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Nevone A, Lattarulo F, Russo M, Panno G, Milani P, Basset M, Avanzini MA, Merlini G, Palladini G, Nuvolone M. A Strategy for the Selection of RT-qPCR Reference Genes Based on Publicly Available Transcriptomic Datasets. Biomedicines 2023; 11:1079. [PMID: 37189697 PMCID: PMC10135859 DOI: 10.3390/biomedicines11041079] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 03/23/2023] [Accepted: 03/27/2023] [Indexed: 04/05/2023] Open
Abstract
In the next-generation sequencing era, RT-qPCR is still widely employed to quantify levels of nucleic acids of interest due to its popularity, versatility, and limited costs. The measurement of transcriptional levels through RT-qPCR critically depends on reference genes used for normalization. Here, we devised a strategy to select appropriate reference genes for a specific clinical/experimental setting based on publicly available transcriptomic datasets and a pipeline for RT-qPCR assay design and validation. As a proof-of-principle, we applied this strategy to identify and validate reference genes for transcriptional studies of bone-marrow plasma cells from patients with AL amyloidosis. We performed a systematic review of published literature to compile a list of 163 candidate reference genes for RT-qPCR experiments employing human samples. Next, we interrogated the Gene Expression Omnibus to assess expression levels of these genes in published transcriptomic studies on bone-marrow plasma cells from patients with different plasma cell dyscrasias and identified the most stably expressed genes as candidate normalizing genes. Experimental validation on bone-marrow plasma cells showed the superiority of candidate reference genes identified through this strategy over commonly employed "housekeeping" genes. The strategy presented here may apply to other clinical and experimental settings for which publicly available transcriptomic datasets are available.
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Affiliation(s)
- Alice Nevone
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy
- Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | - Francesca Lattarulo
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy
- Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | - Monica Russo
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy
- Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | - Giada Panno
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy
- Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | - Paolo Milani
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy
- Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | - Marco Basset
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy
- Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | - Maria Antonietta Avanzini
- Pediatric Hematology Oncology, Cell Factory, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | - Giampaolo Merlini
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy
- Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | - Giovanni Palladini
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy
- Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | - Mario Nuvolone
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy
- Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
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Nilles J, Weiss J, Theile D. Crystal violet staining is a reliable alternative to bicinchoninic acid assay-based normalization. Biotechniques 2022; 73:131-135. [PMID: 36000337 DOI: 10.2144/btn-2022-0064] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Experimental data with cells often require normalization. The frequently used bicinchoninic acid (BCA) assay, in fact, indicates protein content but is influenced by incubation time, pH etc. A simple, rapid and reliable alternative is desirable. Crystal violet stains nucleic acids and proteins and was used to reflect the cell number in 96-well plates. Calibration curves and comparison with BCA confirmed excellent goodness of fit (R2: 0.98), conformity (nonsignificant difference of BCA to crystal violet) and reliability of this staining methodology. Crystal violet staining can be used to normalize experimental data to the number of adherent cells present in cell culture plates.
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Affiliation(s)
- Julie Nilles
- Department of Clinical Pharmacology & Pharmacoepidemiology, Heidelberg University Hospital, Im Neuenheimer Feld 410, Heidelberg, 69120, Germany
| | - Johanna Weiss
- Department of Clinical Pharmacology & Pharmacoepidemiology, Heidelberg University Hospital, Im Neuenheimer Feld 410, Heidelberg, 69120, Germany
| | - Dirk Theile
- Department of Clinical Pharmacology & Pharmacoepidemiology, Heidelberg University Hospital, Im Neuenheimer Feld 410, Heidelberg, 69120, Germany
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Theile D, Wagner L, Bay C, Haefeli WE, Weiss J. Time-Resolved Effect of Interferon-Alpha 2a on Activities of Nuclear Factor Kappa B, Pregnane X Receptor and on Drug Disposition Genes. Pharmaceutics 2021; 13:808. [PMID: 34071580 PMCID: PMC8229072 DOI: 10.3390/pharmaceutics13060808] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 05/26/2021] [Accepted: 05/27/2021] [Indexed: 11/16/2022] Open
Abstract
Interferon-alpha (IFN-α) is suggested to cause pharmacokinetic drug interactions by lowering expression of drug disposition genes through affecting the activities of nuclear factor kappa B (NF-ĸB) and pregnane X receptor (PXR). The time-resolved impact of IFN-α 2a (1000 U/mL; 5000 U/mL; 2 h to 30 h) on the activities of NF-ĸB and PXR and mRNA expression (5000 U/mL; 24 h, 48 h) of selected drug disposition genes and on cytochrome P450 (CYP3A4) activity in LS180 cells (5000 U/mL; 24 h, 48 h) was evaluated using luciferase-based reporter gene assays, reverse transcription polymerase chain reaction, and luminescence-based CYP3A4 activity assays. The cross-talk between NF-ĸB activation and PXR suppression was evaluated by NF-ĸB blockage (10 µM parthenolide). IFN-α 2a initially (2 h, 6 h) enhanced NF-ĸB activity 2-fold and suppressed PXR activity by 30%. mRNA of CYP3A4 was halved, whereas UGT1A1 was increased (1.35-fold) after 24 h. After 48 h, ABCB1 expression was increased (1.76-fold). CYP3A4 activity remained unchanged after 24 h, but was enhanced after 48 h (1.35-fold). IFN-α 2a demonstrated short-term suppressive effects on PXR activity and CYP3A4 mRNA expression, likely mediated by activated NF-ĸB. Longer exposure enhanced CYP3A4 activity. Clinical trials should evaluate the relevance by investigating the temporal effects of IFN-α on CYP3A4 using a sensitive marker substrate.
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Affiliation(s)
| | | | | | | | - Johanna Weiss
- Department of Clinical Pharmacology and Pharmacoepidemiology, Heidelberg University Hospital, Im Neuenheimer Feld 410, 69120 Heidelberg, Germany; (D.T.); (L.W.); (C.B.); (W.E.H.)
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Theile D, Hohmann N, Kiemel D, Gattuso G, Barreca D, Mikus G, Haefeli WE, Schwenger V, Weiss J. Clementine juice has the potential for drug interactions – In vitro comparison with grapefruit and mandarin juice. Eur J Pharm Sci 2017; 97:247-256. [DOI: 10.1016/j.ejps.2016.11.021] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Revised: 11/07/2016] [Accepted: 11/19/2016] [Indexed: 02/07/2023]
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Klenke S, Renckhoff K, Engler A, Peters J, Frey UH. Easy-to-use strategy for reference gene selection in quantitative real-time PCR experiments. Naunyn Schmiedebergs Arch Pharmacol 2016; 389:1353-1366. [PMID: 27650728 DOI: 10.1007/s00210-016-1305-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Accepted: 09/09/2016] [Indexed: 12/19/2022]
Abstract
Real-time PCR is an indispensable technique for mRNA expression analysis but conclusions depend on appropriate reference gene selection. However, while reference gene selection has been a topic of publications, this issue is often disregarded when measuring target mRNA expression. Therefore, we (1) evaluated the frequency of appropriate reference gene selection, (2) suggest an easy-to-use tool for least variability reference gene selection, (3) demonstrate application of this tool, and (4) show effects on target gene expression profiles. All 2015 published articles in Naunyn-Schmiedeberg's Archives of Pharmacology were screened for the use of quantitative real-time PCR analysis and selection of reference genes. Target gene expression (Vegfa, Grk2, Sirt4, and Timp3) in H9c2 cells was analyzed following various interventions (hypoxia, hyperglycemia, and/or isoflurane exposure with and without subsequent hypoxia) in relation to putative reference genes (Actb, Gapdh, B2m, Sdha, and Rplp1) using the least variability method vs. an arbitrarily selected but established reference gene. In the vast majority (18 of 21) of papers, no information was provided regarding selection of an appropriate reference gene. In only 1 of 21 papers, a method of appropriate reference gene selection was described and in 2 papers reference gene selection remains unclear. The method of reference gene selection had major impact on interpretation of target gene expression. With hypoxia, for instance, the least variability gene was Rplp1 and target gene expression (Vefga) heavily showed a 2-fold up-regulation (p = 0.022) but no change (p = 0.3) when arbitrarily using Gapdh. Frequency of appropriate reference gene selection in this journal is low, and we propose our strategy for reference gene selection as an easy tool for proper target gene expression.
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Affiliation(s)
- Stefanie Klenke
- Klinik für Anästhesiologie & Intensivmedizin, Universität Duisburg-Essen and Universitätsklinikum Essen, Hufelandstr. 55, D-45122, Essen, Germany.
| | - Kristina Renckhoff
- Klinik für Anästhesiologie & Intensivmedizin, Universität Duisburg-Essen and Universitätsklinikum Essen, Hufelandstr. 55, D-45122, Essen, Germany
| | - Andrea Engler
- Klinik für Anästhesiologie & Intensivmedizin, Universität Duisburg-Essen and Universitätsklinikum Essen, Hufelandstr. 55, D-45122, Essen, Germany
| | - Jürgen Peters
- Klinik für Anästhesiologie & Intensivmedizin, Universität Duisburg-Essen and Universitätsklinikum Essen, Hufelandstr. 55, D-45122, Essen, Germany
| | - Ulrich H Frey
- Klinik für Anästhesiologie & Intensivmedizin, Universität Duisburg-Essen and Universitätsklinikum Essen, Hufelandstr. 55, D-45122, Essen, Germany
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Witte LPW, Teitsma CA, de la Rosette JJMCH, Michel MC. Muscarinic receptor subtype mRNA expression in the human prostate: association with age, pathological diagnosis, prostate size, or potentially interfering medications? Naunyn Schmiedebergs Arch Pharmacol 2013; 387:207-14. [PMID: 24193354 DOI: 10.1007/s00210-013-0934-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Accepted: 10/21/2013] [Indexed: 12/20/2022]
Abstract
As the prostate abundantly expresses muscarinic receptors and antagonists for such receptors are increasingly used in the treatment of men with voiding function and large prostates, we have explored an association of the mRNA expression of human M1, M2, M3, M4, and M5 receptors in human prostate with patient age, prostate size, prostate-specific antigen level, pathological diagnosis, and concomitant medication. mRNA was isolated from prostate chips of 110 consecutive patients undergoing transurethral resection of the prostate for the treatment of benign prostatic hyperplasia or prostate cancer. Expression of each of the five muscarinic receptor subtype transcripts was assessed by real-time PCR and association with patient age, prostate size, prostate-specific antigen level, pathological diagnosis, and concomitant medication were explored. M1 and M4 receptors were the most and least prevalently expressed subtypes in the human prostate, respectively. M1 receptor mRNA expression was weakly but significantly associated with prostate size (r = 0.2494, p = 0.0451), but mRNA expression of none of the five subtypes was significantly associated with age, prostate-specific antigen level, pathological diagnosis (benign prostatic hyperplasia vs. prostate cancer), or concomitant medication (5α-reductase inhibitors, α1- or β-adrenoceptor antagonists). We conclude that human prostate muscarinic receptor subtype transcripts apparently undergo only a very limited regulation by a variety of physiological, pathophysiological, or treatment factors. In light of the growing use of muscarinic receptor antagonists in men with voiding dysfunction including those with large prostates, the functional role of the weak association between M1 receptor mRNA expression and prostate size merits further investigation.
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Bollmann F, Casper I, Henke J, Pautz A. qRT-PCR: a method and its difficulties. NAUNYN-SCHMIEDEBERG'S ARCHIVES OF PHARMACOLOGY 2012; 385:949-51. [PMID: 22864909 DOI: 10.1007/s00210-012-0786-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Subscribe] [Scholar Register] [Received: 07/16/2012] [Accepted: 07/18/2012] [Indexed: 11/30/2022]
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