1
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Williamson HK, Mendes PM. An integrated perspective on measuring cytokines to inform CAR-T bioprocessing. Biotechnol Adv 2024; 75:108405. [PMID: 38997052 DOI: 10.1016/j.biotechadv.2024.108405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Accepted: 07/09/2024] [Indexed: 07/14/2024]
Abstract
Chimeric antigen receptor (CAR)-T cells are emerging as a generation-defining therapeutic however their manufacture remains a major barrier to meeting increased market demand. Monitoring critical quality attributes (CQAs) and critical process parameters (CPPs) during manufacture would vastly enrich acquired information related to the process and product, providing feedback to enable real-time decision making. Here we identify specific CAR-T cytokines as value-adding analytes and discuss their roles as plausible CPPs and CQAs. High sensitivity sensing technologies which can be easily integrated into manufacture workflows are essential to implement real-time monitoring of these cytokines. We therefore present biosensors as enabling technologies and evaluate recent advancements in cytokine detection in cell cultures, offering promising translatability to CAR-T biomanufacture. Finally, we outline emerging sensing technologies with future promise, and provide an overall outlook on existing gaps to implementation and the optimal sensing platform to enable cytokine monitoring in CAR-T biomanufacture.
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Affiliation(s)
- Hannah K Williamson
- School of Chemical Engineering, University of Birmingham, Birmingham, B15 2TT, UK
| | - Paula M Mendes
- School of Chemical Engineering, University of Birmingham, Birmingham, B15 2TT, UK.
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2
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Luecke S, Guo X, Sheu KM, Singh A, Lowe SC, Han M, Diaz J, Lopes F, Wollman R, Hoffmann A. Dynamical and combinatorial coding by MAPK p38 and NFκB in the inflammatory response of macrophages. Mol Syst Biol 2024; 20:898-932. [PMID: 38872050 PMCID: PMC11297158 DOI: 10.1038/s44320-024-00047-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Revised: 05/27/2024] [Accepted: 05/28/2024] [Indexed: 06/15/2024] Open
Abstract
Macrophages sense pathogens and orchestrate specific immune responses. Stimulus specificity is thought to be achieved through combinatorial and dynamical coding by signaling pathways. While NFκB dynamics are known to encode stimulus information, dynamical coding in other signaling pathways and their combinatorial coordination remain unclear. Here, we established live-cell microscopy to investigate how NFκB and p38 dynamics interface in stimulated macrophages. Information theory and machine learning revealed that p38 dynamics distinguish cytokine TNF from pathogen-associated molecular patterns and high doses from low, but contributed little to information-rich NFκB dynamics when both pathways are considered. This suggests that immune response genes benefit from decoding immune signaling dynamics or combinatorics, but not both. We found that the heterogeneity of the two pathways is surprisingly uncorrelated. Mathematical modeling revealed potential sources of uncorrelated heterogeneity in the branched pathway network topology and predicted it to drive gene expression variability. Indeed, genes dependent on both p38 and NFκB showed high scRNAseq variability and bimodality. These results identify combinatorial signaling as a mechanism to restrict NFκB-AND-p38-responsive inflammatory cytokine expression to few cells.
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Affiliation(s)
- Stefanie Luecke
- Department of Microbiology, Immunology, and Molecular Genetics (MIMG), University of California Los Angeles, Los Angeles, CA, 90095, USA
- Institute for Quantitative and Computational Biosciences, University of California Los Angeles, Los Angeles, CA, 90095, USA
| | - Xiaolu Guo
- Department of Microbiology, Immunology, and Molecular Genetics (MIMG), University of California Los Angeles, Los Angeles, CA, 90095, USA
- Institute for Quantitative and Computational Biosciences, University of California Los Angeles, Los Angeles, CA, 90095, USA
| | - Katherine M Sheu
- Department of Microbiology, Immunology, and Molecular Genetics (MIMG), University of California Los Angeles, Los Angeles, CA, 90095, USA
- Institute for Quantitative and Computational Biosciences, University of California Los Angeles, Los Angeles, CA, 90095, USA
| | - Apeksha Singh
- Department of Microbiology, Immunology, and Molecular Genetics (MIMG), University of California Los Angeles, Los Angeles, CA, 90095, USA
- Institute for Quantitative and Computational Biosciences, University of California Los Angeles, Los Angeles, CA, 90095, USA
| | - Sarina C Lowe
- Department of Microbiology, Immunology, and Molecular Genetics (MIMG), University of California Los Angeles, Los Angeles, CA, 90095, USA
- Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, 90095, USA
| | - Minhao Han
- Department of Microbiology, Immunology, and Molecular Genetics (MIMG), University of California Los Angeles, Los Angeles, CA, 90095, USA
- Institute for Quantitative and Computational Biosciences, University of California Los Angeles, Los Angeles, CA, 90095, USA
| | - Jessica Diaz
- Department of Microbiology, Immunology, and Molecular Genetics (MIMG), University of California Los Angeles, Los Angeles, CA, 90095, USA
- Institute for Quantitative and Computational Biosciences, University of California Los Angeles, Los Angeles, CA, 90095, USA
| | - Francisco Lopes
- Institute for Quantitative and Computational Biosciences, University of California Los Angeles, Los Angeles, CA, 90095, USA
- Grupo de Biologia do Desenvolvimento e Sistemas Dinamicos, Campus Duque de Caxias Professor Geraldo Cidade, Universidade Federal do Rio de Janeiro, Duque de Caxias, 25240-005, Brazil
| | - Roy Wollman
- Institute for Quantitative and Computational Biosciences, University of California Los Angeles, Los Angeles, CA, 90095, USA
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA, 90095, USA
- Department of Integrative Biology and Physiology, University of California Los Angeles, Los Angeles, CA, 90095, USA
| | - Alexander Hoffmann
- Department of Microbiology, Immunology, and Molecular Genetics (MIMG), University of California Los Angeles, Los Angeles, CA, 90095, USA.
- Institute for Quantitative and Computational Biosciences, University of California Los Angeles, Los Angeles, CA, 90095, USA.
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3
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Wang C, Qiu J, Liu M, Wang Y, Yu Y, Liu H, Zhang Y, Han L. Microfluidic Biochips for Single-Cell Isolation and Single-Cell Analysis of Multiomics and Exosomes. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2401263. [PMID: 38767182 PMCID: PMC11267386 DOI: 10.1002/advs.202401263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 04/26/2024] [Indexed: 05/22/2024]
Abstract
Single-cell multiomic and exosome analyses are potent tools in various fields, such as cancer research, immunology, neuroscience, microbiology, and drug development. They facilitate the in-depth exploration of biological systems, providing insights into disease mechanisms and aiding in treatment. Single-cell isolation, which is crucial for single-cell analysis, ensures reliable cell isolation and quality control for further downstream analyses. Microfluidic chips are small lightweight systems that facilitate efficient and high-throughput single-cell isolation and real-time single-cell analysis on- or off-chip. Therefore, most current single-cell isolation and analysis technologies are based on the single-cell microfluidic technology. This review offers comprehensive guidance to researchers across different fields on the selection of appropriate microfluidic chip technologies for single-cell isolation and analysis. This review describes the design principles, separation mechanisms, chip characteristics, and cellular effects of various microfluidic chips available for single-cell isolation. Moreover, this review highlights the implications of using this technology for subsequent analyses, including single-cell multiomic and exosome analyses. Finally, the current challenges and future prospects of microfluidic chip technology are outlined for multiplex single-cell isolation and multiomic and exosome analyses.
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Affiliation(s)
- Chao Wang
- Institute of Marine Science and TechnologyShandong UniversityQingdao266237China
| | - Jiaoyan Qiu
- Institute of Marine Science and TechnologyShandong UniversityQingdao266237China
| | - Mengqi Liu
- Institute of Marine Science and TechnologyShandong UniversityQingdao266237China
| | - Yihe Wang
- Institute of Marine Science and TechnologyShandong UniversityQingdao266237China
| | - Yang Yu
- Department of PeriodontologySchool and Hospital of StomatologyCheeloo College of MedicineShandong UniversityJinan250100China
| | - Hong Liu
- State Key Laboratory of Crystal MaterialsShandong UniversityJinan250100China
| | - Yu Zhang
- Institute of Marine Science and TechnologyShandong UniversityQingdao266237China
| | - Lin Han
- Institute of Marine Science and TechnologyShandong UniversityQingdao266237China
- Shandong Engineering Research Center of Biomarker and Artificial Intelligence ApplicationJinan250100China
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4
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Yang H, Tel J. Engineering global and local signal generators for probing temporal and spatial cellular signaling dynamics. Front Bioeng Biotechnol 2023; 11:1239026. [PMID: 37790255 PMCID: PMC10543096 DOI: 10.3389/fbioe.2023.1239026] [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: 06/12/2023] [Accepted: 08/16/2023] [Indexed: 10/05/2023] Open
Abstract
Cells constantly encounter a wide range of environmental signals and rely on their signaling pathways to initiate reliable responses. Understanding the underlying signaling mechanisms and cellular behaviors requires signal generators capable of providing diverse input signals to deliver to cell systems. Current research efforts are primarily focused on exploring cellular responses to global or local signals, which enable us to understand cellular signaling and behavior in distinct dimensions. This review presents recent advancements in global and local signal generators, highlighting their applications in studying temporal and spatial signaling activity. Global signals can be generated using microfluidic or photochemical approaches. Local signal sources can be created using living or artificial cells in combination with different control methods. We also address the strengths and limitations of each signal generator type, discussing challenges and potential extensions for future research. These approaches are expected to continue to facilitate on-going research to discover novel and intriguing cellular signaling mechanisms.
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Affiliation(s)
- Haowen Yang
- 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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5
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Son M, Wang AG, Kenna E, Tay S. High-throughput co-culture system for analysis of spatiotemporal cell-cell signaling. Biosens Bioelectron 2023; 225:115089. [PMID: 36736159 PMCID: PMC9991101 DOI: 10.1016/j.bios.2023.115089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 01/17/2023] [Accepted: 01/18/2023] [Indexed: 01/31/2023]
Abstract
Study of spatial and temporal aspects of signaling between individual cells is essential in understanding development, the immune response, and host-pathogen interactions. We present an automated high-throughput microfluidic platform that chemically stimulates immune cells to initiate cytokine secretion, and controls the formation of signal gradients that activate neighboring cell populations. Furthermore, our system enables controlling the cell type and density based on distance, and retrieval of cells from different regions for gene expression analysis. Our device performs these tasks in 192 independent chambers to simultaneously test different co-culture conditions. We demonstrate these capabilities by creating various cellular communication scenarios between macrophages and fibroblasts in vitro. We find that spatial distribution of macrophages and heterogeneity in cytokine secretion determine spatiotemporal gene expression responses. Furthermore, we describe how gene expression dynamics depend on a cell's distance from the signaling source. Our device addresses key challenges in the study of cell-to-cell signaling, and provides high-throughput and automated analysis over a wide range of co-culture conditions.
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Affiliation(s)
- Minjun Son
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, 60637, USA; Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL, 60637, USA.
| | - Andrew G Wang
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, 60637, USA; Medical Scientist Training Program, University of Chicago, Chicago, IL, 60637, USA
| | - Emma Kenna
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, 60637, USA
| | - Savaş Tay
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, 60637, USA; Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL, 60637, USA.
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6
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Gebreyesus ST, Muneer G, Huang CC, Siyal AA, Anand M, Chen YJ, Tu HL. Recent advances in microfluidics for single-cell functional proteomics. LAB ON A CHIP 2023; 23:1726-1751. [PMID: 36811978 DOI: 10.1039/d2lc01096h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Single-cell proteomics (SCP) reveals phenotypic heterogeneity by profiling individual cells, their biological states and functional outcomes upon signaling activation that can hardly be probed via other omics characterizations. This has become appealing to researchers as it enables an overall more holistic view of biological details underlying cellular processes, disease onset and progression, as well as facilitates unique biomarker identification from individual cells. Microfluidic-based strategies have become methods of choice for single-cell analysis because they allow facile assay integrations, such as cell sorting, manipulation, and content analysis. Notably, they have been serving as an enabling technology to improve the sensitivity, robustness, and reproducibility of recently developed SCP methods. Critical roles of microfluidics technologies are expected to further expand rapidly in advancing the next phase of SCP analysis to reveal more biological and clinical insights. In this review, we will capture the excitement of the recent achievements of microfluidics methods for both targeted and global SCP, including efforts to enhance the proteomic coverage, minimize sample loss, and increase multiplexity and throughput. Furthermore, we will discuss the advantages, challenges, applications, and future prospects of SCP.
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Affiliation(s)
- Sofani Tafesse Gebreyesus
- Institute of Chemistry, Academia Sinica, Taipei 11529, Taiwan.
- Nano Science and Technology Program, Taiwan International Graduate Program, Academia Sinica, Taipei 11529, Taiwan
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan
| | - Gul Muneer
- Institute of Chemistry, Academia Sinica, Taipei 11529, Taiwan.
- Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica, Taipei 11529, Taiwan
- Institute of Biochemical Sciences, National Taiwan University, Taipei 10617, Taiwan
| | | | - Asad Ali Siyal
- Institute of Chemistry, Academia Sinica, Taipei 11529, Taiwan.
| | - Mihir Anand
- Institute of Chemistry, Academia Sinica, Taipei 11529, Taiwan.
- Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica, Taipei 11529, Taiwan
- Institute of Biochemical Sciences, National Taiwan University, Taipei 10617, Taiwan
| | - Yu-Ju Chen
- Institute of Chemistry, Academia Sinica, Taipei 11529, Taiwan.
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan
- Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica, Taipei 11529, Taiwan
- Genome and Systems Biology Degree Program, Academia Sinica and National Taiwan University, Taipei 10617, Taiwan
| | - Hsiung-Lin Tu
- Institute of Chemistry, Academia Sinica, Taipei 11529, Taiwan.
- Nano Science and Technology Program, Taiwan International Graduate Program, Academia Sinica, Taipei 11529, Taiwan
- Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica, Taipei 11529, Taiwan
- Genome and Systems Biology Degree Program, Academia Sinica and National Taiwan University, Taipei 10617, Taiwan
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7
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Mitchell S, Tsui R, Tan ZC, Pack A, Hoffmann A. The NF-κB multidimer system model: A knowledge base to explore diverse biological contexts. Sci Signal 2023; 16:eabo2838. [PMID: 36917644 PMCID: PMC10195159 DOI: 10.1126/scisignal.abo2838] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 02/22/2023] [Indexed: 03/16/2023]
Abstract
The nuclear factor κB (NF-κB) system is critical for various biological functions in numerous cell types, including the inflammatory response, cell proliferation, survival, differentiation, and pathogenic responses. Each cell type is characterized by a subset of 15 NF-κB dimers whose activity is regulated in a stimulus-responsive manner. Numerous studies have produced different mathematical models that account for cell type-specific NF-κB activities. However, whereas the concentrations or abundances of NF-κB subunits may differ between cell types, the biochemical interactions that constitute the NF-κB signaling system do not. Here, we synthesized a consensus mathematical model of the NF-κB multidimer system, which could account for the cell type-specific repertoires of NF-κB dimers and their cell type-specific activation and cross-talk. Our review demonstrates that these distinct cell type-specific properties of NF-κB signaling can be explained largely as emergent effects of the cell type-specific expression of NF-κB monomers. The consensus systems model represents a knowledge base that may be used to gain insights into the control and function of NF-κB in diverse physiological and pathological scenarios and that describes a path for generating similar regulatory knowledge bases for other pleiotropic signaling systems.
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Affiliation(s)
- Simon Mitchell
- Signaling Systems Laboratory, Department of Microbiology, Immunology, and Molecular Genetics, UCLA, Los Angeles, CA 90095, USA
- Institute for Quantitative and Computational Biosciences, UCLA, Los Angeles, CA 90095, USA
- Brighton and Sussex Medical School, Department of Clinical and Experimental Medicine, University of Sussex, Falmer, East Sussex, BN1 9PX, UK
| | - Rachel Tsui
- Signaling Systems Laboratory, Department of Microbiology, Immunology, and Molecular Genetics, UCLA, Los Angeles, CA 90095, USA
| | - Zhixin Cyrillus Tan
- Institute for Quantitative and Computational Biosciences, UCLA, Los Angeles, CA 90095, USA
| | - Arran Pack
- Brighton and Sussex Medical School, Department of Clinical and Experimental Medicine, University of Sussex, Falmer, East Sussex, BN1 9PX, UK
| | - Alexander Hoffmann
- Signaling Systems Laboratory, Department of Microbiology, Immunology, and Molecular Genetics, UCLA, Los Angeles, CA 90095, USA
- Institute for Quantitative and Computational Biosciences, UCLA, Los Angeles, CA 90095, USA
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8
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Cedillo-Alcantar DF, Rodriguez-Moncayo R, Maravillas-Montero JL, Garcia-Cordero JL. On-Chip Analysis of Protein Secretion from Single Cells Using Microbead Biosensors. ACS Sens 2023; 8:655-664. [PMID: 36710459 DOI: 10.1021/acssensors.2c02148] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The profiling of the effector functions of single immune cells─including cytokine secretion─can lead to a deeper understanding of how the immune system operates and to potential diagnostics and therapeutical applications. Here, we report a microfluidic device that pairs single cells and antibody-functionalized microbeads in hydrodynamic traps to quantitate cytokine secretion. The device contains 1008 microchambers, each with a volume of ∼500 pL, divided into six different sections individually addressed to deliver an equal number of chemical stimuli. Integrating microvalves allowed us to isolate cell/bead pairs, preventing cross-contamination with factors secreted by adjacent cells. We implemented a fluorescence sandwich immunoassay on the biosensing microbeads with a limit of detection of 9 pg/mL and were able to detect interleukin-8 (IL-8) secreted by single blood-derived human monocytes in response to different concentrations of LPS. Finally, our platform allowed us to observe a significant decrease in the number of IL-8-secreting monocytes when paracrine signaling becomes disrupted. Overall, our platform could have a variety of applications for which the analysis of cellular function heterogeneity is necessary, such as cancer research, antibody discovery, or rare cell screening.
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Affiliation(s)
- Diana F Cedillo-Alcantar
- Laboratory of Microtechnologies for Biomedicine, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav), Monterrey 66628, Nuevo León Mexico
| | - Roberto Rodriguez-Moncayo
- Laboratory of Microtechnologies for Biomedicine, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav), Monterrey 66628, Nuevo León Mexico
| | - Jose L Maravillas-Montero
- Red de Apoyo a la Investigación, Universidad Nacional Autónoma de México e Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City 14080, Mexico
| | - Jose L Garcia-Cordero
- Laboratory of Microtechnologies for Biomedicine, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav), Monterrey 66628, Nuevo León Mexico.,Roche Institute for Translational Bioengineering (ITB), Roche Pharma Research and Early Development, Roche Innovation Center Basel, Basel 4058, Switzerland
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9
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Mukherjee P, Park SH, Pathak N, Patino CA, Bao G, Espinosa HD. Integrating Micro and Nano Technologies for Cell Engineering and Analysis: Toward the Next Generation of Cell Therapy Workflows. ACS NANO 2022; 16:15653-15680. [PMID: 36154011 DOI: 10.1021/acsnano.2c05494] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The emerging field of cell therapy offers the potential to treat and even cure a diverse array of diseases for which existing interventions are inadequate. Recent advances in micro and nanotechnology have added a multitude of single cell analysis methods to our research repertoire. At the same time, techniques have been developed for the precise engineering and manipulation of cells. Together, these methods have aided the understanding of disease pathophysiology, helped formulate corrective interventions at the cellular level, and expanded the spectrum of available cell therapeutic options. This review discusses how micro and nanotechnology have catalyzed the development of cell sorting, cellular engineering, and single cell analysis technologies, which have become essential workflow components in developing cell-based therapeutics. The review focuses on the technologies adopted in research studies and explores the opportunities and challenges in combining the various elements of cell engineering and single cell analysis into the next generation of integrated and automated platforms that can accelerate preclinical studies and translational research.
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Affiliation(s)
- Prithvijit Mukherjee
- Department of Mechanical Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Theoretical and Applied Mechanics Program, Northwestern University, Evanston, Illinois 60208, United States
| | - So Hyun Park
- Department of Bioengineering, Rice University, 6500 Main Street, Houston, Texas 77030, United States
| | - Nibir Pathak
- Department of Mechanical Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Theoretical and Applied Mechanics Program, Northwestern University, Evanston, Illinois 60208, United States
| | - Cesar A Patino
- Department of Mechanical Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Gang Bao
- Department of Bioengineering, Rice University, 6500 Main Street, Houston, Texas 77030, United States
| | - Horacio D Espinosa
- Department of Mechanical Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Theoretical and Applied Mechanics Program, Northwestern University, Evanston, Illinois 60208, United States
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10
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Son M, Frank T, Holst-Hansen T, Wang AG, Junkin M, Kashaf SS, Trusina A, Tay S. Spatiotemporal NF-κB dynamics encodes the position, amplitude, and duration of local immune inputs. SCIENCE ADVANCES 2022; 8:eabn6240. [PMID: 36044569 PMCID: PMC9432835 DOI: 10.1126/sciadv.abn6240] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 07/19/2022] [Indexed: 05/31/2023]
Abstract
Infected cells communicate through secreted signaling molecules like cytokines, which carry information about pathogens. How differences in cytokine secretion affect inflammatory signaling over space and how responding cells decode information from propagating cytokines are not understood. By computationally and experimentally studying NF-κB dynamics in cocultures of signal-sending cells (macrophages) and signal-receiving cells (fibroblasts), we find that cytokine signals are transmitted by wave-like propagation of NF-κB activity and create well-defined activation zones in responding cells. NF-κB dynamics in responding cells can simultaneously encode information about cytokine dose, duration, and distance to the cytokine source. Spatially resolved transcriptional analysis reveals that responding cells transmit local cytokine information to distance-specific proinflammatory gene expression patterns, creating "gene expression zones." Despite single-cell variability, the size and duration of the signaling zone are tightly controlled by the macrophage secretion profile. Our results highlight how macrophages tune cytokine secretion to control signal transmission distance and how inflammatory signaling interprets these signals in space and time.
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Affiliation(s)
- Minjun Son
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL 60637, USA
- Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL 60637, USA
| | - Tino Frank
- Department of Biosystems Science and Engineering, ETH Zürich, Basel 4058, Switzerland
| | | | - Andrew G. Wang
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL 60637, USA
| | - Michael Junkin
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL 60637, USA
- Department of Biosystems Science and Engineering, ETH Zürich, Basel 4058, Switzerland
| | - Sara S. Kashaf
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL 60637, USA
| | - Ala Trusina
- Niels Bohr Institute, University of Copenhagen, Copenhagen 2100, Denmark
| | - Savaş Tay
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL 60637, USA
- Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL 60637, USA
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11
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Zielke C, Gutierrez Ramirez AJ, Voss K, Ryan MS, Gholizadeh A, Rathmell JC, Abbyad P. Droplet Microfluidic Technology for the Early and Label-Free Isolation of Highly-Glycolytic, Activated T-Cells. MICROMACHINES 2022; 13:1442. [PMID: 36144067 PMCID: PMC9503730 DOI: 10.3390/mi13091442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 08/24/2022] [Accepted: 08/25/2022] [Indexed: 06/16/2023]
Abstract
A label-free, fixation-free and passive sorting method is presented to isolate activated T-cells shortly after activation and prior to the display of activation surface markers. It uses a recently developed sorting platform dubbed "Sorting by Interfacial Tension" (SIFT) that sorts droplets based on pH. After polyclonal (anti-CD3/CD28 bead) activation and a brief incubation on chip, droplets containing activated T-cells display a lower pH than those containing naive cells due to increased glycolysis. Under specific surfactant conditions, a change in pH can lead to a concurrent increase in droplet interfacial tension. The isolation of activated T-cells on chip is hence achieved as flattened droplets are displaced as they encounter a micro-fabricated trench oriented diagonally with respect to the direction of flow. This technique leads to an enrichment of activated primary CD4+ T-cells to over 95% from an initial mixed population of naive cells and cells activated for as little as 15 min. Moreover, since the pH change is correlated to successful activation, the technique allows the isolation of T-cells with the earliest activation and highest glycolysis, an important feature for the testing of T-cell activation modulators and to determine regulators and predictors of differentiation outcomes.
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Affiliation(s)
- Claudia Zielke
- Department of Chemistry and Biochemistry, Santa Clara University, Santa Clara, CA 95053, USA
| | | | - Kelsey Voss
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Maya S. Ryan
- Department of Chemistry and Biochemistry, Santa Clara University, Santa Clara, CA 95053, USA
| | - Azam Gholizadeh
- Department of Chemistry and Biochemistry, Santa Clara University, Santa Clara, CA 95053, USA
| | - Jeffrey C. Rathmell
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Vanderbilt Center for Immunobiology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Paul Abbyad
- Department of Chemistry and Biochemistry, Santa Clara University, Santa Clara, CA 95053, USA
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12
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Sinha N, Yang H, Janse D, Hendriks L, Rand U, Hauser H, Köster M, van de Vosse FN, de Greef TFA, Tel J. Microfluidic chip for precise trapping of single cells and temporal analysis of signaling dynamics. COMMUNICATIONS ENGINEERING 2022; 1:18. [PMCID: PMC10955935 DOI: 10.1038/s44172-022-00019-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Accepted: 07/12/2022] [Indexed: 06/15/2024]
Abstract
Microfluidic designs are versatile examples of technology miniaturisation that find their applications in various cell biology research, especially to investigate the influence of environmental signals on cellular response dynamics. Multicellular systems operate in intricate cellular microenvironments where environmental signals govern well-orchestrated and robust responses, the understanding of which can be realized with integrated microfluidic systems. In this study, we present a fully automated and integrated microfluidic chip that can deliver input signals to single and isolated suspension or adherent cells in a precisely controlled manner. In respective analyses of different single cell types, we observe, in real-time, the temporal dynamics of caspase 3 activation during DMSO-induced apoptosis in single cancer cells (K562) and the translocation of STAT-1 triggered by interferon γ (IFNγ) in single fibroblasts (NIH3T3). Our investigations establish the employment of our versatile microfluidic system in probing temporal single cell signaling networks where alternations in outputs uncover signal processing mechanisms. Nidhi Sinha, Haowen Yang and colleagues report a microfluidic large-scale integration chip to probe temporal single-cell signalling networks via the delivery of patterns of input signalling molecules. The researchers use their device to investigate drug-induced cancer cell apoptosis and single cell transcription (STAT-1) protein signalling dynamics.
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Affiliation(s)
- Nidhi Sinha
- Laboratory of Immunoengineering, Department of Biomedical Engineering, TU Eindhoven, 5600 MB Eindhoven, Netherlands
- Institute of Complex Molecular Systems, TU Eindhoven, 5600 MB Eindhoven, Netherlands
| | - Haowen Yang
- Laboratory of Immunoengineering, Department of Biomedical Engineering, TU Eindhoven, 5600 MB Eindhoven, Netherlands
- Institute of Complex Molecular Systems, TU Eindhoven, 5600 MB Eindhoven, Netherlands
| | - David Janse
- Laboratory of Immunoengineering, Department of Biomedical Engineering, TU Eindhoven, 5600 MB Eindhoven, Netherlands
| | - Luc Hendriks
- Laboratory of Immunoengineering, Department of Biomedical Engineering, TU Eindhoven, 5600 MB Eindhoven, Netherlands
| | - Ulfert Rand
- Model Systems for Infection and Immunity, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany
| | - Hansjörg Hauser
- Model Systems for Infection and Immunity, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany
| | - Mario Köster
- Model Systems for Infection and Immunity, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany
| | - Frans N. van de Vosse
- Cardiovascular Biomechanics Group, Department of Biomedical Engineering, TU Eindhoven, 5600 MB Eindhoven, Netherlands
| | - Tom F. A. de Greef
- Institute of Complex Molecular Systems, TU Eindhoven, 5600 MB Eindhoven, Netherlands
- Computational Biology Group, Department of Biomedical Engineering, TU Eindhoven, 5600 MB Eindhoven, Netherlands
| | - Jurjen Tel
- Laboratory of Immunoengineering, Department of Biomedical Engineering, TU Eindhoven, 5600 MB Eindhoven, Netherlands
- Institute of Complex Molecular Systems, TU Eindhoven, 5600 MB Eindhoven, Netherlands
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13
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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] [Grants] [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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14
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Tischler J, Swank Z, Hsiung HA, Vianello S, Lutolf MP, Maerkl SJ. An automated do-it-yourself system for dynamic stem cell and organoid culture in standard multi-well plates. CELL REPORTS METHODS 2022; 2:100244. [PMID: 35880022 PMCID: PMC9308133 DOI: 10.1016/j.crmeth.2022.100244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 05/25/2022] [Accepted: 06/09/2022] [Indexed: 11/24/2022]
Abstract
We present a low-cost, do-it-yourself system for complex mammalian cell culture under dynamically changing medium formulations by integrating conventional multi-well tissue culture plates with simple microfluidic control and system automation. We demonstrate the generation of complex concentration profiles, enabling the investigation of sophisticated input-response relations. We further apply our automated cell-culturing platform to the dynamic stimulation of two widely employed stem-cell-based in vitro models for early mammalian development: the conversion of naive mouse embryonic stem cells into epiblast-like cells and mouse 3D gastruloids. Performing automated medium-switch experiments, we systematically investigate cell fate commitment along the developmental trajectory toward mouse epiblast fate and examine symmetry-breaking, germ layer formation, and cardiac differentiation in mouse 3D gastruloids as a function of time-varying Wnt pathway activation. With these proof-of-principle examples, we demonstrate a highly versatile and scalable tool that can be adapted to specific research questions, experimental demands, and model systems.
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Affiliation(s)
- Julia Tischler
- Laboratory of Biological Network Characterization, Institute of Bioengineering, School of Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, 1015 Vaud, Switzerland
| | - Zoe Swank
- Laboratory of Biological Network Characterization, Institute of Bioengineering, School of Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, 1015 Vaud, Switzerland
- Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Hao-An Hsiung
- Laboratory of Stem Cell Bioengineering, Institute of Bioengineering, School of Life Sciences and School of Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, 1015 Vaud, Switzerland
| | - Stefano Vianello
- Laboratory of Stem Cell Bioengineering, Institute of Bioengineering, School of Life Sciences and School of Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, 1015 Vaud, Switzerland
| | - Matthias P. Lutolf
- Laboratory of Stem Cell Bioengineering, Institute of Bioengineering, School of Life Sciences and School of Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, 1015 Vaud, Switzerland
- Roche Institute for Translational Bioengineering (TB), Pharma Research and Early Development (pRED), F. Hoffman-La Roche Ltd, Basel, Switzerland
| | - Sebastian J. Maerkl
- Laboratory of Biological Network Characterization, Institute of Bioengineering, School of Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, 1015 Vaud, Switzerland
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15
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Kizilirmak C, Bianchi ME, Zambrano S. Insights on the NF-κB System Using Live Cell Imaging: Recent Developments and Future Perspectives. Front Immunol 2022; 13:886127. [PMID: 35844496 PMCID: PMC9277462 DOI: 10.3389/fimmu.2022.886127] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 05/25/2022] [Indexed: 11/29/2022] Open
Abstract
The transcription factor family of nuclear factor kappa B (NF-κB) proteins is widely recognized as a key player in inflammation and the immune responses, where it plays a fundamental role in translating external inflammatory cues into precise transcriptional programs, including the timely expression of a wide variety of cytokines/chemokines. Live cell imaging in single cells showed approximately 15 years ago that the canonical activation of NF-κB upon stimulus is very dynamic, including oscillations of its nuclear localization with a period close to 1.5 hours. This observation has triggered a fruitful interdisciplinary research line that has provided novel insights on the NF-κB system: how its heterogeneous response differs between cell types but also within homogeneous populations; how NF-κB dynamics translate external cues into intracellular signals and how NF-κB dynamics affects gene expression. Here we review the main features of this live cell imaging approach to the study of NF-κB, highlighting the key findings, the existing gaps of knowledge and hinting towards some of the potential future steps of this thriving research field.
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Affiliation(s)
- Cise Kizilirmak
- School of Medicine, Vita-Salute San Raffaele University, Milan, Italy
- Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Marco E. Bianchi
- School of Medicine, Vita-Salute San Raffaele University, Milan, Italy
- Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Samuel Zambrano
- School of Medicine, Vita-Salute San Raffaele University, Milan, Italy
- Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milan, Italy
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16
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Yang H, Sinha N, Rand U, Hauser H, Köster M, de Greef TFA, Tel J. A universal microfluidic approach for integrated analysis of temporal homocellular and heterocellular signaling and migration dynamics. Biosens Bioelectron 2022; 211:114353. [PMID: 35594624 DOI: 10.1016/j.bios.2022.114353] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 04/26/2022] [Accepted: 05/06/2022] [Indexed: 11/24/2022]
Abstract
Microfluidics offers precise and dynamic control of microenvironments for the study of temporal cellular responses. However, recent research focusing solely on either homocellular (single-cell, population) or heterocellular response may yield insufficient output, which possibly leads to partial comprehension about the underlying mechanisms of signaling events and corresponding cellular behaviors. Here, a universal microfluidic approach is developed for integrated analysis of temporal signaling and cell migration dynamics in multiple cellular contexts (single-cell, population and coculture). This approach allows to confine the desired number or mixture of specific cell sample types in a single device. Precise single cell seeding was achieved manually with bidirectional controllability. Coupled with time-lapse imaging, temporal cellular responses can be observed with single-cell resolution. Using NIH3T3 cells stably expressing signal transducer and activator of transcription 1/2 (STAT1/2) activity biosensors, temporal STAT1/2 activation and cell migration dynamics were explored in isolated single cells, populations and cocultures stimulated with temporal inputs, such as single-pulse and continuous signals of interferon γ (IFNγ) or lipopolysaccharide (LPS). We demonstrate distinct dynamic responses of fibroblasts in different cellular contexts. Our presented approach facilitates a multi-dimensional understanding of STAT signaling and corresponding migration behaviors.
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Affiliation(s)
- Haowen Yang
- Laboratory of Immunoengineering, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, 5600MB, the Netherlands; Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, 5600 MB, the Netherlands
| | - Nidhi Sinha
- Laboratory of Immunoengineering, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, 5600MB, the Netherlands; Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, 5600 MB, the Netherlands
| | - Ulfert Rand
- Model Systems for Infection and Immunity, Helmholtz Centre for Infection Research, 38124, Braunschweig, Germany
| | - Hansjörg Hauser
- Model Systems for Infection and Immunity, Helmholtz Centre for Infection Research, 38124, Braunschweig, Germany
| | - Mario Köster
- Model Systems for Infection and Immunity, Helmholtz Centre for Infection Research, 38124, Braunschweig, Germany
| | - Tom F A de Greef
- Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, 5600 MB, the Netherlands; Computational Biology Group, Department of Biomedical Engineering, Eindhoven University of Technology, 5600MB, Eindhoven, the Netherlands
| | - Jurjen Tel
- Laboratory of Immunoengineering, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, 5600MB, the Netherlands; Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, 5600 MB, the Netherlands.
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17
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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: 25] [Impact Index Per Article: 12.5] [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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18
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Wong KU, Shi J, Li P, Wang H, Jia Y, Deng C, Jang L, Wong AHH. Assessment of chimeric antigen receptor T (CAR-T) cytotoxicity by droplet microfluidics in vitro. Antib Ther 2022; 5:85-99. [PMID: 35441124 PMCID: PMC9014740 DOI: 10.1093/abt/tbac008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 03/08/2022] [Accepted: 03/17/2022] [Indexed: 11/17/2022] Open
Abstract
Chimeric antigen receptor T (CAR-T) cells are cytotoxic T cells engineered to specifically kill cancer cells expressing specific target receptor(s). Prior CAR-T efficacy tests include CAR expression analysis by qPCR or ELISA, in vitro measurement of interferon-γ (IFNγ) or interleukin-2 (IL-2), and xenograft models. However, the in vitro measurements did not reflect CAR-T cytotoxicity, whereas xenograft models are low throughput and costly. Here, we presented a robust in vitro droplet microfluidic assay for CAR-T cytotoxicity assessment. This method not only enabled assessment of CAR-T cytotoxic activity under different fluid viscosity conditions, but also facilitated measurement of CAR-T expansion and dissection of mechanism of action via phenotype analysis in vitro. Furthermore, our data suggested that label-free cytotoxicity analysis is feasible by acquiring data before and after treatment. Hence, this study presented a novel in vitro method for assessment of cellular cytotoxicity that could potentially be applied to any cytotoxicity experiment with varying solvent composition.
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Affiliation(s)
- Kuan Un Wong
- Cancer Centre, Faculty of Health Sciences, University of Macau, Macau S.A.R., China
| | - Jingxuan Shi
- Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong 510530, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong 510530, China
- University of Chinese Academy of Sciences, Shijingshan District, Beijing 100049, China
| | - Peng Li
- Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong 510530, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong 510530, China
- Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, Guangdong 510005, China
| | - Haitao Wang
- Cancer Centre, Faculty of Health Sciences, University of Macau, Macau S.A.R., China
| | - Yanwei Jia
- Cancer Centre, Faculty of Health Sciences, University of Macau, Macau S.A.R., China
- State Key Laboratory of Analog and Mixed Signal VLSI, University of Macau, Macau S.A.R., China
- Faculty of Science and Technology, University of Macau, Macau S.A.R., China
| | - Chuxia Deng
- Cancer Centre, Faculty of Health Sciences, University of Macau, Macau S.A.R., China
| | - Lianmei Jang
- ARC Excellence Centre for Nanoscale BioPhotonics (CNBP), Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Ada Hang-Heng Wong
- Cancer Centre, Faculty of Health Sciences, University of Macau, Macau S.A.R., China
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19
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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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20
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Wen Y, Zhao J, He H, Zhao Q, Liu Z. Multiplexed Single-Cell Plasmonic Immunoassay of Intracellular Signaling Proteins Enables Non-Destructive Monitoring of Cell Fate. Anal Chem 2021; 93:14204-14213. [PMID: 34648273 DOI: 10.1021/acs.analchem.1c03062] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
It is of significant importance in cancer biology to identify signaling pathways that play key roles in cell fate determination. Dissecting cellular signaling pathways requires the measurement of a large number of signaling proteins. However, tools for simultaneously monitoring multiple signaling pathway components in single living cells remain limited at present. Herein, we describe an approach, termed multiplexed single-cell plasmonic immunosandwich assay (mxscPISA), for simultaneous detection of multiple signaling proteins in individual living cells. This approach enabled simultaneous non-destructive monitoring of multiple (up to five, currently the highest multiplexing capacity in living cells) cytoplasmic and nucleus signaling proteins in individual cells with ultrahigh detection sensitivity. As a proof of principle, the epidermal growth factor receptor (EGFR) pathway, which plays a central role in cell fate determination, was investigated using this approach in this study. We found that there were differential attenuation rate of pro-survival and accumulation rate of pro-death signaling protein of the EGFR pathway in response to EGFR inactivation. These findings implicate that, after EGFR inactivation, a transient imbalance between survival and apoptotic signaling outputs contributed to the final cell fate of death. The mxscPISA approach can be a promising tool to reveal a signaling dynamic pattern at the single-cell level and to identify key components of signaling pathways that contribute to the final cell fate using only a limited number of cells.
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Affiliation(s)
- Yanrong Wen
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Jialing Zhao
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Hui He
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Quan Zhao
- School of Life Science, Nanjing University, 163 Xianlin Avenue, Nanjing 210023, China
| | - Zhen Liu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
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21
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Stimulus-specific responses in innate immunity: Multilayered regulatory circuits. Immunity 2021; 54:1915-1932. [PMID: 34525335 DOI: 10.1016/j.immuni.2021.08.018] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 03/07/2021] [Accepted: 08/16/2021] [Indexed: 12/24/2022]
Abstract
Immune sentinel cells initiate immune responses to pathogens and tissue injury and are capable of producing highly stimulus-specific responses. Insight into the mechanisms underlying such specificity has come from the identification of regulatory factors and biochemical pathways, as well as the definition of signaling circuits that enable combinatorial and temporal coding of information. Here, we review the multi-layered molecular mechanisms that underlie stimulus-specific gene expression in macrophages. We categorize components of inflammatory and anti-pathogenic signaling pathways into five layers of regulatory control and discuss unifying mechanisms determining signaling characteristics at each layer. In this context, we review mechanisms that enable combinatorial and temporal encoding of information, identify recurring regulatory motifs and principles, and present strategies for integrating experimental and computational approaches toward the understanding of signaling specificity in innate immunity.
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22
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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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23
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Zeming KK, Lu R, Woo KL, Sun G, Quek KY, Cheow LF, Chen CH, Han J, Lim SL. Multiplexed Single-Cell Leukocyte Enzymatic Secretion Profiling from Whole Blood Reveals Patient-Specific Immune Signature. Anal Chem 2021; 93:4374-4382. [PMID: 33600165 DOI: 10.1021/acs.analchem.0c03512] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Enzymatic secretion of immune cells (leukocytes) plays a dominant role in host immune responses to a myriad of biological triggers, including infections, cancers, and cardiovascular diseases. Current tools to probe these leukocytes inadequately profile these vital biomarkers; the need for sample preprocessing steps of cell lysis, labeling, washing, and pipetting inevitably triggers the cells, changes its basal state, and dilutes the individual cell secretion in bulk assays. Using a fully integrated system for multiplexed profiling of native immune single-cell enzyme secretion from 50 μL of undiluted blood, we eliminate sample handling. With a total analysis time of 60 min, the integrated platform performs six tasks of leukocyte extraction, cell washing, fluorescent enzyme substrate mixing, single-cell droplet making, droplet incubation, and real-time readout for leukocyte secretion profiling of neutrophil elastase, granzyme B, and metalloproteinase. We calibrated the device, optimized the protocols, and tested the leukocyte secretion of acute heart failure (AHF) patients at admission and predischarge. This paper highlights the presence of single-cell enzymatic immune phenotypes independent of CD marker labeling, which could potentially elucidate the innate immune response states. We found that patients recovering from AHF showed a corresponding reduction in immune-cell enzymatic secretion levels and donor-specific enzymatic signatures were observed, which suggests patient-to-patient heterogeneous immune response. This platform presents opportunities to elucidate the complexities of the immune response from a single drop of blood and bridge the current technological, biological, and medical gap in understanding immune response and biological triggers.
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Affiliation(s)
- Kerwin Kwek Zeming
- Critical Analytics for Manufacturing of Personalised Medicine, Singapore-MIT Alliance for Research and Technology, 1 Create Way, Enterprise Wing #04-13/14, 138602 Singapore
| | - Ri Lu
- Critical Analytics for Manufacturing of Personalised Medicine, Singapore-MIT Alliance for Research and Technology, 1 Create Way, Enterprise Wing #04-13/14, 138602 Singapore.,Graduate School for Integrative Sciences and Engineering, National University of Singapore, University Hall, Tan Chin Tuan Wing Level 04, #04-02, 21 Lower Kent Ridge Road, 119077 Singapore
| | - Kai Lee Woo
- Department of Cardiology, National University Heart Center, 1E Kent Ridge Road, 119228, Singapore
| | - Guoyun Sun
- Graduate School for Integrative Sciences and Engineering, National University of Singapore, University Hall, Tan Chin Tuan Wing Level 04, #04-02, 21 Lower Kent Ridge Road, 119077 Singapore
| | - Kai Yun Quek
- Critical Analytics for Manufacturing of Personalised Medicine, Singapore-MIT Alliance for Research and Technology, 1 Create Way, Enterprise Wing #04-13/14, 138602 Singapore
| | - Lih Feng Cheow
- Critical Analytics for Manufacturing of Personalised Medicine, Singapore-MIT Alliance for Research and Technology, 1 Create Way, Enterprise Wing #04-13/14, 138602 Singapore.,Graduate School for Integrative Sciences and Engineering, National University of Singapore, University Hall, Tan Chin Tuan Wing Level 04, #04-02, 21 Lower Kent Ridge Road, 119077 Singapore.,Department of Biomedical Engineering, National University of Singapore, 4 Engineering Drive 3, 117583 Singapore
| | - Chia-Hung Chen
- Department of Biomedical Engineering, College of Engineering, City University of Hong Kong, YEUNG-B5121A, Hong Kong
| | - Jongyoon Han
- Critical Analytics for Manufacturing of Personalised Medicine, Singapore-MIT Alliance for Research and Technology, 1 Create Way, Enterprise Wing #04-13/14, 138602 Singapore.,Department of Electrical Engineering, Massachusetts Institute of Technology, 50 Vassar Street, Cambridge, Massachusetts 02142, United States.,Department of Biological Engineering, Massachusetts Institute of Technology, 21 Ames Street, #56-651, Cambridge, Massachusetts 02142, United States
| | - Shir Lynn Lim
- Yong Loo Lin School of Medicine, National University of Singapore, 10 Medical Drive, 117597 Singapore.,Department of Cardiology, National University Heart Center, 1E Kent Ridge Road, 119228, Singapore
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24
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Pereiro I, Aubert J, Kaigala GV. Micro-scale technologies propel biology and medicine. BIOMICROFLUIDICS 2021; 15:021302. [PMID: 33948133 PMCID: PMC8081554 DOI: 10.1063/5.0047196] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 04/05/2021] [Indexed: 05/05/2023]
Abstract
Historically, technology has been central to new discoveries in biology and progress in medicine. Among various technologies, microtechnologies, in particular, have had a prominent role in the revolution experienced by the life sciences in the last few decades, which will surely continue in the years to come. In this Perspective, we illustrate how microtechnologies, with a focus on microfluidics, have evolved in trends/waves to tackle the boundary of knowledge in the life sciences. We provide illustrative examples of technology-enabled biological breakthroughs and their current and future use in clinics. Finally, we take a closer look at the translational process to understand why the incorporation of new micro-scale technologies in medicine has been comparatively slow so far.
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25
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Son M, Wang AG, Tu HL, Metzig MO, Patel P, Husain K, Lin J, Murugan A, Hoffmann A, Tay S. NF-κB responds to absolute differences in cytokine concentrations. Sci Signal 2021; 14. [PMID: 34211635 DOI: 10.1126/scisignal.aaz4382] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Cells receive a wide range of dynamic signaling inputs during immune regulation, but how gene regulatory networks measure such dynamic inputs is not well understood. Here, we used microfluidic single-cell analysis and mathematical modeling to study how the NF-κB pathway responds to immune inputs that vary over time such as increasing, decreasing, or fluctuating cytokine signals. We found that NF-κB activity responded to the absolute difference in cytokine concentration and not to the concentration itself. Our analyses revealed that negative feedback by the regulatory proteins A20 and IκBα enabled differential responses to changes in cytokine dose by providing a short-term memory of previous cytokine concentrations and by continuously resetting kinase cycling and receptor abundance. Investigation of NF-κB target gene expression showed that cells exhibited distinct transcriptional responses under different dynamic cytokine profiles. Our results demonstrate how cells use simple network motifs and transcription factor dynamics to efficiently extract information from complex signaling environments.
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Affiliation(s)
- Minjun Son
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL 60637, USA.,Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL 60637, USA
| | - Andrew G Wang
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL 60637, USA
| | - Hsiung-Lin Tu
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL 60637, USA.,Institute of Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Marie Oliver Metzig
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA 90095, USA.,Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, CA 90095, USA
| | - Parthiv Patel
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL 60637, USA
| | - Kabir Husain
- James Franck Institute and Department of Physics, University of Chicago, Chicago, IL 60637, USA
| | - Jing Lin
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL 60637, USA
| | - Arvind Murugan
- James Franck Institute and Department of Physics, University of Chicago, Chicago, IL 60637, USA
| | - Alexander Hoffmann
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA 90095, USA.,Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, CA 90095, USA
| | - Savaş Tay
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL 60637, USA.,Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL 60637, USA
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26
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Saint-Sardos A, Sart S, Lippera K, Brient-Litzler E, Michelin S, Amselem G, Baroud CN. High-Throughput Measurements of Intra-Cellular and Secreted Cytokine from Single Spheroids Using Anchored Microfluidic Droplets. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2020; 16:e2002303. [PMID: 33185938 DOI: 10.1002/smll.202002303] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 09/18/2020] [Indexed: 06/11/2023]
Abstract
While many single-cell approaches have been developed to measure secretions from anchorage-independent cells, these protocols cannot be applied to adherent cells, especially when these cells require to be cultured in 3D formats. Here, a platform to measure secretions from individual spheroids of human mesenchymal stem cells, cultured within microfluidic droplets is introduced. The platform allows to quantify the secretions from hundreds of individual spheroids in each device, by using a secondary droplet to bring functionalized micro-beads in proximity to each spheroid. Vascular endothelial growth factor (VEGF-A) is measured on and a broad distribution of secretion levels within the population of spheroids is observed. The intra-cellular level of VEGF-A on each spheroid, measured through immuno-staining, correlates well with the extra-cellular measurement, indicating that the heterogeneities observed at the spheroid level result from variations at the intra-cellular level. Further, the molecular accumulation within the droplets is modeled and it is found that physical confinement is crucial for measurements of protein secretions. The model predicts that the time to achieve a measurement scales with droplet volume. These first measurements of secretions from individual spheroids provide several new biological and technological insights.
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Affiliation(s)
- Adrien Saint-Sardos
- LadHyX & Department of Mechanics, Ecole Polytechnique, CNRS-UMR 7646, Palaiseau, Cedex, 91128, France
- Physical Microfluidics and Bioengineering, Department of Genomes and Genetics, Institut Pasteur, Paris, 75015, France
| | - Sébastien Sart
- Physical Microfluidics and Bioengineering, Department of Genomes and Genetics, Institut Pasteur, Paris, 75015, France
| | - Kevin Lippera
- LadHyX & Department of Mechanics, Ecole Polytechnique, CNRS-UMR 7646, Palaiseau, Cedex, 91128, France
| | | | - Sébastien Michelin
- LadHyX & Department of Mechanics, Ecole Polytechnique, CNRS-UMR 7646, Palaiseau, Cedex, 91128, France
| | - Gabriel Amselem
- LadHyX & Department of Mechanics, Ecole Polytechnique, CNRS-UMR 7646, Palaiseau, Cedex, 91128, France
| | - Charles N Baroud
- LadHyX & Department of Mechanics, Ecole Polytechnique, CNRS-UMR 7646, Palaiseau, Cedex, 91128, France
- Physical Microfluidics and Bioengineering, Department of Genomes and Genetics, Institut Pasteur, Paris, 75015, France
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27
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Akther F, Yakob SB, Nguyen NT, Ta HT. Surface Modification Techniques for Endothelial Cell Seeding in PDMS Microfluidic Devices. BIOSENSORS 2020; 10:E182. [PMID: 33228050 PMCID: PMC7699314 DOI: 10.3390/bios10110182] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 11/13/2020] [Accepted: 11/15/2020] [Indexed: 12/14/2022]
Abstract
Microfluidic lab-on-a-chip cell culture techniques have been gaining popularity by offering the possibility of reducing the amount of samples and reagents and greater control over cellular microenvironment. Polydimethylsiloxane (PDMS) is the commonly used polymer for microfluidic cell culture devices because of the cheap and easy fabrication techniques, non-toxicity, biocompatibility, high gas permeability, and optical transparency. However, the intrinsic hydrophobic nature of PDMS makes cell seeding challenging when applied on PDMS surface. The hydrophobicity of the PDMS surface also allows the non-specific absorption/adsorption of small molecules and biomolecules that might affect the cellular behaviour and functions. Hydrophilic modification of PDMS surface is indispensable for successful cell seeding. This review collates different techniques with their advantages and disadvantages that have been used to improve PDMS hydrophilicity to facilitate endothelial cells seeding in PDMS devices.
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Affiliation(s)
- Fahima Akther
- Australian Institute for Bioengineering and Nanotechnology, the University of Queensland, Brisbane, QLD 4072, Australia;
- Queensland Micro-and Nanotechnology Centre, Griffith University, Brisbane, QLD 4111, Australia;
| | - Shazwani Binte Yakob
- School of Pharmacy, the University of Queensland, Brisbane, QLD 4102, Australia;
| | - Nam-Trung Nguyen
- Queensland Micro-and Nanotechnology Centre, Griffith University, Brisbane, QLD 4111, Australia;
| | - Hang T. Ta
- Australian Institute for Bioengineering and Nanotechnology, the University of Queensland, Brisbane, QLD 4072, Australia;
- Queensland Micro-and Nanotechnology Centre, Griffith University, Brisbane, QLD 4111, Australia;
- School of Environment and Science, Griffith University, Brisbane, QLD 4111, Australia
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28
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LaBelle CA, Massaro A, Cortés-Llanos B, Sims CE, Allbritton NL. Image-Based Live Cell Sorting. Trends Biotechnol 2020; 39:613-623. [PMID: 33190968 DOI: 10.1016/j.tibtech.2020.10.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 10/13/2020] [Accepted: 10/14/2020] [Indexed: 12/11/2022]
Abstract
Technologies capable of cell separation based on cell images provide powerful tools enabling cell selection criteria that rely on spatially or temporally varying properties. Image-based cell sorting (IBCS) systems utilize microfluidic or microarray platforms, each having unique characteristics and applications. The advent of IBCS marks a new paradigm in which cell phenotype and behavior can be explored with high resolution and tied to cellular physiological and omics data, providing a deeper understanding of single-cell physiology and the creation of cell lines with unique properties. Cell sorting guided by high-content image information has far-reaching implications in biomedical research, clinical medicine, and pharmaceutical development.
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Affiliation(s)
- Cody A LaBelle
- Joint Department of Biomedical Engineering, University of North Carolina, Chapel Hill, NC, and North Carolina State University, Raleigh, NC, USA; Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Angelo Massaro
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | | | - Christopher E Sims
- Department of Bioengineering, University of Washington, Seattle, WA, USA; Department of Medicine, University of Washington, Seattle, WA, USA
| | - Nancy L Allbritton
- Department of Bioengineering, University of Washington, Seattle, WA, USA.
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29
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Craig M, Jenner AL, Namgung B, Lee LP, Goldman A. Engineering in Medicine To Address the Challenge of Cancer Drug Resistance: From Micro- and Nanotechnologies to Computational and Mathematical Modeling. Chem Rev 2020; 121:3352-3389. [PMID: 33152247 DOI: 10.1021/acs.chemrev.0c00356] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Drug resistance has profoundly limited the success of cancer treatment, driving relapse, metastasis, and mortality. Nearly all anticancer drugs and even novel immunotherapies, which recalibrate the immune system for tumor recognition and destruction, have succumbed to resistance development. Engineers have emerged across mechanical, physical, chemical, mathematical, and biological disciplines to address the challenge of drug resistance using a combination of interdisciplinary tools and skill sets. This review explores the developing, complex, and under-recognized role of engineering in medicine to address the multitude of challenges in cancer drug resistance. Looking through the "lens" of intrinsic, extrinsic, and drug-induced resistance (also referred to as "tolerance"), we will discuss three specific areas where active innovation is driving novel treatment paradigms: (1) nanotechnology, which has revolutionized drug delivery in desmoplastic tissues, harnessing physiochemical characteristics to destroy tumors through photothermal therapy and rationally designed nanostructures to circumvent cancer immunotherapy failures, (2) bioengineered tumor models, which have benefitted from microfluidics and mechanical engineering, creating a paradigm shift in physiologically relevant environments to predict clinical refractoriness and enabling platforms for screening drug combinations to thwart resistance at the individual patient level, and (3) computational and mathematical modeling, which blends in silico simulations with molecular and evolutionary principles to map mutational patterns and model interactions between cells that promote resistance. On the basis that engineering in medicine has resulted in discoveries in resistance biology and successfully translated to clinical strategies that improve outcomes, we suggest the proliferation of multidisciplinary science that embraces engineering.
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Affiliation(s)
- Morgan Craig
- Department of Mathematics and Statistics, University of Montreal, Montreal, Quebec H3C 3J7, Canada.,Sainte-Justine University Hospital Research Centre, Montreal, Quebec H3S 2G4, Canada
| | - Adrianne L Jenner
- Department of Mathematics and Statistics, University of Montreal, Montreal, Quebec H3C 3J7, Canada.,Sainte-Justine University Hospital Research Centre, Montreal, Quebec H3S 2G4, Canada
| | - Bumseok Namgung
- Division of Engineering in Medicine, Brigham and Women's Hospital, Boston, Massachusetts 02115, United States.,Department of Medicine, Harvard Medical School, Boston, Massachusetts 02139, United States
| | - Luke P Lee
- Division of Engineering in Medicine, Brigham and Women's Hospital, Boston, Massachusetts 02115, United States.,Department of Medicine, Harvard Medical School, Boston, Massachusetts 02139, United States
| | - Aaron Goldman
- Division of Engineering in Medicine, Brigham and Women's Hospital, Boston, Massachusetts 02115, United States.,Department of Medicine, Harvard Medical School, Boston, Massachusetts 02139, United States
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30
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Schuster B, Junkin M, Kashaf SS, Romero-Calvo I, Kirby K, Matthews J, Weber CR, Rzhetsky A, White KP, Tay S. Automated microfluidic platform for dynamic and combinatorial drug screening of tumor organoids. Nat Commun 2020; 11:5271. [PMID: 33077832 PMCID: PMC7573629 DOI: 10.1038/s41467-020-19058-4] [Citation(s) in RCA: 187] [Impact Index Per Article: 46.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 09/25/2020] [Indexed: 12/13/2022] Open
Abstract
Three-dimensional (3D) cell culture technologies, such as organoids, are physiologically relevant models for basic and clinical applications. Automated microfluidics offers advantages in high-throughput and precision analysis of cells but is not yet compatible with organoids. Here, we present an automated, high-throughput, microfluidic 3D organoid culture and analysis system to facilitate preclinical research and personalized therapies. Our system provides combinatorial and dynamic drug treatments to hundreds of cultures and enables real-time analysis of organoids. We validate our system by performing individual, combinatorial, and sequential drug screens on human-derived pancreatic tumor organoids. We observe significant differences in the response of individual patient-based organoids to drug treatments and find that temporally-modified drug treatments can be more effective than constant-dose monotherapy or combination therapy in vitro. This integrated platform advances organoids models to screen and mirror real patient treatment courses with potential to facilitate treatment decisions for personalized therapy. The use of organoids in personalized medicine is promising but high throughput platforms are needed. Here the authors develop an automated, high-throughput, microfluidic 3D organoid culture system that allows combinatorial and dynamic drug treatments and real-time analysis of organoids.
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Affiliation(s)
- Brooke Schuster
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, IL, 60637, USA.,Institute for Genomics and Systems Biology, The University of Chicago, Chicago, IL, 60637, USA.,Department of Chemistry, The University of Chicago, Chicago, IL, 60637, USA
| | - Michael Junkin
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, IL, 60637, USA.,Institute for Genomics and Systems Biology, The University of Chicago, Chicago, IL, 60637, USA
| | - Sara Saheb Kashaf
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, IL, 60637, USA.,Institute for Genomics and Systems Biology, The University of Chicago, Chicago, IL, 60637, USA
| | - Isabel Romero-Calvo
- Institute for Genomics and Systems Biology, The University of Chicago, Chicago, IL, 60637, USA
| | - Kori Kirby
- Institute for Genomics and Systems Biology, The University of Chicago, Chicago, IL, 60637, USA
| | - Jonathan Matthews
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, IL, 60637, USA.,Institute for Genomics and Systems Biology, The University of Chicago, Chicago, IL, 60637, USA
| | - Christopher R Weber
- Department of Pathology, The University of Chicago Medicine, Chicago, IL, 60637, USA
| | - Andrey Rzhetsky
- Institute for Genomics and Systems Biology, The University of Chicago, Chicago, IL, 60637, USA.,Committee on Genetics, Genomics and Systems Biology, Departments of Medicine and Human Genetics, The University of Chicago, Chicago, IL, 60637, USA
| | - Kevin P White
- Institute for Genomics and Systems Biology, The University of Chicago, Chicago, IL, 60637, USA.,Tempus Labs, Chicago, IL, 60654, USA
| | - Savaş Tay
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, IL, 60637, USA. .,Institute for Genomics and Systems Biology, The University of Chicago, Chicago, IL, 60637, USA.
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31
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Gene-Specific Linear Trends Constrain Transcriptional Variability of the Toll-like Receptor Signaling. Cell Syst 2020; 11:300-314.e8. [PMID: 32918862 PMCID: PMC7521480 DOI: 10.1016/j.cels.2020.08.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 04/08/2020] [Accepted: 08/06/2020] [Indexed: 12/13/2022]
Abstract
Single-cell gene expression is inherently variable, but how this variability is controlled in response to stimulation remains unclear. Here, we use single-cell RNA-seq and single-molecule mRNA counting (smFISH) to study inducible gene expression in the immune toll-like receptor system. We show that mRNA counts of tumor necrosis factor α conform to a standard stochastic switch model, while transcription of interleukin-1β involves an additional regulatory step resulting in increased heterogeneity. Despite different modes of regulation, systematic analysis of single-cell data for a range of genes demonstrates that the variability in transcript count is linearly constrained by the mean response over a range of conditions. Mathematical modeling of smFISH counts and experimental perturbation of chromatin state demonstrates that linear constraints emerge through modulation of transcriptional bursting along with gene-specific relationships. Overall, our analyses demonstrate that the variability of the inducible single-cell mRNA response is constrained by transcriptional bursting. Single-cell TNF-α and IL-1β mRNA responses are differentially controlled Variability of TLR-induced responses scale linearly with mean mRNA counts Gene-specific constraints emerge via modulation of transcriptional bursting Chromatin state regulates transcriptional bursting of IL-1β
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32
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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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33
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Jammes FC, Maerkl SJ. How single-cell immunology is benefiting from microfluidic technologies. MICROSYSTEMS & NANOENGINEERING 2020; 6:45. [PMID: 34567657 PMCID: PMC8433390 DOI: 10.1038/s41378-020-0140-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 01/14/2020] [Accepted: 01/25/2020] [Indexed: 05/03/2023]
Abstract
The immune system is a complex network of specialized cells that work in concert to protect against invading pathogens and tissue damage. Imbalances in this network often result in excessive or absent immune responses leading to allergies, autoimmune diseases, and cancer. Many of the mechanisms and their regulation remain poorly understood. Immune cells are highly diverse, and an immune response is the result of a large number of molecular and cellular interactions both in time and space. Conventional bulk methods are often prone to miss important details by returning population-averaged results. There is a need in immunology to measure single cells and to study the dynamic interplay of immune cells with their environment. Advances in the fields of microsystems and microengineering gave rise to the field of microfluidics and its application to biology. Microfluidic systems enable the precise control of small volumes in the femto- to nanoliter range. By controlling device geometries, surface chemistry, and flow behavior, microfluidics can create a precisely defined microenvironment for single-cell studies with spatio-temporal control. These features are highly desirable for single-cell analysis and have made microfluidic devices useful tools for studying complex immune systems. In addition, microfluidic devices can achieve high-throughput measurements, enabling in-depth studies of complex systems. Microfluidics has been used in a large panel of biological applications, ranging from single-cell genomics, cell signaling and dynamics to cell-cell interaction and cell migration studies. In this review, we give an overview of state-of-the-art microfluidic techniques, their application to single-cell immunology, their advantages and drawbacks, and provide an outlook for the future of single-cell technologies in research and medicine.
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Affiliation(s)
- Fabien C. Jammes
- Institute of Bioengineering, School of Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Sebastian J. Maerkl
- Institute of Bioengineering, School of Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
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34
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Yang L, George J, Wang J. Deep Profiling of Cellular Heterogeneity by Emerging Single-Cell Proteomic Technologies. Proteomics 2020; 20:e1900226. [PMID: 31729152 PMCID: PMC7225074 DOI: 10.1002/pmic.201900226] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 10/14/2019] [Indexed: 12/20/2022]
Abstract
The ability to comprehensively profile cellular heterogeneity in functional proteome is crucial in advancing the understanding of cell behavior, organism development, and disease mechanisms. Conventional bulk measurement by averaging the biological responses across a population often loses the information of cellular variations. Single-cell proteomic technologies are becoming increasingly important to understand and discern cellular heterogeneity. The well-established methods for single-cell protein analysis based on flow cytometry and fluorescence microscopy are limited by the low multiplexing ability owing to the spectra overlap of fluorophores for labeling antibodies. Recent advances in mass spectrometry (MS), microchip, and reiterative staining-based techniques for single-cell proteomics have enabled the evaluation of cellular heterogeneity with high throughput, increased multiplexity, and improved sensitivity. In this review, the principles, developments, advantages, and limitations of these advanced technologies in analysis of single-cell proteins, along with their biological applications to study cellular heterogeneity, are described. At last, the remaining challenges, possible strategies, and future opportunities that will facilitate the improvement and broad applications of single-cell proteomic technologies in cell biology and medical research are discussed.
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Affiliation(s)
- Liwei Yang
- Multiplex Biotechnology Laboratory, Department of Biomedical Engineering, State University of New York at Stony Brook, Stony Brook, NY 11794
| | - Justin George
- Department of Chemistry, State University of New York, University at Albany, Albany, NY 12222
| | - Jun Wang
- Multiplex Biotechnology Laboratory, Department of Biomedical Engineering, State University of New York at Stony Brook, Stony Brook, NY 11794
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35
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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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Chen P, Li S, Guo Y, Zeng X, Liu BF. A review on microfluidics manipulation of the extracellular chemical microenvironment and its emerging application to cell analysis. Anal Chim Acta 2020; 1125:94-113. [PMID: 32674786 DOI: 10.1016/j.aca.2020.05.065] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 05/22/2020] [Accepted: 05/26/2020] [Indexed: 12/22/2022]
Abstract
Spatiotemporal manipulation of extracellular chemical environments with simultaneous monitoring of cellular responses plays an essential role in exploring fundamental biological processes and expands our understanding of underlying mechanisms. Despite the rapid progress and promising successes in manipulation strategies, many challenges remain due to the small size of cells and the rapid diffusion of chemical molecules. Fortunately, emerging microfluidic technology has become a powerful approach for precisely controlling the extracellular chemical microenvironment, which benefits from its integration capacity, automation, and high-throughput capability, as well as its high resolution down to submicron. Here, we summarize recent advances in microfluidics manipulation of the extracellular chemical microenvironment, including the following aspects: i) Spatial manipulation of chemical microenvironments realized by convection flow-, diffusion-, and droplet-based microfluidics, and surface chemical modification; ii) Temporal manipulation of chemical microenvironments enabled by flow switching/shifting, moving/flowing cells across laminar flows, integrated microvalves/pumps, and droplet manipulation; iii) Spatiotemporal manipulation of chemical microenvironments implemented by a coupling strategy and open-space microfluidics; and iv) High-throughput manipulation of chemical microenvironments. Finally, we briefly present typical applications of the above-mentioned technical advances in cell-based analyses including cell migration, cell signaling, cell differentiation, multicellular analysis, and drug screening. We further discuss the future improvement of microfluidics manipulation of extracellular chemical microenvironments to fulfill the needs of biological and biomedical research and applications.
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Affiliation(s)
- Peng Chen
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Shunji Li
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Yiran Guo
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Xuemei Zeng
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Bi-Feng Liu
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China.
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Makaryan SZ, Cess CG, Finley SD. Modeling immune cell behavior across scales in cancer. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2020; 12:e1484. [PMID: 32129950 PMCID: PMC7317398 DOI: 10.1002/wsbm.1484] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 01/07/2020] [Accepted: 02/04/2020] [Indexed: 12/17/2022]
Abstract
Detailed, mechanistic models of immune cell behavior across multiple scales in the context of cancer provide clinically relevant insights needed to understand existing immunotherapies and develop more optimal treatment strategies. We highlight mechanistic models of immune cells and their ability to become activated and promote tumor cell killing. These models capture various aspects of immune cells: (a) single‐cell behavior by predicting the dynamics of intracellular signaling networks in individual immune cells, (b) multicellular interactions between tumor and immune cells, and (c) multiscale dynamics across space and different levels of biological organization. Computational modeling is shown to provide detailed quantitative insight into immune cell behavior and immunotherapeutic strategies. However, there are gaps in the literature, and we suggest areas where additional modeling efforts should be focused to more prominently impact our understanding of the complexities of the immune system in the context of cancer. This article is categorized under:Biological Mechanisms > Cell Signaling Models of Systems Properties and Processes > Mechanistic Models Models of Systems Properties and Processes > Cellular Models
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Affiliation(s)
- Sahak Z Makaryan
- Department of Biomedical Engineering, University of Southern California, Los Angeles, California, USA
| | - Colin G Cess
- Department of Biomedical Engineering, University of Southern California, Los Angeles, California, USA
| | - Stacey D Finley
- Department of Biomedical Engineering, Mork Family Department of Chemical Engineering and Materials Science, Department of Biological Sciences, University of Southern California, Los Angeles, California, USA
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38
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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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Ramji R, Alexander AF, Muñoz-Rojas AR, Kellman LN, Miller-Jensen K. Microfluidic platform enables live-cell imaging of signaling and transcription combined with multiplexed secretion measurements in the same single cells. Integr Biol (Camb) 2020; 11:142-153. [PMID: 31242304 DOI: 10.1093/intbio/zyz013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 04/18/2019] [Accepted: 05/16/2019] [Indexed: 01/17/2023]
Abstract
Innate immune cells, including macrophages and dendritic cells, protect the host from pathogenic assaults in part through secretion of a program of cytokines and chemokines (C/Cs). Cell-to-cell variability in C/C secretion appears to contribute to the regulation of the immune response, but the sources of secretion variability are largely unknown. To begin to track the biological sources that control secretion variability, we developed and validated a microfluidic device to integrate live-cell imaging of fluorescent reporter proteins with a single-cell assay of protein secretion. We used this device to image NF-κB RelA nuclear translocation dynamics and Tnf transcription dynamics in macrophages in response to stimulation with the bacterial component lipopolysaccharide (LPS), followed by quantification of secretion of TNF, CCL2, CCL3, and CCL5. We found that the timing of the initial peak of RelA signaling in part determined the relative level of TNF and CCL3 secretion, but not CCL2 and CCL5 secretion. Our results support evidence that differences in timing across cell processes partly account for cell-to-cell variability in downstream responses, but that other factors introduce variability at each biological step.
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Affiliation(s)
- Ramesh Ramji
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
| | - Amanda F Alexander
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
| | | | - Laura N Kellman
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
| | - Kathryn Miller-Jensen
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA.,Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT, USA
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Abstract
The existence of cellular heterogeneity and its central relevance to biological phenomena provides a strong rationale for a need for analytical methods that enable analysis at the single-cell level. Analysis of the genome and transcriptome is possible at the single-cell level, but the comprehensive interrogation of the proteome with this level of resolution remains challenging. Single-cell protein analysis tools are advancing rapidly, however, and providing insights into collections of proteins with great relevance to cell and disease biology. Here, we review single-cell protein analysis technologies and assess their advantages and limitations. The emerging technologies presented have the potential to reveal new insights into tumour heterogeneity and therapeutic resistance, elucidate mechanisms of immune response and immunotherapy, and accelerate drug discovery.
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Fan H, Zhang S, Li N, Fan P, Hu X, Liang K, Cheng X, Wu Y. Stable expression ratios of five pyroptosis-inducing cytokines in the spleen and thymus of mice showed potential immune regulation at the organ level. Lupus 2020; 29:290-302. [PMID: 32041506 DOI: 10.1177/0961203320903802] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
BACKGROUND The immune system is one of the most complex regulatory systems in the body and is essential for the maintenance of homeostasis. Despite recent breakthroughs in immunology, the regulation of the immune system and the etiology of autoimmune diseases such as lupus remain unclear. Systemic lupus erythematosus is a systemic autoimmune disease with abnormally and inconsistently expressed pro-inflammatory cytokines. Pyroptosis is a pro-inflammatory form of programmed cell death that is associated with systemic lupus erythematosus. The thymus and spleen are important immune organs involved in systemic lupus erythematosus. Therefore, this study investigated the difference in expression of pyroptosis-inducing pro-inflammatory cytokines between the spleen and thymus in lupus model mice and in control mice, to describe immune regulation at the organ level. OBJECTIVE To investigate differences in the expression of pyroptosis-inducing cytokines in the spleen and thymus and to explore immune regulatory networks at the organ level. METHODS Two groups of lupus mice and two groups of control mice were utilized for this study. Using the thymus and spleen of experimental animals, mRNA expression levels of five pyroptosis-inducing cytokines (interleukin 1β, interleukin 18, NLRP3, caspase-1 and TNF-α) were determined via quantitative polymerase chain reaction. In addition, tissue distribution of these cytokines was investigated via immunohistochemistry. RESULTS All five pyroptosis-inducing inflammatory cytokines showed higher expression in the spleen than in the thymus (p < 0.05). Moreover, the spleen/thymus expression ratios of all five pyroptosis-inducing cytokines were not statistically different between the four experimental groups. Expression of all five cytokines exhibited a stable ratio (spleen/thymus ratios). This distinctive stable spleen/thymus ratio was consistent in all four experimental groups. The stable spleen/thymus ratios of the five inflammatory cytokines were as follows: interleukin 1β (2.02 ± 0.9), interleukin 18 (2.07 ± 1.06), caspase-1 (1.93 ± 0.66), NLRP3 (3.14 ± 1.61) and TNF-α (3.16 ± 1.36). Immunohistochemical analysis showed the cytokines were mainly expressed in the red pulp region of the spleen and the medullary region of the thymus, where immune-activated cells aggregated. CONCLUSION The stable spleen/thymus expression ratios of pyroptosis-inducing cytokines indicated that immune organs exhibit strictly regulated functions to maintain immune homeostasis and adapt to the environment.
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Affiliation(s)
- H Fan
- Department of Dermatology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - S Zhang
- Department of Dermatology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - N Li
- Department of Dermatology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - P Fan
- Department of Dermatology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - X Hu
- Department of Dermatology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - K Liang
- Department of Dermatology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - X Cheng
- Department of Dermatology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Y Wu
- Department of Dermatology, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
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42
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Liu M, Jin M, Li L, Ji Y, Zhu F, Luo Y, Liu T, Lin B, Lu Y. PDMS Microwell Stencil Based Multiplexed Single‐Cell Secretion Analysis. Proteomics 2020; 20:e1900231. [DOI: 10.1002/pmic.201900231] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 11/13/2019] [Indexed: 11/05/2022]
Affiliation(s)
- Meimei Liu
- Department of Materials Science and EngineeringDalian Maritime University Dalian 116026 China
- Department of BiotechnologyDalian Institute of Chemical PhysicsChinese Academy of Sciences Dalian 116023 China
| | - Meihua Jin
- Department of Materials Science and EngineeringDalian Maritime University Dalian 116026 China
| | - Linmei Li
- Department of BiotechnologyDalian Institute of Chemical PhysicsChinese Academy of Sciences Dalian 116023 China
| | - Yahui Ji
- Department of BiotechnologyDalian Institute of Chemical PhysicsChinese Academy of Sciences Dalian 116023 China
| | - Fengjiao Zhu
- Department of BiotechnologyDalian Institute of Chemical PhysicsChinese Academy of Sciences Dalian 116023 China
| | - Yong Luo
- State Key Laboratory of Fine ChemicalsDepartment of Chemical EngineeringDalian University of Technology Dalian 116024 China
| | - Tingjiao Liu
- College of StomatologyDalian Medical University Dalian 116044 China
| | - Bingcheng Lin
- Department of BiotechnologyDalian Institute of Chemical PhysicsChinese Academy of Sciences Dalian 116023 China
| | - Yao Lu
- Department of BiotechnologyDalian Institute of Chemical PhysicsChinese Academy of Sciences Dalian 116023 China
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43
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Affiliation(s)
- Iulia M. Lazar
- Department of Biological Sciences, Academy of Integrated Sciences, Virginia Tech, Blacksburg, Virginia 24061, United States
- Carilion School of Medicine, Academy of Integrated Sciences, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Nicholas S. Gulakowski
- Systems Biology, Academy of Integrated Sciences, Virginia Tech, Blacksburg, Virginia 24061, United States
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44
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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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45
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Feng Y, Wang B, Tian Y, Chen H, Liu Y, Fan H, Wang K, Zhang C. Active fluidic chip produced using 3D-printing for combinatorial therapeutic screening on liver tumor spheroid. Biosens Bioelectron 2019; 151:111966. [PMID: 31999576 DOI: 10.1016/j.bios.2019.111966] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 11/19/2019] [Accepted: 12/13/2019] [Indexed: 12/12/2022]
Abstract
Known for their capabilities in automated fluid manipulation, microfluidic devices integrated with pneumatic valves are broadly used for researches in life science and clinical practice. The application is, however, hindered by the high cost and overly complex fabrication procedure. Here, we present an approach for fabricating molds of active fluidic devices using a benchtop 3D printer and a simple 2-step protocol (i.e. 3D printing and polishing). The entire workflow can be completed within 6 h, costing less than US$ 5 to produce all necessary templates for PDMS replica molding, which have smooth surface and round-shaped pneumatic valve structures. Moreover, 3D printing can create unique bespoke on-off objects of a wide range of dimensions. The millimeter- and centimeter-sized features allow examination of large-scale biological samples. Our results demonstrate that the 3D-printed active fluidic device has valve control capacities on par with those made by photolithography. Controlled nutrients and ligands delivery by on-off active valves allows generation of dynamic signals mimicking the ever-changing environmental stimuli, and combinatorial/sequential drug inputs for therapeutic screening on liver tumor spheroid. We believe that the proposed methodology can pave the way for integration of active fluidic systems in research labs, clinical settings and even household appliances for a broad range of application.
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Affiliation(s)
- Yibo Feng
- Institute of Photonics and Photon-Technology, State Key Laboratory of Cultivation Base for Photoelectric Technology and Functional Materials, Northwest University, 1 Xue Fu Avenue, Xi'an, 710127, Shaanxi, China
| | - Bingquan Wang
- Institute of Photonics and Photon-Technology, State Key Laboratory of Cultivation Base for Photoelectric Technology and Functional Materials, Northwest University, 1 Xue Fu Avenue, Xi'an, 710127, Shaanxi, China
| | - Yin Tian
- Laboratory of Stem Cell and Tissue Engineering, Chongqing Medical University, Chongqing, 400016, China
| | - Hao Chen
- College of Chemistry and Material Sciences, Northwest University, Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, Northwest University, 1 Xue Fu Avenue, Xi'an, 710127, Shaanxi, China
| | - Yonggang Liu
- Laboratory of Stem Cell and Tissue Engineering, Chongqing Medical University, Chongqing, 400016, China
| | - Haiming Fan
- College of Chemistry and Material Sciences, Northwest University, Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, Northwest University, 1 Xue Fu Avenue, Xi'an, 710127, Shaanxi, China
| | - Kaige Wang
- Institute of Photonics and Photon-Technology, State Key Laboratory of Cultivation Base for Photoelectric Technology and Functional Materials, Northwest University, 1 Xue Fu Avenue, Xi'an, 710127, Shaanxi, China
| | - Ce Zhang
- Institute of Photonics and Photon-Technology, State Key Laboratory of Cultivation Base for Photoelectric Technology and Functional Materials, Northwest University, 1 Xue Fu Avenue, Xi'an, 710127, Shaanxi, China.
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Pavillon N, Smith NI. Immune cell type, cell activation, and single cell heterogeneity revealed by label-free optical methods. Sci Rep 2019; 9:17054. [PMID: 31745140 PMCID: PMC6864054 DOI: 10.1038/s41598-019-53428-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 10/31/2019] [Indexed: 01/06/2023] Open
Abstract
Measurement techniques that allow the global analysis of cellular responses while retaining single-cell sensitivity are increasingly needed in order to understand complex and dynamic biological processes. In this context, compromises between sensitivity, degree of multiplexing, throughput, and invasiveness are often unavoidable. We present here a noninvasive optical approach that can retrieve quantitative biomarkers of both morphological and molecular phenotypes of individual cells, based on a combination of quantitative phase imaging and Raman spectroscopy measurements. We then develop generalized statistical tools to assess the influence of both controlled (cell sub-populations, immune stimulation) and uncontrolled (culturing conditions, animal variations, etc.) experimental parameters on the label-free biomarkers. These indicators can detect different macrophage cell sub-populations originating from different progenitors as well as their activation state, and how these changes are related to specific differences in morphology and molecular content. The molecular indicators also display further sensitivity that allow identification of other experimental conditions, such as differences between cells originating from different animals, allowing the detection of outlier behaviour from given cell sub-populations.
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Affiliation(s)
- Nicolas Pavillon
- Biophotonics Laboratory, Immunology Frontier Research Center (IFReC), Osaka University, Yamadaoka 3-1, 565-0871, Suita, Osaka, Japan.
| | - Nicholas I Smith
- Biophotonics Laboratory, Immunology Frontier Research Center (IFReC), Osaka University, Yamadaoka 3-1, 565-0871, Suita, Osaka, Japan.
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47
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Wei SC, Hsu MN, Chen CH. Plasmonic droplet screen for single-cell secretion analysis. Biosens Bioelectron 2019; 144:111639. [DOI: 10.1016/j.bios.2019.111639] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 08/11/2019] [Accepted: 08/26/2019] [Indexed: 01/16/2023]
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48
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Abdullah MAA, Wang J. Ultrasimple Single-Cell Detection of Multiple Cytokines by a Nanowell Chip Integrated with Encoded Microarrays. ACS Sens 2019; 4:2296-2302. [PMID: 31423780 DOI: 10.1021/acssensors.9b00765] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Cytokine production is often regarded as the marker of immune cells' activation status. The spectrum and temporal secretion of cytokines are dramatically varied between cell phenotypes and even within the same phenotype. Multiparameter analysis of individual immune cell's cytokine secretion has always been a challenging and complicated process that needs special facilities in a laboratory setting. Herein, we present an ultrasimple method with high sensitivity and high robustness to quantify cytokine expression at the single-cell resolution. A microchip is developed based on poly(dimethylsiloxane) nanowells on sticky tape, while each nanowell is integrated with a DNA-antibody convertible microarray. Only pipetting is needed for the whole single-cell analysis process. The sensitivity of the assay is evaluated by measuring various concentrations of six recombinant cytokine proteins, which was found comparable to conventional methods. Once single cells are loaded to nanowells and incubated there, a Fluorinert FC-40 is used to isolate nanowells; so, cytokines from those cells are captured by separate microarrays. The rest of the sandwich enzyme-linked immunosorbent assay detection process is also executed simply by pipetting of various reagents. This method is validated by measuring cytokine production from hundreds of single cells. It has simplified a typically sophisticated multiplex single-cell assay into an instrument-free, point-of-detection technology, and thus it may find a broad utility in clinical diagnostics.
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Affiliation(s)
- Mohammed A. A. Abdullah
- Multiplex Biotechnology Laboratory, Department of Chemistry, University at Albany, State University of New York, Albany, New York 12222, United States
| | - Jun Wang
- Multiplex Biotechnology Laboratory, Department of Chemistry, University at Albany, State University of New York, Albany, New York 12222, United States
- Cancer Research Center, University at Albany, State University of New York, Rensselaer, New York 12144, United States
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49
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Muldoon JJ, Yu JS, Fassia MK, Bagheri N. Network inference performance complexity: a consequence of topological, experimental and algorithmic determinants. Bioinformatics 2019; 35:3421-3432. [PMID: 30932143 PMCID: PMC6748731 DOI: 10.1093/bioinformatics/btz105] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 01/24/2019] [Accepted: 02/11/2019] [Indexed: 12/21/2022] Open
Abstract
MOTIVATION Network inference algorithms aim to uncover key regulatory interactions governing cellular decision-making, disease progression and therapeutic interventions. Having an accurate blueprint of this regulation is essential for understanding and controlling cell behavior. However, the utility and impact of these approaches are limited because the ways in which various factors shape inference outcomes remain largely unknown. RESULTS We identify and systematically evaluate determinants of performance-including network properties, experimental design choices and data processing-by developing new metrics that quantify confidence across algorithms in comparable terms. We conducted a multifactorial analysis that demonstrates how stimulus target, regulatory kinetics, induction and resolution dynamics, and noise differentially impact widely used algorithms in significant and previously unrecognized ways. The results show how even if high-quality data are paired with high-performing algorithms, inferred models are sometimes susceptible to giving misleading conclusions. Lastly, we validate these findings and the utility of the confidence metrics using realistic in silico gene regulatory networks. This new characterization approach provides a way to more rigorously interpret how algorithms infer regulation from biological datasets. AVAILABILITY AND IMPLEMENTATION Code is available at http://github.com/bagherilab/networkinference/. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Joseph J Muldoon
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL, USA
| | - Jessica S Yu
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA
| | - Mohammad-Kasim Fassia
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA
| | - Neda Bagheri
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, USA
- Northwestern Institute on Complex Systems, Northwestern University, Evanston, IL, USA
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50
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Abstract
Given the many cell types and molecular components of the human immune system, along with vast variations across individuals, how should we go about developing causal and predictive explanations of immunity? A central strategy in human studies is to leverage natural variation to find relationships among variables, including DNA variants, epigenetic states, immune phenotypes, clinical descriptors, and others. Here, we focus on how natural variation is used to find patterns, infer principles, and develop predictive models for two areas: (a) immune cell activation-how single-cell profiling boosts our ability to discover immune cell types and states-and (b) antigen presentation and recognition-how models can be generated to predict presentation of antigens on MHC molecules and their detection by T cell receptors. These are two examples of a shift in how we find the drivers and targets of immunity, especially in the human system in the context of health and disease.
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Affiliation(s)
- Alexandra-Chloé Villani
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.,Center for Immunology and Inflammatory Diseases, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts 02129, USA.,Harvard Medical School, Boston, Massachusetts 02115, USA;
| | - Siranush Sarkizova
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.,Harvard Medical School, Boston, Massachusetts 02115, USA; .,Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts 02142, USA
| | - Nir Hacohen
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.,Harvard Medical School, Boston, Massachusetts 02115, USA; .,Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
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