1
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Zhao J, Wang Z, Tian Y, Ning J, Ye H. T cell exhaustion and senescence for ovarian cancer immunotherapy. Semin Cancer Biol 2024; 104-105:1-15. [PMID: 39032717 DOI: 10.1016/j.semcancer.2024.07.001] [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: 05/16/2024] [Revised: 06/30/2024] [Accepted: 07/09/2024] [Indexed: 07/23/2024]
Abstract
Ovarian cancer is a common gynecological malignancy, and its treatment remains challenging. Although ovarian cancer may respond to immunotherapy because of endogenous immunity at the molecular or T cell level, immunotherapy has so far not had the desired effect. The functional status of preexisting T cells is an indispensable determinant of powerful antitumor immunity and immunotherapy. T cell exhaustion and senescence are two crucial states of T cell dysfunction, which share some overlapping phenotypic and functional features, but each status possesses unique molecular and developmental signatures. It has been widely accepted that exhaustion and senescence of T cells are important strategies for cancer cells to evade immunosurveillance and maintain the immunosuppressive microenvironment. Herein, this review summarizes the phenotypic and functional features of exhaust and senescent T cells, and describes the key drivers of the two T cell dysfunctional states in the tumor microenvironment and their functional roles in ovarian cancer. Furthermore, we present a summary of the molecular machinery and signaling pathways governing T cell exhaustion and senescence. Possible strategies that can prevent and/or reverse T cell dysfunction are also explored. An in-depth understanding of exhausted and senescent T cells will provide novel strategies to enhance immunotherapy of ovarian cancer through redirecting tumor-specific T cells away from a dysfunctional developmental trajectory.
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Affiliation(s)
- Jiao Zhao
- Department of Gynecology Surgery 3, Cancer Hospital of Dalian University of Technology, Liaoning Cancer Hospital & Institute, Shenyang, Liaoning 110042, China
| | - Zhongmiao Wang
- Department of Digestive Diseases 1, Cancer Hospital of Dalian University of Technology, Liaoning Cancer Hospital & Institute, Shenyang, Liaoning 110042, China
| | - Yingying Tian
- Department of Oncology Radiotherapy 2, Qingdao Central Hospital, University of Health and Rehabilitation Sciences, Qingdao, Shandong 266042, China
| | - Jing Ning
- Department of General Internal Medicine (VIP Ward), Cancer Hospital of Dalian University of Technology, Liaoning Cancer Hospital & Institute, Shenyang, Liaoning 110042, China.
| | - Huinan Ye
- Department of Digestive Diseases 1, Cancer Hospital of Dalian University of Technology, Liaoning Cancer Hospital & Institute, Shenyang, Liaoning 110042, China.
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2
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Rezvan A, Romain G, Fathi M, Heeke D, Martinez-Paniagua M, An X, Bandey IN, Montalvo MJ, Adolacion JRT, Saeedi A, Sadeghi F, Fousek K, Puebla-Osorio N, Cooper LJN, Bernatchez C, Singh H, Ahmed N, Mattie M, Bot A, Neelapu S, Varadarajan N. Identification of a clinically efficacious CAR T cell subset in diffuse large B cell lymphoma by dynamic multidimensional single-cell profiling. NATURE CANCER 2024; 5:1010-1023. [PMID: 38750245 DOI: 10.1038/s43018-024-00768-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 04/10/2024] [Indexed: 05/24/2024]
Abstract
Chimeric antigen receptor (CAR) T cells used for the treatment of B cell malignancies can identify T cell subsets with superior clinical activity. Here, using infusion products of individuals with large B cell lymphoma, we integrated functional profiling using timelapse imaging microscopy in nanowell grids with subcellular profiling and single-cell RNA sequencing to identify a signature of multifunctional CD8+ T cells (CD8-fit T cells). CD8-fit T cells are capable of migration and serial killing and harbor balanced mitochondrial and lysosomal volumes. Using independent datasets, we validate that CD8-fit T cells (1) are present premanufacture and are associated with clinical responses in individuals treated with axicabtagene ciloleucel, (2) longitudinally persist in individuals after treatment with CAR T cells and (3) are tumor migrating cytolytic cells capable of intratumoral expansion in solid tumors. Our results demonstrate the power of multimodal integration of single-cell functional assessments for the discovery and application of CD8-fit T cells as a T cell subset with optimal fitness in cell therapy.
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Affiliation(s)
- Ali Rezvan
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, USA
| | - Gabrielle Romain
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, USA
| | | | | | | | - Xingyue An
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, USA
| | - Irfan N Bandey
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, USA
| | - Melisa J Montalvo
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, USA
| | - Jay R T Adolacion
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, USA
| | - Arash Saeedi
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, USA
| | - Fatemeh Sadeghi
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, USA
| | - Kristen Fousek
- Texas Children's Hospital, Baylor College of Medicine, Houston, TX, USA
| | - Nahum Puebla-Osorio
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | - Chantale Bernatchez
- Department of Biologics Development, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Harjeet Singh
- Divsion of Pediatrics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Nabil Ahmed
- Texas Children's Hospital, Baylor College of Medicine, Houston, TX, USA
| | - Mike Mattie
- Kite, a Gilead Company, Santa Monica, CA, USA
| | - Adrian Bot
- Kite, a Gilead Company, Santa Monica, CA, USA
| | - Sattva Neelapu
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Navin Varadarajan
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, USA.
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3
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Alieva M, Barrera Román M, de Blank S, Petcu D, Zeeman AL, Dautzenberg NMM, Cornel AM, van de Ven C, Pieters R, den Boer ML, Nierkens S, Calkoen FGJ, Clevers H, Kuball J, Sebestyén Z, Wehrens EJ, Dekkers JF, Rios AC. BEHAV3D: a 3D live imaging platform for comprehensive analysis of engineered T cell behavior and tumor response. Nat Protoc 2024; 19:2052-2084. [PMID: 38504137 DOI: 10.1038/s41596-024-00972-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 01/04/2024] [Indexed: 03/21/2024]
Abstract
Modeling immuno-oncology by using patient-derived material and immune cell co-cultures can advance our understanding of immune cell tumor targeting in a patient-specific manner, offering leads to improve cellular immunotherapy. However, fully exploiting these living cultures requires analysis of the dynamic cellular features modeled, for which protocols are currently limited. Here, we describe the application of BEHAV3D, a platform that implements multi-color live 3D imaging and computational tools for: (i) analyzing tumor death dynamics at both single-organoid or cell and population levels, (ii) classifying T cell behavior and (iii) producing data-informed 3D images and videos for visual inspection and further insight into obtained results. Together, this enables a refined assessment of how solid and liquid tumors respond to cellular immunotherapy, critically capturing both inter- and intratumoral heterogeneity in treatment response. In addition, BEHAV3D uncovers T cell behavior involved in tumor targeting, offering insight into their mode of action. Our pipeline thereby has strong implications for comparing, prioritizing and improving immunotherapy products by highlighting the behavioral differences between individual tumor donors, distinct T cell therapy concepts or subpopulations. The protocol describes critical wet lab steps, including co-culture preparations and fast 3D imaging with live cell dyes, a segmentation-based image processing tool to track individual organoids, tumor and immune cells and an analytical pipeline for behavioral profiling. This 1-week protocol, accessible to users with basic cell culture, imaging and programming expertise, can easily be adapted to any type of co-culture to visualize and exploit cell behavior, having far-reaching implications for the immuno-oncology field and beyond.
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Affiliation(s)
- Maria Alieva
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.
- Instituto de Investigaciones Biomédicas Sols-Morreale (IIBM), CSIC-UAM, Madrid, Spain.
| | - Mario Barrera Román
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Sam de Blank
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Diana Petcu
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Amber L Zeeman
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | | | - Annelisa M Cornel
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Center for Translational Immunology, University Medical Centre (UMC) Utrecht, Utrecht, the Netherlands
| | - Cesca van de Ven
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Rob Pieters
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Monique L den Boer
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Stefan Nierkens
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Center for Translational Immunology, University Medical Centre (UMC) Utrecht, Utrecht, the Netherlands
| | - Friso G J Calkoen
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Hans Clevers
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and UMC Utrecht, Utrecht, the Netherlands
- Pharma, Research and Early Development (pRED), F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Jürgen Kuball
- Center for Translational Immunology, University Medical Centre (UMC) Utrecht, Utrecht, the Netherlands
- Department of Hematology, UMC Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Zsolt Sebestyén
- Center for Translational Immunology, University Medical Centre (UMC) Utrecht, Utrecht, the Netherlands
| | - Ellen J Wehrens
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Johanna F Dekkers
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Anne C Rios
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.
- Oncode Institute, Utrecht, the Netherlands.
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4
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Montalvo MJ, Bandey IN, Rezvan A, Wu KL, Saeedi A, Kulkarni R, Li Y, An X, Sefat KMSR, Varadarajan N. Decoding the mechanisms of chimeric antigen receptor (CAR) T cell-mediated killing of tumors: insights from granzyme and Fas inhibition. Cell Death Dis 2024; 15:109. [PMID: 38307835 PMCID: PMC10837176 DOI: 10.1038/s41419-024-06461-8] [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: 09/04/2023] [Revised: 01/03/2024] [Accepted: 01/09/2024] [Indexed: 02/04/2024]
Abstract
Chimeric antigen receptor (CAR) T cell show promise in cancer treatments, but their mechanism of action is not well understood. Decoding the mechanisms used by individual T cells can help improve the efficacy of T cells while also identifying mechanisms of T cell failure leading to tumor escape. Here, we used a suite of assays including dynamic single-cell imaging of cell-cell interactions, dynamic imaging of fluorescent reporters to directly track cytotoxin activity in tumor cells, and scRNA-seq on patient infusion products to investigate the cytotoxic mechanisms used by individual CAR T cells in killing tumor cells. We show that surprisingly, overexpression of the Granzyme B (GZMB) inhibitor, protease inhibitor-9 (PI9), does not alter the cytotoxicity mediated by CD19-specific CAR T cells against either the leukemic cell line, NALM6; or the ovarian cancer cell line, SkOV3-CD19. We designed and validated reporters to directly assay T cell delivered GZMB activity in tumor cells and confirmed that while PI9 overexpression inhibits GZMB activity at the molecular level, this is not sufficient to impact the kinetics or magnitude of killing mediated by the CAR T cells. Altering cytotoxicity mediated by CAR T cells required combined inhibition of multiple pathways that are tumor cell specific: (a) B-cell lines like NALM6, Raji and Daudi were sensitive to combined GZMB and granzyme A (GZMA) inhibition; whereas (b) solid tumor targets like SkOV3-CD19 and A375-CD19 (melanoma) were sensitive to combined GZMB and Fas ligand inhibition. We realized the translational relevance of these findings by examining the scRNA-seq profiles of Tisa-cel and Axi-cel infusion products and show a significant correlation between GZMB and GZMA expression at the single-cell level in a T cell subset-dependent manner. Our findings highlight the importance of the redundancy in killing mechanisms of CAR T cells and how this redundancy is important for efficacious T cells.
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Affiliation(s)
- Melisa J Montalvo
- William A. Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, USA
| | - Irfan N Bandey
- William A. Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, USA
| | - Ali Rezvan
- William A. Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, USA
| | - Kwan-Ling Wu
- William A. Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, USA
| | - Arash Saeedi
- William A. Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, USA
| | - Rohan Kulkarni
- William A. Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, USA
| | - Yongshuai Li
- William A. Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, USA
| | - Xingyue An
- William A. Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, USA
| | - K M Samiur Rahman Sefat
- William A. Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, USA
| | - Navin Varadarajan
- William A. Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, USA.
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5
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Colina AS, Shah V, Shah RK, Kozlik T, Dash RK, Terhune S, Zamora AE. Current advances in experimental and computational approaches to enhance CAR T cell manufacturing protocols and improve clinical efficacy. FRONTIERS IN MOLECULAR MEDICINE 2024; 4:1310002. [PMID: 39086435 PMCID: PMC11285593 DOI: 10.3389/fmmed.2024.1310002] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 01/08/2024] [Indexed: 08/02/2024]
Abstract
Since the FDA's approval of chimeric antigen receptor (CAR) T cells in 2017, significant improvements have been made in the design of chimeric antigen receptor constructs and in the manufacturing of CAR T cell therapies resulting in increased in vivo CAR T cell persistence and improved clinical outcome in certain hematological malignancies. Despite the remarkable clinical response seen in some patients, challenges remain in achieving durable long-term tumor-free survival, reducing therapy associated malignancies and toxicities, and expanding on the types of cancers that can be treated with this therapeutic modality. Careful analysis of the biological factors demarcating efficacious from suboptimal CAR T cell responses will be of paramount importance to address these shortcomings. With the ever-expanding toolbox of experimental approaches, single-cell technologies, and computational resources, there is renowned interest in discovering new ways to streamline the development and validation of new CAR T cell products. Better and more accurate prognostic and predictive models can be developed to help guide and inform clinical decision making by incorporating these approaches into translational and clinical workflows. In this review, we provide a brief overview of recent advancements in CAR T cell manufacturing and describe the strategies used to selectively expand specific phenotypic subsets. Additionally, we review experimental approaches to assess CAR T cell functionality and summarize current in silico methods which have the potential to improve CAR T cell manufacturing and predict clinical outcomes.
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Affiliation(s)
- Alfredo S. Colina
- Department of Microbiology & Immunology, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Viren Shah
- Department of Biomedical Engineering, Medical College of Wisconsin and Marquette University, Milwaukee, WI, United States
| | - Ravi K. Shah
- Department of Medicine, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Tanya Kozlik
- Department of Microbiology & Immunology, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Ranjan K. Dash
- Department of Biomedical Engineering, Medical College of Wisconsin and Marquette University, Milwaukee, WI, United States
| | - Scott Terhune
- Department of Microbiology & Immunology, Medical College of Wisconsin, Milwaukee, WI, United States
- Department of Biomedical Engineering, Medical College of Wisconsin and Marquette University, Milwaukee, WI, United States
| | - Anthony E. Zamora
- Department of Microbiology & Immunology, Medical College of Wisconsin, Milwaukee, WI, United States
- Department of Medicine, Medical College of Wisconsin, Milwaukee, WI, United States
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6
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Alieva M, Wezenaar AKL, Wehrens EJ, Rios AC. Bridging live-cell imaging and next-generation cancer treatment. Nat Rev Cancer 2023; 23:731-745. [PMID: 37704740 DOI: 10.1038/s41568-023-00610-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/25/2023] [Indexed: 09/15/2023]
Abstract
By providing spatial, molecular and morphological data over time, live-cell imaging can provide a deeper understanding of the cellular and signalling events that determine cancer response to treatment. Understanding this dynamic response has the potential to enhance clinical outcome by identifying biomarkers or actionable targets to improve therapeutic efficacy. Here, we review recent applications of live-cell imaging for uncovering both tumour heterogeneity in treatment response and the mode of action of cancer-targeting drugs. Given the increasing uses of T cell therapies, we discuss the unique opportunity of time-lapse imaging for capturing the interactivity and motility of immunotherapies. Although traditionally limited in the number of molecular features captured, novel developments in multidimensional imaging and multi-omics data integration offer strategies to connect single-cell dynamics to molecular phenotypes. We review the effect of these recent technological advances on our understanding of the cellular dynamics of tumour targeting and discuss their implication for next-generation precision medicine.
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Affiliation(s)
- Maria Alieva
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
- Instituto de Investigaciones Biomedicas Sols-Morreale (IIBM), CSIC-UAM, Madrid, Spain
| | - Amber K L Wezenaar
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Ellen J Wehrens
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands.
- Oncode Institute, Utrecht, The Netherlands.
| | - Anne C Rios
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands.
- Oncode Institute, Utrecht, The Netherlands.
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7
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Pierzynowska K, Gaffke L, Zaucha JM, Węgrzyn G. Transcriptomic Approaches in Studies on and Applications of Chimeric Antigen Receptor T Cells. Biomedicines 2023; 11:biomedicines11041107. [PMID: 37189725 DOI: 10.3390/biomedicines11041107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 04/01/2023] [Accepted: 04/03/2023] [Indexed: 04/08/2023] Open
Abstract
Chimeric antigen receptor T (CAR-T) cells are specifically modified T cells which bear recombinant receptors, present at the cell surface and devoted to detect selected antigens of cancer cells, and due to the presence of transmembrane and activation domains, able to eliminate the latter ones. The use of CAR-T cells in anti-cancer therapies is a relatively novel approach, providing a powerful tool in the fight against cancer and bringing new hope for patients. However, despite huge possibilities and promising results of preclinical studies and clinical efficacy, there are various drawbacks to this therapy, including toxicity, possible relapses, restrictions to specific kinds of cancers, and others. Studies desiring to overcome these problems include various modern and advanced methods. One of them is transcriptomics, a set of techniques that analyze the abundance of all RNA transcripts present in the cell at certain moment and under certain conditions. The use of this method gives a global picture of the efficiency of expression of all genes, thus revealing the physiological state and regulatory processes occurring in the investigated cells. In this review, we summarize and discuss the use of transcriptomics in studies on and applications of CAR-T cells, especially in approaches focused on improved efficacy, reduced toxicity, new target cancers (like solid tumors), monitoring the treatment efficacy, developing novel analytical methods, and others.
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Affiliation(s)
- Karolina Pierzynowska
- Department of Molecular Biology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Lidia Gaffke
- Department of Molecular Biology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Jan M. Zaucha
- Department of Hematology and Transplantology, Medical University of Gdansk, Smoluchowskiego 17, 80-214 Gdansk, Poland
| | - Grzegorz Węgrzyn
- Department of Molecular Biology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
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8
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Romain G, Strati P, Rezvan A, Fathi M, Bandey IN, Adolacion JR, Heeke DS, Liadi I, Marques-Piubelli ML, Solis Soto LM, Mahendra A, Vega F, Cooper LJ, Singh H, Mattie M, Bot A, Neelapu S, Varadarajan N. Multidimensional single-cell analysis identifies a role for CD2-CD58 interactions in clinical antitumor T cell responses. J Clin Invest 2022; 132:159402. [PMID: 35881486 PMCID: PMC9433104 DOI: 10.1172/jci159402] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 07/12/2022] [Indexed: 11/17/2022] Open
Abstract
The in vivo persistence of adoptively transferred T cells is predictive of antitumor response. Identifying functional properties of infused T cells that lead to in vivo persistence and tumor eradication has remained elusive. We profiled CD19-specific chimeric antigen receptor (CAR) T cells as the infusion products used to treat large B cell lymphomas using high-throughput single-cell technologies based on time-lapse imaging microscopy in nanowell grids (TIMING), which integrates killing, cytokine secretion, and transcriptional profiling. Our results show that the directional migration of CD19-specific CAR T cells is correlated with multifunctionality. We showed that CD2 on T cells is associated with directional migration and that the interaction between CD2 on T cells and CD58 on lymphoma cells accelerates killing and serial killing. Consistent with this, we observed that elevated CD58 expression on pretreatment tumor samples in patients with relapsed or refractory large B cell lymphomas treated with CD19-specific CAR T cell therapy was associated with complete clinical response and survival. These results highlight the importance of studying dynamic T cell–tumor cell interactions in identifying optimal antitumor responses.
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Affiliation(s)
- Gabrielle Romain
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, United States of America
| | - Paolo Strati
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, United States of America
| | - Ali Rezvan
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, United States of America
| | | | - Irfan N Bandey
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, United States of America
| | - Jay Rt Adolacion
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, United States of America
| | - Darren S Heeke
- Kite, Gilead company, Santa Monica, United States of America
| | - Ivan Liadi
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, United States of America
| | - Mario L Marques-Piubelli
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, United States of America
| | - Luisa M Solis Soto
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, United States of America
| | - Ankit Mahendra
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, United States of America
| | - Francisco Vega
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, United States of America
| | | | - Harjeet Singh
- Department of Pediatrics, The University of Texas MD Anderson Cancer Center, Houston, United States of America
| | - Mike Mattie
- Kite, a Gilead company, Santa Monica, United States of America
| | - Adrian Bot
- Chief Scientific Officer, Kite, a Gilead company, Santa Monica, United States of America
| | - Sattva Neelapu
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, United States of America
| | - Navin Varadarajan
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, United States of America
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9
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Sandström N, Brandt L, Sandoz PA, Zambarda C, Guldevall K, Schulz-Ruhtenberg M, Rösener B, Krüger RA, Önfelt B. Live single cell imaging assays in glass microwells produced by laser-induced deep etching. LAB ON A CHIP 2022; 22:2107-2121. [PMID: 35470832 DOI: 10.1039/d2lc00090c] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Miniaturization of cell culture substrates enables controlled analysis of living cells in confined micro-scale environments. This is particularly suitable for imaging individual cells over time, as they can be monitored without escaping the imaging field-of-view (FoV). Glass materials are ideal for most microscopy applications. However, with current methods used in life sciences, glass microfabrication is limited in terms of either freedom of design, quality, or throughput. In this work, we introduce laser-induced deep etching (LIDE) as a method for producing glass microwell arrays for live single cell imaging assays. We demonstrate novel microwell arrays with deep, high-aspect ratio wells that have rounded, dimpled or flat bottom profiles in either single-layer or double-layer glass chips. The microwells are evaluated for microscopy-based analysis of long-term cell culture, clonal expansion, laterally organized cell seeding, subcellular mechanics during migration and immune cell cytotoxicity assays of both adherent and suspension cells. It is shown that all types of microwells can support viable cell cultures and imaging with single cell resolution, and we highlight specific benefits of each microwell design for different applications. We believe that high-quality glass microwell arrays enabled by LIDE provide a great option for high-content and high-resolution imaging-based live cell assays with a broad range of potential applications within life sciences.
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Affiliation(s)
- Niklas Sandström
- Department of Applied Physics, Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden.
| | - Ludwig Brandt
- Department of Applied Physics, Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden.
| | - Patrick A Sandoz
- Department of Applied Physics, Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden.
| | - Chiara Zambarda
- Department of Applied Physics, Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden.
| | - Karolin Guldevall
- Department of Applied Physics, Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden.
| | | | | | | | - Björn Önfelt
- Department of Applied Physics, Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden.
- Department of Microbiology, Tumour and Cell Biology, Karolinska Institutet, Stockholm, Sweden
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10
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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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