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This S, Costantino S, Melichar HJ. Machine learning predictions of T cell antigen specificity from intracellular calcium dynamics. SCIENCE ADVANCES 2024; 10:eadk2298. [PMID: 38446885 PMCID: PMC10917351 DOI: 10.1126/sciadv.adk2298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 01/29/2024] [Indexed: 03/08/2024]
Abstract
Adoptive T cell therapies rely on the production of T cells with an antigen receptor that directs their specificity toward tumor-specific antigens. Methods for identifying relevant T cell receptor (TCR) sequences, predominantly achieved through the enrichment of antigen-specific T cells, represent a major bottleneck in the production of TCR-engineered cell therapies. Fluctuation of intracellular calcium is a proximal readout of TCR signaling and candidate marker for antigen-specific T cell identification that does not require T cell expansion; however, calcium fluctuations downstream of TCR engagement are highly variable. We propose that machine learning algorithms may allow for T cell classification from complex datasets such as polyclonal T cell signaling events. Using deep learning tools, we demonstrate accurate prediction of TCR-transgenic CD8+ T cell activation based on calcium fluctuations and test the algorithm against T cells bearing a distinct TCR as well as polyclonal T cells. This provides the foundation for an antigen-specific TCR sequence identification pipeline for adoptive T cell therapies.
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Affiliation(s)
- Sébastien This
- Centre de recherche de l'Hôpital Maisonneuve-Rosemont, Montréal, Québec, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, Québec, Canada
- Department of Microbiology and Immunology, Goodman Cancer Institute, McGill University, Montréal, Québec, Canada
| | - Santiago Costantino
- Centre de recherche de l'Hôpital Maisonneuve-Rosemont, Montréal, Québec, Canada
- Département d’Ophtalmologie, Université de Montréal, Montréal, Québec, Canada
| | - Heather J. Melichar
- Centre de recherche de l'Hôpital Maisonneuve-Rosemont, Montréal, Québec, Canada
- Department of Microbiology and Immunology, Goodman Cancer Institute, McGill University, Montréal, Québec, Canada
- Département de Médecine, Université de Montréal, Montréal, Québec, Canada
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Kempster C, Butler G, Kuznecova E, Taylor KA, Kriek N, Little G, Sowa MA, Sage T, Johnson LJ, Gibbins JM, Pollitt AY. Fully automated platelet differential interference contrast image analysis via deep learning. Sci Rep 2022; 12:4614. [PMID: 35301400 PMCID: PMC8931011 DOI: 10.1038/s41598-022-08613-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 03/08/2022] [Indexed: 11/12/2022] Open
Abstract
Platelets mediate arterial thrombosis, a leading cause of myocardial infarction and stroke. During injury, platelets adhere and spread over exposed subendothelial matrix substrates of the damaged blood vessel wall. The mechanisms which govern platelet activation and their interaction with a range of substrates are therefore regularly investigated using platelet spreading assays. These assays often use differential interference contrast (DIC) microscopy to assess platelet morphology and analysis performed using manual annotation. Here, a convolutional neural network (CNN) allowed fully automated analysis of platelet spreading assays captured by DIC microscopy. The CNN was trained using 120 generalised training images. Increasing the number of training images increases the mean average precision of the CNN. The CNN performance was compared to six manual annotators. Significant variation was observed between annotators, highlighting bias when manual analysis is performed. The CNN effectively analysed platelet morphology when platelets spread over a range of substrates (CRP-XL, vWF and fibrinogen), in the presence and absence of inhibitors (dasatinib, ibrutinib and PRT-060318) and agonist (thrombin), with results consistent in quantifying spread platelet area which is comparable to published literature. The application of a CNN enables, for the first time, automated analysis of platelet spreading assays captured by DIC microscopy.
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Affiliation(s)
- Carly Kempster
- School of Biological Sciences, University of Reading, Reading, UK
| | - George Butler
- School of Biological Sciences, University of Reading, Reading, UK.,The Brady Urological Institute, Johns Hopkins School of Medicine, Baltimore, USA
| | - Elina Kuznecova
- School of Biological Sciences, University of Reading, Reading, UK
| | - Kirk A Taylor
- School of Biological Sciences, University of Reading, Reading, UK
| | - Neline Kriek
- School of Biological Sciences, University of Reading, Reading, UK
| | - Gemma Little
- School of Biological Sciences, University of Reading, Reading, UK
| | - Marcin A Sowa
- School of Biological Sciences, University of Reading, Reading, UK
| | - Tanya Sage
- School of Biological Sciences, University of Reading, Reading, UK
| | - Louise J Johnson
- School of Biological Sciences, University of Reading, Reading, UK
| | | | - Alice Y Pollitt
- School of Biological Sciences, University of Reading, Reading, UK.
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