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Zhou WM, Yan YY, Guo QR, Ji H, Wang H, Xu TT, Makabel B, Pilarsky C, He G, Yu XY, Zhang JY. Microfluidics applications for high-throughput single cell sequencing. J Nanobiotechnology 2021; 19:312. [PMID: 34635104 PMCID: PMC8507141 DOI: 10.1186/s12951-021-01045-6] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 09/16/2021] [Indexed: 12/22/2022] Open
Abstract
The inherent heterogeneity of individual cells in cell populations plays significant roles in disease development and progression, which is critical for disease diagnosis and treatment. Substantial evidences show that the majority of traditional gene profiling methods mask the difference of individual cells. Single cell sequencing can provide data to characterize the inherent heterogeneity of individual cells, and reveal complex and rare cell populations. Different microfluidic technologies have emerged for single cell researches and become the frontiers and hot topics over the past decade. In this review article, we introduce the processes of single cell sequencing, and review the principles of microfluidics for single cell analysis. Also, we discuss the common high-throughput single cell sequencing technologies along with their advantages and disadvantages. Lastly, microfluidics applications in single cell sequencing technology for the diagnosis of cancers and immune system diseases are briefly illustrated.
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Affiliation(s)
- Wen-Min Zhou
- Key Laboratory of Molecular Target & Clinical Pharmacology , The State & NMPA Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences & the Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou, 511436, People's Republic of China
| | - Yan-Yan Yan
- School of Medicine, Shanxi Datong University, Datong, 037009, People's Republic of China
| | - Qiao-Ru Guo
- Key Laboratory of Molecular Target & Clinical Pharmacology , The State & NMPA Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences & the Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou, 511436, People's Republic of China
| | - Hong Ji
- Key Laboratory of Molecular Target & Clinical Pharmacology , The State & NMPA Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences & the Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou, 511436, People's Republic of China
| | - Hui Wang
- Guangzhou Institute of Pediatrics/Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510623, People's Republic of China
| | - Tian-Tian Xu
- Guangzhou Institute of Pediatrics/Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510623, People's Republic of China
| | - Bolat Makabel
- Xinjiang Institute of Materia Medica, Urumqi, 830004, People's Republic of China
| | - Christian Pilarsky
- Department of Surgery, Friedrich-Alexander University of Erlangen-Nuremberg (FAU), University Hospital of Erlangen, Erlangen, Germany
| | - Gen He
- Key Laboratory of Molecular Target & Clinical Pharmacology , The State & NMPA Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences & the Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou, 511436, People's Republic of China.
| | - Xi-Yong Yu
- Key Laboratory of Molecular Target & Clinical Pharmacology , The State & NMPA Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences & the Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou, 511436, People's Republic of China.
| | - Jian-Ye Zhang
- Key Laboratory of Molecular Target & Clinical Pharmacology , The State & NMPA Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences & the Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou, 511436, People's Republic of China.
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Microfluidic and Microscale Assays to Examine Regenerative Strategies in the Neuro Retina. MICROMACHINES 2020; 11:mi11121089. [PMID: 33316971 PMCID: PMC7763644 DOI: 10.3390/mi11121089] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 12/03/2020] [Accepted: 12/05/2020] [Indexed: 12/15/2022]
Abstract
Bioengineering systems have transformed scientific knowledge of cellular behaviors in the nervous system (NS) and pioneered innovative, regenerative therapies to treat adult neural disorders. Microscale systems with characteristic lengths of single to hundreds of microns have examined the development and specialized behaviors of numerous neuromuscular and neurosensory components of the NS. The visual system is comprised of the eye sensory organ and its connecting pathways to the visual cortex. Significant vision loss arises from dysfunction in the retina, the photosensitive tissue at the eye posterior that achieves phototransduction of light to form images in the brain. Retinal regenerative medicine has embraced microfluidic technologies to manipulate stem-like cells for transplantation therapies, where de/differentiated cells are introduced within adult tissue to replace dysfunctional or damaged neurons. Microfluidic systems coupled with stem cell biology and biomaterials have produced exciting advances to restore vision. The current article reviews contemporary microfluidic technologies and microfluidics-enhanced bioassays, developed to interrogate cellular responses to adult retinal cues. The focus is on applications of microfluidics and microscale assays within mammalian sensory retina, or neuro retina, comprised of five types of retinal neurons (photoreceptors, horizontal, bipolar, amacrine, retinal ganglion) and one neuroglia (Müller), but excludes the non-sensory, retinal pigmented epithelium.
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Iijima K, Ohyama S, Yuyama K, Shono A, Hashizume M. Selective fabrication of hollow and solid polysaccharide composite fibers using a microfluidic device by controlling polyion complex formation. Polym J 2018. [DOI: 10.1038/s41428-018-0105-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Yu Z, Boehm CR, Hibberd JM, Abell C, Haseloff J, Burgess SJ, Reyna-Llorens I. Droplet-based microfluidic analysis and screening of single plant cells. PLoS One 2018; 13:e0196810. [PMID: 29723275 PMCID: PMC5933695 DOI: 10.1371/journal.pone.0196810] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Accepted: 04/22/2018] [Indexed: 01/18/2023] Open
Abstract
Droplet-based microfluidics has been used to facilitate high-throughput analysis of individual prokaryote and mammalian cells. However, there is a scarcity of similar workflows applicable to rapid phenotyping of plant systems where phenotyping analyses typically are time-consuming and low-throughput. We report on-chip encapsulation and analysis of protoplasts isolated from the emergent plant model Marchantia polymorpha at processing rates of >100,000 cells per hour. We use our microfluidic system to quantify the stochastic properties of a heat-inducible promoter across a population of transgenic protoplasts to demonstrate its potential for assessing gene expression activity in response to environmental conditions. We further demonstrate on-chip sorting of droplets containing YFP-expressing protoplasts from wild type cells using dielectrophoresis force. This work opens the door to droplet-based microfluidic analysis of plant cells for applications ranging from high-throughput characterisation of DNA parts to single-cell genomics to selection of rare plant phenotypes.
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Affiliation(s)
- Ziyi Yu
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Christian R. Boehm
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Julian M. Hibberd
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Chris Abell
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Jim Haseloff
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Steven J. Burgess
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
- * E-mail: (SJB); (IR-L)
| | - Ivan Reyna-Llorens
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
- * E-mail: (SJB); (IR-L)
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Khanmohammadi M, Sakai S, Ashida T, Taya M. Production of hyaluronic-acid-based cell-enclosing microparticles and microcapsules via enzymatic reaction using a microfluidic system. J Appl Polym Sci 2015. [DOI: 10.1002/app.43107] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Mehdi Khanmohammadi
- Division of Chemical Engineering, Department of Materials Science and Engineering, Graduate School of Engineering Science; Osaka University; Toyonaka Osaka Japan
| | - Shinji Sakai
- Division of Chemical Engineering, Department of Materials Science and Engineering, Graduate School of Engineering Science; Osaka University; Toyonaka Osaka Japan
| | - Tomoaki Ashida
- Division of Chemical Engineering, Department of Materials Science and Engineering, Graduate School of Engineering Science; Osaka University; Toyonaka Osaka Japan
| | - Masahito Taya
- Division of Chemical Engineering, Department of Materials Science and Engineering, Graduate School of Engineering Science; Osaka University; Toyonaka Osaka Japan
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Sakai S, Kawakami K. Development of Subsieve-Size Capsules and Application to Cell Therapy. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2010; 670:22-30. [DOI: 10.1007/978-1-4419-5786-3_3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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Clausell-Tormos J, Lieber D, Baret JC, El-Harrak A, Miller OJ, Frenz L, Blouwolff J, Humphry KJ, Köster S, Duan H, Holtze C, Weitz DA, Griffiths AD, Merten CA. Droplet-Based Microfluidic Platforms for the Encapsulation and Screening of Mammalian Cells and Multicellular Organisms. ACTA ACUST UNITED AC 2008; 15:427-37. [DOI: 10.1016/j.chembiol.2008.04.004] [Citation(s) in RCA: 497] [Impact Index Per Article: 31.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2007] [Revised: 04/02/2008] [Accepted: 04/08/2008] [Indexed: 10/22/2022]
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Choi CH, Jung JH, Rhee YW, Kim DP, Shim SE, Lee CS. Generation of monodisperse alginate microbeads and in situ encapsulation of cell in microfluidic device. Biomed Microdevices 2008; 9:855-62. [PMID: 17578667 DOI: 10.1007/s10544-007-9098-7] [Citation(s) in RCA: 156] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A microfluidic method for the in situ production of monodispersed alginate hydrogels using chaotic mixing is described. Aqueous droplets comprising of alginate and calcium as a cross-linking agent were formed as an immiscible continuous phase, and then the alginate and calcium in the droplet came into contact and were rapidly mixed. Gelation of the hydrogel was achieved in situ by the chaotic mixing of the droplets in the microfluidic device. Important operating parameters included: the capillary number (Ca) and the flow rate of the continuous phase, which mainly influenced the formation of three distinctive flow regimes, such as fluctuation, stable droplets, and laminar flow. Under the stable formation of droplets regime, monodispersed alginate microbeads having a narrow size distribution (below 3% of CV) were produced in the microfluidic device and the size of the microbeads, ranging from 60 to 95 microm, could be easily modulated by varying the flow rate, viscosity, and interfacial tension. In addition, this approach can be applied to the encapsulation of yeast cells in alginate hydrogels with a high monodispersity. This simple microfluidic technique for the production of monodispersed hydrogels and encapsulation of biomolecules shows strong potential for use in biosensors, cell sensors, drug delivery systems, and cell transplantation applications.
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Affiliation(s)
- Chang-Hyung Choi
- Department of Chemical Engineering, Chungnam National University, Yuseong-gu, Daejeon 305-764, South Korea
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Takei T, Sakai S, Ijima H, Kawakami K. Development of mammalian cell-enclosing calcium-alginate hydrogel fibers in a co-flowing stream. Biotechnol J 2006; 1:1014-7. [PMID: 16941441 DOI: 10.1002/biot.200600055] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
A jetting technique in a liquid-liquid co-flowing stream was applied to the preparation of mammalian cell-enclosing calcium-alginate (Ca-alg) hydrogel fibers of several hundred micrometers in cross-sectional diameter. One percent alginate aqueous solution was extruded from needles (270, 480, 940 microm inner diameter) into a co-flowing laminar stream of 100 mM aqueous calcium chloride solution. The extruded alginate solution was stretched by the CaCl(2) solution, which is known as a "jetting process", and the Ca-alg hydrogel fibers were formed by gelation of the alginate solution through the uptake of calcium ions in the CaCl(2) solution. The cross-sectional diameter of the hydrogel fibers could be controlled from approximately 100-800 microm by changing the velocities of the alginate and CaCl(2) solution, and the inner diameter of the needle. Approximately 95% of bovine carotid artery vascular endothelial cells remained alive after the process of preparing hydrogel fibers in a co-flowing stream, demonstrating that the cell-enclosing process scarcely influences the viability of the enclosed cells.
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Affiliation(s)
- Takayuki Takei
- Department of Chemical Engineering, Faculty of Engineering, Kyushu University, Fukuoka, Japan.
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Usefulness of flow focusing technology for producing subsieve-size cell enclosing capsules: Application for agarose capsules production. Biochem Eng J 2006. [DOI: 10.1016/j.bej.2006.04.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Sakai S, Hashimoto I, Kawakami K. Development of alginate–agarose subsieve-size capsules for subsequent modification with a polyelectrolyte complex membrane. Biochem Eng J 2006. [DOI: 10.1016/j.bej.2006.02.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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