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Fathi M, Charley L, Cooper LJ, Varadarajan N, Meyer DD. Cytotoxic T lymphocytes targeting a conserved SARS-CoV-2 spike epitope are efficient serial killers. Biotechniques 2022; 72:113-120. [PMID: 35297693 PMCID: PMC8929396 DOI: 10.2144/btn-2022-0016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Understanding immune response to infections and vaccines lags understanding humoral responses. While neutralizing antibody responses wane over time, T cells are instrumental in long-term immunity. We apply machine learning and time-lapse imaging microscopy in nanowell grids (TIMING) to study thousands of videos of T cells with specificity for SARS-CoV-2 eliminating targets bearing spike protein as a surrogate for viral infection. The data on effector functions, including cytokine secretion and cytotoxicity, provide the first direct evidence that cytotoxic T lymphocytes from a convalescent patient targeting an epitope conserved across all known variants of concern are serial killers capable of eliminating multiple infected target cells. These data have implications for vaccine development and for the recovery and monitoring of infected individuals. We loaded target cells expressing spike protein, SARS-CoV-2-specific HLA A2-restricted cytotoxic T cells, and beads functionalized with antibodies against IFN-γ onto nanowell arrays. We acquired images of the nanoarray for 8 h at 5-min intervals using an epifluorescent microscope and processed the images using machine learning algorithms for the tracking and segmentation of cells. Artificial intelligence-powered time-lapse imaging microscopy in nanowell grids assays show SARS-CoV-2 T cells are serial killers.
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Affiliation(s)
| | | | | | - Navin Varadarajan
- CellChorus, Inc., Houston, TX 77023, USA.,Department of Chemical & Biomolecular Engineering, University of Houston, Houston, TX 77204, USA
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Fathi M, Charley L, Cooper LJN, Varadarajan N, Meyer D. Cytotoxic T lymphocytes targeting a conserved SARS-CoV-2 spike epitope are efficient serial killers. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.01.24.477535. [PMID: 35118465 PMCID: PMC8811896 DOI: 10.1101/2022.01.24.477535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
UNLABELLED Understanding the cellular immune response to infections, cancers and vaccines lags behind the investigation of humoral responses. While neutralizing antibody responses wane over time, the ability of T cells to recognize viruses including SARS-CoV-2 is instrumental to providing long-term immunity. Although T-cell receptor (TCR) repertoire screening can provide insights into the skewing of a T-cell response elicited upon vaccination or infection, they unfortunately provide no assessment into the functional capacity of T cells or their ability to eliminate virally infected targets. We have used time-lapse imaging microscopy in nanowell grids (TIMING) to integrate the migration of individual T cells with analysis of effector functions including cytokine secretion and cytotoxicity. Machine learning is then applied to study thousands of videos of dynamic interactions as T cells with specificity for SARS-CoV-2 eliminate targets bearing spike protein as a surrogate for viral infection. Our data provide the first direct evidence that cytotoxic T lymphocytes from a convalescent patient targeting an epitope conserved across all known variants of concern (VoC) are serial killers capable of eliminating multiple infected targets. These data have implications for development of vaccines to provide broad and sustained cellular immunity and for the recovery and monitoring of individuals who have been exposed to SARS-CoV-2. MULTIDISCIPLINARY ABSTRACT We present an imaging platform that uses artificial intelligence (AI) to track thousands of individual cell-cell interactions within nanowell arrays. We apply this platform to quantify how the T cell component of adaptive immunity responds to infections. Our results show that T cells specific for a conserved epitope within the SARS-CoV-2 spike protein are serial killers that can rapidly eliminate virally infected targets. The ability to map the functional capacity of T cells and their ability to kill infected cells provides fundamental insights into the immunology of vaccines and recovery from infections.
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Xie H, Appelt JW, Jenkins RW. Going with the Flow: Modeling the Tumor Microenvironment Using Microfluidic Technology. Cancers (Basel) 2021; 13:cancers13236052. [PMID: 34885161 PMCID: PMC8656483 DOI: 10.3390/cancers13236052] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 11/20/2021] [Accepted: 11/25/2021] [Indexed: 12/12/2022] Open
Abstract
Simple Summary The clinical success of cancer immunotherapy targeting immune checkpoints (e.g., PD-1, CTLA-4) has ushered in a new era of cancer therapeutics aimed at promoting antitumor immunity in hopes of offering durable clinical responses for patients with advanced, metastatic cancer. This success has also reinvigorated interest in developing tumor model systems that recapitulate key features of antitumor immune responses to complement existing in vivo tumor models. Patient-derived tumor models have emerged in recent years to facilitate study of tumor–immune dynamics. Microfluidic technology has enabled development of microphysiologic systems (MPSs) for the evaluation of the tumor microenvironment, which have shown early promise in studying tumor–immune dynamics. Further development of microfluidic-based “tumor-on-a-chip” MPSs to study tumor–immune interactions may overcome several key challenges currently facing tumor immunology. Abstract Recent advances in cancer immunotherapy have led a paradigm shift in the treatment of multiple malignancies with renewed focus on the host immune system and tumor–immune dynamics. However, intrinsic and acquired resistance to immunotherapy limits patient benefits and wider application. Investigations into the mechanisms of response and resistance to immunotherapy have demonstrated key tumor-intrinsic and tumor-extrinsic factors. Studying complex interactions with multiple cell types is necessary to understand the mechanisms of response and resistance to cancer therapies. The lack of model systems that faithfully recapitulate key features of the tumor microenvironment (TME) remains a challenge for cancer researchers. Here, we review recent advances in TME models focusing on the use of microfluidic technology to study and model the TME, including the application of microfluidic technologies to study tumor–immune dynamics and response to cancer therapeutics. We also discuss the limitations of current systems and suggest future directions to utilize this technology to its highest potential.
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Affiliation(s)
- Hongyan Xie
- Massachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA; (H.X.); (J.W.A.)
| | - Jackson W. Appelt
- Massachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA; (H.X.); (J.W.A.)
| | - Russell W. Jenkins
- Massachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA; (H.X.); (J.W.A.)
- Laboratory of Systems Pharmacology, Harvard Program in Therapeutic Sciences, Harvard Medical School, Boston, MA 02215, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Correspondence: ; Tel.: +617-726-9372; Fax: +844-542-5959
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Briones J, Espulgar W, Koyama S, Takamatsu H, Tamiya E, Saito M. The future of microfluidics in immune checkpoint blockade. Cancer Gene Ther 2021; 28:895-910. [PMID: 33110208 DOI: 10.1038/s41417-020-00248-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 10/02/2020] [Accepted: 10/09/2020] [Indexed: 01/30/2023]
Abstract
Recent advances in microfluidic techniques have enabled researchers to study sensitivities to immune checkpoint therapy, to determine patients' response to particular antibody treatment. Utilization of this technology is helpful in antibody discovery and in the design of personalized medicine. A variety of microfluidic approaches can provide several functions in processes such as immunologic, genomic, and/or transcriptomic analysis with the aim of improving the efficacy and coverage of immunotherapy, particularly immune checkpoint blockade (ICB). To achieve this requires researchers to overcome the challenges in the current state of the technology. This review looks into the advancements in microfluidic technologies applied to researches on immune checkpoint blockade treatment and its potential shift from proof-of-principle stage to clinical application.
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Affiliation(s)
- Jonathan Briones
- Graduate School of Engineering, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Wilfred Espulgar
- Graduate School of Engineering, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Shohei Koyama
- Graduate School of Medicine, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Hyota Takamatsu
- Graduate School of Medicine, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Eiichi Tamiya
- AIST PhotoBIO-OIL, Osaka University, Suita, Osaka, 565-0871, Japan.,The Institute of Scientific and Industrial Research, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Masato Saito
- Graduate School of Engineering, Osaka University, Suita, Osaka, 565-0871, Japan. .,AIST PhotoBIO-OIL, Osaka University, Suita, Osaka, 565-0871, Japan.
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A design and optimization of a high throughput valve based microfluidic device for single cell compartmentalization and analysis. Sci Rep 2021; 11:12995. [PMID: 34155296 PMCID: PMC8217553 DOI: 10.1038/s41598-021-92472-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 06/08/2021] [Indexed: 12/04/2022] Open
Abstract
The need for high throughput single cell screening platforms has been increasing with advancements in genomics and proteomics to identify heterogeneity, unique cell subsets or super mutants from thousands of cells within a population. For real-time monitoring of enzyme kinetics and protein expression profiling, valve-based microfluidics or pneumatic valving that can compartmentalize single cells is advantageous by providing on-demand fluid exchange capability for several steps in assay protocol and on-chip culturing. However, this technique is throughput limited by the number of compartments in the array. Thus, one big challenge lies in increasing the number of microvalves to several thousand that can be actuated in the microfluidic device to confine enzymes and substrates in picoliter volumes. This work explores the design and optimizations done on a microfluidic platform to achieve high-throughput single cell compartmentalization as applied to single-cell enzymatic assay for protein expression quantification. Design modeling through COMSOL Multiphysics was utilized to determine the circular microvalve’s optimized parameters, which can close thousands of microchambers in an array at lower sealing pressure. Multiphysical modeling results demonstrated the relationships of geometry, valve dimensions, and sealing pressure, which were applied in the fabrication of a microfluidic device comprising of up to 5000 hydrodynamic traps and corresponding microvalves. Comparing the effects of geometry, actuation media and fabrication technique, a sealing pressure as low as 0.04 MPa was achieved. Applying to single cell enzymatic assay, variations in granzyme B activity in Jurkat and human PBMC cells were observed. Improvement in the microfluidic chip’s throughput is significant in single cell analysis applications, especially in drug discovery and treatment personalization.
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Desalvo A, Bateman F, James E, Morgan H, Elliott T. Time-resolved microwell cell-pairing array reveals multiple T cell activation profiles. LAB ON A CHIP 2020; 20:3772-3783. [PMID: 32902549 DOI: 10.1039/d0lc00628a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The differences in behaviour between individual cells in a large population are often important, yet are masked in bulk analyses where only average parameters are measured. One unresolved question in the field of immunology is the extent to which important immunological phenomena such as immunodominance to cancer antigens correlates with the average activity of a population of antigen-specific T lymphocytes, or with the activity of individual "outlier" cells. Despite progress in single cell technologies, few platforms are available that can deliver time-resolved, functional analysis at single cell resolution, for these investigations. We have developed an accessible high-throughput platform to measure single T cell signalling in real time following time-controlled stimulation by live antigen presenting cells. The cell-trap array consists of thousands of individual microwells cast in an agarose block, which is biocompatible and permeable to nutrients. Single T cells are isolated in wells via passive sedimentation and size exclusion, achieving up to 90% occupancy. The device enables simultaneous activation of thousands of single CD8+ cells. Stimulation with soluble reagents (ionomycin, anti-CD3 antibodies) or antigen presenting cells leads to changes in intracellular calcium concentrations which were measured using calcium-chelating fluorophore dyes. The platform was used to demonstrate a range of activation profiles among individual cells of a cloned, antigen specific CD8+ T cell hybridoma in response to both nonspecific stimuli and specific, physiologically relevant antigen stimulation. The presence of two different activation profiles was demonstrated, together with rare outlier behaviour among cells that are essentially clonal.
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Affiliation(s)
- Anna Desalvo
- Centre for Cancer Immunology, University of Southampton, Southampton, UK.
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Briones JC, Espulgar WV, Koyama S, Yoshikawa H, Park J, Naito Y, Kumanogoh A, Tamiya E, Takamatsu H, Saito M. A Microfluidic Platform for Single Cell Fluorometric Granzyme B Profiling. Theranostics 2020; 10:123-132. [PMID: 31903110 PMCID: PMC6929635 DOI: 10.7150/thno.37728] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 07/24/2019] [Indexed: 12/19/2022] Open
Abstract
Granzyme B (GrB) is an essential cytotoxic effector in cancer immunotherapy as it can be a potential biomarker to predict the efficacy of immunotherapies including checkpoint inhibitors. Monitoring the Granzyme B activity in cells would help determine a patient's clinical response to treatment and lead to better treatment strategies by preventing administration of ineffective therapies and avoid adverse events resulting in a delay in subsequent treatment. Methods: A microfluidic device with hydrodynamic traps and pneumatic valving system was fabricated using photo and soft lithography. Single cell Granzyme B (GrB) activity was detected and measured fluorometrically using a commercial assay kit with a peptide substrate containing GrB recognition sequence (Ac-IEPD-AFC) and AFC (7-Amino-4-trifluoromethylcoumarin) label. Fluorescence was observed and measured using a confocal microscope with CSU-W1 scanner unit and CCD camera as well as an inverted microscope with photodetector. Model cells (NK-92, GrB-transduced Jurkat, and THP1 cells) and human PBMCs from healthy donor and lung cancer patients including an anti-PD-1 antibody treated patient were profiled of its GrB activity as proof of concept. Results: GrB expression from the model cells was found to be markedly different. NK-92 cells were found to have higher GrB activity than the GrB-transduced Jurkat cells. THP-1 was found to have relatively no significant activity. A marked increase in GrB expression was also observed in anti-PD-1 treated lung cancer patient sample in comparison to PBMC from a healthy donor. TCR+ Ig-G4+ PBMC cells were found to have high activity which signifies a clear response to PD-1 blockade. Conclusion: As proof of concept, we have shown the capability of a microfluidic platform to measure GrB production through a single cell enzymatic activity assay. Our platform might be a promising tool for evaluating the sensitivity of immunotherapies and identifying specific T cell subset responsible for the anti-tumor response.
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Editorial overview - Biological engineering: Emerging strategies to understand & engineer the human immune system. Curr Opin Chem Eng 2018. [DOI: 10.1016/j.coche.2018.02.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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