1
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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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Verma S, Bradley MC, Gray J, Dogra P, Caron DP, Maurrasse S, Grunstein E, Waldman E, Jang M, Pethe K, Farber DL, Connors TJ. Distinct Localization, Transcriptional Profiles, and Functionality in Early Life Tonsil Regulatory T Cells. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2024; 213:306-316. [PMID: 38905110 PMCID: PMC11304551 DOI: 10.4049/jimmunol.2300890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Accepted: 05/27/2024] [Indexed: 06/23/2024]
Abstract
CD4+ regulatory T cells (Tregs) are key orchestrators of the immune system, fostering the establishment of protective immunity while preventing deleterious responses. Infancy and childhood are crucial periods of rapid immunologic development, but how Tregs mediate immune responses at these earliest timepoints of human life is poorly understood. In this study, we compare blood and tissue (tonsil) Tregs across pediatric and adult subjects to investigate age-related differences in Treg biology. We observed increased FOXP3 expression and proportions of Tregs in tonsil compared with paired blood samples in children. Within tonsil, early life Tregs accumulated in extrafollicular regions with cellular interactions biased toward CD8+ T cells. Tonsil Tregs in both children and adults expressed transcriptional profiles enriched for lineage defining signatures and canonical functionality compared with blood, suggesting tissue as the primary site of Treg activity. Early life tonsil Tregs transcriptional profiles were further defined by pathways associated with activation, proliferation, and polyfunctionality. Observed differences in pediatric tonsil Treg transcriptional signatures were associated with phenotypic differences, high proliferative capacity, and robust production of IL-10 compared with adult Tregs. These results identify tissue as a major driver of Treg identity, provide new insights into developmental differences in Treg biology across the human lifespan, and demonstrate unique functional properties of early life Tregs.
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Affiliation(s)
- Shivali Verma
- Department of Microbiology and Immunology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY
| | - Marissa C Bradley
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY
| | - Joshua Gray
- Department of Microbiology and Immunology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY
| | - Pranay Dogra
- Department of Microbiology and Immunology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY
| | - Daniel P Caron
- Department of Microbiology and Immunology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY
| | - Sarah Maurrasse
- Department of Otolaryngology-Head and Neck Surgery, Columbia University Vagelos College of Physicians and Surgeons, New York, NY
| | - Eli Grunstein
- Department of Otolaryngology-Head and Neck Surgery, Columbia University Vagelos College of Physicians and Surgeons, New York, NY
| | - Erik Waldman
- Department of Otolaryngology-Head and Neck Surgery, Columbia University Vagelos College of Physicians and Surgeons, New York, NY
| | - Minyoung Jang
- Department of Otolaryngology-Head and Neck Surgery, Columbia University Vagelos College of Physicians and Surgeons, New York, NY
| | - Kalpana Pethe
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY
| | - Donna L Farber
- Department of Microbiology and Immunology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY
- Department of Surgery, Columbia University Vagelos College of Physicians and Surgeons, New York, NY
| | - Thomas J Connors
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY
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3
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Rebuffet L, Melsen JE, Escalière B, Basurto-Lozada D, Bhandoola A, Björkström NK, Bryceson YT, Castriconi R, Cichocki F, Colonna M, Davis DM, Diefenbach A, Ding Y, Haniffa M, Horowitz A, Lanier LL, Malmberg KJ, Miller JS, Moretta L, Narni-Mancinelli E, O'Neill LAJ, Romagnani C, Ryan DG, Sivori S, Sun D, Vagne C, Vivier E. High-dimensional single-cell analysis of human natural killer cell heterogeneity. Nat Immunol 2024; 25:1474-1488. [PMID: 38956378 PMCID: PMC11291291 DOI: 10.1038/s41590-024-01883-0] [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: 01/16/2024] [Accepted: 05/23/2024] [Indexed: 07/04/2024]
Abstract
Natural killer (NK) cells are innate lymphoid cells (ILCs) contributing to immune responses to microbes and tumors. Historically, their classification hinged on a limited array of surface protein markers. Here, we used single-cell RNA sequencing (scRNA-seq) and cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq) to dissect the heterogeneity of NK cells. We identified three prominent NK cell subsets in healthy human blood: NK1, NK2 and NK3, further differentiated into six distinct subgroups. Our findings delineate the molecular characteristics, key transcription factors, biological functions, metabolic traits and cytokine responses of each subgroup. These data also suggest two separate ontogenetic origins for NK cells, leading to divergent transcriptional trajectories. Furthermore, we analyzed the distribution of NK cell subsets in the lung, tonsils and intraepithelial lymphocytes isolated from healthy individuals and in 22 tumor types. This standardized terminology aims at fostering clarity and consistency in future research, thereby improving cross-study comparisons.
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Grants
- Wellcome Trust
- P01 CA111412 NCI NIH HHS
- E.V laboratory at CIML and Assistance-Publique des Hôpitaux de Marseille is supported by funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (TILC, grant agreement No. 694502 and MInfla-TILC, grand agreement No. 875102), the Agence Nationale de la Recherche including the PIONEER Project (ANR-17-RHUS-0007), MSDAvenir, Innate Pharma and institutional grants awarded to the CIML (INSERM, CNRS and Aix-Marseille University) and Marseille Immunopole.
- D.M.D laboratory is funded by the Medical Research Council (MR/W031698/1) and the Wellcome Trust (110091/Z/15/Z).
- A.D. laboratory is supported by the European Research Council (ERC AdG ILCAdapt, 101055309 to A.D.) and by the German Research Foundation (DFG) (SFB 1444/427826188 and TRR 241/375876048 to A.D., SPP1937/Di764 /9-2 to A.D.). We are grateful to the Benjamin Franklin Flow Cytometry Facility (BFFC) for support in cell sorting. BFFC is supported by DFG Instrument Grants INST 335/597-1 FUGG und INST 335/777-1 FUGG.
- KJM was supported by the Research Council of Norway, Center of Excellence: Precision Immunotherapy Alliance (332727), the US National Cancer Institute (P01 CA111412, P009500901).
- L.M. is funded by Associazione Italiana contro il Cancro (AIRC), 5xmille project n. 21147.
- C.R. laboratory is supported by the ERC Advanced Grant ‘MEM-CLONK’ (101055157) and the Deutsche Forschungsgemeinschaft (DFG) grants SFB TRR241 B02 and RO 3565/7-1.
- D.G.R is supported by funding from the Medical Research Council (MRC) (MC_UU_00028) and Wellcome Trust-Academy of Medical Sciences (WT-AMS) (SBF009\1119).
- S.S. is funded by Ministero dell’Istruzione, dell’Università e della Ricerca: PRIN 2017WC8499_004 and Fondazione AIRC: AIRC 5×1000 project id. 21147.
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Affiliation(s)
- Lucas Rebuffet
- Aix Marseille Université, CNRS, INSERM, Centre d'Immunologie de Marseille-Luminy, Marseille, France
| | - Janine E Melsen
- Leiden University Medical Center, Willem-Alexander Children's Hospital, Laboratory for Pediatric Immunology, Leiden, the Netherlands
- Leiden University Medical Center, Department of Immunology, Leiden, the Netherlands
| | - Bertrand Escalière
- Aix Marseille Université, CNRS, INSERM, Centre d'Immunologie de Marseille-Luminy, Marseille, France
| | - Daniela Basurto-Lozada
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Avinash Bhandoola
- T Cell Biology and Development Unit, Laboratory of Genome Integrity, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Niklas K Björkström
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Yenan T Bryceson
- Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
- Division of Clinical Immunology and Transfusion Medicine, Karolinska University Hospital, Stockholm, Sweden
- Sweden Broegelmann Research Laboratory, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Roberta Castriconi
- Department of Experimental Medicine (DIMES), University of Genoa, Genoa, Italy
- Laboratory of Clinical and Experimental Immunology, IRCCS Istituto Giannina Gaslini, Genova, Italy
| | - Frank Cichocki
- Department of Medicine, University of Minnesota, Minneapolis, MN, USA
| | - Marco Colonna
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Daniel M Davis
- Department of Life Sciences, Imperial College London, Sir Alexander Fleming Building, South Kensington, London, UK
| | - Andreas Diefenbach
- Laboratory of Innate Immunity, Institute of Microbiology, Infectious Diseases and Immunology (I-MIDI), Campus Benjamin Franklin, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Mucosal and Developmental Immunology, Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, Berlin, Germany
| | - Yi Ding
- T Cell Biology and Development Unit, Laboratory of Genome Integrity, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Muzlifah Haniffa
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
- Department of Dermatology and NIHR Biomedical Research Centre, Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Amir Horowitz
- Department of Immunology & Immunotherapy, The Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Lewis L Lanier
- Department of Microbiology and Immunology and the Parker Institute for Cancer Immunotherapy, University of California, San Francisco, San Francisco, CA, USA
| | - Karl-Johan Malmberg
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
- Precision Immunotherapy Alliance, The University of Oslo, Oslo, Norway
- The Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Jeffrey S Miller
- Department of Medicine, University of Minnesota, Minneapolis, MN, USA
| | - Lorenzo Moretta
- Tumor Immunology Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Emilie Narni-Mancinelli
- Aix Marseille Université, CNRS, INSERM, Centre d'Immunologie de Marseille-Luminy, Marseille, France
| | - Luke A J O'Neill
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin, Ireland
| | - Chiara Romagnani
- Institute of Medical Immunology, Charité Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt Universität zu Berlin, Berlin, Germany
- Innate Immunity, Deutsches Rheuma-Forschungszentrum Berlin (DRFZ), ein Leibniz Institut, Berlin, Germany
- Berlin University Alliance, Berlin, Germany
| | - Dylan G Ryan
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
| | - Simona Sivori
- Department of Experimental Medicine (DIMES), University of Genoa, Genoa, Italy
- IRCCS Ospedale Policlinico San Martino, Genova, Italy
| | - Dan Sun
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Constance Vagne
- Innate Pharma Research Laboratories, Innate Pharma, Marseille, France
| | - Eric Vivier
- Aix Marseille Université, CNRS, INSERM, Centre d'Immunologie de Marseille-Luminy, Marseille, France.
- Innate Pharma Research Laboratories, Innate Pharma, Marseille, France.
- APHM, Hôpital de la Timone, Marseille-Immunopôle, Marseille, France.
- Paris-Saclay Cancer Cluster, Le Kremlin-Bicêtre, France.
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4
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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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5
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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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6
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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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7
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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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8
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Hegewisch-Solloa E, Melsen JE, Ravichandran H, Rendeiro AF, Freud AG, Mundy-Bosse B, Melms JC, Eisman SE, Izar B, Grunstein E, Connors TJ, Elemento O, Horowitz A, Mace EM. Mapping human natural killer cell development in pediatric tonsil by imaging mass cytometry and high-resolution microscopy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.05.556371. [PMID: 37732282 PMCID: PMC10508773 DOI: 10.1101/2023.09.05.556371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/22/2023]
Abstract
Natural killer (NK) cells develop from CD34+ progenitors in a stage-specific manner defined by changes in cell surface receptor expression and function. Secondary lymphoid tissues, including tonsil, are sites of human NK cell development. Here we present new insights into human NK cell development in pediatric tonsil using cyclic immunofluorescence and imaging mass cytometry. We show that NK cell subset localization and interactions are dependent on NK cell developmental stage and tissue residency. NK cell progenitors are found in the interfollicular domain in proximity to cytokine-expressing stromal cells that promote proliferation and maturation. Mature NK cells are primarily found in the T-cell rich parafollicular domain engaging in cell-cell interactions that differ depending on their stage and tissue residency. The presence of local inflammation results in changes in NK cell interactions, abundance, and localization. This study provides the first comprehensive atlas of human NK cell development in secondary lymphoid tissue.
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Affiliation(s)
- Everardo Hegewisch-Solloa
- Department of Pediatrics, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York NY 10032
| | - Janine E Melsen
- Department of Immunology, Leiden University Medical Center, Leiden, The Netherlands
- Laboratory for Pediatric Immunology, Willem-Alexander Children's Hospital, Leiden University Medical Center, Leiden, The Netherlands
| | - Hiranmayi Ravichandran
- Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, NY, 10065
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
| | - André F Rendeiro
- Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, NY, 10065
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14 AKH BT 25.3, 1090, Vienna, Austria
| | - Aharon G Freud
- Department of Pathology, The Ohio State University, Columbus, OH 43210, USA; Comprehensive Cancer Center and The James Cancer Hospital and Solove Research Institute, The Ohio State University, Columbus, OH 43210
| | - Bethany Mundy-Bosse
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH 43210, USA; Comprehensive Cancer Center and The James Cancer Hospital and Solove Research Institute, The Ohio State University, Columbus, OH 43210
| | - Johannes C Melms
- Department of Medicine, Division of Hematology/Oncology, Columbia University Irving Medical Center, New York, NY, 10032
- Columbia Center for Translational Immunology, 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
| | - Benjamin Izar
- Department of Medicine, Division of Hematology/Oncology, Columbia University Irving Medical Center, New York, NY, 10032
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY, 10032
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, 10032
- Program for Mathematical Genomics, Columbia University, New York, NY, 10032
| | - Eli Grunstein
- Department of Otolaryngology - Head and Neck Surgery, Columbia University Medical Center, New York, New York 10032
| | - Thomas J Connors
- Department of Pediatrics, Division of Pediatric Critical Care and Hospital Medicine, Columbia University Irving Medical Center, New York, NY 10024
| | - Olivier Elemento
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, 10065
| | - Amir Horowitz
- Department of Oncological Sciences, Precision Immunology Institute, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029
| | - 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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9
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From the Catastrophic Objective Irreproducibility of Cancer Research and Unavoidable Failures of Molecular Targeted Therapies to the Sparkling Hope of Supramolecular Targeted Strategies. Int J Mol Sci 2023; 24:ijms24032796. [PMID: 36769134 PMCID: PMC9917659 DOI: 10.3390/ijms24032796] [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: 11/30/2022] [Revised: 01/22/2023] [Accepted: 01/23/2023] [Indexed: 02/05/2023] Open
Abstract
The unprecedented non-reproducibility of the results published in the field of cancer research has recently come under the spotlight. In this short review, we try to highlight some general principles in the organization and evolution of cancerous tumors, which objectively lead to their enormous variability and, consequently, the irreproducibility of the results of their investigation. This heterogeneity is also extremely unfavorable for the effective use of molecularly targeted medicine. Against the seemingly comprehensive background of this heterogeneity, we single out two supramolecular characteristics common to all tumors: the clustered nature of tumor interactions with their microenvironment and the formation of biomolecular condensates with tumor-specific distinctive features. We suggest that these features can form the basis of strategies for tumor-specific supramolecular targeted therapies.
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Forkel H, Grabarczyk P, Depke M, Troschke-Meurer S, Simm S, Hammer E, Michalik S, Hentschker C, Corleis B, Loyal L, Zumpe M, Siebert N, Dorhoi A, Thiel A, Lode H, Völker U, Schmidt CA. BCL11B depletion induces the development of highly cytotoxic innate T cells out of IL-15 stimulated peripheral blood αβ CD8+ T cells. Oncoimmunology 2022; 11:2148850. [PMID: 36507091 PMCID: PMC9728472 DOI: 10.1080/2162402x.2022.2148850] [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: 12/12/2022] Open
Abstract
BCL11B, an essential transcription factor for thymopoiesis, regulates also vital processes in post-thymic lymphocytes. Increased expression of BCL11B was recently correlated with the maturation of NK cells, whereas reduced BCL11B levels were observed in native and induced T cell subsets displaying NK cell features. We show that BCL11B-depleted CD8+ T cells stimulated with IL-15 acquired remarkable innate characteristics. These induced innate CD8+ (iiT8) cells expressed multiple innate receptors like NKp30, CD161, and CD16 as well as factors regulating migration and tissue homing while maintaining their T cell phenotype. The iiT8 cells effectively killed leukemic cells spontaneously and neuroblastoma spheroids in the presence of a tumor-specific monoclonal antibody mediated by CD16 receptor activation. These iiT8 cells integrate the innate natural killer cell activity with adaptive T cell longevity, promising an interesting therapeutic potential. Our study demonstrates that innate T cells, albeit of limited clinical applicability given their low frequency, can be efficiently generated from peripheral blood and applied for adoptive transfer, CAR therapy, or combined with therapeutic antibodies.
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Affiliation(s)
- Hannes Forkel
- Internal Medicine Clinic C, University Medicine Greifswald, Greifswald, Germany
| | - Piotr Grabarczyk
- Internal Medicine Clinic C, University Medicine Greifswald, Greifswald, Germany
| | - Maren Depke
- Internal Medicine Clinic C, University Medicine Greifswald, Greifswald, Germany
| | - Sascha Troschke-Meurer
- Department of Pediatric Hematology and Oncology, University Medicine Greifswald, Greifswald, Germany
| | - Stefan Simm
- Institute of Bioinformatics, University Medicine Greifswald, Greifswald, Germany
| | - Elke Hammer
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Stephan Michalik
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Christian Hentschker
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Björn Corleis
- Institute for Immunology, Friedrich-Loeffler-Institute, Federal Research Institute for Animal Health, Greifswald, Germany
| | - Lucie Loyal
- Si-M/“Der Simulierte Mensch” a science framework of Technische Universität Berlin and Charité - Universitätsmedizin Berlin, Berlin, Germany,Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Maxi Zumpe
- Department of Pediatric Hematology and Oncology, University Medicine Greifswald, Greifswald, Germany
| | - Nikolai Siebert
- Department of Pediatric Hematology and Oncology, University Medicine Greifswald, Greifswald, Germany
| | - Anca Dorhoi
- Institute for Immunology, Friedrich-Loeffler-Institute, Federal Research Institute for Animal Health, Greifswald, Germany
| | - Andreas Thiel
- Si-M/“Der Simulierte Mensch” a science framework of Technische Universität Berlin and Charité - Universitätsmedizin Berlin, Berlin, Germany,Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Holger Lode
- Department of Pediatric Hematology and Oncology, University Medicine Greifswald, Greifswald, Germany
| | - Uwe Völker
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Christian A. Schmidt
- Internal Medicine Clinic C, University Medicine Greifswald, Greifswald, Germany,CONTACT Christian A. Schmidt Internal Medicine Clinic C, University Medicine Greifswald, Greifswald, Germany
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Seo S, Mace EM. Diversity of human NK cell developmental pathways defined by single-cell analyses. Curr Opin Immunol 2022; 74:106-111. [PMID: 34861544 PMCID: PMC8901532 DOI: 10.1016/j.coi.2021.11.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 11/01/2021] [Accepted: 11/09/2021] [Indexed: 02/03/2023]
Abstract
Human natural killer (NK) and innate lymphoid cells (ILCs) include diverse specialized phenotypic and functional subsets that reflect their roles as innate immune effector cells present in tissue and circulation. In recent years, significant advances have been made in better defining their tissue resident phenotypes, developmental pathways, and phenotypic plasticity. Here we offer a brief review of new insights into human NK cell diversity specifically defined by next generation sequencing and single-cell transcriptomic studies and integrate these into our current models of human NK cell developmental trajectories and mature subsets. These studies highlight both a deeper understanding of innate lymphoid cell differentiation and homeostasis and underscore critical questions that remain outstanding in the field.
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Affiliation(s)
- Seungmae Seo
- Vagelos College of Physicians and Surgeons, Department of Pediatrics, Columbia University Irving Medical Center New York NY 10032
| | - Emily M. Mace
- Vagelos College of Physicians and Surgeons, Department of Pediatrics, Columbia University Irving Medical Center New York NY 10032
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