1
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Kieffer C, Rondelez Y, Gines G. Coupling Exponential to Linear Amplification for Endpoint Quantitative Analysis. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2309386. [PMID: 38593401 DOI: 10.1002/advs.202309386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Revised: 03/26/2024] [Indexed: 04/11/2024]
Abstract
Exponential DNA amplification techniques are fundamental in ultrasensitive molecular diagnostics. These systems offer a wide dynamic range, but the quantification requires real-time monitoring of the amplification reaction. Linear amplification schemes, despite their limited sensitivity, can achieve quantitative measurement from a single end-point readout, suitable for low-cost, point-of-care, or massive testing. Reconciling the sensitivity of exponential amplification with the simplicity of end-point readout would thus break through a major design dilemma and open a route to a new generation of massively scalable quantitative bioassays. Here a hybrid nucleic acid-based circuit design is introduced to compute a logarithmic function, therefore providing a wide dynamic range based on a single end-point measurement. CELIA (Coupling Exponential amplification reaction to LInear Amplification) exploits a versatile biochemical circuit architecture to couple a tunable linear amplification stage - optionally embedding an inverter function - downstream of an exponential module in a one-pot format. Applied to the detection of microRNAs, CELIA provides a limit of detection in the femtomolar range and a dynamic range of six decades. This isothermal approach bypasses thermocyclers without compromising sensitivity, thereby opening the way to applications in various diagnostic assays, and providing a simplified, cost-efficient, and high throughput solution for quantitative nucleic acid analysis.
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Affiliation(s)
- Coline Kieffer
- Laboratoire Gulliver, UMR7083 CNRS/ESPCI Paris-PSL Research University, 10 rue Vauquelin, Paris, 75005, France
| | - Yannick Rondelez
- Laboratoire Gulliver, UMR7083 CNRS/ESPCI Paris-PSL Research University, 10 rue Vauquelin, Paris, 75005, France
| | - Guillaume Gines
- Laboratoire Gulliver, UMR7083 CNRS/ESPCI Paris-PSL Research University, 10 rue Vauquelin, Paris, 75005, France
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2
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Ang YS, Yung LYL. Protein-to-DNA Converter with High Signal Gain. ACS NANO 2024; 18:10454-10463. [PMID: 38572806 DOI: 10.1021/acsnano.3c11435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/05/2024]
Abstract
DNA isothermal amplification techniques have been applied extensively for evaluating nucleic acid inputs but cannot be implemented directly on other types of biomolecules. In this work, we designed a proximity activation mechanism that converts protein input into DNA barcodes for the DNA exponential amplification reaction, which we termed PEAR. Several design parameters were identified and experimentally verified, which included the choice of enzymes, sequences of proximity probes and template strand via the NUPACK design tool, and the implementation of a hairpin lock on the proximity probe structure. Our PEAR system was surprisingly more robust against nonspecific DNA amplification, which is a major challenge faced in existing formats of the DNA-based exponential amplification reaction. The as-designed PEAR exhibited good target responsiveness for three protein models with a dynamic range of 4-5 orders of magnitude down to femtomolar input concentration. Overall, our proposed protein-to-DNA converter module led to the development of a stable and robust configuration of the DNA exponential amplification reaction to achieve high signal gain. We foresee this enabling the use of protein inputs for more complex molecular evaluation as well as ultrasensitive protein detection.
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Affiliation(s)
- Yan Shan Ang
- Department of Chemical & Biomolecular Engineering, National University of Singapore, Singapore 117585, Singapore
| | - Lin-Yue Lanry Yung
- Department of Chemical & Biomolecular Engineering, National University of Singapore, Singapore 117585, Singapore
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3
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Takiguchi S, Kambara F, Tani M, Sugiura T, Kawano R. Simultaneous Recognition of Over- and Under-Expressed MicroRNAs Using Nanopore Decoding. Anal Chem 2023; 95:14675-14685. [PMID: 37675494 PMCID: PMC10797591 DOI: 10.1021/acs.analchem.3c02560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 08/28/2023] [Indexed: 09/08/2023]
Abstract
This paper describes a strategy for simultaneous recognition of over- and under-expressed microRNAs (miRNAs) using the method of signal classification-based nanopore decoding. MiRNA has attracted attention as a promising biomarker for cancer diagnosis owing to its cancer-type-specific expression patterns. While nanopore technology has emerged as a simple and label-free method to detect miRNAs and their expression patterns, recognizing patterns involving simultaneous over/under-expression is still challenging due to the inherent working principles. Here, inspired by the sequence design for DNA computation with nanopore decoding, we designed diagnostic DNA probes targeting two individual over/under-expressed miRNAs in the serum of oral squamous cell carcinoma. Through nanopore measurements, our designed probes exhibited characteristic current signals depending on the hybridized miRNA species, which were plotted on the scatter plot of duration versus current blocking ratio. The classified signals reflected the relative abundance of target miRNAs, thereby enabling successful pattern recognition of over/under-expressed miRNAs, even when using clinical samples. We believe that our method paves the way for miRNA-targeting simple diagnosis as a liquid biopsy.
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Affiliation(s)
- Sotaro Takiguchi
- Department
of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, Tokyo 184-8588, Japan
| | - Fumika Kambara
- Department
of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, Tokyo 184-8588, Japan
| | - Mika Tani
- Department
of Maxillofacial Diagnostic and Surgical Science, Field of Oral and
Maxillofacial Rehabilitation, Graduate School of Medical and Dental
Science, Kagoshima University, Kagoshima 890-8544, Japan
| | - Tsuyoshi Sugiura
- Department
of Maxillofacial Diagnostic and Surgical Science, Field of Oral and
Maxillofacial Rehabilitation, Graduate School of Medical and Dental
Science, Kagoshima University, Kagoshima 890-8544, Japan
- Division
of Oral and Maxillofacial Oncology and Surgical Sciences, Graduate
School of Dentistry, Tohoku University, Miyagi 980-8577, Japan
| | - Ryuji Kawano
- Department
of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, Tokyo 184-8588, Japan
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4
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Zhang C, Li Z, Liu J, Liu C, Zhang H, Lee WG, Yao C, Guo H, Xu F. Synthetic Gene Circuit-Based Assay with Multilevel Switch Enables Background-Free and Absolute Quantification of Circulating Tumor DNA. RESEARCH (WASHINGTON, D.C.) 2023; 6:0217. [PMID: 37789988 PMCID: PMC10543738 DOI: 10.34133/research.0217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 08/02/2023] [Indexed: 10/05/2023]
Abstract
Circulating tumor DNA (ctDNA) detection has found widespread applications in tumor diagnostics and treatment, where the key is to obtain accurate quantification of ctDNA. However, this remains challenging due to the issue of background noise associated with existing assays. In this work, we developed a synthetic gene circuit-based assay with multilevel switch (termed CATCH) for background-free and absolute quantification of ctDNA. The multilevel switch combining a small transcription activating RNA and a toehold switch was designed to simultaneously regulate transcription and translation processes in gene circuit to eliminate background noise. Moreover, such a multilevel switch-based gene circuit was integrated with a Cas9 nickase H840A (Cas9n) recognizer and a molecular beacon reporter to form CATCH for ctDNA detection. The CATCH can be implemented in one-pot reaction at 35 °C with virtually no background noise, and achieve robust absolute quantification of ctDNA when integrated with a digital chip (i.e., digital CATCH). Finally, we validated the clinical capability of CATCH by detecting drug-resistant ctDNA mutations from the plasma of 76 non-small cell lung cancer (NSCLC) patients, showing satisfying clinical sensitivity and specificity. We envision that the simple and robust CATCH would be a powerful tool for next-generation ctDNA detection.
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Affiliation(s)
- Chao Zhang
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education,
School of Life Science and Technology, Xi’an Jiaotong University, Xi’an 710049, P.R. China
- Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi’an 710049, P.R. China
| | - Zedong Li
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education,
School of Life Science and Technology, Xi’an Jiaotong University, Xi’an 710049, P.R. China
- Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi’an 710049, P.R. China
- TFX Group-Xi'an Jiaotong University Institute of Life Health, Xi'an 710049, P.R. China
| | - Jie Liu
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education,
School of Life Science and Technology, Xi’an Jiaotong University, Xi’an 710049, P.R. China
- Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi’an 710049, P.R. China
| | - Chang Liu
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education,
School of Life Science and Technology, Xi’an Jiaotong University, Xi’an 710049, P.R. China
- Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi’an 710049, P.R. China
| | - Haoqing Zhang
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education,
School of Life Science and Technology, Xi’an Jiaotong University, Xi’an 710049, P.R. China
- Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi’an 710049, P.R. China
| | - Won Gu Lee
- Department of Mechanical Engineering,
Kyung Hee University, Yongin 17104, Republic of Korea
| | - Chunyan Yao
- Department of Transfusion Medicine, Southwest Hospital,
Third Military Medical University (Army Medical University), Chongqing 400038, P.R. China
| | - Hui Guo
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, P.R. China
| | - Feng Xu
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education,
School of Life Science and Technology, Xi’an Jiaotong University, Xi’an 710049, P.R. China
- Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi’an 710049, P.R. China
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5
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Liu X, Zhang X, Yao Y, Shi P, Zeng C, Zhang Q. Construction of DNA-based molecular circuits using normally open and normally closed switches driven by lambda exonuclease. NANOSCALE 2023; 15:7755-7764. [PMID: 37051702 DOI: 10.1039/d3nr00427a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Building synthetic molecular circuits is an important way to realize ion detection, information processing, and molecular computing. However, it is still challenging to implement the NOT logic controlled by a single molecule input in synthetic molecular circuits wherein the presence or absence of the molecule represents the ON or OFF state of the input. Here, based on lambda exonuclease (λ exo), for the first time, we propose the normally open (NO) and normally closed (NC) switching strategy with a unified signal transmission mechanism to build molecular circuits. Specifically, the opposite logic can be output with or without a single signal, and the state of the switch can be adjusted by the addition order and time interval of the upstream signal and switch signal, which endows the switch with time-responsive characteristics. In addition, a time-delay relay with the function of delayed disconnection is developed to realize quantitative control of outputs, which has the potential to meet the automation control need of the system. Finally, digital square and square root circuits are constructed by cascading the NO and NC switches, which demonstrates the versatility of switches. Our design can be extended to time logic and complex digital computing circuits for use in information processing and nanomachines.
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Affiliation(s)
- Xin Liu
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, P. R. China.
| | - Xun Zhang
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, P. R. China.
| | - Yao Yao
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, P. R. China.
| | - Peijun Shi
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, P. R. China.
| | - Chenyi Zeng
- Key Laboratory of Advanced Design and Intelligent Computing, Dalian University, Dalian 116622, China
| | - Qiang Zhang
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, P. R. China.
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6
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Rondelez Y, Gines G. Programmable Ultrasensitive Molecular Amplifier for Digital and Multiplex MicroRNA Quantification. Methods Mol Biol 2023; 2630:89-102. [PMID: 36689178 DOI: 10.1007/978-1-0716-2982-6_7] [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] [Indexed: 01/24/2023]
Abstract
Digital bioassays, popularized by digital PCR, provide some of the most robust and accurate methods for nucleic acid quantification. In this chapter, we detail a protocol for digital, isothermal, and multiplex detection of microRNAs, which relies on a recently developed amplification method. Our approach uses programmable ultrasensitive molecular amplifiers (PUMAs) to reveal the presence of target microRNAs randomly isolated in picoliter-size microfluidic droplets. Nonspecific amplification in droplets that do not contain a target is eliminated by an active threshold mechanism. Multiple circuits can be assembled for the multiplex digital detection of up to three targets. We finally present the option of using fluorescent dropcodes to streamline the assay and analyze more than a dozen samples in parallel.
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Affiliation(s)
- Yannick Rondelez
- Gulliver Laboratory, ESPCI Paris - Université PSL, Paris, France
| | - Guillaume Gines
- Gulliver Laboratory, ESPCI Paris - Université PSL, Paris, France.
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7
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Fluorescence energy transfer biosensing platform based on hyperbranched rolling circle amplification and multi-site strand displacement for ultrasensitive detection of miRNA. Anal Chim Acta 2022; 1222:340190. [DOI: 10.1016/j.aca.2022.340190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 07/07/2022] [Accepted: 07/18/2022] [Indexed: 11/22/2022]
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8
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Gao S, Wu R, Zhang Q. A novel strategy for programmable DNA tile self-assembly with a DNAzyme-mediated DNA cross circuit. NEW J CHEM 2022. [DOI: 10.1039/d1nj06012k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The proposed strategy promotes the controllability and modularization of trigger elements, realizes programmable molecular self-assembly, and has broad applications for the construction of DNA nanodevices.
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Affiliation(s)
- Siqi Gao
- Key Laboratory of Advanced Design and Intelligent Computing, Dalian University, Ministry of Education, Dalian 116622, China
| | - Ranfeng Wu
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Qiang Zhang
- Key Laboratory of Advanced Design and Intelligent Computing, Dalian University, Ministry of Education, Dalian 116622, China
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China
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9
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Shenshin VA, Lescanne C, Gines G, Rondelez Y. A small-molecule chemical interface for molecular programs. Nucleic Acids Res 2021; 49:7765-7774. [PMID: 34223901 PMCID: PMC8287923 DOI: 10.1093/nar/gkab470] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 05/03/2021] [Accepted: 06/29/2021] [Indexed: 12/17/2022] Open
Abstract
In vitro molecular circuits, based on DNA-programmable chemistries, can perform an increasing range of high-level functions, such as molecular level computation, image or chemical pattern recognition and pattern generation. Most reported demonstrations, however, can only accept nucleic acids as input signals. Real-world applications of these programmable chemistries critically depend on strategies to interface them with a variety of non-DNA inputs, in particular small biologically relevant chemicals. We introduce here a general strategy to interface DNA-based circuits with non-DNA signals, based on input-translating modules. These translating modules contain a DNA response part and an allosteric protein sensing part, and use a simple design that renders them fully tunable and modular. They can be repurposed to either transmit or invert the response associated with the presence of a given input. By combining these translating-modules with robust and leak-free amplification motifs, we build sensing circuits that provide a fluorescent quantitative time-response to the concentration of their small-molecule input, with good specificity and sensitivity. The programmability of the DNA layer can be leveraged to perform DNA based signal processing operations, which we demonstrate here with logical inversion, signal modulation and a classification task on two inputs. The DNA circuits are also compatible with standard biochemical conditions, and we show the one-pot detection of an enzyme through its native metabolic activity. We anticipate that this sensitive small-molecule-to-DNA conversion strategy will play a critical role in the future applications of molecular-level circuitry.
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Affiliation(s)
- Vasily A Shenshin
- Laboratoire Gulliver, CNRS, ESPCI Paris, PSL Research University, 10 rue Vauquelin 75005 Paris, France
| | - Camille Lescanne
- Laboratoire Gulliver, CNRS, ESPCI Paris, PSL Research University, 10 rue Vauquelin 75005 Paris, France
| | - Guillaume Gines
- Laboratoire Gulliver, CNRS, ESPCI Paris, PSL Research University, 10 rue Vauquelin 75005 Paris, France
| | - Yannick Rondelez
- Laboratoire Gulliver, CNRS, ESPCI Paris, PSL Research University, 10 rue Vauquelin 75005 Paris, France
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10
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Zhou C, Cui K, Liu Y, Li L, Zhang L, Hao S, Ge S, Yu J. Bi 2S 3@MoS 2 Nanoflowers on Cellulose Fibers Combined with Octahedral CeO 2 for Dual-Mode Microfluidic Paper-Based MiRNA-141 Sensors. ACS APPLIED MATERIALS & INTERFACES 2021; 13:32780-32789. [PMID: 34228452 DOI: 10.1021/acsami.1c07669] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
An effective dual-mode microfluidic paper-based analysis device (μPAD) was proposed via Bi2S3@MoS2 nanoflowers combined with octahedral CeO2 for ultrasensitive miRNA-141 bioassay. To obtain the amplified electrochemical signal, Bi2S3@MoS2 nanoflowers were first in situ grown onto the surface of cellulose fibers to promote the reduction of H2O2. The prism-anchored octahedral CeO2 nanoparticles with a great catalytic function on the reduction of H2O2 were linked up to the functionalized cellulose fibers through the hybridization chain reaction to further enhance the electrochemical signal. By means of the catalysis effect of Bi2S3@MoS2 nanoflowers and octahedral CeO2 nanoparticles, the obtained signal was amplified, thereby achieving ultrasensitive electrochemical detection of the target. With the help of duplex specific nuclease, the octahedral CeO2 could be released from the electrochemical detection area and flow to the color channel through capillary action, which could initiate the oxidation reaction of 3,3',5,5'-tetramethylbenzidine in the existence of H2O2 to generate a blue visual band, avoiding the error of distinguishing color depth caused by the naked eye and thus improving the accuracy of the visual method. Under the optimal conditions, satisfactory prediction and accurate detection performance were achieved in the range of 10 fM-1 nM and 0.5 fM-1 nM, respectively, by measuring the length of the blue product and the electrochemical signal intensity. The electrochemical/visual detection limits of the proposed μPAD for miRNA-141 were as low as 0.12 and 2.65 fM (S/N = 3). This work provides great potential for the construction of low-cost and high-performance dual-mode biosensors for the detection of biomarkers.
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Affiliation(s)
- Chenxi Zhou
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, PR China
| | - Kang Cui
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, PR China
| | - Yue Liu
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, PR China
| | - Li Li
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, PR China
| | - Lina Zhang
- Shandong Provincial Key Laboratory of Preparation and Measurement of Building Materials, University of Jinan, Jinan 250022, PR China
| | - Shiji Hao
- School of Materials Science & Engineering, Dongguan University of Technology, Dongguan, Guangdong 523808, PR China
| | - Shenguang Ge
- Institute for Advanced Interdisciplinary Research, University of Jinan, Jinan 250022, PR China
| | - Jinghua Yu
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, PR China
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11
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Supadmanaba IGP, Mantini G, Randazzo O, Capula M, Muller IB, Cascioferro S, Diana P, Peters GJ, Giovannetti E. Interrelationship between miRNA and splicing factors in pancreatic ductal adenocarcinoma. Epigenetics 2021; 17:381-404. [PMID: 34057028 PMCID: PMC8993068 DOI: 10.1080/15592294.2021.1916697] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is one of the most lethal cancers because of diagnosis at late stage and inherent/acquired chemoresistance. Recent advances in genomic profiling and biology of this disease have not yet been translated to a relevant improvement in terms of disease management and patient’s survival. However, new possibilities for treatment may emerge from studies on key epigenetic factors. Deregulation of microRNA (miRNA) dependent gene expression and mRNA splicing are epigenetic processes that modulate the protein repertoire at the transcriptional level. These processes affect all aspects of PDAC pathogenesis and have great potential to unravel new therapeutic targets and/or biomarkers. Remarkably, several studies showed that they actually interact with each other in influencing PDAC progression. Some splicing factors directly interact with specific miRNAs and either facilitate or inhibit their expression, such as Rbfox2, which cleaves the well-known oncogenic miRNA miR-21. Conversely, miR-15a-5p and miR-25-3p significantly downregulate the splicing factor hnRNPA1 which acts also as a tumour suppressor gene and is involved in processing of miR-18a, which in turn, is a negative regulator of KRAS expression. Therefore, this review describes the interaction between splicing and miRNA, as well as bioinformatic tools to explore the effect of splicing modulation towards miRNA profiles, in order to exploit this interplay for the development of innovative treatments. Targeting aberrant splicing and deregulated miRNA, alone or in combination, may hopefully provide novel therapeutic approaches to fight the complex biology and the common treatment recalcitrance of PDAC.
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Affiliation(s)
- I Gede Putu Supadmanaba
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, VU University Medical Center (VUMC), Amsterdam, The Netherlands.,Biochemistry Department, Faculty of Medicine, Universitas Udayana, Denpasar, Bali, Indonesia
| | - Giulia Mantini
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, VU University Medical Center (VUMC), Amsterdam, The Netherlands.,Cancer Pharmacology Lab, AIRC Start up Unit, Fondazione Pisana per La Scienza, Pisa, Italy
| | - Ornella Randazzo
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, VU University Medical Center (VUMC), Amsterdam, The Netherlands.,Dipartimento Di Scienze E Tecnologie Biologiche Chimiche E Farmaceutiche (STEBICEF), Università Degli Studi Di Palermo, Palermo, Italy
| | - Mjriam Capula
- Cancer Pharmacology Lab, AIRC Start up Unit, Fondazione Pisana per La Scienza, Pisa, Italy.,Institute of Life Sciences, Sant'Anna School of Advanced Studies, Pisa, Italy
| | - Ittai B Muller
- Department of Clinical Chemistry, Amsterdam UMC, VU University Medical Center (VUMC), Amsterdam, The Netherlands
| | - Stella Cascioferro
- Dipartimento Di Scienze E Tecnologie Biologiche Chimiche E Farmaceutiche (STEBICEF), Università Degli Studi Di Palermo, Palermo, Italy
| | - Patrizia Diana
- Dipartimento Di Scienze E Tecnologie Biologiche Chimiche E Farmaceutiche (STEBICEF), Università Degli Studi Di Palermo, Palermo, Italy
| | - Godefridus J Peters
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, VU University Medical Center (VUMC), Amsterdam, The Netherlands.,Department of Biochemistry, Medical University of Gdansk, Poland
| | - Elisa Giovannetti
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, VU University Medical Center (VUMC), Amsterdam, The Netherlands.,Cancer Pharmacology Lab, AIRC Start up Unit, Fondazione Pisana per La Scienza, Pisa, Italy
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12
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Jet T, Gines G, Rondelez Y, Taly V. Advances in multiplexed techniques for the detection and quantification of microRNAs. Chem Soc Rev 2021; 50:4141-4161. [PMID: 33538706 DOI: 10.1039/d0cs00609b] [Citation(s) in RCA: 127] [Impact Index Per Article: 42.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
MicroRNA detection is currently a crucial analytical chemistry challenge: almost 2000 papers were referenced in PubMed in 2018 and 2019 for the keywords "miRNA detection method". MicroRNAs are potential biomarkers for multiple diseases including cancers, neurodegenerative and cardiovascular diseases. Since miRNAs are stably released in bodily fluids, they are of prime interest for the development of non-invasive diagnosis methods, such as liquid biopsies. Their detection is however challenging, as high levels of sensitivity, specificity and robustness are required. The analysis also needs to be quantitative, since the aim is to detect miRNA concentration changes. Moreover, a high multiplexing capability is also of crucial importance, since the clinical potential of miRNAs probably lays in our ability to perform parallel mapping of multiple miRNA concentrations and recognize typical disease signature from this profile. A plethora of biochemical innovative detection methods have been reported recently and some of them provide new solutions to the problem of sensitive multiplex detection. In this review, we propose to analyze in particular the new developments in multiplexed approaches to miRNA detection. The main aspects of these methods (including sensitivity and specificity) will be analyzed, with a particular focus on the demonstrated multiplexing capability and potential of each of these methods.
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Affiliation(s)
- Thomas Jet
- Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, Université de Paris, CNRS SNC5096, Equipe Labellisée Ligue Nationale Contre le Cancer, F-75006 Paris, France.
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