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Jahanbani I, Almoualem N, Al-Abdallah A. Evaluation of reference genes suitable for studying mRNAs and microRNAs expression in thyroid neoplasms. Pathol Res Pract 2024; 262:155519. [PMID: 39173468 DOI: 10.1016/j.prp.2024.155519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 07/31/2024] [Accepted: 08/09/2024] [Indexed: 08/24/2024]
Abstract
Analysis of gene expression is a pivotal method at the core of biomarkers studies and cancer research. Currently, RT-qPCR is the most commonly used technique to investigate the expression of certain genes. The accurate and reliable result relies on an effective normalization step using suitable reference genes. The present study was designed to evaluate the eligibility of a set of candidate mRNAs and snoRNA as reference genes in the most common human thyroid neoplasms. We tested the expression levels of eleven mRNA and small RNA housekeeping genes in thyroid samples. The stability of the candidate genes was examined in different thyroid lesions and under different experimental conditions. Results were compared to the reported data in the TCGA database. Our results suggested HPRT1 and ACTB as the best mRNA reference genes, SNORD96A, and SNORD95 as the best miRNA reference genes in thyroid tissues. These genes showed the most stable expression pattern among different thyroid lesions as well as different experimental conditions. The findings in this study highlight the effect of reference genes selection on data interpretation and emphasize the importance of testing for suitable reference genes to be used in specific types of cells and experimental conditions to ensure the validity and accuracy of results.
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Affiliation(s)
- Iman Jahanbani
- Pathology Department, Faculty of Medicine, Kuwait University, Kuwait.
| | - Nada Almoualem
- Pathology Department, Faculty of Medicine, Kuwait University, Kuwait.
| | - Abeer Al-Abdallah
- Pathology Department, Faculty of Medicine, Kuwait University, Kuwait.
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2
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Toren Y, Ziv Y, Sragovich S, McKinney RA, Barak S, Shazman S, Gozes I. Sex-Specific ADNP/NAP (Davunetide) Regulation of Cocaine-Induced Plasticity. J Mol Neurosci 2024; 74:76. [PMID: 39251453 DOI: 10.1007/s12031-024-02234-2] [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: 05/25/2024] [Accepted: 05/29/2024] [Indexed: 09/11/2024]
Abstract
Cocaine use disorder (CUD) is a chronic neuropsychiatric disorder estimated to effect 1-3% of the population. Activity-dependent neuroprotective protein (ADNP) is essential for brain development and functioning, shown to be protective in fetal alcohol syndrome and to regulate alcohol consumption in adult mice. The goal of this study was to characterize the role of ADNP, and its active peptide NAP (NAPVSIPQ), which is also known as davunetide (investigational drug) in mediating cocaine-induced neuroadaptations. Real time PCR was used to test levels of Adnp and Adnp2 in the nucleus accumbens (NAc), ventral tegmental area (VTA), and dorsal hippocampus (DH) of cocaine-treated mice (15 mg/kg). Adnp heterozygous (Adnp +/-)and wild-type (Adnp +/-) mice were further tagged with excitatory neuronal membrane-expressing green fluorescent protein (GFP) that allowed for in vivo synaptic quantification. The mice were treated with cocaine (5 injections; 15 mg/kg once every other day) with or without NAP daily injections (0.4 µg/0.1 ml) and sacrificed following the last treatment. We analyzed hippocampal CA1 pyramidal cells from 3D confocal images using the Imaris x64.8.1.2 (Oxford Instruments) software to measure changes in dendritic spine density and morphology. In silico ADNP/NAP/cocaine structural modeling was performed as before. Cocaine decreased Adnp and Adnp2 expression 2 h after injection in the NAc and VTA of male mice, with mRNA levels returning to baseline levels after 24 h. Cocaine further reduced hippocampal spine density, particularly synaptically weaker immature thin and stubby spines, in male Adnp+/+) mice while increasing synaptically stronger mature (mushroom) spines in Adnp+/-) male mice and thin and stubby spines in females. Lastly, we showed that cocaine interacts with ADNP on a zinc finger domain identical to ketamine and adjacent to a NAP-zinc finger interaction site. Our results implicate ADNP in cocaine abuse, further placing the ADNP gene as a key regulator in neuropsychiatric disorders. Ketamine/cocaine and NAP treatment may be interchangeable to some degree, implicating an interaction with adjacent zinc finger motifs on ADNP and suggestive of a potential sex-dependent, non-addictive NAP treatment for CUD.
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Affiliation(s)
- Yael Toren
- The Elton Laboratory for Molecular Neuroendocrinology, Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Sagol School of Neuroscience and Adams Super Center for Brain Studies, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Yarden Ziv
- The Elton Laboratory for Molecular Neuroendocrinology, Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Sagol School of Neuroscience and Adams Super Center for Brain Studies, Tel Aviv University, Tel Aviv, 6997801, Israel
- School of Psychological Sciences, Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Shlomo Sragovich
- The Elton Laboratory for Molecular Neuroendocrinology, Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Sagol School of Neuroscience and Adams Super Center for Brain Studies, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - R Anne McKinney
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Canada
| | - Segev Barak
- School of Psychological Sciences, Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Shula Shazman
- Department of Mathematics and Computer Science, The Open University of Israel, Ra'anana, Israel
| | - Illana Gozes
- The Elton Laboratory for Molecular Neuroendocrinology, Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Sagol School of Neuroscience and Adams Super Center for Brain Studies, Tel Aviv University, Tel Aviv, 6997801, Israel.
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3
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de Sousa PRC, da Silva ASM, de Ponte CGG, Nogueira LL, Frota CC, Antas PRZ. Commentary: Identification of optimal reference genes for gene expression normalization in human osteosarcoma cell lines under proliferative conditions. Front Genet 2024; 15:1342447. [PMID: 38333617 PMCID: PMC10850317 DOI: 10.3389/fgene.2024.1342447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 01/02/2024] [Indexed: 02/10/2024] Open
Affiliation(s)
- Paulo R. C. de Sousa
- Programa de Pós-Graduação em Patologia, Universidade Federal do Ceará, Fortaleza, Brazil
| | | | | | - Lucas L. Nogueira
- Programa de Pós-Graduação em Patologia, Universidade Federal do Ceará, Fortaleza, Brazil
| | - Cristiane C. Frota
- Programa de Pós-Graduação em Patologia, Universidade Federal do Ceará, Fortaleza, Brazil
| | - Paulo R. Z. Antas
- Programa de Pós-Graduação em Patologia, Universidade Federal do Ceará, Fortaleza, Brazil
- Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
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4
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Enhanced Nerve Regeneration by Exosomes Secreted by Adipose-Derived Stem Cells with or without FK506 Stimulation. Int J Mol Sci 2021; 22:ijms22168545. [PMID: 34445251 PMCID: PMC8395161 DOI: 10.3390/ijms22168545] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 07/25/2021] [Accepted: 08/05/2021] [Indexed: 12/13/2022] Open
Abstract
Exosomes secreted by adipose-derived stem cells (ADSC-exo) reportedly improve nerve regeneration after peripheral nerve injury. Herein, we investigated whether pretreatment of ADSCs with FK506, an immunosuppressive drug that enhances nerve regeneration, could secret exosomes (ADSC-F-exo) that further augment nerve regeneration. Designed exosomes were topically applied to injured nerve in a mouse model of sciatic nerve crush injury to assess the nerve regeneration efficacy. Outcomes were determined by histomorphometric analysis of semi-thin nerve sections stained with toluidine blue, mouse neurogenesis PCR array, and neurotrophin expression in distal nerve segments. Isobaric tags for relative and absolute quantitation (iTRAQ) were used to profile potential exosomal proteins facilitating nerve regeneration. We observed that locally applied ADSC-exo and ADSC-F-exo significantly enhanced nerve regeneration after nerve crush injury. Pretreatment of ADSCs with FK506 failed to produce exosomes possessing more potent molecules for enhanced nerve regeneration. Proteomic analysis revealed that of 192 exosomal proteins detected in both ADSC-exo and ADSC-F-exo, histone deacetylases (HDACs), amyloid-beta A4 protein (APP), and integrin beta-1 (ITGB1) might be involved in enhancing nerve regeneration.
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Hiller H, Beachy DE, Lebowitz JJ, Engler S, Mason JR, Miller DR, Kusmarteva I, Jacobsen LM, Posgai AL, Khoshbouei H, Oram RA, Schatz DA, Hattersley AT, Bodenmiller B, Atkinson MA, Nick HS, Wasserfall CH. Monogenic Diabetes and Integrated Stress Response Genes Display Altered Gene Expression in Type 1 Diabetes. Diabetes 2021; 70:1885-1897. [PMID: 34035041 PMCID: PMC8385619 DOI: 10.2337/db21-0070] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 05/16/2021] [Indexed: 11/13/2022]
Abstract
Type 1 diabetes (T1D) has a multifactorial autoimmune etiology, involving environmental prompts and polygenic predisposition. We hypothesized that pancreata from individuals with and at risk for T1D would exhibit dysregulated expression of genes associated with monogenic forms of diabetes caused by nonredundant single-gene mutations. Using a "monogenetic transcriptomic strategy," we measured the expression of these genes in human T1D, autoantibody-positive (autoantibody+), and control pancreas tissues with real-time quantitative PCR in accordance with the Minimum Information for Publication of Quantitative Real-Time PCR Experiments (MIQE) guidelines. Gene and protein expression was visualized in situ with use of immunofluorescence, RNAscope, and confocal microscopy. Two dozen monogenic diabetes genes showed altered expression in human pancreata from individuals with T1D versus unaffected control subjects. Six of these genes also saw dysregulation in pancreata from autoantibody+ individuals at increased risk for T1D. As a subset of these genes are related to cellular stress responses, we measured integrated stress response (ISR) genes and identified 20 with altered expression in T1D pancreata, including three of the four eIF2α-dependent kinases. Equally intriguing, we observed significant repression of the three arms of the ISR in autoantibody+ pancreata. Collectively, these efforts suggest monogenic diabetes and ISR genes are dysregulated early in the T1D disease process and likely contribute to the disorder's pathogenesis.
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Affiliation(s)
- Helmut Hiller
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL
| | - Dawn E Beachy
- Department of Neuroscience, University of Florida, Gainesville, FL
| | | | - Stefanie Engler
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland
| | - Justin R Mason
- Department of Occupational Therapy, University of Florida, Gainesville, FL
| | - Douglas R Miller
- Department of Neuroscience, University of Florida, Gainesville, FL
| | - Irina Kusmarteva
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL
| | - Laura M Jacobsen
- Department of Pediatrics, University of Florida, Gainesville, FL
| | - Amanda L Posgai
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL
| | | | - Richard A Oram
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, U.K
| | - Desmond A Schatz
- Department of Pediatrics, University of Florida, Gainesville, FL
| | - Andrew T Hattersley
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, U.K
| | | | - Mark A Atkinson
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL
| | - Harry S Nick
- Department of Neuroscience, University of Florida, Gainesville, FL
- Department of Pediatrics, University of Florida, Gainesville, FL
| | - Clive H Wasserfall
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL
- Department of Pediatrics, University of Florida, Gainesville, FL
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Ren LY, Zhao H, Liu XL, Zong TK, Qiao M, Liu SY, Liu XY. Transcriptome Reveals Roles of Lignin-Modifying Enzymes and Abscisic Acid in the Symbiosis of Mycena and Gastrodia elata. Int J Mol Sci 2021; 22:6557. [PMID: 34207287 PMCID: PMC8235111 DOI: 10.3390/ijms22126557] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/16/2021] [Accepted: 06/16/2021] [Indexed: 01/17/2023] Open
Abstract
Gastrodia elata is a well-known medicinal and heterotrophic orchid. Its germination, limited by the impermeability of seed coat lignin and inhibition by abscisic acid (ABA), is triggered by symbiosis with fungi such as Mycena spp. However, the molecular mechanisms of lignin degradation by Mycena and ABA biosynthesis and signaling in G. elata remain unclear. In order to gain insights into these two processes, this study analyzed the transcriptomes of these organisms during their dynamic symbiosis. Among the 25 lignin-modifying enzyme genes in Mycena, two ligninolytic class II peroxidases and two laccases were significantly upregulated, most likely enabling Mycena hyphae to break through the lignin seed coats of G. elata. Genes related to reduced virulence and loss of pathogenicity in Mycena accounted for more than half of annotated genes, presumably contributing to symbiosis. After coculture, upregulated genes outnumbered downregulated genes in G. elata seeds, suggesting slightly increased biological activity, while Mycena hyphae had fewer upregulated than downregulated genes, indicating decreased biological activity. ABA biosynthesis in G. elata was reduced by the downregulated expression of 9-cis-epoxycarotenoid dioxygenase (NCED-2), and ABA signaling was blocked by the downregulated expression of a receptor protein (PYL12-like). This is the first report to describe the role of NCED-2 and PYL12-like in breaking G. elata seed dormancy by reducing the synthesis and blocking the signaling of the germination inhibitor ABA. This study provides a theoretical basis for screening germination fungi to identify effective symbionts and for reducing ABA inhibition of G. elata seed germination.
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Affiliation(s)
- Li-Ying Ren
- College of Plant Protection, Jilin Agricultural University, Changchun 130118, China;
- Engineering Research Center of Edible and Medicinal Fungi, Ministry of Education, Jilin Agricultural University, Changchun 130118, China
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (H.Z.); (X.-L.L.)
| | - Heng Zhao
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (H.Z.); (X.-L.L.)
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiao-Ling Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (H.Z.); (X.-L.L.)
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tong-Kai Zong
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming 650224, China;
| | - Min Qiao
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650091, China
| | - Shu-Yan Liu
- College of Plant Protection, Jilin Agricultural University, Changchun 130118, China;
- Engineering Research Center of Edible and Medicinal Fungi, Ministry of Education, Jilin Agricultural University, Changchun 130118, China
| | - Xiao-Yong Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (H.Z.); (X.-L.L.)
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Identification and validation of new reference genes for accurate quantitative reverse transcriptase-PCR normalization in the Antarctic plant Colobanthus quitensis under abiotic stress conditions. Polar Biol 2021. [DOI: 10.1007/s00300-021-02801-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
AbstractThe Antarctic ecotype of Colobanthus quitensis is a vascular plant highly adapted to the harsh environmental conditions of Maritime Antarctica which is now facing with the rapid local warming experienced in the Antarctic Peninsula during the last decades. Thus, the identification of the molecular mechanisms leading to the adaptation to this warming trend is a new target for modern cell physiology. The selection of suitable reference genes for quantification of key stress-responsive genes through quantitative Reverse Transcriptase-Polymerase Chain Reaction (qRT-PCR) is important to ensure accurate and reliable results. In this study, we evaluated the expression stability of eleven candidate genes in C. quitensis under different abiotic stress conditions using geNorm and RefFinder tools. The statistical analysis showed that the appropriate reference genes varied depending on the experimental conditions, even if EF1α and PP2Acs ranked as the most stable reference genes when all stress conditions were considered. To further validate the stability of the selected reference genes, the expression patterns of C. quitensis catalase gene (CqCAT) was analyzed. The reference genes validated in this study will be useful for improving the accuracy of qRT-PCR analysis for gene expression studies of the Antarctic ecotype of C. quitensis and could be extended to other ecotypes adapted to low temperatures.
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8
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Su K, Huang X, Xu K, Du W, Zhu D, Yang M, Yuan W, Li L. Transcriptomics Curation of SARS-CoV-2 Related Host Genes in Mice With COVID-19 Comorbidity: A Pilot Study. INFECTIOUS MICROBES & DISEASES 2020; 2:42-47. [PMID: 38630104 PMCID: PMC8529699 DOI: 10.1097/im9.0000000000000025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 04/23/2020] [Accepted: 04/26/2020] [Indexed: 11/26/2022]
Abstract
The pandemic of coronavirus disease 2019 (COVID-19), a respiratory disease caused by a novel severe acute respiratory syndrome coronavirus-2, is causing substantial morbidity and mortality. Along with the respiratory symptoms, underlying diseases in senior patients, such as diabetes, hypertension, and coronary heart disease, are the most common comorbidities, which cause more severe outcomes and even death. During cellular attachment and entry of severe acute respiratory syndrome coronavirus-2, the key protein involved is the angiotensin I converting enzyme 2 (ACE2), which is located on the membrane of host cells. Here, we aim to curate an expression profile of Ace2 and other COVID-19 related genes across the available diabetes murine strains. Based on strictly manual curation and bioinformatics analysis of the publicly deposited expression datasets, Ace2 and other potentially involved genes such as Furin, Tmprss2, Ang, and Ang2 were examined. We found that Ace2 expression is rather ubiquitous in three selected diabetes prone strains (db/db, ob/ob and diet-induced obese). With the most abundant datasets present, the liver shows a medium Ace2 expression level compared with the lungs, pancreatic islets, brain and even T cells. Age is a more critical factor for Ace2 expression in db/db compared with the other two strains. Besides Ace2, the other four host genes showed varied levels of correlation to each other. To accelerate research on the interaction between COVID-19 and underlying diseases, the Murine4Covid transcriptomics database (www.geneureka.org/Murine4Covid) will facilitate the design of research on COVID-19 and comorbidities.
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Affiliation(s)
- Kunkai Su
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
- KS and XH contributed equally to this study
| | - Xin Huang
- Biotherapeutics Research Center, the Second Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
- KS and XH contributed equally to this study
| | - Kaijin Xu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Weibo Du
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Danhua Zhu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Meifang Yang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Wenji Yuan
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Lanjuan Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
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Liu Q, Xing Y, Li Y, Wang H, Mi T, Zhen Y, Yu Z. Carbon fixation gene expression in Skeletonema marinoi in nitrogen-, phosphate-, silicate-starvation, and low-temperature stress exposure. JOURNAL OF PHYCOLOGY 2020; 56:310-323. [PMID: 31628865 DOI: 10.1111/jpy.12936] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 10/10/2019] [Indexed: 06/10/2023]
Abstract
Diatoms are unicellular algae with a set of extraordinary genes, metabolic pathways, and physiological functions acquired by secondary endosymbiosis, especially for their efficient photosynthetic carbon fixation mechanisms, which can be a reason for their successful environmental adaptation and great contribution to primary production. Based on the available genomic information, the expression patterns of carbon fixation genes were analyzed using transcriptomic sequencing and reverse transcription-quantitative polymerase chain reaction (RT-qPCR) in Skeletonema marinoi. Meanwhile, suitable reference genes applying to specific experimental treatments were selected. In our results, carbon fixation genes were standardized by actin and TATA box-binding protein-coding genes in growth phase samples and stress conditions, respectively. It was found that a series of carbon fixation genes, such as the pyruvate orthophosphate dikinase (PPDK)-coding gene, had significantly up-regulated expression in nitrogen-starvation, phosphate-starvation, and low-temperature conditions, but consistently down-regulated in silicate-starvation treatment. These carbon fixation genes exhibited variable expression levels in different conditions and will be useful for investigating gene expression mechanisms in S. marinoi and improve our understanding of diatom carbon fixation pathways.
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Affiliation(s)
- Qian Liu
- Key laboratory of Marine Environment and Ecology, Ministry of Education, Qingdao, 266100, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
- College of Marine Life Science, Ocean University of China, Qingdao, 266003, China
| | - Yongze Xing
- Key laboratory of Marine Environment and Ecology, Ministry of Education, Qingdao, 266100, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
- College of Environmental Science and Engineering, Ocean University of China, Qingdao, 266100, China
- Guangxi Key Lab of Mangrove Conservation and Utilization, Guangxi Mangrove Research Center, Guangxi Sciences Academy, Beihai, 536000, China
| | - Ying Li
- Key laboratory of Marine Environment and Ecology, Ministry of Education, Qingdao, 266100, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
- College of Environmental Science and Engineering, Ocean University of China, Qingdao, 266100, China
| | - Hualong Wang
- Key laboratory of Marine Environment and Ecology, Ministry of Education, Qingdao, 266100, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
- College of Marine Life Science, Ocean University of China, Qingdao, 266003, China
| | - Tiezhu Mi
- Key laboratory of Marine Environment and Ecology, Ministry of Education, Qingdao, 266100, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
- College of Environmental Science and Engineering, Ocean University of China, Qingdao, 266100, China
| | - Yu Zhen
- Key laboratory of Marine Environment and Ecology, Ministry of Education, Qingdao, 266100, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
- College of Environmental Science and Engineering, Ocean University of China, Qingdao, 266100, China
| | - Zhigang Yu
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
- Key Laboratory of Marine Chemical Theory and Technology, Ministry of Education, Qingdao, 266100, China
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10
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Selection of reference genes suitable for normalization of RT-qPCR data in glioma stem cells. Biotechniques 2019; 68:130-137. [PMID: 31870167 DOI: 10.2144/btn-2019-0098] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Considering the importance of gene expression studies for understanding the biology of glioma stem cells (GSCs), we aimed to identify the reliable reference genes in GSCs that were derived from the glioma cell lines T98G, LN229, 090116 and 091214. Quantitative real-time reverse-transcription PCR was employed using 11 reference genes identified through a PubMed literature search, and the assessment of stability through the geNorm, Normfinder and coefficient of variation methods was performed to select suitable reference genes. We found that HPRT1 and RPL13A were the most suitable reference genes, and validated the geometric mean of these genes to normalize the expression of stemness genes by GSCs. Therefore, it is necessary to select novel cell-specific reference genes with greater expression stability for gene expression studies in GSCs.
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11
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Wang X, Wei L, Zhu J, He B, Kong B, Xue Z, Jin X, Fu Z. Environmentally relevant doses of tetrabromobisphenol A (TBBPA) cause immunotoxicity in murine macrophages. CHEMOSPHERE 2019; 236:124413. [PMID: 31545206 DOI: 10.1016/j.chemosphere.2019.124413] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 07/01/2019] [Accepted: 07/19/2019] [Indexed: 06/10/2023]
Abstract
TBBPA is one of the main brominated flame retardants and is ubiquitous in the environment. TBBPA can directly encounter immune cells via the bloodstream, posing potential immunotoxicity. To understand the immunomodulating effect of TBBPA on macrophages, the murine macrophages, RAW 264.7, were exposed to TBBPA at environmentally relevant concentrations (1-100 nM). The results showed that TBBPA at the selected concentrations did not alter cell viability of RAW 264.7 cells with or without LPS stimulation. TBBPA upregulated the expression of pro-inflammatory cytokines, including IL-1β, IL-6, and TNF-α, whereas it attenuated the LPS-stimulated expression of these pro-inflammatory cytokines, and the expression of anti-inflammatory cytokines, including IL-4, IL-10, and IL-13. In addition, TBBPA reduced the mRNA levels of antigen-presenting-related genes, including H2-K2, H2-Aa, Cd80, and Cd86. Moreover, TBBPA impaired the phagocytic activity of macrophages. Furthermore, exposure to TBBPA significantly elevated the protein levels of phosphorylated NF-κB p65 (p-p65), while it reduced LPS-stimulated p-p65 protein levels. DCFH-DA staining assays showed that TBBPA caused a slight but significant elevation in reactive oxygen species levels. The data obtained in the present study demonstrated that exposure to environmentally relevant concentrations of TBBPA posed immunotoxicity in macrophages and unveiled a potential health risk of TBBPA.
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Affiliation(s)
- Xia Wang
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Lai Wei
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Jianbo Zhu
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Bingnan He
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Baida Kong
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Zimeng Xue
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Xini Jin
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Zhengwei Fu
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, China.
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12
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Validation of Reference Genes for Normalization of Relative qRT-PCR Studies in Papillary Thyroid Carcinoma. Sci Rep 2019; 9:15241. [PMID: 31645594 PMCID: PMC6811563 DOI: 10.1038/s41598-019-49247-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 08/19/2019] [Indexed: 12/21/2022] Open
Abstract
Quantitative reverse transcription polymerase chain reaction (qRT-PCR) in thyroid tumors require accurate data normalization, however, there are no sufficient studies addressing the suitable reference genes for gene expression analysis in malignant and normal thyroid tissue specimens. The purpose of this study was to identify valid internal control genes for normalization of relative qRT-PCR studies in human papillary thyroid carcinoma tissue samples. The expression characteristics of 12 candidate reference genes (GAPDH, ACTB, HPRT1, TBP, B2M, PPIA, 18SrRNA, HMBS, GUSB, PGK1, RPLP0, and PGM1) were assessed by qRT-PCR in 45 thyroid tissue samples (15 papillary thyroid carcinoma, 15 paired normal tissues and 15 multinodular goiters). These twelve candidate reference genes were selected by a systematic literature search. GeNorm, NormFinder, and BestKeeper statistical algorithms were applied to determine the most stable reference genes. The three algorithms were in agreement in identifying GUSB and HPRT1 as the most stably expressed genes in all thyroid tumors investigated. According to the NormFinder software, the pair of genes including ‘GUSB and HPRT1’ or ‘GUSB and HMBS’ or ‘GUSB and PGM1’ were the best combinations for selection of pair reference genes. The optimal number of genes required for reliable normalization of qPCR data in thyroid tissues would be three according to calculations made by GeNorm algorithm. These results suggest that GUSB and HPRT1 are promising reference genes for normalization of relative qRT-PCR studies in papillary thyroid carcinoma.
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13
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Hernandez-Segura A, Rubingh R, Demaria M. Identification of stable senescence-associated reference genes. Aging Cell 2019; 18:e12911. [PMID: 30710410 PMCID: PMC6413663 DOI: 10.1111/acel.12911] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 12/10/2018] [Accepted: 12/23/2018] [Indexed: 01/10/2023] Open
Abstract
Cellular senescence is a state of permanent cell cycle arrest activated in response to damaging stimuli. Many hallmarks associated with senescent cells are measured by quantitative real-time PCR (qPCR). As the selection of stable reference genes for interpretation of qPCR data is often overlooked, we performed a systematic review to understand normalization strategies entailed in experiments involving senescent cells. We found that, in violation of the Minimum Information for publication of qPCR Experiments (MIQE) guidelines, most reports used only one reference gene to normalize qPCR data, and that stability of the reference genes was either not tested or not reported. To identify new and more stable reference genes in senescent fibroblasts, we analyzed the Shapiro-Wilk normality test and the coefficient of variation per gene using in public RNAseq datasets. We then compared the new reference gene candidates with commonly used ones by using both RNAseq and qPCR data. Finally, we defined the best reference genes to be used universally or in a strain-dependent manner. This study intends to raise awareness of the instability of classical reference genes in senescent cells and to serve as a first attempt to define guidelines for the selection of more reliable normalization methods.
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Affiliation(s)
- Alejandra Hernandez-Segura
- European Research Institute for the Biology of Ageing, University Medical Center Groningen; University of Groningen; Groningen The Netherlands
| | - Richard Rubingh
- European Research Institute for the Biology of Ageing, University Medical Center Groningen; University of Groningen; Groningen The Netherlands
| | - Marco Demaria
- European Research Institute for the Biology of Ageing, University Medical Center Groningen; University of Groningen; Groningen The Netherlands
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14
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Krautgasser C, Mandl M, Hatzmann FM, Waldegger P, Mattesich M, Zwerschke W. Reliable reference genes for expression analysis of proliferating and adipogenically differentiating human adipose stromal cells. Cell Mol Biol Lett 2019; 24:14. [PMID: 30815013 PMCID: PMC6377720 DOI: 10.1186/s11658-019-0140-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 02/11/2019] [Indexed: 12/28/2022] Open
Abstract
Background The proliferation and adipogenic differentiation of adipose stromal cells (ASCs) are complex processes comprising major phenotypical alterations driven by up- and downregulation of hundreds of genes. Quantitative RT-PCR can be employed to measure relative changes in the expression of a gene of interest. This approach requires constitutively expressed reference genes for normalization to counteract inter-sample variations due to differences in RNA quality and quantity. Thus, a careful validation of quantitative RT-PCR reference genes is needed to accurately measure fluctuations in the expression of genes. Here, we evaluated candidate reference genes applicable for quantitative RT-PCR analysis of gene expression during proliferation and adipogenesis of human ASCs with the immunophenotype DLK1+/CD34+/CD90+/CD105+/CD45−/CD31−. Methods We evaluated the applicability of 10 candidate reference genes (GAPDH, TBP, RPS18, EF1A, TFRC, GUSB, PSMD5, CCNA2, LMNA and MRPL19) using NormFinder, geNorm and BestKeeper software. Results The results indicate that EF1A and MRPL19 are the most reliable reference genes for quantitative RT-PCR analysis of proliferating ASCs. PSMD5 serves as the most reliable endogenous control in adipogenesis. CCNA2 and LMNA were among the least consistent genes. Conclusions Applying these findings for future gene expression analyses will help elucidate ASC biology. Electronic supplementary material The online version of this article (10.1186/s11658-019-0140-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Claudia Krautgasser
- 1Division of Cell Metabolism and Differentiation Research, Institute for Biomedical Aging Research, University of Innsbruck, Rennweg 10, A-6020 Innsbruck, Austria
| | - Markus Mandl
- 1Division of Cell Metabolism and Differentiation Research, Institute for Biomedical Aging Research, University of Innsbruck, Rennweg 10, A-6020 Innsbruck, Austria
| | - Florian M Hatzmann
- 1Division of Cell Metabolism and Differentiation Research, Institute for Biomedical Aging Research, University of Innsbruck, Rennweg 10, A-6020 Innsbruck, Austria
| | - Petra Waldegger
- 1Division of Cell Metabolism and Differentiation Research, Institute for Biomedical Aging Research, University of Innsbruck, Rennweg 10, A-6020 Innsbruck, Austria
| | - Monika Mattesich
- 2Department of Plastic and Reconstructive Surgery, Innsbruck Medical University, Anichstraße 35, A-6020 Innsbruck, Austria
| | - Werner Zwerschke
- 1Division of Cell Metabolism and Differentiation Research, Institute for Biomedical Aging Research, University of Innsbruck, Rennweg 10, A-6020 Innsbruck, Austria
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15
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Selection and validation of reference genes for quantitative gene expression analyses in black locust (Robinia pseudoacacia L.) using real-time quantitative PCR. PLoS One 2018. [PMID: 29529054 PMCID: PMC5846725 DOI: 10.1371/journal.pone.0193076] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Black locust (Robinia pseudoacacia L.) is an easy to raise, fast growing, medium-sized deciduous tree species highly tolerant to harsh eco-conditions, i.e., drought and harsh winters, and it is widely adaptable to sandy, loamy, and marshy soils. The basis for this adaptability remains to be investigated at the transcriptomic level using real-time quantitative PCR (qPCR). Selection of a reliable gene for the normalization of qPCR data is important for obtaining accurate results in gene expression. The goal of this study was to identify an appropriate reference gene from 12 candidate genes for gene expression analysis in black locust exposed to various stressors such as abscisic acid (ABA), NaCl, polyethylene glycol (PEG) and varying temperatures. In GeNorm and NormFinder analyses, ACT (actin) and GAPDH (glyceraldehyde-3-phosphate dehydrogenase) gene expression were the most stable in all conditions except heat stress, but in BestKeeper analysis, GAPDH and helicase gene expression were the most stable under NaCl and heat stress. In contrast, ACT and GAPDH were highest under abscisic acid (ABA), GAPDH and βTUB (beta tubulin) under cold stress, and helicase and EF1α (elongation factor 1 alpha) under PEG stress. We found that the most stable reference gene combination for all conditions was ACT and GAPDH. Additionally, the expression pattern of NAC2 (a transcription factor) and BGL2 in different tissues and under different stress conditions was analyzed relative to ACT and GAPDH and UBQ (ubiquitin) the least stably expressed gene. NAC2 and BGL2 both had highest expression in flowers and pods under ABA stress at 48h. This study provides useful reference genes for future gene expression studies in black locust.
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16
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Haynes HR, Killick-Cole CL, Hares KM, Redondo J, Kemp KC, Moutasim KA, Faulkner C, Wilkins A, Kurian KM. Evaluation of the quality of RNA extracted from archival FFPE glioblastoma and epilepsy surgical samples for gene expression assays. J Clin Pathol 2018; 71:695-701. [DOI: 10.1136/jclinpath-2017-204969] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2017] [Revised: 01/29/2018] [Accepted: 01/30/2018] [Indexed: 01/05/2023]
Abstract
AimsHistopathological tissue samples are being increasingly used as sources of nucleic acids in molecular pathology translational research. This study investigated the suitability of glioblastoma and control central nervous system (CNS) formalin-fixed paraffin embedded (FFPE) tissue-derived RNA for gene expression analyses.MethodsTotal RNA was extracted from control (temporal lobe resection tissue) and glioblastoma FFPE tissue samples. RNA purity (260/280 ratios) was determined and RNA integrity number (RIN) analysis was performed. RNA was subsequently used for RT-qPCR for two reference genes,18SandGAPDH.ResultsReference gene expression was equivalent between control and glioblastoma tissue when using RNA extracted from FFPE tissue, which has key implications for biological normalisation for CNS gene expression studies. There was a significant difference between the mean RIN values of control and glioblastoma FFPE tissue. There was no significant correlation between 260/280 or RIN values versus total RNA yield. The age of the tissue blocks did not influence RNA yield, fragmentation or purity. There was no significant correlation between RIN or 260/280 ratios and mean qPCR cycle threshold for either reference gene.ConclusionsThis study showed that routinely available CNS FFPE tissue is suitable for RNA extraction and downstream gene expression studies, even after 60 months of storage. Substantial RNA fragmentation associated with glioblastoma and control FFPE tissue blocks did not preclude downstream RT-qPCR gene expression analyses. Cross validation with both archival and prospectively collated FFPE specimens is required to further demonstrate that CNS tissue blocks can be used in novel translational molecular biomarker studies.
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18
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Davie AJ, Wen L, Cust ARE, Beavers R, Fyfe T, Zhou S. The effects of moderate intensity training in a hypoxic environment on transcriptional responses in Thoroughbred horses. Biol Open 2017; 6:1035-1040. [PMID: 28583927 PMCID: PMC5550905 DOI: 10.1242/bio.020388] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
This study investigated the effects of six weeks of normobaric hypoxic training on transcriptional expression of the genes associated with mitochondrial and glycolytic activities in Thoroughbred horses. Eight horses were divided into two groups of four. They completed an identical incremental, moderate intensity training program, except that one group trained in a hypoxic chamber with 15% oxygen for 30 min on alternate days except Sundays (HT), while the other group trained in normal air (NC). Prior to and post training, heart rate and blood lactate were measured during an incremental treadmill test. Muscle biopsy samples were taken prior to and 24 h post the training period for qPCR analysis of mRNA changes in VEGF, PPARγ, HIF-1α, PGC-1α, COX4, AK3, LDH, PFK, PKm and SOD-2. No significant differences between the HT and NC were detected by independent-samples t-test with Bonferroni correction for multiple comparisons (P>0.05) in relative changes of mRNA abundance. There were no significant differences between groups for heart rate and blood lactate during the treadmill test. The outcomes indicated that this hypoxia training program did not cause a significant variation in basal level expression of the selected mRNAs in Thoroughbreds as compared with normoxic training.
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Affiliation(s)
- Allan J Davie
- Southern Cross University, School of Health and Human Sciences, Lismore, NSW 2480, Australia
| | - Li Wen
- Tianjin University of Sports, Tianjin Key Laboratory of Exercise Physiology and Sports Medicine, Tianjin 300381, China
| | | | - Rosalind Beavers
- Southern Cross University, School of Health and Human Sciences, Lismore, NSW 2480, Australia
| | - Tom Fyfe
- Pulford Air and Gas, Sydney, NSW 2141, Australia
| | - Shi Zhou
- Southern Cross University, School of Health and Human Sciences, Lismore, NSW 2480, Australia
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19
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20
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Sun JH, Zhu XY, Dong TN, Zhang XH, Liu QQ, Li SQ, Du QX. An “up, no change, or down” system: Time-dependent expression of mRNAs in contused skeletal muscle of rats used for wound age estimation. Forensic Sci Int 2017; 272:104-110. [DOI: 10.1016/j.forsciint.2017.01.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2016] [Revised: 01/02/2017] [Accepted: 01/09/2017] [Indexed: 12/18/2022]
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21
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Meira-Strejevitch CS, Pereira-Chioccola VL, Maia MM, Carnietto de Hipólito DD, Wang HTL, Motoie G, de Souza Gomes AH, Kanamura CT, Martines RB, de Mattos CCB, Frederico FB, de Mattos LC, de Mattos CCB, Frederico FB, Siqueira RC, Previato M, Barbosa AP, Murata FHA. WITHDRAWN: Selection of reference genes in five types of human tissues for normalization of gene expression studies in infectious diseases. Gene 2016:S0378-1119(16)30816-2. [PMID: 27743995 DOI: 10.1016/j.gene.2016.10.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 10/09/2016] [Indexed: 11/23/2022]
Abstract
This article has been withdrawn at the request of the author(s) and/or editor. The Publisher apologizes for any inconvenience this may cause. The full Elsevier Policy on Article Withdrawal can be found at http://www.elsevier.com/locate/withdrawalpolicy.
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Affiliation(s)
| | | | - Marta Marques Maia
- Centro de Parasitologia e Micologia, Instituto Adolfo Lutz, Sao Paulo Brazil
| | | | - Hui-Tzu Lin Wang
- Laboratório de Investigação Molecular em Cardiologia, Instituto Dante Pazzanese de Cardiologia, Sao Paulo Brazil
| | - Gabriela Motoie
- Centro de Parasitologia e Micologia, Instituto Adolfo Lutz, Sao Paulo Brazil
| | | | | | | | - Cinara Cássia Brandão de Mattos
- Laboratório de Imunogenética, Departamento de Biologia Molecular, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto, Brazil
| | - Fábio Batista Frederico
- Ambulatório de Oftalmologia, Fundação Faculdade Regional de Medicina-Hospital de Base, São José do Rio Preto, Brazil
| | - Luiz Carlos de Mattos
- Laboratório de Imunogenética, Departamento de Biologia Molecular, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto, Brazil
| | - Cinara Cássia Brandão de Mattos
- Laboratório de Imunogenética, Departamento de Biologia Molecular, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto, Brazil
| | - Fábio Batista Frederico
- Ambulatório de Oftalmologia, Fundação Faculdade Regional de Medicina-Hospital de Base, São José do Rio Preto, Brazil
| | - Rubens Camargo Siqueira
- Laboratório de Imunogenética, Departamento de Biologia Molecular, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto, Brazil
| | - Mariana Previato
- Laboratório de Imunogenética, Departamento de Biologia Molecular, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto, Brazil
| | - Amanda Pires Barbosa
- Ambulatório de Oftalmologia, Fundação Faculdade Regional de Medicina-Hospital de Base, São José do Rio Preto, Brazil
| | - Fernando Henrique Antunes Murata
- Laboratório de Imunogenética, Departamento de Biologia Molecular, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto, Brazil
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22
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Galichon P, Amrouche L, Hertig A, Brocheriou I, Rabant M, Xu-Dubois YC, Ouali N, Dahan K, Morin L, Terzi F, Rondeau E, Anglicheau D. Urinary mRNA for the Diagnosis of Renal Allograft Rejection: The Issue of Normalization. Am J Transplant 2016; 16:3033-3040. [PMID: 27232948 DOI: 10.1111/ajt.13891] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Revised: 05/10/2016] [Accepted: 05/25/2016] [Indexed: 01/25/2023]
Abstract
Urinary messenger RNA (mRNA) quantification is a promising method for noninvasive diagnosis of renal allograft rejection (AR), but the quantification of mRNAs in urine remains challenging due to degradation. RNA normalization may be warranted to overcome these issues, but the strategies of gene normalization have been poorly evaluated. Herein, we address this issue in a case-control study of 108 urine samples collected at time of allograft biopsy in kidney recipients with (n = 52) or without (n = 56) AR by comparing the diagnostic value of IP-10 and CD3ε mRNAs-two biomarkers of AR-after normalization by the total amount of RNA, normalization by one of the three widely used reference RNAs-18S, glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and Hypoxanthine-guanine phosphoribosyltransferase (HPRT)-or normalization using uroplakin 1A (UPK) mRNA as a possible urine-specific reference mRNA. Our results show that normalization based on the total quantity of RNA is not substantially improved by additional normalization and may even be worsened with some classical reference genes that are overexpressed during rejection. However, considering that normalization by a reference gene is necessary to ensure polymerase chain reaction (PCR) quality and reproducibility and to suppress the effect of RNA degradation, we suggest that GAPDH and UPK1A are preferable to 18S or HPRT RNA.
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Affiliation(s)
- P Galichon
- INSERM U1155, Hôpital Tenon, Paris, France.,Université Pierre et Marie Curie, Paris 6, Sorbonne Universités, Paris, France.,Urgences Néphrologiques et Transplantation Rénale, Hôpital Tenon, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - L Amrouche
- INSERM U1151, Hôpital Necker, Paris, France
| | - A Hertig
- INSERM U1155, Hôpital Tenon, Paris, France.,Université Pierre et Marie Curie, Paris 6, Sorbonne Universités, Paris, France.,Urgences Néphrologiques et Transplantation Rénale, Hôpital Tenon, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - I Brocheriou
- INSERM U1155, Hôpital Tenon, Paris, France.,Université Pierre et Marie Curie, Paris 6, Sorbonne Universités, Paris, France.,Service d'anatomie pathologique, Hôpital Tenon, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - M Rabant
- Laboratoire d'anatomie pathologique, Hôpital Necker, Assistance Publique-Hôpitaux de Paris, Paris, France
| | | | - N Ouali
- Urgences Néphrologiques et Transplantation Rénale, Hôpital Tenon, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - K Dahan
- Service de Néphrologie et Dialyses, Hôpital Necker, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - L Morin
- Service de Néphrologie et Transplantation Adulte, Hôpital Necker, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - F Terzi
- INSERM U1151, Hôpital Necker, Paris, France
| | - E Rondeau
- INSERM U1155, Hôpital Tenon, Paris, France.,Université Pierre et Marie Curie, Paris 6, Sorbonne Universités, Paris, France.,Urgences Néphrologiques et Transplantation Rénale, Hôpital Tenon, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - D Anglicheau
- INSERM U1151, Hôpital Necker, Paris, France.,Service de Néphrologie et Transplantation Adulte, Hôpital Necker, Assistance Publique-Hôpitaux de Paris, Paris, France.,Université Paris Descartes, Sorbonne Paris Cité, Paris, France.,RTRS "Centaure", Labex "Transplantex", Hôpital Necker, Paris, France
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23
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Onzi GR, Ledur PF, Hainzenreder LD, Bertoni APS, Silva AO, Lenz G, Wink MR. Analysis of the safety of mesenchymal stromal cells secretome for glioblastoma treatment. Cytotherapy 2016; 18:828-37. [PMID: 27210718 DOI: 10.1016/j.jcyt.2016.03.299] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Revised: 03/05/2016] [Accepted: 03/31/2016] [Indexed: 02/06/2023]
Abstract
BACKGROUND AIMS The purpose of this study was to investigate whether the secretome of human adipose-derived stem cells (hADSC) affects human glioblastoma (GBM) cancer stem cell (CSC) subpopulation or has any influence on drug resistance and cell migration, evaluating the safety of hADSCs for novel cancer therapies. METHODS hADSCs were maintained in contact with fresh culture medium to produce hADSCs conditioned medium (CM). GBM U87 cells were cultured with CM and sphere formation, expression of genes related to resistance and CSCs-MGMT, OCT4, SOX2, NOTCH1, MSI1-and protein expression of OCT4 and Nanog were analyzed. The influence of hADSC CM on GBM resistance to temozolomide (TMZ) was evaluated by measuring cumulative population doubling and hADSC CM influence on tumor cell migration was analyzed using transwell assay. RESULTS hADSC CM did not alter CSC-related features such as sphere-forming capacity and expression of genes related to CSC. hADSC CM treatment alone did not change proliferation rate of U87 cells and, most important, did not alter the response of tumor cells to TMZ. However, hADSC CM secretome increased the migration capacity of glioblastoma cells. DISCUSSION hADSC CM neither induced an enrichment of CSCs in U87 cells population nor interfered in the response to TMZ in culture. Nevertheless, paracrine factors released by hADSCs were able to modulate glioblastoma cells migration. These findings provide novel information regarding the safety of using hADSCs against cancer and highlight the importance of considering hADSC-tumor cells interactions in tumor microenvironment in the design of novel cell therapies.
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Affiliation(s)
- Giovana Ravizzoni Onzi
- Laboratory of Cell Biology, Universidade Federal de Ciências da Saúde de Porto Alegre, Porto Alegre, Brazil; Department of Biophysics and Center of Biotechnology, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Pítia Flores Ledur
- Department of Biophysics and Center of Biotechnology, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Luana Dimer Hainzenreder
- Laboratory of Cell Biology, Universidade Federal de Ciências da Saúde de Porto Alegre, Porto Alegre, Brazil
| | - Ana Paula Santin Bertoni
- Laboratory of Cell Biology, Universidade Federal de Ciências da Saúde de Porto Alegre, Porto Alegre, Brazil
| | - Andrew Oliveira Silva
- Department of Biophysics and Center of Biotechnology, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Guido Lenz
- Department of Biophysics and Center of Biotechnology, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Márcia Rosângela Wink
- Laboratory of Cell Biology, Universidade Federal de Ciências da Saúde de Porto Alegre, Porto Alegre, Brazil.
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Liu W, Deng Y, Zhou Y, Chen H, Dong Y, Wang N, Li X, Jameel A, Yang H, Zhang M, Chen K, Wang F, Li H. Normalization for Relative Quantification of mRNA and microRNA in Soybean Exposed to Various Abiotic Stresses. PLoS One 2016; 11:e0155606. [PMID: 27176476 PMCID: PMC4866712 DOI: 10.1371/journal.pone.0155606] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Accepted: 05/02/2016] [Indexed: 11/22/2022] Open
Abstract
Plant microRNAs are small non-coding, endogenic RNA molecule (containing 20-24 nucleotides) produced from miRNA precursors (pri-miRNA and pre-miRNA). Evidence suggests that up and down regulation of the miRNA targets the mRNA genes involved in resistance against biotic and abiotic stresses. Reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR) is a powerful technique to analyze variations in mRNA levels. Normalizing the data using reference genes is essential for the analysis of reliable RT-qPCR data. In this study, two groups of candidate reference mRNAs and miRNAs in soybean leaves and roots treated with various abiotic stresses (PEG-simulated drought, salinity, alkalinity, salinity+alkalinity, and abscisic acid) were analyzed by RT-qPCR. We analyzed the most appropriate reference mRNA/miRNAs using the geNorm, NormFinder, and BestKeeper algorithms. According to the results, Act and EF1b were the most suitable reference mRNAs in leaf and root samples, for mRNA and miRNA precursor data normalization. The most suitable reference miRNAs found in leaf and root samples were 166a and 167a for mature miRNA data normalization. Hence the best combinations of reference mRNAs for mRNA and miRNA precursor data normalization were EF1a + Act or EF1b + Act in leaf samples, and EF1a + EF1b or 60s + EF1b in root samples. For mature miRNA data normalization, the most suitable combinations of reference miRNAs were 166a + 167d in leaf samples, and 171a + 156a or 167a + 171a in root samples. We identified potential reference mRNA/miRNAs for accurate RT-qPCR data normalization for mature miRNA, miRNA precursors, and their targeted mRNAs. Our results promote miRNA-based studies on soybean plants exposed to abiotic stress conditions.
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Affiliation(s)
- Weican Liu
- College of Life Sciences, Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun, Jilin, 130118, China
| | - Yu Deng
- College of Life Sciences, Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun, Jilin, 130118, China
| | - Yonggang Zhou
- College of Life Sciences, Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun, Jilin, 130118, China
| | - Huan Chen
- College of Life Sciences, Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun, Jilin, 130118, China
| | - Yuanyuan Dong
- College of Life Sciences, Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun, Jilin, 130118, China
| | - Nan Wang
- College of Life Sciences, Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun, Jilin, 130118, China
| | - Xiaowei Li
- College of Life Sciences, Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun, Jilin, 130118, China
| | - Aysha Jameel
- College of Life Sciences, Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun, Jilin, 130118, China
| | - He Yang
- College of Life Sciences, Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun, Jilin, 130118, China
| | - Min Zhang
- College of Life Sciences, Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun, Jilin, 130118, China
| | - Kai Chen
- College of Life Sciences, Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun, Jilin, 130118, China
| | - Fawei Wang
- College of Life Sciences, Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun, Jilin, 130118, China
| | - Haiyan Li
- College of Life Sciences, Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun, Jilin, 130118, China
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Andrusiewicz M, Słowikowski B, Skibińska I, Wołuń-Cholewa M, Dera-Szymanowska A. Selection of reliable reference genes in eutopic and ectopic endometrium for quantitative expression studies. Biomed Pharmacother 2016; 78:66-73. [PMID: 26898426 DOI: 10.1016/j.biopha.2015.12.028] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Revised: 12/16/2015] [Accepted: 12/21/2015] [Indexed: 01/16/2023] Open
Abstract
PURPOSE Physiological changes during menstrual cycle cause the endometrium and endometriosis to develop specific kind of tissues, especially in regard to the gene expression profiles, which may include also housekeeping genes, commonly used as reference genes (RGs) in quantitative studies. Reverse transcription, followed by quantitative polymerase chain reaction (RT-qPCR) is the most precise and commonly used method in gene expression studies. In order to reduce effects of technical approaches and biological variability of gene's expression level, the studies often employ RGs in experimental data normalization. However, the expression of RGs is not always stable and depends on several variables. Thus, the selection of appropriate RG is one of the most significant steps to obtain reliable results in RT-qPCR-based methods. MATERIAL AND METHODS With the usage of RT-qPCR, we researched the expression of seven genes (ACTB, B2M, G6PD, GAPD, GUSB, HPRT and PPIA) as reliable reference genes in eutopic and ectopic endometrial tissue specimens obtained during standard surgery of women of reproductive age. Stability of expression level was analyzed by the most universal MS Excel plug-ins including: geNorm, NormFinder and BestKeeper. The descriptive statistics were evaluated using Statistica software. RESULTS The distribution of threshold (Ct) values was not equal. We identified genes with higher expression level (referring to Ct values) such as ACTB and B2M, medium e.g., GAPD and low expression level, e.g., G6PD and HPRT. We demonstrated that the stability of the analyzed reference genes was not homogenous, and different algorithms pointed to PPIA, GAPD and B2M as the most stable ones in eutopic and ectopic endometrium. On the contrary to these, GUSB and G6PD were the most unstable ones. CONCLUSIONS In RT-qPCR-based analyses of gene expression level in eutopic and ectopic endometrium, we strongly recommend that a minimum of two reference genes are to be used and we determined that the most suitable seem to be PPIA and GAPD.
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Affiliation(s)
- Mirosław Andrusiewicz
- Department of Cell Biology, Health Sciences Faculty, Poznan University of Medical Sciences, Rokietnicka str. 5D, 60-806 Poznan, Poland.
| | - Bartosz Słowikowski
- Department of Cell Biology, Health Sciences Faculty, Poznan University of Medical Sciences, Rokietnicka str. 5D, 60-806 Poznan, Poland; Department of Biochemistry and Molecular Biology, Faculty of Medicine I, Poznan University of Medical Sciences, Swiecickiego str. 6, 60-781 Poznan, Poland.
| | - Izabela Skibińska
- Department of Cell Biology, Health Sciences Faculty, Poznan University of Medical Sciences, Rokietnicka str. 5D, 60-806 Poznan, Poland.
| | - Maria Wołuń-Cholewa
- Department of Cell Biology, Health Sciences Faculty, Poznan University of Medical Sciences, Rokietnicka str. 5D, 60-806 Poznan, Poland.
| | - Anna Dera-Szymanowska
- Department of Perinatology and Gynecology, Faculty of Medicine II, Poznan University of Medical Sciences, Polna Street 33, 60-535 Poznan, Poland.
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Stassen QEM, Riemers FM, Reijmerink H, Leegwater PAJ, Penning LC. Reference genes for reverse transcription quantitative PCR in canine brain tissue. BMC Res Notes 2015; 8:761. [PMID: 26654363 PMCID: PMC4673830 DOI: 10.1186/s13104-015-1628-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Accepted: 10/26/2015] [Indexed: 12/20/2022] Open
Abstract
Background In the last decade canine models have been used extensively to study genetic causes of neurological disorders such as epilepsy and Alzheimer’s disease and unravel their pathophysiological pathways. Reverse transcription quantitative polymerase chain reaction is a sensitive and inexpensive method to study expression levels of genes involved in disease processes. Accurate normalisation with stably expressed so-called reference genes is crucial for reliable expression analysis. Results Following the minimum information for publication of quantitative real-time PCR experiments precise guidelines, the expression of ten frequently used reference genes, namely YWHAZ, HMBS, B2M, SDHA, GAPDH, HPRT, RPL13A, RPS5, RPS19 and GUSB was evaluated in seven brain regions (frontal lobe, parietal lobe, occipital lobe, temporal lobe, thalamus, hippocampus and cerebellum) and whole brain of healthy dogs. The stability of expression varied between different brain areas. Using the GeNorm and Normfinder software HMBS, GAPDH and HPRT were the most reliable reference genes for whole brain. Furthermore based on GeNorm calculations it was concluded that as little as two to three reference genes are sufficient to obtain reliable normalisation, irrespective the brain area. Conclusions Our results amend/extend the limited previously published data on canine brain reference genes. Despite the excellent expression stability of HMBS, GAPDH and HRPT, the evaluation of expression stability of reference genes must be a standard and integral part of experimental design and subsequent data analysis. Electronic supplementary material The online version of this article (doi:10.1186/s13104-015-1628-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Quirine E M Stassen
- Department of Clinical Sciences of Companion Animals, Faculty of Veterinary Medicine, Utrecht University, PO Box 80154, 3508 TD, Utrecht, The Netherlands.
| | - Frank M Riemers
- Department of Clinical Sciences of Companion Animals, Faculty of Veterinary Medicine, Utrecht University, PO Box 80154, 3508 TD, Utrecht, The Netherlands.
| | - Hannah Reijmerink
- Department of Clinical Sciences of Companion Animals, Faculty of Veterinary Medicine, Utrecht University, PO Box 80154, 3508 TD, Utrecht, The Netherlands.
| | - Peter A J Leegwater
- Department of Clinical Sciences of Companion Animals, Faculty of Veterinary Medicine, Utrecht University, PO Box 80154, 3508 TD, Utrecht, The Netherlands.
| | - Louis C Penning
- Department of Clinical Sciences of Companion Animals, Faculty of Veterinary Medicine, Utrecht University, PO Box 80154, 3508 TD, Utrecht, The Netherlands.
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Ji N, Li L, Lin L, Lin S. Screening for Suitable Reference Genes for Quantitative Real-Time PCR in Heterosigma akashiwo (Raphidophyceae). PLoS One 2015; 10:e0132183. [PMID: 26133173 PMCID: PMC4489630 DOI: 10.1371/journal.pone.0132183] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 06/10/2015] [Indexed: 11/24/2022] Open
Abstract
The raphidophyte Heterosigma akashiwo is a globally distributed harmful alga that has been associated with fish kills in coastal waters. To understand the mechanisms of H. akashiwo bloom formation, gene expression analysis is often required. To accurately characterize the expression levels of a gene of interest, proper reference genes are essential. In this study, we assessed ten of the previously reported algal candidate genes (rpL17-2, rpL23, cox2, cal, tua, tub, ef1, 18S, gapdh, and mdh) for their suitability as reference genes in this species. We used qRT-PCR to quantify the expression levels of these genes in H. akashiwo grown under different temperatures, light intensities, nutrient concentrations, and time points over a diel cycle. The expression stability of these genes was evaluated using geNorm and NormFinder algorithms. Although none of these genes exhibited invariable expression levels, cal, tub, rpL17-2 and rpL23 expression levels were the most stable across the different conditions tested. For further validation, these selected genes were used to normalize the expression levels of ribulose-1, 5-bisphosphate carboxylase/oxygenase large unite (HrbcL) over a diel cycle. Results showed that the expression of HrbcL normalized against each of these reference genes was the highest at midday and lowest at midnight, similar to the diel patterns typically documented for this gene in algae. While the validated reference genes will be useful for future gene expression studies on H. akashiwo, we expect that the procedure used in this study may be helpful to future efforts to screen reference genes for other algae.
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Affiliation(s)
- Nanjing Ji
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, Fujian 361005, China
| | - Ling Li
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, Fujian 361005, China
| | - Lingxiao Lin
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, Fujian 361005, China
| | - Senjie Lin
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, Fujian 361005, China
- Department of Marine Sciences, University of Connecticut, Groton, Connecticut 06340, United States of America
- * E-mail:
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Grube S, Göttig T, Freitag D, Ewald C, Kalff R, Walter J. Selection of suitable reference genes for expression analysis in human glioma using RT-qPCR. J Neurooncol 2015; 123:35-42. [PMID: 25862007 DOI: 10.1007/s11060-015-1772-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Accepted: 04/02/2015] [Indexed: 12/11/2022]
Abstract
In human glioma research, quantitative real-time reverse-transcription PCR is a frequently used tool. Considering the broad variation in the expression of candidate reference genes among tumor stages and normal brain, studies using quantitative RT-PCR require strict definition of adequate endogenous controls. This study aimed at testing a panel of nine reference genes [beta-2-microglobulin, cytochrome c-1 (CYC1), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), hydroxymethylbilane synthase, hypoxanthine guanine phosphoribosyl transferase 1, ribosomal protein L13a (RPL13A), succinate dehydrogenase, TATA-box binding protein and 14-3-3 protein zeta] to identify and validate the most suitable reference genes for expression studies in human glioma of different grades (World Health Organization grades II-IV). After analysis of the stability values calculated using geNorm, NormFinder, and BestKeeper algorithms, GAPDH, RPL13A, and CYC1 can be indicated as reference genes applicable for accurate normalization of gene expression in glioma compared with normal brain and anaplastic astrocytoma or glioblastoma alone within this experimental setting. Generally, there are no differences in expression levels and variability of candidate genes in glioma tissue compared to normal brain. But stability analyses revealed just a small number of genes suitable for normalization in each of the tumor subgroups and across these groups. Nevertheless, our data show the importance of validation of adequate reference genes prior to every study.
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Affiliation(s)
- Susanne Grube
- Department of Neurosurgery, Section of Experimental Neurooncology, Jena University Hospital, Friedrich-Schiller-University Jena, Erlanger Allee 101, 07747, Jena, Germany,
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Validation of reference genes for normalization gene expression in reverse transcription quantitative PCR in human normal thyroid and goiter tissue. BIOMED RESEARCH INTERNATIONAL 2014; 2014:198582. [PMID: 24900955 PMCID: PMC4037571 DOI: 10.1155/2014/198582] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Accepted: 04/18/2014] [Indexed: 01/01/2023]
Abstract
Reverse transcription quantitative polymerase chain reaction (RT-qPCR) has been recognized as the most accurate method for quantifying mRNA transcripts, but normalization of samples is a prerequisite for correct data interpretation. So, this study aimed to evaluate the most stable reference gene for RT-qPCR in human normal thyroid and goiter tissues. Beta-actin (ACTB); glyceraldehyde-3-phosphate dehydrogenase (GAPDH); succinate dehydrogenase, subunit A, flavoprotein (Fp) (SDHA); hypoxanthine phosphoribosyltransferase I (HPRTI); tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, zeta polypeptide (YWHAZ); and beta-2-microglobulin (B2M) were evaluated in 14 thyroid tissue samples (7 normal and 7 goiter tissues) by RT-qPCR. The mean Cq and the maximum fold change (MFC) and NormFinder software were used to assess the stability of the genes. As a result, ACTB gene was more stable than GAPDH, SDHA, HPRTI, YWHAZ, and B2M. In conclusion, ACTB could be used to normalize RT-qPCR data in normal thyroid and goiter tissues.
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Galetto L, Bosco D, Marzachì C. Selection of reference genes from two leafhopper species challenged by phytoplasma infection, for gene expression studies by RT-qPCR. BMC Res Notes 2013; 6:409. [PMID: 24119747 PMCID: PMC3852609 DOI: 10.1186/1756-0500-6-409] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2013] [Accepted: 09/19/2013] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Phytoplasmas are phloem-limited phytopathogenic wall-less bacteria and represent a major threat to agriculture worldwide. They are transmitted in a persistent, propagative manner by phloem-sucking Hemipteran insects. For gene expression studies based on mRNA quantification by RT-qPCR, stability of housekeeping genes is crucial. The aim of this study was the identification of reference genes to study the effect of phytoplasma infection on gene expression of two leafhopper vector species. The identified reference genes will be useful tools to investigate differential gene expression of leafhopper vectors upon phytoplasma infection. RESULTS The expression profiles of ribosomal 18S, actin, ATP synthase β, glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and tropomyosin were determined in two leafhopper vector species (Hemiptera: Cicadellidae), both healthy and infected by "Candidatus Phytoplasma asteris" (chrysanthemum yellows phytoplasma strain, CYP). Insects were analyzed at three different times post acquisition, and expression stabilities of the selected genes were evaluated with BestKeeper, geNorm and Normfinder algorithms. In Euscelidius variegatus, all genes under all treatments were stable and could serve as reference genes. In Macrosteles quadripunctulatus, BestKeeper and Normfinder analysis indicated ATP synthase β, tropomyosin and GAPDH as the most stable, whereas geNorm identified reliable genes only for early stages of infection. CONCLUSIONS In this study a validation of five candidate reference genes was performed with three algorithms, and housekeeping genes were identified for over time transcript profiling of two leafhopper vector species infected by CYP. This work set up an experimental system to study the molecular basis of phytoplasma multiplication in the insect body, in order to elucidate mechanisms of vector specificity. Most of the sequences provided in this study are new for leafhoppers, which are vectors of economically important plant pathogens. Phylogenetic indications were also drawn from sequence analysis of these genes.
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Affiliation(s)
- Luciana Galetto
- Istituto di Virologia Vegetale, CNR, Strada delle Cacce 73, 10135 Torino, Italy.
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Transcriptome Analysis of Spermophilus lateralis and Spermophilus tridecemlineatus Liver Does Not Suggest the Presence of Spermophilus-Liver-Specific Reference Genes. ISRN BIOINFORMATICS 2013; 2013:361321. [PMID: 25937945 PMCID: PMC4393057 DOI: 10.1155/2013/361321] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Accepted: 04/23/2013] [Indexed: 11/21/2022]
Abstract
The expressions of reference genes used in gene expression studies are assumed to be stable under most circumstances. However, studies had demonstrated that genes assumed to be stably expressed in a species are not necessarily stably expressed in other organisms. This study aims to evaluate the likelihood of genus-specific reference genes for liver using comparable microarray datasets from Spermophilus lateralis and Spermophilus tridecemlineatus. The coefficient of variance (CV) of each probe was calculated and there were 178 probes common between the lowest 10% CV of both datasets (n = 1258). All 3 lists were analysed by NormFinder. Our results suggest that the most invariant probe for S. tridecemlineatus was 02n12, while that for S. lateralis was 24j21. However, our results showed that Probes 02n12 and 24j21 are ranked 8644 and 926 in terms of invariancy for S. lateralis and S. tridecemlineatus respectively. This suggests the lack of common liver-specific reference probes for both S. lateralis and S. tridecemlineatus. Given that S. lateralis and S. tridecemlineatus are closely related species and the datasets are comparable, our results do not support the presence of genus-specific reference genes.
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Selection of suitable reference genes for normalization of quantitative real-time PCR in cartilage tissue injury and repair in rabbits. Int J Mol Sci 2012. [PMID: 23203068 PMCID: PMC3509584 DOI: 10.3390/ijms131114344] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
When studying the altered expression of genes associated with cartilage regeneration by quantitative real-time RT-PCR (RT-qPCR), reference genes with highly stable expression during different stages of chondrocyte developmental are necessary to normalize gene expression accurately. Until now, no reports evaluating expression changes of commonly used reference genes in rabbit articular cartilage have been published. In this study, defects were made in rabbit articular cartilage, with or without insulin-like growth factor 1 (IGF-1) treatment, to create different chondrocyte living environments. The stability and intensity of the expressions of the candidate reference genes glyceraldehyde-3-phosphate dehydrogenase (GAPDH), 18S Ribosomal RNA (18S rRNA), cyclophilin (CYP), hypoxanthine phosphoribosyl transferase (HPRT1), and beta-2-microglobulin (B2M) were evaluated. The data were analyzed by geNorm and NormFinder. B2M and 18S rRNA were identified to be suitable reference genes for rabbit cartilage tissues.
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