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Sun Y, Liu Y, Sun D, Liu K, Li Y, Liu Y, Zhang S. A facile single-cell patterning strategy based on harbor-like microwell microfluidics. Biomed Mater 2024; 19:045018. [PMID: 38772387 DOI: 10.1088/1748-605x/ad4e83] [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: 02/22/2024] [Accepted: 05/21/2024] [Indexed: 05/23/2024]
Abstract
Single-cell analysis is an effective method for conducting comprehensive heterogeneity studies ranging from cell phenotype to gene expression. The ability to arrange different cells in a predetermined pattern at single-cell resolution has a wide range of applications in cell-based analysis and plays an important role in facilitating interdisciplinary research by researchers in various fields. Most existing microfluidic microwell chips is a simple and straightforward method, which typically use small-sized microwells to accommodate single cells. However, this method imposes certain limitations on cells of various sizes, and the single-cell capture efficiency is relatively low without the assistance of external forces. Moreover, the microwells limit the spatiotemporal resolution of reagent replacement, as well as cell-to-cell communication. In this study, we propose a new strategy to prepare a single-cell array on a planar microchannel based on microfluidic flip microwells chip platform with large apertures (50 μm), shallow channels (50 μm), and deep microwells (50 μm). The combination of three configuration characteristics contributes to multi-cell trapping and a single-cell array within microwells, while the subsequent chip flipping accomplishes the transfer of the single-cell array to the opposite planar microchannel for cells adherence and growth. Further assisted by protein coating of bovine serum albumin and fibronectin on different layers, the single-cell capture efficiency in microwells is achieved at 92.1% ± 1%, while ultimately 85% ± 3.4% on planar microchannel. To verify the microfluidic flip microwells chip platform, the real-time and heterogeneous study of calcium release and apoptosis behaviours of single cells is carried out. To our knowledge, this is the first time that high-efficiency single-cell acquisition has been accomplished using a circular-well chip design that combines shallow channel, large aperture and deep microwell together. The chip is effective in avoiding the shearing force of high flow rates on cells, and the large apertures better allows cells to sedimentation. Therefore, this strategy owns the advantages of easy preparation and user-friendliness, which is especially valuable for researchers from different fields.
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Affiliation(s)
- Yingnan Sun
- Shandong Province Key Laboratory of Detection Technology for Tumor Makers, School of Medicine, Linyi University, Linyi 276005, People's Republic of China
| | - Yongshu Liu
- Shandong Province Key Laboratory of Detection Technology for Tumor Makers, School of Medicine, Linyi University, Linyi 276005, People's Republic of China
| | - Dezhi Sun
- Xinjiang Key Laboratory of Signal Detection and Processing, School of Computer Science and Technology, Xinjiang University, Urumqi 830046, People's Republic of China
| | - Kexin Liu
- Shandong Province Key Laboratory of Detection Technology for Tumor Makers, School of Medicine, Linyi University, Linyi 276005, People's Republic of China
| | - Yuyan Li
- Shandong Province Key Laboratory of Detection Technology for Tumor Makers, School of Medicine, Linyi University, Linyi 276005, People's Republic of China
| | - Yumin Liu
- Shandong Province Key Laboratory of Detection Technology for Tumor Makers, School of Medicine, Linyi University, Linyi 276005, People's Republic of China
| | - Shusheng Zhang
- Shandong Province Key Laboratory of Detection Technology for Tumor Makers, School of Medicine, Linyi University, Linyi 276005, People's Republic of China
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Wang X, Wang Z, Yu C, Ge Z, Yang W. Advances in precise single-cell capture for analysis and biological applications. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2022; 14:3047-3063. [PMID: 35946358 DOI: 10.1039/d2ay00625a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Cells are the basic structural and functional units of living organisms. However, conventional cell analysis only averages millions of cell populations, and some important information is lost. It is essential to quantitatively characterize the physiology and pathology of single-cell activities. Precise single-cell capture is an extremely challenging task during cell sample preparation. In this review, we summarize the category of technologies to capture single cells precisely with a focus on the latest development in the last five years. Each technology has its own set of benefits and specific challenges, which provide opportunities for researchers in different fields. Accordingly, we introduce the applications of captured single cells in cancer diagnosis, analysis of metabolism and secretion, and disease treatment. Finally, some perspectives are provided on the current development trends, future research directions, and challenges of single-cell capture.
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Affiliation(s)
- Xiaowen Wang
- School of Electromechanical and Automotive Engineering, Yantai University, Yantai 264005, China.
| | - Zhen Wang
- School of Electromechanical and Automotive Engineering, Yantai University, Yantai 264005, China.
| | - Chang Yu
- College of Computer Science, Chongqing University, Chongqing 400000, China
| | - Zhixing Ge
- State Key Laboratory of Robotics, Shenyang Institute of Automation, Chinese Academy of Sciences, Shenyang 110016, China.
| | - Wenguang Yang
- School of Electromechanical and Automotive Engineering, Yantai University, Yantai 264005, China.
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Lin X, Fang M, Yi C, Jiang Y, Zhang C, Pan X, Luo Z. Functional hydrogel for fast, precise and inhibition-free point-of-care bacteria analysis in crude food samples. Biomaterials 2021; 280:121278. [PMID: 34871876 DOI: 10.1016/j.biomaterials.2021.121278] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 10/30/2021] [Accepted: 11/23/2021] [Indexed: 11/02/2022]
Abstract
In this work, instead of performing nucleic acid amplification in the bulk solution, we report a nanoporous hydrogel with controlled release function for rapid, precise, and inhibition-free nucleic acid analysis in crude food samples. The cross-linked PEG hydrogel with nanoporous structures possesses adsorption, release, separation, restriction and self-cleaning abilities. When digital loop-mediated isothermal amplification (LAMP) was performed inside this hydrogel, the surrounding nanostructure act as a temporary reservoir for reagents storage and release them on demand during or after amplification. Meanwhile, the restricted nanoconfined environment of hydrogel also favor the enzymatic amplification process. Thus, an enhanced signal readout, robust anti-inhibition, faster amplification rate, more products yields and specific amplification without primer-dimers were obtained. Moreover, direct amplification in untreated complex food sample was successfully performed inside hydrogel without any sample pretreatment, while conventional droplets digital LAMP failed for detection. Absolute quantification of Escherichia coli and Salmonella typhi directly in fresh fruit and vegetables was achieved within 20 min, with high precision and sensitivity down to single cell. This novel lab-on-hydrogel concept has an enormous potential for future molecular diagnostic assays, and can be also applied for other point-of-care assays.
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Affiliation(s)
- Xingyu Lin
- College of Biosystems Engineering and Food Science, Fuli Institute of Food Science, Zhejiang University, Hangzhou, 310058, PR China.
| | - Mei Fang
- College of Biosystems Engineering and Food Science, Fuli Institute of Food Science, Zhejiang University, Hangzhou, 310058, PR China; College of Environment, Zhejiang University of Technology, Hangzhou, 310014, PR China
| | - Changyu Yi
- College of Biosystems Engineering and Food Science, Fuli Institute of Food Science, Zhejiang University, Hangzhou, 310058, PR China; College of Environment, Zhejiang University of Technology, Hangzhou, 310014, PR China
| | - Yan Jiang
- Chemistry Instrumentation Center, Department of Chemistry, Zhejiang University, Hangzhou, 310027, China
| | - Chao Zhang
- College of Biosystems Engineering and Food Science, Fuli Institute of Food Science, Zhejiang University, Hangzhou, 310058, PR China
| | - Xiangliang Pan
- College of Environment, Zhejiang University of Technology, Hangzhou, 310014, PR China
| | - Zisheng Luo
- College of Biosystems Engineering and Food Science, Fuli Institute of Food Science, Zhejiang University, Hangzhou, 310058, PR China
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Xu S, Wu L, Qin Y, Jiang Y, Sun K, Holcomb C, Gravett MG, Vojtech L, Schiro PG, Chiu DT. Sequential Ensemble-Decision Aliquot Ranking Isolation and Fluorescence In Situ Hybridization Identification of Rare Cells from Blood by Using Concentrated Peripheral Blood Mononuclear Cells. Anal Chem 2021; 93:3196-3201. [PMID: 33528996 PMCID: PMC9901914 DOI: 10.1021/acs.analchem.0c04629] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Isolation and analysis of circulating rare cells is a promising approach for early detection of cancer and other diseases and for prenatal diagnosis. Isolation of rare cells is usually difficult due to their heterogeneity as well as their low abundance in peripheral blood. We previously reported a two-stage ensemble-decision aliquot ranking platform (S-eDAR) for isolating circulating tumor cells from whole blood with high throughput, high recovery rate (>90%), and good purity (>70%), allowing detection of low surface antigen-expressing cancer cells linked to metastasis. However, due to the scarcity of these cells, large sample volumes and large quantities of antibodies were required to isolate sufficient cells for downstream analysis. Here, we drastically increased the number of nucleated cells analyzed by first concentrating peripheral blood mononuclear cells (PBMCs) from whole blood by density gradient centrifugation. The S-eDAR platform was capable of isolating rare cells from concentrated PBMCs (108/mL, equivalent to processing ∼20 mL of whole blood in the 1 mL sample volume used by our instrument) at a high recovery rate (>85%). We then applied the S-eDAR platform for isolating rare fetal nucleated red blood cells (fNRBCs) from concentrated PBMCs spiked with umbilical cord blood cells and confirmed fNRBC recovery by immunostaining and fluorescence in situ hybridization, demonstrating the potential of the S-eDAR system for isolating rare fetal cells from maternal PBMCs to improve noninvasive prenatal diagnosis.
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Affiliation(s)
- Shihan Xu
- Department of Bioengineering, University of Washington, Seattle, WA, USA,Department of Chemistry, University of Washington, Seattle, WA, USA
| | - Li Wu
- Department of Chemistry, University of Washington, Seattle, WA, USA,School of Public Health, Nantong University, Nantong, Jiangsu, P. R. China
| | - Yuling Qin
- Department of Chemistry, University of Washington, Seattle, WA, USA,School of Public Health, Nantong University, Nantong, Jiangsu, P. R. China
| | - Yifei Jiang
- Department of Chemistry, University of Washington, Seattle, WA, USA
| | - Kai Sun
- Department of Chemistry, University of Washington, Seattle, WA, USA
| | - Chenee Holcomb
- Department of Obstetrics & Gynecology, University of Washington, Seattle, WA, USA
| | - Michael G. Gravett
- Department of Obstetrics & Gynecology, University of Washington, Seattle, WA, USA
| | - Lucia Vojtech
- Department of Obstetrics & Gynecology, University of Washington, Seattle, WA, USA
| | | | - Daniel T. Chiu
- Department of Bioengineering, University of Washington, Seattle, WA, USA,Department of Chemistry, University of Washington, Seattle, WA, USA
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Wei X, Chen K, Guo S, Liu W, Zhao XZ. Emerging Microfluidic Technologies for the Detection of Circulating Tumor Cells and Fetal Nucleated Red Blood Cells. ACS APPLIED BIO MATERIALS 2021; 4:1140-1155. [DOI: 10.1021/acsabm.0c01325] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Xiaoyun Wei
- Key Laboratory of Artificial Micro- and Nano-Structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan 430072, China
- Key Laboratory of Medical Information and 3D Bioprinting of Zhejiang Province, Hangzhou Dianzi University, Hangzhou 310018, China
| | - Keke Chen
- Key Laboratory of Artificial Micro- and Nano-Structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan 430072, China
| | - Shishang Guo
- Key Laboratory of Artificial Micro- and Nano-Structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan 430072, China
| | - Wei Liu
- Key Laboratory of Artificial Micro- and Nano-Structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan 430072, China
| | - Xing-Zhong Zhao
- Key Laboratory of Artificial Micro- and Nano-Structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan 430072, China
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Bao Y, Jiang Y, Xiong E, Tian T, Zhang Z, Lv J, Li Y, Zhou X. CUT-LAMP: Contamination-Free Loop-Mediated Isothermal Amplification Based on the CRISPR/Cas9 Cleavage. ACS Sens 2020; 5:1082-1091. [PMID: 32242409 DOI: 10.1021/acssensors.0c00034] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Loop-mediated isothermal amplification (LAMP) is a sensitive and widely used gene amplification technique. However, high amplification efficiency and amplification products containing multiple inverted repeats make the LAMP reaction extremely vulnerable to false-positive amplification caused by contamination. Herein, a contamination-free LAMP (CUT-LAMP) assisted by the CRISPR/Cas9 cleavage with superior reliability and durability has been reported. The core of CUT-LAMP is the engineering of the forward or backward inner primer in the target-independent region, which makes the LAMP products contain a protospacer adjacent motif (PAM) site for the CRISPR/Cas9 recognition. For the CUT-LAMP reaction, cross-contamination can be efficiently cleaved by the corresponding Cas9/sgRNA, but the target gene can get rid of digestion due to the lack of a PAM site near the recognition region. CUT-LAMP shows impressive contamination resistance but does not significantly increase procedure complexity; thus, it represents a simple and versatile toolkit facilitating the adoption by open- and closed-tube detection format.
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Affiliation(s)
- Yijuan Bao
- College of Biophotonics & School of Life Sciences, South China Normal University, Guangzhou 510631, P. R. China
| | - Yongzhong Jiang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
- Hubei Provincial Center for Disease Control and Prevention, Wuhan 430079, P. R. China
| | - Erhu Xiong
- College of Biophotonics & School of Life Sciences, South China Normal University, Guangzhou 510631, P. R. China
| | - Tian Tian
- College of Biophotonics & School of Life Sciences, South China Normal University, Guangzhou 510631, P. R. China
| | - Zhenzhen Zhang
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510275, P. R. China
| | - Jing Lv
- Hubei Provincial Center for Disease Control and Prevention, Wuhan 430079, P. R. China
| | - Yang Li
- Hubei Provincial Center for Disease Control and Prevention, Wuhan 430079, P. R. China
| | - Xiaoming Zhou
- College of Biophotonics & School of Life Sciences, South China Normal University, Guangzhou 510631, P. R. China
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Zhang W, Li N, Lin L, Huang Q, Uchiyama K, Lin JM. Concentrating Single Cells in Picoliter Droplets for Phospholipid Profiling on a Microfluidic System. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2020; 16:e1903402. [PMID: 31769602 DOI: 10.1002/smll.201903402] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Revised: 11/08/2019] [Indexed: 06/10/2023]
Abstract
Cellular membranes are composed of a variety of lipids in different amounts and proportions, and alterations of them are usually closely related to various diseases. To reveal the intercellular heterogeneity of the lipid variation, an integrated microfluidic system is designed, which consists of droplet-based inkjet printing, dielectrophoretic electrodes, and de-emulsification interface to achieve on-line single-cell encapsulation, manipulation, and mass spectrometry (MS) detection. This integrated system effectively improves the single-cell encapsulation rate, and meanwhile reduces the matrix interference and continuous oil phase interference to the MS detection. Using this system, the heterogeneities between the normal and cancer cells are compared, and the heterogeneity of the same cells before and after the drug treatment changed obviously, indicating that this system can be used as a promising tool for studying the link between the alterations of lipid homeostasis and various diseases.
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Affiliation(s)
- Weifei Zhang
- Department of Chemistry, Beijing Key Laboratory of Microanalytical Methods and Instrumentation, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, 100084, China
| | - Nan Li
- Department of Chemistry, Beijing Key Laboratory of Microanalytical Methods and Instrumentation, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, 100084, China
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, 100190, China
| | - Ling Lin
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, 100190, China
| | - Qiushi Huang
- Department of Chemistry, Beijing Key Laboratory of Microanalytical Methods and Instrumentation, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, 100084, China
| | - Katsumi Uchiyama
- Department of Applied Chemistry, Graduate School of Urban Environmental Sciences, Tokyo Metropolitan University, Minamiohsawa, Hachioji, Tokyo, 192-0397, Japan
| | - Jin-Ming Lin
- Department of Chemistry, Beijing Key Laboratory of Microanalytical Methods and Instrumentation, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, 100084, China
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Chen F, Xue J, Zhang J, Bai M, Yu X, Fan C, Zhao Y. Differentiated Visualization of Single-Cell 5-Hydroxymethylpyrimidines with Microfluidic Hydrogel Encoding. J Am Chem Soc 2020; 142:2889-2896. [PMID: 31986025 DOI: 10.1021/jacs.9b11393] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
5-Hydroxymethyluracil ( 5hmU ) is found in the genomes of a diverse range of organisms as another kind of 5-hydroxymethylpyrimidine, with the exception of 5-hydroxymethylcytosine ( 5hmC ). The biological function of 5hmU has not been well explored due to lacking both specific 5hmU recognition and single-cell analysis methods. Here we report differentiated visualization of single-cell 5hmU and 5hmC with microfluidic hydrogel encoding (sc 5hmU / 5hmC -microgel). Single cells and their genomic DNA after cell lysis can be encapsulated in individual agarose microgels. The 5hmU sites are then specifically labeled with thiophosphate for the first time, followed by labeling 5hmC with azide glucose. These labeled bases are each encoded into respective DNA barcode primers by chemical cross-linking. In situ amplification is triggered for single-molecule fluorescence visualization of single-cell 5hmU and 5hmC . On the basis of the sc 5hmU / 5hmC -microgel, we reveal cell type-specific molecular signatures of these two bases with remarkable single-cell heterogeneity. Utilizing machine learning algorithms to decode four-dimensional signatures of 5hmU / 5hmC , we visualize the discrimination of nontumorigenic, carcinoma and highly invasive breast cell lines. This strategy provides a new route to analyze and decode single-cell DNA epigenetic modifications.
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Affiliation(s)
- Feng Chen
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology , Xi'an Jiaotong University , Xianning West Road , Xi'an , Shaanxi 710049 , P. R. China
| | - Jing Xue
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology , Xi'an Jiaotong University , Xianning West Road , Xi'an , Shaanxi 710049 , P. R. China
| | - Jin Zhang
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology , Xi'an Jiaotong University , Xianning West Road , Xi'an , Shaanxi 710049 , P. R. China
| | - Min Bai
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology , Xi'an Jiaotong University , Xianning West Road , Xi'an , Shaanxi 710049 , P. R. China
| | - Xu Yu
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology , Xi'an Jiaotong University , Xianning West Road , Xi'an , Shaanxi 710049 , P. R. China
| | - Chunhai Fan
- Institute of Molecular Medicine, Renji Hospital, School of Medicine and School of Chemistry and ChemicalEngineering , Shanghai Jiao Tong University , Shanghai 200127 , P. R. China
| | - Yongxi Zhao
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology , Xi'an Jiaotong University , Xianning West Road , Xi'an , Shaanxi 710049 , P. R. China
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9
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Cottrell Scholars 2019. Angew Chem Int Ed Engl 2019; 58:11950-11951. [DOI: 10.1002/anie.201907975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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10
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Cottrell Scholars 2019. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201907975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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