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Podbiel D, Laermer F, Zengerle R, Hoffmann J. Fusing MEMS technology with lab-on-chip: nanoliter-scale silicon microcavity arrays for digital DNA quantification and multiplex testing. MICROSYSTEMS & NANOENGINEERING 2020; 6:82. [PMID: 34567692 PMCID: PMC8433415 DOI: 10.1038/s41378-020-00187-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 05/31/2020] [Accepted: 06/07/2020] [Indexed: 05/18/2023]
Abstract
We report on the development of a microfluidic multiplexing technology for highly parallelized sample analysis via quantitative polymerase chain reaction (PCR) in an array of 96 nanoliter-scale microcavities made from silicon. This PCR array technology features fully automatable aliquoting microfluidics, a robust sample compartmentalization up to temperatures of 95 °C, and an application-specific prestorage of reagents within the 25 nl microcavities. The here presented hybrid silicon-polymer microfluidic chip allows both a rapid thermal cycling of the liquid compartments and a real-time fluorescence read-out for a tracking of the individual amplification reactions taking place inside the microcavities. We demonstrate that the technology provides very low reagent carryover of prestored reagents < 6 × 10-2 and a cross talk rate < 1 × 10-3 per PCR cycle, which facilitate a multi-targeted sample analysis via geometric multiplexing. Furthermore, we apply this PCR array technology to introduce a novel digital PCR-based DNA quantification method: by taking the assay-specific amplification characteristics like the limit of detection into account, the method allows for an absolute gene target quantification by means of a statistical analysis of the amplification results.
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Affiliation(s)
- Daniel Podbiel
- Robert Bosch GmbH, Corporate Sector Research, Microsystems and Nanotechnologies, Robert-Bosch-Campus 1, 71272 Renningen, Germany
| | - Franz Laermer
- Robert Bosch GmbH, Corporate Sector Research, Microsystems and Nanotechnologies, Robert-Bosch-Campus 1, 71272 Renningen, Germany
| | - Roland Zengerle
- IMTEK - Department of Microsystems Engineering, University of Freiburg Georges-Koehler-Allee 103, 79110 Freiburg, Germany
| | - Jochen Hoffmann
- Robert Bosch GmbH, Corporate Sector Research, Microsystems and Nanotechnologies, Robert-Bosch-Campus 1, 71272 Renningen, Germany
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52
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Three-dimensional digital PCR through light-sheet imaging of optically cleared emulsion. Proc Natl Acad Sci U S A 2020; 117:25628-25633. [PMID: 32999068 DOI: 10.1073/pnas.2002448117] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The realization of the vast potential of digital PCR (dPCR) to provide extremely accurate and sensitive measurements in the clinical setting has thus far been hindered by challenges such as assay robustness and high costs. Here we introduce a lossless and contamination-free dPCR technology, termed CLEAR-dPCR, which addresses these challenges by completing the dPCR sample preparation, PCR, and readout all in one tube. Optical clearing of the droplet dPCR emulsion was combined with emerging light-sheet fluorescence microscopy, to acquire a three-dimensional (3D) image of a half million droplets sealed in a tube in seconds. CLEAR-dPCR provides ultrahigh-throughput readout results in situ and fundamentally eliminates the possibility of either sample loss or contamination. This approach exhibits improved accuracy over existing dPCR platforms and enables a greatly increased dynamic range to be comparable to that of real-time quantitative PCR.
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53
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Staufer O, Antona S, Zhang D, Csatári J, Schröter M, Janiesch JW, Fabritz S, Berger I, Platzman I, Spatz JP. Microfluidic production and characterization of biofunctionalized giant unilamellar vesicles for targeted intracellular cargo delivery. Biomaterials 2020; 264:120203. [PMID: 32987317 DOI: 10.1016/j.biomaterials.2020.120203] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 05/27/2020] [Accepted: 06/09/2020] [Indexed: 12/16/2022]
Abstract
Lipid-based vesicles have found widespread applications in the life sciences, allowing for fundamental insights into membrane-based processes in cell biology and as carrier systems for drug delivery purposes. So far, mostly small unilamellar vesicles (SUVs) with diameters of ~100 nm have been applied as carrier systems for biomedical applications. Despite this progress, several systematic limitations have arisen due to SUV dimensions, e.g., the size and total amount of applicable cargo is limited. Giant unilamellar vesicles (GUVs) might offer a pragmatic alternative for efficient cargo delivery. However, due to the lack of reliable high-throughput production technologies for GUV-carrier systems, only little is known about their interaction with cells. Here we present a microfluidic-based mechanical droplet-splitting pipeline for the production of carrier-GUVs with diameters of ~2 μm. The technology developed allows for highly efficient cargo loading and unprecedented control over the biological and physicochemical properties of GUV membranes. By generating differently charged (between -31 and + 28 mV), bioligand-conjugated (e.g. with E-cadherin, NrCam and antibodies) and PEG-conjugated GUVs, we performed a detailed investigation of attractive and repulsive GUV-cell interactions. Fine-tuning of these interactions allowed for targeted cellular GUV delivery. Moreover, we evaluated strategies for intracellular GUV cargo release by lysosomal escape mediated by the pH sensitive lipid DOBAQ, enabling cytoplasmic transmission. The presented GUV delivery technology and the systematic characterization of associated GUV-cell interactions could provide a means for more efficient drug administration and will pave the way for hitherto impossible approaches towards a targeted delivery of advanced cargo such as microparticles, viruses or macromolecular DNA-robots.
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Affiliation(s)
- Oskar Staufer
- Department for Cellular Biophysics, Max Planck Institute for Medical Research, Jahnstraße 29, 69120 Heidelberg, Germany; Institute for Molecular Systems Engineering (IMSE), Heidelberg University, D-69120 Heidelberg, Germany; Max Planck-Bristol Center for Minimal Biology, University of Bristol, 1 Tankard's Close, Bristol BS8 1TD, UK.
| | - Silvia Antona
- Department for Cellular Biophysics, Max Planck Institute for Medical Research, Jahnstraße 29, 69120 Heidelberg, Germany; Institute for Molecular Systems Engineering (IMSE), Heidelberg University, D-69120 Heidelberg, Germany
| | - Dennis Zhang
- Department for Cellular Biophysics, Max Planck Institute for Medical Research, Jahnstraße 29, 69120 Heidelberg, Germany
| | - Júlia Csatári
- Department for Cellular Biophysics, Max Planck Institute for Medical Research, Jahnstraße 29, 69120 Heidelberg, Germany
| | - Martin Schröter
- Department for Cellular Biophysics, Max Planck Institute for Medical Research, Jahnstraße 29, 69120 Heidelberg, Germany; Institute for Molecular Systems Engineering (IMSE), Heidelberg University, D-69120 Heidelberg, Germany
| | - Jan-Willi Janiesch
- Department for Cellular Biophysics, Max Planck Institute for Medical Research, Jahnstraße 29, 69120 Heidelberg, Germany; Institute for Molecular Systems Engineering (IMSE), Heidelberg University, D-69120 Heidelberg, Germany
| | - Sebastian Fabritz
- Department for Chemical Biology, Max Planck Institute for Medical Research, Jahnstraße 29, 69120, Heidelberg, Germany
| | - Imre Berger
- Max Planck-Bristol Center for Minimal Biology, University of Bristol, 1 Tankard's Close, Bristol BS8 1TD, UK; School of Biochemistry, Biomedical Sciences, University of Bristol, 1 Tankard's Close, Bristol BS8 1TD, UK; Bristol Synthetic Biology Centre BrisSynBio, University of Bristol, 4 Tyndall Ave, Bristol BS8 1TQ, UK
| | - Ilia Platzman
- Department for Cellular Biophysics, Max Planck Institute for Medical Research, Jahnstraße 29, 69120 Heidelberg, Germany; Institute for Molecular Systems Engineering (IMSE), Heidelberg University, D-69120 Heidelberg, Germany; Max Planck-Bristol Center for Minimal Biology, University of Bristol, 1 Tankard's Close, Bristol BS8 1TD, UK.
| | - Joachim P Spatz
- Department for Cellular Biophysics, Max Planck Institute for Medical Research, Jahnstraße 29, 69120 Heidelberg, Germany; Institute for Molecular Systems Engineering (IMSE), Heidelberg University, D-69120 Heidelberg, Germany; Max Planck-Bristol Center for Minimal Biology, University of Bristol, 1 Tankard's Close, Bristol BS8 1TD, UK.
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54
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Cohen L, Cui N, Cai Y, Garden PM, Li X, Weitz DA, Walt DR. Single Molecule Protein Detection with Attomolar Sensitivity Using Droplet Digital Enzyme-Linked Immunosorbent Assay. ACS NANO 2020; 14:9491-9501. [PMID: 32589401 DOI: 10.1021/acsnano.0c02378] [Citation(s) in RCA: 105] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Many proteins are present at low concentrations in biological samples, and therefore, techniques for ultrasensitive protein detection are necessary. To overcome challenges with sensitivity, the digital enzyme-linked immunosorbent assay (ELISA) was developed, which is 1000× more sensitive than conventional ELISA and allows sub-femtomolar protein detection. However, this sensitivity is still not sufficient to measure many proteins in various biological samples, thereby limiting our ability to detect and discover biomarkers. To overcome this limitation, we developed droplet digital ELISA (ddELISA), a simple approach for detecting low protein levels using digital ELISA and droplet microfluidics. ddELISA achieves maximal sensitivity by improving the sampling efficiency and counting more target molecules. ddELISA can detect proteins in the low attomolar range and is up to 25-fold more sensitive than digital ELISA using Single Molecule Arrays (Simoa), the current gold standard tool for ultrasensitive protein detection. Using ddELISA, we measured the LINE1/ORF1 protein, a potential cancer biomarker that has not been previously measured in serum. Additionally, due to the simplicity of our device design, ddELISA is promising for point-of-care applications. Thus, ddELISA will facilitate the discovery of biomarkers that have never been measured before for various clinical applications.
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Affiliation(s)
- Limor Cohen
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, United States
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
- Department of Chemical Biology, Harvard University, Boston, Massachusetts 02115, United States
| | - Naiwen Cui
- School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Yamei Cai
- School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Padric M Garden
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, United States
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Xiang Li
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, United States
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - David A Weitz
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, United States
- School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts 02138, United States
| | - David R Walt
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, United States
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
- Department of Chemical Biology, Harvard University, Boston, Massachusetts 02115, United States
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55
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Yin J, Zou Z, Yin F, Liang H, Hu Z, Fang W, Lv S, Zhang T, Wang B, Mu Y. A Self-Priming Digital Polymerase Chain Reaction Chip for Multiplex Genetic Analysis. ACS NANO 2020; 14:10385-10393. [PMID: 32794742 DOI: 10.1021/acsnano.0c04177] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Digital PCR (polymerase chain reaction) is a powerful and attractive tool for the quantification of nucleic acids. However, the multiplex detection capabilities of this system are limited or require expensive instrumentation and reagents, all of which can hinder multiplex detection goals. Here, we propose strategies toward solving these issues regarding digital PCR. We designed and tested a self-priming digital PCR chip containing 6-plex detection capabilities using monochrome fluorescence, which has six detection areas and four-layer structures. This strategy achieved multiplex digital detection by the use of self-priming to preintroduce the specific reaction mix to a certain detection area. This avoids competition when multiple primer pairs coexist, allowing for multiplexing in a shorter time while using less reagents and low-cost instruments. This also prevents the digital PCR chip from experiencing long sample introduction time and evaporation. For further validation, this multiplex digital PCR chip was used to detect five types of EGFR (epidermal growth factor receptor) gene mutations in 15 blood samples from lung cancer patients. We conclude that this technique can precisely quantify EGFR mutations in high-performance diagnostics. This multiplex digital detection chip is a simple and inexpensive test intended for liquid biopsies. It can be applied and used in prenatal diagnostics, the monitoring of residual disease, rapid pathogen detection, and many other procedures.
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Affiliation(s)
- Juxin Yin
- Research Centre for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou, Zhejiang Province 310058, China
| | - Zheyu Zou
- College of Life Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Fangfang Yin
- Weifang People's Hospital, Weifang 261000, China
| | - Hongxiao Liang
- Research Centre for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou, Zhejiang Province 310058, China
| | - Zhenming Hu
- Research Centre for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou, Zhejiang Province 310058, China
| | - Weibo Fang
- Research Centre for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou, Zhejiang Province 310058, China
| | - Shaowu Lv
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, College of Life Science, Jilin University, Changchun 130000, China
| | - Tao Zhang
- Research Centre for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou, Zhejiang Province 310058, China
| | - Ben Wang
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, National Ministry of Education), The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310009, China
- Institute of Translational Medicine, Zhejiang University, Hangzhou 310029, China
| | - Ying Mu
- Research Centre for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou, Zhejiang Province 310058, China
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56
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Jiang Y, Manz A, Wu W. Fully automatic integrated continuous-flow digital PCR device for absolute DNA quantification. Anal Chim Acta 2020; 1125:50-56. [DOI: 10.1016/j.aca.2020.05.044] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Revised: 04/27/2020] [Accepted: 05/02/2020] [Indexed: 01/09/2023]
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57
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Zhang F, Liao P, Sun Y, Chen Z, Pang Y, Huang Y. Surfactant and oil formulations for monodisperse droplet emulsion PCR. LAB ON A CHIP 2020; 20:2328-2333. [PMID: 32458866 DOI: 10.1039/d0lc00052c] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Emulsion PCR has become a popular and widely applied method in biological research and clinical diagnostics to provide evenly amplified products and perform highly quantitative counting of target sequences. However, there is still a lack of information to support further development of appropriate water-in-oil emulsion formulations, which need to be both thermally and mechanically stable for digital amplification reactions. Here, we present a systematic survey of the oil and surfactant components of stable monodisperse w/o emulsions suitable for use with our previously developed micro-capillary array (MiCA)-based centrifugal emulsion generation method. Our findings show that a binary formula consisting of isopropyl palmitate and a silicone copolymer demonstrated the best performance, and provided a general guideline for the development of emulsion systems for digital PCR and emulsion amplification applications.
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Affiliation(s)
- Fangli Zhang
- Department of Materials Science and Engineering, College of Engineering, Peking University, Beijing 100871, China.
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58
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Next-Generation Sequencing in High-Sensitive Detection of Mutations in Tumors: Challenges, Advances, and Applications. J Mol Diagn 2020; 22:994-1007. [PMID: 32480002 DOI: 10.1016/j.jmoldx.2020.04.213] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 03/17/2020] [Accepted: 04/23/2020] [Indexed: 02/06/2023] Open
Abstract
Next-generation sequencing (NGS) technologies have come of age as preferred technologies for screening of genomic variants of pathologic and therapeutic potential. Because of their capability for high-throughput and massively parallel sequencing, they can screen for a variety of genomic changes in multiple samples simultaneously. This has made them platforms of choice for clinical testing of solid tumors and hematological malignancies. Consequently, they are increasingly replacing conventional technologies, such as Sanger sequencing and pyrosequencing, expression arrays, real-time PCR, and fluorescence in situ hybridization methods, for routine molecular testing of tumors. However, one limitation of routinely used NGS technologies is the inability to detect low-level genomic variants with high accuracy. This can be attributed to the frequent occurrence of low-level sequencing errors and artifacts in NGS workflow that need specialized approaches to be identified and eliminated. This review focuses on the origins and nature of these artifacts and recent improvements in the NGS technologies to overcome them to facilitate accurate high-sensitive detection of low-level mutations. Potential applications of high-sensitive NGS in oncology and comparisons with non-NGS technologies of similar capabilities are also summarized.
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59
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He Y, Yin J, Wu W, Liang H, Zhu F, Mu Y, Fan H, Zhang T. Rapid In Situ Photoimmobilization of a Planar Droplet Array for Digital PCR. Anal Chem 2020; 92:8530-8535. [PMID: 32412739 DOI: 10.1021/acs.analchem.0c01304] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Digital PCR (dPCR) is a powerful technique capable of absolute quantification of nucleic acids with good accuracy. Droplet-based dPCR (ddPCR), among others, is one of the most important dPCR techniques. However, the surface tension-controlled droplets may suffer from fusion/fission due to the vigorous temperature change in PCR thermal cycling. Besides, the free movement of droplets makes them unsuitable for real-time fluorescence monitoring. In this paper, we first developed a photoimmobilized planar droplet array (PIPDA) by using a photocurable polyurethane as the continuous oil phase. It is found that uniform water-in-oil droplets of various sizes can be readily generated, and more importantly, the oil phase can be rapidly solidified in just a few seconds upon exposure to UV irradiation. This process will leave the droplets immobilized in the accommodation chamber as a stable planar array and, thus, effectively prevent the movement, coalescence, and breakup of droplets. In addition, a novel multilayered chip design has been proposed, which can thoroughly overcome the evaporation issue that commonly exists in polydimethylsiloxane (PDMS)-based dPCR chips. With these two innovations, the ddPCR experiment could be performed in a robust manner, and shows a promising potential in the development of real-time ddPCR technique. These features may therefore enable the wide application of PIPDA-based ddPCR in various fields.
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Affiliation(s)
- Yu He
- Research Center for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou 310027, China
| | - Juxin Yin
- Research Center for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou 310027, China
| | - Wenshuai Wu
- College of Life Sciences, Zhejiang University, Hangzhou 310027, China
| | - Hongxiao Liang
- Research Center for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou 310027, China
| | - Futianchun Zhu
- Research Center for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou 310027, China
| | - Ying Mu
- Research Center for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou 310027, China.,College of Life Sciences, Zhejiang University, Hangzhou 310027, China
| | - Hongliang Fan
- Department of Environmental Medicine, Institute of Hygiene, Zhejiang Academy of Medical Sciences, Hangzhou 310013, China
| | - Tao Zhang
- Research Center for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou 310027, China
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60
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Mbano IM, Mandizvo T, Rogich J, Kunota TTR, Mackenzie JS, Pillay M, Balagaddé FK. Light Forge: A Microfluidic DNA Melting-based Tuberculosis Test. J Appl Lab Med 2020; 5:440-453. [PMID: 32445364 PMCID: PMC7192548 DOI: 10.1093/jalm/jfaa019] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 10/15/2019] [Indexed: 01/09/2023]
Abstract
BACKGROUND There is a well-documented lack of rapid, low-cost tuberculosis (TB) drug resistance diagnostics in low-income settings across the globe. It is these areas that are plagued with a disproportionately high disease burden and in greatest need of these diagnostics. METHODS In this study, we compared the performance of Light Forge, a microfluidic high-resolution melting analysis (HRMA) prototype for rapid low-cost detection of TB drug resistance with a commercial HRMA device, a predictive "nearest-neighbor" thermodynamic model, DNA sequencing, and phenotypic drug susceptibility testing (DST). The initial development and assessment of the Light Forge assay was performed with 7 phenotypically drug resistant strains of Mycobacterium tuberculosis (M.tb) that had their rpoB gene subsequently sequenced to confirm resistance to Rifampin. These isolates of M.tb were then compared against a drug-susceptible standard, H37Rv. Seven strains of M.tb were isolated from clinical specimens and individually analyzed to characterize the unique melting profile of each strain. RESULTS Light Forge was able to detect drug-resistance linked mutations with 100% concordance to the sequencing, phenotypic DST and the "nearest neighbor" thermodynamic model. Researchers were then blinded to the resistance profile of the seven M.tb strains. In this experiment, Light Forge correctly classified 7 out of 9 strains as either drug resistant or drug susceptible. CONCLUSIONS Light Forge represents a promising prototype for a fast, low-cost diagnostic alternative for detection of drug resistant strains of TB in resource constrained settings.
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Affiliation(s)
- Ian M Mbano
- Africa Health Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu Natal, Durban, South Africa
| | - Tawanda Mandizvo
- Africa Health Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu Natal, Durban, South Africa
| | - Jerome Rogich
- University of Massachusetts Medical School, Worcester, MA
| | - Tafara T R Kunota
- Africa Health Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu Natal, Durban, South Africa
| | - Jared S Mackenzie
- Africa Health Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu Natal, Durban, South Africa
| | - Manormoney Pillay
- Medical Microbiology, School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Frederick K Balagaddé
- Africa Health Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu Natal, Durban, South Africa
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61
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Li B, Li Y, Manz A, Wu W. Miniaturized Continuous-Flow Digital PCR for Clinical-Level Serum Sample Based on the 3D Microfluidics and CMOS Imaging Device. SENSORS 2020; 20:s20092492. [PMID: 32354074 PMCID: PMC7250024 DOI: 10.3390/s20092492] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 04/13/2020] [Accepted: 04/20/2020] [Indexed: 12/19/2022]
Abstract
In recent years, the development of polymerase chain reaction (PCR) technology has focused on digital PCR, which depends on the microfluidics. Based on continuous-flow microfluidic technology, this paper designed a miniaturized digital PCR amplification system, and greatly reduced the area required for microdroplet generation and reaction. The core rod. made of polydimethylsiloxane (PDMS), was combined with the Teflon tube to form 3D microfluidics, which requires only one heating source to form the temperature difference required for gene amplification. Only two 34 g needles can form and transmit micro-droplets in a 4-fold tapered Teflon tube, which is the simplest method to generate digital PCR droplets as far as we know, which allows the microdroplet generation device to be free from dependence on expensive chips. A complementary metal oxide semiconductor (CMOS) camera was used as a detection tool to obtain fluorescence video for the entire loop area or a specified loop area. In addition, we developed a homebrew for automatic image acquisition and processing to realize the function of digital PCR. This technique realizes the analysis of clinical serum samples of hepatitis B virus (HBV) and obtained the same results as real-time quantitative PCR. This system has greatly reduced the size and cost of the entire system, while maintaining a stable response.
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Affiliation(s)
- Bin Li
- State Key Laboratory of Applied Optics, Changchun Institute of Optics, Fine Mechanics and Physics (CIOMP), Chinese Academy of Sciences, Changchun 130033, China
- University of Chinese Academy of Sciences (UCAS), Beijing 100049, China
| | - Yuanming Li
- State Key Laboratory of Applied Optics, Changchun Institute of Optics, Fine Mechanics and Physics (CIOMP), Chinese Academy of Sciences, Changchun 130033, China
| | - Andreas Manz
- Systems Engineering Department, Saarland University, 66123 Saarbrücken, Germany
- Bio Sensor & Materials Group, KIST Europe, 66123 Saarbrücken, Germany
| | - Wenming Wu
- State Key Laboratory of Applied Optics, Changchun Institute of Optics, Fine Mechanics and Physics (CIOMP), Chinese Academy of Sciences, Changchun 130033, China
- Correspondence:
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Dong Z, Fang Q. Automated, flexible and versatile manipulation of nanoliter-to-picoliter droplets based on sequential operation droplet array technique. Trends Analyt Chem 2020. [DOI: 10.1016/j.trac.2020.115812] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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63
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Peng H, Zhu M, Gao Z, Liao C, Jia C, Wang H, Zhou H, Zhao J. A centrifugal microfluidic emulsifier integrated with oil storage structures for robust digital LAMP. Biomed Microdevices 2020; 22:18. [DOI: 10.1007/s10544-020-0475-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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64
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Agnihotri SN, Raveshi MR, Bhardwaj R, Neild A. Microfluidic Valves for Selective on-Chip Droplet Splitting at Multiple Sites. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:1138-1146. [PMID: 31968938 DOI: 10.1021/acs.langmuir.9b03515] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
We describe a microfluidic system for control of droplet division at two locations using a T-junction and expansion channel which are placed one after another. Droplets generated at a standard T-junction are introduced into the droplet division section of the microchannel. In the first set of experiments, the droplet division section consists of two consecutive identical T-junctions branching from the main channel. With this geometry, we were able to produce daughter droplets only at the first junction while there was no droplet division at the second junction. Resistive network analysis is used to redesign the microchannel geometry with an expansion channel in place of the second junction, to have the same quantity of flow entering in both the junctions. We observed five different regimes of droplet breakup, namely, (1) no droplet breakup in both junctions, (2) droplet breakup in the first junction, (3) droplet breakup in both junctions with higher daughter droplet volume in the first junction, (4) daughter droplet volume higher in the second junction, and (5) intermittent droplet breakup in both the junctions. Under specific flow conditions, droplet interaction with both the junctions is similar. We then showed design requirements for location of microvalves, simulated by deformation of the main channel wall and by experiments to break the droplet.
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Affiliation(s)
- Sagar N Agnihotri
- IITB-Monash Research Academy , IIT Bombay , Mumbai 400076 , India
- Department of Mechanical and Aerospace Engineering , Monash University , Melbourne , Victoria 3800 , Australia
- Department of Mechanical Engineering , Indian Institute of Technology Bombay , Mumbai 400076 , India
| | - Mohammad Reza Raveshi
- Department of Mechanical and Aerospace Engineering , Monash University , Melbourne , Victoria 3800 , Australia
| | - Rajneesh Bhardwaj
- Department of Mechanical Engineering , Indian Institute of Technology Bombay , Mumbai 400076 , India
| | - Adrian Neild
- Department of Mechanical and Aerospace Engineering , Monash University , Melbourne , Victoria 3800 , Australia
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Cui X, Wu L, Wu Y, Zhang J, Zhao Q, Jing F, Yi L, Li G. Fast and robust sample self-digitization for digital PCR. Anal Chim Acta 2020; 1107:127-134. [PMID: 32200886 DOI: 10.1016/j.aca.2020.02.010] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 01/14/2020] [Accepted: 02/05/2020] [Indexed: 02/07/2023]
Abstract
We present a facile sample partitioning method to enable rapid and low-cost digital PCR (dPCR) assays. By subdividing a high percentage of the sample volume into a large number of equal volume compartments with a self-digitization (SD) chip, this method can achieve a low-waste and high-order sample discretization in a matter of minutes. The SD chip contains a set of parallel microfluidic channels used for sample delivery, and each channel is connected with two rows of cylindrical wells to hold the discretized sample. By utilizing a degassed PDMS sealing slab as a detachable vacuum pumping source, the SD chip automatically generate large arrays of small sample volumes without requirement of external pumping and valving components. Unlike most microfluidic chamber-based methods for sample discretization, our detachable SD chip allows for discretizing sample with air flushing, then peeling off the cover PDMS slab and sealing the digitized samples with oil layer. Due to obviation of time-consuming oil flushing, such microfluidic device can achieve much faster digitization of sample volumes. Furthermore, this digitization chip can partition more than 90% of a sample volume, which is important for the applications where the amount of material available is small. We also demonstrated the utility of the proposed SD chip by applying it to a dPCR assay.
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Affiliation(s)
- Xu Cui
- Key Laboratory of Optoelectronic Technology and Systems, Ministry of Education, Defense Key Disciplines Lab of Novel Micro-Nano Devices and System Technology, Chongqing University, Chongqing, 400044, China
| | - Lei Wu
- State Key Lab of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai, 200050, China
| | - Yin Wu
- Key Laboratory of Optoelectronic Technology and Systems, Ministry of Education, Defense Key Disciplines Lab of Novel Micro-Nano Devices and System Technology, Chongqing University, Chongqing, 400044, China
| | - Jinghong Zhang
- Shanghai Turtle Technology Company Limited, Shanghai, 200439, China
| | - Qiang Zhao
- Key Laboratory of Optoelectronic Technology and Systems, Ministry of Education, Defense Key Disciplines Lab of Novel Micro-Nano Devices and System Technology, Chongqing University, Chongqing, 400044, China
| | - Fengxiang Jing
- Shanghai Turtle Technology Company Limited, Shanghai, 200439, China.
| | - Lin Yi
- Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital, Chongqing, 400030, China
| | - Gang Li
- Key Laboratory of Optoelectronic Technology and Systems, Ministry of Education, Defense Key Disciplines Lab of Novel Micro-Nano Devices and System Technology, Chongqing University, Chongqing, 400044, China.
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66
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Kim S, Ganapathysubramanian B, Anand RK. Concentration Enrichment, Separation, and Cation Exchange in Nanoliter-Scale Water-in-Oil Droplets. J Am Chem Soc 2020; 142:3196-3204. [DOI: 10.1021/jacs.9b13268] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Sungu Kim
- Department of Chemistry, Iowa State University, 1605 Gilman Hall, 2415 Osborn Drive, Ames, Iowa 50011-1021, United States
- Department of Mechanical Engineering, Iowa State University, 2043 Black Engineering, 2529 Union Drive, Ames, Iowa 50011-2030, United States
| | - Baskar Ganapathysubramanian
- Department of Mechanical Engineering, Iowa State University, 2043 Black Engineering, 2529 Union Drive, Ames, Iowa 50011-2030, United States
| | - Robbyn K. Anand
- Department of Chemistry, Iowa State University, 1605 Gilman Hall, 2415 Osborn Drive, Ames, Iowa 50011-1021, United States
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67
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Longwell SA, Fordyce PM. micrIO: an open-source autosampler and fraction collector for automated microfluidic input-output. LAB ON A CHIP 2020; 20:93-106. [PMID: 31701110 PMCID: PMC6923132 DOI: 10.1039/c9lc00512a] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Microfluidic devices are an enabling technology for many labs, facilitating a wide range of applications spanning high-throughput encapsulation, molecular separations, and long-term cell culture. In many cases, however, their utility is limited by a 'world-to-chip' barrier that makes it difficult to serially interface samples with these devices. As a result, many researchers are forced to rely on low-throughput, manual approaches for managing device input and output (IO) of samples, reagents, and effluent. Here, we present a hardware-software platform for automated microfluidic IO (micrIO). The platform, which is uniquely compatible with positive-pressure microfluidics, comprises an 'AutoSipper' for input and a 'Fraction Collector' for output. To facilitate widespread adoption, both are open-source builds constructed from components that are readily purchased online or fabricated from included design files. The software control library, written in Python, allows the platform to be integrated with existing experimental setups and to coordinate IO with other functions such as valve actuation and assay imaging. We demonstrate these capabilities by coupling both the AutoSipper and Fraction Collector to two microfluidic devices: a simple, valved inlet manifold and a microfluidic droplet generator that produces beads with distinct spectral codes. Analysis of the collected materials in each case establishes the ability of the platform to draw from and output to specific wells of multiwell plates with negligible cross-contamination between samples.
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Affiliation(s)
- Scott A Longwell
- Department of Bioengineering, Stanford University, Stanford, CA, USA.
| | - Polly M Fordyce
- Department of Bioengineering, Stanford University, Stanford, CA, USA. and Department of Genetics, Stanford University, Stanford, CA, USA and ChEM-H Institute, Stanford University, Stanford, CA, USA and Chan Zuckerberg Biohub, San Francisco, CA, USA
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68
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Gupta S, Witas R, Voigt A, Semenova T, Nguyen CQ. Single-Cell Sequencing of T cell Receptors: A Perspective on the Technological Development and Translational Application. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1255:29-50. [PMID: 32949388 DOI: 10.1007/978-981-15-4494-1_3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
T cells recognize peptides bound to major histocompatibility complex (MHC) class I and class II molecules at the cell surface. This recognition is accomplished by the expression of T cell receptors (TCR) which are required to be diverse and adaptable in order to accommodate the various and vast number of antigens presented on the MHCs. Thus, determining TCR repertoires of effector T cells is necessary to understand the immunological process in responding to cancer progression, infection, and autoimmune development. Furthermore, understanding the TCR repertoires will provide a solid framework to predict and test the antigen which is more critical in autoimmunity. However, it has been a technical challenge to sequence the TCRs and provide a conceptual context in correlation to the vast number of TCR repertoires in the immunological system. The exploding field of single-cell sequencing has changed how the repertoires are being investigated and analyzed. In this review, we focus on the biology of TCRs, TCR signaling and its implication in autoimmunity. We discuss important methods in bulk sequencing of many cells. Lastly, we explore the most pertinent platforms in single-cell sequencing and its application in autoimmunity.
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Affiliation(s)
- Shivai Gupta
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, Gainesville, FL, USA
| | - Richard Witas
- Department of Oral Biology, College of Dentistry, Gainesville, FL, USA
| | - Alexandria Voigt
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, Gainesville, FL, USA
| | - Touyana Semenova
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, Gainesville, FL, USA
| | - Cuong Q Nguyen
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, Gainesville, FL, USA. .,Department of Oral Biology, College of Dentistry, Gainesville, FL, USA. .,Center of Orphaned Autoimmune Diseases, University of Florida, Gainesville, FL, USA.
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69
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Padmanabhan S, Han JY, Nanayankkara I, Tran K, Ho P, Mesfin N, White I, DeVoe DL. Enhanced sample filling and discretization in thermoplastic 2D microwell arrays using asymmetric contact angles. BIOMICROFLUIDICS 2020; 14:014113. [PMID: 32095199 PMCID: PMC7028432 DOI: 10.1063/1.5126938] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 02/09/2020] [Indexed: 05/04/2023]
Abstract
Sample filling and discretization within thermoplastic 2D microwell arrays is investigated toward the development of low cost disposable microfluidics for passive sample discretization. By using a high level of contact angle asymmetry between the filling channel and microwell surfaces, a significant increase in the range of well geometries that can be successfully filled is revealed. The performance of various array designs is characterized numerically and experimentally to assess the impact of contact angle asymmetry and device geometry on sample filling and discretization, resulting in guidelines to ensure robust microwell filling and sample isolation over a wide range of well dimensions. Using the developed design rules, reliable and bubble-free sample filling and discretization is achieved in designs with critical dimensions ranging from 20 μm to 800 μm. The resulting devices are demonstrated for discretized nucleic acid amplification by performing loop-mediated isothermal amplification for the detection of the mecA gene associated with methicillin-resistant Staphylococcus aureus.
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Affiliation(s)
- S. Padmanabhan
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, Maryland 20742, USA
| | - J. Y. Han
- Department of Mechanical Engineering, University of Maryland, College Park, Maryland 20742, USA
| | - I. Nanayankkara
- Department of Bioengineering, University of Maryland, College Park, Maryland 20742, USA
| | - K. Tran
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, Maryland 20742, USA
| | - P. Ho
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, Maryland 20742, USA
| | - N. Mesfin
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, Maryland 20742, USA
| | - I. White
- Department of Bioengineering, University of Maryland, College Park, Maryland 20742, USA
| | - D. L. DeVoe
- Author to whom correspondence should be addressed:. Tel.: +1-301-405-8125
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70
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Droplet-based optofluidic systems for measuring enzyme kinetics. Anal Bioanal Chem 2019; 412:3265-3283. [PMID: 31853606 DOI: 10.1007/s00216-019-02294-z] [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: 07/30/2019] [Revised: 10/15/2019] [Accepted: 11/19/2019] [Indexed: 01/05/2023]
Abstract
The study of enzyme kinetics is of high significance in understanding metabolic networks in living cells and using enzymes in industrial applications. To gain insight into the catalytic mechanisms of enzymes, it is necessary to screen an enormous number of reaction conditions, a process that is typically laborious, time-consuming, and costly when using conventional measurement techniques. In recent times, droplet-based microfluidic systems have proved themselves to be of great utility in large-scale biological experimentation, since they consume a minimal sample, operate at high analytical throughput, are characterized by efficient mass and heat transfer, and offer high levels of integration and automation. The primary goal of this review is the introduction of novel microfluidic tools and detection methods for use in high-throughput and sensitive analysis of enzyme kinetics. The first part of this review focuses on introducing basic concepts of enzyme kinetics and describing most common microfluidic approaches, with a particular focus on segmented flow. Herein, the key advantages include accurate control over the flow behavior, efficient mass and heat transfer, multiplexing, and high-level integration with detection modalities. The second part describes the current state-of-the-art platforms for high-throughput and sensitive analysis of enzyme kinetics. In addition to our categorization of recent advances in measuring enzyme kinetics, we have endeavored to critically assess the limitations of each of these detection approaches and propose strategies to improve measurements in droplet-based microfluidics. Graphical abstract.
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71
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Akama K, Iwanaga N, Yamawaki K, Okuda M, Jain K, Ueno H, Soga N, Minagawa Y, Noji H. Wash- and Amplification-Free Digital Immunoassay Based on Single-Particle Motion Analysis. ACS NANO 2019; 13:13116-13126. [PMID: 31675215 DOI: 10.1021/acsnano.9b05917] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Digital enzyme-linked immunosorbent assay (ELISA) is a powerful analytical method for highly sensitive protein biomarker detection. The current protocol of digital ELISA requires multiple washing steps and signal amplification using an enzyme, which could be the potential drawback in in vitro diagnosis. In this study, we propose a digital immunoassay method, which we call "Digital HoNon-ELISA" (digital homogeneous non-enzymatic immunosorbent assay) for highly sensitive detection without washing and signal amplification. Target antigen molecules react with antibody-coated magnetic nanoparticles, which are then magnetically pulled into femtoliter-sized reactors. The antigens on the particles are captured by antibodies anchored on the bottom surface of the reactor via molecular tethers. Magnetic force enhances the efficiency of particle encapsulation in the reactors. Subsequent physical compartmentalization of the particles enhances the binding efficiency of antigen-carrying particles to the antibodies. The tethered particles show characteristic Brownian motion within a limited space by the molecular tethering, which is distinct from free diffusion or nonspecific binding of antigen-free particles. The number of tethered particles directly correlates with the concentration of the target antigen. Digital HoNon-ELISA was used with a prostate-specific antigen to achieve a detection of 0.093 pg/mL, which is over 9.0-fold the sensitivity of commercialized highly sensitive ELISA (0.84 pg/mL) and comparable to digital ELISA (0.055 pg/mL). This digital immunoassay strategy has sensitivity similar to digital ELISA with simplicity similar to homogeneous assay. Such similarity allows for potential application in rapid and simple digital diagnostic tests without the need for washing and enzymatic amplification.
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Affiliation(s)
- Kenji Akama
- Department of Applied Chemistry, Graduate School of Engineering , The University of Tokyo , 7-3-1 Hongo , Bunkyo-ku, Tokyo 113-8656 , Japan
- Central Research Laboratories , Sysmex Corporation , 4-4-4 Takatsukadai , Nishi-ku, Kobe 651-2271 , Japan
| | - Niina Iwanaga
- Central Research Laboratories , Sysmex Corporation , 4-4-4 Takatsukadai , Nishi-ku, Kobe 651-2271 , Japan
| | - Koya Yamawaki
- Central Research Laboratories , Sysmex Corporation , 4-4-4 Takatsukadai , Nishi-ku, Kobe 651-2271 , Japan
| | - Masaki Okuda
- Central Research Laboratories , Sysmex Corporation , 4-4-4 Takatsukadai , Nishi-ku, Kobe 651-2271 , Japan
| | - Krupali Jain
- Central Research Laboratories , Sysmex Corporation , 4-4-4 Takatsukadai , Nishi-ku, Kobe 651-2271 , Japan
| | - Hiroshi Ueno
- Department of Applied Chemistry, Graduate School of Engineering , The University of Tokyo , 7-3-1 Hongo , Bunkyo-ku, Tokyo 113-8656 , Japan
| | - Naoki Soga
- Department of Applied Chemistry, Graduate School of Engineering , The University of Tokyo , 7-3-1 Hongo , Bunkyo-ku, Tokyo 113-8656 , Japan
| | - Yoshihiro Minagawa
- Department of Applied Chemistry, Graduate School of Engineering , The University of Tokyo , 7-3-1 Hongo , Bunkyo-ku, Tokyo 113-8656 , Japan
| | - Hiroyuki Noji
- Department of Applied Chemistry, Graduate School of Engineering , The University of Tokyo , 7-3-1 Hongo , Bunkyo-ku, Tokyo 113-8656 , Japan
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72
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Zhukov DV, Khorosheva EM, Khazaei T, Du W, Selck DA, Shishkin AA, Ismagilov RF. Microfluidic SlipChip device for multistep multiplexed biochemistry on a nanoliter scale. LAB ON A CHIP 2019; 19:3200-3211. [PMID: 31441477 DOI: 10.1039/c9lc00541b] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
We have developed a multistep microfluidic device that expands the current SlipChip capabilities by enabling multiple steps of droplet merging and multiplexing. Harnessing the interfacial energy between carrier and sample phases, this manually operated device accurately meters nanoliter volumes of reagents and transfers them into on-device reaction wells. Judiciously shaped microfeatures and surface-energy traps merge droplets in a parallel fashion. Wells can be tuned for different volumetric capacities and reagent types, including for pre-spotted reagents that allow for unique identification of original well contents even after their contents are pooled. We demonstrate the functionality of the multistep SlipChip by performing RNA transcript barcoding on-device for synthetic spiked-in standards and for biologically derived samples. This technology is a good candidate for a wide range of biological applications that require multiplexing of multistep reactions in nanoliter volumes, including single-cell analyses.
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Affiliation(s)
- Dmitriy V Zhukov
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125, USA.
| | - Eugenia M Khorosheva
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125, USA.
| | - Tahmineh Khazaei
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125, USA
| | - Wenbin Du
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, USA
| | - David A Selck
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125, USA.
| | - Alexander A Shishkin
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125, USA
| | - Rustem F Ismagilov
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125, USA. and Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125, USA
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73
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Danielson C, Pappas G, Phelps L, Melvin AT, Park K. Static microdroplet array generated by spraying and analyzed with automated microscopy and image processing. Anal Biochem 2019; 587:113452. [PMID: 31563443 DOI: 10.1016/j.ab.2019.113452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 09/05/2019] [Accepted: 09/24/2019] [Indexed: 10/25/2022]
Abstract
Microdroplets have received increasing interest as practical platforms for high-throughput biochemical analysis. Typically, numerous discrete aqueous microdroplets containing biochemical targets are generated in a continuous oil phase and characterized using a flow-through configuration. Although this approach is capable of extremely high throughput, it is challenging to provide dynamic characterization of time-dependent reaction kinetics. In this paper, we present a practical and affordable method to create and analyze a massive array of static aqueous microdroplets immersed in oil for biochemical analysis. The discrete microdroplets were produced by an air-spray gun, imaged by automated microscopy, and then characterized by image processing. The location, area, and fluorescence intensity of randomly generated individual microdroplets were automatically registered for high-throughput characterization. With this approach, we rapidly produced and characterized a static microdroplet array of over 0.7 million microdroplets with an average volume of 300 fL and a mean population density of 1.5*105 microdroplets/cm2. Using the developed setup, we demonstrated the dependency of the microdroplets' fluorescence intensity on their volume, as well as characterized the time-dependent enzyme reaction kinetics of β-galactosidase-mediated cleavage of the substrate fluorescein di-β-d-galactopyranoside (FDG). The new approach described herein provides an inexpensive alternative solution for high-throughput analysis of dynamic biochemical processes.
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Affiliation(s)
- Christian Danielson
- Division of Electrical and Computer Engineering, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Gavin Pappas
- Cain Department of Chemical Engineering, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Lance Phelps
- Division of Electrical and Computer Engineering, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Adam T Melvin
- Cain Department of Chemical Engineering, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Kidong Park
- Division of Electrical and Computer Engineering, Louisiana State University, Baton Rouge, LA, 70803, USA.
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74
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Yin J, Suo Y, Zou Z, Sun J, Zhang S, Wang B, Xu Y, Darland D, Zhao JX, Mu Y. Integrated microfluidic systems with sample preparation and nucleic acid amplification. LAB ON A CHIP 2019; 19:2769-2785. [PMID: 31365009 PMCID: PMC8876602 DOI: 10.1039/c9lc00389d] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Rapid, efficient and accurate nucleic acid molecule detection is important in the screening of diseases and pathogens, yet remains a limiting factor at point of care (POC) treatment. Microfluidic systems are characterized by fast, integrated, miniaturized features which provide an effective platform for qualitative and quantitative detection of nucleic acid molecules. The nucleic acid detection process mainly includes sample preparation and target molecule amplification. Given the advancements in theoretical research and technological innovations to date, nucleic acid extraction and amplification integrated with microfluidic systems has advanced rapidly. The primary goal of this review is to outline current approaches used for nucleic acid detection in the context of microfluidic systems. The secondary goal is to identify new approaches that will help shape future trends at the intersection of nucleic acid detection and microfluidics, particularly with regard to increasing disease and pathogen detection for improved diagnosis and treatment.
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Affiliation(s)
- Juxin Yin
- Research Centre for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou, 310058, China.
| | - Yuanjie Suo
- Research Centre for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou, 310058, China.
| | - Zheyu Zou
- Research Centre for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou, 310058, China.
| | - Jingjing Sun
- Research Centre for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou, 310058, China.
| | - Shan Zhang
- Research Centre for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou, 310058, China.
| | - Beng Wang
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, National Ministry of Education), The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310009 China and Institute of Translational Medicine, Zhejiang University, Hangzhou, 310029 China
| | - Yawei Xu
- College of Biological and Pharmaceutical Engineering, Jilin Agricultural Science and Technology University, Jilin, 132000 China
| | - Diane Darland
- Department of Biology, University of North Dakota, USA.
| | | | - Ying Mu
- Research Centre for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou, 310058, China.
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75
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Zhu X, Liu B, Su S, Wang B, Bai Y, Huang H, Liu X, Cheng X, Wang X, Zhu L, Yang W, Gao N, Jing G, Guo Y. A "quasi" confocal droplet reader based on laser-induced fluorescence (LIF) cytometry for highly-sensitive and contamination-free detection. Talanta 2019; 206:120200. [PMID: 31514845 DOI: 10.1016/j.talanta.2019.120200] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 07/29/2019] [Accepted: 07/30/2019] [Indexed: 01/23/2023]
Abstract
Highly-sensitive and contamination-free droplet digital PCR (ddPCR) is an enabling technology and widely needed for accurate quantification of nucleic acid in clinical applications. In this paper, a novel droplet reader was developed by combining a "quasi" confocal laser-induced fluorescence (LIF) cytometry with a delicate microfluidic chip design. The droplets with a size of 90 μm was illuminated at an out-of-focus position by two aligned laser beams to generate maximum fluorescent signal. Additionally, the lateral offset position of the microfluidic chip should be precisely tuned so that the bandwidth of the FAM and VIC channels were configured at the matching sizes. Then, PMT gain voltages and pneumatic pressures were optimized for better droplet detection efficiencies. An aerosol adsorption experiment was performed to demonstrate that there was no aerosol contamination, and detected copy numbers of both mutants and wild types scaled linearly with the expected input copy numbers (r2>0.998) with a LoB of 0.0 copies and LoD of 3.0 copies. The results demonstrated that this droplet reader with the delicate chip is a convenient, highly-sensitive and contamination-free to detect fluorescence signals inside droplets after ddPCR, which is highly promising for broad applications of ddPCR in clinical diagnosis.
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Affiliation(s)
- Xiurui Zhu
- Department of Biomedical Engineering, School of Medicine, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Tsinghua University, Beijing, China
| | - Baoxia Liu
- TargetingOne Corporation, Beijing, China
| | - Shisheng Su
- Department of Biomedical Engineering, School of Medicine, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Tsinghua University, Beijing, China
| | - Bo Wang
- TargetingOne Corporation, Beijing, China
| | - Yu Bai
- TargetingOne Corporation, Beijing, China
| | | | | | - Xin Cheng
- TargetingOne Corporation, Beijing, China
| | | | - Lingxiang Zhu
- TargetingOne Corporation, Beijing, China; National Research Institute for Family Planning, Beijing, China
| | - Wenjun Yang
- Department of Biomedical Engineering, School of Medicine, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Tsinghua University, Beijing, China; TargetingOne Corporation, Beijing, China
| | - Na Gao
- TargetingOne Corporation, Beijing, China
| | - Gaoshan Jing
- Department of Precision Instrument, School of Mechanical Engineering, State Key Laboratory of Precision Measurement Technology and Instruments, Tsinghua University, Beijing, China.
| | - Yong Guo
- Department of Biomedical Engineering, School of Medicine, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Tsinghua University, Beijing, China.
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76
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Madadelahi M, Ghazimirsaeed E, Shamloo A. Design and fabrication of a two-phase diamond nanoparticle aided fast PCR device. Anal Chim Acta 2019; 1068:28-40. [DOI: 10.1016/j.aca.2019.02.050] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2019] [Accepted: 02/27/2019] [Indexed: 01/13/2023]
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77
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O’Keefe CM, Kaushik AM, Wang TH. Highly Efficient Real-Time Droplet Analysis Platform for High-Throughput Interrogation of DNA Sequences by Melt. Anal Chem 2019; 91:11275-11282. [DOI: 10.1021/acs.analchem.9b02346] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Christine M. O’Keefe
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Aniruddha M. Kaushik
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Tza-Huei Wang
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
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78
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Lyu W, Yu M, Qu H, Yu Z, Du W, Shen F. Slip-driven microfluidic devices for nucleic acid analysis. BIOMICROFLUIDICS 2019; 13:041502. [PMID: 31312285 PMCID: PMC6625959 DOI: 10.1063/1.5109270] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 07/01/2019] [Indexed: 05/17/2023]
Abstract
Slip-driven microfluidic devices can manipulate fluid by the relative movement of microfluidic plates that are in close contact. Since the demonstration of the first SlipChip device, many slip-driven microfluidic devices with different form factors have been developed, including SlipPAD, SlipDisc, sliding stripe, and volumetric bar chart chip. Slip-driven microfluidic devices can be fabricated from glass, quartz, polydimethylsiloxane, paper, and plastic with various fabrication methods: etching, casting, wax printing, laser cutting, micromilling, injection molding, etc. The slipping operation of the devices can be performed manually, by a micrometer with a base station, or autonomously, by a clockwork mechanism. A variety of readout methods other than fluorescence microscopy have been demonstrated, including both fluorescence detection and colorimetric detection by mobile phones, direct visual detection, and real-time fluorescence imaging. This review will focus on slip-driven microfluidic devices for nucleic acid analysis, including multiplex nucleic acid detection, digital nucleic acid quantification, real-time nucleic acid amplification, and sample-in-answer-out nucleic acid analysis. Slip-driven microfluidic devices present promising approaches for both life science research and clinical molecular diagnostics.
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Affiliation(s)
- Weiyuan Lyu
- School of Biomedical Engineering, Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai 200030, China
| | - Mengchao Yu
- School of Biomedical Engineering, Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai 200030, China
| | - Haijun Qu
- School of Biomedical Engineering, Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai 200030, China
| | | | - Wenbin Du
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100080, China
| | - Feng Shen
- School of Biomedical Engineering, Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai 200030, China
- Author to whom correspondence should be addressed:
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79
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Gorgannezhad L, Stratton H, Nguyen NT. Microfluidic-Based Nucleic Acid Amplification Systems in Microbiology. MICROMACHINES 2019; 10:E408. [PMID: 31248141 PMCID: PMC6630468 DOI: 10.3390/mi10060408] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 06/14/2019] [Accepted: 06/17/2019] [Indexed: 02/07/2023]
Abstract
Rapid, sensitive, and selective bacterial detection is a hot topic, because the progress in this research area has had a broad range of applications. Novel and innovative strategies for detection and identification of bacterial nucleic acids are important for practical applications. Microfluidics is an emerging technology that only requires small amounts of liquid samples. Microfluidic devices allow for rapid advances in microbiology, enabling access to methods of amplifying nucleic acid molecules and overcoming difficulties faced by conventional. In this review, we summarize the recent progress in microfluidics-based polymerase chain reaction devices for the detection of nucleic acid biomarkers. The paper also discusses the recent development of isothermal nucleic acid amplification and droplet-based microfluidics devices. We discuss recent microfluidic techniques for sample preparation prior to the amplification process.
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Affiliation(s)
- Lena Gorgannezhad
- Queensland Micro- and Nanotechnology Centre, Nathan Campus, Griffith University, 170 Kessels Road, Brisbane QLD 4111, Australia.
- School of Environment and Science, Nathan Campus, Griffith University, 170 Kessels Road, Brisbane QLD 4111, Australia.
| | - Helen Stratton
- School of Environment and Science, Nathan Campus, Griffith University, 170 Kessels Road, Brisbane QLD 4111, Australia.
| | - Nam-Trung Nguyen
- Queensland Micro- and Nanotechnology Centre, Nathan Campus, Griffith University, 170 Kessels Road, Brisbane QLD 4111, Australia.
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80
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Yu M, Chen X, Qu H, Ma L, Xu L, Lv W, Wang H, Ismagilov RF, Li M, Shen F. Multistep SlipChip for the Generation of Serial Dilution Nanoliter Arrays and Hepatitis B Viral Load Quantification by Digital Loop Mediated Isothermal Amplification. Anal Chem 2019; 91:8751-8755. [PMID: 31117407 DOI: 10.1021/acs.analchem.9b01270] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Serial dilution is a commonly used technique that generates a low-concentration working sample from a high-concentration stock solution and is used to set up screening conditions over a large dynamic range for biological study, optimization of reaction conditions, drug screening, etc. Creating an array of serial dilutions usually requires cumbersome manual pipetting steps or a robotic liquid handling system. Moreover, it is very challenging to set up an array of serial dilutions in nanoliter volumes in miniaturized assays. Here, a multistep SlipChip microfluidic device is presented for generating serial dilution nanoliter arrays in high throughput with a series of simple sliding motions. The dilution ratio can be precisely predetermined by the volumes of mother microwells and daughter microwells, and this paper demonstrates devices designed to have dilution ratios of 1:1, 1:2, and 1:4. Furthermore, an eight-step serial dilution SlipChip with a dilution ratio of 1:4 is applied for digital loop-mediated isothermal amplification (LAMP) across a large dynamic range and tested for hepatitis B viral load quantification with clinical samples. With 64 wells of each dilution and fewer than 600 wells in total, the serial dilution SlipChip can achieve a theoretical quantification dynamic range of 7 orders of magnitude.
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Affiliation(s)
- Mengchao Yu
- School of Biomedical Engineering , Shanghai Jiao Tong University , 1954 Hua Shan Road , Shanghai 200030 , China
| | - Xiaoying Chen
- Department of Laboratory Medicine, Renji Hospital, School of Medicine , Shanghai Jiao Tong University , Shanghai 200127 , China
| | - Haijun Qu
- School of Biomedical Engineering , Shanghai Jiao Tong University , 1954 Hua Shan Road , Shanghai 200030 , China
| | - Liang Ma
- Department of Chemistry and Institute for Biophysical Dynamics , The University of Chicago , 929 East 57th Street , Chicago , Illinois 60637 , United States
| | - Lei Xu
- School of Biomedical Engineering , Shanghai Jiao Tong University , 1954 Hua Shan Road , Shanghai 200030 , China
| | - Weiyuan Lv
- School of Biomedical Engineering , Shanghai Jiao Tong University , 1954 Hua Shan Road , Shanghai 200030 , China
| | - Hua Wang
- Department of Laboratory Medicine, Renji Hospital, School of Medicine , Shanghai Jiao Tong University , Shanghai 200127 , China
| | - Rustem F Ismagilov
- Division of Chemistry & Chemical Engineering , California Institute of Technology , 1200 East California Boulevard , Mail Code 210-41, Pasadena , California 91125 , United States.,Division of Biology & Biological Engineering , California Institute of Technology , 1200 East California Boulevard , Mail Code 210-41, Pasadena , California 91125 , United States
| | - Min Li
- Department of Laboratory Medicine, Renji Hospital, School of Medicine , Shanghai Jiao Tong University , Shanghai 200127 , China.,China State Key Laboratory of Microbial Resources, Institute of Microbiology , Chinese Academy of Sciences , Beijing 100080 , China
| | - Feng Shen
- School of Biomedical Engineering , Shanghai Jiao Tong University , 1954 Hua Shan Road , Shanghai 200030 , China
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81
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Gao Z, Peng H, Zhu M, Wu L, Jia C, Zhou H, Zhao J. A Facile Strategy for Visualizing and Modulating Droplet-Based Microfluidics. MICROMACHINES 2019; 10:E291. [PMID: 31035446 PMCID: PMC6562635 DOI: 10.3390/mi10050291] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 04/22/2019] [Accepted: 04/25/2019] [Indexed: 11/23/2022]
Abstract
In droplet-based microfluidics, visualizing and modulating of droplets is often prerequisite. In this paper, we report a facile strategy for visualizing and modulating high-throughput droplets in microfluidics. In the strategy, by modulating the sampling frequency of a flash light with the droplet frequency, we are able to map a real high frequency signal to a low frequency signal, which facilitates visualizing and feedback controlling. Meanwhile, because of not needing synchronization signals, the strategy can be directly implemented on any droplet-based microfluidic chips. The only cost of the strategy is an additional signal generator. Moreover, the strategy can catch droplets with frequency up to several kilohertz, which covers the range of most high-throughput droplet-based microfluidics. In this paper, the principle, setup and procedure were introduced. Finally, as a demonstration, the strategy was also implemented in a miniaturized picoinjector in order to monitor and control the injection dosage to droplets. We expect that this facile strategy supplies a low-cost yet effective imaging system that can be easily implemented in miniaturized microfluidic systems or general laboratories.
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Affiliation(s)
- Zehang Gao
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai 200050, China.
- School of Information Science and Technology, ShanghaiTech University, Shanghai 201210, China.
- University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Huo Peng
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai 200050, China.
- University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Minjie Zhu
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai 200050, China.
- Department of Chemistry, College of Science, Shanghai University, Shanghai 200444, China.
| | - Lei Wu
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai 200050, China.
| | - Chunping Jia
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai 200050, China.
| | - Hongbo Zhou
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai 200050, China.
| | - Jianlong Zhao
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai 200050, China.
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82
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Chen-Yin O, Vu T, Grunwald JT, Toledano M, Zimak J, Toosky M, Shen B, Zell JA, Gratton E, Abram T, Zhao W. An ultrasensitive test for profiling circulating tumor DNA using integrated comprehensive droplet digital detection. LAB ON A CHIP 2019; 19:993-1005. [PMID: 30735225 PMCID: PMC6559803 DOI: 10.1039/c8lc01399c] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Current cancer detection systems lack the required sensitivity to reliably detect minimal residual disease (MRD) and recurrence at the earliest stages when treatment would be most effective. To address this issue, we present a novel liquid biopsy approach that utilizes an integrated comprehensive droplet digital detection (IC3D) digital PCR system which combines microfluidic droplet partitioning, fluorescent multiplex PCR chemistry, and our rapid 3D, large-volume droplet counting technology. The IC3D ddPCR assay can detect cancer-specific, ultra-rare genomic targets due to large sample input and high degree of partitioning. We first demonstrate our droplet digital PCR assay can robustly detect common cancer mutants including KRAS G12D spiked in wild-type genomic background or isolated from patient samples with 100% specificity. We then demonstrate that the IC3D ddPCR system can detect oncogenic KRAS G12D mutant alleles against a background of wild-type genomes at a sensitivity of 0.00125-0.005% with a false positive rate of 0% which is 50 to 1000× more sensitive than existing commercial liquid biopsy ddPCR and qPCR platforms, respectively. In addition, our technology can uniquely enable detection of circulating tumor cells using their genetic markers without a pre-enrichment step, and analysis of total tumor DNA isolated from blood samples, which will increase clinical sensitivity and specificity, and minimize inter-assay variability. Therefore, our technology holds the potential to provide clinicians with a powerful decision-making tool to monitor and treat MRD with unprecedented sensitivity for earlier stage intervention.
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Affiliation(s)
- Ou Chen-Yin
- Velox Biosystems, 5 Mason, Suite 160, Irvine, CA 92618, USA
| | - Tam Vu
- Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA 92697, USA
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA 92697, USA
| | | | - Michael Toledano
- Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA 92697, USA
| | - Jan Zimak
- Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA 92697, USA
| | - Melody Toosky
- Velox Biosystems, 5 Mason, Suite 160, Irvine, CA 92618, USA
| | - Byron Shen
- Velox Biosystems, 5 Mason, Suite 160, Irvine, CA 92618, USA
| | - Jason A. Zell
- Chao Family Comprehensive Cancer Center, University of California, Irvine, Irvine, CA 92697, USA
- Division of Hematology/Oncology, University of California Irvine Medical Center, Orange, USA
| | - Enrico Gratton
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA 92697, USA
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine, USA
| | - Tim Abram
- Velox Biosystems, 5 Mason, Suite 160, Irvine, CA 92618, USA
| | - Weian Zhao
- Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA 92697, USA
- Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA 92697, USA
- Chao Family Comprehensive Cancer Center, University of California, Irvine, Irvine, CA 92697, USA
- Edwards Life Sciences Center for Advanced Cardiovascular Technology, University of California, Irvine, Irvine, CA 92697, USA
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA 92697, USA
- Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA
- Division of Hematology/Oncology, University of California Irvine Medical Center, Orange, USA
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83
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Mobile platform for rapid sub-picogram-per-milliliter, multiplexed, digital droplet detection of proteins. Proc Natl Acad Sci U S A 2019; 116:4489-4495. [PMID: 30765530 PMCID: PMC6410864 DOI: 10.1073/pnas.1814110116] [Citation(s) in RCA: 112] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Digital assays have enormous untapped potential for diagnostics, environmental surveillance, and biosafety monitoring, but are currently confined to laboratory settings due to the instrumentation necessary to generate, control, and measure millions of droplets. We instead use a mobile phone-based imaging technique that is >100× faster than conventional microfluidic droplet detection, does not require expensive optics, is invariant to flow rate, and can simultaneously measure multiple fluorescent dyes in droplets. By using this time domain modulation with cloud computing, we overcome the low frame rate of digital imaging, and achieve throughputs as high as 1 million droplets per second. We integrate on-chip delay lines and a microbead processing unit, resulting in a robust device, suitable for low-cost implementation, with ultrasensitive measurement capabilities. Digital droplet assays—in which biological samples are compartmentalized into millions of femtoliter-volume droplets and interrogated individually—have generated enormous enthusiasm for their ability to detect biomarkers with single-molecule sensitivity. These assays have untapped potential for point-of-care diagnostics but are currently mainly confined to laboratory settings, due to the instrumentation necessary to serially generate, control, and measure tens of millions of droplets/compartments. To address this challenge, we developed an optofluidic platform that miniaturizes digital assays into a mobile format by parallelizing their operation. This technology is based on three key innovations: (i) the integration and parallel operation of a hundred droplet generators onto a single chip that operates >100× faster than a single droplet generator, (ii) the fluorescence detection of droplets at >100× faster than conventional in-flow detection using time domain-encoded mobile phone imaging, and (iii) the integration of on-chip delay lines and sample processing to allow serum-to-answer device operation. To demonstrate the power of this approach, we performed a duplex digital ELISA. We characterized the performance of this assay by first using spiked recombinant proteins in a complex media (FBS) and measured a limit of detection, 0.004 pg/mL (300 aM), a 1,000× improvement over standard ELISA and matching that of the existing laboratory-based gold standard digital ELISA system. We additionally measured endogenous GM-CSF and IL6 in human serum from n = 14 human subjects using our mobile duplex assay, and showed excellent agreement with the gold standard system (R2=0.96).
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84
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Vijayan S, Hashimoto M. 3D printed fittings and fluidic modules for customizable droplet generators. RSC Adv 2019; 9:2822-2828. [PMID: 35520507 PMCID: PMC9059964 DOI: 10.1039/c8ra08686a] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 01/09/2019] [Indexed: 11/21/2022] Open
Abstract
We developed a rapid and simple method to fabricate microfluidic non-planar axisymmetric droplet generators using 3D printed fittings and commercially available components. 3D printing allows facile fabrication of microchannels albeit with limitations in the repeatability at low resolutions. In this work, we used 3D printed fitting to arrange the flow in the axisymmetric configuration, while the commercially available needles formed a flow-focusing nozzle as small as 60 μm in diameter. We assembled 3D printed fitting, needle, and soft tubes as different modules to make a single droplet generator. The design of our device allowed for reconfiguration of the modules after fabrication to achieve customized generation of droplets. We produced droplets of varying diameters by switching the standard needles and the minimum diameter of droplet obtained was 332 ± 10 μm for 34 G (ID = 60 μm). Our method allowed for generating complex emulsions (i.e. double emulsions and compartmented emulsions) by adding 3D printed sub-units with the fluidic connections. Our approach offered characteristics complementary to existing methods to fabricate flow-focusing generators. The standardized needles serving as a module offered well-defined dimensions of the channels not attainable in desktop 3D printers, while the 3D printed components, in turn, offered a facile route to reconfigure and extend the flow pattern in the device. Fabrication can be completed in a plug-and-play manner. Overall, the technology we developed here will provide a standard approachable route to generate customized microfluidic emulsions for specific applications in chemical and biological sciences.
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Affiliation(s)
- Sindhu Vijayan
- Pillar of Engineering Product Development, Singapore University of Technology and Design 8 Somapah Road Singapore 487372 Singapore
- Digital Manufacturing and Design (DManD) Centre, Singapore University of Technology and Design 8 Somapah Road Singapore 487372 Singapore
| | - Michinao Hashimoto
- Pillar of Engineering Product Development, Singapore University of Technology and Design 8 Somapah Road Singapore 487372 Singapore
- Digital Manufacturing and Design (DManD) Centre, Singapore University of Technology and Design 8 Somapah Road Singapore 487372 Singapore
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85
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A highly integrated real-time digital PCR device for accurate DNA quantitative analysis. Biosens Bioelectron 2019; 128:151-158. [PMID: 30660930 DOI: 10.1016/j.bios.2018.12.055] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 12/21/2018] [Accepted: 12/25/2018] [Indexed: 11/23/2022]
Abstract
Misclassification of positive partitions in microfluidic digital polymerase chain reaction (dPCR) can cause the false positives and false negatives, which significantly alter the resulting estimate of target DNA molecules. To address this issue, establishing real-time fluorescence interrogation of each partition in microfluidic arrays is an effective way in which false positive and false negative partitions can be eliminated. However, currently available devices for real-time fluorescence interrogation are either not competent for microfluidic digital array, or they are bulky, expensive and entail peripheral equipment due to low integration. Therefore, in this study, a Raspberry Pi based, low-cost and highly integrated device is presented to achieve real-time fluorescence detection for microfluidic digital array, termed real-time dPCR device. In the device, uniform thermocycler, streamlined real-time fluorescence imaging setup, and compact data processing system are all integrated to undergo on-chip dPCR amplification, real-time fluorescence detection, and data analysis. Using this real-time dPCR device, the accuracy of DNA absolute quantification by dPCR is improved, since the misclassification of positive partitions is efficiently reduced based on the characteristic real-time fluorescence curves of positive partitions in a self-priming microfluidic chip. Compared with end-point dPCR on our device and commercialized QuantStudio™ 3D dPCR system, the real-time dPCR on our device exhibits a higher accuracy for DNA quantification. In addition, this real-time dPCR device is much smaller and cheaper than the commercialized Digital PCR system, but not sacrificing the capability of error correction for absolute quantitation analysis. Conclusively, this highly integrated real-time dPCR device is very beneficial for DNA quantitative analysis where the determination accuracy is pivotal.
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86
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Nie M, Zheng M, Li C, Shen F, Liu M, Luo H, Song X, Lan Y, Pan JZ, Du W. Assembled Step Emulsification Device for Multiplex Droplet Digital Polymerase Chain Reaction. Anal Chem 2019; 91:1779-1784. [DOI: 10.1021/acs.analchem.8b04313] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Mengyue Nie
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, China
- College of Life Sciences, University of the Chinese Academy of Sciences, Beijing, 10049, China
| | - Meng Zheng
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, China
- Savaid Medical School, University of the Chinese Academy of Sciences, Beijing, 10049, China
| | - Caiming Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, China
- College of Life Sciences, University of the Chinese Academy of Sciences, Beijing, 10049, China
| | - Feng Shen
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Manhua Liu
- Department of Instrument Science and Engineering, The School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Haibei Luo
- Pilot Gene Technologies, Hangzhou, 311203, China
| | - Xiaohui Song
- Pilot Gene Technologies, Hangzhou, 311203, China
| | - Ying Lan
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, China
| | - Jian-Zhang Pan
- Institute of Microanalytical Systems, Department of Chemistry, Zhejiang University, Hangzhou, 310058, China
| | - Wenbin Du
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, China
- College of Life Sciences, University of the Chinese Academy of Sciences, Beijing, 10049, China
- Savaid Medical School, University of the Chinese Academy of Sciences, Beijing, 10049, China
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87
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Malic L, Daoud J, Geissler M, Boutin A, Lukic L, Janta M, Elmanzalawy A, Veres T. Epigenetic subtyping of white blood cells using a thermoplastic elastomer-based microfluidic emulsification device for multiplexed, methylation-specific digital droplet PCR. Analyst 2019; 144:6541-6553. [DOI: 10.1039/c9an01316d] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Digital droplet PCR for epigenetic leukocyte subtyping from clinically relevant samples is implemented using a thermoplastic elastomer microfluidic droplet generator as a first step towards an economical, customizable and easily deployable system.
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Affiliation(s)
- Lidija Malic
- Life Sciences Division
- National Research Council of Canada
- Boucherville
- Canada
| | - Jamal Daoud
- Life Sciences Division
- National Research Council of Canada
- Boucherville
- Canada
| | - Matthias Geissler
- Life Sciences Division
- National Research Council of Canada
- Boucherville
- Canada
| | - Alex Boutin
- Life Sciences Division
- National Research Council of Canada
- Boucherville
- Canada
| | - Ljuboje Lukic
- Life Sciences Division
- National Research Council of Canada
- Boucherville
- Canada
| | - Mojra Janta
- Life Sciences Division
- National Research Council of Canada
- Boucherville
- Canada
| | | | - Teodor Veres
- Life Sciences Division
- National Research Council of Canada
- Boucherville
- Canada
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88
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Ning Y, Cui X, Yang C, Jing F, Bian X, Yi L, Li G. A self-digitization chip integrated with hydration layer for low-cost and robust digital PCR. Anal Chim Acta 2018; 1055:65-73. [PMID: 30782371 DOI: 10.1016/j.aca.2018.12.029] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 11/15/2018] [Accepted: 12/17/2018] [Indexed: 11/19/2022]
Abstract
We present a self-discretization and zero-water-loss microfluidic digital PCR (dPCR) device to enable low-cost and robust quantitative nucleic acid assays. In this device, a thin void is integrated beneath the reaction chamber array. By utilizing the permeability of polydimethylsiloxane (PDMS) film, the integrated void serves a dual function: vacuum "accumulator" and hydration "reservoir". The combination of pre-stored pumping energy and water compensation for evaporation loss enables simple, robust and reliable single-DNA-molecule amplification and detection in 10,000 reactors of picoliter volume. Compared to the conventional degassing PDMS pumps, the vacuum accumulator exhibits superior performance due to more vacuum storage and shorter diffusion distance. We also evaluated the performance of the embedded hydration layer in suppressing evaporation loss at elevated temperatures, and verified that zero-water-loss could be achieved for all reaction chambers in our dPCR chip during thermal cycling. By performing quantitative detection of T790M DNA from 10 to 104 copies/μL, the proposed dPCR chip demonstrated high accuracy and excellent performance for the absolute quantification of the target gene with a dynamic range of 104. The simplicity and robustness of our dPCR chip make it well suited for low-cost molecular diagnostic assays under resource-limited settings.
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Affiliation(s)
- Yongfeng Ning
- Key Laboratory of Optoelectronic Technology and Systems, Ministry of Education, Defense Key Disciplines Lab of Novel Micro-Nano Devices and System Technology, Chongqing University, Chongqing, 400044, China
| | - Xu Cui
- Key Laboratory of Optoelectronic Technology and Systems, Ministry of Education, Defense Key Disciplines Lab of Novel Micro-Nano Devices and System Technology, Chongqing University, Chongqing, 400044, China
| | - Chao Yang
- Key Laboratory of Optoelectronic Technology and Systems, Ministry of Education, Defense Key Disciplines Lab of Novel Micro-Nano Devices and System Technology, Chongqing University, Chongqing, 400044, China
| | - Fengxiang Jing
- Shanghai Turtle Technology Company Limited, Shanghai, 200439, China.
| | - Xiaojun Bian
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, 201306, China
| | - Lin Yi
- Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital & Chongqing Cancer Institute & Chongqing Cancer Hospital, Chongqing, 400030, China
| | - Gang Li
- Key Laboratory of Optoelectronic Technology and Systems, Ministry of Education, Defense Key Disciplines Lab of Novel Micro-Nano Devices and System Technology, Chongqing University, Chongqing, 400044, China.
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89
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Postek W, Gargulinski P, Scheler O, Kaminski TS, Garstecki P. Microfluidic screening of antibiotic susceptibility at a single-cell level shows the inoculum effect of cefotaxime on E. coli. LAB ON A CHIP 2018; 18:3668-3677. [PMID: 30375609 DOI: 10.1039/c8lc00916c] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Measurement of antibiotic susceptibility at the level of single cells is important as it reveals the concentration of an antibiotic that leads to drug resistance in bacterial strains. To date, no solution for large-scale studies of antibiotic susceptibility at the single-cell level has been shown. Here, we present a method for production and separation of emulsions consisting of subnanoliter droplets that allows us to identify each emulsion by their spatial position in the train of emulsions without chemical barcoding. The emulsions of droplets are separated by a third immiscible phase, thus forming large compartments-tankers-each filled with an emulsion of droplet reactors. Each tanker in a train can be set under different reaction conditions for hundreds or thousands of replications of the same reaction. The tankers allow for long term incubation - needed to check for growth of bacteria under a screen of conditions. We use microfluidic tankers to analyze susceptibility to cefotaxime in ca. 1900 replications for each concentration of the antibiotic in one experiment. We test cefotaxime susceptibility for different initial concentrations of bacteria, showing the inoculum effect down to the level of single cells for more than a hundred single-cell events per tanker. Lastly, we use tankers to observe the formation of aggregates of bacteria in the presence of cefotaxime in the increasing concentration of the antibiotic. The microfluidic tankers allow for facile studies of the inoculum effect and antibiotic susceptibility, and constitute an attractive, label-free screening method for a variety of other experiments in chemistry and biology.
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Affiliation(s)
- Witold Postek
- Institute of Physical Chemistry of the Polish Academy of Sciences, ul. Kasprzaka 44/52, 01-224 Warszawa, Poland.
| | - Pawel Gargulinski
- Institute of Physical Chemistry of the Polish Academy of Sciences, ul. Kasprzaka 44/52, 01-224 Warszawa, Poland.
| | - Ott Scheler
- Institute of Physical Chemistry of the Polish Academy of Sciences, ul. Kasprzaka 44/52, 01-224 Warszawa, Poland. and Institute of Molecular and Cell Biology, University of Tartu, Riia 23, 51010 Tartu, Estonia and Department of Chemistry and Biotechnology, TalTech, Akadeemia tee 15, 12618 Tallinn, Estonia
| | - Tomasz S Kaminski
- Institute of Physical Chemistry of the Polish Academy of Sciences, ul. Kasprzaka 44/52, 01-224 Warszawa, Poland.
| | - Piotr Garstecki
- Institute of Physical Chemistry of the Polish Academy of Sciences, ul. Kasprzaka 44/52, 01-224 Warszawa, Poland.
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90
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Segaliny AI, Li G, Kong L, Ren C, Chen X, Wang JK, Baltimore D, Wu G, Zhao W. Functional TCR T cell screening using single-cell droplet microfluidics. LAB ON A CHIP 2018; 18:3733-3749. [PMID: 30397689 PMCID: PMC6279597 DOI: 10.1039/c8lc00818c] [Citation(s) in RCA: 106] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Adoptive T cell transfer, in particular TCR T cell therapy, holds great promise for cancer immunotherapy with encouraging clinical results. However, finding the right TCR T cell clone is a tedious, time-consuming, and costly process. Thus, there is a critical need for single cell technologies to conduct fast and multiplexed functional analyses followed by recovery of the clone of interest. Here, we use droplet microfluidics for functional screening and real-time monitoring of single TCR T cell activation upon recognition of target tumor cells. Notably, our platform includes a tracking system for each clone as well as a sorting procedure with 100% specificity validated by downstream single cell reverse-transcription PCR and sequencing of TCR chains. Our TCR screening prototype will facilitate immunotherapeutic screening and development of T cell therapies.
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MESH Headings
- Antigens, Neoplasm/chemistry
- Antigens, Neoplasm/metabolism
- Cell Line, Tumor
- Equipment Design
- Humans
- Immunotherapy, Adoptive
- Microfluidic Analytical Techniques/instrumentation
- Neoplasms/therapy
- Receptors, Antigen, T-Cell/analysis
- Receptors, Antigen, T-Cell/chemistry
- Receptors, Antigen, T-Cell/metabolism
- Single-Cell Analysis/instrumentation
- Single-Cell Analysis/methods
- T-Lymphocytes/chemistry
- T-Lymphocytes/cytology
- T-Lymphocytes/metabolism
- T-Lymphocytes/transplantation
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Affiliation(s)
- Aude I. Segaliny
- Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA 92697, U.S.A
- Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA 92697, U.S.A
- Chao Family Comprehensive Cancer Center, University of California, Irvine, Irvine, CA 92697, U.S.A
- Edwards Life Sciences Center for Advanced Cardiovascular Technology, University of California, Irvine, Irvine, CA 92697, U.S.A
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA 92697, U.S.A
- Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, U.S.A
| | - Guideng Li
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, U.S.A
- Center of Systems Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, China
- Suzhou Institute of Systems Medicine, Suzhou 215123, China
| | - Lingshun Kong
- Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA 92697, U.S.A
- Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA 92697, U.S.A
- Chao Family Comprehensive Cancer Center, University of California, Irvine, Irvine, CA 92697, U.S.A
- Edwards Life Sciences Center for Advanced Cardiovascular Technology, University of California, Irvine, Irvine, CA 92697, U.S.A
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA 92697, U.S.A
- Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, U.S.A
| | - Ci Ren
- Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA 92697, U.S.A
- Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA 92697, U.S.A
- Chao Family Comprehensive Cancer Center, University of California, Irvine, Irvine, CA 92697, U.S.A
- Edwards Life Sciences Center for Advanced Cardiovascular Technology, University of California, Irvine, Irvine, CA 92697, U.S.A
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA 92697, U.S.A
- Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, U.S.A
| | - Xiaoming Chen
- Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA 92697, U.S.A
- Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA 92697, U.S.A
- Chao Family Comprehensive Cancer Center, University of California, Irvine, Irvine, CA 92697, U.S.A
- Edwards Life Sciences Center for Advanced Cardiovascular Technology, University of California, Irvine, Irvine, CA 92697, U.S.A
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA 92697, U.S.A
- Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, U.S.A
| | - Jessica K. Wang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, U.S.A
| | - David Baltimore
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, U.S.A
| | - Guikai Wu
- Amberstone Biosciences LLC, Irvine, CA 92617, U.S.A
| | - Weian Zhao
- Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA 92697, U.S.A
- Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA 92697, U.S.A
- Chao Family Comprehensive Cancer Center, University of California, Irvine, Irvine, CA 92697, U.S.A
- Edwards Life Sciences Center for Advanced Cardiovascular Technology, University of California, Irvine, Irvine, CA 92697, U.S.A
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA 92697, U.S.A
- Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, U.S.A
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91
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Sreejith KR, Ooi CH, Jin J, Dao DV, Nguyen NT. Digital polymerase chain reaction technology - recent advances and future perspectives. LAB ON A CHIP 2018; 18:3717-3732. [PMID: 30402632 DOI: 10.1039/c8lc00990b] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Digital polymerase chain reaction (dPCR) technology has remained a "hot topic" in the last two decades due to its potential applications in cell biology, genetic engineering, and medical diagnostics. Various advanced techniques have been reported on sample dispersion, thermal cycling and output monitoring of digital PCR. However, a fully automated, low-cost and handheld digital PCR platform has not been reported in the literature. This paper attempts to critically evaluate the recent developments in techniques for sample dispersion, thermal cycling and output evaluation for dPCR. The techniques are discussed in terms of hardware simplicity, portability, cost-effectiveness and suitability for automation. The present paper also discusses the research gaps observed in each step of dPCR and concludes with possible improvements toward portable, low-cost and automatic digital PCR systems.
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Affiliation(s)
- Kamalalayam Rajan Sreejith
- Queensland Micro- and Nanotechnology Centre, Griffith University, 170 Kessels Road, 4111 Queensland, Australia.
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92
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Chi J, Shao C, Du X, Liu H, Gu Z. Generating Microdroplet Array on Photonic Pseudo-paper for Absolute Quantification of Nucleic Acids. ACS APPLIED MATERIALS & INTERFACES 2018; 10:39144-39150. [PMID: 30335348 DOI: 10.1021/acsami.8b11552] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Here, we propose a new platform for digital nucleic acid assay based on a microdroplet array. The hydrophilic-superhydrophobic property of the pseudopaper photonic nitrocellulose substrate is employed to divide an aqueous sample containing the target nucleic acid into hundreds of microdroplets for loop-mediated isothermal amplification (LAMP). The LAMP reaction leads to the production of fluorescent calcein. By counting the number of microdroplets that are fluorescent, the target nucleic acid (i.e., Staphylococcus aureus DNA) with the copy number ranging from 1 to 1000 can be absolutely quantified without using sophisticated microfluidic devices. The effect of fluorescence enhancement attributed to the photonic nitrocellulose can effectively amplify the detection signal and reduce the amplification time. Thus, we believe that the proposed platform for digital nucleic acid assay based on the microdroplet array is promising for rapid and cost-effective bioanalytical applications.
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Affiliation(s)
- Junjie Chi
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering , Southeast University , Nanjing 210096 , China
| | - Changmin Shao
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering , Southeast University , Nanjing 210096 , China
| | - Xin Du
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering , Southeast University , Nanjing 210096 , China
| | - Hong Liu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering , Southeast University , Nanjing 210096 , China
| | - Zhongze Gu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering , Southeast University , Nanjing 210096 , China
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93
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Kaushik AM, Hsieh K, Wang TH. Droplet microfluidics for high-sensitivity and high-throughput detection and screening of disease biomarkers. WILEY INTERDISCIPLINARY REVIEWS. NANOMEDICINE AND NANOBIOTECHNOLOGY 2018; 10:e1522. [PMID: 29797414 PMCID: PMC6185786 DOI: 10.1002/wnan.1522] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 03/02/2018] [Accepted: 03/10/2018] [Indexed: 12/17/2022]
Abstract
Biomarkers are nucleic acids, proteins, single cells, or small molecules in human tissues or biological fluids whose reliable detection can be used to confirm or predict disease and disease states. Sensitive detection of biomarkers is therefore critical in a variety of applications including disease diagnostics, therapeutics, and drug screening. Unfortunately for many diseases, low abundance of biomarkers in human samples and low sample volumes render standard benchtop platforms like 96-well plates ineffective for reliable detection and screening. Discretization of bulk samples into a large number of small volumes (fL-nL) via droplet microfluidic technology offers a promising solution for high-sensitivity and high-throughput detection and screening of biomarkers. Several microfluidic strategies exist for high-throughput biomarker digitization into droplets, and these strategies have been utilized by numerous droplet platforms for nucleic acid, protein, and single-cell detection and screening. While the potential of droplet-based platforms has led to burgeoning interest in droplets, seamless integration of sample preparation technologies and automation of platforms from biological sample to answer remain critical components that can render these platforms useful in the clinical setting in the near future. This article is categorized under: Diagnostic Tools > Biosensing Diagnostic Tools > Diagnostic Nanodevices Therapeutic Approaches and Drug Discovery > Emerging Technologies Therapeutic Approaches and Drug Discovery > Nanomedicine for Infectious Disease.
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Affiliation(s)
| | - Kuangwen Hsieh
- Department of Mechanical Engineering, Johns Hopkins University
| | - Tza-Huei Wang
- Department of Mechanical Engineering, Department of Biomedical Engineering, Johns Hopkins University
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94
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Smartphone-based mobile digital PCR device for DNA quantitative analysis with high accuracy. Biosens Bioelectron 2018; 120:144-152. [DOI: 10.1016/j.bios.2018.08.030] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 08/12/2018] [Accepted: 08/13/2018] [Indexed: 11/21/2022]
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95
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Watanabe M, Kenmotsu H, Ko R, Wakuda K, Ono A, Imai H, Taira T, Naito T, Murakami H, Abe M, Endo M, Nakajima T, Koh Y, Takahashi T. Isolation and molecular analysis of circulating tumor cells from lung cancer patients using a microfluidic chip type cell sorter. Cancer Sci 2018; 109:2539-2548. [PMID: 29900633 PMCID: PMC6113429 DOI: 10.1111/cas.13692] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2018] [Accepted: 05/28/2018] [Indexed: 12/26/2022] Open
Abstract
Circulating tumor cells (CTCs) are a tumor‐derived material utilized for liquid‐based biopsy; however, capturing rare CTCs for further molecular analysis remains technically challenging, especially in non‐small‐cell lung cancer. Here, we report the results of a clinical evaluation of On‐chip Sort, a disposable microfluidic chip‐based cell sorter, for capture and molecular analysis of CTCs from patients with lung adenocarcinoma. Peripheral blood was collected from 30 metastatic lung adenocarcinoma patients to enumerate CTCs using both On‐chip Sort and CellSearch in a blind manner. Captured cells by On‐chip Sort were subjected to further molecular analysis. Peripheral blood samples were also used for detection of EGFR mutations in plasma using droplet digital PCR. Significantly more CTCs were detected by On‐chip Sort (22/30; median 5; range, 0–18 cells/5 mL blood) than by CellSearch (9/30; median, 0; range, 0–12 cells/7.5 mL) (P < 0.01). Thirteen of 30 patients who had a negative CTC count by CellSearch had a positive CTC count by On‐chip Sort. EGFR mutations in CTCs captured by On‐chip Sort were observed in 40.0% (8/20) of patients with EGFR‐mutated primary tumor. EGFR mutations were often observed in 53.3% (8/15) of patients detected in plasma DNA. Expressions of EGFR and vimentin protein on CTCs were also successfully assessed using On‐chip Sort. These results suggest that On‐chip Sort is an efficient method to detect and capture rare CTCs from patients with lung adenocarcinoma that are undetectable with CellSearch. Mutation detection using isolated CTCs remains to be further tackled (UMIN000012488).
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Affiliation(s)
- Masaru Watanabe
- Drug Discovery and Development Division, Shizuoka Cancer Center Research Institute, Shizuoka.,Third Department of Internal Medicine, Wakayama Medical University, Wakayama
| | | | - Ryo Ko
- Division of Thoracic Oncology, Shizuoka Cancer Center, Shizuoka
| | | | - Akira Ono
- Division of Thoracic Oncology, Shizuoka Cancer Center, Shizuoka
| | - Hisao Imai
- Division of Thoracic Oncology, Shizuoka Cancer Center, Shizuoka
| | - Tetsuhiko Taira
- Division of Thoracic Oncology, Shizuoka Cancer Center, Shizuoka
| | - Tateaki Naito
- Division of Thoracic Oncology, Shizuoka Cancer Center, Shizuoka
| | | | - Masato Abe
- Division of Diagnostic Pathology, Shizuoka Cancer Center, Shizuoka
| | - Masahiro Endo
- Division of Diagnostic Radiology, Shizuoka Cancer Center, Shizuoka, Japan
| | - Takashi Nakajima
- Division of Diagnostic Pathology, Shizuoka Cancer Center, Shizuoka
| | - Yasuhiro Koh
- Drug Discovery and Development Division, Shizuoka Cancer Center Research Institute, Shizuoka.,Third Department of Internal Medicine, Wakayama Medical University, Wakayama
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96
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Miller BS, Parolo C, Turbé V, Keane CE, Gray ER, McKendry RA. Quantifying Biomolecular Binding Constants using Video Paper Analytical Devices. Chemistry 2018; 24:9783-9787. [PMID: 29772094 PMCID: PMC6055620 DOI: 10.1002/chem.201802394] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Indexed: 01/08/2023]
Abstract
A novel ultra-low-cost biochemical analysis platform to quantify protein dissociation binding constants and kinetics using paper microfluidics is reported. This approach marries video imaging with one of humankind's oldest materials: paper, requiring no large, expensive laboratory equipment, complex microfluidics or external power. Temporal measurements of nanoparticle-antibody conjugates binding on paper is found to follow the Langmuir Adsorption Model. This is exploited to measure a series of antibody-antigen dissociation constants on paper, showing excellent agreement with a gold-standard benchtop interferometer. The concept is demonstrated with a camera and low-end smartphone, 500-fold cheaper than the reference method, and can be multiplexed to measure ten reactions in parallel. These findings will help to widen access to quantitative analytical biochemistry, for diverse applications spanning disease diagnostics, drug discovery, and environmental analysis in resource-limited settings.
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Affiliation(s)
- Benjamin S. Miller
- London Centre for NanotechnologyUniversity College London17–19 Gordon StreetLondonWC1H 0AHUK
- Division of MedicineUniversity College London, Cruciform BuildingGower StreetLondonWC1E 6BTUK
| | - Claudio Parolo
- London Centre for NanotechnologyUniversity College London17–19 Gordon StreetLondonWC1H 0AHUK
| | - Valérian Turbé
- London Centre for NanotechnologyUniversity College London17–19 Gordon StreetLondonWC1H 0AHUK
- Division of MedicineUniversity College London, Cruciform BuildingGower StreetLondonWC1E 6BTUK
| | - Candice E. Keane
- London Centre for NanotechnologyUniversity College London17–19 Gordon StreetLondonWC1H 0AHUK
- Division of MedicineUniversity College London, Cruciform BuildingGower StreetLondonWC1E 6BTUK
| | - Eleanor R. Gray
- London Centre for NanotechnologyUniversity College London17–19 Gordon StreetLondonWC1H 0AHUK
| | - Rachel A. McKendry
- London Centre for NanotechnologyUniversity College London17–19 Gordon StreetLondonWC1H 0AHUK
- Division of MedicineUniversity College London, Cruciform BuildingGower StreetLondonWC1E 6BTUK
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97
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Quan PL, Sauzade M, Brouzes E. dPCR: A Technology Review. SENSORS (BASEL, SWITZERLAND) 2018; 18:E1271. [PMID: 29677144 PMCID: PMC5948698 DOI: 10.3390/s18041271] [Citation(s) in RCA: 333] [Impact Index Per Article: 55.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2018] [Revised: 04/13/2018] [Accepted: 04/15/2018] [Indexed: 12/17/2022]
Abstract
Digital Polymerase Chain Reaction (dPCR) is a novel method for the absolute quantification of target nucleic acids. Quantification by dPCR hinges on the fact that the random distribution of molecules in many partitions follows a Poisson distribution. Each partition acts as an individual PCR microreactor and partitions containing amplified target sequences are detected by fluorescence. The proportion of PCR-positive partitions suffices to determine the concentration of the target sequence without a need for calibration. Advances in microfluidics enabled the current revolution of digital quantification by providing efficient partitioning methods. In this review, we compare the fundamental concepts behind the quantification of nucleic acids by dPCR and quantitative real-time PCR (qPCR). We detail the underlying statistics of dPCR and explain how it defines its precision and performance metrics. We review the different microfluidic digital PCR formats, present their underlying physical principles, and analyze the technological evolution of dPCR platforms. We present the novel multiplexing strategies enabled by dPCR and examine how isothermal amplification could be an alternative to PCR in digital assays. Finally, we determine whether the theoretical advantages of dPCR over qPCR hold true by perusing studies that directly compare assays implemented with both methods.
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Affiliation(s)
- Phenix-Lan Quan
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY 11794, USA.
| | - Martin Sauzade
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY 11794, USA.
| | - Eric Brouzes
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY 11794, USA.
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794, USA.
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98
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Hayat Z, El Abed AI. High-Throughput Optofluidic Acquisition of Microdroplets in Microfluidic Systems. MICROMACHINES 2018; 9:E183. [PMID: 30424116 PMCID: PMC6187520 DOI: 10.3390/mi9040183] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 03/26/2018] [Accepted: 04/04/2018] [Indexed: 12/24/2022]
Abstract
Droplet optofluidics technology aims at manipulating the tiny volume of fluids confined in micro-droplets with light, while exploiting their interaction to create "digital" micro-systems with highly significant scientific and technological interests. Manipulating droplets with light is particularly attractive since the latter provides wavelength and intensity tunability, as well as high temporal and spatial resolution. In this review study, we focus mainly on recent methods developed in order to monitor real-time analysis of droplet size and size distribution, active merging of microdroplets using light, or to use microdroplets as optical probes.
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Affiliation(s)
- Zain Hayat
- Laboratoire de Photonique Quantique et Moléculaire, UMR 8537, Ecole Normale Supérieure Paris Saclay, CentraleSupélec, CNRS, Université Paris-Saclay, 61 avenue du Président Wilson, 94235 Cachan, France.
| | - Abdel I El Abed
- Laboratoire de Photonique Quantique et Moléculaire, UMR 8537, Ecole Normale Supérieure Paris Saclay, CentraleSupélec, CNRS, Université Paris-Saclay, 61 avenue du Président Wilson, 94235 Cachan, France.
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99
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Scanga R, Chrastecka L, Mohammad R, Meadows A, Quan PL, Brouzes E. Click Chemistry Approaches to Expand the Repertoire of PEG-based Fluorinated Surfactants for Droplet Microfluidics. RSC Adv 2018; 8:12960-12974. [PMID: 31592185 PMCID: PMC6779154 DOI: 10.1039/c8ra01254g] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
We report the novel and simplified synthesis of fluorinated surfactants for droplet microfluidics. The range of applications of droplet microfluidics has greatly expanded during the last decade thanks to its ability to manipulate and process tiny amount of sample and reagents at high throughput in independent reactors. A critical component of the technology is the formulation of the immiscible oil phase that contains surfactants to stabilize droplets. The success of droplet microfluidics relies mostly on a single fluorinated formulation that uses a PFPE–PEG triblock surfactant. The synthesis of this surfactant is laborious and requires skills in synthetic chemistry preventing the wider community to explore the synthesis of surfactants with alternate structures. We sought to provide a simplified synthesis for novel PFPE–PEG surfactants based on click chemistry approaches such as copper-catalyzed azide-alkyne cycloaddition (CuAAC) and UV-activated thiol–yne reactions. Our strategy is based on converting a moisture sensitive intermediate typically used in the synthesis of the triblock PFPE–PEG surfactant into a stable and click ready molecule. We successfully combined that fluorinated tail with differently functionalized PEG and glycerol ethoxylate molecules to generate surfactants with diverse structures via CuACC and thiol–yne reactions. We report the characterization, biocompatibility and ability to stabilize emulsions of those surfactants, as well as the unique advantages and challenges of the strategy. Click-synthesis of fluorinated surfactants for droplet microfluidics.![]()
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Affiliation(s)
- Randall Scanga
- Department of chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Lucie Chrastecka
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, New York, USA
| | - Ridhwan Mohammad
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, New York, USA
| | - Austin Meadows
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, New York, USA
| | - Phenix-Lan Quan
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, New York, USA
| | - Eric Brouzes
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, New York, USA.,Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York, USA
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100
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Zhang W, Li N, Koga D, Zhang Y, Zeng H, Nakajima H, Lin JM, Uchiyama K. Inkjet Printing Based Droplet Generation for Integrated Online Digital Polymerase Chain Reaction. Anal Chem 2018; 90:5329-5334. [DOI: 10.1021/acs.analchem.8b00463] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Weifei Zhang
- Department of Applied Chemistry, Graduate School of Urban Environmental Sciences, Tokyo Metropolitan University, Minamiohsawa, Hachioji, Tokyo 192-0397, Japan
- Department of Chemistry, Beijing Key Laboratory of Microanalytical Methods and Instrumentation, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing 100084, China
| | - Nan Li
- Department of Chemistry, Beijing Key Laboratory of Microanalytical Methods and Instrumentation, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing 100084, China
| | - Daisuke Koga
- Department of Applied Chemistry, Graduate School of Urban Environmental Sciences, Tokyo Metropolitan University, Minamiohsawa, Hachioji, Tokyo 192-0397, Japan
| | - Yong Zhang
- Department of Applied Chemistry, Graduate School of Urban Environmental Sciences, Tokyo Metropolitan University, Minamiohsawa, Hachioji, Tokyo 192-0397, Japan
| | - Hulie Zeng
- Department of Applied Chemistry, Graduate School of Urban Environmental Sciences, Tokyo Metropolitan University, Minamiohsawa, Hachioji, Tokyo 192-0397, Japan
| | - Hizuru Nakajima
- Department of Applied Chemistry, Graduate School of Urban Environmental Sciences, Tokyo Metropolitan University, Minamiohsawa, Hachioji, Tokyo 192-0397, Japan
| | - Jin-Ming Lin
- Department of Chemistry, Beijing Key Laboratory of Microanalytical Methods and Instrumentation, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing 100084, China
| | - Katsumi Uchiyama
- Department of Applied Chemistry, Graduate School of Urban Environmental Sciences, Tokyo Metropolitan University, Minamiohsawa, Hachioji, Tokyo 192-0397, Japan
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