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Autour A, Merten CA. Fluorescence-activated droplet sequencing (FAD-seq) directly provides sequences of screening hits in antibody discovery. Proc Natl Acad Sci U S A 2024; 121:e2405342121. [PMID: 39240970 DOI: 10.1073/pnas.2405342121] [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: 03/14/2024] [Accepted: 08/04/2024] [Indexed: 09/08/2024] Open
Abstract
Droplet microfluidics has become a very powerful tool in high-throughput screening, including antibody discovery. Screens are usually carried out by physically sorting droplets hosting cells of the desired phenotype, breaking them, recovering the encapsulated cells, and sequencing the paired antibody light and heavy chain genes at the single-cell level. This series of multiple consecutive manipulation steps of rare screening hits is complex and challenging, resulting in a significant loss of clones with the desired phenotype or large fractions of cells with incomplete antibody information. Here, we present fluorescence-activated droplet sequencing, in which droplets showing the desired phenotype are selectively picoinjected with reagents for RT-PCR. Subsequently, light and heavy chain genes are natively paired, fused into a single-chain fragment variant format, and amplified before off-chip transfer and downstream nanopore sequencing. This workflow is sufficiently sensitive for obtaining different paired full-length antibody sequences from as little as five droplets, fulfilling the desired phenotype. Replacing physical sorting by specific sequencing overcomes a general bottleneck in droplet microfluidic screening and should be compatible with many more applications.
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Affiliation(s)
- Alexis Autour
- Institute of Bioengineering, School of Engineering, École Polytechnique Fédérale de Lausanne, Lausanne 1015, Switzerland
- European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Christoph A Merten
- Institute of Bioengineering, School of Engineering, École Polytechnique Fédérale de Lausanne, Lausanne 1015, Switzerland
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2
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Yu MC, Sun YS. A Droplet-Based Microfluidic Platform for High-Throughput Culturing of Yeast Cells in Various Conditions. MICROMACHINES 2024; 15:1034. [PMID: 39203685 PMCID: PMC11356446 DOI: 10.3390/mi15081034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2024] [Revised: 08/08/2024] [Accepted: 08/13/2024] [Indexed: 09/03/2024]
Abstract
Yeast plays a significant role in a variety of fields. In particular, it is extensively used as a model organism in genetics and cellular biology studies, and is employed in the production of vaccines, pharmaceuticals, and biofuels. Traditional "bulk"-based studies on yeast growth often overlook cellular variability, emphasizing the need for single-cell analysis. Micro-droplets, tiny liquid droplets with high surface-area-to-volume ratios, offer a promising platform for investigating single or a small number of cells, allowing precise control and monitoring of individual cell behaviors. Microfluidic devices, which facilitate the generation of micro-droplets, are advantageous due to their reduced volume requirements and ability to mimic in vivo micro-environments. This study introduces a custom-designed microfluidic device to encapsulate yeasts in micro-droplets under various conditions in a parallel manner. The results reveal that optimal glucose concentrations promoted yeast growth while cycloheximide and Cu2+ ions inhibited it. This platform enhances yeast cultivation strategies and holds potential for high-throughput single-cell investigations in more complex organisms.
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Affiliation(s)
| | - Yung-Shin Sun
- Department of Physics, Fu-Jen Catholic University, New Taipei City 24205, Taiwan;
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3
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Fang W, Liu X, Maiga M, Cao W, Mu Y, Yan Q, Zhu Q. Digital PCR for Single-Cell Analysis. BIOSENSORS 2024; 14:64. [PMID: 38391982 PMCID: PMC10886679 DOI: 10.3390/bios14020064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 01/18/2024] [Accepted: 01/22/2024] [Indexed: 02/24/2024]
Abstract
Single-cell analysis provides an overwhelming strategy for revealing cellular heterogeneity and new perspectives for understanding the biological function and disease mechanism. Moreover, it promotes the basic and clinical research in many fields at a single-cell resolution. A digital polymerase chain reaction (dPCR) is an absolute quantitative analysis technology with high sensitivity and precision for DNA/RNA or protein. With the development of microfluidic technology, digital PCR has been used to achieve absolute quantification of single-cell gene expression and single-cell proteins. For single-cell specific-gene or -protein detection, digital PCR has shown great advantages. So, this review will introduce the significance and process of single-cell analysis, including single-cell isolation, single-cell lysis, and single-cell detection methods, mainly focusing on the microfluidic single-cell digital PCR technology and its biological application at a single-cell level. The challenges and opportunities for the development of single-cell digital PCR are also discussed.
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Affiliation(s)
- Weibo Fang
- Research Center for Analytical Instrumentation, Institute of Cyber-Systems and Control, College of Control Science and Engineering, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou 310027, China; (W.F.); (X.L.); (M.M.); (W.C.); (Y.M.)
| | - Xudong Liu
- Research Center for Analytical Instrumentation, Institute of Cyber-Systems and Control, College of Control Science and Engineering, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou 310027, China; (W.F.); (X.L.); (M.M.); (W.C.); (Y.M.)
| | - Mariam Maiga
- Research Center for Analytical Instrumentation, Institute of Cyber-Systems and Control, College of Control Science and Engineering, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou 310027, China; (W.F.); (X.L.); (M.M.); (W.C.); (Y.M.)
| | - Wenjian Cao
- Research Center for Analytical Instrumentation, Institute of Cyber-Systems and Control, College of Control Science and Engineering, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou 310027, China; (W.F.); (X.L.); (M.M.); (W.C.); (Y.M.)
| | - Ying Mu
- Research Center for Analytical Instrumentation, Institute of Cyber-Systems and Control, College of Control Science and Engineering, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou 310027, China; (W.F.); (X.L.); (M.M.); (W.C.); (Y.M.)
| | - Qiang Yan
- Department of Hepatobiliary and Pancreatic Surgery, Huzhou Central Hospital, Huzhou Key Laboratory of Intelligent and Digital Precision Surgery, Department of General Surgery, Affiliated Huzhou Hospital, School of Medicine, Zhejiang University, Huzhou 313000, China
| | - Qiangyuan Zhu
- Research Center for Analytical Instrumentation, Institute of Cyber-Systems and Control, College of Control Science and Engineering, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou 310027, China; (W.F.); (X.L.); (M.M.); (W.C.); (Y.M.)
- Huzhou Institute of Zhejiang University, Huzhou 313002, China
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4
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Gao Z, Yan J, Shi L, Liu X, Wang M, Li C, Huai Z, Wang C, Wang X, Zhang L, Yan W. Efficient Surfactant-Mediated Photovoltaic Manipulation of fL-Scale Aqueous Microdroplets for Diverse Optofluidic Applications on LiNbO 3 Platform. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023:e2304081. [PMID: 37526054 DOI: 10.1002/adma.202304081] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 07/16/2023] [Indexed: 08/02/2023]
Abstract
The electrodeless biocompatible manipulation of femtoliter-scale aqueous microdroplets remains challenging. The appropriate isolation of electrostatic charges from femtoliter-scale aqueous microdroplets is crucial for electrodeless optoelectronic manipulation based on space-charge-density modulation. Here, surfactant-mediated photovoltaic manipulation is proposed, where the surfactant layers self-assembled at the water-oil and oil-Lithium niobate interfaces are employed to isolate photovoltaic charges. The reduced electrostatic attenuation, remarkable hydrophobicity, and strong electrical breakdown suppression of the surfactant layers enable the stable and swift manipulation of femtoliter-scale aqueous microdroplets using µW-level laser in oil media. By virtue of the surfactant-mediated photovoltaic manipulation, a controllable merging/touching/detaching switch of aqueous microdroplets by adjusting the laser illumination intensity and position is realized and the cascading biochemical operations and microreactions of aqueous microdroplets and microdroplet strings are demonstrated. To demonstrate its potential in photonic Micro-Electro-Mechanical-System assemblies, the end coupling of a focused-laser-beam into a ZnO microrod leveraging the refraction effect occurring at the water/oil interface is demonstrated. Moreover, because of the selective permeability of the droplet-interface-bilayer developed between the touching microdroplets, in situ adjustment of the size of the microdroplets and the fluorescent solute contained in the microdroplets are achieved, aiming at constructing multicomponent fluorescent microdroplets with tunable whispering-gallery-mode characteristics.
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Affiliation(s)
- Zuoxuan Gao
- State Key Laboratory of Reliability and Intelligence of Electrical Equipment, School of Materials Science and Engineering, Hebei University of Technology, Tianjin, 300130, China
- Hebei Engineering Laboratory of Photoelectronic Functional Crystals School of Materials Science and Engineering, Hebei University of Technology, Tianjin, 300130, China
| | - Jinghui Yan
- State Key Laboratory of Reliability and Intelligence of Electrical Equipment, School of Materials Science and Engineering, Hebei University of Technology, Tianjin, 300130, China
- Hebei Engineering Laboratory of Photoelectronic Functional Crystals School of Materials Science and Engineering, Hebei University of Technology, Tianjin, 300130, China
| | - Lihong Shi
- Department of Physics, Tianjin Chengjian University, Tianjin, 300384, China
| | - Xiaohu Liu
- State Key Laboratory of Reliability and Intelligence of Electrical Equipment, School of Materials Science and Engineering, Hebei University of Technology, Tianjin, 300130, China
- Hebei Engineering Laboratory of Photoelectronic Functional Crystals School of Materials Science and Engineering, Hebei University of Technology, Tianjin, 300130, China
| | - Mengtong Wang
- State Key Laboratory of Reliability and Intelligence of Electrical Equipment, School of Materials Science and Engineering, Hebei University of Technology, Tianjin, 300130, China
- Hebei Engineering Laboratory of Photoelectronic Functional Crystals School of Materials Science and Engineering, Hebei University of Technology, Tianjin, 300130, China
| | - Chenyu Li
- State Key Laboratory of Reliability and Intelligence of Electrical Equipment, School of Materials Science and Engineering, Hebei University of Technology, Tianjin, 300130, China
- Hebei Engineering Laboratory of Photoelectronic Functional Crystals School of Materials Science and Engineering, Hebei University of Technology, Tianjin, 300130, China
| | - Zechao Huai
- State Key Laboratory of Reliability and Intelligence of Electrical Equipment, School of Materials Science and Engineering, Hebei University of Technology, Tianjin, 300130, China
- Hebei Engineering Laboratory of Photoelectronic Functional Crystals School of Materials Science and Engineering, Hebei University of Technology, Tianjin, 300130, China
| | - Cheng Wang
- State Key Laboratory of Reliability and Intelligence of Electrical Equipment, School of Materials Science and Engineering, Hebei University of Technology, Tianjin, 300130, China
- Hebei Engineering Laboratory of Photoelectronic Functional Crystals School of Materials Science and Engineering, Hebei University of Technology, Tianjin, 300130, China
| | - Xuan Wang
- State Key Laboratory of Reliability and Intelligence of Electrical Equipment, School of Materials Science and Engineering, Hebei University of Technology, Tianjin, 300130, China
- Hebei Engineering Laboratory of Photoelectronic Functional Crystals School of Materials Science and Engineering, Hebei University of Technology, Tianjin, 300130, China
| | - Lina Zhang
- State Key Laboratory of Reliability and Intelligence of Electrical Equipment, School of Materials Science and Engineering, Hebei University of Technology, Tianjin, 300130, China
- Hebei Engineering Laboratory of Photoelectronic Functional Crystals School of Materials Science and Engineering, Hebei University of Technology, Tianjin, 300130, China
| | - Wenbo Yan
- State Key Laboratory of Reliability and Intelligence of Electrical Equipment, School of Materials Science and Engineering, Hebei University of Technology, Tianjin, 300130, China
- Hebei Engineering Laboratory of Photoelectronic Functional Crystals School of Materials Science and Engineering, Hebei University of Technology, Tianjin, 300130, China
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5
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Khariton M, McClune CJ, Brower KK, Klemm S, Sattely ES, Fordyce PM, Wang B. Alleviating Cell Lysate-Induced Inhibition to Enable RT-PCR from Single Cells in Picoliter-Volume Double Emulsion Droplets. Anal Chem 2023; 95:935-945. [PMID: 36598332 DOI: 10.1021/acs.analchem.2c03475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Microfluidic droplet assays enable single-cell polymerase chain reaction (PCR) and sequencing analyses at unprecedented scales, with most methods encapsulating cells within nanoliter-sized single emulsion droplets (water-in-oil). Encapsulating cells within picoliter double emulsion (DE) (water-in-oil-in-water) allows sorting droplets with commercially available fluorescence-activated cell sorter (FACS) machines, making it possible to isolate single cells based on phenotypes of interest for downstream analyses. However, sorting DE droplets with standard cytometers requires small droplets that can pass FACS nozzles. This poses challenges for molecular biology, as prior reports suggest that reverse transcription (RT) and PCR amplification cannot proceed efficiently at volumes below 1 nL due to cell lysate-induced inhibition. To overcome this limitation, we used a plate-based RT-PCR assay designed to mimic reactions in picoliter droplets to systematically quantify and ameliorate the inhibition. We find that RT-PCR is blocked by lysate-induced cleavage of nucleic acid probes and primers, which can be efficiently alleviated through heat lysis. We further show that the magnitude of inhibition depends on the cell type, but that RT-PCR can proceed in low-picoscale reaction volumes for most mouse and human cell lines tested. Finally, we demonstrate one-step RT-PCR from single cells in 20 pL DE droplets with fluorescence quantifiable via FACS. These results open up new avenues for improving picoscale droplet RT-PCR reactions and expanding microfluidic droplet-based single-cell analysis technologies.
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Affiliation(s)
- Margarita Khariton
- Department of Bioengineering, Stanford University, Stanford, California94305, United States
| | - Conor J McClune
- Department of Chemical Engineering, Stanford University, Stanford, California94305, United States.,Howard Hughes Medical Institute, Stanford University, Stanford, California94305, United States
| | - Kara K Brower
- Department of Bioengineering, Stanford University, Stanford, California94305, United States
| | - Sandy Klemm
- Department of Genetics, Stanford University, Stanford, California94305, United States
| | - Elizabeth S Sattely
- Department of Chemical Engineering, Stanford University, Stanford, California94305, United States.,Howard Hughes Medical Institute, Stanford University, Stanford, California94305, United States
| | - Polly M Fordyce
- Department of Bioengineering, Stanford University, Stanford, California94305, United States.,Department of Genetics, Stanford University, Stanford, California94305, United States.,ChEM-H Institute, Stanford University, Stanford, California94305, United States.,Chan Zuckerberg Biohub, San Francisco, California94110, United States
| | - Bo Wang
- Department of Bioengineering, Stanford University, Stanford, California94305, United States
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6
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Leonaviciene G, Mazutis L. RNA cytometry of single-cells using semi-permeable microcapsules. Nucleic Acids Res 2022; 51:e2. [PMID: 36268865 PMCID: PMC9841424 DOI: 10.1093/nar/gkac918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 09/23/2022] [Accepted: 10/07/2022] [Indexed: 01/29/2023] Open
Abstract
Analytical tools for gene expression profiling of individual cells are critical for studying complex biological systems. However, the techniques enabling rapid measurements of gene expression on thousands of single-cells are lacking. Here, we report a high-throughput RNA cytometry for digital profiling of single-cells isolated in liquid droplets enveloped by a thin semi-permeable membrane (microcapsules). Due to the selective permeability of the membrane, the desirable enzymes and reagents can be loaded, or replaced, in the microcapsule at any given step by simply changing the reaction buffer in which the microcapsules are dispersed. Therefore, complex molecular biology workflows can be readily adapted to conduct nucleic acid analysis on encapsulated mammalian cells, or other biological species. The microcapsules support sequential multi-step enzymatic reactions and remain intact under different biochemical conditions, freezing, thawing, and thermocycling. Combining microcapsules with conventional FACS provides a high-throughput approach for conducting RNA cytometry of individual cells based on their digital gene expression signature.
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Affiliation(s)
- Greta Leonaviciene
- Institute of Biotechnology, Life Sciences Centre, Vilnius University, 7 Sauletekio av., Vilnius, LT-10257, Lithuania
| | - Linas Mazutis
- To whom correspondence should be addressed. Tel: +370 5 2234356;
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7
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Abstract
Microfluidics has enabled a new era of cellular and molecular assays due to the small length scales, parallelization, and the modularity of various analysis and actuation functions. Droplet microfluidics, in particular, has been instrumental in providing new tools for biology with its ability to quickly and reproducibly generate drops that act as individual reactors. A notable beneficiary of this technology has been single-cell RNA sequencing, which has revealed new heterogeneities and interactions for the fundamental unit of life. However, viruses far surpass the diversity of cellular life, affect the dynamics of all ecosystems, and are a chronic source of global health crises. Despite their impact on the world, high-throughput and high-resolution viral profiling has been difficult, with conventional methods being limited to population-level averaging, large sample volumes, and few cultivable hosts. Consequently, most viruses have not been identified and studied. Droplet microfluidics holds the potential to address many of these limitations and offers new levels of sensitivity and throughput for virology. This Feature highlights recent efforts that have applied droplet microfluidics to the detection and study of viruses, including for diagnostics, virus-host interactions, and cell-independent virus assays. In combination with traditional virology methods, droplet microfluidics should prove a potent tool toward achieving a better understanding of the most abundant biological species on Earth.
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Affiliation(s)
- Wenyang Jing
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Hee-Sun Han
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, Illinois 61801, United States
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8
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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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