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Cruz Da Silva E, Gaki P, Flieg F, Messmer M, Gucciardi F, Markovska Y, Reisch A, Fafi-Kremer S, Pfeffer S, Klymchenko AS. Direct Zeptomole Detection of RNA Biomarkers by Ultrabright Fluorescent Nanoparticles on Magnetic Beads. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024:e2404167. [PMID: 39011971 DOI: 10.1002/smll.202404167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Revised: 07/05/2024] [Indexed: 07/17/2024]
Abstract
Nucleic acids are important biomarkers in cancer and viral diseases. However, their ultralow concentration in biological/clinical samples makes direct target detection challenging, because it leads to slow hybridization kinetics with the probe and its insufficient signal-to-noise ratio. Therefore, RNA target detection is done by molecular (target) amplification, notably by RT-PCR, which is a tedious multistep method that includes nucleic acid extraction and reverse transcription. Here, a direct method based on ultrabright dye-loaded polymeric nanoparticles in a sandwich-like hybridization assay with magnetic beads is reported. The ultrabright DNA-functionalized nanoparticle, equivalent to ≈10 000 strongly emissive rhodamine dyes, is hybridized with the magnetic bead to the RNA target, providing the signal amplification for the detection. This concept (magneto-fluorescent sandwich) enables high-throughput detection of DNA and RNA sequences of varied lengths from 48 to 1362 nt with the limit of detection down to 0.3 fm using a plate reader (15 zeptomoles), among the best reported for optical sandwich assays. Moreover, it allows semi-quantitative detection of SARS-CoV-2 viral RNA directly in clinical samples without a dedicated RNA extraction step. The developed technology, combining ultrabright nanoparticles with magnetic beads, addresses fundamental challenges in RNA detection; it is expected to accelerate molecular diagnostics of diseases.
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Affiliation(s)
- Elisabete Cruz Da Silva
- Laboratoire de Bioimagerie et Pathologies, Faculté de Pharmacie, Université de Strasbourg, UMR 7021 CNRS, Illkirch, 67401, France
- BrightSens Diagnostics SAS, 11 Rue de l'Académie, Strasbourg, 67000, France
| | - Paraskevi Gaki
- Laboratoire de Bioimagerie et Pathologies, Faculté de Pharmacie, Université de Strasbourg, UMR 7021 CNRS, Illkirch, 67401, France
- BrightSens Diagnostics SAS, 11 Rue de l'Académie, Strasbourg, 67000, France
| | - Fabien Flieg
- BrightSens Diagnostics SAS, 11 Rue de l'Académie, Strasbourg, 67000, France
| | - Melanie Messmer
- Architecture et Réactivité de l'ARN, Institut de biologie moléculaire et cellulaire du CNRS, Université de Strasbourg, UPR 9002, Strasbourg, 67084, France
| | - Floriane Gucciardi
- Architecture et Réactivité de l'ARN, Institut de biologie moléculaire et cellulaire du CNRS, Université de Strasbourg, UPR 9002, Strasbourg, 67084, France
| | | | - Andreas Reisch
- Laboratoire de Bioimagerie et Pathologies, Faculté de Pharmacie, Université de Strasbourg, UMR 7021 CNRS, Illkirch, 67401, France
| | - Samira Fafi-Kremer
- CHU de Strasbourg, Laboratoire de Virologie, Université de Strasbourg, INSERM, Strasbourg, IRM UMR-S 1109, France
| | - Sébastien Pfeffer
- Architecture et Réactivité de l'ARN, Institut de biologie moléculaire et cellulaire du CNRS, Université de Strasbourg, UPR 9002, Strasbourg, 67084, France
| | - Andrey S Klymchenko
- Laboratoire de Bioimagerie et Pathologies, Faculté de Pharmacie, Université de Strasbourg, UMR 7021 CNRS, Illkirch, 67401, France
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The Future of Biomarkers in Veterinary Medicine: Emerging Approaches and Associated Challenges. Animals (Basel) 2022; 12:ani12172194. [PMID: 36077913 PMCID: PMC9454634 DOI: 10.3390/ani12172194] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 08/20/2022] [Accepted: 08/22/2022] [Indexed: 11/30/2022] Open
Abstract
Simple Summary In this review we seek to outline the role of new technologies in biomarker discovery, particularly within the veterinary field and with an emphasis on ‘omics’, as well as to examine why many biomarkers-despite much excitement-have not yet made it to clinical practice. Further we emphasise the critical need for close collaboration between clinicians, researchers and funding bodies and the need to set clear goals for biomarker requirements and realistic application in the clinical setting, ensuring that biomarker type, method of detection and clinical utility are compatible, and adequate funding, time and sample size are available for all phases of development. Abstract New biomarkers promise to transform veterinary practice through rapid diagnosis of diseases, effective monitoring of animal health and improved welfare and production efficiency. However, the road from biomarker discovery to translation is not always straightforward. This review focuses on molecular biomarkers under development in the veterinary field, introduces the emerging technological approaches transforming this space and the role of ‘omics platforms in novel biomarker discovery. The vast majority of veterinary biomarkers are at preliminary stages of development and not yet ready to be deployed into clinical translation. Hence, we examine the major challenges encountered in the process of biomarker development from discovery, through validation and translation to clinical practice, including the hurdles specific to veterinary practice and to each of the ‘omics platforms–transcriptomics, proteomics, lipidomics and metabolomics. Finally, recommendations are made for the planning and execution of biomarker studies with a view to assisting the success of novel biomarkers in reaching their full potential.
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Zhang Q, Yin B, Hao J, Ma L, Huang Y, Shao X, Li C, Chu Z, Yi C, Wong SHD, Yang M. An AIEgen/graphene oxide nanocomposite (AIEgen@GO)-based two-stage "turn-on" nucleic acid biosensor for rapid detection of SARS-CoV-2 viral sequence. AGGREGATE (HOBOKEN, N.J.) 2022; 4:e195. [PMID: 35539693 PMCID: PMC9073974 DOI: 10.1002/agt2.195] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 02/11/2022] [Accepted: 03/08/2022] [Indexed: 05/24/2023]
Abstract
The ongoing outbreak of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) pandemic has posed significant challenges in early viral diagnosis. Hence, it is urgently desirable to develop a rapid, inexpensive, and sensitive method to aid point-of-care SARS-CoV-2 detection. In this work, we report a highly sequence-specific biosensor based on nanocomposites with aggregation-induced emission luminogens (AIEgen)-labeled oligonucleotide probes on graphene oxide nanosheets (AIEgen@GO) for one step-detection of SARS-CoV-2-specific nucleic acid sequences (Orf1ab or N genes). A dual "turn-on" mechanism based on AIEgen@GO was established for viral nucleic acids detection. Here, the first-stage fluorescence recovery was due to dissociation of the AIEgen from GO surface in the presence of target viral nucleic acid, and the second-stage enhancement of AIE-based fluorescent signal was due to the formation of a nucleic acid duplex to restrict the intramolecular rotation of the AIEgen. Furthermore, the feasibility of our platform for diagnostic application was demonstrated by detecting SARS-CoV-2 virus plasmids containing both Orf1ab and N genes with rapid detection around 1 h and good sensitivity at pM level without amplification. Our platform shows great promise in assisting the initial rapid detection of the SARS-CoV-2 nucleic acid sequence before utilizing quantitative reverse transcription-polymerase chain reaction for second confirmation.
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Affiliation(s)
- Qin Zhang
- Department of Biomedical EngineeringThe Hong Kong Polytechnic UniversityHong KongChina
| | - Bohan Yin
- Department of Biomedical EngineeringThe Hong Kong Polytechnic UniversityHong KongChina
| | - Jianhua Hao
- Department of Applied PhysicsThe Hong Kong Polytechnic UniversityHong KongChina
| | - Linjie Ma
- Department of Electrical and Electronic EngineeringJoint Appointment with School of Biomedical SciencesThe University of Hong KongHong KongChina
| | - Yingying Huang
- Department of Biomedical EngineeringThe Hong Kong Polytechnic UniversityHong KongChina
| | - Xueying Shao
- Department of Electrical and Electronic EngineeringJoint Appointment with School of Biomedical SciencesThe University of Hong KongHong KongChina
| | - Chuanqi Li
- Department of Biomedical EngineeringThe Hong Kong Polytechnic UniversityHong KongChina
| | - Zhiqin Chu
- Department of Electrical and Electronic EngineeringJoint Appointment with School of Biomedical SciencesThe University of Hong KongHong KongChina
| | - Changqing Yi
- Key Laboratory of Sensing Technology and Biomedical Instruments (Guangdong Province)School of Biomedical EngineeringSun Yat‐Sen UniversityGuangzhouPR China
| | - Siu Hong Dexter Wong
- Department of Biomedical EngineeringThe Hong Kong Polytechnic UniversityHong KongChina
| | - Mo Yang
- Department of Biomedical EngineeringThe Hong Kong Polytechnic UniversityHong KongChina
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Abstract
We developed a new label-free biosensor technique for the detection of messenger ribonucleic acid (mRNA) that can be used in the prognosis and diagnosis of certain diseases. We observed a dependence of the negative dielectrophoresis (DEP) force applied to polystyrene microspheres (PMs) in conjugation with different types of mRNA and the frequency of the electric field produced by interdigitated microelectrodes. Since the frequency dependence of the negative DEP force is an effective transduction mechanism for the detection of mRNA, this sensing technology has the potential to be used in the diagnosis and identification of gene expression that is associated with various human disease.
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Islam MN, Gopalan V, Haque MH, Masud MK, Hossain MSA, Yamauchi Y, Nguyen NT, Lam AKY, Shiddiky MJA. A PCR-free electrochemical method for messenger RNA detection in cancer tissue samples. Biosens Bioelectron 2017; 98:227-233. [PMID: 28688308 DOI: 10.1016/j.bios.2017.06.051] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Revised: 06/19/2017] [Accepted: 06/25/2017] [Indexed: 11/17/2022]
Abstract
Despite having reliable and excellent diagnostic performances, the currently available messenger RNA (mRNA) detection methods mostly use enzymatic amplification steps of the target mRNA which is generally affected by the sample manipulations, amplification bias and longer assay time. This paper reports an amplification-free electrochemical approach for the sensitive and selective detection of mRNA using a screen-printed gold electrode (SPE-Au). The target mRNA is selectively isolated by magnetic separation and adsorbed directly onto an unmodified SPE-Au. The surface-attached mRNA is then measured by differential pulse voltammetry (DPV) in the presence of [Fe(CN)6]4-/3- redox system. This method circumvents the PCR amplification steps as well as simplifies the assay construction by avoiding multiple steps involved in conventional biosensing approaches of using recognition and transduction layers. Our method has demonstrated good sensitivity (LOD = 1.0pM) and reproducibility (% RSD = <5%, for n = 3) for detecting FAM134B mRNA in two cancer cell lines and a small cohort of clinical samples (number of samples = 26) collected from patients with oesophageal cancer. The analytical performance of our method is validated with a standard qRT-PCR analysis. We believe that our PCR-free approach holds a great promise for the analysis of tumor-specific mRNA in clinical samples.
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Affiliation(s)
- Md Nazmul Islam
- School of Natural Sciences, Griffith University, Nathan Campus, QLD 4111, Australia; Queensland Micro-, and Nanotechnology Centre, Griffith University, Nathan Campus, QLD 4111, Australia
| | - Vinod Gopalan
- Cancer Molecular Pathology Laboratory in School of Medicine, Menzies Health Institute Queensland, Griffith University, Gold Coast Campus, QLD 4222, Australia
| | - Md Hakimul Haque
- Cancer Molecular Pathology Laboratory in School of Medicine, Menzies Health Institute Queensland, Griffith University, Gold Coast Campus, QLD 4222, Australia
| | - Mostafa Kamal Masud
- Queensland Micro-, and Nanotechnology Centre, Griffith University, Nathan Campus, QLD 4111, Australia; Australian Institute for Innovative Materials (AIIM), University of Wollongong, Squires Way, Innovation Campus, North Wollongong, NSW 2519, Australia
| | - Md Shahriar Al Hossain
- Australian Institute for Innovative Materials (AIIM), University of Wollongong, Squires Way, Innovation Campus, North Wollongong, NSW 2519, Australia
| | - Yusuke Yamauchi
- Australian Institute for Innovative Materials (AIIM), University of Wollongong, Squires Way, Innovation Campus, North Wollongong, NSW 2519, Australia; International Center for Materials Nanoarchitectonics (MANA), National Institute for Materials Science (NIMS), 1-1 Namiki, Tsukuba, Ibaraki 305-0044, Japan
| | - Nam-Trung Nguyen
- Queensland Micro-, and Nanotechnology Centre, Griffith University, Nathan Campus, QLD 4111, Australia
| | - Alfred King-Yin Lam
- Cancer Molecular Pathology Laboratory in School of Medicine, Menzies Health Institute Queensland, Griffith University, Gold Coast Campus, QLD 4222, Australia
| | - Muhammad J A Shiddiky
- School of Natural Sciences, Griffith University, Nathan Campus, QLD 4111, Australia; Queensland Micro-, and Nanotechnology Centre, Griffith University, Nathan Campus, QLD 4111, Australia.
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Haider M, Ji B, Haselgrübler T, Sonnleitner A, Aberger F, Hesse J. A microfluidic multiwell chip for enzyme-free detection of mRNA from few cells. Biosens Bioelectron 2016; 86:20-26. [DOI: 10.1016/j.bios.2016.06.019] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Revised: 06/01/2016] [Accepted: 06/07/2016] [Indexed: 11/16/2022]
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