1
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Dortaj H, Amani AM, Tayebi L, Azarpira N, Ghasemi Toudeshkchouei M, Hassanpour-Dehnavi A, Karami N, Abbasi M, Najafian-Najafabadi A, Zarei Behjani Z, Vaez A. Droplet-based microfluidics: an efficient high-throughput portable system for cell encapsulation. J Microencapsul 2024; 41:479-501. [PMID: 39077800 DOI: 10.1080/02652048.2024.2382744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 07/17/2024] [Indexed: 07/31/2024]
Abstract
One of the goals of tissue engineering and regenerative medicine is restoring primary living tissue function by manufacturing a 3D microenvironment. One of the main challenges is protecting implanted non-autologous cells or tissues from the host immune system. Cell encapsulation has emerged as a promising technique for this purpose. It involves entrapping cells in biocompatible and semi-permeable microcarriers made from natural or synthetic polymers that regulate the release of cellular secretions. In recent years, droplet-based microfluidic systems have emerged as powerful tools for cell encapsulation in tissue engineering and regenerative medicine. These systems offer precise control over droplet size, composition, and functionality, allowing for creating of microenvironments that closely mimic native tissue. Droplet-based microfluidic systems have extensive applications in biotechnology, medical diagnosis, and drug discovery. This review summarises the recent developments in droplet-based microfluidic systems and cell encapsulation techniques, as well as their applications, advantages, and challenges in biology and medicine. The integration of these technologies has the potential to revolutionise tissue engineering and regenerative medicine by providing a precise and controlled microenvironment for cell growth and differentiation. By overcoming the immune system's challenges and enabling the release of cellular secretions, these technologies hold great promise for the future of regenerative medicine.
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Affiliation(s)
- Hengameh Dortaj
- Department of Tissue Engineering and Applied Cell Sciences, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Ali Mohammad Amani
- Department of Medical Nanotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Lobat Tayebi
- Marquette University School of Dentistry, Milwaukee, WI, USA
| | - Negar Azarpira
- Transplant Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | | | - Ashraf Hassanpour-Dehnavi
- Tissue Engineering Lab, Department of Anatomical Sciences, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Neda Karami
- Diagnostic Laboratory Sciences and Technology Research Center, School of Paramedical Sciences, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Milad Abbasi
- Department of Medical Nanotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Atefeh Najafian-Najafabadi
- Department of Tissue Engineering and Applied Cell Sciences, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Zeinab Zarei Behjani
- Department of Tissue Engineering and Applied Cell Sciences, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Ahmad Vaez
- Department of Tissue Engineering and Applied Cell Sciences, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
- Biotechnology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
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2
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Wu Z, Han S, Meng H, Lian D, Wu T, Chu W, Li H, Ning M, Wang B, Gao X, Xu S, Ren J, Yang X. Investigation of piezoelectric printing devices for oil-free and on-demand picolitre monodisperse droplet generation. Sci Rep 2024; 14:17104. [PMID: 39048610 PMCID: PMC11269629 DOI: 10.1038/s41598-024-67849-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Accepted: 07/16/2024] [Indexed: 07/27/2024] Open
Abstract
Picolitre monodisperse droplet printing technology has important applications in biochemistry, such as accounting for quantitative analysis and single-cell analysis, and can be used for parallel high-throughput analysis of biomarkers and chemicals. However, commonly used droplet generation devices require complex control systems or customised microfluidic chips, making them costly and difficult for researchers to operate. Additionally, generating picolitre monodisperse droplets with microfluidic devices necessitates the introduction of an oil phase to block and separate the liquid. This requirement can reduce the throughput of the target droplets and cause cell contamination, hindering the adoption of this technology. By employing a common 1-mm-diameter capillary in the laboratory in combination with a piezoelectric transducer, we have achieved on-demand picolitre droplet printing of less than 100 pL in an oil-free environment. The device was found to be biocompatible with K562 cells. This approach is less costly, offers greater operational freedom, and is easier to integrate with other downstream assay modules or even handheld cell-printing devices. This study holds great potential for application in areas such as single-cell analysis, cell sampling, and pharmaceutical analysis.
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Affiliation(s)
- Zhenlin Wu
- School of Optoelectronic Engineering and Instrumentation Science, Dalian University of Technology, Dalian, 116024, China
| | - Shaoshuai Han
- School of Optoelectronic Engineering and Instrumentation Science, Dalian University of Technology, Dalian, 116024, China
| | - Hu Meng
- School of Optoelectronic Engineering and Instrumentation Science, Dalian University of Technology, Dalian, 116024, China
| | - Di Lian
- School of Optoelectronic Engineering and Instrumentation Science, Dalian University of Technology, Dalian, 116024, China
| | - Tongfei Wu
- School of Optoelectronic Engineering and Instrumentation Science, Dalian University of Technology, Dalian, 116024, China
| | - Wenjie Chu
- School of Optoelectronic Engineering and Instrumentation Science, Dalian University of Technology, Dalian, 116024, China
| | - He Li
- School of Optoelectronic Engineering and Instrumentation Science, Dalian University of Technology, Dalian, 116024, China
| | - Mengting Ning
- School of Optoelectronic Engineering and Instrumentation Science, Dalian University of Technology, Dalian, 116024, China
| | - Bingjie Wang
- School of Optoelectronic Engineering and Instrumentation Science, Dalian University of Technology, Dalian, 116024, China
| | - Xijing Gao
- School of Optoelectronic Engineering and Instrumentation Science, Dalian University of Technology, Dalian, 116024, China
| | - Shizhao Xu
- Dalian Municipal Central Hospital, Central Hospital of Dalian University of Technology, Dalian, 116024, China
| | - Jun Ren
- Liaoning Key Laboratory of Molecular Recognition and Imaging, School of Bioengineering, Dalian University of Technology, Dalian, 116024, China.
| | - Xin Yang
- Department of Electrical and Electronics Engineering, School of Engineering, Cardiff University, Cardiff, CF10 3AT, UK
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3
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Jiang Z, Shi H, Tang X, Qin J. Recent advances in droplet microfluidics for single-cell analysis. Trends Analyt Chem 2023. [DOI: 10.1016/j.trac.2023.116932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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4
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Anyaduba TD, Otoo JA, Schlappi TS. Picoliter Droplet Generation and Dense Bead-in-Droplet Encapsulation via Microfluidic Devices Fabricated via 3D Printed Molds. MICROMACHINES 2022; 13:1946. [PMID: 36363966 PMCID: PMC9695966 DOI: 10.3390/mi13111946] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 11/04/2022] [Accepted: 11/05/2022] [Indexed: 06/16/2023]
Abstract
Picoliter-scale droplets have many applications in chemistry and biology, such as biomolecule synthesis, drug discovery, nucleic acid quantification, and single cell analysis. However, due to the complicated processes used to fabricate microfluidic channels, most picoliter (pL) droplet generation methods are limited to research in laboratories with cleanroom facilities and complex instrumentation. The purpose of this work is to investigate a method that uses 3D printing to fabricate microfluidic devices that can generate droplets with sizes <100 pL and encapsulate single dense beads mechanistically. Our device generated monodisperse droplets as small as ~48 pL and we demonstrated the usefulness of this droplet generation technique in biomolecule analysis by detecting Lactobacillus acidophillus 16s rRNA via digital loop-mediated isothermal amplification (dLAMP). We also designed a mixer that can be integrated into a syringe to overcome dense bead sedimentation and found that the bead-in-droplet (BiD) emulsions created from our device had <2% of the droplets populated with more than 1 bead. This study will enable researchers to create devices that generate pL-scale droplets and encapsulate dense beads with inexpensive and simple instrumentation (3D printer and syringe pump). The rapid prototyping and integration ability of this module with other components or processes can accelerate the development of point-of-care microfluidic devices that use droplet-bead emulsions to analyze biological or chemical samples with high throughput and precision.
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Affiliation(s)
- Tochukwu D. Anyaduba
- Keck Graduate Institute, Riggs School of Applied Life Sciences, Claremont, CA 91711, USA
- Abbott Rapid Diagnostics, 4545 Towne Center Ct, La Jolla, San Diego, CA 92121, USA
| | - Jonas A. Otoo
- Keck Graduate Institute, Riggs School of Applied Life Sciences, Claremont, CA 91711, USA
| | - Travis S. Schlappi
- Keck Graduate Institute, Riggs School of Applied Life Sciences, Claremont, CA 91711, USA
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5
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Miwa H, Dimatteo R, de Rutte J, Ghosh R, Di Carlo D. Single-cell sorting based on secreted products for functionally defined cell therapies. MICROSYSTEMS & NANOENGINEERING 2022; 8:84. [PMID: 35874174 PMCID: PMC9303846 DOI: 10.1038/s41378-022-00422-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 05/18/2022] [Accepted: 06/13/2022] [Indexed: 05/13/2023]
Abstract
Cell therapies have emerged as a promising new class of "living" therapeutics over the last decade and have been particularly successful for treating hematological malignancies. Increasingly, cellular therapeutics are being developed with the aim of treating almost any disease, from solid tumors and autoimmune disorders to fibrosis, neurodegenerative disorders and even aging itself. However, their therapeutic potential has remained limited due to the fundamental differences in how molecular and cellular therapies function. While the structure of a molecular therapeutic is directly linked to biological function, cells with the same genetic blueprint can have vastly different functional properties (e.g., secretion, proliferation, cell killing, migration). Although there exists a vast array of analytical and preparative separation approaches for molecules, the functional differences among cells are exacerbated by a lack of functional potency-based sorting approaches. In this context, we describe the need for next-generation single-cell profiling microtechnologies that allow the direct evaluation and sorting of single cells based on functional properties, with a focus on secreted molecules, which are critical for the in vivo efficacy of current cell therapies. We first define three critical processes for single-cell secretion-based profiling technology: (1) partitioning individual cells into uniform compartments; (2) accumulating secretions and labeling via reporter molecules; and (3) measuring the signal associated with the reporter and, if sorting, triggering a sorting event based on these reporter signals. We summarize recent academic and commercial technologies for functional single-cell analysis in addition to sorting and industrial applications of these technologies. These approaches fall into three categories: microchamber, microfluidic droplet, and lab-on-a-particle technologies. Finally, we outline a number of unmet needs in terms of the discovery, design and manufacturing of cellular therapeutics and how the next generation of single-cell functional screening technologies could allow the realization of robust cellular therapeutics for all patients.
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Affiliation(s)
- Hiromi Miwa
- Department of Bioengineering, University of California - Los Angeles, Los Angeles, CA 90095 USA
| | - Robert Dimatteo
- Department of Chemical and Biomolecular Engineering, University of California - Los Angeles, Los Angeles, CA 90095 USA
| | - Joseph de Rutte
- Department of Bioengineering, University of California - Los Angeles, Los Angeles, CA 90095 USA
- Partillion Bioscience, Los Angeles, CA 90095 USA
| | - Rajesh Ghosh
- Department of Bioengineering, University of California - Los Angeles, Los Angeles, CA 90095 USA
| | - Dino Di Carlo
- Department of Bioengineering, University of California - Los Angeles, Los Angeles, CA 90095 USA
- Department of Mechanical and Aerospace Engineering, University of California - Los Angeles, Los Angeles, CA 90095 USA
- California NanoSystems Institute (CNSI), University of California - Los Angeles, Los Angeles, CA 90095 USA
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6
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Chen Z, Kheiri S, Young EWK, Kumacheva E. Trends in Droplet Microfluidics: From Droplet Generation to Biomedical Applications. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:6233-6248. [PMID: 35561292 DOI: 10.1021/acs.langmuir.2c00491] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Over the past decade, droplet microfluidics has attracted growing interest in biology, medicine, and engineering. In this feature article, we review the advances in droplet microfluidics, primarily focusing on the research conducted by our group. Starting from the introduction to the mechanisms of microfluidic droplet formation and the strategies for cell encapsulation in droplets, we then focus on droplet transformation into microgels. Furthermore, we review three biomedical applications of droplet microfluidics, that is, 3D cell culture, single-cell analysis, and in vitro organ and disease modeling. We conclude with our perspective on future directions in the development of droplet microfluidics for biomedical applications.
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Affiliation(s)
- Zhengkun Chen
- Department of Chemistry, University of Toronto, 80 Saint George Street, Toronto, Ontario, Canada M5S 3H6
| | - Sina Kheiri
- Department of Mechanical and Industrial Engineering, University of Toronto, 5 King's College Road, Toronto, Ontario, Canada, M5S 3G8
| | - Edmond W K Young
- Department of Mechanical and Industrial Engineering, University of Toronto, 5 King's College Road, Toronto, Ontario, Canada, M5S 3G8
- Institute of Biomedical Engineering, University of Toronto, Roseburgh Building, 164 College Street, Toronto, Ontario, Canada M5S 3G9
| | - Eugenia Kumacheva
- Department of Chemistry, University of Toronto, 80 Saint George Street, Toronto, Ontario, Canada M5S 3H6
- Institute of Biomedical Engineering, University of Toronto, Roseburgh Building, 164 College Street, Toronto, Ontario, Canada M5S 3G9
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario, Canada M5S 3E5
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7
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Hatori MN, Modavi C, Xu P, Weisgerber D, Abate AR. Dual-layered hydrogels allow complete genome recovery with nucleic acid cytometry. Biotechnol J 2022; 17:e2100483. [PMID: 35088927 PMCID: PMC9208836 DOI: 10.1002/biot.202100483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 12/09/2021] [Accepted: 12/09/2021] [Indexed: 11/09/2022]
Abstract
Targeting specific cells for sequencing is important for applications in cancer, microbiology, and infectious disease. Nucleic acid cytometry is a powerful approach for accomplishing this because it allows specific cells to be isolated based on sequence biomarkers that are otherwise impossible to detect. However, existing methods require specialized microfluidic devices, limiting adoption. Here, we describe a modified workflow that uses particle-templated emulsification and flow cytometry to conduct the essential steps of cell detection and sorting normally accomplished by microfluidics. Our microfluidic-free workflow allows facile isolation and sequencing of cells, viruses, and nucleic acids and thus provides a powerful enrichment approach for targeted sequencing applications. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Makiko N Hatori
- Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biosciences, University of California, San Francisco, CA, 94158, USA
| | - Cyrus Modavi
- Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biosciences, University of California, San Francisco, CA, 94158, USA
| | - Peng Xu
- Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biosciences, University of California, San Francisco, CA, 94158, USA
| | - Daniel Weisgerber
- Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biosciences, University of California, San Francisco, CA, 94158, USA
| | - Adam R Abate
- Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biosciences, University of California, San Francisco, CA, 94158, USA.,Chan Zuckerberg Biohub, San Francisco, CA, 94158, USA
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8
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Ghaznavi A, Lin Y, Douvidzon M, Szmelter A, Rodrigues A, Blackman M, Eddington D, Carmon T, Deych L, Yang L, Xu J. A Monolithic 3D Printed Axisymmetric Co-Flow Single and Compound Emulsion Generator. MICROMACHINES 2022; 13:188. [PMID: 35208313 PMCID: PMC8877394 DOI: 10.3390/mi13020188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 01/12/2022] [Accepted: 01/12/2022] [Indexed: 11/24/2022]
Abstract
We report a microfluidic droplet generator which can produce single and compound droplets using a 3D axisymmetric co-flow structure. The design considered for the fabrication of the device integrated a user-friendly and cost-effective 3D printing process. To verify the performance of the device, single and compound emulsions of deionized water and mineral oil were generated and their features such as size, generation frequency, and emulsion structures were successfully characterized. In addition, the generation of bio emulsions such as alginate and collagen aqueous droplets in mineral oil was demonstrated in this study. Overall, the monolithic 3D printed axisymmetric droplet generator could offer any user an accessible and easy-to-utilize device for the generation of single and compound emulsions.
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Affiliation(s)
- Amirreza Ghaznavi
- Department of Mechanical and Industrial Engineering, University of Illinois at Chicago, Chicago, IL 60607, USA;
| | - Yang Lin
- Department of Mechanical, Industrial and Systems Engineering, University of Rhode Island, Kingston, RI 02881, USA;
| | - Mark Douvidzon
- Physics Department and Solid-State Institute, Technion, Haifa 3200000, Israel;
| | - Adam Szmelter
- Department of Biomedical Engineering, University of Illinois at Chicago, Chicago, IL 60607, USA; (A.S.); (A.R.); (D.E.)
| | - Alannah Rodrigues
- Department of Biomedical Engineering, University of Illinois at Chicago, Chicago, IL 60607, USA; (A.S.); (A.R.); (D.E.)
| | - Malik Blackman
- Department of Mechanical Engineering, Carnegie Mellon University, Pittsburgh, PA 15213, USA;
| | - David Eddington
- Department of Biomedical Engineering, University of Illinois at Chicago, Chicago, IL 60607, USA; (A.S.); (A.R.); (D.E.)
| | - Tal Carmon
- School of Electrical Engineering, Tel Aviv University, Tel Aviv-Yafo 6997801, Israel;
| | - Lev Deych
- Physics Department, Queens College of CUNY, New York, NY 11367, USA;
| | - Lan Yang
- Department of Electrical and Systems Engineering, Washington University, St. Louis, MO 63130, USA;
| | - Jie Xu
- Department of Mechanical and Industrial Engineering, University of Illinois at Chicago, Chicago, IL 60607, USA;
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9
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Zachos I, Genth R, Sutiono S, Marczynski M, Lieleg O, Sieber V. Hot Flows: Evolving an Archaeal Glucose Dehydrogenase for Ultrastable Carba-NADP+ Using Microfluidics at Elevated Temperatures. ACS Catal 2022. [DOI: 10.1021/acscatal.1c04320] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Ioannis Zachos
- Chair of Chemistry of Biogenic Resources, Technical University of Munich, Campus Straubing for Biotechnology and Sustainability, Schulgasse 16, Straubing 94315, Germany
| | - Robert Genth
- Chair of Chemistry of Biogenic Resources, Technical University of Munich, Campus Straubing for Biotechnology and Sustainability, Schulgasse 16, Straubing 94315, Germany
| | - Samuel Sutiono
- Chair of Chemistry of Biogenic Resources, Technical University of Munich, Campus Straubing for Biotechnology and Sustainability, Schulgasse 16, Straubing 94315, Germany
| | - Matthias Marczynski
- TUM School of Engineering and Design, Department of Materials Engineering, Technical University of Munich, Boltzmannstraße 15, Garching 85748, Germany
- Center for Functional Protein Assemblies, Technical University of Munich, Ernst-Otto-Fischer Straße 8, Garching 85748, Germany
| | - Oliver Lieleg
- TUM School of Engineering and Design, Department of Materials Engineering, Technical University of Munich, Boltzmannstraße 15, Garching 85748, Germany
- Center for Functional Protein Assemblies, Technical University of Munich, Ernst-Otto-Fischer Straße 8, Garching 85748, Germany
| | - Volker Sieber
- Chair of Chemistry of Biogenic Resources, Technical University of Munich, Campus Straubing for Biotechnology and Sustainability, Schulgasse 16, Straubing 94315, Germany
- Catalytic Research Center, Technical University of Munich, Ernst-Otto-Fischer-Straße 1, Garching 85748, Germany
- SynBiofoundry@TUM, Technical University of Munich, Straubing 94315, Germany
- School of Chemistry and Molecular Biosciences, The University of Queensland, 68 Copper Road, St. Lucia 4072, Australia
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10
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Shi N, Mohibullah M, Easley CJ. Active Flow Control and Dynamic Analysis in Droplet Microfluidics. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2021; 14:133-153. [PMID: 33979546 PMCID: PMC8956363 DOI: 10.1146/annurev-anchem-122120-042627] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Droplet-based microfluidics has emerged as an important subfield within the microfluidic and general analytical communities. Indeed, several unique applications such as digital assay readout and single-cell sequencing now have commercial systems based on droplet microfluidics. Yet there remains room for this research area to grow. To date, most analytical readouts are optical in nature, relatively few studies have integrated sample preparation, and passive means for droplet formation and manipulation have dominated the field. Analytical scientists continue to expand capabilities by developing droplet-compatible method adaptations, for example, by interfacing to mass spectrometers or automating droplet sampling for temporally resolved analysis. In this review, we highlight recently developed fluidic control techniques and unique integrations of analytical methodology with droplet microfluidics-focusing on automation and the connections to analog/digital domains-and we conclude by offering a perspective on current challenges and future applications.
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Affiliation(s)
- Nan Shi
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849, USA;
| | - Md Mohibullah
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849, USA;
| | - Christopher J Easley
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849, USA;
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11
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Komazaki Y, Hirama H, Uemura S, Fuchigami K, Torii T. Glass Capillary Microfluidic Device Utilizing Pipette Tips for Droplet Formation. CHEM LETT 2021. [DOI: 10.1246/cl.210144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Yusuke Komazaki
- Sensing System Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Central 5-1, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8565, Japan
| | - Hirotada Hirama
- Sensing System Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Central 5-1, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8565, Japan
| | - Sei Uemura
- Sensing System Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Central 5-1, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8565, Japan
| | - Kiyomi Fuchigami
- Shofu Inc., 11 Kamitakamatsu-cho, Fukuine, Higashiyama-ku, Kyoto 605-0983, Japan
| | - Toru Torii
- Future Center Initiative, The University of Tokyo, 148-4-4 Wakashiba, Kashiwa, Chiba 277-0871, Japan
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12
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Lou Q, Ma Y, Zhao SP, Du GS, Fang Q. A flexible and cost-effective manual droplet operation platform for miniaturized cell assays and single cell analysis. Talanta 2021; 224:121874. [PMID: 33379083 DOI: 10.1016/j.talanta.2020.121874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Revised: 11/01/2020] [Accepted: 11/03/2020] [Indexed: 11/27/2022]
Abstract
Herein, we developed a flexible and cost-effective manual droplet operation system (MDOS) for performing miniaturized cell assays as well as single cell analysis. The MDOS consists of a manual x-y-z translation stage for liquid transferring and switching, a high-precision syringe pump for liquid driving and metering, a tapered capillary probe for droplet manipulation, a droplet array chip for droplet loading and reaction, sample/reagent reservoirs for storage, and a microscope for droplet observation, with a total expense of only $4,000. By using the flexible combination of three elementary operations of the x-y-z stage's moving and the pump's aspirating and depositing, the MDOS can manually achieve multiple droplet handling operations in the nanoliter to picoliter range, including droplet generation, assembling, fusion, diluting, and splitting. On this basis, multiple cell-related operations could be performed, such as nanoliter-scale in-droplet cell culture, cell coculture, drug stimulation, cell washing, and cell staining, as well as formation of picoliter single-cell droplets. The feasibility and flexibility of the MDOS was demonstrated in multi-mode miniaturized cell assays, including cell-based drug test, first-pass effect assay, and single-cell enzyme assay. The MDOS with the features of low cost, easy to build and flexible to use, could provide a promising alternative for performing miniaturized assays in routine laboratories, in addition to conventional microfluidic chip-based systems and automated robot systems.
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Affiliation(s)
- Qi Lou
- Institute of Microanalytical Systems, Department of Chemistry, Key Lab for Biomedical Engineering of Ministry of Education, Zhejiang University, Hangzhou, 310058, China
| | - Yan Ma
- Institute of Microanalytical Systems, Department of Chemistry, Key Lab for Biomedical Engineering of Ministry of Education, Zhejiang University, Hangzhou, 310058, China
| | - Shi-Ping Zhao
- Institute of Microanalytical Systems, Department of Chemistry, Key Lab for Biomedical Engineering of Ministry of Education, Zhejiang University, Hangzhou, 310058, China
| | - Guan-Sheng Du
- Institute of Microanalytical Systems, Department of Chemistry, Key Lab for Biomedical Engineering of Ministry of Education, Zhejiang University, Hangzhou, 310058, China
| | - Qun Fang
- Institute of Microanalytical Systems, Department of Chemistry, Key Lab for Biomedical Engineering of Ministry of Education, Zhejiang University, Hangzhou, 310058, China.
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13
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Soga N, Ota A, Nakajima K, Watanabe R, Ueno H, Noji H. Monodisperse Liposomes with Femtoliter Volume Enable Quantitative Digital Bioassays of Membrane Transporters and Cell-Free Gene Expression. ACS NANO 2020; 14:11700-11711. [PMID: 32864949 DOI: 10.1021/acsnano.0c04354] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Digital bioassays have emerged as a new category of bioanalysis. However, digital bioassays for membrane transporter proteins have not been well established yet despite high demands in molecular physiology and molecular pharmacology due to the lack of biologically functional monodisperse liposomes with femtoliter volumes. Here, we established a simple and robust method to produce femtoliter-sized liposomes (femto-liposomes). We prepared 106 monodispersed water-in-oil droplets stabilized by a lipid monolayer using a polyethylene glycol-coated femtoliter reactor array device. Droplets were subjected to the optimized emulsion transfer process for femto-liposome production. Liposomes were monodispersed (coefficient of variation = 5-15%) and had suitable diameter (0.6-5.3 μm) and uniform volumes of subfemtoliter or a few femtoliters; thus, they were termed uniform femto-liposomes. The unilamellarity of uniform femto-liposomes allowed quantitative single-molecule analysis of passive and active transporter proteins: α-hemolysin and FoF1-ATPase. Digital gene expression in uniform femto-liposomes (cell-free transcription and translation from single DNA molecules) was also demonstrated, showing the versatility of digital assays for membrane transporter proteins and cell-free synthetic biology.
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Affiliation(s)
- Naoki Soga
- Department of Applied Chemistry, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Akira Ota
- Department of Applied Chemistry, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Kota Nakajima
- Department of Applied Chemistry, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Rikiya Watanabe
- Department of Applied Chemistry, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
- PRIME, Japan Agency for Medical Research and Development, 1-7-1 Otemachi, Chiyoda-ku, Tokyo 100-0004, 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
| | - 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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14
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Siu RHP, Liu Y, Chan KHY, Ridzewski C, Slaughter LS, Wu AR. Optimization of on-bead emulsion polymerase chain reaction based on single particle analysis. Talanta 2020; 221:121593. [PMID: 33076127 DOI: 10.1016/j.talanta.2020.121593] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 08/20/2020] [Accepted: 08/26/2020] [Indexed: 10/23/2022]
Abstract
Emulsion polymerase chain reaction (ePCR) enables parallel amplification of millions of different DNA molecules while avoiding bias and chimeric byproducts, essential criteria for applications including next generation sequencing, aptamer selection, and protein-DNA interaction studies. Despite these advantages, ePCR remains underused due to the lack of optimal starting conditions, straightforward methods to evaluate success, and guidelines for tuning the reaction. This knowledge has been elusive for bulk emulsion generation methods, such as stirring and vortexing, the only methods that can emulsify libraries of ≥108 sequences within minutes, because these emulsions have not been characterized in ways that preserve the heterogeneity that defines successful ePCR. Our study quantifies the outcome of ePCR from conditions specified in the literature using single particle analysis, which preserves this heterogeneity. We combine ePCR with magnetic microbeads and quantify the amplification yield via qPCR and the proportion of clonal and saturated beads via flow cytometry. Our single particle level analysis of thousands of beads resolves two key criteria that define the success of ePCR: 1) whether the target fraction of 20% clonal beads predicted by the Poisson distribution is achieved, and 2) whether those beads are partially or maximally covered by amplified DNA. We found that among the two concentrations of polymerase tested, only the higher one, which is 20-fold more than the concentration recommended for conventional PCR, could yield sufficient PCR products. Dramatic increases in the concentrations of reverse primer and nucleotides recommended in literature gave no measurable change in outcome. We thus provide evidence-based starting conditions for effective and economical ePCR for real DNA libraries and a straightforward workflow for evaluating the success of tuning ePCR prior to downstream applications.
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Affiliation(s)
- Ryan H P Siu
- Division of Life Science, Hong Kong University of Science and Technology, Hong Kong
| | - Yang Liu
- Division of Life Science, Hong Kong University of Science and Technology, Hong Kong
| | - Kaitlin H Y Chan
- Division of Life Science, Hong Kong University of Science and Technology, Hong Kong
| | - Clara Ridzewski
- Natural and Environmental Sciences, Zittau/Görlitz University of Applied Sciences, Germany
| | - Liane Siu Slaughter
- Division of Life Science, Hong Kong University of Science and Technology, Hong Kong.
| | - Angela R Wu
- Division of Life Science, Hong Kong University of Science and Technology, Hong Kong; Department of Chemical and Biological Engineering, Hong Kong University of Science and Technology, Hong Kong.
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15
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Xing QR, Cipta NO, Hamashima K, Liou YC, Koh CG, Loh YH. Unraveling Heterogeneity in Transcriptome and Its Regulation Through Single-Cell Multi-Omics Technologies. Front Genet 2020; 11:662. [PMID: 32765578 PMCID: PMC7380244 DOI: 10.3389/fgene.2020.00662] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 06/01/2020] [Indexed: 12/30/2022] Open
Abstract
Cellular heterogeneity plays a pivotal role in tissue homeostasis and the disease development of multicellular organisms. To deconstruct the heterogeneity, a multitude of single-cell toolkits measuring various cellular contents, including genome, transcriptome, epigenome, and proteome, have been developed. More recently, multi-omics single-cell techniques enable the capture of molecular footprints with a higher resolution by simultaneously profiling various cellular contents within an individual cell. Integrative analysis of multi-omics datasets unravels the relationships between cellular modalities, builds sophisticated regulatory networks, and provides a holistic view of the cell state. In this review, we summarize the major developments in the single-cell field and review the current state-of-the-art single-cell multi-omic techniques and the bioinformatic tools for integrative analysis.
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Affiliation(s)
- Qiao Rui Xing
- Epigenetics and Cell Fates Laboratory, Institute of Molecular and Cell Biology, ASTAR, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Nadia Omega Cipta
- Epigenetics and Cell Fates Laboratory, Institute of Molecular and Cell Biology, ASTAR, Singapore, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Kiyofumi Hamashima
- Epigenetics and Cell Fates Laboratory, Institute of Molecular and Cell Biology, ASTAR, Singapore, Singapore
| | - Yih-Cherng Liou
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Cheng Gee Koh
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Yuin-Han Loh
- Epigenetics and Cell Fates Laboratory, Institute of Molecular and Cell Biology, ASTAR, Singapore, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
- NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore, Singapore
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
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16
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Chen X, Shen R, Liu S, Xiao X, Yan J, Zhang Y, Jiang Z, Nie B, Liu J. The sensitive detection of single-cell secreted lactic acid for glycolytic inhibitor screening with a microdroplet biosensor. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2020; 12:3250-3259. [PMID: 32930188 DOI: 10.1039/d0ay00633e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Lactic acid (LA) plays an important role in the tumor metabolism and malignant progression of various cancers. Herein, we have developed a one-step, wash-free microfluidic approach with droplet biosensors for the sensitive detection of LA secreted by a single tumor cell. Our assay integrates the enzyme-assisted chemical conversion of LA in small-volume (4.2 nL) droplets for fluorescence signal readout. The microdroplet assay achieved a limit of detection of 1.02 μM and was more sensitive than the commercial ELISA kit by nearly two orders of magnitude. A good specificity has been demonstrated for this assay by testing various ions and biomolecules from the culture medium. This droplet assay allows us to acquire the profiles of the lactic acid secretion of tumor cells under the influence of glycolytic inhibitors at the single-cell level. It offers a useful research tool to study the cell-to-cell differences of LA secretion and glycolytic inhibitor screening for cancer research.
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Affiliation(s)
- Xuyue Chen
- Institute of Functional Nano and Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-Based Functional Materials and Devices, Soochow University, Suzhou, Jiangsu Province 215123, China.
| | - Rui Shen
- Institute of Functional Nano and Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-Based Functional Materials and Devices, Soochow University, Suzhou, Jiangsu Province 215123, China.
| | - Sidi Liu
- Institute of Functional Nano and Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-Based Functional Materials and Devices, Soochow University, Suzhou, Jiangsu Province 215123, China.
| | - Xiang Xiao
- Institute of Functional Nano and Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-Based Functional Materials and Devices, Soochow University, Suzhou, Jiangsu Province 215123, China.
| | - Jun Yan
- Institute of Functional Nano and Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-Based Functional Materials and Devices, Soochow University, Suzhou, Jiangsu Province 215123, China.
| | - Yiqiu Zhang
- Institute of Functional Nano and Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-Based Functional Materials and Devices, Soochow University, Suzhou, Jiangsu Province 215123, China.
| | - Zhongyun Jiang
- Institute of Functional Nano and Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-Based Functional Materials and Devices, Soochow University, Suzhou, Jiangsu Province 215123, China.
| | - Baoqing Nie
- School of Electronic and Information Engineering, Soochow University, Suzhou, Jiangsu Province 215006, China
| | - Jian Liu
- Institute of Functional Nano and Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-Based Functional Materials and Devices, Soochow University, Suzhou, Jiangsu Province 215123, China.
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17
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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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18
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Xu X, Wang J, Wu L, Guo J, Song Y, Tian T, Wang W, Zhu Z, Yang C. Microfluidic Single-Cell Omics Analysis. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2020; 16:e1903905. [PMID: 31544338 DOI: 10.1002/smll.201903905] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2019] [Revised: 08/26/2019] [Indexed: 05/27/2023]
Abstract
The commonly existing cellular heterogeneity plays a critical role in biological processes such as embryonic development, cell differentiation, and disease progress. Single-cell omics-based heterogeneous studies have great significance for identifying different cell populations, discovering new cell types, revealing informative cell features, and uncovering significant interrelationships between cells. Recently, microfluidics has evolved to be a powerful technology for single-cell omics analysis due to its merits of throughput, sensitivity, and accuracy. Herein, the recent advances of microfluidic single-cell omics analysis, including different microfluidic platform designs, lysis strategies, and omics analysis techniques, are reviewed. Representative applications of microfluidic single-cell omics analysis in complex biological studies are then summarized. Finally, a few perspectives on the future challenges and development trends of microfluidic-assisted single-cell omics analysis are discussed.
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Affiliation(s)
- Xing Xu
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, The Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Junxia Wang
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, The Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Lingling Wu
- Institute of Molecular Medicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Jingjing Guo
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, The Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Yanling Song
- Institute of Molecular Medicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Tian Tian
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, The Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Wei Wang
- Institute of Molecular Medicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Zhi Zhu
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, The Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Chaoyong Yang
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, The Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
- Institute of Molecular Medicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
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19
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Zhang W, Li N, Lin L, Huang Q, Uchiyama K, Lin JM. Concentrating Single Cells in Picoliter Droplets for Phospholipid Profiling on a Microfluidic System. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2020; 16:e1903402. [PMID: 31769602 DOI: 10.1002/smll.201903402] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Revised: 11/08/2019] [Indexed: 06/10/2023]
Abstract
Cellular membranes are composed of a variety of lipids in different amounts and proportions, and alterations of them are usually closely related to various diseases. To reveal the intercellular heterogeneity of the lipid variation, an integrated microfluidic system is designed, which consists of droplet-based inkjet printing, dielectrophoretic electrodes, and de-emulsification interface to achieve on-line single-cell encapsulation, manipulation, and mass spectrometry (MS) detection. This integrated system effectively improves the single-cell encapsulation rate, and meanwhile reduces the matrix interference and continuous oil phase interference to the MS detection. Using this system, the heterogeneities between the normal and cancer cells are compared, and the heterogeneity of the same cells before and after the drug treatment changed obviously, indicating that this system can be used as a promising tool for studying the link between the alterations of lipid homeostasis and various diseases.
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Affiliation(s)
- Weifei Zhang
- 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
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, 100190, China
| | - Ling Lin
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, 100190, China
| | - Qiushi Huang
- 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
| | - 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
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20
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Matuła K, Rivello F, Huck WTS. Single-Cell Analysis Using Droplet Microfluidics. ACTA ACUST UNITED AC 2019; 4:e1900188. [PMID: 32293129 DOI: 10.1002/adbi.201900188] [Citation(s) in RCA: 132] [Impact Index Per Article: 26.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 09/30/2019] [Indexed: 12/12/2022]
Abstract
Droplet microfluidics has revolutionized the study of single cells. The ability to compartmentalize cells within picoliter droplets in microfluidic devices has opened up a wide range of strategies to extract information at the genomic, transcriptomic, proteomic, or metabolomic level from large numbers of individual cells. Studying the different molecular landscapes at single-cell resolution has provided the authors with a detailed picture of intracellular heterogeneity and the resulting changes in cellular phenotypes. In addition, these technologies have aided in the discovery of rare cells in tumors or in the immune system, and left the authors with a deeper understanding of the fundamental biological processes that determine cell fate. This review aims to provide a detailed overview of the various droplet microfluidic strategies reported in the literature, taking into account the sometimes subtle differences in workflow or reagents that enable or improve certain protocols. Specifically, approaches to targeted- and whole-genome analysis, as well as whole-transcriptome profiling techniques, are reviewed. In addition, an up-to-date overview of new methods to characterize and quantify single-cell protein levels, and of developments to screen secreted molecules such as antibodies, cytokines, or metabolites at the single-cell level, is provided.
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Affiliation(s)
- Kinga Matuła
- Radboud University, Institute for Molecules and Materials, Heyendaalseweg 135, 6525AJ, Nijmegen, The Netherlands
| | - Francesca Rivello
- Radboud University, Institute for Molecules and Materials, Heyendaalseweg 135, 6525AJ, Nijmegen, The Netherlands
| | - Wilhelm T S Huck
- Radboud University, Institute for Molecules and Materials, Heyendaalseweg 135, 6525AJ, Nijmegen, The Netherlands
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21
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Li X, Zhang D, Ruan W, Liu W, Yin K, Tian T, Bi Y, Ruan Q, Zhao Y, Zhu Z, Yang C. Centrifugal-Driven Droplet Generation Method with Minimal Waste for Single-Cell Whole Genome Amplification. Anal Chem 2019; 91:13611-13619. [DOI: 10.1021/acs.analchem.9b02786] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Xingrui Li
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Pen-Tung Sah Institute of Micro-Nano Science and Technology, Xiamen University, Xiamen 361005, P. R. China
| | - Dongfeng Zhang
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Pen-Tung Sah Institute of Micro-Nano Science and Technology, Xiamen University, Xiamen 361005, P. R. China
| | - Weidong Ruan
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Pen-Tung Sah Institute of Micro-Nano Science and Technology, Xiamen University, Xiamen 361005, P. R. China
| | - Weizhi Liu
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Pen-Tung Sah Institute of Micro-Nano Science and Technology, Xiamen University, Xiamen 361005, P. R. China
| | - Kun Yin
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Pen-Tung Sah Institute of Micro-Nano Science and Technology, Xiamen University, Xiamen 361005, P. R. China
| | - Tian Tian
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Pen-Tung Sah Institute of Micro-Nano Science and Technology, Xiamen University, Xiamen 361005, P. R. China
| | - Yunpeng Bi
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Pen-Tung Sah Institute of Micro-Nano Science and Technology, Xiamen University, Xiamen 361005, P. R. China
| | - Qingyu Ruan
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Pen-Tung Sah Institute of Micro-Nano Science and Technology, Xiamen University, Xiamen 361005, P. R. China
| | - Yuan Zhao
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Pen-Tung Sah Institute of Micro-Nano Science and Technology, Xiamen University, Xiamen 361005, P. R. China
| | - Zhi Zhu
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Pen-Tung Sah Institute of Micro-Nano Science and Technology, Xiamen University, Xiamen 361005, P. R. China
| | - Chaoyong Yang
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Pen-Tung Sah Institute of Micro-Nano Science and Technology, Xiamen University, Xiamen 361005, P. R. China
- Institute of Molecular Medicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, P. R. China
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22
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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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23
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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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24
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Yin K, Zeng X, Liu W, Xue Y, Li X, Wang W, Song Y, Zhu Z, Yang C. Stable Colloidosomes Formed by Self-Assembly of Colloidal Surfactant for Highly Robust Digital PCR. Anal Chem 2019; 91:6003-6011. [DOI: 10.1021/acs.analchem.9b00470] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Kun Yin
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, Department of Chemical Engineering, College of Chemistry and Chemical Engineering, Pen-Tung Sah Institute of Micro-Nano Science and Technology, Xiamen University, Xiamen 361005, China
| | - Xi Zeng
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, Department of Chemical Engineering, College of Chemistry and Chemical Engineering, Pen-Tung Sah Institute of Micro-Nano Science and Technology, Xiamen University, Xiamen 361005, China
| | - Weizhi Liu
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, Department of Chemical Engineering, College of Chemistry and Chemical Engineering, Pen-Tung Sah Institute of Micro-Nano Science and Technology, Xiamen University, Xiamen 361005, China
| | - Yakun Xue
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, Department of Chemical Engineering, College of Chemistry and Chemical Engineering, Pen-Tung Sah Institute of Micro-Nano Science and Technology, Xiamen University, Xiamen 361005, China
| | - Xingrui Li
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, Department of Chemical Engineering, College of Chemistry and Chemical Engineering, Pen-Tung Sah Institute of Micro-Nano Science and Technology, Xiamen University, Xiamen 361005, China
| | - Wei Wang
- Institute of Molecular Medicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
| | - Yanling Song
- Institute of Molecular Medicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
| | - Zhi Zhu
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, Department of Chemical Engineering, College of Chemistry and Chemical Engineering, Pen-Tung Sah Institute of Micro-Nano Science and Technology, Xiamen University, Xiamen 361005, China
| | - Chaoyong Yang
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, Department of Chemical Engineering, College of Chemistry and Chemical Engineering, Pen-Tung Sah Institute of Micro-Nano Science and Technology, Xiamen University, Xiamen 361005, China
- Institute of Molecular Medicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
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25
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Chen K, Sui C, Wu Y, Ao Z, Guo SS, Guo F. A digital acoustofluidic device for on-demand and oil-free droplet generation. NANOTECHNOLOGY 2019; 30:084001. [PMID: 30523921 DOI: 10.1088/1361-6528/aaf3fd] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
We report a digital acoustofluidic device for on-demand and oil-free droplet generation. By applying a programmed radio frequency signal to a circular interdigital transducer, the dynamic focused acoustic pressure profiles generated rise up and dispense sample liquids from a reservoir to dynamically eject the droplets into the air. Our device allows droplets to be dispensed on demand with precisely controlled generation time and sequence, and accurate droplet volume. Moreover, we also demonstrate the generation of a droplet with a volume of 24 pL within 10 ms, as well as the encapsulation of a single cell into droplets. This acoustofluidic droplet generation technique is simple, biocompatible, and enables the on-demand droplet generation and encapsulation of many different biological materials with precise control, which is promising for single cell sampling and analysis applications.
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Affiliation(s)
- Keke Chen
- Key Laboratory of Artificial Micro- and Nano-structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan 430072, People's Republic of China
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26
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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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27
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Alam MK, Koomson E, Zou H, Yi C, Li CW, Xu T, Yang M. Recent advances in microfluidic technology for manipulation and analysis of biological cells (2007–2017). Anal Chim Acta 2018; 1044:29-65. [DOI: 10.1016/j.aca.2018.06.054] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 06/19/2018] [Accepted: 06/19/2018] [Indexed: 12/17/2022]
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28
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Lactobacillus acidophilus Derived Biosurfactant as a Biofilm Inhibitor: A Promising Investigation Using Microfluidic Approach. APPLIED SCIENCES-BASEL 2018. [DOI: 10.3390/app8091555] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Background: Biomedical devices and implants are adversely affected by biofilm-associated infections that pose serious public health issues. Biosurfactants (BSs) can combat pathogenic biofilms through their antimicrobial, antibiofilm and antiadhesive capabilities. The objective of our research was to produce biosurfactant (BS) from Lactobacillus acidophilus NCIM 2903 and investigate its antibiofilm, antiadhesive potential using microfluidics strategies by mimicking the micro-environment of biofilm. Methods: Antibiofilm and antiadhesive potential was effectively evaluated using different methods like microfluidics assay, catheter assay, polydimethlysiloxane (PDMS) disc assay. Along with this chemical and physical characteristics of BS were also evaluated. Results: Cell free biosurfactant (CFBS) obtained was found to be effective against biofilm which was validated through the microfluidic (MF) or Lab on Chip (LOC) approach. The potency of CFBS was also evaluated on catheter tubing and PDMS surfaces (representative bioimplants). The efficacy of CFBS was also demonstrated through the reduction in surface tension, interfacial tension, contact angle and low critical micelle concentration. Conclusion: CFBS was found to be a potent antimicrobial and antibiofilm agent. We believe that perhaps this is the first report on demonstrating the inhibiting effect of Lactobacillus spp. derived CFBS against selected bacteria via LOC approach. These findings can be explored to design various BSs based formulations exhibiting antimicrobial, antibiofilm and antiadhesive potential for biomedical applications.
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29
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Guo S, Lin WN, Hu Y, Sun G, Phan DT, Chen CH. Ultrahigh-throughput droplet microfluidic device for single-cell miRNA detection with isothermal amplification. LAB ON A CHIP 2018; 18:1914-1920. [PMID: 29877542 DOI: 10.1039/c8lc00390d] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Analysis of microRNA (miRNA), a pivotal primary regulator of fundamental cellular processes, at the single-cell level is essential to elucidate regulated gene expression precisely. Most single-cell gene sequencing methods use the polymerase chain reaction (PCR) to increase the concentration of the target gene for detection, thus requiring a barcoding process for cell identification and creating a challenge for real-time, large-scale screening of sequences in cells to rapidly profile physiological samples. In this study, a rapid, PCR-free, single-cell miRNA assay is developed from a continuous-flow microfluidic process employing a DNA hybridization chain reaction to amplify the target miRNA signal. Individual cells are encapsulated with DNA amplifiers in water-in-oil droplets and then lysed. The released target miRNA interacts with the DNA amplifiers to trigger hybridization reactions, producing fluorescence signals. Afterward, the target sequences are recycled to trigger a cyclic cascade reaction and significantly amplify the fluorescence signals without using PCR thermal cycling. Multiple DNA amplifiers with distinct fluorescence signals can be encapsulated simultaneously in a droplet to measure multiple miRNAs from a single cell simultaneously. Moreover, this process converts the lab bench PCR assay to a real-time droplet assay with the post-reaction fluorescence signal as a readout to allow flow cytometry-like continuous-flow measurement of sequences in a single cell with an ultrahigh throughput (300-500 cells per minute) for rapid biomedical identification.
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Affiliation(s)
- Song Guo
- Department of Biomedical Engineering, National University of Singapore, 21 Lower Kent Ridge Road, 119077 Singapore.
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30
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Jafek AR, Harbertson S, Brady H, Samuel R, Gale BK. Instrumentation for xPCR Incorporating qPCR and HRMA. Anal Chem 2018; 90:7190-7196. [DOI: 10.1021/acs.analchem.7b05176] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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31
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Wang C, Liu W, Wei Q, Ren L, Tan M, Yu Y. A novel dual-well array chip for efficiently trapping single-cell in large isolated micro-well without complicated accessory equipment. BIOMICROFLUIDICS 2018; 12:034103. [PMID: 29774084 PMCID: PMC5938174 DOI: 10.1063/1.5030203] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 04/20/2018] [Indexed: 06/08/2023]
Abstract
Conventional cell-sized well arrays have advantages of high occupancy, simple operation, and low cost for capturing single-cells. However, they have insufficient space for including reagents required for cell treatment or analysis, which restricts the wide application of cell-sized well arrays as a single-cell research tool alone. Here, we present a novel dual-well array chip, which integrates capture-wells (20 μm in diameter) with reaction-wells (100 μm in diameter) and describe a flow method for convenient single-cell analysis requiring neither complicated infra-structure nor high expenditure, while enabling highly efficient single cell trapping (75.8%) with only 11.3% multi-cells. Briefly, the cells are first loaded into the dual-wells by gravity and then multi-cells in the reaction-wells are washed out by phosphate buffer saline. Next, biochemical reagents are loaded into reaction-wells using the scraping method and the chip is packed as a sandwich structure. We thereby successfully measured intracellular β-galactosidase activity of K562 cells at the single-cell level. We also used computational simulations to illustrate the working principle of dual-well structure and found out a relationship between the wall shear stress distribution and the aspect ratio of the dual-well array chip which provides theoretical guidance for designing multi-wells chip for convenient single-cell analysis. Our work produced the first dual-well chip that can simultaneously provide a high occupancy rate for single cells and sufficient space for reagents, as well as being low in cost and simple to operate. We believe that the feasibility and convenience of our method will enhance its use as a practical single-cell research tool.
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Affiliation(s)
| | | | | | | | | | - Yude Yu
- Author to whom correspondence should be addressed: . Tel.: 86-10-82304979
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32
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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: 334] [Impact Index Per Article: 55.7] [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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33
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Guo XL, Wei Y, Lou Q, Zhu Y, Fang Q. Manipulating Femtoliter to Picoliter Droplets by Pins for Single Cell Analysis and Quantitative Biological Assay. Anal Chem 2018; 90:5810-5817. [PMID: 29648445 DOI: 10.1021/acs.analchem.8b00343] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Herein, we developed an automated and flexible system for performing miniaturized liquid-liquid reactions and assays in the femtoliter to picoliter range, by combining the contact printing and the droplet-based microfluidics techniques. The system mainly consisted of solid pins and an oil-covered hydrophilic micropillar array chip fixed on an automated x- y- z translation stage. A novel droplet manipulation mode called "dipping-depositing-moving" (DDM) was proposed, which was based on the programmable combination of three basic operations, dipping liquids and depositing liquids with the solid pins and moving the two-dimensional oil-covered hydrophilic pillar microchip. With the DDM mode, flexible generation and manipulation of small droplets with volumes down to 179 fL could be achieved. For overcoming the scale phenomenon specially appeared in picoliter-scale droplets, we used a design of water moat to protect the femtoliter to picoliter droplets from volume loss through the cover oil during the droplet generation, manipulation, reaction and assay processes. Moreover, we also developed a precise quantitative method, quantitative droplet dilution method, to accurately measure the volumes of femtoliter to picoliter droplets. To demonstrate its feasibility and adaptability, we applied the present system in the determination of kinetics parameter for matrix metalloproteinases (MMP-9) in 1.81 pL reactors and the measurement the activity of β-galactosidase in single cells (HepG2 cells) in picoliter droplet array. The ultrasmall volumes of the droplet reactors avoided the excessive dilution to the reaction solutions and enabled the highly sensitive measurement of enzyme activity in the single cell level.
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Affiliation(s)
- Xiao-Li Guo
- Institute of Microanalytical Systems, Department of Chemistry and Innovation Center for Cell Signaling Network , Zhejiang University , Hangzhou , 310058 , China
| | - Yan Wei
- Institute of Microanalytical Systems, Department of Chemistry and Innovation Center for Cell Signaling Network , Zhejiang University , Hangzhou , 310058 , China
| | - Qi Lou
- Institute of Microanalytical Systems, Department of Chemistry and Innovation Center for Cell Signaling Network , Zhejiang University , Hangzhou , 310058 , China
| | - Ying Zhu
- Institute of Microanalytical Systems, Department of Chemistry and Innovation Center for Cell Signaling Network , Zhejiang University , Hangzhou , 310058 , China
| | - Qun Fang
- Institute of Microanalytical Systems, Department of Chemistry and Innovation Center for Cell Signaling Network , Zhejiang University , Hangzhou , 310058 , China
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34
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Ven K, Vanspauwen B, Pérez-Ruiz E, Leirs K, Decrop D, Gerstmans H, Spasic D, Lammertyn J. Target Confinement in Small Reaction Volumes Using Microfluidic Technologies: A Smart Approach for Single-Entity Detection and Analysis. ACS Sens 2018; 3:264-284. [PMID: 29363316 DOI: 10.1021/acssensors.7b00873] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Over the last decades, the study of cells, nucleic acid molecules, and proteins has evolved from ensemble measurements to so-called single-entity studies. The latter offers huge benefits, not only as biological research tools to examine heterogeneities among individual entities within a population, but also as biosensing tools for medical diagnostics, which can reach the ultimate sensitivity by detecting single targets. Whereas various techniques for single-entity detection have been reported, this review focuses on microfluidic systems that physically confine single targets in small reaction volumes. We categorize these techniques as droplet-, microchamber-, and nanostructure-based and provide an overview of their implementation for studying single cells, nucleic acids, and proteins. We furthermore reflect on the advantages and limitations of these techniques and highlight future opportunities in the field.
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Affiliation(s)
- Karen Ven
- Department
of Biosystems, KU Leuven - University of Leuven, Willem de Croylaan 42, 3001 Leuven, Belgium
| | - Bram Vanspauwen
- Department
of Biosystems, KU Leuven - University of Leuven, Willem de Croylaan 42, 3001 Leuven, Belgium
| | - Elena Pérez-Ruiz
- Department
of Biosystems, KU Leuven - University of Leuven, Willem de Croylaan 42, 3001 Leuven, Belgium
| | - Karen Leirs
- Department
of Biosystems, KU Leuven - University of Leuven, Willem de Croylaan 42, 3001 Leuven, Belgium
| | - Deborah Decrop
- Department
of Biosystems, KU Leuven - University of Leuven, Willem de Croylaan 42, 3001 Leuven, Belgium
| | - Hans Gerstmans
- Department
of Biosystems, KU Leuven - University of Leuven, Willem de Croylaan 42, 3001 Leuven, Belgium
- Department
of Applied biosciences, Ghent University, Valentyn Vaerwyckweg 1 - building
C, 9000 Gent, Belgium
- Department
of Biosystems, KU Leuven - University of Leuven, Kasteelpark Arenberg
21, 3001 Leuven, Belgium
| | - Dragana Spasic
- Department
of Biosystems, KU Leuven - University of Leuven, Willem de Croylaan 42, 3001 Leuven, Belgium
| | - Jeroen Lammertyn
- Department
of Biosystems, KU Leuven - University of Leuven, Willem de Croylaan 42, 3001 Leuven, Belgium
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35
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Li X, Zhang D, Zhang H, Guan Z, Song Y, Liu R, Zhu Z, Yang C. Microwell Array Method for Rapid Generation of Uniform Agarose Droplets and Beads for Single Molecule Analysis. Anal Chem 2018; 90:2570-2577. [PMID: 29350029 DOI: 10.1021/acs.analchem.7b04040] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Compartmentalization of aqueous samples in uniform emulsion droplets has proven to be a useful tool for many chemical, biological, and biomedical applications. Herein, we introduce an array-based emulsification method for rapid and easy generation of monodisperse agarose-in-oil droplets in a PDMS microwell array. The microwells are filled with agarose solution, and subsequent addition of hot oil results in immediate formation of agarose droplets due to the surface-tension of the liquid solution. Because droplet size is determined solely by the array unit dimensions, uniform droplets with preselectable diameters ranging from 20 to 100 μm can be produced with relative standard deviations less than 3.5%. The array-based droplet generation method was used to perform digital PCR for absolute DNA quantitation. The array-based droplet isolation and sol-gel switching property of agarose enable formation of stable beads by chilling the droplet array at -20 °C, thus, maintaining the monoclonality of each droplet and facilitating the selective retrieval of desired droplets. The monoclonality of droplets was demonstrated by DNA sequencing and FACS analysis, suggesting the robustness and flexibility of the approach for single molecule amplification and analysis. We believe our approach will lead to new possibilities for a great variety of applications, such as single-cell gene expression studies, aptamer selection, and oligonucleotide analysis.
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Affiliation(s)
- Xingrui Li
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Pen-Tung Sah Institute of Micro-Nano Science and Technology, Xiamen University , Xiamen 361005, People's Republic of China
| | - Dongfeng Zhang
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Pen-Tung Sah Institute of Micro-Nano Science and Technology, Xiamen University , Xiamen 361005, People's Republic of China
| | - Huimin Zhang
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Pen-Tung Sah Institute of Micro-Nano Science and Technology, Xiamen University , Xiamen 361005, People's Republic of China
| | - Zhichao Guan
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Pen-Tung Sah Institute of Micro-Nano Science and Technology, Xiamen University , Xiamen 361005, People's Republic of China
| | - Yanling Song
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Pen-Tung Sah Institute of Micro-Nano Science and Technology, Xiamen University , Xiamen 361005, People's Republic of China.,The MOE Key Laboratory of Analysis and Detection Technology for Food Safety, State Key Laboratory of Photocatalysis on Energy and Environment, College of Biological Science and Engineering, Fuzhou University , Fuzhou 350116, People's Republic of China
| | - Ruochen Liu
- Department of Chemistry and Chemical Biology, Rutgers University , Piscataway, New Jersey United States
| | - Zhi Zhu
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Pen-Tung Sah Institute of Micro-Nano Science and Technology, Xiamen University , Xiamen 361005, People's Republic of China
| | - Chaoyong Yang
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Pen-Tung Sah Institute of Micro-Nano Science and Technology, Xiamen University , Xiamen 361005, People's Republic of China
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36
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Jiang Y, Du L, Li Y, Mu Q, Cui Z, Zhou J, Wu W. A novel mechanism for user-friendly and self-activated microdroplet generation capable of programmable control. Analyst 2018; 143:3798-3807. [DOI: 10.1039/c8an00035b] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The real-time continuous-flow PCR inside a 3D spiral microchannel is realized by a novel self-activated microdroplet generation/transport mechanism.
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Affiliation(s)
- Yangyang Jiang
- State Key Laboratory of Applied Optics
- Changchun Institute of Optics
- Fine Mechanics and Physics
- Chinese Academy of Sciences
- Changchun
| | - Lin Du
- State Key Laboratory of ASIC and Systems
- Fudan University
- Shanghai 200433
- China
| | - Yuanming Li
- State Key Laboratory of Applied Optics
- Changchun Institute of Optics
- Fine Mechanics and Physics
- Chinese Academy of Sciences
- Changchun
| | - Quanquan Mu
- State Key Laboratory of Applied Optics
- Changchun Institute of Optics
- Fine Mechanics and Physics
- Chinese Academy of Sciences
- Changchun
| | - Zhongxu Cui
- State Key Laboratory of Applied Optics
- Changchun Institute of Optics
- Fine Mechanics and Physics
- Chinese Academy of Sciences
- Changchun
| | - Jia Zhou
- State Key Laboratory of ASIC and Systems
- Fudan University
- Shanghai 200433
- China
| | - Wenming Wu
- State Key Laboratory of Applied Optics
- Changchun Institute of Optics
- Fine Mechanics and Physics
- Chinese Academy of Sciences
- Changchun
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37
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Murphy TW, Zhang Q, Naler LB, Ma S, Lu C. Recent advances in the use of microfluidic technologies for single cell analysis. Analyst 2017; 143:60-80. [PMID: 29170786 PMCID: PMC5839671 DOI: 10.1039/c7an01346a] [Citation(s) in RCA: 103] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The inherent heterogeneity in cell populations has become of great interest and importance as analytical techniques have improved over the past decades. With the advent of personalized medicine, understanding the impact of this heterogeneity has become an important challenge for the research community. Many different microfluidic approaches with varying levels of throughput and resolution exist to study single cell activity. In this review, we take a broad view of the recent microfluidic developments in single cell analysis based on microwell, microchamber, and droplet platforms. We cover physical, chemical, and molecular biology approaches for cellular and molecular analysis including newly emerging genome-wide analysis.
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Affiliation(s)
- Travis W Murphy
- Department of Chemical Engineering, Virginia Tech, Blacksburg, VA 24061, USA.
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38
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Murata Y, Nakashoji Y, Kondo M, Tanaka Y, Hashimoto M. Rapid automatic creation of monodisperse emulsion droplets by microfluidic device with degassed PDMS slab as a detachable suction actuator. Electrophoresis 2017; 39:504-511. [DOI: 10.1002/elps.201700247] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 07/28/2017] [Accepted: 07/31/2017] [Indexed: 12/26/2022]
Affiliation(s)
- Yuki Murata
- Department of Chemical Engineering and Materials Science; Faculty of Science and Engineering; Doshisha University; Kyotanabe Kyoto Japan
| | - Yuta Nakashoji
- Department of Chemical Engineering and Materials Science; Faculty of Science and Engineering; Doshisha University; Kyotanabe Kyoto Japan
| | - Masaki Kondo
- Department of Chemical Engineering and Materials Science; Faculty of Science and Engineering; Doshisha University; Kyotanabe Kyoto Japan
| | - Yugo Tanaka
- Department of Chemical Engineering and Materials Science; Faculty of Science and Engineering; Doshisha University; Kyotanabe Kyoto Japan
| | - Masahiko Hashimoto
- Department of Chemical Engineering and Materials Science; Faculty of Science and Engineering; Doshisha University; Kyotanabe Kyoto Japan
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39
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Caen O, Lu H, Nizard P, Taly V. Microfluidics as a Strategic Player to Decipher Single-Cell Omics? Trends Biotechnol 2017. [DOI: 10.1016/j.tibtech.2017.05.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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40
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Okura N, Nakashoji Y, Koshirogane T, Kondo M, Tanaka Y, Inoue K, Hashimoto M. A compact and facile microfluidic droplet creation device using a piezoelectric diaphragm micropump for droplet digital PCR platforms. Electrophoresis 2017; 38:2666-2672. [DOI: 10.1002/elps.201700039] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Revised: 05/16/2017] [Accepted: 06/11/2017] [Indexed: 11/08/2022]
Affiliation(s)
- Naoaki Okura
- Department of Chemical Engineering and Materials Science, Faculty of Science and Engineering; Doshisha University; Kyotanabe Kyoto Japan
| | - Yuta Nakashoji
- Department of Chemical Engineering and Materials Science, Faculty of Science and Engineering; Doshisha University; Kyotanabe Kyoto Japan
| | - Toshihiro Koshirogane
- Department of Chemical Engineering and Materials Science, Faculty of Science and Engineering; Doshisha University; Kyotanabe Kyoto Japan
| | - Masaki Kondo
- Department of Chemical Engineering and Materials Science, Faculty of Science and Engineering; Doshisha University; Kyotanabe Kyoto Japan
| | - Yugo Tanaka
- Department of Chemical Engineering and Materials Science, Faculty of Science and Engineering; Doshisha University; Kyotanabe Kyoto Japan
| | - Kohei Inoue
- Department of Chemical Engineering and Materials Science, Faculty of Science and Engineering; Doshisha University; Kyotanabe Kyoto Japan
| | - Masahiko Hashimoto
- Department of Chemical Engineering and Materials Science, Faculty of Science and Engineering; Doshisha University; Kyotanabe Kyoto Japan
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41
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Wang C, Liu W, Tan M, Sun H, Yu Y. An open-pattern droplet-in-oil planar array for single cell analysis based on sequential inkjet printing technology. BIOMICROFLUIDICS 2017; 11:044106. [PMID: 28794816 PMCID: PMC5519398 DOI: 10.1063/1.4995294] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Accepted: 07/10/2017] [Indexed: 05/08/2023]
Abstract
Cellular heterogeneity represents a fundamental principle of cell biology for which a readily available single-cell research tool is urgently required. Here, we present a novel method combining cell-sized well arrays with sequential inkjet printing. Briefly, K562 cells with phosphate buffer saline buffer were captured at high efficiency (74.5%) in a cell-sized well as a "primary droplet" and sealed using fluorinated oil. Then, piezoelectric inkjet printing technology was adapted to precisely inject the cell lysis buffer and the fluorogenic substrate, fluorescein-di-β-D-galactopyranoside, as a "secondary droplet" to penetrate the sealing oil and fuse with the "primary droplet." We thereby successfully measured the intracellular β-galactosidase activity of K562 cells at the single-cell level. Our method allows, for the first time, the ability to simultaneously accommodate the high occupancy rate of single cells and sequential addition of reagents while retaining an open structure. We believe that the feasibility and flexibility of our method will enhance its use as a universal single-cell research tool as well as accelerate the adoption of inkjet printing in the study of cellular heterogeneity.
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Affiliation(s)
| | | | | | - Hongbo Sun
- State Key Laboratory on Integrated Optoelectronics, College of Electronic Science and Engineering, Jilin University, Changchun 130012, People's Republic of China
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42
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Sauzade M, Brouzes E. Deterministic trapping, encapsulation and retrieval of single-cells. LAB ON A CHIP 2017; 17:2186-2192. [PMID: 28585962 PMCID: PMC5541261 DOI: 10.1039/c7lc00283a] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
We present a novel method for conducting true single-cell encapsulation at very high efficiency for the manipulation of precious samples. Our unique strategy is based on the sequential capture and original encapsulation of single-cells into a series of hydrodynamic traps. We identified two distinct modes of encapsulation and we established their associated design rules. We improved the trapping scheme to reach a near perfect capture efficiency and make it compatible with the encapsulation process. Finally, we developed the complete device operation that permits highly efficient single-cell encapsulation and droplet retrieval. This platform provides the foundation to a fully integrated multiparameter platform that will impact the analysis of tissues at single-cell resolution.
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Affiliation(s)
- M Sauzade
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY 11794-5281, USA.
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43
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Clark IC, Abate AR. Finding a helix in a haystack: nucleic acid cytometry with droplet microfluidics. LAB ON A CHIP 2017; 17:2032-2045. [PMID: 28540956 PMCID: PMC6005652 DOI: 10.1039/c7lc00241f] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Nucleic acids encode the information of life, programming cellular functions and dictating many biological outcomes. Differentiating between cells based on their nucleic acid programs is, thus, a powerful way to unravel the genetic bases of many phenotypes. This is especially important considering that most cells exist in heterogeneous populations, requiring them to be isolated before they can be studied. Existing flow cytometry techniques, however, are unable to reliably recover specific cells based on nucleic acid content. Nucleic acid cytometry is a new field built on droplet microfluidics that allows robust identification, sorting, and sequencing of cells based on specific nucleic acid biomarkers. This review highlights applications that immediately benefit from the approach, biological questions that can be addressed for the first time with it, and considerations for building successful workflows.
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Affiliation(s)
- Iain C Clark
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA.
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Abstract
Droplet microfluidics generates and manipulates discrete droplets through immiscible multiphase flows inside microchannels. Due to its remarkable advantages, droplet microfluidics bears significant value in an extremely wide range of area. In this review, we provide a comprehensive and in-depth insight into droplet microfluidics, covering fundamental research from microfluidic chip fabrication and droplet generation to the applications of droplets in bio(chemical) analysis and materials generation. The purpose of this review is to convey the fundamentals of droplet microfluidics, a critical analysis on its current status and challenges, and opinions on its future development. We believe this review will promote communications among biology, chemistry, physics, and materials science.
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Affiliation(s)
- Luoran Shang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University , Nanjing 210096, China
| | - Yao Cheng
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University , Nanjing 210096, China
| | - Yuanjin Zhao
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University , Nanjing 210096, China
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45
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Multiple pathogen biomarker detection using an encoded bead array in droplet PCR. J Microbiol Methods 2017; 139:22-28. [PMID: 28434824 DOI: 10.1016/j.mimet.2017.04.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Revised: 04/19/2017] [Accepted: 04/19/2017] [Indexed: 11/23/2022]
Abstract
We present a droplet PCR workflow for detection of multiple pathogen DNA biomarkers using fluorescent color-coded Luminex® beads. This strategy enables encoding of multiple singleplex droplet PCRs using a commercially available bead set of several hundred distinguishable fluorescence codes. This workflow provides scalability beyond the limited number offered by fluorescent detection probes such as TaqMan probes, commonly used in current multiplex droplet PCRs. The workflow was validated for three different Luminex bead sets coupled to target specific capture oligos to detect hybridization of three microorganisms infecting poultry: avian influenza, infectious laryngotracheitis virus and Campylobacter jejuni. In this assay, the target DNA was amplified with fluorescently labeled primers by PCR in parallel in monodisperse picoliter droplets, to avoid amplification bias. The color codes of the Luminex detection beads allowed concurrent and accurate classification of the different bead sets used in this assay. The hybridization assay detected target DNA of all three microorganisms with high specificity, from samples with average target concentration of a single DNA template molecule per droplet. This workflow demonstrates the possibility of increasing the droplet PCR assay detection panel to detect large numbers of targets in parallel, utilizing the scalability offered by the color-coded Luminex detection beads.
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46
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Prakadan SM, Shalek AK, Weitz DA. Scaling by shrinking: empowering single-cell 'omics' with microfluidic devices. Nat Rev Genet 2017; 18:345-361. [PMID: 28392571 DOI: 10.1038/nrg.2017.15] [Citation(s) in RCA: 212] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Recent advances in cellular profiling have demonstrated substantial heterogeneity in the behaviour of cells once deemed 'identical', challenging fundamental notions of cell 'type' and 'state'. Not surprisingly, these findings have elicited substantial interest in deeply characterizing the diversity, interrelationships and plasticity among cellular phenotypes. To explore these questions, experimental platforms are needed that can extensively and controllably profile many individual cells. Here, microfluidic structures - whether valve-, droplet- or nanowell-based - have an important role because they can facilitate easy capture and processing of single cells and their components, reducing labour and costs relative to conventional plate-based methods while also improving consistency. In this article, we review the current state-of-the-art methodologies with respect to microfluidics for mammalian single-cell 'omics' and discuss challenges and future opportunities.
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Affiliation(s)
- Sanjay M Prakadan
- Institute for Medical Engineering &Science (IMES) and Department of Chemistry, MIT, Cambridge, Massachusetts 02139, USA.,Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts 02139, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Alex K Shalek
- Institute for Medical Engineering &Science (IMES) and Department of Chemistry, MIT, Cambridge, Massachusetts 02139, USA.,Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts 02139, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - David A Weitz
- School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts 02138, USA.,Department of Physics, Harvard University, Cambridge, Massachusetts 02138, USA
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47
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Ding Y, Choo J, deMello AJ. From single-molecule detection to next-generation sequencing: microfluidic droplets for high-throughput nucleic acid analysis. MICROFLUIDICS AND NANOFLUIDICS 2017; 21:58. [PMID: 32214953 PMCID: PMC7087872 DOI: 10.1007/s10404-017-1889-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2016] [Accepted: 02/22/2017] [Indexed: 05/27/2023]
Abstract
Droplet-based microfluidic technologies have proved themselves to be of significant utility in the performance of high-throughput chemical and biological experiments. By encapsulating and isolating reagents within femtoliter-nanoliter droplet, millions of (bio) chemical reactions can be processed in a parallel fashion and on ultra-short timescales. Recent applications of such technologies to genetic analysis have suggested significant utility in low-cost, efficient and rapid workflows for DNA amplification, rare mutation detection, antibody screening and next-generation sequencing. To this end, we describe and highlight some of the most interesting recent developments and applications of droplet-based microfluidics in the broad area of nucleic acid analysis. In addition, we also present a cursory description of some of the most essential functional components, which allow the creation of integrated and complex workflows based on flowing streams of droplets.
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Affiliation(s)
- Yun Ding
- Institute for Chemical and Bioengineering, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir Prelog Weg 1, 8093 Zurich, Switzerland
| | - Jaebum Choo
- Department of Bionano Technology, Hanyang University, Ansan, 15588 Republic of Korea
| | - Andrew J. deMello
- Institute for Chemical and Bioengineering, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir Prelog Weg 1, 8093 Zurich, Switzerland
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48
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Quan HH, Li M, Huang Y, Hahn JH. A hydrophobic ionic liquid compartmentalized sampling/labeling and its separation techniques in polydimethylsiloxane microchip capillary electrophoresis. Electrophoresis 2016; 38:372-379. [PMID: 27739089 DOI: 10.1002/elps.201600305] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 09/07/2016] [Accepted: 09/08/2016] [Indexed: 01/18/2023]
Abstract
This paper demonstrates a novel compartmentalized sampling/labeling method and its separation techniques using a hydrophobic ionic liquid (IL)-1-butyl-3-methylimidazolium bis(trifluoromethylsulfonyl)-imidate (BmimNTf2 )-as the immiscible phase, which is capable of minimizing signal losses during microchip capillary electrophoresis (MCE). The MCE device consists of a silica tube connected to a straight polydimethylsiloxane (PDMS) separation channel. Poly(diallyldimethylammonium chloride) (PDDAC) was coated on the inner surface of channel to ease the introduction of IL plugs and enhance the IL wetting on the PDMS surface for sample releasing. Electroosmotic flow (EOF)-based sample compartmentalization was carried out through a sequenced injection into sampling tubes with the following order: leading IL plug/sample segment/terminal IL plug. The movement of the sample segment was easily controlled by applying an electrical voltage across both ends of the chip without a sample volume change. This approach effectively prevented analyte diffusion before injection into MCE channels. When the sample segment was manipulated to the PDDAC-modified PDMS channel, the sample plug then was released from isolation under EOF while IL plugs adsorbed onto channel surfaces owing to strong adhesion. A mixture of flavin adenine nucleotides (FAD) and flavin mononucleotides (FMN) was successfully separated on a 2.5 cm long separation channel, for which the theoretical numbers of plates were 15 000 and 17 000, respectively. The obtained peak intensity was increased 6.3-fold over the corresponding value from conventional electrokinetic injection with the same sampling time. Furthermore, based on the compartmented sample segment serving as an interim reactor, an on-chip fluorescence labeling is demonstrated.
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Affiliation(s)
- Hong Hua Quan
- Jiangsu Key Laboratory of Environmental Material & Environmental Engineering, College of Environmental Science and Engineering, Yangzhou University, Yangzhou, P. R. China
| | - Ming Li
- Jiangsu Key Laboratory of Environmental Material & Environmental Engineering, College of Environmental Science and Engineering, Yangzhou University, Yangzhou, P. R. China
| | - Yan Huang
- Department of Chemistry, Pohang University of Science and Technology, Pohang, Korea
| | - Jong Hoon Hahn
- Department of Chemistry, Pohang University of Science and Technology, Pohang, Korea
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49
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Seiffert S. Microfluidics and Macromolecules: Top-Down Analytics and Bottom-Up Engineering of Soft Matter at Small Scales. MACROMOL CHEM PHYS 2016. [DOI: 10.1002/macp.201600280] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Sebastian Seiffert
- Johannes Gutenberg-Universität Mainz; Institute of Physical Chemistry; Duesbergweg 10-14 55128 Mainz Germany
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50
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Wen N, Zhao Z, Fan B, Chen D, Men D, Wang J, Chen J. Development of Droplet Microfluidics Enabling High-Throughput Single-Cell Analysis. Molecules 2016; 21:E881. [PMID: 27399651 PMCID: PMC6272933 DOI: 10.3390/molecules21070881] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Revised: 06/27/2016] [Accepted: 06/28/2016] [Indexed: 12/20/2022] Open
Abstract
This article reviews recent developments in droplet microfluidics enabling high-throughput single-cell analysis. Five key aspects in this field are included in this review: (1) prototype demonstration of single-cell encapsulation in microfluidic droplets; (2) technical improvements of single-cell encapsulation in microfluidic droplets; (3) microfluidic droplets enabling single-cell proteomic analysis; (4) microfluidic droplets enabling single-cell genomic analysis; and (5) integrated microfluidic droplet systems enabling single-cell screening. We examine the advantages and limitations of each technique and discuss future research opportunities by focusing on key performances of throughput, multifunctionality, and absolute quantification.
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Affiliation(s)
- Na Wen
- Institute of Electronics, Chinese Academy of Sciences, Beijing 100190, China.
| | - Zhan Zhao
- Institute of Electronics, Chinese Academy of Sciences, Beijing 100190, China.
| | - Beiyuan Fan
- Institute of Electronics, Chinese Academy of Sciences, Beijing 100190, China.
| | - Deyong Chen
- Institute of Electronics, Chinese Academy of Sciences, Beijing 100190, China.
| | - Dong Men
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China.
| | - Junbo Wang
- Institute of Electronics, Chinese Academy of Sciences, Beijing 100190, China.
| | - Jian Chen
- Institute of Electronics, Chinese Academy of Sciences, Beijing 100190, China.
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