of reference genes showing invariant expression across various pathological conditions. Only few data exist on appropriate reference genes for the human heart. The objective of this study was to determine a set of suitable reference genes in human atrial and ventricular tissues, from right and left cavities in control and in cardiac diseases. Methods and results We assessed the expression of 16 reference genes (ACTB, B2M, GAPDH, GUSB, HMBS, HPRT1, IPO8, PGK1, POLR2A, PPIA, RPLP0, TBP, TFRC, UBC, YWHAZ, 18S) in tissues from: right and left ventricles from healthy controls and heart failure (HF) patients; right-atrial tissue from patients in sinus rhythm with (SRd) or without (SRnd) atrial dilatation, patients with paroxysmal (pAF) or chronic (cAF) atrial fibrillation or with HF; and left-atrial tissue from patients in SR or cAF. Consensual analysis (by geNorm and Normfinder algorithms, BestKeeper software tool and comparative delta-Ct method) of the variability scores obtained for each reference gene expression shows that the most stably expressed genes are: GAPDH, GUSB, IPO8, POLR2A, and YWHAZ when comparing either right and left ventricle or ventricle from healthy controls and HF patients; GAPDH, IPO8, POLR2A, PPIA, and RPLP0 when comparing either right and left atrium or right atria from all pathological groups. ACTB, TBP, TFRC, and 18S genes were identified as the least stable. Conclusions The overall most stable reference genes across different heart cavities and disease conditions were GAPDH, IPO8, POLR2A and PPIA. YWHAZ or GUSB could be added to this set for some specific experiments. This study should provide useful guidelines for reference gene selection in RT-qPCR studies in human heart.
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Affiliation(s)
- Cristina E Molina
- Inserm, UMR-S 1180, University of Paris-Sud, Université Paris-Saclay, Châtenay-Malabry, France.,Institute of Pharmacology and Toxicology, Heart Research Center Göttingen, University Medical Center, Georg-August University Göttingen, Germany.,German Center for Cardiovascular Research (DZHK), Partner Site Göttingen, Germany
| | - Eric Jacquet
- Institut de Chimie des Substances Naturelles, UPR 2301, CNRS, University of Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Prishila Ponien
- Institut de Chimie des Substances Naturelles, UPR 2301, CNRS, University of Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | | | - Istvan Baczkó
- Department Pharmacology and Pharmacotherapy, University of Szeged, Hungary
| | - Lars S Maier
- Department Internal Medicine II, University Heart Center, University Hospital Regensburg, Regensburg, Germany
| | | | - Dobromir Dobrev
- West German Heart and Vascular Center, Institute of Pharmacology, University Duisburg-Essen, Essen, Germany
| | - Rodolphe Fischmeister
- Inserm, UMR-S 1180, University of Paris-Sud, Université Paris-Saclay, Châtenay-Malabry, France
| | - Anne Garnier
- Inserm, UMR-S 1180, University of Paris-Sud, Université Paris-Saclay, Châtenay-Malabry, France
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