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Yamagishi M, Miyata K, Kamatani T, Kabata H, Baba R, Tanaka Y, Suzuki N, Matsusaka M, Motomura Y, Kiniwa T, Koga S, Goda K, Ohara O, Funatsu T, Fukunaga K, Moro K, Uemura S, Shirasaki Y. Quantitative live-cell imaging of secretion activity reveals dynamic immune responses. iScience 2024; 27:109840. [PMID: 38779479 PMCID: PMC11109006 DOI: 10.1016/j.isci.2024.109840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 01/19/2024] [Accepted: 04/25/2024] [Indexed: 05/25/2024] Open
Abstract
Quantification of cytokine secretion has facilitated advances in the field of immunology, yet the dynamic and varied secretion profiles of individual cells, particularly those obtained from limited human samples, remain obscure. Herein, we introduce a technology for quantitative live-cell imaging of secretion activity (qLCI-S) that enables high-throughput and dual-color monitoring of secretion activity at the single-cell level over several days, followed by transcriptome analysis of individual cells based on their phenotype. The efficacy of qLCI-S was demonstrated by visualizing the characteristic temporal pattern of cytokine secretion of group 2 innate lymphoid cells, which constitute less than 0.01% of human peripheral blood mononuclear cells, and by revealing minor subpopulations with enhanced cytokine production. The underlying mechanism of this feature was linked to the gene expression of stimuli receptors. This technology paves the way for exploring gene expression signatures linked to the spatiotemporal dynamic nature of various secretory functions.
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Affiliation(s)
- Mai Yamagishi
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo 113-0033, Japan
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
- Live Cell Diagnosis, Ltd., Saitama 351-0022, Japan
| | - Kaede Miyata
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - Takashi Kamatani
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
- Division of Pulmonary Medicine, Department of Medicine, Keio University School of Medicine, Tokyo 160-8582, Japan
- Department of AI Technology Development, M&D Data Science Center, Tokyo Medical and Dental University, Tokyo 113-8519, Japan
- Division of Precision Cancer Medicine, Tokyo Medical and Dental University, Tokyo 113-8519, Japan
| | - Hiroki Kabata
- Division of Pulmonary Medicine, Department of Medicine, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Rie Baba
- Division of Pulmonary Medicine, Department of Medicine, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Yumiko Tanaka
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - Nobutake Suzuki
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo 113-0033, Japan
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - Masako Matsusaka
- Division of Pulmonary Medicine, Department of Medicine, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Yasutaka Motomura
- Department of Microbiology and Immunology, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan
| | - Tsuyoshi Kiniwa
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Satoshi Koga
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Keisuke Goda
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Institute of Technological Sciences, Wuhan University, Hubei 430072, China
| | - Osamu Ohara
- KAZUSA DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
| | - Takashi Funatsu
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo 113-0033, Japan
| | - Koichi Fukunaga
- Division of Pulmonary Medicine, Department of Medicine, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Kazuyo Moro
- Department of Microbiology and Immunology, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Sotaro Uemura
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - Yoshitaka Shirasaki
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo 113-0033, Japan
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
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Lin S, Feng D, Han X, Li L, Lin Y, Gao H. Microfluidic platform for omics analysis on single cells with diverse morphology and size: A review. Anal Chim Acta 2024; 1294:342217. [PMID: 38336406 DOI: 10.1016/j.aca.2024.342217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 01/04/2024] [Accepted: 01/04/2024] [Indexed: 02/12/2024]
Abstract
BACKGROUND Microfluidic techniques have emerged as powerful tools in single-cell research, facilitating the exploration of omics information from individual cells. Cell morphology is crucial for gene expression and physiological processes. However, there is currently a lack of integrated analysis of morphology and single-cell omics information. A critical challenge remains: what platform technologies are the best option to decode omics data of cells that are complex in morphology and size? RESULTS This review highlights achievements in microfluidic-based single-cell omics and isolation of cells based on morphology, along with other cell sorting methods based on physical characteristics. Various microfluidic platforms for single-cell isolation are systematically presented, showcasing their diversity and adaptability. The discussion focuses on microfluidic devices tailored to the distinct single-cell isolation requirements in plants and animals, emphasizing the significance of considering cell morphology and cell size in optimizing single-cell omics strategies. Simultaneously, it explores the application of microfluidic single-cell sorting technologies to single-cell sequencing, aiming to effectively integrate information about cell shape and size. SIGNIFICANCE AND NOVELTY The novelty lies in presenting a comprehensive overview of recent accomplishments in microfluidic-based single-cell omics, emphasizing the integration of different microfluidic platforms and their implications for cell morphology-based isolation. By underscoring the pivotal role of the specialized morphology of different cells in single-cell research, this review provides robust support for delving deeper into the exploration of single-cell omics data.
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Affiliation(s)
- Shujin Lin
- Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, 350025, China; Central Laboratory at the Second Affiliated Hospital of Fujian University of Traditional Chinese Medicine, Fujian-Macao Science and Technology Cooperation Base of Traditional Chinese Medicine-Oriented Chronic Disease Prevention and Treatment, Innovation and Transformation Center, Fujian University of Traditional Chinese Medicine, China
| | - Dan Feng
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xiao Han
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, 350108, China.
| | - Ling Li
- Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, 350025, China; The First Clinical Medical College of Fujian Medical University, Fuzhou, 350004, China; Hepatopancreatobiliary Surgery Department, The First Affiliated Hospital of Fujian Medical University, Fuzhou, 350004, China.
| | - Yao Lin
- Central Laboratory at the Second Affiliated Hospital of Fujian University of Traditional Chinese Medicine, Fujian-Macao Science and Technology Cooperation Base of Traditional Chinese Medicine-Oriented Chronic Disease Prevention and Treatment, Innovation and Transformation Center, Fujian University of Traditional Chinese Medicine, China; Collaborative Innovation Center for Rehabilitation Technology, Fujian University of Traditional Chinese Medicine, China.
| | - Haibing Gao
- Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, 350025, China.
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Labib M, Wang Z, Kim Y, Lin S, Abdrabou A, Yousefi H, Lo PY, Angers S, Sargent EH, Kelley SO. Identification of druggable regulators of cell secretion via a kinome-wide screen and high-throughput immunomagnetic cell sorting. Nat Biomed Eng 2024; 8:263-277. [PMID: 38012306 DOI: 10.1038/s41551-023-01135-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 10/16/2023] [Indexed: 11/29/2023]
Abstract
The identification of genetic regulators of cell secretions is challenging because it requires the sorting of a large number of cells according to their secretion patterns. Here we report the development and applicability of a high-throughput microfluidic method for the analysis of the secretion levels of large populations of immune cells. The method is linked with a kinome-wide loss-of-function CRISPR screen, immunomagnetically sorting the cells according to their secretion levels, and the sequencing of their genomes to identify key genetic modifiers of cell secretion. We used the method, which we validated against flow cytometry for cytokines secreted from primary mouse CD4+ (cluster of differentiation 4-positive) T cells, to discover a subgroup of highly co-expressed kinase-coding genes that regulate interferon-gamma secretion by these cells. We validated the function of the kinases identified using RNA interference, CRISPR knockouts and kinase inhibitors and confirmed the druggability of selected kinases via the administration of a kinase inhibitor in an animal model of colitis. The technique may facilitate the discovery of regulatory mechanisms for immune-cell activation and of therapeutic targets for autoimmune diseases.
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Affiliation(s)
- Mahmoud Labib
- Peninsula Medical School, Faculty of Health, University of Plymouth, Plymouth, UK
- Department of Chemistry, Northwestern University, Evanston, IL, USA
- Department of Pharmaceutical Sciences, University of Toronto, Toronto, Ontario, Canada
| | - Zongjie Wang
- Department of Biomedical Engineering, McCormick School of Engineering, Northwestern University, Evanston, IL, USA
| | - Yunhye Kim
- Department of Pharmaceutical Sciences, University of Toronto, Toronto, Ontario, Canada
| | - Sichun Lin
- Department of Pharmaceutical Sciences, University of Toronto, Toronto, Ontario, Canada
| | - Abdalla Abdrabou
- Robert H. Laurie Comprehensive Cancer Center, Northwestern University, Chicago, IL, USA
| | - Hanie Yousefi
- Department of Chemistry, Northwestern University, Evanston, IL, USA
| | - Pei-Ying Lo
- Department of Biomedical Engineering, McCormick School of Engineering, Northwestern University, Evanston, IL, USA
| | - Stéphane Angers
- Department of Pharmaceutical Sciences, University of Toronto, Toronto, Ontario, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
- Donnelly Centre for Cellular and Biomolecular Research, Toronto, Ontario, Canada
| | - Edward H Sargent
- Department of Biomedical Engineering, McCormick School of Engineering, Northwestern University, Evanston, IL, USA
- Department of Electrical & Computer Engineering, University of Toronto, Toronto, Ontario, Canada
| | - Shana O Kelley
- Department of Chemistry, Northwestern University, Evanston, IL, USA.
- Department of Pharmaceutical Sciences, University of Toronto, Toronto, Ontario, Canada.
- Department of Biomedical Engineering, McCormick School of Engineering, Northwestern University, Evanston, IL, USA.
- Robert H. Laurie Comprehensive Cancer Center, Northwestern University, Chicago, IL, USA.
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada.
- Donnelly Centre for Cellular and Biomolecular Research, Toronto, Ontario, Canada.
- Institute for Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada.
- Chan Zuckerberg Biohub Chicago, Chicago, IL, USA.
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Schlotheuber LJ, Lüchtefeld I, Eyer K. Antibodies, repertoires and microdevices in antibody discovery and characterization. LAB ON A CHIP 2024; 24:1207-1225. [PMID: 38165819 PMCID: PMC10898418 DOI: 10.1039/d3lc00887h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 12/01/2023] [Indexed: 01/04/2024]
Abstract
Therapeutic antibodies are paramount in treating a wide range of diseases, particularly in auto-immunity, inflammation and cancer, and novel antibody candidates recognizing a vast array of novel antigens are needed to expand the usefulness and applications of these powerful molecules. Microdevices play an essential role in this challenging endeavor at various stages since many general requirements of the overall process overlap nicely with the general advantages of microfluidics. Therefore, microfluidic devices are rapidly taking over various steps in the process of new candidate isolation, such as antibody characterization and discovery workflows. Such technologies can allow for vast improvements in time-lines and incorporate conservative antibody stability and characterization assays, but most prominently screenings and functional characterization within integrated workflows due to high throughput and standardized workflows. First, we aim to provide an overview of the challenges of developing new therapeutic candidates, their repertoires and requirements. Afterward, this review focuses on the discovery of antibodies using microfluidic systems, technological aspects of micro devices and small-scale antibody protein characterization and selection, as well as their integration and implementation into antibody discovery workflows. We close with future developments in microfluidic detection and antibody isolation principles and the field in general.
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Affiliation(s)
- Luca Johannes Schlotheuber
- ETH Laboratory for Functional Immune Repertoire Analysis, Institute of Pharmaceutical Sciences, D-CHAB, ETH Zürich, 8093 Zürich, Switzerland.
| | - Ines Lüchtefeld
- ETH Laboratory for Functional Immune Repertoire Analysis, Institute of Pharmaceutical Sciences, D-CHAB, ETH Zürich, 8093 Zürich, Switzerland.
- ETH Laboratory for Tumor and Stem Cell Dynamics, Institute of Molecular Health Sciences, D-BIOL, ETH Zürich, 8093 Zürich, Switzerland
| | - Klaus Eyer
- ETH Laboratory for Functional Immune Repertoire Analysis, Institute of Pharmaceutical Sciences, D-CHAB, ETH Zürich, 8093 Zürich, Switzerland.
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5
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Fang W, Liu X, Maiga M, Cao W, Mu Y, Yan Q, Zhu Q. Digital PCR for Single-Cell Analysis. BIOSENSORS 2024; 14:64. [PMID: 38391982 PMCID: PMC10886679 DOI: 10.3390/bios14020064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 01/18/2024] [Accepted: 01/22/2024] [Indexed: 02/24/2024]
Abstract
Single-cell analysis provides an overwhelming strategy for revealing cellular heterogeneity and new perspectives for understanding the biological function and disease mechanism. Moreover, it promotes the basic and clinical research in many fields at a single-cell resolution. A digital polymerase chain reaction (dPCR) is an absolute quantitative analysis technology with high sensitivity and precision for DNA/RNA or protein. With the development of microfluidic technology, digital PCR has been used to achieve absolute quantification of single-cell gene expression and single-cell proteins. For single-cell specific-gene or -protein detection, digital PCR has shown great advantages. So, this review will introduce the significance and process of single-cell analysis, including single-cell isolation, single-cell lysis, and single-cell detection methods, mainly focusing on the microfluidic single-cell digital PCR technology and its biological application at a single-cell level. The challenges and opportunities for the development of single-cell digital PCR are also discussed.
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Affiliation(s)
- Weibo Fang
- Research Center for Analytical Instrumentation, Institute of Cyber-Systems and Control, College of Control Science and Engineering, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou 310027, China; (W.F.); (X.L.); (M.M.); (W.C.); (Y.M.)
| | - Xudong Liu
- Research Center for Analytical Instrumentation, Institute of Cyber-Systems and Control, College of Control Science and Engineering, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou 310027, China; (W.F.); (X.L.); (M.M.); (W.C.); (Y.M.)
| | - Mariam Maiga
- Research Center for Analytical Instrumentation, Institute of Cyber-Systems and Control, College of Control Science and Engineering, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou 310027, China; (W.F.); (X.L.); (M.M.); (W.C.); (Y.M.)
| | - Wenjian Cao
- Research Center for Analytical Instrumentation, Institute of Cyber-Systems and Control, College of Control Science and Engineering, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou 310027, China; (W.F.); (X.L.); (M.M.); (W.C.); (Y.M.)
| | - Ying Mu
- Research Center for Analytical Instrumentation, Institute of Cyber-Systems and Control, College of Control Science and Engineering, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou 310027, China; (W.F.); (X.L.); (M.M.); (W.C.); (Y.M.)
| | - Qiang Yan
- Department of Hepatobiliary and Pancreatic Surgery, Huzhou Central Hospital, Huzhou Key Laboratory of Intelligent and Digital Precision Surgery, Department of General Surgery, Affiliated Huzhou Hospital, School of Medicine, Zhejiang University, Huzhou 313000, China
| | - Qiangyuan Zhu
- Research Center for Analytical Instrumentation, Institute of Cyber-Systems and Control, College of Control Science and Engineering, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou 310027, China; (W.F.); (X.L.); (M.M.); (W.C.); (Y.M.)
- Huzhou Institute of Zhejiang University, Huzhou 313002, China
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Wang C, Wang C, Wu Y, Gao J, Han Y, Chu Y, Qiang L, Qiu J, Gao Y, Wang Y, Song F, Wang Y, Shao X, Zhang Y, Han L. High-Throughput, Living Single-Cell, Multiple Secreted Biomarker Profiling Using Microfluidic Chip and Machine Learning for Tumor Cell Classification. Adv Healthc Mater 2022; 11:e2102800. [PMID: 35368151 DOI: 10.1002/adhm.202102800] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 03/02/2022] [Indexed: 11/09/2022]
Abstract
Secreted proteins provide abundant functional information on living cells and can be used as important tumor diagnostic markers, of which profiling at the single-cell level is helpful for accurate tumor cell classification. Currently, achieving living single-cell multi-index, high-sensitivity, and quantitative secretion biomarker profiling remains a great challenge. Here, a high-throughput living single-cell multi-index secreted biomarker profiling platform is proposed, combined with machine learning, to achieve accurate tumor cell classification. A single-cell culture microfluidic chip with self-assembled graphene oxide quantum dots (GOQDs) enables high-activity single-cell culture, ensuring normal secretion of biomarkers and high-throughput single-cell separation, providing sufficient statistical data for machine learning. At the same time, the antibody barcode chip with self-assembled GOQDs performs multi-index, highly sensitive, and quantitative detection of secreted biomarkers, in which each cell culture chamber covers a whole barcode array. Importantly, by combining the K-means strategy with machine learning, thousands of single tumor cell secretion data are analyzed, enabling tumor cell classification with a recognition accuracy of 95.0%. In addition, further profiling of the grouping results reveals the unique secretion characteristics of subgroups. This work provides an intelligent platform for high-throughput living single-cell multiple secretion biomarker profiling, which has broad implications for cancer investigation and biomedical research.
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Affiliation(s)
- Chao Wang
- Institute of Marine Science and Technology Shandong University Tsingdao 266237 China
| | - Chunhua Wang
- Institute of Marine Science and Technology Shandong University Tsingdao 266237 China
| | - Yu Wu
- Obstetrics and Gynecology Department Peking University Third Hospital Beijing 100191 China
| | - Jianwei Gao
- Institute of Marine Science and Technology Shandong University Tsingdao 266237 China
| | - Yingkuan Han
- Institute of Marine Science and Technology Shandong University Tsingdao 266237 China
| | - Yujin Chu
- Institute of Marine Science and Technology Shandong University Tsingdao 266237 China
| | - Le Qiang
- Institute of Marine Science and Technology Shandong University Tsingdao 266237 China
| | - Jiaoyan Qiu
- Institute of Marine Science and Technology Shandong University Tsingdao 266237 China
| | - Yakun Gao
- Institute of Marine Science and Technology Shandong University Tsingdao 266237 China
| | - Yanhao Wang
- Institute of Marine Science and Technology Shandong University Tsingdao 266237 China
| | - Fangteng Song
- Institute of Marine Science and Technology Shandong University Tsingdao 266237 China
| | - Yihe Wang
- Institute of Marine Science and Technology Shandong University Tsingdao 266237 China
| | - Xiaowei Shao
- Institute of Marine Science and Technology Shandong University Tsingdao 266237 China
| | - Yu Zhang
- Institute of Marine Science and Technology Shandong University Tsingdao 266237 China
| | - Lin Han
- Institute of Marine Science and Technology Shandong University Tsingdao 266237 China
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Xie H, Ding X. The Intriguing Landscape of Single-Cell Protein Analysis. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2105932. [PMID: 35199955 PMCID: PMC9036017 DOI: 10.1002/advs.202105932] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 01/27/2022] [Indexed: 05/15/2023]
Abstract
Profiling protein expression at single-cell resolution is essential for fundamental biological research (such as cell differentiation and tumor microenvironmental examination) and clinical precision medicine where only a limited number of primary cells are permitted. With the recent advances in engineering, chemistry, and biology, single-cell protein analysis methods are developed rapidly, which enable high-throughput and multiplexed protein measurements in thousands of individual cells. In combination with single cell RNA sequencing and mass spectrometry, single-cell multi-omics analysis can simultaneously measure multiple modalities including mRNAs, proteins, and metabolites in single cells, and obtain a more comprehensive exploration of cellular signaling processes, such as DNA modifications, chromatin accessibility, protein abundance, and gene perturbation. Here, the recent progress and applications of single-cell protein analysis technologies in the last decade are summarized. Current limitations, challenges, and possible future directions in this field are also discussed.
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Affiliation(s)
- Haiyang Xie
- State Key Laboratory of Oncogenes and Related GenesInstitute for Personalized MedicineSchool of Biomedical EngineeringShanghai Jiao Tong UniversityShanghai200030China
| | - Xianting Ding
- State Key Laboratory of Oncogenes and Related GenesInstitute for Personalized MedicineSchool of Biomedical EngineeringShanghai Jiao Tong UniversityShanghai200030China
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8
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Broketa M, Bruhns P. Single-Cell Technologies for the Study of Antibody-Secreting Cells. Front Immunol 2022; 12:821729. [PMID: 35173713 PMCID: PMC8841722 DOI: 10.3389/fimmu.2021.821729] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 12/29/2021] [Indexed: 01/05/2023] Open
Abstract
Antibody-secreting cells (ASC), plasmablasts and plasma cells, are terminally differentiated B cells responsible for large-scale production and secretion of antibodies. ASC are derived from activated B cells, which may differentiate extrafollicularly or form germinal center (GC) reactions within secondary lymphoid organs. ASC therefore consist of short-lived, poorly matured plasmablasts that generally secrete lower-affinity antibodies, or long-lived, highly matured plasma cells that generally secrete higher-affinity antibodies. The ASC population is responsible for producing an immediate humoral B cell response, the polyclonal antibody repertoire, as well as in parallel building effective humoral memory and immunity, or potentially driving pathology in the case of autoimmunity. ASC are phenotypically and transcriptionally distinct from other B cells and further distinguishable by morphology, varied lifespans, and anatomical localization. Single cell analyses are required to interrogate the functional and transcriptional diversity of ASC and their secreted antibody repertoire and understand the contribution of individual ASC responses to the polyclonal humoral response. Here we summarize the current and emerging functional and molecular techniques for high-throughput characterization of ASC with single cell resolution, including flow and mass cytometry, spot-based and microfluidic-based assays, focusing on functional approaches of the secreted antibodies: specificity, affinity, and secretion rate.
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Affiliation(s)
- Matteo Broketa
- Institut Pasteur, Université de Paris, INSERM UMR 1222, Unit of Antibodies in Therapy and Pathology, Paris, France
- Sorbonne Université, Collège doctoral, Paris, France
- *Correspondence: Matteo Broketa, ; Pierre Bruhns,
| | - Pierre Bruhns
- Institut Pasteur, Université de Paris, INSERM UMR 1222, Unit of Antibodies in Therapy and Pathology, Paris, France
- *Correspondence: Matteo Broketa, ; Pierre Bruhns,
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9
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Luo X, Chen JY, Ataei M, Lee A. Microfluidic Compartmentalization Platforms for Single Cell Analysis. BIOSENSORS 2022; 12:58. [PMID: 35200319 PMCID: PMC8869497 DOI: 10.3390/bios12020058] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/17/2022] [Accepted: 01/18/2022] [Indexed: 12/25/2022]
Abstract
Many cellular analytical technologies measure only the average response from a cell population with an assumption that a clonal population is homogenous. The ensemble measurement often masks the difference among individual cells that can lead to misinterpretation. The advent of microfluidic technology has revolutionized single-cell analysis through precise manipulation of liquid and compartmentalizing single cells in small volumes (pico- to nano-liter). Due to its advantages from miniaturization, microfluidic systems offer an array of capabilities to study genomics, transcriptomics, and proteomics of a large number of individual cells. In this regard, microfluidic systems have emerged as a powerful technology to uncover cellular heterogeneity and expand the depth and breadth of single-cell analysis. This review will focus on recent developments of three microfluidic compartmentalization platforms (microvalve, microwell, and microdroplets) that target single-cell analysis spanning from proteomics to genomics. We also compare and contrast these three microfluidic platforms and discuss their respective advantages and disadvantages in single-cell analysis.
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Affiliation(s)
- Xuhao Luo
- Department of Biomedical Engineering, University of California, Irvine, CA 92697, USA; (X.L.); (J.-Y.C.)
| | - Jui-Yi Chen
- Department of Biomedical Engineering, University of California, Irvine, CA 92697, USA; (X.L.); (J.-Y.C.)
| | - Marzieh Ataei
- Department of Mechanical and Aerospace Engineering, University of California, Irvine, CA 92697, USA;
| | - Abraham Lee
- Department of Biomedical Engineering, University of California, Irvine, CA 92697, USA; (X.L.); (J.-Y.C.)
- Department of Mechanical and Aerospace Engineering, University of California, Irvine, CA 92697, USA;
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Miwa H, Dimatteo R, de Rutte J, Ghosh R, Di Carlo D. Single-cell sorting based on secreted products for functionally defined cell therapies. MICROSYSTEMS & NANOENGINEERING 2022; 8:84. [PMID: 35874174 PMCID: PMC9303846 DOI: 10.1038/s41378-022-00422-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 05/18/2022] [Accepted: 06/13/2022] [Indexed: 05/13/2023]
Abstract
Cell therapies have emerged as a promising new class of "living" therapeutics over the last decade and have been particularly successful for treating hematological malignancies. Increasingly, cellular therapeutics are being developed with the aim of treating almost any disease, from solid tumors and autoimmune disorders to fibrosis, neurodegenerative disorders and even aging itself. However, their therapeutic potential has remained limited due to the fundamental differences in how molecular and cellular therapies function. While the structure of a molecular therapeutic is directly linked to biological function, cells with the same genetic blueprint can have vastly different functional properties (e.g., secretion, proliferation, cell killing, migration). Although there exists a vast array of analytical and preparative separation approaches for molecules, the functional differences among cells are exacerbated by a lack of functional potency-based sorting approaches. In this context, we describe the need for next-generation single-cell profiling microtechnologies that allow the direct evaluation and sorting of single cells based on functional properties, with a focus on secreted molecules, which are critical for the in vivo efficacy of current cell therapies. We first define three critical processes for single-cell secretion-based profiling technology: (1) partitioning individual cells into uniform compartments; (2) accumulating secretions and labeling via reporter molecules; and (3) measuring the signal associated with the reporter and, if sorting, triggering a sorting event based on these reporter signals. We summarize recent academic and commercial technologies for functional single-cell analysis in addition to sorting and industrial applications of these technologies. These approaches fall into three categories: microchamber, microfluidic droplet, and lab-on-a-particle technologies. Finally, we outline a number of unmet needs in terms of the discovery, design and manufacturing of cellular therapeutics and how the next generation of single-cell functional screening technologies could allow the realization of robust cellular therapeutics for all patients.
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Affiliation(s)
- Hiromi Miwa
- Department of Bioengineering, University of California - Los Angeles, Los Angeles, CA 90095 USA
| | - Robert Dimatteo
- Department of Chemical and Biomolecular Engineering, University of California - Los Angeles, Los Angeles, CA 90095 USA
| | - Joseph de Rutte
- Department of Bioengineering, University of California - Los Angeles, Los Angeles, CA 90095 USA
- Partillion Bioscience, Los Angeles, CA 90095 USA
| | - Rajesh Ghosh
- Department of Bioengineering, University of California - Los Angeles, Los Angeles, CA 90095 USA
| | - Dino Di Carlo
- Department of Bioengineering, University of California - Los Angeles, Los Angeles, CA 90095 USA
- Department of Mechanical and Aerospace Engineering, University of California - Los Angeles, Los Angeles, CA 90095 USA
- California NanoSystems Institute (CNSI), University of California - Los Angeles, Los Angeles, CA 90095 USA
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11
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Khajvand T, Huang P, Li L, Zhang M, Zhu F, Xu X, Huang M, Yang C, Lu Y, Zhu Z. Interfacing droplet microfluidics with antibody barcodes for multiplexed single-cell protein secretion profiling. LAB ON A CHIP 2021; 21:4823-4830. [PMID: 34792068 DOI: 10.1039/d1lc00567g] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Multiplexed protein secretion analysis of single cells is important to understand the heterogeneity of cellular functions and processes in healthy and disease states. However, current single-cell platforms, such as microwell-, microchamber-, or droplet-based assays, suffer from low single-cell occupancy, waste of reagents, limited sensitivity, or inability to perform necessary operations, etc. To overcome these drawbacks, we present an integrated droplet microfluidic device that interfaces with spatially patterned antibody barcodes for multiplexed single-cell secretome analysis. The trapping array of 100 picoliter-sized isolation chambers could achieve >80% single-cell capture efficiency with >90% viability. The single-cell analysis microchip was validated by the detection of four-plexed cytokines, including IL-8, MCP-1, MIP-1b, and TNF-a/IL-10, from unstimulated and lipopolysaccharide (LPS)-stimulated individual human macrophages. We also successfully applied the platform to profile protein secretions of human tumor cell lines and primary/metastatic cancer cells dissociated from cancer patients to observe the secretion heterogeneity among cells. This unique microfluidic platform enables multiplexed secretion assays for static droplet microfluidics, provides a reliable and straightforward workflow for protein secretion assays based on a low number of single cells in a short incubation time (∼4 h), and could have widespread applications for studying secretion-mediated cellular heterogeneity.
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Affiliation(s)
- Tahereh Khajvand
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Key Laboratory for Chemical Biology of Fujian Province, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China.
| | - Peifeng Huang
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Key Laboratory for Chemical Biology of Fujian Province, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China.
| | - Linmei Li
- Department of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, China.
| | - Mingxia Zhang
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Key Laboratory for Chemical Biology of Fujian Province, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China.
| | - Fengjiao Zhu
- Department of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, China.
| | - Xing Xu
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Key Laboratory for Chemical Biology of Fujian Province, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China.
| | - Mengjiao Huang
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Key Laboratory for Chemical Biology of Fujian Province, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China.
| | - Chaoyong Yang
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Key Laboratory for Chemical Biology of Fujian Province, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China.
- Institute of Molecular Medicine, Department of Obstetrics and Gynecology, Renji Hospital Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Yao Lu
- Department of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, China.
| | - Zhi Zhu
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Key Laboratory for Chemical Biology of Fujian Province, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China.
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12
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Li Q, Bencherif SA, Su M. Edge-Enhanced Microwell Immunoassay for Highly Sensitive Protein Detection. Anal Chem 2021; 93:10292-10300. [PMID: 34251806 DOI: 10.1021/acs.analchem.1c01754] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Highly sensitive biosensors that can detect low concentrations of protein biomarkers at the early stages of diseases or proteins secreted from single cells are of importance for disease diagnosis and treatment assessment. This work reports a new signal amplification mechanism, that is, edge enhancement based on the vertical sidewalls of microwells for ultra-sensitive protein detection. The fluorescence emission at the edge of the microwells is highly amplified due to the microscopic axial resolution (depth of field) and demonstrates a microring effect. The enhanced fluorescence intensity from microrings is calibrated for bovine serum albumin detection, which shows a 6-fold sensitivity enhancement and a lower limit of detection at the microwell edge, compared to those obtained on a flat surface. The microwell chip is used to separate single cells, and the wall of each microwell is used to detect interferon-γ secretion from T cells stimulated with a peptide and whole cancer cells. Given its edge-enhancement ability, the microwell technique can be a highly sensitive biosensing platform for disease diagnosis at an early stage and for assessing potential treatments at the single-cell level.
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Affiliation(s)
- Qingxuan Li
- Department of Chemical Engineering, Northeastern University, Boston, Massachusetts 02115, United States
| | - Sidi A Bencherif
- Department of Chemical Engineering, Northeastern University, Boston, Massachusetts 02115, United States.,Department of Bioengineering, Northeastern University, Boston, Massachusetts 02115, United States
| | - Ming Su
- Department of Chemical Engineering, Northeastern University, Boston, Massachusetts 02115, United States
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13
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Zhou Y, Shao N, Bessa de Castro R, Zhang P, Ma Y, Liu X, Huang F, Wang RF, Qin L. Evaluation of Single-Cell Cytokine Secretion and Cell-Cell Interactions with a Hierarchical Loading Microwell Chip. Cell Rep 2021; 31:107574. [PMID: 32348757 PMCID: PMC7583657 DOI: 10.1016/j.celrep.2020.107574] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 02/21/2020] [Accepted: 04/02/2020] [Indexed: 02/01/2023] Open
Abstract
Comprehensive evaluation of single T cell functions such as cytokine secretion and cytolysis of target cells is greatly needed in adoptive cell therapy (ACT) but has never been fully fulfilled by current approaches. Herein, we develop a hierarchical loading microwell chip (HL-Chip) that aligns multiple cells and functionalized beads in a high-throughput microwell array with single-cell/bead precision based on size differences. We demonstrate the potential of the HL-Chip in evaluating single T cell functions by three applications: high-throughput longitudinal secretory profiling of single T cells, large-scale evaluation of cytolytic activity of single T cells, and integrated T cell-tumor cell interactions. The HL-Chip is a simple and robust technology that constructs arrays of defined cell/object combinations for multiple measurements and material retrieval.
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Affiliation(s)
- Yufu Zhou
- Department of Nanomedicine, Houston Methodist Research Institute, Houston, TX 77030, USA; The Third Xiangya Hospital, Central South University, Changsha 410008, China; Center for inflammation and Epigenetics, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Ning Shao
- Department of Nanomedicine, Houston Methodist Research Institute, Houston, TX 77030, USA; Department of Cell and Developmental Biology, Weill Cornell Medical College, New York, NY 10065, USA
| | - Ricardo Bessa de Castro
- Department of Nanomedicine, Houston Methodist Research Institute, Houston, TX 77030, USA; Department of Cell and Developmental Biology, Weill Cornell Medical College, New York, NY 10065, USA
| | - Pengchao Zhang
- Department of Nanomedicine, Houston Methodist Research Institute, Houston, TX 77030, USA; Department of Cell and Developmental Biology, Weill Cornell Medical College, New York, NY 10065, USA
| | - Yuan Ma
- Department of Nanomedicine, Houston Methodist Research Institute, Houston, TX 77030, USA; Department of Cell and Developmental Biology, Weill Cornell Medical College, New York, NY 10065, USA
| | - Xin Liu
- Center for inflammation and Epigenetics, Houston Methodist Research Institute, Houston, TX 77030, USA; Department of Medicine and Norris Comprehensive Cancer Center, The Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Feizhou Huang
- The Third Xiangya Hospital, Central South University, Changsha 410008, China
| | - Rong-Fu Wang
- Center for inflammation and Epigenetics, Houston Methodist Research Institute, Houston, TX 77030, USA; Department of Pediatrics, Children's Hospital of Los Angeles, The Keck School of Medicine, University of Southern California, Los Angeles, CA 90027, USA; Department of Medicine and Norris Comprehensive Cancer Center, The Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA.
| | - Lidong Qin
- Department of Nanomedicine, Houston Methodist Research Institute, Houston, TX 77030, USA; Department of Cell and Developmental Biology, Weill Cornell Medical College, New York, NY 10065, USA.
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14
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Impact of Immunotherapy on CD4 T Cell Phenotypes and Function in Cancer. Vaccines (Basel) 2021; 9:vaccines9050454. [PMID: 34064410 PMCID: PMC8147771 DOI: 10.3390/vaccines9050454] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 04/29/2021] [Accepted: 05/02/2021] [Indexed: 12/29/2022] Open
Abstract
Immunotherapy has become a standard treatment in many cancers and it is based on three main therapeutic axes: immune checkpoint blockade (ICB), vaccination and adoptive cell transfer (ACT). If originally these therapies mainly focused on exploiting CD8 T cells given their role in the direct elimination of tumor cells, increasing evidence highlights the crucial role CD4 T cells play in the antitumor immune response. Indeed, these cells can profoundly modulate the tumor microenvironment (TME) by secreting different types of cytokine or by directly eliminating cancer cells. In this review, we describe how different CD4 T cell subsets can contribute to tumor immune responses during immunotherapy and the novel high-throughput immune monitoring tools that are expected to facilitate the study of CD4 T cells, at antigen-specific and single cell level, thus accelerating bench-to-bed translational research in cancer.
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15
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Bucheli OTM, Sigvaldadóttir I, Eyer K. Measuring single-cell protein secretion in immunology: Technologies, advances, and applications. Eur J Immunol 2021; 51:1334-1347. [PMID: 33734428 PMCID: PMC8252417 DOI: 10.1002/eji.202048976] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 01/12/2021] [Accepted: 03/15/2021] [Indexed: 12/19/2022]
Abstract
The dynamics, nature, strength, and ultimately protective capabilities of an active immune response are determined by the extracellular constitution and concentration of various soluble factors. Generated effector cells secrete such mediators, including antibodies, chemo‐ and cytokines to achieve functionality. These secreted factors organize the individual immune cells into functional tissues, initiate, orchestrate, and regulate the immune response. Therefore, a single‐cell resolved analysis of protein secretion is a valuable tool for studying the heterogeneity and functionality of immune cells. This review aims to provide a comparative overview of various methods to characterize immune reactions by measuring single‐cell protein secretion. Spot‐based and cytometry‐based assays, such as ELISpot and flow cytometry, respectively, are well‐established methods applied in basic research and clinical settings. Emerging novel technologies, such as microfluidic platforms, offer new ways to measure and exploit protein secretion in immune reactions. Further technological advances will allow the deciphering of protein secretion in immunological responses with unprecedented detail, linking secretion to functionality. Here, we summarize the development and recent advances of tools that allow the analysis of protein secretion at the single‐cell level, and discuss and contrast their applications within immunology.
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Affiliation(s)
- Olivia T M Bucheli
- ETH Laboratory for Functional Immune Repertoire Analysis, Institute of Pharmaceutical Sciences, D-CHAB, ETH Zürich, Zürich, Switzerland
| | - Ingibjörg Sigvaldadóttir
- ETH Laboratory for Functional Immune Repertoire Analysis, Institute of Pharmaceutical Sciences, D-CHAB, ETH Zürich, Zürich, Switzerland
| | - Klaus Eyer
- ETH Laboratory for Functional Immune Repertoire Analysis, Institute of Pharmaceutical Sciences, D-CHAB, ETH Zürich, Zürich, Switzerland
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16
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Choi JR, Lee JH, Xu A, Matthews K, Xie S, Duffy SP, Ma H. Monolithic hydrogel nanowells-in-microwells enabling simultaneous single cell secretion and phenotype analysis. LAB ON A CHIP 2020; 20:4539-4551. [PMID: 33201962 DOI: 10.1039/d0lc00965b] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Cytokine secretion is a form of cellular communication that regulates a wide range of biological processes. A common approach for measuring cytokine secretion from single cells is to confine individual cells in arrays of nanoliter wells (nanowells) fabricated using polydimethylsiloxane. However, this approach cannot be easily integrated in standard microwell plates in order to take advantage of high-throughput infrastructure for automated and multiplexed analysis. Here, we used laser micropatterning to fabricate monolithic hydrogel nanowells inside wells in a microwell plate (microwells) using polyethylene glycol diacrylate (PEGDA). This approach produces high-aspect ratio nanowells that retain cells and beads during reagent exchange, enabling simultaneous profiling of single cell secretion and phenotyping via immunostaining. To limit contamination between nanowells, we used methylcellulose as a media additive to reduce diffusion distance. Patterning nanowells monolithically in microwells also dramatically increases density, providing ∼1200 nanowells per microwell in a microwell plate. Using this approach, we profiled IL-8 secretion from single MDA-MB-231 cells, which showed significant heterogeneity. We further profiled the polarization of THP-1 cells into M1 and M2 macrophages, along with their associated IL-1β and CCL-22 secretion profiles. These results demonstrate the potential to use this approach for high-throughput secretion and phenotype analysis on single cells.
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Affiliation(s)
- Jane Ru Choi
- Department of Mechanical Engineering, University of British Columbia, Canada. and Centre for Blood Research, University of British Columbia, Canada
| | - Jeong Hyun Lee
- Department of Mechanical Engineering, University of British Columbia, Canada. and Centre for Blood Research, University of British Columbia, Canada
| | - Alec Xu
- Department of Mechanical Engineering, University of British Columbia, Canada. and Centre for Blood Research, University of British Columbia, Canada
| | - Kerryn Matthews
- Department of Mechanical Engineering, University of British Columbia, Canada. and Centre for Blood Research, University of British Columbia, Canada
| | - Shuyong Xie
- Department of Mechanical Engineering, University of British Columbia, Canada. and Centre for Blood Research, University of British Columbia, Canada
| | - Simon P Duffy
- Department of Mechanical Engineering, University of British Columbia, Canada. and Centre for Blood Research, University of British Columbia, Canada and British Columbia Institute of Technology, Canada
| | - Hongshen Ma
- Department of Mechanical Engineering, University of British Columbia, Canada. and Centre for Blood Research, University of British Columbia, Canada and School of Biomedical Engineering, University of British Columbia, Canada and Vancouver Prostate Centre, Vancouver General Hospital, Canada
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17
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Zhang W, Li R, Jia F, Hu Z, Li Q, Wei Z. A microfluidic chip for screening high-producing hybridomas at single cell level. LAB ON A CHIP 2020; 20:4043-4051. [PMID: 33005908 DOI: 10.1039/d0lc00847h] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Hybridomas are a commonly used, or even the only option, for laboratory study and pilot production of monoclonal antibodies (mAbs), which are crucial for both targeted therapy and biomedical study. A long-term culture of hybridomas will inevitably induce a heterogenization of the whole hybridoma population, resulting in a continuous growth of non-producing hybridomas. To overcome the limits of existing methods of screening heterogeneous hybridomas, in which the whole multi-round screening process is performed in multi-well plates or other discrete modules, this study presents a novel method in which all processing steps of a multi-round hybridoma screening are finished in a single microfluidic chip. This microfluidic chip comprehensively performs hybridoma trapping/proliferating/transferring and fluorescent identification of protein-antibody binding at single cell level. By performing a two-round screening of anti-CD45 mAb secreting hybridomas, the novel microfluidic chip was proved capable of screening several single high-producing hybridomas with minimum cell loss/human labor/time cost, and more importantly, enhanced accuracy and definite monoclonality, which is one of the most important properties of mAb production.
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Affiliation(s)
- Weikai Zhang
- Department of Biomedical Engineering, School of Life Science, Beijing Institute of Technology, Beijing 100081, China.
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18
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Donatti A, Canto AM, Godoi AB, da Rosa DC, Lopes-Cendes I. Circulating Metabolites as Potential Biomarkers for Neurological Disorders-Metabolites in Neurological Disorders. Metabolites 2020; 10:E389. [PMID: 33003305 PMCID: PMC7601919 DOI: 10.3390/metabo10100389] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 09/17/2020] [Accepted: 09/18/2020] [Indexed: 12/11/2022] Open
Abstract
There are, still, limitations to predicting the occurrence and prognosis of neurological disorders. Biomarkers are molecules that can change in different conditions, a feature that makes them potential tools to improve the diagnosis of disease, establish a prognosis, and monitor treatments. Metabolites can be used as biomarkers, and are small molecules derived from the metabolic process found in different biological media, such as tissue samples, cells, or biofluids. They can be identified using various strategies, targeted or untargeted experiments, and by different techniques, such as high-performance liquid chromatography, mass spectrometry, or nuclear magnetic resonance. In this review, we aim to discuss the current knowledge about metabolites as biomarkers for neurological disorders. We will present recent developments that show the need and the feasibility of identifying such biomarkers in different neurological disorders, as well as discuss relevant research findings in the field of metabolomics that are helping to unravel the mechanisms underlying neurological disorders. Although several relevant results have been reported in metabolomic studies in patients with neurological diseases, there is still a long way to go for the clinical use of metabolites as potential biomarkers in these disorders, and more research in the field is needed.
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Affiliation(s)
- Amanda Donatti
- Department of Medical Genetics and Genomic Medicine, School of Medical Sciences, University of Campinas (UNICAMP), Tessália Vieira de Camargo, 126 Cidade Universitária “Zeferino Vaz”, Campinas SP 13083-887, Brazil; (A.D.); (A.M.C.); (A.B.G.); (D.C.d.R.)
- Brazilian Institute of Neuroscience and Neurotechnology, Campinas SP 13083-887, Brazil
| | - Amanda M. Canto
- Department of Medical Genetics and Genomic Medicine, School of Medical Sciences, University of Campinas (UNICAMP), Tessália Vieira de Camargo, 126 Cidade Universitária “Zeferino Vaz”, Campinas SP 13083-887, Brazil; (A.D.); (A.M.C.); (A.B.G.); (D.C.d.R.)
- Brazilian Institute of Neuroscience and Neurotechnology, Campinas SP 13083-887, Brazil
| | - Alexandre B. Godoi
- Department of Medical Genetics and Genomic Medicine, School of Medical Sciences, University of Campinas (UNICAMP), Tessália Vieira de Camargo, 126 Cidade Universitária “Zeferino Vaz”, Campinas SP 13083-887, Brazil; (A.D.); (A.M.C.); (A.B.G.); (D.C.d.R.)
- Brazilian Institute of Neuroscience and Neurotechnology, Campinas SP 13083-887, Brazil
| | - Douglas C. da Rosa
- Department of Medical Genetics and Genomic Medicine, School of Medical Sciences, University of Campinas (UNICAMP), Tessália Vieira de Camargo, 126 Cidade Universitária “Zeferino Vaz”, Campinas SP 13083-887, Brazil; (A.D.); (A.M.C.); (A.B.G.); (D.C.d.R.)
- Brazilian Institute of Neuroscience and Neurotechnology, Campinas SP 13083-887, Brazil
| | - Iscia Lopes-Cendes
- Department of Medical Genetics and Genomic Medicine, School of Medical Sciences, University of Campinas (UNICAMP), Tessália Vieira de Camargo, 126 Cidade Universitária “Zeferino Vaz”, Campinas SP 13083-887, Brazil; (A.D.); (A.M.C.); (A.B.G.); (D.C.d.R.)
- Brazilian Institute of Neuroscience and Neurotechnology, Campinas SP 13083-887, Brazil
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19
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Abstract
The immune system is composed of heterogeneous populations of immune cells that regulate physiological processes and protect organisms against diseases. Single cell technologies have been used to assess immune cell responses at the single cell level, which are crucial for identifying the causes of diseases and elucidating underlying biological mechanisms to facilitate medical therapy. In the present review we first discuss the most recent advances in the development of single cell technologies to investigate cell signaling, cell-cell interactions and cell migration. Each technology's advantages and limitations and its applications in immunology are subsequently reviewed. The latest progress toward commercialization, the remaining challenges and future perspectives for single cell technologies in immunology are also briefly discussed.
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Affiliation(s)
- Jane Ru Choi
- Centre for Blood Research, Life Sciences Centre, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada.,Department of Mechanical Engineering, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
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20
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Yamagishi M, Ohara O, Shirasaki Y. Microfluidic Immunoassays for Time-Resolved Measurement of Protein Secretion from Single Cells. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2020; 13:67-84. [PMID: 32031877 DOI: 10.1146/annurev-anchem-091619-101212] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Measurement of humoral factors secreted from cells has served as an indispensable method to monitor the states of a cell ensemble because humoral factors play crucial roles in cell-cell interaction and aptly reflect the states of individual cells. Although a cell ensemble consisting of a large number of cells has conventionally been the object of such measurements, recent advances in microfluidic technology together with highly sensitive immunoassays have enabled us to quantify secreted humoral factors even from individual cells in either a population or a temporal context. Many groups have reported various miniaturized platforms for immunoassays of proteins secreted from single cells. This review focuses on the current status of time-resolved assay platforms for protein secretion with single-cell resolution. We also discuss future perspectives of time-resolved immunoassays from the viewpoint of systems biology.
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Affiliation(s)
- Mai Yamagishi
- Department of Biological Sciences, The University of Tokyo, Tokyo 113-0033, Japan;
| | - Osamu Ohara
- Department of Applied Genomics, Kazusa DNA Research Institute, Chiba 292-0818, Japan
- Laboratory for Integrative Genomics, RIKEN Center for Integrative Medical Sciences, Kanagawa 230-0045, Japan
- The Futuristic Medical Care Education and Research Organization, Chiba University, Chiba 260-8670, Japan
| | - Yoshitaka Shirasaki
- Department of Biological Sciences, The University of Tokyo, Tokyo 113-0033, Japan;
- Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency (JST), Saitama 332-0012, Japan
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21
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Yuan Y, Brouchon J, Calvo-Calle JM, Xia J, Sun L, Zhang X, Clayton KL, Ye F, Weitz DA, Heyman JA. Droplet encapsulation improves accuracy of immune cell cytokine capture assays. LAB ON A CHIP 2020; 20:1513-1520. [PMID: 32242586 PMCID: PMC7313394 DOI: 10.1039/c9lc01261c] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Quantification of cell-secreted molecules, e.g., cytokines, is fundamental to the characterization of immune responses. Cytokine capture assays that use engineered antibodies to anchor the secreted molecules to the secreting cells are widely used to characterize immune responses because they allow both sensitive identification and recovery of viable responding cells. However, if the cytokines diffuse away from the secreting cells, non-secreting cells will also be identified as responding cells. Here we encapsulate immune cells in microfluidic droplets and perform in-droplet cytokine capture assays to limit the diffusion of the secreted cytokines. We use microfluidic devices to rapidly encapsulate single natural killer NK-92 MI cells and their target K562 cells into microfluidic droplets. We perform in-droplet IFN-γ capture assays and demonstrate that NK-92 MI cells recognize target cells within droplets and become activated to secrete IFN-γ. Droplet encapsulation prevents diffusion of secreted products to neighboring cells and dramatically reduces both false positives and false negatives, relative to assays performed without droplets. In a sample containing 1% true positives, encapsulation reduces, from 94% to 2%, the number of true-positive cells appearing as negatives; in a sample containing 50% true positives, the number of non-stimulated cells appearing as positives is reduced from 98% to 1%. After cells are released from the droplets, secreted cytokine remains captured onto secreting immune cells, enabling FACS-isolation of populations highly enriched for activated effector immune cells. Droplet encapsulation can be used to reduce background and improve detection of any single-cell secretion assay.
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Affiliation(s)
- Yuan Yuan
- Beijing National Laboratory for Condensed Matter Physics and CAS Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China
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22
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Nakao T, Kazoe Y, Mori E, Morikawa K, Fukasawa T, Yoshizaki A, Kitamori T. Cytokine analysis on a countable number of molecules from living single cells on nanofluidic devices. Analyst 2020; 144:7200-7208. [PMID: 31691693 DOI: 10.1039/c9an01702j] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Analysis of proteins released from living single cells is strongly required in the fields of biology and medicine to elucidate the mechanism of gene expression, cell-cell communication and cytopathology. However, as living single-cell analysis involves fL sample volumes with ultra-small amounts of analyte, comprehensive integration of entire chemical processing for single cells and proteins into spaces smaller than single cells (pL) would be indispensable to prevent dispersion-associated analyte loss. In this study, we proposed and developed a living single-cell protein analysis device based on micro/nanofluidics and demonstrated analysis of cytokines released from living single B cells by enzyme-linked immunosorbent assay. Based on our integration method and technologies including top-down nanofabrication, surface modifications and pressure-driven flow control, we designed and prepared the device where pL-microfluidic- and fL-nanofluidic channels are hierarchically allocated for cellular and molecular processing, respectively, and succeeded in micro/nanofluidic control for manipulating single cells and molecules. 13-unit operations for pL-cellular processing including single-cell trapping and stimulation and fL-molecular processing including fL-volumetry, antigen-antibody reactions and detection were entirely integrated into a microchip. The results suggest analytical performances for countable interleukin (IL)-6 molecules at the limit of detection of 5.27 molecules and that stimulated single B cells secrete 3.41 IL-6 molecules per min. The device is a novel tool for single-cell targeted proteomics, and the methodology of device integration is applicable to other single-cell analyses such as single-cell shotgun proteomics. This study thus provides a general approach and technical breakthroughs that will facilitate further advances in micro/nanofluidics, single-cell life science research, and other fields.
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Affiliation(s)
- Tatsuro Nakao
- Department of Bioengineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo 113-8656, Japan.
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23
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Rodriguez-Moncayo R, Jimenez-Valdes RJ, Gonzalez-Suarez AM, Garcia-Cordero JL. Integrated Microfluidic Device for Functional Secretory Immunophenotyping of Immune Cells. ACS Sens 2020; 5:353-361. [PMID: 31927915 DOI: 10.1021/acssensors.9b01786] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Integrated platforms for automatic assessment of cellular functional secretory immunophenotyping could have a widespread use in the diagnosis, real-time monitoring, and therapy evaluation of several pathologies. We present a microfluidic platform with integrated biosensors and culture chambers to measure cytokine secretion from a consistent and uniform number of immune cells. The biosensor relies on a fluorescence sandwich immunoassay enabled by the mechanically induced trapping of molecular interactions method. The platform contains 32 cell culture chambers, each patterned with an array of 492 microwells, to capture and analyze both adherent and nonadherent immune cells. Multiple stimuli can be delivered to a set of culture chambers. Per chamber, we were able to capture consistently 1113 ± 191 of blood-derived monocytes and neutrophils and 348 ± 37 THP-1 monocytes. Good occupancy efficiencies of ∼70% with a uniformity of ∼90% across all of the culture chambers of the device were achieved. Furthermore, we demonstrate that up to 96% of cells remain viable for the first 48 h. The employment of epoxy-modified glass substrates and active mixing enhanced the biosensing performance compared to the use of bare glass and simple diffusion. Finally, we performed functional secretory analysis of interleukin-8 and tumor necrosis factor alpha from human neutrophils and monocytes, stimulated with various doses of lipopolysaccharide and phorbol 12-myristate 13-acetate-ionomycin, respectively. We foresee the employment of our microfluidic platform in the diagnosis of different pathologies where alterations in cytokine secretion patterns can be used as biomarkers.
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Affiliation(s)
- Roberto Rodriguez-Moncayo
- Unidad Monterrey, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Parque PIIT, Apodaca, Nuevo León 66628, Mexico
| | - Rocio Jimena Jimenez-Valdes
- Unidad Monterrey, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Parque PIIT, Apodaca, Nuevo León 66628, Mexico
| | - Alan Mauricio Gonzalez-Suarez
- Unidad Monterrey, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Parque PIIT, Apodaca, Nuevo León 66628, Mexico
| | - Jose Luis Garcia-Cordero
- Unidad Monterrey, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Parque PIIT, Apodaca, Nuevo León 66628, Mexico
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Gupta S, Witas R, Voigt A, Semenova T, Nguyen CQ. Single-Cell Sequencing of T cell Receptors: A Perspective on the Technological Development and Translational Application. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1255:29-50. [PMID: 32949388 DOI: 10.1007/978-981-15-4494-1_3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
T cells recognize peptides bound to major histocompatibility complex (MHC) class I and class II molecules at the cell surface. This recognition is accomplished by the expression of T cell receptors (TCR) which are required to be diverse and adaptable in order to accommodate the various and vast number of antigens presented on the MHCs. Thus, determining TCR repertoires of effector T cells is necessary to understand the immunological process in responding to cancer progression, infection, and autoimmune development. Furthermore, understanding the TCR repertoires will provide a solid framework to predict and test the antigen which is more critical in autoimmunity. However, it has been a technical challenge to sequence the TCRs and provide a conceptual context in correlation to the vast number of TCR repertoires in the immunological system. The exploding field of single-cell sequencing has changed how the repertoires are being investigated and analyzed. In this review, we focus on the biology of TCRs, TCR signaling and its implication in autoimmunity. We discuss important methods in bulk sequencing of many cells. Lastly, we explore the most pertinent platforms in single-cell sequencing and its application in autoimmunity.
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Affiliation(s)
- Shivai Gupta
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, Gainesville, FL, USA
| | - Richard Witas
- Department of Oral Biology, College of Dentistry, Gainesville, FL, USA
| | - Alexandria Voigt
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, Gainesville, FL, USA
| | - Touyana Semenova
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, Gainesville, FL, USA
| | - Cuong Q Nguyen
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, Gainesville, FL, USA. .,Department of Oral Biology, College of Dentistry, Gainesville, FL, USA. .,Center of Orphaned Autoimmune Diseases, University of Florida, Gainesville, FL, USA.
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25
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Chintapula U, M Iqbal S, Kim YT. A compendium of single cell analysis in aging and disease. AIMS MOLECULAR SCIENCE 2020. [DOI: 10.3934/molsci.2020004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
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Methods for Single-Cell Isolation and Preparation. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1255:7-27. [PMID: 32949387 DOI: 10.1007/978-981-15-4494-1_2] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Within the last decade, single-cell analysis has revolutionized our understanding of cellular processes and heterogeneity across all disciplines of life science. As the transcriptome, genome, or epigenome of individual cells can nowadays be analyzed at low cost and in high-throughput within a few days by modern techniques, tremendous improvements in disease diagnosis on the one hand and the investigation of disease-relevant mechanisms on the other were achieved so far. This relies on the parallel development of reliable cell capturing and single-cell sequencing approaches that have paved the way for comprehensive single-cell studies. Apart from single-cell isolation methods in high-throughput, a variety of methods with distinct specializations were developed, allowing for correlation of transcriptomics with cellular parameters like electrophysiology or morphology.For all single-cell-based approaches, accurate and reliable isolation with proper quality controls is prerequisite, whereby different options exist dependent on sample type and tissue properties. Careful consideration of an appropriate method is required to avoid incorrect or biased data that may lead to misinterpretations.In this chapter, we will provide a broad overview of the current state of the art in matters of single-cell isolation methods mostly applied for sequencing-based downstream analysis, and their respective advantages and drawbacks. Distinct technologies will be discussed in detail addressing key parameters like sample compatibility, viability, purity, throughput, and isolation efficiency.
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Germeys C, Vandoorne T, Bercier V, Van Den Bosch L. Existing and Emerging Metabolomic Tools for ALS Research. Genes (Basel) 2019; 10:genes10121011. [PMID: 31817338 PMCID: PMC6947647 DOI: 10.3390/genes10121011] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 11/23/2019] [Accepted: 12/03/2019] [Indexed: 12/12/2022] Open
Abstract
Growing evidence suggests that aberrant energy metabolism could play an important role in the pathogenesis of amyotrophic lateral sclerosis (ALS). Despite this, studies applying advanced technologies to investigate energy metabolism in ALS remain scarce. The rapidly growing field of metabolomics offers exciting new possibilities for ALS research. Here, we review existing and emerging metabolomic tools that could be used to further investigate the role of metabolism in ALS. A better understanding of the metabolic state of motor neurons and their surrounding cells could hopefully result in novel therapeutic strategies.
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Affiliation(s)
- Christine Germeys
- Department of Neurosciences, Experimental Neurology, and Leuven Brain Institute (LBI), KU Leuven—University of Leuven, 3000 Leuven, Belgium; (C.G.); (T.V.); (V.B.)
- VIB, Center for Brain & Disease Research, Laboratory of Neurobiology, 3000 Leuven, Belgium
| | - Tijs Vandoorne
- Department of Neurosciences, Experimental Neurology, and Leuven Brain Institute (LBI), KU Leuven—University of Leuven, 3000 Leuven, Belgium; (C.G.); (T.V.); (V.B.)
- VIB, Center for Brain & Disease Research, Laboratory of Neurobiology, 3000 Leuven, Belgium
| | - Valérie Bercier
- Department of Neurosciences, Experimental Neurology, and Leuven Brain Institute (LBI), KU Leuven—University of Leuven, 3000 Leuven, Belgium; (C.G.); (T.V.); (V.B.)
- VIB, Center for Brain & Disease Research, Laboratory of Neurobiology, 3000 Leuven, Belgium
| | - Ludo Van Den Bosch
- Department of Neurosciences, Experimental Neurology, and Leuven Brain Institute (LBI), KU Leuven—University of Leuven, 3000 Leuven, Belgium; (C.G.); (T.V.); (V.B.)
- VIB, Center for Brain & Disease Research, Laboratory of Neurobiology, 3000 Leuven, Belgium
- Correspondence: ; Tel.: +32-16-33-06-81
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Jarzębska NT, Yamaguchi S, Izuta S, Kosaka T, Yamahira S, Nagamune T, Okamoto A. Photo-responsive materials with strong cell trapping ability for light-guided manipulation of nonadherent cells. Biomater Sci 2019; 7:4514-4518. [PMID: 31602442 DOI: 10.1039/c9bm01200a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
We report a photo-cleavable material for tight trapping of nonadherent cells to substrate surfaces. Model immunocytes were selectively trapped in a non-irradiated area as single cells after the projection of a light pattern and withstood high-speed laminar flow, achieving light-guided cell release from the substrates.
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Affiliation(s)
- Natalia Teresa Jarzębska
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan.
| | - Satoshi Yamaguchi
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan. and PRESTO, Japan Science and Technology Agency (JST), 4-1-8 Hon-cho, Kawaguchi, Saitama 351-0198, Japan
| | - Shin Izuta
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan.
| | - Takahiro Kosaka
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan.
| | - Shinya Yamahira
- Center for Medical Sciences, St. Luke's International University, 10-1 Akashi-Cho, Chuo-ku, Tokyo, 104-0044, Japan
| | - Teruyuki Nagamune
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan.
| | - Akimitsu Okamoto
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan. and Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan.
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29
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Single identical cell toxicity assay on coordinately ordered patterns. Anal Chim Acta 2019; 1065:56-63. [DOI: 10.1016/j.aca.2019.02.040] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 02/11/2019] [Accepted: 02/14/2019] [Indexed: 12/25/2022]
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30
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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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31
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Kshitiz, Ellison DD, Suhail Y, Afzal J, Woo L, Kilic O, Spees J, Levchenko A. Dynamic secretome of bone marrow-derived stromal cells reveals a cardioprotective biochemical cocktail. Proc Natl Acad Sci U S A 2019; 116:14374-14383. [PMID: 31239339 PMCID: PMC6628676 DOI: 10.1073/pnas.1902598116] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Transplanted stromal cells have demonstrated considerable promise as therapeutic agents in diverse disease settings. Paracrine signaling can be an important mediator of these therapeutic effects at the sites of acute or persistent injury and inflammation. As many stromal cell types, including bone marrow-derived stromal cells (BMSCs), display tissue-specific responses, there is a need to explore their secretory dynamics in the context of tissue and injury type. Paracrine signals are not static, and could encode contextual dynamics in the kinetic changes of the concentrations of the secreted ligands. However, precise measurement of dynamic and context-specific cellular secretory signatures, particularly in adherent cells, remains challenging. Here, by creating an experimental and computational analysis platform, we reconstructed dynamic secretory signatures of cells based on a very limited number of time points. By using this approach, we demonstrate that the secretory signatures of CD133-positive BMSCs are uniquely defined by distinct biological contexts, including signals from injured cardiac cells undergoing oxidative stress, characteristic of cardiac infarction. Furthermore, we show that the mixture of recombinant factors reproducing the dynamics of BMSC-generated secretion can mediate a highly effective rescue of cells injured by oxidative stress and an improved cardiac output. These results support the importance of the dynamic multifactorial paracrine signals in mediating remedial effects of stromal stem cells, and pave the way for stem cell-inspired cell-free treatments of cardiac and other injuries.
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Affiliation(s)
- Kshitiz
- Yale Institute of Systems Biology, Yale University, West Haven, CT 06516;
- Department of Biomedical Engineering, University of Connecticut Health Center, Farmington, CT 06030
| | - David D Ellison
- Department of Medicine, The Johns Hopkins School of Medicine, Baltimore, MD 21205
| | - Yasir Suhail
- Department of Biomedical Engineering, University of Connecticut Health Center, Farmington, CT 06030
| | - Junaid Afzal
- Department of Cardiology, University of California, San Francisco, CA 94115
| | - Laura Woo
- Department of Medicine, The Johns Hopkins School of Medicine, Baltimore, MD 21205
| | - Onur Kilic
- Yale Institute of Systems Biology, Yale University, West Haven, CT 06516
| | - Jeffrey Spees
- Department of Cellular Molecular and Biomedical Sciences, University of Vermont, Burlington, VT 05405
| | - Andre Levchenko
- Yale Institute of Systems Biology, Yale University, West Haven, CT 06516;
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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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33
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Su EJ, Jeeawoody S, Herr AE. Protein diffusion from microwells with contrasting hydrogel domains. APL Bioeng 2019; 3:026101. [PMID: 31069338 PMCID: PMC6481738 DOI: 10.1063/1.5078650] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 04/03/2019] [Indexed: 12/11/2022] Open
Abstract
Understanding and controlling molecular transport in hydrogel materials is important for biomedical tools, including engineered tissues and drug delivery, as well as life sciences tools for single-cell analysis. Here, we scrutinize the ability of microwells-micromolded in hydrogel slabs-to compartmentalize lysate from single cells. We consider both (i) microwells that are "open" to a large fluid (i.e., liquid) reservoir and (ii) microwells that are "closed," having been capped with either a slab of high-density polyacrylamide gel or an impermeable glass slide. We use numerical modeling to gain insight into the sensitivity of time-dependent protein concentration distributions on hydrogel partition and protein diffusion coefficients and open and closed microwell configurations. We are primarily concerned with diffusion-driven protein loss from the microwell cavity. Even for closed microwells, confocal fluorescence microscopy reports that a fluid (i.e., liquid) film forms between the hydrogel slabs (median thickness of 1.7 μm). Proteins diffuse from the microwells and into the fluid (i.e., liquid) layer, yet concentration distributions are sensitive to the lid layer partition coefficients and the protein diffusion coefficient. The application of a glass lid or a dense hydrogel retains protein in the microwell, increasing the protein solute concentration in the microwell by ∼7-fold for the first 15 s. Using triggered release of Protein G from microparticles, we validate our simulations by characterizing protein diffusion in a microwell capped with a high-density polyacrylamide gel lid (p > 0.05, Kolmogorov-Smirnov test). Here, we establish and validate a numerical model useful for understanding protein transport in and losses from a hydrogel microwell across a range of boundary conditions.
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Liu Y, Chen X, Zhang Y, Liu J. Advancing single-cell proteomics and metabolomics with microfluidic technologies. Analyst 2019; 144:846-858. [PMID: 30351310 DOI: 10.1039/c8an01503a] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Recent advances in single-cell analysis have unraveled substantial heterogeneity among seemingly identical cells at genomic and transcriptomic levels. These discoveries have urged scientists to develop new tools that are capable of investigating single cells from a broader set of "omics". Proteomics and metabolomics, for instance, are of particular interest as they are closely correlated with a dynamic picture of cellular behaviors and phenotypic identities. The development of such tools requires highly efficient isolation and processing of a large number of individual cells, where techniques such as microfluidics are extremely useful. Here, we review the recent advances in single-cell proteomics and metabolomics, with a focus on microfluidics-based platforms. We highlight a vast array of emerging microfluidic formats for single-cell isolation and manipulation, and how the state-of-the-art analytical tools are coupled with such platforms for proteomic and metabolomic profiling.
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Affiliation(s)
- Yifan Liu
- Jiangsu Key Laboratory for Carbon-based Functional Materials and Devices, Institute of Functional Nano and Soft Materials (FUNSOM), Soochow University, Suzhou, Jiangsu Province 215123, China.
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Bandaru P, Chu D, Sun W, Lasli S, Zhao C, Hou S, Zhang S, Ni J, Cefaloni G, Ahadian S, Dokmeci MR, Sengupta S, Lee J, Khademhosseini A. A Microfabricated Sandwiching Assay for Nanoliter and High-Throughput Biomarker Screening. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2019; 15:e1900300. [PMID: 30884183 DOI: 10.1002/smll.201900300] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 02/14/2019] [Indexed: 05/03/2023]
Abstract
Cells secrete substances that are essential to the understanding of numerous immunological phenomena and are extensively used in clinical diagnoses. Countless techniques for screening of biomarker secretion in living cells have generated valuable information on cell function and physiology, but low volume and real-time analysis is a bottleneck for a range of approaches. Here, a simple, highly sensitive assay using a high-throughput micropillar and microwell array chip (MIMIC) platform is presented for monitoring of biomarkers secreted by cancer cells. The sensing element is a micropillar array that uses the enzyme-linked immunosorbent assay (ELISA) mechanism to detect captured biomolecules. When integrated with a microwell array where few cells are localized, interleukin 8 (IL-8) secretion can be monitored with nanoliter volume using multiple micropillar arrays. The trend of cell secretions measured using MIMICs matches the results from conventional ELISA well while it requires orders of magnitude less cells and volumes. Moreover, the proposed MIMIC is examined to be used as a drug screening platform by delivering drugs using micropillar arrays in combination with a microfluidic system and then detecting biomolecules from cells as exposed to drugs.
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Affiliation(s)
- Praveen Bandaru
- Department of Bioengineering, Henry Samueli School of Engineering and Applied Sciences, University of California-Los Angeles, Los Angeles, CA, 90095, USA
- Center for Minimally Invasive Therapeutics (C-MIT), University of California-Los Angeles, Los Angeles, CA, 90095, USA
| | - Dafeng Chu
- Department of Bioengineering, Henry Samueli School of Engineering and Applied Sciences, University of California-Los Angeles, Los Angeles, CA, 90095, USA
- Center for Minimally Invasive Therapeutics (C-MIT), University of California-Los Angeles, Los Angeles, CA, 90095, USA
| | - Wujin Sun
- Department of Bioengineering, Henry Samueli School of Engineering and Applied Sciences, University of California-Los Angeles, Los Angeles, CA, 90095, USA
- Center for Minimally Invasive Therapeutics (C-MIT), University of California-Los Angeles, Los Angeles, CA, 90095, USA
| | - Soufian Lasli
- Department of Bioengineering, Henry Samueli School of Engineering and Applied Sciences, University of California-Los Angeles, Los Angeles, CA, 90095, USA
- Center for Minimally Invasive Therapeutics (C-MIT), University of California-Los Angeles, Los Angeles, CA, 90095, USA
| | - Chuanzhen Zhao
- Department of Chemistry and Biochemistry, University of California-Los Angeles, Los Angeles, CA, 90095, USA
| | - Shuang Hou
- Department of Molecular and Medical Pharmacology, University of California-Los Angeles, Los Angeles, CA, 90095, USA
| | - Shiming Zhang
- Department of Bioengineering, Henry Samueli School of Engineering and Applied Sciences, University of California-Los Angeles, Los Angeles, CA, 90095, USA
- Center for Minimally Invasive Therapeutics (C-MIT), University of California-Los Angeles, Los Angeles, CA, 90095, USA
| | - Jiahua Ni
- Department of Bioengineering, Henry Samueli School of Engineering and Applied Sciences, University of California-Los Angeles, Los Angeles, CA, 90095, USA
- Center for Minimally Invasive Therapeutics (C-MIT), University of California-Los Angeles, Los Angeles, CA, 90095, USA
| | - Giorgia Cefaloni
- Department of Bioengineering, Henry Samueli School of Engineering and Applied Sciences, University of California-Los Angeles, Los Angeles, CA, 90095, USA
- Center for Minimally Invasive Therapeutics (C-MIT), University of California-Los Angeles, Los Angeles, CA, 90095, USA
| | - Samad Ahadian
- Department of Bioengineering, Henry Samueli School of Engineering and Applied Sciences, University of California-Los Angeles, Los Angeles, CA, 90095, USA
- Center for Minimally Invasive Therapeutics (C-MIT), University of California-Los Angeles, Los Angeles, CA, 90095, USA
| | - Mehmet Remzi Dokmeci
- Center for Minimally Invasive Therapeutics (C-MIT), University of California-Los Angeles, Los Angeles, CA, 90095, USA
- Department of Radiology, David Geffen School of Medicine, University of California-Los Angeles, Los Angeles, CA, 90095, USA
| | - Shiladitya Sengupta
- Department of Medicine, Division of Engineering in Medicine, Brigham and Women's Hospital, Harvard Medical School, Cambridge, MA, 02139, USA
- Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Junmin Lee
- Department of Bioengineering, Henry Samueli School of Engineering and Applied Sciences, University of California-Los Angeles, Los Angeles, CA, 90095, USA
- Center for Minimally Invasive Therapeutics (C-MIT), University of California-Los Angeles, Los Angeles, CA, 90095, USA
| | - Ali Khademhosseini
- Department of Bioengineering, Henry Samueli School of Engineering and Applied Sciences, University of California-Los Angeles, Los Angeles, CA, 90095, USA
- Center for Minimally Invasive Therapeutics (C-MIT), University of California-Los Angeles, Los Angeles, CA, 90095, USA
- Department of Radiology, David Geffen School of Medicine, University of California-Los Angeles, Los Angeles, CA, 90095, USA
- Department of Chemical and Biomolecular Engineering, Henry Samueli School of Engineering and Applied Sciences, University of California-Los Angeles, Los Angeles, CA, 90095, USA
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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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Sinha N, Subedi N, Tel J. Integrating Immunology and Microfluidics for Single Immune Cell Analysis. Front Immunol 2018; 9:2373. [PMID: 30459757 PMCID: PMC6232771 DOI: 10.3389/fimmu.2018.02373] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 09/24/2018] [Indexed: 12/16/2022] Open
Abstract
The field of immunoengineering aims to develop novel therapies and modern vaccines to manipulate and modulate the immune system and applies innovative technologies toward improved understanding of the immune system in health and disease. Microfluidics has proven to be an excellent technology for analytics in biology and chemistry. From simple microsystem chips to complex microfluidic designs, these platforms have witnessed an immense growth over the last decades with frequent emergence of new designs. Microfluidics provides a highly robust and precise tool which led to its widespread application in single-cell analysis of immune cells. Single-cell analysis allows scientists to account for the heterogeneous behavior of immune cells which often gets overshadowed when conventional bulk study methods are used. Application of single-cell analysis using microfluidics has facilitated the identification of several novel functional immune cell subsets, quantification of signaling molecules, and understanding of cellular communication and signaling pathways. Single-cell analysis research in combination with microfluidics has paved the way for the development of novel therapies, point-of-care diagnostics, and even more complex microfluidic platforms that aid in creating in vitro cellular microenvironments for applications in drug and toxicity screening. In this review, we provide a comprehensive overview on the integration of microsystems and microfluidics with immunology and focus on different designs developed to decode single immune cell behavior and cellular communication. We have categorized the microfluidic designs in three specific categories: microfluidic chips with cell traps, valve-based microfluidics, and droplet microfluidics that have facilitated the ongoing research in the field of immunology at single-cell level.
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Affiliation(s)
- Nidhi Sinha
- Laboratory of Immunoengineering, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, Netherlands
- Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, Netherlands
| | - Nikita Subedi
- Laboratory of Immunoengineering, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, Netherlands
- Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, Netherlands
| | - Jurjen Tel
- Laboratory of Immunoengineering, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, Netherlands
- Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, Netherlands
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38
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Tentori AM, Nagarajan MB, Kim JJ, Zhang WC, Slack FJ, Doyle PS. Quantitative and multiplex microRNA assays from unprocessed cells in isolated nanoliter well arrays. LAB ON A CHIP 2018; 18:2410-2424. [PMID: 29998262 PMCID: PMC6081239 DOI: 10.1039/c8lc00498f] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
MicroRNAs (miRNAs) have recently emerged as promising biomarkers for the profiling of diseases. Translation of miRNA biomarkers to clinical practice, however, remains a challenge due to the lack of analysis platforms for sensitive, quantitative, and multiplex miRNA assays that have simple and robust workflows suitable for translation. The platform we present here utilizes functionalized hydrogel posts contained within isolated nanoliter well reactors for quantitative and multiplex assays directly from unprocessed cell samples without the need of prior nucleic acid extraction. Simultaneous reactor isolation and delivery of miRNA extraction reagents is achieved by sealing an array of wells containing the functionalized hydrogel posts and cells against another array of wells containing lysis and extraction reagents. The nanoliter well array platform features >100× better sensitivity compared to previous technology utilizing hydrogel particles without relying on signal amplification and enables >100 parallel assays in a single device. These advances provided by this platform lay the groundwork for translatable and robust analysis technologies for miRNA expression profiling in samples with small populations of cells and in precious, material-limited samples.
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Affiliation(s)
- Augusto M. Tentori
- Department of Chemical Engineering
, Massachusetts Institute of Technology
,
Cambridge
, USA
.
; Tel: +1 617 253 4534
| | - Maxwell B. Nagarajan
- Department of Chemical Engineering
, Massachusetts Institute of Technology
,
Cambridge
, USA
.
; Tel: +1 617 253 4534
| | - Jae Jung Kim
- Department of Chemical Engineering
, Massachusetts Institute of Technology
,
Cambridge
, USA
.
; Tel: +1 617 253 4534
| | - Wen Cai Zhang
- Department of Pathology
, Beth Israel Deaconess Medical Center/Harvard Medical School
,
Boston
, USA
| | - Frank J. Slack
- Department of Pathology
, Beth Israel Deaconess Medical Center/Harvard Medical School
,
Boston
, USA
| | - Patrick S. Doyle
- Department of Chemical Engineering
, Massachusetts Institute of Technology
,
Cambridge
, USA
.
; Tel: +1 617 253 4534
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39
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Ohiri KA, Kelly ST, Motschman JD, Lin KH, Wood KC, Yellen BB. An acoustofluidic trap and transfer approach for organizing a high density single cell array. LAB ON A CHIP 2018; 18:2124-2133. [PMID: 29931016 PMCID: PMC6078799 DOI: 10.1039/c8lc00196k] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
We demonstrate a hybrid microfluidic system that combines fluidic trapping and acoustic switching to organize an array of single cells at high density. The fluidic trapping step is achieved by balancing the hydrodynamic resistances of three parallel channel segments forming a microfluidic trifurcation, the purpose of which was to capture single cells in a high-density array. Next, the cells were transferred into adjacent larger compartments by generating an array of streaming micro-vortices to move the cells to the desired streamlines in a massively parallel format. This approach can compartmentalize single cells with efficiencies of ≈67% in compartments that have diameters on the order of ∼100 um, which is an appropriate size for single cell proliferation studies and other single cell biochemical measurements.
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Affiliation(s)
- Korine A Ohiri
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC 27708, USA.
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40
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Li X, Soler M, Szydzik C, Khoshmanesh K, Schmidt J, Coukos G, Mitchell A, Altug H. Label-Free Optofluidic Nanobiosensor Enables Real-Time Analysis of Single-Cell Cytokine Secretion. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2018; 14:e1800698. [PMID: 29806234 DOI: 10.1002/smll.201800698] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 04/06/2018] [Indexed: 05/23/2023]
Abstract
Single-cell analysis of cytokine secretion is essential to understand the heterogeneity of cellular functionalities and develop novel therapies for multiple diseases. Unraveling the dynamic secretion process at single-cell resolution reveals the real-time functional status of individual cells. Fluorescent and colorimetric-based methodologies require tedious molecular labeling that brings inevitable interferences with cell integrity and compromises the temporal resolution. An innovative label-free optofluidic nanoplasmonic biosensor is introduced for single-cell analysis in real time. The nanobiosensor incorporates a novel design of a multifunctional microfluidic system with small volume microchamber and regulation channels for reliable monitoring of cytokine secretion from individual cells for hours. Different interleukin-2 secretion profiles are detected and distinguished from single lymphoma cells. The sensor configuration combined with optical spectroscopic imaging further allows us to determine the spatial single-cell secretion fingerprints in real time. This new biosensor system is anticipated to be a powerful tool to characterize single-cell signaling for basic and clinical research.
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Affiliation(s)
- Xiaokang Li
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - Maria Soler
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - Crispin Szydzik
- School of Engineering, RMIT University, Melbourne, 3001, Australia
| | | | - Julien Schmidt
- Ludwig Institute for Cancer Research, University of Lausanne and Department of Oncology, University of Lausanne, CH-1007, Lausanne, Switzerland
| | - George Coukos
- Ludwig Institute for Cancer Research, University of Lausanne and Department of Oncology, University of Lausanne, CH-1007, Lausanne, Switzerland
| | - Arnan Mitchell
- School of Engineering, RMIT University, Melbourne, 3001, Australia
| | - Hatice Altug
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
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41
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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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42
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Park H, Kim H, Doh J. Multifunctional Microwell Arrays for Single Cell Level Functional Analysis of Lymphocytes. Bioconjug Chem 2017; 29:672-679. [DOI: 10.1021/acs.bioconjchem.7b00620] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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43
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Murphy TW, Zhang Q, Naler LB, Ma S, Lu C. Recent advances in the use of microfluidic technologies for single cell analysis. Analyst 2017; 143:60-80. [PMID: 29170786 PMCID: PMC5839671 DOI: 10.1039/c7an01346a] [Citation(s) in RCA: 103] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The inherent heterogeneity in cell populations has become of great interest and importance as analytical techniques have improved over the past decades. With the advent of personalized medicine, understanding the impact of this heterogeneity has become an important challenge for the research community. Many different microfluidic approaches with varying levels of throughput and resolution exist to study single cell activity. In this review, we take a broad view of the recent microfluidic developments in single cell analysis based on microwell, microchamber, and droplet platforms. We cover physical, chemical, and molecular biology approaches for cellular and molecular analysis including newly emerging genome-wide analysis.
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Affiliation(s)
- Travis W Murphy
- Department of Chemical Engineering, Virginia Tech, Blacksburg, VA 24061, USA.
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44
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Timm AC, Warrick JW, Yin J. Quantitative profiling of innate immune activation by viral infection in single cells. Integr Biol (Camb) 2017; 9:782-791. [PMID: 28831492 PMCID: PMC5603422 DOI: 10.1039/c7ib00082k] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Cells infected by viruses can exhibit diverse patterns of viral and cellular gene expression. The patterns arise in part from the stochastic or noisy reaction kinetics associated with the small number of genomes, enzymes, and other molecules that typically initiate virus replication and activate cellular anti-viral defenses. It is not known what features, if any, of the early viral or cellular gene expression correlate with later processes of viral replication or cell survival. Here we used two fluorescent reporters to visualize innate immune activation of human prostate cancer (PC3) cells against infection by vesicular stomatitis virus. The cells were engineered to express green-fluorescent protein under control of the promoter for IFIT2, an interferon-sensitive component of the anti-viral response, while red-fluorescent protein was expressed as a byproduct of virus infection. To isolate and quantitatively analyze single-cells, we used a unique microwell array device and open-source image processing software. Kinetic analysis of viral and cellular reporter profiles from hundreds of cells revealed novel relationships between gene expression and the outcome of infection. Specifically, the relative timing rather than the magnitude of the viral gene expression and innate immune activation correlated with the infection outcome. Earlier viral or anti-viral gene expression favored or hindered virus growth, respectively. Further, analysis of kinetic parameters estimated from these data suggests a trade-off between robust antiviral signaling and cell death, as indicated by a higher rate of detectable cell lysis in infected cells with a detectable immune response. In short, cells that activate an immune response lyse at a higher rate. More broadly, we demonstrate how the intrinsic heterogeneity of individual cell behaviors can be exploited to discover features of viral and host gene expression that correlate with single-cell outcomes, which will ultimately impact whether or not infections spread.
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Affiliation(s)
- Andrea C Timm
- Systems Biology Theme, Wisconsin Institute for Discovery, Department of Chemical and Biological Engineering, University of Wisconsin, Madison, WI, USA.
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45
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An X, Sendra VG, Liadi I, Ramesh B, Romain G, Haymaker C, Martinez-Paniagua M, Lu Y, Radvanyi LG, Roysam B, Varadarajan N. Single-cell profiling of dynamic cytokine secretion and the phenotype of immune cells. PLoS One 2017; 12:e0181904. [PMID: 28837583 PMCID: PMC5570329 DOI: 10.1371/journal.pone.0181904] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 07/10/2017] [Indexed: 01/05/2023] Open
Abstract
Natural killer (NK) cells are a highly heterogeneous population of innate lymphocytes that constitute our first line of defense against several types of tumors and microbial infections. Understanding the heterogeneity of these lymphocytes requires the ability to integrate their underlying phenotype with dynamic functional behaviors. We have developed and validated a single-cell methodology that integrates cellular phenotyping and dynamic cytokine secretion based on nanowell arrays and bead-based molecular biosensors. We demonstrate the robust passivation of the polydimethylsiloxane (PDMS)-based nanowells arrays with polyethylene glycol (PEG) and validated our assay by comparison to enzyme-linked immunospot (ELISPOT) assays. We used numerical simulations to optimize the molecular density of antibodies on the surface of the beads as a function of the capture efficiency of cytokines within an open-well system. Analysis of hundreds of individual human peripheral blood NK cells profiled ex vivo revealed that CD56dimCD16+ NK cells are immediate secretors of interferon gamma (IFN-γ) upon activation by phorbol 12-myristate 13-acetate (PMA) and ionomycin (< 3 h), and that there was no evidence of cooperation between NK cells leading to either synergistic activation or faster IFN-γ secretion. Furthermore, we observed that both the amount and rate of IFN-γ secretion from individual NK cells were donor-dependent. Collectively, these results establish our methodology as an investigational tool for combining phenotyping and real-time protein secretion of individual cells in a high-throughput manner.
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Affiliation(s)
- Xingyue An
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, Texas, United States of America
| | - Victor G. Sendra
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, Texas, United States of America
| | - Ivan Liadi
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, Texas, United States of America
| | - Balakrishnan Ramesh
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, Texas, United States of America
| | - Gabrielle Romain
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, Texas, United States of America
| | - Cara Haymaker
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Melisa Martinez-Paniagua
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, Texas, United States of America
| | - Yanbin Lu
- Department of Electrical and Computer Engineering, University of Houston, Houston, Texas, United States of America
| | - Laszlo G. Radvanyi
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Badrinath Roysam
- Department of Electrical and Computer Engineering, University of Houston, Houston, Texas, United States of America
| | - Navin Varadarajan
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, Texas, United States of America
- * E-mail:
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46
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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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47
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Ross AE, Belanger MC, Woodroof JF, Pompano RR. Spatially resolved microfluidic stimulation of lymphoid tissue ex vivo. Analyst 2017; 142:649-659. [PMID: 27900374 PMCID: PMC7863610 DOI: 10.1039/c6an02042a] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The lymph node is a structurally complex organ of the immune system, whose dynamic cellular arrangements are thought to control much of human health. Currently, no methods exist to precisely stimulate substructures within the lymph node or analyze local stimulus-response behaviors, making it difficult to rationally design therapies for inflammatory disease. Here we describe a novel integration of live lymph node slices with a microfluidic system for local stimulation. Slices maintained the cellular organization of the lymph node while making its core experimentally accessible. The 3-layer polydimethylsiloxane device consisted of a perfusion chamber stacked atop stimulation ports fed by underlying microfluidic channels. Fluorescent dextrans similar in size to common proteins, 40 and 70 kDa, were delivered to live lymph node slices with 284 ± 9 μm and 202 ± 15 μm spatial resolution, respectively, after 5 s, which is sufficient to target functional zones of the lymph node. The spread and quantity of stimulation were controlled by varying the flow rates of delivery; these were predictable using a computational model of isotropic diffusion and convection through the tissue. Delivery to two separate regions simultaneously was demonstrated, to mimic complex intercellular signaling. Delivery of a model therapeutic, glucose-conjugated albumin, to specific regions of the lymph node indicated that retention of the drug was greater in the B-cell zone than in the T-cell zone. Together, this work provides a novel platform, the lymph node slice-on-a-chip, to target and study local events in the lymph node and to inform the development of new immunotherapeutics.
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Affiliation(s)
- Ashley E Ross
- University of Virginia, Dept. of Chemistry, PO Box 400319, McCormick Rd, Charlottesville, VA 22904, USA.
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48
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An on-chip imaging droplet-sorting system: a real-time shape recognition method to screen target cells in droplets with single cell resolution. Sci Rep 2017; 7:40072. [PMID: 28059147 PMCID: PMC5216404 DOI: 10.1038/srep40072] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 11/30/2016] [Indexed: 12/29/2022] Open
Abstract
A microfluidic on-chip imaging cell sorter has several advantages over conventional cell sorting methods, especially to identify cells with complex morphologies such as clusters. One of the remaining problems is how to efficiently discriminate targets at the species level without labelling. Hence, we developed a label-free microfluidic droplet-sorting system based on image recognition of cells in droplets. To test the applicability of this method, a mixture of two plankton species with different morphologies (Dunaliella tertiolecta and Phaeodactylum tricornutum) were successfully identified and discriminated at a rate of 10 Hz. We also examined the ability to detect the number of objects encapsulated in a droplet. Single cell droplets sorted into collection channels showed 91 ± 4.5% and 90 ± 3.8% accuracy for D. tertiolecta and P. tricornutum, respectively. Because we used image recognition to confirm single cell droplets, we achieved highly accurate single cell sorting. The results indicate that the integrated method of droplet imaging cell sorting can provide a complementary sorting approach capable of isolating single target cells from a mixture of cells with high accuracy without any staining.
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49
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Son KJ, Rahimian A, Shin DS, Siltanen C, Patel T, Revzin A. Microfluidic compartments with sensing microbeads for dynamic monitoring of cytokine and exosome release from single cells. Analyst 2017; 141:679-88. [PMID: 26525740 DOI: 10.1039/c5an01648g] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Monitoring activity of single cells has high significance for basic science and diagnostic applications. Here we describe a reconfigurable microfluidic device for confining single cells along with antibody-modified sensing beads inside 20 picoliter (pL) microcompartments for monitoring cellular secretory activity. An array of ∼7000 microchambers fabricated in the roof of the reconfigurable microfluidic device could be raised or lowered by applying negative pressure. The floor of the device was micropatterned to contain cell attachment sites in registration with the microcompartments. Using this set-up, we demonstrated the detection of inflammatory cytokine IFN-γ and exosomes from single immune cells and cancer cells respectively. The detection scheme was similar in both cases: cells were first captured on the surface inside the microfluidic device, then sensing microbeads were introduced into the device so that, once the microcompartments were lowered, single cells and microbeads became confined together. The liquid bathing the beads and the cells inside the compartments also contained fluorescently-labeled secondary antibodies (Abs). The capture of cell-secreted molecules onto microbeads was followed by binding of secondary antibodies - this caused microbeads to become fluorescent. The fluorescence intensity of the microbeads changed over time, providing dynamics of single cell secretory activity. The microdevice described here may be particularly useful in the cases where panning upstream of sensing is required or to analyze secretory activity of anchorage-dependent cells.
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Affiliation(s)
- Kyung Jin Son
- Department of Biomedical Engineering, University of California, Davis, California 95616, USA.
| | - Ali Rahimian
- Department of Biomedical Engineering, University of California, Davis, California 95616, USA.
| | - Dong-Sik Shin
- Department of Biomedical Engineering, University of California, Davis, California 95616, USA. and Department of Medical & Pharmaceutical Sciences, Sookmyung Women's University, Seoul, Korea
| | - Christian Siltanen
- Department of Biomedical Engineering, University of California, Davis, California 95616, USA.
| | - Tushar Patel
- Department of Cancer Biology, Mayo Clinic, Jacksonville, Florida 32224, USA
| | - Alexander Revzin
- Department of Biomedical Engineering, University of California, Davis, California 95616, USA.
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50
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Fast and Inexpensive Detection of Bacterial Viability and Drug Effectiveness through Metabolic Monitoring. SENSORS 2016; 16:s16111879. [PMID: 27834850 PMCID: PMC5134538 DOI: 10.3390/s16111879] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 10/19/2016] [Accepted: 10/26/2016] [Indexed: 01/10/2023]
Abstract
Conventional methods for the detection of bacterial infection such as DNA or immunoassays are expensive, time consuming, or not definitive and thus may not provide all the information sought by medical professionals. In particular, it is difficult to obtain information about viability or drug effectiveness, which is crucial to formulate a treatment. Bacterial culture tests are the “gold standard” because they are inexpensive and do not require extensive sample preparation, and most importantly, provide all the necessary information sought by healthcare professionals, such as bacterial presence, viability and drug effectiveness. These conventional culture methods, however, have a long turnaround time, anywhere between 1 day and 4 weeks. Here, we solve this problem by monitoring the growth of bacteria in thousands of nanowells simultaneously to more quickly identify their presence in the sample and their viability. The segmentation of a sample with low bacterial concentration into thousands of nanoliter wells digitizes the samples and increases the effective concentration in those wells that contain bacteria. We monitor the metabolism of aerobic bacteria by using an oxygen-sensitive fluorophore, ruthenium tris (2,2’-diprydl) dichloride hexahydrate (RTDP), which allows us to monitor the dissolved oxygen concentration in the nanowells. Using E. coli K12 as a model pathogen, we demonstrate that the detection time of E. coli can be as fast as 35–60 min with sample concentrations varying from 104 (62 min for detection), 106 (42 min) and 108 cells/mL (38 min). More importantly, we also demonstrate that reducing the well size can reduce the detection time. Finally we show that drug effectiveness information can be obtained in this format by loading the wells with the drug and monitoring the metabolism of the bacteria. The method that we have developed is low cost, simple, requires minimal sample preparation and can potentially be used with a wide variety of samples in a resource-poor setting to detect bacterial infections such as tuberculosis.
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