1
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Qiao Y, Cheng T, Miao Z, Cui Y, Tu J. Recent Innovations and Technical Advances in High-Throughput Parallel Single-Cell Whole-Genome Sequencing Methods. SMALL METHODS 2024:e2400789. [PMID: 38979872 DOI: 10.1002/smtd.202400789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2024] [Indexed: 07/10/2024]
Abstract
Single-cell whole-genome sequencing (scWGS) detects cell heterogeneity at the aspect of genomic variations, which are inheritable and play an important role in life processes such as aging and cancer progression. The recent explosive development of high-throughput single-cell sequencing methods has enabled high-performance heterogeneity detection through a vast number of novel strategies. Despite the limitation on total cost, technical advances in high-throughput single-cell whole-genome sequencing methods are made for higher genome coverage, parallel throughput, and level of integration. This review highlights the technical advancements in high-throughput scWGS in the aspects of strategies design, data efficiency, parallel handling platforms, and their applications on human genome. The experimental innovations, remaining challenges, and perspectives are summarized and discussed.
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Affiliation(s)
- Yi Qiao
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Tianguang Cheng
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Zikun Miao
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Yue Cui
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Jing Tu
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
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2
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Bartkova S, Zapotoczna M, Sanka I, Scheler O. A Guide to Biodetection in Droplets. Anal Chem 2024; 96:9745-9755. [PMID: 38842026 PMCID: PMC11190884 DOI: 10.1021/acs.analchem.3c04282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 05/21/2024] [Accepted: 05/22/2024] [Indexed: 06/07/2024]
Abstract
Droplet-based methods for optical biodetection enable unprecedented high-throughput experimental parameters. The methods, however, remain underused due to the accompanying multidisciplinary and complicated experimental workflows. Here, we provide a tutorial for droplet-based optical biodetection workflows with a focus on the key aspect of label selection. By discussing and guiding readers through recent state-of-the-art studies, we aim to make droplet-based approaches more accessible to the general scientific public.
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Affiliation(s)
- Simona Bartkova
- Department
of Chemistry and Biotechnology, Tallinn
University of Technology (TalTech), Akadeemia tee 15, Tallinn 12618, Estonia
| | - Marta Zapotoczna
- Faculty
of Biology, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02-089 Warsaw, Poland
| | - Immanuel Sanka
- Department
of Chemistry and Biotechnology, Tallinn
University of Technology (TalTech), Akadeemia tee 15, Tallinn 12618, Estonia
| | - Ott Scheler
- Department
of Chemistry and Biotechnology, Tallinn
University of Technology (TalTech), Akadeemia tee 15, Tallinn 12618, Estonia
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3
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Liang L, Liang M, Zuo Z, Ai Y. Label-free single-cell analysis in microdroplets using a light-scattering-based optofluidic chip. Biosens Bioelectron 2024; 253:116148. [PMID: 38428071 DOI: 10.1016/j.bios.2024.116148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 02/01/2024] [Accepted: 02/19/2024] [Indexed: 03/03/2024]
Abstract
Droplet-based single-cell analysis is a very powerful tool for studying phenotypic and genomic heterogeneity at single-cell resolution for a variety of biological problems. In conventional two-phase droplet microfluidics, due to the mismatch in optical properties between oil and aqueous phases, light scattering mainly happens at the oil/water interface that disables light-scattering-based cell analysis confined in microdroplets. Detection and analysis of cells in microdroplets thus mostly rely on the fluorescence labeling of cell samples, which may suffer from complex operation, cytotoxicity, and low fluorescence stability. In this work, we propose a novel light-scattering-based droplet screening (LSDS) that can effectively detect and characterize single cells confined in droplets by adjusting the optical properties of droplets in a multiangle optofluidic chip. Theoretical and simulated calculations suggest that refractive index (RI) matching in droplet two-phase materials can reduce or eliminate droplets' scattered signals (background signal), enabling the differentiation of scattered signals from single cells and particles within droplets. Furthermore, by using a set of multiangle (from -145° to 140°) optical fibers integrated into the optofluidic chip, the scattered light properties of droplets with the RI ranging from 1.334 to 1.429 are measured. We find that the smaller the RI and size of microparticles inside droplets are, the smaller the RI difference between two-phase materials Δn is required. Especially, when Δn is smaller than 0.02, single cells in droplets can be detected and analyzed solely based on light scattering. This capability allows to accurately detect droplets containing one single cell and one single gel bead, a typical droplet encapsulation for single-cell sequencing. Altogether, this work provides a powerful platform for high-throughput label-free single-cell analysis in microdroplets for diverse single-cell related biological assays.
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Affiliation(s)
- Li Liang
- School of Physics and Electronic Information, Anhui Normal University, Wuhu, 241000, China
| | - Minhui Liang
- Pillar of Engineering Product Development, Singapore University of Technology and Design, Singapore, 487372, Singapore
| | - Zewen Zuo
- School of Physics and Electronic Information, Anhui Normal University, Wuhu, 241000, China
| | - Ye Ai
- Pillar of Engineering Product Development, Singapore University of Technology and Design, Singapore, 487372, Singapore.
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4
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Ding Y, Peng YY, Li S, Tang C, Gao J, Wang HY, Long ZY, Lu XM, Wang YT. Single-Cell Sequencing Technology and Its Application in the Study of Central Nervous System Diseases. Cell Biochem Biophys 2024; 82:329-342. [PMID: 38133792 DOI: 10.1007/s12013-023-01207-3] [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: 08/21/2023] [Accepted: 11/30/2023] [Indexed: 12/23/2023]
Abstract
The mammalian central nervous system consists of a large number of cells, which contain not only different types of neurons, but also a large number of glial cells, such as astrocytes, oligodendrocytes, and microglia. These cells are capable of performing highly refined electrophysiological activities and providing the brain with functions such as nutritional support, information transmission and pathogen defense. The diversity of cell types and individual differences between cells have brought inspiration to the study of the mechanism of central nervous system diseases. In order to explore the role of different cells, a new technology, single-cell sequencing technology has emerged to perform specific analysis of high-throughput cell populations, and has been continuously developed. Single-cell sequencing technology can accurately analyze single-cell expression in mixed-cell populations and collect cells from different spatial locations, time stages and types. By using single-cell sequencing technology to compare gene expression profiles of normal and diseased cells, it is possible to discover cell subsets associated with specific diseases and their associated genes. Therefore, scientists can understand the development process, related functions and disease state of the nervous system from an unprecedented depth. In conclusion, single-cell sequencing technology provides a powerful technology for the discovery of novel therapeutic targets for central nervous system diseases.
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Affiliation(s)
- Yang Ding
- College of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, 400054, China
- State Key Laboratory of Trauma and Chemical Poisoning, Daping Hospital, Army Medical University, Chongqing, 400042, China
| | - Yu-Yuan Peng
- College of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, 400054, China
| | - Sen Li
- State Key Laboratory of Trauma and Chemical Poisoning, Daping Hospital, Army Medical University, Chongqing, 400042, China
| | - Can Tang
- College of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, 400054, China
| | - Jie Gao
- College of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, 400054, China
| | - Hai-Yan Wang
- State Key Laboratory of Trauma and Chemical Poisoning, Daping Hospital, Army Medical University, Chongqing, 400042, China
| | - Zai-Yun Long
- State Key Laboratory of Trauma and Chemical Poisoning, Daping Hospital, Army Medical University, Chongqing, 400042, China
| | - Xiu-Min Lu
- College of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, 400054, China.
| | - Yong-Tang Wang
- State Key Laboratory of Trauma and Chemical Poisoning, Daping Hospital, Army Medical University, Chongqing, 400042, China.
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5
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Kim S, Lam PY, Jayaraman A, Han A. Uniform sized cancer spheroids production using hydrogel-based droplet microfluidics: a review. Biomed Microdevices 2024; 26:26. [PMID: 38806765 PMCID: PMC11241584 DOI: 10.1007/s10544-024-00712-3] [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] [Accepted: 05/16/2024] [Indexed: 05/30/2024]
Abstract
Three-dimensional (3D) cell culture models have been extensively utilized in various mechanistic studies as well as for drug development studies as superior in vitro platforms than conventional two-dimensional (2D) cell culture models. This is especially the case in cancer biology, where 3D cancer models, such as spheroids or organoids, have been utilized extensively to understand the mechanisms of cancer development. Recently, many sophisticated 3D models such as organ-on-a-chip models are emerging as advanced in vitro models that can more accurately mimic the in vivo tissue functions. Despite such advancements, spheroids are still considered as a powerful 3D cancer model due to the relatively simple structure and compatibility with existing laboratory instruments, and also can provide orders of magnitude higher throughput than complex in vitro models, an extremely important aspects for drug development. However, creating well-defined spheroids remain challenging, both in terms of throughputs in generation as well as reproducibility in size and shape that can make it challenging for drug testing applications. In the past decades, droplet microfluidics utilizing hydrogels have been highlighted due to their potentials. Importantly, core-shell structured gel droplets can avoid spheroid-to-spheroid adhesion that can cause large variations in assays while also enabling long-term cultivation of spheroids with higher uniformity by protecting the core organoid area from external environment while the outer porous gel layer still allows nutrient exchange. Hence, core-shell gel droplet-based spheroid formation can improve the predictivity and reproducibility of drug screening assays. This review paper will focus on droplet microfluidics-based technologies for cancer spheroid production using various gel materials and structures. In addition, we will discuss emerging technologies that have the potential to advance the production of spheroids, prospects of such technologies, and remaining challenges.
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Affiliation(s)
- Sungjin Kim
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX, USA
| | - Po Yi Lam
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX, USA
| | - Arul Jayaraman
- Department of Chemical Engineering, Texas A&M University, College Station, TX, USA
| | - Arum Han
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX, USA.
- Department of Biomedical Engineering, Texas A&M University, College Station, TX, USA.
- Department of Chemical Engineering, Texas A&M University, College Station, TX, USA.
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6
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Zia AB, Farrell J, Foulds IG. Automated dynamic inlet microfluidics system: 3D printer adaptation for cost-effective, low volume, on-demand multi-analyte droplet generator. LAB ON A CHIP 2024; 24:3015-3026. [PMID: 38745471 DOI: 10.1039/d4lc00075g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
The paper demonstrates an adaptation of a 3D printer (Prusa Mini+) with novel modules to develop a droplet generation system that generates combinatorial droplets from a standard 96 well plate. The calibration methodology developed would allow any fused deposition modeling (FDM) printer to generate monodisperse droplets (coefficient of variance (CV%) < 5%) from well plates or vials of any geometry. The system maintains precision across various volumes while maintaining a C.V. range of 0.81% to 3.61%, with an increased precision for larger volumes. The cost of the system developed is 70% less than commercially available droplet generation packages. Successful droplet library storage is accomplished via 3D printed cartridge connectors. The implemented system has been calibrated for Tygon® and PTFE at different velocities and volumetric configurations.
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Affiliation(s)
- Abdul Basit Zia
- School of Engineering, The University of British Columbia, Okanagan Campus, Kelowna, BC, Canada.
| | - Justin Farrell
- School of Engineering, The University of British Columbia, Okanagan Campus, Kelowna, BC, Canada.
| | - Ian G Foulds
- School of Engineering, The University of British Columbia, Okanagan Campus, Kelowna, BC, Canada.
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7
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Xu F, Ma L, Fan Y. Air trap and removal on a pressure driven PDMS-based microfluidic device. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2024; 95:055003. [PMID: 38739426 DOI: 10.1063/5.0190337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 04/23/2024] [Indexed: 05/14/2024]
Abstract
With the development of microfluidic technology, microfluidic chips have played a positive role in applications such as cell culture, microfluidic PCR, and nanopore gene sequencing. However, the presence of bubbles interferes with fluid flow and has a significant impact on experimental results. There are many reasons for the generation of bubbles in microfluidic chips, such as pressure changes inside the chip, air vibration inside the chip, and the open chip guiding air into the chip when driving fluid. This study designed and prepared a microfluidic device based on polydimethylsiloxane. First, air was actively introduced into the microfluidic chip, and bubbles were captured through the microfluidic device to simulate the presence of bubbles inside the chip in biological experiments. To remove bubbles trapped in the microfluidic chip, distilled water, distilled water containing surfactants, and mineral oil were pumped into the microfluidic chip. We compared and discussed the bubble removal efficiency under different driving fluids, driving pressures, and open/closed channel configurations. This study helps to understand the mechanism of bubble formation and removal in microfluidic devices, optimize chip structure design and experimental reagent selection, prevent or eliminate bubbles, and reduce the impact of bubbles on experiments.
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Affiliation(s)
- Fan Xu
- School of Mechanical and Electrical Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Liang Ma
- Department of Clinical Laboratory, China-Japan Friendship Hospital, Beijing 100029, China
| | - Yiqiang Fan
- School of Mechanical and Electrical Engineering, Beijing University of Chemical Technology, Beijing 100029, China
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8
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Tanaka D, Zheng S, Furuya M, Kobayashi M, Fujita H, Akitsu T, Sekiguchi T, Shoji S. Efficient Separation of Methanol Single-Micron Droplets by Tailing Phenomenon Using a PDMS Microfluidic Device. Molecules 2024; 29:1949. [PMID: 38731440 PMCID: PMC11085517 DOI: 10.3390/molecules29091949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 04/11/2024] [Accepted: 04/17/2024] [Indexed: 05/13/2024] Open
Abstract
Microdroplet-based fluidic systems have the advantages of small size, short diffusion time, and no cross-contamination; consequently, droplets often provide a fast and precise reaction environment as well as an analytical environment for individual molecules. In order to handle diverse reactions, we developed a method to create organic single-micron droplets (S-MDs) smaller than 5 μm in diameter dispersed in silicone oil without surfactant. The S-MD generation microflow device consists of a mother droplet (MoD) generator and a tapered separation channel featuring multiple side channels. The tapered channel enhanced the shear forces to form tails from the MoDs, causing them to break up. Surface treatment with the fluoropolymer CYTOP protected PDMS fluid devices from organic fluids. The tailing separation of methanol droplets was accomplished without the use of surfactants. The generation of tiny organic droplets may offer new insights into chemical separation and help study the scaling effects of various chemical reactions.
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Affiliation(s)
- Daiki Tanaka
- Department of Electronic and Physical Systems, School of Fundamental Science and Engineering, Waseda University, Tokyo 145-0065, Japan; (S.Z.); (S.S.)
| | - Shengqi Zheng
- Department of Electronic and Physical Systems, School of Fundamental Science and Engineering, Waseda University, Tokyo 145-0065, Japan; (S.Z.); (S.S.)
| | - Masahiro Furuya
- Cooperative Major in Nuclear Energy, Waseda University, Tokyo 169-8555, Japan; (M.F.); (M.K.)
| | - Masashi Kobayashi
- Cooperative Major in Nuclear Energy, Waseda University, Tokyo 169-8555, Japan; (M.F.); (M.K.)
| | | | - Takashiro Akitsu
- Department of Chemistry, Faculty of Science, Tokyo University of Science, Tokyo 162-0825, Japan;
| | - Tetsushi Sekiguchi
- Research Organization for Nano & Life Innovation, Waseda University, Tokyo 162-0041, Japan;
| | - Shuichi Shoji
- Department of Electronic and Physical Systems, School of Fundamental Science and Engineering, Waseda University, Tokyo 145-0065, Japan; (S.Z.); (S.S.)
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9
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Ahmadpour A, Shojaeian M, Tasoglu S. Deep learning-augmented T-junction droplet generation. iScience 2024; 27:109326. [PMID: 38510144 PMCID: PMC10951907 DOI: 10.1016/j.isci.2024.109326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 01/13/2024] [Accepted: 02/20/2024] [Indexed: 03/22/2024] Open
Abstract
Droplet generation technology has become increasingly important in a wide range of applications, including biotechnology and chemical synthesis. T-junction channels are commonly used for droplet generation due to their integration capability of a larger number of droplet generators in a compact space. In this study, a finite element analysis (FEA) approach is employed to simulate droplet production and its dynamic regimes in a T-junction configuration and collect data for post-processing analysis. Next, image analysis was performed to calculate the droplet length and determine the droplet generation regime. Furthermore, machine learning (ML) and deep learning (DL) algorithms were applied to estimate outputs through examination of input parameters within the simulation range. At the end, a graphical user interface (GUI) was developed for estimation of the droplet characteristics based on inputs, enabling the users to preselect their designs with comparable microfluidic configurations within the studied range.
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Affiliation(s)
- Abdollah Ahmadpour
- Mechanical Engineering Department, School of Engineering, Koç University, Istanbul 34450, Türkiye
| | - Mostafa Shojaeian
- Mechanical Engineering Department, School of Engineering, Koç University, Istanbul 34450, Türkiye
| | - Savas Tasoglu
- Mechanical Engineering Department, School of Engineering, Koç University, Istanbul 34450, Türkiye
- Koç University Arçelik Research Center for Creative Industries (KUAR), Koç University, Istanbul 34450, Türkiye
- Koç University Is Bank Artificial Intelligence Lab (KUIS AILab), Koç University, Sariyer, Istanbul 34450, Türkiye
- Koç University Translational Medicine Research Center (KUTTAM), Koç University, Istanbul 34450, Türkiye
- Boğaziçi Institute of Biomedical Engineering, Boğaziçi University, Istanbul 34684, Türkiye
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10
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Asama R, Liu CJS, Tominaga M, Cheng YR, Nakamura Y, Kondo A, Wang HY, Ishii J. Droplet-based microfluidic platform for detecting agonistic peptides that are self-secreted by yeast expressing a G-protein-coupled receptor. Microb Cell Fact 2024; 23:104. [PMID: 38594681 PMCID: PMC11005146 DOI: 10.1186/s12934-024-02379-0] [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: 01/12/2024] [Accepted: 03/22/2024] [Indexed: 04/11/2024] Open
Abstract
BACKGROUND Single-cell droplet microfluidics is an important platform for high-throughput analyses and screening because it provides an independent and compartmentalized microenvironment for reaction or cultivation by coencapsulating individual cells with various molecules in monodisperse microdroplets. In combination with microbial biosensors, this technology becomes a potent tool for the screening of mutant strains. In this study, we demonstrated that a genetically engineered yeast strain that can fluorescently sense agonist ligands via the heterologous expression of a human G-protein-coupled receptor (GPCR) and concurrently secrete candidate peptides is highly compatible with single-cell droplet microfluidic technology for the high-throughput screening of new agonistically active peptides. RESULTS The water-in-oil microdroplets were generated using a flow-focusing microfluidic chip to encapsulate engineered yeast cells coexpressing a human GPCR [i.e., angiotensin II receptor type 1 (AGTR1)] and a secretory agonistic peptide [i.e., angiotensin II (Ang II)]. The single yeast cells cultured in the droplets were then observed under a microscope and analyzed using image processing incorporating machine learning techniques. The AGTR1-mediated signal transduction elicited by the self-secreted Ang II peptide was successfully detected via the expression of a fluorescent reporter in single-cell yeast droplet cultures. The system could also distinguish Ang II analog peptides with different agonistic activities. Notably, we further demonstrated that the microenvironment of the single-cell droplet culture enabled the detection of rarely existing positive (Ang II-secreting) yeast cells in the model mixed cell library, whereas the conventional batch-culture environment using a shake flask failed to do so. Thus, our approach provided compartmentalized microculture environments, which can prevent the diffusion, dilution, and cross-contamination of peptides secreted from individual single yeast cells for the easy identification of GPCR agonists. CONCLUSIONS We established a droplet-based microfluidic platform that integrated an engineered yeast biosensor strain that concurrently expressed GPCR and self-secreted the agonistic peptides. This offers individually isolated microenvironments that allow the culture of single yeast cells secreting these peptides and gaging their signaling activities, for the high-throughput screening of agonistic peptides. Our platform base on yeast GPCR biosensors and droplet microfluidics will be widely applicable to metabolic engineering, environmental engineering, and drug discovery.
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Affiliation(s)
- Ririka Asama
- Graduate School of Science, Technology, and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan
| | - Cher J S Liu
- Department of Engineering and System Science, National Tsing Hua University, Hsinchu, 30013, Taiwan
| | - Masahiro Tominaga
- Graduate School of Science, Technology, and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan
- Engineering Biology Research Center, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan
| | - Yu-Ru Cheng
- Department of Engineering and System Science, National Tsing Hua University, Hsinchu, 30013, Taiwan
| | - Yasuyuki Nakamura
- Graduate School of Science, Technology, and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan
- Engineering Biology Research Center, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan
- Bacchus Bio Innovation Co., Ltd., 6-3-7 Minatojima-Minami, Chuo, Kobe, 650-0047, Japan
| | - Akihiko Kondo
- Graduate School of Science, Technology, and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan
- Engineering Biology Research Center, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan
- Department of Chemical Science and Engineering, Faculty of Engineering, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan
- Center for Sustainable Resource Science, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama, 230-0045, Japan
| | - Hsiang-Yu Wang
- Department of Engineering and System Science, National Tsing Hua University, Hsinchu, 30013, Taiwan.
| | - Jun Ishii
- Graduate School of Science, Technology, and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan.
- Engineering Biology Research Center, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan.
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11
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Jyoti TP, Chandel S, Singh R. Unveiling the epigenetic landscape of plants using flow cytometry approach. Cytometry A 2024; 105:231-241. [PMID: 38437027 DOI: 10.1002/cyto.a.24834] [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: 09/23/2023] [Revised: 01/12/2024] [Accepted: 02/22/2024] [Indexed: 03/06/2024]
Abstract
Plants are sessile creatures that have to adapt constantly changing environmental circumstances. Plants are subjected to a range of abiotic stressors as a result of unpredictable climate change. Understanding how stress-responsive genes are regulated can help us better understand how plants can adapt to changing environmental conditions. Epigenetic markers that dynamically change in response to stimuli, such as DNA methylation and histone modifications are known to regulate gene expression. Individual cells or particles' physical and/or chemical properties can be measured using the method known as flow cytometry. It may therefore be used to evaluate changes in DNA methylation, histone modifications, and other epigenetic markers, making it a potent tool for researching epigenetics in plants. We explore the use of flow cytometry as a technique for examining epigenetic traits in this thorough discussion. The separation of cell nuclei and their subsequent labeling with fluorescent antibodies, offering information on the epigenetic mechanisms in plants when utilizing flow cytometry. We also go through the use of high-throughput data analysis methods to unravel the complex epigenetic processes occurring inside plant systems.
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Affiliation(s)
- Thakur Prava Jyoti
- Department of Pharmacognosy, ISF College of Pharmacy, Moga, Punjab, India
| | - Shivani Chandel
- Department of Pharmacognosy, ISF College of Pharmacy, Moga, Punjab, India
| | - Rajveer Singh
- Department of Pharmacognosy, ISF College of Pharmacy, Moga, Punjab, India
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12
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Jiang L, Guo K, Chen Y, Xiang N. Droplet Microfluidics for Current Cancer Research: From Single-Cell Analysis to 3D Cell Culture. ACS Biomater Sci Eng 2024; 10:1335-1354. [PMID: 38420753 DOI: 10.1021/acsbiomaterials.3c01866] [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] [Indexed: 03/02/2024]
Abstract
Cancer is the second leading cause of death worldwide. Differences in drug resistance and treatment response caused by the heterogeneity of cancer cells are the primary reasons for poor cancer therapy outcomes in patients. In addition, current in vitro anticancer drug-screening methods rely on two-dimensional monolayer-cultured cancer cells, which cannot accurately predict drug behavior in vivo. Therefore, a powerful tool to study the heterogeneity of cancer cells and produce effective in vitro tumor models is warranted to leverage cancer research. Droplet microfluidics has become a powerful platform for the single-cell analysis of cancer cells and three-dimensional cell culture of in vitro tumor spheroids. In this review, we discuss the use of droplet microfluidics in cancer research. Droplet microfluidic technologies, including single- or double-emulsion droplet generation and passive- or active-droplet manipulation, are concisely discussed. Recent advances in droplet microfluidics for single-cell analysis of cancer cells, circulating tumor cells, and scaffold-free/based 3D cell culture of tumor spheroids have been systematically introduced. Finally, the challenges that must be overcome for the further application of droplet microfluidics in cancer research are discussed.
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Affiliation(s)
- Lin Jiang
- School of Mechanical Engineering, and Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, Southeast University, Nanjing 211189, China
| | - Kefan Guo
- School of Mechanical Engineering, and Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, Southeast University, Nanjing 211189, China
| | - Yao Chen
- School of Mechanical Engineering, and Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, Southeast University, Nanjing 211189, China
| | - Nan Xiang
- School of Mechanical Engineering, and Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, Southeast University, Nanjing 211189, China
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13
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Britel A, Tomagra G, Aprà P, Varzi V, Sturari S, Amine NH, Olivero P, Picollo F. 3D printing in microfluidics: experimental optimization of droplet size and generation time through flow focusing, phase, and geometry variation. RSC Adv 2024; 14:7770-7778. [PMID: 38444974 PMCID: PMC10913413 DOI: 10.1039/d4ra00752b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 02/26/2024] [Indexed: 03/07/2024] Open
Abstract
Droplet-based microfluidics systems have become widely used in recent years thanks to their advantages, varying from the possibility of handling small fluid volumes to directly synthesizing and encapsulating various living forms for biological-related applications. The effectiveness of such systems mainly depends on the ability to control some of these systems' parameters, such as produced droplet size and formation time, which represents a challenging task. This work reports an experimental study on tuning droplet size and generation time in a flow-focusing geometry fabricated with stereolithography 3D printing by exploring the interplay of phase and geometrical parameters. We produced droplets at different low flow rates of continuous and dispersed phases to assess the effect of each of these phases on the droplets' size and formation time. We observed that smaller droplets were produced for high viscosity oil and water phase, along with high flow rates. In addition, changing the microfluidics channels' width, and morphology of the orifice has shown a similar effect on droplet size, as shown in the case of high-viscosity solutions. The variation of the bifurcation angle shows a noticeable variation in terms of the achieved droplet size and formation time. We further investigated the impact of modifying the width ratio of the continuous and dispersed phases on droplet formation.
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Affiliation(s)
- Adam Britel
- Department of Physics, "NIS" Inter-departmental Centre, University of Torino, National Institute of Nuclear Physics Sect. Torino, Via Pietro Giuria 1 10125 Torino Italy
| | - Giulia Tomagra
- Department of Drug and Science Technology, NIS Interdepartmental Centre, University of Torino Corso Raffaello 30 10125 Torino Italy
| | - Pietro Aprà
- Department of Physics, "NIS" Inter-departmental Centre, University of Torino, National Institute of Nuclear Physics Sect. Torino, Via Pietro Giuria 1 10125 Torino Italy
| | - Veronica Varzi
- Department of Physics, "NIS" Inter-departmental Centre, University of Torino, National Institute of Nuclear Physics Sect. Torino, Via Pietro Giuria 1 10125 Torino Italy
| | - Sofia Sturari
- Department of Physics, "NIS" Inter-departmental Centre, University of Torino, National Institute of Nuclear Physics Sect. Torino, Via Pietro Giuria 1 10125 Torino Italy
| | - Nour-Hanne Amine
- Department of Physics, "NIS" Inter-departmental Centre, University of Torino, National Institute of Nuclear Physics Sect. Torino, Via Pietro Giuria 1 10125 Torino Italy
| | - Paolo Olivero
- Department of Physics, "NIS" Inter-departmental Centre, University of Torino, National Institute of Nuclear Physics Sect. Torino, Via Pietro Giuria 1 10125 Torino Italy
| | - Federico Picollo
- Department of Physics, "NIS" Inter-departmental Centre, University of Torino, National Institute of Nuclear Physics Sect. Torino, Via Pietro Giuria 1 10125 Torino Italy
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14
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Tang T, Zhao H, Shen S, Yang L, Lim CT. Enhancing single-cell encapsulation in droplet microfluidics with fine-tunable on-chip sample enrichment. MICROSYSTEMS & NANOENGINEERING 2024; 10:3. [PMID: 38169721 PMCID: PMC10758392 DOI: 10.1038/s41378-023-00631-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 10/17/2023] [Accepted: 10/30/2023] [Indexed: 01/05/2024]
Abstract
Single-cell encapsulation in droplet microfluidics is commonly hindered by the tradeoff between cell suspension density and on-chip focusing performance. In this study, we introduce a novel droplet microfluidic chip to overcome this challenge. The chip comprises a double spiral focusing unit, a flow resistance-based sample enrichment module with fine-tunable outlets, and a crossflow droplet generation unit. Utilizing a low-density cell/bead suspension (2 × 106 objects/mL), cells/beads are focused into a near-equidistant linear arrangement within the double spiral microchannel. The excess water phase is diverted while cells/beads remain focused and sequentially encapsulated in individual droplets. Focusing performance was assessed through numerical simulations and experiments at three flow rates (40, 60, 80 μL/min), demonstrating successful focusing at 40 and 80 μL/min for beads and cells, respectively. In addition, both simulation and experimental results revealed that the flow resistance at the sample enrichment module is adjustable by punching different outlets, allowing over 50% of the aqueous phase to be removed. YOLOv8n-based droplet detection algorithms realized the counting of cells/beads in droplets, statistically demonstrating single-cell and bead encapsulation rates of 72.2% and 79.2%, respectively. All the results indicate that this on-chip sample enrichment approach can be further developed and employed as a critical component in single-cell encapsulation in water-in-oil droplets.
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Affiliation(s)
- Tao Tang
- Department of Biomedical Engineering, National University of Singapore, 117583 Singapore, Singapore
| | - Hao Zhao
- Department of Biomedical Engineering, National University of Singapore, 117583 Singapore, Singapore
- Integrative Sciences and Engineering Programme, NUS Graduate School, National University of Singapore, 119077 Singapore, Singapore
| | - Shaofei Shen
- Shanxi Key Lab for Modernization of TCVM, College of Life Science, Shanxi Agricultural University, Taigu, Shanxi 030801 China
| | - Like Yang
- Department of Biomedical Engineering, National University of Singapore, 117583 Singapore, Singapore
| | - Chwee Teck Lim
- Department of Biomedical Engineering, National University of Singapore, 117583 Singapore, Singapore
- Institute for Health Innovation & Technology, National University of Singapore, 117599 Singapore, Singapore
- Mechanobiology Institute, National University of Singapore, 117411 Singapore, Singapore
- Institute for Digital Molecular Analytics and Science, Nanyang Technological University, 636921 Singapore, Singapore
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15
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Zhong R, Sullivan M, Upreti N, Chen R, De Ganzó A, Yang K, Yang S, Jin K, He Y, Li K, Xia J, Ma Z, Lee LP, Konry T, Huang TJ. Cellular immunity analysis by a modular acoustofluidic platform: CIAMAP. SCIENCE ADVANCES 2023; 9:eadj9964. [PMID: 38134285 PMCID: PMC10745697 DOI: 10.1126/sciadv.adj9964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Accepted: 11/22/2023] [Indexed: 12/24/2023]
Abstract
The study of molecular mechanisms at the single-cell level holds immense potential for enhancing immunotherapy and understanding neuroinflammation and neurodegenerative diseases by identifying previously concealed pathways within a diverse range of paired cells. However, existing single-cell pairing platforms have limitations in low pairing efficiency, complex manual operation procedures, and single-use functionality. Here, we report a multiparametric cellular immunity analysis by a modular acoustofluidic platform: CIAMAP. This platform enables users to efficiently sort and collect effector-target (i.e., NK92-K562) cell pairs and monitor the real-time dynamics of immunological response formation. Furthermore, we conducted transcriptional and protein expression analyses to evaluate the pathways that mediate effector cytotoxicity toward target cells, as well as the synergistic effect of doxorubicin on the cellular immune response. Our CIAMAP can provide promising building blocks for high-throughput quantitative single-cell level coculture to understand intercellular communication while also empowering immunotherapy by precision analysis of immunological synapses.
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Affiliation(s)
- Ruoyu Zhong
- Thomas Lord Department of Mechanical Engineering & Materials Science, Duke University, Durham, NC 27708, USA
| | - Matthew Sullivan
- Department of Pharmaceutical Sciences, Bouvé College of Health Sciences, Northeastern University, Boston, MA 02115, USA
| | - Neil Upreti
- Biomedical Engineering Department, Pratt School of Engineering, Duke University, Durham, NC 27708, USA
| | - Roy Chen
- Biomedical Engineering Department, Pratt School of Engineering, Duke University, Durham, NC 27708, USA
| | - Agustin De Ganzó
- Department of Pharmaceutical Sciences, Bouvé College of Health Sciences, Northeastern University, Boston, MA 02115, USA
| | - Kaichun Yang
- Thomas Lord Department of Mechanical Engineering & Materials Science, Duke University, Durham, NC 27708, USA
| | - Shujie Yang
- Thomas Lord Department of Mechanical Engineering & Materials Science, Duke University, Durham, NC 27708, USA
- Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Ke Jin
- Thomas Lord Department of Mechanical Engineering & Materials Science, Duke University, Durham, NC 27708, USA
| | - Ye He
- Thomas Lord Department of Mechanical Engineering & Materials Science, Duke University, Durham, NC 27708, USA
| | - Ke Li
- Thomas Lord Department of Mechanical Engineering & Materials Science, Duke University, Durham, NC 27708, USA
| | - Jianping Xia
- Thomas Lord Department of Mechanical Engineering & Materials Science, Duke University, Durham, NC 27708, USA
| | - Zhiteng Ma
- Thomas Lord Department of Mechanical Engineering & Materials Science, Duke University, Durham, NC 27708, USA
| | - Luke P. Lee
- Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Department of Bioengineering, Department of Electrical Engineering and Computer Science, University of California, Berkeley, Berkeley, CA 94720, USA
- Institute of Quantum Biophysics, Department of Biophysics, Sungkyunkwan University, Suwon 16419, Republic of Korea
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Tania Konry
- Department of Pharmaceutical Sciences, Bouvé College of Health Sciences, Northeastern University, Boston, MA 02115, USA
| | - Tony Jun Huang
- Thomas Lord Department of Mechanical Engineering & Materials Science, Duke University, Durham, NC 27708, USA
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16
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Yang G, Gao C, Chen D, Wang J, Huo X, Chen J. Multiplex fluorescence detection of single-cell droplet microfluidics and its application in quantifying protein expression levels. BIOMICROFLUIDICS 2023; 17:064106. [PMID: 38162228 PMCID: PMC10754627 DOI: 10.1063/5.0179121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 11/29/2023] [Indexed: 01/03/2024]
Abstract
This study presented a platform of multiplex fluorescence detection of single-cell droplet microfluidics with demonstrative applications in quantifying protein expression levels. The platform of multiplex fluorescence detection mainly included optical paths adopted from conventional microscopy enabling the generation of three optical spots from three laser sources for multiple fluorescence excitation and capture of multiple fluorescence signals by four photomultiplier tubes. As to platform characterization, microscopic images of three optical spots were obtained where clear Gaussian distributions of intensities without skewness confirmed the functionality of the scanning lens, while the controllable distances among three optical spots validated the functionality of fiber collimators and the reflector lens. As to demonstration, this platform was used to quantify single-cell protein expression within droplets where four-type protein expression of α-tubulin, Ras, c-Myc, and β-tubulin of CAL 27 (Ncell = 1921) vs WSU-HN6 (Ncell = 1881) were quantitatively estimated, which were (2.85 ± 0.72) × 105 vs (4.83 ± 1.58) × 105, (3.69 ± 1.41) × 104 vs (5.07 ± 2.13) × 104, (5.90 ± 1.45) × 104 vs (9.57 ± 2.85) × 104, and (3.84 ± 1.28) × 105 vs (3.30 ± 1.10) × 105, respectively. Neural pattern recognition was utilized for the classification of cell types, achieving successful rates of 69.0% (α-tubulin), 75.4% (Ras), 89.1% (c-Myc), 65.8% (β-tubulin), and 99.1% in combination, validating the capability of this platform of multiplex fluorescence detection to quantify various types of single-cell proteins, which could provide comprehensive evaluations on cell status.
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Affiliation(s)
| | | | | | - Junbo Wang
- Authors to whom correspondence should be addressed:; ; and
| | - Xiaoye Huo
- Authors to whom correspondence should be addressed:; ; and
| | - Jian Chen
- Authors to whom correspondence should be addressed:; ; and
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17
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Murakami T, Teratani H, Aoki D, Noguchi M, Tsugane M, Suzuki H. Single-cell trapping and retrieval in open microfluidics. iScience 2023; 26:108323. [PMID: 38026163 PMCID: PMC10656270 DOI: 10.1016/j.isci.2023.108323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 09/28/2023] [Accepted: 10/20/2023] [Indexed: 12/01/2023] Open
Abstract
Among various single-cell analysis platforms, hydrodynamic cell trapping systems remain relevant because of their versatility. Among those, deterministic hydrodynamic cell-trapping systems have received significant interest; however, their applications are limited because trapped cells are kept within the closed microchannel, thus prohibiting access to external cell-picking devices. In this study, we develop a hydrodynamic cell-trapping system in an open microfluidics architecture to allow external access to trapped cells. A technique to render only the inside of a polydimethylsiloxane (PDMS) microchannel hydrophilic is developed, which allows the precise confinement of spontaneous capillary flow in the open-type microchannel with a width on the order of several tens of micrometers. Efficient trapping of single beads and single cells is achieved, in which trapped cells can be retrieved via automated robotic pipetting. The present system can facilitate the development of new single-cell analytical systems by bridging between microfluidic devices and macro-scale apparatus used in conventional biology.
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Affiliation(s)
- Tomoki Murakami
- Department of Precision Mechanics, Graduate School of Science and Engineering, Chuo University, Kasuga 1-13-27, Bunkyo-ku, Tokyo 112-8551, Japan
| | - Hiroto Teratani
- Department of Precision Mechanics, Graduate School of Science and Engineering, Chuo University, Kasuga 1-13-27, Bunkyo-ku, Tokyo 112-8551, Japan
| | - Dai’ichiro Aoki
- Aeternus Co., Ltd, Minamidai 2-1-14, Fujimino, Saitama 356-0036, Japan
| | - Masao Noguchi
- Caravell Co., Ltd, Surugadai 1-29-39, Funabashi, Chiba 273-0862, Japan
| | - Mamiko Tsugane
- Department of Precision Mechanics, Graduate School of Science and Engineering, Chuo University, Kasuga 1-13-27, Bunkyo-ku, Tokyo 112-8551, Japan
| | - Hiroaki Suzuki
- Department of Precision Mechanics, Graduate School of Science and Engineering, Chuo University, Kasuga 1-13-27, Bunkyo-ku, Tokyo 112-8551, Japan
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18
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Liu D, Xuanyuan T, Liu X, Fu W, Liu W. Massive and efficient encapsulation of single cells in monodisperse droplets and collagen-alginate microgels using a microfluidic device. Front Bioeng Biotechnol 2023; 11:1281375. [PMID: 38033813 PMCID: PMC10684782 DOI: 10.3389/fbioe.2023.1281375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 10/30/2023] [Indexed: 12/02/2023] Open
Abstract
Single-cell manipulation is the key foundation of life exploration at individual cell resolution. Constructing easy-to-use, high-throughput, and biomimetic manipulative tools for efficient single-cell operation is quite necessary. In this study, a facile and efficient encapsulation of single cells relying on the massive and controllable production of droplets and collagen-alginate microgels using a microfluidic device is presented. High monodispersity and geometric homogeneity of both droplet and microgel generation were experimentally demonstrated based on the well-investigated microfluidic fabricating procedure. The reliability of the microfluidic platform for controllable, high-throughput, and improved single-cell encapsulation in monodisperse droplets and microgels was also confirmed. A single-cell encapsulation rate of up to 33.6% was achieved based on the established microfluidic operation. The introduction of stromal material in droplets/microgels for encapsulation provided single cells an in vivo simulated microenvironment. The single-cell operation achievement offers a methodological approach for developing simple and miniaturized devices to perform single-cell manipulation and analysis in a high-throughput and microenvironment-biomimetic manner. We believe that it holds great potential for applications in precision medicine, cell microengineering, drug discovery, and biosensing.
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Affiliation(s)
| | | | | | | | - Wenming Liu
- Departments of Biomedical Engineering and Pathology, School of Basic Medical Science, Central South University, Changsha, Hunan, China
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19
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Li W, Huberman-Shlaes J, Tian B. Perspectives on Multiscale Colloid-Based Materials for Biomedical Applications. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:13759-13769. [PMID: 37733490 PMCID: PMC10552542 DOI: 10.1021/acs.langmuir.3c01274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Indexed: 09/23/2023]
Abstract
Colloid-based materials with tunable biophysical and chemical properties have demonstrated significant potential in a wide range of biomedical applications. The ability to manipulate these properties across various size scales, encompassing nano-, micro-, and macrodomains, is essential to enhancing current biomedical technologies and facilitating the development of novel applications. Focusing on material design, we explore various synthetic colloid-based materials at the nano- and microscales and investigate their correlation with biological systems. Furthermore, we examine the utilization of the self-assembly of colloids to construct monolithic and macroscopic materials suitable for biointerfaces. By probing the potential of spatial imaging and localized drug delivery, enhanced functionality, and colloidal manipulation, we highlight emerging opportunities that could significantly advance the field of colloid-based materials in biomedical applications.
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Affiliation(s)
- Wen Li
- Department
of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
| | - Judah Huberman-Shlaes
- Department
of Biology, The University of Chicago, Chicago, Illinois 60637, United States
| | - Bozhi Tian
- Department
of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
- The
James Franck Institute, The University of
Chicago, Chicago, Illinois 60637, United States
- The
Institute for Biophysical Dynamics, The
University of Chicago, Chicago, Illinois 60637, United States
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20
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Han X, Xu X, Yang C, Liu G. Microfluidic design in single-cell sequencing and application to cancer precision medicine. CELL REPORTS METHODS 2023; 3:100591. [PMID: 37725985 PMCID: PMC10545941 DOI: 10.1016/j.crmeth.2023.100591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 07/01/2023] [Accepted: 08/24/2023] [Indexed: 09/21/2023]
Abstract
Single-cell sequencing (SCS) is a crucial tool to reveal the genetic and functional heterogeneity of tumors, providing unique insights into the clonal evolution, microenvironment, drug resistance, and metastatic progression of cancers. Microfluidics is a critical component of many SCS technologies and workflows, conferring advantages in throughput, economy, and automation. Here, we review the current landscape of microfluidic architectures and sequencing techniques for single-cell omics analysis and highlight how these have enabled recent applications in oncology research. We also discuss the challenges and the promise of microfluidics-based single-cell analysis in the future of precision oncology.
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Affiliation(s)
- Xin Han
- CUHK(SZ)-Boyalife Joint Laboratory of Regenerative Medicine Engineering, Biomedical Engineering Programme, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China; Ciechanover Institute of Precision and Regenerative Medicine, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China
| | - Xing Xu
- State Key Laboratory of Physical Chemistry of Solid Surfaces, MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Key Laboratory for Chemical Biology of Fujian Province, Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P.R. China; Institute of Molecular Medicine, State Key Laboratory of Oncogenes and Related 12 Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, P.R. China
| | - Chaoyang Yang
- State Key Laboratory of Physical Chemistry of Solid Surfaces, MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Key Laboratory for Chemical Biology of Fujian Province, Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P.R. China; Institute of Molecular Medicine, State Key Laboratory of Oncogenes and Related 12 Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, P.R. China.
| | - Guozhen Liu
- CUHK(SZ)-Boyalife Joint Laboratory of Regenerative Medicine Engineering, Biomedical Engineering Programme, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China; Ciechanover Institute of Precision and Regenerative Medicine, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China.
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21
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Robinson JP, Ostafe R, Iyengar SN, Rajwa B, Fischer R. Flow Cytometry: The Next Revolution. Cells 2023; 12:1875. [PMID: 37508539 PMCID: PMC10378642 DOI: 10.3390/cells12141875] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 07/06/2023] [Accepted: 07/13/2023] [Indexed: 07/30/2023] Open
Abstract
Unmasking the subtleties of the immune system requires both a comprehensive knowledge base and the ability to interrogate that system with intimate sensitivity. That task, to a considerable extent, has been handled by an iterative expansion in flow cytometry methods, both in technological capability and also in accompanying advances in informatics. As the field of fluorescence-based cytomics matured, it reached a technological barrier at around 30 parameter analyses, which stalled the field until spectral flow cytometry created a fundamental transformation that will likely lead to the potential of 100 simultaneous parameter analyses within a few years. The simultaneous advance in informatics has now become a watershed moment for the field as it competes with mature systematic approaches such as genomics and proteomics, allowing cytomics to take a seat at the multi-omics table. In addition, recent technological advances try to combine the speed of flow systems with other detection methods, in addition to fluorescence alone, which will make flow-based instruments even more indispensable in any biological laboratory. This paper outlines current approaches in cell analysis and detection methods, discusses traditional and microfluidic sorting approaches as well as next-generation instruments, and provides an early look at future opportunities that are likely to arise.
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Affiliation(s)
- J Paul Robinson
- Department of Basic Medical Sciences, Purdue University, West Lafayette, IN 47907, USA
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN 47907, USA
| | - Raluca Ostafe
- Molecular Evolution, Protein Engineering and Production Facility (PI4D), Purdue University, West Lafayette, IN 47907, USA
| | | | - Bartek Rajwa
- Bindley Bioscience Center, Purdue University, West Lafayette, IN 47907, USA
| | - Rainer Fischer
- Department of Comparative Pathobiology, College of Veterinary Medicine, Purdue University, West Lafayette, IN 47907, USA
- Purdue Institute of Inflammation, Immunology and Infectious Diseases, Purdue University, West Lafayette, IN 47907, USA
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22
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Cardoso BD, Castanheira EMS, Lanceros-Méndez S, Cardoso VF. Recent Advances on Cell Culture Platforms for In Vitro Drug Screening and Cell Therapies: From Conventional to Microfluidic Strategies. Adv Healthc Mater 2023; 12:e2202936. [PMID: 36898671 DOI: 10.1002/adhm.202202936] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 02/27/2023] [Indexed: 03/12/2023]
Abstract
The clinical translations of drugs and nanomedicines depend on coherent pharmaceutical research based on biologically accurate screening approaches. Since establishing the 2D in vitro cell culture method, the scientific community has improved cell-based drug screening assays and models. Those advances result in more informative biochemical assays and the development of 3D multicellular models to describe the biological complexity better and enhance the simulation of the in vivo microenvironment. Despite the overall dominance of conventional 2D and 3D cell macroscopic culture methods, they present physicochemical and operational challenges that impair the scale-up of drug screening by not allowing a high parallelization, multidrug combination, and high-throughput screening. Their combination and complementarity with microfluidic platforms enable the development of microfluidics-based cell culture platforms with unequivocal advantages in drug screening and cell therapies. Thus, this review presents an updated and consolidated view of cell culture miniaturization's physical, chemical, and operational considerations in the pharmaceutical research scenario. It clarifies advances in the field using gradient-based microfluidics, droplet-based microfluidics, printed-based microfluidics, digital-based microfluidics, SlipChip, and paper-based microfluidics. Finally, it presents a comparative analysis of the performance of cell-based methods in life research and development to achieve increased precision in the drug screening process.
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Affiliation(s)
- Beatriz D Cardoso
- Physics Centre of Minho and Porto Universities (CF-UM-UP), Campus de Gualtar, University of Minho, Braga, 4710-057, Portugal
- LaPMET-Laboratory of Physics for Materials and Emergent Technologies, University of Minho, 4710-057, Braga, Portugal
- Center for MicroElectromechanical Systems (CMEMS-UMinho), Campus de Azurém, University of Minho, 4800-058, Guimarães, Portugal
- LABBELS-Associate Laboratory in Biotechnology and Bioengineering and Microelectromechanical Systems, University of Minho, Braga/Guimarães, Portugal
| | - Elisabete M S Castanheira
- Physics Centre of Minho and Porto Universities (CF-UM-UP), Campus de Gualtar, University of Minho, Braga, 4710-057, Portugal
- LaPMET-Laboratory of Physics for Materials and Emergent Technologies, University of Minho, 4710-057, Braga, Portugal
| | - Senentxu Lanceros-Méndez
- Physics Centre of Minho and Porto Universities (CF-UM-UP), Campus de Gualtar, University of Minho, Braga, 4710-057, Portugal
- LaPMET-Laboratory of Physics for Materials and Emergent Technologies, University of Minho, 4710-057, Braga, Portugal
- BCMaterials, Basque Center for Materials, Applications and Nanostructures, UPV/EHU Science Park, Leioa, 48940, Spain
- IKERBASQUE, Basque Foundation for Science, Bilbao, 48009, Spain
| | - Vanessa F Cardoso
- Center for MicroElectromechanical Systems (CMEMS-UMinho), Campus de Azurém, University of Minho, 4800-058, Guimarães, Portugal
- LABBELS-Associate Laboratory in Biotechnology and Bioengineering and Microelectromechanical Systems, University of Minho, Braga/Guimarães, Portugal
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23
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Jiang J, Yang G, Ma F. Fluorescence coupling strategies in fluorescence-activated droplet sorting (FADS) for ultrahigh-throughput screening of enzymes, metabolites, and antibodies. Biotechnol Adv 2023; 66:108173. [PMID: 37169102 DOI: 10.1016/j.biotechadv.2023.108173] [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: 01/11/2023] [Revised: 04/17/2023] [Accepted: 05/06/2023] [Indexed: 05/13/2023]
Abstract
Fluorescence-activated droplet sorting (FADS) has emerged as a powerful tool for ultrahigh-throughput screening of enzymes, metabolites, and antibodies. Fluorescence coupling strategies (FCSs) are key to the development of new FADS methods through their coupling of analyte properties such as concentration, activities, and affinity with fluorescence signals. Over the last decade, a series of FCSs have been developed, greatly expanding applications of FADS. Here, we review recent advances in FCS for different analyte types, providing a critical comparison of the available FCSs and further classification into four categories according to their principles. We also summarize successful FADS applications employing FCSs in enzymes, metabolites, and antibodies. Further, we outline possible future developments in this area.
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Affiliation(s)
- Jingjie Jiang
- Medical Enzyme Engineering Center, CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, Jiangsu 215163, China
| | - Guangyu Yang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Fuqiang Ma
- Medical Enzyme Engineering Center, CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, Jiangsu 215163, China.
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24
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Ma X, Guo G, Wu X, Wu Q, Liu F, Zhang H, Shi N, Guan Y. Advances in Integration, Wearable Applications, and Artificial Intelligence of Biomedical Microfluidics Systems. MICROMACHINES 2023; 14:mi14050972. [PMID: 37241596 DOI: 10.3390/mi14050972] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 04/20/2023] [Accepted: 04/25/2023] [Indexed: 05/28/2023]
Abstract
Microfluidics attracts much attention due to its multiple advantages such as high throughput, rapid analysis, low sample volume, and high sensitivity. Microfluidics has profoundly influenced many fields including chemistry, biology, medicine, information technology, and other disciplines. However, some stumbling stones (miniaturization, integration, and intelligence) strain the development of industrialization and commercialization of microchips. The miniaturization of microfluidics means fewer samples and reagents, shorter times to results, and less footprint space consumption, enabling a high throughput and parallelism of sample analysis. Additionally, micro-size channels tend to produce laminar flow, which probably permits some creative applications that are not accessible to traditional fluid-processing platforms. The reasonable integration of biomedical/physical biosensors, semiconductor microelectronics, communications, and other cutting-edge technologies should greatly expand the applications of current microfluidic devices and help develop the next generation of lab-on-a-chip (LOC). At the same time, the evolution of artificial intelligence also gives another strong impetus to the rapid development of microfluidics. Biomedical applications based on microfluidics normally bring a large amount of complex data, so it is a big challenge for researchers and technicians to analyze those huge and complicated data accurately and quickly. To address this problem, machine learning is viewed as an indispensable and powerful tool in processing the data collected from micro-devices. In this review, we mainly focus on discussing the integration, miniaturization, portability, and intelligence of microfluidics technology.
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Affiliation(s)
- Xingfeng Ma
- School of Communication and Information Engineering, Shanghai University, Shanghai 200000, China
- Department of Microelectronics, Shanghai University, Shanghai 200000, China
| | - Gang Guo
- Department of Microelectronics, Shanghai University, Shanghai 200000, China
| | - Xuanye Wu
- Department of Microelectronics, Shanghai University, Shanghai 200000, China
- Shanghai Industrial μTechnology Research Institute, Shanghai 200000, China
| | - Qiang Wu
- Shanghai Aure Technology Limited Company, Shanghai 200000, China
| | - Fangfang Liu
- Shanghai Industrial μTechnology Research Institute, Shanghai 200000, China
| | - Hua Zhang
- Shanghai Aure Technology Limited Company, Shanghai 200000, China
| | - Nan Shi
- Shanghai Industrial μTechnology Research Institute, Shanghai 200000, China
- Institute of Translational Medicine, Shanghai University, Shanghai 200000, China
| | - Yimin Guan
- Department of Microelectronics, Shanghai University, Shanghai 200000, China
- Shanghai Aure Technology Limited Company, Shanghai 200000, China
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Zhong J, Liang M, Tang Q, Ai Y. Selectable encapsulated cell quantity in droplets via label-free electrical screening and impedance-activated sorting. Mater Today Bio 2023; 19:100594. [PMID: 36910274 PMCID: PMC9999206 DOI: 10.1016/j.mtbio.2023.100594] [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: 01/02/2023] [Revised: 02/21/2023] [Accepted: 02/22/2023] [Indexed: 03/02/2023] Open
Abstract
Single-cell encapsulation in droplets has become a powerful tool in immunotherapy, medicine discovery, and single-cell analysis, thanks to its capability for cell confinement in picoliter volumes. However, the purity and throughput of single-cell droplets are limited by random encapsulation process, which resuts in a majority of empty and multi-cells droplets. Herein we introduce the first label-free selectable cell quantity encapsulation in droplets sorting system to overcome this problem. The system utilizes a simple and reliable electrical impedance based screening (98.9% of accuracy) integrated with biocompatible acoustic sorting to select single-cell droplets, achieving 90.3% of efficiency and up to 200 Hz of throughput, by removing multi-cells (∼60% of rejection) and empty droplets (∼90% of rejection). We demonstrate the use of the droplet sorting to improve the throughput of single-cell encapsulation by ∼9-fold compared to the conventional random encapsulation process.
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Affiliation(s)
- Jianwei Zhong
- Pillar of Engineering Product Development, Singapore University of Technology and Design, 8 Somapah Road, Singapore, 487372, Singapore
| | - Minhui Liang
- Pillar of Engineering Product Development, Singapore University of Technology and Design, 8 Somapah Road, Singapore, 487372, Singapore
| | - Qiang Tang
- Jiangsu Provincial Engineering Research Center for Biomedical Materials and Advanced Medical Devices, Faculty of Mechanical and Material Engineering, Huaiyin Institute of Technology, Huaian, 223003, China
| | - Ye Ai
- Pillar of Engineering Product Development, Singapore University of Technology and Design, 8 Somapah Road, Singapore, 487372, Singapore
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26
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Ryu J, Kim J, Han KH. dDrop-Chip: disposable film-chip microfluidic device for real-time droplet feedback control. LAB ON A CHIP 2023; 23:1896-1904. [PMID: 36877075 DOI: 10.1039/d2lc01069k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
A cost-effective, simple to use, and automated technique that can provide real-time feedback control for droplet generation is required to obtain droplets with high-throughput, stability, and uniformity. This study introduces a disposable droplet generation microfluidic device (dDrop-Chip) that can simultaneously control both droplet size and production rate in real time. The dDrop-Chip consists of a reusable sensing substrate and a disposable microchannel that can be assembled using vacuum pressure. It also integrates a droplet detector and a flow sensor on-chip, enabling real-time measurement and feedback control of droplet size and sample flow rate. The dDrop-Chip has the additional advantage of being disposable, which can prevent chemical and biological contamination, due to low manufacturing cost by the film-chip technique. We demonstrate benefits of the dDrop-Chip by controlling droplet size at a fixed sample flow rate and the production rate at a fixed droplet size using real-time feedback control. The experimental results show that the dDrop-Chip consistently generates monodisperse droplets with a length of 219.36 ± 0.08 μm (CV 0.036%) at a production rate of 32.38 ± 0.48 Hz using the feedback control, while without feedback control, there is a significant deviation in droplet length (224.18 ± 6.69 μm, CV 2.98%) and production rate (33.94 ± 1.72 Hz) despite the use of identical devices. Therefore, the dDrop-Chip is a reliable, cost-effective, and automated technique for generating droplets of controlled size and production rate in real time, making it suitable for various droplet-based applications.
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Affiliation(s)
- Jaewook Ryu
- Department of Nanoscience and Engineering, Center for Nano Manufacturing, Inje University, 197, Inje-Ro, Gimhae 50834, Gyeongnam, Republic of Korea.
| | - Junhyeong Kim
- Department of Nanoscience and Engineering, Center for Nano Manufacturing, Inje University, 197, Inje-Ro, Gimhae 50834, Gyeongnam, Republic of Korea.
| | - Ki-Ho Han
- Department of Nanoscience and Engineering, Center for Nano Manufacturing, Inje University, 197, Inje-Ro, Gimhae 50834, Gyeongnam, Republic of Korea.
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27
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Gebreyesus ST, Muneer G, Huang CC, Siyal AA, Anand M, Chen YJ, Tu HL. Recent advances in microfluidics for single-cell functional proteomics. LAB ON A CHIP 2023; 23:1726-1751. [PMID: 36811978 DOI: 10.1039/d2lc01096h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Single-cell proteomics (SCP) reveals phenotypic heterogeneity by profiling individual cells, their biological states and functional outcomes upon signaling activation that can hardly be probed via other omics characterizations. This has become appealing to researchers as it enables an overall more holistic view of biological details underlying cellular processes, disease onset and progression, as well as facilitates unique biomarker identification from individual cells. Microfluidic-based strategies have become methods of choice for single-cell analysis because they allow facile assay integrations, such as cell sorting, manipulation, and content analysis. Notably, they have been serving as an enabling technology to improve the sensitivity, robustness, and reproducibility of recently developed SCP methods. Critical roles of microfluidics technologies are expected to further expand rapidly in advancing the next phase of SCP analysis to reveal more biological and clinical insights. In this review, we will capture the excitement of the recent achievements of microfluidics methods for both targeted and global SCP, including efforts to enhance the proteomic coverage, minimize sample loss, and increase multiplexity and throughput. Furthermore, we will discuss the advantages, challenges, applications, and future prospects of SCP.
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Affiliation(s)
- Sofani Tafesse Gebreyesus
- Institute of Chemistry, Academia Sinica, Taipei 11529, Taiwan.
- Nano Science and Technology Program, Taiwan International Graduate Program, Academia Sinica, Taipei 11529, Taiwan
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan
| | - Gul Muneer
- Institute of Chemistry, Academia Sinica, Taipei 11529, Taiwan.
- Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica, Taipei 11529, Taiwan
- Institute of Biochemical Sciences, National Taiwan University, Taipei 10617, Taiwan
| | | | - Asad Ali Siyal
- Institute of Chemistry, Academia Sinica, Taipei 11529, Taiwan.
| | - Mihir Anand
- Institute of Chemistry, Academia Sinica, Taipei 11529, Taiwan.
- Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica, Taipei 11529, Taiwan
- Institute of Biochemical Sciences, National Taiwan University, Taipei 10617, Taiwan
| | - Yu-Ju Chen
- Institute of Chemistry, Academia Sinica, Taipei 11529, Taiwan.
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan
- Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica, Taipei 11529, Taiwan
- Genome and Systems Biology Degree Program, Academia Sinica and National Taiwan University, Taipei 10617, Taiwan
| | - Hsiung-Lin Tu
- Institute of Chemistry, Academia Sinica, Taipei 11529, Taiwan.
- Nano Science and Technology Program, Taiwan International Graduate Program, Academia Sinica, Taipei 11529, Taiwan
- Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica, Taipei 11529, Taiwan
- Genome and Systems Biology Degree Program, Academia Sinica and National Taiwan University, Taipei 10617, Taiwan
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28
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Tang W, He M, Chen B, Ruan G, Xia Y, Xu P, Song G, Bi Y, Hu B. Investigation of toxic effect of mercury on Microcystis aeruginosa: Correlation between intracellular mercury content at single cells level and algae physiological responses. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 858:159894. [PMID: 36336050 DOI: 10.1016/j.scitotenv.2022.159894] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 10/28/2022] [Accepted: 10/29/2022] [Indexed: 06/16/2023]
Abstract
Single-cell studies can help to understand individual differences and obtain atypical cellular characteristics in view of cellular heterogeneity. Herein, the accumulation of mercury (Hg) in single algae cells was studied by droplet chip-time resolved inductively coupled plasma mass spectrometry analytical system, and the relation of Hg accumulation to the physiological responses of algae cell was explored. When low concentrations of Hg2+ (5-20 μg/L) were used in the exposure experiment, the content of Hg in single cells increased in first 2 h, then decreased with further increase of exposure time to 96 h, probably due to the growth dilution effect of the algae. When exposed to 30 μg/L Hg2+, the uptake of Hg by individual cells increased over time, which was associated with increased cell membrane permeability. The exposure to Hg2+ (5-30 μg/L) inhibited the growth of algae in a concentration-dependent manner and serious growth inhibition occurred under the exposure concentration of 30 μg/L. While the exposure concentration was lower than 20 μg/L, algal cells exhibited a recover tendency due to the self-protection mechanism of algal cells. Bivariate results showed that intracellular Hg accumulation was significantly negatively correlated with cells growth in terms of OD680, photosynthetic pigments, Fv/Fm and PIabs. On the contrast, reactive oxygen species content, superoxide dismutase activity, and cell membrane permeability were significantly positively correlated with the accumulation of intracellular Hg. These results are helpful to further understand the toxic effect of Hg on algae.
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Affiliation(s)
- Wenxiao Tang
- Department of Chemistry, Wuhan University, Wuhan 430072, China
| | - Man He
- Department of Chemistry, Wuhan University, Wuhan 430072, China
| | - Beibei Chen
- Department of Chemistry, Wuhan University, Wuhan 430072, China
| | - Gang Ruan
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Yixue Xia
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Pingping Xu
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Gaofei Song
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Yonghong Bi
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Bin Hu
- Department of Chemistry, Wuhan University, Wuhan 430072, China.
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29
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Jiang L, Yang H, Cheng W, Ni Z, Xiang N. Droplet microfluidics for CTC-based liquid biopsy: a review. Analyst 2023; 148:203-221. [PMID: 36508171 DOI: 10.1039/d2an01747d] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Circulating tumor cells (CTCs) are important biomarkers of liquid biopsy. The number and heterogeneity of CTCs play an important role in cancer diagnosis and personalized medicine. However, owing to the low-abundance biomarkers of CTCs, conventional assays are only able to detect CTCs at the population level. Therefore, there is a pressing need for a highly sensitive method to analyze CTCs at the single-cell level. As an important branch of microfluidics, droplet microfluidics is a high-throughput and sensitive single-cell analysis platform for the quantitative detection and heterogeneity analysis of CTCs. In this review, we focus on the quantitative detection and heterogeneity analysis of CTCs using droplet microfluidics. Technologies that enable droplet microfluidics, particularly high-throughput droplet generation and high-efficiency droplet manipulation, are first discussed. Then, recent advances in detecting and analyzing CTCs using droplet microfluidics from the different aspects of nucleic acids, proteins, and metabolites are introduced. The purpose of this review is to provide guidance for the continued study of droplet microfluidics for CTC-based liquid biopsy.
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Affiliation(s)
- Lin Jiang
- School of Mechanical Engineering, and Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, Southeast University, Nanjing, 211189, China.
| | - Hang Yang
- School of Mechanical Engineering, and Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, Southeast University, Nanjing, 211189, China.
| | - Weiqi Cheng
- School of Mechanical Engineering, and Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, Southeast University, Nanjing, 211189, China.
| | - Zhonghua Ni
- School of Mechanical Engineering, and Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, Southeast University, Nanjing, 211189, China.
| | - Nan Xiang
- School of Mechanical Engineering, and Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, Southeast University, Nanjing, 211189, China.
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30
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Single-cell extracellular vesicle analysis by microfluidics and beyond. Trends Analyt Chem 2023. [DOI: 10.1016/j.trac.2023.116930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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31
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Li B, Ma X, Cheng J, Tian T, Guo J, Wang Y, Pang L. Droplets microfluidics platform-A tool for single cell research. Front Bioeng Biotechnol 2023; 11:1121870. [PMID: 37152651 PMCID: PMC10154550 DOI: 10.3389/fbioe.2023.1121870] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 04/03/2023] [Indexed: 05/09/2023] Open
Abstract
Cells are the most basic structural and functional units of living organisms. Studies of cell growth, differentiation, apoptosis, and cell-cell interactions can help scientists understand the mysteries of living systems. However, there is considerable heterogeneity among cells. Great differences between individuals can be found even within the same cell cluster. Cell heterogeneity can only be clearly expressed and distinguished at the level of single cells. The development of droplet microfluidics technology opens up a new chapter for single-cell analysis. Microfluidic chips can produce many nanoscale monodisperse droplets, which can be used as small isolated micro-laboratories for various high-throughput, precise single-cell analyses. Moreover, gel droplets with good biocompatibility can be used in single-cell cultures and coupled with biomolecules for various downstream analyses of cellular metabolites. The droplets are also maneuverable; through physical and chemical forces, droplets can be divided, fused, and sorted to realize single-cell screening and other related studies. This review describes the channel design, droplet generation, and control technology of droplet microfluidics and gives a detailed overview of the application of droplet microfluidics in single-cell culture, single-cell screening, single-cell detection, and other aspects. Moreover, we provide a recent review of the application of droplet microfluidics in tumor single-cell immunoassays, describe in detail the advantages of microfluidics in tumor research, and predict the development of droplet microfluidics at the single-cell level.
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Affiliation(s)
- Bixuan Li
- Xi’an Key Laboratory of Pathogenic Microorganism and Tumor Immunity, Xi’an, China
- School of Basic Medicine, Xi’an Medical University, Xi’an, China
| | - Xi Ma
- Xi’an Key Laboratory of Pathogenic Microorganism and Tumor Immunity, Xi’an, China
- School of Basic Medicine, Xi’an Medical University, Xi’an, China
| | - Jianghong Cheng
- Xi’an Key Laboratory of Pathogenic Microorganism and Tumor Immunity, Xi’an, China
- School of Basic Medicine, Xi’an Medical University, Xi’an, China
| | - Tian Tian
- Xi’an Key Laboratory of Pathogenic Microorganism and Tumor Immunity, Xi’an, China
- School of Basic Medicine, Xi’an Medical University, Xi’an, China
| | - Jiao Guo
- Xi’an Key Laboratory of Pathogenic Microorganism and Tumor Immunity, Xi’an, China
- School of Basic Medicine, Xi’an Medical University, Xi’an, China
| | - Yang Wang
- Xi’an Key Laboratory of Pathogenic Microorganism and Tumor Immunity, Xi’an, China
- School of Basic Medicine, Xi’an Medical University, Xi’an, China
- *Correspondence: Yang Wang,
| | - Long Pang
- Xi’an Key Laboratory of Pathogenic Microorganism and Tumor Immunity, Xi’an, China
- School of Basic Medicine, Xi’an Medical University, Xi’an, China
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32
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Huang C, Jiang Y, Li Y, Zhang H. Droplet Detection and Sorting System in Microfluidics: A Review. MICROMACHINES 2022; 14:mi14010103. [PMID: 36677164 PMCID: PMC9867185 DOI: 10.3390/mi14010103] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 12/23/2022] [Accepted: 12/26/2022] [Indexed: 05/26/2023]
Abstract
Since being invented, droplet microfluidic technologies have been proven to be perfect tools for high-throughput chemical and biological functional screening applications, and they have been heavily studied and improved through the past two decades. Each droplet can be used as one single bioreactor to compartmentalize a big material or biological population, so millions of droplets can be individually screened based on demand, while the sorting function could extract the droplets of interest to a separate pool from the main droplet library. In this paper, we reviewed droplet detection and active sorting methods that are currently still being widely used for high-through screening applications in microfluidic systems, including the latest updates regarding each technology. We analyze and summarize the merits and drawbacks of each presented technology and conclude, with our perspectives, on future direction of development.
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Affiliation(s)
- Can Huang
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX 77842, USA
| | - Yuqian Jiang
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Yuwen Li
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX 77842, USA
| | - Han Zhang
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX 77842, USA
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33
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Recent advances in microfluidic single-cell analysis and its applications in drug development. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116796] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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34
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Yang G, Yang H, Zhang T, Gao C, Chen D, Wang J, Chen J. Quantitative flow cytometry leveraging
droplet‐based
constriction microchannels with high reliability and high sensitivity. Cytometry A 2022; 103:429-438. [PMID: 36420790 DOI: 10.1002/cyto.a.24705] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 10/08/2022] [Accepted: 11/08/2022] [Indexed: 11/24/2022]
Abstract
This study presented a quantitative flow cytometry leveraging droplet-based constriction microchannels with high reliability and high sensitivity. Droplets encapsulating single cells and even distribution of fluorescein labeled antibodies removed from targeted cells deformed through the constriction microchannel where the excited fluorescent signals were sampled and interpreted into numbers of proteins based on volume equivalence in measurement of droplets and calibration of fluorescence. To improve the detection reliability, a comprehensive analysis and comparison of multiple stripping agents such as proteinase K, guanidine hydrochloride, and urea was conducted. To improve the detection sensitivity, light modulation was used to address electrical noises and quartz microchannels were fabricated to address optical noises. As a demonstration, based on this quantitative flow cytometry of droplet microfluidics, (1) mutant p53 expressions of single cells were quantified as 1.95 ± 0.60 × 105 (ncell = 2918 of A431) and 1.30 ± 0.70 × 105 (ncell = 3954 of T47D); (2) single-cell expressions of Ras, c-Myc, and β-tubulin were quantified as 1.90 ± 0.59 × 105 , 4.39 ± 1.44 × 105 , and 2.97 ± 0.81 × 105 (ncell = 3298 of CAL 27), 1.83 ± 0.58 × 105 , 2.08 ± 0.13 × 106 , and 1.96 ± 0.74 × 105 (ncell = 5459 of WSU-HN6). As a microfluidic tool capable of quantitatively estimating single-cell protein expressions, this methodology may provide a new quantitative perspective for the field of flow cytometry.
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Affiliation(s)
- Guang Yang
- State Key Laboratory of Transducer Technology Aerospace Information Research Institute of Chinese Academy of Sciences Beijing China
- School of Electronic, Electrical and Communication Engineering University of Chinese Academy of Sciences Beijing China
| | - Hongyu Yang
- State Key Laboratory of Transducer Technology Aerospace Information Research Institute of Chinese Academy of Sciences Beijing China
- School of Future Technology University of Chinese Academy of Sciences Beijing China
| | - Ting Zhang
- State Key Laboratory of Transducer Technology Aerospace Information Research Institute of Chinese Academy of Sciences Beijing China
- School of Future Technology University of Chinese Academy of Sciences Beijing China
| | - Chiyuan Gao
- State Key Laboratory of Transducer Technology Aerospace Information Research Institute of Chinese Academy of Sciences Beijing China
- School of Future Technology University of Chinese Academy of Sciences Beijing China
| | - Deyong Chen
- State Key Laboratory of Transducer Technology Aerospace Information Research Institute of Chinese Academy of Sciences Beijing China
- School of Electronic, Electrical and Communication Engineering University of Chinese Academy of Sciences Beijing China
- School of Future Technology University of Chinese Academy of Sciences Beijing China
| | - Junbo Wang
- State Key Laboratory of Transducer Technology Aerospace Information Research Institute of Chinese Academy of Sciences Beijing China
- School of Electronic, Electrical and Communication Engineering University of Chinese Academy of Sciences Beijing China
- School of Future Technology University of Chinese Academy of Sciences Beijing China
| | - Jian Chen
- State Key Laboratory of Transducer Technology Aerospace Information Research Institute of Chinese Academy of Sciences Beijing China
- School of Electronic, Electrical and Communication Engineering University of Chinese Academy of Sciences Beijing China
- School of Future Technology University of Chinese Academy of Sciences Beijing China
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