1
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Jang W, Song EL, Mun SJ, Bong KW. Efficient isolation of encoded microparticles in a degassed micromold for highly sensitive and multiplex immunoassay with signal amplification. Biosens Bioelectron 2024; 261:116465. [PMID: 38850735 DOI: 10.1016/j.bios.2024.116465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 05/29/2024] [Accepted: 06/02/2024] [Indexed: 06/10/2024]
Abstract
Multiplex detection of low-abundance protein biomarkers in biofluids can contribute to diverse biomedical fields such as early diagnosis and precision medicine. However, conventional techniques such as digital ELISA, microarray, and hydrogel-based assay still face limitations in terms of efficient protein detection due to issues with multiplexing capability, sensitivity, or complicated assay procedures. In this study, we present the degassed micromold-based particle isolation technique for highly sensitive and multiplex immunoassay with enzymatic signal amplification. Using degassing treatment of nanoporous polydimethylsiloxane (PDMS) micromold, the encoded particles are isolated in the mold within 5 min absorbing trapped air bubbles into the mold by air suction capability. Through 10 min of signal amplification in the isolated spaces by fluorogenic substrate and horseradish peroxidase labeled in the particle, the assay signal is amplified with one order of magnitude compared to that of the standard hydrogel-based assay. Using the signal amplification assay, vascular endothelial growth factor (VEGF) and chorionic gonadotropin beta (CG beta), the preeclampsia-related protein biomarkers, are quantitatively detected with a limit of detection (LoD) of 249 fg/mL and 476 fg/mL in phosphate buffer saline. The multiplex immunoassay is conducted to validate negligible non-specific detection signals and robust recovery rates in the multiplex assay. Finally, the VEGF and CG beta in real urine samples are simultaneously and quantitatively detected by the developed assay. Given the high sensitivity, multiplexing capability, and process simplicity, the presented particle isolation-based signal amplification assay holds significant potential in biomedical and proteomic fields.
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Affiliation(s)
- Wookyoung Jang
- Department of Chemical and Biological Engineering, Korea University, Seoul, 02841, Republic of Korea
| | - E Loomee Song
- Department of Chemical and Biological Engineering, Korea University, Seoul, 02841, Republic of Korea
| | - Seok Joon Mun
- Department of Chemical and Biological Engineering, Korea University, Seoul, 02841, Republic of Korea
| | - Ki Wan Bong
- Department of Chemical and Biological Engineering, Korea University, Seoul, 02841, Republic of Korea.
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2
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Ghosh R, Arnheim A, van Zee M, Shang L, Soemardy C, Tang RC, Mellody M, Baghdasarian S, Sanchez Ochoa E, Ye S, Chen S, Williamson C, Karunaratne A, Di Carlo D. Lab on a Particle Technologies. Anal Chem 2024; 96:7817-7839. [PMID: 38650433 PMCID: PMC11112544 DOI: 10.1021/acs.analchem.4c01510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 04/14/2024] [Accepted: 04/16/2024] [Indexed: 04/25/2024]
Affiliation(s)
- Rajesh Ghosh
- Department
of Bioengineering, University of California,
Los Angeles, Los Angeles, California 90095, United States
| | - Alyssa Arnheim
- Department
of Bioengineering, University of California,
Los Angeles, Los Angeles, California 90095, United States
| | - Mark van Zee
- Department
of Bioengineering, University of California,
Los Angeles, Los Angeles, California 90095, United States
| | - Lily Shang
- Department
of Bioengineering, University of California,
Los Angeles, Los Angeles, California 90095, United States
| | - Citradewi Soemardy
- Department
of Bioengineering, University of California,
Los Angeles, Los Angeles, California 90095, United States
| | - Rui-Chian Tang
- Department
of Bioengineering, University of California,
Los Angeles, Los Angeles, California 90095, United States
| | - Michael Mellody
- Department
of Bioengineering, University of California,
Los Angeles, Los Angeles, California 90095, United States
| | - Sevana Baghdasarian
- Department
of Bioengineering, University of California,
Los Angeles, Los Angeles, California 90095, United States
| | - Edwin Sanchez Ochoa
- Department
of Bioengineering, University of California,
Los Angeles, Los Angeles, California 90095, United States
| | - Shun Ye
- Department
of Bioengineering, University of California,
Los Angeles, Los Angeles, California 90095, United States
| | - Siyu Chen
- Department
of Bioengineering, University of California,
Los Angeles, Los Angeles, California 90095, United States
| | - Cayden Williamson
- Department
of Bioengineering, University of California,
Los Angeles, Los Angeles, California 90095, United States
| | - Amrith Karunaratne
- Department
of Bioengineering, University of California,
Los Angeles, Los Angeles, California 90095, United States
| | - Dino Di Carlo
- Department
of Bioengineering, University of California,
Los Angeles, Los Angeles, California 90095, United States
- Jonsson
Comprehensive Cancer Center, University
of California, Los Angeles, Los Angeles, California 90095, United States
- Department
of Mechanical and Aerospace Engineering, University of California, Los Angeles, Los Angeles, California 90095, United States
- California
NanoSystems Institute, Los Angeles, California 90095, United States
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3
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Sahin MA, Shehzad M, Destgeer G. Stopping Microfluidic Flow. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2307956. [PMID: 38143295 DOI: 10.1002/smll.202307956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 11/13/2023] [Indexed: 12/26/2023]
Abstract
A cross-comparison of three stop-flow configurations-such as low-pressure (LSF), high-pressure open-circuit (OC-HSF), and high-pressure short-circuit (SC-HSF) stop-flow-is presented to rapidly bring a high velocity flow O(m s-1) within a microchannel to a standstill O(µm s-1). The performance of three stop-flow configurations is assessed by measuring residual flow velocities within microchannels having three orders of magnitude different flow resistances. The LSF configuration outperforms the OC-HSF and SC-HSF configurations within a high flow resistance microchannel and results in a residual velocity of <10 µm s-1. The OC-HSF configuration results in a residual velocity of <150 µm s-1 within a low flow resistance microchannel. The SC-HSF configuration results in a residual velocity of <200 µm s-1 across the three orders-of-magnitude different flow resistance microchannels, and <100 µm s-1 for the low flow resistance channel. It is hypothesized that residual velocity results from compliance in fluidic circuits, which is further investigated by varying the elasticity of microchannel walls and connecting tubing. A numerical model is developed to estimate the expanded volumes of the compliant microchannel and connecting tubings under a pressure gradient and to calculate the distance traveled by the sample fluid. A comparison of the numerically and experimentally obtained traveling distances confirms the hypothesis that the residual velocities are an outcome of the compliance in the fluidic circuit.
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Affiliation(s)
- Mehmet Akif Sahin
- Control and Manipulation of Microscale Living Objects, Department of Electrical Engineering, School of Computation, Information and Technology (CIT), Center for Translational Cancer Research (TranslaTUM), Technical University of Munich, Einsteinstraße 25, 81675, Munich, Germany
| | - Muhammad Shehzad
- Control and Manipulation of Microscale Living Objects, Department of Electrical Engineering, School of Computation, Information and Technology (CIT), Center for Translational Cancer Research (TranslaTUM), Technical University of Munich, Einsteinstraße 25, 81675, Munich, Germany
| | - Ghulam Destgeer
- Control and Manipulation of Microscale Living Objects, Department of Electrical Engineering, School of Computation, Information and Technology (CIT), Center for Translational Cancer Research (TranslaTUM), Technical University of Munich, Einsteinstraße 25, 81675, Munich, Germany
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4
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Choi JH, Jang W, Lim YJ, Mun SJ, Bong KW. Highly Flexible Deep-Learning-Based Automatic Analysis for Graphically Encoded Hydrogel Microparticles. ACS Sens 2023; 8:3158-3166. [PMID: 37489756 DOI: 10.1021/acssensors.3c00857] [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: 07/26/2023]
Abstract
Graphically encoded hydrogel microparticle (HMP)-based bioassay is a diagnostic tool characterized by exceptional multiplex detectability and robust sensitivity and specificity. Specifically, deep learning enables highly fast and accurate analyses of HMPs with diverse graphical codes. However, previous related studies have found the use of plain particles as data to be disadvantageous for accurate analyses of HMPs loaded with functional nanomaterials. Furthermore, the manual data annotation method used in existing approaches is highly labor-intensive and time-consuming. In this study, we present an efficient deep-learning-based analysis of encoded HMPs with diverse graphical codes and functional nanomaterials, utilizing the auto-annotation and synthetic data mixing methods for model training. The auto-annotation enhanced the throughput of dataset preparation up to 0.11 s/image. Using synthetic data mixing, a mean average precision of 0.88 was achieved in the analysis of encoded HMPs with magnetic nanoparticles, representing an approximately twofold improvement over the standard method. To evaluate the practical applicability of the proposed automatic analysis strategy, a single-image analysis was performed after the triplex immunoassay for the preeclampsia-related protein biomarkers. Finally, we accomplished a processing throughput of 0.353 s per sample for analyzing the result image.
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Affiliation(s)
- Jun Hee Choi
- Department of Chemical and Biological Engineering, Korea University, Seoul 02841, South Korea
| | - Wookyoung Jang
- Department of Chemical and Biological Engineering, Korea University, Seoul 02841, South Korea
| | - Yong Jun Lim
- Department of Chemical and Biological Engineering, Korea University, Seoul 02841, South Korea
| | - Seok Joon Mun
- Department of Chemical and Biological Engineering, Korea University, Seoul 02841, South Korea
| | - Ki Wan Bong
- Department of Chemical and Biological Engineering, Korea University, Seoul 02841, South Korea
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5
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De Masi A, Scognamiglio PL, Battista E, Netti PA, Causa F. Hydrogel particles-on-chip (HyPoC): a fluorescence micro-sensor array for IgG immunoassay. LAB ON A CHIP 2023; 23:2458-2468. [PMID: 37092599 DOI: 10.1039/d2lc01080a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Novel microparticles have generated growing interest in diagnostics for potential sensitivity and specificity in biomolecule detection and for the possibility to be integrated in a micro-system array as a lab-on-chip. Indeed, bead-based technologies integrated in microfluidics could speed up incubation steps, reduce reagent consumption and improve accessibility of diagnostic devices to non-expert users. To limit non-specific interactions with interfering molecules and to exploit the whole particle volume for bioconjugation, hydrogel microparticles, particularly polyethylene glycol-based, have emerged as promising materials to develop high-performing biosensors since their network can be functionalized to concentrate the target and improve detection. However, the limitations in positioning, trapping and mainly fine manipulation of a precise number of particles in microfluidics have largely impaired point-of-care applications. Herein, we developed an on-chip sandwich immunoassay for the detection of human immunoglobulin G in biological fluids. The detection system is based on finely engineered cleavable PEG-based microparticles, functionalized with specific monoclonal antibodies. By changing the particle number, we demonstrated tuneable specificity and sensitivity (down to 3 pM) in serum and urine. Therefore, a controlled number of hydrogel particles have been integrated in a microfluidic device for on-chip detection (HyPoC) allowing for their precise positioning and fluid exchange for incubation, washing and target detection. HyPoC dramatically decreases incubation time from 180 minutes to one minute and reduces washing volumes from 3.5 ml to 90 μL, achieving a limit of detection of 0.07 nM (with a dynamic range of 0.07-1 nM). Thus, the developed approach represents a versatile, fast and easy point-of-care testing platform for immunoassays.
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Affiliation(s)
- Alessandra De Masi
- Center for Advanced Biomaterials for Healthcare@CRIB, Istituto Italiano di Tecnologia (IIT), Largo Barsanti e Matteucci 53, 80125 Naples, Italy.
- Dipartimento di Ingegneria Chimica del Materiali e della Produzione Industriale (DICMAPI), University "Federico II", Piazzale Tecchio 80, 80125 Naples, Italy
| | - Pasqualina Liana Scognamiglio
- Center for Advanced Biomaterials for Healthcare@CRIB, Istituto Italiano di Tecnologia (IIT), Largo Barsanti e Matteucci 53, 80125 Naples, Italy.
| | - Edmondo Battista
- Center for Advanced Biomaterials for Healthcare@CRIB, Istituto Italiano di Tecnologia (IIT), Largo Barsanti e Matteucci 53, 80125 Naples, Italy.
- Interdisciplinary Research Centre on Biomaterials (CRIB), University "Federico II", Piazzale Tecchio 80, 80125 Naples, Italy
| | - Paolo Antonio Netti
- Center for Advanced Biomaterials for Healthcare@CRIB, Istituto Italiano di Tecnologia (IIT), Largo Barsanti e Matteucci 53, 80125 Naples, Italy.
- Interdisciplinary Research Centre on Biomaterials (CRIB), University "Federico II", Piazzale Tecchio 80, 80125 Naples, Italy
- Dipartimento di Ingegneria Chimica del Materiali e della Produzione Industriale (DICMAPI), University "Federico II", Piazzale Tecchio 80, 80125 Naples, Italy
| | - Filippo Causa
- Center for Advanced Biomaterials for Healthcare@CRIB, Istituto Italiano di Tecnologia (IIT), Largo Barsanti e Matteucci 53, 80125 Naples, Italy.
- Interdisciplinary Research Centre on Biomaterials (CRIB), University "Federico II", Piazzale Tecchio 80, 80125 Naples, Italy
- Dipartimento di Ingegneria Chimica del Materiali e della Produzione Industriale (DICMAPI), University "Federico II", Piazzale Tecchio 80, 80125 Naples, Italy
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6
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Sahin MA, Werner H, Udani S, Di Carlo D, Destgeer G. Flow lithography for structured microparticles: fundamentals, methods and applications. LAB ON A CHIP 2022; 22:4007-4042. [PMID: 35920614 DOI: 10.1039/d2lc00421f] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Structured microparticles, with unique shapes, customizable sizes, multiple materials, and spatially-defined chemistries, are leading the way for emerging 'lab on a particle' technologies. These microparticles with engineered designs find applications in multiplexed diagnostics, drug delivery, single-cell secretion assays, single-molecule detection assays, high throughput cytometry, micro-robotics, self-assembly, and tissue engineering. In this article we review state-of-the-art particle manufacturing technologies based on flow-assisted photolithography performed inside microfluidic channels. Important physicochemical concepts are discussed to provide a basis for understanding the fabrication technologies. These photolithography technologies are compared based on the structural as well as compositional complexity of the fabricated particles. Particles are categorized, from 1D to 3D particles, based on the number of dimensions that can be independently controlled during the fabrication process. After discussing the advantages of the individual techniques, important applications of the fabricated particles are reviewed. Lastly, a future perspective is provided with potential directions to improve the throughput of particle fabrication, realize new particle shapes, measure particles in an automated manner, and adopt the 'lab on a particle' technologies to other areas of research.
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Affiliation(s)
- Mehmet Akif Sahin
- Control and Manipulation of Microscale Living Objects, Central Institute for Translational Cancer Research (TranslaTUM), Department of Electrical and Computer Engineering, Technical University of Munich, Einsteinstraße 25, Munich 81675, Germany.
| | - Helen Werner
- Control and Manipulation of Microscale Living Objects, Central Institute for Translational Cancer Research (TranslaTUM), Department of Electrical and Computer Engineering, Technical University of Munich, Einsteinstraße 25, Munich 81675, Germany.
| | - Shreya Udani
- Department of Bioengineering, University of California, Los Angeles, California 90095, USA.
| | - Dino Di Carlo
- Department of Bioengineering, University of California, Los Angeles, California 90095, USA.
- Department of Mechanical and Aerospace Engineering, California NanoSystems Institute and Jonsson Comprehensive Cancer Center, University of California, Los Angeles, California 90095, USA
| | - Ghulam Destgeer
- Control and Manipulation of Microscale Living Objects, Central Institute for Translational Cancer Research (TranslaTUM), Department of Electrical and Computer Engineering, Technical University of Munich, Einsteinstraße 25, Munich 81675, Germany.
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7
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Bae S, Lee D, Na H, Jang J, Kwon S. One-step assembly of barcoded planar microparticles for efficient readout of multiplexed immunoassay. LAB ON A CHIP 2022; 22:2090-2096. [PMID: 35579061 DOI: 10.1039/d2lc00174h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Barcoded planar microparticles are suitable for developing cost-efficient multiplexed assays, but the robustness and efficiency of the readout process still needs improvement. Here, we designed a one-step microparticle assembling chip that produces efficient and accurate multiplex immunoassay readout results. Our design was also compatible with injection molding for mass production.
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Affiliation(s)
- Sangwook Bae
- Bio-MAX/N-Bio, Seoul National University, Seoul 08826, South Korea.
| | - Daewon Lee
- Education and Research Program for Future ICT Pioneers, Seoul National University, Seoul 08826, South Korea
- SOFT Foundry Institute, Seoul National University, Seoul 08826, South Korea
| | - Hunjong Na
- Department of Electrical and Computer Engineering, Seoul National University, Seoul 08826, South Korea
- QuantaMatrix Inc., Medical Innovation Center, Seoul National University Hospital, Seoul, 03080, South Korea
| | - Jisung Jang
- QuantaMatrix Inc., Medical Innovation Center, Seoul National University Hospital, Seoul, 03080, South Korea
| | - Sunghoon Kwon
- Bio-MAX/N-Bio, Seoul National University, Seoul 08826, South Korea.
- Education and Research Program for Future ICT Pioneers, Seoul National University, Seoul 08826, South Korea
- Department of Electrical and Computer Engineering, Seoul National University, Seoul 08826, South Korea
- QuantaMatrix Inc., Medical Innovation Center, Seoul National University Hospital, Seoul, 03080, South Korea
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8
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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: 122] [Impact Index Per Article: 40.7] [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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9
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Zou Z, Liu Y, Xia L, Hu Z, Yin J, Mu Y. A multiplex and fast detection platform for microRNAs based on a self-priming microfluidic chip and duplex-specific nuclease. Analyst 2021; 146:628-635. [DOI: 10.1039/d0an01691h] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
A self-priming microfluidic chip for multiplex and fast detection of microRNAs was developed.
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Affiliation(s)
- Zheyu Zou
- Research Centre for Analytical Instrumentation
- Institute of Cyber-Systems and Control
- State Key Laboratory of Industrial Control Technology
- Zhejiang University
- Hangzhou
| | - Yuanhui Liu
- Research Centre for Analytical Instrumentation
- Institute of Cyber-Systems and Control
- State Key Laboratory of Industrial Control Technology
- Zhejiang University
- Hangzhou
| | - Liping Xia
- Research Centre for Analytical Instrumentation
- Institute of Cyber-Systems and Control
- State Key Laboratory of Industrial Control Technology
- Zhejiang University
- Hangzhou
| | - Zhenming Hu
- Research Centre for Analytical Instrumentation
- Institute of Cyber-Systems and Control
- State Key Laboratory of Industrial Control Technology
- Zhejiang University
- Hangzhou
| | - Juxin Yin
- Research Centre for Analytical Instrumentation
- Institute of Cyber-Systems and Control
- State Key Laboratory of Industrial Control Technology
- Zhejiang University
- Hangzhou
| | - Ying Mu
- Research Centre for Analytical Instrumentation
- Institute of Cyber-Systems and Control
- State Key Laboratory of Industrial Control Technology
- Zhejiang University
- Hangzhou
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10
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Juthani N, Doyle PS. A platform for multiplexed colorimetric microRNA detection using shape-encoded hydrogel particles. Analyst 2020; 145:5134-5140. [PMID: 32567641 PMCID: PMC7392806 DOI: 10.1039/d0an00938e] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
We report a platform utilizing a reporter enzyme, which produces a chromogenic indigo precipitate that preferentially localizes within a hydrogel microparticle. The 3D network of the hydrogel maintains the rapid target binding kinetics found in solution, while multiplexed target detection is achieved through shape-encoding of the particles. Moreover, the precipitate-laden hydrogels can be imaged with a simple phone camera setup. We used this system to detect microRNA (miRNA) down to 0.22 fmol. We then showed the compatibility of this system with real samples by performing multiplexed miRNA measurements from total RNA from matched colon cancer and normal adjacent tissue.
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Affiliation(s)
- Nidhi Juthani
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.
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11
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Ye WQ, Wei YX, Zhang YZ, Yang CG, Xu ZR. Multiplexed detection of micro-RNAs based on microfluidic multi-color fluorescence droplets. Anal Bioanal Chem 2019; 412:647-655. [PMID: 31836924 DOI: 10.1007/s00216-019-02266-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 10/12/2019] [Accepted: 11/08/2019] [Indexed: 12/29/2022]
Abstract
In this work, simple, rapid, and low-cost multiplexed detection of tumor-related micro-RNAs (miRNAs) was achieved based on multi-color fluorescence on a microfluidic droplet chip, which simplified the complexity of light path to a half. A four-T-junction structure was fabricated to form uniform nano-volume droplet arrays with customized contents. Multi-color quantum dots (QDs) used as the fluorescence labels were encapsulated into droplets to develop the multi-path fluorescence detection module. We designed an integrated multiplex fluorescence resonance energy transfer system assisted by multiple QDs (four colors) and one quencher to detect four tumor-related miRNAs (miRNA-20a, miRNA-21, miRNA-155, and miRNA-221). The qualitative analysis of miRNAs was realized by the color identification of QDs, while the quantitative detection of miRNAs was achieved based on the linear relationship between the quenching efficiency of QDs and the concentration of miRNAs. The practicability of the multiplex detection device was further confirmed by detecting four tumor-related miRNAs in real human serum samples. The detection limits of four miRNAs ranged from 35 to 39 pmol/L was achieved without any target amplification. And the linear range was from 0.1 nmol/L to 1 μmol/L using 10 nL detection volume (one droplet) under the detection speed of 320 droplets per minute. The multiple detection system for miRNAs is simple, fast, and low-cost and will be a powerful platform for clinical diagnostic analysis. Graphical abstract.
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Affiliation(s)
- Wen-Qi Ye
- Research Center for Analytical Sciences, Northeastern University, 3-11 Wenhua Road, Shenyang, 110819, Liaoning, China
| | - Yi-Xuan Wei
- Research Center for Analytical Sciences, Northeastern University, 3-11 Wenhua Road, Shenyang, 110819, Liaoning, China
| | - Ying-Zhi Zhang
- Research Center for Analytical Sciences, Northeastern University, 3-11 Wenhua Road, Shenyang, 110819, Liaoning, China
| | - Chun-Guang Yang
- Research Center for Analytical Sciences, Northeastern University, 3-11 Wenhua Road, Shenyang, 110819, Liaoning, China.
| | - Zhang-Run Xu
- Research Center for Analytical Sciences, Northeastern University, 3-11 Wenhua Road, Shenyang, 110819, Liaoning, China
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12
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13
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Caputo TM, Battista E, Netti PA, Causa F. Supramolecular Microgels with Molecular Beacons at the Interface for Ultrasensitive, Amplification-Free, and SNP-Selective miRNA Fluorescence Detection. ACS APPLIED MATERIALS & INTERFACES 2019; 11:17147-17156. [PMID: 31021070 DOI: 10.1021/acsami.8b22635] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
In this study, a supramolecular structure with femtomolar biorecognition properties is proposed for use in analytical devices. It is obtained by an innovative interface between synthetic hydrogel polymers and molecular beacon (mb) probes. Supramolecularly structured microgels are synthetized with a core-shell architecture with specific dyes polymerized in a desired compartment. Mb probes are opportunely conjugated at the microgel interface so that their recognition mechanism is preserved and their spatial distribution is optimized to avoid crowding effects. The miR-21, a microRNA involved in various biological processes and usually used as a biomarker in early cancer diagnosis, has been selected as the target. The results demonstrate that by tuning the spatial distribution of molecular probes immobilized on the microgel and/or the amount of microgels, the assay shows scalable sensitivity reaching a limit of detection down to about 10 fM, without amplification steps and with detection time as short as 1 h. The assay results specific toward single mutated targets, and it is stable in the presence of high-interfering oligonucleotides concentrations. The miRNA target is also detected in human serum with performances similar to those observed in PBS buffer because of microgel antifouling properties without the need of any surface treatment. All tests were performed in a low sample volume (20 μL). As a result, mb-microgel represents an innovative biosensor to precisely quantify microRNAs in a direct (mix&read), scalable, and selective way. Such an approach paves the way for creating innovative biosensing interfaces with other probes, such as hairpins, aptamers, and PNA.
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Affiliation(s)
- Tania M Caputo
- Center for Advanced Biomaterials for Healthcare@CRIB , Istituto Italiano di Tecnologia (IIT) , Largo Barsanti e Matteucci 53 , 80125 Naples , Italy
| | - Edmondo Battista
- Center for Advanced Biomaterials for Healthcare@CRIB , Istituto Italiano di Tecnologia (IIT) , Largo Barsanti e Matteucci 53 , 80125 Naples , Italy
- InterdisciplinaryResearch Centre on Biomaterials (CRIB) , Università degli Studi di Napoli "Federico II" , Piazzale Tecchio 80 , 80125 Naples , Italy
| | - Paolo A Netti
- Center for Advanced Biomaterials for Healthcare@CRIB , Istituto Italiano di Tecnologia (IIT) , Largo Barsanti e Matteucci 53 , 80125 Naples , Italy
- InterdisciplinaryResearch Centre on Biomaterials (CRIB) , Università degli Studi di Napoli "Federico II" , Piazzale Tecchio 80 , 80125 Naples , Italy
- Dipartimento di Ingegneria Chimica del Materiali e della Produzione Industriale (DICMAPI) , University "Federico II" , Piazzale Tecchio 80 , 80125 Naples , Italy
| | - Filippo Causa
- Center for Advanced Biomaterials for Healthcare@CRIB , Istituto Italiano di Tecnologia (IIT) , Largo Barsanti e Matteucci 53 , 80125 Naples , Italy
- InterdisciplinaryResearch Centre on Biomaterials (CRIB) , Università degli Studi di Napoli "Federico II" , Piazzale Tecchio 80 , 80125 Naples , Italy
- Dipartimento di Ingegneria Chimica del Materiali e della Produzione Industriale (DICMAPI) , University "Federico II" , Piazzale Tecchio 80 , 80125 Naples , Italy
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14
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Nagarajan MB, Tentori AM, Zhang WC, Slack FJ, Doyle PS. Nonfouling, Encoded Hydrogel Microparticles for Multiplex MicroRNA Profiling Directly from Formalin-Fixed, Paraffin-Embedded Tissue. Anal Chem 2018; 90:10279-10285. [PMID: 30106558 DOI: 10.1021/acs.analchem.8b02010] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
MicroRNAs (miRNA) are short, noncoding RNAs that have been implicated in many diseases, including cancers. Because miRNAs are dysregulated in disease, miRNAs show promise as highly stable biomarkers. Formalin-fixed, paraffin-embedded (FFPE) tissue is a valuable sample type to assay for biomolecules because it is a convenient storage method and is often used by pathologists for histological staining. However, extracting biomolecules from FFPE tissue is challenging because of the presence of cellular and extracellular proteins, formaldehyde cross-links, and paraffin. Moreover, most protocols to measure miRNA in FFPE tissue are time-consuming and laborious. Here, we report a simple protocol to directly measure miRNA from formalin-fixed cells, FFPE tissue sections after paraffin is removed, and FFPE tissue sections using encoded hydrogel microparticles fabricated using stop flow lithography. Measurements by these particles show agreement between formalin-fixed cells and fresh cells, and measurement of FFPE tissue with paraffin is 10% less than FFPE tissue when paraffin is removed before the assay. When normal and tumor FFPE tissue are compared using this microparticle assay, we observe differential miRNA signal for oncogenic miRNAs and tumor suppressing miRNAs. This approach reduces assay times, reduces the use of hazardous chemicals to remove paraffin, and provides a sensitive, quantitative, and multiplexed measurement of miRNA in FFPE tissue.
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Affiliation(s)
- Maxwell B Nagarajan
- Department of Chemical Engineering , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States
| | - Augusto M Tentori
- Department of Chemical Engineering , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States
| | - Wen Cai Zhang
- HMS Initiative for RNA Medicine, Department of Pathology, Beth Israel Deaconess Medical Center , Harvard Medical School , 330 Brookline Avenue , Boston , Massachusetts 02215 , United States
| | - Frank J Slack
- HMS Initiative for RNA Medicine, Department of Pathology, Beth Israel Deaconess Medical Center , Harvard Medical School , 330 Brookline Avenue , Boston , Massachusetts 02215 , United States
| | - Patrick S Doyle
- Department of Chemical Engineering , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States
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15
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Tentori AM, Nagarajan MB, Kim JJ, Zhang WC, Slack FJ, Doyle PS. Quantitative and multiplex microRNA assays from unprocessed cells in isolated nanoliter well arrays. LAB ON A CHIP 2018; 18:2410-2424. [PMID: 29998262 PMCID: PMC6081239 DOI: 10.1039/c8lc00498f] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
MicroRNAs (miRNAs) have recently emerged as promising biomarkers for the profiling of diseases. Translation of miRNA biomarkers to clinical practice, however, remains a challenge due to the lack of analysis platforms for sensitive, quantitative, and multiplex miRNA assays that have simple and robust workflows suitable for translation. The platform we present here utilizes functionalized hydrogel posts contained within isolated nanoliter well reactors for quantitative and multiplex assays directly from unprocessed cell samples without the need of prior nucleic acid extraction. Simultaneous reactor isolation and delivery of miRNA extraction reagents is achieved by sealing an array of wells containing the functionalized hydrogel posts and cells against another array of wells containing lysis and extraction reagents. The nanoliter well array platform features >100× better sensitivity compared to previous technology utilizing hydrogel particles without relying on signal amplification and enables >100 parallel assays in a single device. These advances provided by this platform lay the groundwork for translatable and robust analysis technologies for miRNA expression profiling in samples with small populations of cells and in precious, material-limited samples.
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Affiliation(s)
- Augusto M. Tentori
- Department of Chemical Engineering
, Massachusetts Institute of Technology
,
Cambridge
, USA
.
; Tel: +1 617 253 4534
| | - Maxwell B. Nagarajan
- Department of Chemical Engineering
, Massachusetts Institute of Technology
,
Cambridge
, USA
.
; Tel: +1 617 253 4534
| | - Jae Jung Kim
- Department of Chemical Engineering
, Massachusetts Institute of Technology
,
Cambridge
, USA
.
; Tel: +1 617 253 4534
| | - Wen Cai Zhang
- Department of Pathology
, Beth Israel Deaconess Medical Center/Harvard Medical School
,
Boston
, USA
| | - Frank J. Slack
- Department of Pathology
, Beth Israel Deaconess Medical Center/Harvard Medical School
,
Boston
, USA
| | - Patrick S. Doyle
- Department of Chemical Engineering
, Massachusetts Institute of Technology
,
Cambridge
, USA
.
; Tel: +1 617 253 4534
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16
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Chen L, Kim JJ, Doyle PS. Microfluidic platform for selective microparticle parking and paired particle isolation in droplet arrays. BIOMICROFLUIDICS 2018; 12:024102. [PMID: 29576834 PMCID: PMC5832466 DOI: 10.1063/1.5011342] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 02/16/2018] [Indexed: 05/11/2023]
Abstract
Immobilizing microscale objects (e.g., cells, spheroids, and microparticles) in arrays for direct observation and analysis is a critical step of many biological and chemical assays; however, existing techniques are often limited in their ability to precisely capture, arrange, isolate, and recollect objects of interest. In this work, we present a microfluidic platform that selectively parks microparticles in hydrodynamic traps based on particle physical characteristics (size, stiffness, and internal structure). We present an accompanying scaling analysis for the particle parking process to enable rational design of microfluidic traps and selection of operating conditions for successful parking of desired particles with specific size and elastic modulus. Our platform also enables parking of encoded particle pairs in defined spatial arrangements and subsequent isolation of these pairs in aqueous droplets, creating distinct microenvironments with no cross-contamination. In addition, we demonstrate the ability to recollect objects of interest (i.e., one particle from each pair) after observation within the channel. This integrated device is ideal for multiplexed assays or microenvironment fabrication for controlled biological studies.
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Affiliation(s)
- Lynna Chen
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Jae Jung Kim
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Patrick S Doyle
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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