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Ebrahimi A, Gharanjik S, Azadvari E, Rashidi-Monfared S. Characterizing reference genes for high-fidelity gene expression analysis under different abiotic stresses and elicitor treatments in fenugreek leaves. PLANT METHODS 2024; 20:40. [PMID: 38491388 PMCID: PMC10943880 DOI: 10.1186/s13007-024-01167-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Accepted: 02/28/2024] [Indexed: 03/18/2024]
Abstract
BACKGROUND Quantifying gene expression is a critical aspect of applied genomics research across all organisms, and real-time PCR has emerged as a powerful tool for this purpose. However, selecting appropriate internal control genes for data normalization presents specific challenges. This study aimed to identify suitable reference genes for gene expression analysis under various conditions, encompassing salinity, low and high-temperature stresses, and different elicitor treatments. These treatments included titanium dioxide, cold plasma, 24-epibrassinolide, and melatonin, resulting in a total of 13 unique treatments and 148 treatment combinations applied to fenugreek plants. RESULTS As per the analysis performed with the BestKeeper tool, EEF-1α, and GAPDH were recognized as the most stable reference genes under the majority of conditions. Furthermore, the GeNorm and NormFinder tools identified β-tubulin and EEF-1α as the most stable reference genes. The findings of this research demonstrated that, although the stability of three reference genes expression was acceptable in almost all evaluated treatments, fluctuations in their expression were observed under the treatments of cold stress with TiO2 NPs application, cold plasma application with salinity stress, and cold plasma application with high-temperature stress compared to others. Simultaneously, the GeNorm analysis results demonstrated that in the mentioned treatments, relying on only one reference gene is inadequate. To corroborate the results, we examined the expression profile of the SSR gene, a pivotal gene in diosgenin biosynthesis, under all investigated treatments and treatment combinations. The outcomes suggested that employing stable reference genes yielded highly consistent results. CONCLUSIONS The varying expression patterns of the target genes emphasize the crucial need for precise optimization of experimental conditions and selecting stable reference genes to achieve accurate results in gene expression studies utilizing real-time PCR. These findings offer valuable insights into the selection of appropriate reference genes for gene expression analysis under diverse conditions using real-time PCR.
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Affiliation(s)
- Amin Ebrahimi
- Agronomy and Plant Breeding Department, Faculty of Agriculture, Shahrood University of Technology, Semnan, Iran.
| | - Shahrokh Gharanjik
- Department of Plant Breeding and Biotechnology, Faculty of Agricultural Engineering, Shahrood University of Technology, Shahrood, Iran.
| | - Elham Azadvari
- Horticultural Sciences Department, Faculty of Agriculture, Shahrood University of Technology, Shahrood, Iran
| | - Sajad Rashidi-Monfared
- Plant Breeding and Biotechnology Department, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran
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Abstract
Northern hybridization is used to measure the amount and size of RNAs transcribed from eukaryotic genes and to estimate their abundance. No other method is capable of obtaining these pieces of information simultaneously from a large number of RNA preparations; northern analysis is therefore fundamental to studies of gene expression in eukaryotic cells. To prepare a northern blot for hybridization, RNA must be separated according to size through a denaturing agarose or polyacrylamide gel and transferred to a solid support in a way that preserves its topological distribution within the gel. These important steps in northern analysis are discussed here.
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Zhou L, Meng JY, Ruan HY, Yang CL, Zhang CY. Expression stability of candidate RT-qPCR housekeeping genes in Spodoptera frugiperda (Lepidoptera: Noctuidae). ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2021; 108:e21831. [PMID: 34240760 DOI: 10.1002/arch.21831] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Revised: 06/01/2021] [Accepted: 06/04/2021] [Indexed: 05/28/2023]
Abstract
Reverse-transcription quantitative polymerase chain reaction (RT-qPCR) is commonly used to quantify gene expression. For normalization, the expression of each gene is compared with a reference "housekeeping" gene that is stably expressed under relevant stress. Unfortunately, there have been no reports on the stability of such reference genes under various treatments of the Spodoptera frugiperda. In this study, we used five tools (RefFinder, GeNorm, NormFinder, BestKeeper, and ΔCt methods) to evaluate the stability of 12 candidate reference genes (RPS18, β-tubulin, GAPDH, RPS7, RPS15, RPL7, RPL32, Actin-5C, EF1-α, EF1-γ, RPL27, and ACE) in different instars, tissues, and treatments (high and low temperature, UV-A, and emamectin benzoate). Several ribosomal proteins (RPS7, RPS15, RPL32, RPS18, and RPL7), GAPDH, Actin-5C, and β-tubulin, were relatively stable, suggesting that they are ideal housekeeping genes for various treatments. ACE was extremely unstable under various experimental treatments, rendering it unsuitable as an internal reference. This study identified the reference housekeeping genes stably expressed by S. frugiperda under different treatments, thus setting a foundation for further exploration of the physiological and biochemical mechanisms.
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Affiliation(s)
- Lv Zhou
- Guizhou Provincial Key Laboratory for Agricultural Pest Management of the Mountainous Region, Institute of Entomology, Guizhou University, Guiyang, China
| | - Jian-Yu Meng
- Guizhou Tobacco Science Research Institute, Guiyang, China
| | - Hong-Yun Ruan
- Guizhou Provincial Key Laboratory for Agricultural Pest Management of the Mountainous Region, Institute of Entomology, Guizhou University, Guiyang, China
| | - Chang-Li Yang
- Guizhou Provincial Key Laboratory for Agricultural Pest Management of the Mountainous Region, Institute of Entomology, Guizhou University, Guiyang, China
| | - Chang-Yu Zhang
- Guizhou Provincial Key Laboratory for Agricultural Pest Management of the Mountainous Region, Institute of Entomology, Guizhou University, Guiyang, China
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Jain N, Nitisa D, Pirsko V, Cakstina I. Selecting suitable reference genes for qPCR normalization: a comprehensive analysis in MCF-7 breast cancer cell line. BMC Mol Cell Biol 2020; 21:68. [PMID: 32977762 PMCID: PMC7519550 DOI: 10.1186/s12860-020-00313-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 09/16/2020] [Indexed: 02/08/2023] Open
Abstract
Background MCF-7 breast cancer cell line is undoubtedly amongst the most extensively studied patient-derived research models, providing pivotal results that have over the decades translated to constantly improving patient care. Many research groups, have previously identified suitable reference genes for qPCR normalization in MCF-7 cell line. However, over the course of identification of suitable reference genes, a comparative analysis comprising these genes together in a single study has not been reported. Furthermore, the expression dynamics of these reference genes within sub-clones cultured over multiple passages (p) has attracted limited attention from research groups. Therefore, we investigated the expression dynamics of 12 previously suggested reference genes within two sub-clones (culture A1 and A2) cultured identically over multiple passages. Additionally, the effect of nutrient stress on reference gene expression was examined to postulate an evidence-based recommendation of the least variable reference genes that could be employed in future gene expression studies. Results The analysis revealed the presence of differential reference gene expression within the sub-clones of MCF-7. In culture A1, GAPDH-CCSER2 were identified as the least variable reference genes while for culture A2, GAPDH-RNA28S were identified. However, upon validation using genes of interest, both these pairs were found to be unsuitable control pairs. Normalization of AURKA and KRT19 with triplet pair GAPDH-CCSER2-PCBP1 yielded successful results. The triplet also proved its capability to handle variations arising from nutrient stress. Conclusions The variance in expression behavior amongst sub-clones highlights the potential need for exercising caution while selecting reference genes for MCF-7. GAPDH-CCSER2-PCBP1 triplet offers a reliable alternative to otherwise traditionally used internal controls for optimizing intra- and inter-assay gene expression differences. Furthermore, we suggest avoiding the use of ACTB, GAPDH and PGK1 as single internal controls.
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Affiliation(s)
- Nityanand Jain
- Laboratory of Molecular Genetics, Institute of Oncology, Riga Stradiņš University, Dzirciema street 16, Riga, LV-1007, Latvia
| | - Dina Nitisa
- Laboratory of Molecular Genetics, Institute of Oncology, Riga Stradiņš University, Dzirciema street 16, Riga, LV-1007, Latvia
| | - Valdis Pirsko
- Laboratory of Molecular Genetics, Institute of Oncology, Riga Stradiņš University, Dzirciema street 16, Riga, LV-1007, Latvia
| | - Inese Cakstina
- Laboratory of Molecular Genetics, Institute of Oncology, Riga Stradiņš University, Dzirciema street 16, Riga, LV-1007, Latvia.
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Athanasiou AT, Nussbaumer T, Kummer S, Hofer M, Johnston IG, Staltner M, Allmer DM, Scott MC, Vogl C, Fenger JM, Modiano JF, Walter I, Steinborn R. S100A4 mRNA-protein relationship uncovered by measurement noise reduction. J Mol Med (Berl) 2020; 98:735-749. [PMID: 32296879 PMCID: PMC7241963 DOI: 10.1007/s00109-020-01898-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 02/28/2020] [Accepted: 03/12/2020] [Indexed: 10/30/2022]
Abstract
Intrinsic biological fluctuation and/or measurement error can obscure the association of gene expression patterns between RNA and protein levels. Appropriate normalization of reverse-transcription quantitative PCR (RT-qPCR) data can reduce technical noise in transcript measurement, thus uncovering such relationships. The accuracy of gene expression measurement is often challenged in the context of cancer due to the genetic instability and "splicing weakness" involved. Here, we sequenced the poly(A) cancer transcriptome of canine osteosarcoma using mRNA-Seq. Expressed sequences were resolved at the level of two consecutive exons to enable the design of exon-border spanning RT-qPCR assays and ranked for stability based on the coefficient of variation (CV). Using the same template type for RT-qPCR validation, i.e. poly(A) RNA, avoided skewing of stability assessment by circular RNAs (circRNAs) and/or rRNA deregulation. The strength of the relationship between mRNA expression of the tumour marker S100A4 and its proportion score of quantitative immunohistochemistry (qIHC) was introduced as an experimental readout to fine-tune the normalization choice. Together with the essential logit transformation of qIHC scores, this approach reduced the noise of measurement as demonstrated by uncovering a highly significant, strong association between mRNA and protein expressions of S100A4 (Spearman's coefficient ρ = 0.72 (p = 0.006)). KEY MESSAGES: • RNA-seq identifies stable pairs of consecutive exons in a heterogeneous tumour. • Poly(A) RNA templates for RT-qPCR avoid bias from circRNA and rRNA deregulation. • HNRNPL is stably expressed across various cancer tissues and osteosarcoma. • Logit transformed qIHC score better associates with mRNA amount. • Quantification of minor S100A4 mRNA species requires poly(A) RNA templates and dPCR.
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Affiliation(s)
| | - Thomas Nussbaumer
- Computational Systems Biology, University of Vienna, Althanstrasse 14, A-1090, Vienna, Austria
| | - Stefan Kummer
- VetBioBank, VetCore, University of Veterinary Medicine, Veterinärplatz 1, A-1210, Vienna, Austria
| | - Martin Hofer
- Genomics Core Facility, VetCore, University of Veterinary Medicine, Veterinärplatz 1, A-1210, Vienna, Austria
| | - Iain G Johnston
- Department of Mathematics, University of Bergen, Bergen, Norway
| | - Moritz Staltner
- Genomics Core Facility, VetCore, University of Veterinary Medicine, Veterinärplatz 1, A-1210, Vienna, Austria
| | - Daniela M Allmer
- Genomics Core Facility, VetCore, University of Veterinary Medicine, Veterinärplatz 1, A-1210, Vienna, Austria
| | - Milcah C Scott
- College of Veterinary Medicine and Masonic Cancer Center, University of Minnesota, 425 East River Road, Minneapolis, MN, USA
| | - Claus Vogl
- Institute of Animal Breeding and Genetics, Department for Biomedical Sciences, University of Veterinary Medicine, Veterinärplatz 1, A-1210, Vienna, Austria
| | - Joelle M Fenger
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, The Ohio State University, 1900 Coffey Road, Columbus, OH, USA
| | - Jaime F Modiano
- College of Veterinary Medicine and Masonic Cancer Center, University of Minnesota, 425 East River Road, Minneapolis, MN, USA
| | - Ingrid Walter
- VetBioBank, VetCore, University of Veterinary Medicine, Veterinärplatz 1, A-1210, Vienna, Austria
- Institute of Pathology, Department of Pathobiology, University of Veterinary Medicine, Veterinärplatz 1, A-1210, Vienna, Austria
| | - Ralf Steinborn
- Genomics Core Facility, VetCore, University of Veterinary Medicine, Veterinärplatz 1, A-1210, Vienna, Austria.
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Ma D, Fan J, Tian Y, Jiang P, Wang J, Zhu H, Bai J. Selection of reference genes for quantitative real-time PCR normalisation in largemouth bass Micropterus salmoides fed on alternative diets. JOURNAL OF FISH BIOLOGY 2019; 95:393-400. [PMID: 31017661 DOI: 10.1111/jfb.13991] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 04/23/2019] [Indexed: 06/09/2023]
Abstract
The partial cDNA sequences of eight reference genes (actb, tuba1, gapdh58, gapdh59, eef1a1, RNA 18 s, pabpc1, ube2I) were cloned from largemouth bass Micropterus salmoides. The expression levels of these eight genes were compared in the various tissues (eye, spleen, kidney, gill, muscle, brain, liver, heart, gut and gonad) of M. salmoides fed on forage fish. The results showed that the candidate genes exhibited tissue-specific expression to various degrees and the stability ranking order was eef1a1 > tuba1 > RNA 18 s > pabpc1 > ube2I > actb > gapdh58 > gapdh59 among tissue types. Four candidate genes eef1a1, tuba1, RNA 18 s and actb were used to analyse the stability in liver tissues of largemouth bass between the forage-fish group and the formulated-feed group. The candidate genes also showed some changes in expression levels in the livers, while eef1a1 and tuba1 had the most stable expression in livers of fish fed on alternative diets within 10 candidates. So eef1a1 and tuba1 were recommended as optimal reference gene in quantitative real-time PCR analysis to normalise the expression levels of target genes in tissues and lives of the M. salmoides fed on alternative diets. In livers, the expression levels of gck normalised by eef1a1 and tuba1 showed the significant up-regulation in formulated feed group (P < 0.05) than those in forage-fish group. While sex difference has no significant effects on the expression levels of gck in both groups.
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Affiliation(s)
- Dongmei Ma
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation, Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Jiajia Fan
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation, Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Yuanyuan Tian
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation, Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Peng Jiang
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation, Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Junjie Wang
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation, Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Huaping Zhu
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation, Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Junjie Bai
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation, Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
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Ma F, Liu Z, Huang J, Kang Y, Wang J. Evaluation of reference genes for quantitative real-time PCR analysis of messenger RNAs and microRNAs in rainbow trout Oncorhynchus mykiss under heat stress. JOURNAL OF FISH BIOLOGY 2019; 95:540-554. [PMID: 30993691 DOI: 10.1111/jfb.13986] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 04/15/2019] [Indexed: 06/09/2023]
Abstract
We assessed the expression stability of several messenger (m)RNAs and micro (mi)RNAs from liver and head kidney of rainbow trout Oncorhynchus mykiss using high-throughput RNA sequencing (RNA-seq) and miRNA-seq data. Additionally, four commonly used reference genes and one small non-coding RNA (u6) were also selected to identify ideal reference mRNAs and miRNAs for quantitative real-time (qrt)-PCR analysis of heat stress responses. GeNorm, NormFinder, BestKeeper and comparative ΔCt were employed for analysis of qrt-PCR data to systematically assess the expression stability of candidate mRNAs and miRNAs and stability was ranked using geometric means. β-actin and ef1-α were the most stably expressed reference mRNAs in liver and head kidney, respectively and ssa-mir-26a-5p and ssa-mir-462b-5p were the most stably expressed miRNAs in these tissues. This is the first identification of appropriate reference mRNAs and miRNAs for qrt-PCR analysis of O. mykiss under heat stress.
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Affiliation(s)
- Fang Ma
- College of Animal Science and Technology, Gansu Agricultural University, No. 1 Yingmencun, Anning District, Lanzhou, Gansu, China
| | - Zhe Liu
- College of Animal Science and Technology, Gansu Agricultural University, No. 1 Yingmencun, Anning District, Lanzhou, Gansu, China
| | - Jinqiang Huang
- College of Animal Science and Technology, Gansu Agricultural University, No. 1 Yingmencun, Anning District, Lanzhou, Gansu, China
| | - Yujun Kang
- College of Animal Science and Technology, Gansu Agricultural University, No. 1 Yingmencun, Anning District, Lanzhou, Gansu, China
| | - Jianfu Wang
- College of Animal Science and Technology, Gansu Agricultural University, No. 1 Yingmencun, Anning District, Lanzhou, Gansu, China
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Singh S, Gupta M, Pandher S, Kaur G, Goel N, Rathore P, Palli SR. RNA sequencing, selection of reference genes and demonstration of feeding RNAi in Thrips tabaci (Lind.) (Thysanoptera: Thripidae). BMC Mol Biol 2019; 20:6. [PMID: 30777032 PMCID: PMC6380046 DOI: 10.1186/s12867-019-0123-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 02/12/2019] [Indexed: 11/21/2022] Open
Abstract
Background Thrips tabaci is a severe pest of onion and cotton. Due to lack of information on its genome or transcriptome, not much is known about this insect at the molecular level. To initiate molecular studies in this insect, RNA was sequenced; de novo transcriptome assembly and analysis were performed. The RNAseq data was used to identify reference and RNAi pathway genes in this insect. Additionally, feeding RNAi was demonstrated in T. tabaci for the first time. Results From the assembled transcriptome, 27,836 coding sequence (CDS) with an average size of 1236 bp per CDS were identified. About 85.4% of CDS identified showed positive Blast hits. The homologs of most of the core RNAi machinery genes were identified in this transcriptome. To select reference genes for reverse-transcriptase real-time quantitative PCR (RT-qPCR) experiments, 14 housekeeping genes were identified in the transcriptome and their expression was analyzed by (RT-qPCR). UbiCE in adult, 28s in nymphs and SOD under starvation stress were identified as the most stable reference genes for RT-qPCR. Feeding dsSNF7 and dsAQP caused 16.4- and 14.47-fold reduction in SNF7 and AQP mRNA levels respectively, when compared to their levels in dsGFP fed control insects. Feeding dsSNF7 or dsAQP also caused 62 and 72% mortality in T. tabaci. Interestingly, simultaneous feeding of dsRNAs targeting SNF7 or AQP and one of the RNAi pathway genes (Dicer-2/Aubergine/Staufen) resulted in a significant reduction in RNAi of target genes. These data suggest the existence of robust RNAi machinery in T. tabaci. Conclusion The current research is the first report of the assembled, analyzed and annotated RNAseq resource for T. tabaci, which may be used for future molecular studies in this insect. Reference genes validated across stages and starvation stress provides first-hand information on stable genes in T. tabaci. The information on RNAi machinery genes and significant knockdown of the target gene through dsRNA feeding in synthetic diet confirms the presence of efficient RNAi in this insect. These data provide a solid foundation for further research on developing RNAi as a method to manage this pest. Electronic supplementary material The online version of this article (10.1186/s12867-019-0123-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Satnam Singh
- Punjab Agricultural University, Regional Station, Faridkot, Punjab, 151203, India.
| | - Mridula Gupta
- Punjab Agricultural University, Regional Station, Faridkot, Punjab, 151203, India
| | - Suneet Pandher
- Punjab Agricultural University, Regional Station, Faridkot, Punjab, 151203, India
| | - Gurmeet Kaur
- Punjab Agricultural University, Regional Station, Faridkot, Punjab, 151203, India
| | - Neha Goel
- Forest Research Institute, Dehradun, Uttaranchal, India
| | - Pankaj Rathore
- Punjab Agricultural University, Regional Station, Faridkot, Punjab, 151203, India
| | - Subba Reddy Palli
- Department of Entomology, University of Kentucky, Lexington, KY, USA
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Busato S, Mezzetti M, Logan P, Aguilera N, Bionaz M. What's the norm in normalization? A frightening note on the use of RT-qPCR in the livestock science. Gene 2019; 721S:100003. [PMID: 34531001 PMCID: PMC7285961 DOI: 10.1016/j.gene.2018.100003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 11/29/2018] [Accepted: 12/10/2018] [Indexed: 11/26/2022]
Abstract
Reverse-Transcription quantitative PCR (RT-qPCR) provides a valuable tool to study gene expression with exquisite sensitivity. To retain its inferential power, user-introduced technical variability must be reduced and accounted for. Selecting a set of stably expressed internal control genes (ICG), validated for each experimental condition/sample set, is widely accepted as a reliable way to normalize RT-qPCR data and account for said variability. Despite significant efforts in establishing standardized and resource-efficient normalization approaches, numerous recent reports have underlined deficiencies in the state of RT-qPCR normalization. Livestock science has benefitted tremendously from the use of RT-qPCR; however, the issue of lack of proper normalization likely affects this discipline as well. We thus decided to determine whether this is true, and to which extent. We conducted an in-depth analysis of all (225) RT-qPCR articles published in the six most prominent livestock journals in the field from 2013 to 2017. A quantitative scale was constructed, and values were assigned to each article based on the number of ICG used, the use of a publicly available algorithm to assess the reliability of ICG, and the reporting of pertinent information related to ICG (ranges from 0 = total noncompliance - to 100 = total compliance). Out of the surveyed group, only 10.7% of the publications obtained a score of 100, while the largest group (n = 158) was represented by articles that scored 0. Subdividing articles based on whether an algorithm to validate ICG was used (YAL) or not (NAL) revealed the use of a larger number of ICG to normalize RT-qPCR in the YAL group compared to NAL (1.4-fold more, 95% C.I.: 1.11–1.84) and was closer to the “gold standard” of three ICG. Using an algorithm also increased the diversity of ICG and significantly reduced the use of RNA18S, whose suitability as ICG has been thoroughly debated. These remarkably low normalization standards are likely to generate questionable results that can severely hinder the advance of transcriptomic studies in livestock science and related fields. Subpar normalization of reverse transcription qPCR was reported for the five major livestock journals over the period 2013-2017 The use of algorithms for validation led to a greater number of ICG used, and greater variety of ICGs The issue could be solved by editors by enforcing the use of the standardized MIQE guidelines for RT-qPCR
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Affiliation(s)
- Sebastiano Busato
- Department of Animal and Rangeland Sciences, Oregon State University, Corvallis, OR 97331, United States of America
| | - Matteo Mezzetti
- Istituto di Zootecnica, Facoltà di Agraria, Università Cattolica del Sacro Cuore, 29122 Piacenza, Italy
| | - Paul Logan
- Department of Animal and Rangeland Sciences, Oregon State University, Corvallis, OR 97331, United States of America
| | - Nicolas Aguilera
- Department of Animal and Rangeland Sciences, Oregon State University, Corvallis, OR 97331, United States of America
| | - Massimo Bionaz
- Department of Animal and Rangeland Sciences, Oregon State University, Corvallis, OR 97331, United States of America.
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Identification and Validation of Reference Genes for RT-qPCR Normalization in Mythimna separata (Lepidoptera: Noctuidae). BIOMED RESEARCH INTERNATIONAL 2018; 2018:1828253. [PMID: 30151374 PMCID: PMC6091413 DOI: 10.1155/2018/1828253] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 05/28/2018] [Accepted: 06/21/2018] [Indexed: 11/18/2022]
Abstract
Mythimna separata is a major agricultural pest with seasonal migrating trait in China. Formation and regulation mechanism of migration behavior has resulted in a large number of fundamental researches involving quantitative studies of gene expression in this species. Using appropriate reference gene is critical in RT-qPCR data normalization. A comprehensive study on the reference genes in M. separata is lacking. In this paper, expression stabilities of ten candidate reference genes were evaluated in M. separata under various biotic and abiotic conditions by employing four different software geNorm, NormFinder, BestKeeper, and the comparative ΔCT method. The comprehensive stabilities ranking of these genes were suggested by RefFinder. PKG as a target gene was employed to justify the number of reference genes in four larval tissues and two photoperiod treatments. Results demonstrate that the first three most stable genes were as follows: EF, CypA, and β-TUB for developmental stages; EF, CypA, and RPL12 for larval tissues; EF, TBP, and β-TUB for adult tissues. RPL12, β-TUB, and EF for densities; EF, RPL12, and GAPDH for photoperiod treatments; β-TUB, EF, and ATPase for temperature treatments. Stable reference gene combinations may reduce bias in normalization. This work provides for the first time a comprehensive list of appropriate reference genes and facilitates future studies on gene function of M. separata.
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Singh S, Gupta M, Pandher S, Kaur G, Rathore P, Palli SR. Selection of housekeeping genes and demonstration of RNAi in cotton leafhopper, Amrasca biguttula biguttula (Ishida). PLoS One 2018; 13:e0191116. [PMID: 29329327 PMCID: PMC5766320 DOI: 10.1371/journal.pone.0191116] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2017] [Accepted: 12/28/2017] [Indexed: 01/14/2023] Open
Abstract
Amrasca biguttula biguttula (Ishida) commonly known as cotton leafhopper is a severe pest of cotton and okra. Not much is known on this insect at molecular level due to lack of genomic and transcriptomic data. To prepare for functional genomic studies in this insect, we evaluated 15 common housekeeping genes (Tub, B-Tub, EF alpha, GADPH, UbiCF, RP13, Ubiq, G3PD, VATPase, Actin, 18s, 28s, TATA, ETF, SOD and Cytolytic actin) during different developmental stages and under starvation stress. We selected early (1st and 2nd), late (3rd and 4th) stage nymphs and adults for identification of stable housekeeping genes using geNorm, NormFinder, BestKeeper and RefFinder software. Based on the different algorithms, RP13 and VATPase are identified as the most suitable reference genes for quantification of gene expression by reverse transcriptase quantitative PCR (RT-qPCR). Based on RefFinder which comprehended the results of three algorithms, RP13 in adults, Tubulin (Tub) in late nymphs, 28S in early nymph and UbiCF under starvation stress were identified as the most stable genes. We also developed methods for feeding double-stranded RNA (dsRNA) incorporated in the diet. Feeding dsRNA targeting Snf7, IAP, AQP1, and VATPase caused 56.17-77.12% knockdown of targeted genes compared to control and 16 to 48% mortality of treated insects when compared to control.
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Affiliation(s)
- Satnam Singh
- Punjab Agricultural University, Regional Station, Faridkot, Punjab, India
| | - Mridula Gupta
- Punjab Agricultural University, Regional Station, Faridkot, Punjab, India
| | - Suneet Pandher
- Punjab Agricultural University, Regional Station, Faridkot, Punjab, India
| | - Gurmeet Kaur
- Punjab Agricultural University, Regional Station, Faridkot, Punjab, India
| | - Pankaj Rathore
- Punjab Agricultural University, Regional Station, Faridkot, Punjab, India
| | - Subba Reddy Palli
- Department of Entomology, University of Kentucky, Lexington, KY, United States of America
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12
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Titov SE, Demenkov PS, Ivanov MK, Malakhina ES, Poloz TL, Tsivlikova EV, Ganzha MS, Shevchenko SP, Gulyaeva LF, Kolesnikov NN. Selection and validation of miRNAs as normalizers for profiling expression of microRNAs isolated from thyroid fine needle aspiration smears. Oncol Rep 2016; 36:2501-2510. [PMID: 27666315 PMCID: PMC5055203 DOI: 10.3892/or.2016.5113] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 09/01/2016] [Indexed: 11/16/2022] Open
Abstract
Fine needle aspiration cytology (FNAC) is currently the method of choice for malignancy prediction in thyroid nodules. Nevertheless, in some cases the interpretation of FNAC results may be problematic due to limitations of the method. The expression level of some microRNAs changes with the development of thyroid tumors, and its quantitation can be used to refine the FNAC results. For this quantitation to be reliable, the obtained data must be adequately normalized. Currently, no reference genes are universally recognized for quantitative assessments of microRNAs in thyroid nodules. The aim of the present study was the selection and validation of such reference genes. Expression of 800 microRNAs in 5 paired samples of thyroid surgical material corresponding to different histotypes of tumors was analyzed using NanoString technology and four of these (hsa-miR-151a-3p, -197-3p, -99a-5p and -214-3p) with the relatively low variation coefficient were selected. The possibility of use of the selected microRNAs and their combination as references was estimated by RT-qPCR on a sampling of cytological smears: benign (n=226), atypia of undetermined significance (n=9), suspicious for follicular neoplasm (n=61), suspicious for malignancy (n=19), medullary thyroid carcinoma (MTC) (n=32), papillary thyroid carcinoma (PTC) (n=54) and non-diagnostic material (ND) (n=34). In order to assess the expression stability of the references, geNorm algorithm was used. The maximum stability was observed for the normalization factor obtained by the combination of all 4 microRNAs. Further validation of the complex normalizer and individual selected microRNAs was performed using 5 different classification methods on 3 groups of FNAC smears from the analyzed batch: benign neoplasms, MTC and PTC. In all cases, the use of the complex classifier resulted in the reduced number of errors. On using the complex microRNA normalizer, the decision-tree method C4.5 makes it possible to distinguish between malignant and benign thyroid neoplasms in cytological smears with high overall accuracy (>91%).
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Affiliation(s)
- Sergei E Titov
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Pavel S Demenkov
- The Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Mikhail K Ivanov
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Ekaterina S Malakhina
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Tatiana L Poloz
- Non-governmental Healthcare Institution 'Railroad Clinical Hospital on the Station Novosibirsk-Glavny', Joint Stock Company 'Russian Railways', Novosibirsk 630003, Russia
| | | | | | - Sergei P Shevchenko
- Novosibirsk Municipal Budgetary Healthcare Institution 'Municipal Clinical Hospital #1', Novosibirsk 630047, Russia
| | - Lyudmila F Gulyaeva
- Institute of Molecular Biology and Biophysics, Siberian Branch of the Russian Academy of Medical Sciences, Novosibirsk 630117, Russia
| | - Nikolay N Kolesnikov
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia
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13
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Cale JM, Millican DS, Itoh H, Magness RR, Bird IM. Pregnancy Induces an Increase in the Expression of Glyceraldehyde-3-Phosphate Dehydrogenase in Uterine Artery Endothelial Cells. ACTA ACUST UNITED AC 2016. [DOI: 10.1177/107155769700400604] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
| | | | | | - Ronald R. Magness
- Department of Obstetrics and Gynecology, Perinatal Research Laboratories, and the Department of Meat and Animal Science, University of Wisconsin-Madison, Madison, Wisconsin
| | - Ian M. Bird
- University of Wisconsin-Madison, Department of Obstetrics and Gynecology, Perinatal Research Laboratories, 7E Meriter Hospital/Park, 202 South Park Street, Madison, WI 53715
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14
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Yu S, Hwang HE, Yun N, Goldenring JR, Nam KT. The mRNA and Protein Levels of Tubulin and β-Actin Are Greatly Reduced in the Proximal Duodenum of Mice Relative to the Rest of the Small Intestines. Dig Dis Sci 2015; 60:2670-6. [PMID: 25976623 DOI: 10.1007/s10620-015-3688-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Accepted: 04/24/2015] [Indexed: 12/09/2022]
Abstract
To accurately quantify mRNA and protein levels, it is critical to choose appropriate internal standards. As the expression of housekeeping genes is assumed to remain constant, they are often employed to normalize signals to correct for sample-to-sample variations. However, recent studies have documented that β-actin and Glyceraldehyde 3-phosphate dehydrogenase (GAPDH) expression levels change in response to various stimuli during proliferation, activation, and differentiation. We investigated levels of α-, β-, γ-tubulin, β-actin, and GAPDH vary across the gastrointestinal tract of mice. We found that different regions of the small intestines had dramatically different expression profiles, as measured by western blot, quantitative Reverse transcription polymerase chain reaction (RT-PCR), and immunohistochemical staining. These results revealed that the expression levels of tubulins and β-actin were dramatically lower in the proximal duodenum, relative to the rest of the small intestines. These varying levels of housekeeping genes may reflect differences in the activities of specialized tissues and suggest unique requirements for tubulins in these tissue types. We conclude that the use of a single housekeeping gene to normalize gene expression in the gastrointestinal tracts of mice may introduce errors, as measured differences in gene expression may reflect regulation of the internal control rather than the mRNA or protein under investigation.
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Affiliation(s)
- Sungsook Yu
- Severance Biomedical Science Institute, Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 120-752, Korea
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15
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The expression and distributions of ANP32A in the developing brain. BIOMED RESEARCH INTERNATIONAL 2015; 2015:207347. [PMID: 25866766 PMCID: PMC4383345 DOI: 10.1155/2015/207347] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Revised: 08/20/2014] [Accepted: 08/20/2014] [Indexed: 12/25/2022]
Abstract
Acidic (leucine-rich) nuclear phosphoprotein 32 family, member A (ANP32A), has multiple functions involved in neuritogenesis, transcriptional regulation, and apoptosis. However, whether ANP32A has an effect on the mammalian developing brain is still in question. In this study, it was shown that brain was the organ that expressed the most abundant ANP32A by human multiple tissue expression (MTE) array. The distribution of ANP32A in the different adult brain areas was diverse dramatically, with high expression in cerebellum, temporal lobe, and cerebral cortex and with low expression in pons, medulla oblongata, and spinal cord. The expression of ANP32A was higher in the adult brain than in the fetal brain of not only humans but also mice in a time-dependent manner. ANP32A signals were dispersed accordantly in embryonic mouse brain. However, ANP32A was abundant in the granular layer of the cerebellum and the cerebral cortex when the mice were growing up, as well as in the Purkinje cells of the cerebellum. The variation of expression levels and distribution of ANP32A in the developing brain would imply that ANP32A may play an important role in mammalian brain development, especially in the differentiation and function of neurons in the cerebellum and the cerebral cortex.
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16
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Rueda-Martínez C, Lamas O, Mataró MJ, Robledo-Carmona J, Sánchez-Espín G, Jiménez-Navarro M, Such-Martínez M, Fernández B. Selection of reference genes for quantitative real time PCR (qPCR) assays in tissue from human ascending aorta. PLoS One 2014; 9:e97449. [PMID: 24841551 PMCID: PMC4026239 DOI: 10.1371/journal.pone.0097449] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2013] [Accepted: 04/21/2014] [Indexed: 11/18/2022] Open
Abstract
Dilatation of the ascending aorta (AAD) is a prevalent aortopathy that occurs frequently associated with bicuspid aortic valve (BAV), the most common human congenital cardiac malformation. The molecular mechanisms leading to AAD associated with BAV are still poorly understood. The search for differentially expressed genes in diseased tissue by quantitative real-time PCR (qPCR) is an invaluable tool to fill this gap. However, studies dedicated to identify reference genes necessary for normalization of mRNA expression in aortic tissue are scarce. In this report, we evaluate the qPCR expression of six candidate reference genes in tissue from the ascending aorta of 52 patients with a variety of clinical and demographic characteristics, normal and dilated aortas, and different morphologies of the aortic valve (normal aorta and normal valve n = 30; dilated aorta and normal valve n = 10; normal aorta and BAV n = 4; dilated aorta and BAV n = 8). The expression stability of the candidate reference genes was determined with three statistical algorithms, GeNorm, NormFinder and Bestkeeper. The expression analyses showed that the most stable genes for the three algorithms employed were CDKN1β, POLR2A and CASC3, independently of the structure of the aorta and the valve morphology. In conclusion, we propose the use of these three genes as reference genes for mRNA expression analysis in human ascending aorta. However, we suggest searching for specific reference genes when conducting qPCR experiments with new cohort of samples.
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Affiliation(s)
- Carmen Rueda-Martínez
- UGC del Corazón, Instituto de Investigación Biomédica de Málaga (IBIMA), Hospital Clínico Universitario Virgen de la Victoria, Málaga, Spain
| | - Oscar Lamas
- UGC del Corazón, Instituto de Investigación Biomédica de Málaga (IBIMA), Hospital Clínico Universitario Virgen de la Victoria, Málaga, Spain
| | - María José Mataró
- UGC del Corazón, Instituto de Investigación Biomédica de Málaga (IBIMA), Hospital Clínico Universitario Virgen de la Victoria, Málaga, Spain
| | - Juan Robledo-Carmona
- UGC del Corazón, Instituto de Investigación Biomédica de Málaga (IBIMA), Hospital Clínico Universitario Virgen de la Victoria, Málaga, Spain
| | - Gemma Sánchez-Espín
- UGC del Corazón, Instituto de Investigación Biomédica de Málaga (IBIMA), Hospital Clínico Universitario Virgen de la Victoria, Málaga, Spain
| | - Manuel Jiménez-Navarro
- UGC del Corazón, Instituto de Investigación Biomédica de Málaga (IBIMA), Hospital Clínico Universitario Virgen de la Victoria, Málaga, Spain
- Departamento de Medicina, Facultad de Medicina, Universidad de Málaga, Málaga, Spain
| | - Miguel Such-Martínez
- UGC del Corazón, Instituto de Investigación Biomédica de Málaga (IBIMA), Hospital Clínico Universitario Virgen de la Victoria, Málaga, Spain
| | - Borja Fernández
- Departamento de Biología Animal, Instituto de Investigación Biomédica de Málaga (IBIMA), Facultad de Ciencias, Universidad de Málaga, Málaga, Spain
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Han TU, Park J, Domingues CF, Moretti-Ferreira D, Paris E, Sainz E, Gutierrez J, Drayna D. A study of the role of the FOXP2 and CNTNAP2 genes in persistent developmental stuttering. Neurobiol Dis 2014; 69:23-31. [PMID: 24807205 DOI: 10.1016/j.nbd.2014.04.019] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Revised: 04/09/2014] [Accepted: 04/27/2014] [Indexed: 11/24/2022] Open
Abstract
A number of speech disorders including stuttering have been shown to have important genetic contributions, as indicated by high heritability estimates from twin and other studies. We studied the potential contribution to stuttering from variants in the FOXP2 gene, which have previously been associated with developmental verbal dyspraxia, and from variants in the CNTNAP2 gene, which have been associated with specific language impairment (SLI). DNA sequence analysis of these two genes in a group of 602 unrelated cases, all with familial persistent developmental stuttering, revealed no excess of potentially deleterious coding sequence variants in the cases compared to a matched group of 487 well characterized neurologically normal controls. This was compared to the distribution of variants in the GNPTAB, GNPTG, and NAGPA genes which have previously been associated with persistent stuttering. Using an expanded subject data set, we again found that NAGPA showed significantly different mutation frequencies in North Americans of European descent (p=0.0091) and a significant difference existed in the mutation frequency of GNPTAB in Brazilians (p=0.00050). No significant differences in mutation frequency in the FOXP2 and CNTNAP2 genes were observed between cases and controls. To examine the pattern of expression of these five genes in the human brain, real time quantitative reverse transcription PCR was performed on RNA purified from 27 different human brain regions. The expression patterns of FOXP2 and CNTNAP2 were generally different from those of GNPTAB, GNPTG and NAPGA in terms of relatively lower expression in the cerebellum. This study provides an improved estimate of the contribution of mutations in GNPTAB, GNPTG and NAGPA to persistent stuttering, and suggests that variants in FOXP2 and CNTNAP2 are not involved in the genesis of familial persistent stuttering. This, together with the different brain expression patterns of GNPTAB, GNPTG, and NAGPA compared to that of FOXP2 and CNTNAP2, suggests that the genetic neuropathological origins of stuttering differ from those of verbal dyspraxia and SLI.
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Affiliation(s)
- Tae-Un Han
- National Institute on Deafness and Other Communication Disorders, NIH, Bethesda, MD 20892, USA
| | - John Park
- National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD 20892, USA
| | - Carlos F Domingues
- National Institute on Deafness and Other Communication Disorders, NIH, Bethesda, MD 20892, USA; Department of Genetics, Institute of Bioscience, São Paulo State University (UNESP), Botucatu, São Paulo 18618-000, Brazil
| | - Danilo Moretti-Ferreira
- Department of Genetics, Institute of Bioscience, São Paulo State University (UNESP), Botucatu, São Paulo 18618-000, Brazil
| | - Emily Paris
- National Institute on Deafness and Other Communication Disorders, NIH, Bethesda, MD 20892, USA
| | - Eduardo Sainz
- National Institute on Deafness and Other Communication Disorders, NIH, Bethesda, MD 20892, USA
| | - Joanne Gutierrez
- National Institute on Deafness and Other Communication Disorders, NIH, Bethesda, MD 20892, USA
| | - Dennis Drayna
- National Institute on Deafness and Other Communication Disorders, NIH, Bethesda, MD 20892, USA.
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18
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Kam WWY, McNamara AL, Lake V, Banos C, Davies JB, Kuncic Z, Banati RB. Predicted ionisation in mitochondria and observed acute changes in the mitochondrial transcriptome after gamma irradiation: A Monte Carlo simulation and quantitative PCR study. Mitochondrion 2013; 13:736-42. [DOI: 10.1016/j.mito.2013.02.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2012] [Revised: 01/14/2013] [Accepted: 02/13/2013] [Indexed: 10/27/2022]
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19
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Fong SW, Ibrahim S, Mohamed MS, Few LL, Too WCS, Khoo BY, Yusof Z, Rahman ARA, Yvonne-Tee GB. Identification of endogenous control genes for gene expression studies in peripheral blood of patients with coronary artery disease. Mol Biol 2013. [DOI: 10.1134/s0026893313020064] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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20
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Leelatanawit R, Klanchui A, Uawisetwathana U, Karoonuthaisiri N. Validation of reference genes for real-time PCR of reproductive system in the black tiger shrimp. PLoS One 2012; 7:e52677. [PMID: 23285145 PMCID: PMC3532477 DOI: 10.1371/journal.pone.0052677] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2012] [Accepted: 11/19/2012] [Indexed: 11/19/2022] Open
Abstract
Gene expression of reproductive system of the black tiger shrimp (Peneaus monodon) has been widely studied to address poor maturation problem in captivity. However, a systematic evaluation of reference genes in quantitative real-time PCR (qPCR) for P. monodon reproductive organs is lacking. In this study, the stability of four potential reference genes (18s rRNA, GAPDH, β-actin, and EF1-α) was examined in the reproductive tissues in various conditions using bioinformatic tools: NormFinder and geNorm. For NormFinder, EF1-α and GAPDH ranked first and second as the most stable genes in testis groups whereas GAPDH and EF1-α were for ovaries from wild-caught broodstock and domesticated groups. EF1-α and β-actin ranked first and second for the eyestalk ablated ovaries. For geNorm, EF1-α and GAPDH had the best stability in all testis and ovaries from domesticated groups whereas EF1-α and β-actin were the best for ovaries from wild-caught and eyestalk ablated groups. Moreover, the expression levels of two well-known reproductive genes, Dmc1 and Vitellogenin, were used to validate these reference genes. When normalized to EF1-α, the expected expression patterns were obtained in all cases. Therefore, this work suggests that EF1-α is more versatile as reference genes in qPCR analysis for reproductive system in P. monodon.
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Affiliation(s)
- Rungnapa Leelatanawit
- Microarray Laboratory, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Klong Luang, Pathumthani, Thailand
| | - Amornpan Klanchui
- Microarray Laboratory, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Klong Luang, Pathumthani, Thailand
| | - Umaporn Uawisetwathana
- Microarray Laboratory, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Klong Luang, Pathumthani, Thailand
| | - Nitsara Karoonuthaisiri
- Microarray Laboratory, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Klong Luang, Pathumthani, Thailand
- * E-mail:
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21
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Vázquez-Blomquist D, Fernández JR, Miranda J, Bello C, Silva JA, Estrada RC, Novoa LI, Palenzuela D, Bello I. Selection of reference genes for use in quantitative reverse transcription PCR assays when using interferons in U87MG. Mol Biol Rep 2012; 39:11167-75. [DOI: 10.1007/s11033-012-2026-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2012] [Accepted: 10/02/2012] [Indexed: 10/27/2022]
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22
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Zhao DJ, Guo K, Kang L. Identification of condition-specific reference genes from microarray data for locusts exposed to hypobaric hypoxia. FEBS Open Bio 2012; 2:235-40. [PMID: 23650605 PMCID: PMC3642161 DOI: 10.1016/j.fob.2012.08.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2012] [Revised: 08/01/2012] [Accepted: 08/03/2012] [Indexed: 12/11/2022] Open
Abstract
Real-time quantitative polymerase chain reaction (qPCR) is a routine and robust approach for measuring gene expression. The stability of reference genes in qPCR is crucial for the accurate quantification of gene expression. To provide reliable reference genes for studying the transcriptional responses of locust muscles to hypobaric hypoxia, we first examined the gene expression stability of the frequently used housekeeping genes 18S, GAPDH, and β-actin. However, the expression of these three housekeeping genes was influenced by hypobaric hypoxia. Consequently, we identified five novel candidate reference genes from the locust microarray data. The gene expression stability of the five candidates, together with the three classical housekeeping genes, were evaluated using two distinct algorithms implemented in geNorm and NormFinder. GeNorm identified Ach (acetyl-CoA hydrolase) and Pgp (phosphoglycolate phosphatase-like) as the most stable genes and NormFinder further distinguished Ach as the most stable one. The validity of Ach as a reference gene was confirmed through comparison with 18S. This study exemplifies the necessity of validating reference genes before their application and the feasibility of identifying condition-specific reference genes from large-scale gene expression data.
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Affiliation(s)
- De-Jian Zhao
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
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23
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Sokolenko S, George S, Wagner A, Tuladhar A, Andrich JMS, Aucoin MG. Co-expression vs. co-infection using baculovirus expression vectors in insect cell culture: Benefits and drawbacks. Biotechnol Adv 2012; 30:766-81. [PMID: 22297133 PMCID: PMC7132753 DOI: 10.1016/j.biotechadv.2012.01.009] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2011] [Revised: 01/13/2012] [Accepted: 01/17/2012] [Indexed: 12/12/2022]
Abstract
The baculovirus expression vector system (BEVS) is a versatile and powerful platform for protein expression in insect cells. With the ability to approach similar post-translational modifications as in mammalian cells, the BEVS offers a number of advantages including high levels of expression as well as an inherent safety during manufacture and of the final product. Many BEVS products include proteins and protein complexes that require expression from more than one gene. This review examines the expression strategies that have been used to this end and focuses on the distinguishing features between those that make use of single polycistronic baculovirus (co-expression) and those that use multiple monocistronic baculoviruses (co-infection). Three major areas in which researchers have been able to take advantage of co-expression/co-infection are addressed, including compound structure-function studies, insect cell functionality augmentation, and VLP production. The core of the review discusses the parameters of interest for co-infection and co-expression with time of infection (TOI) and multiplicity of infection (MOI) highlighted for the former and the choice of promoter for the latter. In addition, an overview of modeling approaches is presented, with a suggested trajectory for future exploration. The review concludes with an examination of the gaps that still remain in co-expression/co-infection knowledge and practice.
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Affiliation(s)
- Stanislav Sokolenko
- Department of Chemical Engineering, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario, Canada N2L 3G1
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Lomashvili KA, Wang X, Wallin R, O'Neill WC. Matrix Gla protein metabolism in vascular smooth muscle and role in uremic vascular calcification. J Biol Chem 2011; 286:28715-28722. [PMID: 21705322 PMCID: PMC3190679 DOI: 10.1074/jbc.m111.251462] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2011] [Revised: 06/22/2011] [Indexed: 01/07/2023] Open
Abstract
Matrix Gla protein (MGP) is an inhibitor of vascular calcification but its mechanism of action and pathogenic role are unclear. This was examined in cultured rat aortas and in a model of vascular calcification in rats with renal failure. Both carboxylated (GlaMGP) and uncarboxylated (GluMGP) forms were present in aorta and disappeared during culture with warfarin. MGP was also released into the medium and removed by ultracentrifugation, and similarly affected by warfarin. In a high-phosphate medium, warfarin increased aortic calcification but only in the absence of pyrophosphate, another endogenous inhibitor of vascular calcification. Although GlaMGP binds and inactivates bone morphogenic protein (BMP)-2, a proposed mediator of vascular calcification through up-regulation of the osteogenic transcription factor runx2, neither warfarin, BMP-2, nor the BMP-2 antagonist noggin altered runx2 mRNA content in aortas, and noggin did not prevent warfarin-induced calcification. Aortic content of MGP mRNA was increased 5-fold in renal failure but did not differ between calcified and noncalcified aortas. Immunoblots showed increased GlaMGP in noncalcified (5-fold) and calcified (20-fold) aortas from rats with renal failure, with similar increases in GluMGP. We conclude that rat aortic smooth muscle produces both GlaMGP and GluMGP in tissue-bound and soluble, presumably vesicular, forms. MGP inhibits calcification independent of BMP-2-driven osteogenesis and only in the absence of pyrophosphate, consistent with direct inhibition of hydroxyapatite formation. Synthesis of MGP is increased in renal failure and deficiency of GlaMGP is not a primary cause of medial calcification in this condition.
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Affiliation(s)
- Koba A Lomashvili
- Department of Medicine, Renal Division, Emory University, Atlanta, Georgia 30322 and
| | - Xiaonan Wang
- Department of Medicine, Renal Division, Emory University, Atlanta, Georgia 30322 and
| | - Reidar Wallin
- Department of Medicine, Wake Forest University, Winston-Salem, North Carolina 27109
| | - W Charles O'Neill
- Department of Medicine, Renal Division, Emory University, Atlanta, Georgia 30322 and.
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25
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Kulkarni B, Mohammed I, Hopkinson A, Dua HS. Validation of endogenous control genes for gene expression studies on human ocular surface epithelium. PLoS One 2011; 6:e22301. [PMID: 21857920 PMCID: PMC3152287 DOI: 10.1371/journal.pone.0022301] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2011] [Accepted: 06/21/2011] [Indexed: 11/18/2022] Open
Abstract
Purpose To evaluate a panel of ten known endogenous control genes (ECG) with quantitative reverse transcription PCR (qPCR), for identification of stably expressed endogenous control genes in the ocular surface (OS) epithelial regions including cornea, limbus, limbal epithelial crypt and conjunctiva to normalise the quantitative reverse transcription PCR data of genes of interest expressed in above-mentioned regions. Method The lasermicrodissected (LMD) OS epithelial regions of cryosectioned corneoscleral buttons from the cadaver eyes were processed for RNA extraction and cDNA synthesis to detect genes of interest with qPCR. Gene expression of 10 known ECG—glyceraldehyde-3-phosphate dehydrogenase (GAPDH), beta actin (ACTB), peptidylprolyl isomerase (PPIA), TATA-box binding protein (TBP1), hypoxanthine guanine phosphoribosyl transferase (HPRT1), beta glucuronidase (GUSB), Eucaryotic 18S ribosomal RNA (18S), phosphoglycerate kinase (PGK1), beta-2-microglobulin (B2M), ribosomal protein, large, P0 (RPLP0)—was measured in the OS epithelial regions by qPCR method and the data collected was further analysed using geNorm software. Results The expression stability of ECGs in the OS epithelial regions in increasing order as determined with geNorm software is as follows: ACTB<18S<TBP<B2M<PGK1<HPRT1<GUSB<GAPDH<PPIA-RPLP0. In this study, geNorm analysis has shown the following ECGs pairs to be most stably expressed in individual OS epithelial regions: HPRT1-TBP in cornea, GUSB-PPIA in limbus, B2M-PPIA and RPLP0-TBP in LEC and conjunctiva respectively. However, across the entire ocular surface including all the regions mentioned above, PPIA-RPLP0 pair was shown to be most stable. Conclusion This study has identified stably expressed ECGs on the OS epithelial regions for effective qPCR results in genes of interest. The results from this study are broadly applicable to quantitative reverse transcription PCR studies on human OS epithelium and provide evidence for the use of PPIA-RPLP0 ECGs pair in quantitative reverse transcription PCR across the OS epithelium.
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Affiliation(s)
- Bina Kulkarni
- Division of Ophthalmology and Visual Sciences, Queen's Medical Centre, Nottingham, United Kingdom
| | - Imran Mohammed
- Division of Ophthalmology and Visual Sciences, Queen's Medical Centre, Nottingham, United Kingdom
- Institute for Translational Medicine and Therapeutics, Department of Pharmacology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Andrew Hopkinson
- Division of Ophthalmology and Visual Sciences, Queen's Medical Centre, Nottingham, United Kingdom
| | - Harminder Singh Dua
- Division of Ophthalmology and Visual Sciences, Queen's Medical Centre, Nottingham, United Kingdom
- * E-mail:
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Yurube T, Takada T, Hirata H, Kakutani K, Maeno K, Zhang Z, Yamamoto J, Doita M, Kurosaka M, Nishida K. Modified house-keeping gene expression in a rat tail compression loading-induced disc degeneration model. J Orthop Res 2011; 29:1284-90. [PMID: 21387398 DOI: 10.1002/jor.21406] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/30/2010] [Accepted: 02/15/2011] [Indexed: 02/04/2023]
Abstract
House-keeping genes (HKGs) are generally used as endogenous controls for molecular normalization in quantitative PCR analysis. However, whether all the so-called HKGs are useful for intervertebral disc research is controversial. Our objective was, using a prevalidated rat tail static compression loading-induced disc degeneration model, to clarify the feasibility of common HKGs for gene-quantification in the nucleus pulposus cells. In real-time RT-PCR for five HKGs [β-actin, β-glucuronidase, β-2 microglobulin, glyceraldehyde 3-phosphate dehydrogenase (GAPDH), and lactate dehydrogenase A (LDHA)], static compression at 1.3 MPa for up to 56 days demonstrated messenger RNA (mRNA) expression levels of consistent β-2 microglobulin and GAPDH, slightly up-regulated β-glucuronidase, and fairly down-regulated β-actin and LDHA. Especially, β-actin had a drastic suppression to 0.15-fold in the loaded relative to unloaded discs at 7 days. In immunofluorescence, β-actin showed a significant down-regulation to almost undetectable levels from 28 days, while GAPDH was constantly detected throughout. β-Actin mRNA and protein-distribution are thought to be affected by the loading treatment, however, GAPDH mRNA and protein-distribution can retain relatively stable expressions. Under prolonged static compression, β-actin and probably LDHA are inappropriate, and GAPDH is a feasible HKG as internal references in the disc cells.
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Affiliation(s)
- Takashi Yurube
- Department of Orthopaedic Surgery, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe 650-0017, Japan
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Kroupova H, Trubiroha A, Wuertz S, Kloas W. Stage-dependent differences in RNA composition and content affect the outcome of expression profiling in roach (Rutilus rutilus) ovary. Comp Biochem Physiol A Mol Integr Physiol 2011; 159:141-9. [DOI: 10.1016/j.cbpa.2011.02.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2011] [Revised: 02/07/2011] [Accepted: 02/07/2011] [Indexed: 10/18/2022]
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Xiao X, Li M, Wang K, Qin Q, Chen X. Characterization of large yellow croaker (Pseudosciaena crocea) β-actin promoter supports β-actin gene as an internal control for gene expression modulation and its potential application in transgenic studies in fish. FISH & SHELLFISH IMMUNOLOGY 2011; 30:1072-1079. [PMID: 21316460 DOI: 10.1016/j.fsi.2011.02.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2010] [Revised: 01/31/2011] [Accepted: 02/06/2011] [Indexed: 05/30/2023]
Abstract
As a housekeeping gene, β-actin is one of the most commonly used reference gene and its promoter is widely used in transgenic studies in mammals and fish. In this study, we used genomic walker technology to clone the β-actin gene (Lycβ-actin) promoter sequence from large yellow croaker, an economically important marine fish in China. The Lycβ-actin promoter region spans 3350 nucleotides (nt) and contains several transcription factor binding sites and a conserved enhancer motif (ATGGTAATAA) in the first intron. A promoter activity assay showed that this promoter region can drive enhanced green fluorescent protein (EGFP) gene expression in the fish cell line, EPC. Luciferase activity analysis demonstrated that the activity of the Lycβ-actin promoter is not affected by poly(I:C) or lipopolysaccharide (LPS) stimulation. Absolute real-time PCR analysis of various tissues revealed that Lycβ-actin expression levels are not significantly altered by poly(I:C) or inactivated trivalent bacterial vaccine (P > 0.05). These results suggest that β-actin can be used as a suitable internal control for gene expression modulation in response to immune stimulations in large yellow croaker. In vivo transgenic experiments showed that the Lycβ-actin promoter region can drive efficient EGFP expression in large yellow croaker fries or fertilized zebrafish eggs, supporting its potential application in transgenic studies in fish.
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Affiliation(s)
- Xiaoqiang Xiao
- School of Life Sciences, Zhongshan University, Guangzhou 510275, PR China
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Selection and validation of reference genes for gene expression studies by reverse transcription quantitative PCR in Xanthomonas citri subsp. citri during infection of Citrus sinensis. Biotechnol Lett 2011; 33:1177-84. [PMID: 21318633 DOI: 10.1007/s10529-011-0552-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2010] [Accepted: 01/25/2011] [Indexed: 01/06/2023]
Abstract
Xanthomonas citri subsp. citri (Xcc) causes citrus canker, a worldwide disease found mainly in sweet oranges (Citrus sinensis (L.) Osbeck). The expression of nine candidate internal reference genes was analyzed in Xcc grown alone and during C. sinensis infection to identify genes most suitable for comparative expression studies in Xcc using reverse transcription quantitative PCR (qRT-PCR). The stability of these genes was determined using the programs geNorm, NormFinder and BestKeeper. The genes most suitable for data normalization during C. sinensis infection were atpD, rpoB, gyrA and gyrB. The use of at least three reference genes is essential for accurate data normalization in Xcc.
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Tunbridge EM, Eastwood SL, Harrison PJ. Changed relative to what? Housekeeping genes and normalization strategies in human brain gene expression studies. Biol Psychiatry 2011; 69:173-9. [PMID: 20673871 DOI: 10.1016/j.biopsych.2010.05.023] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/11/2010] [Revised: 04/25/2010] [Accepted: 05/20/2010] [Indexed: 10/19/2022]
Abstract
Many studies in biological psychiatry compare the abundance of individual messenger RNAs between cases and control subjects or, more recently, between genotype groups. Most utilize some form of normalization procedure, usually expressing the transcript(s) of interest relative to that of a housekeeping gene or genes (also called reference genes), to overcome various sources of experimental error. Indeed, normalization is such a standard procedure that its purpose, principles, and limitations are sometimes overlooked, and some papers lack sufficient information as to its implementation. Here, we review the rationales for normalization and argue that in well-conducted psychiatric gene expression studies using human brain tissue, it is reducing intersubject variability rather than experimental error that is the major benefit of normalization. We also review the conceptual and empirical basis for the category of housekeeping genes-i.e., genes with a ubiquitous and invariant expression. We conclude that the evidence is against any such simple categorization and that a more pragmatic, less dogmatic, approach to the selection and implementation of reference genes is required, which takes into account the particular issues that pertain to human brain tissue studies. This pragmatism extends to the issue of whether normalization should be to one or multiple reference genes. We end by making several recommendations toward a more flexible, transparent, and comprehensive approach to data presentation and analysis. We illustrate the review with examples from studies of schizophrenia and mood disorder.
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Affiliation(s)
- Elizabeth M Tunbridge
- Department of Psychiatry, University of Oxford, Warneford Hospital, Oxford, United Kingdom
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Fernandez P, Di Rienzo JA, Moschen S, Dosio GAA, Aguirrezábal LAN, Hopp HE, Paniego N, Heinz RA. Comparison of predictive methods and biological validation for qPCR reference genes in sunflower leaf senescence transcript analysis. PLANT CELL REPORTS 2011; 30:63-74. [PMID: 21076836 DOI: 10.1007/s00299-010-0944-3] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2010] [Revised: 10/21/2010] [Accepted: 10/22/2010] [Indexed: 05/22/2023]
Abstract
The selection and validation of reference genes constitute a key point for gene expression analysis based on qPCR, requiring efficient normalization approaches. In this work, the expression profiles of eight genes were evaluated to identify novel reference genes for transcriptional studies associated to the senescence process in sunflower. Three alternative strategies were applied for the evaluation of gene expression stability in leaves of different ages and exposed to different treatments affecting the senescence process: algorithms implemented in geNorm, BestKeeper software, and the fitting of a statistical linear mixed model (LMModel). The results show that geNorm suggested the use of all combined genes, although identifying α-TUB1 as the most stable expressing gene. BestKeeper revealed α-TUB and β-TUB as stable genes, scoring β-TUB as the most stable one. The statistical LMModel identified α-TUB, actin, PEP, and EF-1α as stable genes in this order. The model-based approximation allows not only the estimation of systematic changes in gene expression, but also the identification of sources of random variation through the estimation of variance components, considering the experimental design applied. Validation of α-TUB and EF-1α as reference genes for expression studies of three sunflower senescence associated genes showed that the first one was more stable for the assayed conditions. We conclude that, when biological replicates are available, LMModel allows a more reliable selection under the assayed conditions. This study represents the first analysis of identification and validation of genuine reference genes for use as internal control in qPCR expression studies in sunflower, experimentally validated throughout six different controlled leaf senescence conditions.
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Affiliation(s)
- Paula Fernandez
- Instituto de Biotecnología, CICVyA, INTA Castelar, Las Cabañas y Los Reseros, (1686) Hurlingham, Buenos Aires, Argentina.
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Moreno-Igoa M, Manzano R, Oliván S, Calvo AC, Toivonen JM, Osta R. Effects of gene therapy on muscle 18S rRNA expression in mouse model of ALS. BMC Res Notes 2010; 3:275. [PMID: 21044297 PMCID: PMC2987871 DOI: 10.1186/1756-0500-3-275] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2010] [Accepted: 11/02/2010] [Indexed: 01/14/2023] Open
Abstract
Background The efficiency of gene therapy experiments is frequently evaluated by measuring the impact of the treatment on the expression of genes of interest by quantitative real time PCR (qRT-PCR) and by normalizing these values to those of housekeeping (HK) genes constitutively expressed throughout the experiment. The objective of this work was to study the effects of muscle gene therapy on the expression of 18 S ribosomal RNA (Rn18S), a commonly used HK gene. Findings Mouse model of motor neuron disease (SOD1-G93A) was injected intramuscularly with Brain-derived neurotrophic factor (BDNF-TTC) encoding or control naked DNA plasmids. qRT-PCR expression analysis was performed for BDNF and HK genes Rn18 S, glyceraldehyde-3-phosphate dehydrogenase (Gapdh) and β-actin (Actb). We report that elevated BDNF expression in the injected muscle was accompanied with increased Rn18 S expression, whereas Gapdh and Actb were not affected. Increased "ribosomal output" upon BDNF stimulation was supported by increased steady-state levels of ribosomal protein mRNAs. Conclusions Ribosomal RNA transcription may be directly stimulated by administration of trophic factors. Caution should be taken in using Rn18 S as a HK gene in experiments where muscle metabolism is likely to be altered by therapeutic intervention.
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Affiliation(s)
- María Moreno-Igoa
- LAGENBIO-I3A, Veterinary Faculty, Aragon Institute of Health Sciences (IACS), Universidad de Zaragoza, Miguel Servet 177, 50013 Zaragoza, Spain.
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Li Z, Yang L, Wang J, Shi W, Pawar RA, Liu Y, Xu C, Cong W, Hu Q, Lu T, Xia F, Guo W, Zhao M, Zhang Y. beta-Actin is a useful internal control for tissue-specific gene expression studies using quantitative real-time PCR in the half-smooth tongue sole Cynoglossus semilaevis challenged with LPS or Vibrio anguillarum. FISH & SHELLFISH IMMUNOLOGY 2010; 29:89-93. [PMID: 20227507 DOI: 10.1016/j.fsi.2010.02.021] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2009] [Revised: 02/20/2010] [Accepted: 02/22/2010] [Indexed: 05/25/2023]
Abstract
beta-Actin has been frequently used as an internal control (gene) or as a housekeeping gene to normalize the expression of the target gene(s) or mRNA levels between different samples. However, the beta-actin expression has been shown to be influenced by the sample type and experimental conditions. If beta-actin could be used as a reference gene for the half-smooth tongue sole Cynoglossus semilaevis remains ill-defined. Here we evaluate the tissue-specific beta-actin gene expression pattern in C. semilaevis when challenged with antigenic agents namely, lipopolysaccharide (LPS) or Vibrio anguillarum employing absolute quantitative real-time PCR. The real-time PCR was performed based on the standard curve generated from recombinant plasmids. No significant differences in beta-actin expression were found between treated and untreated tissue samples. We thus conclude that beta-actin could be used as a reliable internal reference gene for real-time PCR based quantitation of gene expression studies in various tissue samples of C. semilaevis challenged with LPS or pathogenic bacteria.
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Affiliation(s)
- Zhaojie Li
- The Technology Center of Weihai Entry-exit Inspection and Quarantine Bureau, Weihai 264205, PR China
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Hurtado del Pozo C, Calvo RM, Vesperinas-García G, Gómez-Ambrosi J, Frühbeck G, Corripio-Sánchez R, Rubio MA, Obregon MJ. IPO8 and FBXL10: new reference genes for gene expression studies in human adipose tissue. Obesity (Silver Spring) 2010; 18:897-903. [PMID: 19876011 DOI: 10.1038/oby.2009.374] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Housekeeping genes frequently used in gene expression studies are highly regulated in human adipose tissue. To ensure a correct interpretation of results, it is critical to select appropriate reference genes. Subcutaneous (SC) and omental (OM) adipose tissue expression was analyzed from lean and obese subjects using whole genome complementary DNA (cDNA) microarrays to identify stably expressed genes and commercial TaqMan low density arrays (LDAs), with 16 common control genes. The best candidate gene from microarrays analysis was F-box and leucine-rich repeat protein-10 (FBXL10) (fold-change 10(-3) P < 0.01), an ubiquitous nucleolar protein evolutionarily conserved. Hypoxanthine phosphoribosyltransferase 1 (HPRT1) and importin 8 (IPO8), were the best reference genes among the 16 genes in the LDAs with coefficient of variation (CV) of 4.51 and 4.55%, respectively. However, when the LDAs data were further analyzed by the geNorm and NormFinder softwares, IPO8, a nuclear protein mediating import of proteins, was the first and the third better reference gene, respectively. IPO8 and FBXL10 were further validated by real-time PCR in additional OM and SC fat samples and primary cultured preadipocytes. According to their CV, IPO8 resulted more suitable than FBXL10 in both adipose tissue depots and SC preadipocytes, whereas FBXL10 performed better than IPO8 in OM cultured preadipocytes. Both genes expression levels did not change throughout adipogenesis. Thus, we provide clear evidence that IPO8 and FBXL10 are good candidates to use as reference genes in gene expression studies in human OM and SC adipose tissues as well as differentiated primary preadipocytes.
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Affiliation(s)
- Carmen Hurtado del Pozo
- Instituto de Investigaciones Biomedicas, Consejo Superior de Investigaciones Cientificas-UAM, Madrid, Spain
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Boava LP, Laia ML, Jacob TR, Dabbas KM, Gonçalves JF, Ferro JA, Ferro MI, Furtado EL. Selection of endogenous genes for gene expression studies in Eucalyptus under biotic (Puccinia psidii) and abiotic (acibenzolar-S-methyl) stresses using RT-qPCR. BMC Res Notes 2010; 3:43. [PMID: 20181283 PMCID: PMC2854107 DOI: 10.1186/1756-0500-3-43] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2009] [Accepted: 02/24/2010] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Rust caused by Puccinia psidii Winter has been limiting for the establishment of new Eucalyptus plantations, as well as for resprouting of susceptible genetic materials. Identifying host genes involved in defense responses is important to elucidate resistance mechanisms. Reverse transcription-quantitative PCR is the most common method of mRNA quantitation for gene expression analysis. This method generally employs a reference gene as an internal control to normalize results. A good endogenous control transcript shows minimal variation due to experimental conditions. FINDINGS We analyzed the expression of 13 genes to identify transcripts with minimal variation in leaves of 60-day-old clonal seedlings of two Eucalyptus clones (rust-resistant and susceptible) subjected to biotic (P. psidii) and abiotic (acibenzolar-S-methyl, ASM) stresses. CONCLUSIONS For tissue samples of clones that did not receive any stimulus, a combination of the eEF2 and EglDH genes was the best control for normalization. When pathogen-inoculated and uninoculated plant samples were compared, eEF2 and UBQ together were more appropriate as normalizers. In ASM-treated and untreated leaves of both clones, transcripts of the CYP and elF4B genes combined were the ones with minimal variation. Finally, when comparing expression in both clones for ASM-treated leaves, P. psidii-inoculated leaves, ASM-treated plus P. psidii-inoculated leaves, and their respective controls, the genes with the most stable expression were EgIDH and UBQ. The chitinase gene, which is highly expressed in studies on plant resistance to phytopathogens, was used to confirm variation in gene expression due to the treatments.
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Affiliation(s)
- Leonardo P Boava
- Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista - UNESP, Via de Acesso Prof, Paulo Donato Castellane, s/n, CEP: 14884-900, Jaboticabal, SP, Brazil.
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Yang Y, Hou S, Cui G, Chen S, Wei J, Huang L. Characterization of reference genes for quantitative real-time PCR analysis in various tissues of Salvia miltiorrhiza. Mol Biol Rep 2009; 37:507-13. [PMID: 19680786 DOI: 10.1007/s11033-009-9703-3] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2009] [Accepted: 07/29/2009] [Indexed: 11/25/2022]
Abstract
Five reference genes, 18S, EF1alpha, alpha-Tubulin, Ubiquitin and Actin, from Salvia miltiorrhiza were analyzed as internal controls for gene expression profiling assay using quantitative real-time polymerase chain reaction (qRT-PCR). The five candidate genes were measured for their transcriptional level in seven tissues, including roots, stems, leaves, sepals, petals, stamens and pistils. Then they were ranked by the GeNorm tool. The results showed that Actin and Ubiquitin were the most stable whereas EF1alpha and 18S did not favor normalization of qRT-PCR results in these tissues. Expression levels of the SmDXR gene were studied in parallel, with Actin and Ubiquitin both or each as reference in the seven tissues, and varying relative quantifications of the SmDXR gene in seven tissues. This study indicated that selection of the most stable genes plays an important role in gene expression profiling assays.
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Affiliation(s)
- Yanfang Yang
- Institute of Medicinal Plant Development, Chinese Academy of Medicinal Sciences and Peking Union Medical College, Beijing, China
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Guénin S, Mauriat M, Pelloux J, Van Wuytswinkel O, Bellini C, Gutierrez L. Normalization of qRT-PCR data: the necessity of adopting a systematic, experimental conditions-specific, validation of references. JOURNAL OF EXPERIMENTAL BOTANY 2009; 60:487-93. [PMID: 19264760 DOI: 10.1093/jxb/ern305] [Citation(s) in RCA: 368] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Quantitative RT-PCR (reverse transcription polymerase chain reaction, also known as qRT-PCR or real-time RT-PCR) has been used in large proportions of transcriptome analyses published to date. The accuracy of the results obtained by this method strongly depends on accurate transcript normalization using stably expressed genes, known as references. Statistical algorithms have been developed recently to help validate reference genes but, surprisingly, this robust approach is under-utilized in plants. Instead, putative 'housekeeping' genes tend to be used as references without any proper validation. The concept of normalization in transcript quantification is introduced here and the factors affecting its reliability in qRT-PCR are discussed in an attempt to convince molecular biologists, and non-specialists, that systematic validation of reference genes is essential for producing accurate, reliable data in qRT-PCR analyses, and thus should be an integral component of them.
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Affiliation(s)
- Stéphanie Guénin
- Molecular Biology Centre, Centre de Ressources Régionales en Biologie Moléculaire, Université de Picardie Jules Verne, Faculté des Sciences, 33 Rue St Leu, F-80039 Amiens, France
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Cicinnati VR, Shen Q, Sotiropoulos GC, Radtke A, Gerken G, Beckebaum S. Validation of putative reference genes for gene expression studies in human hepatocellular carcinoma using real-time quantitative RT-PCR. BMC Cancer 2008. [PMID: 19036168 DOI: 10.1186/1471-2407-8-350.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Reference genes, which are often referred to as housekeeping genes are frequently used to normalize mRNA levels between different samples in quantitative reverse transcription polymerase chain reaction (qRT-PCR). The selection of reference genes is critical for gene expression studies because the expression of these genes may vary among tissues or cells and may change under certain circumstances. Here, a systematic evaluation of six putative reference genes for gene expression studies in human hepatocellular carcinoma (HCC) is presented. METHODS Six genes, beta-2-microglobulin (B2M), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), hydroxymethyl-bilane synthase (HMBS), hypoxanthine phosphoribosyl-transferase 1 (HPRT1), succinate dehydrogenase complex, subunit A (SDHA) and ubiquitin C (UBC), with distinct functional characteristics and expression patterns were evaluated by qRT-PCR. Inhibitory substances in RNA samples were quantitatively assessed and controlled using an external RNA control. The stability of selected reference genes was analyzed using both geNorm and NormFinder software. RESULTS HMBS and GAPDH were identified as the optimal reference genes for normalizing gene expression data between paired tumoral and adjacent non-tumoral tissues derived from patients with HCC. HMBS, GAPDH and UBC were identified to be suitable for the normalization of gene expression data among tumor tissues; whereas the combination of HMBS, B2M, SDHA and GAPDH was suitable for normalizing gene expression data among five liver cancer cell lines, namely Hep3B, HepG2, HuH7, SK-HEP-1 and SNU-182. The determined gene stability was increased after exclusion of RNA samples containing relatively higher inhibitory substances. CONCLUSION Of six genes studied, HMBS was found to be the single best reference gene for gene expression studies in HCC. The appropriate choice of combination of more than one reference gene to improve qRT-PCR accuracy depends on the kind of liver tissues or cells under investigation. Quantitative assessment and control of qRT-PCR inhibitors using an external RNA control can reduce the variation of qRT-PCR assay and facilitate the evaluation of gene stability. Our results may facilitate the choice of reference genes for expression studies in HCC.
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Affiliation(s)
- Vito R Cicinnati
- Department of Gastroenterology and Hepatology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany.
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Cicinnati VR, Shen Q, Sotiropoulos GC, Radtke A, Gerken G, Beckebaum S. Validation of putative reference genes for gene expression studies in human hepatocellular carcinoma using real-time quantitative RT-PCR. BMC Cancer 2008; 8:350. [PMID: 19036168 PMCID: PMC2607287 DOI: 10.1186/1471-2407-8-350] [Citation(s) in RCA: 99] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2008] [Accepted: 11/27/2008] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Reference genes, which are often referred to as housekeeping genes are frequently used to normalize mRNA levels between different samples in quantitative reverse transcription polymerase chain reaction (qRT-PCR). The selection of reference genes is critical for gene expression studies because the expression of these genes may vary among tissues or cells and may change under certain circumstances. Here, a systematic evaluation of six putative reference genes for gene expression studies in human hepatocellular carcinoma (HCC) is presented. METHODS Six genes, beta-2-microglobulin (B2M), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), hydroxymethyl-bilane synthase (HMBS), hypoxanthine phosphoribosyl-transferase 1 (HPRT1), succinate dehydrogenase complex, subunit A (SDHA) and ubiquitin C (UBC), with distinct functional characteristics and expression patterns were evaluated by qRT-PCR. Inhibitory substances in RNA samples were quantitatively assessed and controlled using an external RNA control. The stability of selected reference genes was analyzed using both geNorm and NormFinder software. RESULTS HMBS and GAPDH were identified as the optimal reference genes for normalizing gene expression data between paired tumoral and adjacent non-tumoral tissues derived from patients with HCC. HMBS, GAPDH and UBC were identified to be suitable for the normalization of gene expression data among tumor tissues; whereas the combination of HMBS, B2M, SDHA and GAPDH was suitable for normalizing gene expression data among five liver cancer cell lines, namely Hep3B, HepG2, HuH7, SK-HEP-1 and SNU-182. The determined gene stability was increased after exclusion of RNA samples containing relatively higher inhibitory substances. CONCLUSION Of six genes studied, HMBS was found to be the single best reference gene for gene expression studies in HCC. The appropriate choice of combination of more than one reference gene to improve qRT-PCR accuracy depends on the kind of liver tissues or cells under investigation. Quantitative assessment and control of qRT-PCR inhibitors using an external RNA control can reduce the variation of qRT-PCR assay and facilitate the evaluation of gene stability. Our results may facilitate the choice of reference genes for expression studies in HCC.
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Affiliation(s)
- Vito R Cicinnati
- Department of Gastroenterology and Hepatology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany.
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McCurley AT, Callard GV. Characterization of housekeeping genes in zebrafish: male-female differences and effects of tissue type, developmental stage and chemical treatment. BMC Mol Biol 2008; 9:102. [PMID: 19014500 PMCID: PMC2588455 DOI: 10.1186/1471-2199-9-102] [Citation(s) in RCA: 447] [Impact Index Per Article: 27.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2008] [Accepted: 11/12/2008] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Research using the zebrafish model has experienced a rapid growth in recent years. Although real-time reverse transcription PCR (QPCR), normalized to an internal reference ("housekeeping") gene, is a frequently used method for quantifying gene expression changes in zebrafish, many commonly used housekeeping genes are known to vary with experimental conditions. To identify housekeeping genes that are stably expressed under different experimental conditions, and thus suitable as normalizers for QPCR in zebrafish, the present study evaluated the expression of eight commonly used housekeeping genes as a function of stage and hormone/toxicant exposure during development, and by tissue type and sex in adult fish. RESULTS QPCR analysis was used to quantify mRNA levels of bactin1, tubulin alpha 1(tuba1), glyceraldehyde-3-phosphate dehydrogenase (gapdh), glucose-6-phosphate dehydrogenase (g6pd), TATA-box binding protein (tbp), beta-2-microglobulin (b2m), elongation factor 1 alpha (elfa), and 18s ribosomal RNA (18s) during development (2 - 120 hr postfertilization, hpf); in different tissue types (brain, eye, liver, heart, muscle, gonads) of adult males and females; and after treatment of embryos/larvae (24 - 96 hpf) with commonly used vehicles for administration and agents that represent known environmental endocrine disruptors. All genes were found to have some degree of variability under the conditions tested here. Rank ordering of expression stability using geNorm analysis identified 18s, b2m, and elfa as most stable during development and across tissue types, while gapdh, tuba1, and tpb were the most variable. Following chemical treatment, tuba1, bactin1, and elfa were the most stably expressed whereas tbp, 18s, and b2m were the least stable. Data also revealed sex differences that are gene- and tissue-specific, and treatment effects that are gene-, vehicle- and ligand-specific. When the accuracy of QPCR analysis was tested using different reference genes to measure suppression of cyp19a1b by an estrogen receptor antagonist and induction of cyp1a by an arylhydrocarbon receptor agonist, the direction and magnitude of effects with stable and unstable genes differed. CONCLUSION This study provides data that can be expected to aid zebrafish researchers in their initial choice of housekeeping genes for future studies, but underlines the importance of further validating housekeeping genes for each new experimental paradigm and fish species.
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Affiliation(s)
- Amy T McCurley
- Department of Biology, Boston University, Boston, MA 02215, USA.
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Small BC, Murdock CA, Bilodeau-Bourgeois AL, Peterson BC, Waldbieser GC. Stability of reference genes for real-time PCR analyses in channel catfish (Ictalurus punctatus) tissues under varying physiological conditions. Comp Biochem Physiol B Biochem Mol Biol 2008; 151:296-304. [DOI: 10.1016/j.cbpb.2008.07.010] [Citation(s) in RCA: 98] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2008] [Revised: 07/14/2008] [Accepted: 07/17/2008] [Indexed: 01/15/2023]
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Mori R, Wang Q, Danenberg KD, Pinski JK, Danenberg PV. Both beta-actin and GAPDH are useful reference genes for normalization of quantitative RT-PCR in human FFPE tissue samples of prostate cancer. Prostate 2008; 68:1555-60. [PMID: 18651557 DOI: 10.1002/pros.20815] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
BACKGROUND Beta-actin and glyceraldehyde-3-phosphate dehydrogenase (GAPDH) have been frequently considered as constitutive house keeping genes for RT-PCR and used to normalize changes in specific gene expressions. However, these expressions have been shown to be affected by the sample type and experimental conditions. We investigated which housekeeping gene is useful to study gene expression of paraffin embedded human tissue samples of prostate cancer. METHODS Fifteen pairs of cancer and corresponding normal tissue were obtained from patients with prostate cancer. We evaluated gene expression of beta-actin, GAPDH, androgen receptor (AR), and heat-shock 70-kd protein 5 (HSPA5) using laser captured microdissection and quantitative RT-PCR. AR and HSPA5 gene expression were normalized to each of these reference genes using the 2(-DeltaDeltaCt) method of relative quantification. The quantity 2(Ct(normal)-Ct(cancer)) divided by ratio of cDNA(cancer)/cDNA (normal) was used for comparing differences between cancer and normal tissue in GAPDH and beta-actin expression. RESULTS Ct value of beta-actin was significantly correlated with that of GAPDH (r = 0.443, P = 0.014). AR and HSPA5 gene expression levels using beta-actin for normalization were significantly correlated with these gene expression levels using GAPDH (AR; r = 0.689, P = 0.004, HSPA5; r = 0.879, P < 0.001). Both reference genes were expressed more highly in cancer tissue than in normal tissue, with that of GAPDH being significantly different between cancer tissue and normal tissue (P = 0.029). CONCLUSIONS The good correlation between gene expression values obtained when using beta-actin and GAPDH as reference genes suggests that either gene is a valid denominator for gene expression studies in prostate cancer.
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Affiliation(s)
- Ryutaro Mori
- Department of Biochemistry & Molecular Biology, University of Southern California Keck School of Medicine, Los Angeles, California 90033, USA
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43
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Yoo WG, Kim TI, Li S, Kwon OS, Cho PY, Kim TS, Kim K, Hong SJ. Reference genes for quantitative analysis on Clonorchis sinensis gene expression by real-time PCR. Parasitol Res 2008; 104:321-8. [PMID: 18815810 DOI: 10.1007/s00436-008-1195-x] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2008] [Accepted: 09/09/2008] [Indexed: 02/06/2023]
Abstract
The accuracies of relative gene expressions as determined by quantitative real-time polymerase chain reaction are largely dependent on the variabilities of the reference genes used. Validation of the stabilities of reference genes under experimental conditions is an essential initial step for comparative studies on the expression levels of target genes in experimental groups. Using three total RNA samples extracted independently from Clonorchis sinensis metacercariae and adults, we determined the gene expression stabilities of eight reference gene candidates and the relative transcript levels of three target genes using the geNorm program. The reference genes found to be stably expressed in metacercariae and adults were phosphoglycerate kinase, beta-actin, and calcyphosine; reference genes found to be stably expressed under gamma-irradiated and non-irradiated conditions were succinate dehydrogenase, small nuclear ribonucleoprotein, and beta-actin; and those stably expressed regardless of bile treatment were small nuclear ribonucleoprotein, phosphoglycerate kinase, and succinate dehydrogenase. According to our data, the expression levels of target genes are dependent on normalization factors, such as the C (T) values of single reference genes and the geometric mean of the C (T) values of three reference genes. When comparing C. sinensis gene expressions, we propose to employ the geometric mean of the C (T) values of more than three reference genes validated in the same experimental setting.
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Affiliation(s)
- Won Gi Yoo
- Department of Medical Environmental Biology, Chung-Ang University College of Medicine, Tongjak-gu, Seoul 156-756, Republic of Korea
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44
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Gutierrez L, Mauriat M, Guénin S, Pelloux J, Lefebvre JF, Louvet R, Rusterucci C, Moritz T, Guerineau F, Bellini C, Van Wuytswinkel O. The lack of a systematic validation of reference genes: a serious pitfall undervalued in reverse transcription-polymerase chain reaction (RT-PCR) analysis in plants. PLANT BIOTECHNOLOGY JOURNAL 2008; 6:609-18. [PMID: 18433420 DOI: 10.1111/j.1467-7652.2008.00346.x] [Citation(s) in RCA: 438] [Impact Index Per Article: 27.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Reverse transcription-polymerase chain reaction (RT-PCR) approaches have been used in a large proportion of transcriptome analyses published to date. The accuracy of the results obtained by this method strongly depends on accurate transcript normalization using stably expressed genes, known as references. Statistical algorithms have been developed recently to help validate reference genes, and most studies of gene expression in mammals, yeast and bacteria now include such validation. Surprisingly, this important approach is under-utilized in plant studies, where putative housekeeping genes tend to be used as references without any appropriate validation. Using quantitative RT-PCR, the expression stability of several genes commonly used as references was tested in various tissues of Arabidopsis thaliana and hybrid aspen (Populus tremula x Populus tremuloides). It was found that the expression of most of these genes was unstable, indicating that their use as references is inappropriate. The major impact of the use of such inappropriate references on the results obtained by RT-PCR is demonstrated in this study. Using aspen as a model, evidence is presented indicating that no gene can act as a universal reference, implying the need for a systematic validation of reference genes. For the first time, the extent to which the lack of a systematic validation of reference genes is a stumbling block to the reliability of results obtained by RT-PCR in plants is clearly shown.
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Affiliation(s)
- Laurent Gutierrez
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 901 83 Umeå, Sweden.
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Thal SC, Wyschkon S, Pieter D, Engelhard K, Werner C. Selection of Endogenous Control Genes for Normalization of Gene Expression Analysis after Experimental Brain Trauma in Mice. J Neurotrauma 2008; 25:785-94. [DOI: 10.1089/neu.2007.0497] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Affiliation(s)
- Serge C. Thal
- Department of Anesthesiology, Johannes Gutenberg University, Mainz, Germany
| | - Sebastian Wyschkon
- Department of Anesthesiology, Johannes Gutenberg University, Mainz, Germany
| | - Dana Pieter
- Department of Anesthesiology, Johannes Gutenberg University, Mainz, Germany
| | - Kristin Engelhard
- Department of Anesthesiology, Johannes Gutenberg University, Mainz, Germany
| | - Christian Werner
- Department of Anesthesiology, Johannes Gutenberg University, Mainz, Germany
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Glenn ST, Jones CA, Liang P, Kaushik D, Gross KW, Kim HL. Expression profiling of archival renal tumors by quantitative PCR to validate prognostic markers. Biotechniques 2007; 43:639-40, 642-3, 647. [DOI: 10.2144/000112562] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Formalin-fixed paraffin-embedded (FFPE) tissues are routinely stored by most pathology departments and are a widely available resource for discovery of clinically useful biomarkers. We describe our method for optimizing quantitative reverse transcription PCR (RT-PCR) for expression analysis using frozen and archival tissue. Commonly used reference genes were evaluated for stability of expression in normal kidney and clear cell renal cell carcinoma (RCC). Optimal reference genes for calculating normalization factors for RT-PCR were ACTB, RPL13A, GUS, RPLP0, HPRT1, and SDHA when using FFPE RCC. The optimal reference genes when using frozen RCC were ACTB, RPL13A, and GUS, confirming that use of multiple reference genes improves accuracy when intact RNA from frozen renal tumors are used. Expression of 16 markers previously reported to have prognostic significance in RCC was determined in 23 matching frozen and FFPE renal tumors, representing a range of tumor grades and stages; correlation coefficient for expression measured in frozen and FFPE tumors was 0.921 (P<0.001). All markers predicted survival when frozen tumors were used and 14 of the 16 markers predicted survival when FFPE tumors were used as the source of RNA. An optimized RT-PCR assay can accurately measure expression of most prognostic tumor markers.
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Affiliation(s)
| | | | - Ping Liang
- Roswell Park Cancer Institute, Buffalo, NY, USA
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de Jonge HJM, Fehrmann RSN, de Bont ESJM, Hofstra RMW, Gerbens F, Kamps WA, de Vries EGE, van der Zee AGJ, te Meerman GJ, ter Elst A. Evidence based selection of housekeeping genes. PLoS One 2007; 2:e898. [PMID: 17878933 PMCID: PMC1976390 DOI: 10.1371/journal.pone.0000898] [Citation(s) in RCA: 546] [Impact Index Per Article: 32.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2007] [Accepted: 08/27/2007] [Indexed: 12/31/2022] Open
Abstract
For accurate and reliable gene expression analysis, normalization of gene expression data against housekeeping genes (reference or internal control genes) is required. It is known that commonly used housekeeping genes (e.g. ACTB, GAPDH, HPRT1, and B2M) vary considerably under different experimental conditions and therefore their use for normalization is limited. We performed a meta-analysis of 13,629 human gene array samples in order to identify the most stable expressed genes. Here we show novel candidate housekeeping genes (e.g. RPS13, RPL27, RPS20 and OAZ1) with enhanced stability among a multitude of different cell types and varying experimental conditions. None of the commonly used housekeeping genes were present in the top 50 of the most stable expressed genes. In addition, using 2,543 diverse mouse gene array samples we were able to confirm the enhanced stability of the candidate novel housekeeping genes in another mammalian species. Therefore, the identified novel candidate housekeeping genes seem to be the most appropriate choice for normalizing gene expression data.
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Affiliation(s)
- Hendrik J. M. de Jonge
- Division of Pediatric Oncology/Hematology, Department of Pediatrics, Beatrix Children's Hospital, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Rudolf S. N. Fehrmann
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- Department of Gynecology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- Department of Medical Oncology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Eveline S. J. M. de Bont
- Division of Pediatric Oncology/Hematology, Department of Pediatrics, Beatrix Children's Hospital, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Robert M. W. Hofstra
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Frans Gerbens
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Willem A. Kamps
- Division of Pediatric Oncology/Hematology, Department of Pediatrics, Beatrix Children's Hospital, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Elisabeth G. E. de Vries
- Department of Medical Oncology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Ate G. J. van der Zee
- Department of Gynecology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Gerard J. te Meerman
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Arja ter Elst
- Division of Pediatric Oncology/Hematology, Department of Pediatrics, Beatrix Children's Hospital, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- * To whom correspondence should be addressed. E-mail:
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Pálsdóttir HM, Gudmundsdóttir A. Development of a qRT-PCR assay to determine the relative mRNA expression of two different trypsins in Atlantic cod (Gadus morhua). Comp Biochem Physiol B Biochem Mol Biol 2007; 146:26-34. [PMID: 17081791 DOI: 10.1016/j.cbpb.2006.08.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2006] [Revised: 08/24/2006] [Accepted: 08/30/2006] [Indexed: 11/24/2022]
Abstract
A fluorescence resonance energy transfer (FRET) based quantitative RT-PCR method (qRT PCR) was developed in this study for measuring the mRNA expression of trypsins Y and I in the Atlantic cod. Atlantic cod beta-actin was used as the reference gene and standard curves were created for quantification of the mRNA expression levels. For yet unknown reasons, the Atlantic cod (Gadus morhua) produces several trypsins with different characteristics. Trypsin I is the most common and best characterized of these but trypsin Y is a recently discovered enzyme. The recombinant form of trypsin Y was found to have unique characteristics relative to trypsin I. The native form of trypsin Y has proven difficult to isolate from the cod and activity assays do not distinguish between the activities of trypsin I and trypsin Y. The results show that trypsin Y mRNA is expressed in a very low copy number relative to that of trypsin I (ratio of 1:1340), which may explain the difficulty of isolating the native form of trypsin Y.
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Affiliation(s)
- Helga Margrét Pálsdóttir
- Science Institute, University of Iceland, Laeknagardi, Vatnsmýrarvegi 16, Reykjavík, IS-101, Iceland
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Abstract
Quantifying the level of mRNA is central to the study of mammalian gene expression. Conventional approaches such as Northern blotting are often prone to low sensitivity and reproducibility. The RNase protection assay (RPA) provides a sensitive alternative for the detection and quantification of mRNA. The RPA is based on the hybridization in solution of a labeled single-stranded antisense RNA probe with a target mRNA. After hybridization, single-strand specific RNases are then used to digest away unhybridized RNA. The hybrid can be resolved by a denaturing gel. Subsequent detection will reveal the appropriate-sized gel band corresponding to the target mRNA. The major advantage of RPA is the high sensitivity and the simultaneous detection and quantification of multiple mRNA targets in a single RNA sample. The primary limitation of RPA is the lack of information on transcript size.
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Affiliation(s)
- Yongxia Qu
- VA New York Harbor Healthcare System, SUNY Downstate Medical Center, Brooklyn, NY, USA
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50
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Baumbusch LO, Myhre S, Langerød A, Bergamaschi A, Geisler SB, Lønning PE, Deppert W, Dornreiter I, Børresen-Dale AL. Expression of full-length p53 and its isoform Deltap53 in breast carcinomas in relation to mutation status and clinical parameters. Mol Cancer 2006; 5:47. [PMID: 17054774 PMCID: PMC1636663 DOI: 10.1186/1476-4598-5-47] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2006] [Accepted: 10/20/2006] [Indexed: 11/22/2022] Open
Abstract
Background The tumor suppressor gene p53 (TP53) controls numerous signaling pathways and is frequently mutated in human cancers. Novel p53 isoforms suggest alternative splicing as a regulatory feature of p53 activity. Results In this study we have analyzed mRNA expression of both wild-type and mutated p53 and its respective Δp53 isoform in 88 tumor samples from breast cancer in relation to clinical parameters and molecular subgroups. Three-dimensional structure differences for the novel internally deleted p53 isoform Δp53 have been predicted. We confirmed the expression of Δp53 mRNA in tumors using quantitative real-time PCR technique. The mRNA expression levels of the two isoforms were strongly correlated in both wild-type and p53-mutated tumors, with the level of the Δp53 isoform being approximately 1/3 of that of the full-length p53 mRNA. Patients expressing mutated full-length p53 and non-mutated (wild-type) Δp53, "mutational hybrids", showed a slightly higher frequency of patients with distant metastasis at time of diagnosis compared to other patients with p53 mutations, but otherwise did not differ significantly in any other clinical parameter. Interestingly, the p53 wild-type tumors showed a wide range of mRNA expression of both p53 isoforms. Tumors with mRNA expression levels in the upper or lower quartile were significantly associated with grade and molecular subtypes. In tumors with missense or in frame mutations the mRNA expression levels of both isoforms were significantly elevated, and in tumors with nonsense, frame shift or splice mutations the mRNA levels were significantly reduced compared to those expressing wild-type p53. Conclusion Expression of p53 is accompanied by the functionally different isoform Δp53 at the mRNA level in cell lines and human breast tumors. Investigations of "mutational hybrid" patients highlighted that wild-type Δp53 does not compensates for mutated p53, but rather may be associated with a worse prognosis. In tumors, both isoforms show strong correlations in different mutation-dependent mRNA expression patterns.
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Affiliation(s)
- Lars O Baumbusch
- Department of Genetics, Institute for Cancer Research, Rikshospitalet-Radiumhospitalet Medical Center, 0310 Oslo, Norway
| | - Simen Myhre
- Department of Genetics, Institute for Cancer Research, Rikshospitalet-Radiumhospitalet Medical Center, 0310 Oslo, Norway
| | - Anita Langerød
- Department of Genetics, Institute for Cancer Research, Rikshospitalet-Radiumhospitalet Medical Center, 0310 Oslo, Norway
| | - Anna Bergamaschi
- Department of Genetics, Institute for Cancer Research, Rikshospitalet-Radiumhospitalet Medical Center, 0310 Oslo, Norway
- Medical Faculty, University of Oslo, Oslo, Norway
| | - Stephanie B Geisler
- Department of Medicine, Section of Oncology, Haukeland University Hospital, 5021 Bergen, Norway
| | - Per E Lønning
- Department of Medicine, Section of Oncology, Haukeland University Hospital, 5021 Bergen, Norway
| | - Wolfgang Deppert
- Heinrich-Pette-Institut für Experimentelle Virologie und Immunologie an der Universität Hamburg, Martinistr. 52, 20251 Hamburg, Germany
| | - Irene Dornreiter
- Heinrich-Pette-Institut für Experimentelle Virologie und Immunologie an der Universität Hamburg, Martinistr. 52, 20251 Hamburg, Germany
| | - Anne-Lise Børresen-Dale
- Department of Genetics, Institute for Cancer Research, Rikshospitalet-Radiumhospitalet Medical Center, 0310 Oslo, Norway
- Medical Faculty, University of Oslo, Oslo, Norway
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