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Munguía-Ramírez B, Giménez-Lirola L, Zimmerman J. Assessment of Strategies for Preserving Swine Viral RNA Targets in Diagnostic Specimens. Microorganisms 2024; 12:410. [PMID: 38399814 PMCID: PMC10892022 DOI: 10.3390/microorganisms12020410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 02/13/2024] [Accepted: 02/15/2024] [Indexed: 02/25/2024] Open
Abstract
Successful downstream molecular analyses of viral ribonucleic acid (RNA) in diagnostic laboratories, e.g., reverse transcription-quantitative polymerase chain reaction (RT-qPCR) or next-generation sequencing, are dependent on the quality of the RNA in the specimen. In swine specimens, preserving the integrity of RNA requires proper sample handling at the time the sample is collected on the farm, during transport, and in the laboratory until RNA extraction is performed. Options for proper handling are limited to maintaining the cold chain or using commercial specimen storage matrices. Herein, we reviewed the refereed literature for evidence that commercial specimen storage matrices can play a role in preserving swine viral RNA in clinical specimens. Refereed publications were included if they compared RNA detection in matrix-treated vs. untreated samples. At present, the small number of refereed studies and the inconsistency in reported results preclude the routine use of commercial specimen storage matrices. For example, specimen storage matrices may be useful under specific circumstances, e.g., where it is mandatory to render the virus inactive. In a broader view, statistically sound side-by-side comparisons between specimens, viral RNA targets, and storage conditions are needed to establish if, when, and how commercial specimen storage matrices could be used in diagnostic medicine.
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Affiliation(s)
- Berenice Munguía-Ramírez
- Veterinary Diagnostic and Production Animal Medicine Department, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA; (L.G.-L.); (J.Z.)
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He L, Wang JY, Su QJ, Chen ZH, Xie F. Selection and validation of reference genes for RT-qPCR in ophiocordyceps sinensis under different experimental conditions. PLoS One 2024; 19:e0287882. [PMID: 38319940 PMCID: PMC10846742 DOI: 10.1371/journal.pone.0287882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 06/14/2023] [Indexed: 02/08/2024] Open
Abstract
The Chinese caterpillar mushroom, Ophiocordyceps sinensis (O. sinensis), is a rarely medicinal fungus in traditional chinese herbal medicine due to its unique medicinal values, and the expression stability of reference genes is essential to normalize its gene expression analysis. In this study, BestKeeper, NormFinder and geNorm, three authoritative statistical arithmetics, were applied to evaluate the expression stability of sixteen candidate reference genes (CRGs) in O. sinensis under different stress [low temperature (4°C), light treatment (300 lx), NaCl (3.8%)] and different development stages (mycelia, primordia and fruit bodies) and formation of morphologic mycelium (aeriasubstrate, hyphae knot mycelium). The paired variation values indicated that two genes could be enough to accurate standardization exposed to different conditions of O.sinensis. Among these sixteen CRGs, 18S ribosomal RNA (18S rRNA) and beta-Tubulin (β-TUB) showed the topmost expression stability in O.sinensis exposed to all conditions, while glutathione hydrolase proenzym (GGT) and Phosphoglucose isomerase (PGI) showed the least expression stability. The optimal reference gene in different conditions was various. β-TUB and Ubiquitin (UBQ) were identified as the two most stable genes in different primordia developmental stage, while phosphoglucomutase (PGM) with elongation factor 1-alpha (EF1-α) and 18S rRNA with UBQ were the most stably expressed for differentially morphologic mycelium stages and different stresses, respectively. These results will contribute to more accurate evaluation of the gene relative expression levels in O.sinensis under different conditions using the optimal reference gene in real-time quantitative PCR (RT-qPCR) analysis.
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Affiliation(s)
- Li He
- School of Biological and Pharmaceutical Engineering, Lanzhou Jiaotong University, Lanzhou, GanSu, P. R. China
| | - Jin Yi Wang
- School of Biological and Pharmaceutical Engineering, Lanzhou Jiaotong University, Lanzhou, GanSu, P. R. China
| | - Qiang Jun Su
- School of Biological and Pharmaceutical Engineering, Lanzhou Jiaotong University, Lanzhou, GanSu, P. R. China
| | - Zhao He Chen
- School of Biological and Pharmaceutical Engineering, Lanzhou Jiaotong University, Lanzhou, GanSu, P. R. China
| | - Fang Xie
- School of Biological and Pharmaceutical Engineering, Lanzhou Jiaotong University, Lanzhou, GanSu, P. R. China
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Munguía-Ramírez B, Armenta-Leyva B, Henao-Díaz A, Cheng TY, Zhang J, Rawal G, Ye F, Giménez-Lirola L, Zimmerman JJ. Effect of extrinsic factors on the detection of PRRSV and a porcine-specific internal sample control in serum, oral fluid, and fecal specimens tested by RT-rtPCR. J Vet Diagn Invest 2023; 35:374-383. [PMID: 37166086 PMCID: PMC10331379 DOI: 10.1177/10406387231174556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023] Open
Abstract
We characterized the effect of 1) temperature × time, 2) freeze-thaw cycles, and 3) high porcine reproductive and respiratory syndrome virus (PRRSV) RNA concentrations on the detection of PRRSV and a porcine-specific internal sample control (ISC) in serum, oral fluid, and fecal samples using a commercial PRRSV RT-rtPCR assay (Idexx). In study 1, the effect of temperature × time on PRRSV and ISC detection was shown to be specimen dependent. In serum stored at 4, 10, or 20°C, PRRSV detection was consistent for up to 168 h, but storage at 30°C reduced detectable PRRSV RNA. ISC RNA was stable in serum held at 4 and 10°C, but not at 20 and 30°C. In contrast, PRRSV and ISC RNAs in oral fluid and fecal samples continuously decreased at all temperature × time treatments. Based on these data, serum samples should be stored at ≤ 20°C to optimize PRRSV RNA detection. Oral fluid and fecal samples should be frozen in a non-self-defrosting freezer until tested. In study 2, freeze-thaw cycles had little impact on PRRSV and ISC detection, but more so in oral fluids than serum or fecal samples. Thus, freeze-thaw cycles in oral fluids should be minimized before RT-rtPCR testing. In study 3, the ISC was not affected by high concentrations of PRRSV RNA in serum, oral fluid, or fecal samples. It should not be assumed that data from our PRRSV study are applicable to other pathogens; additional pathogen-specific studies are required.
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Affiliation(s)
- Berenice Munguía-Ramírez
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Betsy Armenta-Leyva
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | | | - Ting-Yu Cheng
- Department of Veterinary Preventive Medicine, The Ohio State University, Columbus, OH, USA
| | - Jianqiang Zhang
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Gaurav Rawal
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Fangshu Ye
- Department of Statistics, College of Liberal Arts and Sciences, Iowa State University, Ames, IA, USA
| | - Luis Giménez-Lirola
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Jeffrey J. Zimmerman
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
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Bohan AE, Purvis KN, Sawyer JT, Bergen WG, Brandebourg TD. Sampling Adipose and Muscle Tissue following Post-Harvest Scalding Does Not Affect RNA Integrity or Real-Time PCR Results in Market Weight Yorkshire Pigs. Foods 2022; 11:foods11121741. [PMID: 35741939 PMCID: PMC9222963 DOI: 10.3390/foods11121741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 06/06/2022] [Accepted: 06/11/2022] [Indexed: 11/16/2022] Open
Abstract
Improving production efficiency while enhancing pork quality is pivotal for strengthening sustainable pork production. Being able to study both gene expression and indices of pork quality from the same anatomical location of an individual animal would better enable research conducted to study relationships between animal growth and carcass merit. To facilitate gene expression studies, adipose and muscle tissue samples are often collected immediately following exsanguination to maximize RNA integrity, which is a primary determinant of the sensitivity of RNA-based assays, such as real-time PCR. However, collecting soft tissue samples requires cutting through the hide or skin. This leaves the underlying tissue exposed during scalding, poses possible food safety issues, and potentially confounds pork quality measures. To overcome these limitations, the effect of tissue sample timing post-harvest on RNA integrity, real-time PCR results, and pork quality measurements was investigated by sampling subcutaneous adipose tissue and longissimus thoracis et lumborum muscle immediately following either exsanguination, scalding, or chilling. Sampling time did not affect RNA quality, as determined by the RNA integrity number of RNA samples purified from either adipose (RIN; p > 0.54) or muscle tissue (p > 0.43). Likewise, the sampling time did not influence the results of real-time PCR analysis of gene expression when comparing RNA samples prepared from adipose or muscle tissue immediately following either exsanguination or scalding (p > 0.92). However, sampling tissue prior to scalding resulted in a greater visual color score (p < 0.001) and lesser L* (p < 0.001) and b* (p < 0.001) values without impacting the 24 h pH (p < 0.41). These results suggested that if both RNA-based assays and meat quality endpoints are to be performed at the same anatomical location on an animal, tissue sampling to facilitate RNA-based assays should occur at a time point immediately following scalding. These findings demonstrated that sampling of adipose and muscle tissue can be delayed until after scalding/dehairing without decreasing the RNA integrity or altering the results of real-time PCR assays, while doing so was associated with little impact on measures of pork quality.
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Brouns I, Verckist L, Pintelon I, Timmermans JP, Adriaensen D. Pulmonary Sensory Receptors. ADVANCES IN ANATOMY EMBRYOLOGY AND CELL BIOLOGY 2021; 233:1-65. [PMID: 33950466 DOI: 10.1007/978-3-030-65817-5_1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Inge Brouns
- Laboratory of Cell Biology and Histology, Department of Veterinary Sciences, University of Antwerp, Antwerpen (Wilrijk), Belgium.
| | - Line Verckist
- Laboratory of Cell Biology and Histology, Department of Veterinary Sciences, University of Antwerp, Antwerpen (Wilrijk), Belgium
| | - Isabel Pintelon
- Laboratory of Cell Biology and Histology, Department of Veterinary Sciences, University of Antwerp, Antwerpen (Wilrijk), Belgium
| | - Jean-Pierre Timmermans
- Laboratory of Cell Biology and Histology, Department of Veterinary Sciences, University of Antwerp, Antwerpen (Wilrijk), Belgium
| | - Dirk Adriaensen
- Laboratory of Cell Biology and Histology, Department of Veterinary Sciences, University of Antwerp, Antwerpen (Wilrijk), Belgium
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Studying the Pulmonary NEB ME: A Multidisciplinary Approach. ADVANCES IN ANATOMY EMBRYOLOGY AND CELL BIOLOGY 2021. [PMID: 33950468 DOI: 10.1007/978-3-030-65817-5_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register]
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7
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Gaafar ARZ, Al-Qurainy F, Alshameri A, Khan S, Nadeem M, Tarroum M, Alansi S, Shaikhaldein HO, Salih AM, Arrak Alenezi N. High RNA quality extracted from the tolerant crop Cyamopsis tetragonoloba (L.) despite possession of low RNA integrity number. BIOTECHNOL BIOTEC EQ 2021. [DOI: 10.1080/13102818.2021.1910567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Affiliation(s)
| | - Fahad Al-Qurainy
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Aref Alshameri
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Salim Khan
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Mohammad Nadeem
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Mohamed Tarroum
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Saleh Alansi
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Hassan O. Shaikhaldein
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Abdalrhaman M. Salih
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Norah Arrak Alenezi
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
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Stable Reference Genes for qPCR Analysis in BM-MSCs Undergoing Osteogenic Differentiation within 3D Hyaluronan-Based Hydrogels. Int J Mol Sci 2020; 21:ijms21239195. [PMID: 33276559 PMCID: PMC7729573 DOI: 10.3390/ijms21239195] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 11/22/2020] [Accepted: 11/30/2020] [Indexed: 11/17/2022] Open
Abstract
Reverse transcription quantitative polymerase chain reaction (RT-qPCR) enables the monitoring of changes in cell phenotype via the high-throughput screening of numerous genes. RT-qPCR is a fundamental approach in numerous research fields, including biomaterials, yet little attention has been given to the potential impact of 3D versus monolayer (2D) cell culture and to the requirement for a constant validation of the multiple steps of gene expression analysis. The aim of this study is to use high-quality RNA to identify the most suitable reference genes for RT-qPCR analysis during the osteogenic differentiation of human bone marrow mesenchymal stem/stromal cells (BM-MSCs). BM-MSCs are cultured under osteogenic conditions for 28 days in 2D or within hyaluronic acid hydrogels (3D). RNA is subject to quality controls and is then used to identify the most stable reference genes using geNorm, NormFinder, and the ∆Cq method. The effect of the reverse transcriptase is investigated, as well as the expression of osteogenic-related markers. This study shows marked differences in the stability of reference genes between 2D (RPLP0/GAPDH) and 3D (OAZ1/PPIA) culture, suggesting that it is critical to choose appropriate reference genes for 3D osteogenic cell cultures. Thus, a thorough validation under specific experimental settings is essential to obtain meaningful gene expression results.
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Alfieri CM, Mattinzoli D, Ikehata M, Cresseri D, Moroni G, Vaira V, Ferri G, Ferrero S, Messa P. Laser capture microdissection on formalin-fixed and paraffin-embedded renal transplanted biopsies: Technical perspectives for clinical practice application. Exp Mol Pathol 2020; 116:104516. [PMID: 32853636 DOI: 10.1016/j.yexmp.2020.104516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 04/22/2020] [Accepted: 08/03/2020] [Indexed: 11/30/2022]
Abstract
Renal biopsy (RBx) is an essential tool in the diagnostic and therapeutic process of most native kidney diseases and in the renal transplanted graft. Laser capture microdissection (LCM), combined with molecular biology, might improve the diagnostic power of RBx. However, the limited amount of available renal tissue is often an obstacle for achieving a satisfactory qualitative and quantitative analysis. In our work we present a method which allows us to obtain good quality and quantity of RNA from formalin-fixed and paraffin-embedded (FFPE) renal tissue derived from RBx performed in transplanted patients. Histology, immunohistochemistry, LCM, pre-amplify system and qRT-PCR of biomarkers related to tubular damage, inflammation and fibrosis on FFPE RBx were performed. Glomeruli, tubules and interstitium of three RBx (RB-A: no alteration; RB-B and -C: the progressive rise of creatinine) were compared. The method proposed, could well be useful in future clinical practice. It is quick, easy to perform and allows the analyses of many biomarkers. In addition, it could be extended to all types of RBx without any limitation on the sample amount. Nevertheless, the need for a higher number of well-trained technicians might represent some limitation, counterbalanced by the opportunity to elaborate more accurate diagnosis and, consequently, more targeted therapies.
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Affiliation(s)
- Carlo Maria Alfieri
- Renal Research Laboratory, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy; Unit of Nephrology, Dialysis and Renal Transplant, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy; Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy
| | - Deborah Mattinzoli
- Renal Research Laboratory, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Masami Ikehata
- Renal Research Laboratory, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Donata Cresseri
- Unit of Nephrology, Dialysis and Renal Transplant, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Gabriella Moroni
- Unit of Nephrology, Dialysis and Renal Transplant, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Valentina Vaira
- Department of Pathophysiology and Transplantation, University of Milan, Divisions of Pathology, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Giulia Ferri
- Renal Research Laboratory, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Stefano Ferrero
- Department of Pathophysiology and Transplantation, University of Milan, Divisions of Pathology, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Piergiorgio Messa
- Renal Research Laboratory, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy; Unit of Nephrology, Dialysis and Renal Transplant, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy; Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy.
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Comparative Evaluation of RNAlater Solution and Snap Frozen Methods for Gene Expression Studies in Different Tissues. REV ROMANA MED LAB 2020. [DOI: 10.2478/rrlm-2020-0024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Abstract
Introduction: Freezing of tissues with liquid nitrogen is the most common method in studies performed at the RNA level. However, the use of RNA stabilization solutions has become a popular alternative method. The aim of this study is to investigate the effectiveness of RNAlater on RNA stabilization in different tissues.
Material and Methods: In this study, RNA were isolated from the lung, heart, liver and skeletal muscle tissues of rats that were frozen with liquid nitrogen (snap frozen, SF group) or stored in RNAlater solution (RL group), and the changes in concentration, purity, reference genes expression, and fold-change levels between groups were analyzed.
Results: In the RL group, the concentration of RNA isolated from the liver tissues was higher (P<0.05), whereas the A260/280 ratio was lower in the heart and liver tissues (P<0.05). PPIA and SRP72 genes were found to have lower Ct values in the heart tissues of rats in the RL group (P<0.05 and P<0.001, respectively) than the SF group. Expression levels of PPIA, ACTB, and SRP72 genes across the tissues were found to be different between the groups (P<0.05). The gene expression level examined in terms of fold-change was significantly different in the RL group (upregulated up to 4 folds and downregulated about 0.5 fold) (P< 0.05).
Conclusions: The results showed that RNAlater can maintain the RNA integrity and can also change the results of gene expression because it does not inhibit biological activity. The snap freezing method is more reliable because gene expression is more stable in tissues frozen with liquid nitrogen.
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Alsamadany H. De novo leaf transcriptome assembly of Bougainvillea spectabilis for the identification of genes involves in the secondary metabolite pathways. Gene 2020; 746:144660. [PMID: 32275998 DOI: 10.1016/j.gene.2020.144660] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2020] [Revised: 03/20/2020] [Accepted: 04/06/2020] [Indexed: 12/25/2022]
Abstract
Bougainvillea spectabilis is known as a vital medicinal, ornamental as well as an essential oil producing plant. It is also a rich source of important secondary metabolites with several therapeutic properties. Various studies on its pharmacological and toxicological aspects have been published but there is no genomic or transcriptomic resource available in the public databases. To address this important issue, the de-novo transcriptome assembly of B. spectabilis leaf tissue has been done for the identification of genes involved in various important secondary metabolites, Single nucleotide polymorphism (SNPs) and Simple sequence repeats (SSRs). The transcriptome sequencing of B. spectabilis leaf tissue generated 79,811,024 raw reads with GC value 42.77%. The transcriptomic assembly was performed by Trinity software which generated 100,374 transcripts and 99,793 unigenes with minimum and maximum length of 201 bp and 13,237 bp and N50 value of 1470 and 1472 respectively. Annotation of these unigenes was performed using seven databases including NR, PFAM, GO and KEGG. Approximately, 44,302 unigenes were annotated in GO database. The KEGG pathway analysis revealed 23,102 unigenes in which 19,054 genes were assigned to five groups in KEGG and 130 biochemical pathways. The highest group among the five groups was Metabolism with 9230 unigenes. Moreover, about 63,226 SNPs and 30,333 SSRs in the leaf transcriptome of B. spectabilis were identified. To the best of my understanding it will be the first comprehensive transcriptome analysis of B. spectabilis from family Nyctaginaceae which will help as a reference line for further genomic and transcriptomic studies.
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Affiliation(s)
- Hameed Alsamadany
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia.
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Esteva-Socias M, Gómez-Romano F, Carrillo-Ávila JA, Sánchez-Navarro AL, Villena C. Impact of different stabilization methods on RT-qPCR results using human lung tissue samples. Sci Rep 2020; 10:3579. [PMID: 32108147 PMCID: PMC7046779 DOI: 10.1038/s41598-020-60618-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 01/20/2020] [Indexed: 02/06/2023] Open
Abstract
Aiming to increase the reproducibility of biomedical research results, biobanks obtain human tissues of the highest quality and carry out different storage methods adapted to the needs of analytical technique to be performed by the biomedical researchers. However, there is much controversy and little data concerning the real impact of different stabilization methods on tissue quality, integrity and functionality of derived biomolecules. The influence of four stabilization methods [RNAlater (RNL), snap freezing (SF), snap freezing using Optimal Cutting Tissue compound (SF-OCT) and formalin-fixed paraffin-embedded (FFPE)] on RNA quality and integrity was evaluated in paired samples of lung tissue. RNA integrity was evaluated through PCR-endpoint assays amplifying six fragments of different length of the HPRT1 gene and RNA Integrity Number (RIN). To evaluate the difference of tissue functionality among the stabilization methods tested, RT-qPCRs were performed focusing on the differential expression of the HPRT1, SNRPD3 and Jun genes. RNA from the samples preserved with the RNL or SF-OCT method showed better integrity compared to SF and FFPE, measured by PCR-endpoint and RT-qPCR assays. However, only statistically significant differences were observed between the RNA from FFPE and other stabilization methods when gene expression of HPRT1, SNRPD3 and Jun housekeeping genes were determined by RT-qPCR. For the three mentioned genes, Cq and RIN values were highly correlated. The present work describes the fragility of SF samples, being critical the moment just before RNA extraction, although further experiments of tissue RNA are needed. Standardization pre-analytic workflow can lead to improved reproducibility between biomedical research studies. The present study demonstrated clear evidences about the impact of the stabilization method on RNA derived from lung human tissue samples.
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Affiliation(s)
- Margalida Esteva-Socias
- Centro de Investigación Biomédica en Red in Respiratory Diseases (CIBERES), Plataforma Biobanco Pulmonar CIBERES, Hospital Universitari Son Espases, Palma, Spain
- Grupo de Inflamación, reparación y cáncer en enfermedades respiratorias, Institut d'Investigació Sanitària de les Illes Balears (IdISBa), Hospital Universitari Son Espases, Palma, Spain
- Spanish Biobank Network, Instituto de Salud Carlos III, Madrid, Spain
| | - Fernando Gómez-Romano
- Centro de Investigación Biomédica en Red in Respiratory Diseases (CIBERES), Plataforma Biobanco Pulmonar CIBERES, Hospital Universitari Son Espases, Palma, Spain
- Grupo de Inflamación, reparación y cáncer en enfermedades respiratorias, Institut d'Investigació Sanitària de les Illes Balears (IdISBa), Hospital Universitari Son Espases, Palma, Spain
- Spanish Biobank Network, Instituto de Salud Carlos III, Madrid, Spain
| | - José Antonio Carrillo-Ávila
- Spanish Biobank Network, Instituto de Salud Carlos III, Madrid, Spain
- Andalusian Public Health System Biobank, Granada. Instituto de Investigación Biosanitaria ibs. Granada. Complejo Universitario de Granada/Universidad de Granada, Granada, Spain
| | - Alicia Loreto Sánchez-Navarro
- Centro de Investigación Biomédica en Red in Respiratory Diseases (CIBERES), Plataforma Biobanco Pulmonar CIBERES, Hospital Universitari Son Espases, Palma, Spain
- Grupo de Inflamación, reparación y cáncer en enfermedades respiratorias, Institut d'Investigació Sanitària de les Illes Balears (IdISBa), Hospital Universitari Son Espases, Palma, Spain
- Spanish Biobank Network, Instituto de Salud Carlos III, Madrid, Spain
| | - Cristina Villena
- Centro de Investigación Biomédica en Red in Respiratory Diseases (CIBERES), Plataforma Biobanco Pulmonar CIBERES, Hospital Universitari Son Espases, Palma, Spain.
- Grupo de Inflamación, reparación y cáncer en enfermedades respiratorias, Institut d'Investigació Sanitària de les Illes Balears (IdISBa), Hospital Universitari Son Espases, Palma, Spain.
- Spanish Biobank Network, Instituto de Salud Carlos III, Madrid, Spain.
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13
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Wang G, Cheng H, Li M, Zhang C, Deng W, Li T. Selection and validation of reliable reference genes for Tolypocladium guangdongense gene expression analysis under differentially developmental stages and temperature stresses. Gene 2020; 734:144380. [PMID: 31978511 DOI: 10.1016/j.gene.2020.144380] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 12/16/2019] [Accepted: 01/16/2020] [Indexed: 01/23/2023]
Abstract
Tolypocladium guangdongense, formerly known as Cordyceps guangdongensis, is a widely cultivated fungus of the Cordyceps s.l. species that has been investigated over the last 12 years. It has the potential to be used in a number of applications in the health and pharmaceutical industries for it has shown its high nutritional and medicinal values according to previous animal studies. qRT-PCR (quantitative reverse transcription polymerase chain reaction) is extensively used to analyze the expression pattern and molecular mechanisms of functional genes under differentially experimental conditions. The expression stability of reference genes used for normalization determines the reliability of qRT-PCR results, indicating the importance of selection and validation of reference genes before gene expression analysis. In the present study, three statistical algorithms, geNorm, NormFinder and BestKeeper, were used for analyzing the expression stability of nineteen candidate reference genes (CRGs) in T. guangdongense. Investigation were carried out under differentially experimental conditions, which included differentially developmential stages (mycelia, primordia, young and mature fruiting bodies), different carbon sources, cold and heat stresses. The results showed that histone H4 and tubulin beta chain 2 (β-tub2) were the most and least stable genes, respectively, across all the experimental samples. Moreover, analysis of individual data sets exhibited different stability and expression profiles of reference genes. The vacuolar protein sorting gene VPS was the most stable gene expressed under the differentially developmental stages and temperature stresses, whereas H4 was the most stably expressed gene under different carbon sources. Therefore, it can be proposed that VPS and H4 are the preferred reference genes for normalization of gene expression under different experimental conditions. The results of our present study will enable more accurate evaluation of gene expression in T. guangdongense using the optimal reference gene for qRT-PCR analysis.
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Affiliation(s)
- Gangzheng Wang
- Guangdong Institute of Microbiology, Guangdong Academy of Sciences, State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangzhou 510070, China
| | - Huijiao Cheng
- Guangdong Institute of Microbiology, Guangdong Academy of Sciences, State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangzhou 510070, China; South China Agricultural University, Guangzhou 510642, China
| | - Min Li
- Guangdong Institute of Microbiology, Guangdong Academy of Sciences, State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangzhou 510070, China; College of Agriculture and Animal Husbandry, Tibet University, Nyingchi 860000, Tibet, China
| | - Chenghua Zhang
- Guangdong Institute of Microbiology, Guangdong Academy of Sciences, State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangzhou 510070, China.
| | - Wangqiu Deng
- Guangdong Institute of Microbiology, Guangdong Academy of Sciences, State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangzhou 510070, China.
| | - Taihui Li
- Guangdong Institute of Microbiology, Guangdong Academy of Sciences, State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangzhou 510070, China.
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14
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Pistochini A, Rossi F, Gallo S, Pirrone C, Preti A, Gornati R, Bernardini G, Castelnuovo P. Multiple gene expression profiling suggests epithelial dysfunction in polypoid chronic rhinosinusitis. ACTA ACUST UNITED AC 2019; 39:169-177. [PMID: 31131836 PMCID: PMC6536031 DOI: 10.14639/0392-100x-2361] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 03/13/2019] [Indexed: 12/13/2022]
Abstract
Chronic rhinosinusitis (CRS) is a heterogeneous inflammatory disorder resulting from a complex gene-environment interaction. Although its aetiology remains elusive, numerous studies reported gene expression alterations of factors apparently implicated in all aspects of the inflammatory response. However, most investigations are limited, unconfirmed analyses of a single gene. Moreover, studies concerning multiple gene expression analyses, usually on inflammatory mediators (e.g. cytokines), show contrasting outcomes in part due to use of heterogeneous samples or methodologies with limited power. In this scenario, our goal was to simultaneously evaluate the expression of a panel of selected genes (AQP5, MUC5AC, CAV1, LTF, COX2, PGDS, TNFα, TGFβ1, MGB1) potentially involved in CRS inflammatory mechanisms. While most of the samples collected were excluded from the analysis because of poor quality RNA, we were able to demonstrate statistically significant downregulation of the AQP5, CAV1, LTF, MGB1 genes in a specific subset of polypoid CRS (patients without typical comorbidities), which might suggest relevant underlying epithelial dysfunction. Further studies are needed to enrich our knowledge on the pathogenesis of CRS. Forthcoming approaches might utilise next-generation RNA sequencing and comprehensive bioinformatics analyses to better characterise the transcriptome profiles of CRS endotypes.
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Affiliation(s)
- A Pistochini
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy.,Department of Otorhinolaryngology, University of Insubria and ASST Sette Laghi, Varese, Italy
| | - F Rossi
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - S Gallo
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy.,Department of Otorhinolaryngology, University of Insubria and ASST Sette Laghi, Varese, Italy
| | - C Pirrone
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - A Preti
- Department of Otorhinolaryngology, University of Milan and IRCCS Multimedica, Ospedale San Giuseppe, Milan, Italy
| | - R Gornati
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy.,"The Protein Factory" Research Center, Politecnico of Milano, ICRM-CNR Milan and University of Insubria, Milan, Italy
| | - G Bernardini
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy.,"The Protein Factory" Research Center, Politecnico of Milano, ICRM-CNR Milan and University of Insubria, Milan, Italy
| | - P Castelnuovo
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy.,Department of Otorhinolaryngology, University of Insubria and ASST Sette Laghi, Varese, Italy
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15
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Fan XJ, Huang Y, Wu PH, Yin XK, Yu XH, Fu XH, Feng LL, Wang YL, Yi HJ, Chen ZT, Yin JX, Zhang DL, Feng WX, Bai SM, Kim T, Mills GB, Lu YL, Wan XB, Wang L. Impact of Cold Ischemic Time and Freeze-Thaw Cycles on RNA, DNA and Protein Quality in Colorectal Cancer Tissues Biobanking. J Cancer 2019; 10:4978-4988. [PMID: 31598170 PMCID: PMC6775519 DOI: 10.7150/jca.29372] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 06/23/2019] [Indexed: 12/20/2022] Open
Abstract
Tissue-derived RNA, DNA and protein samples become more and more crucial for molecular detection in clinical research, personalized and targeted cancer therapy. This study evaluated how to biobanking colorectal tissues through examining the influences of cold ischemic time and freeze-thaw cycles on RNA, DNA and protein integrity. Here, 144 pairs of tumor and normal colorectal tissues were used to investigate the impact of cold ischemic times (0-48h) on RNA, DNA and protein integrity at on ice or room temperature conditions. Additionally, 45 pairs of tissues experienced 0-9 freeze-thaw cycles, and then the RNA, DNA and protein quality were analyzed. On ice, RNA, DNA and protein from colorectal tumor and normal tissues were all stable up to 48h after surgery. At room temperature, RNA in colorectal tumor and normal tissues began to degrade at 8h and 24h, respectively. Meanwhile, the tumor tissues DNA degradation occurred at 24h after surgery at room temperature. Similarly, the protein expression level of tumor and normal tissues began to change at 24h after the surgery at room temperature. Interestingly, tissue RNA and DNA remained stable even after 9 freeze-thaw cycles, whereas the proteins levels were remarkably changed after 7 freeze-thaw cycles. This study provided a useful evidence on how to store human colorectal tissues for biobanking. Preserving the surgical colorectal tissue on ice was an effective way to prevent RNA, DNA and protein degradation. Importantly, more than 7 repeated freeze-thaw cycles were not recommended for colorectal tissues.
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Affiliation(s)
- Xin-Juan Fan
- Guangdong Institute of Gastrointestinal, Guangzhou, Guangdong, China.,Department of Pathology, the Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Yan Huang
- Department of Pathology, the Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Pei-Huang Wu
- Guangdong Institute of Gastrointestinal, Guangzhou, Guangdong, China
| | - Xin-Ke Yin
- Guangdong Institute of Gastrointestinal, Guangzhou, Guangdong, China
| | - Xi-Hu Yu
- Guangdong Institute of Gastrointestinal, Guangzhou, Guangdong, China.,Department of Gastrointestinal Surgery, the Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Xin-Hui Fu
- Guangdong Institute of Gastrointestinal, Guangzhou, Guangdong, China
| | - Li-Li Feng
- Guangdong Institute of Gastrointestinal, Guangzhou, Guangdong, China
| | - Yun-Long Wang
- Guangdong Institute of Gastrointestinal, Guangzhou, Guangdong, China
| | - Hong-Jun Yi
- Department of Pathology, the Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Zhi-Ting Chen
- Guangdong Institute of Gastrointestinal, Guangzhou, Guangdong, China
| | - Jun-Xiang Yin
- China National Center for Biotechnology Development, Beijing, China
| | - Da-Lu Zhang
- China National Center for Biotechnology Development, Beijing, China
| | - Wei-Xing Feng
- Guangdong Institute of Gastrointestinal, Guangzhou, Guangdong, China
| | - Shao-Mei Bai
- Guangdong Institute of Gastrointestinal, Guangzhou, Guangdong, China
| | - Taewan Kim
- The Ohio State University Comprehensive Cancer Center, Columbus, Ohio, USA
| | - Gordon B Mills
- Department of Systems Biology, Division of Basic Science Research, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yi-Ling Lu
- Department of Systems Biology, Division of Basic Science Research, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Xiang-Bo Wan
- Guangdong Institute of Gastrointestinal, Guangzhou, Guangdong, China.,Department of Radiation Oncology, the Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Lei Wang
- Guangdong Institute of Gastrointestinal, Guangzhou, Guangdong, China.,Department of Gastrointestinal Surgery, the Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
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16
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Luo Y, Wang G, Wang C, Gong Y, Bian Y, Zhou Y. Selection and Validation of Reference Genes for qRT-PCR in Lentinula edodes under Different Experimental Conditions. Genes (Basel) 2019; 10:genes10090647. [PMID: 31461882 PMCID: PMC6770232 DOI: 10.3390/genes10090647] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 08/17/2019] [Accepted: 08/22/2019] [Indexed: 12/04/2022] Open
Abstract
Lentinula edodes is the most consumed mushroom in Asia due to its nutritional and medicinal values, and the optimal reference gene is crucial for normalization of its gene expression analysis. Here, the expression stability of 18 candidate reference genes (CRGs) in L. edodes was analyzed by three statistical algorithms (geNorm, NormFinder and BestKeeper) under different stresses (heat, cadmium excess and Trichoderma atroviride infection), different substrates (straw, sawdust and corn stalk) and different development stages (mycelia, primordia and fruit bodies). Among the 18 CRGs, 28S, Actin and α-tub exhibited the highest expression stability in L. edodes under all conditions, while GPD, SPRYP and MSF showed the least stable expression. The best reference gene in different conditions was different. The pairwise variation values showed that two genes would be sufficient for accurate normalization under different conditions of L. edodes. This study will contribute to more accurate estimation of the gene relative expression levels under different conditions using the optimal reference gene in qRT-PCR (quantitative reverse transcription polymerase chain reaction) analysis.
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Affiliation(s)
- Yi Luo
- Institute of Applied Mycology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Gangzheng Wang
- Institute of Applied Mycology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangzhou 510070, China
| | - Chen Wang
- Institute of Applied Mycology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Yuhua Gong
- Institute of Applied Mycology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Yinbing Bian
- Institute of Applied Mycology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Yan Zhou
- Institute of Applied Mycology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China.
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17
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Loontiens S, Depestel L, Vanhauwaert S, Dewyn G, Gistelinck C, Verboom K, Van Loocke W, Matthijssens F, Willaert A, Vandesompele J, Speleman F, Durinck K. Purification of high-quality RNA from a small number of fluorescence activated cell sorted zebrafish cells for RNA sequencing purposes. BMC Genomics 2019; 20:228. [PMID: 30894119 PMCID: PMC6425699 DOI: 10.1186/s12864-019-5608-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 03/14/2019] [Indexed: 11/30/2022] Open
Abstract
Background Transgenic zebrafish lines with the expression of a fluorescent reporter under the control of a cell-type specific promoter, enable transcriptome analysis of FACS sorted cell populations. RNA quality and yield are key determinant factors for accurate expression profiling. Limited cell number and FACS induced cellular stress make RNA isolation of sorted zebrafish cells a delicate process. We aimed to optimize a workflow to extract sufficient amounts of high-quality RNA from a limited number of FACS sorted cells from Tg(fli1a:GFP) zebrafish embryos, which can be used for accurate gene expression analysis. Results We evaluated two suitable RNA isolation kits (the RNAqueous micro and the RNeasy plus micro kit) and determined that sorting cells directly into lysis buffer is a critical step for success. For low cell numbers, this ensures direct cell lysis, protects RNA from degradation and results in a higher RNA quality and yield. We showed that this works well up to 0.5× dilution of the lysis buffer with sorted cells. In our sort settings, this corresponded to 30,000 and 75,000 cells for the RNAqueous micro kit and RNeasy plus micro kit respectively. Sorting more cells dilutes the lysis buffer too much and requires the use of a collection buffer. We also demonstrated that an additional genomic DNA removal step after RNA isolation is required to completely clear the RNA from any contaminating genomic DNA. For cDNA synthesis and library preparation, we combined SmartSeq v4 full length cDNA library amplification, Nextera XT tagmentation and sample barcoding. Using this workflow, we were able to generate highly reproducible RNA sequencing results. Conclusions The presented optimized workflow enables to generate high quality RNA and allows accurate transcriptome profiling of small populations of sorted zebrafish cells. Electronic supplementary material The online version of this article (10.1186/s12864-019-5608-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Siebe Loontiens
- Department of Biomolecular Medicine & Center for Medical Genetics, Ghent University, 9000, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), 9000, Ghent, Belgium
| | - Lisa Depestel
- Department of Biomolecular Medicine & Center for Medical Genetics, Ghent University, 9000, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), 9000, Ghent, Belgium
| | - Suzanne Vanhauwaert
- Department of Biomolecular Medicine & Center for Medical Genetics, Ghent University, 9000, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), 9000, Ghent, Belgium
| | - Givani Dewyn
- Department of Biomolecular Medicine & Center for Medical Genetics, Ghent University, 9000, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), 9000, Ghent, Belgium
| | - Charlotte Gistelinck
- Department of Biomolecular Medicine & Center for Medical Genetics, Ghent University, 9000, Ghent, Belgium.,Department of Orthopedics and Sports Medicine, University of Washington, Seattle, WA, 98195, USA
| | - Karen Verboom
- Department of Biomolecular Medicine & Center for Medical Genetics, Ghent University, 9000, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), 9000, Ghent, Belgium
| | - Wouter Van Loocke
- Department of Biomolecular Medicine & Center for Medical Genetics, Ghent University, 9000, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), 9000, Ghent, Belgium
| | - Filip Matthijssens
- Department of Biomolecular Medicine & Center for Medical Genetics, Ghent University, 9000, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), 9000, Ghent, Belgium
| | - Andy Willaert
- Department of Biomolecular Medicine & Center for Medical Genetics, Ghent University, 9000, Ghent, Belgium
| | - Jo Vandesompele
- Department of Biomolecular Medicine & Center for Medical Genetics, Ghent University, 9000, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), 9000, Ghent, Belgium
| | - Frank Speleman
- Department of Biomolecular Medicine & Center for Medical Genetics, Ghent University, 9000, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), 9000, Ghent, Belgium
| | - Kaat Durinck
- Department of Biomolecular Medicine & Center for Medical Genetics, Ghent University, 9000, Ghent, Belgium. .,Cancer Research Institute Ghent (CRIG), 9000, Ghent, Belgium.
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18
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Gao S, Wang G, Huang Z, Lei X, Bian Y, Liu Y, Huang W. Selection of Reference Genes for qRT-PCR Analysis in Lentinula edodes after Hot-Air Drying. Molecules 2018; 24:molecules24010136. [PMID: 30602709 PMCID: PMC6337709 DOI: 10.3390/molecules24010136] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2018] [Revised: 12/24/2018] [Accepted: 12/25/2018] [Indexed: 12/31/2022] Open
Abstract
Volatile sulfur compounds gradually develop in Lentinula edodes after hot-air drying, and many genes are involved in the generation of these sulfur compounds. The expression stability of reference genes may vary in a particular experimental treatment when analyzing their expressions by quantitative real-time polymerase chain reaction (qRT-PCR). In this study, the expression profile of 17 candidate genes was assessed in L. edodes under treatment at 50 °C for 0, 1, 2, and 3 h, and the expression stability of each reference gene was analyzed by three statistical algorithms, including geNorm, NormFinder, and BestKeeper. Results indicated that the two optimal reference genes for mycelium and fruiting body were CAC and DAHP as well as CAC and NUP, respectively. Additionally, CAC and DAHP were found to be the two most stable reference genes across the mycelium and fruiting body set. Our results will provide a genetic foundation for further research on the metabolism genes of sulfur compounds in L. edodes.
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Affiliation(s)
- Shuangshuang Gao
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China.
| | - Gangzheng Wang
- Institute of Applied Mycology, Plant Science and Technology College, Huazhong Agricultural University, Wuhan, Hubei 430070, China.
| | - Zhicheng Huang
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China.
| | - Xiaoyu Lei
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China.
| | - Yinbing Bian
- Institute of Applied Mycology, Plant Science and Technology College, Huazhong Agricultural University, Wuhan, Hubei 430070, China.
| | - Ying Liu
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China.
| | - Wen Huang
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China.
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19
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Sanders R, Bustin S, Huggett J, Mason D. Improving the standardization of mRNA measurement by RT-qPCR. BIOMOLECULAR DETECTION AND QUANTIFICATION 2018; 15:13-17. [PMID: 29922589 PMCID: PMC6006386 DOI: 10.1016/j.bdq.2018.03.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 02/09/2018] [Accepted: 03/06/2018] [Indexed: 12/31/2022]
Abstract
Human health and safety depend on reliable measurements in medical diagnosis and on tests that support the selection and evaluation of therapeutic intervention and newly discovered molecular biomarkers must pass a rigorous evaluation process if they are to be of benefit to patients. Measurement standardization helps to maximize data quality and confidence and ultimately improves the reproducibility of published research. Failure to consider how a given experiment may be standardized can be costly, both financially as well as in time and failure to perform and report pre-clinical research in an appropriately rigorous manner will hinder the development of diagnostic methods. Hence standardization is a crucial step in maintaining the integrity of scientific studies and is a key feature of robust investigation.
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Affiliation(s)
- Rebecca Sanders
- Molecular and Cell Biology, Science and Innovation, LGC, Queens Road, Teddington, Middlesex TW11 0LY, UK
| | - Stephen Bustin
- Faculty of Medical Science, Anglia Ruskin University, Michael Salmon Building, Chelmsford, Essex CM1 1SQ, UK
| | - Jim Huggett
- Molecular and Cell Biology, Science and Innovation, LGC, Queens Road, Teddington, Middlesex TW11 0LY, UK
| | - Deborah Mason
- School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff CF10 3AX, UK
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20
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Nakayama T, Okada N, Yoshikawa M, Asaka D, Kuboki A, Kojima H, Tanaka Y, Haruna SI. Assessment of suitable reference genes for RT-qPCR studies in chronic rhinosinusitis. Sci Rep 2018; 8:1568. [PMID: 29371606 PMCID: PMC5785529 DOI: 10.1038/s41598-018-19834-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Accepted: 01/09/2018] [Indexed: 11/09/2022] Open
Abstract
Reverse transcription–quantitative polymerase chain reaction is a valuable and reliable method for gene quantification. Target gene expression is usually quantified by normalization using reference genes (RGs), and accurate normalization is critical for producing reliable data. However, stable RGs in nasal polyps and sinonasal tissues from patients with chronic rhinosinusitis (CRS) have not been well investigated. Here, we used a two-stage study design to identify stable RGs. We assessed the stability of 15 commonly used candidate RGs using five programs—geNorm, NormFinder, BestKeeper, ΔCT, and RefFinder. Ribosomal protein lateral stalk subunit P1 (RPLP1) and ribosomal protein lateral stalk subunit P0 (RPLP0) were the two most stable RGs in the first stage of the study, and these results were validated in the second stage. The commonly used RGs β-actin (ACTB) and glyceraldehyde 3-phosphate dehydrogenase (GAPDH) were unstable according to all of the algorithms used. The findings were further validated via relative quantification of IL-5, CCL11, IFN-γ, and IL-17A using the stable and unstable RGs. The relative expression levels varied greatly according to normalization with the selected RGs. Appropriate selection of stable RGs will allow more accurate determination of target gene expression levels in patients with CRS.
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Affiliation(s)
- Tsuguhisa Nakayama
- Department of Otorhinolaryngology, Jikei University School of Medicine, Tokyo, Japan.
| | - Naoko Okada
- Department of Allergy and Immunology, National Research Institute of Child Health and Development, Tokyo, Japan
| | - Mamoru Yoshikawa
- Department of Otorhinolaryngology, Toho University, Tokyo, Japan
| | - Daiya Asaka
- Department of Otorhinolaryngology, Jikei University School of Medicine, Tokyo, Japan
| | - Akihito Kuboki
- Department of Otorhinolaryngology, Jikei University School of Medicine, Tokyo, Japan
| | - Hiromi Kojima
- Department of Otorhinolaryngology, Jikei University School of Medicine, Tokyo, Japan
| | - Yasuhiro Tanaka
- Department of Otorhinolaryngology Head and Neck Surgery, Dokkyo Medical University Koshigaya Hospital, Saitama, Japan
| | - Shin-Ichi Haruna
- Department of Otorhinolaryngology Head and Neck Surgery, Dokkyo Medical University, Tochigi, Japan
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21
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McGovern F, Boland T, Ryan M, Sweeney T. Assessment of RNA Stability in Postmortem Tissue from New-Born Lambs. Anim Biotechnol 2017; 29:269-275. [PMID: 29172984 DOI: 10.1080/10495398.2017.1378226] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The recovery of high quality RNA from postmortem tissue is crucial to gene expression analyses. The acquisition of postmortem tissue has inherent time delays and, hence, understanding the temporal variation in the stability of total RNA is imperative. This experiment aimed: ( 1 ) to qualitatively and quantitatively assess the integrity of total RNA derived from a range of new-born ovine tissues (liver, spleen, thyroid, skeletal muscle, ileum, and perirenal adipose tissue) which were stored at ambient temperature until extraction at 0, 3, 6, and 9 h postmortem; and ( 2 ) to analyze the stability of the reference gene(s) and expression of specific target genes in these tissues. Postmortem sampling time resulted in variable reductions in the relative integrity number (RIN) values across the tissues, ranging from 0.9 to 1.8% in liver, spleen, skeletal muscle, and ileum to 5.7-11.1% in the thyroid and perirenal adipose tissues, respectively (P < 0.05). In conclusion, tissues with small reductions in RIN value can exhibit disproportionately large differences in the normalization factor used to calculate the target gene expression. Hence, changes in transcript abundance due to RNA degradation are not always sufficiently buffered through normalization with reference genes. The normalization factor should be presented alongside the RIN value in postmortem tissue studies.
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Affiliation(s)
- Fiona McGovern
- a UCD School of Agriculture and Food Science , University College Dublin, Lyons Research Farm , Newcastle , Dublin , Ireland.,b UCD School of Veterinary Medicine , University College Dublin , Belfield , Dublin , Ireland
| | - Tommy Boland
- a UCD School of Agriculture and Food Science , University College Dublin, Lyons Research Farm , Newcastle , Dublin , Ireland
| | - Marion Ryan
- b UCD School of Veterinary Medicine , University College Dublin , Belfield , Dublin , Ireland
| | - Torres Sweeney
- b UCD School of Veterinary Medicine , University College Dublin , Belfield , Dublin , Ireland
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22
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Bustin S, Nolan T. Talking the talk, but not walking the walk: RT-qPCR as a paradigm for the lack of reproducibility in molecular research. Eur J Clin Invest 2017; 47:756-774. [PMID: 28796277 DOI: 10.1111/eci.12801] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 08/07/2017] [Indexed: 12/11/2022]
Abstract
Poorly executed and inadequately reported molecular measurement methods are amongst the causes underlying the lack of reproducibility of much biomedical research. Although several high impact factor journals have acknowledged their past failure to scrutinise adequately the technical soundness of manuscripts, there is a perplexing reluctance to implement basic corrective measures. The reverse transcription real-time quantitative PCR (RT-qPCR) is probably the most straightforward measurement technique available for RNA quantification and is widely used in research, diagnostic, forensic and biotechnology applications. Despite the impact of the minimum information for the publication of quantitative PCR experiments (MIQE) guidelines, which aim to improve the robustness and the transparency of reporting of RT-qPCR data, we demonstrate that elementary protocol errors, inappropriate data analysis and inadequate reporting continue to be rife and conclude that the majority of published RT-qPCR data are likely to represent technical noise.
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Affiliation(s)
- Stephen Bustin
- Postgraduate Medical Institute, Faculty of Medical Science, Anglia Ruskin University, Chelmsford, Essex, UK
| | - Tania Nolan
- Institute of Population Health, Faculty of Medical and Human Sciences, University of Manchester, Manchester, UK
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Ji X, Wang M, Li L, Chen F, Zhang Y, Li Q, Zhou J. The Impact of Repeated Freeze–Thaw Cycles on the Quality of Biomolecules in Four Different Tissues. Biopreserv Biobank 2017; 15:475-483. [PMID: 28930488 DOI: 10.1089/bio.2017.0064] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Xiaoli Ji
- Department of Central Laboratory, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Min Wang
- Department of Central Laboratory, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Lingling Li
- Department of Central Laboratory, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Fang Chen
- Department of Urology, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Yanyang Zhang
- Department of Central Laboratory, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Qian Li
- Department of Central Laboratory, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Junmei Zhou
- Department of Central Laboratory, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China
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Verckist L, Lembrechts R, Thys S, Pintelon I, Timmermans JP, Brouns I, Adriaensen D. Selective gene expression analysis of the neuroepithelial body microenvironment in postnatal lungs with special interest for potential stem cell characteristics. Respir Res 2017; 18:87. [PMID: 28482837 PMCID: PMC5422937 DOI: 10.1186/s12931-017-0571-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 05/01/2017] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND The pulmonary neuroepithelial body (NEB) microenvironment (ME) consists of innervated cell clusters that occur sparsely distributed in the airway epithelium, an organization that has so far hampered reliable selective gene expression analysis. Although the NEB ME has been suggested to be important for airway epithelial repair after ablation, little is known about their potential stem cell characteristics in healthy postnatal lungs. Here we report on a large-scale selective gene expression analysis of the NEB ME. METHODS A GAD67-GFP mouse model was used that harbors GFP-fluorescent NEBs, allowing quick selection and pooling by laser microdissection (LMD) without further treatment. A panel of stem cell-related PCR arrays was used to selectively compare mRNA expression in the NEB ME to control airway epithelium (CAE). For genes that showed a higher expression in the NEB ME, a ranking was made based on the relative expression level. Single qPCR and immunohistochemistry were used to validate and quantify the PCR array data. RESULTS Careful optimization of all protocols appeared to be essential to finally obtain high-quality RNA from pooled LMD samples of NEB ME. About 30% of the more than 600 analyzed genes showed an at least two-fold higher expression compared to CAE. The gene that showed the highest relative expression in the NEB ME, Delta-like ligand 3 (Dll3), was investigated in more detail. Selective Dll3 gene expression in the NEB ME could be quantified via single qPCR experiments, and Dll3 protein expression could be localized specifically to NEB cell surface membranes. CONCLUSIONS This study emphasized the importance of good protocols and RNA quality controls because of the, often neglected, fast RNA degradation in postnatal lung samples. It was shown that sufficient amounts of high-quality RNA for reliable complex gene expression analysis can be obtained from pooled LMD-collected NEB ME samples of postnatal lungs. Dll3 expression, which has also been reported to be important in high-grade pulmonary tumor-initiating cells, was used as a proof-of-concept to confirm that the described methodology represents a promising tool for further unraveling the molecular basis of NEB ME physiology in general, and its postnatal stem cell capacities in particular.
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Affiliation(s)
- Line Verckist
- Laboratory of Cell Biology and Histology, Department of Veterinary Sciences, University of Antwerp, Universiteitsplein 1, BE-2610, Antwerpen, Wilrijk, Belgium
| | - Robrecht Lembrechts
- Laboratory of Cell Biology and Histology, Department of Veterinary Sciences, University of Antwerp, Universiteitsplein 1, BE-2610, Antwerpen, Wilrijk, Belgium
| | - Sofie Thys
- Laboratory of Cell Biology and Histology, Department of Veterinary Sciences, University of Antwerp, Universiteitsplein 1, BE-2610, Antwerpen, Wilrijk, Belgium
| | - Isabel Pintelon
- Laboratory of Cell Biology and Histology, Department of Veterinary Sciences, University of Antwerp, Universiteitsplein 1, BE-2610, Antwerpen, Wilrijk, Belgium
| | - Jean-Pierre Timmermans
- Laboratory of Cell Biology and Histology, Department of Veterinary Sciences, University of Antwerp, Universiteitsplein 1, BE-2610, Antwerpen, Wilrijk, Belgium
| | - Inge Brouns
- Laboratory of Cell Biology and Histology, Department of Veterinary Sciences, University of Antwerp, Universiteitsplein 1, BE-2610, Antwerpen, Wilrijk, Belgium
| | - Dirk Adriaensen
- Laboratory of Cell Biology and Histology, Department of Veterinary Sciences, University of Antwerp, Universiteitsplein 1, BE-2610, Antwerpen, Wilrijk, Belgium.
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25
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Pop LA, Pileczki V, Cojocneanu-Petric RM, Petrut B, Braicu C, Jurj AM, Buiga R, Achimas-Cadariu P, Berindan-Neagoe I. Normalization of gene expression measurement of tissue samples obtained by transurethral resection of bladder tumors. Onco Targets Ther 2016; 9:3369-80. [PMID: 27330317 PMCID: PMC4898429 DOI: 10.2147/ott.s97519] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Background Sample processing is a crucial step for all types of genomic studies. A major challenge for researchers is to understand and predict how RNA quality affects the identification of transcriptional differences (by introducing either false-positive or false-negative errors). Nanotechnologies help improve the quality and quantity control for gene expression studies. Patients and methods The study was performed on 14 tumor and matched normal pairs of tissue from patients with bladder urothelial carcinomas. We assessed the RNA quantity by using the NanoDrop spectrophotometer and the quality by nano-microfluidic capillary electrophoresis technology provided by Agilent 2100 Bioanalyzer. We evaluated the amplification status of three housekeeping genes and one small nuclear RNA gene using the ViiA 7 platform, with specific primers. Results Every step of the sample handling protocol, which begins with sample harvest and ends with the data analysis, is of utmost importance due to the fact that it is time consuming, labor intensive, and highly expensive. High temperature of the surgical procedure does not affect the small nucleic acid sequences in comparison with the mRNA. Conclusion Gene expression is clearly affected by the RNA quality, but less affected in the case of small nuclear RNAs. We proved that the high-temperature, highly invasive transurethral resection of bladder tumor procedure damages the tissue and affects the integrity of the RNA from biological specimens.
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Affiliation(s)
- Laura A Pop
- The Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Haţieganu University of Medicine and Pharmacy, Cluj-Napoca, Cluj, Romania
| | - Valentina Pileczki
- The Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Haţieganu University of Medicine and Pharmacy, Cluj-Napoca, Cluj, Romania; Department of Analytical Chemistry, Iuliu Haţieganu University of Medicine and Pharmacy, Cluj-Napoca, Cluj, Romania
| | - Roxana M Cojocneanu-Petric
- The Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Haţieganu University of Medicine and Pharmacy, Cluj-Napoca, Cluj, Romania
| | - Bogdan Petrut
- Department of Surgery II - Urology, The Oncology Institute "Prof Dr Ion Chiricuţă", Cluj-Napoca, Cluj, Romania; Department of Urology, Iuliu Haţieganu University of Medicine and Pharmacy, Cluj-Napoca, Cluj, Romania
| | - Cornelia Braicu
- The Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Haţieganu University of Medicine and Pharmacy, Cluj-Napoca, Cluj, Romania
| | - Ancuta M Jurj
- The Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Haţieganu University of Medicine and Pharmacy, Cluj-Napoca, Cluj, Romania
| | - Rares Buiga
- Department of Pathology, The Oncology Institute "Prof. Dr Ion Chiricuţă", Cluj-Napoca, Cluj, Romania
| | - Patriciu Achimas-Cadariu
- Department of Surgery, The Oncology Institute "Prof Dr Ion Chiricuţă", Cluj-Napoca, Cluj, Romania; Department of Surgical Oncology and Gynecological Oncology, Iuliu Haţieganu University of Medicine and Pharmacy, Cluj-Napoca, Cluj, Romania
| | - Ioana Berindan-Neagoe
- The Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Haţieganu University of Medicine and Pharmacy, Cluj-Napoca, Cluj, Romania; Department of Functional Genomics and Experimental Pathology, The Oncology Institute "Prof Dr Ion Chiricuţă", Cluj-Napoca, Cluj, Romania
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26
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LTD4 and TGF-β1 Induce the Expression of Metalloproteinase-1 in Chronic Rhinosinusitis via a Cysteinyl Leukotriene Receptor 1-Related Mechanism. SINUSITIS 2016. [DOI: 10.3390/sinusitis1010065] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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27
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Campbell EM, McIntosh CH, Bowman AS. A Toolbox for Quantitative Gene Expression in Varroa destructor: RNA Degradation in Field Samples and Systematic Analysis of Reference Gene Stability. PLoS One 2016; 11:e0155640. [PMID: 27182699 PMCID: PMC4868281 DOI: 10.1371/journal.pone.0155640] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Accepted: 05/02/2016] [Indexed: 11/29/2022] Open
Abstract
Varroa destructor is the major pest of Apis mellifera and contributes to the global honey bee health crisis threatening food security. Developing new control strategies to combat Varroa will require the application of molecular biology, including gene expression studies by quantitative real-time reverse transcription-polymerase chain reaction (qRT-PCR). Both high quality RNA samples and suitable stable internal reference genes are required for accurate gene expression studies. In this study, ten candidate genes (succinate dehydrogenase (SDHA), NADH dehydrogenase (NADH), large ribsosmal subunit, TATA-binding protein, glyceraldehyde-3-phosphate dehydrogenase, 18S rRNA (18S), heat-shock protein 90 (HSP90), cyclophilin, α-tubulin, actin), were evaluated for their suitability as normalization genes using the geNorm, Normfinder, BestKeeper, and comparative ΔCq algorithims. Our study proposes the use of no more than two of the four most stable reference genes (NADH, 18S, SDHA and HSP90) in Varroa gene expression studies. These four genes remain stable in phoretic and reproductive stage Varroa and are unaffected by Deformed wing virus load. When used for determining changes in vitellogenin gene expression, the signal-to-noise ratio (SNR) for the relatively unstable genes actin and α-tubulin was much lower than for the stable gene combinations (NADH + HSP90 +18S; NADH + HSP90; or NADH). Using both electropherograms and RT-qPCR for short and long amplicons as quality controls, we demonstrate that high quality RNA can be recovered from Varroa up to 10 days later stored at ambient temperature if collected into RNAlater and provided the body is pierced. This protocol allows the exchange of Varroa samples between international collaborators and field sample collectors without requiring frozen collection or shipping. Our results make important contributions to gene expression studies in Varroa by proposing a validated sampling protocol to obtain high quality Varroa RNA and the validation of suitable reference genes for expression studies in this globally important pest.
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Affiliation(s)
- Ewan M Campbell
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Catriona H McIntosh
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Alan S Bowman
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, United Kingdom
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Differential miRNA-Expression as an Adjunctive Diagnostic Tool in Neuroendocrine Tumors of the Lung. Cancers (Basel) 2016; 8:cancers8040038. [PMID: 27023611 PMCID: PMC4846847 DOI: 10.3390/cancers8040038] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2015] [Revised: 02/07/2016] [Accepted: 03/10/2016] [Indexed: 11/17/2022] Open
Abstract
Pulmonary malignancies with neuroendocrine differentiation represent a rare subclass of lung carcinomas, which vary in the extent of differentiation and grade of biological aggressiveness. In particular, neuroendocrine tumors are classified into well differentiated typical and atypical carcinoids as well as poorly differentiated large cell neuroendocrine and small cell lung carcinomas. Tiny MicroRNAs have been identified as reliable classifiers in distinct cancer types and seem to play important roles in cellular processes like regulation of cell growth, differentiation and apoptosis. In the present study, two different microRNAs (miR-21 and miR-34a) were explored for their involvements in pathogenesis of subtypes and finally in differential diagnosis of pulmonary neuroendocrine tumors. miR-21 was upregulated in poorly differentiated neuroendocrine tumors (mean rank: 26.8; 28.75) as compared to carcinoids (mean rank: 12.33; 12.07) with a significance of 0.00033. High-expression levels of miR-34a were associated with atypical carcinoids (p = 0.010). A close association is implicated between the elevated miR-21 values in high-grade and miR-34a patterns in low-grade atypical neuroendocrine lung carcinomas, which could potentially be exploited as practical supportive markers for differential lung cancer diagnosis in routine. However, some additional extended research and validation studies are needed to utilize them as routine markers or potential molecular targets for personalized medicine.
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29
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Quantitative Evaluation and Selection of Reference Genes for Quantitative RT-PCR in Mouse Acute Pancreatitis. BIOMED RESEARCH INTERNATIONAL 2016; 2016:8367063. [PMID: 27069927 PMCID: PMC4812220 DOI: 10.1155/2016/8367063] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Revised: 01/19/2016] [Accepted: 02/07/2016] [Indexed: 02/05/2023]
Abstract
The analysis of differences in gene expression is dependent on normalization using reference genes. However, the expression of many of these reference genes, as evaluated by quantitative RT-PCR, is upregulated in acute pancreatitis, so they cannot be used as the standard for gene expression in this condition. For this reason, we sought to identify a stable reference gene, or a suitable combination, for expression analysis in acute pancreatitis. The expression stability of 10 reference genes (ACTB, GAPDH, 18sRNA, TUBB, B2M, HPRT1, UBC, YWHAZ, EF-1α, and RPL-13A) was analyzed using geNorm, NormFinder, and BestKeeper software and evaluated according to variations in the raw Ct values. These reference genes were evaluated using a comprehensive method, which ranked the expression stability of these genes as follows (from most stable to least stable): RPL-13A, YWHAZ > HPRT1 > GAPDH > UBC > EF-1α > 18sRNA > B2M > TUBB > ACTB. RPL-13A was the most suitable reference gene, and the combination of RPL-13A and YWHAZ was the most stable group of reference genes in our experiments. The expression levels of ACTB, TUBB, and B2M were found to be significantly upregulated during acute pancreatitis, whereas the expression level of 18sRNA was downregulated. Thus, we recommend the use of RPL-13A or a combination of RPL-13A and YWHAZ for normalization in qRT-PCR analyses of gene expression in mouse models of acute pancreatitis.
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Oh TS, Kang HY, Nam YS, Kim YJ, You EK, Lee MY, Cho SY, Lee HJ. An Effective Method of RNA Extraction from Mycobacterium tuberculosis. ANNALS OF CLINICAL MICROBIOLOGY 2016. [DOI: 10.5145/acm.2016.19.1.20] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Affiliation(s)
- Tae Sang Oh
- Department of Biomedical Science, Graduate School, Kyung Hee University, Seoul, Korea
| | - Hee Yoon Kang
- Department of Laboratory Medicine, Kyung Hee University School of Medicine, Seoul, Korea
| | - You Sun Nam
- Department of Biomedical Science, Graduate School, Kyung Hee University, Seoul, Korea
| | - Young Jin Kim
- Department of Laboratory Medicine, Kyung Hee University School of Medicine, Seoul, Korea
| | - Eun Kyung You
- Department of Laboratory Medicine, Kyung Hee University School of Medicine, Seoul, Korea
| | - Min Young Lee
- Department of Laboratory Medicine, Kyung Hee University School of Medicine, Seoul, Korea
| | - Sun Young Cho
- Department of Laboratory Medicine, Kyung Hee University School of Medicine, Seoul, Korea
| | - Hee Joo Lee
- Department of Laboratory Medicine, Kyung Hee University School of Medicine, Seoul, Korea
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31
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Lee DD, Schwarz MA. Adapted approach to profile genes while reconciling Vegf-a mRNA expression in the developing and injured lung. Am J Physiol Lung Cell Mol Physiol 2015; 308:L1202-11. [PMID: 25868151 DOI: 10.1152/ajplung.00053.2015] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Accepted: 04/09/2015] [Indexed: 12/12/2022] Open
Abstract
During lung development and injury, messenger RNA (mRNA) transcript levels of genes fluctuate over both space and time. Quantitative PCR (qPCR) is a highly sensitive, widely used technique to measure the mRNA levels. The sensitivity of this technique can be disadvantageous and errors amplified when each qPCR assay is not validated. In contrast to other organs, lungs have high RNase activity, resulting in less than optimal RNA integrity. We implemented a strategy to address these limitations in developing and injured lungs. Parameters were established and a filter designed that optimized amplicon length and included or excluded samples based on RNA integrity. This approach was illustrated and validated by measuring mRNA levels including Vegf-a in newborn mouse lungs that were injured by 85% oxygen (hyperoxia) for 12 days and compared with control (normoxia). We demonstrate that, in contrast to contradictory Vegf-a expression when normalized to the least suitable housekeeping genes, application of this filter and normalization to most suitable three housekeeping genes, Hprt, Eef2, and Rpl13a, gave reproducible Vegf-a expression, thus corroborating the sample filter. Accordingly, both short amplicon length and proper normalization to ranked, evaluated genes minimized erroneous fluctuation and qPCR amplification issues associated with nonideal RNA integrity in injured and developing lungs. Furthermore, our work uncovers how RNA integrity, purity, amplicon length, and discovery of stable candidate reference genes enhance precision of qPCR results and utilizes the advantages of qPCR in developmental studies.
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Affiliation(s)
- Daniel D Lee
- Department of Pediatrics, Indiana University School of Medicine, South Bend, Indiana
| | - Margaret A Schwarz
- Department of Pediatrics, Indiana University School of Medicine, South Bend, Indiana
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Bustin S, Dhillon HS, Kirvell S, Greenwood C, Parker M, Shipley GL, Nolan T. Variability of the reverse transcription step: practical implications. Clin Chem 2014; 61:202-12. [PMID: 25361949 DOI: 10.1373/clinchem.2014.230615] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
BACKGROUND The reverse transcription (RT) of RNA to cDNA is a necessary first step for numerous research and molecular diagnostic applications. Although RT efficiency is known to be variable, little attention has been paid to the practical implications of that variability. METHODS We investigated the reproducibility of the RT step with commercial reverse transcriptases and RNA samples of variable quality and concentration. We quantified several mRNA targets with either singleplex SYBR Green I or dualplex probe-based reverse transcription real-time quantitative PCR (RT-qPCR), with the latter used to calculate the correlation between quantification cycles (Cqs) of mRNA targets amplified in the same real-time quantitative PCR (qPCR) assay. RESULTS RT efficiency is enzyme, sample, RNA concentration, and assay dependent and can lead to variable correlation between mRNAs from the same sample. This translates into relative mRNA expression levels that generally vary between 2- and 3-fold, although higher levels are also observed. CONCLUSIONS Our study demonstrates that the variability of the RT step is sufficiently large to call into question the validity of many published data that rely on quantification of cDNA. Variability can be minimized by choosing an appropriate RTase and high concentrations of RNA and characterizing the variability of individual assays by use of multiple RT replicates.
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Affiliation(s)
- Stephen Bustin
- Postgraduate Medical Institute, Faculty of Medical Science, Anglia Ruskin University, Chelmsford, UK;
| | - Harvinder S Dhillon
- Postgraduate Medical Institute, Faculty of Medical Science, Anglia Ruskin University, Chelmsford, UK
| | - Sara Kirvell
- Postgraduate Medical Institute, Faculty of Medical Science, Anglia Ruskin University, Chelmsford, UK
| | - Christina Greenwood
- Postgraduate Medical Institute, Faculty of Medical Science, Anglia Ruskin University, Chelmsford, UK
| | - Michael Parker
- Postgraduate Medical Institute, Faculty of Medical Science, Anglia Ruskin University, Chelmsford, UK
| | | | - Tania Nolan
- Institute of Population Health, Faculty of Medical and Human Sciences, University of Manchester, Manchester, UK
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Vrtačnik P, Kos Š, Bustin SA, Marc J, Ostanek B. Influence of trypsinization and alternative procedures for cell preparation before RNA extraction on RNA integrity. Anal Biochem 2014; 463:38-44. [PMID: 24983903 DOI: 10.1016/j.ab.2014.06.017] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2014] [Revised: 06/18/2014] [Accepted: 06/19/2014] [Indexed: 10/25/2022]
Abstract
The accuracy of techniques such as microarrays, reverse transcription polymerase chain reaction, and whole transcriptome shotgun sequencing is critically dependent on RNA quality. We have repeatedly observed extensive RNA degradation following trypsinization, a routine procedure used to dissociate adherent tissue culture cells prior to RNA extraction. This study investigated the cause of this degradation and identifies an alternative procedure that enables extraction of intact high-quality RNA. Trypsinization and several alternative procedures were used to dissociate a range of different cell lines prior to RNA extraction. The contribution of exogenous ribonucleases or induction of endogenous ribonucleases by trypsin reagent proteases to RNA degradation was examined. Trypsinization resulted in a complete degradation of RNA regardless of cell line type, differentiation stage, or passage number. This occurred when intact RNA was incubated directly with trypsin and was not suppressed by inhibiting trypsin's protease activity. Prevention of degradation by sodium hypochlorite treatment of trypsin reagent identified the presence of ribonucleases in trypsin derived from animal pancreas. Consistent extraction of high-quality RNA requires the use of direct cell lysis with a phenol guanidine-based reagent or an animal origin-free protease-based dissociation agent if enzymatic detachment prior to RNA extraction cannot be avoided.
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Affiliation(s)
- Peter Vrtačnik
- Department of Clinical Biochemistry, Faculty of Pharmacy, University of Ljubljana, Ljubljana 1000, Slovenia
| | - Špela Kos
- Department of Clinical Biochemistry, Faculty of Pharmacy, University of Ljubljana, Ljubljana 1000, Slovenia
| | - Stephen A Bustin
- Postgraduate Medical Institute, Anglia Ruskin University, Chelmsford CM1 1SQ, UK
| | - Janja Marc
- Department of Clinical Biochemistry, Faculty of Pharmacy, University of Ljubljana, Ljubljana 1000, Slovenia
| | - Barbara Ostanek
- Department of Clinical Biochemistry, Faculty of Pharmacy, University of Ljubljana, Ljubljana 1000, Slovenia.
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Sanders R, Mason DJ, Foy CA, Huggett JF. Considerations for accurate gene expression measurement by reverse transcription quantitative PCR when analysing clinical samples. Anal Bioanal Chem 2014; 406:6471-83. [PMID: 24858468 PMCID: PMC4182594 DOI: 10.1007/s00216-014-7857-x] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Revised: 04/17/2014] [Accepted: 04/24/2014] [Indexed: 01/04/2023]
Abstract
Reverse transcription quantitative PCR is an established, simple and effective method for RNA measurement. However, technical standardisation challenges combined with frequent insufficient experimental detail render replication of many published findings challenging. Consequently, without adequate consideration of experimental standardisation, such findings may be sufficient for a given publication but cannot be translated to wider clinical application. This article builds on earlier standardisation work and the MIQE guidelines, discussing processes that need consideration for accurate, reproducible analysis when dealing with patient samples. By applying considerations common to the science of measurement (metrology), one can maximise the impact of gene expression studies, increasing the likelihood of their translation to clinical tools.
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Affiliation(s)
- Rebecca Sanders
- Molecular & Cell Biology, LGC, Queens Road, Teddington, TW11 0LY, UK,
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35
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Simultaneous isolation of mRNA and native protein from minute samples of cells. Biotechniques 2014; 56:229-37. [PMID: 24806223 DOI: 10.2144/000114165] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2013] [Accepted: 03/04/2014] [Indexed: 11/23/2022] Open
Abstract
Precious biological samples often lack a sufficient number of cells for multiple procedures, such as extraction of mRNA while maintaining protein in a non-denatured state suitable for subsequent characterization. Here we present a new method for the simultaneous purification of mRNA and native proteins from samples containing small numbers of cells. Our approach utilizes oligodeoxythymidylate [oligo(dT)25]-coated paramagnetic beads in an optimized reaction buffer to isolate mRNA comparable in quantity and quality to mRNA isolated with existing methods, while maintaining the proteins in their native state for traditional protein assays. We validated the procedure using neonatal rat ovaries and small numbers of human granulosa cells, demonstrating the extraction of mRNA suitable for gene expression analysis with simultaneous isolation of native proteins suitable for downstream characterization using different protein assays.
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36
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Ma Y, Kang XN, Ding WB, Yang HZ, Wang Y, Zhang J, Huang YR, Dai HL. Renal tissue thawed for 30 minutes is still suitable for gene expression analysis. PLoS One 2014; 9:e93175. [PMID: 24687048 PMCID: PMC3970958 DOI: 10.1371/journal.pone.0093175] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Accepted: 03/03/2014] [Indexed: 11/19/2022] Open
Abstract
Some biosamples obtained from biobanks may go through thawing before processing. We aim to evaluate the effects of thawing at room temperature for different time periods on gene expression analysis. A time course study with four time points was conducted to investigate the expression profiling on 10 thawed normal mice renal tissue samples through Affymetrix GeneChip mouse gene 2.0 st array. Microarray results were validated by quantitative real time polymerase chain reactions (qPCR) on 6 candidate reference genes and 11 target genes. Additionally, we used geNorm plus and NormFinder to identify the most stably expressed reference genes over time. The results showed RNA degraded more after longer incubation at room temperature. However, microarray results showed only 240 genes (0.91%) altered significantly in response to thawing at room temperature. The signal of majority altered probe sets decreased with thawing time, and the crossing point (Cp) values of all candidate reference genes correlated positively with the thawing time (p<0.05). The combination of B2M, ACTB and PPIA was identified as the best choice for qPCR normalization. We found most target genes were stable by using this normalization method. However, serious gene quantification errors were resulted from improper reference genes. In conclusion, thirty minutes of thawing at room temperature has a limited impact on microarray and qPCR analysis, gene expression variations due to RNA degradation in early period after thawing can be largely reduced by proper normalization.
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Affiliation(s)
- Yi Ma
- Department of Biobank, Renji Hospital, School of Medicine, Shanghai JiaoTong University, Shanghai, China
- Department of Urology, Renji Hospital, School of Medicine, Shanghai JiaoTong University, Shanghai, China
| | - Xiao-Nan Kang
- Department of Biobank, Renji Hospital, School of Medicine, Shanghai JiaoTong University, Shanghai, China
| | - Wen-Bin Ding
- Department of Biobank, Renji Hospital, School of Medicine, Shanghai JiaoTong University, Shanghai, China
| | - Hao-Zheng Yang
- Department of Central Laboratory, Renji Hospital, School of Medicine, Shanghai JiaoTong University, Shanghai, China
| | - Ye Wang
- Department of Biobank, Renji Hospital, School of Medicine, Shanghai JiaoTong University, Shanghai, China
| | - Jin Zhang
- Department of Urology, Renji Hospital, School of Medicine, Shanghai JiaoTong University, Shanghai, China
| | - Yi-Ran Huang
- Department of Urology, Renji Hospital, School of Medicine, Shanghai JiaoTong University, Shanghai, China
- * E-mail: (YRH); (HLD)
| | - Hui-Li Dai
- Department of Biobank, Renji Hospital, School of Medicine, Shanghai JiaoTong University, Shanghai, China
- * E-mail: (YRH); (HLD)
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Chen H, Osuna D, Colville L, Lorenzo O, Graeber K, Küster H, Leubner-Metzger G, Kranner I. Transcriptome-wide mapping of pea seed ageing reveals a pivotal role for genes related to oxidative stress and programmed cell death. PLoS One 2013; 8:e78471. [PMID: 24205239 PMCID: PMC3812160 DOI: 10.1371/journal.pone.0078471] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Accepted: 09/13/2013] [Indexed: 01/19/2023] Open
Abstract
Understanding of seed ageing, which leads to viability loss during storage, is vital for ex situ plant conservation and agriculture alike. Yet the potential for regulation at the transcriptional level has not been fully investigated. Here, we studied the relationship between seed viability, gene expression and glutathione redox status during artificial ageing of pea (Pisum sativum) seeds. Transcriptome-wide analysis using microarrays was complemented with qRT-PCR analysis of selected genes and a multilevel analysis of the antioxidant glutathione. Partial degradation of DNA and RNA occurred from the onset of artificial ageing at 60% RH and 50°C, and transcriptome profiling showed that the expression of genes associated with programmed cell death, oxidative stress and protein ubiquitination were altered prior to any sign of viability loss. After 25 days of ageing viability started to decline in conjunction with progressively oxidising cellular conditions, as indicated by a shift of the glutathione redox state towards more positive values (>-190 mV). The unravelling of the molecular basis of seed ageing revealed that transcriptome reprogramming is a key component of the ageing process, which influences the progression of programmed cell death and decline in antioxidant capacity that ultimately lead to seed viability loss.
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Affiliation(s)
- Hongying Chen
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, People's Republic of China
- Seed Conservation Department, Royal Botanic Gardens, Kew, Ardingly, West Sussex, United Kingdom
| | - Daniel Osuna
- Departamento de Fisiología Vegetal, Centro Hispano-Luso de Investigaciones Agrarias (CIALE), Facultad de Biología. Universidad de Salamanca, Salamanca, Spain
| | - Louise Colville
- Seed Conservation Department, Royal Botanic Gardens, Kew, Ardingly, West Sussex, United Kingdom
| | - Oscar Lorenzo
- Departamento de Fisiología Vegetal, Centro Hispano-Luso de Investigaciones Agrarias (CIALE), Facultad de Biología. Universidad de Salamanca, Salamanca, Spain
| | - Kai Graeber
- Institute for Biology II, Botany/Plant Physiology, Faculty of Biology, Albert-Ludwigs-University Freiburg, Freiburg, Germany
- Institute for Plant Genetics, Unit IV – Plant Genomics, Leibniz Universität Hannover, Hannover, Germany
| | - Helge Küster
- Institute for Plant Genetics, Unit IV – Plant Genomics, Leibniz Universität Hannover, Hannover, Germany
| | - Gerhard Leubner-Metzger
- Institute for Biology II, Botany/Plant Physiology, Faculty of Biology, Albert-Ludwigs-University Freiburg, Freiburg, Germany
| | - Ilse Kranner
- Seed Conservation Department, Royal Botanic Gardens, Kew, Ardingly, West Sussex, United Kingdom
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Sanders R, Mason DJ, Foy CA, Huggett JF. Evaluation of digital PCR for absolute RNA quantification. PLoS One 2013; 8:e75296. [PMID: 24073259 PMCID: PMC3779174 DOI: 10.1371/journal.pone.0075296] [Citation(s) in RCA: 130] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2013] [Accepted: 08/15/2013] [Indexed: 12/29/2022] Open
Abstract
Gene expression measurements detailing mRNA quantities are widely employed in molecular biology and are increasingly important in diagnostic fields. Reverse transcription (RT), necessary for generating complementary DNA, can be both inefficient and imprecise, but remains a quintessential RNA analysis tool using qPCR. This study developed a Transcriptomic Calibration Material and assessed the RT reaction using digital (d)PCR for RNA measurement. While many studies characterise dPCR capabilities for DNA quantification, less work has been performed investigating similar parameters using RT-dPCR for RNA analysis. RT-dPCR measurement using three, one-step RT-qPCR kits was evaluated using single and multiplex formats when measuring endogenous and synthetic RNAs. The best performing kit was compared to UV quantification and sensitivity and technical reproducibility investigated. Our results demonstrate assay and kit dependent RT-dPCR measurements differed significantly compared to UV quantification. Different values were reported by different kits for each target, despite evaluation of identical samples using the same instrument. RT-dPCR did not display the strong inter-assay agreement previously described when analysing DNA. This study demonstrates that, as with DNA measurement, RT-dPCR is capable of accurate quantification of low copy RNA targets, but the results are both kit and target dependent supporting the need for calibration controls.
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Affiliation(s)
- Rebecca Sanders
- Molecular and Cell Biology, LGC, Teddington, United Kingdom ; Cardiff School of BioSciences, The Sir Martin Evans Building, Cardiff, United Kingdom
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Chionh YH, Ho CH, Pruksakorn D, Ramesh Babu I, Ng CS, Hia F, McBee ME, Su D, Pang YLJ, Gu C, Dong H, Prestwich EG, Shi PY, Preiser PR, Alonso S, Dedon PC. A multidimensional platform for the purification of non-coding RNA species. Nucleic Acids Res 2013; 41:e168. [PMID: 23907385 PMCID: PMC3783195 DOI: 10.1093/nar/gkt668] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A renewed interest in non-coding RNA (ncRNA) has led to the discovery of novel RNA species and post-transcriptional ribonucleoside modifications, and an emerging appreciation for the role of ncRNA in RNA epigenetics. Although much can be learned by amplification-based analysis of ncRNA sequence and quantity, there is a significant need for direct analysis of RNA, which has led to numerous methods for purification of specific ncRNA molecules. However, no single method allows purification of the full range of cellular ncRNA species. To this end, we developed a multidimensional chromatographic platform to resolve, isolate and quantify all canonical ncRNAs in a single sample of cells or tissue, as well as novel ncRNA species. The applicability of the platform is demonstrated in analyses of ncRNA from bacteria, human cells and plasmodium-infected reticulocytes, as well as a viral RNA genome. Among the many potential applications of this platform are a system-level analysis of the dozens of modified ribonucleosides in ncRNA, characterization of novel long ncRNA species, enhanced detection of rare transcript variants and analysis of viral genomes.
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Affiliation(s)
- Yok Hian Chionh
- Singapore-MIT Alliance for Research and Technology, Infectious Disease Interdisciplinary Research Group, Campus for Research Excellence and Technological Enterprise, Singapore 138602, Department of Microbiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Department of Biological Engineering and Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA, Applied Biological Science Program, Chulabhorn Graduate Institute, Bangkok 10210, Thailand, Division of Molecular Genetics & Cell Biology, School of Biological Sciences, Nanyang Technological University, Singapore 637551, Immunology Programme, Life Science Institute, Centre for Life Science, Singapore 117456 and Novartis Institute for Tropical Disease, Singapore 138670
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Identification of accurate reference genes for RT-qPCR analysis of formalin-fixed paraffin-embedded tissue from primary Non-Small Cell Lung Cancers and brain and lymph node metastases. Lung Cancer 2013; 81:180-6. [DOI: 10.1016/j.lungcan.2013.04.007] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2013] [Revised: 03/28/2013] [Accepted: 04/06/2013] [Indexed: 11/18/2022]
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41
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A robust and efficient method for the isolation of DNA-free, pure and intact RNA from Mycobacterium tuberculosis. J Microbiol Methods 2013; 93:198-202. [DOI: 10.1016/j.mimet.2013.03.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2013] [Revised: 03/21/2013] [Accepted: 03/21/2013] [Indexed: 11/19/2022]
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Van Bruaene N, C PN, Van Crombruggen K, De Ruyck N, Holtappels G, Van Cauwenberge P, Gevaert P, Bachert C. Inflammation and remodelling patterns in early stage chronic rhinosinusitis. Clin Exp Allergy 2013; 42:883-90. [PMID: 22093003 DOI: 10.1111/j.1365-2222.2011.03898.x] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
BACKGROUND A distinct set of inflammatory and remodelling factors have been found elevated in chronic rhinosinusitis. OBJECTIVE The investigation of their expression in early stage disease may reveal early events in this common disease. METHODS Sinonasal mucosal samples from nine patients with early stage CRSsNP were taken from the inferior and middle turbinates, the uncinate process, maxillary sinus, anterior ethmoid, bulla ethmoidalis and the posterior ethmoid and measured for TGF-beta 1 and it's receptors, MPO protein as well as pro-inflammatory cytokines (TNF-alpha and IL-1beta) and the Th1 cell signature (IFN-gamma and T-bet). As outcome parameter for TGF-beta signalling collagen deposition was analysed. Inferior turbinates from patients undergoing (rhino-) septoplasty were collected as controls. RESULTS TGF-beta 1 protein concentrations were significantly increased in the maxillary sinuses (P = 0.006), the uncinate process (P = 0.01), the anterior ethmoid including the bulla ethmoidalis (P = 0.005) and the posterior ethmoid (P = 0.037) when compared to the inferior and middle turbinates. Collagen deposition was significantly increased in the maxillary sinus when compared to the inferior turbinates (P = 0.008). In contrast, mRNA for TGF-beta receptors, Th1 related markers (IFN-gamma and T-bet), pro-inflammatory cytokines (IL-1 beta and TNF-alpha), and MPO protein as neutrophil marker were expressed at all locations but showed no significant differences between the various locations. TGF-beta 1 mRNA expression in inferior turbinates of CRSsNP was significantly higher when compared to inferior turbinates of controls (P = 0.017). The pro-inflammatory cytokines and Th1-related cytokines did not show an upregulation in inferior turbinates of CRSsNP when compared to controls. CONCLUSIONS In early stage chronic sinus disease, TGF-beta protein is expressed in significantly higher concentrations within the paranasal sinuses when compared to turbinates, whereas pro-inflammatory, neutrophilic and Th1 markers did not show any difference. These findings suggest that TGF-beta plays a central role in the initiation of CRSsNP, and represents a major target for further research and future intervention.
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Affiliation(s)
- N Van Bruaene
- Upper Airway Research Laboratory, Department of Oto-Rhino-Laryngology, Ghent University Hospital, Ghent, Belgium.
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Román B, González-Verdejo CI, Peña F, Nadal S, Gómez P. Evaluation of different pulverisation methods for RNA extraction in squash fruit: lyophilisation, cryogenic mill and mortar grinding. PHYTOCHEMICAL ANALYSIS : PCA 2012; 23:622-626. [PMID: 22517615 DOI: 10.1002/pca.2364] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2011] [Revised: 02/17/2012] [Accepted: 03/06/2012] [Indexed: 05/31/2023]
Abstract
INTRODUCTION Quality and integrity of RNA are critical for transcription studies in plant molecular biology. In squash fruit and other high water content crops, the grinding of tissue with mortar and pestle in liquid nitrogen fails to produce a homogeneous and fine powered sample desirable to ensure a good penetration of the extraction reagent. OBJECTIVE To develop an improved pulverisation method to facilitate the homogenisation process of squash fruit tissue prior to RNA extraction without reducing quality and yield of the extracted RNA. METHODOLOGY Three methods of pulverisation, each followed by the same extraction protocol, were compared. The first approach consisted of the lyophilisation of the sample in order to remove the excess of water before grinding, the second one used a cryogenic mill and the control one a mortar grinding of frozen tissue. The quality of the isolated RNA was tested by carrying out a quantitative real time downstream amplification. RESULTS In the three situations considered, mean values for A(260) /A(280) indicated minimal interference by proteins and RNA quality indicator (RQI) values were considered appropriate for quantitative real-time polymerase chain reaction (qRT-PCR) amplification. Successful qRT-PCR amplifications were obtained with cDNA isolated with the three protocols. CONCLUSION Both apparatus can improve and facilitate the grinding step in the RNA extraction process in zucchini, resulting in isolated RNA of high quality and integrity as revealed by qRT-PCR downstream application. This is apparently the first time that a cryogenic mill has been used to prepare fruit samples for RNA extraction, thereby improving the sampling strategy because the fine powder obtained represents a homogeneous mix of the organ tissue.
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Affiliation(s)
- Belén Román
- IFAPA-Centro Alameda del Obispo., Área de Mejora y Biotecnología, Avda. Menéndez Pidal s/n, Apdo. 3092, 14080, Córdoba, Spain.
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Ali SA, Alman B. RNA extraction from human articular cartilage by chondrocyte isolation. Anal Biochem 2012; 429:39-41. [PMID: 22776092 DOI: 10.1016/j.ab.2012.06.028] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2012] [Revised: 06/26/2012] [Accepted: 06/28/2012] [Indexed: 11/30/2022]
Abstract
We report an optimized method for RNA extraction from human articular cartilage that does not require the use of specialized equipment or column purification. To maximize RNA yield while minimizing degradation and contamination, chondrocytes are isolated from the extracellular matrix and the traditional TRIzol protocol is modified to include two RNA-DNA-protein phase separations. We compared RNA extracted using this modified method with the traditional TRIzol method by spectrophotometry, Bioanalyzer, and real-time polymerase chain reaction (PCR). With the modified method, RNA recovery is increased by nearly 1μg per 100mg of cartilage, and RNA integrity number (RIN) is improved from 2.0 to 7.5.
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Affiliation(s)
- Shabana Amanda Ali
- Program in Developmental and Stem Cell Biology, Hospital for Sick Children, Toronto, Ontario, Canada M5G 1X8
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Kraemer N, Neubert G, Issa L, Ninnemann O, Seiler AEM, Kaindl AM. Reference genes in the developing murine brain and in differentiating embryonic stem cells. Neurol Res 2012; 34:664-8. [PMID: 22735032 DOI: 10.1179/1743132812y.0000000060] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
Abstract
OBJECTIVES Gene expression analysis via quantitative real-time PCR (qPCR) is a key approach in biological and medical research. Here, variations between runs and samples are compensated for by in-parallel analysis of reference genes, which require a most stable expression throughout all samples and experimental procedures to function as internal standards. In reality, there is no universal reference gene; but rather, assumed reference genes vary widely among various cell types. This demands an evaluation of reference genes for each specific experimental purpose, especially in the case of developmental studies. The aim of the present study was to identify suitable reference genes for gene expression analysis in the developing murine brain neocortex in vivo and in mouse embryonic stem cells (mESC) throughout differentiation in vitro. METHODS The five candidate genes Actb, 18s, Gapdh, Hprt, and RpII were analyzed throughout development in vivo and in vitro using the quartiles of C(q) values, fold change, coefficient of variation (CV) and the difference between maximum minus twofold standard deviation and mean as the criteria to evaluate their expression stability. RESULTS We found that RpII was the most stable expressed gene in mESC throughout differentiation, while in the developing murine neocortex Gapdh showed the highest expression stability. CONCLUSIONS Based on our results, we suggest for gene expression analysis in the context of neurodevelopment the usage of RpII as a reference gene for mESC and Gapdh or Hprt for the murine neocortex.
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Affiliation(s)
- Nadine Kraemer
- Institute of Neuroanatomy and Cell Biology, Charité - Universitätsmedizin Berlin, Germany.
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46
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Ma Y, Dai H, Kong X. Impact of warm ischemia on gene expression analysis in surgically removed biosamples. Anal Biochem 2012; 423:229-35. [DOI: 10.1016/j.ab.2012.02.003] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2011] [Revised: 01/15/2012] [Accepted: 02/03/2012] [Indexed: 02/01/2023]
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Ibusuki M, Fu P, Yamamoto S, Fujiwara S, Yamamoto Y, Honda Y, Iyama KI, Iwase H. Establishment of a standardized gene-expression analysis system using formalin-fixed, paraffin-embedded, breast cancer specimens. Breast Cancer 2011; 20:159-66. [DOI: 10.1007/s12282-011-0318-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2011] [Accepted: 11/06/2011] [Indexed: 11/24/2022]
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Mee BC, Carroll P, Donatello S, Connolly E, Griffin M, Dunne B, Burke L, Flavin R, Rizkalla H, Ryan C, Hayes B, D'Adhemar C, Banville N, Faheem N, Muldoon C, Gaffney EF. Maintaining Breast Cancer Specimen Integrity and Individual or Simultaneous Extraction of Quality DNA, RNA, and Proteins from Allprotect-Stabilized and Nonstabilized Tissue Samples. Biopreserv Biobank 2011; 9:389-398. [PMID: 23386926 PMCID: PMC3558729 DOI: 10.1089/bio.2011.0034] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2011] [Accepted: 08/25/2011] [Indexed: 12/13/2022] Open
Abstract
The Saint James's Hospital Biobank was established in 2008, to develop a high-quality breast tissue BioResource, as a part of the breast cancer clinical care pathway. The aims of this work were: (1) to ascertain the quality of RNA, DNA, and protein in biobanked carcinomas and normal breast tissues, (2) to assess the efficacy of AllPrep(®) (Qiagen) in isolating RNA, DNA, and protein simultaneously, (3) to compare AllPrep with RNEasy(®) and QIAamp(®) (both Qiagen), and (4) to examine the effectiveness of Allprotect(®) (Qiagen), a new tissue stabilization medium in preserving DNA, RNA, and proteins. One hundred eleven frozen samples of carcinoma and normal breast tissue were analyzed. Tumor and normal tissue morphology were confirmed by frozen sections. Tissue type, tissue treatment (Allprotect vs. no Allprotect), extraction kit, and nucleic acid quantification were analyzed by utilizing a 4 factorial design (SPSS PASW 18 Statistics Software(®)). QIAamp (DNA isolation), AllPrep (DNA, RNA, and Protein isolation), and RNeasy (RNA isolation) kits were assessed and compared. Mean DNA yield and A(260/280) values using QIAamp were 33.2 ng/μL and 1.86, respectively, and using AllPrep were 23.2 ng/μL and 1.94. Mean RNA yield and RNA Integrity Number (RIN) values with RNeasy were 73.4 ng/μL and 8.16, respectively, and with AllPrep were 74.8 ng/μL and 7.92. Allprotect-treated tissues produced higher RIN values of borderline significance (P=0.055). No discernible loss of RNA stability was detected after 6 h incubation of stabilized or nonstabilized tissues at room temperature or 4°C or in 9 freeze-thaw cycles. Allprotect requires further detailed evaluation, but we consider AllPrep to be an excellent option for the simultaneous extraction of RNA, DNA, and protein from tumor and normal breast tissues. The essential presampling procedures that maintain the diagnostic integrity of pathology specimens do not appear to compromise the quality of molecular isolates.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Ciara Ryan
- St. James's Hospital Biobank, Dublin, Ireland
| | - Brian Hayes
- St. James's Hospital Biobank, Dublin, Ireland
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Condori J, Nopo-Olazabal C, Medrano G, Medina-Bolivar F. Selection of reference genes for qPCR in hairy root cultures of peanut. BMC Res Notes 2011; 4:392. [PMID: 21985172 PMCID: PMC3199266 DOI: 10.1186/1756-0500-4-392] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2011] [Accepted: 10/10/2011] [Indexed: 11/10/2022] Open
Abstract
Background Hairy root cultures produced via Agrobacterium rhizogenes-mediated transformation have emerged as practical biological models to elucidate the biosynthesis of specialized metabolites. To effectively understand the expression patterns of the genes involved in the metabolic pathways of these compounds, reference genes need to be systematically validated under specific experimental conditions as established by the MIQE (Minimum Information for Publication of Quantitative Real-Time PCR Experiments) guidelines. In the present report we describe the first validation of reference genes for RT-qPCR in hairy root cultures of peanut which produce stilbenoids upon elicitor treatments. Results A total of 21 candidate reference genes were evaluated. Nineteen genes were selected based on previous qPCR studies in plants and two were from the T-DNAs transferred from A. rhizogenes. Nucleotide sequences of peanut candidate genes were obtained using their homologous sequences in Arabidopsis. To identify the suitable primers, calibration curves were obtained for each candidate reference gene. After data analysis, 12 candidate genes meeting standard efficiency criteria were selected. The expression stability of these genes was analyzed using geNorm and NormFinder algorithms and a ranking was established based on expression stability of the genes. Candidate reference gene expression was shown to have less variation in methyl jasmonate (MeJA) treated root cultures than those treated with sodium acetate (NaOAc). Conclusions This work constitutes the first effort to validate reference genes for RT-qPCR in hairy roots. While these genes were selected under conditions of NaOAc and MeJA treatment, we anticipate these genes to provide good targets for reference genes for hairy roots under a variety of stress conditions. The lead reference genes were a gene encoding for a TATA box binding protein (TBP2) and a gene encoding a ribosomal protein (RPL8C). A commonly used reference gene GAPDH showed low stability of expression suggesting that its use may lead to inaccurate gene expression profiles when used for data normalization in stress-stimulated hairy roots. Likewise the A. rhizogenes transgene rolC showed less expression stability than GAPDH. This study proposes that a minimum of two reference genes should be used for a normalization procedure in gene expression profiling using elicited hairy roots.
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Affiliation(s)
- Jose Condori
- Arkansas Biosciences Institute, Arkansas State University, P,O, Box 639, State University, AR 72467, USA.
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Graeber K, Linkies A, Wood AT, Leubner-Metzger G. A guideline to family-wide comparative state-of-the-art quantitative RT-PCR analysis exemplified with a Brassicaceae cross-species seed germination case study. THE PLANT CELL 2011; 23:2045-63. [PMID: 21666000 PMCID: PMC3160028 DOI: 10.1105/tpc.111.084103] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2011] [Revised: 05/06/2011] [Accepted: 05/27/2011] [Indexed: 05/20/2023]
Abstract
Comparative biology includes the comparison of transcriptome and quantitative real-time RT-PCR (qRT-PCR) data sets in a range of species to detect evolutionarily conserved and divergent processes. Transcript abundance analysis of target genes by qRT-PCR requires a highly accurate and robust workflow. This includes reference genes with high expression stability (i.e., low intersample transcript abundance variation) for correct target gene normalization. Cross-species qRT-PCR for proper comparative transcript quantification requires reference genes suitable for different species. We addressed this issue using tissue-specific transcriptome data sets of germinating Lepidium sativum seeds to identify new candidate reference genes. We investigated their expression stability in germinating seeds of L. sativum and Arabidopsis thaliana by qRT-PCR, combined with in silico analysis of Arabidopsis and Brassica napus microarray data sets. This revealed that reference gene expression stability is higher for a given developmental process between distinct species than for distinct developmental processes within a given single species. The identified superior cross-species reference genes may be used for family-wide comparative qRT-PCR analysis of Brassicaceae seed germination. Furthermore, using germinating seeds, we exemplify optimization of the qRT-PCR workflow for challenging tissues regarding RNA quality, transcript stability, and tissue abundance. Our work therefore can serve as a guideline for moving beyond Arabidopsis by establishing high-quality cross-species qRT-PCR.
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Affiliation(s)
- Kai Graeber
- University of Freiburg, Faculty of Biology, Institute for Biology II, Botany/Plant Physiology, D-79104 Freiburg, Germany
| | - Ada Linkies
- University of Freiburg, Faculty of Biology, Institute for Biology II, Botany/Plant Physiology, D-79104 Freiburg, Germany
| | - Andrew T.A. Wood
- University of Nottingham, Division of Statistics, School of Mathematical Sciences, University Park, Nottingham NG7 2RD, United Kingdom
| | - Gerhard Leubner-Metzger
- University of Freiburg, Faculty of Biology, Institute for Biology II, Botany/Plant Physiology, D-79104 Freiburg, Germany
- Address correspondence to
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