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Detassis S, Precazzini F, Brentari I, Ruffilli R, Ress C, Maglione A, Pernagallo S, Denti MA. SA-ODG platform: a semi-automated and PCR-free method to analyse microRNAs in solid tissues. Analyst 2024; 149:3891-3899. [PMID: 38994789 DOI: 10.1039/d4an00783b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/13/2024]
Abstract
Over the past two decades, numerous techniques have been developed for analysing microRNAs in body fluids and tissues. However, these techniques still face technical challenges, particularly when compared to well-established techniques for proteins and metabolites. Recently, the ODG platform was introduced, which is an innovative technology that allows for the direct detection and quantification of microRNAs in liquid biopsies without requiring extraction or amplification. This study presents the implementation of the ODG platform within a semi-automated protocol to create the "SA-ODG" platform, enhancing the efficiency and precision of microRNA testing while reducing hands-on time required by laboratory staff. For the first time, the SA-ODG platform has been used to directly quantify microRNAs in solid tissues. The results demonstrate precise analysis of miR-122-5p in mouse liver tissues using SA-ODG. These developments represent a crucial step forward in advancing the field of extraction and amplification-free microRNA detection and quantification.
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Affiliation(s)
- S Detassis
- OPTOI SRL, Via Vienna 8, 38121, Trento, Italy.
| | - F Precazzini
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Via Sommarive 9, 38123, Trento, Italy
| | - I Brentari
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Via Sommarive 9, 38123, Trento, Italy
| | - R Ruffilli
- OPTOI SRL, Via Vienna 8, 38121, Trento, Italy.
| | - C Ress
- OPTOI SRL, Via Vienna 8, 38121, Trento, Italy.
| | - A Maglione
- OPTOI SRL, Via Vienna 8, 38121, Trento, Italy.
| | - S Pernagallo
- DESTINA Genomica SL, Parque Tecnológico de la Salud (PTS), Avenida de la Innovación 1, 18016 Granada, Spain
| | - M A Denti
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Via Sommarive 9, 38123, Trento, Italy
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2
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Afari MNK, Lönnberg T. Base-Filling in Double-Helical Nucleic Acids. ChemistryOpen 2024:e202400088. [PMID: 38709096 DOI: 10.1002/open.202400088] [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: 03/18/2024] [Revised: 04/10/2024] [Indexed: 05/07/2024] Open
Abstract
Base-filling, i. e., post-synthetic furnishing of an oligonucleotide scaffold with base moieties or their analogues, is an interesting alternative to the conventional approach of sequential coupling of building blocks (modified or otherwise). Reversible attachment of the base moieties is particularly attractive as it allows the use of dynamic combinatorial chemistry and usually leads to higher fidelity. This concept article summarizes the various backbones and coupling reactions used for base-filling over the past fifteen years, discusses the impact of base stacking and pairing on efficiency and fidelity and highlights potential and realized applications.
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Affiliation(s)
| | - Tuomas Lönnberg
- Department of Chemistry, University of Turku, Henrikinkatu 2, 20500, Turku, Finland
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3
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Marín-Romero A, Pernagallo S. A comprehensive review of Dynamic Chemical Labelling on Luminex xMAP technology: a journey towards Drug-Induced Liver Injury testing. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2023; 15:6139-6149. [PMID: 37965948 DOI: 10.1039/d3ay01481a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2023]
Abstract
Drug-Induced Liver Injury (DILI) is a grave global adverse event that can result in fatal consequences, causing drug failures, market withdrawals, and regulatory warnings, leading to substantial financial losses. The early detection of DILI remains a significant challenge in global healthcare. Although circulating microRNAs (miRs) show promise as clinical biomarkers for DILI, the current analytical methods for their measurement are insufficient. There is a pressing need for rapid and reliable miR detection methods that eliminate the need for nucleic acid extraction and PCR-based amplification. This review highlights recent advancements achieved by integrating Dynamic Chemical Labelling (DCL) with Luminex xMAP technology. This powerful combination has resulted in groundbreaking bead-based assays that allow (1) the direct, multiplex detection of miRs, and (2) the simultaneous testing of miR and protein biomarkers. This triple capability enables a comprehensive assessment that significantly enhances the detection and analysis of crucial biomarkers, thus improving the understanding and diagnosis of DILI. In conclusion, this review offers valuable insights into the capabilities and potential applications of these groundbreaking assays in DILI research, as well as their potential use in other diagnostic and research domains that require direct or multiplex analysis of miRs or analysis of miRs in combination with proteins.
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Affiliation(s)
- Antonio Marín-Romero
- DESTINA Genomica S.L., Parque Tecnológico Ciencias de la Salud (PTS), Avenida de la Innovación 1, Edificio BIC, Armilla, Granada 18100, Spain.
| | - Salvatore Pernagallo
- DESTINA Genomica S.L., Parque Tecnológico Ciencias de la Salud (PTS), Avenida de la Innovación 1, Edificio BIC, Armilla, Granada 18100, Spain.
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4
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Wu Y, Fu Y, Guo J, Guo J. Single-molecule immunoassay technology: Recent advances. Talanta 2023; 265:124903. [PMID: 37418954 DOI: 10.1016/j.talanta.2023.124903] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 06/29/2023] [Accepted: 07/01/2023] [Indexed: 07/09/2023]
Abstract
Detecting diseases at the molecular level aids in early diagnosis and treatment. However, traditional immunological detection techniques, such as enzyme-linked immunosorbent assay (ELISA) and chemiluminescence, have detection sensitivities between 10-16 and 10-12 mol/L, which are inadequate for early diagnosis. Single-molecule immunoassays can reach detection sensitivities of 10-18 mol/L and can detect biomarkers that are difficult to measure using conventional detection techniques. It can confine molecules to be detected in a small spatial area and provide absolute counting of the detected signal, offering the advantage of high efficiency and accuracy. Herein, we demonstrate the principles and equipment of two single-molecule immunoassay techniques and discuss their applications. It is shown that the detection sensitivity can be improved by 2-3 orders of magnitude compared to common chemiluminescence or ELISA assays. The microarray-based single-molecule immunoassay technique can test 66 samples in 1 h, which is more efficient than conventional immunological detection techniques. In contrast, microdroplet-based single-molecule immunoassay techniques can generate 107 droplets in 10 min, which is more than 100 times faster than a single droplet generator. By comparing the two single-molecule immunoassay techniques, we highlight our personal perspectives on the current limitations of point-of-care applications and future development trends.
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Affiliation(s)
- Yi Wu
- University of Electronic Science and Technology of China, Chengdu, China
| | - Yusheng Fu
- University of Electronic Science and Technology of China, Chengdu, China
| | - Jiuchuan Guo
- University of Electronic Science and Technology of China, Chengdu, China.
| | - Jinhong Guo
- School of Sensing Science and Engineering, Shanghai Jiao Tong University, Shanghai, China; The M.O.E. Key Laboratory of Laboratory Medical Diagnostics, The College of Laboratory Medicine, Chongqing Medical University, #1 Yixueyuan Road, Yuzhong District, Chongqing, 400016, China.
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5
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SARS-CoV-2 viral RNA detection using the novel CoVradar device associated with the CoVreader smartphone app. Biosens Bioelectron 2023; 230:115268. [PMID: 37030262 PMCID: PMC10060197 DOI: 10.1016/j.bios.2023.115268] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Accepted: 03/25/2023] [Indexed: 04/01/2023]
Abstract
The COVID-19 pandemic has highlighted the need for innovative approaches to its diagnosis. Here we present CoVradar, a novel and simple colorimetric method that combines nucleic acid analysis with dynamic chemical labeling (DCL) technology and the Spin-Tube device to detect SARS-CoV-2 RNA in saliva samples. The assay includes a fragmentation step to increase the number of RNA templates for analysis, using abasic peptide nucleic acid probes (DGL probes) immobilized to nylon membranes in a specific dot pattern to capture RNA fragments. Duplexes are formed by labeling complementary RNA fragments with biotinylated SMART bases, which act as templates for DCL. Signals are generated by recognizing biotin with streptavidin alkaline phosphatase and incubating with a chromogenic substrate to produce a blue precipitate. CoVradar results are analysed by CoVreader, a smartphone-based image processing system that can display and interpret the blotch pattern. CoVradar and CoVreader provide a unique molecular assay capable of detecting SARS-CoV-2 viral RNA without the need for extraction, preamplification, or prelabeling steps, offering advantages in terms of time (∼3 h/test), cost (∼€1/test manufacturing cost) and simplicity (does not require large equipment). This solution is also promising for the development of assays for other infectious diseases.
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6
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Robles-Remacho A, Luque-Gonzalez MA, López-Delgado FJ, Guardia-Monteagudo JJ, Fara MA, Pernagallo S, Sanchez-Martin RM, Diaz-Mochon JJ. Direct detection of alpha satellite DNA with single-base resolution by using abasic Peptide Nucleic Acids and Fluorescent in situ Hybridization. Biosens Bioelectron 2023; 219:114770. [PMID: 36270082 DOI: 10.1016/j.bios.2022.114770] [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: 05/18/2022] [Revised: 09/15/2022] [Accepted: 09/28/2022] [Indexed: 11/19/2022]
Abstract
The detection of repetitive sequences with single-base resolution is becoming increasingly important aiming to understand the biological implications of genomic variation in these sequences. However, there is a lack of techniques to experimentally validate sequencing data from repetitive sequences obtained by Next-Generation Sequencing methods, especially in the case of Single-Nucleotide Variations (SNVs). That is one of the reasons why repetitive sequences have been poorly studied and excluded from most genomic studies. Therefore, in addition to sequencing data, there is an urgent need for efficient validation methods of genomic variation in these sequences. Herein we report the development of chemFISH, an alternative method for the detection of SNVs in repetitive sequences. ChemFISH is an innovative method based on dynamic chemistry labelling and abasic Peptide Nucleic Acid (PNA) probes to detect in situ the α-satellite DNA, organized in tandem repeats, with single-base resolution in a direct and rapid reaction. With this approach, we detected by microscopy the α-satellite DNA in a variety of human cell lines, we quantified the detection showing a low coefficient of variation among samples (13.16%-25.33%) and we detected single-base specificity with high sensitivity (82.41%-88.82%). These results indicate that chemFISH can serve as a rapid method to validate previously detected SNVs in sequencing data, as well as to find novel SNVs in repetitive sequences. Furthermore, the versatile chemistry behind chemFISH can lead to develop novel molecular assays for the in situ detection of nucleic acids.
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Affiliation(s)
- Agustín Robles-Remacho
- GENYO, Centre for Genomics and Oncological Research, Pfizer, University of Granada, Andalusian Regional Government, PTS Granada, Avenida de la Ilustración, 114, 18016, Granada, Spain; Department of Medicinal and Organic Chemistry, School of Pharmacy, University of Granada, Campus Cartuja s/n, 18071, Granada, Spain; Biosanitary Research Institute of Granada (ibs.GRANADA), University Hospital of Granada/University of Granada, Avenida del Conocimiento, s/n, 18016, Granada, Spain
| | - M Angelica Luque-Gonzalez
- GENYO, Centre for Genomics and Oncological Research, Pfizer, University of Granada, Andalusian Regional Government, PTS Granada, Avenida de la Ilustración, 114, 18016, Granada, Spain; Department of Medicinal and Organic Chemistry, School of Pharmacy, University of Granada, Campus Cartuja s/n, 18071, Granada, Spain; Biosanitary Research Institute of Granada (ibs.GRANADA), University Hospital of Granada/University of Granada, Avenida del Conocimiento, s/n, 18016, Granada, Spain
| | - F Javier López-Delgado
- DESTINA Genomica S.L, PTS Granada, Avenida de la Innovación 1, Edificio BIC, Armilla, 18100, Granada, Spain
| | - Juan J Guardia-Monteagudo
- DESTINA Genomica S.L, PTS Granada, Avenida de la Innovación 1, Edificio BIC, Armilla, 18100, Granada, Spain
| | - Mario Antonio Fara
- DESTINA Genomica S.L, PTS Granada, Avenida de la Innovación 1, Edificio BIC, Armilla, 18100, Granada, Spain
| | - Salvatore Pernagallo
- DESTINA Genomica S.L, PTS Granada, Avenida de la Innovación 1, Edificio BIC, Armilla, 18100, Granada, Spain
| | - Rosario M Sanchez-Martin
- GENYO, Centre for Genomics and Oncological Research, Pfizer, University of Granada, Andalusian Regional Government, PTS Granada, Avenida de la Ilustración, 114, 18016, Granada, Spain; Department of Medicinal and Organic Chemistry, School of Pharmacy, University of Granada, Campus Cartuja s/n, 18071, Granada, Spain; Biosanitary Research Institute of Granada (ibs.GRANADA), University Hospital of Granada/University of Granada, Avenida del Conocimiento, s/n, 18016, Granada, Spain.
| | - Juan Jose Diaz-Mochon
- GENYO, Centre for Genomics and Oncological Research, Pfizer, University of Granada, Andalusian Regional Government, PTS Granada, Avenida de la Ilustración, 114, 18016, Granada, Spain; Department of Medicinal and Organic Chemistry, School of Pharmacy, University of Granada, Campus Cartuja s/n, 18071, Granada, Spain; Biosanitary Research Institute of Granada (ibs.GRANADA), University Hospital of Granada/University of Granada, Avenida del Conocimiento, s/n, 18016, Granada, Spain.
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7
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Schofield AL, Brown JP, Brown J, Wilczynska A, Bell C, Glaab WE, Hackl M, Howell L, Lee S, Dear JW, Remes M, Reeves P, Zhang E, Allmer J, Norris A, Falciani F, Takeshita LY, Seyed Forootan S, Sutton R, Park BK, Goldring C. Systems analysis of miRNA biomarkers to inform drug safety. Arch Toxicol 2021; 95:3475-3495. [PMID: 34510227 PMCID: PMC8492583 DOI: 10.1007/s00204-021-03150-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 08/23/2021] [Indexed: 02/06/2023]
Abstract
microRNAs (miRNAs or miRs) are short non-coding RNA molecules which have been shown to be dysregulated and released into the extracellular milieu as a result of many drug and non-drug-induced pathologies in different organ systems. Consequently, circulating miRs have been proposed as useful biomarkers of many disease states, including drug-induced tissue injury. miRs have shown potential to support or even replace the existing traditional biomarkers of drug-induced toxicity in terms of sensitivity and specificity, and there is some evidence for their improved diagnostic and prognostic value. However, several pre-analytical and analytical challenges, mainly associated with assay standardization, require solutions before circulating miRs can be successfully translated into the clinic. This review will consider the value and potential for the use of circulating miRs in drug-safety assessment and describe a systems approach to the analysis of the miRNAome in the discovery setting, as well as highlighting standardization issues that at this stage prevent their clinical use as biomarkers. Highlighting these challenges will hopefully drive future research into finding appropriate solutions, and eventually circulating miRs may be translated to the clinic where their undoubted biomarker potential can be used to benefit patients in rapid, easy to use, point-of-care test systems.
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Affiliation(s)
- Amy L Schofield
- MRC Centre for Drug Safety Science, Department of Pharmacology and Therapeutics, University of Liverpool, Sherrington Buildings, Ashton Street, Liverpool, L69 3GE, UK
| | - Joseph P Brown
- MRC Centre for Drug Safety Science, Department of Pharmacology and Therapeutics, University of Liverpool, Sherrington Buildings, Ashton Street, Liverpool, L69 3GE, UK
| | - Jack Brown
- MRC Centre for Drug Safety Science, Department of Pharmacology and Therapeutics, University of Liverpool, Sherrington Buildings, Ashton Street, Liverpool, L69 3GE, UK
| | - Ania Wilczynska
- bit.bio, Babraham Research Campus, The Dorothy Hodgkin Building, Cambridge, CB22 3FH, UK
| | - Catherine Bell
- CVRM Safety, Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Warren E Glaab
- Merck & Co., Inc, 770 Sumneytown Pike, West Point, PA, 19486, USA
| | | | - Lawrence Howell
- GlaxoSmithKline (GSK), Stevenage, Greater Cambridge Area, UK
| | - Stephen Lee
- ABHI, 1 Duchess St, 4th Floor, Suite 2, London, W1W 6AN, UK
| | - James W Dear
- Centre for Cardiovascular Science, The Queen's Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh, EH16 4TJ, UK
| | - Mika Remes
- Genomics EMEA, QIAGEN Aarhus, Prismet, Silkeborgvej 2, 8000, Aarhus C, Denmark
| | - Paul Reeves
- Arcis Biotechnology Limited, Suite S07, Techspace One, Sci-tech Daresbury, Keckwick Lane, Daresbury, Warrington, WA4 4AB, UK
| | - Eunice Zhang
- Wolfson Centre for Personalised Medicine, Department of Pharmacology and Therapeutics, University of Liverpool, Crown Street, Liverpool, L69 3BX, UK
| | - Jens Allmer
- Applied Bioinformatics, Bioscience, Wageningen University and Research, Droevendaalsesteeg 4, 6708 PB, Wageningen, The Netherlands
| | - Alan Norris
- MRC Centre for Drug Safety Science, Department of Pharmacology and Therapeutics, University of Liverpool, Sherrington Buildings, Ashton Street, Liverpool, L69 3GE, UK
| | - Francesco Falciani
- Computational Biology Facility, MerseyBio, University of Liverpool, Crown Street, Liverpool, L69 7ZB, UK
| | - Louise Y Takeshita
- Computational Biology Facility, MerseyBio, University of Liverpool, Crown Street, Liverpool, L69 7ZB, UK
| | - Shiva Seyed Forootan
- MRC Centre for Drug Safety Science, Department of Pharmacology and Therapeutics, University of Liverpool, Sherrington Buildings, Ashton Street, Liverpool, L69 3GE, UK
| | - Robert Sutton
- Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Biosciences Building, Crown Street, Liverpool, L69 7BE, UK
| | - B Kevin Park
- MRC Centre for Drug Safety Science, Department of Pharmacology and Therapeutics, University of Liverpool, Sherrington Buildings, Ashton Street, Liverpool, L69 3GE, UK
| | - Chris Goldring
- MRC Centre for Drug Safety Science, Department of Pharmacology and Therapeutics, University of Liverpool, Sherrington Buildings, Ashton Street, Liverpool, L69 3GE, UK.
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8
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Simultaneous Detection of Drug-Induced Liver Injury Protein and microRNA Biomarkers Using Dynamic Chemical Labelling on a Luminex MAGPIX System. ANALYTICA 2021. [DOI: 10.3390/analytica2040013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
Drug-induced liver injury (DILI) is a potentially fatal adverse event and a leading cause for pre- and post-marketing drug withdrawal. Several multinational DILI initiatives have now recommended a panel of protein and microRNA (miRNA) biomarkers that can detect early liver injury and inform about mechanistic basis. This manuscript describes the development of seqCOMBO, a unique combo-multiplexed assay which combines the dynamic chemical labelling approach and an antibody-dependant method on the Luminex MAGPIX system. SeqCOMBO enables a versatile multiplexing platform to perform qualitative and quantitative analysis of proteins and miRNAs in patient serum samples simultaneously. To the best of our knowledge, this is the first method to profile protein and miRNA biomarkers to diagnose DILI in a single-step assay.
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9
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Kaysheva AL, Isaeva AI, Pleshakova TO, Shumov ID, Valueva AA, Ershova MO, Ivanova IA, Ziborov VS, Iourov IY, Vorsanova SG, Ryabtsev SV, Archakov AI, Ivanov YD. Detection of Circulating Serum microRNA/Protein Complexes in ASD Using Functionalized Chips for an Atomic Force Microscope. Molecules 2021; 26:5979. [PMID: 34641523 PMCID: PMC8512613 DOI: 10.3390/molecules26195979] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 09/17/2021] [Accepted: 09/29/2021] [Indexed: 11/17/2022] Open
Abstract
MicroRNAs, which circulate in blood, are characterized by high diagnostic value; in biomedical research, they can be considered as candidate markers of various diseases. Mature microRNAs of glial cells and neurons can cross the blood-brain barrier and can be detected in the serum of patients with autism spectrum disorders (ASD) as components of macrovesicles, macromolecular protein and low-density lipoprotein particles. In our present study, we have proposed an approach, in which microRNAs in protein complexes can be concentrated on the surface of AFM chips with oligonucleotide molecular probes, specific against the target microRNAs. MicroRNAs, associated with the development of ASD in children, were selected as targets. The chips with immobilized molecular probes were incubated in serum samples of ASD patients and healthy volunteers. By atomic force microscopy (AFM), objects on the AFM chip surface have been revealed after incubation in the serum samples. The height of these objects amounted to 10 nm and 6 nm in the case of samples of ASD patients and healthy volunteers, respectively. MALDI-TOF-MS analysis of protein components on the chip surface allowed us to identify several cell proteins. These proteins are involved in the binding of nucleic acids (GBG10, RT24, RALYL), in the organization of proteasomes and nucleosomes (PSA4, NP1L4), and participate in the functioning of the channel of active potassium transport (KCNE5, KCNV2).
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Affiliation(s)
- Anna L. Kaysheva
- Laboratory of Nanobiotechnology, Institute of Biomedical Chemistry, Pogodinskaya St. 10/8, 119121 Moscow, Russia; (A.L.K.); (T.O.P.); (I.D.S.); (A.A.V.); (M.O.E.); (I.A.I.); (V.S.Z.); (A.I.A.); (Y.D.I.)
| | - Arina I. Isaeva
- Laboratory of Nanobiotechnology, Institute of Biomedical Chemistry, Pogodinskaya St. 10/8, 119121 Moscow, Russia; (A.L.K.); (T.O.P.); (I.D.S.); (A.A.V.); (M.O.E.); (I.A.I.); (V.S.Z.); (A.I.A.); (Y.D.I.)
| | - Tatyana O. Pleshakova
- Laboratory of Nanobiotechnology, Institute of Biomedical Chemistry, Pogodinskaya St. 10/8, 119121 Moscow, Russia; (A.L.K.); (T.O.P.); (I.D.S.); (A.A.V.); (M.O.E.); (I.A.I.); (V.S.Z.); (A.I.A.); (Y.D.I.)
| | - Ivan D. Shumov
- Laboratory of Nanobiotechnology, Institute of Biomedical Chemistry, Pogodinskaya St. 10/8, 119121 Moscow, Russia; (A.L.K.); (T.O.P.); (I.D.S.); (A.A.V.); (M.O.E.); (I.A.I.); (V.S.Z.); (A.I.A.); (Y.D.I.)
| | - Anastasia A. Valueva
- Laboratory of Nanobiotechnology, Institute of Biomedical Chemistry, Pogodinskaya St. 10/8, 119121 Moscow, Russia; (A.L.K.); (T.O.P.); (I.D.S.); (A.A.V.); (M.O.E.); (I.A.I.); (V.S.Z.); (A.I.A.); (Y.D.I.)
| | - Maria O. Ershova
- Laboratory of Nanobiotechnology, Institute of Biomedical Chemistry, Pogodinskaya St. 10/8, 119121 Moscow, Russia; (A.L.K.); (T.O.P.); (I.D.S.); (A.A.V.); (M.O.E.); (I.A.I.); (V.S.Z.); (A.I.A.); (Y.D.I.)
| | - Irina A. Ivanova
- Laboratory of Nanobiotechnology, Institute of Biomedical Chemistry, Pogodinskaya St. 10/8, 119121 Moscow, Russia; (A.L.K.); (T.O.P.); (I.D.S.); (A.A.V.); (M.O.E.); (I.A.I.); (V.S.Z.); (A.I.A.); (Y.D.I.)
| | - Vadim S. Ziborov
- Laboratory of Nanobiotechnology, Institute of Biomedical Chemistry, Pogodinskaya St. 10/8, 119121 Moscow, Russia; (A.L.K.); (T.O.P.); (I.D.S.); (A.A.V.); (M.O.E.); (I.A.I.); (V.S.Z.); (A.I.A.); (Y.D.I.)
- Laboratory of Shock Wave Impacts, Joint Institute for High Temperatures of the Russian Academy of Sciences, Izhorskaya St. 13 Bd.2, 125412 Moscow, Russia
| | | | - Svetlana G. Vorsanova
- Veltischev Research and Clinical Institute for Pediatrics, Pirogov Russian National Research Medical University, Ministry of Health of Russian Federation, Taldomskaya St. 2, 125412 Moscow, Russia;
| | | | - Alexander I. Archakov
- Laboratory of Nanobiotechnology, Institute of Biomedical Chemistry, Pogodinskaya St. 10/8, 119121 Moscow, Russia; (A.L.K.); (T.O.P.); (I.D.S.); (A.A.V.); (M.O.E.); (I.A.I.); (V.S.Z.); (A.I.A.); (Y.D.I.)
| | - Yuri D. Ivanov
- Laboratory of Nanobiotechnology, Institute of Biomedical Chemistry, Pogodinskaya St. 10/8, 119121 Moscow, Russia; (A.L.K.); (T.O.P.); (I.D.S.); (A.A.V.); (M.O.E.); (I.A.I.); (V.S.Z.); (A.I.A.); (Y.D.I.)
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10
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Robles-Remacho A, Luque-González MA, González-Casín RA, Cano-Cortés MV, Lopez-Delgado FJ, Guardia-Monteagudo JJ, Antonio Fara M, Sánchez-Martín RM, Díaz-Mochón JJ. Development of a nanotechnology-based approach for capturing and detecting nucleic acids by using flow cytometry. Talanta 2021; 226:122092. [PMID: 33676649 PMCID: PMC7794053 DOI: 10.1016/j.talanta.2021.122092] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 01/04/2021] [Accepted: 01/05/2021] [Indexed: 12/16/2022]
Abstract
Nucleic acid-based molecular diagnosis has gained special importance for the detection and early diagnosis of genetic diseases as well as for the control of infectious disease outbreaks. The development of systems that allow for the detection and analysis of nucleic acids in a low-cost and easy-to-use way is of great importance. In this context, we present a combination of a nanotechnology-based approach with the already validated dynamic chemical labeling (DCL) technology, capable of reading nucleic acids with single-base resolution. This system allows for the detection of biotinylated molecular products followed by simple detection using a standard flow cytometer, a widely used platform in clinical and molecular laboratories, and therefore, is easy to implement. This proof-of-concept assay has been developed to detect mutations in KRAS codon 12, as these mutations are highly important in cancer development and cancer treatments.
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Affiliation(s)
- Agustín Robles-Remacho
- GENYO. Centre for Genomics and Oncological Research: Pfizer / University of Granada / Andalusian Regional Government, PTS Granada, Avenida de La Ilustracion, 114, 18016, Granada, Spain,Department of Medicinal and Organic Chemistry, School of Pharmacy, University of Granada, Campus Cartuja S/n, 18071, Granada, Spain,Biosanitary Research Institute of Granada (ibs.GRANADA), University Hospital of Granada/University of Granada, Avenida Del Conocimiento, S/n, 18016, Granada, Spain
| | - M. Angélica Luque-González
- GENYO. Centre for Genomics and Oncological Research: Pfizer / University of Granada / Andalusian Regional Government, PTS Granada, Avenida de La Ilustracion, 114, 18016, Granada, Spain,Department of Medicinal and Organic Chemistry, School of Pharmacy, University of Granada, Campus Cartuja S/n, 18071, Granada, Spain,Biosanitary Research Institute of Granada (ibs.GRANADA), University Hospital of Granada/University of Granada, Avenida Del Conocimiento, S/n, 18016, Granada, Spain
| | - Roberto A. González-Casín
- GENYO. Centre for Genomics and Oncological Research: Pfizer / University of Granada / Andalusian Regional Government, PTS Granada, Avenida de La Ilustracion, 114, 18016, Granada, Spain
| | - M. Victoria Cano-Cortés
- GENYO. Centre for Genomics and Oncological Research: Pfizer / University of Granada / Andalusian Regional Government, PTS Granada, Avenida de La Ilustracion, 114, 18016, Granada, Spain,Department of Medicinal and Organic Chemistry, School of Pharmacy, University of Granada, Campus Cartuja S/n, 18071, Granada, Spain,Biosanitary Research Institute of Granada (ibs.GRANADA), University Hospital of Granada/University of Granada, Avenida Del Conocimiento, S/n, 18016, Granada, Spain
| | - F. Javier Lopez-Delgado
- DestiNA Genomica S.L, PTS Granada, Avenida de La Innovación 1, Edificio BIC, 18100, Armilla, Granada, Spain
| | - Juan J. Guardia-Monteagudo
- DestiNA Genomica S.L, PTS Granada, Avenida de La Innovación 1, Edificio BIC, 18100, Armilla, Granada, Spain
| | - Mario Antonio Fara
- DestiNA Genomica S.L, PTS Granada, Avenida de La Innovación 1, Edificio BIC, 18100, Armilla, Granada, Spain
| | - Rosario M. Sánchez-Martín
- GENYO. Centre for Genomics and Oncological Research: Pfizer / University of Granada / Andalusian Regional Government, PTS Granada, Avenida de La Ilustracion, 114, 18016, Granada, Spain,Department of Medicinal and Organic Chemistry, School of Pharmacy, University of Granada, Campus Cartuja S/n, 18071, Granada, Spain,Biosanitary Research Institute of Granada (ibs.GRANADA), University Hospital of Granada/University of Granada, Avenida Del Conocimiento, S/n, 18016, Granada, Spain,Corresponding author. GENYO. Centre for Genomics and Oncological Research: Pfizer / University of Granada / Andalusian Regional Government, PTS Granada, Avenida de la Ilustracion, 114, 18016, Granada, Spain
| | - Juan José Díaz-Mochón
- GENYO. Centre for Genomics and Oncological Research: Pfizer / University of Granada / Andalusian Regional Government, PTS Granada, Avenida de La Ilustracion, 114, 18016, Granada, Spain,Department of Medicinal and Organic Chemistry, School of Pharmacy, University of Granada, Campus Cartuja S/n, 18071, Granada, Spain,Biosanitary Research Institute of Granada (ibs.GRANADA), University Hospital of Granada/University of Granada, Avenida Del Conocimiento, S/n, 18016, Granada, Spain,Corresponding author. GENYO. Centre for Genomics and Oncological Research: Pfizer / University of Granada / Andalusian Regional Government, PTS Granada, Avenida de la Ilustracion, 114, 18016, Granada, Spain
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11
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Measurements Methods for the Development of MicroRNA-Based Tests for Cancer Diagnosis. Int J Mol Sci 2021; 22:ijms22031176. [PMID: 33503982 PMCID: PMC7865473 DOI: 10.3390/ijms22031176] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 01/15/2021] [Accepted: 01/22/2021] [Indexed: 12/19/2022] Open
Abstract
Studies investigating microRNAs as potential biomarkers for cancer, immune-related diseases, or cardiac pathogenic diseases, among others, have exponentially increased in the last years. In particular, altered expression of specific miRNAs correlates with the occurrence of several diseases, making these molecules potential molecular tools for non-invasive diagnosis, prognosis, and response to therapy. Nonetheless, microRNAs are not in clinical use yet, due to inconsistencies in the literature regarding the specific miRNAs identified as biomarkers for a specific disease, which in turn can be attributed to several reasons, including lack of assay standardization and reproducibility. Technological limitations in circulating microRNAs measurement have been, to date, the biggest challenge for using these molecules in clinical settings. In this review we will discuss pre-analytical, analytical, and post-analytical challenges to address the potential technical biases and patient-related parameters that can have an influence and should be improved to translate miRNA biomarkers to the clinical stage. Moreover, we will describe the currently available methods for circulating miRNA expression profiling and measurement, underlining their advantages and potential pitfalls.
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12
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Marín-Romero A, Tabraue-Chávez M, Dear JW, Sánchez-Martín RM, Ilyine H, Guardia-Monteagudo JJ, Fara MA, López-Delgado FJ, Díaz-Mochón JJ, Pernagallo S. Amplification-free profiling of microRNA-122 biomarker in DILI patient serums, using the luminex MAGPIX system. Talanta 2020; 219:121265. [PMID: 32887156 DOI: 10.1016/j.talanta.2020.121265] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 06/04/2020] [Accepted: 06/07/2020] [Indexed: 01/08/2023]
Abstract
Dynamic chemical labelling is a single-base specific method to enable detection and quantification of micro-Ribonucleic Acids in biological fluids without extraction and pre-amplification. In this study, dynamic chemical labelling was combined with the Luminex MAGPIX system to profile levels of microRNA-122 biomarker in serum from patients with Drug-Induced Liver Injury.
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Affiliation(s)
- Antonio Marín-Romero
- DESTINA Genomica S.L. Parque Tecnológico Ciencias de la Salud (PTS), Avenida de la Innovación 1, Edificio BIC, Armilla, Granada, 18100, Spain; GENYO. Centre for Genomics and Oncological Research: Pfizer / University of Granada, Andalusian Regional Government, PTS Granada - Avenida de la Ilustración, 114 - 18016, GRANADA, Spain; Universidad de Granada. Facultad de Farmacia. Departamento de Quimica Farmacéutica y Orgánica, Campus Cartuja s/n, 18071, Granada, Spain
| | - Mavys Tabraue-Chávez
- DESTINA Genomica S.L. Parque Tecnológico Ciencias de la Salud (PTS), Avenida de la Innovación 1, Edificio BIC, Armilla, Granada, 18100, Spain
| | - James W Dear
- Pharmacology,Therapeutics and Toxicology, Centre for Cardiovascular Science, University of Edinburgh, The Queen's Medical Research Institute, 47, Little France Crescent, Edinburgh, EH16, 4TJ, UK
| | - Rosario M Sánchez-Martín
- GENYO. Centre for Genomics and Oncological Research: Pfizer / University of Granada, Andalusian Regional Government, PTS Granada - Avenida de la Ilustración, 114 - 18016, GRANADA, Spain; Universidad de Granada. Facultad de Farmacia. Departamento de Quimica Farmacéutica y Orgánica, Campus Cartuja s/n, 18071, Granada, Spain
| | - Hugh Ilyine
- DESTINA Genomics Ltd, 7-11 Melville St, Edinburgh, EH3 7PE, UK
| | - Juan J Guardia-Monteagudo
- DESTINA Genomica S.L. Parque Tecnológico Ciencias de la Salud (PTS), Avenida de la Innovación 1, Edificio BIC, Armilla, Granada, 18100, Spain
| | - Mario A Fara
- DESTINA Genomica S.L. Parque Tecnológico Ciencias de la Salud (PTS), Avenida de la Innovación 1, Edificio BIC, Armilla, Granada, 18100, Spain
| | - Francisco J López-Delgado
- DESTINA Genomica S.L. Parque Tecnológico Ciencias de la Salud (PTS), Avenida de la Innovación 1, Edificio BIC, Armilla, Granada, 18100, Spain
| | - Juan J Díaz-Mochón
- GENYO. Centre for Genomics and Oncological Research: Pfizer / University of Granada, Andalusian Regional Government, PTS Granada - Avenida de la Ilustración, 114 - 18016, GRANADA, Spain; Universidad de Granada. Facultad de Farmacia. Departamento de Quimica Farmacéutica y Orgánica, Campus Cartuja s/n, 18071, Granada, Spain.
| | - Salvatore Pernagallo
- DESTINA Genomica S.L. Parque Tecnológico Ciencias de la Salud (PTS), Avenida de la Innovación 1, Edificio BIC, Armilla, Granada, 18100, Spain.
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13
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Garcia-Fernandez E, Gonzalez-Garcia MC, Pernagallo S, Ruedas-Rama MJ, Fara MA, López-Delgado FJ, Dear JW, Ilyine H, Ress C, Díaz-Mochón JJ, Orte A. miR-122 direct detection in human serum by time-gated fluorescence imaging. Chem Commun (Camb) 2019; 55:14958-14961. [PMID: 31774422 DOI: 10.1039/c9cc08069d] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
A simple method for direct detection of microRNAs (miRs) in human serum without the use of polymerase amplification is presented, achieving low miR-122 concentrations and importantly, discerning effectively single-base sequence mutations. The method is based on the capture of target miRs with synthetic peptide nucleic acid oligomers, dynamic chemical labelling, separation with quaternary amine microplatforms and detection using time-gated fluorescence imaging.
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Affiliation(s)
- Emilio Garcia-Fernandez
- Departamento de Fisicoquimica. Unidad de Excelencia de Química aplicada a Biomedicina y Medioambiente, Facultad de Farmacia, Universidad de Granada, Campus de Cartuja s/n, 18071-Granada, Spain.
| | - M Carmen Gonzalez-Garcia
- Departamento de Fisicoquimica. Unidad de Excelencia de Química aplicada a Biomedicina y Medioambiente, Facultad de Farmacia, Universidad de Granada, Campus de Cartuja s/n, 18071-Granada, Spain.
| | - Salvatore Pernagallo
- DestiNA Genomica S.L., Parque Tecnológico Ciencias de la Salud (PTS), Av. de la Innovación 1, Edificio BIC, Armilla, Granada, Spain and DestiNA Genomics Ltd, 7-11 Melville St, Edinburgh EH3 7PE, UK
| | - Maria J Ruedas-Rama
- Departamento de Fisicoquimica. Unidad de Excelencia de Química aplicada a Biomedicina y Medioambiente, Facultad de Farmacia, Universidad de Granada, Campus de Cartuja s/n, 18071-Granada, Spain.
| | - Mario A Fara
- DestiNA Genomica S.L., Parque Tecnológico Ciencias de la Salud (PTS), Av. de la Innovación 1, Edificio BIC, Armilla, Granada, Spain
| | - Francisco J López-Delgado
- DestiNA Genomica S.L., Parque Tecnológico Ciencias de la Salud (PTS), Av. de la Innovación 1, Edificio BIC, Armilla, Granada, Spain
| | - James W Dear
- Centre for Cardiovascular Science, University of Edinburgh, The Queen's Medical Research Institute, 47 Little France Crescent, Edinburgh, EH16 4TJ, UK
| | - Hugh Ilyine
- DestiNA Genomics Ltd, 7-11 Melville St, Edinburgh EH3 7PE, UK
| | - Cristina Ress
- Optoi Microelectronics, Via Vienna n°8, Trento, 38121 Gardolo, Italy
| | - Juan J Díaz-Mochón
- DestiNA Genomica S.L., Parque Tecnológico Ciencias de la Salud (PTS), Av. de la Innovación 1, Edificio BIC, Armilla, Granada, Spain and GENYO, Centre for Genomics and Oncological Research, Pfizer/University of Granada/Andalusian Regional Government, Av. de la Ilustración, 114, 18016-Granada, Spain and Departamento de Quimica Farmaceutica y Organica, Facultad de Farmacia, Universidad de Granada, Campus de Cartuja s/n, 18071-Granada, Spain
| | - Angel Orte
- Departamento de Fisicoquimica. Unidad de Excelencia de Química aplicada a Biomedicina y Medioambiente, Facultad de Farmacia, Universidad de Granada, Campus de Cartuja s/n, 18071-Granada, Spain.
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14
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Detassis S, Grasso M, Tabraue-Chávez M, Marín-Romero A, López-Longarela B, Ilyine H, Ress C, Ceriani S, Erspan M, Maglione A, Díaz-Mochón JJ, Pernagallo S, Denti MA. New Platform for the Direct Profiling of microRNAs in Biofluids. Anal Chem 2019; 91:5874-5880. [PMID: 30994325 DOI: 10.1021/acs.analchem.9b00213] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Circulating microRNAs have been identified as potential biomarkers for early detection, prognosis, and prediction of several diseases. Their use in clinical diagnostics has been limited by the lack of suitable detection techniques. Most of the current technologies suffer from requiring complex protocols, not yet able to deliver robust and cost-effective assays in the field of clinical diagnostics. In this work, we report the development of a breakthrough platform for profiling circulating microRNAs. The platform comprises a novel silicon photomultiplier-based reader in conjunction with a chemical-based method for nucleic acid detection. Accurate microRNAs profiling without extraction, pre-amplification, or pre-labeling of the target is now achievable. We designed and synthesized a set of reagents that combined the chemical-based method with a chemiluminescent reaction. The signals generated were read out using a novel, compact silicon photomultiplier-based reader. The platform sensitivity was determined by measuring known concentrations of hsa-miR-21-5p spike-ins. The limit of detection was calculated as 4.7 pmol/L. The platform was also successfully used to directly detect hsa-miR-21-5p in eight non-small cell lung cancer plasma samples. Levels of plasma hsa-miR-21-5p expression were also measured via TaqMan RT-qPCR. The successful integration of the unique chemical-based method for nucleic acid detection with the novel silicon photomultiplier-based reader created an innovative product (ODG platform) with diagnostic utility, for the direct qualitative and quantitative analysis of microRNA biomarkers in biological fluids.
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Affiliation(s)
- Simone Detassis
- Department of Cellular, Computational and Integrative Biology (CIBIO) , Via Sommarive 9 , 38123 Trento , Italy
| | - Margherita Grasso
- Department of Cellular, Computational and Integrative Biology (CIBIO) , Via Sommarive 9 , 38123 Trento , Italy
| | - Mavys Tabraue-Chávez
- DestiNA Genomica S.L. Parque Tecnológico de la Salud (PTS) , Avenida de la Innovación 1 , 18016 Granada , Spain
| | - Antonio Marín-Romero
- DestiNA Genomica S.L. Parque Tecnológico de la Salud (PTS) , Avenida de la Innovación 1 , 18016 Granada , Spain.,Centro Pfizer-Universidad de Granada-Junta de Andalucía de Genómica e Investigación Oncológica (GENYO), Parque Tecnológico de la Salud (PTS) , Avenida de la Ilustración 114 , Granada 18016 , Spain.,Faculty of Pharmacy , University of Granada , Campus Cartuja s/n , Granada 18016 , Spain
| | - Bárbara López-Longarela
- DestiNA Genomica S.L. Parque Tecnológico de la Salud (PTS) , Avenida de la Innovación 1 , 18016 Granada , Spain
| | - Hugh Ilyine
- DestiNA Genomica S.L. Parque Tecnológico de la Salud (PTS) , Avenida de la Innovación 1 , 18016 Granada , Spain.,DestiNA Genomics Ltd. , 7-11 Melville St , Edinburgh EH3 7PE , United Kingdom
| | - Cristina Ress
- Optoelettronica Italia Srl , Via Vienna 8 , 38121 Trento , Italy
| | - Silvia Ceriani
- Optoelettronica Italia Srl , Via Vienna 8 , 38121 Trento , Italy
| | - Mirko Erspan
- Optoelettronica Italia Srl , Via Vienna 8 , 38121 Trento , Italy
| | - Alfredo Maglione
- Optoelettronica Italia Srl , Via Vienna 8 , 38121 Trento , Italy
| | - Juan J Díaz-Mochón
- DestiNA Genomica S.L. Parque Tecnológico de la Salud (PTS) , Avenida de la Innovación 1 , 18016 Granada , Spain.,DestiNA Genomics Ltd. , 7-11 Melville St , Edinburgh EH3 7PE , United Kingdom.,Centro Pfizer-Universidad de Granada-Junta de Andalucía de Genómica e Investigación Oncológica (GENYO), Parque Tecnológico de la Salud (PTS) , Avenida de la Ilustración 114 , Granada 18016 , Spain.,Faculty of Pharmacy , University of Granada , Campus Cartuja s/n , Granada 18016 , Spain
| | - Salvatore Pernagallo
- DestiNA Genomica S.L. Parque Tecnológico de la Salud (PTS) , Avenida de la Innovación 1 , 18016 Granada , Spain.,DestiNA Genomics Ltd. , 7-11 Melville St , Edinburgh EH3 7PE , United Kingdom
| | - Michela A Denti
- Department of Cellular, Computational and Integrative Biology (CIBIO) , Via Sommarive 9 , 38123 Trento , Italy
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15
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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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