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Wang C, Qiu J, Liu M, Wang Y, Yu Y, Liu H, Zhang Y, Han L. Microfluidic Biochips for Single-Cell Isolation and Single-Cell Analysis of Multiomics and Exosomes. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2401263. [PMID: 38767182 PMCID: PMC11267386 DOI: 10.1002/advs.202401263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 04/26/2024] [Indexed: 05/22/2024]
Abstract
Single-cell multiomic and exosome analyses are potent tools in various fields, such as cancer research, immunology, neuroscience, microbiology, and drug development. They facilitate the in-depth exploration of biological systems, providing insights into disease mechanisms and aiding in treatment. Single-cell isolation, which is crucial for single-cell analysis, ensures reliable cell isolation and quality control for further downstream analyses. Microfluidic chips are small lightweight systems that facilitate efficient and high-throughput single-cell isolation and real-time single-cell analysis on- or off-chip. Therefore, most current single-cell isolation and analysis technologies are based on the single-cell microfluidic technology. This review offers comprehensive guidance to researchers across different fields on the selection of appropriate microfluidic chip technologies for single-cell isolation and analysis. This review describes the design principles, separation mechanisms, chip characteristics, and cellular effects of various microfluidic chips available for single-cell isolation. Moreover, this review highlights the implications of using this technology for subsequent analyses, including single-cell multiomic and exosome analyses. Finally, the current challenges and future prospects of microfluidic chip technology are outlined for multiplex single-cell isolation and multiomic and exosome analyses.
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Affiliation(s)
- Chao Wang
- Institute of Marine Science and TechnologyShandong UniversityQingdao266237China
| | - Jiaoyan Qiu
- Institute of Marine Science and TechnologyShandong UniversityQingdao266237China
| | - Mengqi Liu
- Institute of Marine Science and TechnologyShandong UniversityQingdao266237China
| | - Yihe Wang
- Institute of Marine Science and TechnologyShandong UniversityQingdao266237China
| | - Yang Yu
- Department of PeriodontologySchool and Hospital of StomatologyCheeloo College of MedicineShandong UniversityJinan250100China
| | - Hong Liu
- State Key Laboratory of Crystal MaterialsShandong UniversityJinan250100China
| | - Yu Zhang
- Institute of Marine Science and TechnologyShandong UniversityQingdao266237China
| | - Lin Han
- Institute of Marine Science and TechnologyShandong UniversityQingdao266237China
- Shandong Engineering Research Center of Biomarker and Artificial Intelligence ApplicationJinan250100China
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2
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Briones J, Espulgar W, Koyama S, Takamatsu H, Tamiya E, Saito M. The future of microfluidics in immune checkpoint blockade. Cancer Gene Ther 2021; 28:895-910. [PMID: 33110208 DOI: 10.1038/s41417-020-00248-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 10/02/2020] [Accepted: 10/09/2020] [Indexed: 01/30/2023]
Abstract
Recent advances in microfluidic techniques have enabled researchers to study sensitivities to immune checkpoint therapy, to determine patients' response to particular antibody treatment. Utilization of this technology is helpful in antibody discovery and in the design of personalized medicine. A variety of microfluidic approaches can provide several functions in processes such as immunologic, genomic, and/or transcriptomic analysis with the aim of improving the efficacy and coverage of immunotherapy, particularly immune checkpoint blockade (ICB). To achieve this requires researchers to overcome the challenges in the current state of the technology. This review looks into the advancements in microfluidic technologies applied to researches on immune checkpoint blockade treatment and its potential shift from proof-of-principle stage to clinical application.
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Affiliation(s)
- Jonathan Briones
- Graduate School of Engineering, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Wilfred Espulgar
- Graduate School of Engineering, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Shohei Koyama
- Graduate School of Medicine, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Hyota Takamatsu
- Graduate School of Medicine, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Eiichi Tamiya
- AIST PhotoBIO-OIL, Osaka University, Suita, Osaka, 565-0871, Japan.,The Institute of Scientific and Industrial Research, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Masato Saito
- Graduate School of Engineering, Osaka University, Suita, Osaka, 565-0871, Japan. .,AIST PhotoBIO-OIL, Osaka University, Suita, Osaka, 565-0871, Japan.
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3
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Molinski J, Tadimety A, Burklund A, Zhang JXJ. Scalable Signature-Based Molecular Diagnostics Through On-chip Biomarker Profiling Coupled with Machine Learning. Ann Biomed Eng 2020; 48:2377-2399. [PMID: 32816167 PMCID: PMC7785517 DOI: 10.1007/s10439-020-02593-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 08/11/2020] [Indexed: 02/07/2023]
Abstract
Molecular diagnostics have traditionally relied on discrete biological substances as diagnostic markers. In recent years however, advances in on-chip biomarker screening technologies and data analytics have enabled signature-based diagnostics. Such diagnostics aim to utilize unique combinations of multiple biomarkers or diagnostic 'fingerprints' rather than discrete analyte measurements. This approach has shown to improve both diagnostic accuracy and diagnostic specificity. In this review, signature-based diagnostics enabled by microfluidic and micro-/nano- technologies will be reviewed with a focus on device design and data analysis pipelines and methodologies. With increasing amounts of data available from microfluidic biomarker screening, isolation, and detection platforms, advanced data handling and analytics approaches can be employed. Thus, current data analysis approaches including machine learning and recent advances with image processing, along with potential future directions will be explored. Lastly, the needs and gaps in current literature will be elucidated to inform future efforts towards development of molecular diagnostics and biomarker screening technologies.
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Affiliation(s)
- John Molinski
- Thayer School of Engineering at Dartmouth, 14 Engineering Drive, Hanover, NH, 03755, USA
| | - Amogha Tadimety
- Thayer School of Engineering at Dartmouth, 14 Engineering Drive, Hanover, NH, 03755, USA
| | - Alison Burklund
- Thayer School of Engineering at Dartmouth, 14 Engineering Drive, Hanover, NH, 03755, USA
| | - John X J Zhang
- Thayer School of Engineering at Dartmouth, 14 Engineering Drive, Hanover, NH, 03755, USA.
- Norris Cotton Cancer Center, Dartmouth Hitchcock Medical Center, Lebanon, NH, USA.
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4
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Jammes FC, Maerkl SJ. How single-cell immunology is benefiting from microfluidic technologies. MICROSYSTEMS & NANOENGINEERING 2020; 6:45. [PMID: 34567657 PMCID: PMC8433390 DOI: 10.1038/s41378-020-0140-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 01/14/2020] [Accepted: 01/25/2020] [Indexed: 05/03/2023]
Abstract
The immune system is a complex network of specialized cells that work in concert to protect against invading pathogens and tissue damage. Imbalances in this network often result in excessive or absent immune responses leading to allergies, autoimmune diseases, and cancer. Many of the mechanisms and their regulation remain poorly understood. Immune cells are highly diverse, and an immune response is the result of a large number of molecular and cellular interactions both in time and space. Conventional bulk methods are often prone to miss important details by returning population-averaged results. There is a need in immunology to measure single cells and to study the dynamic interplay of immune cells with their environment. Advances in the fields of microsystems and microengineering gave rise to the field of microfluidics and its application to biology. Microfluidic systems enable the precise control of small volumes in the femto- to nanoliter range. By controlling device geometries, surface chemistry, and flow behavior, microfluidics can create a precisely defined microenvironment for single-cell studies with spatio-temporal control. These features are highly desirable for single-cell analysis and have made microfluidic devices useful tools for studying complex immune systems. In addition, microfluidic devices can achieve high-throughput measurements, enabling in-depth studies of complex systems. Microfluidics has been used in a large panel of biological applications, ranging from single-cell genomics, cell signaling and dynamics to cell-cell interaction and cell migration studies. In this review, we give an overview of state-of-the-art microfluidic techniques, their application to single-cell immunology, their advantages and drawbacks, and provide an outlook for the future of single-cell technologies in research and medicine.
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Affiliation(s)
- Fabien C. Jammes
- Institute of Bioengineering, School of Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Sebastian J. Maerkl
- Institute of Bioengineering, School of Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
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5
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Liu M, Jin M, Li L, Ji Y, Zhu F, Luo Y, Liu T, Lin B, Lu Y. PDMS Microwell Stencil Based Multiplexed Single‐Cell Secretion Analysis. Proteomics 2020; 20:e1900231. [DOI: 10.1002/pmic.201900231] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 11/13/2019] [Indexed: 11/05/2022]
Affiliation(s)
- Meimei Liu
- Department of Materials Science and EngineeringDalian Maritime University Dalian 116026 China
- Department of BiotechnologyDalian Institute of Chemical PhysicsChinese Academy of Sciences Dalian 116023 China
| | - Meihua Jin
- Department of Materials Science and EngineeringDalian Maritime University Dalian 116026 China
| | - Linmei Li
- Department of BiotechnologyDalian Institute of Chemical PhysicsChinese Academy of Sciences Dalian 116023 China
| | - Yahui Ji
- Department of BiotechnologyDalian Institute of Chemical PhysicsChinese Academy of Sciences Dalian 116023 China
| | - Fengjiao Zhu
- Department of BiotechnologyDalian Institute of Chemical PhysicsChinese Academy of Sciences Dalian 116023 China
| | - Yong Luo
- State Key Laboratory of Fine ChemicalsDepartment of Chemical EngineeringDalian University of Technology Dalian 116024 China
| | - Tingjiao Liu
- College of StomatologyDalian Medical University Dalian 116044 China
| | - Bingcheng Lin
- Department of BiotechnologyDalian Institute of Chemical PhysicsChinese Academy of Sciences Dalian 116023 China
| | - Yao Lu
- Department of BiotechnologyDalian Institute of Chemical PhysicsChinese Academy of Sciences Dalian 116023 China
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6
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Wei W, Fan R. Special Issue on Single-Cell Multiomics for Immuno-Oncology and Cancer Systems Biology. Proteomics 2019; 19:e1900235. [PMID: 31411816 DOI: 10.1002/pmic.201900235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Indexed: 11/10/2022]
Affiliation(s)
- Wei Wei
- Institute for Systems Biology, Seattle, WA, 98109, USA
| | - Rong Fan
- Department of Biomedical Engineering, Yale University, New Haven, CT, 06520, USA
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7
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Chen P, Chen D, Li S, Ou X, Liu BF. Microfluidics towards single cell resolution protein analysis. Trends Analyt Chem 2019. [DOI: 10.1016/j.trac.2019.06.022] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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8
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Chen Z, Chen JJ, Fan R. Single-Cell Protein Secretion Detection and Profiling. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2019; 12:431-449. [PMID: 30978293 DOI: 10.1146/annurev-anchem-061318-115055] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Secreted proteins play important roles in mediating various biological processes such as cell-cell communication, differentiation, migration, and homeostasis at the population or tissue level. Here, we review bioanalytical technologies and devices for detecting protein secretions from single cells. We begin by discussing conventional approaches followed by detailing the latest advances in microengineered systems for detecting single-cell protein secretions with an emphasis on multiplex measurement. These platforms include droplet microfluidics, micro-/nanowell-based assays, and microchamber-based assays, among which the advantages and limitations are compared. Microscale systems also enable the tracking of protein secretion dynamics in single cells, further empowering the study of the cell-cell communication network. Looking forward, we discuss the remaining challenges and future opportunities that will transform basic research of cellular secretion functions at the systems level and the clinical applications for immune monitoring and cancer treatment.
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Affiliation(s)
- Zhuo Chen
- Department of Biomedical Engineering, Yale University, New Haven, Connecticut 06520, USA;
| | - Jonathan J Chen
- Department of Biomedical Engineering, Yale University, New Haven, Connecticut 06520, USA;
| | - Rong Fan
- Department of Biomedical Engineering, Yale University, New Haven, Connecticut 06520, USA;
- Yale Cancer Center, Yale Stem Cell Center, Human and Translational Immunology Program, Yale School of Medicine, New Haven, Connecticut 06520, USA
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9
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Abstract
Single-cell omics studies provide unique information regarding cellular heterogeneity at various levels of the molecular biology central dogma. This knowledge facilitates a deeper understanding of how underlying molecular and architectural changes alter cell behavior, development, and disease processes. The emerging microchip-based tools for single-cell omics analysis are enabling the evaluation of cellular omics with high throughput, improved sensitivity, and reduced cost. We review state-of-the-art microchip platforms for profiling genomics, epigenomics, transcriptomics, proteomics, metabolomics, and multi-omics at single-cell resolution. We also discuss the background of and challenges in the analysis of each molecular layer and integration of multiple levels of omics data, as well as how microchip-based methodologies benefit these fields. Additionally, we examine the advantages and limitations of these approaches. Looking forward, we describe additional challenges and future opportunities that will facilitate the improvement and broad adoption of single-cell omics in life science and medicine.
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Affiliation(s)
- Yanxiang Deng
- Department of Biomedical Engineering, Yale University, New Haven, Connecticut 06511, USA; , ,
| | - Amanda Finck
- Department of Biomedical Engineering, Yale University, New Haven, Connecticut 06511, USA; , ,
| | - Rong Fan
- Department of Biomedical Engineering, Yale University, New Haven, Connecticut 06511, USA; , ,
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10
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Wang Z, Zhang X. Single Cell Proteomics for Molecular Targets in Lung Cancer: High-Dimensional Data Acquisition and Analysis. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1068:73-87. [PMID: 29943297 DOI: 10.1007/978-981-13-0502-3_7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
In the proteomic and genomic era, lung cancer researchers are increasingly under challenge with traditional protein analyzing tools. High output, multiplexed analytical procedures are in demand for disclosing the post-translational modification, molecular interactions and signaling pathways of proteins precisely, specifically, dynamically and systematically, as well as for identifying novel proteins and their functions. This could be better realized by single-cell proteomic methods than conventional proteomic methods. Using single-cell proteomic tools including flow cytometry, mass cytometry, microfluidics and chip technologies, chemical cytometry, single-cell western blotting, the quantity and functions of proteins are analyzed simultaneously. Aside from deciphering disease mechanisms, single-cell proteomic techniques facilitate the identification and screening of biomarkers, molecular targets and promising compounds as well. This review summarized single-cell proteomic tools and their use in lung cancer.
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Affiliation(s)
- Zheng Wang
- Department of Respiratory and Critical Care Medicine, Zhengzhou University People's Hospital, Zhengzhou, China
| | - Xiaoju Zhang
- Department of Respiratory and Critical Care Medicine, Zhengzhou University People's Hospital, Zhengzhou, China. .,Biomedical Research Center, Zhengzhou University People's Hospital, Zhengzhou, China.
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11
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Pan Q, Yamauchi KA, Herr AE. Controlling Dispersion during Single-Cell Polyacrylamide-Gel Electrophoresis in Open Microfluidic Devices. Anal Chem 2018; 90:13419-13426. [PMID: 30346747 PMCID: PMC6777840 DOI: 10.1021/acs.analchem.8b03233] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
New tools for measuring protein expression in individual cells complement single-cell genomics and transcriptomics. To characterize a population of individual mammalian cells, hundreds to thousands of microwells are arrayed on a polyacrylamide-gel-coated glass microscope slide. In this "open" fluidic device format, we explore the feasibility of mitigating diffusional losses during lysis and polyacrylamide-gel electrophoresis (PAGE) through spatial control of the pore-size of the gel layer. To reduce in-plane diffusion-driven dilution of each single-cell lysate during in-microwell chemical lysis, we photopattern and characterize microwells with small-pore-size sidewalls ringing the microwell except at the injection region. To reduce out-of-plane-diffusion-driven-dilution-caused signal loss during both lysis and single-cell PAGE, we scrutinize a selectively permeable agarose lid layer. To reduce injection dispersion, we photopattern and study a stacking-gel feature at the head of each <1 mm separation axis. Lastly, we explore a semienclosed device design that reduces the cross-sectional area of the chip, thus reducing Joule-heating-induced dispersion during single-cell PAGE. As a result, we observed a 3-fold increase in separation resolution during a 30 s separation and a >2-fold enhancement of the signal-to-noise ratio. We present well-integrated strategies for enhancing overall single-cell-PAGE performance.
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Affiliation(s)
- Qiong Pan
- Department of Bioengineering, University of California, Berkeley, California 94720, United States
| | - Kevin A. Yamauchi
- Department of Bioengineering, University of California, Berkeley, California 94720, United States
| | - Amy E. Herr
- Department of Bioengineering, University of California, Berkeley, California 94720, United States
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12
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Microfluidic Analyzer Enabling Quantitative Measurements of Specific Intracellular Proteins at the Single-Cell Level. MICROMACHINES 2018; 9:mi9110588. [PMID: 30424565 PMCID: PMC6265747 DOI: 10.3390/mi9110588] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Revised: 11/02/2018] [Accepted: 11/08/2018] [Indexed: 12/29/2022]
Abstract
This paper presents a microfluidic instrument capable of quantifying single-cell specific intracellular proteins, which are composed of three functioning modules and two software platforms. Under the control of a LabVIEW platform, a pressure module flushed cells stained with fluorescent antibodies through a microfluidic module with fluorescent intensities quantified by a fluorescent module and translated into the numbers of specific intracellular proteins at the single-cell level using a MATLAB platform. Detection ranges and resolutions of the analyzer were characterized as 896.78–6.78 × 105 and 334.60 nM for Alexa 488, 314.60–2.11 × 105 and 153.98 nM for FITC, and 77.03–5.24 × 104 and 37.17 nM for FITC-labelled anti-beta-actin antibodies. As a demonstration, the numbers of single-cell beta-actins of two paired oral tumor cell types and two oral patient samples were quantified as: 1.12 ± 0.77 × 106/cell (salivary adenoid cystic carcinoma parental cell line (SACC-83), ncell = 13,689) vs. 0.90 ± 0.58 × 105/cell (salivary adenoid cystic carcinoma lung metastasis cell line (SACC-LM), ncell = 15,341); 0.89 ± 0.69 × 106/cell (oral carcinoma cell line (CAL 27), ncell = 7357) vs. 0.93 ± 0.69 × 106/cell (oral carcinoma lymphatic metastasis cell line (CAL 27-LN2), ncell = 6276); and 0.86 ± 0.52 × 106/cell (patient I) vs. 0.85 ± 0.58 × 106/cell (patient II). These results (1) validated the developed analyzer with a throughput of 10 cells/s and a processing capability of ~10,000 cells for each cell type, and (2) revealed that as an internal control in cell analysis, the expressions of beta-actins remained stable in oral tumors with different malignant levels.
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13
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Li X, Fan B, Liu L, Chen D, Cao S, Men D, Wang J, Chen J. A Microfluidic Fluorescent Flow Cytometry Capable of Quantifying Cell Sizes and Numbers of Specific Cytosolic Proteins. Sci Rep 2018; 8:14229. [PMID: 30242168 PMCID: PMC6155059 DOI: 10.1038/s41598-018-32333-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Accepted: 07/06/2018] [Indexed: 12/20/2022] Open
Abstract
This study presents a microfluidics based cytometry capable of characterizing cell sizes and counting numbers of specific cytosolic proteins where cells were first bound by antibodies labelled with fluorescence and then aspirated into a constriction microchannel in which fluorescent levels were measured. These raw fluorescent pulses were further divided into a rising domain, a stable domain and a declining domain. In addition, antibody solutions with labelled fluorescence were aspirated through the constriction microchannel, yielding curves to translate raw fluorescent levels to protein concentrations. By using key parameters of three domains as well as the calibration curves, cell diameters and the absolute number of β-actins at the single-cell level were quantified as 14.2 ± 1.7 μm and 9.62 ± 4.29 × 105 (A549, ncell = 14 242), 13.0 ± 2.0 μm and 6.46 ± 3.34 × 105 (Hep G2, ncell = 35 932), 13.8 ± 1.9 μm and 1.58 ± 0.90 × 106 (MCF 10 A, ncell = 16 650), and 12.7 ± 1.5 μm and 1.09 ± 0.49 × 106 (HeLa, ncell = 26 246). This platform could be further adopted to measure numbers of various cytosolic proteins, providing key insights in proteomics at the single-cell level.
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Affiliation(s)
- Xiufeng Li
- State Key Lab of Transducer Technology, Institute of Electronics of Chinese Academy of Sciences, Beijing City, China.,University of Chinese Academy of Sciences, Beijing City, China
| | - Beiyuan Fan
- State Key Lab of Transducer Technology, Institute of Electronics of Chinese Academy of Sciences, Beijing City, China.,University of Chinese Academy of Sciences, Beijing City, China
| | - Lixing Liu
- State Key Lab of Transducer Technology, Institute of Electronics of Chinese Academy of Sciences, Beijing City, China.,University of Chinese Academy of Sciences, Beijing City, China
| | - Deyong Chen
- State Key Lab of Transducer Technology, Institute of Electronics of Chinese Academy of Sciences, Beijing City, China.,University of Chinese Academy of Sciences, Beijing City, China
| | - Shanshan Cao
- State Key Lab of Virology, Wuhan Institute of Virology of Chinese Academy of Sciences, Wuhan City, Hubei Province, China
| | - Dong Men
- State Key Lab of Virology, Wuhan Institute of Virology of Chinese Academy of Sciences, Wuhan City, Hubei Province, China.
| | - Junbo Wang
- State Key Lab of Transducer Technology, Institute of Electronics of Chinese Academy of Sciences, Beijing City, China. .,University of Chinese Academy of Sciences, Beijing City, China.
| | - Jian Chen
- State Key Lab of Transducer Technology, Institute of Electronics of Chinese Academy of Sciences, Beijing City, China. .,University of Chinese Academy of Sciences, Beijing City, China.
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14
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Mincarelli L, Lister A, Lipscombe J, Macaulay IC. Defining Cell Identity with Single-Cell Omics. Proteomics 2018; 18:e1700312. [PMID: 29644800 PMCID: PMC6175476 DOI: 10.1002/pmic.201700312] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Revised: 03/23/2018] [Indexed: 01/17/2023]
Abstract
Cells are a fundamental unit of life, and the ability to study the phenotypes and behaviors of individual cells is crucial to understanding the workings of complex biological systems. Cell phenotypes (epigenomic, transcriptomic, proteomic, and metabolomic) exhibit dramatic heterogeneity between and within the different cell types and states underlying cellular functional diversity. Cell genotypes can also display heterogeneity throughout an organism, in the form of somatic genetic variation-most notably in the emergence and evolution of tumors. Recent technical advances in single-cell isolation and the development of omics approaches sensitive enough to reveal these aspects of cell identity have enabled a revolution in the study of multicellular systems. In this review, we discuss the technologies available to resolve the genomes, epigenomes, transcriptomes, proteomes, and metabolomes of single cells from a wide variety of living systems.
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Affiliation(s)
- Laura Mincarelli
- Earlham InstituteNorwich Research ParkNorwichNR4 7UZUnited Kingdom
| | - Ashleigh Lister
- Earlham InstituteNorwich Research ParkNorwichNR4 7UZUnited Kingdom
| | - James Lipscombe
- Earlham InstituteNorwich Research ParkNorwichNR4 7UZUnited Kingdom
| | - Iain C. Macaulay
- Earlham InstituteNorwich Research ParkNorwichNR4 7UZUnited Kingdom
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15
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Fujiwara M, Anstadt EJ, Flynn B, Morse K, Ng C, Paczkowski P, Zhou J, Mackay S, Wasko N, Nichols F, Clark RB. Enhanced TLR2 responses in multiple sclerosis. Clin Exp Immunol 2018; 193:313-326. [PMID: 30043528 PMCID: PMC6150258 DOI: 10.1111/cei.13150] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 03/29/2018] [Accepted: 04/18/2018] [Indexed: 12/17/2022] Open
Abstract
The roles of the microbiome and innate immunity in the pathogenesis of multiple sclerosis (MS) remain unclear. We have previously documented abnormally low levels of a microbiome‐derived Toll‐like receptor (TLR)2‐stimulating bacterial lipid in the blood of MS patients and postulated that this is indicative of a deficiency in the innate immune regulating function of the microbiome in MS. We postulated further that the resulting enhanced TLR2 responsiveness plays a critical role in the pathogenesis of MS. As proof‐of‐concept, we reported that decreasing systemic TLR2 responsiveness by administering very low‐dose TLR2 ligands attenuated significantly the mouse model of MS, experimental autoimmune encephalomyelitis. Studies of Toll‐like receptor responses in patients with MS have been conflicting. Importantly, most of these investigations have focused on the response to TLR4 ligation and few have characterized TLR2 responses in MS. In the present study, our goal was to characterize TLR2 responses of MS patients using multiple approaches. Studying a total of 26 MS patients and 32 healthy controls, we now document for the first time that a large fraction of MS patients (50%) demonstrate enhanced responsiveness to TLR2 stimulation. Interestingly, the enhanced TLR2 responders include a significant fraction of those with progressive forms of MS, a subset of patients considered unresponsive to adaptive immune system‐targeting therapies. Our results suggest the presence of a pathologically relevant TLR2 related innate immune abnormality in patients with both relapsing–remitting and progressive MS. These findings may have significant implications for understanding the role of innate immunity in the pathogenesis of MS.
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Affiliation(s)
- M Fujiwara
- Departments of Immunology and Medicine, University of Connecticut School of Medicine, Farmington, CT, USA
| | - E J Anstadt
- Departments of Immunology and Medicine, University of Connecticut School of Medicine, Farmington, CT, USA
| | - B Flynn
- IsoPlexis, Branford, CT, USA
| | - K Morse
- IsoPlexis, Branford, CT, USA
| | - C Ng
- IsoPlexis, Branford, CT, USA
| | | | - J Zhou
- IsoPlexis, Branford, CT, USA
| | | | - N Wasko
- Departments of Immunology and Medicine, University of Connecticut School of Medicine, Farmington, CT, USA
| | - F Nichols
- Division of Periodontology, University of Connecticut School of Medicine and School of Dental Health, Farmington, CT, USA
| | - R B Clark
- Departments of Immunology and Medicine, University of Connecticut School of Medicine, Farmington, CT, USA
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16
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Bulbul G, Chaves G, Olivier J, Ozel RE, Pourmand N. Nanopipettes as Monitoring Probes for the Single Living Cell: State of the Art and Future Directions in Molecular Biology. Cells 2018; 7:E55. [PMID: 29882813 PMCID: PMC6024992 DOI: 10.3390/cells7060055] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 06/01/2018] [Accepted: 06/05/2018] [Indexed: 02/07/2023] Open
Abstract
Examining the behavior of a single cell within its natural environment is valuable for understanding both the biological processes that control the function of cells and how injury or disease lead to pathological change of their function. Single-cell analysis can reveal information regarding the causes of genetic changes, and it can contribute to studies on the molecular basis of cell transformation and proliferation. By contrast, whole tissue biopsies can only yield information on a statistical average of several processes occurring in a population of different cells. Electrowetting within a nanopipette provides a nanobiopsy platform for the extraction of cellular material from single living cells. Additionally, functionalized nanopipette sensing probes can differentiate analytes based on their size, shape or charge density, making the technology uniquely suited to sensing changes in single-cell dynamics. In this review, we highlight the potential of nanopipette technology as a non-destructive analytical tool to monitor single living cells, with particular attention to integration into applications in molecular biology.
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Affiliation(s)
- Gonca Bulbul
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95064, USA.
| | - Gepoliano Chaves
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95064, USA.
| | - Joseph Olivier
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95064, USA.
| | - Rifat Emrah Ozel
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95064, USA.
| | - Nader Pourmand
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95064, USA.
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17
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Gao Y, Li B, Singhal R, Fontecchio A, Pelleg B, Orynbayeva Z, Gogotsi Y, Friedman G. Perfusion double-channel micropipette probes for oxygen flux mapping with single-cell resolution. BEILSTEIN JOURNAL OF NANOTECHNOLOGY 2018; 9:850-860. [PMID: 29600146 PMCID: PMC5852649 DOI: 10.3762/bjnano.9.79] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Accepted: 02/21/2018] [Indexed: 06/08/2023]
Abstract
Measuring cellular respiration with single-cell spatial resolution is a significant challenge, even with modern tools and techniques. Here, a double-channel micropipette is proposed and investigated as a probe to achieve this goal by sampling fluid near the point of interest. A finite element model (FEM) of this perfusion probe is validated by comparing simulation results with experimental results of hydrodynamically confined fluorescent molecule diffusion. The FEM is then used to investigate the dependence of the oxygen concentration variation and the measurement signal on system parameters, including the pipette's shape, perfusion velocity, position of the oxygen sensors within the pipette, and proximity of the pipette to the substrate. The work demonstrates that the use of perfusion double-barrel micropipette probes enables the detection of oxygen consumption signals with micrometer spatial resolution, while amplifying the signal, as compared to sensors without the perfusion system. In certain flow velocity ranges (depending on pipette geometry and configuration), the perfusion flow increases oxygen concentration gradients formed due to cellular oxygen consumption. An optimal perfusion velocity for respiratory measurements on single cells can be determined for different system parameters (e.g., proximity of the pipette to the substrate). The optimum perfusion velocities calculated in this paper range from 1.9 to 12.5 μm/s. Finally, the FEM model is used to show that the spatial resolution of the probe may be varied by adjusting the pipette tip diameter, which may allow oxygen consumption mapping of cells within tissue, as well as individual cells at subcellular resolution.
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Affiliation(s)
- Yang Gao
- Department of Electrical and Computer Engineering, Drexel University, 3141 Chestnut Street, Philadelphia, PA 19104, USA
| | - Bin Li
- Department of Electrical and Computer Engineering, Drexel University, 3141 Chestnut Street, Philadelphia, PA 19104, USA
| | - Riju Singhal
- Department of Material Science and Engineering, Drexel University, 3141 Chestnut Street, Philadelphia, PA 19104, USA
| | - Adam Fontecchio
- Department of Electrical and Computer Engineering, Drexel University, 3141 Chestnut Street, Philadelphia, PA 19104, USA
| | - Ben Pelleg
- Department of Electrical and Computer Engineering, Drexel University, 3141 Chestnut Street, Philadelphia, PA 19104, USA
| | - Zulfiya Orynbayeva
- Department of Surgery, Drexel University, 245 N. 15th Street, Philadelphia, PA 19102, USA
| | - Yury Gogotsi
- Department of Material Science and Engineering, Drexel University, 3141 Chestnut Street, Philadelphia, PA 19104, USA
| | - Gary Friedman
- Department of Electrical and Computer Engineering, Drexel University, 3141 Chestnut Street, Philadelphia, PA 19104, USA
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18
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Abstract
Quantification of single-cell proteomics provides key insights in the field of cellular heterogeneity. This chapter discusses the emerging techniques that are being used to measure the protein copy numbers at the single-cell level, which includes flow cytometry, mass cytometry, droplet cytometry, microengraving, and single-cell barcoding microchip. The advantages and limitations of each technique are compared, and future research opportunities are highlighted.
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19
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Wei J, Hu X, Zou X, Tian T. Reverse-engineering of gene networks for regulating early blood development from single-cell measurements. BMC Med Genomics 2017; 10:72. [PMID: 29297370 PMCID: PMC5751697 DOI: 10.1186/s12920-017-0312-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Recent advances in omics technologies have raised great opportunities to study large-scale regulatory networks inside the cell. In addition, single-cell experiments have measured the gene and protein activities in a large number of cells under the same experimental conditions. However, a significant challenge in computational biology and bioinformatics is how to derive quantitative information from the single-cell observations and how to develop sophisticated mathematical models to describe the dynamic properties of regulatory networks using the derived quantitative information. METHODS This work designs an integrated approach to reverse-engineer gene networks for regulating early blood development based on singel-cell experimental observations. The wanderlust algorithm is initially used to develop the pseudo-trajectory for the activities of a number of genes. Since the gene expression data in the developed pseudo-trajectory show large fluctuations, we then use Gaussian process regression methods to smooth the gene express data in order to obtain pseudo-trajectories with much less fluctuations. The proposed integrated framework consists of both bioinformatics algorithms to reconstruct the regulatory network and mathematical models using differential equations to describe the dynamics of gene expression. RESULTS The developed approach is applied to study the network regulating early blood cell development. A graphic model is constructed for a regulatory network with forty genes and a dynamic model using differential equations is developed for a network of nine genes. Numerical results suggests that the proposed model is able to match experimental data very well. We also examine the networks with more regulatory relations and numerical results show that more regulations may exist. We test the possibility of auto-regulation but numerical simulations do not support the positive auto-regulation. In addition, robustness is used as an importantly additional criterion to select candidate networks. CONCLUSION The research results in this work shows that the developed approach is an efficient and effective method to reverse-engineer gene networks using single-cell experimental observations.
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Affiliation(s)
- Jiangyong Wei
- School of Statistics and Mathematics, Zhongnan University of Economics and Law, Wuhan, 430073 China
| | - Xiaohua Hu
- School of Computer, Central China Normal University, Wuhan, 430079 China
| | - Xiufen Zou
- School of Mathematics and Statistics, Wuhan University, Wuhan, 430072 China
| | - Tianhai Tian
- School of Mathematical Sciences, Monash University, Melbourne, VIC 3800 Australia
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20
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Su Y, Shi Q, Wei W. Single cell proteomics in biomedicine: High-dimensional data acquisition, visualization, and analysis. Proteomics 2017; 17. [PMID: 28128880 DOI: 10.1002/pmic.201600267] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 01/20/2017] [Accepted: 01/23/2017] [Indexed: 11/11/2022]
Abstract
New insights on cellular heterogeneity in the last decade provoke the development of a variety of single cell omics tools at a lightning pace. The resultant high-dimensional single cell data generated by these tools require new theoretical approaches and analytical algorithms for effective visualization and interpretation. In this review, we briefly survey the state-of-the-art single cell proteomic tools with a particular focus on data acquisition and quantification, followed by an elaboration of a number of statistical and computational approaches developed to date for dissecting the high-dimensional single cell data. The underlying assumptions, unique features, and limitations of the analytical methods with the designated biological questions they seek to answer will be discussed. Particular attention will be given to those information theoretical approaches that are anchored in a set of first principles of physics and can yield detailed (and often surprising) predictions.
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Affiliation(s)
- Yapeng Su
- NanoSystems Biology Cancer Center, Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Qihui Shi
- Key Laboratory of Systems Biomedicine (Ministry of Education), School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Wei Wei
- NanoSystems Biology Cancer Center, Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA.,Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California - Los Angeles, Los Angeles, CA, USA
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21
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Li X, Fan B, Cao S, Chen D, Zhao X, Men D, Yue W, Wang J, Chen J. A microfluidic flow cytometer enabling absolute quantification of single-cell intracellular proteins. LAB ON A CHIP 2017; 17:3129-3137. [PMID: 28805868 DOI: 10.1039/c7lc00546f] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Quantification of single-cell proteomics provides key insights into cellular heterogeneity while conventional flow cytometry cannot provide absolute quantification of intracellular proteins of single cells due to the lack of calibration approaches. This paper presents a constriction channel (with a cross sectional area smaller than cells) based microfluidic flow cytometer, capable of collecting copy numbers of specific intracellular proteins. In this platform, single cells stained with fluorescence labelled antibodies were forced to squeeze through the constriction channel with the fluorescence intensities quantified and since cells fully filled the constriction channel during the squeezing process, solutions with fluorescence labelled antibodies were flushed into the constriction channel to obtain calibration curves. By combining raw fluorescence data and calibration curves, absolute quantification of intracellular proteins was realized. As a demonstration, copy numbers of beta-actin of single tumour cells were quantified to be 0.90 ± 0.30 μM (A549, ncell = 14 228), 2.34 ± 0.70 μM (MCF 10A, ncell = 2455), and 0.98 ± 0.65 μM (Hep G2, ncell = 6945). The travelling time for individual cells was quantified to be roughly 10 ms and thus a throughput of 100 cells per s can be achieved. This microfluidic system can be used to quantify the copy numbers of intracellular proteins in a high-throughput manner, which may function as an enabling technique in the field of single-cell proteomics.
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Affiliation(s)
- Xiufeng Li
- State Key Laboratory of Transducer Technology, Institute of Electronics, Chinese Academy of Sciences, Beijing, P.R. China.
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22
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Lyons YA, Wu SY, Overwijk WW, Baggerly KA, Sood AK. Immune cell profiling in cancer: molecular approaches to cell-specific identification. NPJ Precis Oncol 2017; 1:26. [PMID: 29872708 PMCID: PMC5871917 DOI: 10.1038/s41698-017-0031-0] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Revised: 07/10/2017] [Accepted: 07/24/2017] [Indexed: 01/22/2023] Open
Abstract
The immune system has many important regulatory roles in cancer development and progression. Given the emergence of effective immune therapies against many cancers, reliable predictors of response are needed. One method of determining response is by evaluating immune cell populations from treated and untreated tumor samples. The amount of material obtained from tumor biopsies can be limited; therefore, gene-based or protein-based analyses may be attractive because they require minimal tissue. Cell-specific signatures are being analyzed with use of the latest technologies, including NanoString’s nCounter technology, intracellular staining flow cytometry, cytometry by time-of-flight, RNA-Seq, and barcoding antibody-based protein arrays. These signatures provide information about the contributions of specific types of immune cells to bulk tumor samples. To date, both tumor tissue and immune cells have been analyzed for molecular expression profiles that can assess genes and proteins that are specific to immune cells, yielding results of varying specificity. Here, we discuss the importance of profiling tumor tissue and immune cells to identify immune-cell-associated genes and proteins and specific gene profiles of immune cells. We also discuss the use of these signatures in cancer treatment and the challenges faced in molecular expression profiling of immune cell populations.
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Affiliation(s)
- Yasmin A Lyons
- 1Department of Gynecologic Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, Texas 77030 USA
| | - Sherry Y Wu
- 1Department of Gynecologic Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, Texas 77030 USA
| | - Willem W Overwijk
- 2Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, Texas 77030 USA
| | - Keith A Baggerly
- 3Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, Texas 77030 USA
| | - Anil K Sood
- 1Department of Gynecologic Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, Texas 77030 USA.,4Center for RNA Interference and Non-Coding RNA, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, Texas 77030 USA.,5Cancer Biology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, Texas 77030 USA
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23
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24
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Lu Y, Yang L, Wei W, Shi Q. Microchip-based single-cell functional proteomics for biomedical applications. LAB ON A CHIP 2017; 17:1250-1263. [PMID: 28280819 PMCID: PMC5459479 DOI: 10.1039/c7lc00037e] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Cellular heterogeneity has been widely recognized but only recently have single cell tools become available that allow characterizing heterogeneity at the genomic and proteomic levels. We review the technological advances in microchip-based toolkits for single-cell functional proteomics. Each of these tools has distinct advantages and limitations, and a few have advanced toward being applied to address biological or clinical problems that traditional population-based methods fail to address. High-throughput single-cell proteomic assays generate high-dimensional data sets that contain new information and thus require developing new analytical frameworks to extract new biology. In this review article, we highlight a few biological and clinical applications in which microchip-based single-cell proteomic tools provide unique advantages. The examples include resolving functional heterogeneity and dynamics of immune cells, dissecting cell-cell interaction by creating a well-controlled on-chip microenvironment, capturing high-resolution snapshots of immune system functions in patients for better immunotherapy and elucidating phosphoprotein signaling networks in cancer cells for guiding effective molecularly targeted therapies.
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Affiliation(s)
- Yao Lu
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Liu Yang
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China.
| | - Wei Wei
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA. and Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Qihui Shi
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China.
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25
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Tadimety A, Syed A, Nie Y, Long CR, Kready KM, Zhang JXJ. Liquid biopsy on chip: a paradigm shift towards the understanding of cancer metastasis. Integr Biol (Camb) 2017; 9:22-49. [DOI: 10.1039/c6ib00202a] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Amogha Tadimety
- Thayer School of Engineering at Dartmouth College, Hanover NH, 03755, USA
| | - Abeer Syed
- Thayer School of Engineering at Dartmouth College, Hanover NH, 03755, USA
| | - Yuan Nie
- Thayer School of Engineering at Dartmouth College, Hanover NH, 03755, USA
| | - Christina R. Long
- Thayer School of Engineering at Dartmouth College, Hanover NH, 03755, USA
| | - Kasia M. Kready
- Thayer School of Engineering at Dartmouth College, Hanover NH, 03755, USA
| | - John X. J. Zhang
- Thayer School of Engineering at Dartmouth College, Hanover NH, 03755, USA
- Dartmouth-Hitchcock Norris Cotton Cancer Center, Lebanon NH, 03766, USA
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26
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Abstract
Hematopoiesis is probably the best-understood stem cell differentiation system; hematopoietic stem cell (HSC) transplantation represents the most widely used regenerative therapy. The classical view of lineage hierarchy in hematopoiesis is built on cell type definition system by a group of cell surface markers. However, the traditional model is facing increasing challenges, as many classical cell types are proved to be heterogeneous. Recently, the developments of new technologies allow genome, transcriptome, proteome, and epigenome analysis at the single-cell level. For the first time, we can study hematopoietic system at single-cell resolution on a multi-omic scale. Here, we review recent technical advances in single-cell analysis technology, as well as their current applications. We will also discuss the impact of single-cell technologies on both basic research and clinical application in hematology.
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27
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Eiden L, Yamanishi C, Takayama S, Dishinger JF. Aqueous Two-Phase System Rehydration of Antibody–Polymer Microarrays Enables Convenient Compartmentalized Multiplex Immunoassays. Anal Chem 2016; 88:11328-11334. [DOI: 10.1021/acs.analchem.6b02960] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Lisa Eiden
- PHASIQ, Inc., Ann Arbor, Michigan 48109, United States
| | - Cameron Yamanishi
- Department
of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Shuichi Takayama
- Department
of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department
of Macromolecular Science and Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States
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28
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Yang L, Wang Z, Deng Y, Li Y, Wei W, Shi Q. Single-Cell, Multiplexed Protein Detection of Rare Tumor Cells Based on a Beads-on-Barcode Antibody Microarray. Anal Chem 2016; 88:11077-11083. [PMID: 27644430 PMCID: PMC5519775 DOI: 10.1021/acs.analchem.6b03086] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Circulating tumor cells (CTCs) shed from tumor sites and represent the molecular characteristics of the tumor. Besides genetic and transcriptional characterization, it is important to profile a panel of proteins with single-cell precision for resolving CTCs' phenotype, organ-of-origin, and drug targets. We describe a new technology that enables profiling multiple protein markers of extraordinarily rare tumor cells at the single-cell level. This technology integrates a microchip consisting of 15000 60 pL-sized microwells and a novel beads-on-barcode antibody microarray (BOBarray). The BOBarray allows for multiplexed protein detection by assigning two independent identifiers (bead size and fluorescent color) of the beads to each protein. Four bead sizes (1.75, 3, 4.5, and 6 μm) and three colors (blue, green, and yellow) are utilized to encode up to 12 different proteins. The miniaturized BOBarray can fit an array of 60 pL-sized microwells that isolate single cells for cell lysis and the subsequent detection of protein markers. An enclosed 60 pL-sized microchamber defines a high concentration of proteins released from lysed single cells, leading to single-cell resolution of protein detection. The protein markers assayed in this study include organ-specific markers and drug targets that help to characterize the organ-of-origin and drug targets of isolated rare tumor cells from blood samples. This new approach enables handling a very small number of cells and achieves single-cell, multiplexed protein detection without loss of rare but clinically important tumor cells.
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Affiliation(s)
- Liu Yang
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai, People’s Republic of China
| | - Zhihua Wang
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai, People’s Republic of China
| | - Yuliang Deng
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai, People’s Republic of China
| | - Yan Li
- Shanghai Municipal Hospital of Traditional Chinese Medicine, Shanghai, People’s Republic of China
| | - Wei Wei
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, United States
| | - Qihui Shi
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai, People’s Republic of China
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
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29
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Tentori AM, Yamauchi KA, Herr AE. Detection of Isoforms Differing by a Single Charge Unit in Individual Cells. Angew Chem Int Ed Engl 2016; 55:12431-5. [PMID: 27595864 PMCID: PMC5201312 DOI: 10.1002/anie.201606039] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Indexed: 11/10/2022]
Abstract
To measure protein isoforms in individual mammalian cells, we report single-cell resolution isoelectric focusing (scIEF) and high-selectivity immunoprobing. Microfluidic design and photoactivatable materials establish the tunable pH gradients required by IEF and precisely control the transport and handling of each 17-pL cell lysate during analysis. The scIEF assay resolves protein isoforms with resolution down to a single-charge unit, including both endogenous cytoplasmic and nuclear proteins from individual mammalian cells.
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Affiliation(s)
- Augusto M Tentori
- The UC Berkeley/UCSF Graduate Program in Bioengineering, Berkeley, CA, USA
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Kevin A Yamauchi
- The UC Berkeley/UCSF Graduate Program in Bioengineering, Berkeley, CA, USA
| | - Amy E Herr
- The UC Berkeley/UCSF Graduate Program in Bioengineering, Berkeley, CA, USA.
- Department of Bioengineering, UC Berkeley, 308B Stanley Hall, Berkeley, CA, 94720, USA.
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30
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Tentori AM, Yamauchi KA, Herr AE. Detection of Isoforms Differing by a Single Charge Unit in Individual Cells. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201606039] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Augusto M. Tentori
- The UC Berkeley/UCSF Graduate Program in Bioengineering Berkeley CA USA
- Department of Chemical Engineering Massachusetts Institute of Technology Cambridge MA USA
| | - Kevin A. Yamauchi
- The UC Berkeley/UCSF Graduate Program in Bioengineering Berkeley CA USA
| | - Amy E. Herr
- The UC Berkeley/UCSF Graduate Program in Bioengineering Berkeley CA USA
- Department of Bioengineering UC Berkeley 308B Stanley Hall Berkeley CA 94720 USA
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Abstract
INTRODUCTION Cellular heterogeneity has challenged current cancer therapeutics and hindered the discovery and development of cancer drugs. The heterogeneity in functional proteome is of particular interest because many cancer drugs are developed to target signaling proteins. The complex nature of tumor systems calls for more advanced multiplexed single-cell tools to address the heterogeneity issue. AREA COVERED Over the past five years, there are a few single-cell functional proteomics tools introduced with unprecedented multiplexity and performance that are transforming the oncology field. Those tools are generally categorized as cytometry-based tools and microfluidics-based tools, and we discuss the representatives in both categories. Expert commentary: The single-cell tools have provided an avenue to understand the multifaceted differences of cancer cells, the complex signaling networks, and the relationship of intercellular interaction and tumor architecture. We also provide an outlook of single-cell tools in five years and the challenges to address before a greater impact on oncology can be made.
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Affiliation(s)
- Jun Wang
- a Multiplex Biotechnology Laboratory, Department of Chemistry , University at Albany, State University of New York , Albany , NY , USA.,b Cancer Research Center , University at Albany, State University of New York , Rensselaer , NY , USA
| | - Fan Yang
- a Multiplex Biotechnology Laboratory, Department of Chemistry , University at Albany, State University of New York , Albany , NY , USA
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32
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Wen N, Zhao Z, Fan B, Chen D, Men D, Wang J, Chen J. Development of Droplet Microfluidics Enabling High-Throughput Single-Cell Analysis. Molecules 2016; 21:E881. [PMID: 27399651 PMCID: PMC6272933 DOI: 10.3390/molecules21070881] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Revised: 06/27/2016] [Accepted: 06/28/2016] [Indexed: 12/20/2022] Open
Abstract
This article reviews recent developments in droplet microfluidics enabling high-throughput single-cell analysis. Five key aspects in this field are included in this review: (1) prototype demonstration of single-cell encapsulation in microfluidic droplets; (2) technical improvements of single-cell encapsulation in microfluidic droplets; (3) microfluidic droplets enabling single-cell proteomic analysis; (4) microfluidic droplets enabling single-cell genomic analysis; and (5) integrated microfluidic droplet systems enabling single-cell screening. We examine the advantages and limitations of each technique and discuss future research opportunities by focusing on key performances of throughput, multifunctionality, and absolute quantification.
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Affiliation(s)
- Na Wen
- Institute of Electronics, Chinese Academy of Sciences, Beijing 100190, China.
| | - Zhan Zhao
- Institute of Electronics, Chinese Academy of Sciences, Beijing 100190, China.
| | - Beiyuan Fan
- Institute of Electronics, Chinese Academy of Sciences, Beijing 100190, China.
| | - Deyong Chen
- Institute of Electronics, Chinese Academy of Sciences, Beijing 100190, China.
| | - Dong Men
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China.
| | - Junbo Wang
- Institute of Electronics, Chinese Academy of Sciences, Beijing 100190, China.
| | - Jian Chen
- Institute of Electronics, Chinese Academy of Sciences, Beijing 100190, China.
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33
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Liu Z, Han X, Qin L. Recent Progress of Microfluidics in Translational Applications. Adv Healthc Mater 2016; 5:871-88. [PMID: 27091777 PMCID: PMC4922259 DOI: 10.1002/adhm.201600009] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Revised: 02/16/2016] [Indexed: 12/12/2022]
Abstract
Microfluidics, featuring microfabricated structures, is a technology for manipulating fluids at the micrometer scale. The small dimension and flexibility of microfluidic systems are ideal for mimicking molecular and cellular microenvironment, and show great potential in translational research and development. Here, the recent progress of microfluidics in biological and biomedical applications, including molecular analysis, cellular analysis, and chip-based material delivery and biomimetic design is presented. The potential future developments in the translational microfluidics field are also discussed.
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Affiliation(s)
- Zongbin Liu
- Department of Nanomedicine, Houston Methodist Research Institute, Houston, TX 77030, USA
- Department of Cell and Developmental Biology, Weill Medical College of Cornell University, New York, NY 10065, USA
| | - Xin Han
- Department of Nanomedicine, Houston Methodist Research Institute, Houston, TX 77030, USA
- Department of Cell and Developmental Biology, Weill Medical College of Cornell University, New York, NY 10065, USA
| | - Lidong Qin
- Department of Nanomedicine, Houston Methodist Research Institute, Houston, TX 77030, USA
- Department of Cell and Developmental Biology, Weill Medical College of Cornell University, New York, NY 10065, USA
- Department of Molecular and Cellular Oncology, The University of Texas M. D. Anderson Cancer Center, Houston, TX 77030, USA
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Development of Microfluidic Systems Enabling High-Throughput Single-Cell Protein Characterization. SENSORS 2016; 16:232. [PMID: 26891303 PMCID: PMC4801608 DOI: 10.3390/s16020232] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Revised: 01/21/2016] [Accepted: 02/02/2016] [Indexed: 01/09/2023]
Abstract
This article reviews recent developments in microfluidic systems enabling high-throughput characterization of single-cell proteins. Four key perspectives of microfluidic platforms are included in this review: (1) microfluidic fluorescent flow cytometry; (2) droplet based microfluidic flow cytometry; (3) large-array micro wells (microengraving); and (4) large-array micro chambers (barcode microchips). We examine the advantages and limitations of each technique and discuss future research opportunities by focusing on three key performance parameters (absolute quantification, sensitivity, and throughput).
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Abstract
Protein phosphorylation is a ubiquitous posttranslational modification, which is heavily involved in signal transduction. Misregulation of protein phosphorylation is often associated with a decrease in cell viability and complex diseases such as cancer. The dynamic and low abundant nature of phosphorylated proteins makes studying phosphoproteome a challenging task. In this review, we summarize state of the art proteomic techniques to study and quantify peptide phosphorylation in biological systems and discuss their limitations. Due to its short-lived nature, the phosphorylation event cannot be precisely traced in a heterogonous cell population, which highlights the importance of analyzing phosphorylation events at the single cell level. Mainly, we focus on the methodical and instrumental developments in proteomics and nanotechnology, which will help to build more accurate and robust systems for the feasibility of phosphorylation analysis at the single cell level. We propose that an automated and miniaturized construction of analytical systems holds the key to the future of phosphoproteomics; therefore, we highlight the benchmark studies in this direction. Having advanced and automated microfluidic chip LC systems will allow us to analyze single-cell phosphoproteomics and quantitatively compare it with others. The progress in the microfluidic chip LC systems and feasibility of the single-cell phosphoproteomics will be beneficial for early diagnosis and detection of the treatment response of many crucial diseases.
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Affiliation(s)
- Ayse Nur Polat
- Department of Molecular Biology and Genetics, Science Faculty, Koç University, Istanbul, Turkey.
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36
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Pellowe AS, Gonzalez AL. Extracellular matrix biomimicry for the creation of investigational and therapeutic devices. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2015; 8:5-22. [PMID: 26053111 DOI: 10.1002/wnan.1349] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2014] [Revised: 01/26/2015] [Accepted: 03/27/2015] [Indexed: 01/24/2023]
Abstract
The extracellular matrix (ECM) is a web of fibrous proteins that serves as a scaffold for tissues and organs, and is important for maintaining homeostasis and facilitating cellular adhesion. Integrin transmembrane receptors are the primary adhesion molecules that anchor cells to the ECM, thus integrating cells with their microenvironments. Integrins play a critical role in facilitating cell-matrix interactions and promoting signal transduction, both from the cell to the ECM and vice versa, ultimately mediating cell behavior. For this reason, many advanced biomaterials employ biomimicry by replicating the form and function of fibrous ECM proteins. The ECM also acts as a reservoir for small molecules and growth factors, wherein fibrous proteins directly bind and present these bioactive moieties that facilitate cell activity. Therefore biomimicry can be enhanced by incorporating small molecules into ECM-like substrates. Biomimetic ECM materials have served as invaluable research tools for studying interactions between cells and the surrounding ECM, revealing that cell-matrix signaling is driven by mechanical forces, integrin engagement, and small molecules. Mimicking pathological ECMs has also elucidated disease specific cell behaviors. For example, biomimetic tumor microenvironments have been used to induce metastatic cell behaviors, and have thereby shown promise for in vitro cancer drug testing and targeting. Further, ECM-like substrates have been successfully employed for autologous cell recolonization for tissue engineering and wound healing. As we continue to learn more about the mechanical and biochemical characteristics of the ECM, these properties can be harnessed to develop new biomaterials, biomedical devices, and therapeutics.
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Affiliation(s)
- Amanda S Pellowe
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
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37
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Abstract
Single-cell analysis heralds a new era that allows “omics” analysis, notably genomics, transcriptomics, epigenomics and proteomics at the single-cell level. It enables the identification of the minor subpopulations that may play a critical role in a biological process of a population of cells, which conventionally are regarded as homogeneous. It provides an ultra-sensitive tool to clarify specific molecular mechanisms and pathways and reveal the nature of cell heterogeneity. It also facilitates the clinical investigation of patients when a very low quantity or a single cell is available for analysis, such as noninvasive prenatal diagnosis and cancer screening, and genetic evaluation for in vitro fertilization. Within a few short years, single-cell analysis, especially whole genomic sequencing and transcriptomic sequencing, is becoming robust and broadly accessible, although not yet a routine practice. Here, with single cell RNA-seq emphasized, an overview of the discipline, progresses, and prospects of single-cell analysis and its applications in biology and medicine are given with a series of logic and theoretical considerations.
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Affiliation(s)
- Xinghua Pan
- Department of Genetics, School of Medicine, Yale University, New Haven, CT, USA
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38
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Remacle F, Levine RD. [Prediction of the molecular response to pertubations from single cell measurements]. Med Sci (Paris) 2014; 30:1129-35. [PMID: 25537043 DOI: 10.1051/medsci/20143012016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The response of protein signalization networks to perturbations is analysed from single cell measurements. This experimental approach allows characterizing the fluctuations in protein expression levels from cell to cell. The analysis is based on an information theoretic approach grounded in thermodynamics leading to a quantitative version of Le Chatelier principle which allows to predict the molecular response. Two systems are investigated: human macrophages subjected to lipopolysaccharide challenge, analogous to the immune response against Gram-negative bacteria and the response of the proteins involved in the mTOR signalizing network of GBM cancer cells to changes in partial oxygen pressure.
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Affiliation(s)
- Françoise Remacle
- Université de Liège, département de chimie, chimie-physique théorique, B6c, allée de la Chimie, 3, B4000 Liège, Belgique
| | - Raphael D Levine
- Crump institute for molecular imaging, department of molecular and medical pharmacology, university of California, department of chemistry and biochemistry, David Geffen school of medicine, Los Angeles, CA 90095, États-Unis
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Deng Y, Zhang Y, Sun S, Wang Z, Wang M, Yu B, Czajkowsky DM, Liu B, Li Y, Wei W, Shi Q. An integrated microfluidic chip system for single-cell secretion profiling of rare circulating tumor cells. Sci Rep 2014; 4:7499. [PMID: 25511131 PMCID: PMC4266859 DOI: 10.1038/srep07499] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Accepted: 11/27/2014] [Indexed: 02/08/2023] Open
Abstract
Genetic and transcriptional profiling, as well as surface marker identification of single circulating tumor cells (CTCs) have been demonstrated. However, quantitatively profiling of functional proteins at single CTC resolution has not yet been achieved, owing to the limited purity of the isolated CTC populations and a lack of single-cell proteomic approaches to handle and analyze rare CTCs. Here, we develop an integrated microfluidic system specifically designed for streamlining isolation, purification and single-cell secretomic profiling of CTCs from whole blood. Key to this platform is the use of photocleavable ssDNA-encoded antibody conjugates to enable a highly purified CTC population with <75 ‘contaminated' blood cells. An enhanced poly-L-lysine barcode pattern is created on the single-cell barcode chip for efficient capture rare CTC cells in microchambers for subsequent secreted protein profiling. This system was extensively evaluated and optimized with EpCAM-positive HCT116 cells seeded into whole blood. Patient blood samples were employed to assess the utility of the system for isolation, purification and single-cell secretion profiling of CTCs. The CTCs present in patient blood samples exhibit highly heterogeneous secretion profile of IL-8 and VEGF. The numbers of secreting CTCs are found not in accordance with CTC enumeration based on immunostaining in the parallel experiments.
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Affiliation(s)
- Yuliang Deng
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai, China
| | - Yu Zhang
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai, China
| | - Shuai Sun
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai, China
| | - Zhihua Wang
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai, China
| | - Minjiao Wang
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai, China
| | - Beiqin Yu
- Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Daniel M Czajkowsky
- 1] Center for Bio-Detection and Bio-Instrumentation, Shanghai Jiao Tong University, Shanghai, China [2] School of Biomedicial Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Bingya Liu
- 1] Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai, China [2] Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yan Li
- Shanghai Municipal Hospital of Traditional Chinese Medicine, Shanghai, China
| | - Wei Wei
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Qihui Shi
- 1] Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai, China [2] State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University, Shanghai, China [3] Center for Bio-Detection and Bio-Instrumentation, Shanghai Jiao Tong University, Shanghai, China [4] School of Biomedicial Engineering, Shanghai Jiao Tong University, Shanghai, China
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40
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Elitas M, Brower K, Lu Y, Chen JJ, Fan R. A microchip platform for interrogating tumor-macrophage paracrine signaling at the single-cell level. LAB ON A CHIP 2014; 14:3582-8. [PMID: 25057779 PMCID: PMC4145007 DOI: 10.1039/c4lc00676c] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
It is increasingly recognized that infiltrating immune cells contribute to the pathogenesis of a wide range of solid tumors. The paracrine signaling between the tumor and the immune cells alters the functional state of individual tumor cells and, correspondingly, the anticipated response to radiation or chemotherapies, which is of great importance to clinical oncology. Here we present a high-density microchip platform capable of measuring a panel of paracrine signals associated with heterotypic tumor-immune cell interactions in the single-cell, pair-wise manner. The device features a high-content cell capture array of 5000+ sub-nanoliter microchambers for the isolation of single and multi-cell combinations and a multi-plex antibody "barcode" array for multiplexed protein secretion analysis from each microchamber. In this work, we measured a panel of 16 proteins produced from individual glioma cells, individual macrophage cells and varying heterotypic multi-cell combinations of both on the same device. The results show changes of tumor cell functional phenotypes that cannot be explained by an additive effect from isolated single cells and, presumably, can be attributed to the paracrine signaling between macrophage and glioma cells. The protein correlation analysis reveals the key signaling nodes altered by tumor-macrophage communication. This platform enables the novel pair-wise interrogation of heterotypic cell-cell paracrine signaling at the individual cell level with an in-depth analysis of the changing functional phenotypes for different co-culture cell combinations.
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Affiliation(s)
- Meltem Elitas
- Department of Biomedical Engineering, Yale University, New Haven, Connecticut 06520, USA.
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41
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Hughes AJ, Spelke DP, Xu Z, Kang CC, Schaffer DV, Herr AE. Single-cell western blotting. Nat Methods 2014; 11:749-55. [PMID: 24880876 PMCID: PMC4077215 DOI: 10.1038/nmeth.2992] [Citation(s) in RCA: 292] [Impact Index Per Article: 29.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Accepted: 04/28/2014] [Indexed: 02/06/2023]
Abstract
To measure cell-to-cell variation in protein-mediated functions, we developed an approach to conduct ∼10(3) concurrent single-cell western blots (scWesterns) in ∼4 h. A microscope slide supporting a 30-μm-thick photoactive polyacrylamide gel enables western blotting: settling of single cells into microwells, lysis in situ, gel electrophoresis, photoinitiated blotting to immobilize proteins and antibody probing. We applied this scWestern method to monitor single-cell differentiation of rat neural stem cells and responses to mitogen stimulation. The scWestern quantified target proteins even with off-target antibody binding, multiplexed to 11 protein targets per single cell with detection thresholds of <30,000 molecules, and supported analyses of low starting cell numbers (∼200) when integrated with FACS. The scWestern overcomes limitations of antibody fidelity and sensitivity in other single-cell protein analysis methods and constitutes a versatile tool for the study of complex cell populations at single-cell resolution.
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Affiliation(s)
- Alex J Hughes
- 1] Department of Bioengineering, University of California (UC) Berkeley, Berkeley, California, USA. [2] California Institute for Quantitative Biosciences, UC Berkeley, Berkeley, California, USA. [3] [4]
| | - Dawn P Spelke
- 1] Department of Bioengineering, University of California (UC) Berkeley, Berkeley, California, USA. [2] California Institute for Quantitative Biosciences, UC Berkeley, Berkeley, California, USA. [3] The UC Berkeley-UC San Francisco Graduate Program in Bioengineering, UC Berkeley, Berkeley, California, USA. [4]
| | - Zhuchen Xu
- 1] Department of Bioengineering, University of California (UC) Berkeley, Berkeley, California, USA. [2] California Institute for Quantitative Biosciences, UC Berkeley, Berkeley, California, USA
| | - Chi-Chih Kang
- 1] Department of Bioengineering, University of California (UC) Berkeley, Berkeley, California, USA. [2] California Institute for Quantitative Biosciences, UC Berkeley, Berkeley, California, USA
| | - David V Schaffer
- 1] Department of Bioengineering, University of California (UC) Berkeley, Berkeley, California, USA. [2] California Institute for Quantitative Biosciences, UC Berkeley, Berkeley, California, USA. [3] The UC Berkeley-UC San Francisco Graduate Program in Bioengineering, UC Berkeley, Berkeley, California, USA. [4] Department of Chemical and Biomolecular Engineering, UC Berkeley, Berkeley, California, USA. [5] Helen Wills Neuroscience Institute, UC Berkeley, Berkeley, California, USA
| | - Amy E Herr
- 1] Department of Bioengineering, University of California (UC) Berkeley, Berkeley, California, USA. [2] California Institute for Quantitative Biosciences, UC Berkeley, Berkeley, California, USA. [3] The UC Berkeley-UC San Francisco Graduate Program in Bioengineering, UC Berkeley, Berkeley, California, USA
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Yu J, Zhou J, Sutherland A, Wei W, Shin YS, Xue M, Heath JR. Microfluidics-based single-cell functional proteomics for fundamental and applied biomedical applications. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2014; 7:275-95. [PMID: 24896308 DOI: 10.1146/annurev-anchem-071213-020323] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
We review an emerging microfluidics-based toolkit for single-cell functional proteomics. Functional proteins include, but are not limited to, the secreted signaling proteins that can reflect the biological behaviors of immune cells or the intracellular phosphoproteins associated with growth factor-stimulated signaling networks. Advantages of the microfluidics platforms are multiple. First, 20 or more functional proteins may be assayed simultaneously from statistical numbers of single cells. Second, cell behaviors (e.g., motility) may be correlated with protein assays. Third, extensions to quantized cell populations can permit measurements of cell-cell interactions. Fourth, rare cells can be functionally identified and then separated for further analysis or culturing. Finally, certain assay types can provide a conduit between biology and the physicochemical laws. We discuss the history and challenges of the field then review design concepts and uses of the microchip platforms that have been reported, with an eye toward biomedical applications. We then look to the future of the field.
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Affiliation(s)
- Jing Yu
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125;
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