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El-Daly SM, Gouhar SA, Abd Elmageed ZY. Circulating microRNAs as Reliable Tumor Biomarkers: Opportunities and Challenges Facing Clinical Application. J Pharmacol Exp Ther 2023; 384:35-51. [PMID: 35809898 PMCID: PMC9827506 DOI: 10.1124/jpet.121.000896] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 06/23/2022] [Accepted: 06/24/2022] [Indexed: 01/13/2023] Open
Abstract
MicroRNAs (miRNAs) are involved in the development of human malignancies, and cells have the ability to secrete these molecules into extracellular compartments. Thus, cell-free miRNAs (circulating miRNAs) can potentially be used as biomarkers to evaluate pathophysiological changes. Although circulating miRNAs have been proposed as potential noninvasive tumor biomarkers for diagnosis, prognosis, and response to therapy, their routine application in the clinic is far from being achieved. This review focuses on the recent progress regarding the value of circulating miRNAs as noninvasive biomarkers, with specific consideration of their relevant clinical applications. In addition, we provide an in-depth analysis of the technical challenges that impact the assessment of circulating miRNAs. We also highlight the significance of integrating circulating miRNAs with the standard laboratory biomarkers to boost sensitivity and specificity. The current status of circulating miRNAs in clinical trials as tumor biomarkers is also covered. These insights and general guidelines will assist researchers in experimental practice to ensure quality standards and repeatability, thus improving future studies on circulating miRNAs. SIGNIFICANCE STATEMENT: Our review will boost the knowledge behind the inconsistencies and contradictory results observed among studies investigating circulating miRNAs. It will also provide a solid platform for better-planned strategies and standardized techniques to optimize the assessment of circulating cell-free miRNAs.
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Affiliation(s)
- Sherien M El-Daly
- Medical Biochemistry Department, Medicine and Clinical Studies Research Institute, National Research Centre, Dokki, Cairo, Egypt (S.M.E-D., S.A.G.); Cancer Biology and Genetics Laboratory, Centre of Excellence for Advanced Sciences, National Research Centre, Cairo, Egypt (S.M.E-D.); and Department of Biomedical Sciences, Discipline of Pharmacology, Edward Via College of Osteopathic Medicine, University of Louisiana-Monroe, Monroe, Louisiana (Z.Y.A.)
| | - Shaimaa A Gouhar
- Medical Biochemistry Department, Medicine and Clinical Studies Research Institute, National Research Centre, Dokki, Cairo, Egypt (S.M.E-D., S.A.G.); Cancer Biology and Genetics Laboratory, Centre of Excellence for Advanced Sciences, National Research Centre, Cairo, Egypt (S.M.E-D.); and Department of Biomedical Sciences, Discipline of Pharmacology, Edward Via College of Osteopathic Medicine, University of Louisiana-Monroe, Monroe, Louisiana (Z.Y.A.)
| | - Zakaria Y Abd Elmageed
- Medical Biochemistry Department, Medicine and Clinical Studies Research Institute, National Research Centre, Dokki, Cairo, Egypt (S.M.E-D., S.A.G.); Cancer Biology and Genetics Laboratory, Centre of Excellence for Advanced Sciences, National Research Centre, Cairo, Egypt (S.M.E-D.); and Department of Biomedical Sciences, Discipline of Pharmacology, Edward Via College of Osteopathic Medicine, University of Louisiana-Monroe, Monroe, Louisiana (Z.Y.A.)
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Larocque É, Lévesque V, Lambert D. Crystal digital RT-PCR for the detection and quantification of norovirus and hepatitis A virus RNA in frozen raspberries. Int J Food Microbiol 2022; 380:109884. [PMID: 36055105 DOI: 10.1016/j.ijfoodmicro.2022.109884] [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: 02/07/2022] [Revised: 08/17/2022] [Accepted: 08/18/2022] [Indexed: 10/31/2022]
Abstract
Berries are important vehicles for norovirus (NoV) and hepatitis A virus (HAV) foodborne outbreaks. Sensitive and quantitative detection of these viruses in food samples currently relies on RT-qPCR, but remains challenging due to their low concentration and the presence of RT-qPCR inhibitors. Moreover, quantification requires a standard curve. In this study, crystal digital RT-PCR (RT-cdPCR) assays were adapted from RT-qPCR sets of primers and probe currently used in our diagnostic laboratory for the detection and precise quantification of norovirus genogroups I and II (NoV GI, GII) and hepatitis A virus (HAV) RNA in frozen raspberry samples. We selected assay conditions based on optimal separation of positive and negative droplets, and peak resolution. Using virus-specific in vitro RNA transcripts diluted in raspberry RNA extracts, we showed that all three RT-cdPCR assays were sensitive, and we estimated the 95 % detection limit at 9 copies per RT-cdPCR reaction for NoV GI, 3 for NoV GII, and 14 for HAV. Serial dilutions of the RNA transcripts showed excellent linearity over a range of four orders of magnitude. We achieved precise quantification (CV ≤ 35 %) of the RNA transcripts between runs down to 15-145 copies per reaction for NoV GI, <20 for NoV GII, and < 15 for HAV. The three RT-cdPCR assays also proved to be tolerant to inhibitors from frozen raspberries, although not as tolerant as the RT-qPCR assays in the case of NoV GI and HAV. We further evaluated the assays with inoculated frozen raspberry samples and compared their performance to that of the RT-qPCR assays. As compared to the corresponding RT-qPCR assays, the NoV GI and HAV RT-cdPCR assays showed a decreased qualitative sensitivity, while the NoV GII RT-cdPCR assay had an increased sensitivity. As for quantification, the NoV GI and NoV GII RT-cdPCR assays produced similar estimates of RNA copy number than their respective RT-qPCR assays, whereas for HAV, the RT-cdPCR assay produced lower estimates than the RT-qPCR assay. However, all the RT-cdPCR assays provided more precise quantitative measurements at low levels of contamination than the RT-qPCR assays. In conclusion, the potential of the RT-cdPCR assays in this study to detect viral RNA from frozen raspberries varied according to assay, but these RT-cdPCR assays should be considered for precise absolute quantification in difficult matrices such as frozen raspberries.
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Affiliation(s)
- Émilie Larocque
- Food Virology National Reference Centre, St. Hyacinthe Laboratory, Canadian Food Inspection Agency (CFIA), 3400 Casavant Boulevard West, St. Hyacinthe, QC J2S 8E3, Canada.
| | - Valérie Lévesque
- Food Virology National Reference Centre, St. Hyacinthe Laboratory, Canadian Food Inspection Agency (CFIA), 3400 Casavant Boulevard West, St. Hyacinthe, QC J2S 8E3, Canada
| | - Dominic Lambert
- Food Virology National Reference Centre, St. Hyacinthe Laboratory, Canadian Food Inspection Agency (CFIA), 3400 Casavant Boulevard West, St. Hyacinthe, QC J2S 8E3, Canada
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3
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Considerations and Suggestions for the Reliable Analysis of miRNA in Plasma Using qRT-PCR. Genes (Basel) 2022; 13:genes13020328. [PMID: 35205372 PMCID: PMC8872398 DOI: 10.3390/genes13020328] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 02/08/2022] [Accepted: 02/08/2022] [Indexed: 12/12/2022] Open
Abstract
MicroRNAs (miRNAs) are promising molecules that can regulate gene expression, and their expression level and type have been associated with early diagnosis, targeted therapy, and prognosis of various diseases. Therefore, analysis of miRNA in the plasma or serum is useful for the discovery of biomarkers and the diagnosis of implicated diseases to achieve potentially unprecedented progress in early treatment. Numerous methods to improve sensitivity have recently been proposed and confirmed to be valuable in miRNA detection. Specifically, quantitative reverse-transcription polymerase chain reaction (qRT-PCR) is an effective and common method for sensitive and specific analysis of miRNA from biological fluids, such as plasma or serum. Despite this, the application of qRT-PCR is limited, as it can be affected by various contaminants. Therefore, extraction studies have been frequently conducted to maximize the extracted miRNA amount while simultaneously minimizing contaminants. Moreover, studies have evaluated extraction efficiency and normalization of the extracted sample. However, variability in results among laboratories still exists. In this review, we aimed to summarize the factors influencing the qualification and quantification of miRNAs in the plasma using qRT-PCR. Factors influencing reliable analysis of miRNA using qRT-PCR are described in detail. Additionally, we aimed to describe the importance of evaluating extraction and normalization for reliable miRNA analysis and to explore how miRNA detection accuracy, especially from plasma, can be improved.
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Unger C, Lokmer N, Lehmann D, Axmann IM. Detection of phenol contamination in RNA samples and its impact on qRT-PCR results. Anal Biochem 2019; 571:49-52. [PMID: 30742799 DOI: 10.1016/j.ab.2019.02.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 02/06/2019] [Accepted: 02/06/2019] [Indexed: 12/14/2022]
Abstract
Residual phenol, carried over from RNA purification, can alter RNA concentration measurements and is assumed to inhibit PCR. Here, we demonstrate that Impurities A260 values of spectral content profiling (SCP) UV/Vis measurements correlated with phenol concentration, whereas absorbance ratios of classical UV/Vis systems failed to reliably detect phenol in RNA samples. Phenol contamination led to over- or underestimation of RNA concentration on UV/Vis systems, whereas it had no influence on fluorometry quantification. Wrong RNA concentration results led to altered template input in qRT-PCR and consequently caused quantification cycle (Cq) shifts, although ≤ 0.01% phenol had no direct influence.
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Affiliation(s)
- Conny Unger
- QIAGEN GmbH, Qiagen Strasse 1, 40724, Hilden, Germany; Institute for Synthetic Microbiology, Heinrich Heine University Düsseldorf, Universitätsstraße 1, Düsseldorf, 40225, Germany.
| | - Nicole Lokmer
- QIAGEN GmbH, Qiagen Strasse 1, 40724, Hilden, Germany
| | | | - Ilka M Axmann
- Institute for Synthetic Microbiology, Heinrich Heine University Düsseldorf, Universitätsstraße 1, Düsseldorf, 40225, Germany
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Garcia-Elias A, Alloza L, Puigdecanet E, Nonell L, Tajes M, Curado J, Enjuanes C, Díaz O, Bruguera J, Martí-Almor J, Comín-Colet J, Benito B. Defining quantification methods and optimizing protocols for microarray hybridization of circulating microRNAs. Sci Rep 2017; 7:7725. [PMID: 28798363 PMCID: PMC5552704 DOI: 10.1038/s41598-017-08134-3] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Accepted: 07/05/2017] [Indexed: 12/22/2022] Open
Abstract
MicroRNAs (miRNAs) have emerged as promising biomarkers of disease. Their potential use in clinical practice requires standardized protocols with very low miRNA concentrations, particularly in plasma samples. Here we tested the most appropriate method for miRNA quantification and validated the performance of a hybridization platform using lower amounts of starting RNA. miRNAs isolated from human plasma and from a reference sample were quantified using four platforms and profiled with hybridization arrays and RNA sequencing (RNA-seq). Our results indicate that the Infinite® 200 PRO Nanoquant and Nanodrop 2000 spectrophotometers magnified the miRNA concentration by detecting contaminants, proteins, and other forms of RNA. The Agilent 2100 Bioanalyzer PicoChip and SmallChip gave valuable information on RNA profile but were not a reliable quantification method for plasma samples. The Qubit® 2.0 Fluorometer provided the most accurate quantification of miRNA content, although RNA-seq confirmed that only ~58% of small RNAs in plasma are true miRNAs. On the other hand, reducing the starting RNA to 70% of the recommended amount for miRNA profiling with arrays yielded results comparable to those obtained with the full amount, whereas a 50% reduction did not. These findings provide important clues for miRNA determination in human plasma samples.
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Affiliation(s)
- Anna Garcia-Elias
- Group of Biomedical Research in Heart Diseases, IMIM (Hospital del Mar Medical Research Institute), C/Doctor Aiguader 88, 08003, Barcelona, Spain.
| | - Leonor Alloza
- Microarray Analysis Service, IMIM (Hospital del Mar Medical Research Institute), C/Doctor Aiguader 88, 08003, Barcelona, Spain
| | - Eulàlia Puigdecanet
- Microarray Analysis Service, IMIM (Hospital del Mar Medical Research Institute), C/Doctor Aiguader 88, 08003, Barcelona, Spain
| | - Lara Nonell
- Microarray Analysis Service, IMIM (Hospital del Mar Medical Research Institute), C/Doctor Aiguader 88, 08003, Barcelona, Spain
| | - Marta Tajes
- Group of Biomedical Research in Heart Diseases, IMIM (Hospital del Mar Medical Research Institute), C/Doctor Aiguader 88, 08003, Barcelona, Spain
| | - Joao Curado
- Group of Biomedical Research in Heart Diseases, IMIM (Hospital del Mar Medical Research Institute), C/Doctor Aiguader 88, 08003, Barcelona, Spain.,Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader, 88, 08003, Barcelona, Spain.,Universitat Pompeu Fabra, C/Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Cristina Enjuanes
- Group of Biomedical Research in Heart Diseases, IMIM (Hospital del Mar Medical Research Institute), C/Doctor Aiguader 88, 08003, Barcelona, Spain.,Cardiology Department, Hospital del Mar, Passeig Marítim 25-29, 08003, Barcelona, Spain
| | - Oscar Díaz
- Cardiovascular Risk and Nutrition Group, IMIM (Hospital del Mar Medical Research Institute), C/Doctor Aiguader 88, 08003, Barcelona, Spain
| | - Jordi Bruguera
- Group of Biomedical Research in Heart Diseases, IMIM (Hospital del Mar Medical Research Institute), C/Doctor Aiguader 88, 08003, Barcelona, Spain.,Cardiology Department, Hospital del Mar, Passeig Marítim 25-29, 08003, Barcelona, Spain
| | - Julio Martí-Almor
- Group of Biomedical Research in Heart Diseases, IMIM (Hospital del Mar Medical Research Institute), C/Doctor Aiguader 88, 08003, Barcelona, Spain.,Cardiology Department, Hospital del Mar, Passeig Marítim 25-29, 08003, Barcelona, Spain
| | - Josep Comín-Colet
- Group of Biomedical Research in Heart Diseases, IMIM (Hospital del Mar Medical Research Institute), C/Doctor Aiguader 88, 08003, Barcelona, Spain.,Cardiology Department, Hospital del Mar, Passeig Marítim 25-29, 08003, Barcelona, Spain
| | - Begoña Benito
- Group of Biomedical Research in Heart Diseases, IMIM (Hospital del Mar Medical Research Institute), C/Doctor Aiguader 88, 08003, Barcelona, Spain.,Cardiology Department, Hospital del Mar, Passeig Marítim 25-29, 08003, Barcelona, Spain
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Lee JTY, Cheung KMC, Leung VYL. Systematic study of cell isolation from bovine nucleus pulposus: Improving cell yield and experiment reliability. J Orthop Res 2015; 33:1743-55. [PMID: 26036782 DOI: 10.1002/jor.22942] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Accepted: 05/08/2015] [Indexed: 02/04/2023]
Abstract
Differences in matrix compositions in human nucleus pulposus (NP) clinical samples demand different cell isolation protocols for optimal results but there is no clear guide about this to date. Sub-optimal protocols may result in low cell yield, limited reliability of results or even failure of experiments. Cell yield, viability and attachment of cells isolated from bovine NP tissue with different protocols were estimated by cell counting, Trypan blue staining and cell culturing respectively. RNA was extracted from isolated cells and quantified by Nanodrop spectrometry and RT-qPCR. Higher collagenase concentration, longer digestion duration and pronase pre-treatment increased the cell yield. Cell viability remained high (<5% dead cells) even after 0.2% collagenase treatment for overnight. NP cells remained to have high ACAN, COL2A1, CDH2, KRT18, and KRT19 expression compared to muscle cells for different cell isolation conditions tested. Digestion by collagenase alone without the use of pronase could isolate cells from human degenerated NP tissue but clusters of cells were observed. We suggest the use of the disappearance of tissue as an indirect measure of cells released. This study provides a guide for researchers to decide the parameters involved in NP cell isolation for optimal outcome.
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Affiliation(s)
- Juliana T Y Lee
- Department of Orthopaedics and Traumatology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Kenneth M C Cheung
- Department of Orthopaedics and Traumatology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Victor Y L Leung
- Department of Orthopaedics and Traumatology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
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Sanchez I, Remm M, Frasquilho S, Betsou F, Mathieson W. How Severely Is DNA Quantification Hampered by RNA Co-extraction? Biopreserv Biobank 2015; 13:320-4. [PMID: 26418169 DOI: 10.1089/bio.2015.0008] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The optional RNase digest that is part of many DNA extraction protocols is often omitted, either because RNase is not provided in the kit or because users do not want to risk contaminating their laboratory. Consequently, co-eluting RNA can become a "contaminant" of unknown magnitude in a DNA extraction. We extracted DNA from liver, lung, kidney, and heart tissues and established that 28-52% of the "DNA" as assessed by spectrophotometry is actually RNA (depending on tissue type). Including an RNase digest in the extraction protocol reduced 260:280 purity ratios. Co-eluting RNA drives an overestimation of DNA yield when quantification is carried out using OD 260 nm spectrophotometry, or becomes an unquantified contaminant when spectrofluorometry is used for DNA quantification. This situation is potentially incompatible with the best practice guidelines for biobanks issued by organizations such as the International Society for Biological and Environmental Repositories, which state that biospecimens should be accurately characterized in terms of their identity, purity, concentration, and integrity. Consequently, we conclude that an RNase digest must be included in DNA extractions if pure DNA is required. We also discuss the implications of unquantified RNA contamination in DNA samples in the context of laboratory accreditation schemes.
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Affiliation(s)
| | - Matthieu Remm
- 1 Integrated Biobank of Luxembourg , Luxembourg .,2 Departement Genie Biologique, University of Lorraine , Yutz, France
| | | | - Fay Betsou
- 1 Integrated Biobank of Luxembourg , Luxembourg
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