1
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Shibayama S, Osumi Y, Takatsu A, Kato M. Identification and optimization of parameters for accurate quantification of RNA by RT-dPCR. Anal Bioanal Chem 2024:10.1007/s00216-024-05447-x. [PMID: 39046502 DOI: 10.1007/s00216-024-05447-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Revised: 06/28/2024] [Accepted: 07/02/2024] [Indexed: 07/25/2024]
Abstract
Reverse transcription-digital PCR (RT-dPCR) is attracting attention as a method that enables SI-traceable RNA quantification without calibration, but its accuracy and bias have not been thoroughly studied. In this study, the accurate quantification of RNA by the RT-dPCR method was investigated using NMIJ CRM 6204-b, an RNA certified reference material whose certified value was assigned by orthogonal chemical measurement methods. Moreover, a two-step RT-dPCR method was adopted to examine in detail the conditions for the RT reaction process, which was expected to be the major uncertainty component in the RT-dPCR measurement. Optimization experiments revealed that the type of reverse transcriptase, the concentration of template RNA, and the type and concentration of primers in the RT reaction affected the value quantified by RT-dPCR. Under the optimal conditions, the value quantified by RT-dPCR, 76.4 ng/μL ± 6.7 ng/μL (the quantified value ± expanded uncertainty (k = 2)), was consistent with the certified value, 68.2 ng/μL ± 5.8 ng/μL, of NMIJ CRM 6204-b RNA 1000-A within the expanded uncertainty. From the results of the uncertainty evaluation, the relative combined uncertainty of the RT-dPCR method was 4.42%, and the major uncertainty components in the RT-dPCR method were the preparation of RT solution (3.68%), the inter-day difference (1.80%), and the RT reaction (1.30%). Together, the results suggested that the contribution of the RT reaction process to the total uncertainty was greater than that of the dPCR process.
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Affiliation(s)
- Sachie Shibayama
- National Metrology Institute of Japan (NMIJ), National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan.
| | - Yukiko Osumi
- National Metrology Institute of Japan (NMIJ), National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
| | - Akiko Takatsu
- National Metrology Institute of Japan (NMIJ), National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
| | - Megumi Kato
- National Metrology Institute of Japan (NMIJ), National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
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2
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Micheel J, Safrastyan A, Aron F, Wollny D. Exploring the impact of primer length on efficient gene detection via high-throughput sequencing. Nat Commun 2024; 15:5858. [PMID: 38997264 PMCID: PMC11245535 DOI: 10.1038/s41467-024-49685-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 06/14/2024] [Indexed: 07/14/2024] Open
Abstract
Reverse transcription (RT) is a crucial step in most RNA analysis methods. Optimizing protocols for this initial stage is critical for effective target detection, particularly when working with limited input RNA. Several factors, such as the input material quality and reaction conditions, influence RT efficiency. However, the effect of RT primer length on gene detection efficiency remains largely unknown. Thus, we investigate its impact by generating RNA-seq libraries with random RT primers of 6, 12, 18, or 24 nucleotides. To our surprise, the 18mer primer shows superior efficiency in overall transcript detection compared to the commonly used 6mer primer, especially in detecting longer RNA transcripts in complex human tissue samples. This study highlights the critical role of primer length in RT efficiency, which has significant potential to benefit various transcriptomic assays, from basic research to clinical diagnostics, given the central role of RT in RNA-related analyses.
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Affiliation(s)
- Julia Micheel
- RNA Bioinformatics and High Throughput Analysis, Friedrich Schiller University, Jena, Germany
- Leibniz Institute on Aging-Fritz Lipmann Institute (FLI), Jena, Germany
| | - Aram Safrastyan
- RNA Bioinformatics and High Throughput Analysis, Friedrich Schiller University, Jena, Germany
- Leibniz Institute on Aging-Fritz Lipmann Institute (FLI), Jena, Germany
| | - Franziska Aron
- RNA Bioinformatics and High Throughput Analysis, Friedrich Schiller University, Jena, Germany
- Leibniz Institute on Aging-Fritz Lipmann Institute (FLI), Jena, Germany
| | - Damian Wollny
- RNA Bioinformatics and High Throughput Analysis, Friedrich Schiller University, Jena, Germany.
- Leibniz Institute on Aging-Fritz Lipmann Institute (FLI), Jena, Germany.
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
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3
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Gao N, Huo Y, Yu D, Cheng F, Wang T, Zhang X, Zhang L, Hu W, Li J, Yuan P, Liu J, Wang Y, Yan J. Evaluation of reverse transcription yield of RNA standards and forensic samples based on droplet digital PCR. Biochem Biophys Res Commun 2024; 711:149909. [PMID: 38615573 DOI: 10.1016/j.bbrc.2024.149909] [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] [Received: 03/24/2024] [Accepted: 04/05/2024] [Indexed: 04/16/2024]
Abstract
RNA analysis has shown great value in forensic science, such as body fluids and tissue identification, postmortem interval estimation, biological age prediction, etc. Currently, most RNA follow-up experiments involve reverse transcription (RT) procedures. It has been shown that the RT step is variable and has a greater impact on subsequent data analysis, especially for forensic trace samples. However, the pattern of variation between different RNA template inputs and complementary DNA (cDNA) yield is unclear. In this study, a series of 2-fold gradient dilutions of RNA standards (1 μg/μL - 0.24 ng/μL) and forensic samples (including blood samples, saliva samples, bloodstains, and saliva stains) were reverse-transcribed using EasyQuick RT MasterMix. The obtained cDNA was quantified by droplet digital PCR (ddPCR) to assess the RT yield of the ACTB gene. The results showed that the 125 ng RNA template had the highest RT yield in a 10 μL RT reaction system with the selected kit. For all stain samples, the RT yield improved as the amount of RNA template input increased since RNA quantities were below 125 ng. As many commercialized reverse transcription kits using different kinds of enzymes are available for forensic RNA research, we recommend that systematic experiments should be performed in advance to determine the amount of RNA input at the optimum RT yield when using any kit for reverse transcription experiments.
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Affiliation(s)
- Niu Gao
- School of Forensic Medicine, Shanxi Medical University, No. 55 Wenhua Street, Yuci District, Jinzhong, Shanxi, China; Shanxi Key Laboratory of Forensic Medicine, Yuci District, Jinzhong, Shanxi, China
| | - Yumei Huo
- School of Forensic Medicine, Shanxi Medical University, No. 55 Wenhua Street, Yuci District, Jinzhong, Shanxi, China; Shanxi Key Laboratory of Forensic Medicine, Yuci District, Jinzhong, Shanxi, China
| | - Daijing Yu
- School of Forensic Medicine, Shanxi Medical University, No. 55 Wenhua Street, Yuci District, Jinzhong, Shanxi, China; Shanxi Key Laboratory of Forensic Medicine, Yuci District, Jinzhong, Shanxi, China
| | - Feng Cheng
- School of Forensic Medicine, Shanxi Medical University, No. 55 Wenhua Street, Yuci District, Jinzhong, Shanxi, China; Shanxi Key Laboratory of Forensic Medicine, Yuci District, Jinzhong, Shanxi, China
| | - Tian Wang
- School of Forensic Medicine, Shanxi Medical University, No. 55 Wenhua Street, Yuci District, Jinzhong, Shanxi, China; Shanxi Key Laboratory of Forensic Medicine, Yuci District, Jinzhong, Shanxi, China
| | - Xiaomeng Zhang
- School of Forensic Medicine, Shanxi Medical University, No. 55 Wenhua Street, Yuci District, Jinzhong, Shanxi, China; Shanxi Key Laboratory of Forensic Medicine, Yuci District, Jinzhong, Shanxi, China
| | - Liwei Zhang
- School of Forensic Medicine, Shanxi Medical University, No. 55 Wenhua Street, Yuci District, Jinzhong, Shanxi, China; Shanxi Key Laboratory of Forensic Medicine, Yuci District, Jinzhong, Shanxi, China
| | - Wenjing Hu
- School of Forensic Medicine, Shanxi Medical University, No. 55 Wenhua Street, Yuci District, Jinzhong, Shanxi, China; Shanxi Key Laboratory of Forensic Medicine, Yuci District, Jinzhong, Shanxi, China
| | - Junli Li
- School of Forensic Medicine, Shanxi Medical University, No. 55 Wenhua Street, Yuci District, Jinzhong, Shanxi, China; Shanxi Key Laboratory of Forensic Medicine, Yuci District, Jinzhong, Shanxi, China
| | - Piao Yuan
- School of Forensic Medicine, Shanxi Medical University, No. 55 Wenhua Street, Yuci District, Jinzhong, Shanxi, China; Shanxi Key Laboratory of Forensic Medicine, Yuci District, Jinzhong, Shanxi, China
| | - Jinding Liu
- School of Forensic Medicine, Shanxi Medical University, No. 55 Wenhua Street, Yuci District, Jinzhong, Shanxi, China; Shanxi Key Laboratory of Forensic Medicine, Yuci District, Jinzhong, Shanxi, China.
| | - Yan Wang
- School of Forensic Medicine, Shanxi Medical University, No. 55 Wenhua Street, Yuci District, Jinzhong, Shanxi, China; Shanxi Key Laboratory of Forensic Medicine, Yuci District, Jinzhong, Shanxi, China; Clinical Biobank Center, Medical Innovation Research Division of Chinese, PLA General Hospital, Beijing, China.
| | - Jiangwei Yan
- School of Forensic Medicine, Shanxi Medical University, No. 55 Wenhua Street, Yuci District, Jinzhong, Shanxi, China; Shanxi Key Laboratory of Forensic Medicine, Yuci District, Jinzhong, Shanxi, China.
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4
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Luna Santamaría M, Andersson D, Parris TZ, Helou K, Österlund T, Ståhlberg A. Digital RNA sequencing using unique molecular identifiers enables ultrasensitive RNA mutation analysis. Commun Biol 2024; 7:249. [PMID: 38429519 PMCID: PMC10907754 DOI: 10.1038/s42003-024-05955-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 02/22/2024] [Indexed: 03/03/2024] Open
Abstract
Mutation analysis is typically performed at the DNA level since most technical approaches are developed for DNA analysis. However, some applications, like transcriptional mutagenesis, RNA editing and gene expression analysis, require RNA analysis. Here, we combine reverse transcription and digital DNA sequencing to enable low error digital RNA sequencing. We evaluate yield, reproducibility, dynamic range and error correction rate for seven different reverse transcription conditions using multiplexed assays. The yield, reproducibility and error rate vary substantially between the specific conditions, where the yield differs 9.9-fold between the best and worst performing condition. Next, we show that error rates similar to DNA sequencing can be achieved for RNA using appropriate reverse transcription conditions, enabling detection of mutant allele frequencies <0.1% at RNA level. We also detect mutations at both DNA and RNA levels in tumor tissue using a breast cancer panel. Finally, we demonstrate that digital RNA sequencing can be applied to liquid biopsies, analyzing cell-free gene transcripts. In conclusion, we demonstrate that digital RNA sequencing is suitable for ultrasensitive RNA mutation analysis, enabling several basic research and clinical applications.
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Affiliation(s)
- Manuel Luna Santamaría
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Daniel Andersson
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Toshima Z Parris
- Sahlgrenska Center for Cancer Research, Department of Oncology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Khalil Helou
- Sahlgrenska Center for Cancer Research, Department of Oncology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Tobias Österlund
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Gothenburg, Sweden
- Region Västra Götaland, Sahlgrenska University Hospital, Department of Clinical Genetics and Genomics, Gothenburg, Sweden
| | - Anders Ståhlberg
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden.
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Gothenburg, Sweden.
- Region Västra Götaland, Sahlgrenska University Hospital, Department of Clinical Genetics and Genomics, Gothenburg, Sweden.
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5
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Jeon E, Koo B, Kim S, Kim J, Yu Y, Jang H, Lee M, Kim SH, Kang T, Kim SK, Kwak R, Shin Y, Lee J. Biporous silica nanostructure-induced nanovortex in microfluidics for nucleic acid enrichment, isolation, and PCR-free detection. Nat Commun 2024; 15:1366. [PMID: 38355558 PMCID: PMC10866868 DOI: 10.1038/s41467-024-45467-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 01/24/2024] [Indexed: 02/16/2024] Open
Abstract
Efficient pathogen enrichment and nucleic acid isolation are critical for accurate and sensitive diagnosis of infectious diseases, especially those with low pathogen levels. Our study introduces a biporous silica nanofilms-embedded sample preparation chip for pathogen and nucleic acid enrichment/isolation. This chip features unique biporous nanostructures comprising large and small pore layers. Computational simulations confirm that these nanostructures enhance the surface area and promote the formation of nanovortex, resulting in improved capture efficiency. Notably, the chip demonstrates a 100-fold lower limit of detection compared to conventional methods used for nucleic acid detection. Clinical validations using patient samples corroborate the superior sensitivity of the chip when combined with the luminescence resonance energy transfer assay. The enhanced sample preparation efficiency of the chip, along with the facile and straightforward synthesis of the biporous nanostructures, offers a promising solution for polymer chain reaction-free detection of nucleic acids.
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Affiliation(s)
- Eunyoung Jeon
- Department of Chemistry, Hanyang University, Seoul, 04763, Republic of Korea
- Research Institute for Natural Science, Hanyang University, Seoul, 04763, Republic of Korea
- Research Institute for Convergence of Basic Sciences, Hanyang University, Seoul, 04763, Republic of Korea
| | - Bonhan Koo
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea
| | - Suyeon Kim
- Department of Chemistry, Hanyang University, Seoul, 04763, Republic of Korea
- Research Institute for Natural Science, Hanyang University, Seoul, 04763, Republic of Korea
- Research Institute for Convergence of Basic Sciences, Hanyang University, Seoul, 04763, Republic of Korea
| | - Jieun Kim
- Department of Mechanical Convergence Engineering, Hanyang University, Seoul, 04763, Republic of Korea
| | - Yeonuk Yu
- Department of Mechanical Convergence Engineering, Hanyang University, Seoul, 04763, Republic of Korea
| | - Hyowon Jang
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Minju Lee
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea
| | - Sung-Han Kim
- Department of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, Seoul, 05505, Republic of Korea
| | - Taejoon Kang
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Sang Kyung Kim
- Center for Augmented Safety Systems with Intelligence, Sensing and Tracking (ASSIST), Korea Institute of Science and Technology (KIST), Seoul, 02792, Republic of Korea
| | - Rhokyun Kwak
- Department of Mechanical Convergence Engineering, Hanyang University, Seoul, 04763, Republic of Korea.
| | - Yong Shin
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea.
| | - Joonseok Lee
- Department of Chemistry, Hanyang University, Seoul, 04763, Republic of Korea.
- Research Institute for Natural Science, Hanyang University, Seoul, 04763, Republic of Korea.
- Research Institute for Convergence of Basic Sciences, Hanyang University, Seoul, 04763, Republic of Korea.
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6
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Gasch K, Hykollari A, Habe M, Haubensak P, Painer-Gigler J, Smith S, Stalder G, Arnold W. Summer fades, deer change: Photoperiodic control of cellular seasonal acclimatization of skeletal muscle. iScience 2024; 27:108619. [PMID: 38155774 PMCID: PMC10753075 DOI: 10.1016/j.isci.2023.108619] [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: 08/11/2023] [Revised: 10/23/2023] [Accepted: 11/30/2023] [Indexed: 12/30/2023] Open
Abstract
We found major seasonal changes of polyunsaturated fatty acids (PUFAs) in muscular phospholipids (PL) in a large non-hibernating mammal, the red deer (Cervus elaphus). Dietary supply of essential linoleic acid (LA) and α-linolenic acid (ALA) had no, or only weak influence, respectively. We further found correlations of PL PUFA concentrations with the activity of key metabolic enzymes, independent of higher winter expression. Activity of the sarcoplasmic reticulum (SR) Ca++-ATPase increased with SR PL concentrations of n-6 PUFA, and of cytochrome c oxidase and citrate synthase, indicators of ATP-production, with concentrations of eicosapentaenoic acid in mitochondrial PL. All detected cyclic molecular changes were controlled by photoperiod and are likely of general relevance for mammals living in seasonal environments, including humans. During winter, these changes at the molecular level presumably compensate for Arrhenius effects in the colder peripheral body parts and thus enable a thrifty life at lower body temperature.
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Affiliation(s)
- Kristina Gasch
- Research Institute of Wildlife Ecology, Department of Interdisciplinary Life Science, University of Veterinary Medicine Vienna, 1160 Vienna, Austria
| | - Alba Hykollari
- Research Institute of Wildlife Ecology, Department of Interdisciplinary Life Science, University of Veterinary Medicine Vienna, 1160 Vienna, Austria
| | - Manuela Habe
- Research Institute of Wildlife Ecology, Department of Interdisciplinary Life Science, University of Veterinary Medicine Vienna, 1160 Vienna, Austria
| | - Patricia Haubensak
- Konrad Lorenz Institute of Ethology, Department of Interdisciplinary Life Science, University of Veterinary Medicine Vienna, 1160 Vienna, Austria
| | - Johanna Painer-Gigler
- Research Institute of Wildlife Ecology, Department of Interdisciplinary Life Science, University of Veterinary Medicine Vienna, 1160 Vienna, Austria
| | - Steve Smith
- Konrad Lorenz Institute of Ethology, Department of Interdisciplinary Life Science, University of Veterinary Medicine Vienna, 1160 Vienna, Austria
| | - Gabrielle Stalder
- Research Institute of Wildlife Ecology, Department of Interdisciplinary Life Science, University of Veterinary Medicine Vienna, 1160 Vienna, Austria
| | - Walter Arnold
- Research Institute of Wildlife Ecology, Department of Interdisciplinary Life Science, University of Veterinary Medicine Vienna, 1160 Vienna, Austria
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7
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Lewis CA, Seashols-Williams SJ. A combined molecular approach utilizing microbial DNA and microRNAs in a qPCR multiplex for the classification of five forensically relevant body fluids. J Forensic Sci 2024; 69:282-290. [PMID: 37818748 DOI: 10.1111/1556-4029.15400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 09/13/2023] [Accepted: 09/26/2023] [Indexed: 10/13/2023]
Abstract
Body fluid identification is an essential step in the forensic biology workflow that can assist DNA analysts in determining where to collect DNA evidence. Current presumptive tests lack the specificity that molecular techniques can achieve; therefore, molecular methods, including microRNA (miRNA) and microbial signature characterization, have been extensively researched in the forensic community. Limitations of each method suggest combining molecular markers to increase the discrimination efficiency of multiple body fluids from a single assay. While microbial signatures have been successful in identifying fluids with high bacterial abundances, microRNAs have shown promise in fluids with low microbial abundance (blood and semen). This project synergized the benefits of microRNAs and microbial DNA to identify multiple body fluids using DNA extracts. A reverse transcription (RT)-qPCR duplex targeting miR-891a and let-7g was validated, and miR-891a differential expression was significantly different between blood and semen. The miRNA duplex was incorporated into a previously reported qPCR multiplex targeting 16S rRNA genes of Lactobacillus crispatus, Bacteroides uniformis, and Streptococcus salivarius to presumptively identify vaginal/menstrual secretions, feces, and saliva, respectively. The combined classification regression tree model resulted in the presumptive classification of five body fluids with 94.6% overall accuracy, now including blood and semen identification. These results provide proof of concept that microRNAs and microbial DNA can classify multiple body fluids simultaneously at the quantification step of the current forensic DNA workflow.
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Affiliation(s)
- Carolyn A Lewis
- Integrative Life Sciences Doctoral Program, Virginia Commonwealth University, Richmond, Virginia, USA
- Department of Forensic Science, Virginia Commonwealth University, Richmond, Virginia, USA
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8
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Casmil IC, Huang C, Blakney AK. A duplex droplet digital PCR assay for absolute quantification and characterization of long self-amplifying RNA. Sci Rep 2023; 13:19050. [PMID: 37923834 PMCID: PMC10624827 DOI: 10.1038/s41598-023-46314-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 10/30/2023] [Indexed: 11/06/2023] Open
Abstract
Self-amplifying messenger ribonucleic acid (saRNA) provides extended expression of genes of interest by encoding an alphavirus-derived RNA replicase and thus is 2-3 times larger than conventional messenger RNA. However, quality assessment of long RNA transcripts is challenging using standard techniques. Here, we utilized a multiplex droplet digital polymerase chain reaction (ddPCR) assay to assess the quality of saRNA produced from an in vitro transcription reaction and the replication kinetics in human cell lines. Using the one-step reverse transcription ddPCR, we show that an in vitro transcription generates 50-60% full-length saRNA transcripts. However, we note that the two-step reverse transcription ddPCR assay results in a 20% decrease from results obtained using the one-step and confirmed using capillary gel electrophoresis. Additionally, we provided three formulas that differ in the level of stringency and assumptions made to calculate the fraction of intact saRNA. Using ddPCR, we also showed that subgenomic transcripts of saRNA were 19-to-108-fold higher than genomic transcripts at different hours post-transfection of mammalian cells in copies. Therefore, we demonstrate that multiplex ddPCR is well suited for quality assessment of long RNA and replication kinetics of saRNA based on absolute quantification.
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Affiliation(s)
- Irafasha C Casmil
- Michael Smith Laboratories, School of Biomedical Engineering, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Cynthia Huang
- Michael Smith Laboratories, School of Biomedical Engineering, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Anna K Blakney
- Michael Smith Laboratories, School of Biomedical Engineering, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.
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9
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DeJaco RF, Roberts MJ, Romsos EL, Vallone PM, Kearsley AJ. Reducing Bias and Quantifying Uncertainty in Fluorescence Produced by PCR. Bull Math Biol 2023; 85:83. [PMID: 37574503 PMCID: PMC10423706 DOI: 10.1007/s11538-023-01182-z] [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] [Received: 11/16/2022] [Accepted: 06/20/2023] [Indexed: 08/15/2023]
Abstract
We present a new approach for relating nucleic-acid content to fluorescence in a real-time Polymerase Chain Reaction (PCR) assay. By coupling a two-type branching process for PCR with a fluorescence analog of Beer's Law, the approach reduces bias and quantifies uncertainty in fluorescence. As the two-type branching process distinguishes between complementary strands of DNA, it allows for a stoichiometric description of reactions between fluorescent probes and DNA and can capture the initial conditions encountered in assays targeting RNA. Analysis of the expected copy-number identifies additional dynamics that occur at short times (or, equivalently, low cycle numbers), while investigation of the variance reveals the contributions from liquid volume transfer, imperfect amplification, and strand-specific amplification (i.e., if one strand is synthesized more efficiently than its complement). Linking the branching process to fluorescence by the Beer's Law analog allows for an a priori description of background fluorescence. It also enables uncertainty quantification (UQ) in fluorescence which, in turn, leads to analytical relationships between amplification efficiency (probability) and limit of detection. This work sets the stage for UQ-PCR, where both the input copy-number and its uncertainty are quantified from fluorescence kinetics.
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Affiliation(s)
- Robert F. DeJaco
- Applied and Computational Mathematics Division, National Institute of Standards and Technology, 100 Bureau Dr., MS 8910, Gaithersburg, MD 20899-8910 USA
- Department of Chemistry and Biochemistry, University of Maryland, 8051 Regents Dr., College Park, MD 20742-4454 USA
| | - Matthew J. Roberts
- Applied and Computational Mathematics Division, National Institute of Standards and Technology, 100 Bureau Dr., MS 8910, Gaithersburg, MD 20899-8910 USA
- Cost Analysis and Research Division, Institute for Defense Analyses, 730 E. Glebe Rd., Alexandria, VA 22305-3086 USA
| | - Erica L. Romsos
- Biomolecular Measurement Division, National Institute of Standards and Technology, 100 Bureau Dr., MS 8314, Gaithersburg, MD 20899-8314 USA
| | - Peter M. Vallone
- Biomolecular Measurement Division, National Institute of Standards and Technology, 100 Bureau Dr., MS 8314, Gaithersburg, MD 20899-8314 USA
| | - Anthony J. Kearsley
- Applied and Computational Mathematics Division, National Institute of Standards and Technology, 100 Bureau Dr., MS 8910, Gaithersburg, MD 20899-8910 USA
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10
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Santiago NA, He B, Howard SL, Beaudin S, Strupp BJ, Smith DR. Developmental Manganese Exposure Causes Lasting Attention Deficits Accompanied by Dysregulation of mTOR Signaling and Catecholaminergic Gene Expression in Brain Prefrontal Cortex. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.16.549215. [PMID: 37503220 PMCID: PMC10370122 DOI: 10.1101/2023.07.16.549215] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Elevated manganese (Mn) exposure is associated with attentional deficits in children, and is an environmental risk factor for attention deficit hyperactivity disorder (ADHD). We have shown that developmental Mn exposure causes lasting attention and sensorimotor deficits in a rat model of early childhood Mn exposure, and that these deficits are associated with a hypofunctioning catecholaminergic system in the prefrontal cortex (PFC), though the mechanistic basis for these deficits is not well understood. To address this, male Long-Evans rats were exposed orally to Mn (50 mg/kg/d) over PND 1-21 and attentional function was assessed in adulthood using the 5-Choice Serial Reaction Time Task. Targeted catecholaminergic system and epigenetic gene expression, followed by unbiased differential DNA methylation and gene regulation expression transcriptomics in the PFC, were performed in young adult littermates. Results show that developmental Mn exposure causes lasting focused attention deficits that are associated with reduced gene expression of tyrosine hydroxylase, dopamine transporter, and DNA methyltransferase 3a. Further, developmental Mn exposure causes broader lasting methylation and gene expression dysregulation associated with epigenetic regulation, inflammation, cell development, and hypofunctioning catecholaminergic neuronal systems. Pathway enrichment analyses uncovered mTOR and Wnt signaling pathway genes as significant transcriptomic regulators of the Mn altered transcriptome, and Western blot of total, C1 and C2 phospho-mTOR confirmed mTOR pathway dysregulation. Our findings deepen our understanding of the mechanistic basis of how developmental Mn exposure leads to lasting catecholaminergic dysfunction and attention deficits, which may aid future therapeutic interventions of environmental exposure associated disorders. Significance Statement Attention deficit hyperactivity disorder (ADHD) is associated with environmental risk factors, including exposure to neurotoxic agents. Here we used a rodent model of developmental manganese (Mn) exposure producing lasting attention deficits to show broad epigenetic and gene expression changes in the prefrontal cortex, and to identify disrupted mTOR and Wnt signaling pathways as a novel mechanism for how developmental Mn exposure may induce lasting attention and catecholaminergic system impairments. Importantly, our findings establish early development as a critical period of susceptibility to lasting deficits in attentional function caused by elevated environmental toxicant exposure. Given that environmental health threats disproportionately impact communities of color and low socioeconomic status, our findings can aid future studies to assess therapeutic interventions for vulnerable populations.
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11
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Verwilt J, Mestdagh P, Vandesompele J. Artifacts and biases of the reverse transcription reaction in RNA sequencing. RNA (NEW YORK, N.Y.) 2023; 29:889-897. [PMID: 36990512 DOI: 10.1261/rna.079623.123] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
RNA sequencing has spurred a significant number of research areas in recent years. Most protocols rely on synthesizing a more stable complementary DNA (cDNA) copy of the RNA molecule during the reverse transcription reaction. The resulting cDNA pool is often wrongfully assumed to be quantitatively and molecularly similar to the original RNA input. Sadly, biases and artifacts confound the resulting cDNA mixture. These issues are often overlooked or ignored in the literature by those that rely on the reverse transcription process. In this review, we confront the reader with intra- and intersample biases and artifacts caused by the reverse transcription reaction during RNA sequencing experiments. To fight the reader's despair, we also provide solutions to most issues and inform on good RNA sequencing practices. We hope the reader can use this review to their advantage, thereby contributing to scientifically sound RNA studies.
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Affiliation(s)
- Jasper Verwilt
- OncoRNALab, Cancer Research Institute Ghent, 9000 Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium
- Center for Medical Genetics, Ghent University, 9000 Ghent, Belgium
| | - Pieter Mestdagh
- OncoRNALab, Cancer Research Institute Ghent, 9000 Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium
- Center for Medical Genetics, Ghent University, 9000 Ghent, Belgium
| | - Jo Vandesompele
- OncoRNALab, Cancer Research Institute Ghent, 9000 Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium
- Center for Medical Genetics, Ghent University, 9000 Ghent, Belgium
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12
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Accurate quantification of SARS-CoV-2 RNA by isotope dilution mass spectrometry and providing a correction of reverse transcription efficiency in droplet digital PCR. Anal Bioanal Chem 2022; 414:6771-6777. [PMID: 35941317 PMCID: PMC9360635 DOI: 10.1007/s00216-022-04238-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 07/13/2022] [Accepted: 07/18/2022] [Indexed: 11/01/2022]
Abstract
The novel coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has infected more than 505 million confirmed cases, including over 6 million deaths. Reference materials (RMs) of SARS-CoV-2 RNA played a crucial role in performance evaluation and quality control of testing laboratories. As the potential primary characterization method of RMs, reverse transcription digital PCR (RT-dPCR) measures the copy number of RNA, but the accuracy of reverse transcription (RT) efficiency has yet to be confirmed. This study established a method of enzymatic digestion followed by isotope dilution mass spectrometry (IDMS), which does not require an RT reaction, to quantify in vitro-transcribed SARS-CoV-2 RNA. RNA was digested to nucleotide monophosphate (NMP) within 15 min and analyzed by IDMS within 5 min. The consistency among the results of four different NMPs demonstrated the reliability of the proposed method. Compared to IDMS, the quantitative result of RT-dPCR turned out to be about 10% lower, possibly attributed to the incompleteness of the reverse transcription process. Therefore, the proposed approach could be valuable and reliable for quantifying RNA molecules and evaluating the RT efficiency of RT-based methods.
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13
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Yang J, Li D, Wang J, Zhang R, Li J. Design, optimization, and application of multiplex rRT-PCR in the detection of respiratory viruses. Crit Rev Clin Lab Sci 2022:1-18. [PMID: 35559711 DOI: 10.1080/10408363.2022.2072467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Viral respiratory infections are common and serious diseases. Because there is no effective treatment method or vaccine for respiratory tract infection, early diagnosis is vital to identify the pathogen so as to determine the infectivity of the patient and to quickly take measures to curb the spread of the virus, if warranted, to avoid serious public health problems. Real-time reverse transcriptase PCR (rRT-PCR), which has high sensitivity and specificity, is the best approach for early diagnosis. Among rRT-PCR methods, multiplex rRT-PCR can resolve issues arising from various types of viruses, high mutation frequency, coinfection, and low concentrations of virus. However, the design, optimization, and validation of multiplex rRT-PCR are more complicated than singleplex rRT-PCR, and comprehensive research on multiplex rRT-PCR methodology is lacking. This review summarizes recent progress in multiplex rRT-PCR methodology, outlines the principles of design, optimization and validation, and describes a scheme to help diagnostic companies to design and optimize their multiplex rRT-PCR detection panel and to assist laboratory staff to solve problems in their daily work. In addition, the analytical validity, clinical validity and clinical utility of multiplex rRT-PCR in viral respiratory tract infection diagnosis are assessed to provide theoretical guidance and useful information for physicians to understand the test results.
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Affiliation(s)
- Jing Yang
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/ National Center of Gerontology, P.R. China.,Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, P.R. China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, P.R. China
| | - Dandan Li
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/ National Center of Gerontology, P.R. China.,Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, P.R. China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, P.R. China
| | - Jie Wang
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/ National Center of Gerontology, P.R. China.,Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, P.R. China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, P.R. China
| | - Rui Zhang
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/ National Center of Gerontology, P.R. China.,Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, P.R. China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, P.R. China
| | - Jinming Li
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/ National Center of Gerontology, P.R. China.,Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, P.R. China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, P.R. China
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14
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Wade MJ, Lo Jacomo A, Armenise E, Brown MR, Bunce JT, Cameron GJ, Fang Z, Farkas K, Gilpin DF, Graham DW, Grimsley JMS, Hart A, Hoffmann T, Jackson KJ, Jones DL, Lilley CJ, McGrath JW, McKinley JM, McSparron C, Nejad BF, Morvan M, Quintela-Baluja M, Roberts AMI, Singer AC, Souque C, Speight VL, Sweetapple C, Walker D, Watts G, Weightman A, Kasprzyk-Hordern B. Understanding and managing uncertainty and variability for wastewater monitoring beyond the pandemic: Lessons learned from the United Kingdom national COVID-19 surveillance programmes. JOURNAL OF HAZARDOUS MATERIALS 2022; 424:127456. [PMID: 34655869 PMCID: PMC8498793 DOI: 10.1016/j.jhazmat.2021.127456] [Citation(s) in RCA: 81] [Impact Index Per Article: 40.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 09/23/2021] [Accepted: 10/05/2021] [Indexed: 05/18/2023]
Abstract
The COVID-19 pandemic has put unprecedented pressure on public health resources around the world. From adversity, opportunities have arisen to measure the state and dynamics of human disease at a scale not seen before. In the United Kingdom, the evidence that wastewater could be used to monitor the SARS-CoV-2 virus prompted the development of National wastewater surveillance programmes. The scale and pace of this work has proven to be unique in monitoring of virus dynamics at a national level, demonstrating the importance of wastewater-based epidemiology (WBE) for public health protection. Beyond COVID-19, it can provide additional value for monitoring and informing on a range of biological and chemical markers of human health. A discussion of measurement uncertainty associated with surveillance of wastewater, focusing on lessons-learned from the UK programmes monitoring COVID-19 is presented, showing that sources of uncertainty impacting measurement quality and interpretation of data for public health decision-making, are varied and complex. While some factors remain poorly understood, we present approaches taken by the UK programmes to manage and mitigate the more tractable sources of uncertainty. This work provides a platform to integrate uncertainty management into WBE activities as part of global One Health initiatives beyond the pandemic.
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Affiliation(s)
- Matthew J Wade
- UK Health Security Agency, Environmental Monitoring for Health Protection, Windsor House, Victoria Street, London SW1H 0TL, UK; Newcastle University, School of Engineering, Cassie Building, Newcastle-upon-Tyne NE1 7RU, UK.
| | - Anna Lo Jacomo
- UK Health Security Agency, Environmental Monitoring for Health Protection, Windsor House, Victoria Street, London SW1H 0TL, UK; Bristol University, Department of Engineering Mathematics, Bristol BS8 1TW, UK
| | - Elena Armenise
- Environment Agency, Research, Horizon House, Deanery Road, Bristol BS1 5AH, UK
| | - Mathew R Brown
- UK Health Security Agency, Environmental Monitoring for Health Protection, Windsor House, Victoria Street, London SW1H 0TL, UK; Newcastle University, School of Engineering, Cassie Building, Newcastle-upon-Tyne NE1 7RU, UK
| | - Joshua T Bunce
- UK Health Security Agency, Environmental Monitoring for Health Protection, Windsor House, Victoria Street, London SW1H 0TL, UK; Newcastle University, School of Engineering, Cassie Building, Newcastle-upon-Tyne NE1 7RU, UK; Department for Environment, Food and Rural Affairs, Seacole Building, 2 Marsham Street, London SW1P 4DF, UK
| | - Graeme J Cameron
- Scottish Environment Protection Agency, Strathallan House, Stirling FK9 4TZ, UK
| | - Zhou Fang
- Biomathematics and Statistics Scotland, James Clerk Maxwell Building, Peter Guthrie Tait Road, Edinburgh EH9 3FD, UK
| | - Kata Farkas
- Bangor University, School of Natural Sciences, Deiniol Road, Bangor LL57 2UW, UK
| | - Deidre F Gilpin
- Queen's University Belfast, School of Pharmacy, Lisburn Road, Belfast BT9 7BL, UK
| | - David W Graham
- Newcastle University, School of Engineering, Cassie Building, Newcastle-upon-Tyne NE1 7RU, UK
| | - Jasmine M S Grimsley
- UK Health Security Agency, Environmental Monitoring for Health Protection, Windsor House, Victoria Street, London SW1H 0TL, UK
| | - Alwyn Hart
- Environment Agency, Research, Horizon House, Deanery Road, Bristol BS1 5AH, UK
| | - Till Hoffmann
- UK Health Security Agency, Environmental Monitoring for Health Protection, Windsor House, Victoria Street, London SW1H 0TL, UK; Imperial College London, Department of Mathematics, London SW7 2AZ, UK
| | - Katherine J Jackson
- Environment Agency, Research, Horizon House, Deanery Road, Bristol BS1 5AH, UK
| | - David L Jones
- Bangor University, School of Natural Sciences, Deiniol Road, Bangor LL57 2UW, UK; The University of Western Australia, UWA School of Agriculture and Environment, Perth, WA 6009, Australia
| | - Chris J Lilley
- UK Health Security Agency, Environmental Monitoring for Health Protection, Windsor House, Victoria Street, London SW1H 0TL, UK
| | - John W McGrath
- Queen's University Belfast, School of Biological Sciences, Chlorine Gardens, Belfast BT9 5DL, UK
| | - Jennifer M McKinley
- Queen's University Belfast, School of Natural and Built Environment, Stranmills Road, Belfast BT9 5AG, UK
| | - Cormac McSparron
- Queen's University Belfast, School of Natural and Built Environment, Stranmills Road, Belfast BT9 5AG, UK
| | - Behnam F Nejad
- Queen's University Belfast, School of Natural and Built Environment, Stranmills Road, Belfast BT9 5AG, UK
| | - Mario Morvan
- UK Health Security Agency, Environmental Monitoring for Health Protection, Windsor House, Victoria Street, London SW1H 0TL, UK; University College London, Department of Physics and Astronomy, Gower Street, London WC1E 6BT, UK
| | - Marcos Quintela-Baluja
- Newcastle University, School of Engineering, Cassie Building, Newcastle-upon-Tyne NE1 7RU, UK
| | - Adrian M I Roberts
- Biomathematics and Statistics Scotland, James Clerk Maxwell Building, Peter Guthrie Tait Road, Edinburgh EH9 3FD, UK
| | - Andrew C Singer
- UK Centre for Ecology and Hydrology, Benson Lane, Wallingford OX10 8BB, UK
| | - Célia Souque
- UK Health Security Agency, Environmental Monitoring for Health Protection, Windsor House, Victoria Street, London SW1H 0TL, UK; University of Oxford, Department of Zoology, Mansfield Road, Oxford OX1 3SZ, UK
| | - Vanessa L Speight
- University of Sheffield, Department of Civil and Structural Engineering, Mappin Street, Sheffield S1 3JD, UK
| | - Chris Sweetapple
- UK Health Security Agency, Environmental Monitoring for Health Protection, Windsor House, Victoria Street, London SW1H 0TL, UK; University of Exeter, Centre for Water Systems, College of Engineering, Mathematics and Physical Sciences, Exeter EX4 4QF, UK
| | - David Walker
- Centre for Environment, Fisheries and Aquaculture Science, Barrack Road, Weymouth DT4 8UB, UK
| | - Glenn Watts
- Environment Agency, Research, Horizon House, Deanery Road, Bristol BS1 5AH, UK
| | - Andrew Weightman
- Cardiff University, Cardiff School of Biosciences, The Sir Martin Evans Building, Museum Avenue, Cardiff CF10 3AX, UK
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15
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RT-qPCR Detection of SARS-CoV-2: No Need for a Dedicated Reverse Transcription Step. Int J Mol Sci 2022; 23:ijms23031303. [PMID: 35163227 PMCID: PMC8835954 DOI: 10.3390/ijms23031303] [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: 12/06/2021] [Revised: 12/27/2021] [Accepted: 01/21/2022] [Indexed: 11/16/2022] Open
Abstract
Reverse transcription of RNA coupled to amplification of the resulting cDNA by the polymerase chain reaction (RT-PCR) is one of the principal molecular technologies in use today, with applications across all areas of science and medicine. In its real-time, fluorescence-based usage (RT-qPCR), it has long been a core technology driving the accurate, rapid and sensitive laboratory diagnosis of infectious diseases. However, RT-qPCR protocols have changed little over the past 30 years, with the RT step constituting a significant percentage of the time taken to complete a typical RT-qPCR assay. When applied to research investigations, reverse transcription has been evaluated by criteria such as maximum yield, length of transcription, fidelity, and faithful representation of an RNA pool. Crucially, however, these are of less relevance in a diagnostic RT-PCR test, where speed and sensitivity are the prime RT imperatives, with specificity contributed by the PCR component. We propose a paradigm shift that omits the requirement for a separate high-temperature RT step at the beginning of an RT-qPCR assay. This is achieved by means of an innovative protocol that incorporates suitable reagents with a revised primer and amplicon design and we demonstrate a proof of principle that incorporates the RT step as part of the PCR assay setup at room temperature. Use of this modification as part of a diagnostic assay will of course require additional characterisation, validation and optimisation of the PCR step. Combining this revision with our previous development of fast qPCR protocols allows completion of a 40 cycle RT-qPCR run on a suitable commercial instrument in approximately 15 min. Even faster times, in combination with extreme PCR procedures, can be achieved.
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16
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Jiang R, Sun T, Song D, Li JJ. Statistics or biology: the zero-inflation controversy about scRNA-seq data. Genome Biol 2022; 23:31. [PMID: 35063006 PMCID: PMC8783472 DOI: 10.1186/s13059-022-02601-5] [Citation(s) in RCA: 122] [Impact Index Per Article: 61.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 01/04/2022] [Indexed: 12/13/2022] Open
Abstract
Researchers view vast zeros in single-cell RNA-seq data differently: some regard zeros as biological signals representing no or low gene expression, while others regard zeros as missing data to be corrected. To help address the controversy, here we discuss the sources of biological and non-biological zeros; introduce five mechanisms of adding non-biological zeros in computational benchmarking; evaluate the impacts of non-biological zeros on data analysis; benchmark three input data types: observed counts, imputed counts, and binarized counts; discuss the open questions regarding non-biological zeros; and advocate the importance of transparent analysis.
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Affiliation(s)
- Ruochen Jiang
- Department of Statistics, University of California, Los Angeles, 90095-1554, CA, USA
| | - Tianyi Sun
- Department of Statistics, University of California, Los Angeles, 90095-1554, CA, USA
| | - Dongyuan Song
- Bioinformatics Interdepartmental Ph.D. Program, University of California, Los Angeles, 90095-7246, CA, USA
| | - Jingyi Jessica Li
- Department of Statistics, University of California, Los Angeles, 90095-1554, CA, USA.
- Department of Human Genetics, University of California, Los Angeles, 90095-7088, CA, USA.
- Department of Computational Medicine, University of California, Los Angeles, 90095-1766, CA, USA.
- Department of Biostatistics, University of California, Los Angeles, 90095-1772, CA, USA.
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17
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Pereira LA, Lapinscki BA, Debur MC, Santos JS, Petterle RR, Nogueira MB, Vidal LRR, De Almeida SM, Raboni SM. Standardization of a high-performance RT-qPCR for viral load absolute quantification of influenza A. J Virol Methods 2021; 301:114439. [PMID: 34942203 DOI: 10.1016/j.jviromet.2021.114439] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 12/13/2021] [Accepted: 12/17/2021] [Indexed: 12/26/2022]
Abstract
Influenza is an acute viral infectious respiratory disease worldwide, presenting in different clinical forms, from influenza-like illness (ILI) to severe acute respiratory infection (SARI). Although real-time quantitative polymerase chain reaction (qPCR) is already an important tool for both diagnosis and treatment monitoring of several viral infections, the correlation between the clinical aspects and the viral load of influenza is still unclear. This lack of clarity is primarily due to the low accuracy and reproducibility of the methodologies developed to quantify the influenza virus. Thus, this study aimed to develop and standardize a universal absolute quantification for influenza A by reverse transcription-quantitative PCR (RT-qPCR), using a plasmid DNA. The assay showed efficiency (Eff%) 98.6, determination coefficient (R2) 0.998, linear range 10^1 to 10^10, limit of detection (LOD) 6.77, limit of quantification (LOQ) 20.52 copies/reaction. No inter and intra assay variability was shown, and neither was the matrix effect observed. Serial measurements of clinical samples collected at a 72h interval showed no change in viral load. By contrast, immunocompetent patients have a significantly lower viral load than immunosuppressed ones. Absolute quantification in clinical samples showed some predictors associated with increased viral load: (H1N1)pdm09 (0.045); women (p = 0.049) and asthmatics (p = 0.035). The high efficiency, precision, and previous performance in clinical samples suggest the assay can be used as an accurate universal viral load quantification of influenza A. Its applicability in predicting severity and response to antivirals needs to be evaluated.
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Affiliation(s)
- L A Pereira
- Graduate Program in Internal Medicine and Health Science, Universidade Federal, do Paraná, Curitiba, Brazil
| | - B A Lapinscki
- Graduate Program in Internal Medicine and Health Science, Universidade Federal, do Paraná, Curitiba, Brazil
| | - M C Debur
- Public Health Laboratory, Curitiba, Brazil
| | - J S Santos
- Virology Laboratory, Hospital de Clínicas, Universidade Federal do Paraná, Brazil
| | - R R Petterle
- Sector of Health Sciences, Medical School, Universidade Federal do Paraná, Curitiba, Brazil
| | - M B Nogueira
- Virology Laboratory, Hospital de Clínicas, Universidade Federal do Paraná, Brazil
| | - L R R Vidal
- Virology Laboratory, Hospital de Clínicas, Universidade Federal do Paraná, Brazil
| | - S M De Almeida
- Virology Laboratory, Hospital de Clínicas, Universidade Federal do Paraná, Brazil
| | - S M Raboni
- Virology Laboratory, Hospital de Clínicas, Universidade Federal do Paraná, Brazil; Infectious Diseases Division, Hospital de Clínicas, Universidade Federal do Paraná, Brazil.
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18
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Zucha D, Kubista M, Valihrach L. Tutorial: Guidelines for Single-Cell RT-qPCR. Cells 2021; 10:cells10102607. [PMID: 34685587 PMCID: PMC8534298 DOI: 10.3390/cells10102607] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 09/24/2021] [Accepted: 09/27/2021] [Indexed: 01/05/2023] Open
Abstract
Reverse transcription quantitative PCR (RT-qPCR) has delivered significant insights in understanding the gene expression landscape. Thanks to its precision, sensitivity, flexibility, and cost effectiveness, RT-qPCR has also found utility in advanced single-cell analysis. Single-cell RT-qPCR now represents a well-established method, suitable for an efficient screening prior to single-cell RNA sequencing (scRNA-Seq) experiments, or, oppositely, for validation of hypotheses formulated from high-throughput approaches. Here, we aim to provide a comprehensive summary of the scRT-qPCR method by discussing the limitations of single-cell collection methods, describing the importance of reverse transcription, providing recommendations for the preamplification and primer design, and summarizing essential data processing steps. With the detailed protocol attached in the appendix, this tutorial provides a set of guidelines that allow any researcher to perform scRT-qPCR measurements of the highest standard.
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Affiliation(s)
- Daniel Zucha
- Laboratory of Gene Expression, Institute of Biotechnology CAS, 252 50 Vestec, Czech Republic; (D.Z.); (M.K.)
- Department of Informatics and Chemistry, Faculty of Chemical Technology, University of Chemistry and Technology, 166 28 Prague, Czech Republic
| | - Mikael Kubista
- Laboratory of Gene Expression, Institute of Biotechnology CAS, 252 50 Vestec, Czech Republic; (D.Z.); (M.K.)
- TATAA Biocenter AB, 411 03 Gothenburg, Sweden
| | - Lukas Valihrach
- Laboratory of Gene Expression, Institute of Biotechnology CAS, 252 50 Vestec, Czech Republic; (D.Z.); (M.K.)
- Correspondence:
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19
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Borchardt MA, Boehm AB, Salit M, Spencer SK, Wigginton KR, Noble RT. The Environmental Microbiology Minimum Information (EMMI) Guidelines: qPCR and dPCR Quality and Reporting for Environmental Microbiology. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:10210-10223. [PMID: 34286966 DOI: 10.1021/acs.est.1c01767] [Citation(s) in RCA: 85] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Real-time quantitative polymerase chain reaction (qPCR) and digital PCR (dPCR) methods have revolutionized environmental microbiology, yielding quantitative organism-specific data of nucleic acid targets in the environment. Such data are essential for characterizing interactions and processes of microbial communities, assessing microbial contaminants in the environment (water, air, fomites), and developing interventions (water treatment, surface disinfection, air purification) to curb infectious disease transmission. However, our review of recent qPCR and dPCR literature in our field of health-related environmental microbiology showed that many researchers are not reporting necessary and sufficient controls and methods, which would serve to strengthen their study results and conclusions. Here, we describe the application, utility, and interpretation of the suite of controls needed to make high quality qPCR and dPCR measurements of microorganisms in the environment. Our presentation is organized by the discrete steps and operations typical of this measurement process. We propose systematic terminology to minimize ambiguity and aid comparisons among studies. Example schemes for batching and combining controls for efficient work flow are demonstrated. We describe critical reporting elements for enhancing data credibility, and we provide an element checklist in the Supporting Information. Additionally, we present several key principles in metrology as context for laboratories to devise their own quality assurance and quality control reporting framework. Following the EMMI guidelines will improve comparability and reproducibility among qPCR and dPCR studies in environmental microbiology, better inform engineering and public health actions for preventing disease transmission through environmental pathways, and for the most pressing issues in the discipline, focus the weight of evidence in the direction toward solutions.
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Affiliation(s)
- Mark A Borchardt
- Environmentally Integrated Dairy Management Research Unit, USDA Agricultural Research Service, 2615 Yellowstone Drive, Marshfield, Wisconsin 54449, United States
| | - Alexandria B Boehm
- Department of Civil and Environmental Engineering, Stanford University, Stanford, California 94305, United States
| | - Marc Salit
- Departments of Pathology and Bioengineering, Stanford University, Stanford, California 94305, United States
- Joint Initiative for Metrology in Biology, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Susan K Spencer
- Environmentally Integrated Dairy Management Research Unit, USDA Agricultural Research Service, 2615 Yellowstone Drive, Marshfield, Wisconsin 54449, United States
| | - Krista R Wigginton
- Department of Civil and Environmental Engineering, University of Michigan, Ann Arbor Michigan 48109, United States
| | - Rachel T Noble
- Insitute for the Environment, University of North Carolina, Chapel Hill, North Carolina 27517, United States
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20
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Myklebust MP, Thor A, Rosenlund B, Gjengstø P, Karlsdottir Á, Brydøy M, Bercea BS, Olsen C, Johnson I, Berg MI, Langberg CW, Andreassen KE, Kjellman A, Haugnes HS, Dahl O. Serum miR371 in testicular germ cell cancer before and after orchiectomy, assessed by digital-droplet PCR in a prospective study. Sci Rep 2021; 11:15582. [PMID: 34341387 PMCID: PMC8329070 DOI: 10.1038/s41598-021-94812-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 07/16/2021] [Indexed: 11/09/2022] Open
Abstract
MicroRNA-371a-3p (miR371) has been suggested as a sensitive biomarker in testicular germ cell cancer (TGCC). We aimed to compare miR371 with the classical biomarkers α-fetoprotein (AFP) and β-human chorionic gonadotropin (hCGβ). Overall, 180 patients were prospectively enrolled in the study, with serum samples collected before and after orchiectomy. We compared the use of digital droplet PCR (RT-ddPCR) with the quantitative PCR used by others for detection of miR371. The novel RT-ddPCR protocol showed high performance in detection of miR371 in serum samples. In the study cohort, miR371 was measured using RT-ddPCR. MiR371 detected CS1 of the seminoma and the non-seminoma sub-types with a sensitivity of 87% and 89%, respectively. The total sensitivity was 89%. After orchiectomy, miR371 levels declined in 154 of 159 TGCC cases. The ratio of miR371 pre- and post-orchiectomy was 20.5 in CS1 compared to 6.5 in systemic disease. AFP and hCGβ had sensitivities of 52% and 51% in the non-seminomas. MiR371 is a sensitive marker that performs better than the classical markers in all sub-types and clinical stages. Especially for the seminomas CS1, the high sensitivity of miR371 in detecting TGCC cells may have clinical implications.
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Affiliation(s)
- Mette Pernille Myklebust
- Mohn Cancer Research Laboratory, Department of Oncology and Medical Physics, Haukeland University Hospital, Jonas Lies vei 91B, 5021, Bergen, Norway.
| | - Anna Thor
- Department of Urology and CLINTEC Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Benedikte Rosenlund
- Mohn Cancer Research Laboratory, Department of Oncology and Medical Physics, Haukeland University Hospital, Jonas Lies vei 91B, 5021, Bergen, Norway
| | - Peder Gjengstø
- Department of Urology, Haukeland University Hospital, Bergen, Norway
| | - Ása Karlsdottir
- Mohn Cancer Research Laboratory, Department of Oncology and Medical Physics, Haukeland University Hospital, Jonas Lies vei 91B, 5021, Bergen, Norway
| | - Marianne Brydøy
- Mohn Cancer Research Laboratory, Department of Oncology and Medical Physics, Haukeland University Hospital, Jonas Lies vei 91B, 5021, Bergen, Norway
| | | | - Christian Olsen
- Mohn Cancer Research Laboratory, Department of Oncology and Medical Physics, Haukeland University Hospital, Jonas Lies vei 91B, 5021, Bergen, Norway
| | - Ida Johnson
- Department of Urology, Oslo University Hospital, Oslo, Norway
| | - Mathilde I Berg
- Department of Urology, Oslo University Hospital, Oslo, Norway
| | | | | | - Anders Kjellman
- Department of Urology and CLINTEC Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Hege S Haugnes
- Department of Oncology, University Hospital of North Norway, Tromsø, Norway.,Department of Clinical Medicine, UIT-The Arctic University, Tromsø, Norway
| | - Olav Dahl
- Mohn Cancer Research Laboratory, Department of Oncology and Medical Physics, Haukeland University Hospital, Jonas Lies vei 91B, 5021, Bergen, Norway
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21
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Assessment of Circulating Nucleic Acids in Cancer: From Current Status to Future Perspectives and Potential Clinical Applications. Cancers (Basel) 2021; 13:cancers13143460. [PMID: 34298675 PMCID: PMC8307284 DOI: 10.3390/cancers13143460] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 07/01/2021] [Accepted: 07/06/2021] [Indexed: 02/06/2023] Open
Abstract
Current approaches for cancer detection and characterization are based on radiological procedures coupled with tissue biopsies, despite relevant limitations in terms of overall accuracy and feasibility, including relevant patients' discomfort. Liquid biopsies enable the minimally invasive collection and analysis of circulating biomarkers released from cancer cells and stroma, representing therefore a promising candidate for the substitution or integration in the current standard of care. Despite the potential, the current clinical applications of liquid biopsies are limited to a few specific purposes. The lack of standardized procedures for the pre-analytical management of body fluids samples and the detection of circulating biomarkers is one of the main factors impacting the effective advancement in the applicability of liquid biopsies to clinical practice. The aim of this work, besides depicting current methods for samples collection, storage, quality check and biomarker extraction, is to review the current techniques aimed at analyzing one of the main circulating biomarkers assessed through liquid biopsy, namely cell-free nucleic acids, with particular regard to circulating tumor DNA (ctDNA). ctDNA current and potential applications are reviewed as well.
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22
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Lim JM, Tevatia R, Saraf RF. Quantitative PCR of Small Nucleic Acids: Size Matters. ChemistrySelect 2021; 6:2975-2979. [PMID: 36819227 PMCID: PMC9937448 DOI: 10.1002/slct.202100807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Quantitative dysregulation in small nucleic acids (NA), such as microRNA (miRNA), extracted from minimally invasive biopsies, such as, blood, stool, urine, nose, throat, are promising biomarker for diseases diagnosis and management. We quantify the effect of the extra step of poly(A) ligation for cDNA synthesis and small size of the NA on the limit of quantification (LOQ) of quantitative PCR (qPCR), the gold standard to measure copy number. It was discovered that for small NA, the cycle threshold, Ct that is proportional to -log[c], where [c] is the concentration of the target NA exhibits a sharp transition. The results indicate that although the limit of detection (LOD) of qPCR can be in femtomolar range, the LOQ is significantly reduced by well over three orders of magnitude, in picomolar range. Specifically, the study reveals that the PCR product length is the primary reason the limitation on LOQ and is explicitly shown to be an important consideration for primer design for qPCR in general.
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Affiliation(s)
- Jay Min Lim
- Vajra Instruments Inc., 8300 Cody Drive, Ste C, Lincoln, NE 68512, USA
| | - Rahul Tevatia
- Vajra Instruments Inc., 8300 Cody Drive, Ste C, Lincoln, NE 68512, USA
| | - Ravi F. Saraf
- Department of Chemical and Biomolecular Engineering, University of Nebraska-Lincoln, Lincoln NE 68588, USA
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23
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Jing Y, Lv Y, Ye J, Yao L, Chen L, Mi L, Fei Y, Yu Y, Dong B, Lv H, Ma J. Quantifying tagged mRNA export flux via nuclear pore complexes in single live cells. Biochem Biophys Res Commun 2021; 545:138-144. [PMID: 33548627 DOI: 10.1016/j.bbrc.2021.01.049] [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] [Received: 01/15/2021] [Accepted: 01/18/2021] [Indexed: 02/08/2023]
Abstract
The mRNA export flux through nuclear pore complexes (NPC) changes under DNA manipulation and hence affects protein translation. However, monitoring the flux of a specific mRNA in single live cell is beyond reach of traditional techniques. We developed a fluorescence-based detection method for measuring the export flux of mRNA through NPC in single live cell using a snapshot image, which had been tested on exogenous genes' expression in HeLa cells, with transfection or infection, and endogenous genes' expression in yeast cells, during incubation and carbon catabolite repression. With its speediness, explicitness and noninvasiveness, we believe that it would be valuable in direct monitoring of gene behavior, and the understanding of gene regulation at a single cell level.
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Affiliation(s)
- Yueyue Jing
- Department of Optical Science and Engineering, Shanghai Engineering Research Center of Ultra-Precision Optical Manufacturing, Key Laboratory of Micro and Nano Photonic Structures (Ministry of Education), Green Photoelectron Platform, Fudan University, Shanghai, China
| | - Yilin Lv
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China; Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, 200438, China
| | - Jingya Ye
- National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Sichuan, 610041, China
| | - Longfang Yao
- Department of Optical Science and Engineering, Shanghai Engineering Research Center of Ultra-Precision Optical Manufacturing, Key Laboratory of Micro and Nano Photonic Structures (Ministry of Education), Green Photoelectron Platform, Fudan University, Shanghai, China
| | - Liwen Chen
- Department of Optical Science and Engineering, Shanghai Engineering Research Center of Ultra-Precision Optical Manufacturing, Key Laboratory of Micro and Nano Photonic Structures (Ministry of Education), Green Photoelectron Platform, Fudan University, Shanghai, China
| | - Lan Mi
- Department of Optical Science and Engineering, Shanghai Engineering Research Center of Ultra-Precision Optical Manufacturing, Key Laboratory of Micro and Nano Photonic Structures (Ministry of Education), Green Photoelectron Platform, Fudan University, Shanghai, China
| | - Yiyan Fei
- Department of Optical Science and Engineering, Shanghai Engineering Research Center of Ultra-Precision Optical Manufacturing, Key Laboratory of Micro and Nano Photonic Structures (Ministry of Education), Green Photoelectron Platform, Fudan University, Shanghai, China
| | - Yao Yu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China; Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, 200438, China
| | - Biao Dong
- National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Sichuan, 610041, China.
| | - Hong Lv
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China; Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, 200438, China.
| | - Jiong Ma
- Department of Optical Science and Engineering, Shanghai Engineering Research Center of Ultra-Precision Optical Manufacturing, Key Laboratory of Micro and Nano Photonic Structures (Ministry of Education), Green Photoelectron Platform, Fudan University, Shanghai, China; Institute of Biomedical Engineering and Technology, Academy for Engineer and Technology, Fudan University, Shanghai, China; Shanghai Engineering Research Center of Industrial Microorganisms, Multiscale Research Institute of Complex Systems (MRICS), School of Life Sciences, Fudan University, Shanghai, China.
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24
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Bustin S, Mueller R, Shipley G, Nolan T. COVID-19 and Diagnostic Testing for SARS-CoV-2 by RT-qPCR-Facts and Fallacies. Int J Mol Sci 2021; 22:2459. [PMID: 33671091 PMCID: PMC7957603 DOI: 10.3390/ijms22052459] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 02/24/2021] [Accepted: 02/24/2021] [Indexed: 12/19/2022] Open
Abstract
Although molecular testing, and RT-qPCR in particular, has been an indispensable component in the scientific armoury targeting SARS-CoV-2, there are numerous falsehoods, misconceptions, assumptions and exaggerated expectations with regards to capability, performance and usefulness of the technology. It is essential that the true strengths and limitations, although publicised for at least twenty years, are restated in the context of the current COVID-19 epidemic. The main objective of this commentary is to address and help stop the unfounded and debilitating speculation surrounding its use.
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Affiliation(s)
- Stephen Bustin
- Medical Technology Research Centre, Anglia Ruskin University, Chelmsford CM1 1SQ, UK;
| | | | | | - Tania Nolan
- Medical Technology Research Centre, Anglia Ruskin University, Chelmsford CM1 1SQ, UK;
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25
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Niu C, Dong L, Gao Y, Zhang Y, Wang X, Wang J. Quantitative analysis of RNA by HPLC and evaluation of RT-dPCR for coronavirus RNA quantification. Talanta 2021; 228:122227. [PMID: 33773731 PMCID: PMC7898971 DOI: 10.1016/j.talanta.2021.122227] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Revised: 01/31/2021] [Accepted: 02/13/2021] [Indexed: 01/23/2023]
Abstract
Nucleic acid detection and quantification have been known to be important at various fields, from genetically modified organisms and gene expression to virus detection. For DNA molecules, digital PCR has been developed as an absolute quantification method which is not dependent on external calibrators. While when it comes to RNA molecules, reverse transcription (RT) step must be taken before PCR amplification to obtain cDNA. With different kinds of reverse transcriptase (RTase) and RT reaction conditions being used in laboratory assays, the efficiency of RT process differs a lot which led variety in quantification results of RNA molecules. In this study, we developed HPLC method combined with enzymatic digestion of RNA to nucleotides for quantification of RNA without RT process. This method was metrologically traceable to four nuceloside monophosphate (NMP) Certification Reference Materials of National Institute of Metrology, China (NIMC) for insurance of accuracy. The established method was used to evaluate the reverse transcription digital polymerase chain reaction (RT-dPCR) of three target genes of Middle East Respiratory Syndrome Coronavirus (MERS-CoV) RNA, including open reading frame 1ab (ORF1ab), nucleocapsid protein (N) and envelope protein (E) gene. Three available RT kits had been evaluated and disparities were observed for the RT efficiency varied from 9% to 182%. It is thus demonstrated that HPLC combined with enzymatic digestion could be a useful method to quantify RNA molecules and evaluate RT efficiency. It is suggested that RT process should be optimized and identified in RNA quantification assays.
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Affiliation(s)
- Chunyan Niu
- Center for Advanced Measurement Science, National Institute of Metrology, Beijing, 100013, China.
| | - Lianhua Dong
- Center for Advanced Measurement Science, National Institute of Metrology, Beijing, 100013, China
| | - Yunhua Gao
- Center for Advanced Measurement Science, National Institute of Metrology, Beijing, 100013, China
| | - Yongzhuo Zhang
- Center for Advanced Measurement Science, National Institute of Metrology, Beijing, 100013, China
| | - Xia Wang
- Center for Advanced Measurement Science, National Institute of Metrology, Beijing, 100013, China
| | - Jing Wang
- Department of Metrological Services and Quality System, National Institute of Metrology, Beijing, 100013, China
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26
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Fitzpatrick AH, Rupnik A, O'Shea H, Crispie F, Keaveney S, Cotter P. High Throughput Sequencing for the Detection and Characterization of RNA Viruses. Front Microbiol 2021; 12:621719. [PMID: 33692767 PMCID: PMC7938315 DOI: 10.3389/fmicb.2021.621719] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 01/20/2021] [Indexed: 12/12/2022] Open
Abstract
This review aims to assess and recommend approaches for targeted and agnostic High Throughput Sequencing of RNA viruses in a variety of sample matrices. HTS also referred to as deep sequencing, next generation sequencing and third generation sequencing; has much to offer to the field of environmental virology as its increased sequencing depth circumvents issues with cloning environmental isolates for Sanger sequencing. That said however, it is important to consider the challenges and biases that method choice can impart to sequencing results. Here, methodology choices from RNA extraction, reverse transcription to library preparation are compared based on their impact on the detection or characterization of RNA viruses.
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Affiliation(s)
- Amy H. Fitzpatrick
- Food Biosciences, Teagasc Food Research Centre, Fermoy, Ireland
- Shellfish Microbiology, Marine Institute, Oranmore, Ireland
- Biological Sciences, Munster Technological University, Cork, Ireland
| | | | - Helen O'Shea
- Biological Sciences, Munster Technological University, Cork, Ireland
| | - Fiona Crispie
- Food Biosciences, Teagasc Food Research Centre, Fermoy, Ireland
| | | | - Paul Cotter
- Food Biosciences, Teagasc Food Research Centre, Fermoy, Ireland
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27
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Measurements Methods for the Development of MicroRNA-Based Tests for Cancer Diagnosis. Int J Mol Sci 2021; 22:ijms22031176. [PMID: 33503982 PMCID: PMC7865473 DOI: 10.3390/ijms22031176] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 01/15/2021] [Accepted: 01/22/2021] [Indexed: 12/19/2022] Open
Abstract
Studies investigating microRNAs as potential biomarkers for cancer, immune-related diseases, or cardiac pathogenic diseases, among others, have exponentially increased in the last years. In particular, altered expression of specific miRNAs correlates with the occurrence of several diseases, making these molecules potential molecular tools for non-invasive diagnosis, prognosis, and response to therapy. Nonetheless, microRNAs are not in clinical use yet, due to inconsistencies in the literature regarding the specific miRNAs identified as biomarkers for a specific disease, which in turn can be attributed to several reasons, including lack of assay standardization and reproducibility. Technological limitations in circulating microRNAs measurement have been, to date, the biggest challenge for using these molecules in clinical settings. In this review we will discuss pre-analytical, analytical, and post-analytical challenges to address the potential technical biases and patient-related parameters that can have an influence and should be improved to translate miRNA biomarkers to the clinical stage. Moreover, we will describe the currently available methods for circulating miRNA expression profiling and measurement, underlining their advantages and potential pitfalls.
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28
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Moriarty RV, Fesser N, Sutton MS, Venturi V, Davenport MP, Schlub T, O'Connor SL. Validation of multiplex PCR sequencing assay of SIV. Virol J 2021; 18:21. [PMID: 33451356 PMCID: PMC7810186 DOI: 10.1186/s12985-020-01473-0] [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: 06/22/2020] [Accepted: 12/21/2020] [Indexed: 11/24/2022] Open
Abstract
Background The generation of accurate and reproducible viral sequence data is necessary to understand the diversity present in populations of RNA viruses isolated from clinical samples. While various sequencing methods are available, they often require high quality templates and high viral titer to ensure reliable data. Methods We modified a multiplex PCR and sequencing approach to characterize populations of simian immunodeficiency virus (SIV) isolated from nonhuman primates. We chose this approach with the aim of reducing the number of required input templates while maintaining fidelity and sensitivity. We conducted replicate sequencing experiments using different numbers of quantified viral RNA (vRNA) or viral cDNA as input material. We performed assays with clonal SIVmac239 to detect false positives, and we mixed SIVmac239 and a variant with 24 point mutations (SIVmac239-24X) to measure variant detection sensitivity. Results We found that utilizing a starting material of quantified viral cDNA templates had a lower rate of false positives and increased reproducibility when compared to that of quantified vRNA templates. This study identifies the importance of rigorously validating deep sequencing methods and including replicate samples when using a new method to characterize low frequency variants in a population with a small number of templates. Conclusions Because the need to generate reproducible and accurate sequencing data from diverse viruses from low titer samples, we modified a multiplex PCR and sequencing approach to characterize SIV from populations from non-human primates. We found that increasing starting template numbers increased the reproducibility and decreased the number of false positives identified, and this was further seen when cDNA was used as a starting material. Ultimately, we highlight the importance of vigorously validating methods to prevent overinterpretation of low frequency variants in a sample.
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Affiliation(s)
- Ryan V Moriarty
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, 555 Science Dr, Madison, WI, 53711, USA
| | - Nicolas Fesser
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, 555 Science Dr, Madison, WI, 53711, USA
| | - Matthew S Sutton
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, 555 Science Dr, Madison, WI, 53711, USA
| | - Vanessa Venturi
- Infection Analytics Program, Kirby Institute for Infection and Immunity, UNSW Sydney, Sydney, NSW, 2052, Australia
| | - Miles P Davenport
- Infection Analytics Program, Kirby Institute for Infection and Immunity, UNSW Sydney, Sydney, NSW, 2052, Australia
| | - Timothy Schlub
- Faculty of Medicine and Health, Sydney School of Public Health, University of Sydney, Sydney, NSW, 2000, Australia
| | - Shelby L O'Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, 555 Science Dr, Madison, WI, 53711, USA.
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29
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de Almeida PR, Eisen AKA, Demoliner M, Spilki FR. RT-dPCR in Mosquito Samples for ZIKV Detection: Effects of RNA Extraction and Reverse Transcription in Target Concentration. Viruses 2020; 12:v12080827. [PMID: 32751540 PMCID: PMC7472166 DOI: 10.3390/v12080827] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 07/25/2020] [Accepted: 07/27/2020] [Indexed: 01/04/2023] Open
Abstract
Zika virus (ZIKV) is an important arbovirus, responsible for recent outbreaks of Guillain Barré Syndrome and Congenital Zika Syndrome (CZS). After thousands of CZS cases, ZIKV is under constant surveillance in Brazil. Reliable and robust detection techniques are required to minimize the influence of host inhibitors from clinical samples and mosquito pool samples. Reverse transcription Digital Polymerase Chain Reaction (RT-dPCR) is a technique that allows the accurate quantification of DNA targets with high sensitivity, and it is usually less affected by inhibitors than RT-qPCR. This study aimed to assess the influence of mosquito tissue, RNA extraction and cDNA synthesis in ZIKV PCR detection. Samples containing 0, 3 and 10 mosquitoes were spiked with ZIKV MR766 and serially diluted prior to RNA extraction and RT-dPCR for ZIKV. Two reverse transcription protocols were tested. Assay sensitivity allowed the detection of 1.197 copies/µL. A higher correlation between dilution factor and target quantification was observed in 10 mosquito pool samples. The lower quantification in samples diluted without mosquitoes highlights the critical role of the reverse transcription step in RNA detection, since it could be attributed to reverse transcriptase variable performance in samples with low overall RNA concentration. The results in mosquito pools indicate that mosquito tissues do not inhibit ZIKV RT-dPCR, and the RT-dPCR technique has good sensitivity and robustness for ZIKV detection in mosquito pool samples regardless of mosquito tissue concentration.
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30
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Zucha D, Androvic P, Kubista M, Valihrach L. Performance Comparison of Reverse Transcriptases for Single-Cell Studies. Clin Chem 2020; 66:217-228. [PMID: 31699702 DOI: 10.1373/clinchem.2019.307835] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 09/23/2019] [Indexed: 12/21/2022]
Abstract
BACKGROUND Recent advances allowing quantification of RNA from single cells are revolutionizing biology and medicine. Currently, almost all single-cell transcriptomic protocols rely on reverse transcription (RT). However, RT is recognized as a known source of variability, particularly with low amounts of RNA. Recently, several new reverse transcriptases (RTases) with the potential to decrease the loss of information have been developed, but knowledge of their performance is limited. METHODS We compared the performance of 11 RTases in quantitative reverse transcription PCR (RT-qPCR) on single-cell and 100-cell bulk templates, using 2 priming strategies: a conventional mixture of random hexamers with oligo(dT)s and a reduced concentration of oligo(dT)s mimicking common single-cell RNA-sequencing protocols. Depending on their performance, 2 RTases were further tested in a high-throughput single-cell experiment. RESULTS All tested RTases demonstrated high precision (R2 > 0.9445). The most pronounced differences were found in their ability to capture rare transcripts (0%-90% reaction positivity rate) and in their absolute reaction yield (7.3%-137.9%). RTase performance and reproducibility were compared with Z scores. The 2 best-performing enzymes were Maxima H- and SuperScript IV. The validity of the obtained results was confirmed in a follow-up single-cell model experiment. The better-performing enzyme (Maxima H-) increased the sensitivity of the single-cell experiment and improved resolution in the clustering analysis over the commonly used RTase (SuperScript II). CONCLUSIONS Our comprehensive comparison of 11 RTases in low RNA input conditions identified 2 best-performing enzymes. Our results provide a point of reference for the improvement of current single-cell quantification protocols.
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Affiliation(s)
- Daniel Zucha
- Laboratory of Gene Expression, Institute of Biotechnology CAS, Vestec, Czech Republic.,Faculty of Science, Charles University, Prague, Czech Republic
| | - Peter Androvic
- Laboratory of Gene Expression, Institute of Biotechnology CAS, Vestec, Czech Republic.,Laboratory of Growth Regulators, Faculty of Science, Palacky University, Olomouc, Czech Republic
| | - Mikael Kubista
- Laboratory of Gene Expression, Institute of Biotechnology CAS, Vestec, Czech Republic.,TATAA Biocenter AB, Gothenburg, Sweden
| | - Lukas Valihrach
- Laboratory of Gene Expression, Institute of Biotechnology CAS, Vestec, Czech Republic
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31
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Khoury S, Tran N. qPCR multiplex detection of microRNA and messenger RNA in a single reaction. PeerJ 2020; 8:e9004. [PMID: 32617186 PMCID: PMC7321665 DOI: 10.7717/peerj.9004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 03/26/2020] [Indexed: 11/30/2022] Open
Abstract
Reverse Transcription-Quantitative PCR (RT-qPCR) is one of the standards for analytical measurement of different RNA species in biological models. However, current Reverse Transcription (RT) based priming strategies are unable to synthesize differing RNAs and ncRNAs especially miRNAs, within a single tube. We present a new methodology, referred to as RNAmp, that measures in parallel miRNA and mRNA expression. We demonstrate this in various cell lines, then evaluate clinical utility by quantifying several miRNAs and mRNA simultaneously in sera. PCR efficiency in RNAmp was estimated between 1.8 and 1.9 which is comparable to standard miRNA and random primer RT approaches. Furthermore, when using RNAmp to detect selected mRNA and miRNAs, the quantification cycle (Cq) was several cycles lower. This low volume single-tube duplex protocol reduces technical variation and reagent usage and is suitable for uniform analysis of single or multiple miRNAs and/or mRNAs within a single qPCR reaction.
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Affiliation(s)
- Samantha Khoury
- Office of the Deputy Vice Chancellor Innovation and Enterprise, University of Technology Sydney, Sydney, New South Wales, Australia
| | - Nham Tran
- Centre for Health Technologies and School of Biomedical Engineering, University of Technology Sydney, Sydney, New South Wales, Australia.,The Sydney Head and Neck Cancer Institute, Royal Prince Alfred Hospital, Sydney, New South Wales, Australia
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32
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Bustin SA, Nolan T. RT-qPCR Testing of SARS-CoV-2: A Primer. Int J Mol Sci 2020; 21:E3004. [PMID: 32344568 PMCID: PMC7215906 DOI: 10.3390/ijms21083004] [Citation(s) in RCA: 104] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 04/22/2020] [Accepted: 04/23/2020] [Indexed: 01/14/2023] Open
Abstract
Testing for the presence of coronavirus is an essential diagnostic tool for monitoring and managing the current COVID-19 pandemic. The only reliable test in current use for testing acute infection targets the genome of SARS-CoV-2, and the most widely used method is quantitative fluorescence-based reverse transcription polymerase chain reaction (RT-qPCR). Despite its ubiquity, there is a significant amount of uncertainty about how this test works, potential throughput and reliability. This has resulted in widespread misrepresentation of the problems faced using this test during the current COVID-19 epidemic. This primer provides simple, straightforward and impartial information about RT-qPCR.
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Affiliation(s)
- Stephen A. Bustin
- Medical Technology Research Centre, Faculty of Health, Education, Medicine and Social Care, Anglia Ruskin University, Chelmsford, Essex CM1 1SQ, UK
| | - Tania Nolan
- Institute of Population Health, Faculty of Medical and Human Sciences, University of Manchester; Manchester M13 9NT, UK;
- The Gene Team, Bury St Edmunds, Suffolk IP31 1AA, UK
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33
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Gines G, Menezes R, Nara K, Kirstetter AS, Taly V, Rondelez Y. Isothermal digital detection of microRNAs using background-free molecular circuit. SCIENCE ADVANCES 2020; 6:eaay5952. [PMID: 32010788 PMCID: PMC6976291 DOI: 10.1126/sciadv.aay5952] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 11/20/2019] [Indexed: 05/04/2023]
Abstract
MicroRNAs, a class of transcripts involved in the regulation of gene expression, are emerging as promising disease-specific biomarkers accessible from tissues or bodily fluids. However, their accurate quantification from biological samples remains challenging. We report a sensitive and quantitative microRNA detection method using an isothermal amplification chemistry adapted to a droplet digital readout. Building on molecular programming concepts, we design a DNA circuit that converts, thresholds, amplifies, and reports the presence of a specific microRNA, down to the femtomolar concentration. Using a leak absorption mechanism, we were able to suppress nonspecific amplification, classically encountered in other exponential amplification reactions. As a result, we demonstrate that this isothermal amplification scheme is adapted to digital counting of microRNAs: By partitioning the reaction mixture into water-in-oil droplets, resulting in single microRNA encapsulation and amplification, the method provides absolute target quantification. The modularity of our approach enables to repurpose the assay for various microRNA sequences.
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Affiliation(s)
- Guillaume Gines
- Laboratoire Gulliver, CNRS, ESPCI Paris, PSL Research University, 10 rue Vauquelin, 75005 Paris, France
| | - Roberta Menezes
- Centre de Recherche des Cordeliers, INSERM, CNRS, Sorbonne Université, USPC, Université Paris Descartes, Université Paris Diderot, Equipe Labellisée Ligue Nationale Contre le Cancer, Paris, France
| | - Kaori Nara
- Laboratoire Gulliver, CNRS, ESPCI Paris, PSL Research University, 10 rue Vauquelin, 75005 Paris, France
| | - Anne-Sophie Kirstetter
- Laboratoire Gulliver, CNRS, ESPCI Paris, PSL Research University, 10 rue Vauquelin, 75005 Paris, France
| | - Valerie Taly
- Centre de Recherche des Cordeliers, INSERM, CNRS, Sorbonne Université, USPC, Université Paris Descartes, Université Paris Diderot, Equipe Labellisée Ligue Nationale Contre le Cancer, Paris, France
- Corresponding author. (Y.R.); (V.T.)
| | - Yannick Rondelez
- Laboratoire Gulliver, CNRS, ESPCI Paris, PSL Research University, 10 rue Vauquelin, 75005 Paris, France
- Corresponding author. (Y.R.); (V.T.)
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34
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Hu Z, Xu F, Sun G, Zhang S, Zhang X. Homogeneous multiplexed digital detection of microRNA with ligation-rolling circle amplification. Chem Commun (Camb) 2020; 56:5409-5412. [DOI: 10.1039/d0cc01530j] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
MicroRNA was transformed into a DNA nanoflower ball by LRCA reaction for homogeneous multiplexed digital detection using flow cytometry.
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Affiliation(s)
- Zhian Hu
- Department of Chemistry
- Tsinghua University
- Beijing 100084
- China
| | - Fujian Xu
- Department of Chemistry
- Tsinghua University
- Beijing 100084
- China
| | - Gongwei Sun
- Department of Chemistry
- Tsinghua University
- Beijing 100084
- China
| | - Sichun Zhang
- Department of Chemistry
- Tsinghua University
- Beijing 100084
- China
| | - Xinrong Zhang
- Department of Chemistry
- Tsinghua University
- Beijing 100084
- China
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35
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Abstract
Deregulation of microRNA expression has been shown to play an important role in human malignancies. The identification of circulating-free miRNAs in biofluids a decade ago led to great enthusiasm and motivation to develop non-invasive tests based on the expression of these small non-coding RNAs. Herein, we review the progress within the field of research for identifying circulating miRNA cancer biomarkers and discuss the advantages and challenges associated with this. We also discuss the methodological and analytical variables, which may influence the final miRNA quantification and the importance of standardizing pre-analytical, analytical, and post-analytical processes in order to enable a successful translation of the results from basic research into the clinics.
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Affiliation(s)
- Gitte Brinch Andersen
- Department of Biomedicine, Aarhus University, The Bartholin Building, Bartholin Allé 6, 8000, Aarhus C, Denmark.,Laboratory for Epigenetics and Environment, Centre National de Recherche en Génomique Humaine, CEA-Institut de Biologie Francois Jacob, Bâtiment G2, 2 rue Gaston Crémieux, 91000, Evry, France
| | - Jörg Tost
- Laboratory for Epigenetics and Environment, Centre National de Recherche en Génomique Humaine, CEA-Institut de Biologie Francois Jacob, Bâtiment G2, 2 rue Gaston Crémieux, 91000, Evry, France.
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Forero DA, González-Giraldo Y, Castro-Vega LJ, Barreto GE. qPCR-based methods for expression analysis of miRNAs. Biotechniques 2019; 67:192-199. [PMID: 31560239 DOI: 10.2144/btn-2019-0065] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Several approaches for miRNA expression analysis have been developed in recent years. In this article, we provide an updated and comprehensive review of available qPCR-based methods for miRNA expression analysis and discuss their advantages and disadvantages. Existing techniques involve the use of stem-loop reverse transcriptase-PCR, polyadenylation of RNAs, ligation of adapters or RT with complex primers, using universal or miRNA-specific qPCR primers and/or probes. Many of these methods are oriented towards the expression analysis of mature miRNAs and few are designed for the study of pre-miRNAs and pri-miRNAs. We also discuss findings from articles that compare results from existing methods. Finally, we suggest key points for the improvement of available techniques and for the future development of additional methods.
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Affiliation(s)
- Diego A Forero
- Laboratory of NeuroPsychiatric Genetics, Biomedical Sciences Research Group, School of Medicine, Universidad Antonio Nariño, Bogotá, Colombia.,PhD Program in Health Sciences, School of Medicine, Universidad Antonio Nariño, Bogotá, Colombia
| | - Yeimy González-Giraldo
- Departamento de Nutrición y Bioquímica, Pontificia Universidad Javeriana, Bogotá, Colombia
| | - Luis J Castro-Vega
- INSERM, UMR970, Paris-Cardiovascular Research Center, Equipe Labellisée par la Ligue contre le Cancer, Paris, France.,Université Paris Descartes, Sorbonne Paris Cité, Faculté de Médecine, Paris, France
| | - George E Barreto
- Departamento de Nutrición y Bioquímica, Pontificia Universidad Javeriana, Bogotá, Colombia
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Abstract
Over the past decade, the amount of research and the number of publications on associations between circulating small and long non-coding RNAs (ncRNAs) and cancer have grown exponentially. Particular focus has been placed on the development of diagnostic and prognostic biomarkers to enable efficient patient management - from early detection of cancer to monitoring for disease recurrence or progression after treatment. Owing to their high abundance and stability, circulating ncRNAs have potential utility as non-invasive, blood-based biomarkers that can provide information on tumour biology and the effects of treatments, such as targeted therapies and immunotherapies. Increasing evidence highlights the roles of ncRNAs in cell-to-cell communication, with a number of ncRNAs having the capacity to regulate gene expression outside of the cell of origin through extracellular vesicle-mediated transfer to recipient cells, with implications for cancer progression and therapy resistance. Moreover, 'foreign' microRNAs (miRNAs) encoded by non-human genomes (so-called xeno-miRNAs), such as viral miRNAs, have been shown to be present in human body fluids and can be used as biomarkers. Herein, we review the latest developments in the use of circulating ncRNAs as diagnostic and prognostic biomarkers and discuss their roles in cell-to-cell communication in the context of cancer. We provide a compendium of miRNAs and long ncRNAs that have been reported in the literature to be present in human body fluids and that have the potential to be used as diagnostic and prognostic cancer biomarkers.
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Koch L, Poyot T, Schnetterle M, Guillier S, Soulé E, Nolent F, Gorgé O, Neulat-Ripoll F, Valade E, Sebbane F, Biot F. Transcriptomic studies and assessment of Yersinia pestis reference genes in various conditions. Sci Rep 2019; 9:2501. [PMID: 30792499 PMCID: PMC6385181 DOI: 10.1038/s41598-019-39072-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 12/14/2018] [Indexed: 12/27/2022] Open
Abstract
Reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR) is a very sensitive widespread technique considered as the gold standard to explore transcriptional variations. While a particular methodology has to be followed to provide accurate results many published studies are likely to misinterpret results due to lack of minimal quality requirements. Yersinia pestis is a highly pathogenic bacterium responsible for plague. It has been used to propose a ready-to-use and complete approach to mitigate the risk of technical biases in transcriptomic studies. The selection of suitable reference genes (RGs) among 29 candidates was performed using four different methods (GeNorm, NormFinder, BestKeeper and the Delta-Ct method). An overall comprehensive ranking revealed that 12 following candidate RGs are suitable for accurate normalization: gmk, proC, fabD, rpoD, nadB, rho, thrA, ribD, mutL, rpoB, adk and tmk. Some frequently used genes like 16S RNA had even been found as unsuitable to study Y. pestis. This methodology allowed us to demonstrate, under different temperatures and states of growth, significant transcriptional changes of six efflux pumps genes involved in physiological aspects as antimicrobial resistance or virulence. Previous transcriptomic studies done under comparable conditions had not been able to highlight these transcriptional modifications. These results highlight the importance of validating RGs prior to the normalization of transcriptional expression levels of targeted genes. This accurate methodology can be extended to any gene of interest in Y. pestis. More generally, the same workflow can be applied to identify and validate appropriate RGs in other bacteria to study transcriptional variations.
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Affiliation(s)
- Lionel Koch
- Institut de Recherche Biomédicale des Armées (IRBA), Brétigny-sur-Orge, France
- Ecole du Val de Grace (EVDG), Paris, France
- Aix Marseille University, INSERM, SSA, IRBA, MCT, Marseille, France
| | - Thomas Poyot
- Institut de Recherche Biomédicale des Armées (IRBA), Brétigny-sur-Orge, France
| | - Marine Schnetterle
- Institut de Recherche Biomédicale des Armées (IRBA), Brétigny-sur-Orge, France
- Aix Marseille University, INSERM, SSA, IRBA, MCT, Marseille, France
| | - Sophie Guillier
- Institut de Recherche Biomédicale des Armées (IRBA), Brétigny-sur-Orge, France
- Aix Marseille University, INSERM, SSA, IRBA, MCT, Marseille, France
| | - Estelle Soulé
- Institut de Recherche Biomédicale des Armées (IRBA), Brétigny-sur-Orge, France
- Aix Marseille University, INSERM, SSA, IRBA, MCT, Marseille, France
| | - Flora Nolent
- Institut de Recherche Biomédicale des Armées (IRBA), Brétigny-sur-Orge, France
- Aix Marseille University, INSERM, SSA, IRBA, MCT, Marseille, France
| | - Olivier Gorgé
- Institut de Recherche Biomédicale des Armées (IRBA), Brétigny-sur-Orge, France
- Aix Marseille University, INSERM, SSA, IRBA, MCT, Marseille, France
| | - Fabienne Neulat-Ripoll
- Institut de Recherche Biomédicale des Armées (IRBA), Brétigny-sur-Orge, France
- Aix Marseille University, INSERM, SSA, IRBA, MCT, Marseille, France
| | - Eric Valade
- Institut de Recherche Biomédicale des Armées (IRBA), Brétigny-sur-Orge, France
- Ecole du Val de Grace (EVDG), Paris, France
- Aix Marseille University, INSERM, SSA, IRBA, MCT, Marseille, France
| | - Florent Sebbane
- Inserm, University of Lille, CNRS, CHU Lille, Institut Pasteur de Lille, U1019-UMR8204-CIIL-Center for Infection and Immunity of Lille, Lille, France
| | - Fabrice Biot
- Institut de Recherche Biomédicale des Armées (IRBA), Brétigny-sur-Orge, France.
- Aix Marseille University, INSERM, SSA, IRBA, MCT, Marseille, France.
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Schwaber J, Andersen S, Nielsen L. Shedding light: The importance of reverse transcription efficiency standards in data interpretation. BIOMOLECULAR DETECTION AND QUANTIFICATION 2019; 17:100077. [PMID: 30805297 PMCID: PMC6374950 DOI: 10.1016/j.bdq.2018.12.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2018] [Revised: 12/10/2018] [Accepted: 12/17/2018] [Indexed: 12/20/2022]
Abstract
The RNA-to-cDNA conversion step in transcriptomics experiments is widely recognised as inefficient and variable, casting doubt on the ability to do quantitative transcriptomics analyses. Multiple studies have focused on ways to optimise this process, resulting in contradictory recommendations. Here we explore the problem of reverse transcription efficiency using digital PCR and the RT method’s impact on subsequent data analysis. Using synthetic RNA standards, an example experiment is presented, outlining a method to (1) determine relevant efficiency and variability values and then to (2) incorporate this information into downstream analyses as a way to improve the accuracy of quantitative transcriptomics experiments.
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Affiliation(s)
- Jessica Schwaber
- Centre for Commercialization of Regenerative Medicine, Toronto, ON, M5G 1M1, Canada
| | - Stacey Andersen
- Australian Institute for Bioengineering and Nanotechnology, Building 75, Corner College and Cooper Roads, The University of Queensland, St Lucia 4067 QLD, Australia
| | - Lars Nielsen
- Australian Institute for Bioengineering and Nanotechnology, Building 75, Corner College and Cooper Roads, The University of Queensland, St Lucia 4067 QLD, Australia
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Immunomics of Renal Allograft Acute T Cell-Mediated Rejection Biopsies of Tacrolimus- and Belatacept-Treated Patients. Transplant Direct 2018; 5:e418. [PMID: 30656216 PMCID: PMC6324913 DOI: 10.1097/txd.0000000000000857] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 11/02/2018] [Accepted: 11/10/2018] [Indexed: 12/14/2022] Open
Abstract
Supplemental digital content is available in the text. Background Belatacept-based therapy in kidney transplant recipient has been shown to increase long-term renal allograft and patient survival compared with calcineurin inhibitor–based therapy, however, with an increased risk of acute T cell-mediated rejection (aTCMR). An improved understanding of costimulation blockade-resistant rejections could lead to a more personalized approach to belatacept therapy. Here, immunomic profiles of aTCMR biopsies of patients treated with either tacrolimus or belatacept were compared. Methods Formalin-fixed paraffin-embedded renal transplant biopsies were used for immunohistochemistry and gene expression analysis using the innovative NanoString technique. To validate NanoString, transcriptomic profiles of patients with and without biopsy-proven aTCMR were compared. Biopsies from 31 patients were studied: 14 tacrolimus-treated patients with aTCMR, 11 belatacept-treated patients with aTCMR, and 6 controls without rejection. Results A distinct pattern was seen in biopsies with aTCMR compared to negative controls: 78 genes had a higher expression in the aTCMR group (false discovery rate P value <.05 to 1.42e–05). The most significant were T cell-associated genes (CD3, CD8, and CD4; P < 1.98e-04), γ-interferon-inducible genes (CCL5, CXCL9, CXCL11, CXCL10, TBX21; P < 1.33e-04) plus effector genes (GNLY, GZMB, ITGAX; P < 2.82e-03). Immunophenotypical analysis of the classic immune markers of the innate and adaptive immune system was comparable between patients treated with either tacrolimus or belatacept. In addition, the transcriptome of both groups was not significantly different. Conclusions In this small pilot study, no difference was found in immunomics of aTCMR biopsies of tacrolimus- and belatacept-treated patients. This suggests that clinically diagnosed aTCMR reflects a final common pathway of allorecognition which is unaffected by the type of immunosuppressive therapy.
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Yedahalli S, Rehmann L, Bassi A. High throughput screening of β-glucuronidase (GUS) reporter in transgenic microalgae transformed by Agrobacterium tumefaciens. ALGAL RES 2018. [DOI: 10.1016/j.algal.2018.06.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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Bevilacqua C, Ducos B. Laser microdissection: A powerful tool for genomics at cell level. Mol Aspects Med 2017; 59:5-27. [PMID: 28927943 DOI: 10.1016/j.mam.2017.09.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 09/13/2017] [Indexed: 12/18/2022]
Abstract
Laser microdissection (LM) has become widely democratized over the last fifteen years. Instruments have evolved to offer more powerful and efficient lasers as well as new options for sample collection and preparation. Technological evolutions have also focused on the post-microdissection analysis capabilities, opening up investigations in all disciplines of experimental and clinical biology, thanks to the advent of new high-throughput methods of genome analysis, including RNAseq and proteomics, now globally known as microgenomics, i.e. analysis of biomolecules at the cell level. In spite of the advances these rapidly developing methods have allowed, the workflow for sampling and collection by LM remains a critical step in insuring sample integrity in terms of histology (accurate cell identification) and biochemistry (reliable analyzes of biomolecules). In this review, we describe the sample processing as well as the strengths and limiting factors of LM applied to the specific selection of one or more cells of interest from a heterogeneous tissue. We will see how the latest developments in protocols and methods have made LM a powerful and sometimes essential tool for genomic and proteomic analyzes of tiny amounts of biomolecules extracted from few cells isolated from a complex tissue, in their physiological context, thus offering new opportunities for understanding fundamental physiological and/or patho-physiological processes.
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Affiliation(s)
- Claudia Bevilacqua
- GABI, Plateforme @BRIDGE, INRA, AgroParisTech, Université Paris-Saclay, Domaine de Vilvert, 78350 Jouy en Josas, France.
| | - Bertrand Ducos
- LPS-ENS, CNRS UMR 8550, UPMC, Université Denis Diderot, PSL Research University, 24 Rue Lhomond, 75005 Paris France; High Throughput qPCR Core Facility, IBENS, 46 Rue d'Ulm, 75005 Paris France; Laser Microdissection Facility of Montagne Sainte Geneviève, CIRB Collège de France, Place Marcellin Berthelot, 75005 Paris France.
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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: 69] [Impact Index Per Article: 9.9] [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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Baebler Š, Svalina M, Petek M, Stare K, Rotter A, Pompe-Novak M, Gruden K. quantGenius: implementation of a decision support system for qPCR-based gene quantification. BMC Bioinformatics 2017; 18:276. [PMID: 28545393 PMCID: PMC5445471 DOI: 10.1186/s12859-017-1688-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Accepted: 05/16/2017] [Indexed: 12/21/2022] Open
Abstract
Background Quantitative molecular biology remains a challenge for researchers due to inconsistent approaches for control of errors in the final results. Due to several factors that can influence the final result, quantitative analysis and interpretation of qPCR data are still not trivial. Together with the development of high-throughput qPCR platforms, there is a need for a tool allowing for robust, reliable and fast nucleic acid quantification. Results We have developed “quantGenius” (http://quantgenius.nib.si), an open-access web application for a reliable qPCR-based quantification of nucleic acids. The quantGenius workflow interactively guides the user through data import, quality control (QC) and calculation steps. The input is machine- and chemistry–independent. Quantification is performed using the standard curve approach, with normalization to one or several reference genes. The special feature of the application is the implementation of user-guided QC-based decision support system, based on qPCR standards, that takes into account pipetting errors, assay amplification efficiencies, limits of detection and quantification of the assays as well as the control of PCR inhibition in individual samples. The intermediate calculations and final results are exportable in a data matrix suitable for further statistical analysis or visualization. We additionally compare the most important features of quantGenius with similar advanced software tools and illustrate the importance of proper QC system in the analysis of qPCR data in two use cases. Conclusions To our knowledge, quantGenius is the only qPCR data analysis tool that integrates QC-based decision support and will help scientists to obtain reliable results which are the basis for biologically meaningful data interpretation. Electronic supplementary material The online version of this article (doi:10.1186/s12859-017-1688-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Špela Baebler
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, 1000, SI, Slovenia.
| | - Miha Svalina
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, 1000, SI, Slovenia
| | - Marko Petek
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, 1000, SI, Slovenia
| | - Katja Stare
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, 1000, SI, Slovenia
| | - Ana Rotter
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, 1000, SI, Slovenia
| | - Maruša Pompe-Novak
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, 1000, SI, Slovenia
| | - Kristina Gruden
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, 1000, SI, Slovenia
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Bustin SA, Huggett JF. Reproducibility of biomedical research - The importance of editorial vigilance. BIOMOLECULAR DETECTION AND QUANTIFICATION 2017; 11:1-3. [PMID: 28331813 PMCID: PMC5348116 DOI: 10.1016/j.bdq.2017.01.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Many journal editors are a failing to implement their own authors' instructions, resulting in the publication of many articles that do not meet basic standards of transparency, employ unsuitable data analysis methods and report overly optimistic conclusions. This problem is particularly acute where quantitative measurements are made and results in the publication of papers that lack scientific rigor and contributes to the concerns with regard to the reproducibility of biomedical research. This hampers research areas such as biomarker identification, as reproducing all but the most striking changes is challenging and translation to patient care rare.
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Affiliation(s)
- Stephen A Bustin
- Faculty of Medical Science , Anglia Ruskin University, Chelmsford, CM1 1SQ, United Kingdom
| | - Jim F Huggett
- Analytical Microbiology, School of Bioscience and Medicine, Faculty of Health and Medical Science, University of Surrey, Guildford, GU2 7XH, United Kingdom
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Assays for precise quantification of total (including short) and elongated HIV-1 transcripts. J Virol Methods 2016; 242:1-8. [PMID: 28034670 DOI: 10.1016/j.jviromet.2016.12.017] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Revised: 12/21/2016] [Accepted: 12/23/2016] [Indexed: 11/24/2022]
Abstract
Despite intensive study, it is unclear which mechanisms are responsible for latent HIV infection in vivo. One potential mechanism is inhibition of HIV transcriptional elongation, which results in short abortive transcripts containing the trans-activation response (TAR) region. Because the relative levels of total (including short) and processive transcripts provide measures of HIV transcriptional initiation and elongation, there is a compelling need for techniques that accurately measure both. Nonetheless, prior assays for total transcripts have been semi-quantitative and have seen limited application to patient samples. This manuscript reports the validation of quantitative reverse transcription (RT) droplet digital PCR assays for measurement of total (TAR) and processive (R-U5/gag) HIV transcripts. Traditional RT priming strategies can efficiently detect the TAR region on long HIV transcripts but detect <4% of true short transcripts. The TAR assay presented here utilizes an initial polyadenylation step, which provides an accessible RT priming site and detects short and long transcripts with approximately equal efficiency (70%). By applying these assays to blood samples from 8 ART-treated HIV+ individuals, total HIV transcripts were detected at levels >10-fold higher than elongated transcripts, implying a substantial block to transcriptional elongation in vivo. This approach may be applied to other difficult-to-prime RNA targets.
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Haider M, Ji B, Haselgrübler T, Sonnleitner A, Aberger F, Hesse J. A microfluidic multiwell chip for enzyme-free detection of mRNA from few cells. Biosens Bioelectron 2016; 86:20-26. [DOI: 10.1016/j.bios.2016.06.019] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Revised: 06/01/2016] [Accepted: 06/07/2016] [Indexed: 11/16/2022]
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Pett H, Gonçalves BP, Dicko A, Nébié I, Tiono AB, Lanke K, Bradley J, Chen I, Diawara H, Mahamar A, Soumare HM, Traore SF, Baber I, Sirima SB, Sauerwein R, Brown J, Gosling R, Felger I, Drakeley C, Bousema T. Comparison of molecular quantification of Plasmodium falciparum gametocytes by Pfs25 qRT-PCR and QT-NASBA in relation to mosquito infectivity. Malar J 2016; 15:539. [PMID: 27821171 PMCID: PMC5100312 DOI: 10.1186/s12936-016-1584-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2016] [Accepted: 10/28/2016] [Indexed: 11/24/2022] Open
Abstract
Background Quantifying gametocyte densities in natural malaria infections is important to estimate malaria transmission potential. Two molecular methods (Pfs25 mRNA quantitative reverse transcriptase PCR (qRT-PCR) and Pfs25 mRNA quantitative nucleic acid sequence based amplification (QT-NASBA)) are commonly used to determine gametocyte densities in clinical and epidemiological studies and allow gametocyte detection at densities below the microscopic threshold for detection. Here, reproducibility of these measurements and the association between estimated gametocyte densities and mosquito infection rates were compared. Methods To quantify intra- and inter-assay variation of QT-NASBA and qRT-PCR, a series of experiments was performed using culture-derived mature Plasmodium falciparum gametocytes from three different parasite isolates (NF54, NF135, NF166). Pfs25 mRNA levels were also determined in samples from clinical trials in Mali and Burkina Faso using both methods. Agreement between the two methods and association with mosquito infection rates in membrane feeding assays were assessed. Results Intra- and inter-assay variability was larger in QT-NASBA compared to qRT-PCR, particularly at low gametocyte densities (< 1 gametocyte per μL). Logistic models, including log-transformed gametocytaemia estimated by QT-NASBA, explained variability in mosquito feeding experiment results as well as log-transformed gametocytaemia by qRT-PCR (marginal R2 0.28 and 0.22, respectively). Densities determined by both methods strongly correlated with mosquito infection rates [Spearman’s rank correlation coefficient, 0.59 for qRT-PCR and 0.64 for QT-NASBA (P < 0.001 for both)]. Gametocyte densities estimated by qRT-PCR were higher than levels estimated by QT-NASBA or light microscopy at high densities (>100 gametocyte per μL). Samples collected in one of the two transmission studies had extremely low gametocyte densities by both molecular methods, which is suggestive of RNA degradation due to an unknown number of freeze–thaw cycles and illustrates the reliance of molecular gametocyte diagnostics on a reliable cold-chain. Conclusions The experiments indicate that both qRT-PCR and QT-NASBA are of value for quantifying mature gametocytes in samples collected in field studies. For both assays, estimated gametocyte densities correlated well with mosquito infection rates. QT-NASBA is less reproducible than qRT-PCR, particularly for low gametocyte densities. Electronic supplementary material The online version of this article (doi:10.1186/s12936-016-1584-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Helmi Pett
- Department of Medical Microbiology, Radboud University Medical Center, Geert Grooteplein Zuid 26-28, 6500 HB, Nijmegen, The Netherlands
| | - Bronner P Gonçalves
- Department of Immunology and Infection, London School of Hygiene & Tropical Medicine, London, UK
| | - Alassane Dicko
- Malaria Research and Training Centre, Faculty of Pharmacy and Faculty of Medicine and Dentistry, University of Science, Techniques and Technologies of Bamako, Bamako, Mali
| | - Issa Nébié
- Centre National de Recherche et de Formation sur le Paludisme, Ouagadougou, Burkina Faso
| | - Alfred B Tiono
- Centre National de Recherche et de Formation sur le Paludisme, Ouagadougou, Burkina Faso
| | - Kjerstin Lanke
- Department of Medical Microbiology, Radboud University Medical Center, Geert Grooteplein Zuid 26-28, 6500 HB, Nijmegen, The Netherlands
| | - John Bradley
- MRC Tropical Epidemiology Group, Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK
| | - Ingrid Chen
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA
| | - Halimatou Diawara
- Malaria Research and Training Centre, Faculty of Pharmacy and Faculty of Medicine and Dentistry, University of Science, Techniques and Technologies of Bamako, Bamako, Mali
| | - Almahamoudou Mahamar
- Malaria Research and Training Centre, Faculty of Pharmacy and Faculty of Medicine and Dentistry, University of Science, Techniques and Technologies of Bamako, Bamako, Mali
| | - Harouna M Soumare
- Malaria Research and Training Centre, Faculty of Pharmacy and Faculty of Medicine and Dentistry, University of Science, Techniques and Technologies of Bamako, Bamako, Mali
| | - Sekou F Traore
- Malaria Research and Training Centre, Faculty of Pharmacy and Faculty of Medicine and Dentistry, University of Science, Techniques and Technologies of Bamako, Bamako, Mali
| | - Ibrahima Baber
- Malaria Research and Training Centre, Faculty of Pharmacy and Faculty of Medicine and Dentistry, University of Science, Techniques and Technologies of Bamako, Bamako, Mali
| | - Sodiomon B Sirima
- Centre National de Recherche et de Formation sur le Paludisme, Ouagadougou, Burkina Faso
| | - Robert Sauerwein
- Department of Medical Microbiology, Radboud University Medical Center, Geert Grooteplein Zuid 26-28, 6500 HB, Nijmegen, The Netherlands
| | - Joelle Brown
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA
| | - Roly Gosling
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA
| | - Ingrid Felger
- Molecular Diagnostics Unit, Swiss Tropical and Public Health Institute, Basel, Switzerland
| | - Chris Drakeley
- Department of Immunology and Infection, London School of Hygiene & Tropical Medicine, London, UK
| | - Teun Bousema
- Department of Medical Microbiology, Radboud University Medical Center, Geert Grooteplein Zuid 26-28, 6500 HB, Nijmegen, The Netherlands.
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Campomenosi P, Gini E, Noonan DM, Poli A, D'Antona P, Rotolo N, Dominioni L, Imperatori A. A comparison between quantitative PCR and droplet digital PCR technologies for circulating microRNA quantification in human lung cancer. BMC Biotechnol 2016; 16:60. [PMID: 27538962 PMCID: PMC4991011 DOI: 10.1186/s12896-016-0292-7] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Accepted: 08/13/2016] [Indexed: 12/18/2022] Open
Abstract
Background Selected microRNAs (miRNAs) that are abnormally expressed in the serum of patients with lung cancer have recently been proposed as biomarkers of this disease. The measurement of circulating miRNAs, however, requires a highly reliable quantification method. Quantitative real-time PCR (qPCR) is the most commonly used method, but it lacks reliable endogenous reference miRNAs for normalization of results in biofluids. When used in absolute quantification, it must rely on the use of external calibrators. Droplet digital PCR (ddPCR) is a recently introduced technology that overcomes the normalization issue and may facilitate miRNA measurement. Here we compared the performance of absolute qPCR and ddPCR techniques for quantifying selected miRNAs in the serum. Results In the first experiment, three miRNAs, proposed in the literature as lung cancer biomarkers (miR-21, miR-126 and let-7a), were analyzed in a set of 15 human serum samples. Four independent qPCR and four independent ddPCR amplifications were done on the same samples and used to estimate the precision and correlation of miRNA measurements obtained with the two techniques. The precision of the two methods was evaluated by calculating the Coefficient of Variation (CV) of the four independent measurements obtained with each technique. The CV was similar or smaller in ddPCR than in qPCR for all miRNAs tested, and was significantly smaller for let-7a (p = 0.028). Linear regression analysis of the miRNA values obtained with qPCR and ddPCR showed strong correlation (p < 0.001). To validate the correlation obtained with the two techniques in the first experiment, in a second experiment the same miRNAs were measured in a larger cohort (70 human serum samples) by both qPCR and ddPCR. The correlation of miRNA analyses with the two methods was significant for all three miRNAs. Moreover, in our experiments the ddPCR technique had higher throughput than qPCR, at a similar cost-per-sample. Conclusions Analyses of serum miRNAs performed with qPCR and ddPCR were largely concordant. Both qPCR and ddPCR can reliably be used to quantify circulating miRNAs, however, ddPCR revealed similar or greater precision and higher throughput of analysis. Electronic supplementary material The online version of this article (doi:10.1186/s12896-016-0292-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Paola Campomenosi
- Department of Biotechnology and Life Sciences (DBSV) and "The Protein Factory", University of Insubria, Via JH Dunant, 3, 21100, Varese, Italy. .,The Protein Factory, Centro Interuniversitario di Ricerca in Biotecnologie Proteiche, Politecnico di Milano, ICRM-CNR Milano and University of Insubria, Varese, Italy.
| | - Elisabetta Gini
- Department of Biotechnology and Life Sciences (DBSV) and "The Protein Factory", University of Insubria, Via JH Dunant, 3, 21100, Varese, Italy.,Department of Surgical Sciences and Human Morphology, DSCM, University of Insubria, Via Guicciardini, 9, 21100, Varese, Italy
| | - Douglas M Noonan
- Department of Biotechnology and Life Sciences (DBSV) and "The Protein Factory", University of Insubria, Via JH Dunant, 3, 21100, Varese, Italy.,Scientific and Technological Pole, IRCCS MultiMedica, Milan, Italy
| | - Albino Poli
- Department of Public Health and Community Medicine, University of Verona, Verona, Italy
| | - Paola D'Antona
- Department of Biotechnology and Life Sciences (DBSV) and "The Protein Factory", University of Insubria, Via JH Dunant, 3, 21100, Varese, Italy.,Department of Surgical Sciences and Human Morphology, DSCM, University of Insubria, Via Guicciardini, 9, 21100, Varese, Italy
| | - Nicola Rotolo
- Department of Surgical Sciences and Human Morphology, DSCM, University of Insubria, Via Guicciardini, 9, 21100, Varese, Italy
| | - Lorenzo Dominioni
- Department of Surgical Sciences and Human Morphology, DSCM, University of Insubria, Via Guicciardini, 9, 21100, Varese, Italy
| | - Andrea Imperatori
- Department of Surgical Sciences and Human Morphology, DSCM, University of Insubria, Via Guicciardini, 9, 21100, Varese, Italy
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Obolenskaya MY, Kuklin AV, Rodrigez RR, Martsenyuk OP, Korneyeva K, Docenko VA, Draguschenko OO. Practical approach to quantification of mRNA abundance using RT-qPCR, normalization of experimental data and MIQE. ACTA ACUST UNITED AC 2016. [DOI: 10.7124/bc.00091a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
| | - A. V. Kuklin
- Institute of Molecular Biology and Genetics, NAS of Ukraine
| | - R. R. Rodrigez
- Institute of Molecular Biology and Genetics, NAS of Ukraine
| | | | - K. Korneyeva
- Institute of Molecular Biology and Genetics, NAS of Ukraine
| | - V. A. Docenko
- Institute of Molecular Biology and Genetics, NAS of Ukraine
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