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Zhang H, Vandesompele J, Braeckmans K, De Smedt SC, Remaut K. Nucleic acid degradation as barrier to gene delivery: a guide to understand and overcome nuclease activity. Chem Soc Rev 2024; 53:317-360. [PMID: 38073448 DOI: 10.1039/d3cs00194f] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
Gene therapy is on its way to revolutionize the treatment of both inherited and acquired diseases, by transferring nucleic acids to correct a disease-causing gene in the target cells of patients. In the fight against infectious diseases, mRNA-based therapeutics have proven to be a viable strategy in the recent Covid-19 pandemic. Although a growing number of gene therapies have been approved, the success rate is limited when compared to the large number of preclinical and clinical trials that have been/are being performed. In this review, we highlight some of the hurdles which gene therapies encounter after administration into the human body, with a focus on nucleic acid degradation by nucleases that are extremely abundant in mammalian organs, biological fluids as well as in subcellular compartments. We overview the available strategies to reduce the biodegradation of gene therapeutics after administration, including chemical modifications of the nucleic acids, encapsulation into vectors and co-administration with nuclease inhibitors and discuss which strategies are applied for clinically approved nucleic acid therapeutics. In the final part, we discuss the currently available methods and techniques to qualify and quantify the integrity of nucleic acids, with their own strengths and limitations.
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Affiliation(s)
- Heyang Zhang
- Laboratory for General Biochemistry and Physical Pharmacy, Department of Pharmaceutical Sciences, Ghent University, 9000 Ghent, Belgium.
- Leiden Academic Centre for Drug Research, Leiden University, 2333 CC Leiden, The Netherlands
| | - Jo Vandesompele
- Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Kevin Braeckmans
- Laboratory for General Biochemistry and Physical Pharmacy, Department of Pharmaceutical Sciences, Ghent University, 9000 Ghent, Belgium.
- Centre for Nano- and Biophotonics, Ghent University, 9000 Ghent, Belgium
| | - Stefaan C De Smedt
- Laboratory for General Biochemistry and Physical Pharmacy, Department of Pharmaceutical Sciences, Ghent University, 9000 Ghent, Belgium.
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
- Centre for Nano- and Biophotonics, Ghent University, 9000 Ghent, Belgium
| | - Katrien Remaut
- Laboratory for General Biochemistry and Physical Pharmacy, Department of Pharmaceutical Sciences, Ghent University, 9000 Ghent, Belgium.
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
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2
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Benedetto A, Biasibetti E, Robotti E, Marengo E, Audino V, Bozzetta E, Pezzolato M. Transcriptional Biomarkers and Immunohistochemistry for Detection of Illicit Dexamethasone Administration in Veal Calves. Foods 2022; 11:foods11121810. [PMID: 35742008 PMCID: PMC9222442 DOI: 10.3390/foods11121810] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 06/10/2022] [Accepted: 06/14/2022] [Indexed: 02/05/2023] Open
Abstract
Corticosteroids such as Dexamethasone (DEX) are commonly licensed for therapy in meat animals due to their known pharmacological properties. However, their misuse aimed to achieve anabolic effects is often found by National Residues Control Plans. The setup of a complementary “biomarker based” methods to unveil such illicit practices is encouraged by current European legislation. In this study, the combined use of molecular and histological quantitative techniques was applied on formalin fixed paraffin embedded (FFPE) muscle samples to assess the effects of illicit DEX treatment on veal calves. A PCR array, including 28 transcriptional biomarkers related to DEX exposure, was combined with a histochemical analysis of muscle fiber. An analysis based on unsupervised (PCA) and supervised (PLS-DA and Kohonen’s SOM) methods, was applied in order to define multivariate models able to classify animals suspected of illicit treatment by DEX. According to the conventional univariate approach, a not-significant reduction in type I fibres was recorded in the DEX-treated group, and only 12 out of 28 targeted genes maintained their expected differential expression, confirming the technical limitations of a quantitative analysis on FFPE samples. However, the multivariate models developed highlighted the possibility to establish complementary screening strategies, particularly when based on transcriptional biomarkers characterised by low expression profiles.
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Affiliation(s)
- Alessandro Benedetto
- Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d’Aosta, Via Bologna 148, 10154 Torino, Italy; (A.B.); (V.A.); (E.B.); (M.P.)
| | - Elena Biasibetti
- Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d’Aosta, Via Bologna 148, 10154 Torino, Italy; (A.B.); (V.A.); (E.B.); (M.P.)
- Correspondence: (E.B.); (E.R.); Tel.: +39-0112686254 (E.B.); +39-1031360272 (E.R.)
| | - Elisa Robotti
- Department of Sciences and Technological Innovation, University of Piemonte Orientale, Viale Michel 11, 15121 Alessandria, Italy;
- Correspondence: (E.B.); (E.R.); Tel.: +39-0112686254 (E.B.); +39-1031360272 (E.R.)
| | - Emilio Marengo
- Department of Sciences and Technological Innovation, University of Piemonte Orientale, Viale Michel 11, 15121 Alessandria, Italy;
| | - Valentina Audino
- Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d’Aosta, Via Bologna 148, 10154 Torino, Italy; (A.B.); (V.A.); (E.B.); (M.P.)
| | - Elena Bozzetta
- Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d’Aosta, Via Bologna 148, 10154 Torino, Italy; (A.B.); (V.A.); (E.B.); (M.P.)
| | - Marzia Pezzolato
- Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d’Aosta, Via Bologna 148, 10154 Torino, Italy; (A.B.); (V.A.); (E.B.); (M.P.)
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Profiling of transcriptional biomarkers in FFPE liver samples: PLS-DA applications for detection of illicit administration of sex steroids and clenbuterol in veal calves. Food Control 2021. [DOI: 10.1016/j.foodcont.2021.108149] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Huggett JF. The Digital MIQE Guidelines Update: Minimum Information for Publication of Quantitative Digital PCR Experiments for 2020. Clin Chem 2021; 66:1012-1029. [PMID: 32746458 DOI: 10.1093/clinchem/hvaa125] [Citation(s) in RCA: 216] [Impact Index Per Article: 72.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 05/18/2020] [Indexed: 12/17/2022]
Abstract
Digital PCR (dPCR) has developed considerably since the publication of the Minimum Information for Publication of Digital PCR Experiments (dMIQE) guidelines in 2013, with advances in instrumentation, software, applications, and our understanding of its technological potential. Yet these developments also have associated challenges; data analysis steps, including threshold setting, can be difficult and preanalytical steps required to purify, concentrate, and modify nucleic acids can lead to measurement error. To assist independent corroboration of conclusions, comprehensive disclosure of all relevant experimental details is required. To support the community and reflect the growing use of dPCR, we present an update to dMIQE, dMIQE2020, including a simplified dMIQE table format to assist researchers in providing key experimental information and understanding of the associated experimental process. Adoption of dMIQE2020 by the scientific community will assist in standardizing experimental protocols, maximize efficient utilization of resources, and further enhance the impact of this powerful technology.
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Benedetto A, Biasibetti E, Beltramo C, Audino V, Peletto S, Bozzetta EM, Pezzolato M. Regucalcin expression profiles in veal calf testis: validation of histological and molecular tests to detect sex steroids illicit administration. PeerJ 2021; 9:e10894. [PMID: 33643712 PMCID: PMC7899017 DOI: 10.7717/peerj.10894] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 01/13/2021] [Indexed: 12/25/2022] Open
Abstract
Background Sex steroids administration in meat producing animals is forbidden within the EU to preserve consumers’ safety, but continuous monitoring to identify resurgence of their misuse is needed. Among biomarkers related to sex steroids abuse in veal calves the regucalcin (RGN) mRNA perturbations in testis have been described in RNAlater samples. To setup novel diagnostic method, to update current tests available in National Residue Control Plans (NRCPs) and in legal dispute when illicit practices on farm animals are suspected, the reliability of RGN profiling was assessed by histological and molecular techniques. Methods Formalin fixed paraffin embedded (FFPE) testis samples, chosen being the most effective preservation strategy adopted by histological NRCPs and allowing easier retrospective analysis if required by legal disputes, were analyzed from veal calves treated with nandrolone, 17β-estradiol and a cocktail of the two hormones. RGN levels were determined by quantitative Real Time PCR and Immunohistochemistry assays. Test performances were assessed and compared by multiple ROC curves. Results Both tests resulted sensitive and specific, allowing to enrich, in future field investigation, novel integrated diagnostic protocols needed to unveil sex steroid abuse. Discussion Developed RT-qPCR and IHC methods confirmed RGN as a useful and robust biomarker to detect illegal administration of sex steroid hormones in veal calves. The developed methods, successfully applied to ten years old FFPE blocks, could allow both retrospective analysis, when supplementary investigations are requested by authorities, and future implementation of current NRCPs.
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Affiliation(s)
- Alessandro Benedetto
- Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d'Aosta, Turin, Italy
| | - Elena Biasibetti
- Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d'Aosta, Turin, Italy
| | - Chiara Beltramo
- Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d'Aosta, Turin, Italy
| | - Valentina Audino
- Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d'Aosta, Turin, Italy
| | - Simone Peletto
- Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d'Aosta, Turin, Italy
| | - Elena Maria Bozzetta
- Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d'Aosta, Turin, Italy
| | - Marzia Pezzolato
- Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d'Aosta, Turin, Italy
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Fattorini P, Forzato C, Tierno D, De Martino E, Azzalini E, Canzonieri V, Stanta G, Bonin S. A Novel HPLC-Based Method to Investigate on RNA after Fixation. Int J Mol Sci 2020; 21:ijms21207540. [PMID: 33066070 PMCID: PMC7588918 DOI: 10.3390/ijms21207540] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 09/24/2020] [Accepted: 10/09/2020] [Indexed: 12/13/2022] Open
Abstract
RNA isolated from fixed and paraffin-embedded tissues is widely used in biomedical research and molecular pathology for diagnosis. In the present study, we have set-up a method based on high performance liquid chromatography (HPLC) to investigate the effects of different fixatives on RNA. By the application of the presented method, which is based on the Nuclease S1 enzymatic digestion of RNA extracts followed by a HPLC analysis, it is possible to quantify the unmodified nucleotide monophosphates (NMPs) in the mixture and recognize their hydroxymethyl derivatives as well as other un-canonical RNA moieties. The results obtained from a set of mouse livers fixed/embedded with different protocols as well from a set of clinical samples aged 0 to 30 years-old show that alcohol-based fixatives do not induce chemical modification of the nucleic acid under ISO standard recommendations and confirm that pre-analytical conditions play a major role in RNA preservation.
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Affiliation(s)
- Paolo Fattorini
- DSM-Department of Medical Sciences, University of Trieste, 34149 Trieste, Italy; (P.F.); (D.T.); (E.D.M.); (E.A.); (V.C.); (G.S.)
| | - Cristina Forzato
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, 34127 Trieste, Italy;
| | - Domenico Tierno
- DSM-Department of Medical Sciences, University of Trieste, 34149 Trieste, Italy; (P.F.); (D.T.); (E.D.M.); (E.A.); (V.C.); (G.S.)
- Doctorate of Nanotechnology, University of Trieste, 34100 Trieste, Italy
| | - Eleonora De Martino
- DSM-Department of Medical Sciences, University of Trieste, 34149 Trieste, Italy; (P.F.); (D.T.); (E.D.M.); (E.A.); (V.C.); (G.S.)
| | - Eros Azzalini
- DSM-Department of Medical Sciences, University of Trieste, 34149 Trieste, Italy; (P.F.); (D.T.); (E.D.M.); (E.A.); (V.C.); (G.S.)
| | - Vincenzo Canzonieri
- DSM-Department of Medical Sciences, University of Trieste, 34149 Trieste, Italy; (P.F.); (D.T.); (E.D.M.); (E.A.); (V.C.); (G.S.)
- Pathology Unit, IRCCS CRO Aviano-National Cancer Institute, 33081 Aviano, Italy
| | - Giorgio Stanta
- DSM-Department of Medical Sciences, University of Trieste, 34149 Trieste, Italy; (P.F.); (D.T.); (E.D.M.); (E.A.); (V.C.); (G.S.)
| | - Serena Bonin
- DSM-Department of Medical Sciences, University of Trieste, 34149 Trieste, Italy; (P.F.); (D.T.); (E.D.M.); (E.A.); (V.C.); (G.S.)
- Correspondence: ; Tel.: +39-040-399-3266
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Rochow H, Franz A, Jung M, Weickmann S, Ralla B, Kilic E, Stephan C, Fendler A, Jung K. Instability of circular RNAs in clinical tissue samples impairs their reliable expression analysis using RT-qPCR: from the myth of their advantage as biomarkers to reality. Am J Cancer Res 2020; 10:9268-9279. [PMID: 32802191 PMCID: PMC7415809 DOI: 10.7150/thno.46341] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 06/25/2020] [Indexed: 12/11/2022] Open
Abstract
Background: Circular RNAs (circRNAs) are a new class of RNAs with medical significance. Compared to that of linear mRNA transcripts, the stability of circRNAs against degradation owing to their circular structure is considered advantageous for their use as biomarkers. As systematic studies on the stability of circRNAs depending on the RNA integrity, determined as RNA integrity number (RIN), in clinical tissue samples are lacking, we have investigated this aspect in the present study under model and clinical conditions. Methods: Total RNA isolated from kidney cancer tissue and cell lines (A-498 and HEK-293) with different RIN after thermal degradation was used in model experiments. Further, RNA isolated from kidney cancer and prostate cancer tissue collected under routine surgical conditions, representing clinical samples with RIN ranging from 2 to 9, were examined. Quantitative real-time reverse-transcription polymerase chain reaction (RT-qPCR) analysis of several circRNAs (circEGLN3, circRHOBTB3, circCSNK1G3, circRNA4, and circRNA9), their corresponding linear counterparts, tissue-specific reference genes, and three microRNAs (as controls) was performed. The quantification cycles were converted into relative quantities and normalized to the expression of specific reference genes for the corresponding tissue. The effect of RIN on the expression of different RNA entities was determined using linear regression analysis, and clinical samples were classified into two groups based on RIN greater or lesser than 6. Results: The results of model experiments and clinical sample analyses showed that all relative circRNA expression gradually decreased with reduction in RIN values. The adverse effect of RIN was partially compensated after normalizing the data and limiting the samples to only those with RIN values > 6. Conclusions: Our results suggested that circRNAs are not stable in clinical tissue samples, but are subjected to degradative processes similar to mRNAs. This has not been investigated extensively in circRNA expression studies, and hence must be considered in future for obtaining reliable circRNA expression data. This can be achieved by applying the principles commonly used in mRNA expression studies.
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Benedetto A, Pezzolato M, Beltramo C, Audino V, Ingravalle F, Pillitteri C, Foschini S, Peletto S, Bozzetta E. Real-time PCR assay for detecting illicit steroid administration in veal calves allows reliable biomarker profiling of formalin-fixed, paraffin-embedded (FFPE) archival tissue samples. Food Chem 2020; 312:126061. [DOI: 10.1016/j.foodchem.2019.126061] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 11/14/2019] [Accepted: 12/13/2019] [Indexed: 11/30/2022]
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9
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Fattorini P, Bonin S, Marrubini G, Bertoglio B, Grignani P, Recchia E, Pitacco P, Zupanič Pajnič I, Sorçaburu-Ciglieri S, Previderè C. Highly degraded RNA can still provide molecular information: An in vitro approach. Electrophoresis 2020; 41:386-393. [PMID: 31967656 DOI: 10.1002/elps.201900200] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2019] [Revised: 01/13/2020] [Accepted: 01/15/2020] [Indexed: 01/01/2023]
Abstract
The long-term survival of RNA in postmortem tissues is a tricky topic. Many aged/forensic specimens show, in fact, high rates of null/inconclusive PCR-based results, while reliable outcomes were sometimes achieved from archaeological samples. On the other hand, several data show that the RNA is a molecule that survives even to several physical-chemical stresses. In the present study, a simple protocol, which was already developed for the prolonged hydrolysis of DNA, was applied to a RNA sample extracted from blood. This protocol is based on the heat-mediated (70°C) hydrolysis for up to 36 h using ultrapure water and di-ethyl-pyro-carbonate-water as hydrolysis medium. Measurable levels of depurination were not found even if microfluidic devices showed a progressive pattern of degradation. The reverse transcription/quantitative PCR analysis of two (60 bp long) housekeeping targets (glyceraldehyde-3-phosphate dehydrogenase and porphobilinogen deaminase) showed that the percentage of amplifiable target (%AT) decreased in relation to the duration of the damaging treatment (r2 > 0.973). The comparison of the %AT in the degraded RNA and in the DNA samples that underwent the same damaging treatment showed that the %AT is always higher in RNA, reaching up to three orders of magnitude. Lastly, even the end-point PCR of blood-specific markers gave reliable results, which is in agreement with the body fluid origin of the sample. In conclusion, all the PCR-based results show that RNA maintains the ability to be retro-transcribed in short cDNA fragments even after 36 h of incubation at 70°C in mildly acidic buffers. It is therefore likely that the long-term survival of RNA samples depends mainly on the protection against RNAase attacks rather than on environmental factors (such as humidity and acidity) that are instead of great importance for the stability of DNA. As a final remark, our results suggest that the RNA analysis can be successfully performed even when DNA profiling failed.
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Affiliation(s)
- Paolo Fattorini
- Department of Medicine, Surgery and Health, University of Trieste, Trieste, Italy
| | - Serena Bonin
- Department of Medicine, Surgery and Health, University of Trieste, Trieste, Italy
| | | | - Barbara Bertoglio
- Department of Public Health, Experimental and Forensic Medicine, Section of Legal Medicine and Forensic Sciences, University of Pavia, Pavia, Italy
| | - Pierangela Grignani
- Department of Public Health, Experimental and Forensic Medicine, Section of Legal Medicine and Forensic Sciences, University of Pavia, Pavia, Italy
| | - Elisa Recchia
- Department of Medicine, Surgery and Health, University of Trieste, Trieste, Italy
| | - Paola Pitacco
- Department of Medicine, Surgery and Health, University of Trieste, Trieste, Italy
| | - Irena Zupanič Pajnič
- Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | | | - Carlo Previderè
- Department of Public Health, Experimental and Forensic Medicine, Section of Legal Medicine and Forensic Sciences, University of Pavia, Pavia, Italy
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Cholet F, Ijaz UZ, Smith CJ. Differential ratio amplicons (R amp ) for the evaluation of RNA integrity extracted from complex environmental samples. Environ Microbiol 2019; 21:827-844. [PMID: 30585386 PMCID: PMC6392129 DOI: 10.1111/1462-2920.14516] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 12/07/2018] [Accepted: 12/20/2018] [Indexed: 12/31/2022]
Abstract
Reliability and reproducibility of transcriptomics‐based studies are dependent on RNA integrity. In microbial ecology, microfluidics‐based techniques, such as the Ribosomal Integrity Number (RIN), targeting rRNA are currently the only approaches to evaluate RNA integrity. However, the relationship between rRNA and mRNA integrity is unknown. Here, we present an integrity index, the Ratio Amplicon, Ramp, adapted from human clinical studies, to directly monitor mRNA integrity from complex environmental samples. We show, in a suite of experimental degradations of RNA extracted from sediment, that while the RIN generally reflected the degradation status of RNA the Ramp mapped mRNA degradation better. Furthermore, we examined the effect of degradation on transcript community structure by amplicon sequencing of 16S rRNA, amoA and glnA transcripts. We successfully sequenced transcripts for all three targets even from highly‐degraded RNA samples. While RNA degradation changed the community structure of the mRNA profiles, no changes were observed for the 16S rRNA transcript profiles. Since both RT‐Q‐PCR and sequencing results were obtained, even from highly degraded samples, we strongly recommend evaluating RNA integrity prior to downstream processing to ensure meaningful results. For this, both the RIN and Ramp are useful, with the Ramp better evaluating mRNA integrity in this study.
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Affiliation(s)
- Fabien Cholet
- Infrastructure and Environment Research Division, School of Engineering, University of Glasgow, Glasgow, G12 8LT, UK
| | - Umer Z Ijaz
- Infrastructure and Environment Research Division, School of Engineering, University of Glasgow, Glasgow, G12 8LT, UK
| | - Cindy J Smith
- Infrastructure and Environment Research Division, School of Engineering, University of Glasgow, Glasgow, G12 8LT, UK
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11
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Padhi BK, Singh M, Rosales M, Pelletier G, Cakmak S. A PCR-based quantitative assay for the evaluation of mRNA integrity in rat samples. BIOMOLECULAR DETECTION AND QUANTIFICATION 2018; 15:18-23. [PMID: 29922590 PMCID: PMC6006387 DOI: 10.1016/j.bdq.2018.02.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/03/2017] [Revised: 02/23/2018] [Accepted: 02/27/2018] [Indexed: 01/22/2023]
Abstract
Reverse Transcription quantitative real-time PCR (RT-qPCR) is applied to quantify gene transcript levels in a wide range of investigations. Proper assessment of RNA integrity is essential for reliable assessment of gene expression levels, as RNA molecules are acutely vulnerable to degradation. However, RNA quality control measures are still infrequently reported in rat toxicological studies, which impede proper evaluation of gene expression data reliability. The high operational cost of microfluidic capillary electrophoresis systems along with paucity of alternative methods for the quantitative assessment of rat RNA integrity constitute potential hurdles to the systematic implementation and reporting of RNA integrity assessment in rat studies. This manuscript describes the adaptation of an alternative RT-qPCR-based 3':5' assay as an additional option for the quantitative assessment of rat RNA integrity. Two PCR primer sets were designed on the 3' and 5' regions of a rat housekeeping gene to evaluate RNA integrity by measuring the relative expression (3':5' ratio) of these amplicons. The 3':5' ratios were then compared to Agilent Bioanalyzer's RNA integrity number (RIN) for a wide range of RNA samples originating from different tissues, cultured cell lines and rat strains that were prepared freshly, stored for years at -80 °C, purchased commercially or intentionally degraded. The 3':5' ratios and RIN values presented similar assessment of RNA integrity status from intact to heavily degraded samples. Based on the LOWESS regression of this large comparison dataset, 3':5' ratio threshold criteria equivalent to RIN cut-off values can be proposed for the selection of RNA samples for RT-qPCR analyses. This qPCR-based assay is easy to implement, cost-effective, and provides a reliable quantification of RNA integrity to assist in the selection of rat RNA samples suitable for downstream RT-qPCR gene expression analyses.
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Affiliation(s)
- Bhaja K. Padhi
- Hazard Identification Division, Environmental Health Science and Research Bureau, Health Canada, Ottawa, Ontario, K1A 0K9, Canada
- Corresponding author at: 50 Colombine driveway, P.L. 0803B, Ottawa, Ontario, K1A 0K9, Canada.
| | - Manjeet Singh
- Hazard Identification Division, Environmental Health Science and Research Bureau, Health Canada, Ottawa, Ontario, K1A 0K9, Canada
| | - Marianela Rosales
- Hazard Identification Division, Environmental Health Science and Research Bureau, Health Canada, Ottawa, Ontario, K1A 0K9, Canada
| | - Guillaume Pelletier
- Hazard Identification Division, Environmental Health Science and Research Bureau, Health Canada, Ottawa, Ontario, K1A 0K9, Canada
| | - Sabit Cakmak
- Population Studies Division, Environmental Health Science and Research Bureau, Health Canada, Ottawa, Ontario, K1A 0K9, Canada
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12
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White K, Yang P, Li L, Farshori A, Medina AE, Zielke HR. Effect of Postmortem Interval and Years in Storage on RNA Quality of Tissue at a Repository of the NIH NeuroBioBank. Biopreserv Biobank 2018; 16:148-157. [PMID: 29498539 PMCID: PMC5906728 DOI: 10.1089/bio.2017.0099] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Brain tissue from 1068 donors was analyzed for RNA quality as a function of postmortem interval (PMI) and years in storage. Approximately 83% of the cortical and cerebellar samples had an RNA integrity number (RIN) of 6 or greater, indicating their likely suitability for real-time quantitative polymerase chain reaction research. The average RIN value was independent of the PMI, up to at least 36 hours. The RNA quality for specific donated brains could not be predicted based on the PMI. Individual samples with a low PMI could have a poor RIN value, while a sample with a PMI over 36 hours may have a high RIN value. The RIN values for control brain donors, all of whom died suddenly and unexpectedly, were marginally higher than for individuals with clinical brain disorders. Polymerase chain reaction (PCR) analysis of samples confirmed that RIN values were more critical than PMI for determining suitability of tissue for molecular biological studies and samples should be matched by their RIN values rather than PMI. Importantly, PCR analysis established that tissue stored up to 23 years at −80°C yielded high-quality RNA. These results confirm that postmortem human brain tissue collected by brain and tissue banks over decades can serve as high quality material for the study of human disorders.
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Affiliation(s)
- Kimberly White
- 1 Department of Pediatrics, University of Maryland School of Medicine , Baltimore, Maryland
| | - Peixin Yang
- 2 Department of Obstetrics and Gynecology, University of Maryland School of Medicine , Baltimore, Maryland
| | - Ling Li
- 1 Department of Pediatrics, University of Maryland School of Medicine , Baltimore, Maryland.,3 Office of the Chief Medical Examiner, Baltimore, Maryland
| | - Amna Farshori
- 4 Degree Program in Osteopathic Medicine, Edward Via College of Osteopathic Medicine , Blacksburg, Virginia
| | - Alexandre E Medina
- 1 Department of Pediatrics, University of Maryland School of Medicine , Baltimore, Maryland
| | - Horst Ronald Zielke
- 1 Department of Pediatrics, University of Maryland School of Medicine , Baltimore, Maryland
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Baena-Del Valle JA, Zheng Q, Hicks JL, Fedor H, Trock BJ, Morrissey C, Corey E, Cornish TC, Sfanos KS, De Marzo AM. Rapid Loss of RNA Detection by In Situ Hybridization in Stored Tissue Blocks and Preservation by Cold Storage of Unstained Slides. Am J Clin Pathol 2017; 148:398-415. [PMID: 29106457 DOI: 10.1093/ajcp/aqx094] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVES Recent commercialization of methods for in situ hybridization using Z-pair probe/branched DNA amplification has led to increasing adoption of this technology for interrogating RNA expression in formalin-fixed, paraffin-embedded (FFPE) tissues. Current practice for FFPE block storage is to maintain them at room temperature, often for many years. METHODS To examine the effects of block storage time on FFPE tissues using a number of RNA in situ probes with the Advanced Cellular Diagnostic's RNAscope assay. RESULTS We report marked reductions in signals after 5 years and significant reductions often after 1 year. Furthermore, storing unstained slides cut from recent cases (<1 year old) at -20°C can preserve hybridization signals significantly better than storing the blocks at room temperature and cutting the slides fresh when needed. CONCLUSIONS We submit that the standard practice of storing FFPE tissue blocks at room temperature should be reevaluated to better preserve RNA for in situ hybridization.
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Affiliation(s)
- Javier A Baena-Del Valle
- From the Department of Pathology
- Department of Pathology and Laboratory Medicine, Fundacion Santa Fe de Bogota University Hospital, Bogota DC, Colombia
| | | | | | | | - Bruce J Trock
- Departments of Urology and Oncology
- Sidney Kimmel Comprehensive Cancer Center
- The Brady Urological Research Institute, The Johns Hopkins University School of Medicine, Baltimore, MD
| | - Colm Morrissey
- Department of Urology, University of Washington, Seattle
| | - Eva Corey
- Department of Urology, University of Washington, Seattle
| | - Toby C Cornish
- From the Department of Pathology
- Department of Pathology, University of Colorado School of Medicine, Aurora
| | - Karen S Sfanos
- From the Department of Pathology
- Departments of Urology and Oncology
- Sidney Kimmel Comprehensive Cancer Center
- The Brady Urological Research Institute, The Johns Hopkins University School of Medicine, Baltimore, MD
| | - Angelo M De Marzo
- From the Department of Pathology
- Departments of Urology and Oncology
- Sidney Kimmel Comprehensive Cancer Center
- The Brady Urological Research Institute, The Johns Hopkins University School of Medicine, Baltimore, MD
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14
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Doucet M, Becker KF, Björkman J, Bonnet J, Clément B, Daidone MG, Duyckaerts C, Erb G, Haslacher H, Hofman P, Huppertz B, Junot C, Lundeberg J, Metspalu A, Lavitrano M, Litton JE, Moore HM, Morente M, Naimi BY, Oelmueller U, Ollier B, Parodi B, Ruan L, Stanta G, Turano P, Vaught J, Watson P, Wichmann HE, Yuille M, Zaomi M, Zatloukal K, Dagher G. Quality Matters: 2016 Annual Conference of the National Infrastructures for Biobanking. Biopreserv Biobank 2016; 15:270-276. [PMID: 27992240 DOI: 10.1089/bio.2016.0053] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Affiliation(s)
- Marika Doucet
- 1 BIOBANQUES Infrastructure, Inserm US13, Hôpital de la Pitié Salpêtrière , Paris, France
| | | | | | - Jacques Bonnet
- 4 Inserm U916, Institut Bergonié, Université de Bordeaux , Bordeaux, France
| | - Bruno Clément
- 1 BIOBANQUES Infrastructure, Inserm US13, Hôpital de la Pitié Salpêtrière , Paris, France .,5 Inserm UMR991, Rennes, France
| | | | | | | | | | - Paul Hofman
- 1 BIOBANQUES Infrastructure, Inserm US13, Hôpital de la Pitié Salpêtrière , Paris, France .,10 Hospital-Integrated Biobank (BB-0033-00025), FHU OncoAge, University of Nice Sophia Antipolis , Nice, France
| | | | | | - Joakim Lundeberg
- 13 Science for Life Laboratory, KTH Royal Institute of Technology , Stockholm, Sweden
| | - Andres Metspalu
- 14 Estonian Genome Center, University of Tartu , Tartu, Estonia
| | | | | | - Helen M Moore
- 17 National Cancer Institute Biorepositories and Biospecimen Research Branch (BBRB) , Rockville, Maryland
| | - Manuel Morente
- 18 Biobank Unit of the Spanish national cancer center (CNIO) , Madrid, Spain
| | | | | | - Bill Ollier
- 21 University of Manchester , Manchester, United Kingdom
| | - Barbara Parodi
- 22 Biological Resource Center of the National Institute for Cancer Research (IRCCS AOU San Martino-IST) , Genoa, Italy
| | | | | | | | - Jim Vaught
- 26 International Society for Biological and Environmental Repositories (ISBER) , Bethesda, Maryland
| | - Peter Watson
- 27 British Columbia Cancer Agency's Vancouver Island Cancer Center , Victoria, Canada
| | - H-Erich Wichmann
- 28 Helmholtz Zentrum München, Institute of Epidemiology II , Munich, Germany
| | - Martin Yuille
- 21 University of Manchester , Manchester, United Kingdom
| | - Myriam Zaomi
- 1 BIOBANQUES Infrastructure, Inserm US13, Hôpital de la Pitié Salpêtrière , Paris, France
| | | | - Georges Dagher
- 1 BIOBANQUES Infrastructure, Inserm US13, Hôpital de la Pitié Salpêtrière , Paris, France
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15
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Korenkova V, Slyskova J, Novosadova V, Pizzamiglio S, Langerova L, Bjorkman J, Vycital O, Liska V, Levy M, Veskrna K, Vodicka P, Vodickova L, Kubista M, Verderio P. The focus on sample quality: Influence of colon tissue collection on reliability of qPCR data. Sci Rep 2016; 6:29023. [PMID: 27383461 PMCID: PMC4935944 DOI: 10.1038/srep29023] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Accepted: 06/14/2016] [Indexed: 01/12/2023] Open
Abstract
Successful molecular analyses of human solid tissues require intact biological material with well-preserved nucleic acids, proteins, and other cell structures. Pre-analytical handling, comprising of the collection of material at the operating theatre, is among the first critical steps that influence sample quality. The aim of this study was to compare the experimental outcomes obtained from samples collected and stored by the conventional means of snap freezing and by PAXgene Tissue System (Qiagen). These approaches were evaluated by measuring rRNA and mRNA integrity of the samples (RNA Quality Indicator and Differential Amplification Method) and by gene expression profiling. The collection procedures of the biological material were implemented in two hospitals during colon cancer surgery in order to identify the impact of the collection method on the experimental outcome. Our study shows that the pre-analytical sample handling has a significant effect on the quality of RNA and on the variability of qPCR data. PAXgene collection mode proved to be more easily implemented in the operating room and moreover the quality of RNA obtained from human colon tissues by this method is superior to the one obtained by snap freezing.
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Affiliation(s)
- Vlasta Korenkova
- Institute of Biotechnology, BIOCEV Centre, Czech Academy of Sciences, Průmyslová 595, 252 42, Vestec u Prahy, Czech Republic
| | - Jana Slyskova
- Institute of Experimental Medicine, Czech Academy of Sciences, Prague, Czech Republic
| | - Vendula Novosadova
- Institute of Biotechnology, BIOCEV Centre, Czech Academy of Sciences, Průmyslová 595, 252 42, Vestec u Prahy, Czech Republic
| | - Sara Pizzamiglio
- Unit of Medical Statistics, Biometry and Bioinformatics, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Istituto Nazionale dei Tumori, Milan, Italy
| | - Lucie Langerova
- Institute of Biotechnology, BIOCEV Centre, Czech Academy of Sciences, Průmyslová 595, 252 42, Vestec u Prahy, Czech Republic
| | | | - Ondrej Vycital
- Deparment of Surgery, Teaching Hospital and Medical School Pilsen, Charles University in Prague, Pilsen, Czech Republic.,Biomedical Centre, Medical School Pilsen, Charles University in Prague, Pilsen, Czech Republic
| | - Vaclav Liska
- Deparment of Surgery, Teaching Hospital and Medical School Pilsen, Charles University in Prague, Pilsen, Czech Republic.,Biomedical Centre, Medical School Pilsen, Charles University in Prague, Pilsen, Czech Republic
| | - Miroslav Levy
- Surgical Department, Thomayer Hospital, First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Karel Veskrna
- Surgical Department, Thomayer Hospital, First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Pavel Vodicka
- Institute of Experimental Medicine, Czech Academy of Sciences, Prague, Czech Republic.,Biomedical Centre, Medical School Pilsen, Charles University in Prague, Pilsen, Czech Republic.,Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Ludmila Vodickova
- Institute of Experimental Medicine, Czech Academy of Sciences, Prague, Czech Republic.,Biomedical Centre, Medical School Pilsen, Charles University in Prague, Pilsen, Czech Republic.,Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Mikael Kubista
- Institute of Biotechnology, BIOCEV Centre, Czech Academy of Sciences, Průmyslová 595, 252 42, Vestec u Prahy, Czech Republic.,TATAA Biocenter AB, Göteborg, Sweden
| | - Paolo Verderio
- Unit of Medical Statistics, Biometry and Bioinformatics, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Istituto Nazionale dei Tumori, Milan, Italy
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16
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Karlsson O, Segerström L, Sjöback R, Nylander I, Borén M. qPCR based mRNA quality score show intact mRNA after heat stabilization. BIOMOLECULAR DETECTION AND QUANTIFICATION 2016; 7:21-6. [PMID: 27077049 PMCID: PMC4827693 DOI: 10.1016/j.bdq.2016.01.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Revised: 01/21/2016] [Accepted: 01/26/2016] [Indexed: 11/29/2022]
Abstract
Analysis of multiple analytes from biological samples can be challenging as different analytes require different preservation measures. Heat induced enzymatic inactivation is an efficient way to preserve proteins and their modifications in biological samples but RNA quality, as measured by RIN value, has been a concern in such samples. Here, we investigate the effect of heat stabilization compared with standard snap freezing on RNA quality using two RNA extraction protocols, QiaZol with and without urea pre-solubilization, and two RNA quality measurements: RIN value, as defined by the Agilent Bioanalyzer, and an alternative qPCR based method. DNA extraction from heat stabilized brain samples was also examined. The snap frozen samples had RIN values about 1 unit higher than heat stabilized samples for the direct QiaZol extraction but equal with stabilized samples using urea pre-solubilization. qPCR based RNA quality measurement showed no difference in quality between snap frozen and heat inactivated samples. The probable explanation for this discrepancy is that the RIN value is an indirect measure based on rRNA, while the qPCR score is based on actual measurement of mRNA quality. The DNA yield from heat stabilized brain tissue samples was significantly increased, compared to the snap frozen tissue, without any effects on purity or quality. Hence, heat stabilization of tissues opens up the possibility for a two step preservation protocol, where proteins and their modifications can be preserved in the first heat based step, while in a second step, using standard RNA preservation strategies, mRNA be preserved. This collection strategy will enable biobanking of samples where the ultimate analysis is not determined without loss of sample quality.
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Affiliation(s)
- Oskar Karlsson
- Department of Clinical Neuroscience, Karolinska Institutet, The Center for Molecular Medicine, Stockholm, Sweden
| | - Lova Segerström
- Department of Pharmaceutical Biosciences/Pharmacology/Neuropharmacology, Addiction & Behavior, Uppsala University, Uppsala, Sweden
| | | | - Ingrid Nylander
- Department of Pharmaceutical Biosciences/Pharmacology/Neuropharmacology, Addiction & Behavior, Uppsala University, Uppsala, Sweden
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