1
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Davies KA, Welch SR, Sorvillo TE, Coleman-McCray JD, Martin ML, Brignone JM, Montgomery JM, Spiropoulou CF, Spengler JR. Optimal reference genes for RNA tissue analysis in small animal models of hemorrhagic fever viruses. Sci Rep 2023; 13:19384. [PMID: 37938597 PMCID: PMC10632498 DOI: 10.1038/s41598-023-45740-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 10/23/2023] [Indexed: 11/09/2023] Open
Abstract
Reverse-transcription quantitative polymerase chain reaction assays are frequently used to evaluate gene expression in animal model studies. Data analyses depend on normalization using a suitable reference gene (RG) to minimize effects of variation due to sample collection, sample processing, or experimental set-up. Here, we investigated the suitability of nine potential RGs in laboratory animals commonly used to study viral hemorrhagic fever infection. Using tissues (liver, spleen, gonad [ovary or testis], kidney, heart, lung, eye, brain, and blood) collected from naïve animals and those infected with Crimean-Congo hemorrhagic fever (mice), Nipah (hamsters), or Lassa (guinea pigs) viruses, optimal species-specific RGs were identified based on five web-based algorithms to assess RG stability. Notably, the Ppia RG demonstrated stability across all rodent tissues tested. Optimal RG pairs that include Ppia were determined for each rodent species (Ppia and Gusb for mice; Ppia and Hrpt for hamsters; and Ppia and Gapdh for guinea pigs). These RG pair assays were multiplexed with viral targets to improve assay turnaround time and economize sample usage. Finally, a pan-rodent Ppia assay capable of detecting Ppia across multiple rodent species was developed and successfully used in ecological investigations of field-caught rodents, further supporting its pan-species utility.
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Affiliation(s)
- Katherine A Davies
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA, USA
- U.S. Department of Agriculture, Agricultural Research Service, Zoonotic and Emerging Disease Research Unit, National Bio and Agro-Defense Facility, Manhattan, KS, USA
| | - Stephen R Welch
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Teresa E Sorvillo
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - JoAnn D Coleman-McCray
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - María Laura Martin
- Departamento Investigación, Instituto Nacional de Enfermedades Virales Humanas (INEVH) "Dr. Julio I. Maiztegui", Pergamino, Argentina
| | - Julia M Brignone
- Departamento Investigación, Instituto Nacional de Enfermedades Virales Humanas (INEVH) "Dr. Julio I. Maiztegui", Pergamino, Argentina
| | - Joel M Montgomery
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Christina F Spiropoulou
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Jessica R Spengler
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA, USA.
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2
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Mishra M, Kane AE, Young AP, Howlett SE. Age, sex, and frailty modify the expression of common reference genes in skeletal muscle from ageing mice. Mech Ageing Dev 2023; 210:111762. [PMID: 36509213 DOI: 10.1016/j.mad.2022.111762] [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: 09/26/2022] [Revised: 11/30/2022] [Accepted: 12/06/2022] [Indexed: 12/14/2022]
Abstract
Changes in gene expression with age are typically normalised to constitutively expressed reference genes (RGs). However, RG expression may be affected by age or overall health and most studies use only male animals. We investigated whether expression of common RGs (Gapdh, Gusb, Rplp0, B2m, Tubb5, Rpl7l1, Hprt, Rer1) was affected by age, sex and/or overall health (frailty index) in skeletal muscle from young (4-mos) and aged (25-26-mos) mice. Standard RG selection programs recommended Gapdh (RefFinder/Genorm/NormFinder) or Rpl7l1 (BestKeeper) without considering age and sex. Analysis of raw Cq values showed only Rplp0 was stable in both sexes at both ages. When qPCR data were normalised to Rplp0, age affected RG expression, especially in females. For example, Hprt expression declined with age (Hprt=9.8 ×10-2 ± 4.7 ×10-2 vs. 6.5 ×10-3 ± 8.8 ×10-4; mean±SEM), while Gusb expression increased (6.0 ×10-4 ± 5.5 ×10-5 vs. 1.7 ×10-3 ± 3.1 ×10-4; n = 5/group; p < 0.05). These effects were not seen in males. Tubb5 and Gapdh were not affected by age or sex when normalised to Rplp0. Similar results were seen with normalisation by Gapdh or the Rplp0/Gapdh pair. Interestingly, RG expression was graded not only by age but by frailty. These data demonstrate that age, sex, and frailty of animals must be carefully considered when selecting RGs to normalise mRNA abundance data.
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Affiliation(s)
- Manish Mishra
- Department of Pharmacology, Dalhousie University, Halifax, Nova Scotia, Canada.
| | - Alice E Kane
- Department of Pharmacology, Dalhousie University, Halifax, Nova Scotia, Canada; Blavatnik Institute, Department of Genetics, Paul F. Glenn Center for Biology of Aging Research at Harvard Medical School, Boston, MA, USA.
| | - Alexander P Young
- Department of Pharmacology, Dalhousie University, Halifax, Nova Scotia, Canada.
| | - Susan E Howlett
- Department of Pharmacology, Dalhousie University, Halifax, Nova Scotia, Canada; Department of Medicine (Geriatric Medicine), Dalhousie University, Halifax, Nova Scotia, Canada.
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3
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Xu Y, Wang J, Ren H, Dai H, Zhou Y, Ren X, Wang Y, Feng S, Deng X, Wu J, Fu T, Nie T, He H, Wei T, Zhu B, Hui L, Li B, Wang J, Wang H, Chen L, Shi X, Cheng X. Human endoderm stem cells reverse inflammation-related acute liver failure through cystatin SN-mediated inhibition of interferon signaling. Cell Res 2023; 33:147-164. [PMID: 36670290 PMCID: PMC9892047 DOI: 10.1038/s41422-022-00760-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 11/25/2022] [Indexed: 01/22/2023] Open
Abstract
Acute liver failure (ALF) is a life-threatening disease that occurs secondary to drug toxicity, infection or a devastating immune response. Orthotopic liver transplantation is an effective treatment but limited by the shortage of donor organs, the requirement for life-long immune suppression and surgical challenges. Stem cell transplantation is a promising alternative therapy for fulminant liver failure owing to the immunomodulatory abilities of stem cells. Here, we report that when transplanted into the liver, human endoderm stem cells (hEnSCs) that are germ layer-specific and nontumorigenic cells derived from pluripotent stem cells are able to effectively ameliorate hepatic injury in multiple rodent and swine drug-induced ALF models. We demonstrate that hEnSCs tune the local immune microenvironment by skewing macrophages/Kupffer cells towards an anti-inflammatory state and by reducing the infiltrating monocytes/macrophages and inflammatory T helper cells. Single-cell transcriptomic analyses of infiltrating and resident monocytes/macrophages isolated from animal livers revealed dramatic changes, including changes in gene expression that correlated with the change of activation states, and dynamic population heterogeneity among these cells after hEnSC transplantation. We further demonstrate that hEnSCs modulate the activation state of macrophages/Kupffer cells via cystatin SN (CST1)-mediated inhibition of interferon signaling and therefore highlight CST1 as a candidate therapeutic agent for diseases that involve over-activation of interferons. We propose that hEnSC transplantation represents a novel and powerful cell therapeutic treatment for ALF.
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Affiliation(s)
- Yilin Xu
- grid.410726.60000 0004 1797 8419State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Jinglin Wang
- grid.428392.60000 0004 1800 1685Department of Hepatobiliary Surgery, the Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, Jiangsu China ,grid.41156.370000 0001 2314 964XHepatobiliary Institute Nanjing University, Nanjing, Jiangsu China
| | - Haozhen Ren
- grid.428392.60000 0004 1800 1685Department of Hepatobiliary Surgery, the Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, Jiangsu China ,grid.41156.370000 0001 2314 964XHepatobiliary Institute Nanjing University, Nanjing, Jiangsu China
| | - Hao Dai
- grid.410726.60000 0004 1797 8419State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China ,grid.510564.3Institute of Brain-Intelligence Technology, Zhangjiang Laboratory, Shanghai, China
| | - Ying Zhou
- grid.410726.60000 0004 1797 8419State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Xiongzhao Ren
- grid.410726.60000 0004 1797 8419State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Yang Wang
- grid.16821.3c0000 0004 0368 8293Department of Immunology and Microbiology, Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Sisi Feng
- grid.410726.60000 0004 1797 8419State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Xiaogang Deng
- grid.410726.60000 0004 1797 8419State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Jiaying Wu
- grid.410726.60000 0004 1797 8419State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Tianlong Fu
- grid.410726.60000 0004 1797 8419State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Tengfei Nie
- grid.410726.60000 0004 1797 8419State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Haifeng He
- grid.410726.60000 0004 1797 8419State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Tongkun Wei
- grid.410726.60000 0004 1797 8419State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Bing Zhu
- grid.9227.e0000000119573309National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Lijian Hui
- grid.410726.60000 0004 1797 8419State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Bin Li
- grid.16821.3c0000 0004 0368 8293Department of Immunology and Microbiology, Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jing Wang
- grid.16821.3c0000 0004 0368 8293Department of Immunology and Microbiology, Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Hongyan Wang
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China.
| | - Luonan Chen
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China. .,Key Laboratory of Systems Biology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Hangzhou, Zhejiang, China.
| | - Xiaolei Shi
- Department of Hepatobiliary Surgery, the Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, Jiangsu, China. .,Hepatobiliary Institute Nanjing University, Nanjing, Jiangsu, China.
| | - Xin Cheng
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China.
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4
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Unkovič A, Boštjančič E, Belič A, Perše M. Selection and Evaluation of mRNA and miRNA Reference Genes for Expression Studies (qPCR) in Archived Formalin-Fixed and Paraffin-Embedded (FFPE) Colon Samples of DSS-Induced Colitis Mouse Model. BIOLOGY 2023; 12:190. [PMID: 36829468 PMCID: PMC9952917 DOI: 10.3390/biology12020190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 01/21/2023] [Accepted: 01/25/2023] [Indexed: 01/28/2023]
Abstract
The choice of appropriate reference genes is essential for correctly interpreting qPCR data and results. However, the majority of animal studies use a single reference gene without any prior evaluation. Therefore, many qPCR results from rodent studies can be misleading, affecting not only reproducibility but also translatability. In this study, the expression stability of reference genes for mRNA and miRNA in archived FFPE samples of 117 C57BL/6JOlaHsd mice (males and females) from 9 colitis experiments (dextran sulfate sodium; DSS) were evaluated and their expression analysis was performed. In addition, we investigated whether normalization reduced/neutralized the influence of inter/intra-experimental factors which we systematically included in the study. Two statistical algorithms (NormFinder and Bestkeeper) were used to determine the stability of reference genes. Multivariate analysis was made to evaluate the influence of normalization with different reference genes on target gene expression in regard to inter/intra-experimental factors. Results show that archived FFPE samples are a reliable source of RNA and imply that the FFPE procedure does not change the ranking of stability of reference genes obtained in fresh tissues. Multivariate analysis showed that the histological picture is an important factor affecting the expression levels of target genes.
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Affiliation(s)
- Ana Unkovič
- Medical Experimental Centre, Institute of Pathology, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Emanuela Boštjančič
- Institute of Pathology, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Aleš Belič
- Statistics and Modelling, Technical Development Biologics, Novartis Technical Research & Development, Lek Pharmaceuticals d.d., 1000 Ljubljana, Slovenia
| | - Martina Perše
- Medical Experimental Centre, Institute of Pathology, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
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5
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Hoja-Łukowicz D, Maciążek D, Kościelniak P, Janik ME. Innovative GenExpA software for selecting suitable reference genes for reliable normalization of gene expression in melanoma. Sci Rep 2022; 12:3331. [PMID: 35228606 PMCID: PMC8885735 DOI: 10.1038/s41598-022-07257-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 02/14/2022] [Indexed: 11/17/2022] Open
Abstract
The algorithms commonly used to select the best stable reference gene in RT-qPCR data analysis have their limitations. We showed that simple selection of the reference gene or pair of genes with the lowest stability value from the pool of potential reference genes—a commonly used approach—is not sufficient to accurately and reliably normalize the target gene transcript and can lead to biologically incorrect conclusions. For reliable assessment of changes in a target gene expression level, we propose our innovative GenExpA software, which works in a manner independent of the experimental model and the normalizer used. GenExpA software selects the best reference by combining the NormFinder algorithm with progressive removal of the least stable gene from the candidate genes in a given experimental model and in the set of daughter models assigned to it. The reliability of references is validated based on the consistency of the statistical analyses of normalized target gene expression levels through all models, described by the coherence score (CS). The use of the CS value imparts a new quality to qPCR analysis because it clarifies how low the stability value of reference must be in order for biologically correct conclusions to be drawn. We tested our method on qPCR data for the B4GALT genes family in melanoma, which is characterized by a high mutation rate, and in melanocytes. GenExpA is available at https://github.com/DorotaHojaLukowicz/GenExpA or https://www.sciencemarket.pl/baza-programow-open-source#oferty.
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6
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Banerjee S, Hayes AM, Shapiro BH. Early expression of requisite developmental growth hormone imprinted cytochromes P450 and dependent transcription factors. Endocr Connect 2021; 10:1167-1179. [PMID: 34424855 PMCID: PMC8494408 DOI: 10.1530/ec-21-0143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 08/20/2021] [Indexed: 11/22/2022]
Abstract
The sexually dimorphic expression of cytochromes P450 (CYP) drug metabolizing enzymes has been reported in all species examined. These sex differences are initially expressed during puberty and are solely regulated by sex differences in the circulating growth hormone (GH) profiles. Once established, however, the different male- and female-dependent CYP isoforms are permanent and immutable, suggesting that adult CYP expression requires imprinting. Since the hormone that regulates an adult function is likely the same hormone that imprints the function, we selectively blocked GH secretion in some newborn male rats while others also received a concurrent physiologic replacement of rat GH. Rats were subsequently challenged, peripubertally, with either a masculine-like episodic GH regimen or the GH vehicle alone. The results demonstrate that episodic GH regulation of male-specific CYP2C11 and CYP3A2, as well as female-predominant CYP2C6, are dependent on developmental GH imprinting. Moreover, the induction and/or activation of major components in the signal transduction pathway regulating the expression of the principal CYP2C11 isoform is obligatorily dependent on perinatal GH imprinting without which CYP2C11 and drug metabolism would be permanently and profoundly suppressed. Since there are additional adult metabolic functions also regulated by GH, pediatric drug therapy that is known to disrupt GH secretion could unintentionally impair adult health.
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Affiliation(s)
- Sarmistha Banerjee
- Department of Biomedical Sciences, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Allison M Hayes
- Department of Biomedical Sciences, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Bernard H Shapiro
- Department of Biomedical Sciences, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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7
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Lu X, Liu Y, Zhang D, Liu K, Wang Q, Wang H. Determination of the panel of reference genes for quantitative real-time PCR in fetal and adult rat intestines. Reprod Toxicol 2021; 104:68-75. [PMID: 34242779 DOI: 10.1016/j.reprotox.2021.07.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 06/30/2021] [Accepted: 07/04/2021] [Indexed: 02/07/2023]
Abstract
In quantitative real-time PCR (qRT-PCR) detection, the stability of reference genes varies with different organs, tissue locations, sex and developmental stages. This study aimed to screen out and determine the optimal panel of reference genes of the intestine in pre- and post-natal rats of different sex. We used qRT-PCR to detect the mRNA expression of six commonly used reference genes (ACTB, GAPDH, HPRT1, B2M, RPLPO and SDHA) in rat intestines at gestational day 21 (GD21) and postnatal week 12 (PW12). Using GeNorm, BestKeeper and NormFinder software comprehensively analyzed the stability of candidate reference genes and screened out stable reference genes. Further, we used the pathological model of prenatal dexamethasone exposure (PDE) to verify the stability of the selected panel of reference genes. Based on the results of the software analysis, the optimal panel of reference genes in the fetal rat intestine was SDHA + ACTB, and the adult rat small intestine and colon were ACTB + HPRT1 and RPLP0 + GAPDH, respectively. There was no significant sex difference in the above results. Besides, in the PDE model, the results were consistent with those under physiological conditions. Therefore, the stability of intestinal reference genes in fetal rats and adult rats was different, and the intestinal reference genes of adult rats were intestinal segments-specific. The selected panel of reference genes was still stable under pathological conditions. This study determined the optimal panel of reference genes of pre- and post-natal rat intestines and provided reliable reference genes for the qRT-PCR analysis of rat intestines.
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Affiliation(s)
- Xiaoqian Lu
- Department of Pharmacology, Basic Medical School of Wuhan University, Wuhan, 430071, China
| | - Yi Liu
- Department of Pharmacology, Basic Medical School of Wuhan University, Wuhan, 430071, China
| | - Dingmei Zhang
- Department of Pharmacology, Basic Medical School of Wuhan University, Wuhan, 430071, China
| | - Kexin Liu
- Department of Pharmacology, Basic Medical School of Wuhan University, Wuhan, 430071, China
| | - Qian Wang
- Department of Pharmacology, Basic Medical School of Wuhan University, Wuhan, 430071, China
| | - Hui Wang
- Department of Pharmacology, Basic Medical School of Wuhan University, Wuhan, 430071, China; Hubei Provincial Key Laboratory of Developmentally Originated Disease, Wuhan, 430071, China.
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8
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Panel of suitable reference genes and its gender differences of fetal rat liver under physiological conditions and exposure to dexamethasone during pregnancy. Reprod Toxicol 2021; 100:74-82. [PMID: 33453333 DOI: 10.1016/j.reprotox.2021.01.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Revised: 12/17/2020] [Accepted: 01/11/2021] [Indexed: 01/04/2023]
Abstract
The panel of suitable reference genes in the fetal liver have not been reported. In this study, five commonly used reference genes (GAPDH, β-actin, Rn18 s, Rpl13a, and Rps29) were firstly selected as candidates. Bestkeeper, GeNorm, and NormFinder software were then used to screen out the panel of suitable reference genes of male and female fetal rat liver under physiological and prenatal dexamethasone exposure (PDE) conditions. Finally, we verified the reliability of the screened panel of reference genes by standardizing sterol regulatory element binding protein 1c (SREBP1c) expression with different reference genes. The results showed that GAPDH + Rn18 s and GAPDH + Rpl13a were respectively the panel of suitable reference genes in male and female rat fetal liver under the physiological model, while Rn18 s + Rps29 and GAPDH + Rn18 s were respectively under the PDE model. The results showed that different reference genes affected the statistical results of SREBP1c expression, and the screened panel of suitable reference genes under the PDE model had smaller intragroup differences, when compared with other reference genes under physiological and PDE models. In conclusion, we screened and determined that the panel of suitable reference genes were GAPDH + Rn18 s and Rn18 s + Rps29 in the male rat fetal liver under physiological and PDE models, while they were GAPDH + Rpl13a and GAPDH + Rn18 s in the females, and confirmed that the selection of the panel of suitable reference genes in the fetal liver had gender differences and pathological model specificity.
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9
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Sarker N, Fabijan J, Emes RD, Hemmatzadeh F, Meers J, Moreton J, Owen H, Seddon JM, Simmons G, Speight N, Trott D, Woolford L, Tarlinton RE. Identification of stable reference genes for quantitative PCR in koalas. Sci Rep 2018; 8:3364. [PMID: 29463845 PMCID: PMC5820254 DOI: 10.1038/s41598-018-21723-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 02/09/2018] [Indexed: 11/17/2022] Open
Abstract
To better understand host and immune response to diseases, gene expression studies require identification of reference genes with stable expression for accurate normalisation. This study describes the identification and testing of reference genes with stable expression profiles in koala lymph node tissues across two genetically distinct koala populations. From the 25 most stable genes identified in transcriptome analysis, 11 genes were selected for verification using reverse transcription quantitative PCR, in addition to the commonly used ACTB and GAPDH genes. The expression data were analysed using stable genes statistical software - geNorm, BestKeeper, NormFinder, the comparative ΔCt method and RefFinder. All 13 genes showed relative stability in expression in koala lymph node tissues, however Tmem97 and Hmg20a were identified as the most stable genes across the two koala populations.
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Affiliation(s)
- N Sarker
- School of Veterinary Science, The University of Queensland, Gatton, QLD, Australia
| | - J Fabijan
- School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, SA, Australia
| | - R D Emes
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, United Kingdom.,Advanced Data Analysis Centre (ADAC), University of Nottingham, Sutton Bonington, United Kingdom
| | - F Hemmatzadeh
- School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, SA, Australia
| | - J Meers
- School of Veterinary Science, The University of Queensland, Gatton, QLD, Australia
| | - J Moreton
- Advanced Data Analysis Centre (ADAC), University of Nottingham, Sutton Bonington, United Kingdom
| | - H Owen
- School of Veterinary Science, The University of Queensland, Gatton, QLD, Australia
| | - J M Seddon
- School of Veterinary Science, The University of Queensland, Gatton, QLD, Australia
| | - G Simmons
- School of Veterinary Science, The University of Queensland, Gatton, QLD, Australia
| | - N Speight
- School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, SA, Australia
| | - D Trott
- School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, SA, Australia
| | - L Woolford
- School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, SA, Australia
| | - R E Tarlinton
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, United Kingdom.
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10
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Khanna P, Johnson KL, Maron JL. Optimal reference genes for RT-qPCR normalization in the newborn. Biotech Histochem 2017; 92:459-466. [PMID: 28910197 DOI: 10.1080/10520295.2017.1362474] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
It is difficult to identify reliable reference genes for transcriptomic analyses in biofluids such as saliva. This situation is particularly relevant for the newborn population, where rapid development is associated with dynamic changes in gene expression. Real-time gene expression monitoring holds great promise for elucidating disrupted pathways that result in morbidities unique to this population, such as retinopathy of prematurity, but its impact depends on identifying stable and consistently expressed genes across a wide range of gestational ages. We extracted total RNA from 400 neonatal saliva samples (postconceptional ages: 32 5/7 to 48 2/7 weeks), converted it to cDNA, and pre-amplified and analyzed it by qPCR for three commonly used reference genes, ACTB, GAPDH, and YWHAZ. Relative quantification was determined using the Δ Ct method. Data were analyzed as a whole and also stratified by age and sex. Descriptive statistics and homogeneity of variance were performed to identify optimal reference genes. Data analyzed from all ages and both sexes showed significant expression variation for ACTB, while GAPDH and YWHAZ showed greater stability. Male infants exhibited increased expression variation compared to females for ACTB, but neither GAPDH nor YWHAZ showed significant variance for either sex. We suggest that ACTB is an unreliable reference gene for the newborn population. Males showed significantly more variation in ACTB expression compared to females, which suggests a sex-specific developmental role for this biomarker. By contrast, GAPDH and YWHAZ were less variable and therefore preferable for use in neonates. Our findings may improve the use of reference genes for the RT-qPCR platform in the newborn over a wide range of gestational ages, thereby minimizing the likelihood of erroneous interpretation of gene expression during rapid growth, development, and differentiation.
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Affiliation(s)
- P Khanna
- a Sackler School of Graduate Biomedical Sciences
| | | | - J L Maron
- c Mother Infant Research Institute, Floating Hospital for Children, Tufts Medical Center , Boston , Massachusetts
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11
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Gholami K, Loh SY, Salleh N, Lam SK, Hoe SZ. Selection of suitable endogenous reference genes for qPCR in kidney and hypothalamus of rats under testosterone influence. PLoS One 2017; 12:e0176368. [PMID: 28591185 PMCID: PMC5462341 DOI: 10.1371/journal.pone.0176368] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2016] [Accepted: 04/10/2017] [Indexed: 12/21/2022] Open
Abstract
Real-time quantitative PCR (qPCR) is the most reliable and accurate technique for analyses of gene expression. Endogenous reference genes are being used to normalize qPCR data even though their expression may vary under different conditions and in different tissues. Nonetheless, verification of expression of reference genes in selected studied tissue is essential in order to accurately assess the level of expression of target genes of interest. Therefore, in this study, we attempted to examine six commonly used reference genes in order to identify the gene being expressed most constantly under the influence of testosterone in the kidneys and hypothalamus. The reference genes include glyceraldehyde-3-phosphate dehydrogenase (GAPDH), actin beta (ACTB), beta-2 microglobulin (B2m), hypoxanthine phosphoribosyltransferase 1 (HPRT), peptidylprolylisomerase A (Ppia) and hydroxymethylbilane synthase (Hmbs). The cycle threshold (Ct) value for each gene was determined and data obtained were analyzed using the software programs NormFinder, geNorm, BestKeeper, and rank aggregation. Results showed that Hmbs and Ppia genes were the most stably expressed in the hypothalamus. Meanwhile, in kidneys, Hmbs and GAPDH appeared to be the most constant genes. In conclusion, variations in expression levels of reference genes occur in kidneys and hypothalamus under similar conditions; thus, it is important to verify reference gene levels in these tissues prior to commencing any studies.
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Affiliation(s)
- Khadijeh Gholami
- Division of Human Biology, School of Medicine, International Medical University, Kuala Lumpur, Malaysia
- * E-mail:
| | - Su Yi Loh
- Division of Human Biology, School of Medicine, International Medical University, Kuala Lumpur, Malaysia
| | - Naguib Salleh
- Department of Physiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Sau Kuen Lam
- Department of Physiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - See Ziau Hoe
- Department of Physiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
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12
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Das RK, Banerjee S, Shapiro BH. Growth hormone: a newly identified developmental organizer. J Endocrinol 2017; 232:377-389. [PMID: 27980003 PMCID: PMC5241097 DOI: 10.1530/joe-16-0471] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 12/15/2016] [Indexed: 01/23/2023]
Abstract
The sexually dimorphic expression of cytochromes P450 (CYP) drug-metabolizing enzymes has been reported in all species examined. These sex differences are only expressed during adulthood and are solely regulated by sex differences in circulating growth hormone (GH) profiles. Once established, however, the different male- and female-dependent CYP isoform profiles are permanent and immutable, suggesting that adult CYP expression requires imprinting. As the hormone that regulates an adult function is likely the same hormone that imprints the function, we selectively blocked GH secretion in some newborn male rats, whereas others received concurrent physiologic replacement of rat GH. The results demonstrate that adult male GH activation of the signal transduction pathway regulating expression of the principal CYP2C11 isoform is obligatorily dependent on perinatal GH imprinting, without which CYP2C11 and drug metabolism would be permanently and profoundly suppressed. As there are other adult metabolic functions also regulated by GH, pediatric drug therapy known to disrupt GH secretion could unintentionally impair adult health.
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Affiliation(s)
| | | | - Bernard H Shapiro
- Department of Biomedical SciencesUniversity of Pennsylvania, School of Veterinary Medicine, Philadelphia, Pennsylvania, USA
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13
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Schaeck M, De Spiegelaere W, De Craene J, Van den Broeck W, De Spiegeleer B, Burvenich C, Haesebrouck F, Decostere A. Laser capture microdissection of intestinal tissue from sea bass larvae using an optimized RNA integrity assay and validated reference genes. Sci Rep 2016; 6:21092. [PMID: 26883391 PMCID: PMC4756658 DOI: 10.1038/srep21092] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Accepted: 01/11/2016] [Indexed: 12/28/2022] Open
Abstract
The increasing demand for a sustainable larviculture has promoted research regarding environmental parameters, diseases and nutrition, intersecting at the mucosal surface of the gastrointestinal tract of fish larvae. The combination of laser capture microdissection (LCM) and gene expression experiments allows cell specific expression profiling. This study aimed at optimizing an LCM protocol for intestinal tissue of sea bass larvae. Furthermore, a 3′/5′ integrity assay was developed for LCM samples of fish tissue, comprising low RNA concentrations. Furthermore, reliable reference genes for performing qPCR in larval sea bass gene expression studies were identified, as data normalization is critical in gene expression experiments using RT-qPCR. We demonstrate that a careful optimization of the LCM procedure allows recovery of high quality mRNA from defined cell populations in complex intestinal tissues. According to the geNorm and Normfinder algorithms, ef1a, rpl13a, rps18 and faua were the most stable genes to be implemented as reference genes for an appropriate normalization of intestinal tissue from sea bass across a range of experimental settings. The methodology developed here, offers a rapid and valuable approach to characterize cells/tissues in the intestinal tissue of fish larvae and their changes following pathogen exposure, nutritional/environmental changes, probiotic supplementation or a combination thereof.
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Affiliation(s)
- M Schaeck
- Department of Morphology, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820 Merelbeke, Belgium
| | - W De Spiegelaere
- Department of Internal Medicine, Faculty of Medicine and Health Sciences, Ghent University, De Pintelaan 185, 9000 Ghent, Belgium
| | - J De Craene
- Department of Morphology, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820 Merelbeke, Belgium
| | - W Van den Broeck
- Department of Morphology, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820 Merelbeke, Belgium
| | - B De Spiegeleer
- Department of Pharmaceutical Analysis, Laboratory of Drug Quality &Registration, Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteenweg 460, 9000 Ghent, Belgium
| | - C Burvenich
- Department of Comparative Physiology and Biometrics, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820 Merelbeke, Belgium
| | - F Haesebrouck
- Department of Pathology, Bacteriology and Avian Diseases, Ghent University, Salisburylaan 133, 9820 Merelbeke, Belgium
| | - A Decostere
- Department of Morphology, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820 Merelbeke, Belgium
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14
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Pohóczky K, Kun J, Szalontai B, Szőke É, Sághy É, Payrits M, Kajtár B, Kovács K, Környei JL, Garai J, Garami A, Perkecz A, Czeglédi L, Helyes Z. Estrogen-dependent up-regulation of TRPA1 and TRPV1 receptor proteins in the rat endometrium. J Mol Endocrinol 2016; 56:135-49. [PMID: 26643912 DOI: 10.1530/jme-15-0184] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 12/04/2015] [Indexed: 01/15/2023]
Abstract
Transient receptor potential ankyrin 1 (TRPA1) and vanilloid 1 (TRPV1) receptors expressed predominantly in sensory nerves are activated by inflammatory stimuli and mediate inflammation and pain. Although they have been shown in the human endometrium, their regulation and function are unknown. Therefore, we investigated their estrogen- and progesterone-dependent alterations in the rat endometrium in comparison with the estrogen-regulated inflammatory cytokine macrophage migration inhibitory factor (MIF). Four-week-old (sexually immature) and four-month-old (sexually mature) female rats were treated with the non-selective estrogen receptor (ER) agonist diethylstilboestrol (DES), progesterone and their combination, or ovariectomized. RT-PCR and immunohistochemistry were performed to determine mRNA and protein expression levels respectively. Channel function was investigated with ratiometric [Ca(2+)]i measurement in cultured primary rat endometrial cells. Both TRP receptors and MIF were detected in the endometrium at mRNA and protein levels, and their localizations were similar. Immunostaining was observed in the immature epithelium, while stromal, glandular and epithelial positivity were observed in adults. Functionally active TRP receptor proteins were shown in endometrial cells by activation-induced calcium influx. In adults, Trpa1 and Trpv1 mRNA levels were significantly up-regulated after DES treatment. TRPA1 increased after every treatment, but TRPV1 remained unchanged following the combined treatment and ovariectomy. In immature rats, DES treatment resulted in increased mRNA expression of both channels and elevated TRPV1 immunopositivity. MIF expression changed in parallel with TRPA1/TRPV1 in most cases. DES up-regulated Trpa1, Trpv1 and Mif mRNA levels in endometrial cell cultures, but 17β-oestradiol having ERα-selective potency increased only the expression of Trpv1. We provide the first evidence for TRPA1/TRPV1 expression and their estrogen-induced up-regulation in the rat endometrium in correlation with the MIF.
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Affiliation(s)
- Krisztina Pohóczky
- Department of Pharmacology and PharmacotherapyUniversity of Pécs Medical School, Szigeti Street 12, H-7624 Pécs, HungaryJanos Szentagothai Research CentreUniversity of Pécs, Ifjúság Street 20, H-7624 Pécs, HungaryDepartments of PathologyUniversity of Pécs Medical School, Szigeti Street 12, H-7624 Pécs, HungaryDepartment of PhysiologyUniversity of Pécs Medical School, Szigeti Street 12, H-7624 Pécs, HungaryDepartment of Pathophysiology and GerontologyUniversity of Pécs Medical School, Szigeti Street 12, H-7624 Pécs, HungaryMTA-PTE NAP B Chronic Pain Research GroupHungary, Szigeti Street 12, H-7624 Pécs, HungaryInstitute of Animal ScienceCentre for Agricultural and Applied Economic Sciences, University of Debrecen, PO Box 36, H-4015 Debrecen, Hungary Department of Pharmacology and PharmacotherapyUniversity of Pécs Medical School, Szigeti Street 12, H-7624 Pécs, HungaryJanos Szentagothai Research CentreUniversity of Pécs, Ifjúság Street 20, H-7624 Pécs, HungaryDepartments of PathologyUniversity of Pécs Medical School, Szigeti Street 12, H-7624 Pécs, HungaryDepartment of PhysiologyUniversity of Pécs Medical School, Szigeti Street 12, H-7624 Pécs, HungaryDepartment of Pathophysiology and GerontologyUniversity of Pécs Medical School, Szigeti Street 12, H-7624 Pécs, HungaryMTA-PTE NAP B Chronic Pain Research GroupHungary, Szigeti Street 12, H-7624 Pécs, HungaryInstitute of Animal ScienceCentre for Agricultural and Applied Economic Sciences, University of Debrecen, PO Box 36, H-4015 Debrecen, Hungary
| | - József Kun
- Department of Pharmacology and PharmacotherapyUniversity of Pécs Medical School, Szigeti Street 12, H-7624 Pécs, HungaryJanos Szentagothai Research CentreUniversity of Pécs, Ifjúság Street 20, H-7624 Pécs, HungaryDepartments of PathologyUniversity of Pécs Medical School, Szigeti Street 12, H-7624 Pécs, HungaryDepartment of PhysiologyUniversity of Pécs Medical School, Szigeti Street 12, H-7624 Pécs, HungaryDepartment of Pathophysiology and GerontologyUniversity of Pécs Medical School, Szigeti Street 12, H-7624 Pécs, HungaryMTA-PTE NAP B Chronic Pain Research GroupHungary, Szigeti Street 12, H-7624 Pécs, HungaryInstitute of Animal ScienceCentre for Agricultural and Applied Economic Sciences, University of Debrecen, PO Box 36, H-4015 Debrecen, Hungary Department of Pharmacology and PharmacotherapyUniversity of Pécs Medical School, Szigeti Street 12, H-7624 Pécs, HungaryJanos Szentagothai Research CentreUniversity of Pécs, Ifjúság Street 20, H-7624 Pécs, HungaryDepartments of PathologyUniversity of Pécs Medical School, Szigeti Street 12, H-7624 Pécs, HungaryDepartment of PhysiologyUniversity of Pécs Medical School, Szigeti Street 12, H-7624 Pécs, HungaryDepartment of Pathophysiology and GerontologyUniversity of Pécs Medical School, Szigeti Street 12, H-7624 Pécs, HungaryMTA-PTE NAP B Chronic Pain Research GroupHungary, Szigeti Street 12, H-7624 Pécs, HungaryInstitute of Animal ScienceCentre for Agricultural and Applied Economic Sciences, University of Debrecen, PO Box 36, H-4015 Debrecen, Hungary Department of Pharmacology and PharmacotherapyUniversity of Pécs Medical School, Szigeti Street 12, H-7624 Pécs, HungaryJanos Szentagothai Research CentreUniversity of Pécs, Ifjúság Street 20, H-7624 Pécs, HungaryDepartments of PathologyUniversity of Pécs Medical School, Szigeti Street 12, H-7624 Pécs, HungaryDepartment of PhysiologyUniversity of Pécs Medical School, Szigeti Street 12, H-7624 Pécs, HungaryDepartment of Pathophysiology and Ger
| | - Bálint Szalontai
- Department of Pharmacology and PharmacotherapyUniversity of Pécs Medical School, Szigeti Street 12, H-7624 Pécs, HungaryJanos Szentagothai Research CentreUniversity of Pécs, Ifjúság Street 20, H-7624 Pécs, HungaryDepartments of PathologyUniversity of Pécs Medical School, Szigeti Street 12, H-7624 Pécs, HungaryDepartment of PhysiologyUniversity of Pécs Medical School, Szigeti Street 12, H-7624 Pécs, HungaryDepartment of Pathophysiology and GerontologyUniversity of Pécs Medical School, Szigeti Street 12, H-7624 Pécs, HungaryMTA-PTE NAP B Chronic Pain Research GroupHungary, Szigeti Street 12, H-7624 Pécs, HungaryInstitute of Animal ScienceCentre for Agricultural and Applied Economic Sciences, University of Debrecen, PO Box 36, H-4015 Debrecen, Hungary
| | - Éva Szőke
- Department of Pharmacology and PharmacotherapyUniversity of Pécs Medical School, Szigeti Street 12, H-7624 Pécs, HungaryJanos Szentagothai Research CentreUniversity of Pécs, Ifjúság Street 20, H-7624 Pécs, HungaryDepartments of PathologyUniversity of Pécs Medical School, Szigeti Street 12, H-7624 Pécs, HungaryDepartment of PhysiologyUniversity of Pécs Medical School, Szigeti Street 12, H-7624 Pécs, HungaryDepartment of Pathophysiology and GerontologyUniversity of Pécs Medical School, Szigeti Street 12, H-7624 Pécs, HungaryMTA-PTE NAP B Chronic Pain Research GroupHungary, Szigeti Street 12, H-7624 Pécs, HungaryInstitute of Animal ScienceCentre for Agricultural and Applied Economic Sciences, University of Debrecen, PO Box 36, H-4015 Debrecen, Hungary Department of Pharmacology and PharmacotherapyUniversity of Pécs Medical School, Szigeti Street 12, H-7624 Pécs, HungaryJanos Szentagothai Research CentreUniversity of Pécs, Ifjúság Street 20, H-7624 Pécs, HungaryDepartments of PathologyUniversity of Pécs Medical School, Szigeti Street 12, H-7624 Pécs, HungaryDepartment of PhysiologyUniversity of Pécs Medical School, Szigeti Street 12, H-7624 Pécs, HungaryDepartment of Pathophysiology and GerontologyUniversity of Pécs Medical School, Szigeti Street 12, H-7624 Pécs, HungaryMTA-PTE NAP B Chronic Pain Research GroupHungary, Szigeti Street 12, H-7624 Pécs, HungaryInstitute of Animal ScienceCentre for Agricultural and Applied Economic Sciences, University of Debrecen, PO Box 36, H-4015 Debrecen, Hungary Department of Pharmacology and PharmacotherapyUniversity of Pécs Medical School, Szigeti Street 12, H-7624 Pécs, HungaryJanos Szentagothai Research CentreUniversity of Pécs, Ifjúság Street 20, H-7624 Pécs, HungaryDepartments of PathologyUniversity of Pécs Medical School, Szigeti Street 12, H-7624 Pécs, HungaryDepartment of PhysiologyUniversity of Pécs Medical School, Szigeti Street 12, H-7624 Pécs, HungaryDepartment of Pathophysiology and Ger
| | - Éva Sághy
- Department of Pharmacology and PharmacotherapyUniversity of Pécs Medical School, Szigeti Street 12, H-7624 Pécs, HungaryJanos Szentagothai Research CentreUniversity of Pécs, Ifjúság Street 20, H-7624 Pécs, HungaryDepartments of PathologyUniversity of Pécs Medical School, Szigeti Street 12, H-7624 Pécs, HungaryDepartment of PhysiologyUniversity of Pécs Medical School, Szigeti Street 12, H-7624 Pécs, HungaryDepartment of Pathophysiology and GerontologyUniversity of Pécs Medical School, Szigeti Street 12, H-7624 Pécs, HungaryMTA-PTE NAP B Chronic Pain Research GroupHungary, Szigeti Street 12, H-7624 Pécs, HungaryInstitute of Animal ScienceCentre for Agricultural and Applied Economic Sciences, University of Debrecen, PO Box 36, H-4015 Debrecen, Hungary Department of Pharmacology and PharmacotherapyUniversity of Pécs Medical School, Szigeti Street 12, H-7624 Pécs, HungaryJanos Szentagothai Research CentreUniversity of Pécs, Ifjúság Street 20, H-7624 Pécs, HungaryDepartments of PathologyUniversity of Pécs Medical School, Szigeti Street 12, H-7624 Pécs, HungaryDepartment of PhysiologyUniversity of Pécs Medical School, Szigeti Street 12, H-7624 Pécs, HungaryDepartment of Pathophysiology and GerontologyUniversity of Pécs Medical School, Szigeti Street 12, H-7624 Pécs, HungaryMTA-PTE NAP B Chronic Pain Research GroupHungary, Szigeti Street 12, H-7624 Pécs, HungaryInstitute of Animal ScienceCentre for Agricultural and Applied Economic Sciences, University of Debrecen, PO Box 36, H-4015 Debrecen, Hungary
| | - Maja Payrits
- Department of Pharmacology and PharmacotherapyUniversity of Pécs Medical School, Szigeti Street 12, H-7624 Pécs, HungaryJanos Szentagothai Research CentreUniversity of Pécs, Ifjúság Street 20, H-7624 Pécs, HungaryDepartments of PathologyUniversity of Pécs Medical School, Szigeti Street 12, H-7624 Pécs, HungaryDepartment of PhysiologyUniversity of Pécs Medical School, Szigeti Street 12, H-7624 Pécs, HungaryDepartment of Pathophysiology and GerontologyUniversity of Pécs Medical School, Szigeti Street 12, H-7624 Pécs, HungaryMTA-PTE NAP B Chronic Pain Research GroupHungary, Szigeti Street 12, H-7624 Pécs, HungaryInstitute of Animal ScienceCentre for Agricultural and Applied Economic Sciences, University of Debrecen, PO Box 36, H-4015 Debrecen, Hungary Department of Pharmacology and PharmacotherapyUniversity of Pécs Medical School, Szigeti Street 12, H-7624 Pécs, HungaryJanos Szentagothai Research CentreUniversity of Pécs, Ifjúság Street 20, H-7624 Pécs, HungaryDepartments of PathologyUniversity of Pécs Medical School, Szigeti Street 12, H-7624 Pécs, HungaryDepartment of PhysiologyUniversity of Pécs Medical School, Szigeti Street 12, H-7624 Pécs, HungaryDepartment of Pathophysiology and GerontologyUniversity of Pécs Medical School, Szigeti Street 12, H-7624 Pécs, HungaryMTA-PTE NAP B Chronic Pain Research GroupHungary, Szigeti Street 12, H-7624 Pécs, HungaryInstitute of Animal ScienceCentre for Agricultural and Applied Economic Sciences, University of Debrecen, PO Box 36, H-4015 Debrecen, Hungary
| | - Béla Kajtár
- Department of Pharmacology and PharmacotherapyUniversity of Pécs Medical School, Szigeti Street 12, H-7624 Pécs, HungaryJanos Szentagothai Research CentreUniversity of Pécs, Ifjúság Street 20, H-7624 Pécs, HungaryDepartments of PathologyUniversity of Pécs Medical School, Szigeti Street 12, H-7624 Pécs, HungaryDepartment of PhysiologyUniversity of Pécs Medical School, Szigeti Street 12, H-7624 Pécs, HungaryDepartment of Pathophysiology and GerontologyUniversity of Pécs Medical School, Szigeti Street 12, H-7624 Pécs, HungaryMTA-PTE NAP B Chronic Pain Research GroupHungary, Szigeti Street 12, H-7624 Pécs, HungaryInstitute of Animal ScienceCentre for Agricultural and Applied Economic Sciences, University of Debrecen, PO Box 36, H-4015 Debrecen, Hungary
| | - Krisztina Kovács
- Department of Pharmacology and PharmacotherapyUniversity of Pécs Medical School, Szigeti Street 12, H-7624 Pécs, HungaryJanos Szentagothai Research CentreUniversity of Pécs, Ifjúság Street 20, H-7624 Pécs, HungaryDepartments of PathologyUniversity of Pécs Medical School, Szigeti Street 12, H-7624 Pécs, HungaryDepartment of PhysiologyUniversity of Pécs Medical School, Szigeti Street 12, H-7624 Pécs, HungaryDepartment of Pathophysiology and GerontologyUniversity of Pécs Medical School, Szigeti Street 12, H-7624 Pécs, HungaryMTA-PTE NAP B Chronic Pain Research GroupHungary, Szigeti Street 12, H-7624 Pécs, HungaryInstitute of Animal ScienceCentre for Agricultural and Applied Economic Sciences, University of Debrecen, PO Box 36, H-4015 Debrecen, Hungary
| | - József László Környei
- Department of Pharmacology and PharmacotherapyUniversity of Pécs Medical School, Szigeti Street 12, H-7624 Pécs, HungaryJanos Szentagothai Research CentreUniversity of Pécs, Ifjúság Street 20, H-7624 Pécs, HungaryDepartments of PathologyUniversity of Pécs Medical School, Szigeti Street 12, H-7624 Pécs, HungaryDepartment of PhysiologyUniversity of Pécs Medical School, Szigeti Street 12, H-7624 Pécs, HungaryDepartment of Pathophysiology and GerontologyUniversity of Pécs Medical School, Szigeti Street 12, H-7624 Pécs, HungaryMTA-PTE NAP B Chronic Pain Research GroupHungary, Szigeti Street 12, H-7624 Pécs, HungaryInstitute of Animal ScienceCentre for Agricultural and Applied Economic Sciences, University of Debrecen, PO Box 36, H-4015 Debrecen, Hungary
| | - János Garai
- Department of Pharmacology and PharmacotherapyUniversity of Pécs Medical School, Szigeti Street 12, H-7624 Pécs, HungaryJanos Szentagothai Research CentreUniversity of Pécs, Ifjúság Street 20, H-7624 Pécs, HungaryDepartments of PathologyUniversity of Pécs Medical School, Szigeti Street 12, H-7624 Pécs, HungaryDepartment of PhysiologyUniversity of Pécs Medical School, Szigeti Street 12, H-7624 Pécs, HungaryDepartment of Pathophysiology and GerontologyUniversity of Pécs Medical School, Szigeti Street 12, H-7624 Pécs, HungaryMTA-PTE NAP B Chronic Pain Research GroupHungary, Szigeti Street 12, H-7624 Pécs, HungaryInstitute of Animal ScienceCentre for Agricultural and Applied Economic Sciences, University of Debrecen, PO Box 36, H-4015 Debrecen, Hungary
| | - András Garami
- Department of Pharmacology and PharmacotherapyUniversity of Pécs Medical School, Szigeti Street 12, H-7624 Pécs, HungaryJanos Szentagothai Research CentreUniversity of Pécs, Ifjúság Street 20, H-7624 Pécs, HungaryDepartments of PathologyUniversity of Pécs Medical School, Szigeti Street 12, H-7624 Pécs, HungaryDepartment of PhysiologyUniversity of Pécs Medical School, Szigeti Street 12, H-7624 Pécs, HungaryDepartment of Pathophysiology and GerontologyUniversity of Pécs Medical School, Szigeti Street 12, H-7624 Pécs, HungaryMTA-PTE NAP B Chronic Pain Research GroupHungary, Szigeti Street 12, H-7624 Pécs, HungaryInstitute of Animal ScienceCentre for Agricultural and Applied Economic Sciences, University of Debrecen, PO Box 36, H-4015 Debrecen, Hungary
| | - Anikó Perkecz
- Department of Pharmacology and PharmacotherapyUniversity of Pécs Medical School, Szigeti Street 12, H-7624 Pécs, HungaryJanos Szentagothai Research CentreUniversity of Pécs, Ifjúság Street 20, H-7624 Pécs, HungaryDepartments of PathologyUniversity of Pécs Medical School, Szigeti Street 12, H-7624 Pécs, HungaryDepartment of PhysiologyUniversity of Pécs Medical School, Szigeti Street 12, H-7624 Pécs, HungaryDepartment of Pathophysiology and GerontologyUniversity of Pécs Medical School, Szigeti Street 12, H-7624 Pécs, HungaryMTA-PTE NAP B Chronic Pain Research GroupHungary, Szigeti Street 12, H-7624 Pécs, HungaryInstitute of Animal ScienceCentre for Agricultural and Applied Economic Sciences, University of Debrecen, PO Box 36, H-4015 Debrecen, Hungary
| | - Levente Czeglédi
- Department of Pharmacology and PharmacotherapyUniversity of Pécs Medical School, Szigeti Street 12, H-7624 Pécs, HungaryJanos Szentagothai Research CentreUniversity of Pécs, Ifjúság Street 20, H-7624 Pécs, HungaryDepartments of PathologyUniversity of Pécs Medical School, Szigeti Street 12, H-7624 Pécs, HungaryDepartment of PhysiologyUniversity of Pécs Medical School, Szigeti Street 12, H-7624 Pécs, HungaryDepartment of Pathophysiology and GerontologyUniversity of Pécs Medical School, Szigeti Street 12, H-7624 Pécs, HungaryMTA-PTE NAP B Chronic Pain Research GroupHungary, Szigeti Street 12, H-7624 Pécs, HungaryInstitute of Animal ScienceCentre for Agricultural and Applied Economic Sciences, University of Debrecen, PO Box 36, H-4015 Debrecen, Hungary
| | - Zsuzsanna Helyes
- Department of Pharmacology and PharmacotherapyUniversity of Pécs Medical School, Szigeti Street 12, H-7624 Pécs, HungaryJanos Szentagothai Research CentreUniversity of Pécs, Ifjúság Street 20, H-7624 Pécs, HungaryDepartments of PathologyUniversity of Pécs Medical School, Szigeti Street 12, H-7624 Pécs, HungaryDepartment of PhysiologyUniversity of Pécs Medical School, Szigeti Street 12, H-7624 Pécs, HungaryDepartment of Pathophysiology and GerontologyUniversity of Pécs Medical School, Szigeti Street 12, H-7624 Pécs, HungaryMTA-PTE NAP B Chronic Pain Research GroupHungary, Szigeti Street 12, H-7624 Pécs, HungaryInstitute of Animal ScienceCentre for Agricultural and Applied Economic Sciences, University of Debrecen, PO Box 36, H-4015 Debrecen, Hungary Department of Pharmacology and PharmacotherapyUniversity of Pécs Medical School, Szigeti Street 12, H-7624 Pécs, HungaryJanos Szentagothai Research CentreUniversity of Pécs, Ifjúság Street 20, H-7624 Pécs, HungaryDepartments of PathologyUniversity of Pécs Medical School, Szigeti Street 12, H-7624 Pécs, HungaryDepartment of PhysiologyUniversity of Pécs Medical School, Szigeti Street 12, H-7624 Pécs, HungaryDepartment of Pathophysiology and GerontologyUniversity of Pécs Medical School, Szigeti Street 12, H-7624 Pécs, HungaryMTA-PTE NAP B Chronic Pain Research GroupHungary, Szigeti Street 12, H-7624 Pécs, HungaryInstitute of Animal ScienceCentre for Agricultural and Applied Economic Sciences, University of Debrecen, PO Box 36, H-4015 Debrecen, Hungary Department of Pharmacology and PharmacotherapyUniversity of Pécs Medical School, Szigeti Street 12, H-7624 Pécs, HungaryJanos Szentagothai Research CentreUniversity of Pécs, Ifjúság Street 20, H-7624 Pécs, HungaryDepartments of PathologyUniversity of Pécs Medical School, Szigeti Street 12, H-7624 Pécs, HungaryDepartment of PhysiologyUniversity of Pécs Medical School, Szigeti Street 12, H-7624 Pécs, HungaryDepartment of Pathophysiology and Ger
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15
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Chapman JR, Waldenström J. With Reference to Reference Genes: A Systematic Review of Endogenous Controls in Gene Expression Studies. PLoS One 2015; 10:e0141853. [PMID: 26555275 PMCID: PMC4640531 DOI: 10.1371/journal.pone.0141853] [Citation(s) in RCA: 203] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 10/13/2015] [Indexed: 12/20/2022] Open
Abstract
The choice of reference genes that are stably expressed amongst treatment groups is a crucial step in real-time quantitative PCR gene expression studies. Recent guidelines have specified that a minimum of two validated reference genes should be used for normalisation. However, a quantitative review of the literature showed that the average number of reference genes used across all studies was 1.2. Thus, the vast majority of studies continue to use a single gene, with β-actin (ACTB) and/or glyceraldehyde 3-phosphate dehydrogenase (GAPDH) being commonly selected in studies of vertebrate gene expression. Few studies (15%) tested a panel of potential reference genes for stability of expression before using them to normalise data. Amongst studies specifically testing reference gene stability, few found ACTB or GAPDH to be optimal, whereby these genes were significantly less likely to be chosen when larger panels of potential reference genes were screened. Fewer reference genes were tested for stability in non-model organisms, presumably owing to a dearth of available primers in less well characterised species. Furthermore, the experimental conditions under which real-time quantitative PCR analyses were conducted had a large influence on the choice of reference genes, whereby different studies of rat brain tissue showed different reference genes to be the most stable. These results highlight the importance of validating the choice of normalising reference genes before conducting gene expression studies.
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Affiliation(s)
- Joanne R. Chapman
- Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, Kalmar, Sweden
- * E-mail:
| | - Jonas Waldenström
- Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, Kalmar, Sweden
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Mesnage R, Arno M, Costanzo M, Malatesta M, Séralini GE, Antoniou MN. Transcriptome profile analysis reflects rat liver and kidney damage following chronic ultra-low dose Roundup exposure. Environ Health 2015; 14:70. [PMID: 26302742 PMCID: PMC4549093 DOI: 10.1186/s12940-015-0056-1] [Citation(s) in RCA: 105] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Accepted: 08/11/2015] [Indexed: 05/17/2023]
Abstract
BACKGROUND Glyphosate-based herbicides (GBH) are the major pesticides used worldwide. Converging evidence suggests that GBH, such as Roundup, pose a particular health risk to liver and kidneys although low environmentally relevant doses have not been examined. To address this issue, a 2-year study in rats administering 0.1 ppb Roundup (50 ng/L glyphosate equivalent) via drinking water (giving a daily intake of 4 ng/kg bw/day of glyphosate) was conducted. A marked increased incidence of anatomorphological and blood/urine biochemical changes was indicative of liver and kidney structure and functional pathology. In order to confirm these findings we have conducted a transcriptome microarray analysis of the liver and kidneys from these same animals. RESULTS The expression of 4224 and 4447 transcript clusters (a group of probes corresponding to a known or putative gene) were found to be altered respectively in liver and kidney (p < 0.01, q < 0.08). Changes in gene expression varied from -3.5 to 3.7 fold in liver and from -4.3 to 5.3 in kidneys. Among the 1319 transcript clusters whose expression was altered in both tissues, ontological enrichment in 3 functional categories among 868 genes were found. First, genes involved in mRNA splicing and small nucleolar RNA were mostly upregulated, suggesting disruption of normal spliceosome activity. Electron microscopic analysis of hepatocytes confirmed nucleolar structural disruption. Second, genes controlling chromatin structure (especially histone-lysine N-methyltransferases) were mostly upregulated. Third, genes related to respiratory chain complex I and the tricarboxylic acid cycle were mostly downregulated. Pathway analysis suggests a modulation of the mTOR and phosphatidylinositol signalling pathways. Gene disturbances associated with the chronic administration of ultra-low dose Roundup reflect a liver and kidney lipotoxic condition and increased cellular growth that may be linked with regeneration in response to toxic effects causing damage to tissues. Observed alterations in gene expression were consistent with fibrosis, necrosis, phospholipidosis, mitochondrial membrane dysfunction and ischemia, which correlate with and thus confirm observations of pathology made at an anatomical, histological and biochemical level. CONCLUSION Our results suggest that chronic exposure to a GBH in an established laboratory animal toxicity model system at an ultra-low, environmental dose can result in liver and kidney damage with potential significant health implications for animal and human populations.
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Affiliation(s)
- Robin Mesnage
- Gene Expression and Therapy Group, Faculty of Life Sciences & Medicine, Department of Medical and Molecular Genetics, King's College London, 8th Floor Tower Wing, Guy's Hospital, Great Maze Pond, London, SE1 9RT, UK
| | - Matthew Arno
- Genomics Centre, King's College London, Waterloo Campus, 150 Stamford Street, London, SE1 9NH, UK
| | - Manuela Costanzo
- Department of Neurological and Movement Sciences, University of Verona, Verona, 37134, Italy
| | - Manuela Malatesta
- Department of Neurological and Movement Sciences, University of Verona, Verona, 37134, Italy
| | - Gilles-Eric Séralini
- Institute of Biology, EA 2608 and Risk Pole, MRSH-CNRS, Esplanade de la Paix, University of Caen, Caen, 14032, Cedex, France
| | - Michael N Antoniou
- Gene Expression and Therapy Group, Faculty of Life Sciences & Medicine, Department of Medical and Molecular Genetics, King's College London, 8th Floor Tower Wing, Guy's Hospital, Great Maze Pond, London, SE1 9RT, UK.
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Svingen T, Letting H, Hadrup N, Hass U, Vinggaard AM. Selection of reference genes for quantitative RT-PCR (RT-qPCR) analysis of rat tissues under physiological and toxicological conditions. PeerJ 2015; 3:e855. [PMID: 25825680 PMCID: PMC4375968 DOI: 10.7717/peerj.855] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Accepted: 03/05/2015] [Indexed: 11/20/2022] Open
Abstract
In biological research the analysis of gene expression levels in cells and tissues can be a powerful tool to gain insights into biological processes. For this, quantitative RT-PCR (RT-qPCR) is a popular method that often involve the use of constitutively expressed endogenous reference (or ‘housekeeping’) gene for normalization of data. Thus, it is essential to use reference genes that have been verified to be stably expressed within the specific experimental setting. Here, we have analysed the expression stability of 12 commonly used reference genes (Actb, B2m, Gapdh, Hprt, Pgk1, Rn18s, Rpl13a, Rps18, Rps29, Sdha, Tbp and Ubc) across several juvenile and adult rat tissues (liver, adrenal, prostate, fat pad, testis and ovaries), both under normal conditions and following exposure to various chemicals during development. Employing NormFinder and BestKeeper softwares, we found Hprt and Sdha to be amongst the most stable genes across normal and manipulated tissues, with several others also being suitable for most tissues. Tbp and B2m displayed highest variability in transcript levels between tissues and developmental stages. It was also observed that the reference genes were most unstable in liver and testis following toxicological exposure. For future studies, we propose the use of more than one verified reference gene and the continuous monitoring of their suitability under various experimental conditions, including toxicological studies, based on changes in threshold (Ct) values from cDNA samples having been reverse-transcribed from a constant input concentration of RNA.
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Affiliation(s)
- Terje Svingen
- Division of Toxicology and Risk Assessment, National Food Institute, Technical University of Denmark , Søborg , Denmark
| | - Heidi Letting
- Division of Toxicology and Risk Assessment, National Food Institute, Technical University of Denmark , Søborg , Denmark
| | - Niels Hadrup
- Division of Toxicology and Risk Assessment, National Food Institute, Technical University of Denmark , Søborg , Denmark
| | - Ulla Hass
- Division of Toxicology and Risk Assessment, National Food Institute, Technical University of Denmark , Søborg , Denmark
| | - Anne Marie Vinggaard
- Division of Toxicology and Risk Assessment, National Food Institute, Technical University of Denmark , Søborg , Denmark
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Das RK, Banerjee S, Shapiro BH. Irreversible perinatal imprinting of adult expression of the principal sex-dependent drug-metabolizing enzyme CYP2C11. FASEB J 2014; 28:4111-22. [PMID: 24942648 DOI: 10.1096/fj.13-248864] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Accepted: 06/02/2014] [Indexed: 01/17/2023]
Abstract
We proposed to determine whether, like other sexual dimorphisms, drug metabolism is permanently imprinted by perinatal hormones, resulting in its irreversible sex-dependent expression. We treated newborn male rats with monosodium glutamate (MSG), a total growth hormone (GH) blocker, and, using cultured hepatocytes, examined expression of adult CYP2C11, the predominant cytochrome-P450 expressed only in males, as well as the signal transduction pathway by which episodic GH solely regulates the isoform's expression. In addition, adolescent hypophysectomized (hypox) male rats served as controls in which GH was eliminated after the critical imprinting period. Whereas renaturalization of the masculine episodic GH profile restored normal male-like levels of CYP2C11, as well as CYP2C12, in hepatocytes from hypox rats, the cells derived from the MSG-treated rats were completely unresponsive. Moreover, GH exposure of hepatocytes from hypox rats resulted in normal induction, activation, nuclear translocation, and binding to the CYP2C11 promoter of the signal transducers mediating GH regulation of CYP2C11 expression, which dramatically contrasted with the complete unresponsiveness of the MSG-derived hepatocytes, also associated with hypermethylation of GH-response elements in the CYP2C11 promoter. Lastly, neonatal MSG treatment had no adverse effect on postnatal and adult testosterone levels. The results demonstrate that the sexually dimorphic expression of CYP2C11 is irreversibly imprinted shortly after birth by a hormone other than the customary testosterone, but likely by GH.
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Affiliation(s)
- Rajat Kumar Das
- Laboratories of Biochemistry, University of Pennsylvania, School of Veterinary Medicine, Philadelphia, Pennsylvania, USA
| | - Sarmistha Banerjee
- Laboratories of Biochemistry, University of Pennsylvania, School of Veterinary Medicine, Philadelphia, Pennsylvania, USA
| | - Bernard H Shapiro
- Laboratories of Biochemistry, University of Pennsylvania, School of Veterinary Medicine, Philadelphia, Pennsylvania, USA
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