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Waerlop G, Leroux-Roels G, Pagnon A, Begue S, Salaun B, Janssens M, Medaglini D, Pettini E, Montomoli E, Gianchecchi E, Lambe T, Godfrey L, Bull M, Bellamy D, Amdam H, Bredholt G, Cox RJ, Clement F. Proficiency tests to evaluate the impact on assay outcomes of harmonized influenza-specific Intracellular Cytokine Staining (ICS) and IFN-ɣ Enzyme-Linked ImmunoSpot (ELISpot) protocols. J Immunol Methods 2023; 523:113584. [PMID: 37918618 DOI: 10.1016/j.jim.2023.113584] [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: 04/16/2023] [Revised: 09/30/2023] [Accepted: 10/28/2023] [Indexed: 11/04/2023]
Abstract
The magnitude and quality of cell-mediated immune responses elicited by natural infection or vaccination are commonly measured by Interferon-ɣ (IFN-ɣ) Enzyme-Linked ImmunoSpot (ELISpot) and Intracellular Cytokine Staining (ICS). To date, laboratories apply a variety of in-house procedures which leads to diverging results, complicates interlaboratory comparisons and hampers vaccine evaluations. During the FLUCOP project, efforts have been made to develop harmonized Standard Operating Procedures (SOPs) for influenza-specific IFN-ɣ ELISpot and ICS assays. Exploratory pilot studies provided information about the interlaboratory variation before harmonization efforts were initiated. Here we report the results of two proficiency tests organized to evaluate the impact of the harmonization effort on assay results and the performance of participating FLUCOP partners. The introduction of the IFN-ɣ ELISpot SOP reduced variation of both background and stimulated responses. Post-harmonization background responses were all lower than an arbitrary threshold of 50 SFU/million cells. When stimulated with A/California and B/Phuket, a statistically significant reduction in variation (p < 0.0001) was observed and CV values were strongly reduced, from 148% to 77% for A/California and from 126% to 73% for B/Phuket. The harmonizing effect of applying an ICS SOP was also confirmed by an increased homogeneity of data obtained by the individual labs. The application of acceptance criteria on cell viability and background responses further enhanced the data homogeneity. Finally, as the same set of samples was analyzed by both the IFN-ɣ ELISpot and the ICS assays, a method comparison was performed. A clear correlation between the two methods was observed, but they cannot be considered interchangeable. In conclusion, proficiency tests show that a limited harmonization effort consisting of the introduction of SOPs and the use of the same in vitro stimulating antigens leads to a reduction of the interlaboratory variation of IFN-ɣ ELISpot data and demonstrate that substantial improvements for the ICS assay are achieved as comparable laboratory datasets could be generated. Additional steps to further reduce the interlaboratory variation of ICS data can consist of standardized gating templates and detailed data reporting instructions as well as further efforts to harmonize reagent and instrument use.
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Affiliation(s)
- Gwenn Waerlop
- Center for Vaccinology (CEVAC), Ghent University and University Hospital, Ghent, Belgium.
| | - Geert Leroux-Roels
- Center for Vaccinology (CEVAC), Ghent University and University Hospital, Ghent, Belgium
| | - Anke Pagnon
- Sanofi, Research Global Immunology, Marcy l'Etoile, France
| | - Sarah Begue
- Sanofi, Research Global Immunology, Marcy l'Etoile, France
| | | | | | - Donata Medaglini
- Laboratory of Molecular Microbiology and Biotechnology, Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Elena Pettini
- Laboratory of Molecular Microbiology and Biotechnology, Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Emanuele Montomoli
- Department of Molecular and Developmental Medicine, University of Siena, Siena, Italy; VisMederi srl, 53100 Siena, Italy
| | | | - Teresa Lambe
- Oxford Vaccine Group, Department of Paediatrics, Medical Sciences Division, University of Oxford, UK; Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, United Kingdom
| | - Leila Godfrey
- Oxford Vaccine Group, Department of Paediatrics, Medical Sciences Division, University of Oxford, UK
| | - Maireid Bull
- Oxford Vaccine Group, Department of Paediatrics, Medical Sciences Division, University of Oxford, UK; Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, United Kingdom
| | - Duncan Bellamy
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Håkon Amdam
- Influenza Centre, Department of Clinical Science, University of Bergen, N5021 Bergen, Norway
| | - Geir Bredholt
- Influenza Centre, Department of Clinical Science, University of Bergen, N5021 Bergen, Norway
| | - Rebecca Jane Cox
- Influenza Centre, Department of Clinical Science, University of Bergen, N5021 Bergen, Norway
| | - Frédéric Clement
- Center for Vaccinology (CEVAC), Ghent University and University Hospital, Ghent, Belgium
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2
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Baldzhieva A, Burnusuzov HA, Murdjeva MA, Dimcheva TD, Taskov HB. A concise review of flow cytometric methods for minimal residual disease assessment in childhood B-cell precursor acute lymphoblastic leukemia. Folia Med (Plovdiv) 2023; 65:355-361. [PMID: 38351809 DOI: 10.3897/folmed.65.e96440] [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: 10/17/2022] [Accepted: 01/04/2023] [Indexed: 02/16/2024] Open
Abstract
Minimal residual disease refers to a leukemia cell population that is resistant to chemotherapy or radiotherapy and leads to disease relapse. The assessment of MRD is crucial for making an accurate prognosis of the disease and for the choice of optimal treatment strategy. Here, we review the advantages and disadvantages of the available genetic and phenotypic methods and focus on the multiparametric flow cytometry as a promising method with greater sensitivity, speed, and standardization options. In addition, we discuss how the application of automated data analysis outweighs the use of complex combinations of windows and gates in classical analysis, thus eliminating subjective evaluation.
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3
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Baumgaertner P, Sankar M, Herrera F, Benedetti F, Barras D, Thierry AC, Dangaj D, Kandalaft LE, Coukos G, Xenarios I, Guex N, Harari A. Unsupervised Analysis of Flow Cytometry Data in a Clinical Setting Captures Cell Diversity and Allows Population Discovery. Front Immunol 2021; 12:633910. [PMID: 33995353 PMCID: PMC8119773 DOI: 10.3389/fimmu.2021.633910] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 04/12/2021] [Indexed: 11/13/2022] Open
Abstract
Data obtained with cytometry are increasingly complex and their interrogation impacts the type and quality of knowledge gained. Conventional supervised analyses are limited to pre-defined cell populations and do not exploit the full potential of data. Here, in the context of a clinical trial of cancer patients treated with radiotherapy, we performed longitudinal flow cytometry analyses to identify multiple distinct cell populations in circulating whole blood. We cross-compared the results from state-of-the-art recommended supervised analyses with results from MegaClust, a high-performance data-driven clustering algorithm allowing fast and robust identification of cell-type populations. Ten distinct cell populations were accurately identified by supervised analyses, including main T, B, dendritic cell (DC), natural killer (NK) and monocytes subsets. While all ten subsets were also identified with MegaClust, additional cell populations were revealed (e.g. CD4+HLA-DR+ and NKT-like subsets), and DC profiling was enriched by the assignment of additional subset-specific markers. Comparison between transcriptomic profiles of purified DC populations and publicly available datasets confirmed the accuracy of the unsupervised clustering algorithm and demonstrated its potential to identify rare and scarcely described cell subsets. Our observations show that data-driven analyses of cytometry data significantly enrich the amount and quality of knowledge gained, representing an important step in refining the characterization of immune responses.
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Affiliation(s)
- Petra Baumgaertner
- Centre of Experimental Therapeutics, Department of Oncology, University Hospital of Lausanne (CHUV), Lausanne, Switzerland.,Department of Oncology, University Hospital of Lausanne (CHUV), Lausanne, Switzerland
| | - Martial Sankar
- Vital-IT, Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Fernanda Herrera
- Department of Oncology, University Hospital of Lausanne (CHUV), Lausanne, Switzerland
| | - Fabrizio Benedetti
- Centre of Experimental Therapeutics, Department of Oncology, University Hospital of Lausanne (CHUV), Lausanne, Switzerland.,Department of Oncology, University Hospital of Lausanne (CHUV), Lausanne, Switzerland
| | - David Barras
- Centre of Experimental Therapeutics, Department of Oncology, University Hospital of Lausanne (CHUV), Lausanne, Switzerland.,Department of Oncology, University Hospital of Lausanne (CHUV), Lausanne, Switzerland
| | - Anne-Christine Thierry
- Centre of Experimental Therapeutics, Department of Oncology, University Hospital of Lausanne (CHUV), Lausanne, Switzerland.,Department of Oncology, University Hospital of Lausanne (CHUV), Lausanne, Switzerland
| | - Denarda Dangaj
- Centre of Experimental Therapeutics, Department of Oncology, University Hospital of Lausanne (CHUV), Lausanne, Switzerland.,Department of Oncology, University Hospital of Lausanne (CHUV), Lausanne, Switzerland.,Ludwig Institute for Cancer Research, University of Lausanne (UNIL), Lausanne, Switzerland
| | - Lana E Kandalaft
- Centre of Experimental Therapeutics, Department of Oncology, University Hospital of Lausanne (CHUV), Lausanne, Switzerland.,Department of Oncology, University Hospital of Lausanne (CHUV), Lausanne, Switzerland.,Ludwig Institute for Cancer Research, University of Lausanne (UNIL), Lausanne, Switzerland
| | - George Coukos
- Department of Oncology, University Hospital of Lausanne (CHUV), Lausanne, Switzerland.,Ludwig Institute for Cancer Research, University of Lausanne (UNIL), Lausanne, Switzerland
| | - Ioannis Xenarios
- Department of Oncology, University Hospital of Lausanne (CHUV), Lausanne, Switzerland
| | - Nicolas Guex
- Vital-IT, Swiss Institute of Bioinformatics, Lausanne, Switzerland.,Bioinformatics Competence Center (BICC), University of Lausanne, Lausanne, Switzerland
| | - Alexandre Harari
- Centre of Experimental Therapeutics, Department of Oncology, University Hospital of Lausanne (CHUV), Lausanne, Switzerland.,Department of Oncology, University Hospital of Lausanne (CHUV), Lausanne, Switzerland.,Ludwig Institute for Cancer Research, University of Lausanne (UNIL), Lausanne, Switzerland
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4
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Sun J, Kroeger JL, Markowitz J. Introduction to Multiparametric Flow Cytometry and Analysis of High-Dimensional Data. Methods Mol Biol 2021; 2194:239-253. [PMID: 32926370 PMCID: PMC7868168 DOI: 10.1007/978-1-0716-0849-4_13] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Multiparametric flow cytometry is a technique utilized in translational experiments that utilizes fluorescently tagged antibodies and functional fluorescent dyes to measure proteins on the surface or in the cytoplasm of cells and to measure processes occurring within cells themselves. These fluorescent molecules, or fluorophores, can be tagged to antibodies to measure specific biological molecules such as proteins inside or on the surface of cells. Small organic compounds such as the nucleic acid binding dye propidium iodide (PI) can permeate compromised cell membranes when cells are no longer viable or used to measure DNA content of cycling cells. Successful completion of flow cytometry experiments requires expertise in both the preparation of the samples, acquisition of the samples on instruments, and analyses of the results. This chapter describes the principles needed to conduct a successful multiparameter flow cytometry experiment needed for drug development with references to well established internet resources that are useful to those less experienced in the field. In addition, we provide a brief introduction to data analysis including complex analysis of 10+ parameters simultaneously. These high-dimensional datasets require novel methods for analysis due to the volume of data collected, which are also introduced in this chapter.
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Affiliation(s)
- James Sun
- Department of Cutaneous Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Jodi L Kroeger
- The Flow Cytometry Core Facility, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Joseph Markowitz
- Department of Oncologic Sciences, University of South Florida, Morsani School of Medicine, Tampa, FL, USA.
- Department of Cutaneous Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA.
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5
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Cesano A, Cannarile MA, Gnjatic S, Gomes B, Guinney J, Karanikas V, Karkada M, Kirkwood JM, Kotlan B, Masucci GV, Meeusen E, Monette A, Naing A, Thorsson V, Tschernia N, Wang E, Wells DK, Wyant TL, Rutella S. Society for Immunotherapy of Cancer clinical and biomarkers data sharing resource document: Volume II-practical challenges. J Immunother Cancer 2020; 8:e001472. [PMID: 33323463 PMCID: PMC7745522 DOI: 10.1136/jitc-2020-001472] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/06/2020] [Indexed: 01/10/2023] Open
Abstract
The development of strongly predictive validated biomarkers is essential for the field of immuno-oncology (IO) to advance. The highly complex, multifactorial data sets required to develop these biomarkers necessitate effective, responsible data-sharing efforts in order to maximize the scientific knowledge and utility gained from their collection. While the sharing of clinical- and safety-related trial data has already been streamlined to a large extent, the sharing of biomarker-aimed clinical trial derived data and data sets has been met with a number of hurdles that have impaired the progression of biomarkers from hypothesis to clinical use. These hurdles include technical challenges associated with the infrastructure, technology, workforce, and sustainability required for clinical biomarker data sharing. To provide guidance and assist in the navigation of these challenges, the Society for Immunotherapy of Cancer (SITC) Biomarkers Committee convened to outline the challenges that researchers currently face, both at the conceptual level (Volume I) and at the technical level (Volume II). The committee also suggests possible solutions to these problems in the form of professional standards and harmonized requirements for data sharing, assisting in continued progress toward effective, clinically relevant biomarkers in the IO setting.
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Affiliation(s)
| | - Michael A Cannarile
- Roche Pharmaceutical Research and Early Development Oncology, Roche Innovation Center Munich, Penzberg, Germany
| | - Sacha Gnjatic
- Department of Medicine, Tisch Cancer Institute, Icahn School of Medicine, New York, New York, USA
| | - Bruno Gomes
- Roche Pharmaceutical Research and Early Development Oncology, Roche Innovation Center, Basel, Switzerland
| | | | - Vaios Karanikas
- Roche Pharmaceutical Research and Early Development Oncology, Roche Innovation Center, Zürich, Switzerland
| | - Mohan Karkada
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, USA
| | - John M Kirkwood
- Department of Medicine, Division of Hematology/Oncology, University of Pittsburgh School of Medicine and Melanoma Center at UPMC Hillman Cancer Center, Pittsburgh, Pennsylvania, USA
| | - Beatrix Kotlan
- National Institute of Oncology, Budapest, Budapest, Hungary
| | | | - Els Meeusen
- CancerProbe Pty Ltd, Prahran, Victoria, Australia
| | - Anne Monette
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
| | - Aung Naing
- Department of Investigational Cancer Therapeutics, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | | | - Nicholas Tschernia
- Department of Medicine, Division of Hematology/Oncology, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - Ena Wang
- Allogene Therapeutics, South San Francisco, California, USA
| | - Daniel K Wells
- Parker Institute for Cancer Immunotherapy, San Francisco, California, USA
| | | | - Sergio Rutella
- John van Geest Cancer Research Centre, Nottingham Trent University, Nottingham, Nottinghamshire, UK
- Centre for Health, Ageing and Understanding Disease (CHAUD), Nottingham Trent University, Nottingham, Nottinghamshire, UK
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6
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Lucchesi S, Furini S, Medaglini D, Ciabattini A. From Bivariate to Multivariate Analysis of Cytometric Data: Overview of Computational Methods and Their Application in Vaccination Studies. Vaccines (Basel) 2020; 8:vaccines8010138. [PMID: 32244919 PMCID: PMC7157606 DOI: 10.3390/vaccines8010138] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 03/17/2020] [Accepted: 03/18/2020] [Indexed: 12/15/2022] Open
Abstract
Flow and mass cytometry are used to quantify the expression of multiple extracellular or intracellular molecules on single cells, allowing the phenotypic and functional characterization of complex cell populations. Multiparametric flow cytometry is particularly suitable for deep analysis of immune responses after vaccination, as it allows to measure the frequency, the phenotype, and the functional features of antigen-specific cells. When many parameters are investigated simultaneously, it is not feasible to analyze all the possible bi-dimensional combinations of marker expression with classical manual analysis and the adoption of advanced automated tools to process and analyze high-dimensional data sets becomes necessary. In recent years, the development of many tools for the automated analysis of multiparametric cytometry data has been reported, with an increasing record of publications starting from 2014. However, the use of these tools has been preferentially restricted to bioinformaticians, while few of them are routinely employed by the biomedical community. Filling the gap between algorithms developers and final users is fundamental for exploiting the advantages of computational tools in the analysis of cytometry data. The potentialities of automated analyses range from the improvement of the data quality in the pre-processing steps up to the unbiased, data-driven examination of complex datasets using a variety of algorithms based on different approaches. In this review, an overview of the automated analysis pipeline is provided, spanning from the pre-processing phase to the automated population analysis. Analysis based on computational tools might overcame both the subjectivity of manual gating and the operator-biased exploration of expected populations. Examples of applications of automated tools that have successfully improved the characterization of different cell populations in vaccination studies are also presented.
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Affiliation(s)
- Simone Lucchesi
- Laboratory of Molecular Microbiology and Biotechnology (LA.M.M.B.), Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy; (S.L.); (D.M.)
| | - Simone Furini
- Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy;
| | - Donata Medaglini
- Laboratory of Molecular Microbiology and Biotechnology (LA.M.M.B.), Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy; (S.L.); (D.M.)
| | - Annalisa Ciabattini
- Laboratory of Molecular Microbiology and Biotechnology (LA.M.M.B.), Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy; (S.L.); (D.M.)
- Correspondence:
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7
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Roshal M. Measurable disease evaluation in patients with myeloma. Best Pract Res Clin Haematol 2020; 33:101154. [PMID: 32139019 DOI: 10.1016/j.beha.2020.101154] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 01/30/2020] [Indexed: 01/09/2023]
Abstract
Recent years saw significant breakthroughs in treatment of multiple myeloma. Durable remissions are now seen in a significant proportion of patients with the previously uniformly incurable and progressive disease. Yet because of deep suppression of the neoplastic myeloma clones by the newer therapies, older disease monitoring techniques are insufficient to distinguish between the patients at high risk of imminent relapse and those in whom durable remission is expected. This review briefly describes prognostic and therapeutic implications of measurable disease (MRD) evaluation, explains why deep MRD evaluation is needed for patients without morphologic evidence of disease, and reviews the state of the art of evaluation of myeloma MRD by flow cytometry.
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Affiliation(s)
- Mikhail Roshal
- Hematopathology Service, Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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8
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Pedersen NW, Laske K, Maurer D, Welters M, Walter S, Gouttefangeas C, Hadrup SR. Optimization in Detection of Antigen-Specific T Cells Through Differentially Labeled MHC Multimers. Cytometry A 2019; 97:955-964. [PMID: 31808999 PMCID: PMC7540688 DOI: 10.1002/cyto.a.23942] [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: 05/22/2019] [Revised: 11/15/2019] [Accepted: 11/19/2019] [Indexed: 11/09/2022]
Abstract
A large variety of fluorescent molecules are used on a regular basis to tag major histocompatibility complex (MHC) multimers for detection of antigen-specific T cells. We have evaluated the way in which the choice of fluorescent label can impact the detection of MHC multimer binding T cells in an exploratory proficiency panel where detection of MHC multimer binding T cells was assessed across 16 different laboratories. We found that the staining index (SI) of the multimer reagent provided the best direct correlation with the value of a given fluorochrome for T cell detection studies. The SI is dependent on flow cytometer settings and chosen antibody panel; hence, the optimal fluorochrome selection may differ from lab to lab. Consequently, we describe a strategy to evaluate performance of the detection channels and optimize the SI for selected fluorescent molecules. This approach can easily be used to test and optimize fluorescence detection in relation to MHC multimer staining and in general, for antibody-based identification of rare cell populations. © 2019 The Authors. Cytometry Part A published by Wiley Periodicals, Inc. on behalf of International Society for Advancement of Cytometry.
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Affiliation(s)
| | - Karoline Laske
- Department of Immunology, Institute of Cell Biology, University of Tübingen, Tübingen, Germany.,Immatics Biotechnologies GmbH, Tübingen, Germany
| | | | - Marij Welters
- Department of Clinical Oncology, Leiden University Medical Center, Leiden, Netherlands
| | | | - Cécile Gouttefangeas
- Department of Immunology, Institute of Cell Biology, University of Tübingen, Tübingen, Germany
| | - Sine Reker Hadrup
- Department of Health Technology, Technical University of Denmark, Copenhagen, Denmark
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9
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Gouttefangeas C, Schuhmacher J, Dimitrov S. Adhering to adhesion: assessing integrin conformation to monitor T cells. Cancer Immunol Immunother 2019; 68:1855-1863. [PMID: 31309255 PMCID: PMC11028104 DOI: 10.1007/s00262-019-02365-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 07/02/2019] [Indexed: 11/27/2022]
Abstract
Monitoring T cells is of major importance for the development of immunotherapies. Recent sophisticated assays can address particular aspects of the anti-tumor T-cell repertoire or support very large-scale immune screening for biomarker discovery. Robust methods for the routine assessment of the quantity and quality of antigen-specific T cells remain, however, essential. This review discusses selected methods that are commonly used for T-cell monitoring and summarizes the advantages and limitations of these assays. We also present a new functional assay, which specifically detects activated β2 integrins within a very short time following CD8+ T-cell stimulation. Because of its unique and favorable characteristics, this assay could be useful for implementation into our T-cell monitoring toolbox.
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Affiliation(s)
- Cécile Gouttefangeas
- Department of Immunology, Interfaculty Institute for Cell Biology, Eberhard Karls University, Auf der Morgenstelle 15, 72076, Tübingen, Germany.
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Partner Site Tübingen, Tübingen, Germany.
| | - Juliane Schuhmacher
- Department of Immunology, Interfaculty Institute for Cell Biology, Eberhard Karls University, Auf der Morgenstelle 15, 72076, Tübingen, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Partner Site Tübingen, Tübingen, Germany
| | - Stoyan Dimitrov
- Institute of Medical Psychology and Behavioral Neurobiology, Eberhard Karls University, Otfried-Müller Straße 25, 72076, Tübingen, Germany.
- German Center for Diabetes Research, 72076, Tübingen, Germany.
- Institute for Diabetes Research and Metabolic Diseases, Helmholtz Center Munich at the University of Tübingen (IDM), Otfried-Müller Straße 10, 72076, Tübingen, Germany.
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10
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Vazquez J, Ong IM, Stanic AK. Single-cell technologies in reproductive immunology. Am J Reprod Immunol 2019; 82:e13157. [PMID: 31206899 PMCID: PMC6697222 DOI: 10.1111/aji.13157] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 06/06/2019] [Accepted: 06/07/2019] [Indexed: 11/29/2022] Open
Abstract
The maternal-fetal interface represents a unique immune privileged site that maintains the ability to defend against pathogens while orchestrating the necessary tissue remodeling required for placentation. The recent discovery of novel cellular families (innate lymphoid cells, tissue-resident NK cells) suggests that our understanding of the decidual immunome is incomplete. To understand this complex milieu, new technological developments allow reproductive immunologists to collect increasingly complex data at a cellular resolution. Polychromatic flow cytometry allows for greater resolution in the identification of novel cell types by surface and intracellular protein. Single-cell RNA-seq coupled with microfluidics allows for efficient cellular transcriptomics. The extreme dimensionality and size of data sets generated, however, requires the application of novel computational approaches for unbiased analysis. There are now multiple dimensionality reduction (tSNE, SPADE) and visualization tools (SPICE) that allow researchers to efficiently analyze flow cytometry data. Development of computational tools has also been extended to RNA-seq data (including scRNA-seq), which requires specific analytical tools. Here, we provide an overview and a brief primer for the reproductive immunology community on data acquisition and computational tools for the analysis of complex flow cytometry and RNA-seq data.
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Affiliation(s)
- Jessica Vazquez
- Division of Reproductive Sciences, University of Wisconsin-Madison, Madison, WI
| | - Irene M Ong
- Division of Reproductive Sciences, University of Wisconsin-Madison, Madison, WI
- Division of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI
| | - Aleksandar K. Stanic
- Division of Reproductive Sciences, University of Wisconsin-Madison, Madison, WI
- Division of Reproductive Endocrinology and Infertility, Departments of Obstetrics and Gynecology, University of Wisconsin-Madison, Madison, WI
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11
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Chandran PA, Laske K, Cazaly A, Rusch E, Schmid-Horch B, Rammensee HG, Ottensmeier CH, Gouttefangeas C. Validation of Immunomonitoring Methods for Application in Clinical Studies: The HLA-Peptide Multimer Staining Assay. CYTOMETRY. PART B, CLINICAL CYTOMETRY 2018; 94:342-353. [PMID: 27363684 DOI: 10.1002/cyto.b.21397] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Revised: 05/27/2016] [Accepted: 06/28/2016] [Indexed: 11/11/2022]
Abstract
BACKGROUND Validated assays are essential to generate data with defined specificity, consistency, and reliability. Although the process of validation is required for applying immunoassays in the context of clinical studies, reports on systematic validation of in vitro T cell assays are scarce so far. We recently validated our HLA-peptide multimer staining assay in a systematic manner so as to qualify the method for monitoring antigen-specific T cell responses after immunotherapy. METHODS Parameters of the assay, specificity, precision, linearity, sensitivity, and robustness were assessed systematically. Experiments were designed to address specifically each parameter and are detailed. RESULTS Nonspecific multimer staining was below the acceptance limit of 0.02% multimer(+) CD8(+) cells. The assay showed acceptable precision in all dimensions it was repeated (CV < 10%) and also demonstrated a linear detection (R2 > 0.99) of antigen specific cells. CONCLUSIONS We succeeded in validating the HLA-multimer staining assay in a systematic manner. Additionally, we propose a technical framework and recommendations that can be applied for validating other T cell assessment methods. © 2016 International Clinical Cytometry Society.
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Affiliation(s)
- P Anoop Chandran
- Department of Immunology, Institute for Cell Biology, Eberhard Karls University, and German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ) Partner Site Tuebingen, Tuebingen, Germany
| | - Karoline Laske
- Department of Immunology, Institute for Cell Biology, Eberhard Karls University, and German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ) Partner Site Tuebingen, Tuebingen, Germany
| | - Angelica Cazaly
- Cancer Sciences Unit, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton, SO16 6YD, United Kingdom
| | - Elisa Rusch
- Department of Immunology, Institute for Cell Biology, Eberhard Karls University, and German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ) Partner Site Tuebingen, Tuebingen, Germany
| | | | - Hans-Georg Rammensee
- Department of Immunology, Institute for Cell Biology, Eberhard Karls University, and German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ) Partner Site Tuebingen, Tuebingen, Germany
| | - Christian H Ottensmeier
- Cancer Sciences Unit, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton, SO16 6YD, United Kingdom
| | - Cécile Gouttefangeas
- Department of Immunology, Institute for Cell Biology, Eberhard Karls University, and German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ) Partner Site Tuebingen, Tuebingen, Germany
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12
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Pedersen NW, Chandran PA, Qian Y, Rebhahn J, Petersen NV, Hoff MD, White S, Lee AJ, Stanton R, Halgreen C, Jakobsen K, Mosmann T, Gouttefangeas C, Chan C, Scheuermann RH, Hadrup SR. Automated Analysis of Flow Cytometry Data to Reduce Inter-Lab Variation in the Detection of Major Histocompatibility Complex Multimer-Binding T Cells. Front Immunol 2017; 8:858. [PMID: 28798746 PMCID: PMC5526901 DOI: 10.3389/fimmu.2017.00858] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Accepted: 07/07/2017] [Indexed: 12/22/2022] Open
Abstract
Manual analysis of flow cytometry data and subjective gate-border decisions taken by individuals continue to be a source of variation in the assessment of antigen-specific T cells when comparing data across laboratories, and also over time in individual labs. Therefore, strategies to provide automated analysis of major histocompatibility complex (MHC) multimer-binding T cells represent an attractive solution to decrease subjectivity and technical variation. The challenge of using an automated analysis approach is that MHC multimer-binding T cell populations are often rare and therefore difficult to detect. We used a highly heterogeneous dataset from a recent MHC multimer proficiency panel to assess if MHC multimer-binding CD8+ T cells could be analyzed with computational solutions currently available, and if such analyses would reduce the technical variation across different laboratories. We used three different methods, FLOw Clustering without K (FLOCK), Scalable Weighted Iterative Flow-clustering Technique (SWIFT), and ReFlow to analyze flow cytometry data files from 28 laboratories. Each laboratory screened for antigen-responsive T cell populations with frequency ranging from 0.01 to 1.5% of lymphocytes within samples from two donors. Experience from this analysis shows that all three programs can be used for the identification of high to intermediate frequency of MHC multimer-binding T cell populations, with results very similar to that of manual gating. For the less frequent populations (<0.1% of live, single lymphocytes), SWIFT outperformed the other tools. As used in this study, none of the algorithms offered a completely automated pipeline for identification of MHC multimer populations, as varying degrees of human interventions were needed to complete the analysis. In this study, we demonstrate the feasibility of using automated analysis pipelines for assessing and identifying even rare populations of antigen-responsive T cells and discuss the main properties, differences, and advantages of the different methods tested.
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Affiliation(s)
- Natasja Wulff Pedersen
- Division of Immunology and Vaccinology, Veterinary Institute, Technical University of Denmark, Copenhagen, Denmark
| | - P. Anoop Chandran
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tuebingen, Tuebingen, Germany
| | - Yu Qian
- Department of Informatics, J. Craig Venter Institute, La Jolla, CA, United States
| | - Jonathan Rebhahn
- David H. Smith Center for Vaccine Biology and Immunology, University of Rochester Medical Center, Rochester, NY, United States
| | - Nadia Viborg Petersen
- Division of Immunology and Vaccinology, Veterinary Institute, Technical University of Denmark, Copenhagen, Denmark
| | - Mathilde Dalsgaard Hoff
- Division of Immunology and Vaccinology, Veterinary Institute, Technical University of Denmark, Copenhagen, Denmark
| | - Scott White
- Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, NC, United States
| | - Alexandra J. Lee
- Department of Informatics, J. Craig Venter Institute, La Jolla, CA, United States
| | - Rick Stanton
- Human Longevity Inc., San Diego, CA, United States
| | | | | | - Tim Mosmann
- David H. Smith Center for Vaccine Biology and Immunology, University of Rochester Medical Center, Rochester, NY, United States
| | - Cécile Gouttefangeas
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tuebingen, Tuebingen, Germany
| | - Cliburn Chan
- Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, NC, United States
| | - Richard H. Scheuermann
- Department of Informatics, J. Craig Venter Institute, La Jolla, CA, United States
- Department of Pathology, University of California, San Diego, La Jolla, CA, United States
| | - Sine Reker Hadrup
- Division of Immunology and Vaccinology, Veterinary Institute, Technical University of Denmark, Copenhagen, Denmark
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13
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Saeys Y, Van Gassen S, Lambrecht BN. Computational flow cytometry: helping to make sense of high-dimensional immunology data. Nat Rev Immunol 2016; 16:449-62. [PMID: 27320317 DOI: 10.1038/nri.2016.56] [Citation(s) in RCA: 299] [Impact Index Per Article: 37.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Recent advances in flow cytometry allow scientists to measure an increasing number of parameters per cell, generating huge and high-dimensional datasets. To analyse, visualize and interpret these data, newly available computational techniques should be adopted, evaluated and improved upon by the immunological community. Computational flow cytometry is emerging as an important new field at the intersection of immunology and computational biology; it allows new biological knowledge to be extracted from high-throughput single-cell data. This Review provides non-experts with a broad and practical overview of the many recent developments in computational flow cytometry.
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Affiliation(s)
- Yvan Saeys
- VIB Inflammation Research Center, Technologiepark 927, Ghent B-9052, Belgium.,Department of Internal Medicine, Ghent University, De Pintelaan 185, Ghent B-9000, Belgium
| | - Sofie Van Gassen
- VIB Inflammation Research Center, Technologiepark 927, Ghent B-9052, Belgium.,Department of Information Technology, Technologiepark 15, Ghent B-9052, Belgium
| | - Bart N Lambrecht
- VIB Inflammation Research Center, Technologiepark 927, Ghent B-9052, Belgium.,Department of Internal Medicine, Ghent University, De Pintelaan 185, Ghent B-9000, Belgium.,Department of Pulmonary Medicine, Erasmus MC Rotterdam, Dr Molewaterplein 50, Rotterdam 3015 GE, The Netherlands
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14
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Mandruzzato S, Brandau S, Britten CM, Bronte V, Damuzzo V, Gouttefangeas C, Maurer D, Ottensmeier C, van der Burg SH, Welters MJP, Walter S. Toward harmonized phenotyping of human myeloid-derived suppressor cells by flow cytometry: results from an interim study. Cancer Immunol Immunother 2016; 65:161-9. [PMID: 26728481 PMCID: PMC4726716 DOI: 10.1007/s00262-015-1782-5] [Citation(s) in RCA: 139] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Accepted: 12/12/2015] [Indexed: 01/02/2023]
Abstract
There is an increasing interest for monitoring circulating myeloid-derived suppressor cells (MDSCs) in cancer patients, but there are also divergences in their phenotypic definition. To overcome this obstacle, the Cancer Immunoguiding Program under the umbrella of the Association of Cancer Immunotherapy is coordinating a proficiency panel program that aims at harmonizing MDSC phenotyping. After a consultation period, a two-stage approach was designed to harmonize MDSC phenotype. In the first step, an international consortium of 23 laboratories immunophenotyped 10 putative MDSC subsets on pretested, peripheral blood mononuclear cells of healthy donors to assess the level of concordance and define robust marker combinations for the identification of circulating MDSCs. At this stage, no mandatory requirements to standardize reagents or protocols were introduced. Data analysis revealed a small intra-laboratory, but very high inter-laboratory variance for all MDSC subsets, especially for the granulocytic subsets. In particular, the use of a dead-cell marker altered significantly the reported percentage of granulocytic MDSCs, confirming that these cells are especially sensitive to cryopreservation and/or thawing. Importantly, the gating strategy was heterogeneous and associated with high inter-center variance. Overall, our results document the high variability in MDSC phenotyping in the multicenter setting if no harmonization/standardization measures are applied. Although the observed variability depended on a number of identified parameters, the main parameter associated with variation was the gating strategy. Based on these findings, we propose further efforts to harmonize marker combinations and gating parameters to identify strategies for a robust enumeration of MDSC subsets.
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Affiliation(s)
- Susanna Mandruzzato
- Section of Oncology and Immunology, Department of Surgery, Oncology and Gastroenterology, University of Padova, Via Gattamelata, 64, 35128, Padua, Italy.
- Veneto Institute of Oncology IOV - IRCCS, Padua, Italy.
| | - Sven Brandau
- Department of Otorhinolaryngology, University Hospital Essen, Essen, Germany
| | - Cedrik M Britten
- TRON Translationale Onkologie an der Universitätsmedizin der Johannes Gutenberg-Universität Mainz GmbH, Mainz, Germany
- Cell Therapy Group, Immuno-Oncology and Combinations, GlaxoSmithKline, Stevenage, UK
| | - Vincenzo Bronte
- Section of Immunology, Department of Pathology and Diagnostics, Verona University Hospital, Verona, Italy
| | - Vera Damuzzo
- Section of Oncology and Immunology, Department of Surgery, Oncology and Gastroenterology, University of Padova, Via Gattamelata, 64, 35128, Padua, Italy
- Veneto Institute of Oncology IOV - IRCCS, Padua, Italy
| | - Cécile Gouttefangeas
- Department of Immunology, Institute for Cell Biology, University of Tübingen, Tübingen, Germany
| | | | - Christian Ottensmeier
- Cancer Sciences Unit, Faculty of Medicine, Experimental Cancer Medicine Centre, Southampton General Hospital, University of Southampton, Tremona Road, Southampton, UK
| | - Sjoerd H van der Burg
- Department of Clinical Oncology, Leiden University Medical Center, Leiden, The Netherlands
| | - Marij J P Welters
- Department of Clinical Oncology, Leiden University Medical Center, Leiden, The Netherlands
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15
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Verschoor CP, Lelic A, Bramson JL, Bowdish DME. An Introduction to Automated Flow Cytometry Gating Tools and Their Implementation. Front Immunol 2015; 6:380. [PMID: 26284066 PMCID: PMC4515551 DOI: 10.3389/fimmu.2015.00380] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Accepted: 07/12/2015] [Indexed: 12/18/2022] Open
Abstract
Current flow cytometry (FCM) reagents and instrumentation allow for the measurement of an unprecedented number of parameters for any given cell within a homogenous or heterogeneous population. While this provides a great deal of power for hypothesis testing, it also generates a vast amount of data, which is typically analyzed manually through a processing called “gating.” For large experiments, such as high-content screens, in which many parameters are measured, the time required for manual analysis as well as the technical variability inherent to manual gating can increase dramatically, even becoming prohibitive depending on the clinical or research goal. In the following article, we aim to provide the reader an overview of automated FCM analysis as well as an example of the implementation of FLOw Clustering without K, a tool that we consider accessible to researchers of all levels of computational expertise. In most cases, computational assistance methods are more reproducible and much faster than manual gating, and for some, also allow for the discovery of cellular populations that might not be expected or evident to the researcher. We urge any researcher who is planning or has previously performed large FCM experiments to consider implementing computational assistance into their analysis pipeline.
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Affiliation(s)
- Chris P Verschoor
- Department of Pathology and Molecular Medicine, McMaster Immunology Research Centre (MIRC), McMaster University , Hamilton, ON , Canada
| | - Alina Lelic
- Department of Pathology and Molecular Medicine, McMaster Immunology Research Centre (MIRC), McMaster University , Hamilton, ON , Canada
| | - Jonathan L Bramson
- Department of Pathology and Molecular Medicine, McMaster Immunology Research Centre (MIRC), McMaster University , Hamilton, ON , Canada
| | - Dawn M E Bowdish
- Department of Pathology and Molecular Medicine, McMaster Immunology Research Centre (MIRC), McMaster University , Hamilton, ON , Canada
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