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Bustin SA. Improving the quality of quantitative polymerase chain reaction experiments: 15 years of MIQE. Mol Aspects Med 2024; 96:101249. [PMID: 38290180 DOI: 10.1016/j.mam.2024.101249] [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: 10/24/2023] [Revised: 01/02/2024] [Accepted: 01/15/2024] [Indexed: 02/01/2024]
Abstract
The quantitative polymerase chain reaction (qPCR) is fundamental to molecular biology. It is not just a laboratory technique, qPCR is a bridge between research and clinical practice. Its theoretical foundations guide the design of experiments, while its practical implications extend to diagnostics, treatment, and research advancements in the life sciences, human and veterinary medicine, agriculture, and forensics. However, the accuracy, reliability and reproducibility of qPCR data face challenges arising from various factors associated with experimental design, execution, data analysis and inadequate reporting details. Addressing these concerns, the Minimum Information for the Publication of Quantitative Real-Time PCR Experiments (MIQE) guidelines have emerged as a cohesive framework offering a standardised set of recommendations that describe the essential information required for assessing qPCR experiments. By emphasising the importance of methodological rigour, the MIQE guidelines have made a major contribution to improving the trustworthiness, consistency, and transparency of many published qPCR results. However, major challenges related to awareness, resources, and publication pressures continue to affect their consistent application.
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Affiliation(s)
- Stephen A Bustin
- Medical Technology Research Centre, Anglia Ruskin University, Chelmsford, Essex, CM1 1SQ, UK.
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Tavallaie M, Khafaei M. An Enhanced Quantitative Reverse Transcription-PCR Approach for Measuring Circulating MicroRNAs. Methods Mol Biol 2024; 2745:227-231. [PMID: 38060189 DOI: 10.1007/978-1-0716-3577-3_14] [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: 12/08/2023]
Abstract
Short (22 nt) RNAs called microRNAs (miRNAs) bind to and inhibit target messenger RNAs in gene regulatory networks. Recent study suggests that miRNAs circulate in a stable, cell-free form and that particular miRNAs in plasma or serum may be biomarkers for cancer and other diseases. Circulating miRNAs as biomarkers provide distinct challenges including pre-analytic variance and data standardization. We describe our qRT-PCR approach for measuring circulating miRNAs as biomarkers, as well as sample preparation, experimental design, and data processing issues.
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Affiliation(s)
| | - Mostafa Khafaei
- National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
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3
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Guterres A. Viral load: We need a new look at an old problem? J Med Virol 2023; 95:e29061. [PMID: 37638475 DOI: 10.1002/jmv.29061] [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: 01/27/2023] [Revised: 07/22/2023] [Accepted: 08/17/2023] [Indexed: 08/29/2023]
Abstract
The concept of viral load was introduced in the 1980s to measure the amount of viral genetic material in a person's blood, primarily for human immunodeficiency virus (HIV). It has since become crucial for monitoring HIV infection progression and assessing the efficacy of antiretroviral therapy. However, during the coronavirus disease 2019 pandemic, the term "viral load" became widely popularized, not only for the scientific community but for the general population. Viral load plays a critical role in both clinical patient management and research, providing valuable insights for antiviral treatment strategies, vaccination efforts, and epidemiological control measures. As measuring viral load is so important, why don't researchers discuss the best way to do it? Is it simply acceptable to use raw Ct values? Relying solely on Ct values for viral load estimation can be problematic due to several reasons. First, Ct values can vary between different quantitative polymerase chain reaction assays, platforms, and laboratories, making it difficult to compare data across studies. Second, Ct values do not directly measure the quantity of viral particles in a sample and they can be influenced by various factors such as initial viral load, sample quality, and assay sensitivity. Moreover, variations in viral RNA extraction and reverse-transcription steps can further impact the accuracy of viral load estimation, emphasizing the need for careful interpretation of Ct values in viral load assessment. Interestingly, we did not observe scientific articles addressing different strategies to quantify viral load. The absence of standardized and validated methods impedes the implementation of viral load monitoring in clinical management. The variability in cell quantities within samples and the variation in viral particle numbers within infected cells further challenge accurate viral load measurement and interpretation. To advance the field and improve patient outcomes, there is an urgent need for the development and validation of tailored, standardized methods for precise viral load quantification.
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Affiliation(s)
- Alexandro Guterres
- Laboratório de Hantaviroses e Rickettsioses, Instituto Oswaldo Cruz Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro, Brazil
- Laboratório de Tecnologia Imunológica, Instituto de Tecnologia em Imunobiológicos, Vice-Diretoria de Desenvolvimento Tecnológico, Bio-Manguinhos, Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro, Brazil
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4
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Lee CJ, Shin W, Song M, Shin SS, Park Y, Srikulnath K, Kim DH, Han K. Comparison of digital PCR platforms using the molecular marker. Genomics Inform 2023; 21:e24. [PMID: 37704210 PMCID: PMC10326530 DOI: 10.5808/gi.23008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 03/27/2023] [Accepted: 03/29/2023] [Indexed: 07/08/2023] Open
Abstract
Assays of clinical diagnosis and species identification using molecular markers are performed according to a quantitative method in consideration of sensitivity, cost, speed, convenience, and specificity. However, typical polymerase chain reaction (PCR) assay is difficult to quantify and have various limitations. In addition, to perform quantitative analysis with the quantitative real-time PCR (qRT-PCR) equipment, a standard curve or normalization using reference genes is essential. Within the last a decade, previous studies have reported that the digital PCR (dPCR) assay, a third-generation PCR, can be applied in various fields by overcoming the shortcomings of typical PCR and qRT-PCR assays. We selected Stilla Naica System (Stilla Technologies), Droplet Digital PCR Technology (Bio-Rad), and Lab on an Array Digital Real-Time PCR analyzer system (OPTOLANE) for comparative analysis among the various droplet digital PCR platforms currently in use commercially. Our previous study discovered a molecular marker that can distinguish Hanwoo species (Korean native cattle) using Hanwoo-specific genomic structural variation. Here, we report the pros and cons of the operation of each dPCR platform from various perspectives using this species identification marker. In conclusion, we hope that this study will help researchers to select suitable dPCR platforms according to their purpose and resources.
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Affiliation(s)
- Cherl-Joon Lee
- Department of Bio-Convergence Engineering, Dankook University, Yongin 16890, Korea
| | - Wonseok Shin
- NGS Clinical Laboratory, Dankook University Hospital, Cheonan 31116, Korea
| | | | | | - Yujun Park
- Department of Microbiology, College of Science & Technology, Dankook University, Cheonan 31116, Korea
| | - Kornsorn Srikulnath
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Facult y of Science, Kasetsart University, Bangkok 10900, Thailand
| | - Dong Hee Kim
- Department of Anesthesiology and Pain Management, Dankook University College of Medicine, Cheonan 31116, Korea
| | - Kyudong Han
- Department of Bio-Convergence Engineering, Dankook University, Yongin 16890, Korea
- Department of Microbiology, College of Science & Technology, Dankook University, Cheonan 31116, Korea
- HuNBiome Co., Ltd., R&D Center, Seoul 08507, Korea
- Bio-Medical Engineering Research Center, Dankook University, Cheonan 31116, Korea
- DKU-Theragen Institute for NGS Analysis (DTiNa), Cheonan 31116, Korea
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5
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Cerda A, Rivera M, Armijo G, Ibarra-Henriquez C, Reyes J, Blázquez-Sánchez P, Avilés J, Arce A, Seguel A, Brown AJ, Vásquez Y, Cortez-San Martín M, Cubillos FA, García P, Ferres M, Ramírez-Sarmiento CA, Federici F, Gutiérrez RA. An Open One-Step RT-qPCR for SARS-CoV-2 detection. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2021.11.29.21267000. [PMID: 34909786 PMCID: PMC8669853 DOI: 10.1101/2021.11.29.21267000] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The COVID-19 pandemic has resulted in millions of deaths globally, and while several diagnostic systems were proposed, real-time reverse transcription polymerase chain reaction (RT-PCR) remains the gold standard. However, diagnostic reagents, including enzymes used in RT-PCR, are subject to centralized production models and intellectual property restrictions, which present a challenge for less developed countries. With the aim of generating a standardized One-Step open RT-qPCR protocol to detect SARS-CoV-2 RNA in clinical samples, we purified and tested recombinant enzymes and a non-proprietary buffer. The protocol utilized M-MLV RT and Taq DNA pol enzymes to perform a Taqman probe-based assay. Synthetic RNA samples were used to validate the One-Step RT-qPCR components, and the kit showed comparable sensitivity to approved commercial kits. The One-Step RT-qPCR was then tested on clinical samples and demonstrated similar performance to commercial kits in terms of positive and negative calls. This study represents a proof of concept for an open approach to developing diagnostic kits for viral infections and diseases, which could provide a cost-effective and accessible solution for less developed countries.
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Affiliation(s)
- Ariel Cerda
- ANID - Millennium Science Initiative Program - Millennium Institute for Integrative Biology (iBio)
- FONDAP Center for Genome Regulation. Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago, 8331150, Chile
| | - Maira Rivera
- ANID - Millennium Science Initiative Program - Millennium Institute for Integrative Biology (iBio)
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Grace Armijo
- ANID - Millennium Science Initiative Program - Millennium Institute for Integrative Biology (iBio)
- FONDAP Center for Genome Regulation. Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago, 8331150, Chile
| | - Catalina Ibarra-Henriquez
- ANID - Millennium Science Initiative Program - Millennium Institute for Integrative Biology (iBio)
- FONDAP Center for Genome Regulation. Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago, 8331150, Chile
| | - Javiera Reyes
- ANID - Millennium Science Initiative Program - Millennium Institute for Integrative Biology (iBio)
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Paula Blázquez-Sánchez
- ANID - Millennium Science Initiative Program - Millennium Institute for Integrative Biology (iBio)
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Javiera Avilés
- ANID - Millennium Science Initiative Program - Millennium Institute for Integrative Biology (iBio)
| | - Aníbal Arce
- ANID - Millennium Science Initiative Program - Millennium Institute for Integrative Biology (iBio)
| | - Aldo Seguel
- ANID - Millennium Science Initiative Program - Millennium Institute for Integrative Biology (iBio)
| | - Alexander J. Brown
- Department of Biomedical Research, National Jewish Health, Denver, CO, USA
- Department of Immunology & Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Yesseny Vásquez
- Escuela de Ciencias Médicas. Facultad de Medicina. Universidad de Santiago de Chile. USACH, Santiago, Chile
| | - Marcelo Cortez-San Martín
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, USACH, Santiago, Chile
| | - Francisco A. Cubillos
- ANID - Millennium Science Initiative Program - Millennium Institute for Integrative Biology (iBio)
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, USACH, Santiago, Chile
| | - Patricia García
- Departamento de Laboratorios Clínicos. Escuela de Medicina. Facultad de Medicina. Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Marcela Ferres
- Departamento de Laboratorios Clínicos. Escuela de Medicina. Facultad de Medicina. Pontificia Universidad Católica de Chile, Santiago, Chile
| | - César A. Ramírez-Sarmiento
- ANID - Millennium Science Initiative Program - Millennium Institute for Integrative Biology (iBio)
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Fernán Federici
- ANID - Millennium Science Initiative Program - Millennium Institute for Integrative Biology (iBio)
- FONDAP Center for Genome Regulation. Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago, 8331150, Chile
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Rodrigo A. Gutiérrez
- ANID - Millennium Science Initiative Program - Millennium Institute for Integrative Biology (iBio)
- FONDAP Center for Genome Regulation. Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago, 8331150, Chile
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Napoletano S, Battista E, Martone N, Netti PA, Causa F. Direct, precise, enzyme-free detection of miR-103–3p in real samples by microgels with highly specific molecular beacons. Talanta 2023; 259:124468. [PMID: 37011564 DOI: 10.1016/j.talanta.2023.124468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 03/13/2023] [Accepted: 03/16/2023] [Indexed: 03/29/2023]
Abstract
Low abundance, small size, and sequence similarities render microRNA (miRNAs) detection challenging, particularly in real samples, where quantifying weakly expressed miRNAs can be arduous due to interference of more abundant molecules. The standard quantitative reverse transcription polymerase chain reaction (qRT-PCR) requires multiple steps, thermal cycles, and costly enzymatic reactions that can negatively affect results. Here we present a direct, precise, enzyme-free assay based on microgels particles conjugating molecular beacons (MB) capable of optically detecting low abundant miRNAs in real samples. We validate the applicability of microgels assay using qRT-PCR as a reference technology. As a relevant case, we chose miR-103-3p, a valuable diagnostic biomarker for breast cancer, both in serum samples and MCF7 cells. As a result, microgels assay quantifies miRNA molecules at room temperature in a single step, 1 h (vs. 4 hrs for qRT-PCR) without complementary DNA synthesis, amplification, or expensive reagents. Microgels assay exhibits femtomolar sensitivity, single nucleotide specificity, and a wide linear range (102-107 fM) (wider than qRT-PCR), with low sample consumption (2 μL) and excellent linearity (R2= 0.98). To test the selectivity of the microgel assay in real samples, MCF7 cells were considered where the pool of 8 other miRNAs were further upregulated with respect to miRNA 103-3p. In such complex environments, microgels assay selectively detects the miRNA target, mainly due to MB advanced stability and specificity as well as high microgel antifouling properties. These results show the reliability of microgels assay to detect miRNAs in real samples.
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7
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Hue SSS, Jin Y, Cheng H, Bin Masroni MS, Tang LWT, Ho YH, Ong DBL, Leong SM, Tan SY. Tissue-Specific microRNA Expression Profiling to Derive Novel Biomarkers for the Diagnosis and Subtyping of Small B-Cell Lymphomas. Cancers (Basel) 2023; 15:cancers15020453. [PMID: 36672402 PMCID: PMC9856483 DOI: 10.3390/cancers15020453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 12/23/2022] [Accepted: 12/30/2022] [Indexed: 01/13/2023] Open
Abstract
Accurate diagnosis of the most common histological subtypes of small B-cell lymphomas is challenging due to overlapping morphological features and limitations of ancillary testing, which involves a large number of immunostains and molecular investigations. In addition, a common diagnostic challenge is to distinguish reactive lymphoid hyperplasia that do not require additional stains from such lymphomas that need ancillary investigations. We investigated if tissue-specific microRNA (miRNA) expression may provide potential biomarkers to improve the pathology diagnostic workflow. This study seeks to distinguish reactive lymphoid proliferation (RL) from small B-cell lymphomas, and to further distinguish the four main subtypes of small B-cell lymphomas. Two datasets were included: a discovery cohort (n = 100) to screen for differentially expressed miRNAs and a validation cohort (n = 282) to develop classification models. The models were evaluated for accuracy in subtype prediction. MiRNA gene set enrichment was also performed to identify differentially regulated pathways. 306 miRNAs were detected and quantified, resulting in 90-miRNA classification models from which smaller panels of miRNAs biomarkers with good accuracy were derived. Bioinformatic analysis revealed the upregulation of known and other potentially relevant signaling pathways in such lymphomas. In conclusion, this study suggests that miRNA expression profiling may serve as a promising tool to aid the diagnosis of common lymphoid lesions.
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Affiliation(s)
- Susan Swee-Shan Hue
- Department of Pathology, National University Hospital, Level 3 NUH Main Building, 21 Lower Kent Ridge Road, Singapore 119077, Singapore
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Level 3 NUH Main Building, 21 Lower Kent Ridge Road, Singapore 119077, Singapore
| | - Yu Jin
- MiRXES Pte Ltd., 2 Tukang Innovation Grove, JTC MedTech Hub, #08-01, Singapore 618305, Singapore
| | - He Cheng
- MiRXES Pte Ltd., 2 Tukang Innovation Grove, JTC MedTech Hub, #08-01, Singapore 618305, Singapore
| | - Muhammad Sufyan Bin Masroni
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Level 3 NUH Main Building, 21 Lower Kent Ridge Road, Singapore 119077, Singapore
| | - Lloyd Wei Tat Tang
- Department of Pharmacy, Faculty of Science, National University of Singapore, Block S4A, Level 3, 18 Science Drive 4, Singapore 117543, Singapore
| | - Yong Howe Ho
- Department of Pathology, Tan Tock Seng Hospital, Level 2 Podium Block, 11 Jalan Tan Tock Seng, Singapore 308433, Singapore
| | - Diana Bee-Lan Ong
- Department of Pathology, University of Malaya, Lembah Pantai, Kuala Lumpur 50603, Malaysia
| | - Sai Mun Leong
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Level 3 NUH Main Building, 21 Lower Kent Ridge Road, Singapore 119077, Singapore
| | - Soo Yong Tan
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Level 3 NUH Main Building, 21 Lower Kent Ridge Road, Singapore 119077, Singapore
- Advanced Molecular Pathology Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore 138673, Singapore
- Correspondence:
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Lin T, Wu N, Guo J, Li M, Zhong Z, Yu W. Establishment of quantitative nested-PCR of Abelson interactor 1 transcript variant-11. Heliyon 2022; 8:e12119. [PMID: 36561701 PMCID: PMC9764186 DOI: 10.1016/j.heliyon.2022.e12119] [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: 06/22/2022] [Revised: 09/14/2022] [Accepted: 11/28/2022] [Indexed: 12/12/2022] Open
Abstract
Abelson interactor 1 (ABI1), which presents 18 Transcript Variants (TSV), plays an important role in CRC metastasis. Different ABI1-TSVs play synergistic or antagonistic roles in the same pathophysiological events. ABI1 Transcript Variant-11 (ABI1-TSV-11) functionally promotes lymph node metastasis of left-sided colorectal cancer (LsCC) and is an independent molecular marker to evaluate the prognosis of patients with LsCC. However, there is still lack of a quick and accurate method to detect the expression of ABI-TSV-11, distinguishing ABI1-TSV-11 from other 17 TSVs. To establish a rapid method specific for ABI1-TSV-11detection, we developed a quantitative nested-PCR method composed of pre-amplification regular PCR using ABI1 universal primer pair and the followed Real Time (RT)-qPCR using ABI1-TSV-11 specific primer pair spanning exon-exon junction. ABI1-TSV-11-overexpressed SW480 and LoVo cell lines were used to verify the quantitative nested-PCR assay, and the sequencing data was used to evaluate the accuracy of ABI1-TSV-11 quantitative nested-PCR assay. The detection limit was 5.24×104 copies/ml. ABI1-TSV-11 quantitative nested-PCR provides a new technical means for the detection of ABI1-TSV-11.
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Affiliation(s)
- Tingru Lin
- Department of Central Laboratory and Institute of Clinical Molecular Biology, Peking University People's Hospital, Beijing 100044, China,Department of Gastroenterology, Peking University People's Hospital, Beijing 100044, China
| | - Na Wu
- Department of Central Laboratory and Institute of Clinical Molecular Biology, Peking University People's Hospital, Beijing 100044, China
| | - Jingzhu Guo
- Department of Pediatric, Peking University People's Hospital, Beijing 100044, China
| | - Mei Li
- Department of Central Laboratory and Institute of Clinical Molecular Biology, Peking University People's Hospital, Beijing 100044, China
| | - Zhaohui Zhong
- Department of General Surgery, Peking University People's Hospital, Beijing 100044, China
| | - Weidong Yu
- Department of Central Laboratory and Institute of Clinical Molecular Biology, Peking University People's Hospital, Beijing 100044, China,Corresponding author.
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Leonaviciene G, Mazutis L. RNA cytometry of single-cells using semi-permeable microcapsules. Nucleic Acids Res 2022; 51:e2. [PMID: 36268865 PMCID: PMC9841424 DOI: 10.1093/nar/gkac918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 09/23/2022] [Accepted: 10/07/2022] [Indexed: 01/29/2023] Open
Abstract
Analytical tools for gene expression profiling of individual cells are critical for studying complex biological systems. However, the techniques enabling rapid measurements of gene expression on thousands of single-cells are lacking. Here, we report a high-throughput RNA cytometry for digital profiling of single-cells isolated in liquid droplets enveloped by a thin semi-permeable membrane (microcapsules). Due to the selective permeability of the membrane, the desirable enzymes and reagents can be loaded, or replaced, in the microcapsule at any given step by simply changing the reaction buffer in which the microcapsules are dispersed. Therefore, complex molecular biology workflows can be readily adapted to conduct nucleic acid analysis on encapsulated mammalian cells, or other biological species. The microcapsules support sequential multi-step enzymatic reactions and remain intact under different biochemical conditions, freezing, thawing, and thermocycling. Combining microcapsules with conventional FACS provides a high-throughput approach for conducting RNA cytometry of individual cells based on their digital gene expression signature.
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Affiliation(s)
- Greta Leonaviciene
- Institute of Biotechnology, Life Sciences Centre, Vilnius University, 7 Sauletekio av., Vilnius, LT-10257, Lithuania
| | - Linas Mazutis
- To whom correspondence should be addressed. Tel: +370 5 2234356;
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Bohan AE, Purvis KN, Sawyer JT, Bergen WG, Brandebourg TD. Sampling Adipose and Muscle Tissue following Post-Harvest Scalding Does Not Affect RNA Integrity or Real-Time PCR Results in Market Weight Yorkshire Pigs. Foods 2022; 11:foods11121741. [PMID: 35741939 PMCID: PMC9222963 DOI: 10.3390/foods11121741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 06/06/2022] [Accepted: 06/11/2022] [Indexed: 11/16/2022] Open
Abstract
Improving production efficiency while enhancing pork quality is pivotal for strengthening sustainable pork production. Being able to study both gene expression and indices of pork quality from the same anatomical location of an individual animal would better enable research conducted to study relationships between animal growth and carcass merit. To facilitate gene expression studies, adipose and muscle tissue samples are often collected immediately following exsanguination to maximize RNA integrity, which is a primary determinant of the sensitivity of RNA-based assays, such as real-time PCR. However, collecting soft tissue samples requires cutting through the hide or skin. This leaves the underlying tissue exposed during scalding, poses possible food safety issues, and potentially confounds pork quality measures. To overcome these limitations, the effect of tissue sample timing post-harvest on RNA integrity, real-time PCR results, and pork quality measurements was investigated by sampling subcutaneous adipose tissue and longissimus thoracis et lumborum muscle immediately following either exsanguination, scalding, or chilling. Sampling time did not affect RNA quality, as determined by the RNA integrity number of RNA samples purified from either adipose (RIN; p > 0.54) or muscle tissue (p > 0.43). Likewise, the sampling time did not influence the results of real-time PCR analysis of gene expression when comparing RNA samples prepared from adipose or muscle tissue immediately following either exsanguination or scalding (p > 0.92). However, sampling tissue prior to scalding resulted in a greater visual color score (p < 0.001) and lesser L* (p < 0.001) and b* (p < 0.001) values without impacting the 24 h pH (p < 0.41). These results suggested that if both RNA-based assays and meat quality endpoints are to be performed at the same anatomical location on an animal, tissue sampling to facilitate RNA-based assays should occur at a time point immediately following scalding. These findings demonstrated that sampling of adipose and muscle tissue can be delayed until after scalding/dehairing without decreasing the RNA integrity or altering the results of real-time PCR assays, while doing so was associated with little impact on measures of pork quality.
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11
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Hanson PJ, Liu-Fei F, Minato TA, Hossain AR, Rai H, Chen VA, Ng C, Ask K, Hirota JA, McManus BM. Advanced detection strategies for cardiotropic virus infection in a cohort study of heart failure patients. J Transl Med 2022; 102:14-24. [PMID: 34608239 PMCID: PMC8488924 DOI: 10.1038/s41374-021-00669-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 08/20/2021] [Indexed: 12/11/2022] Open
Abstract
The prevalence and contribution of cardiotropic viruses to various expressions of heart failure are increasing, yet primarily underappreciated and underreported due to variable clinical syndromes, a lack of consensus diagnostic standards and insufficient clinical laboratory tools. In this study, we developed an advanced methodology for identifying viruses across a spectrum of heart failure patients. We designed a custom tissue microarray from 78 patients with conditions commonly associated with virus-related heart failure, conditions where viral contribution is typically uncertain, or conditions for which the etiological agent remains suspect but elusive. Subsequently, we employed advanced, highly sensitive in situ hybridization to probe for common cardiotropic viruses: adenovirus 2, coxsackievirus B3, cytomegalovirus, Epstein-Barr virus, hepatitis C and E, influenza B and parvovirus B19. Viral RNA was detected in 46.4% (32/69) of heart failure patients, with 50% of virus-positive samples containing more than one virus. Adenovirus 2 was the most prevalent, detected in 27.5% (19/69) of heart failure patients, while in contrast to previous reports, parvovirus B19 was detected in only 4.3% (3/69). As anticipated, viruses were detected in 77.8% (7/9) of patients with viral myocarditis and 37.5% (6/16) with dilated cardiomyopathy. Additionally, viruses were detected in 50% of patients with coronary artery disease (3/6) and hypertrophic cardiomyopathy (2/4) and in 28.6% (2/7) of transplant rejection cases. We also report for the first time viral detection within a granulomatous lesion of cardiac sarcoidosis and in giant cell myocarditis, conditions for which etiological agents remain unknown. Our study has revealed a higher than anticipated prevalence of cardiotropic viruses within cardiac muscle tissue in a spectrum of heart failure conditions, including those not previously associated with a viral trigger or exacerbating role. Our work forges a path towards a deeper understanding of viruses in heart failure pathogenesis and opens possibilities for personalized patient therapeutic approaches.
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Affiliation(s)
- Paul J Hanson
- UBC Centre for Heart Lung Innovation, Vancouver, BC, Canada.
- UBC Department of Pathology and Laboratory Medicine, Vancouver, BC, Canada.
| | | | | | | | - Harpreet Rai
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON, Canada
| | | | - Coco Ng
- UBC Centre for Heart Lung Innovation, Vancouver, BC, Canada
| | - Kjetil Ask
- Firestone Institute for Respiratory Health - Division of Respirology, Department of Medicine, McMaster University, Hamilton, ON, Canada
| | - Jeremy A Hirota
- Firestone Institute for Respiratory Health - Division of Respirology, Department of Medicine, McMaster University, Hamilton, ON, Canada
| | - Bruce M McManus
- UBC Centre for Heart Lung Innovation, Vancouver, BC, Canada
- UBC Department of Pathology and Laboratory Medicine, Vancouver, BC, Canada
- PROOF Centre of Excellence, Vancouver, BC, Canada
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12
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Huebner T, Steffens M, Scholl C. Molecular Genetic Techniques in Biomarker Analysis Relevant for Drugs Centrally Approved in Europe. Mol Diagn Ther 2021; 26:89-103. [PMID: 34905151 PMCID: PMC8766366 DOI: 10.1007/s40291-021-00567-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/18/2021] [Indexed: 11/26/2022]
Abstract
On the basis of scientific evidence, information on the option, recommendation or requirement to test for pharmacogenetic or pharmacogenomic biomarkers is incorporated in the Summary of Product Characteristics of an increasing number of drugs in Europe. A screening of the Genetic Testing Registry (GTR) showed that a variety of molecular genetic testing methods is currently offered worldwide in testing services with regard to according drugs and biomarkers. Thereby, among the methodology indicated in the screened GTR category ‘Molecular Genetics’, next-generation sequencing is applied for identification of the largest proportion of evaluated biomarkers that are relevant for therapeutic management of centrally approved drugs in Europe. However, sufficient information on regulatory clearances, clinical utility, analytical and clinical validity of applied methods is rarely provided.
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Affiliation(s)
- Tatjana Huebner
- Research Division, Federal Institute for Drugs and Medical Devices (BfArM), Kurt-Georg-Kiesinger-Allee 3, 53175, Bonn, North Rhine-Westphalia, Germany.
| | - Michael Steffens
- Research Division, Federal Institute for Drugs and Medical Devices (BfArM), Kurt-Georg-Kiesinger-Allee 3, 53175, Bonn, North Rhine-Westphalia, Germany
| | - Catharina Scholl
- Research Division, Federal Institute for Drugs and Medical Devices (BfArM), Kurt-Georg-Kiesinger-Allee 3, 53175, Bonn, North Rhine-Westphalia, Germany
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13
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Lee CJ, Shin W, Mun S, Yu M, Choi YB, Kim DH, Han K. Diagnostic evaluation of qRT-PCR-based kit and dPCR-based kit for COVID-19. Genes Genomics 2021; 43:1277-1288. [PMID: 34524612 PMCID: PMC8441239 DOI: 10.1007/s13258-021-01162-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Accepted: 09/01/2021] [Indexed: 11/25/2022]
Abstract
Background Coronavirus disease of 2019 (COVID-19) is well known as a fatal disease, first discovered at Wuhan in China, ranging from mild to death, such as shortness of breath and fever. Early diagnosis of COVID-19 is a crucial point in preventing global prevalence. Objective We aimed to evaluate the diagnostic competency and efficiency with the Allplex™ 2019-nCoV Assay kit and the Dr. PCR 20 K COVID-19 Detection kit, designed based on the qRT-PCR and dPCR technologies, respectively. Methods A total of 30 negative and 20 COVID-19 positive specimens were assigned to the diagnostic test by using different COVID-19 diagnosis kits. Diagnostic accuracy was measured by statistical testing with sensitivity, specificity, and co-efficiency calculations. Results Comparing both diagnostic kits, we confirmed that the diagnostic results of 30 negative and 20 positive cases were the same pre-diagnostic results. The diagnostic statistics test results were perfectly matched with value (1). Cohen’s Kappa coefficient was demonstrated that the given kits in two different ways were “almost perfect” with value (1). In evaluating the detection capability, the dilutional linearity experiments substantiate that the Dr. PCR 20 K COVID-19 Detection kit could detect SARS-CoV-2 viral load at a concentration ten times lower than that of the Allplex™ 2019-nCoV Assay kit. Conclusions In this study, we propose that the dPCR diagnosis using LOAA dPCR could be a powerful method for COVID-19 point-of-care tests requiring immediate diagnosis in a limited time and space through the advantages of relatively low sample concentration and small equipment size compared to conventional qRT-PCR. Supplementary Information The online version contains supplementary material available at 10.1007/s13258-021-01162-4.
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Affiliation(s)
- Cherl-Joon Lee
- Department of Bio-Convergence Engineering, Dankook University, Jukjeon, 16890, Republic of Korea
| | - Wonseok Shin
- NGS Clinical Laboratory, Dankook University Hospital, Cheonan, 31116, Republic of Korea
| | - Seyoung Mun
- Department of Nanobiomedical Science, Dankook University, Cheonan, 31116, Republic of Korea.,Center for Bio-Medical Engineering Core Facility, Dankook University, Cheonan, 31116, Republic of Korea.,DKU-Theragen institute for NGS analysis (DTiNa), Cheonan, 31116, Republic of Korea
| | - Minjae Yu
- DKU-Theragen institute for NGS analysis (DTiNa), Cheonan, 31116, Republic of Korea.,Department of Microbiology, College of Science and Technology, Dankook University, Cheonan, 31116, Republic of Korea
| | - Young-Bong Choi
- Department of Chemistry, College of Science and Technology, Dankook University, Cheonan, 31116, Republic of Korea
| | - Dong Hee Kim
- Department of Anesthesiology and Pain Management, Dankook University College of Medicine, Cheonan, 31116, Republic of Korea.
| | - Kyudong Han
- Department of Bio-Convergence Engineering, Dankook University, Jukjeon, 16890, Republic of Korea. .,NGS Clinical Laboratory, Dankook University Hospital, Cheonan, 31116, Republic of Korea. .,Center for Bio-Medical Engineering Core Facility, Dankook University, Cheonan, 31116, Republic of Korea. .,DKU-Theragen institute for NGS analysis (DTiNa), Cheonan, 31116, Republic of Korea. .,Department of Microbiology, College of Science and Technology, Dankook University, Cheonan, 31116, Republic of Korea.
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14
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Bustin S, Kirvell S, Huggett JF, Nolan T. RT-qPCR Diagnostics: The "Drosten" SARS-CoV-2 Assay Paradigm. Int J Mol Sci 2021; 22:ijms22168702. [PMID: 34445406 PMCID: PMC8395416 DOI: 10.3390/ijms22168702] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 07/31/2021] [Accepted: 08/11/2021] [Indexed: 12/23/2022] Open
Abstract
The reverse transcription quantitative polymerase chain reaction (RT-qPCR) is an established tool for the diagnosis of RNA pathogens. Its potential for automation has caused it to be used as a presence/absence diagnostic tool even when RNA quantification is not required. This technology has been pushed to the forefront of public awareness by the COVID-19 pandemic, as its global application has enabled rapid and analytically sensitive mass testing, with the first assays targeting three viral genes published within days of the publication of the SARS-CoV-2 genomic sequence. One of those, targeting the RNA-dependent RNA polymerase gene, has been heavily criticised for supposed scientific flaws at the molecular and methodological level, and this criticism has been extrapolated to doubts about the validity of RT-qPCR for COVID-19 testing in general. We have analysed this assay in detail, and our findings reveal some limitations but also highlight the robustness of the RT-qPCR methodology for SARS-CoV-2 detection. Nevertheless, whilst our data show that some errors can be tolerated, it is always prudent to confirm that the primer and probe sequences complement their intended target, since, when errors do occur, they may result in a reduction in the analytical sensitivity. However, in this case, it is unlikely that a mismatch will result in poor specificity or a significant number of false-positive SARS-CoV-2 diagnoses, especially as this is routinely checked by diagnostic laboratories as part of their quality assurance.
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Affiliation(s)
- Stephen Bustin
- Medical Technology Research Centre, Faculty of Health, Education, Medicine and Social Care, Anglia Ruskin University Chelmsford, Chelmsford CM1 1SQ, UK; (S.K.); (T.N.)
- Correspondence:
| | - Sara Kirvell
- Medical Technology Research Centre, Faculty of Health, Education, Medicine and Social Care, Anglia Ruskin University Chelmsford, Chelmsford CM1 1SQ, UK; (S.K.); (T.N.)
| | - Jim F. Huggett
- National Measurement Laboratory, LGC, Queens Rd, Teddington, London TW11 0LY, UK;
| | - Tania Nolan
- Medical Technology Research Centre, Faculty of Health, Education, Medicine and Social Care, Anglia Ruskin University Chelmsford, Chelmsford CM1 1SQ, UK; (S.K.); (T.N.)
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15
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Kozłowska J, Kolenda T, Poter P, Sobocińska J, Guglas K, Stasiak M, Bliźniak R, Teresiak A, Lamperska K. Long Intergenic Non-Coding RNAs in HNSCC: From "Junk DNA" to Important Prognostic Factor. Cancers (Basel) 2021; 13:2949. [PMID: 34204634 PMCID: PMC8231241 DOI: 10.3390/cancers13122949] [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: 05/24/2021] [Revised: 06/08/2021] [Accepted: 06/09/2021] [Indexed: 12/24/2022] Open
Abstract
Head and neck squamous cell carcinoma is one of the most common and fatal cancers worldwide. Even a multimodal approach consisting of standard chemo- and radiotherapy along with surgical resection is only effective in approximately 50% of the cases. The rest of the patients develop a relapse of the disease and acquire resistance to treatment. Especially this group of individuals needs novel, personalized, targeted therapy. The first step to discovering such solutions is to investigate the tumor microenvironment, thus understanding the role and mechanism of the function of coding and non-coding sequences of the human genome. In recent years, RNA molecules gained great interest when the complex character of their impact on our biology allowed them to come out of the shadows of the "junk DNA" label. Furthermore, long non-coding RNAs (lncRNA), specifically the intergenic subgroup (lincRNA), are one of the most aberrantly expressed in several malignancies, which makes them particularly promising future diagnostic biomarkers and therapeutic targets. This review contains characteristics of known and validated lincRNAs in HNSCC, such as XIST, MALAT, HOTAIR, HOTTIP, lincRNA-p21, LINC02487, LINC02195, LINC00668, LINC00519, LINC00511, LINC00460, LINC00312, and LINC00052, with a description of their prognostic abilities. Even though much work remains to be done, lincRNAs are important factors in cancer biology that will become valuable biomarkers of tumor stage, outcome prognosis, and contribution to personalized medicine.
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Affiliation(s)
- Joanna Kozłowska
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, Garbary 15, 61-866 Poznan, Poland; (T.K.); (J.S.); (K.G.); (M.S.); (R.B.); (A.T.)
- Research and Implementation Unit, Greater Poland Cancer Centre, Garbary 15, 61-866 Poznan, Poland;
| | - Tomasz Kolenda
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, Garbary 15, 61-866 Poznan, Poland; (T.K.); (J.S.); (K.G.); (M.S.); (R.B.); (A.T.)
- Research and Implementation Unit, Greater Poland Cancer Centre, Garbary 15, 61-866 Poznan, Poland;
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, 8 Rokietnicka Street, 60-806 Poznan, Poland
| | - Paulina Poter
- Research and Implementation Unit, Greater Poland Cancer Centre, Garbary 15, 61-866 Poznan, Poland;
- Department of Oncologic Pathology and Prophylaxis, Poznan University of Medical Sciences, Greater Poland Cancer Centere, Garbary 15, 61-866 Poznan, Poland
- Department of Pathology, Pomeranian Medical University, Rybacka 1, 70-204 Szczecin, Poland
| | - Joanna Sobocińska
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, Garbary 15, 61-866 Poznan, Poland; (T.K.); (J.S.); (K.G.); (M.S.); (R.B.); (A.T.)
- Research and Implementation Unit, Greater Poland Cancer Centre, Garbary 15, 61-866 Poznan, Poland;
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, 8 Rokietnicka Street, 60-806 Poznan, Poland
| | - Kacper Guglas
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, Garbary 15, 61-866 Poznan, Poland; (T.K.); (J.S.); (K.G.); (M.S.); (R.B.); (A.T.)
- Research and Implementation Unit, Greater Poland Cancer Centre, Garbary 15, 61-866 Poznan, Poland;
- Postgraduate School of Molecular Medicine, Medical University of Warsaw, ul. Zwirki 61 and ul. Wigury, 02-091 Warsaw, Poland
| | - Maciej Stasiak
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, Garbary 15, 61-866 Poznan, Poland; (T.K.); (J.S.); (K.G.); (M.S.); (R.B.); (A.T.)
- Research and Implementation Unit, Greater Poland Cancer Centre, Garbary 15, 61-866 Poznan, Poland;
| | - Renata Bliźniak
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, Garbary 15, 61-866 Poznan, Poland; (T.K.); (J.S.); (K.G.); (M.S.); (R.B.); (A.T.)
- Research and Implementation Unit, Greater Poland Cancer Centre, Garbary 15, 61-866 Poznan, Poland;
| | - Anna Teresiak
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, Garbary 15, 61-866 Poznan, Poland; (T.K.); (J.S.); (K.G.); (M.S.); (R.B.); (A.T.)
- Research and Implementation Unit, Greater Poland Cancer Centre, Garbary 15, 61-866 Poznan, Poland;
| | - Katarzyna Lamperska
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, Garbary 15, 61-866 Poznan, Poland; (T.K.); (J.S.); (K.G.); (M.S.); (R.B.); (A.T.)
- Research and Implementation Unit, Greater Poland Cancer Centre, Garbary 15, 61-866 Poznan, Poland;
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16
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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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17
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Kim MY, Jung S, Kim J, Lee HJ, Jeong S, Sim SJ, Kim SK. Highly sensitive and multiplexed one-step RT-qPCR for profiling genes involved in the circadian rhythm using microparticles. Sci Rep 2021; 11:6463. [PMID: 33742035 PMCID: PMC7979730 DOI: 10.1038/s41598-021-85728-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2020] [Accepted: 11/09/2020] [Indexed: 11/09/2022] Open
Abstract
Given the growing interest in molecular diagnosis, highly extensive and selective detection of genetic targets from a very limited amount of samples is in high demand. We demonstrated the highly sensitive and multiplexed one-step RT-qPCR platform for RNA analysis using microparticles as individual reactors. Those particles are equipped with a controlled release system of thermo-responsive materials, and are able to capture RNA targets inside. The particle-based assay can successfully quantify multiple target RNAs from only 200 pg of total RNA. The assay can also quantify target RNAs from a single cell with the aid of a pre-concentration process. We carried out 8-plex one-step RT-qPCR using tens of microparticles, which allowed extensive mRNA profiling. The circadian cycles were shown by the multiplex one-step RT-qPCR in human cell and human hair follicles. Reliable 24-plex one-step RT-qPCR was developed using a single operation in a PCR chip without any loss of performance (i.e., selectivity and sensitivity), even from a single hair. Many other disease-related transcripts can be monitored using this versatile platform. It can also be used non–invasively for samples obtained in clinics.
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Affiliation(s)
- Mi Yeon Kim
- Center for Molecular Recognition Research, Materials and Life Science Research Division, Korea Institute of Science and Technology(KIST), Seoul, KS013, Korea.,Department of Chemical Biological Engineering, Korea University, Seoul, KS013, Korea
| | - Seungwon Jung
- Center for Molecular Recognition Research, Materials and Life Science Research Division, Korea Institute of Science and Technology(KIST), Seoul, KS013, Korea
| | - Junsun Kim
- Center for Molecular Recognition Research, Materials and Life Science Research Division, Korea Institute of Science and Technology(KIST), Seoul, KS013, Korea.,Department of Chemical Biological Engineering, Korea University, Seoul, KS013, Korea
| | - Heon Jeong Lee
- Department of Psychiatry and Chronobiology Institute, Korea University College of Medicine, Seoul, KS013, Korea
| | - Seunghwa Jeong
- Department of Psychiatry and Chronobiology Institute, Korea University College of Medicine, Seoul, KS013, Korea
| | - Sang Jun Sim
- Department of Chemical Biological Engineering, Korea University, Seoul, KS013, Korea
| | - Sang Kyung Kim
- Center for Molecular Recognition Research, Materials and Life Science Research Division, Korea Institute of Science and Technology(KIST), Seoul, KS013, Korea.
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18
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Xiong F, Cheng X, Zhang C, Klar RM, He T. Optimizations for identifying reference genes in bone and cartilage bioengineering. BMC Biotechnol 2021; 21:25. [PMID: 33731065 PMCID: PMC7972220 DOI: 10.1186/s12896-021-00685-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Accepted: 03/08/2021] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR) remains one of the best-established techniques to assess gene expression patterns. However, appropriate reference gene(s) selection remains a critical and challenging subject in which inappropriate reference gene selction can distort results leading to false interpretations. To date, mixed opinions still exist in how to choose the most optimal reference gene sets in accodrance to the Minimum Information for Publication of Quantitative Real-Time PCR Experiments (MIQE) guideline. Therefore, the purpose of this study was to investigate which schemes were the most feasible for the identification of reference genes in a bone and cartilage bioengineering experimental setting. In this study, rat bone mesenchymal stem cells (rBMSCs), skeletal muscle tissue and adipose tissue were utilized, undergoing either chondrogenic or osteogenic induction, to investigate the optimal reference gene set identification scheme that would subsequently ensure stable and accurate interpretation of gene expression in bone and cartilage bioengineering. RESULTS The stability and pairwise variance of eight candidate reference genes were analyzed using geNorm. The V0.15- vs. Vmin-based normalization scheme in rBMSCs had no significant effect on the eventual normalization of target genes. In terms of the muscle tissue, the results of the correlation of NF values between the V0.15 and Vmin schemes and the variance of target genes expression levels generated by these two schemes showed that different schemes do indeed have a significant effect on the eventual normalization of target genes. Three selection schemes were adopted in terms of the adipose tissue, including the three optimal reference genes (Opt3), V0.20 and Vmin schemes, and the analysis of NF values with eventual normalization of target genes showed that the different selection schemes also have a significant effect on the eventual normalization of target genes. CONCLUSIONS Based on these results, the proposed cut-off value of Vn/n + 1 under 0.15, according to the geNorm algorithm, should be considered with caution. For cell only experiments, at least rBMSCs, a Vn/n + 1 under 0.15 is sufficient in RT-qPCR studies. However, when using certain tissue types such as skeletal muscle and adipose tissue the minimum Vn/n + 1 should be used instead as this provides a far superior mode of generating accurate gene expression results. We thus recommended that when the stability and variation of a candidate reference genes in a specific study is unclear the minimum Vn/n + 1 should always be used as this ensures the best and most accurate gene expression value is achieved during RT-qPCR assays.
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Affiliation(s)
- Fei Xiong
- Department of Sports Medicine, Wuxi 9th People's Hospital affiliated to Soochow University, Wuxi, Jiangsu, China
| | - Xiangyun Cheng
- Department of Orthopedics, Renji Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Chao Zhang
- Department of Orthopedics, Renji Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Roland Manfred Klar
- Department of Orthopedics, Physical Medicine and Rehabilitation, University Hospital of Munich (LMU), Munich, Germany.
| | - Tao He
- Department of Orthopedics, Renji Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China.
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19
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RNA Extraction from Equine Samples for Equine Influenza Virus. Methods Mol Biol 2021. [PMID: 32170703 DOI: 10.1007/978-1-0716-0346-8_28] [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: 09/09/2023]
Abstract
The primary goals of this chapter are to discuss common viral RNA isolation and purification methods that are routinely used by various diagnostic laboratories and to highlight the advantages and drawbacks of each method and to identify the most suitable and reliable method to increase the sensitivity and specificity of RT-PCR assays for the detection of equine influenza virus (EIV) in clinical specimens. Our experiences and review of literature show that magnetic bead-based nucleic extraction methods (manual and automatic) work well for isolation and purification of EIV RNA from nasal swab specimens. Furthermore, most of the information presented in this chapter could be directly applicable to isolation and purification of nucleic acids (both DNA and RNA) from other equine clinical samples.
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20
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Drag MH, Kilpeläinen TO. Cell-free DNA and RNA-measurement and applications in clinical diagnostics with focus on metabolic disorders. Physiol Genomics 2020; 53:33-46. [PMID: 33346689 DOI: 10.1152/physiolgenomics.00086.2020] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Circulating cell-free DNA (cfDNA) and RNA (cfRNA) hold enormous potential as a new class of biomarkers for the development of noninvasive liquid biopsies in many diseases and conditions. In recent years, cfDNA and cfRNA have been studied intensely as tools for noninvasive prenatal testing, solid organ transplantation, cancer screening, and monitoring of tumors. In obesity, higher cfDNA concentration indicates accelerated cellular turnover of adipocytes during expansion of adipose mass and may be directly involved in the development of adipose tissue insulin resistance by inducing inflammation. Furthermore, cfDNA and cfRNA have promising diagnostic value in a range of obesity-related metabolic disorders, such as nonalcoholic fatty liver disease, type 2 diabetes, and diabetic complications. Here, we review the current and future applications of cfDNA and cfRNA within clinical diagnostics, discuss technical and analytical challenges in the field, and summarize the opportunities of using cfDNA and cfRNA in the diagnostics and prognostics of obesity-related metabolic disorders.
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Affiliation(s)
- Markus H Drag
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Tuomas O Kilpeläinen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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21
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Zhang Y, Gu Z, Zhao J, Shao L, Kan Y. Sequence-Specific Detection of DNA Strands Using a Solid-State Nanopore Assisted by Microbeads. MICROMACHINES 2020; 11:mi11121097. [PMID: 33322605 PMCID: PMC7763196 DOI: 10.3390/mi11121097] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 12/08/2020] [Accepted: 12/10/2020] [Indexed: 01/30/2023]
Abstract
Simple, rapid, and low-cost detection of DNA with specific sequence is crucial for molecular diagnosis and therapy applications. In this research, the target DNA molecules are bonded to the streptavidin-coated microbeads, after hybridizing with biotinylated probes. A nanopore with a diameter significantly smaller than the microbeads is used to detect DNA molecules through the ionic pulse signals. Because the DNA molecules attached on the microbead should dissociate from the beads before completely passing through the pore, the signal duration time for the target DNA is two orders of magnitude longer than free DNA. Moreover, the high local concentration of target DNA molecules on the surface of microbeads leads to multiple DNA molecules translocating through the pore simultaneously, which generates pulse signals with amplitude much larger than single free DNA translocation events. Therefore, the DNA molecules with specific sequence can be easily identified by a nanopore sensor assisted by microbeads according to the ionic pulse signals.
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22
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Bossuyt PM. Testing COVID-19 tests faces methodological challenges. J Clin Epidemiol 2020; 126:172-176. [PMID: 32622902 PMCID: PMC7332449 DOI: 10.1016/j.jclinepi.2020.06.037] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 06/25/2020] [Accepted: 06/30/2020] [Indexed: 01/08/2023]
Abstract
In battling the COVID-19 pandemic, testing is essential. The detection of viral RNA allows the identification of infected persons, whereas the detection of antibodies may reveal a response to a previous infection. Tests for coronavirus should be rigorously evaluated in terms of their analytical and clinical performance. This poses not only logistic challenges, but also methodological ones. Some of these are generic for the diagnostic accuracy paradigm, whereas others are more specific for tests for viruses. Problematic for evaluations of the clinical performance of tests for viral RNA is the absence of an independent reference standard. Many studies lack rigor in terms of the recruitment of study participants. Study reports are often insufficiently informative, which makes it difficult to assess the applicability of study findings. Attempts to summarize the performance of these tests in terms of a single estimate of the clinical sensitivity fail to do justice to the identifiable sources of the large heterogeneity in mechanisms for generating false negative results.
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Affiliation(s)
- Patrick M Bossuyt
- Department of Epidemiology & Data Science, Amsterdam Public Health, Amsterdam University Medical Centers, Room J1B-214, PO Box 22660, 1100 DD Amsterdam, The Netherlands.
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23
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González-González E, Trujillo-de Santiago G, Lara-Mayorga IM, Martínez-Chapa SO, Alvarez MM. Portable and accurate diagnostics for COVID-19: Combined use of the miniPCR thermocycler and a well-plate reader for SARS-CoV-2 virus detection. PLoS One 2020; 15:e0237418. [PMID: 32790779 PMCID: PMC7425953 DOI: 10.1371/journal.pone.0237418] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Accepted: 07/27/2020] [Indexed: 02/04/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic has crudely demonstrated the need for massive and rapid diagnostics. By the first week of July, more than 10,000,000 positive cases of COVID-19 have been reported worldwide, although this number could be greatly underestimated. In the case of an epidemic emergency, the first line of response should be based on commercially available and validated resources. Here, we demonstrate the use of the miniPCR, a commercial compact and portable PCR device recently available on the market, in combination with a commercial well-plate reader as a diagnostic system for detecting genetic material of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causal agent of COVID-19. We used the miniPCR to detect and amplify SARS-CoV-2 DNA sequences using the sets of initiators recommended by the World Health Organization (WHO) for targeting three different regions that encode for the N protein. Prior to amplification, samples were combined with a DNA intercalating reagent (i.e., EvaGreen Dye). Sample fluorescence after amplification was then read using a commercial 96-well plate reader. This straightforward method allows the detection and amplification of SARS-CoV-2 nucleic acids in the range of ~625 to 2×105 DNA copies. The accuracy and simplicity of this diagnostics strategy may provide a cost-efficient and reliable alternative for COVID-19 pandemic testing, particularly in underdeveloped regions where RT-QPCR instrument availability may be limited. The portability, ease of use, and reproducibility of the miniPCR makes it a reliable alternative for deployment in point-of-care SARS-CoV-2 detection efforts during pandemics.
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Affiliation(s)
- Everardo González-González
- Centro de Biotecnología-FEMSA, Escuela de Ingeniería y Ciencias, Tecnologico de Monterrey, Monterrey, Nuevo León, México
- Departamento de Bioingeniería, Escuela de Ingeniería y Ciencias, Tecnologico de Monterrey, Monterrey, Nuevo León, México
| | - Grissel Trujillo-de Santiago
- Centro de Biotecnología-FEMSA, Escuela de Ingeniería y Ciencias, Tecnologico de Monterrey, Monterrey, Nuevo León, México
- Departamento de Ingeniería Mecátrónica y Eléctrica, Escuela de Ingeniería y Ciencias, Tecnologico de Monterrey, Monterrey, Nuevo León, México
| | - Itzel Montserrat Lara-Mayorga
- Centro de Biotecnología-FEMSA, Escuela de Ingeniería y Ciencias, Tecnologico de Monterrey, Monterrey, Nuevo León, México
- Departamento de Bioingeniería, Escuela de Ingeniería y Ciencias, Tecnologico de Monterrey, Monterrey, Nuevo León, México
| | - Sergio Omar Martínez-Chapa
- Departamento de Ingeniería Mecátrónica y Eléctrica, Escuela de Ingeniería y Ciencias, Tecnologico de Monterrey, Monterrey, Nuevo León, México
| | - Mario Moisés Alvarez
- Centro de Biotecnología-FEMSA, Escuela de Ingeniería y Ciencias, Tecnologico de Monterrey, Monterrey, Nuevo León, México
- Departamento de Bioingeniería, Escuela de Ingeniería y Ciencias, Tecnologico de Monterrey, Monterrey, Nuevo León, México
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Abstract
Accurate, rapid and simple detection methods are required to facilitate early diagnosis of various disorders including infectious and lifestyle diseases as well as cancer. These detection approaches reduce the window of infection, i.e., the period between infection and reliable detection. Optimally, these methods should target protein as an indicator of pathogenic microbes as well as other biomarkers. For example, although nucleic acid is easily detected by polymerase chain reaction (PCR), these markers are also present in dead microbes, and, in the case of mRNA, it is not known whether this target was successfully translated. Accordingly, early diagnostic approaches require the development of ultrasensitive protein detection methods. In this chapter, we introduce an ultrasensitive enzyme-linked immunosorbent assay (ELISA) which combines a traditional sandwich-based immunoassay with thionicotinamide adenine dinucleotide (thio-NAD) cycling. The performance characteristics of this unique approach are reviewed as well as its potential role in providing a novel and ultrasensitive diagnostic tool in the clinical laboratory.
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Affiliation(s)
- Etsuro Ito
- Department of Biology, Waseda University, Tokyo, Japan; Waseda Research Institute for Science and Engineering, Waseda University, Tokyo, Japan; Graduate Institute of Medicine, School of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan.
| | - Kanako Iha
- Department of Biology, Waseda University, Tokyo, Japan
| | - Teruki Yoshimura
- School of Pharmaceutical Sciences, Health Sciences University of Hokkaido, Sapporo, Hokkaido, Japan
| | - Kazunari Nakaishi
- Waseda Research Institute for Science and Engineering, Waseda University, Tokyo, Japan; R&D Headquarters, TAUNS Laboratories, Inc., Izunokuni, Japan
| | - Satoshi Watabe
- Waseda Research Institute for Science and Engineering, Waseda University, Tokyo, Japan; R&D Headquarters, TAUNS Laboratories, Inc., Izunokuni, Japan
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25
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Gunawan I, Hatta M, Fachruddin Benyamin A, Asadul Islam A. The Hypoxic Response Expression as a Survival Biomarkers in Treatment-Naive Advanced Breast Cancer. Asian Pac J Cancer Prev 2020; 21:629-637. [PMID: 32212787 PMCID: PMC7437329 DOI: 10.31557/apjcp.2020.21.3.629] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2019] [Accepted: 03/13/2020] [Indexed: 12/24/2022] Open
Abstract
OBJECTIVE Hypoxia-associated biomarkers profiling may provide information for prognosis, staging, and subsequent therapy. We aim to evaluate whether the quantitative gene and protein expression of hypoxic response tumor markers - carbonic anhydrase IX (CAIX) and hypoxia- inducible factor 1 alpha (HIF1A) - may have a role in predicting survival in advanced breast cancer of Indonesian population. METHODS Tumor tissues and peripheral blood samples were collected from treatment - naïve locally advanced (LABC) or metastatic breast cancer patients (MBC) at Wahidin Sudirohusodo General Hospital (Makassar, South Sulawesi) and its referral network hospitals from July 2017 to March 2019. The level of mRNA (of blood and tumor tissue samples) and soluble protein (of blood samples) of CAIX and HIF1A were measured by RT-qPCR and ELISA methods, respectively, besides the standard histopathological grading and molecular subtype assessment. The CAIX and HIF1A expression, patients' age, tumor characteristics, surgery status, and neoadjuvant chemotherapy drug classes were further involved in survival analyses for overall survival (OS) and progression-free survival (PFS). RESULTS Forty (30 LABC, 10 MBC) eligible patients examined were 21 hormone-receptors positives (15 Luminal A, 6 Luminal B) and 19 hormone-receptors negatives (10 HER2-enriched, 9 triple-negative). The CAIX blood mRNA and CAIX soluble protein levels in hormone-receptors negative patients were higher than in hormone-receptor-positive patients (p < 0.05). In univariate analysis, both CAIX and HIF1A levels predict OS (except HIF1A protein) with CAIX tissue mRNA has the highest hazard ratio (HR 8.04, 95%CI:2.45-26.39), but not PFS. Cox proportional hazard model confirmed that CAIX tissue mRNA is the independent predictor of OS (HR 6.10, 95%CI: 1.16-32.13) along with surgical status and tumor advancement type (LABC or MBC). CONCLUSIONS CAIX mRNA expression of tumor tissue in treatment-naïve advanced breast cancer has a predictive value for OS. .
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Affiliation(s)
| | | | | | - Andi Asadul Islam
- 4Department of Surgery, Faculty of Medicine, Hasanuddin University, Makassar, Indonesia.
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26
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Lyophilized Matrix Containing Ready-to-Use Primers and Probe Solution for Standardization of Real-Time PCR and RT-qPCR Diagnostics in Virology. Viruses 2020; 12:v12020159. [PMID: 32019076 PMCID: PMC7077261 DOI: 10.3390/v12020159] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 01/28/2020] [Indexed: 01/06/2023] Open
Abstract
Real-time molecular techniques have become the reference methods for direct diagnosis of pathogens. The reduction of steps is a key factor in order to decrease the risk of human errors resulting in invalid series and delayed results. We describe here a process of preparation of oligonucleotide primers and hydrolysis probe in a single tube at predefined optimized concentrations that are stabilized via lyophilization (Lyoph-P&P). Lyoph-P&P was compared versus the classic protocol using extemporaneously prepared liquid reagents using (i) sensitivity study, (ii) long-term stability at 4 °C, and (iii) long-term stability at 37 °C mimicking transportation without cold chain. Two previously published molecular assays were selected for this study. They target two emerging viruses that are listed on the blueprint of the WHO as to be considered for preparedness and response actions: chikungunya virus (CHIKV) and Rift Valley fever phlebovirus (RVFV). Results of our study demonstrate that (i) Lyoph-P&P is stable for at least 4 days at 37 °C supporting shipping without the need of cold chain, (ii) Lyoph-P&P rehydrated solution is stable at +4 °C for at least two weeks, (iii) sensitivity observed with Lyoph-P&P is at least equal to, often better than, that observed with liquid formulation, (iv) validation of results observed with low-copy specimens is rendered easier by higher fluorescence level. In conclusion, Lyoph-P&P holds several advantages over extemporaneously preparer liquid formulation that merit to be considered when a novel real-time molecular assay is implemented in a laboratory in charge of routine diagnostic activity.
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27
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Shen Z, He L, Wang W, Tan L, Gan N. Highly sensitive and simultaneous detection of microRNAs in serum using stir-bar assisted magnetic DNA nanospheres-encoded probes. Biosens Bioelectron 2019; 148:111831. [PMID: 31706172 DOI: 10.1016/j.bios.2019.111831] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 10/28/2019] [Accepted: 10/29/2019] [Indexed: 11/17/2022]
Abstract
There are critical interests in the detection of microRNA (miRNA) because it can be a blood-borne biomarker, but analytical strategies are still limited by its small size, high sequence homology among family members and low abundance. In this work, three-dimensional magnetic DNA nanospheres were synthesized and immobilized on a gold stir-bar as encoded probes for miRNA capture and signal amplification. Electrochemical tags-labeled DNAs were immobilized on gold coated magnetic nanospheres via a hyperbranched hybridization chain reaction (HHCR). Subsequently, the magnetic DNA nanospheres were immobilized on the gold stir-bar as encoded probes. Target miRNAs were captured on the surface of the stir-bar by replacing the magnetic DNA nanospheres-encoded probes, and the probes were magnetically enriched for highly sensitive and selective electrochemical detection. The gold stir-bar assisted magnetic DNA nanospheres-encoded probes possess dual functions: They are as a nanocarrier to increase the loading amounts of HHCR products, and they are also a platform for efficient electrochemical signal amplification via magnetic enrichment. The method was successfully applied for the detection of miRNA21 and miRNA155 in a wide linear range of 5 fM to 2 nM, and with detection limits of 1.5 fM and 1.8 fM, respectively. The preliminary application of the method suggests that it has great potential in the detection of miRNAs in serum samples.
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Affiliation(s)
- Zhipeng Shen
- Faculty of Materials Science and Chemical Engineering, Ningbo University, Ningbo, 315211, China
| | - Liyong He
- Faculty of Materials Science and Chemical Engineering, Ningbo University, Ningbo, 315211, China
| | - Wenhai Wang
- Faculty of Materials Science and Chemical Engineering, Ningbo University, Ningbo, 315211, China
| | - Lei Tan
- Guangzhou Center for Disease Control and Prevention, Guangzhou, 510440, China.
| | - Ning Gan
- Faculty of Materials Science and Chemical Engineering, Ningbo University, Ningbo, 315211, China.
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28
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Locher K, Roscoe D, Jassem A, Wong T, Hoang LMN, Charles M, Bryce E, Grant J, Stefanovic A. FilmArray respiratory panel assay: An effective method for detecting viral and atypical bacterial pathogens in bronchoscopy specimens. Diagn Microbiol Infect Dis 2019; 95:114880. [PMID: 31607515 PMCID: PMC7132745 DOI: 10.1016/j.diagmicrobio.2019.114880] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 07/05/2019] [Accepted: 07/30/2019] [Indexed: 12/17/2022]
Abstract
The BioFire FilmArray Respiratory Panel (FA RP) is a rapid multiplexed molecular assay approved for detection of viral and atypical bacterial pathogens in nasopharyngeal specimens. This study aimed to evaluate the performance of the BioFire FilmArray Respiratory Panel v1.7 on bronchoscopy specimens. We tested 133 bronchial specimens (87 archived and 46 prospectively collected) with the FA RP and compared the results to the Luminex NxTAG Respiratory Pathogen Panel (NxTAG RPP). After discordant analysis, 123 specimens gave concordant results using the FA RP and the NxTAG RPP for an overall agreement of 93.9% (kappa = 0.88 [95% CI 0.80–0.96]), a positive percent agreement of 93.7% (95% CI 83.7–97.7) and a negative percent agreement of 94.1% (95% CI 84.9–98.1). In conclusion, the BioFire FilmArray RP performed reliably to detect a broad range of respiratory pathogens in bronchoscopy specimens.
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Affiliation(s)
- Kerstin Locher
- Division of Medical Microbiology, Department of Pathology and Laboratory Medicine, Vancouver Coastal Health, British Columbia, Canada; University of British Columbia, Faculty of Medicine, Vancouver, British Columbia, Canada.
| | - Diane Roscoe
- Division of Medical Microbiology, Department of Pathology and Laboratory Medicine, Vancouver Coastal Health, British Columbia, Canada; University of British Columbia, Faculty of Medicine, Vancouver, British Columbia, Canada
| | - Agatha Jassem
- British Columbia Center for Disease Control, Public Health Laboratory, Vancouver, British Columbia, Canada; University of British Columbia, Faculty of Medicine, Vancouver, British Columbia, Canada
| | - Titus Wong
- Division of Medical Microbiology, Department of Pathology and Laboratory Medicine, Vancouver Coastal Health, British Columbia, Canada; University of British Columbia, Faculty of Medicine, Vancouver, British Columbia, Canada
| | - Linda M N Hoang
- British Columbia Center for Disease Control, Public Health Laboratory, Vancouver, British Columbia, Canada; University of British Columbia, Faculty of Medicine, Vancouver, British Columbia, Canada
| | - Marthe Charles
- Division of Medical Microbiology, Department of Pathology and Laboratory Medicine, Vancouver Coastal Health, British Columbia, Canada; University of British Columbia, Faculty of Medicine, Vancouver, British Columbia, Canada
| | - Elizabeth Bryce
- Division of Medical Microbiology, Department of Pathology and Laboratory Medicine, Vancouver Coastal Health, British Columbia, Canada; University of British Columbia, Faculty of Medicine, Vancouver, British Columbia, Canada
| | - Jennifer Grant
- Division of Medical Microbiology, Department of Pathology and Laboratory Medicine, Vancouver Coastal Health, British Columbia, Canada; University of British Columbia, Faculty of Medicine, Vancouver, British Columbia, Canada
| | - Aleksandra Stefanovic
- Division of Medical Microbiology, Department of Pathology and Laboratory Medicine, Vancouver Coastal Health, British Columbia, Canada; University of British Columbia, Faculty of Medicine, Vancouver, British Columbia, Canada
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29
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Zhang L, Dong R, Wei S, Zhou HC, Zhang MX, Alagarsamy K. A novel data processing method CyC* for quantitative real time polymerase chain reaction minimizes cumulative error. PLoS One 2019; 14:e0218159. [PMID: 31185064 PMCID: PMC6559663 DOI: 10.1371/journal.pone.0218159] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 05/28/2019] [Indexed: 11/18/2022] Open
Abstract
Quantitative real-time polymerase chain reaction (qPCR) is routinely conducted for DNA quantitative analysis using the cycle-threshold (Ct) method, which assumes uniform/optimum template amplification. In practice, amplification efficiencies vary from cycle to cycle in a PCR reaction, and often decline as the amplification proceeds, which results in substantial errors in measurement. This study reveals the cumulative error for quantification of initial template amounts, due to the difference between the assumed perfect amplification efficiency and actual one in each amplification cycle. The novel CyC* method involves determination of both the earliest amplification cycle detectable above background (“outlier” C*) and the amplification efficiency over the cycle range from C* to the next two amplification cycles; subsequent analysis allows the calculation of initial template amount with minimal cumulative error. Simulation tests indicated that the CyC* method resulted in significantly less variation in the predicted initial DNA level represented as fluorescence intensity F0 when the outlier cycle C* was advanced to an earlier cycle. Performance comparison revealed that CyC* was better than the majority of 13 established qPCR data analysis methods in terms of bias, linearity, reproducibility, and resolution. Actual PCR test also suggested that relative expression levels of nine genes in tea leaves obtained using CyC* were much closer to the real value than those obtained with the conventional 2-ΔΔCt method. Our data indicated that increasing the input of initial template was effective in advancing emergence of the earliest amplification cycle among the tested variants. A computer program (CyC* method) was compiled to perform the data processing. This novel method can minimize cumulative error over the amplification process, and thus, can improve qPCR analysis.
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Affiliation(s)
- Linzhong Zhang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, Anhui, China
- School of Science, Anhui Agricultural University, Hefei, Anhui, China
| | - Rui Dong
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, Anhui, China
| | - Shu Wei
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, Anhui, China
- * E-mail:
| | - Han-Chen Zhou
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, Anhui, China
- Tea Research Institution, Anhui Academy of Agricultural Sciences, Huangshan, Anhui, China
| | - Meng-Xian Zhang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, Anhui, China
| | - Karthikeyan Alagarsamy
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, Anhui, China
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30
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Ouyang T, Liu Z, Han Z, Ge Q. MicroRNA Detection Specificity: Recent Advances and Future Perspective. Anal Chem 2019; 91:3179-3186. [DOI: 10.1021/acs.analchem.8b05909] [Citation(s) in RCA: 91] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Tinglan Ouyang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Zhiyu Liu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Zhiyi Han
- Department of Liver Diseases, Shenzhen Traditional Chinese Medicine Hospital, Shenzhen 518033, China
| | - Qinyu Ge
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
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31
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Robetorye RS, Maguire A, Rosenthal AC, Rimsza LM. Profiling of lymphoma from formalin-fixed paraffin-embedded tissue. Semin Hematol 2018; 56:46-51. [PMID: 30573044 DOI: 10.1053/j.seminhematol.2018.05.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 05/07/2018] [Indexed: 12/21/2022]
Abstract
Molecular profiling of lymphoma samples has contributed enormously to our understanding of disease biology leading to detailed descriptions of diagnostic categories. These studies have also helped the field to recognize different subtypes of disease, different diseases that share similar cellular pathway perturbations, different immune responses, and different prognostic groups. While nearly all of these discoveries were made using unfixed, snap-frozen materials, with few exceptions, clinical biopsy materials are comprised of formalin-fixed and paraffin-embedded (FFPE) tissues. Here, we describe the impact of molecular profiling on the field of lymphoma, the challenges associated with using FFPE tissues for downstream molecular diagnostic testing, the various molecular profiling techniques, and also provide an example of the clinical application of a molecular profiling test of lymphoma using FFPE tissues.
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Affiliation(s)
- Ryan S Robetorye
- Department of Laboratory Medicine and Pathology, Mayo Clinic Arizona, Phoenix, AZ.
| | - Alanna Maguire
- Department of Research, Mayo Clinic Arizona, Phoenix, AZ
| | - Alison C Rosenthal
- Department of Medicine, Division of Hematology-Oncology, Mayo Clinic Arizona, Phoenix, AZ
| | - Lisa M Rimsza
- Department of Laboratory Medicine and Pathology, Mayo Clinic Arizona, Phoenix, AZ
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32
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MicroRNAs as Biomarkers in Amyotrophic Lateral Sclerosis. Cells 2018; 7:cells7110219. [PMID: 30463376 PMCID: PMC6262636 DOI: 10.3390/cells7110219] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 11/15/2018] [Accepted: 11/17/2018] [Indexed: 12/30/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is an incurable and fatal disorder characterized by the progressive loss of motor neurons in the cerebral cortex, brain stem, and spinal cord. Sporadic ALS form accounts for the majority of patients, but in 1–13.5% of cases the disease is inherited. The diagnosis of ALS is mainly based on clinical assessment and electrophysiological examinations with a history of symptom progression and is then made with a significant delay from symptom onset. Thus, the identification of biomarkers specific for ALS could be of a fundamental importance in the clinical practice. An ideal biomarker should display high specificity and sensitivity for discriminating ALS from control subjects and from ALS-mimics and other neurological diseases, and should then monitor disease progression within individual patients. microRNAs (miRNAs) are considered promising biomarkers for neurodegenerative diseases, since they are remarkably stable in human body fluids and can reflect physiological and pathological processes relevant for ALS. Here, we review the state of the art of miRNA biomarker identification for ALS in cerebrospinal fluid (CSF), blood and muscle tissue; we discuss advantages and disadvantages of different approaches, and underline the limits but also the great potential of this research for future practical applications.
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33
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Venkateshwari V, Vijayakumar A, Vijayakumar AK, Reddy LPA, Srinivasan M, Rajasekharan R. Leaf lipidome and transcriptome profiling of Portulaca oleracea: characterization of lysophosphatidylcholine acyltransferase. PLANTA 2018; 248:347-367. [PMID: 29736624 DOI: 10.1007/s00425-018-2908-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2018] [Accepted: 04/16/2018] [Indexed: 06/08/2023]
Abstract
Portulaca leaves serve as an alternative bioresource for edible PUFAs. Transcriptome data provide information to explore Portulaca as a model system for galactolipids, leaf lipid metabolism, and PUFA-rich designer lipids. Poly-unsaturated fatty acids (PUFAs) are gaining importance due to their innumerable health benefits, and hence, understanding their biosynthesis in plants has attained prominence in recent years. The most common source of PUFAs is of marine origin. Although reports have identified Portulaca oleracea (purslane) as a leaf source of omega-3 fatty acids in the form of alpha-linolenic acid (ALA), the mechanism of ALA accumulation and its distribution into various lipids has not been elucidated. Here, we present the lipid profiles of leaves and seeds of several accessions of P. oleracea. Among the nineteen distinct accessions, the RR04 accession has the highest amount of ALA and is primarily associated with galactolipids. In addition, we report the transcriptome of RR04, and we have mapped the potential genes involved in lipid metabolism. Phosphatidylcholine (PC) is the major site of acyl editing, which is catalyzed by lysophosphatidylcholine acyltransferase (LPCAT), an integral membrane protein that plays a major role in supplying oleate to the PC pool for further unsaturation. Our investigations using mass spectrometric analysis of leaf microsomal fractions identified LPCAT as part of a membrane protein complex. Both native and recombinant LPCAT showed strong acyltransferase activity with various acyl-CoA substrates. Altogether, the results suggest that ALA-rich glycerolipid biosynthetic machinery is highly active in nutritionally important Portulaca leaves. Furthermore, lipidome, transcriptome, and mass spectrometric analyses of RR04 provide novel information for exploring Portulaca as a potential resource and a model system for studying leaf lipid metabolism.
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Affiliation(s)
- Varadarajan Venkateshwari
- Department of Lipid Science, Central Food Technological Research Institute, Mysore, 570020, Karnataka, India
- Academy of Scientific and Innovative Research, New Delhi, India
| | - Anitha Vijayakumar
- Department of Lipid Science, Central Food Technological Research Institute, Mysore, 570020, Karnataka, India
| | - Arun Kumar Vijayakumar
- Food Safety and Analytical Quality Control Department, Central Food Technological Research Institute, Mysore, 570020, Karnataka, India
| | - L Prasanna Anjaneya Reddy
- Department of Lipid Science, Central Food Technological Research Institute, Mysore, 570020, Karnataka, India
| | - Malathi Srinivasan
- Department of Lipid Science, Central Food Technological Research Institute, Mysore, 570020, Karnataka, India
- Academy of Scientific and Innovative Research, New Delhi, India
| | - Ram Rajasekharan
- Department of Lipid Science, Central Food Technological Research Institute, Mysore, 570020, Karnataka, India.
- Academy of Scientific and Innovative Research, New Delhi, India.
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Gürtler C, Laible M, Schwabe W, Steinhäuser H, Li X, Liu S, Schlombs K, Sahin U. Transferring a Quantitative Molecular Diagnostic Test to Multiple Real-Time Quantitative PCR Platforms. J Mol Diagn 2018; 20:398-414. [DOI: 10.1016/j.jmoldx.2018.02.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Revised: 01/16/2018] [Accepted: 02/28/2018] [Indexed: 12/22/2022] Open
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35
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Wanke KA, Devanna P, Vernes SC. Understanding Neurodevelopmental Disorders: The Promise of Regulatory Variation in the 3'UTRome. Biol Psychiatry 2018; 83:548-557. [PMID: 29289333 DOI: 10.1016/j.biopsych.2017.11.006] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 11/02/2017] [Accepted: 11/02/2017] [Indexed: 01/28/2023]
Abstract
Neurodevelopmental disorders have a strong genetic component, but despite widespread efforts, the specific genetic factors underlying these disorders remain undefined for a large proportion of affected individuals. Given the accessibility of exome sequencing, this problem has thus far been addressed from a protein-centric standpoint; however, protein-coding regions only make up ∼1% to 2% of the human genome. With the advent of whole genome sequencing we are in the midst of a paradigm shift as it is now possible to interrogate the entire sequence of the human genome (coding and noncoding) to fill in the missing heritability of complex disorders. These new technologies bring new challenges, as the number of noncoding variants identified per individual can be overwhelming, making it prudent to focus on noncoding regions of known function, for which the effects of variation can be predicted and directly tested to assess pathogenicity. The 3'UTRome is a region of the noncoding genome that perfectly fulfills these criteria and is of high interest when searching for pathogenic variation related to complex neurodevelopmental disorders. Herein, we review the regulatory roles of the 3'UTRome as binding sites for microRNAs or RNA binding proteins, or during alternative polyadenylation. We detail existing evidence that these regions contribute to neurodevelopmental disorders and outline strategies for identification and validation of novel putatively pathogenic variation in these regions. This evidence suggests that studying the 3'UTRome will lead to the identification of new risk factors, new candidate disease genes, and a better understanding of the molecular mechanisms contributing to neurodevelopmental disorders.
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Affiliation(s)
- Kai A Wanke
- Neurogenetics of Vocal Communication Group, Max Planck Institute for Psycholinguistics, Nijmegen, the Netherlands; Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, the Netherlands
| | - Paolo Devanna
- Neurogenetics of Vocal Communication Group, Max Planck Institute for Psycholinguistics, Nijmegen, the Netherlands
| | - Sonja C Vernes
- Neurogenetics of Vocal Communication Group, Max Planck Institute for Psycholinguistics, Nijmegen, the Netherlands; Donders Institute for Brain, Cognition and Behaviour, Nijmegen, the Netherlands.
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36
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Kim SU, Batule BS, Mun H, Shim WB, Kim MG. Ultrasensitive colorimetric detection of Salmonella enterica Typhimurium on lettuce leaves by HRPzyme-Integrated polymerase chain reaction. Food Control 2018. [DOI: 10.1016/j.foodcont.2017.09.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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37
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Nakayama T, Okada N, Yoshikawa M, Asaka D, Kuboki A, Kojima H, Tanaka Y, Haruna SI. Assessment of suitable reference genes for RT-qPCR studies in chronic rhinosinusitis. Sci Rep 2018; 8:1568. [PMID: 29371606 PMCID: PMC5785529 DOI: 10.1038/s41598-018-19834-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Accepted: 01/09/2018] [Indexed: 11/09/2022] Open
Abstract
Reverse transcription–quantitative polymerase chain reaction is a valuable and reliable method for gene quantification. Target gene expression is usually quantified by normalization using reference genes (RGs), and accurate normalization is critical for producing reliable data. However, stable RGs in nasal polyps and sinonasal tissues from patients with chronic rhinosinusitis (CRS) have not been well investigated. Here, we used a two-stage study design to identify stable RGs. We assessed the stability of 15 commonly used candidate RGs using five programs—geNorm, NormFinder, BestKeeper, ΔCT, and RefFinder. Ribosomal protein lateral stalk subunit P1 (RPLP1) and ribosomal protein lateral stalk subunit P0 (RPLP0) were the two most stable RGs in the first stage of the study, and these results were validated in the second stage. The commonly used RGs β-actin (ACTB) and glyceraldehyde 3-phosphate dehydrogenase (GAPDH) were unstable according to all of the algorithms used. The findings were further validated via relative quantification of IL-5, CCL11, IFN-γ, and IL-17A using the stable and unstable RGs. The relative expression levels varied greatly according to normalization with the selected RGs. Appropriate selection of stable RGs will allow more accurate determination of target gene expression levels in patients with CRS.
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Affiliation(s)
- Tsuguhisa Nakayama
- Department of Otorhinolaryngology, Jikei University School of Medicine, Tokyo, Japan.
| | - Naoko Okada
- Department of Allergy and Immunology, National Research Institute of Child Health and Development, Tokyo, Japan
| | - Mamoru Yoshikawa
- Department of Otorhinolaryngology, Toho University, Tokyo, Japan
| | - Daiya Asaka
- Department of Otorhinolaryngology, Jikei University School of Medicine, Tokyo, Japan
| | - Akihito Kuboki
- Department of Otorhinolaryngology, Jikei University School of Medicine, Tokyo, Japan
| | - Hiromi Kojima
- Department of Otorhinolaryngology, Jikei University School of Medicine, Tokyo, Japan
| | - Yasuhiro Tanaka
- Department of Otorhinolaryngology Head and Neck Surgery, Dokkyo Medical University Koshigaya Hospital, Saitama, Japan
| | - Shin-Ichi Haruna
- Department of Otorhinolaryngology Head and Neck Surgery, Dokkyo Medical University, Tochigi, Japan
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38
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Kim SU, Batule BS, Mun H, Byun JY, Shim WB, Kim MG. Colorimetric molecular diagnosis of the HIV gag gene using DNAzyme and a complementary DNA-extended primer. Analyst 2018; 143:695-699. [PMID: 29299545 DOI: 10.1039/c7an01520h] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
We have developed a novel strategy for the colorimetric detection of PCR products by utilizing a target-specific primer modified at the 5'-end with an anti-DNAzyme sequence. A single-stranded DNAzyme sequence folds into a G-quadruplex structure with hemin and shows strong peroxidase activity. When the complementary strand binds to the DNAzyme sequence, it blocks the formation of the G-quadraduplex structure and loses its peroxidase activity. In the presence of the target gene, PCR amplification proceeds, and anti-DNAzyme sequence modified primers present in the reaction mixture form a double strand through primer extension. Therefore, it does not block the DNAzyme sequence. Further, a colorimetric signal is generated by the addition of 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonate) (ABTS) and H2O2 at the end of the reaction. We have successfully detected a single copy of the HIV type 1 gag gene in buffer and 10 copies in human serum. The strategy developed could be used to detect DNA and RNA in complex biological samples by simple primer designing that includes DNAzyme and a DNA extended primer.
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Affiliation(s)
- Seong U Kim
- Advanced Photonics Research Institute, Gwangju Institute of Science and Technology, 261 Chemdan-gwagiro, Gwangju 500-712, Republic of Korea.
| | - Bhagwan S Batule
- Department of Chemistry, School of Physics and Chemistry, Gwangju Institute of Science and Technology, 261 Chemdan-gwagiro, Gwangju 500-712, Republic of Korea
| | - Hyoyoung Mun
- Department of Chemistry, School of Physics and Chemistry, Gwangju Institute of Science and Technology, 261 Chemdan-gwagiro, Gwangju 500-712, Republic of Korea
| | - Ju-Young Byun
- Department of Chemistry, School of Physics and Chemistry, Gwangju Institute of Science and Technology, 261 Chemdan-gwagiro, Gwangju 500-712, Republic of Korea
| | - Won-Bo Shim
- Department of Agricultural Chemistry and Food Science and Technology, Gyeongsang National University, 900 Gajwa-dong Jinju, Gyeongnam 660-701, Republic of Korea
| | - Min-Gon Kim
- Advanced Photonics Research Institute, Gwangju Institute of Science and Technology, 261 Chemdan-gwagiro, Gwangju 500-712, Republic of Korea. and Department of Chemistry, School of Physics and Chemistry, Gwangju Institute of Science and Technology, 261 Chemdan-gwagiro, Gwangju 500-712, Republic of Korea
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Zhang Y, Rana A, Stratton Y, Czyzyk-Krzeska MF, Esfandiari L. Sequence-Specific Detection of MicroRNAs Related to Clear Cell Renal Cell Carcinoma at fM Concentration by an Electroosmotically Driven Nanopore-Based Device. Anal Chem 2017; 89:9201-9208. [PMID: 28832110 DOI: 10.1021/acs.analchem.7b01944] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
MicroRNAs (miRs) are small noncoding RNAs that play a critical role in gene regulation. Recently, traces of cancer-related miRs have been identified in body fluids, which make them remarkable noninvasive biomarkers. In this study, a new nanopore-based detection scheme utilizing a borosilicate micropipette and an assay of complementary γ-peptide nucleic acid (γ-PNA) probes conjugated to polystyrene beads have been reported for the detection of miR-204 and miR-210 related to the clear cell Renal Cell Carcinoma (ccRCC). Electroosmotic flow (EOF) is induced as the driving force to transport PNA-beads harboring target miRs to the tip of the pore (sensing zone), which results in pore blockades with unique and easily distinguishable serrated shape electrical signals. The concentration detection limit is investigated to be 1 and 10 fM for miR-204 and miR-210, respectively. The EOF transport mechanism enables highly sensitive detection of molecules with low surface charge density with 97.6% detection accuracy compared to the conventional electrophoretically driven methods. Furthermore, resistive-pulse experiments are conducted to study the correlation of the particles' surface charge density with their translocation time and verify the detection principle.
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Affiliation(s)
- Yuqian Zhang
- Department of Electrical Engineering and Computing Systems, University of Cincinnati , Cincinnati, Ohio 45221, United States
| | - Ankit Rana
- Department of Electrical Engineering and Computing Systems, University of Cincinnati , Cincinnati, Ohio 45221, United States
| | - Yiwen Stratton
- Department of Cancer Biology, University of Cincinnati , Cincinnati, Ohio 45267, United States
| | - Maria F Czyzyk-Krzeska
- Department of Cancer Biology, University of Cincinnati , Cincinnati, Ohio 45267, United States.,Department of Veterans Affairs, VA Research Service , Cincinnati, Ohio 45220, United States
| | - Leyla Esfandiari
- Department of Electrical Engineering and Computing Systems, University of Cincinnati , Cincinnati, Ohio 45221, United States.,Department of Biomedical Chemical and Environmental Engineering, University of Cincinnati , Cincinnati, Ohio 45221, United States
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40
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Ivica J, Williamson PTF, de Planque MRR. Salt Gradient Modulation of MicroRNA Translocation through a Biological Nanopore. Anal Chem 2017; 89:8822-8829. [DOI: 10.1021/acs.analchem.7b01246] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Josip Ivica
- Electronics
and Computer Science, ‡Centre for Biological Sciences, and §Institute for
Life Sciences, University of Southampton, Southampton SO17 1BJ, United Kingdom
| | - Philip T. F. Williamson
- Electronics
and Computer Science, ‡Centre for Biological Sciences, and §Institute for
Life Sciences, University of Southampton, Southampton SO17 1BJ, United Kingdom
| | - Maurits R. R. de Planque
- Electronics
and Computer Science, ‡Centre for Biological Sciences, and §Institute for
Life Sciences, University of Southampton, Southampton SO17 1BJ, United Kingdom
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41
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Lv Y, Zhao SG, Lu G, Leung CK, Xiong ZQ, Su XW, Ma JL, Chan WY, Liu HB. Identification of reference genes for qRT-PCR in granulosa cells of healthy women and polycystic ovarian syndrome patients. Sci Rep 2017; 7:6961. [PMID: 28761164 PMCID: PMC5537281 DOI: 10.1038/s41598-017-07346-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 06/26/2017] [Indexed: 02/06/2023] Open
Abstract
Comparative gene expression analysis by qRT-PCR is commonly used to detect differentially expressed genes in studies of PCOS pathology. Impaired GC function is strongly associated with PCOS pathogenesis, and a growing body of studies has been dedicated to identifying differentially expressed genes in GCs in PCOS patients and healthy women by qRT-PCR. It is necessary to validate the expression stability of the selected reference genes across the tested samples for target gene expression normalization. We examined the variability and stability of expression of the 15 commonly used reference genes in GCs from 44 PCOS patients and 45 healthy women using the GeNorm, BestKeeper, and NormFinder statistical algorithms. We combined the rankings of the three programs to produce a final ranking based on the geometric means of their stability scores. We found that HPRT1, RPLP0, and HMBS out of 15 examined commonly used reference genes are stably expressed in GCs in both controls and PCOS patients and can be used for normalization in gene expression profiling by qRT-PCR. Future gene-expression studies should consider using these reference genes in GCs in PCOS patients for more accurate quantitation of target gene expression and data interpretation.
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Affiliation(s)
- Yue Lv
- Center for Reproductive Medicine, Shandong University, Jinan, Shandong, 250001, China.,CUHK-SDU Joint Laboratory on Reproductive Genetics, School of Biomedical Sciences, the Chinese University of Hong Kong, Hong Kong, China.,National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Jinan, Shandong, 250001, China
| | - Shi Gang Zhao
- Center for Reproductive Medicine, Shandong University, Jinan, Shandong, 250001, China.,National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Jinan, Shandong, 250001, China
| | - Gang Lu
- CUHK-SDU Joint Laboratory on Reproductive Genetics, School of Biomedical Sciences, the Chinese University of Hong Kong, Hong Kong, China. .,National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Jinan, Shandong, 250001, China.
| | - Chi Kwan Leung
- Center for Reproductive Medicine, Shandong University, Jinan, Shandong, 250001, China.,National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Jinan, Shandong, 250001, China.,SDIVF R&D Centre, Hong Kong Science and Technology Parks, Hong Kong, China
| | - Zhi Qiang Xiong
- Center for Reproductive Medicine, Shandong University, Jinan, Shandong, 250001, China.,National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Jinan, Shandong, 250001, China.,SDIVF R&D Centre, Hong Kong Science and Technology Parks, Hong Kong, China
| | - Xian Wei Su
- Center for Reproductive Medicine, Shandong University, Jinan, Shandong, 250001, China.,National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Jinan, Shandong, 250001, China.,SDIVF R&D Centre, Hong Kong Science and Technology Parks, Hong Kong, China
| | - Jin Long Ma
- Center for Reproductive Medicine, Shandong University, Jinan, Shandong, 250001, China.,CUHK-SDU Joint Laboratory on Reproductive Genetics, School of Biomedical Sciences, the Chinese University of Hong Kong, Hong Kong, China.,National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Jinan, Shandong, 250001, China.,SDIVF R&D Centre, Hong Kong Science and Technology Parks, Hong Kong, China
| | - Wai Yee Chan
- CUHK-SDU Joint Laboratory on Reproductive Genetics, School of Biomedical Sciences, the Chinese University of Hong Kong, Hong Kong, China.,National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Jinan, Shandong, 250001, China
| | - Hong Bin Liu
- Center for Reproductive Medicine, Shandong University, Jinan, Shandong, 250001, China. .,CUHK-SDU Joint Laboratory on Reproductive Genetics, School of Biomedical Sciences, the Chinese University of Hong Kong, Hong Kong, China. .,National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Jinan, Shandong, 250001, China.
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42
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Transcriptome Profiling in Human Diseases: New Advances and Perspectives. Int J Mol Sci 2017; 18:ijms18081652. [PMID: 28758927 PMCID: PMC5578042 DOI: 10.3390/ijms18081652] [Citation(s) in RCA: 146] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 07/21/2017] [Accepted: 07/27/2017] [Indexed: 12/14/2022] Open
Abstract
In the last decades, transcriptome profiling has been one of the most utilized approaches to investigate human diseases at the molecular level. Through expression studies, many molecular biomarkers and therapeutic targets have been found for several human pathologies. This number is continuously increasing thanks to total RNA sequencing. Indeed, this new technology has completely revolutionized transcriptome analysis allowing the quantification of gene expression levels and allele-specific expression in a single experiment, as well as to identify novel genes, splice isoforms, fusion transcripts, and to investigate the world of non-coding RNA at an unprecedented level. RNA sequencing has also been employed in important projects, like ENCODE (Encyclopedia of the regulatory elements) and TCGA (The Cancer Genome Atlas), to provide a snapshot of the transcriptome of dozens of cell lines and thousands of primary tumor specimens. Moreover, these studies have also paved the way to the development of data integration approaches in order to facilitate management and analysis of data and to identify novel disease markers and molecular targets to use in the clinics. In this scenario, several ongoing clinical trials utilize transcriptome profiling through RNA sequencing strategies as an important instrument in the diagnosis of numerous human pathologies.
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43
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RNA splicing in human disease and in the clinic. Clin Sci (Lond) 2017; 131:355-368. [PMID: 28202748 DOI: 10.1042/cs20160211] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Revised: 12/06/2016] [Accepted: 12/15/2016] [Indexed: 01/12/2023]
Abstract
Defects at the level of the pre-mRNA splicing process represent a major cause of human disease. Approximately 15-50% of all human disease mutations have been shown to alter functioning of basic and auxiliary splicing elements. These elements are required to ensure proper processing of pre-mRNA splicing molecules, with their disruption leading to misprocessing of the pre-mRNA molecule and disease. The splicing process is a complex process, with much still to be uncovered before we are able to accurately predict whether a reported genomic sequence variant (GV) represents a splicing-associated disease mutation or a harmless polymorphism. Furthermore, even when a mutation is correctly identified as affecting the splicing process, there still remains the difficulty of providing an exact evaluation of the potential impact on disease onset, severity and duration. In this review, we provide a brief overview of splicing diagnostic methodologies, from in silico bioinformatics approaches to wet lab in vitro and in vivo systems to evaluate splicing efficiencies. In particular, we provide an overview of how the latest developments in high-throughput sequencing can be applied to the clinic, and are already changing clinical approaches.
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44
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Oostendorp C, Meyer S, Sobrio M, van Arendonk J, Reichmann E, Daamen WF, van Kuppevelt TH. Evaluation of cultured human dermal- and dermo-epidermal substitutes focusing on extracellular matrix components: Comparison of protein and RNA analysis. Burns 2017; 43:520-530. [PMID: 28041746 DOI: 10.1016/j.burns.2016.10.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Revised: 10/02/2016] [Accepted: 10/04/2016] [Indexed: 02/07/2023]
Abstract
Treatment of full-thickness skin defects with split-thickness skin grafts is generally associated with contraction and scar formation and cellular skin substitutes have been developed to improve skin regeneration. The evaluation of cultured skin substitutes is generally based on qualitative parameters focusing on histology. In this study we focused on quantitative evaluation to provide a template for comparison of human bio-engineered skin substitutes between clinical and/or research centers, and to supplement histological data. We focused on extracellular matrix proteins since these components play an important role in skin regeneration. As a model we analyzed the human dermal substitute denovoDerm and the dermo-epidermal skin substitute denovoSkin. The quantification of the extracellular matrix proteins type III collagen and laminin 5 in tissue homogenates using western blotting analysis and ELISA was not successful. The same was true for assaying lysyl oxidase, an enzyme involved in crosslinking of matrix molecules. As an alternative, gene expression levels were measured using qPCR. Various RNA isolation procedures were probed. The gene expression profile for specific dermal and epidermal genes could be measured reliably and reproducibly. Differences caused by changes in the cell culture conditions could easily be detected. The number of cells in the skin substitutes was measured using the PicoGreen dsDNA assay, which was found highly quantitative and reproducible. The (dis) advantages of assays used for quantitative evaluation of skin substitutes are discussed.
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Affiliation(s)
- Corien Oostendorp
- Department of Biochemistry, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein 28, 6525 GA, Nijmegen, The Netherlands.
| | - Sarah Meyer
- Tissue Biology Research Unit, Department of Surgery, Zurich University Children's Hospital, August Forel Strasse 7, 8008 Zurich, Switzerland
| | - Monia Sobrio
- Tissue Biology Research Unit, Department of Surgery, Zurich University Children's Hospital, August Forel Strasse 7, 8008 Zurich, Switzerland.
| | - Joyce van Arendonk
- Department of Biochemistry, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein 28, 6525 GA, Nijmegen, The Netherlands
| | - Ernst Reichmann
- Tissue Biology Research Unit, Department of Surgery, Zurich University Children's Hospital, August Forel Strasse 7, 8008 Zurich, Switzerland.
| | - Willeke F Daamen
- Department of Biochemistry, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein 28, 6525 GA, Nijmegen, The Netherlands.
| | - Toin H van Kuppevelt
- Department of Biochemistry, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein 28, 6525 GA, Nijmegen, The Netherlands.
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45
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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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46
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Wei T, Du D, Wang Z, Zhang W, Lin Y, Dai Z. Rapid and sensitive detection of microRNA via the capture of fluorescent dyes-loaded albumin nanoparticles around functionalized magnetic beads. Biosens Bioelectron 2017; 94:56-62. [PMID: 28257975 DOI: 10.1016/j.bios.2017.02.044] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2016] [Revised: 02/20/2017] [Accepted: 02/24/2017] [Indexed: 12/29/2022]
Abstract
MicroRNAs (miRNAs) play important roles in gene regulation and cancer development. Nowadays, it is still a challenge to detect low-abundance miRNAs. Here, we present a magnetic fluorescent miRNA sensing system for the rapid and sensitive detection of miRNAs from cell lysates and serum samples. In this system, albumin nanoparticles (Alb NPs) were prepared from inherent biocompatible bovine serum albumin (BSA). A large number of fluorescent dyes were loaded into Alb NPs to make Alb NPs serve as signal molecular nanocarriers for signal amplification. Benefited from the reactive functional groups-carboxyl groups of Alb NPs, p19 protein, a viral protein that can bind and sequester short RNA duplex effectively and selectively, was modified successfully to the surface of the fluorescent dyes-loaded Alb NPs, thus enabling the probe:target miRNA duplex recognition and binding. Followed by the introduction of gold nanoparticles coated magnetic microbeads (Au NPs-MBs), which were prepared through a novel and simple method, the system combined the merits of the rapid and efficient collection given by MBs with the good affinities to attach probe molecules endowed by the coated gold layer. A broad linear detection range of 10fM-10nM and a low detection limit of 9fM were obtained within 100min by detecting a model target miRNA-21. The feasibility of this method for rapid and sensitive quantification might advance the use of miRNAs as biomarkers in clinical praxis significantly.
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Affiliation(s)
- Tianxiang Wei
- Jiangsu Collaborative Innovation Centre of Biomedical Functional Materials and Jiangsu Key Laboratory of Biofunctional Materials, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, PR China; School of Mechanical and Materials Engineering, Washington State University, Pullman, WA 99164, USA; School of Environment, Nanjing Normal University, Nanjing 210023, PR China
| | - Dan Du
- School of Mechanical and Materials Engineering, Washington State University, Pullman, WA 99164, USA
| | - Zhaoyin Wang
- Jiangsu Collaborative Innovation Centre of Biomedical Functional Materials and Jiangsu Key Laboratory of Biofunctional Materials, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, PR China
| | - Weiwei Zhang
- Jiangsu Collaborative Innovation Centre of Biomedical Functional Materials and Jiangsu Key Laboratory of Biofunctional Materials, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, PR China
| | - Yuehe Lin
- School of Mechanical and Materials Engineering, Washington State University, Pullman, WA 99164, USA.
| | - Zhihui Dai
- Jiangsu Collaborative Innovation Centre of Biomedical Functional Materials and Jiangsu Key Laboratory of Biofunctional Materials, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, PR China.
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47
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Fattahi S, Pilehchian Langroudi M, Samadani AA, Nikbakhsh N, Asouri M, Akhavan-Niaki H. Application of unique sequence index (USI) barcode to gene expression profiling in gastric adenocarcinoma. J Cell Commun Signal 2017; 11:97-104. [PMID: 28120184 DOI: 10.1007/s12079-017-0376-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Accepted: 01/10/2017] [Indexed: 01/15/2023] Open
Abstract
Accurate expression profiling is imperative for understanding the biological roles of mRNAs. Real-time PCR have been at the forefront of biological innovation in detection and monitoring of gene expression, however, fluorophore-labeled oligonucleotides and double-stranded DNA binding dyes, the two most frequently used dyes in RNA detection, are not very cost effective and have poor specificity, respectively. We have developed a cost effective and specific approach for mRNA expression profiling via added unique sequence index (USI) to cDNAs before amplification. USI is a barcode which enable the detection of each target RNA. Using this method, caudal type homeobox 1 (CDX1) and FAT atypical cadherin 4 (FAT4) expressions were investigated in tumoral and non-tumoral tissues of gastric cancer patients and compared with commercial ABI kit. Both methods indicated that FAT4 and CDX1 expression were significantly reduced in gastric cancer tissues compared with adjacent noncancerous tissues. Moreover, we have shown that this assay is highly sensitive, linear and reproducible. USI barcode not only provides a powerful tool for mRNA detection due to its sensitivity, specificity and cost-effectiveness, but also allows comfortable design for real-time qPCR assays within the least time and empowers the analysis of many transcripts of virtually any organism. Furthermore, USI barcode is highly affordable for large numbers of different samples or small sample sizes without microarray and expensive commercial platforms.
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Affiliation(s)
- Sadegh Fattahi
- Cellular and Molecular Biology Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran.,North Research Center-Pasteur Institute of Iran, Amol, Iran
| | | | | | - Novin Nikbakhsh
- Department of Surgery, Rouhani hospital, Babol University of Medical Sciences, Babol, Iran
| | - Mohsen Asouri
- North Research Center-Pasteur Institute of Iran, Amol, Iran
| | - Haleh Akhavan-Niaki
- North Research Center-Pasteur Institute of Iran, Amol, Iran. .,Department of Genetics, Faculty of Medicine, Babol University of Medical Sciences, Babol, Iran.
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48
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Verheul RC, van Deutekom JCT, Datson NA. Digital Droplet PCR for the Absolute Quantification of Exon Skipping Induced by Antisense Oligonucleotides in (Pre-)Clinical Development for Duchenne Muscular Dystrophy. PLoS One 2016; 11:e0162467. [PMID: 27612288 PMCID: PMC5017733 DOI: 10.1371/journal.pone.0162467] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 08/23/2016] [Indexed: 01/15/2023] Open
Abstract
Antisense oligonucleotides (AONs) in clinical development for Duchenne muscular dystrophy (DMD) aim to induce skipping of a specific exon of the dystrophin transcript during pre-mRNA splicing. This results in restoration of the open reading frame and consequently synthesis of a dystrophin protein with a shorter yet functional central rod domain. To monitor the molecular therapeutic effect of exon skip-inducing AONs in clinical studies, accurate quantification of pre- and post-treatment exon skip levels is required. With the recent introduction of 3rd generation digital droplet PCR (ddPCR), a state-of-the-art technology became available which allows absolute quantification of transcript copy numbers with and without specific exon skip with high precision, sensitivity and reproducibility. Using Taqman assays with probes targeting specific exon-exon junctions, we here demonstrate that ddPCR reproducibly quantified cDNA fragments with and without exon 51 of the DMD gene over a 4-log dynamic range. In a comparison of conventional nested PCR, qPCR and ddPCR using cDNA constructs with and without exon 51 mixed in different molar ratios using, ddPCR quantification came closest to the expected outcome over the full range of ratios (0–100%), while qPCR and in particular nested PCR overestimated the relative percentage of the construct lacking exon 51. Highest accuracy was similarly obtained with ddPCR in DMD patient-derived muscle cells treated with an AON inducing exon 51 skipping. We therefore recommend implementation of ddPCR for quantification of exon skip efficiencies of AONs in (pre)clinical development for DMD.
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49
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Hackl M, Heilmeier U, Weilner S, Grillari J. Circulating microRNAs as novel biomarkers for bone diseases - Complex signatures for multifactorial diseases? Mol Cell Endocrinol 2016; 432:83-95. [PMID: 26525415 DOI: 10.1016/j.mce.2015.10.015] [Citation(s) in RCA: 115] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Revised: 10/20/2015] [Accepted: 10/20/2015] [Indexed: 02/07/2023]
Abstract
Biomarkers are essential tools in clinical research and practice. Useful biomarkers must combine good measurability, validated association with biological processes or outcomes, and should support clinical decision making if used in clinical practice. Several types of validated biomarkers have been reported in the context of bone diseases. However, because these biomarkers face certain limitations there is an interest in the identification of novel biomarkers for bone diseases, specifically in those that are tightly linked to the disease pathology leading to increased fracture-risk. MicroRNAs (miRNAs) are the most abundant RNA species to be found in cell-free blood. Encapsulated within microvesicles or bound to proteins, circulating miRNAs are remarkably stable analytes that can be measured using gold-standard technologies such as quantitative polymerase-chain-reaction (qPCR). Nevertheless, the analysis of circulating miRNAs faces several pre-analytical as well as analytical challenges. From a biological view, there is accumulating evidence that miRNAs play essential roles in the regulation of various biological processes including bone homeostasis. Moreover, specific changes in miRNA transcription levels or miRNA secretory levels have been linked to the development and progression of certain bone diseases. Only recently, results from circulating miRNAs analysis in patients with osteopenia, osteoporosis and fragility fractures have been reported. By comparing these findings to studies on circulating miRNAs in cellular senescence and aging or muscle physiology and sarcopenia, several overlaps were observed. This suggests that signatures observed during osteoporosis might not be specific to the pathophysiology in bone, but rather integrate information from several tissue types. Despite these promising first data, more work remains to be done until circulating miRNAs can serve as established and robust diagnostic tools for bone diseases in clinical research, clinical routine and in personalized medicine.
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Affiliation(s)
| | - Ursula Heilmeier
- Musculoskeletal Quantitative Imaging Research Group, Department of Radiology & Biomedical Imaging, University of California San Francisco, San Francisco, CA, USA
| | | | - Johannes Grillari
- Evercyte GmbH, 1190 Vienna, Austria; Christian Doppler Laboratory for Biotechnology of Skin Aging, Department of Biotechnology, BOKU - University of Natural Resources and Life Sciences Vienna, 1190 Vienna, Austria.
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50
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