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Walker SN, Lucas K, Dewey MJ, Badylak SF, Hussey GS, Flax J, McGrath JL. Rapid Assessment of Biomarkers on Single Extracellular Vesicles Using "Catch and Display" on Ultrathin Nanoporous Silicon Nitride Membranes. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024:e2405505. [PMID: 39358943 DOI: 10.1002/smll.202405505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2024] [Revised: 08/27/2024] [Indexed: 10/04/2024]
Abstract
Extracellular vesicles (EVs) are particles released from cells that facilitate intercellular communication and have tremendous diagnostic and therapeutic potential. Bulk assays lack the sensitivity to detect rare EV subsets relevant to disease, and while single EV analysis techniques remedy this, they are often undermined by complicated detection schemes and prohibitive instrumentation. To address these issues, a microfluidic technique for EV characterization called "catch and display for liquid biopsy (CAD-LB)" is proposed. In this method, minimally processed samples are pipette-injected and fluorescently labeled EVs are captured in the nanopores of an ultrathin membrane. This enables the rapid assessment of EV number and biomarker colocalization by light microscopy. Here, nanoparticles are used to define the accuracy and dynamic range for counting and colocalization. The same assessments are then made for purified EVs and for unpurified EVs in plasma. Biomarker detection is validated using CD9 and Western blot analysis to confirm that CAD-LB accurately reports relative protein expression levels. Using unprocessed conditioned media, CAD-LB captures the known increase in EV-associated ICAM-1 following endothelial cell cytokine stimulation. Finally, to demonstrate CAD-LB's clinical potential, EV biomarkers indicative of immunotherapy responsiveness are successfully detected in the plasma of bladder cancer patients treated with immune checkpoint blockade.
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Affiliation(s)
- Samuel N Walker
- Department of Biomedical Engineering, University of Rochester, Rochester, NY, 14627, USA
| | - Kilean Lucas
- Department of Biomedical Engineering, University of Rochester, Rochester, NY, 14627, USA
| | - Marley J Dewey
- McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, PA, 15219, USA
| | - Stephen F Badylak
- McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, PA, 15219, USA
| | - George S Hussey
- McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, PA, 15219, USA
| | - Jonathan Flax
- Department of Biomedical Engineering, University of Rochester, Rochester, NY, 14627, USA
- Department of Urology, University of Rochester Medical Center, Rochester, NY, 14642, USA
| | - James L McGrath
- Department of Biomedical Engineering, University of Rochester, Rochester, NY, 14627, USA
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Fike BJ, Curtin K, Li P. Nucleic Acid Target Sensing Using a Vibrating Sharp-Tip Capillary and Digital Droplet Loop-Mediated Isothermal Amplification (ddLAMP). SENSORS (BASEL, SWITZERLAND) 2024; 24:4266. [PMID: 39001045 PMCID: PMC11243892 DOI: 10.3390/s24134266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/28/2024] [Revised: 06/24/2024] [Accepted: 06/28/2024] [Indexed: 07/16/2024]
Abstract
Nucleic acid tests are key tools for the detection and diagnosis of many diseases. In many cases, the amplification of the nucleic acids is required to reach a detectable level. To make nucleic acid amplification tests more accessible to a point-of-care (POC) setting, isothermal amplification can be performed with a simple heating source. Although these tests are being performed in bulk reactions, the quantification is not as accurate as it would be with digital amplification. Here, we introduce the use of the vibrating sharp-tip capillary for a simple and portable system for tunable on-demand droplet generation. Because of the large range of droplet sizes possible and the tunability of the vibrating sharp-tip capillary, a high dynamic range (~2 to 6000 copies/µL) digital droplet loop-mediated isothermal amplification (ddLAMP) system has been developed. It was also noted that by changing the type of capillary on the vibrating sharp-tip capillary, the same mechanism can be used for simple and portable DNA fragmentation. With the incorporation of these elements, the present work paves the way for achieving digital nucleic acid tests in a POC setting with limited resources.
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Affiliation(s)
- Bethany J Fike
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV 26506, USA
| | - Kathrine Curtin
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV 26506, USA
- Department of Mechanical and Aerospace Engineering, West Virginia University, Morgantown, WV 26506, USA
| | - Peng Li
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV 26506, USA
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Walker SN, Lucas K, Dewey MJ, Badylak S, Hussey G, Flax J, McGrath JL. Rapid Assessment of Biomarkers on Single Extracellular Vesicles Using 'Catch and Display' on Ultrathin Nanoporous Silicon Nitride Membranes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.29.589900. [PMID: 38746341 PMCID: PMC11092443 DOI: 10.1101/2024.04.29.589900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Extracellular vesicles (EVs) are particles secreted by all cells that carry bioactive cargo and facilitate intercellular communication with roles in normal physiology and disease pathogenesis. EVs have tremendous diagnostic and therapeutic potential and accordingly, the EV field has grown exponentially in recent years. Bulk assays lack the sensitivity to detect rare EV subsets relevant to disease, and while single EV analysis techniques remedy this, they are undermined by complicated detection schemes often coupled with prohibitive instrumentation. To address these issues, we propose a microfluidic technique for EV characterization called 'catch and display for liquid biopsy (CAD-LB)'. CAD-LB rapidly captures fluorescently labeled EVs in the similarly-sized pores of an ultrathin silicon nitride membrane. Minimally processed sample is introduced via pipette injection into a simple microfluidic device which is directly imaged using fluorescence microscopy for a rapid assessment of EV number and biomarker colocalization. In this work, nanoparticles were first used to define the accuracy and dynamic range for counting and colocalization by CAD-LB. Following this, the same assessments were made for purified EVs and for unpurified EVs in plasma. Biomarker detection was validated using CD9 in which Western blot analysis confirmed that CAD-LB faithfully recapitulated differing expression levels among samples. We further verified that CAD-LB captured the known increase in EV-associated ICAM-1 following the cytokine stimulation of endothelial cells. Finally, to demonstrate CAD-LB's clinical potential, we show that EV biomarkers indicative of immunotherapy responsiveness are successfully detected in the plasma of bladder cancer patients undergoing immune checkpoint blockade.
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Affiliation(s)
- Samuel N. Walker
- Department of Biomedical Engineering, University of Rochester, Rochester, NY 14627, United States
| | - Kilean Lucas
- Department of Biomedical Engineering, University of Rochester, Rochester, NY 14627, United States
| | - Marley J. Dewey
- McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, PA 15219, United States
| | - Stephen Badylak
- McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, PA 15219, United States
| | - George Hussey
- McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, PA 15219, United States
| | - Jonathan Flax
- Department of Biomedical Engineering, University of Rochester, Rochester, NY 14627, United States
- Department of Urology, University of Rochester Medical Center, Rochester, NY 14642, United States
| | - James L. McGrath
- Department of Biomedical Engineering, University of Rochester, Rochester, NY 14627, United States
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Bail R, Lee DH. Displacement Mapping as a Highly Flexible Surface Texturing Tool for Additively Photopolymerized Components. MICROMACHINES 2024; 15:575. [PMID: 38793148 PMCID: PMC11123137 DOI: 10.3390/mi15050575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 04/23/2024] [Accepted: 04/24/2024] [Indexed: 05/26/2024]
Abstract
Displacement mapping is a computer graphics technique that enables the design of components with regularly or randomly textured surfaces that can be quickly materialized on a three-dimensional (3D) printer when needed. This approach is, in principle, more flexible, faster, and more economical compared to conventional texturing methods, but the accuracy of the texture depends heavily on the parameters used. The purpose of this study is to demonstrate how to produce a surface-textured part using polygonal (mesh) modeling software and a photopolymerizable resin and to develop a universal methodology to predict the dimensional accuracy of the model file log combined with a resin 3D printer. The printed components were characterized on a scanning confocal microscope. In the setup used in this study, the mesh size had to be reduced to 10% of the smallest feature size, and the textured layer had to be heavily (×4.5) overexposed to achieve the desired accuracy. As a practical application, two functional stamps with a regular (honeycomb) and a random texture, respectively, were successfully manufactured. The insights gained will be of great benefit for quickly and cost-effectively producing components with innovative patterns and textures for a variety of hobby, industrial, and biomedical applications.
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Affiliation(s)
- Robert Bail
- Graduate School of Convergent Systems Engineering, Dankook University, Yongin 16890, Republic of Korea
| | - Dong Hyun Lee
- Department of Polymer Science and Engineering, Dankook University, Yongin 16890, Republic of Korea
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Wang Z, Wei P. Shifting the paradigm in RNA virus detection: integrating nucleic acid testing and immunoassays through single-molecule digital ELISA. Front Immunol 2024; 14:1331981. [PMID: 38235132 PMCID: PMC10791976 DOI: 10.3389/fimmu.2023.1331981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 12/12/2023] [Indexed: 01/19/2024] Open
Abstract
In this review article, we explore the characteristics of RNA viruses and their potential threats to humanity. We also provide a brief overview of the primary contemporary techniques used for the early detection of such viruses. After thoroughly analyzing the strengths and limitations of these methods, we highlight the importance of integrating nucleic acid testing with immunological assays in RNA virus detection. Although notable methodological differences between nucleic acid testing and immune assays pose challenges, the emerging single-molecule immunoassay-digital ELISA may be applied to technically integrate these techniques. We emphasize that the greatest value of digital ELISA is its extensive compatibility, which creates numerous opportunities for real-time, large-scale testing of RNA viruses. Furthermore, we describe the possible developmental trends of digital ELISA in various aspects, such as reaction carriers, identification elements, signal amplification, and data reading, thus revealing the remarkable potential of single-molecule digital ELISA in future RNA virus detection.
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Affiliation(s)
| | - Pei Wei
- Department of Immunology, Zunyi Medical University, Zhuhai, China
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Shan X, Gong F, Yang Y, Qian J, Tan Z, Tian S, He Z, Ji X. Nucleic Acid Amplification-Free Digital Detection Method for SARS-CoV-2 RNA Based on Droplet Microfluidics and CRISPR-Cas13a. Anal Chem 2023; 95:16489-16495. [PMID: 37910547 DOI: 10.1021/acs.analchem.3c02007] [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: 11/03/2023]
Abstract
Most of the methods currently developed for RNA detection based on CRISPR were combined with nucleic acid amplification. As a result, such methods inevitably led to certain disadvantages such as multiple operations, expensive reagents, and amplification bias. To solve the above problems, we developed a highly sensitive and specific nucleic acid amplification-free digital detection method for SARS-CoV-2 RNA based on droplet microfluidics and CRISPR-Cas13a. In this assay, thousands of monodisperse droplets with a size of 30 μm were generated within 2 min by a negative pressure-driven microfluidic chip. By confining a single target RNA recognition event to an independent droplet, the collateral cleavage products of activated Cas13a could be accumulated in one droplet. By combining the droplet microfluidics and CRISPR-Cas13a, SARS-CoV-2 RNA could be easily detected within 30 min with a detection limit of 470 aM. The performance of this assay was verified by specificity experiments and spiking and recovery experiments with human saliva. Compared with many developed methods for SARS-CoV-2 RNA detection, our method is time- and reagent-saving and easy to operate. Taken together, this digital detection method based on droplet microfluidics and CRISPR-Cas13a provides a promising approach for RNA detection in clinical diagnostics.
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Affiliation(s)
- Xiaoyun Shan
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| | - Feng Gong
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| | - Yixia Yang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| | - Jingjing Qian
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| | - Zhiyou Tan
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| | - Songbai Tian
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| | - Zhike He
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
- Wuhan Research Center for Infectious Diseases and Cancer, Chinese Academy of Medical Sciences, Wuhan 430071, China
| | - Xinghu Ji
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
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Heidari-Bafroui H, Kumar A, Hahn C, Scholz N, Charbaji A, Rahmani N, Anagnostopoulos C, Faghri M. Development of a New Lab-on-Paper Microfluidics Platform Using Bi-Material Cantilever Actuators for ELISA on Paper. BIOSENSORS 2023; 13:310. [PMID: 36979522 PMCID: PMC10046564 DOI: 10.3390/bios13030310] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 02/16/2023] [Accepted: 02/22/2023] [Indexed: 06/18/2023]
Abstract
In this paper, we present a novel and cost-effective lab-on-paper microfluidics platform for performing ELISA autonomously, with no user intervention beyond adding the sample. The platform utilizes two Bi-Material Cantilever Valves placed in a specially designed housing. The integration of these valves in a specific channel network forms a complete fluidic logic circuit for performing ELISA on paper. The housing also incorporates an innovative reagent storage and release mechanism that minimizes variability in the volume of reagents released into the reagent pads. The platform design was optimized to minimize variance in the time of fluid wicking from the reagent pad, using a randomized design of experiment. The platform adheres to the World Health Organization's ASSURED principles. The optimized design was used to conduct an ELISA for detecting rabbit immunoglobulin G (IgG) in a buffer, with a limit of detection of 2.27 ng/mL and a limit of quantification of 8.33 ng/mL. This represents a 58% improvement over previous ELISA methods for detecting rabbit IgG in buffer using portable microfluidic technology.
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Affiliation(s)
- Hojat Heidari-Bafroui
- Microfluidics Laboratory, Department of Mechanical, Industrial, and Systems Engineering, University of Rhode Island, 2 East Alumni Avenue, Kingston, RI 02881, USA
| | - Ashutosh Kumar
- Microfluidics Laboratory, Department of Mechanical, Industrial, and Systems Engineering, University of Rhode Island, 2 East Alumni Avenue, Kingston, RI 02881, USA
| | - Cameron Hahn
- Microfluidics Laboratory, Department of Mechanical, Industrial, and Systems Engineering, University of Rhode Island, 2 East Alumni Avenue, Kingston, RI 02881, USA
| | - Nicholas Scholz
- Microfluidics Laboratory, Department of Mechanical, Industrial, and Systems Engineering, University of Rhode Island, 2 East Alumni Avenue, Kingston, RI 02881, USA
| | - Amer Charbaji
- Microfluidics Laboratory, Department of Mechanical, Industrial, and Systems Engineering, University of Rhode Island, 2 East Alumni Avenue, Kingston, RI 02881, USA
| | - Nassim Rahmani
- Microfluidics Laboratory, Department of Mechanical, Industrial, and Systems Engineering, University of Rhode Island, 2 East Alumni Avenue, Kingston, RI 02881, USA
| | - Constantine Anagnostopoulos
- Microfluidics Laboratory, Department of Mechanical, Industrial, and Systems Engineering, University of Rhode Island, 2 East Alumni Avenue, Kingston, RI 02881, USA
| | - Mohammad Faghri
- Microfluidics Laboratory, Department of Mechanical, Industrial, and Systems Engineering, University of Rhode Island, 2 East Alumni Avenue, Kingston, RI 02881, USA
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