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Aggarwal A, Jamwal M, Viswanathan GK, Sharma P, Sachdeva MS, Bansal D, Malhotra P, Das R. Optimal Reference Gene Selection for Expression Studies in Human Reticulocytes. J Mol Diagn 2018; 20:326-333. [PMID: 29474985 DOI: 10.1016/j.jmoldx.2018.01.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Revised: 12/28/2017] [Accepted: 01/25/2018] [Indexed: 11/29/2022] Open
Abstract
Reference genes are indispensable for normalizing mRNA levels across samples in real-time quantitative PCR. Their expression levels vary under different experimental conditions and because of several inherent characteristics. Appropriate reference gene selection is thus critical for gene-expression studies. This study aimed at selecting optimal reference genes for gene-expression analysis of reticulocytes and at validating them in hereditary spherocytosis (HS) and β-thalassemia intermedia (βTI) patients. Seven reference genes (PGK1, MPP1, HPRT1, ACTB, GAPDH, RN18S1, and SDHA) were selected because of published reports. Real-time quantitative PCR was performed on reticulocytes in 20 healthy volunteers, 15 HS patients, and 10 βTI patients. Threshold cycle values were compared with fold-change method and RefFinder software. The stable reference genes recommended by RefFinder were validated with SLC4A1 and flow cytometric eosin-5'-maleimide binding assay values in HS patients and HBG2 and high performance liquid chromatography-derived percentage of hemoglobin F in βTI. Comprehensive ranking predicted MPP1 and GAPDH as optimal reference genes for reticulocytes that were not affected in HS and βTI. This was further confirmed on validation with eosin-5'-maleimide results and percentage of hemoglobin F in HS and βTI patients, respectively. Hence, MPP1 and GAPDH are good reference genes for reticulocyte expression studies compared with ACTB and RN18S1, the two most commonly used reference genes.
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Affiliation(s)
- Anu Aggarwal
- Department of Hematology, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Manu Jamwal
- Department of Hematology, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Ganesh K Viswanathan
- Department of Hematology, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Prashant Sharma
- Department of Hematology, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - ManUpdesh S Sachdeva
- Department of Hematology, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Deepak Bansal
- Hematology-Oncology Unit, Department of Pediatrics, Advanced Pediatrics Centre, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Pankaj Malhotra
- Department of Internal Medicine, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Reena Das
- Department of Hematology, Post Graduate Institute of Medical Education and Research, Chandigarh, India.
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Identification of Reference Genes for Analysis of microRNA Expression Patterns in Equine Chorioallantoic Membrane and Serum. Mol Biotechnol 2017; 60:62-73. [DOI: 10.1007/s12033-017-0047-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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53
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The temporal expression of adipokines during spinal fusion. Spine J 2017. [PMID: 28647583 DOI: 10.1016/j.spinee.2017.06.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
BACKGROUND CONTEXT Adipokines are secreted by white adipose tissue and have been associated with fracture healing. Our goal was to report the temporal expression of adipokines during spinal fusion in an established rabbit model. PURPOSE Our goal was to report the temporal expression of adipokines during spinal fusion in an established rabbit model. STUDY DESIGN The study design included a laboratory animal model. METHODS New Zealand white rabbits were assigned to either sham surgery (n=2), unilateral posterior spinal fusion (n=14), or bilateral posterior spinal fusion (n=14). Rabbits were euthanized 1-6 and 10 weeks out from surgery. Fusion was evaluated by radiographs, manual palpation, and histology. Reverse transcription-polymerase chain reaction on the bone fusion mass catalogued the gene expression of leptin, adiponectin, resistin, and vascular endothelial growth factor (VEGF) at each time point. Results were normalized to the internal control gene, glyceraldehyde-3-phosphate dehydrogenase (GAPDH) (2^ΔCt), and control bone sites (2^ΔΔCt). Quantitative data were analyzed by two-factor analysis of variance (p<.05). RESULTS Manual palpation scores, radiograph scores, and histologic findings showed progression of boney fusion over time (p<.0003). The frequency of fusion by palpation after 4 weeks was 68.75%. Leptin expression in decortication and bone graft sites peaked at 5 weeks after the fusion procedure (p=.0143), adiponectin expression was greatest 1 week after surgery (p<.001), VEGF expression peaked at 4 weeks just after initial increases in leptin expression (p<.001), and resistin decreased precipitously 1 week after the fusion procedure (p<.001). CONCLUSIONS Leptin expression is likely associated with the maturation phase of bone fusion. Adiponectin and resistin may play a role early on during the fusion process. Our results suggest that leptin expression may be upstream of VEGF expression during spinal fusion, and both appear to play an important role in bone spinal fusion.
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Xiao J, Li X, Liu J, Fan X, Lei H, Li C. Identification of reference genes in blood before and after entering the plateau for SYBR green RT-qPCR studies. PeerJ 2017; 5:e3726. [PMID: 28970964 PMCID: PMC5622608 DOI: 10.7717/peerj.3726] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 08/01/2017] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Tibetans have lived at high altitudes for thousands of years, and they have unique physiological traits that enable them to tolerate this hypoxic environment. However, the genetic basis of these traits is still unknown. As a sensitive and highly efficient technique, RT-qPCR is widely used in gene expression analyses to provide insight into the molecular mechanisms underlying environmental changes. However, the quantitative analysis of gene expression in blood is limited by a shortage of stable reference genes for the normalization of mRNA levels. Thus, systematic approaches were used to identify potential reference genes. RESULTS The expression levels of eight candidate human reference genes (GAPDH, ACTB, 18S RNA, β2-MG, PPIA, RPL13A, TBP and SDHA) were assessed in blood from hypoxic environments. The expression stability of these selected reference genes was evaluated using the geNorm, NormFinder and BestKeeper programs. Interestingly, RPL13A was identified as the ideal reference gene for normalizing target gene expression in human blood before and after exposure to high-altitude conditions. CONCLUSION These results indicate that different reference genes should be selected for the normalization of gene expression in blood from different environmental settings.
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Affiliation(s)
- Jun Xiao
- Department of Blood Transfusion, General Hospital of Air Force, PLA, Beijing, China
| | - Xiaowei Li
- Department of Blood Transfusion, General Hospital of Air Force, PLA, Beijing, China
| | - Juan Liu
- Department of Blood Transfusion, General Hospital of Air Force, PLA, Beijing, China
| | - Xiu Fan
- Department of Blood Transfusion, General Hospital of Air Force, PLA, Beijing, China
| | - Huifen Lei
- Department of Blood Transfusion, General Hospital of Air Force, PLA, Beijing, China
| | - Cuiying Li
- Department of Blood Transfusion, General Hospital of Air Force, PLA, Beijing, China
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55
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Sood TJ, Lagah SV, Sharma A, Singla SK, Mukesh M, Chauhan MS, Manik R, Palta P. Selection of Suitable Internal Control Genes for Accurate Normalization of Real-Time Quantitative PCR Data of Buffalo (Bubalus bubalis) Blastocysts Produced by SCNT and IVF. Cell Reprogram 2017; 19:302-310. [PMID: 28880574 DOI: 10.1089/cell.2017.0010] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
We evaluated the suitability of 10 candidate internal control genes (ICGs), belonging to different functional classes, namely ACTB, EEF1A1, GAPDH, HPRT1, HMBS, RPS15, RPS18, RPS23, SDHA, and UBC for normalizing the real-time quantitative polymerase chain reaction (qPCR) data of blastocyst-stage buffalo embryos produced by hand-made cloning and in vitro fertilization (IVF). Total RNA was isolated from three pools, each of cloned and IVF blastocysts (n = 50/pool) for cDNA synthesis. Two different statistical algorithms geNorm and NormFinder were used for evaluating the stability of these genes. Based on gene stability measure (M value) and pairwise variation (V value), calculated by geNorm analysis, the most stable ICGs were RPS15, HPRT1, and ACTB for cloned blastocysts, HMBS, UBC, and HPRT1 for IVF blastocysts and RPS15, GAPDH, and HPRT1 for both the embryo types analyzed together. RPS18 was the least stable gene for both cloned and IVF blastocysts. Following NormFinder analysis, the order of stability was RPS15 = HPRT1>GAPDH for cloned blastocysts, HMBS = UBC>RPS23 for IVF blastocysts, and HPRT1>GAPDH>RPS15 for cloned and IVF blastocysts together. These results suggest that despite overlapping of the three most stable ICGs between cloned and IVF blastocysts, the panel of ICGs selected for normalization of qPCR data of cloned and IVF blastocyst-stage embryos should be different.
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Affiliation(s)
- Tanushri Jerath Sood
- 1 Animal Biotechnology Center, ICAR-National Dairy Research Institute , Karnal, India
| | - Swati Viviyan Lagah
- 1 Animal Biotechnology Center, ICAR-National Dairy Research Institute , Karnal, India
| | - Ankita Sharma
- 2 ICAR-National Bureau of Animal Genetic Resources , Karnal, India
| | - Suresh Kumar Singla
- 1 Animal Biotechnology Center, ICAR-National Dairy Research Institute , Karnal, India
| | - Manishi Mukesh
- 2 ICAR-National Bureau of Animal Genetic Resources , Karnal, India
| | | | - Radheysham Manik
- 1 Animal Biotechnology Center, ICAR-National Dairy Research Institute , Karnal, India
| | - Prabhat Palta
- 1 Animal Biotechnology Center, ICAR-National Dairy Research Institute , Karnal, India
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Podlesniy P, Trullas R. Absolute measurement of gene transcripts with Selfie-digital PCR. Sci Rep 2017; 7:8328. [PMID: 28827685 PMCID: PMC5566441 DOI: 10.1038/s41598-017-08270-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 07/06/2017] [Indexed: 01/19/2023] Open
Abstract
Absolute measurement of the number of RNA transcripts per gene is necessary to compare gene transcription among different tissues or experimental conditions and to assess transcription of genes that have a variable copy number per cell such as mitochondrial DNA. Here, we present a method called Selfie-digital PCR that measures the absolute amount of an RNA transcript produced by its own coding DNA at a particular moment. Overcoming the limitations of previous approaches, Selfie-digital PCR allows for the quantification of nuclear and mitochondrial gene transcription in a strand-specific manner that is comparable among tissues and cell types that differ in gene copy number or metabolic state. Using Selfie-digital PCR, we found that, with the exception of the liver, different organs exhibit marked variations in mitochondrial DNA copy number but similar transcription of mitochondrial DNA heavy and light chains, thus suggesting a preferential role of mitochondrial DNA abundance over its transcription in organ function. Moreover, the strand-specific analysis of mitochondrial transcription afforded by Selfie-digital PCR showed that transcription of the heavy strand was significantly higher than that of the light strand in all the tissues studied.
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Affiliation(s)
- Petar Podlesniy
- Neurobiology Unit. Institut d'Investigacions Biomèdiques de Barcelona (IIBB), Consejo Superior de Investigaciones Científicas (CSIC), Barcelona, 08036, Spain.,Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Barcelona, 08036, Spain
| | - Ramon Trullas
- Neurobiology Unit. Institut d'Investigacions Biomèdiques de Barcelona (IIBB), Consejo Superior de Investigaciones Científicas (CSIC), Barcelona, 08036, Spain. .,Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, 08036, Spain. .,Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Barcelona, 08036, Spain. .,Neurobiology Unit, IIBB/CSIC, IDIBAPS, CIBERNED, Rosselló 161, sexta planta, 08036, Barcelona, Spain.
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57
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Lv Y, Zhao SG, Lu G, Leung CK, Xiong ZQ, Su XW, Ma JL, Chan WY, Liu HB. Identification of reference genes for qRT-PCR in granulosa cells of healthy women and polycystic ovarian syndrome patients. Sci Rep 2017; 7:6961. [PMID: 28761164 PMCID: PMC5537281 DOI: 10.1038/s41598-017-07346-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 06/26/2017] [Indexed: 02/06/2023] Open
Abstract
Comparative gene expression analysis by qRT-PCR is commonly used to detect differentially expressed genes in studies of PCOS pathology. Impaired GC function is strongly associated with PCOS pathogenesis, and a growing body of studies has been dedicated to identifying differentially expressed genes in GCs in PCOS patients and healthy women by qRT-PCR. It is necessary to validate the expression stability of the selected reference genes across the tested samples for target gene expression normalization. We examined the variability and stability of expression of the 15 commonly used reference genes in GCs from 44 PCOS patients and 45 healthy women using the GeNorm, BestKeeper, and NormFinder statistical algorithms. We combined the rankings of the three programs to produce a final ranking based on the geometric means of their stability scores. We found that HPRT1, RPLP0, and HMBS out of 15 examined commonly used reference genes are stably expressed in GCs in both controls and PCOS patients and can be used for normalization in gene expression profiling by qRT-PCR. Future gene-expression studies should consider using these reference genes in GCs in PCOS patients for more accurate quantitation of target gene expression and data interpretation.
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Affiliation(s)
- Yue Lv
- Center for Reproductive Medicine, Shandong University, Jinan, Shandong, 250001, China.,CUHK-SDU Joint Laboratory on Reproductive Genetics, School of Biomedical Sciences, the Chinese University of Hong Kong, Hong Kong, China.,National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Jinan, Shandong, 250001, China
| | - Shi Gang Zhao
- Center for Reproductive Medicine, Shandong University, Jinan, Shandong, 250001, China.,National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Jinan, Shandong, 250001, China
| | - Gang Lu
- CUHK-SDU Joint Laboratory on Reproductive Genetics, School of Biomedical Sciences, the Chinese University of Hong Kong, Hong Kong, China. .,National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Jinan, Shandong, 250001, China.
| | - Chi Kwan Leung
- Center for Reproductive Medicine, Shandong University, Jinan, Shandong, 250001, China.,National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Jinan, Shandong, 250001, China.,SDIVF R&D Centre, Hong Kong Science and Technology Parks, Hong Kong, China
| | - Zhi Qiang Xiong
- Center for Reproductive Medicine, Shandong University, Jinan, Shandong, 250001, China.,National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Jinan, Shandong, 250001, China.,SDIVF R&D Centre, Hong Kong Science and Technology Parks, Hong Kong, China
| | - Xian Wei Su
- Center for Reproductive Medicine, Shandong University, Jinan, Shandong, 250001, China.,National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Jinan, Shandong, 250001, China.,SDIVF R&D Centre, Hong Kong Science and Technology Parks, Hong Kong, China
| | - Jin Long Ma
- Center for Reproductive Medicine, Shandong University, Jinan, Shandong, 250001, China.,CUHK-SDU Joint Laboratory on Reproductive Genetics, School of Biomedical Sciences, the Chinese University of Hong Kong, Hong Kong, China.,National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Jinan, Shandong, 250001, China.,SDIVF R&D Centre, Hong Kong Science and Technology Parks, Hong Kong, China
| | - Wai Yee Chan
- CUHK-SDU Joint Laboratory on Reproductive Genetics, School of Biomedical Sciences, the Chinese University of Hong Kong, Hong Kong, China.,National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Jinan, Shandong, 250001, China
| | - Hong Bin Liu
- Center for Reproductive Medicine, Shandong University, Jinan, Shandong, 250001, China. .,CUHK-SDU Joint Laboratory on Reproductive Genetics, School of Biomedical Sciences, the Chinese University of Hong Kong, Hong Kong, China. .,National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Jinan, Shandong, 250001, China.
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58
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Mathur D, Riffo-Campos AL, Castillo J, Haines JD, Vidaurre OG, Zhang F, Coret-Ferrer F, Casaccia P, Casanova B, Lopez-Rodas G. Bioenergetic Failure in Rat Oligodendrocyte Progenitor Cells Treated with Cerebrospinal Fluid Derived from Multiple Sclerosis Patients. Front Cell Neurosci 2017; 11:209. [PMID: 28775680 PMCID: PMC5517784 DOI: 10.3389/fncel.2017.00209] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 07/03/2017] [Indexed: 01/09/2023] Open
Abstract
In relapsing-remitting multiple sclerosis (RRMS) subtype, the patient’s brain itself is capable of repairing the damage, remyelinating the axon and recovering the neurological function. Cerebrospinal fluid (CSF) is in close proximity with brain parenchyma and contains a host of proteins and other molecules, which influence the cellular physiology, that may balance damage and repair of neurons and glial cells. The purpose of this study was to determine the pathophysiological mechanisms underpinning myelin repair in distinct clinical forms of MS and neuromyelitis optica (NMO) patients by studying the effect of diseased CSF on glucose metabolism and ATP synthesis. A cellular model with primary cultures of oligodendrocyte progenitor cells (OPCs) from rat cerebrum was employed, and cells were treated with CSF from distinct clinical forms of MS, NMO patients and neurological controls. Prior to comprehending mechanisms underlying myelin repair, we determine the best stably expressed reference genes in our experimental condition to accurately normalize our target mRNA transcripts. The GeNorm and NormFinder algorithms showed that mitochondrial ribosomal protein (Mrpl19), hypoxanthine guanine phosphoribosyl transferase (Hprt), microglobulin β2 (B2m), and transferrin receptor (Tfrc) were identified as the best reference genes in OPCs treated with MS subjects and were used for normalizing gene transcripts. The main findings on microarray gene expression profiling analysis on CSF treated OPCs cells revealed a disturbed carbohydrate metabolism and ATP synthesis in MS and NMO derived CSF treated OPCs. In addition, using STRING program, we investigate whether gene–gene interaction affected the whole network in our experimental conditions. Our findings revealed downregulated expression of genes involved in carbohydrate metabolism, and that glucose metabolism impairment and reduced ATP availability for cellular damage repair clearly differentiate more benign forms from the most aggressive forms and worst prognosis in MS patients.
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Affiliation(s)
- Deepali Mathur
- Department of Functional Biology, University of ValenciaValencia, Spain.,Department of Biochemistry and Molecular Biology, INCLIVA Biomedical Research Institute, University of ValenciaValencia, Spain
| | - Angela L Riffo-Campos
- Department of Biochemistry and Molecular Biology, INCLIVA Biomedical Research Institute, University of ValenciaValencia, Spain.,Laboratory of Molecular Pathology, Faculty of Medicine, University of La FronteraTemuco, Chile
| | - Josefa Castillo
- Department of Biochemistry and Molecular Biology, INCLIVA Biomedical Research Institute, University of ValenciaValencia, Spain
| | - Jeffery D Haines
- Department of Neuroscience, Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New YorkNY, United States
| | - Oscar G Vidaurre
- Department of Neuroscience, Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New YorkNY, United States
| | - Fan Zhang
- Department of Neuroscience, Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New YorkNY, United States
| | | | - Patrizia Casaccia
- Department of Neuroscience, Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New YorkNY, United States
| | - Bonaventura Casanova
- CSUR-Esclerosi Múltiple, Unitat Mixta d'Esclerosi Múltiple i Neurorregeneració del'IIS-La Fe, Hospital Universitari i Politécnic La FeValencia, Spain
| | - Gerardo Lopez-Rodas
- Department of Biochemistry and Molecular Biology, INCLIVA Biomedical Research Institute, University of ValenciaValencia, Spain
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59
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Guelfi G, Stefanetti V, De Luca S, Giontella A, Barile VL, Barbato O. Serum microRNAs in buffalo cows: Potential biomarkers of pregnancy. Res Vet Sci 2017. [PMID: 28628844 DOI: 10.1016/j.rvsc.2017.06.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
MiRNAs (microRNA) constitute a large family of single-stranded, non-coding small RNAs. Although the functions and target genes of most miRNAs are still unknown, it has been well established that they are involved in embryogenesis, organogenesis and neonatal birth. In recent decades, interest in buffalo breeding has largely increased worldwide thus focusing the attention on this species as a dairy purpose animal. Problems related to long calving interval, late puberty and seasonal anestrus hamper reproductive efficiency in this species. Early pregnancy diagnosis is important to shorten the calving interval and increase lifetime production on dairy animals. MicroRNAs have recently emerged as key molecules in fertilization of several species even though in buffalo, few previous studies have investigated miRNAs. The aim of this research was to identify the best miRNA reference in serum among miR-191, miR-25-3p, SNORD44, and SNORD48. Consequently, assess the expression levels of miR-103, miR-200b, miR-301a, miR-423-5p, miR-375, miR-451 and miR-452 involved in buffalo progesterone-maturation oocyte and pregnancy. Interestingly, we found that all the miRNAs analyzed at 40days after artificial insemination were differentially expressed among pregnant and non-pregnant buffalo. Our research may be a first step for gain further insight in the biological function of circulating miRNAs in this species.
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Affiliation(s)
- Gabriella Guelfi
- Department of Veterinary Medicine, via San Costanzo 4, 06126 Perugia, Italy.
| | | | - Silvio De Luca
- Department of Veterinary Medicine, via San Costanzo 4, 06126 Perugia, Italy
| | - Andrea Giontella
- Department of Veterinary Medicine, via San Costanzo 4, 06126 Perugia, Italy
| | - Vittoria Lucia Barile
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria (CREA), Animal Production Research Centre, Monterotondo, 00015, Rome, Italy
| | - Olimpia Barbato
- Department of Veterinary Medicine, via San Costanzo 4, 06126 Perugia, Italy
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60
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Piazza VG, Bartke A, Miquet JG, Sotelo AI. Analysis of Different Approaches for the Selection of Reference Genes in RT-qPCR Experiments: A Case Study in Skeletal Muscle of Growing Mice. Int J Mol Sci 2017; 18:ijms18051060. [PMID: 28509880 PMCID: PMC5454972 DOI: 10.3390/ijms18051060] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2017] [Revised: 05/09/2017] [Accepted: 05/11/2017] [Indexed: 11/18/2022] Open
Abstract
The reliability of reverse transcription-quantitative PCR (RT-qPCR) results in gene expression studies depends on the approaches used to account for non-biological variations. In order to find a proper normalization strategy for the study of genes related to growth hormone signaling in skeletal muscle of growing mice, nine unrelated genes were evaluated as internal controls. According to the most used algorithms–geNorm, the Comparative ΔCq method, NormFinder and BestKeeper–GSK3B, YWHAZ, RPL13A and RN18S were found as the most stable. However, the relative expression levels of eight of the potential reference genes assessed decreased with age in cDNA samples obtained from the same amount of total RNA. In a different approach to analyze this apparent discrepancy, experiments were performed with cDNA obtained from equal amounts of purified mRNA. Since the decline was still observed, the hypothesis of an age-related change in mRNA to total RNA ratio that could account for the systematic decrease was rejected. Differences among experimental groups could be due to a substantial increase with age in highly expressed mRNAs, which would bias the quantitation of the remaining genes. Consequently, those reference genes reflecting this dilution effect, which would have been discarded considering their variable relative expression levels, arose as suitable internal controls.
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Affiliation(s)
- Verónica G Piazza
- Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Instituto de Química y Fisicoquímica Biológicas (IQUIFIB), Facultad de Farmacia y Bioquímica, Buenos Aires C1113AAD, Argentina.
| | - Andrzej Bartke
- Department of Internal Medicine and Physiology, Division of Geriatric Research, School of Medicine, Southern Illinois University, Springfield, IL 62794-9628, USA.
| | - Johanna G Miquet
- Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Instituto de Química y Fisicoquímica Biológicas (IQUIFIB), Facultad de Farmacia y Bioquímica, Buenos Aires C1113AAD, Argentina.
| | - Ana I Sotelo
- Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Instituto de Química y Fisicoquímica Biológicas (IQUIFIB), Facultad de Farmacia y Bioquímica, Buenos Aires C1113AAD, Argentina.
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61
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Sagri E, Koskinioti P, Gregoriou ME, Tsoumani KT, Bassiakos YC, Mathiopoulos KD. Housekeeping in Tephritid insects: the best gene choice for expression analyses in the medfly and the olive fly. Sci Rep 2017; 7:45634. [PMID: 28368031 PMCID: PMC5377319 DOI: 10.1038/srep45634] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 03/01/2017] [Indexed: 02/07/2023] Open
Abstract
Real-time quantitative-PCR has been a priceless tool for gene expression analyses. The reaction, however, needs proper normalization with the use of housekeeping genes (HKGs), whose expression remains stable throughout the experimental conditions. Often, the combination of several genes is required for accurate normalization. Most importantly, there are no universal HKGs which can be used since their expression varies among different organisms, tissues or experimental conditions. In the present study, nine common HKGs (RPL19, tbp, ubx, GAPDH, α-TUB, β-TUB, 14-3-3zeta, RPE and actin3) are evaluated in thirteen different body parts, developmental stages and reproductive and olfactory tissues of two insects of agricultural importance, the medfly and the olive fly. Three software programs based on different algorithms were used (geNorm, NormFinder and BestKeeper) and gave different ranking of HKG stabilities. This confirms once again that the stability of common HKGs should not be taken for granted and demonstrates the caution that is needed in the choice of the appropriate HKGs. Finally, by estimating the average of a standard score of the stability values resulted by the three programs we were able to provide a useful consensus key for the choice of the best HKG combination in various tissues of the two insects.
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Affiliation(s)
- Efthimia Sagri
- Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
| | - Panagiota Koskinioti
- Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
| | - Maria-Eleni Gregoriou
- Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
| | | | - Yiannis C Bassiakos
- Department of Economic Sciences, National and Kapodistrian University of Athens, Athens, 10559, Greece
| | - Kostas D Mathiopoulos
- Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
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Volland M, Blasco J, Hampel M. Validation of reference genes for RT-qPCR in marine bivalve ecotoxicology: Systematic review and case study using copper treated primary Ruditapes philippinarum hemocytes. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2017; 185:86-94. [PMID: 28189915 DOI: 10.1016/j.aquatox.2017.01.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2016] [Revised: 01/06/2017] [Accepted: 01/09/2017] [Indexed: 06/06/2023]
Abstract
The appropriate selection of reference genes for the normalization of non-biological variance in reverse transcription real-time quantitative PCR (RT-qPCR) is essential for the accurate interpretation of the collected data. The use of multiple validated reference genes has been shown to substantially increase the robustness of the normalization. It is therefore considered good practice to validate putative genes under specific conditions, determine the optimal number of genes to be employed, and report the method or methods used. Under this premise, we assessed the current state of reference gene based normalization in RT-qPCR bivalve ecotoxicology studies (post 2011), employing a systematic quantitative literature review. A total of 52 papers met our criteria and were analysed for genes used, the use of multiple reference genes, as well as the validation method employed. We further critically discuss methods for reference gene validation based on a case study using copper exposed primary hemocytes from the marine bivalve Ruditapes philippinarum; including the established algorithms geNorm, NormFinder and BestKeeper, as well as the popular online tool RefFinder. We identified that RT-qPCR normalization is largely performed using single reference genes, while less than 40% of the studies attempted to experimentally validate the expression stability of the genes used. 18s rRNA and β-Actin were the most popular genes, yet their un-validated use did introduce artefactual variance that altered the interpretation of the resulting data. Our findings further suggest that combining the results from multiple individual algorithms and calculating the overall best-ranked gene, as computed by the RefFinder tool, does not by default lead to the identification of the most suitable reference genes.
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Affiliation(s)
- Moritz Volland
- Instituto de Ciencias Marinas de Andalucía (CSIC), Campus Universitario Río San Pedro s/n, 11510 Puerto Real, Cadiz, Spain.
| | - Julián Blasco
- Instituto de Ciencias Marinas de Andalucía (CSIC), Campus Universitario Río San Pedro s/n, 11510 Puerto Real, Cadiz, Spain
| | - Miriam Hampel
- Department for Physical Chemistry, Faculty of Marine and Environmental Sciences, University of Cadiz, Campus Universitario Río San Pedro s/n, 11510 Puerto Real, Cadiz, Spain; Andalusian Center of Marine Science and Technology (CACYTMAR), Campus Universitario Río San Pedro s/n, 11510 Puerto Real, Cadiz, Spain
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63
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Batra A, Maier HJ, Fife MS. Selection of reference genes for gene expression analysis by real-time qPCR in avian cells infected with infectious bronchitis virus. Avian Pathol 2017; 46:173-180. [PMID: 27624876 DOI: 10.1080/03079457.2016.1235258] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Accepted: 08/19/2016] [Indexed: 10/21/2022]
Abstract
Infectious bronchitis virus (IBV) causes infectious bronchitis in poultry, a respiratory disease that is a source of major economic loss to the poultry industry. Detection and the study of the molecular pathogenesis of the virus often involve the use of real-time quantitative PCR assays (qPCR). To account for error within the experiments, the levels of target gene transcription are normalized to that of suitable reference genes. Despite publication of the MIQE (Minimum Information for Publication of Quantitative Real-Time PCR Experiments) guidelines in 2009, single un-tested reference genes are often used for normalization of qPCR assays in avian research studies. Here, we use the geNorm algorithm to identify suitable reference genes in different avian cell types during infection with apathogenic and pathogenic strains of IBV. We discuss the importance of selecting an appropriate experimental sample subset for geNorm analysis, and show the effect that this selection can have on resultant reference gene selection. The effects of inappropriate normalization on the transcription pattern of a cellular signalling gene, AKT1, and the interferon-inducible, MX1, were studied. We identify the possibility of the misinterpretation of qPCR data when an inappropriate normalization strategy is employed. This is most notable when measuring the transcription of AKT1, where changes are minimal during infection.
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Affiliation(s)
- Ambalika Batra
- a Avian Viral Diseases , The Pirbright Institute , Pirbright , UK
- b Institute of Infection and Global Health, University of Liverpool , Liverpool , UK
| | - Helena J Maier
- a Avian Viral Diseases , The Pirbright Institute , Pirbright , UK
| | - Mark S Fife
- a Avian Viral Diseases , The Pirbright Institute , Pirbright , UK
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64
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Usarek E, Barańczyk-Kuźma A, Kaźmierczak B, Gajewska B, Kuźma-Kozakiewicz M. Validation of qPCR reference genes in lymphocytes from patients with amyotrophic lateral sclerosis. PLoS One 2017; 12:e0174317. [PMID: 28328930 PMCID: PMC5362213 DOI: 10.1371/journal.pone.0174317] [Citation(s) in RCA: 9] [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: 06/23/2016] [Accepted: 03/07/2017] [Indexed: 12/12/2022] Open
Abstract
Quantitative polymerase chain reaction (qPCR) is the most specific and reliable method for determination of mRNA gene expression. Crucial point for its accurate normalization is the choice of appropriate internal control genes (ICGs). In the present work we determined and compare the expression of eight commonly used ICGs in lymphocytes from 26 patients with amyotrophic lateral sclerosis (ALS) and 30 control subjects. Peripheral blood mononuclear cells (PBMCs) before and after immortalization by EBV transfection (lymphoblast cell lines—LCLs) were used for qPCR analysis. LCLs were studied before and after liquid nitrogen cryopreservation and culturing (groups LCL1 and LCL2, respectively). qPCR data of 8 ICGs expression was analyzed by BestKeeper, NormFinder and geNorm methods. All studied genes (18SRNA, ACTB, B2M, GUSB,GAPDH, HPRT1, MT-ATP6 and RPS17) were expressed in PBMCs, whereas only first four in LCLs. LCLs cryopreservation had no effect on ICGs expression. Comprehensive ranking indicated RPS17 with MT-ATP6 as the best ICGs for qPCR in PBMCs of control and ALS subjects, and RPS17 with 18RNA or MT-ATP6 in LCLs from ALS. In PBMCs 18RNA shouldn’t be used as ICG.
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Affiliation(s)
- Ewa Usarek
- Department of Biochemistry, Medical University of Warsaw, Warsaw, Poland
| | - Anna Barańczyk-Kuźma
- Department of Biochemistry, Medical University of Warsaw, Warsaw, Poland
- Neurodegenerative Diseases Research Group, Medical University of Warsaw, Warsaw, Poland
| | - Beata Kaźmierczak
- Department of Biochemistry, Medical University of Warsaw, Warsaw, Poland
- Neurodegenerative Diseases Research Group, Medical University of Warsaw, Warsaw, Poland
| | - Beata Gajewska
- Department of Biochemistry, Medical University of Warsaw, Warsaw, Poland
- Neurodegenerative Diseases Research Group, Medical University of Warsaw, Warsaw, Poland
| | - Magdalena Kuźma-Kozakiewicz
- Neurodegenerative Diseases Research Group, Medical University of Warsaw, Warsaw, Poland
- Department of Neurology, Medical University of Warsaw, Warsaw, Poland
- * E-mail:
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65
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El Hadi H, Abdellaoui-Maane I, Kottwitz D, El Amrani M, Bouchoutrouch N, Qmichou Z, Karkouri M, ElAttar H, Errihani H, Fernandez PL, Bakri Y, Sefrioui H, Moumen A. Development and evaluation of a novel RT-qPCR based test for the quantification of HER2 gene expression in breast cancer. Gene 2017; 605:114-122. [DOI: 10.1016/j.gene.2016.12.027] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Revised: 12/08/2016] [Accepted: 12/23/2016] [Indexed: 10/20/2022]
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66
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Hernández PA, Mendoza GD, Castro A, Lara A, Plata FX, Martínez JA, Ferraro S. Effects of grain level on lamb performance, ruminal metabolism and leptin mRNA expression in perirenal adipose tissue. ANIMAL PRODUCTION SCIENCE 2017. [DOI: 10.1071/an15564] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The effects of four different grain composition diets of finishing lambs on lamb performance, dry matter (DM) digestibility, rumen fermentation and leptin mRNA expression were evaluated. Thirty-two Pelibuey lambs (25.35 ± 4.73 kg bodyweight) were used in a completely randomised experiment in which lambs were fed diets that contained 30%, 45%, 60% or 75% grain (DM basis). The results indicated that increasing the grain level improved the average daily weight gain, hot carcass weight, DM digestibility and feed conversion linearly (P < 0.01); however, feed intake was not affected. Ruminal pH decreased linearly as the grain content was increased (P < 0.01). Ruminal propionate concentration increased and acetate concentration declined with increased grain content (P < 0.01). Leptin mRNA expression in perirenal adipose tissue increased linearly (P < 0.05) as grain content increased. Based on these results, we conclude that increasing grain level in the diets of finishing feedlot lambs improved weight gain and feed efficiency; however, because weight gain and feed efficiency were similar at the higher grain levels, our data suggest including 60% grain in lamb finishing rations.
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Ranganathan S, Ningappa M, Ashokkumar C, Higgs BW, Min J, Sun Q, Schmitt L, Subramaniam S, Hakonarson H, Sindhi R. Loss of EGFR-ASAP1 signaling in metastatic and unresectable hepatoblastoma. Sci Rep 2016; 6:38347. [PMID: 27910913 PMCID: PMC5133573 DOI: 10.1038/srep38347] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 11/09/2016] [Indexed: 02/08/2023] Open
Abstract
Hepatoblastoma (HBL), the most common childhood liver cancer is cured with surgical resection after chemotherapy or with liver transplantation if local invasion and multifocality preclude resection. However, variable survival rates of 60-80% and debilitating chemotherapy sequelae argue for more informed treatment selection, which is not possible by grading the Wnt-β-catenin over activity present in most HBL tumors. A hypothesis-generating whole transcriptome analysis shows that HBL tumors removed at transplantation are enriched most for cancer signaling pathways which depend predominantly on epidermal growth factor (EGF) signaling, and to a lesser extent, on aberrant Wnt-β-catenin signaling. We therefore evaluated whether EGFR, ASAP1, ERBB2 and ERBB4, which signal downstream after ligation of EGF, and which show aberrant expression in several other invasive cancers, would also predict HBL tumor invasiveness. Immunohistochemistry of HBL tumors (n = 60), which are histologically heterogeneous, shows that compared with well-differentiated fetal cells, less differentiated embryonal and undifferentiated small cells (SCU) progressively lose EGFR and ASAP1 expression. This trend is exaggerated in unresectable, locally invasive or metastatic tumors, in which embryonal tumor cells are EGFR-negative, while SCU cells are EGFR-negative and ASAP1-negative. Loss of EGFR-ASAP1 signaling characterizes undifferentiated and invasive HBL. EGFR-expressing HBL tumors present novel therapeutic targeting opportunities.
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Affiliation(s)
- Sarangarajan Ranganathan
- Children’s Hospital of Pittsburgh of University of Pittsburgh Medical Center, 4401 Penn Avenue, Department of Pathology, Pittsburgh, PA 15224, USA
| | - Mylarappa Ningappa
- Children’s Hospital of Pittsburgh of University of Pittsburgh Medical Center, 4401 Penn Avenue, Pediatric Abdominal Transplant Surgery, Pittsburgh, PA 15224, USA
| | - Chethan Ashokkumar
- Children’s Hospital of Pittsburgh of University of Pittsburgh Medical Center, 4401 Penn Avenue, Pediatric Abdominal Transplant Surgery, Pittsburgh, PA 15224, USA
| | - Brandon W. Higgs
- Children’s Hospital of Pittsburgh of University of Pittsburgh Medical Center, 4401 Penn Avenue, Pediatric Abdominal Transplant Surgery, Pittsburgh, PA 15224, USA
| | - Jun Min
- Department of Bioengineering, University of California San Diego, LA Jolla, CA, USA
| | - Qing Sun
- Children’s Hospital of Pittsburgh of University of Pittsburgh Medical Center, 4401 Penn Avenue, Pediatric Abdominal Transplant Surgery, Pittsburgh, PA 15224, USA
| | - Lori Schmitt
- Children’s Hospital of Pittsburgh of University of Pittsburgh Medical Center, 4401 Penn Avenue, Department of Pathology, Pittsburgh, PA 15224, USA
| | - Shankar Subramaniam
- Department of Bioengineering, University of California San Diego, LA Jolla, CA, USA
| | - Hakon Hakonarson
- Center for Applied Genomics, Children’s Hospital of Philadelphia, 1216 E. Abramson’s Research Center, 34th and Civic Center Blvd., ARC 1216E, Philadelphia, PA. 19104, USA
| | - Rakesh Sindhi
- Children’s Hospital of Pittsburgh of University of Pittsburgh Medical Center, 4401 Penn Avenue, Pediatric Abdominal Transplant Surgery, Pittsburgh, PA 15224, USA
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68
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An H, Zhu Q, Pei W, Fan J, Liang Y, Cui Y, Lv N, Wang W. Whole-Transcriptome Selection and Evaluation of Internal Reference Genes for Expression Analysis in Protocorm Development of Dendrobium officinale Kimura et Migo. PLoS One 2016; 11:e0163478. [PMID: 27814359 PMCID: PMC5096709 DOI: 10.1371/journal.pone.0163478] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Accepted: 09/10/2016] [Indexed: 11/18/2022] Open
Abstract
Dendrobium officinale Kimu et Migo has increased many researchers' interest for its high medical and horticultural values and the molecular mechanism of its protocorm development remains unclear. In this study, 19 genes from 26 most stably expressed genes in whole transcriptome of protocorms and 5 housekeeping genes were used as candidate reference genes and screened with 4 application softwares (geNorm, NormFinder, BestKeeper and RefFinder). The results showed that a few reference genes could effectively normalize expression level of specific genes in protocorm development and the optimal top 2 reference genes were ASS and APH1L. Meanwhile, validation of GNOM, AP2 and temperature induced gene (TIL) for normalization demonstrates the usefulness of the validated candidate reference genes. The expression profiles of these genes varied under protocorms and temperature stress according to the stablest and unstablest reference genes, which proved the importance of the choice of appropriate reference genes. The first systematic evaluation of stably expressed genes will be very useful in the future analysis of specific genes expression in D. officinale.
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Affiliation(s)
- Hongqiang An
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu 610031, the People’s Republic of China
| | - Qiankun Zhu
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu 610031, the People’s Republic of China
| | - Wei Pei
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu 610031, the People’s Republic of China
| | - Jing Fan
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu 610031, the People’s Republic of China
| | - Yi Liang
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu 610031, the People’s Republic of China
| | - Yihui Cui
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu 610031, the People’s Republic of China
| | - Nan Lv
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu 610031, the People’s Republic of China
| | - Wanjun Wang
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu 610031, the People’s Republic of China
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69
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Ham S, Harrison C, Southwick G, Temple-Smith P. Selection of internal control genes for analysis of gene expression in normal and diseased human dermal fibroblasts using quantitative real-time PCR. Exp Dermatol 2016; 25:911-914. [DOI: 10.1111/exd.13091] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/25/2016] [Indexed: 11/26/2022]
Affiliation(s)
- Seungmin Ham
- Hudson Institute of Medical Research; Monash University; Melbourne Vic. Australia
- Department of Obstetrics and Gynaecology; Monash University; Melbourne Vic. Australia
| | - Craig Harrison
- Hudson Institute of Medical Research; Monash University; Melbourne Vic. Australia
- Department of Biochemistry and Molecular Biology; Monash University; Melbourne Vic. Australia
| | - Graeme Southwick
- Hudson Institute of Medical Research; Monash University; Melbourne Vic. Australia
- Department of Anatomy and Developmental Biology; Monash University; Melbourne Vic. Australia
- Melbourne Institute of Plastic Surgery, Malvern; Vic. Australia
| | - Peter Temple-Smith
- Hudson Institute of Medical Research; Monash University; Melbourne Vic. Australia
- Department of Obstetrics and Gynaecology; Monash University; Melbourne Vic. Australia
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70
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Cellular thiamine status is coupled to function of mitochondrial 2-oxoglutarate dehydrogenase. Neurochem Int 2016; 101:66-75. [PMID: 27773789 DOI: 10.1016/j.neuint.2016.10.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Revised: 10/16/2016] [Accepted: 10/17/2016] [Indexed: 12/15/2022]
Abstract
Decreased thiamine and reduced activity of thiamine diphosphate (ThDP)-dependent 2-oxoglutarate dehydrogenase (OGDH) cause neurodegeneration. We hypothesized on concerted cell-specific regulation of the thiamine metabolism and ThDP-dependent reactions. We identified a smaller thiamine pool, a lower expression of the mitochondrial ThDP transporter, and a higher expression of OGDH in rat astrocytes versus neuroblastoma N2A. According to the data, the astrocytic OGDH may be up-regulated by an increase in intracellular ThDP, while the neuroblastomal OGDH functions at full ThDP saturation. Indeed, in rat astrocytes and brain cortex, OGDH inhibition by succinyl phosphonate (SP) enlarged the pool of thiamine compounds. Increased ThDP level in response to the OGDH inhibition presumably up-regulated the enzyme to compensate for a decrease in reducing power which occurred in SP-treated astrocytes. Under the same SP treatment of N2A cells, their thiamine pool and reducing power were unchanged, although SP action was evident from accumulation of glutamate. The presented data indicate that functional interplay between OGDH, other proteins of the tricarbocylic acid cycle and proteins of thiamine metabolism is an important determinant of physiology-specific networks and their homeostatic mechanisms.
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71
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Harrison OJ, Moorjani N, Torrens C, Ohri SK, Cagampang FR. Endogenous Reference Genes for Gene Expression Studies on Bicuspid Aortic Valve Associated Aortopathy in Humans. PLoS One 2016; 11:e0164329. [PMID: 27727313 PMCID: PMC5058495 DOI: 10.1371/journal.pone.0164329] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 09/25/2016] [Indexed: 01/18/2023] Open
Abstract
Bicuspid aortic valve (BAV) disease is the most common congenital cardiac abnormality and predisposes patients to life-threatening aortic complications including aortic aneurysm. Quantitative real-time reverse transcription PCR (qRT-PCR) is one of the most commonly used methods to investigate underlying molecular mechanisms involved in aortopathy. The accuracy of the gene expression data is dependent on normalization by appropriate housekeeping (HK) genes, whose expression should remain constant regardless of aortic valve morphology, aortic diameter and other factors associated with aortopathy. Here, we identified an appropriate set of HK genes to be used as endogenous reference for quantifying gene expression in ascending aortic tissue using a spin column-based RNA extraction method. Ascending aortic biopsies were collected intra-operatively from patients undergoing aortic valve and/or ascending aortic surgery. These patients had BAV or tricuspid aortic valve (TAV), and the aortas were either dilated (≥4.5cm) or undilated. The cohort had an even distribution of gender, valve disease and hypertension. The expression stability of 12 reference genes were investigated (ATP5B, ACTB, B2M, CYC1, EIF4A2, GAPDH, SDHA, RPL13A, TOP1, UBC, YWHAZ, and 18S) using geNorm software. The most stable HK genes were found to be GAPDH, UBC and ACTB. Both GAPDH and UBC demonstrated relative stability regardless of valve morphology, aortic diameter, gender and age. The expression of B2M and SDHA were found to be the least stable HK genes. We propose the use of GAPDH, UBC and ACTB as reference genes for gene expression studies of BAV aortopathy using ascending aortic tissue.
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Affiliation(s)
- Oliver J. Harrison
- Institute of Developmental Sciences, University of Southampton Faculty of Medicine, Southampton, United Kingdom
- * E-mail:
| | - Narain Moorjani
- Department of Cardiac Surgery, Papworth Hospital NHS Foundation Trust, Cambridge, United Kingdom
| | - Christopher Torrens
- Institute of Developmental Sciences, University of Southampton Faculty of Medicine, Southampton, United Kingdom
| | - Sunil K. Ohri
- Department of Cardiac Surgery, University Hospital Southampton, Southampton, United Kingdom
| | - Felino R. Cagampang
- Institute of Developmental Sciences, University of Southampton Faculty of Medicine, Southampton, United Kingdom
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72
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Ortega Serrano PV, Guzmán A, Hernández-Coronado CG, Castillo-Juárez H, Rosales-Torres AM. Reduction in the mRNA expression of sVEGFR1 and sVEGFR2 is associated with the selection of dominant follicle in cows. Reprod Domest Anim 2016; 51:985-991. [PMID: 27650571 DOI: 10.1111/rda.12777] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 08/02/2016] [Indexed: 11/28/2022]
Abstract
The vascular endothelial growth factor (VEGF) is essential for follicular development by promoting follicular angiogenesis, as well as for the proliferation and survival of granulosa cells. The biological effects of VEGF are regulated by two membrane receptors, VEGFR1 and VEGFR2, and two soluble receptors, sVEGFR1 and sVEGFR2, which play an antagonistic role. Thus, the objective of this study was to identify the mRNA expression pattern of total VEGF, VEGFR1, VEGFR2, sVEGFR1 and sVEGFR2 in bovine preselected follicles (PRF) and post-selected follicles (POF). The mRNA expression of these five genes in both granulosa cells (GC) and theca cells (TC) was compared between follicles classified as PRF and POF based on their diameter and on their ratio of estradiol/progesterone (E2/P4). Results showed a lower expression of mRNA of sVEGFR1 and sVEGFR2 in POF than in PRF (p < .05). Regarding the mRNA expression of total VEGF, VEGFR1 and VEGFR2, there was no difference between POF and PRF follicles (p > .05). Our results showed that the mRNA expression of VEGFR2 and sVEGFR1 was more abundant than the expression of VEGFR1 and sVEGFR2, while GC was the main source of mRNA for total VEGF. On the other hand, TC was the follicular compartment where the receptors were most expressed. Our results suggest that non-dominant follicles maintain a greater concentration of the mRNA expression of both membrane and soluble VEGF receptors. On the other hand, follicular dominance is related to a reduction in the mRNA expression of sVEGFR1 and sVEGFR2, which may favour VEGF binding with VEGFR2 and, hence, improve the follicular health and development.
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Affiliation(s)
- P V Ortega Serrano
- Universidad Autónoma Metropolitana-Xochimilco Estudiante de Posgrado en Ciencias Agropecuarias, Ciudad de México, México
| | - A Guzmán
- Laboratorio Bioquímica de la Reproducción, Departamento de Producción Agrícola y Animal, Universidad Autónoma Metropolitana-Xochimilco, Ciudad de México, México
| | - C G Hernández-Coronado
- Universidad Autónoma Metropolitana-Xochimilco Estudiante de Posgrado en Ciencias Agropecuarias, Ciudad de México, México
| | - H Castillo-Juárez
- Laboratorio Bioquímica de la Reproducción, Departamento de Producción Agrícola y Animal, Universidad Autónoma Metropolitana-Xochimilco, Ciudad de México, México
| | - A M Rosales-Torres
- Laboratorio Bioquímica de la Reproducción, Departamento de Producción Agrícola y Animal, Universidad Autónoma Metropolitana-Xochimilco, Ciudad de México, México
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73
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Klenke S, Renckhoff K, Engler A, Peters J, Frey UH. Easy-to-use strategy for reference gene selection in quantitative real-time PCR experiments. Naunyn Schmiedebergs Arch Pharmacol 2016; 389:1353-1366. [PMID: 27650728 DOI: 10.1007/s00210-016-1305-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Accepted: 09/09/2016] [Indexed: 12/19/2022]
Abstract
Real-time PCR is an indispensable technique for mRNA expression analysis but conclusions depend on appropriate reference gene selection. However, while reference gene selection has been a topic of publications, this issue is often disregarded when measuring target mRNA expression. Therefore, we (1) evaluated the frequency of appropriate reference gene selection, (2) suggest an easy-to-use tool for least variability reference gene selection, (3) demonstrate application of this tool, and (4) show effects on target gene expression profiles. All 2015 published articles in Naunyn-Schmiedeberg's Archives of Pharmacology were screened for the use of quantitative real-time PCR analysis and selection of reference genes. Target gene expression (Vegfa, Grk2, Sirt4, and Timp3) in H9c2 cells was analyzed following various interventions (hypoxia, hyperglycemia, and/or isoflurane exposure with and without subsequent hypoxia) in relation to putative reference genes (Actb, Gapdh, B2m, Sdha, and Rplp1) using the least variability method vs. an arbitrarily selected but established reference gene. In the vast majority (18 of 21) of papers, no information was provided regarding selection of an appropriate reference gene. In only 1 of 21 papers, a method of appropriate reference gene selection was described and in 2 papers reference gene selection remains unclear. The method of reference gene selection had major impact on interpretation of target gene expression. With hypoxia, for instance, the least variability gene was Rplp1 and target gene expression (Vefga) heavily showed a 2-fold up-regulation (p = 0.022) but no change (p = 0.3) when arbitrarily using Gapdh. Frequency of appropriate reference gene selection in this journal is low, and we propose our strategy for reference gene selection as an easy tool for proper target gene expression.
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Affiliation(s)
- Stefanie Klenke
- Klinik für Anästhesiologie & Intensivmedizin, Universität Duisburg-Essen and Universitätsklinikum Essen, Hufelandstr. 55, D-45122, Essen, Germany.
| | - Kristina Renckhoff
- Klinik für Anästhesiologie & Intensivmedizin, Universität Duisburg-Essen and Universitätsklinikum Essen, Hufelandstr. 55, D-45122, Essen, Germany
| | - Andrea Engler
- Klinik für Anästhesiologie & Intensivmedizin, Universität Duisburg-Essen and Universitätsklinikum Essen, Hufelandstr. 55, D-45122, Essen, Germany
| | - Jürgen Peters
- Klinik für Anästhesiologie & Intensivmedizin, Universität Duisburg-Essen and Universitätsklinikum Essen, Hufelandstr. 55, D-45122, Essen, Germany
| | - Ulrich H Frey
- Klinik für Anästhesiologie & Intensivmedizin, Universität Duisburg-Essen and Universitätsklinikum Essen, Hufelandstr. 55, D-45122, Essen, Germany
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74
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Su X, Yao X, Sun Z, Han Q, Zhao RC. Optimization of Reference Genes for Normalization of Reverse Transcription Quantitative Real-Time Polymerase Chain Reaction Results in Senescence Study of Mesenchymal Stem Cells. Stem Cells Dev 2016; 25:1355-65. [PMID: 27484587 DOI: 10.1089/scd.2016.0031] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Recently, it has been suggested that cellular senescence is associated with stem cell exhaustion, which reduces the regenerative potential of tissues and contributes to aging and age-related diseases. Mesenchymal stem cells (MSCs) attract a large amount of attention in stem cell research and regeneration medicine because they possess multiple advantages and senescent MSCs could be one of the most useful stem cell models in aging studies. It is important to quantitatively evaluate senescence markers to both identify and study the mechanisms involved in MSC senescence. Reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR) is currently the most widely used tool to quantify the mRNA levels of markers. However, no report has demonstrated the optimal reference genes that should be used to normalize RT-qPCR in senescence studies of MSCs. In this study, we compared 16 commonly used reference genes (GAPDH, ACTB, RPL13A, TBP, B2M, GUSB, RPLPO, YWHAZ, RPS18, EEF1A1, ATP5F1, HPRT1, PGK1, TFRC, UBC, and PPIA) in proliferating or replicative-senescent human adipose-derived MSCs (hAD-MSCs) that were isolated from seven healthy donors aged 29-59 years old. Three algorithms (geNorm, NormFinder, and BestKeeper) were used to determine the most optimal reference gene. The results showed that PPIA exhibited the most stable expression during senescence, while the widely used ACTB exhibited the lowest stability. We also confirmed that different reference genes lead to different evaluations of senescence markers. Our work ensures that results obtained from senescence studies of hAD-MSCs will be appropriately evaluated in both basic research and clinical trials.
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Affiliation(s)
- Xiaodong Su
- 1 Institute of Basic Medical Sciences, School of Basic Medicine, Peking Union Medical College, Center of Excellence in Tissue Engineering, Chinese Academy of Medical Sciences , Beijing, People's Republic of China
| | - Xinglei Yao
- 1 Institute of Basic Medical Sciences, School of Basic Medicine, Peking Union Medical College, Center of Excellence in Tissue Engineering, Chinese Academy of Medical Sciences , Beijing, People's Republic of China .,2 State Key Laboratory of Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences , Beijing, People's Republic of China
| | - Zhao Sun
- 3 Department of Oncology, School of Basic Medicine, Peking Union Medical College, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences , Beijing, People's Republic of China
| | - Qin Han
- 1 Institute of Basic Medical Sciences, School of Basic Medicine, Peking Union Medical College, Center of Excellence in Tissue Engineering, Chinese Academy of Medical Sciences , Beijing, People's Republic of China
| | - Robert Chunhua Zhao
- 1 Institute of Basic Medical Sciences, School of Basic Medicine, Peking Union Medical College, Center of Excellence in Tissue Engineering, Chinese Academy of Medical Sciences , Beijing, People's Republic of China
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75
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Liu F, Guo DD, Tu YH, Xue YR, Gao Y, Guo ML. Identification of reference genes for gene expression normalization in safflower (Carthamus tinctorius). REVISTA BRASILEIRA DE FARMACOGNOSIA-BRAZILIAN JOURNAL OF PHARMACOGNOSY 2016. [DOI: 10.1016/j.bjp.2016.05.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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76
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Screening Reliable Reference Genes for RT-qPCR Analysis of Gene Expression in Moringa oleifera. PLoS One 2016; 11:e0159458. [PMID: 27541138 PMCID: PMC4991797 DOI: 10.1371/journal.pone.0159458] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 07/01/2016] [Indexed: 01/29/2023] Open
Abstract
Moringa oleifera is a promising plant species for oil and forage, but its genetic improvement is limited. Our current breeding program in this species focuses on exploiting the functional genes associated with important agronomical traits. Here, we screened reliable reference genes for accurately quantifying the expression of target genes using the technique of real-time quantitative polymerase chain reaction (RT-qPCR) in M. oleifera. Eighteen candidate reference genes were selected from a transcriptome database, and their expression stabilities were examined in 90 samples collected from the pods in different developmental stages, various tissues, and the roots and leaves under different conditions (low or high temperature, sodium chloride (NaCl)- or polyethyleneglycol (PEG)- simulated water stress). Analyses with geNorm, NormFinder and BestKeeper algorithms revealed that the reliable reference genes differed across sample designs and that ribosomal protein L1 (RPL1) and acyl carrier protein 2 (ACP2) were the most suitable reference genes in all tested samples. The experiment results demonstrated the significance of using the properly validated reference genes and suggested the use of more than one reference gene to achieve reliable expression profiles. In addition, we applied three isotypes of the superoxide dismutase (SOD) gene that are associated with plant adaptation to abiotic stress to confirm the efficacy of the validated reference genes under NaCl and PEG water stresses. Our results provide a valuable reference for future studies on identifying important functional genes from their transcriptional expressions via RT-qPCR technique in M. oleifera.
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77
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Chao J, Yang S, Chen Y, Tian WM. Evaluation of Reference Genes for Quantitative Real-Time PCR Analysis of the Gene Expression in Laticifers on the Basis of Latex Flow in Rubber Tree (Hevea brasiliensis Muell. Arg.). FRONTIERS IN PLANT SCIENCE 2016; 7:1149. [PMID: 27524995 PMCID: PMC4965454 DOI: 10.3389/fpls.2016.01149] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Accepted: 07/18/2016] [Indexed: 05/29/2023]
Abstract
Latex exploitation-caused latex flow is effective in enhancing latex regeneration in laticifer cells of rubber tree. It should be suitable for screening appropriate reference gene for analysis of the expression of latex regeneration-related genes by quantitative real-time PCR (qRT-PCR). In the present study, the expression stability of 23 candidate reference genes was evaluated on the basis of latex flow by using geNorm and NormFinder algorithms. Ubiquitin-protein ligase 2a (UBC2a) and ubiquitin-protein ligase 2b (UBC2b) were the two most stable genes among the selected candidate references in rubber tree clones with differential duration of latex flow. The two genes were also high-ranked in previous reference gene screening across different tissues and experimental conditions. By contrast, the transcripts of latex regeneration-related genes fluctuated significantly during latex flow. The results suggest that screening reference gene during latex flow should be an efficient and effective clue for selection of reference genes in qRT-PCR.
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78
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Kosinová L, Cahová M, Fábryová E, Týcová I, Koblas T, Leontovyč I, Saudek F, Kříž J. Unstable Expression of Commonly Used Reference Genes in Rat Pancreatic Islets Early after Isolation Affects Results of Gene Expression Studies. PLoS One 2016; 11:e0152664. [PMID: 27035827 PMCID: PMC4817981 DOI: 10.1371/journal.pone.0152664] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2015] [Accepted: 03/17/2016] [Indexed: 12/15/2022] Open
Abstract
The use of RT-qPCR provides a powerful tool for gene expression studies; however, the proper interpretation of the obtained data is crucially dependent on accurate normalization based on stable reference genes. Recently, strong evidence has been shown indicating that the expression of many commonly used reference genes may vary significantly due to diverse experimental conditions. The isolation of pancreatic islets is a complicated procedure which creates severe mechanical and metabolic stress leading possibly to cellular damage and alteration of gene expression. Despite of this, freshly isolated islets frequently serve as a control in various gene expression and intervention studies. The aim of our study was to determine expression of 16 candidate reference genes and one gene of interest (F3) in isolated rat pancreatic islets during short-term cultivation in order to find a suitable endogenous control for gene expression studies. We compared the expression stability of the most commonly used reference genes and evaluated the reliability of relative and absolute quantification using RT-qPCR during 0-120 hrs after isolation. In freshly isolated islets, the expression of all tested genes was markedly depressed and it increased several times throughout the first 48 hrs of cultivation. We observed significant variability among samples at 0 and 24 hrs but substantial stabilization from 48 hrs onwards. During the first 48 hrs, relative quantification failed to reflect the real changes in respective mRNA concentrations while in the interval 48-120 hrs, the relative expression generally paralleled the results determined by absolute quantification. Thus, our data call into question the suitability of relative quantification for gene expression analysis in pancreatic islets during the first 48 hrs of cultivation, as the results may be significantly affected by unstable expression of reference genes. However, this method could provide reliable information from 48 hrs onwards.
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Affiliation(s)
- Lucie Kosinová
- Laboratory of Pancreatic Islets, Center of Experimental Medicine, Institute for Clinical and Experimental Medicine, Prague, Czech Republic
- First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Monika Cahová
- Department of Metabolism and Diabetes, Center of Experimental Medicine, Institute for Clinical and Experimental Medicine, Prague, Czech Republic
| | - Eva Fábryová
- Laboratory of Pancreatic Islets, Center of Experimental Medicine, Institute for Clinical and Experimental Medicine, Prague, Czech Republic
| | - Irena Týcová
- Transplant Laboratory, Center of Experimental Medicine, Institute for Clinical and Experimental Medicine, Prague, Czech Republic
| | - Tomáš Koblas
- Laboratory of Pancreatic Islets, Center of Experimental Medicine, Institute for Clinical and Experimental Medicine, Prague, Czech Republic
| | - Ivan Leontovyč
- Laboratory of Pancreatic Islets, Center of Experimental Medicine, Institute for Clinical and Experimental Medicine, Prague, Czech Republic
| | - František Saudek
- Laboratory of Pancreatic Islets, Center of Experimental Medicine, Institute for Clinical and Experimental Medicine, Prague, Czech Republic
- Department of Diabetes, Center of Diabetes, Institute for Clinical and Experimental Medicine, Prague, Czech Republic
| | - Jan Kříž
- Department of Diabetes, Center of Diabetes, Institute for Clinical and Experimental Medicine, Prague, Czech Republic
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79
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Pacheco-Marín R, Melendez-Zajgla J, Castillo-Rojas G, Mandujano-Tinoco E, Garcia-Venzor A, Uribe-Carvajal S, Cabrera-Orefice A, Gonzalez-Torres C, Gaytan-Cervantes J, Mitre-Aguilar IB, Maldonado V. Transcriptome profile of the early stages of breast cancer tumoral spheroids. Sci Rep 2016; 6:23373. [PMID: 27021602 PMCID: PMC4810430 DOI: 10.1038/srep23373] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Accepted: 03/02/2016] [Indexed: 12/15/2022] Open
Abstract
Oxygen or nutrient deprivation of early stage tumoral spheroids can be used to reliably mimic the initial growth of primary and metastatic cancer cells. However, cancer cell growth during the initial stages has not been fully explored using a genome-wide approach. Thus, in the present study, we investigated the transcriptome of breast cancer cells during the initial stages of tumoral growth using RNAseq in a model of Multicellular Tumor Spheroids (MTS). Network analyses showed that a metastatic signature was enriched as several adhesion molecules were deregulated, including EPCAM, E-cadherin, integrins and syndecans, which were further supported by an increase in cell migration. Interestingly, we also found that the cancer cells at this stage of growth exhibited a paradoxical hyperactivation of oxidative mitochondrial metabolism. In addition, we found a large number of regulated (long non coding RNA) lncRNAs, several of which were co-regulated with neighboring genes. The regulatory role of some of these lncRNAs on mRNA expression was demonstrated with gain of function assays. This is the first report of an early-stage MTS transcriptome, which not only reveals a complex expression landscape, but points toward an important contribution of long non-coding RNAs in the final phenotype of three-dimensional cellular models.
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Affiliation(s)
- Rosario Pacheco-Marín
- Epigenetics, National Institute of Genomic Medicine, Periférico Sur No. 4809, Col Arenal Tepepan, Delegación Tlalpan, México, D.F., C.P 14610.,Posgraduate Program in Biological Sciences, Faculty of Medicine (UNAM), University City Avenue 3000 C.P. 04510, Coyoacan, Mexico City
| | - Jorge Melendez-Zajgla
- Functional Genomics laboratories, National Institute of Genomic Medicine, Periférico Sur No. 4809, Col Arenal Tepepan, Delegación Tlalpan, México, D.F., C.P 14610
| | - Gonzalo Castillo-Rojas
- Microbial Molecular Immunology Program, Department of Microbiology and Parasitology, Faculty of Medicine, National Autonomous University of Mexico (UNAM), University City Avenue 3000 C.P. 04510, Coyoacan, Mexico City
| | - Edna Mandujano-Tinoco
- Functional Genomics laboratories, National Institute of Genomic Medicine, Periférico Sur No. 4809, Col Arenal Tepepan, Delegación Tlalpan, México, D.F., C.P 14610
| | - Alfredo Garcia-Venzor
- Functional Genomics laboratories, National Institute of Genomic Medicine, Periférico Sur No. 4809, Col Arenal Tepepan, Delegación Tlalpan, México, D.F., C.P 14610
| | - Salvador Uribe-Carvajal
- Department of Molecular Genetics, Institute of Cellular Physiology (UNAM), University City Avenue 3000 C.P. 04510, Coyoacan, Mexico City
| | - Alfredo Cabrera-Orefice
- Department of Molecular Genetics, Institute of Cellular Physiology (UNAM), University City Avenue 3000 C.P. 04510, Coyoacan, Mexico City
| | - Carolina Gonzalez-Torres
- Functional Genomics laboratories, National Institute of Genomic Medicine, Periférico Sur No. 4809, Col Arenal Tepepan, Delegación Tlalpan, México, D.F., C.P 14610
| | - Javier Gaytan-Cervantes
- Functional Genomics laboratories, National Institute of Genomic Medicine, Periférico Sur No. 4809, Col Arenal Tepepan, Delegación Tlalpan, México, D.F., C.P 14610
| | - Irma B Mitre-Aguilar
- Unit of Biochemistry, National Institute of Medical Sciences and Nutrition Salvador Zubirán (INCMNSZ), Av. Vasco de Quiroga N° 15, Colonia Belisario Domínguez Sección XVI, Delegación Tlalpan. CP.14080, México D. F., México
| | - Vilma Maldonado
- Epigenetics, National Institute of Genomic Medicine, Periférico Sur No. 4809, Col Arenal Tepepan, Delegación Tlalpan, México, D.F., C.P 14610
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80
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Quantitative Evaluation and Selection of Reference Genes for Quantitative RT-PCR in Mouse Acute Pancreatitis. BIOMED RESEARCH INTERNATIONAL 2016; 2016:8367063. [PMID: 27069927 PMCID: PMC4812220 DOI: 10.1155/2016/8367063] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Revised: 01/19/2016] [Accepted: 02/07/2016] [Indexed: 02/05/2023]
Abstract
The analysis of differences in gene expression is dependent on normalization using reference genes. However, the expression of many of these reference genes, as evaluated by quantitative RT-PCR, is upregulated in acute pancreatitis, so they cannot be used as the standard for gene expression in this condition. For this reason, we sought to identify a stable reference gene, or a suitable combination, for expression analysis in acute pancreatitis. The expression stability of 10 reference genes (ACTB, GAPDH, 18sRNA, TUBB, B2M, HPRT1, UBC, YWHAZ, EF-1α, and RPL-13A) was analyzed using geNorm, NormFinder, and BestKeeper software and evaluated according to variations in the raw Ct values. These reference genes were evaluated using a comprehensive method, which ranked the expression stability of these genes as follows (from most stable to least stable): RPL-13A, YWHAZ > HPRT1 > GAPDH > UBC > EF-1α > 18sRNA > B2M > TUBB > ACTB. RPL-13A was the most suitable reference gene, and the combination of RPL-13A and YWHAZ was the most stable group of reference genes in our experiments. The expression levels of ACTB, TUBB, and B2M were found to be significantly upregulated during acute pancreatitis, whereas the expression level of 18sRNA was downregulated. Thus, we recommend the use of RPL-13A or a combination of RPL-13A and YWHAZ for normalization in qRT-PCR analyses of gene expression in mouse models of acute pancreatitis.
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81
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Dowling CM, Walsh D, Coffey JC, Kiely PA. The importance of selecting the appropriate reference genes for quantitative real time PCR as illustrated using colon cancer cells and tissue. F1000Res 2016. [PMID: 26962435 DOI: 10.12688/f1000research.7656.1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Quantitative real-time reverse-transcription polymerase chain reaction (RT-qPCR) remains the most sensitive technique for nucleic acid quantification. Its popularity is reflected in the remarkable number of publications reporting RT-qPCR data. Careful normalisation within RT-qPCR studies is imperative to ensure accurate quantification of mRNA levels. This is commonly achieved through the use of reference genes as an internal control to normalise the mRNA levels between different samples. The selection of appropriate reference genes can be a challenge as transcript levels vary with physiology, pathology and development, making the information within the transcriptome flexible and variable. In this study, we examined the variation in expression of a panel of nine candidate reference genes in HCT116 and HT29 2-dimensional and 3-dimensional cultures, as well as in normal and cancerous colon tissue. Using normfinder we identified the top three most stable genes for all conditions. Further to this we compared the change in expression of a selection of PKC coding genes when the data was normalised to one reference gene and three reference genes. Here we demonstrated that there is a variation in the fold changes obtained dependent on the number of reference genes used. As well as this, we highlight important considerations namely; assay efficiency tests, inhibition tests and RNA assessment which should also be implemented into all RT-qPCR studies. All this data combined demonstrates the need for careful experimental design in RT-qPCR studies to help eliminate false interpretation and reporting of results.
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Affiliation(s)
- Catríona M Dowling
- Department of Life Sciences, and Materials and Surface Science Institute, University of Limerick, Limerick, Ireland; Health Research Institute, University of Limerick, Limerick, Ireland; Graduate Entry Medical School, University of Limerick, Limerick, Ireland
| | - Dara Walsh
- 4i Centre for Interventions in Infection, Inflammation and Immunity, Graduate Entry Medical School, University of Limerick, Limerick, Ireland
| | - John C Coffey
- 4i Centre for Interventions in Infection, Inflammation and Immunity, Graduate Entry Medical School, University of Limerick, Limerick, Ireland
| | - Patrick A Kiely
- Department of Life Sciences, and Materials and Surface Science Institute, University of Limerick, Limerick, Ireland; Health Research Institute, University of Limerick, Limerick, Ireland; Graduate Entry Medical School, University of Limerick, Limerick, Ireland
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82
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Boulter N, Suarez FG, Schibeci S, Sunderland T, Tolhurst O, Hunter T, Hodge G, Handelsman D, Simanainen U, Hendriks E, Duggan K. A simple, accurate and universal method for quantification of PCR. BMC Biotechnol 2016; 16:27. [PMID: 26956612 PMCID: PMC4784296 DOI: 10.1186/s12896-016-0256-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 02/25/2016] [Indexed: 11/10/2022] Open
Abstract
Background Research into gene expression enables scientists to decipher the complex regulatory networks that control fundamental biological processes. Quantitative real-time PCR (qPCR) is a powerful and ubiquitous method for interrogation of gene expression. Accurate quantification is essential for correct interpretation of qPCR data. However, conventional relative and absolute quantification methodologies often give erroneous results or are laborious to perform. To overcome these failings, we developed an accurate, simple to use, universal calibrator, AccuCal. Results Herein, we show that AccuCal quantification can be used with either dye- or probe-based detection methods and is accurate over a dynamic range of ≥105 copies, for amplicons up to 500 base pairs (bp). By providing absolute quantification of all genes of interest, AccuCal exposes, and circumvents, the well-known biases of qPCR, thus allowing objective experimental conclusions to be drawn. Conclusion We propose that AccuCal supersedes the traditional quantification methods of PCR. Electronic supplementary material The online version of this article (doi:10.1186/s12896-016-0256-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nicky Boulter
- Accugen Pty Ltd, 11 Julius Avenue, North Ryde, NSW, 2113, Australia.
| | | | - Stephen Schibeci
- Westmead Millennium Institute, 176 Hawkesbury Road, Westmead, NSW, 2145, Australia.
| | - Trevor Sunderland
- Bitfuturistic Solutions, 9623 Lawndale Avenue SW, Lakewood, WA, 98498, USA.
| | - Ornella Tolhurst
- Accugen Pty Ltd, 11 Julius Avenue, North Ryde, NSW, 2113, Australia. .,Vectus Biosystems Pty Ltd, 11 Julius Avenue, North Ryde, NSW, 2113, Australia.
| | - Tegan Hunter
- Accugen Pty Ltd, 11 Julius Avenue, North Ryde, NSW, 2113, Australia. .,Vectus Biosystems Pty Ltd, 11 Julius Avenue, North Ryde, NSW, 2113, Australia.
| | - George Hodge
- Vectus Biosystems Pty Ltd, 11 Julius Avenue, North Ryde, NSW, 2113, Australia.
| | - David Handelsman
- ANZAC Research Institute, University of Sydney, Sydney, NSW, 2139, Australia.
| | - Ulla Simanainen
- ANZAC Research Institute, University of Sydney, Sydney, NSW, 2139, Australia.
| | - Edward Hendriks
- Accugen Pty Ltd, 11 Julius Avenue, North Ryde, NSW, 2113, Australia. .,Vectus Biosystems Pty Ltd, 11 Julius Avenue, North Ryde, NSW, 2113, Australia.
| | - Karen Duggan
- Accugen Pty Ltd, 11 Julius Avenue, North Ryde, NSW, 2113, Australia. .,Vectus Biosystems Pty Ltd, 11 Julius Avenue, North Ryde, NSW, 2113, Australia.
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83
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Vanhauwaert S, Lefever S, Coucke P, Speleman F, De Paepe A, Vandesompele J, Willaert A. RT-qPCR gene expression analysis in zebrafish: Preanalytical precautions and use of expressed repetitive elements for normalization. Methods Cell Biol 2016; 135:329-42. [PMID: 27443934 DOI: 10.1016/bs.mcb.2016.02.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Gene expression analysis is increasingly important in many fields of biological research. Understanding patterns of expressed genes is assumed to provide insight into complex regulatory networks and can lead to the identification of genes relevant to specific biological processes, including disease. Among different techniques, reverse transcription quantitative polymerase chain reaction (RT-qPCR) is currently regarded as the gold standard for targeted quantification of RNA gene expression, especially because of its high sensitivity, specificity, accuracy, and precision, and also because of its practical simplicity and processing speed. However, different critical factors can influence the outcome of RT-qPCR studies, including isolation of RNA, reverse transcription to cDNA, and data analysis. These factors need to be addressed in order to obtain biologically meaningful results. In this chapter, we describe how RT-qPCR can be used in a reliable way to successfully study differential gene expression in zebrafish. Hereby, we especially focus on how expressed repetitive elements can be employed as reference targets in zebrafish RT-qPCR studies and how they can further improve the quality of the data.
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Affiliation(s)
| | | | - P Coucke
- Ghent University, Ghent, Belgium
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84
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Wang Z, Wang Y, Yang J, Hu K, An B, Deng X, Li Y. Reliable Selection and Holistic Stability Evaluation of Reference Genes for Rice Under 22 Different Experimental Conditions. Appl Biochem Biotechnol 2016; 179:753-75. [PMID: 26940571 DOI: 10.1007/s12010-016-2029-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2015] [Accepted: 02/22/2016] [Indexed: 01/26/2023]
Abstract
Stable and uniform expression of reference genes across samples plays a key role in accurate normalization of gene expression by reverse-transcription quantitative polymerase chain reaction (RT-qPCR). For rice study, there is still a lack of validation and recommendation of appropriate reference genes with high stability depending on experimental conditions. Eleven candidate reference genes potentially owning high stability were evaluated by geNorm and NormFinder for their expression stability in 22 various experimental conditions. Best combinations of multiple reference genes were recommended depending on experimental conditions, and the holistic stability of reference genes was also evaluated. Reference genes would become more variable and thus needed to be critically selected in experimental groups of tissues, heat, 6-benzylamino purine, and drought, but they were comparatively stable under cold, wound, and ultraviolet-B stresses. Triosephosphate isomerase (TI), profilin-2 (Profilin-2), ubiquitin-conjugating enzyme E2 (UBC), endothelial differentiation factor (Edf), and ADP-ribosylation factor (ARF) were stable in most of our experimental conditions. No universal reference gene showed good stability in all experimental conditions. To get accurate expression result, suitable combination of multiple reference genes for a specific experimental condition would be a better choice. This study provided an application guideline to select stable reference genes for rice gene expression study.
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Affiliation(s)
- Zhaohai Wang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Hubei, 430072, People's Republic of China
| | - Ya Wang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Hubei, 430072, People's Republic of China
| | - Jing Yang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Hubei, 430072, People's Republic of China
| | - Keke Hu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Hubei, 430072, People's Republic of China
| | - Baoguang An
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Hubei, 430072, People's Republic of China
| | - Xiaolong Deng
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Hubei, 430072, People's Republic of China
| | - Yangsheng Li
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Hubei, 430072, People's Republic of China. .,State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice, Ministry of Agriculture, College of Life Sciences, Wuhan University, Hubei, 430072, People's Republic of China.
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85
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Bustin SA. Improving the reliability of peer-reviewed publications: We are all in it together. BIOMOLECULAR DETECTION AND QUANTIFICATION 2016; 7:A1-5. [PMID: 27077047 PMCID: PMC4827640 DOI: 10.1016/j.bdq.2015.11.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Revised: 11/20/2015] [Accepted: 11/26/2015] [Indexed: 12/20/2022]
Abstract
The current, and welcome, focus on standardization of techniques and transparency of reporting in the biomedical, peer-reviewed literature is commendable. However, that focus has been intermittent as well as lacklustre and so failed to tackle the alarming lack of reliability and reproducibly of biomedical research. Authors have access to numerous recommendations, ranging from simple standards dealing with technical issues to those regulating clinical trials, suggesting that improved reporting guidelines are not the solution. The elemental solution is for editors to require meticulous implementation of their journals' instructions for authors and reviewers and stipulate that no paper is published without a transparent, complete and accurate materials and methods section.
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Affiliation(s)
- Stephen A. Bustin
- Faculty of Medical Science, Postgraduate Medical Institute, Anglia Ruskin University, Chelmsford CM1 1SQ, UK
- The Gene Team Ltd., UK
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86
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Zhao H, Liu J, Li Y, Yang C, Zhao S, Liu J, Liu A, Liu G, Yin H, Guan G, Luo J. Validation of Reference Genes for Quantitative Real-Time PCR in Bovine PBMCs Transformed and Non-transformed by Theileria annulata. THE KOREAN JOURNAL OF PARASITOLOGY 2016; 54:39-46. [PMID: 26951977 PMCID: PMC4792322 DOI: 10.3347/kjp.2016.54.1.39] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Revised: 10/17/2015] [Accepted: 11/01/2015] [Indexed: 11/23/2022]
Abstract
Theileria annulata is a tick-borne intracellular protozoan parasite that causes tropical theileriosis, a fatal bovine lymphoproliferative disease. The parasite predominantly invades bovine B lymphocytes and macrophages and induces host cell transformation by a mechanism that is not fully comprehended. Analysis of signaling pathways by quantitative real-time PCR (qPCR) could be a highly efficient means to understand this transformation mechanism. However, accurate analysis of qPCR data relies on selection of appropriate reference genes for normalization, yet few papers on T. annulata contain evidence of reference gene validation. We therefore used the geNorm and NormFinder programs to evaluate the stability of 5 candidate reference genes; 18S rRNA, glyceraldehyde-3-phosphate dehydrogenase (GAPDH), ACTB (β-actin), PRKG1 (protein kinase cGMP-dependent, type I) and TATA box binding protein (TBP). The results showed that 18S rRNA was the reference gene most stably expressed in bovine PBMCs transformed and non-transformed with T. annulata, followed by GAPDH and TBP. While 18S rRNA and GAPDH were the best combination, these 2 genes were chosen as references to study signaling pathways involved in the transformation mechanism of T. annulata.
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Affiliation(s)
- Hongxi Zhao
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, People's Republic of China ; Agricultural College of Ningxia University, Yinchuan 750021, People's Republic of China
| | - Junlong Liu
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, People's Republic of China
| | - Youquan Li
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, People's Republic of China
| | - Congshan Yang
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, People's Republic of China
| | - Shuaiyang Zhao
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, People's Republic of China
| | - Juan Liu
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, People's Republic of China
| | - Aihong Liu
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, People's Republic of China
| | - Guangyuan Liu
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, People's Republic of China
| | - Hong Yin
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, People's Republic of China ; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou 225009, People's Republic of China
| | - Guiquan Guan
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, People's Republic of China
| | - Jianxun Luo
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, People's Republic of China
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Barrett GL, Naim T, Trieu J, Huang M. In vivo knockdown of basal forebrain p75 neurotrophin receptor stimulates choline acetyltransferase activity in the mature hippocampus. J Neurosci Res 2016; 94:389-400. [DOI: 10.1002/jnr.23717] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2015] [Revised: 12/15/2015] [Accepted: 01/11/2016] [Indexed: 11/09/2022]
Affiliation(s)
- Graham L. Barrett
- Department of Physiology; University of Melbourne; Melbourne Victoria Australia
| | - Timur Naim
- Department of Physiology; University of Melbourne; Melbourne Victoria Australia
| | - Jennifer Trieu
- Department of Physiology; University of Melbourne; Melbourne Victoria Australia
| | - Mengjie Huang
- Department of Physiology; University of Melbourne; Melbourne Victoria Australia
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88
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Dowling CM, Walsh D, Coffey JC, Kiely PA. The importance of selecting the appropriate reference genes for quantitative real time PCR as illustrated using colon cancer cells and tissue. F1000Res 2016; 5:99. [PMID: 26962435 PMCID: PMC4768652 DOI: 10.12688/f1000research.7656.2] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/04/2016] [Indexed: 12/16/2022] Open
Abstract
Quantitative real-time reverse-transcription polymerase chain reaction (RT-qPCR) remains the most sensitive technique for nucleic acid quantification. Its popularity is reflected in the remarkable number of publications reporting RT-qPCR data. Careful normalisation within RT-qPCR studies is imperative to ensure accurate quantification of mRNA levels. This is commonly achieved through the use of reference genes as an internal control to normalise the mRNA levels between different samples. The selection of appropriate reference genes can be a challenge as transcript levels vary with physiology, pathology and development, making the information within the transcriptome flexible and variable. In this study, we examined the variation in expression of a panel of nine candidate reference genes in HCT116 and HT29 2-dimensional and 3-dimensional cultures, as well as in normal and cancerous colon tissue. Using normfinder we identified the top three most stable genes for all conditions. Further to this we compared the change in expression of a selection of PKC coding genes when the data was normalised to one reference gene and three reference genes. Here we demonstrated that there is a variation in the fold changes obtained dependent on the number of reference genes used. As well as this, we highlight important considerations namely; assay efficiency tests, inhibition tests and RNA assessment which should also be implemented into all RT-qPCR studies. All this data combined demonstrates the need for careful experimental design in RT-qPCR studies to help eliminate false interpretation and reporting of results.
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Affiliation(s)
- Catríona M Dowling
- Department of Life Sciences, and Materials and Surface Science Institute, University of Limerick, Limerick, Ireland; Health Research Institute, University of Limerick, Limerick, Ireland; Graduate Entry Medical School, University of Limerick, Limerick, Ireland
| | - Dara Walsh
- 4i Centre for Interventions in Infection, Inflammation and Immunity, Graduate Entry Medical School, University of Limerick, Limerick, Ireland
| | - John C Coffey
- 4i Centre for Interventions in Infection, Inflammation and Immunity, Graduate Entry Medical School, University of Limerick, Limerick, Ireland
| | - Patrick A Kiely
- Department of Life Sciences, and Materials and Surface Science Institute, University of Limerick, Limerick, Ireland; Health Research Institute, University of Limerick, Limerick, Ireland; Graduate Entry Medical School, University of Limerick, Limerick, Ireland
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89
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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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Valenza M, Picetti R, Yuferov V, Butelman ER, Kreek MJ. Strain and cocaine-induced differential opioid gene expression may predispose Lewis but not Fischer rats to escalate cocaine self-administration. Neuropharmacology 2016; 105:639-650. [PMID: 26777278 DOI: 10.1016/j.neuropharm.2016.01.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Revised: 12/11/2015] [Accepted: 01/03/2016] [Indexed: 11/24/2022]
Abstract
The aim of the present study was to investigate alterations in gene expression of opioid system components induced by extended access (18 h) cocaine self-administration and to determine the impact of genetic background in the vulnerability to escalate cocaine intake. Comparing two inbred rat strains, we previously reported that Lewis rats progressively escalated cocaine consumption compared to Fischer rats, in a new translational model of intravenous cocaine self-administration, which included 14 sessions of 18-h operant sessions in which rats were allowed to select the cocaine unit dose to self-administer. We compare here Fischer and Lewis rats in the gene expression of endogenous opioid peptides (Pomc, Penk, Pdyn) and cognate receptors (Oprm, Oprk and Oprd) in reward-related brain regions, after exposure to either cocaine self-administration or yoked-saline, in the aforementioned translational paradigm. We performed a correlation analysis between the mRNA level, found in the Dorsal Striatum (DS), Nucleus accumbens (NAcc) shell and core respectively, and individual cocaine intake. Our findings show that the gene expression of all the aforementioned opioid genes exhibit strain-dependent differences in the DS, in absence of cocaine exposure. Also, different strain-specific cocaine-induced mRNA expression of Oprm and Oprk was found in DS. Only few differences were found in the ventral parts of the striatum. Moreover, gene expression level of Pdyn, Penk, Oprk, and Oprm in the DS was significantly correlated with cocaine intake only in Fischer rats. Overall, these data shed light on potential genetic differences which may predispose of subjects to initiate and escalate cocaine consumption.
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Affiliation(s)
- Marta Valenza
- Laboratory of the Biology of Addictive Diseases, The Rockefeller University, New York, NY, USA.
| | - Roberto Picetti
- Laboratory of the Biology of Addictive Diseases, The Rockefeller University, New York, NY, USA; Department of Social and Environmental Health Research, London School of Hygiene and Tropical Medicine, London, UK
| | - Vadim Yuferov
- Laboratory of the Biology of Addictive Diseases, The Rockefeller University, New York, NY, USA
| | - Eduardo R Butelman
- Laboratory of the Biology of Addictive Diseases, The Rockefeller University, New York, NY, USA
| | - Mary Jeanne Kreek
- Laboratory of the Biology of Addictive Diseases, The Rockefeller University, New York, NY, USA
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91
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Reference gene study for forensic body fluid identification. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2015. [DOI: 10.1016/j.fsigss.2015.09.067] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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92
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Appropriate real-time PCR reference genes for fluoride treatment studies performed in vitro or in vivo. Arch Oral Biol 2015; 62:33-42. [PMID: 26615575 DOI: 10.1016/j.archoralbio.2015.11.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Revised: 09/15/2015] [Accepted: 11/05/2015] [Indexed: 01/06/2023]
Abstract
OBJECTIVE Quantitative real-time PCR (qPCR) is routinely performed for experiments designed to identify the molecular mechanisms involved in the pathogenesis of dental fluorosis. Expression of reference gene(s) is expected to remain unchanged in fluoride-treated cells or in rodents relative to the corresponding untreated controls. The aim of this study was to select optimal reference genes for fluoride experiments performed in vitro and in vivo. DESIGN Five candidate genes were evaluated: B2m, Eef1a1, Gapdh, Hprt and Tbp. For in vitro experiments, LS8 cells derived from mouse enamel organ were treated with 0, 1, 3 and/or 5mM sodium fluoride (NaF) for 6 or 18 h followed by RNA isolation. For in vivo experiments, six-week old rats were treated with 0 or 100 ppm fluoride as NaF for six weeks at which time RNA was isolated from enamel organs. RNA from cells and enamel organs were reverse-transcribed and stability of gene expression for the candidate reference genes was evaluated by qPCR in treated versus non-treated samples. RESULTS The most stably expressed genes in vitro according to geNorm were B2m and Tbp, and according to Normfinder were Hprt and Gapdh. The most stable genes in vivo were Eef1a1 and Gapdh. Expression of Ddit3, a gene previously shown to be induced by fluoride, was demonstrated to be accurately calculated only when using an optimal reference gene. CONCLUSIONS This study identifies suitable reference genes for relative quantification of gene expression by qPCR after fluoride treatment both in cultured cells and in the rodent enamel organ.
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93
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Poumpouridou N, Acha-Sagredo A, Goutas N, Vlachodimitropoulos D, Chatziioannidou I, Lianidou E, Liloglou T, Kroupis C. Development and validation of molecular methodologies to assess PALB2 expression in sporadic breast cancer. Clin Biochem 2015; 49:253-9. [PMID: 26526077 DOI: 10.1016/j.clinbiochem.2015.10.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2015] [Revised: 10/11/2015] [Accepted: 10/14/2015] [Indexed: 12/11/2022]
Abstract
OBJECTIVES Recent reports have included PALB2 (Partner and localizer of BRCA2) in the growing list of hereditary cancer genes. PALB2 mutations confer a moderate breast cancer risk in heterozygotes and Fanconi anemia in biallelic mutation carriers. PALB2 protein co-localizes with BRCA2 and BRCA1 in nuclear structures and enables error-free homologous recombination repair of double-stranded DNA breaks. This important contribution could be severely diminished if affected by epigenetic mechanisms such as promoter CpG island methylation. The aim of our study was to develop molecular methodologies in order to assess accurately PALB2 expression in breast cancer tissues. DESIGN AND METHODS DNA and RNA were extracted from 91 sporadic fresh-frozen breast tissues with known histopathological data. DNA was subjected to sodium bisulfite conversion reaction and the CpG island of the PALB2 promoter was analyzed by pyrosequencing. RNA was converted to cDNA and analyzed by a newly developed and validated RT-qPCR assay based on a hydrolysis probe (TaqMan) in the Light Cycler. RESULTS PALB2 promoter was not methylated in any of the samples tested. 87 out of 91 (95.6%) primary tumors were positive for PALB2 expression, as checked at the mRNA level. When levels of PALB2 mRNA were compared to histopathological data (tumor size, grade, lymph node involvement, metastasis, hormone receptors and HER2 overexpression), no significant statistical correlation was found. CONCLUSIONS DNA methylation is an unlike mechanism for PALB2 transcriptional regulation. PALB2 mRNA expression does not seem be a promising prognostic biomarker for sporadic breast cancer.
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Affiliation(s)
- Nikoleta Poumpouridou
- Department of Clinical Biochemistry, Attikon University General Hospital, University of Athens Medical School, Haidari 12462, Greece
| | - Amelia Acha-Sagredo
- Department of Molecular and Clinical Cancer Medicine, University of Liverpool, L3 9TA Liverpool, United Kingdom
| | - Nikolaos Goutas
- Laboratory of Pathologic Anatomy, Evgenidio Hospital, University of Athens Medical School, Athens 15128, Greece
| | | | - Ioanna Chatziioannidou
- Department of Clinical Biochemistry, Attikon University General Hospital, University of Athens Medical School, Haidari 12462, Greece
| | - Evi Lianidou
- Laboratory of Analytical Chemistry, Department of Chemistry, University of Athens, Athens 15771, Greece
| | - Triantafyllos Liloglou
- Department of Molecular and Clinical Cancer Medicine, University of Liverpool, L3 9TA Liverpool, United Kingdom
| | - Christos Kroupis
- Laboratory of Analytical Chemistry, Department of Chemistry, University of Athens, Athens 15771, Greece.
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Yang Z, Kong F. UV-B Exposure Affects the Biosynthesis of Microcystin in Toxic Microcystis aeruginosa Cells and Its Degradation in the Extracellular Space. Toxins (Basel) 2015; 7:4238-52. [PMID: 26492272 PMCID: PMC4626732 DOI: 10.3390/toxins7104238] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Revised: 10/13/2015] [Accepted: 10/14/2015] [Indexed: 11/16/2022] Open
Abstract
Microcystins (MCs) are cyclic hepatotoxic heptapeptides produced by cyanobacteria that can be toxic to aquatic and terrestrial organisms. MC synthesis and degradation are thought to be influenced by several different physical and environmental parameters. In this study, the effects of different intensities of UV-B radiation on MC biosynthesis in Microcystis cells and on its extracellular degradation were investigated by mRNA analysis and degradation experiments. Exposure to UV-B at intensities of 1.02 and 1.45 W/m2 not only remarkably inhibited the growth of Microcystis, but also led to a decrease in the MC concentration. In addition, mcyD transcription was decreased under the same UV-B intensities. These results demonstrated that the effects of UV-B exposure on the biosynthesis of MCs in Microcystis cells could be attributed to the regulation of mcy gene transcription. Moreover, the MC concentration was decreased significantly after exposure to different intensities of UV-B radiation. Of the three MC variants (MC-LR, -RR and -YR, L, R and Y are abbreviations of leucine, arginine and tyrosine), MC-LR and MC-YR were sensitive to UV-B radiation, whereas MC-RR was not. In summary, our results showed that UV-B radiation had a negative effect on MC production in Microcystis cells and MC persistence in the extracellular space.
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Affiliation(s)
- Zhen Yang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, 73 East Beijing Road, Nanjing 210008, China.
| | - Fanxiang Kong
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, 73 East Beijing Road, Nanjing 210008, China.
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95
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Karaglani M, Toumpoulis I, Goutas N, Poumpouridou N, Vlachodimitropoulos D, Vasilaros S, Rizos I, Kroupis C. Development of novel real-time PCR methodology for quantification of COL11A1 mRNA variants and evaluation in breast cancer tissue specimens. BMC Cancer 2015; 15:694. [PMID: 26466668 PMCID: PMC4606509 DOI: 10.1186/s12885-015-1725-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Accepted: 10/08/2015] [Indexed: 12/26/2022] Open
Abstract
Background Collagen XI is a key structural component of the extracellular matrix and consists of three alpha chains. One of these chains, the α1 (XI), is encoded by the COL11A1 gene and is transcribed to four different variants at least (A, B, C and E) that differ in the propensity to N-terminal domain proteolysis and potentially in the way the extracellular matrix is arranged. This could affect the ability of tumor cells to invade the remodeled stroma and metastasize. No study in the literature has so far investigated the expression of these four variants in breast cancer nor does a method for their accurate quantitative detection exist. Methods We developed a conventional PCR for the general detection of the general COL11A1 transcript and real-time qPCR methodologies with dual hybridization probes in the LightCycler platform for the quantitative determination of the variants. Data from 90 breast cancer tissues with known histopathological features were collected. Results The general COL11A1 transcript was detected in all samples. The developed methodologies for each variant were rapid as well as reproducible, sensitive and specific. Variant A was detected in 30 samples (33 %) and variant E in 62 samples (69 %). Variants B and C were not detected at all. A statistically significant correlation was observed between the presence of variant E and lymph nodes involvement (p = 0.037) and metastasis (p = 0.041). Conclusions With the newly developed tools, the possibility of inclusion of COL11A1 variants as prognostic biomarkers in emerging multiparameter technologies examining tissue RNA expression should be further explored. Electronic supplementary material The online version of this article (doi:10.1186/s12885-015-1725-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Makrina Karaglani
- Department of Clinical Biochemistry and Molecular Diagnostics, Attikon University General Hospital, University of Athens Medical School, Rimini 1 St., Haidari, 12462, Greece.
| | - Ioannis Toumpoulis
- Department of Cardiothoracic Surgery, Attikon University General Hospital, University of Athens Medical School, Athens, Greece.
| | - Nikolaos Goutas
- Pathologic Anatomy Laboratory, Evgenidio Hospital, University of Athens Medical School, Athens, Greece.
| | - Nikoleta Poumpouridou
- Department of Clinical Biochemistry and Molecular Diagnostics, Attikon University General Hospital, University of Athens Medical School, Rimini 1 St., Haidari, 12462, Greece.
| | | | | | - Ioannis Rizos
- Department of Cardiology, Attikon University General Hospital, University of Athens Medical School, Athens, Greece.
| | - Christos Kroupis
- Department of Clinical Biochemistry and Molecular Diagnostics, Attikon University General Hospital, University of Athens Medical School, Rimini 1 St., Haidari, 12462, Greece.
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96
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Mathur D, Urena-Peralta JR, Lopez-Rodas G, Casanova B, Coret-Ferrer F, Burgal-Marti M. Bypassing hazard of housekeeping genes: their evaluation in rat granule neurons treated with cerebrospinal fluid of multiple sclerosis subjects. Front Cell Neurosci 2015; 9:375. [PMID: 26441545 PMCID: PMC4585208 DOI: 10.3389/fncel.2015.00375] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 09/07/2015] [Indexed: 01/09/2023] Open
Abstract
Gene expression studies employing real-time PCR has become an intrinsic part of biomedical research. Appropriate normalization of target gene transcript(s) based on stably expressed housekeeping genes is crucial in individual experimental conditions to obtain accurate results. In multiple sclerosis (MS), several gene expression studies have been undertaken, however, the suitability of housekeeping genes to express stably in this disease is not yet explored. Recent research suggests that their expression level may vary under different experimental conditions. Hence it is indispensible to evaluate their expression stability to accurately normalize target gene transcripts. The present study aims to evaluate the expression stability of seven housekeeping genes in rat granule neurons treated with cerebrospinal fluid of MS patients. The selected reference genes were quantified by real time PCR and their expression stability was assessed using GeNorm and NormFinder algorithms. GeNorm identified transferrin receptor (Tfrc) and microglobulin beta-2 (B2m) the most stable genes followed by ribosomal protein L19 (Rpl19) whereas β-actin (ActB) and glyceraldehyde-3-phosphate-dehydrogenase (Gapdh) the most fluctuated ones in these neurons. NormFinder identified Tfrc as the best invariable gene followed by B2m and Rpl19. ActB and Gapdh were the least stable genes as analyzed by NormFinder algorithm. Both methods reported Tfrc and B2m the most stably expressed genes and Gapdh the least stable one. Altogether our data demonstrate the significance of pre-validation of housekeeping genes for accurate normalization and indicates Tfrc and B2m as best endogenous controls in MS. ActB and Gapdh are not recommended in gene expression studies related to current one.
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Affiliation(s)
- Deepali Mathur
- Department of Functional Biology, University of Valencia Valencia, Spain ; Multiple Sclerosis Laboratory, Department of Biomedicine, Prince Felipe Research Center Valencia, Spain
| | - Juan R Urena-Peralta
- Multiple Sclerosis Laboratory, Department of Biomedicine, Prince Felipe Research Center Valencia, Spain
| | - Gerardo Lopez-Rodas
- Department of Biochemistry and Molecular Biology, University of Valencia and INCLIVA Biomedical Research Institute Valencia, Spain
| | - Bonaventura Casanova
- CSUR-Esclerosi Múltiple, Hospital Universitari i Politècnic La Fe, Unitat Mixta d'Esclerosi Múltiple i Neurorregeneració de l'IIS-La Fe València, Spain
| | | | - Maria Burgal-Marti
- Multiple Sclerosis Laboratory, Department of Biomedicine, Prince Felipe Research Center Valencia, Spain
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Hromadnikova I, Kotlabova K, Hympanova L, Krofta L. Cardiovascular and Cerebrovascular Disease Associated microRNAs Are Dysregulated in Placental Tissues Affected with Gestational Hypertension, Preeclampsia and Intrauterine Growth Restriction. PLoS One 2015; 10:e0138383. [PMID: 26394310 PMCID: PMC4579085 DOI: 10.1371/journal.pone.0138383] [Citation(s) in RCA: 94] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Accepted: 08/28/2015] [Indexed: 01/13/2023] Open
Abstract
Aims To demonstrate that pregnancy-related complications are associated with alterations in cardiovascular and cerebrovascular microRNA expression. Gene expression of 32 microRNAs (miR-1-3p, miR-16-5p, miR-17-5p, miR-20a-5p, miR-20b-5p, miR-21-5p, miR-23a-3p, miR-24-3p, miR-26a-5p, miR-29a-3p, miR-33a-5p, miR-92a-3p, miR-100-5p, miR-103a-3p, miR-122-5p, miR-125b-5p, miR-126-3p, miR-130b-3p, miR-133a-3p, miR-143-3p, miR-145-5p, miR-146a-5p, miR-155-5p, miR-181a-5p, miR-195-5p, miR-199a-5p, miR-208a-3p, miR-210-3p, miR-221-3p, miR-342-3p, miR-499a-5p, and miR-574-3p) was assessed in placental tissues, compared between groups (35 gestational hypertension, 80 preeclampsia, 35 intrauterine growth restriction and 20 normal pregnancies) and correlated with the severity of the disease with respect to clinical signs, delivery date, and Doppler ultrasound parameters. Initially, selection and validation of endogenous controls for microRNA expression studies in placental tissues affected by pregnancy-related complications have been carried out. Results The expression profile of microRNAs was different between pregnancy-related complications and controls. The up-regulation of miR-499a-5p was a common phenomenon shared between gestational hypertension, preeclampsia, and intrauterine growth restriction. Preeclamptic pregnancies delivering after 34 weeks of gestation and IUGR with abnormal values of flow rate in the umbilical artery demonstrated up-regulation of miR-1-3b. Preeclampsia and IUGR requiring termination of gestation before 34 weeks of gestation were associated with down-regulation of miR-26a-5p, miR-103a-3p and miR-145-5p. On the other hand, some of microRNAs (miR-16-5p, miR-100-5p, miR-122-5p, miR-125b-5p, miR-126-3p, miR-143-3p, miR-195-5p, miR-199a-5p, miR-221-3p, miR-342-3p, and miR-574-3p) were only down-regulated or showed a trend to down-regulation just in intrauterine growth restriction pregnancies requiring the delivery before 34 weeks of gestation. Conclusion Epigenetic changes induced by pregnancy-related complications in placental tissue may cause later onset of cardiovascular and cerebrovascular diseases in offspring.
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Affiliation(s)
- Ilona Hromadnikova
- Department of Molecular Biology and Cell Pathology, Third Faculty of Medicine, Charles University, Prague, Czech Republic
- * E-mail:
| | - Katerina Kotlabova
- Department of Molecular Biology and Cell Pathology, Third Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Lucie Hympanova
- Department of Molecular Biology and Cell Pathology, Third Faculty of Medicine, Charles University, Prague, Czech Republic
- Institute for the Care of the Mother and Child, Third Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Ladislav Krofta
- Institute for the Care of the Mother and Child, Third Faculty of Medicine, Charles University, Prague, Czech Republic
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98
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Timaru-Kast R, Herbig EL, Luh C, Engelhard K, Thal SC. Influence of Age on Cerebral Housekeeping Gene Expression for Normalization of Quantitative Polymerase Chain Reaction after Acute Brain Injury in Mice. J Neurotrauma 2015; 32:1777-88. [PMID: 26102571 DOI: 10.1089/neu.2014.3784] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
To prevent methodological errors of quantitative PCR (qPCR) normalization with reference genes is obligatory. Although known to influence gene expression, impact of age on housekeeping gene expression has not been determined after acute brain lesions such as traumatic brain injury (TBI). Therefore, expression of eight common control genes was investigated at 15 min, 24 h, and 72 h after experimental TBI in 2- and 21-month-old C57Bl6 mice. Expression of β2-microglobulin (B2M), β-actin (ActB), and porphobilinogen deaminase (PBGD) increased after TBI in both ages. β2M demonstrated age-dependent differences and highest inter- and intragroup variations. Expression of cyclophilin A, glyceraldehyde-3-phosphate dehydrogenase (GAPDH), hypoxanthine ribosyltransferase (HPRT), S100B, and 18SrRNA remained stable. Cyclophilin A and HPRT demonstrated strongest inter- and intragroup stability. The data indicate that the expression of most but not all control genes is stable during aging. The correct choice of housekeeping genes is of key importance to ensure adequate normalization of qPCR data. With respect to insult and age, normalization strategies should consider cyclophilin A as a single normalizer. Normalization with two reference genes is recommended with cyclophilin A and HPRT in young mice and in mixed age studies and with cyclophilin A and GAPDH in old mice. In addition, the present study suggests not to use β2-microglobulin, β-actin or PBGD as single control genes because of strong regulation after CCI in 2- and 21-month-old mice.
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Affiliation(s)
- Ralph Timaru-Kast
- Department of Anesthesiology, Medical Center of Johannes Gutenberg-University , Mainz, Germany
| | - Elina L Herbig
- Department of Anesthesiology, Medical Center of Johannes Gutenberg-University , Mainz, Germany
| | - Clara Luh
- Department of Anesthesiology, Medical Center of Johannes Gutenberg-University , Mainz, Germany
| | - Kristin Engelhard
- Department of Anesthesiology, Medical Center of Johannes Gutenberg-University , Mainz, Germany
| | - Serge C Thal
- Department of Anesthesiology, Medical Center of Johannes Gutenberg-University , Mainz, Germany
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Sørensen BS, Knudsen A, Wittrup CF, Nielsen S, Aggerholm-Pedersen N, Busk M, Horsman M, Høyer M, Bouchelouche PN, Overgaard J, Alsner J. The usability of a 15-gene hypoxia classifier as a universal hypoxia profile in various cancer cell types. Radiother Oncol 2015; 116:346-51. [DOI: 10.1016/j.radonc.2015.06.028] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Revised: 06/19/2015] [Accepted: 06/30/2015] [Indexed: 02/05/2023]
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LEMming: A Linear Error Model to Normalize Parallel Quantitative Real-Time PCR (qPCR) Data as an Alternative to Reference Gene Based Methods. PLoS One 2015; 10:e0135852. [PMID: 26325269 PMCID: PMC4556681 DOI: 10.1371/journal.pone.0135852] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Accepted: 07/27/2015] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Gene expression analysis is an essential part of biological and medical investigations. Quantitative real-time PCR (qPCR) is characterized with excellent sensitivity, dynamic range, reproducibility and is still regarded to be the gold standard for quantifying transcripts abundance. Parallelization of qPCR such as by microfluidic Taqman Fluidigm Biomark Platform enables evaluation of multiple transcripts in samples treated under various conditions. Despite advanced technologies, correct evaluation of the measurements remains challenging. Most widely used methods for evaluating or calculating gene expression data include geNorm and ΔΔCt, respectively. They rely on one or several stable reference genes (RGs) for normalization, thus potentially causing biased results. We therefore applied multivariable regression with a tailored error model to overcome the necessity of stable RGs. RESULTS We developed a RG independent data normalization approach based on a tailored linear error model for parallel qPCR data, called LEMming. It uses the assumption that the mean Ct values within samples of similarly treated groups are equal. Performance of LEMming was evaluated in three data sets with different stability patterns of RGs and compared to the results of geNorm normalization. Data set 1 showed that both methods gave similar results if stable RGs are available. Data set 2 included RGs which are stable according to geNorm criteria, but became differentially expressed in normalized data evaluated by a t-test. geNorm-normalized data showed an effect of a shifted mean per gene per condition whereas LEMming-normalized data did not. Comparing the decrease of standard deviation from raw data to geNorm and to LEMming, the latter was superior. In data set 3 according to geNorm calculated average expression stability and pairwise variation, stable RGs were available, but t-tests of raw data contradicted this. Normalization with RGs resulted in distorted data contradicting literature, while LEMming normalized data did not. CONCLUSIONS If RGs are coexpressed but are not independent of the experimental conditions the stability criteria based on inter- and intragroup variation fail. The linear error model developed, LEMming, overcomes the dependency of using RGs for parallel qPCR measurements, besides resolving biases of both technical and biological nature in qPCR. However, to distinguish systematic errors per treated group from a global treatment effect an additional measurement is needed. Quantification of total cDNA content per sample helps to identify systematic errors.
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