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Manohar SM. Shedding Light on Intracellular Proteins using Flow Cytometry. Cell Biochem Biophys 2024:10.1007/s12013-024-01338-1. [PMID: 38831173 DOI: 10.1007/s12013-024-01338-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/24/2024] [Indexed: 06/05/2024]
Abstract
Intracellular protein abundance is routinely measured in mammalian cells using population-based techniques such as western blotting which fail to capture single cell protein levels or using fluorescence microscopy which is although suitable for single cell protein detection but not for rapid analysis of large no. of cells. Flow cytometry offers rapid, high-throughput, multiparameter-based analysis of intracellular protein expression in statistically significant no. of cells at single cell resolution. In past few decades, customized assays have been developed for flow cytometric detection of specific intracellular proteins. This review discusses the scope of flow cytometry for intracellular protein detection in mammalian cells along with specific applications. Technological advancements to overcome the limitations of traditional flow cytometry for the same are also discussed.
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Affiliation(s)
- Sonal M Manohar
- Department of Biological Sciences, Sunandan Divatia School of Science, SVKM's NMIMS (Deemed-to-be) University, Vile Parle (West), Mumbai, 400056, India.
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2
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Cottignies-Calamarte A, He F, Zhu A, Real F, Bomsel M. Protocol to detect infectious SARS-CoV-2 at low levels using in situ hybridization techniques. STAR Protoc 2023; 4:102593. [PMID: 37738115 PMCID: PMC10520661 DOI: 10.1016/j.xpro.2023.102593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 07/21/2023] [Accepted: 09/05/2023] [Indexed: 09/24/2023] Open
Abstract
Low and persistent levels of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA/protein/virus can be detected in clinical samples months after infection, possibly related to the emergence of SARS-CoV-2 variants or development of long coronavirus disease. Here, we present a protocol to detect low levels of viral RNA together with protein using flow cytometry and microscopy. We describe steps for cell infection with SARS-CoV-2 and quantification by fluorescence in situ hybridization-flow cytometry. We then detail procedures for visualization using immunolabeling and RNAscope. This approach is directly applicable to clinical samples. For complete details on the use and execution of this protocol, please refer to Zhu et al. (2022).1.
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Affiliation(s)
- Andréa Cottignies-Calamarte
- Laboratory of Mucosal Entry of HIV and Mucosal Immunity, Université de Paris Cité, Paris, France; Institut Cochin, INSERM U1016, CNRS UMR8104, Université de Paris Cité, Paris, France
| | - Feifan He
- Laboratory of Mucosal Entry of HIV and Mucosal Immunity, Université de Paris Cité, Paris, France; Institut Cochin, INSERM U1016, CNRS UMR8104, Université de Paris Cité, Paris, France
| | - Aiwei Zhu
- Laboratory of Mucosal Entry of HIV and Mucosal Immunity, Université de Paris Cité, Paris, France; Institut Cochin, INSERM U1016, CNRS UMR8104, Université de Paris Cité, Paris, France
| | - Fernando Real
- Laboratory of Mucosal Entry of HIV and Mucosal Immunity, Université de Paris Cité, Paris, France; Institut Cochin, INSERM U1016, CNRS UMR8104, Université de Paris Cité, Paris, France
| | - Morgane Bomsel
- Laboratory of Mucosal Entry of HIV and Mucosal Immunity, Université de Paris Cité, Paris, France; Institut Cochin, INSERM U1016, CNRS UMR8104, Université de Paris Cité, Paris, France.
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3
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Calianese D, Kreiss T, Kasikara C, Davra V, Lahey KC, Gadiyar V, Geng K, Singh S, Honnen W, Jaijyan DK, Reichman C, Siekierka J, Gennaro ML, Kotenko SV, Ucker DS, Brekken RA, Pinter A, Birge RB, Choudhary A. Phosphatidylserine-Targeting Monoclonal Antibodies Exhibit Distinct Biochemical and Cellular Effects on Anti-CD3/CD28-Stimulated T Cell IFN-γ and TNF-α Production. THE JOURNAL OF IMMUNOLOGY 2021; 207:436-448. [PMID: 34215655 DOI: 10.4049/jimmunol.2000763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 05/11/2021] [Indexed: 11/19/2022]
Abstract
Phosphatidylserine (PS)-targeting monoclonal Abs (mAbs) that directly target PS and target PS via β2-gp1 (β2GP1) have been in preclinical and clinical development for over 10 y for the treatment of infectious diseases and cancer. Although the intended targets of PS-binding mAbs have traditionally included pathogens as well as stressed tumor cells and its associated vasculature in oncology, the effects of PS-targeting mAbs on activated immune cells, notably T cells, which externalize PS upon Ag stimulation, is not well understood. Using human T cells from healthy donor PBMCs activated with an anti-CD3 + anti-CD28 Ab mixture (anti-CD3/CD28) as a model for TCR-mediated PS externalization and T cell stimulation, we investigated effects of two different PS-targeting mAbs, 11.31 and bavituximab (Bavi), on TCR activation and TCR-mediated cytokine production in an ex vivo paradigm. Although 11.31 and Bavi bind selectivity to anti-CD3/28 activated T cells in a PS-dependent manner, surprisingly, they display distinct functional activities in their effect on IFN-γ and TNF-ɑ production, whereby 11.31, but not Bavi, suppressed cytokine production. This inhibitory effect on anti-CD3/28 activated T cells was observed on both CD4+ and CD8+ cells and independently of monocytes, suggesting the effects of 11.31 were directly mediated by binding to externalized PS on activated T cells. Imaging showed 11.31 and Bavi bind at distinct focal depots on the cell membrane. Collectively, our findings indicate that PS-targeting mAb 11.31 suppresses cytokine production by anti-CD3/28 activated T cells.
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Affiliation(s)
- David Calianese
- Department of Microbiology, Biochemistry and Molecular Genetics, New Jersey Medical School Cancer Center, Rutgers University, Newark, NJ
| | - Tamara Kreiss
- Department of Microbiology, Biochemistry and Molecular Genetics, New Jersey Medical School Cancer Center, Rutgers University, Newark, NJ.,Department of Chemistry and Biochemistry, The Herman and Margaret Sokol Institute for Pharmaceutical Life Sciences, Montclair State University, Montclair, NJ
| | - Canan Kasikara
- Department of Microbiology, Biochemistry and Molecular Genetics, New Jersey Medical School Cancer Center, Rutgers University, Newark, NJ
| | - Viralkumar Davra
- Department of Microbiology, Biochemistry and Molecular Genetics, New Jersey Medical School Cancer Center, Rutgers University, Newark, NJ
| | - Kevin C Lahey
- Department of Microbiology, Biochemistry and Molecular Genetics, New Jersey Medical School Cancer Center, Rutgers University, Newark, NJ
| | - Varsha Gadiyar
- Department of Microbiology, Biochemistry and Molecular Genetics, New Jersey Medical School Cancer Center, Rutgers University, Newark, NJ
| | - Ke Geng
- Department of Microbiology, Biochemistry and Molecular Genetics, New Jersey Medical School Cancer Center, Rutgers University, Newark, NJ
| | - Sukhwinder Singh
- Department of Pathology and Laboratory Medicine, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ
| | - William Honnen
- Public Health Research Institute Center, New Jersey Medical School, Rutgers University, Newark, NJ
| | - Dabbu Kumar Jaijyan
- Department of Microbiology, Biochemistry and Molecular Genetics, New Jersey Medical School Cancer Center, Rutgers University, Newark, NJ
| | - Charles Reichman
- Public Health Research Institute Center, New Jersey Medical School, Rutgers University, Newark, NJ
| | - John Siekierka
- Department of Chemistry and Biochemistry, The Herman and Margaret Sokol Institute for Pharmaceutical Life Sciences, Montclair State University, Montclair, NJ
| | - Maria Laura Gennaro
- Public Health Research Institute Center, New Jersey Medical School, Rutgers University, Newark, NJ
| | - Sergei V Kotenko
- Department of Microbiology, Biochemistry and Molecular Genetics, New Jersey Medical School Cancer Center, Rutgers University, Newark, NJ
| | - David S Ucker
- Department of Microbiology and Immunology, University of Illinois College of Medicine, Chicago, IL
| | - Rolf A Brekken
- Division of Surgical Oncology, Department of Surgery, Hamon Center for Therapeutic Oncology Research, Dallas, TX; and.,Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX
| | - Abraham Pinter
- Public Health Research Institute Center, New Jersey Medical School, Rutgers University, Newark, NJ
| | - Raymond B Birge
- Department of Microbiology, Biochemistry and Molecular Genetics, New Jersey Medical School Cancer Center, Rutgers University, Newark, NJ
| | - Alok Choudhary
- Public Health Research Institute Center, New Jersey Medical School, Rutgers University, Newark, NJ;
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Arrigucci R, Lakehal K, Vir P, Handler D, Davidow AL, Herrera R, Estrada-Guzmán JD, Bushkin Y, Tyagi S, Lardizabal AA, Gennaro ML. Active Tuberculosis Is Characterized by Highly Differentiated Effector Memory Th1 Cells. Front Immunol 2018; 9:2127. [PMID: 30283456 PMCID: PMC6156157 DOI: 10.3389/fimmu.2018.02127] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 08/29/2018] [Indexed: 12/22/2022] Open
Abstract
Despite advances in diagnosing latent Mycobacterium tuberculosis infection (LTBI), we still lack a diagnostic test that differentiates LTBI from active tuberculosis (TB) or predicts the risk of progression to active disease. One reason for the absence of such a test may be the failure of current assays to capture the dynamic complexities of the immune responses associated with various stages of TB, since these assays measure only a single parameter (release of IFN-γ) and rely on prolonged (overnight) T cell stimulation. We describe a novel, semi-automated RNA flow cytometry assay to determine whether immunological differences can be identified between LTBI and active TB. We analyzed antigen-induced expression of Th1 cytokine mRNA after short (2- and 6-h) stimulation with antigen, in the context of memory T cell immunophenotyping. IFNG and TNFA mRNA induction was detectable in CD4+ T cells after only 2 h of ex vivo stimulation. Moreover, IFNG- and TNFA-expressing CD4+ T cells (Th1 cells) were more frequent in active TB than in LTBI, a difference that is undetectable with conventional, protein-based cytokine assays. We also found that active TB was associated with higher ratios of effector memory to central memory Th1 cells than LTBI. This effector memory phenotype of active TB was associated with increased T cell differentiation, as defined by loss of the CD27 marker, but not with T cell exhaustion, as determined by PD-1 abundance. These results indicate that single-cell-based, mRNA measurements may help identify time-dependent, quantitative differences in T cell functional status between latent infection and active tuberculosis.
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Affiliation(s)
- Riccardo Arrigucci
- Public Health Research Institute, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ, United States
| | - Karim Lakehal
- Public Health Research Institute, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ, United States
| | - Pooja Vir
- Public Health Research Institute, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ, United States
| | - Deborah Handler
- Global Tuberculosis Institute, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ, United States
| | - Amy L Davidow
- Department of Biostatistics, School of Public Health, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ, United States
| | - Rosa Herrera
- Facultad de Medicina Mexicali, Universidad Autónoma de Baja California, Mexicali, Mexico
| | | | - Yuri Bushkin
- Public Health Research Institute, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ, United States
| | - Sanjay Tyagi
- Public Health Research Institute, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ, United States
| | - Alfred A Lardizabal
- Global Tuberculosis Institute, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ, United States
| | - Maria Laura Gennaro
- Public Health Research Institute, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ, United States
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Arrigucci R, Bushkin Y, Radford F, Lakehal K, Vir P, Pine R, Martin D, Sugarman J, Zhao Y, Yap GS, Lardizabal AA, Tyagi S, Gennaro ML. FISH-Flow, a protocol for the concurrent detection of mRNA and protein in single cells using fluorescence in situ hybridization and flow cytometry. Nat Protoc 2017; 12:1245-1260. [PMID: 28518171 DOI: 10.1038/nprot.2017.039] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
We describe a flow-cytometry-based protocol for intracellular mRNA measurements in nonadherent mammalian cells using fluorescence in situ hybridization (FISH) probes. The method, which we call FISH-Flow, allows for high-throughput multiparametric measurements of gene expression, a task that was not feasible with earlier, microscopy-based approaches. The FISH-Flow protocol involves cell fixation, permeabilization and hybridization with a set of fluorescently labeled oligonucleotide probes. In this protocol, surface and intracellular protein markers can also be stained with fluorescently labeled antibodies for simultaneous protein and mRNA measurement. Moreover, a semiautomated, single-tube version of the protocol can be performed with a commercially available cell-wash device that reduces cell loss, operator time and interoperator variability. It takes ∼30 h to perform this protocol. An example of FISH-Flow measurements of cytokine mRNA induction by ex vivo stimulation of primed T cells with specific antigens is described.
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Affiliation(s)
- Riccardo Arrigucci
- Public Health Research Institute, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, New Jersey, USA
| | - Yuri Bushkin
- Public Health Research Institute, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, New Jersey, USA
| | - Felix Radford
- Public Health Research Institute, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, New Jersey, USA
| | - Karim Lakehal
- Public Health Research Institute, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, New Jersey, USA
| | - Pooja Vir
- Public Health Research Institute, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, New Jersey, USA
| | - Richard Pine
- Public Health Research Institute, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, New Jersey, USA
| | | | | | - Yanlin Zhao
- Center for Immunity and Inflammation, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, New Jersey, USA
| | - George S Yap
- Center for Immunity and Inflammation, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, New Jersey, USA
| | - Alfred A Lardizabal
- Global Tuberculosis Institute, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, New Jersey, USA
| | - Sanjay Tyagi
- Public Health Research Institute, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, New Jersey, USA
| | - Maria Laura Gennaro
- Public Health Research Institute, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, New Jersey, USA
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Radford F, Tyagi S, Gennaro ML, Pine R, Bushkin Y. Flow Cytometric Characterization of Antigen-Specific T Cells Based on RNA and Its Advantages in Detecting Infections and Immunological Disorders. Crit Rev Immunol 2016; 36:359-378. [PMID: 28605344 PMCID: PMC5548664 DOI: 10.1615/critrevimmunol.2017018316] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Fluorescence in situ hybridization coupled with flow cytometry (FISH-Flow) is a highly quantitative, high-throughput platform allowing precise quantification of total mRNA transcripts in single cells. In undiagnosed infections posing a significant health burden worldwide, such as latent tuberculosis or asymptomatic recurrent malaria, an important challenge is to develop accurate diagnostic tools. Antigen-specific T cells create a persistent memory to pathogens, making them useful for diagnosis of infection. Stimulation of memory response initiates T-cell transitions between functional states. Numerous studies have shown that changes in protein levels lag real-time T-cell transitions. However, analysis at the single-cell transcriptional level can determine the differences. FISH-Flow is a powerful tool with which to study the functional states of T-cell subsets and to identify the gene expression profiles of antigen-specific T cells during disease progression. Advances in instrumentation, fluorophores, and FISH methodologies will broaden and deepen the use of FISH-Flow, changing the immunological field by allowing determination of functional immune signatures at the mRNA level and the development of new diagnostic tools.
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Affiliation(s)
- Felix Radford
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520
| | - Sanjay Tyagi
- Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark, NJ 07103
| | - Maria Laura Gennaro
- Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark, NJ 07103
| | - Richard Pine
- Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark, NJ 07103
| | - Yuri Bushkin
- Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark, NJ 07103
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