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Giudice V, Fonseca V, Selleri C, Gadina M. Cell Viability Multiplexing: Quantification of Cellular Viability by Barcode Flow Cytometry and Computational Analysis. Methods Mol Biol 2023; 2644:99-121. [PMID: 37142918 DOI: 10.1007/978-1-0716-3052-5_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Fluorescent cell barcoding (FCB) is a useful flow cytometric technique for high-throughput multiplexed analyses and can minimize technical variations after preliminary optimization and validation of protocols. To date, FCB is widely used for measurement of phosphorylation status of certain proteins, while it can be also employed for cellular viability assessment. In this chapter, we describe the protocol to perform FCB combined with viability assessment on lymphocytes and monocytes using manual and computational analysis. We also provide recommendations for FCB protocol optimization and validation for clinical sample analysis.
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Affiliation(s)
- Valentina Giudice
- Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", University of Salerno, Baronissi, Salerno, Italy.
- Cell Biology Section, Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA.
| | - Victoria Fonseca
- Translational Immunology Section, Office of Science Technology (OST), National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), National Institutes of Health, Bethesda, MD, USA
| | - Carmine Selleri
- Cell Biology Section, Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Massimo Gadina
- Translational Immunology Section, Office of Science Technology (OST), National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), National Institutes of Health, Bethesda, MD, USA.
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2
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Junker F, Camillo Teixeira P. Barcoding of live peripheral blood mononuclear cells to assess immune cell phenotypes using full spectrum flow cytometry. Cytometry A 2022; 101:909-921. [PMID: 35150047 DOI: 10.1002/cyto.a.24543] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 01/11/2022] [Accepted: 02/07/2022] [Indexed: 01/27/2023]
Abstract
Barcoded flow cytometry is a multiplexing technique allowing for the simultaneous acquisition of cells from different donors or experimental conditions in a high-throughput manner. This approach allows to synchronize acquisition of samples and reduce variance introduced through the operator or technical platform. However, to date, only very few flow cytometry barcoding protocols have been developed, which often suffer from technical limitations. Here, we developed a novel barcoding protocol for a full-spectrum flow cytometry platform. We developed a 21-color immunophenotyping assay for up to 20 different samples analyzed simultaneously with comparable variance between repeated single-tube acquisition and postde-multiplexing. Barcoding offers great potential in parallelizing the analysis of complex cell populations such as peripheral blood mononuclear cells (PBMCs). Consequently, we assessed the performance of our method in situations where PBMCs were challenged with phytohaemagglutinin (PHA), a strong mitogen and broad activator of B cells and T cells, and superantigen Staphylococcus enterotoxin B (SEB) that has been reported to induce polyclonal T cell activation. PBMCs were either barcoded before pooled challenge or challenged individually pre-barcoding. Our final workflow included pooled immunophenotyping followed by machine learning aided single-cell data analysis and enabled us to identify robust PHA and SEB mode of action related phenotypic changes in PBMC immune cell lineages. Conclusively, we present a novel technique allowing the barcoded acquisition and analysis of PBMCs from up to 20 different donors and present a valid basis for the future development of complex immunophenotyping protocols.
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Affiliation(s)
- Fabian Junker
- Roche Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel, Switzerland
| | - Priscila Camillo Teixeira
- Roche Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel, Switzerland
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3
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Balsamo JA, Penton KE, Zhao Z, Hayes MJ, Lima SM, Irish JM, Bachmann BO. An immunogenic cell injury module for the single-cell multiplexed activity metabolomics platform to identify promising anti-cancer natural products. J Biol Chem 2022; 298:102300. [PMID: 35931117 PMCID: PMC9424577 DOI: 10.1016/j.jbc.2022.102300] [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] [Received: 03/05/2022] [Revised: 07/14/2022] [Accepted: 07/18/2022] [Indexed: 11/05/2022] Open
Abstract
Natural products constitute and significantly impact many current anti-cancer medical interventions. A subset of natural products induces injury processes in malignant cells that recruit and activate host immune cells to produce an adaptive anti-cancer immune response, a process known as immunogenic cell death. However, a challenge in the field is to delineate forms of cell death and injury that best promote durable antitumor immunity. Addressing this with a single-cell chemical biology natural product discovery platform, like multiplex activity metabolomics, would be especially valuable in human leukemia, where cancer cells are heterogeneous and may react differently to the same compounds. Herein, a new ten-color, fluorescent cell barcoding-compatible module measuring six immunogenic cell injury signaling readouts are as follows: DNA damage response (γH2AX), apoptosis (cCAS3), necroptosis (p-MLKL), mitosis (p-Histone H3), autophagy (LC3), and the unfolded protein response (p-EIF2α). A proof-of-concept screen was performed to validate functional changes in single cells induced by secondary metabolites with known mechanisms within bacterial extracts. This assay was then applied in multiplexed activity metabolomics to reveal an unexpected mammalian cell injury profile induced by the natural product narbomycin. Finally, the functional consequences of injury pathways on immunogenicity were compared with three canonical assays for immunogenic hallmarks, ATP, HMGB1, and calreticulin, to correlate secondary metabolite-induced cell injury profiles with canonical markers of immunogenic cell death. In total, this work demonstrated a new phenotypic screen for discovery of natural products that modulate injury response pathways that can contribute to cancer immunogenicity.
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Affiliation(s)
- Joseph A Balsamo
- Department of Pharmacology, Vanderbilt University, Nashville, Tennessee, US
| | - Kathryn E Penton
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, USA
| | - Zhihan Zhao
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, USA
| | - Madeline J Hayes
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee, USA; Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Sierra M Lima
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee, USA; Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jonathan M Irish
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee, USA; Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA; Vanderbilt Institute of Chemical Biology, Nashville, TN, USA; Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Brian O Bachmann
- Department of Pharmacology, Vanderbilt University, Nashville, Tennessee, US; Department of Chemistry, Vanderbilt University, Nashville, Tennessee, USA; Vanderbilt Institute of Chemical Biology, Nashville, TN, USA.
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Delgado-Gonzalez A, Laz-Ruiz JA, Cano-Cortes MV, Huang YW, Gonzalez VD, Diaz-Mochon JJ, Fantl WJ, Sanchez-Martin RM. Hybrid Fluorescent Mass-Tag Nanotrackers as Universal Reagents for Long-Term Live-Cell Barcoding. Anal Chem 2022; 94:10626-10635. [PMID: 35866879 PMCID: PMC9352147 DOI: 10.1021/acs.analchem.2c00795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Barcoding and pooling cells for processing as a composite
sample
are critical to minimize technical variability in multiplex technologies.
Fluorescent cell barcoding has been established as a standard method
for multiplexing in flow cytometry analysis. In parallel, mass-tag
barcoding is routinely used to label cells for mass cytometry. Barcode
reagents currently used label intracellular proteins in fixed and
permeabilized cells and, therefore, are not suitable for studies with
live cells in long-term culture prior to analysis. In this study,
we report the development of fluorescent palladium-based hybrid-tag
nanotrackers to barcode live cells for flow and mass cytometry dual-modal
readout. We describe the preparation, physicochemical characterization,
efficiency of cell internalization, and durability of these nanotrackers
in live cells cultured over time. In addition, we demonstrate their
compatibility with standardized cytometry reagents and protocols.
Finally, we validated these nanotrackers for drug response assays
during a long-term coculture experiment with two barcoded cell lines.
This method represents a new and widely applicable advance for fluorescent
and mass-tag barcoding that is independent of protein expression levels
and can be used to label cells before long-term drug studies.
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Affiliation(s)
- Antonio Delgado-Gonzalez
- GENYO, Centre for Genomics and Oncological Research, Pfizer/University of Granada/Andalusian Regional Gov-ernment, PTS Granada, Avda. Ilustración 114, 18016 Granada, Spain.,Department of Medicinal & Organic Chemistry and Excellence Research Unit of "Chemistry applied to Biomedi-cine and the Environment", Faculty of Pharmacy, University of Granada, Campus de Cartuja s/n, 18071 Granada, Spain.,Biosanitary Research Institute of Granada (ibs.GRANADA), University Hospitals of Granada-University of Grana-da, 18012 Granada, Spain.,Department of Urology, Stanford University School of Medicine, Stanford, California 94305, United States
| | - Jose Antonio Laz-Ruiz
- GENYO, Centre for Genomics and Oncological Research, Pfizer/University of Granada/Andalusian Regional Gov-ernment, PTS Granada, Avda. Ilustración 114, 18016 Granada, Spain.,Department of Medicinal & Organic Chemistry and Excellence Research Unit of "Chemistry applied to Biomedi-cine and the Environment", Faculty of Pharmacy, University of Granada, Campus de Cartuja s/n, 18071 Granada, Spain.,Biosanitary Research Institute of Granada (ibs.GRANADA), University Hospitals of Granada-University of Grana-da, 18012 Granada, Spain
| | - M Victoria Cano-Cortes
- GENYO, Centre for Genomics and Oncological Research, Pfizer/University of Granada/Andalusian Regional Gov-ernment, PTS Granada, Avda. Ilustración 114, 18016 Granada, Spain.,Department of Medicinal & Organic Chemistry and Excellence Research Unit of "Chemistry applied to Biomedi-cine and the Environment", Faculty of Pharmacy, University of Granada, Campus de Cartuja s/n, 18071 Granada, Spain.,Biosanitary Research Institute of Granada (ibs.GRANADA), University Hospitals of Granada-University of Grana-da, 18012 Granada, Spain
| | - Ying-Wen Huang
- Department of Urology, Stanford University School of Medicine, Stanford, California 94305, United States
| | - Veronica D Gonzalez
- Department of Urology, Stanford University School of Medicine, Stanford, California 94305, United States
| | - Juan Jose Diaz-Mochon
- GENYO, Centre for Genomics and Oncological Research, Pfizer/University of Granada/Andalusian Regional Gov-ernment, PTS Granada, Avda. Ilustración 114, 18016 Granada, Spain.,Department of Medicinal & Organic Chemistry and Excellence Research Unit of "Chemistry applied to Biomedi-cine and the Environment", Faculty of Pharmacy, University of Granada, Campus de Cartuja s/n, 18071 Granada, Spain.,Biosanitary Research Institute of Granada (ibs.GRANADA), University Hospitals of Granada-University of Grana-da, 18012 Granada, Spain
| | - Wendy J Fantl
- Department of Urology, Stanford University School of Medicine, Stanford, California 94305, United States.,Stanford Cancer Institute, Stanford University School of Medicine, Stanford, California 94305, United States.,Department of Obstetrics and Gynecology, Stanford University School of Medicine, Stanford, California 94304, United States
| | - Rosario M Sanchez-Martin
- GENYO, Centre for Genomics and Oncological Research, Pfizer/University of Granada/Andalusian Regional Gov-ernment, PTS Granada, Avda. Ilustración 114, 18016 Granada, Spain.,Department of Medicinal & Organic Chemistry and Excellence Research Unit of "Chemistry applied to Biomedi-cine and the Environment", Faculty of Pharmacy, University of Granada, Campus de Cartuja s/n, 18071 Granada, Spain.,Biosanitary Research Institute of Granada (ibs.GRANADA), University Hospitals of Granada-University of Grana-da, 18012 Granada, Spain
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5
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Kaviany S, Bartkowiak T, Dulek DE, Khan YW, Hayes MJ, Schaefer SG, Ye X, Dahunsi DO, Connelly JA, Irish JM, Rathmell JC. Systems Immunology Analyses of STAT1 Gain-of-Function Immune Phenotypes Reveal Heterogeneous Response to IL-6 and Broad Immunometabolic Roles for STAT1. Immunohorizons 2022; 6:447-464. [PMID: 35840326 PMCID: PMC9623573 DOI: 10.4049/immunohorizons.2200041] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 06/21/2022] [Indexed: 11/19/2022] Open
Abstract
Patients with STAT1 gain-of-function (GOF) pathogenic variants have enhanced or prolonged STAT1 phosphorylation following cytokine stimulation and exhibit increased yet heterogeneous susceptibility to infections, autoimmunity, and cancer. Although disease phenotypes are diverse and other genetic factors contribute, how STAT1 GOF affects cytokine sensitivity and cell biology remains poorly defined. In this study, we analyzed the immune and immunometabolic profiles of two patients with known pathogenic heterozygous STAT1 GOF mutation variants. A systems immunology approach of peripheral blood cells from these patients revealed major changes in multiple immune cell compartments relative to healthy adult and pediatric donors. Although many phenotypes of STAT1 GOF donors were shared, including increased Th1 cells but decreased class-switched B cells and plasmacytoid dendritic cell populations, others were heterogeneous. Mechanistically, hypersensitivity for cytokine-induced STAT1 phosphorylation in memory T cell populations was particularly evident in response to IL-6 in one STAT1 GOF patient. Immune cell metabolism directly influences cell function, and the STAT1 GOF patients shared an immunometabolic phenotype of heightened glucose transporter 1 (GLUT1) and carnitine palmitoyl transferase 1A (CPT1a) expression across multiple immune cell lineages. Interestingly, the metabolic phenotypes of the pediatric STAT1 GOF donors more closely resembled or exceeded those of healthy adult than healthy age-similar pediatric donors, which had low expression of these metabolic markers. These results define new features of STAT1 GOF patients, including a differential hypersensitivity for IL-6 and a shared increase in markers of metabolism in many immune cell types that suggests a role for STAT1 in metabolic regulation of immunity.
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Affiliation(s)
- Saara Kaviany
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN.,Vanderbilt Human Immunology Discovery Initiative of the Vanderbilt Center for Immunobiology, Vanderbilt University Medical Center, Nashville, TN
| | - Todd Bartkowiak
- Vanderbilt Human Immunology Discovery Initiative of the Vanderbilt Center for Immunobiology, Vanderbilt University Medical Center, Nashville, TN.,Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN; and
| | - Daniel E Dulek
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN
| | - Yasmin W Khan
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN
| | - Madeline J Hayes
- Vanderbilt Human Immunology Discovery Initiative of the Vanderbilt Center for Immunobiology, Vanderbilt University Medical Center, Nashville, TN.,Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN; and
| | - Samuel G Schaefer
- Vanderbilt Human Immunology Discovery Initiative of the Vanderbilt Center for Immunobiology, Vanderbilt University Medical Center, Nashville, TN.,Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN
| | - Xiang Ye
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN
| | - Debolanle O Dahunsi
- Vanderbilt Human Immunology Discovery Initiative of the Vanderbilt Center for Immunobiology, Vanderbilt University Medical Center, Nashville, TN.,Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN
| | - James A Connelly
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN.,Vanderbilt Human Immunology Discovery Initiative of the Vanderbilt Center for Immunobiology, Vanderbilt University Medical Center, Nashville, TN
| | - Jonathan M Irish
- Vanderbilt Human Immunology Discovery Initiative of the Vanderbilt Center for Immunobiology, Vanderbilt University Medical Center, Nashville, TN; .,Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN; and
| | - Jeffrey C Rathmell
- Vanderbilt Human Immunology Discovery Initiative of the Vanderbilt Center for Immunobiology, Vanderbilt University Medical Center, Nashville, TN; .,Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN
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