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Delmas A, Oikonomopoulos A, Lacey PN, Fallahi M, Hommes DW, Sundrud MS. Informatics-Based Discovery of Disease-Associated Immune Profiles. PLoS One 2016; 11:e0163305. [PMID: 27669154 PMCID: PMC5036861 DOI: 10.1371/journal.pone.0163305] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 09/07/2016] [Indexed: 01/30/2023] Open
Abstract
Advances in flow and mass cytometry are enabling ultra-high resolution immune profiling in mice and humans on an unprecedented scale. However, the resulting high-content datasets challenge traditional views of cytometry data, which are both limited in scope and biased by pre-existing hypotheses. Computational solutions are now emerging (e.g., Citrus, AutoGate, SPADE) that automate cell gating or enable visualization of relative subset abundance within healthy versus diseased mice or humans. Yet these tools require significant computational fluency and fail to show quantitative relationships between discrete immune phenotypes and continuous disease variables. Here we describe a simple informatics platform that uses hierarchical clustering and nearest neighbor algorithms to associate manually gated immune phenotypes with clinical or pre-clinical disease endpoints of interest in a rapid and unbiased manner. Using this approach, we identify discrete immune profiles that correspond with either weight loss or histologic colitis in a T cell transfer model of inflammatory bowel disease (IBD), and show distinct nodes of immune dysregulation in the IBDs, Crohn’s disease and ulcerative colitis. This streamlined informatics approach for cytometry data analysis leverages publicly available software, can be applied to manually or computationally gated cytometry data, is suitable for any clinical or pre-clinical setting, and embraces ultra-high content flow and mass cytometry as a discovery engine.
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Affiliation(s)
- Amber Delmas
- Department of Cancer Biology, The Scripps Research Institute, Jupiter, Florida, United States of America
- Department of Immunology and Microbial Sciences, The Scripps Research Institute, Jupiter, Florida, United States of America
| | - Angelos Oikonomopoulos
- Division of Digestive Disease, University of California Los Angeles, Los Angeles, California, United States of America
| | - Precious N. Lacey
- Division of Digestive Disease, University of California Los Angeles, Los Angeles, California, United States of America
| | - Mohammad Fallahi
- Informatics Core, The Scripps Institute, Jupiter, Florida, United States of America
| | - Daniel W. Hommes
- Division of Digestive Disease, University of California Los Angeles, Los Angeles, California, United States of America
| | - Mark S. Sundrud
- Department of Cancer Biology, The Scripps Research Institute, Jupiter, Florida, United States of America
- Department of Immunology and Microbial Sciences, The Scripps Research Institute, Jupiter, Florida, United States of America
- * E-mail:
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Mizukami A, Fernandes-Platzgummer A, Carmelo JG, Swiech K, Covas DT, Cabral JMS, da Silva CL. Stirred tank bioreactor culture combined with serum-/xenogeneic-free culture medium enables an efficient expansion of umbilical cord-derived mesenchymal stem/stromal cells. Biotechnol J 2016; 11:1048-59. [PMID: 27168373 DOI: 10.1002/biot.201500532] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Revised: 03/03/2016] [Accepted: 05/10/2016] [Indexed: 01/15/2023]
Abstract
Mesenchymal stem/stromal cells (MSC) are being widely explored as promising candidates for cell-based therapies. Among the different human MSC origins exploited, umbilical cord represents an attractive and readily available source of MSC that involves a non-invasive collection procedure. In order to achieve relevant cell numbers of human MSC for clinical applications, it is crucial to develop scalable culture systems that allow bioprocess control and monitoring, combined with the use of serum/xenogeneic (xeno)-free culture media. In the present study, we firstly established a spinner flask culture system combining gelatin-based Cultispher(®) S microcarriers and xeno-free culture medium for the expansion of umbilical cord matrix (UCM)-derived MSC. This system enabled the production of 2.4 (±1.1) x10(5) cells/mL (n = 4) after 5 days of culture, corresponding to a 5.3 (±1.6)-fold increase in cell number. The established protocol was then implemented in a stirred-tank bioreactor (800 mL working volume) (n = 3) yielding 115 million cells after 4 days. Upon expansion under stirred conditions, cells retained their differentiation ability and immunomodulatory potential. The development of a scalable microcarrier-based stirred culture system, using xeno-free culture medium that suits the intrinsic features of UCM-derived MSC represents an important step towards a GMP compliant large-scale production platform for these promising cell therapy candidates.
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Affiliation(s)
- Amanda Mizukami
- Hemotherapy Center of Ribeirão Preto, Faculty of Medicine of Ribeirão Preto, University of São Paulo, Ribeirão Preto-SP, Brazil
| | - Ana Fernandes-Platzgummer
- Department of Bioengineering and IBB-Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal
| | - Joana G Carmelo
- Department of Bioengineering and IBB-Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal
| | - Kamilla Swiech
- Hemotherapy Center of Ribeirão Preto, Faculty of Medicine of Ribeirão Preto, University of São Paulo, Ribeirão Preto-SP, Brazil. .,Department of Pharmaceutical Sciences, Faculty of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto-SP, Brazil.
| | - Dimas T Covas
- Hemotherapy Center of Ribeirão Preto, Faculty of Medicine of Ribeirão Preto, University of São Paulo, Ribeirão Preto-SP, Brazil
| | - Joaquim M S Cabral
- Department of Bioengineering and IBB-Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal
| | - Cláudia L da Silva
- Department of Bioengineering and IBB-Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal .
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Lakschevitz FS, Hassanpour S, Rubin A, Fine N, Sun C, Glogauer M. Identification of neutrophil surface marker changes in health and inflammation using high-throughput screening flow cytometry. Exp Cell Res 2016; 342:200-9. [PMID: 26970376 DOI: 10.1016/j.yexcr.2016.03.007] [Citation(s) in RCA: 111] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Accepted: 03/06/2016] [Indexed: 01/05/2023]
Abstract
Neutrophils are the most abundant white blood cell and are an essential component of the innate immune system. A complete cataloguing of cell surface markers has not been undertaken for neutrophils isolated from circulation as well as healthy and inflamed tissues. To identify cell-surface markers specific to human neutrophils, we used high-throughput flow cytometry to screen neutrophil populations isolated from blood and oral rinses from healthy and chronic periodontitis patients against a panel of 374 known cluster of differentiation (CD) antibodies. This screen identified CD11b, CD16, and CD66b as markers that are consistently expressed on neutrophils independent of the cell location, level of activation and disease state. Cell sorting against CD11b, CD16 and CD66b allowed for the enrichment of mature neutrophils, yielding neutrophil populations with up to 99% purity. These findings suggest an ideal surface marker set for isolating mature neutrophils from humans. The screen also demonstrated that tissue neutrophils from chronically inflamed tissue display a unique surface marker set compared to tissue neutrophils present in healthy, non-inflamed tissues.
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Affiliation(s)
- Flavia S Lakschevitz
- Department of Periodontology, Faculty of Dentistry, University of Toronto, Toronto, Ontario, Canada; Matrix Dynamics Group, Faculty of Dentistry, University of Toronto, Toronto, Ontario, Canada.
| | - Siavash Hassanpour
- Department of Periodontology, Faculty of Dentistry, University of Toronto, Toronto, Ontario, Canada; Matrix Dynamics Group, Faculty of Dentistry, University of Toronto, Toronto, Ontario, Canada
| | - Ayala Rubin
- Matrix Dynamics Group, Faculty of Dentistry, University of Toronto, Toronto, Ontario, Canada
| | - Noah Fine
- Matrix Dynamics Group, Faculty of Dentistry, University of Toronto, Toronto, Ontario, Canada
| | - Chunxiang Sun
- Department of Periodontology, Faculty of Dentistry, University of Toronto, Toronto, Ontario, Canada; Matrix Dynamics Group, Faculty of Dentistry, University of Toronto, Toronto, Ontario, Canada
| | - Michael Glogauer
- Department of Periodontology, Faculty of Dentistry, University of Toronto, Toronto, Ontario, Canada; Matrix Dynamics Group, Faculty of Dentistry, University of Toronto, Toronto, Ontario, Canada.
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Wang A, Chen L, Li C, Zhu Y. Heterogeneity in cancer stem cells. Cancer Lett 2015; 357:63-68. [DOI: 10.1016/j.canlet.2014.11.040] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Revised: 11/18/2014] [Accepted: 11/18/2014] [Indexed: 01/06/2023]
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Van de Laar E, Clifford M, Hasenoeder S, Kim BR, Wang D, Lee S, Paterson J, Vu NM, Waddell TK, Keshavjee S, Tsao MS, Ailles L, Moghal N. Cell surface marker profiling of human tracheal basal cells reveals distinct subpopulations, identifies MST1/MSP as a mitogenic signal, and identifies new biomarkers for lung squamous cell carcinomas. Respir Res 2014; 15:160. [PMID: 25551685 PMCID: PMC4343068 DOI: 10.1186/s12931-014-0160-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Accepted: 12/17/2014] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND The large airways of the lungs (trachea and bronchi) are lined with a pseudostratified mucociliary epithelium, which is maintained by stem cells/progenitors within the basal cell compartment. Alterations in basal cell behavior can contribute to large airway diseases including squamous cell carcinomas (SQCCs). Basal cells have traditionally been thought of as a uniform population defined by basolateral position, cuboidal cell shape, and expression of pan-basal cell lineage markers like KRT5 and TP63. While some evidence suggests that basal cells are not all functionally equivalent, few heterogeneously expressed markers have been identified to purify and study subpopulations. In addition, few signaling pathways have been identified that regulate their cell behavior. The goals of this work were to investigate tracheal basal cell diversity and to identify new signaling pathways that regulate basal cell behavior. METHODS We used flow cytometry (FACS) to profile cell surface marker expression at a single cell level in primary human tracheal basal cell cultures that maintain stem cell/progenitor activity. FACS results were validated with tissue staining, in silico comparisons with normal basal cell and lung cancer datasets, and an in vitro proliferation assay. RESULTS We identified 105 surface markers, with 47 markers identifying potential subpopulations. These subpopulations generally fell into more (~ > 13%) or less abundant (~ < 6%) groups. Microarray gene expression profiling supported the heterogeneous expression of these markers in the total population, and immunostaining of large airway tissue suggested that some of these markers are relevant in vivo. 24 markers were enriched in lung SQCCs relative to adenocarcinomas, with four markers having prognostic significance in SQCCs. We also identified 33 signaling receptors, including the MST1R/RON growth factor receptor, whose ligand MST1/MSP was mitogenic for basal cells. CONCLUSION This work provides the largest description to date of molecular diversity among human large airway basal cells. Furthermore, these markers can be used to further study basal cell function in repair and disease, and may aid in the classification and study of SQCCs.
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Affiliation(s)
- Emily Van de Laar
- />Department of Medical Biophysics, Ontario Cancer Institute/Campbell Family Cancer Research Institute/Princess Margaret Cancer Centre/University Health Network, University of Toronto, Toronto, ON M5G 1 L7 Canada
| | - Monica Clifford
- />Department of Medical Biophysics, Ontario Cancer Institute/Campbell Family Cancer Research Institute/Princess Margaret Cancer Centre/University Health Network, University of Toronto, Toronto, ON M5G 1 L7 Canada
| | - Stefan Hasenoeder
- />Department of Medical Biophysics, Ontario Cancer Institute/Campbell Family Cancer Research Institute/Princess Margaret Cancer Centre/University Health Network, University of Toronto, Toronto, ON M5G 1 L7 Canada
- />Present address: Helmholtz Zentrum München, Institute of Stem Cell Research, Ingolstädter Landstrasse 1, 85746 Neuherberg, Germany
| | - Bo Ram Kim
- />Department of Medical Biophysics, Ontario Cancer Institute/Campbell Family Cancer Research Institute/Princess Margaret Cancer Centre/University Health Network, University of Toronto, Toronto, ON M5G 1 L7 Canada
| | - Dennis Wang
- />Department of Medical Biophysics, Ontario Cancer Institute/Campbell Family Cancer Research Institute/Princess Margaret Cancer Centre/University Health Network, University of Toronto, Toronto, ON M5G 1 L7 Canada
| | - Sharon Lee
- />Department of Medical Biophysics, Ontario Cancer Institute/Campbell Family Cancer Research Institute/Princess Margaret Cancer Centre/University Health Network, University of Toronto, Toronto, ON M5G 1 L7 Canada
- />Department of Applied Mathematics, University of Waterloo, 200 University Avenue West, Waterloo, ON N2L 3G1 Canada
| | - Josh Paterson
- />Department of Medical Biophysics, Ontario Cancer Institute/Campbell Family Cancer Research Institute/Princess Margaret Cancer Centre/University Health Network, University of Toronto, Toronto, ON M5G 1 L7 Canada
| | - Nancy M Vu
- />Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112 USA
- />Present address: University of Utah School of Medicine, Salt Lake City, UT 84132 USA
| | - Thomas K Waddell
- />Toronto Lung Transplant Program, University Health Network, University of Toronto, Toronto, ON M5G 1 L7 Canada
| | - Shaf Keshavjee
- />Toronto Lung Transplant Program, University Health Network, University of Toronto, Toronto, ON M5G 1 L7 Canada
| | - Ming-Sound Tsao
- />Department of Medical Biophysics, Ontario Cancer Institute/Campbell Family Cancer Research Institute/Princess Margaret Cancer Centre/University Health Network, University of Toronto, Toronto, ON M5G 1 L7 Canada
| | - Laurie Ailles
- />Department of Medical Biophysics, Ontario Cancer Institute/Campbell Family Cancer Research Institute/Princess Margaret Cancer Centre/University Health Network, University of Toronto, Toronto, ON M5G 1 L7 Canada
| | - Nadeem Moghal
- />Department of Medical Biophysics, Ontario Cancer Institute/Campbell Family Cancer Research Institute/Princess Margaret Cancer Centre/University Health Network, University of Toronto, Toronto, ON M5G 1 L7 Canada
- />Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112 USA
- />Present address: Ontario Cancer Institute and Princess Margaret Hospital, University Health Network, Toronto, ON M5G 1 L7 Canada
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