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Shannon MJ, Eisman SE, Lowe AR, Sloan TFW, Mace EM. cellPLATO - an unsupervised method for identifying cell behaviour in heterogeneous cell trajectory data. J Cell Sci 2024; 137:jcs261887. [PMID: 38738282 PMCID: PMC11213520 DOI: 10.1242/jcs.261887] [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: 12/15/2023] [Accepted: 05/01/2024] [Indexed: 05/14/2024] Open
Abstract
Advances in imaging, segmentation and tracking have led to the routine generation of large and complex microscopy datasets. New tools are required to process this 'phenomics' type data. Here, we present 'Cell PLasticity Analysis Tool' (cellPLATO), a Python-based analysis software designed for measurement and classification of cell behaviours based on clustering features of cell morphology and motility. Used after segmentation and tracking, the tool extracts features from each cell per timepoint, using them to segregate cells into dimensionally reduced behavioural subtypes. Resultant cell tracks describe a 'behavioural ID' at each timepoint, and similarity analysis allows the grouping of behavioural sequences into discrete trajectories with assigned IDs. Here, we use cellPLATO to investigate the role of IL-15 in modulating human natural killer (NK) cell migration on ICAM-1 or VCAM-1. We find eight behavioural subsets of NK cells based on their shape and migration dynamics between single timepoints, and four trajectories based on sequences of these behaviours over time. Therefore, by using cellPLATO, we show that IL-15 increases plasticity between cell migration behaviours and that different integrin ligands induce different forms of NK cell migration.
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Affiliation(s)
- Michael J. Shannon
- Department of Pediatrics, Vagelos College of Physicians and Surgeons, Columbia University Medical Center, NYC, NY 10032, USA
| | - Shira E. Eisman
- Department of Pediatrics, Vagelos College of Physicians and Surgeons, Columbia University Medical Center, NYC, NY 10032, USA
| | - Alan R. Lowe
- Institute for the Physics of Living Systems, Institute for Structural and Molecular Biology and London Centre for Nanotechnology, University College London, London WC1H 0AH, UK
| | | | - Emily M. Mace
- Department of Pediatrics, Vagelos College of Physicians and Surgeons, Columbia University Medical Center, NYC, NY 10032, USA
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2
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Martinez AL, Shannon MJ, Sloan T, Mace EM. CD56/NCAM mediates cell migration of human NK cells by promoting integrin-mediated adhesion turnover. Mol Biol Cell 2024; 35:ar64. [PMID: 38507235 PMCID: PMC11151098 DOI: 10.1091/mbc.e23-12-0463] [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: 12/11/2023] [Revised: 03/06/2024] [Accepted: 03/12/2024] [Indexed: 03/22/2024] Open
Abstract
Natural killer (NK) cells patrol tissue to mediate lysis of virally infected and tumorigenic cells. Human NK cells are typically identified by their expression of neural cell adhesion molecule (NCAM, CD56), yet despite its ubiquitous expression on NK cells, CD56 remains a poorly understood protein on immune cells. CD56 has been previously demonstrated to play roles in NK cell cytotoxic function and cell migration. Specifically, CD56-deficient NK cells have impaired cell migration on stromal cells and CD56 is localized to the uropod of NK cells migrating on stroma. Here, we show that CD56 is required for NK cell migration on ICAM-1 and is required for the establishment of persistent cell polarity and unidirectional actin flow. The intracellular domain of CD56 (NCAM-140) is required for its function and the loss of CD56 leads to enlarged actin foci and sequestration of phosphorylated Pyk2 accompanied by increased size and frequency of activated LFA-1 clusters. Together, these data identify a role for CD56 in regulating human NK cell migration through modulation of actin dynamics and integrin turnover.
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Affiliation(s)
- Amera L. Martinez
- Department of Pediatrics, Vagelos College of Physicians and Surgeons, Columbia University Medical Center, New York, NY 10024
| | - Michael J. Shannon
- Department of Pediatrics, Vagelos College of Physicians and Surgeons, Columbia University Medical Center, New York, NY 10024
| | | | - Emily M. Mace
- Department of Pediatrics, Vagelos College of Physicians and Surgeons, Columbia University Medical Center, New York, NY 10024
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3
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Weiner L, Fitzgerald A, Maynard R, Marcisak E, Nasir A, Glasgow E, Jablonski S, Van Der Veken P, Pearson G, Eisman S, Mace E, Fertig E. Fibroblast activation protein regulates natural killer cell migration, extravasation and tumor infiltration. RESEARCH SQUARE 2023:rs.3.rs-3706465. [PMID: 38196606 PMCID: PMC10775390 DOI: 10.21203/rs.3.rs-3706465/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2024]
Abstract
Natural killer (NK) cells play a critical role in physiologic and pathologic conditions such as pregnancy, infection, autoimmune disease and cancer. In cancer, numerous strategies have been designed to exploit the cytolytic properties of NK cells, with variable success. A major hurdle to NK-cell focused therapies is NK cell recruitment and infiltration into tumors. While the chemotaxis pathways regulating NK recruitment to different tissues are well delineated, the mechanisms human NK cells employ to physically migrate are ill-defined. We show for the first time that human NK cells express fibroblast activation protein (FAP), a cell surface protease previously thought to be primarily expressed by activated fibroblasts. FAP degrades the extracellular matrix to facilitate cell migration and tissue remodeling. We used novel in vivo zebrafish and in vitro 3D culture models to demonstrate that FAP knock out and pharmacologic inhibition restrict NK cell migration, extravasation, and invasion through tissue matrix. Notably, forced overexpression of FAP promotes NK cell invasion through matrix in both transwell and tumor spheroid assays, ultimately increasing tumor cell lysis. Additionally, FAP overexpression enhances NK cells invasion into a human tumor in immunodeficient mice. These findings demonstrate the necessity of FAP in NK cell migration and present a new approach to modulate NK cell trafficking and enhance cell-based therapy in solid tumors.
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Affiliation(s)
| | - Allison Fitzgerald
- Lombardi Comprehensive Cancer Center, Georgetown University Medial Center, Washington
| | | | - Emily Marcisak
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine
| | | | | | | | | | | | | | - Emily Mace
- Columbia University Irving Medical Center
| | - Elana Fertig
- Johns Hopkins Convergence Institute, Johns Hopkins Bloomberg Kimmel Institute for Immunotherapy, Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Department of Biomedical Engineeri
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Martinez AL, Shannon MJ, Sloan T, Mace EM. CD56/NCAM mediates cell migration of human NK cells by promoting integrin-mediated adhesion turnover. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.21.567714. [PMID: 38045340 PMCID: PMC10690223 DOI: 10.1101/2023.11.21.567714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
Natural killer (NK) cells patrol tissue to mediate lysis of virally infected and tumorigenic cells. Human NK cells are typically identified by their expression of neural cell adhesion molecule (NCAM, CD56), yet, despite its ubiquitous expression on NK cells, CD56 remains a poorly understand protein on immune cells. CD56 has been previously demonstrated to play roles in NK cell cytotoxic function and cell migration. Specifically, CD56-deficient NK cells have impaired cell migration on stromal cells and CD56 is localized to the uropod of NK cells migrating on stroma. Here, we show that CD56 is required for NK cell migration on ICAM-1 and is required for the establishment of persistent cell polarity and unidirectional actin flow. The intracellular domain of CD56 (NCAM-140) is required for its function, and the loss of CD56 leads to enlarged actin foci and sequestration of phosphorylated Pyk2, accompanied by increased size and frequency of activated LFA-1 clusters. Together, these data identify a role for CD56 in regulating human NK cell migration through modulation of actin dynamics and integrin turnover.
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Affiliation(s)
- Amera L Martinez
- Department of Pediatrics, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York NY 10032
| | - Michael J Shannon
- Department of Pediatrics, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York NY 10032
| | | | - Emily M Mace
- Department of Pediatrics, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York NY 10032
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Shannon MJ, Eisman SE, Lowe AR, Sloan T, Mace EM. cellPLATO: an unsupervised method for identifying cell behaviour in heterogeneous cell trajectory data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.28.564355. [PMID: 37961659 PMCID: PMC10634992 DOI: 10.1101/2023.10.28.564355] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Advances in imaging, cell segmentation, and cell tracking now routinely produce microscopy datasets of a size and complexity comparable to transcriptomics or proteomics. New tools are required to process this 'phenomics' type data. Cell PLasticity Analysis TOol (cellPLATO) is a Python-based analysis software designed for measurement and classification of diverse cell behaviours based on clustering of parameters of cell morphology and motility. cellPLATO is used after segmentation and tracking of cells from live cell microscopy data. The tool extracts morphological and motility metrics from each cell per timepoint, before being using them to segregate cells into behavioural subtypes with dimensionality reduction. Resultant cell tracks have a 'behavioural ID' for each cell per timepoint corresponding to their changing behaviour over time in a sequence. Similarity analysis allows the grouping of behavioural sequences into discrete trajectories with assigned IDs. Trajectories and underlying behaviours generate a phenotypic fingerprint for each experimental condition, and representative cells are mathematically identified and graphically displayed for human understanding of each subtype. Here, we use cellPLATO to investigate the role of IL-15 in modulating NK cell migration on ICAM-1 or VCAM-1. We find 8 behavioural subsets of NK cells based on their shape and migration dynamics, and 4 trajectories of behaviour. Therefore, using cellPLATO we show that IL-15 increases plasticity between cell migration behaviours and that different integrin ligands induce different forms of NK cell migration.
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Affiliation(s)
- Michael J Shannon
- Department of Pediatrics, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York NY 10032
| | - Shira E Eisman
- Department of Pediatrics, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York NY 10032
| | - Alan R Lowe
- Institute for the Physics of Living Systems, Institute for Structural and Molecular Biology and London Centre for Nanotechnology, University College London, London WC1H 0AH, United Kingdom
| | | | - Emily M Mace
- Department of Pediatrics, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York NY 10032
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Hegewisch-Solloa E, Nalin AP, Freud AG, Mace EM. Deciphering the localization and trajectory of human natural killer cell development. J Leukoc Biol 2023; 114:487-506. [PMID: 36869821 DOI: 10.1093/jleuko/qiad027] [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: 11/21/2022] [Revised: 02/07/2023] [Accepted: 02/12/2023] [Indexed: 03/05/2023] Open
Abstract
Innate immune cells represent the first line of cellular immunity, comprised of both circulating and tissue-resident natural killer cells and innate lymphoid cells. These innate lymphocytes arise from a common CD34+ progenitor that differentiates into mature natural killer cells and innate lymphoid cells. The successive stages in natural killer cell maturation are characterized by increased lineage restriction and changes to phenotype and function. Mechanisms of human natural killer cell development have not been fully elucidated, especially the role of signals that drive the spatial localization and maturation of natural killer cells. Cytokines, extracellular matrix components, and chemokines provide maturation signals and influence the trafficking of natural killer cell progenitors to peripheral sites of differentiation. Here we present the latest advances in our understanding of natural killer and innate lymphoid cell development in peripheral sites, including secondary lymphoid tissues (i.e. tonsil). Recent work in the field has provided a model for the spatial distribution of natural killer cell and innate lymphoid cell developmental intermediates in tissue and generated further insights into the developmental niche. In support of this model, future studies using multifaceted approaches seek to fully map the developmental trajectory of human natural killer cells and innate lymphoid cells in secondary lymphoid tissues.
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Affiliation(s)
- Everardo Hegewisch-Solloa
- Department of Pediatrics, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, 630 W 168th St. New York, NY 10032, USA
| | - Ansel P Nalin
- Biomedical Sciences Graduate Program, Medical Scientist Training Program, Comprehensive Cancer Center and The James Cancer Hospital and Solove Research Institute, The Ohio State University, 460 W 10th Ave. Columbus, OH 43210, USA
| | - Aharon G Freud
- Department of Pathology, Comprehensive Cancer Center and The James Cancer Hospital and Solove Research Institute, The Ohio State University, 460 W 12th Ave. Columbus, OH 43210, USA
| | - Emily M Mace
- Department of Pediatrics, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, 630 W 168th St. New York, NY 10032, USA
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Martinez AL, Shannon MJ, Eisman SE, Hegewisch-Solloa E, Asif AN, Ebrahim TAM, Mace EM. Quantifying Human Natural Killer Cell Migration by Imaging and Image Analysis. Methods Mol Biol 2022; 2463:129-151. [PMID: 35344172 PMCID: PMC9159076 DOI: 10.1007/978-1-0716-2160-8_10] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Migration is an important function for natural killer cells. Cell motility has implications in development, tissue infiltration, and cytotoxicity, and measuring the properties of natural killer (NK) cell migration using in vitro assays can be highly informative. Many researchers have an interest in studying properties of NK cell migration in the context of genetic mutation, disease, or in specific tissues and microenvironments. Motility assays can also provide information on the localization of proteins during different phases of cell migration. These assays can be performed on different surfaces for migration or coupled with chemoattractants and/or target cells to test functional outcomes or characterize cell migration speeds and phenotypes. NK cells undergo migration during differentiation in tissue, and these conditions can be modeled by culturing NK cells on a confluent bed of stromal cells on glass and imaging cell migration. Alternatively, fibronectin- or ICAM-1-coated surfaces promote NK cell migration and can be used as substrates. Here, we will describe techniques for the experimental setup and analysis of NK cell motility assays by confocal microscopy or in-incubator imaging using commercially available systems. Finally, we describe open-source software for analyzing cell migration using manual tracking or automated approaches and discuss considerations for the implementation of each of these methods.
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Affiliation(s)
- Amera L Martinez
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA
| | - Michael J Shannon
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA
| | - Shira E Eisman
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA
| | | | - Aneeza N Asif
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA
- Department of Biology, Barnard College, New York, NY, USA
| | - Tasneem A M Ebrahim
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA
- Department of Cell, Developmental, and Regenerative Biology, Icahn School of Medicine at Mt. Sinai, New York, NY, USA
| | - Emily M Mace
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA.
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Three-Dimensional Culture Models to Study Innate Anti-Tumor Immune Response: Advantages and Disadvantages. Cancers (Basel) 2021; 13:cancers13143417. [PMID: 34298630 PMCID: PMC8303518 DOI: 10.3390/cancers13143417] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 06/29/2021] [Accepted: 07/05/2021] [Indexed: 12/12/2022] Open
Abstract
Several approaches have shown that the immune response against tumors strongly affects patients' clinical outcome. Thus, the study of anti-tumor immunity is critical to understand and potentiate the mechanisms underlying the elimination of tumor cells. Natural killer (NK) cells are members of innate immunity and represent powerful anti-tumor effectors, able to eliminate tumor cells without a previous sensitization. Thus, the study of their involvement in anti-tumor responses is critical for clinical translation. This analysis has been performed in vitro, co-incubating NK with tumor cells and quantifying the cytotoxic activity of NK cells. In vivo confirmation has been applied to overcome the limits of in vitro testing, however, the innate immunity of mice and humans is different, leading to discrepancies. Different activating receptors on NK cells and counter-ligands on tumor cells are involved in the antitumor response, and innate immunity is strictly dependent on the specific microenvironment where it takes place. Thus, three-dimensional (3D) culture systems, where NK and tumor cells can interact in a tissue-like architecture, have been created. For example, tumor cell spheroids and primary organoids derived from several tumor types, have been used so far to analyze innate immune response, replacing animal models. Herein, we briefly introduce NK cells and analyze and discuss in detail the properties of 3D tumor culture systems and their use for the study of tumor cell interactions with NK cells.
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Assunção M, Dehghan-Baniani D, Yiu CHK, Später T, Beyer S, Blocki A. Cell-Derived Extracellular Matrix for Tissue Engineering and Regenerative Medicine. Front Bioeng Biotechnol 2020; 8:602009. [PMID: 33344434 PMCID: PMC7744374 DOI: 10.3389/fbioe.2020.602009] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 11/10/2020] [Indexed: 12/12/2022] Open
Abstract
Cell-derived extracellular matrices (CD-ECMs) captured increasing attention since the first studies in the 1980s. The biological resemblance of CD-ECMs to their in vivo counterparts and natural complexity provide them with a prevailing bioactivity. CD-ECMs offer the opportunity to produce microenvironments with costumizable biological and biophysical properties in a controlled setting. As a result, CD-ECMs can improve cellular functions such as stemness or be employed as a platform to study cellular niches in health and disease. Either on their own or integrated with other materials, CD-ECMs can also be utilized as biomaterials to engineer tissues de novo or facilitate endogenous healing and regeneration. This review provides a brief overview over the methodologies used to facilitate CD-ECM deposition and manufacturing. It explores the versatile uses of CD-ECM in fundamental research and therapeutic approaches, while highlighting innovative strategies. Furthermore, current challenges are identified and it is accentuated that advancements in methodologies, as well as innovative interdisciplinary approaches are needed to take CD-ECM-based research to the next level.
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Affiliation(s)
- Marisa Assunção
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong
- Institute for Tissue Engineering and Regenerative Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Dorsa Dehghan-Baniani
- Institute for Tissue Engineering and Regenerative Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Chi Him Kendrick Yiu
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong
- Institute for Tissue Engineering and Regenerative Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Thomas Später
- Institute for Clinical and Experimental Surgery, University of Saarland, Saarbrücken, Germany
| | - Sebastian Beyer
- Department of Biomedical Engineering, Faculty of Engineering, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Anna Blocki
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong
- Institute for Tissue Engineering and Regenerative Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong
- Department of Orthopaedics and Traumatology, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong
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