1
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McCarthy M, Lu X, Ogunleye O, Latham DR, Abravanel M, Pritko D, Huggins JR, Haskell CV, Patel ND, Pittman ZA, Sanabria H, Birtwistle MR. Increasing Signal Intensity of Fluorescent Oligo-Labeled Antibodies to Enable Combination Multiplexing. Bioconjug Chem 2024; 35:1053-1063. [PMID: 38889324 PMCID: PMC11262307 DOI: 10.1021/acs.bioconjchem.4c00246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2024] [Revised: 06/03/2024] [Accepted: 06/05/2024] [Indexed: 06/20/2024]
Abstract
Full-spectrum flow cytometry has increased antibody-based multiplexing, yet further increases remain potentially impactful. We recently proposed how fluorescence multiplexing using spectral imaging and combinatorics (MuSIC) could do so using tandem dyes and an oligo-based antibody labeling method. In this work, we found that such labeled antibodies had significantly lower signal intensities than conventionally labeled antibodies in human cell experiments. To improve signal intensity, we tested moving the fluorophores from the original external (ext.) 5' or 3' end-labeled orientation to internal (int.) fluorophore modifications. Cell-free spectrophotometer measurements showed a ∼6-fold signal intensity increase of the new int. configuration compared to the previous ext. configuration. Time-resolved fluorescence and fluorescence correlation spectroscopy showed that the ∼3-fold brightness difference is due to static quenching most likely by the oligo or solution in the ext. configuration. Spectral flow cytometry experiments using peripheral blood mononuclear cells show int. MuSIC probe-labeled antibodies (i) retained increased signal intensity while having no significant difference in the estimated % of CD8+ lymphocytes and (ii) labeled with Atto488, Atto647, and Atto488/647 combinations can be demultiplexed in triple-stained samples. The antibody labeling approach is general and can be broadly applied to many biological and diagnostic applications where spectral detection is available.
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Affiliation(s)
- Madeline
E. McCarthy
- Department
of Chemical and Biomolecular Engineering, Clemson University, Clemson, South Carolina 29634-0002, United States
| | - Xiaoming Lu
- Department
of Chemical and Biomolecular Engineering, Clemson University, Clemson, South Carolina 29634-0002, United States
| | - Oluwaferanmi Ogunleye
- Department
of Chemistry, Clemson University, Clemson, South Carolina 29634-0002, United
States
| | - Danielle R. Latham
- Department
of Physics and Astronomy, Clemson University, Clemson, South Carolina 29634-0002, United
States
| | - Megan Abravanel
- Department
of Chemical and Biomolecular Engineering, Clemson University, Clemson, South Carolina 29634-0002, United States
| | - Daniel Pritko
- Department
of Chemical and Biomolecular Engineering, Clemson University, Clemson, South Carolina 29634-0002, United States
| | - Jonah R. Huggins
- Department
of Chemical and Biomolecular Engineering, Clemson University, Clemson, South Carolina 29634-0002, United States
| | - Charlotte V. Haskell
- Department
of Chemical and Biomolecular Engineering, Clemson University, Clemson, South Carolina 29634-0002, United States
| | - Nishi D. Patel
- Department
of Chemical and Biomolecular Engineering, Clemson University, Clemson, South Carolina 29634-0002, United States
| | - Zachariah A. Pittman
- Department
of Chemical and Biomolecular Engineering, Clemson University, Clemson, South Carolina 29634-0002, United States
| | - Hugo Sanabria
- Department
of Chemistry, Clemson University, Clemson, South Carolina 29634-0002, United
States
| | - Marc R. Birtwistle
- Department
of Chemical and Biomolecular Engineering, Clemson University, Clemson, South Carolina 29634-0002, United States
- Department
of Bioengineering, Clemson University, Clemson, South Carolina 29634-0002, United
States
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2
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McCarthy ME, Lu X, Ogunleye O, Latham DR, Abravanel M, Pritko D, Huggins JR, Haskell CV, Patel ND, Pittman ZA, Sanabria H, Birtwistle MR. Increasing Signal Intensity of Fluorescent Oligo-Labeled Antibodies to Enable Combination Multiplexing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.07.06.547965. [PMID: 37461453 PMCID: PMC10350089 DOI: 10.1101/2023.07.06.547965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/27/2023]
Abstract
Full-spectrum flow cytometry has increased antibody-based multiplexing, yet further increases remain potentially impactful. We recently proposed how fluorescence Multiplexing using Spectral Imaging and Combinatorics (MuSIC) could do so using tandem dyes and an oligo-based antibody labeling method. In this work, we found that such labeled antibodies had significantly lower signal intensity than conventionally-labeled antibodies in human cell experiments. To improve signal intensity, we tested moving the fluorophores from the original external (ext.) 5' or 3' end-labeled orientation to internal (int.) fluorophore modifications. Cell-free spectrophotometer measurements showed a ~6-fold signal intensity increase of the new int. configuration compared to the previous ext. configuration. Time-resolved fluorescence and fluorescence correlation spectroscopy showed that ~3-fold brightness difference is due to static quenching most likely by the oligo or solution in the ext. configuration. Spectral flow cytometry experiments using peripheral blood mononuclear cells show int. MuSIC probe-labeled antibodies (i) retained increased signal intensity while having no significant difference in the estimated % of CD8+ lymphocytes and (ii) labeled with Atto488, Atto647, and Atto488/647 combinations can be demultiplexed in triple-stained samples. The antibody labeling approach is general and can be broadly applied to many biological and diagnostic applications where spectral detection is available.
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Affiliation(s)
| | - Xiaoming Lu
- Department of Chemical and Biomolecular Engineering, Clemson University
| | | | | | - Megan Abravanel
- Department of Chemical and Biomolecular Engineering, Clemson University
| | - Daniel Pritko
- Department of Chemical and Biomolecular Engineering, Clemson University
| | - Jonah R. Huggins
- Department of Chemical and Biomolecular Engineering, Clemson University
| | | | - Nishi D. Patel
- Department of Chemical and Biomolecular Engineering, Clemson University
| | | | | | - Marc R. Birtwistle
- Department of Chemical and Biomolecular Engineering, Clemson University
- Department of Bioengineering, Clemson University
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3
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G. de Castro C, G. del Hierro A, H-Vázquez J, Cuesta-Sancho S, Bernardo D. State-of-the-art cytometry in the search of novel biomarkers in digestive cancers. Front Oncol 2024; 14:1407580. [PMID: 38868532 PMCID: PMC11167087 DOI: 10.3389/fonc.2024.1407580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Accepted: 05/10/2024] [Indexed: 06/14/2024] Open
Abstract
Despite that colorectal and liver cancer are among the most prevalent tumours in the world, the identification of non-invasive biomarkers to aid on their diagnose and subsequent prognosis is a current unmet need that would diminish both their incidence and mortality rates. In this context, conventional flow cytometry has been widely used in the screening of biomarkers with clinical utility in other malignant processes like leukaemia or lymphoma. Therefore, in this review, we will focus on how advanced cytometry panels covering over 40 parameters can be applied on the study of the immune system from patients with colorectal and hepatocellular carcinoma and how that can be used on the search of novel biomarkers to aid or diagnose, prognosis, and even predict clinical response to different treatments. In addition, these multiparametric and unbiased approaches can also provide novel insights into the specific immunopathogenic mechanisms governing these malignant diseases, hence potentially unravelling novel targets to perform immunotherapy or identify novel mechanisms, rendering the development of novel treatments. As a consequence, computational cytometry approaches are an emerging methodology for the early detection and predicting therapies for gastrointestinal cancers.
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Affiliation(s)
- Carolina G. de Castro
- Mucosal Immunology Lab, Institute of Biomedicine and Molecular Genetics (IBGM), University of Valladolid and Consejo Superior de Investigaciones Científicas (CSIC), Valladolid, Spain
| | - Alejandro G. del Hierro
- Mucosal Immunology Lab, Institute of Biomedicine and Molecular Genetics (IBGM), University of Valladolid and Consejo Superior de Investigaciones Científicas (CSIC), Valladolid, Spain
| | - Juan H-Vázquez
- Mucosal Immunology Lab, Institute of Biomedicine and Molecular Genetics (IBGM), University of Valladolid and Consejo Superior de Investigaciones Científicas (CSIC), Valladolid, Spain
| | - Sara Cuesta-Sancho
- Mucosal Immunology Lab, Institute of Biomedicine and Molecular Genetics (IBGM), University of Valladolid and Consejo Superior de Investigaciones Científicas (CSIC), Valladolid, Spain
| | - David Bernardo
- Mucosal Immunology Lab, Institute of Biomedicine and Molecular Genetics (IBGM), University of Valladolid and Consejo Superior de Investigaciones Científicas (CSIC), Valladolid, Spain
- Centro de Investigaciones Biomedicas en Red de Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain
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4
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Paul Robinson J, Rajwa B. Spectral flow cytometry: Fundamentals and future impact. Methods Cell Biol 2024; 186:311-332. [PMID: 38705605 DOI: 10.1016/bs.mcb.2024.02.022] [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] [Indexed: 05/07/2024]
Abstract
Spectral flow cytometry has emerged as a significant player in the cytometry marketplace, with the potential for rapid growth. Despite a slow start, the technology has made significant strides in advancing various areas of single-cell analysis utilized by the scientific community. The integration of spectral cytometry into clinical laboratories and diagnostic processes is currently underway and is expected to garner a significant level of widespread acceptance in the near future. However, incorporating a new methodological approach into existing research programs can lead to misunderstandings or even misuse. This chapter offers an introductory yet comprehensive explanation of the scientific principles that form the foundation of spectral cytometry. Specifically, it delves into the unmixing processes that are utilized for data analysis. This overview is designed for those who are new to the field and seeking an informative guide to this exciting emerging technology.
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Affiliation(s)
- J Paul Robinson
- Weldon School of Biomedical Engineering, College of Engineering, Purdue University, West Lafayette, IN, United States; Department of Basic Medical Sciences, College of Veterinary Medicine, Purdue University, West Lafayette, IN, United States.
| | - Bartek Rajwa
- Bindley Bioscience Center, Purdue University, West Lafayette, IN, United States
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5
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Ermann J, Lefton M, Wei K, Gutierrez-Arcelus M. Understanding Spondyloarthritis Pathogenesis: The Promise of Single-Cell Profiling. Curr Rheumatol Rep 2024; 26:144-154. [PMID: 38227172 DOI: 10.1007/s11926-023-01132-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/28/2023] [Indexed: 01/17/2024]
Abstract
PURPOSE OF REVIEW Single-cell profiling, either in suspension or within the tissue context, is a rapidly evolving field. The purpose of this review is to outline recent advancements and emerging trends with a specific focus on studies in spondyloarthritis. RECENT FINDINGS The introduction of sequencing-based approaches for the quantification of RNA, protein, or epigenetic modifications at single-cell resolution has provided a major boost to discovery-driven research. Fluorescent flow cytometry, mass cytometry, and image-based cytometry continue to evolve. Spatial transcriptomics and imaging mass cytometry have extended high-dimensional analysis to cells in tissues. Applications in spondyloarthritis include the indexing and functional characterization of cells, discovery of disease-associated cell states, and identification of signatures associated with therapeutic responses. Single-cell TCR-seq has provided evidence for clonal expansion of CD8+ T cells in spondyloarthritis. The use of single-cell profiling approaches in spondyloarthritis research is still in its early stages. Challenges include high cost and limited availability of diseased tissue samples. To harness the full potential of the rapidly expanding technical capabilities, large-scale collaborative efforts are imperative.
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Affiliation(s)
- Joerg Ermann
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women's Hospital, Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
| | - Micah Lefton
- Elson S. Floyd College of Medicine, Washington State University, Spokane, WA, USA
| | - Kevin Wei
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Maria Gutierrez-Arcelus
- Harvard Medical School, Boston, MA, USA
- Boston Children's Hospital, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
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6
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Nalwoga A, Nakibuule M, Roshan R, Kwizera Mbonye M, Miley W, Whitby D, Newton R, Rochford R, Cose S. Immune cell phenotype and function patterns across the life course in individuals from rural Uganda. Front Immunol 2024; 15:1356635. [PMID: 38562926 PMCID: PMC10982424 DOI: 10.3389/fimmu.2024.1356635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 02/28/2024] [Indexed: 04/04/2024] Open
Abstract
Background To determine the pattern of immune cell subsets across the life span in rural sub-Saharan Africa (SSA), and to set a reference standard for cell subsets amongst Africans, we characterised the major immune cell subsets in peripheral blood including T cells, B cells, monocytes, NK cells, neutrophils and eosinophils, in individuals aged 3 to 89 years from Uganda. Methods Immune phenotypes were measured using both conventional flow cytometry in 72 individuals, and full spectrum flow cytometry in 80 individuals. Epstein-Barr virus (EBV) IFN-γ T cell responses were quantified in 332 individuals using an ELISpot assay. Full blood counts of all study participants were also obtained. Results The percentages of central memory (TCM) and senescent CD4+ and CD8+ T cell subsets, effector memory (TEM) CD8+ T cells and neutrophils increased with increasing age. On the other hand, the percentages of naïve T (TN) and B (BN) cells, atypical B cells (BA), total lymphocytes, eosinophils and basophils decreased with increasing age. There was no change in CD4+ or CD8+ T effector memory RA (TEMRA) cells, exhausted T cells, NK cells and monocytes with age. Higher eosinophil and basophil percentages were observed in males compared to females. T cell function as measured by IFN-γ responses to EBV increased with increasing age, peaking at 31-55 years. Conclusion The percentages of cell subsets differ between individuals from SSA compared to those elsewhere, perhaps reflecting a different antigenic milieu. These results serve as a reference for normal values in this population.
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Affiliation(s)
- Angela Nalwoga
- Department of Immunology and Microbiology, University of Colorado, Aurora, CO, United States
- Medical Research Council/ Uganda Virus Research Institute and London School of Hygiene & Tropical Medicine, Entebbe, Uganda
| | - Marjorie Nakibuule
- Medical Research Council/ Uganda Virus Research Institute and London School of Hygiene & Tropical Medicine, Entebbe, Uganda
| | - Romin Roshan
- Frederick National Laboratory for Cancer Research, Viral Oncology Section, AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc., Frederick, MD, United States
| | - Moses Kwizera Mbonye
- Medical Research Council/ Uganda Virus Research Institute and London School of Hygiene & Tropical Medicine, Entebbe, Uganda
| | - Wendell Miley
- Frederick National Laboratory for Cancer Research, Viral Oncology Section, AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc., Frederick, MD, United States
| | - Denise Whitby
- Frederick National Laboratory for Cancer Research, Viral Oncology Section, AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc., Frederick, MD, United States
| | - Robert Newton
- Medical Research Council/ Uganda Virus Research Institute and London School of Hygiene & Tropical Medicine, Entebbe, Uganda
- Department of Health Sciences, University of York, York, United Kingdom
| | - Rosemary Rochford
- Department of Immunology and Microbiology, University of Colorado, Aurora, CO, United States
| | - Stephen Cose
- Medical Research Council/ Uganda Virus Research Institute and London School of Hygiene & Tropical Medicine, Entebbe, Uganda
- Department of Clinical Research, London School of Hygiene & Tropical Medicine, London, United Kingdom
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7
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Iyengar SN, Robinson JP. Spectral analysis and sorting of microbial organisms using a spectral sorter. Methods Cell Biol 2024; 186:189-212. [PMID: 38705599 DOI: 10.1016/bs.mcb.2024.02.017] [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] [Indexed: 05/07/2024]
Abstract
This chapter discusses the problems related to the application of conventional flow cytometers to microbiology. To address some of those limitations, the concept of spectral flow cytometry is introduced and the advantages over conventional flow cytometry for bacterial sorting are presented. We demonstrate by using ThermoFisher's Bigfoot spectral sorter where the spectral signatures of different stains for staining bacteria are demonstrated with an example of performing unmixing on spectral datasets. In addition to the Bigfoot's spectral analysis, the special biosafety features of this instrument are discussed. Utilizing these biosafety features, the sorting and patterning at the single cell level is optimized using non-pathogenic bacteria. Finally, the chapter is concluded by presenting a novel, label free, non-destructive, and rapid phenotypic method called Elastic Light Scattering (ELS) technology for identification of the patterned bacterial cells based on their unique colony scatter patterns.
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Affiliation(s)
- Sharath Narayana Iyengar
- Department of Basic Medical Sciences, College of Veterinary Medicine, Purdue University, West Lafayette, IN, United States
| | - J Paul Robinson
- Department of Basic Medical Sciences, College of Veterinary Medicine, Purdue University, West Lafayette, IN, United States; Weldon School of Biomedical Engineering, College of Engineering, Purdue University, West Lafayette, IN, United States.
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8
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Kwok SJJ, Forward S, Fahlberg MD, Assita ER, Cosgriff S, Lee SH, Abbott GR, Zhu H, Minasian NH, Vote AS, Martino N, Yun SH. High-dimensional multi-pass flow cytometry via spectrally encoded cellular barcoding. Nat Biomed Eng 2024; 8:310-324. [PMID: 38036616 DOI: 10.1038/s41551-023-01144-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 10/21/2023] [Indexed: 12/02/2023]
Abstract
Advances in immunology, immuno-oncology, drug discovery and vaccine development demand improvements in the capabilities of flow cytometry to allow it to measure more protein markers per cell at multiple timepoints. However, the size of panels of fluorophore markers is limited by overlaps in fluorescence-emission spectra, and flow cytometers typically perform cell measurements at one timepoint. Here we describe multi-pass high-dimensional flow cytometry, a method leveraging cellular barcoding via microparticles emitting near-infrared laser light to track and repeatedly measure each cell using more markers and fewer colours. By using live human peripheral blood mononuclear cells, we show that the method enables the time-resolved characterization of the same cells before and after stimulation, their analysis via a 10-marker panel with minimal compensation for spectral spillover and their deep immunophenotyping via a 32-marker panel, where the same cells are analysed in 3 back-to-back cycles with 10-13 markers per cycle, reducing overall spillover and simplifying marker-panel design. Cellular barcoding in flow cytometry extends the utility of the technique for high-dimensional multi-pass single-cell analyses.
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Affiliation(s)
| | | | | | | | | | | | | | - Han Zhu
- LASE Innovation Inc., Woburn, MA, USA
| | | | | | - Nicola Martino
- Harvard Medical School and Wellman Center for Photomedicine, Massachusetts General Hospital, Cambridge, MA, USA
| | - Seok-Hyun Yun
- Harvard Medical School and Wellman Center for Photomedicine, Massachusetts General Hospital, Cambridge, MA, USA.
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9
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Spiteri AG, Pilkington KR, Wishart CL, Macia L, King NJC. High-Dimensional Methods of Single-Cell Microglial Profiling to Enhance Understanding of Neuropathological Disease. Curr Protoc 2024; 4:e985. [PMID: 38439574 DOI: 10.1002/cpz1.985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2024]
Abstract
Microglia are the innate myeloid cells of the central nervous system (CNS) parenchyma, functionally implicated in almost every defined neuroinflammatory and neurodegenerative disorder. Current understanding of disease pathogenesis for many neuropathologies is limited and/or lacks reliable diagnostic markers, vaccines, and treatments. With the increasing aging of society and rise in neurogenerative diseases, improving our understanding of their pathogenesis is essential. Analysis of microglia from murine disease models provides an investigative tool to unravel disease processes. In many neuropathologies, bone-marrow-derived monocytes are recruited to the CNS, adopting a phenotype similar to that of microglia. This significantly confounds the accurate identification of cell-type-specific functions and downstream therapeutic targeting. The increased capacity to analyze more phenotypic markers using spectral-cytometry-based technologies allows improved separation of microglia from monocyte-derived cells. Full-spectrum profiling enables enhanced marker resolution, time-efficient analysis of >40 fluorescence parameters, and extraction of cellular autofluorescence parameters. Coupling this system with additional cytometric technologies, including cell sorting and high-parameter imaging, can improve the understanding of microglial phenotypes in disease. To this end, we provide detailed, step-by-step protocols for the analysis of murine brain tissue by high-parameter ex vivo cytometric analysis using the Aurora spectral cytometer (Cytek), including best practices for unmixing and autofluorescence extraction, cell sorting for single-cell RNA analysis, and imaging mass cytometry. Together, this provides a toolkit for researchers to comprehensively investigate microglial disease processes at protein, RNA, and spatial levels for the identification of therapeutic targets in neuropathology. © 2024 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Processing the mouse brain into a single-cell suspension for microglia isolation Basic Protocol 2: Staining single-cell mouse brain suspensions for microglial phenotyping by spectral cytometry Basic Protocol 3: Flow cytometric sorting of mouse microglia for ex vivo analysis Basic Protocol 4: Processing the mouse brain for imaging mass cytometry for spatial microglia analysis.
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Affiliation(s)
- Alanna G Spiteri
- Viral Immunopathology Laboratory, Infection, Immunity and Inflammation Research Theme, School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, Australia
| | | | - Claire L Wishart
- Viral Immunopathology Laboratory, Infection, Immunity and Inflammation Research Theme, School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, Australia
| | - Laurence Macia
- Charles Perkins Centre, The University of Sydney, Sydney, Australia
- Sydney Cytometry, The University of Sydney and Centenary Institute, Sydney, Australia
| | - Nicholas J C King
- Viral Immunopathology Laboratory, Infection, Immunity and Inflammation Research Theme, School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, Australia
- Sydney Cytometry, The University of Sydney and Centenary Institute, Sydney, Australia
- The University of Sydney Institute for Infectious Diseases, The University of Sydney, Sydney, Australia
- The University of Sydney Nano Institute, The University of Sydney, Sydney, Australia
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10
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Kong WT, Bied M, Ginhoux F. Spectral Flow Cytometry Analysis of Resident Tissue Macrophages. Methods Mol Biol 2024; 2713:269-280. [PMID: 37639129 DOI: 10.1007/978-1-0716-3437-0_18] [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] [Indexed: 08/29/2023]
Abstract
Spectral flow cytometry improves flow cytometry panels by resolving the full emission spectra of individual fluorophores, allowing greater flexibility to incorporate more fluorochromes when designing multicolor panels. Additionally, the spectral approach captures the autofluorescence of a sample or cell population (e.g., macrophages, which are highly autofluorescent) that can be considered during unmixing for improved downstream analyses. As the increased complexity of macrophage heterogeneity unravels in the scientific community, it is crucial to obtain high-dimensional data at the single-cell level to resolve these populations.
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Affiliation(s)
- Wan Ting Kong
- Gustave Roussy Cancer Campus, Villejuif, France
- Institut National de la Santé Et de la Recherche Médicale (INSERM) U1015, Equipe Labellisée-Ligue Nationale contre le Cancer, Villejuif, France
- Université Paris-Saclay, Ile-de-France, France
| | - Mathilde Bied
- Gustave Roussy Cancer Campus, Villejuif, France
- Institut National de la Santé Et de la Recherche Médicale (INSERM) U1015, Equipe Labellisée-Ligue Nationale contre le Cancer, Villejuif, France
| | - Florent Ginhoux
- Gustave Roussy Cancer Campus, Villejuif, France.
- Institut National de la Santé Et de la Recherche Médicale (INSERM) U1015, Equipe Labellisée-Ligue Nationale contre le Cancer, Villejuif, France.
- Université Paris-Saclay, Ile-de-France, France.
- Singapore Immunology Network (SIgN), A*STAR, Singapore, Singapore.
- Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
- Translational Immunology Institute, SingHealth Duke-NUS Academic Medical Centre, Singapore, Singapore.
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11
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Spurgeon BEJ, Frelinger AL. OMIP-097: High-parameter phenotyping of human platelets by spectral flow cytometry. Cytometry A 2023; 103:935-940. [PMID: 37786346 DOI: 10.1002/cyto.a.24797] [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: 04/18/2023] [Revised: 08/24/2023] [Accepted: 09/12/2023] [Indexed: 10/04/2023]
Abstract
Using spectral flow cytometry, we developed a 16-color panel for analysis of platelet phenotype and function in human whole blood. The panel contains markers of clinical relevance and follows an optimized protocol for the high-parameter phenotyping of (phosphatidylserine positive) procoagulant platelets. Inclusion of established markers, such as CD62P and PAC-1, allows the subsetting of classic (proinflammatory and proaggregatory) phenotypes, while addition of novel markers, such as TLR9, allows the resolution of platelets with nonclassic functions. Multiple inducible (C3b, CD63, CD107a, CD154, and TLT-1) and constitutive (CD29, CD31, CD32, CD36, CD42a, CD61, and GPVI) markers are also measurable, and we demonstrate the use of automatic gating for platelet analysis. The panel is widely applicable to research and clinical settings and can be readily modified, should users wish to tailor the panel to more specific needs.
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Affiliation(s)
- Benjamin E J Spurgeon
- Center for Platelet Research Studies, Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Andrew L Frelinger
- Center for Platelet Research Studies, Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Harvard Medical School, Boston, Massachusetts, USA
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12
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Kare AJ, Nichols L, Zermeno R, Raie MN, Tumbale SK, Ferrara KW. OMIP-095: 40-Color spectral flow cytometry delineates all major leukocyte populations in murine lymphoid tissues. Cytometry A 2023; 103:839-850. [PMID: 37768325 PMCID: PMC10843696 DOI: 10.1002/cyto.a.24788] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 07/26/2023] [Accepted: 08/18/2023] [Indexed: 09/29/2023]
Abstract
High-dimensional immunoprofiling is essential for studying host response to immunotherapy, infection, and disease in murine model systems. However, the difficulty of multiparameter panel design combined with a lack of existing murine tools has prevented the comprehensive study of all major leukocyte phenotypes in a single assay. Herein, we present a 40-color flow cytometry panel for deep immunophenotyping of murine lymphoid tissues, including the spleen, blood, Peyer's patches, inguinal lymph nodes, bone marrow, and thymus. This panel uses a robust set of surface markers capable of differentiating leukocyte subsets without the use of intracellular staining, thus allowing for the use of cells in downstream functional experiments or multiomic analyses. Our panel classifies T cells, B cells, natural killer cells, innate lymphoid cells, monocytes, macrophages, dendritic cells, basophils, neutrophils, eosinophils, progenitors, and their functional subsets by using a series of co-stimulatory, checkpoint, activation, migration, and maturation markers. This tool has a multitude of systems immunology applications ranging from serial monitoring of circulating blood signatures to complex endpoint analysis, especially in pre-clinical settings where treatments can modulate leukocyte abundance and/or function. Ultimately, this 40-color panel resolves a diverse array of immune cells on the axes of time, tissue, and treatment, filling the niche for a modern tool dedicated to murine immunophenotyping.
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Affiliation(s)
- Aris J. Kare
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
- Department of Radiology, Stanford University, Stanford, CA 94305, USA
| | - Lisa Nichols
- Stanford Shared FACS Facility, Stanford University, Stanford, CA 94305, USA
| | - Ricardo Zermeno
- Stanford Shared FACS Facility, Stanford University, Stanford, CA 94305, USA
| | - Marina N. Raie
- Department of Radiology, Stanford University, Stanford, CA 94305, USA
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13
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de Graaf JF, Arens R. Immunophenotyping beyond the limits of time. CELL REPORTS METHODS 2023; 3:100612. [PMID: 37883923 PMCID: PMC10626202 DOI: 10.1016/j.crmeth.2023.100612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 09/20/2023] [Accepted: 09/20/2023] [Indexed: 10/28/2023]
Abstract
Immunophenotyping is a powerful approach for deciphering responses of the immune system to drug screening and immunotherapy. In this issue of Cell Report Methods, Liechti et al. have advanced this approach by developing a pipeline, which allows high-throughput but still accurate single-cell immunophenotyping in time.
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Affiliation(s)
- J Fréderique de Graaf
- Department of Immunology, Leiden University Medical Center, 2333ZA Leiden, the Netherlands
| | - Ramon Arens
- Department of Immunology, Leiden University Medical Center, 2333ZA Leiden, the Netherlands.
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14
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Edwards JM, Andrews MC, Burridge H, Smith R, Owens C, Edinger M, Pilkington K, Desfrancois J, Shackleton M, Senthi S, van Zelm MC. Design, optimisation and standardisation of a high-dimensional spectral flow cytometry workflow assessing T-cell immunophenotype in patients with melanoma. Clin Transl Immunology 2023; 12:e1466. [PMID: 37692904 PMCID: PMC10484688 DOI: 10.1002/cti2.1466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 06/26/2023] [Accepted: 08/18/2023] [Indexed: 09/12/2023] Open
Abstract
Objectives Despite the success of immune checkpoint blockade, most metastatic melanoma patients fail to respond to therapy or experience severe toxicity. Assessment of biomarkers and immunophenotypes before or early into treatment will help to understand favourable responses and improve therapeutic outcomes. Methods We present a high-dimensional approach for blood T-cell profiling using three multi-parameter cytometry panels: (1) a TruCount panel for absolute cell counts, (2) a 27-colour spectral panel assessing T-cell markers and (3) a 20-colour spectral panel evaluating intracellular cytokine expression. Pre-treatment blood mononuclear cells from patients and healthy controls were cryopreserved before staining across 11 batches. Batch effects were tracked using a single-donor control and the suitability of normalisation was assessed. The data were analysed using manual gating and high-dimensional strategies. Results Batch-to-batch variation was minimal, as demonstrated by the dimensionality reduction of batch-control samples, and normalisation did not improve manual or high-dimensional analysis. Application of the workflow demonstrated the capacity of the panels and showed that patients had fewer lymphocytes than controls (P = 0.0027), due to lower naive CD4+ (P = 0.015) and CD8+ (P = 0.011) T cells and follicular helper T cells (P = 0.00076). Patients showed trends for higher proportions of Ki67 and IL-2-expressing cells within CD4+ and CD8+ memory subsets, and increased CD57 and EOMES expression within TCRγδ+ T cells. Conclusion Our optimised high-parameter spectral cytometry approach provided in-depth profiling of blood T cells and found differences in patient immunophenotype at baseline. The robustness of our workflow, as demonstrated by minimal batch effects, makes this approach highly suitable for the longitudinal evaluation of immunotherapy effects.
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Affiliation(s)
- Jack M Edwards
- Alfred Health Radiation OncologyThe Alfred HospitalMelbourneVICAustralia
- Department of Immunology, Central Clinical SchoolMonash University and Alfred HospitalMelbourneVICAustralia
| | - Miles C Andrews
- Department of Medicine, Central Clinical SchoolMonash UniversityMelbourneVICAustralia
- Department of Medical OncologyThe Alfred HospitalMelbourneVICAustralia
| | - Hayley Burridge
- Department of Medical OncologyThe Alfred HospitalMelbourneVICAustralia
| | - Robin Smith
- Alfred Health Radiation OncologyThe Alfred HospitalMelbourneVICAustralia
| | - Carole Owens
- Alfred Health Radiation OncologyThe Alfred HospitalMelbourneVICAustralia
| | | | | | | | - Mark Shackleton
- Department of Medicine, Central Clinical SchoolMonash UniversityMelbourneVICAustralia
- Department of Medical OncologyThe Alfred HospitalMelbourneVICAustralia
| | - Sashendra Senthi
- Alfred Health Radiation OncologyThe Alfred HospitalMelbourneVICAustralia
| | - Menno C van Zelm
- Department of Immunology, Central Clinical SchoolMonash University and Alfred HospitalMelbourneVICAustralia
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15
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Mincham KT, Snelgrove RJ. OMIP-086: Full spectrum flow cytometry for high-dimensional immunophenotyping of mouse innate lymphoid cells. Cytometry A 2023; 103:110-116. [PMID: 36331092 PMCID: PMC10953369 DOI: 10.1002/cyto.a.24702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 10/17/2022] [Accepted: 10/24/2022] [Indexed: 11/06/2022]
Abstract
This 25-parameter, 22-color full spectrum flow cytometry panel was designed and optimized for the comprehensive enumeration and functional characterization of innate lymphoid cell (ILC) subsets in mouse tissues. The panel presented here allows the discrimination of ILC progenitors (ILCP), ILC1, ILC2, NCR+ ILC3, NCR- ILC3, CCR6+ lymphoid tissue-inducer (LTi)-like ILC3 and mature natural killer (NK) cell populations. Further characterization of ILC and NK cell functional profiles in response to stimulation is provided by the inclusion of subset-specific cytokine markers, and proliferation markers. Development and optimization of this panel was performed on freshly isolated cells from adult BALB/c lungs and small intestine lamina propria, and ex vivo stimulation with phorbol 12-myrisate 13-acetate, ionomycin, and pro-ILC activating cytokines.
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Affiliation(s)
- Kyle T. Mincham
- National Heart and Lung InstituteImperial College LondonLondonUK
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16
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Spurgeon BEJ, Frelinger AL. Platelet Phenotyping by Full Spectrum Flow Cytometry. Curr Protoc 2023; 3:e687. [PMID: 36779850 DOI: 10.1002/cpz1.687] [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: 02/14/2023]
Abstract
Platelets play key roles in hemostasis, immunity, and inflammation, and tests of platelet phenotype and function are useful in studies of disease biology and pathology. Full spectrum flow cytometry offers distinct advantages over standard tests and enables the sensitive and simultaneous detection of many biomarkers. A typical assay provides a wealth of information on platelet biology and allows the assessment of in vivo activation and in vitro reactivity, as well as the discovery of novel phenotypes. Here, we describe the analysis of platelets by full spectrum flow cytometry and discuss a range of controls and methods for interpreting results. © 2023 Wiley Periodicals LLC. Basic Protocol: Platelet phenotyping by full spectrum flow cytometry Support Protocol 1: Spectral unmixing Support Protocol 2: Data preprocessing.
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Affiliation(s)
- Benjamin E J Spurgeon
- Center for Platelet Research Studies, Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Harvard Medical School, Boston, Massachusetts
| | - Andrew L Frelinger
- Center for Platelet Research Studies, Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Harvard Medical School, Boston, Massachusetts
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17
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Lee J, Campillo B, Hamidian S, Liu Z, Shorey M, St-Pierre F. Automating the High-Throughput Screening of Protein-Based Optical Indicators and Actuators. Biochemistry 2023; 62:169-177. [PMID: 36315460 PMCID: PMC9852035 DOI: 10.1021/acs.biochem.2c00357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Over the last 25 years, protein engineers have developed an impressive collection of optical tools to interface with biological systems: indicators to eavesdrop on cellular activity and actuators to poke and prod native processes. To reach the performance level required for their downstream applications, protein-based tools are usually sculpted by iterative rounds of mutagenesis. In each round, libraries of variants are made and evaluated, and the most promising hits are then retrieved, sequenced, and further characterized. Early efforts to engineer protein-based optical tools were largely manual, suffering from low throughput, human error, and tedium. Here, we describe approaches to automating the screening of libraries generated as colonies on agar, multiwell plates, and pooled populations of single-cell variants. We also briefly discuss emerging approaches for screening, including cell-free systems and machine learning.
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Affiliation(s)
- Jihwan Lee
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
| | - Beatriz Campillo
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
| | - Shaminta Hamidian
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
| | - Zhuohe Liu
- Department of Electrical and Computer Engineering, Rice University, Houston, TX 77005, USA
| | - Matthew Shorey
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
| | - François St-Pierre
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
- Systems, Synthetic, and Physical Biology Program, Rice University, Houston, TX 77005, USA
- Department of Electrical and Computer Engineering, Rice University, Houston, TX 77005, USA
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
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18
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Santinon F, Young YK, Del Rincón SV, Mann KK. Analyzing the Tumor-Immune Microenvironment by Flow Cytometry. Methods Mol Biol 2023; 2614:17-36. [PMID: 36587116 DOI: 10.1007/978-1-0716-2914-7_2] [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] [Indexed: 01/02/2023]
Abstract
Flow cytometry is an essential tool for studying the tumor-immune microenvironment. It allows us to quickly quantify and identify multiple cell types in a heterogeneous sample. This chapter provides an overview of the flow cytometry instrumentation and a discussion of the appropriate considerations and steps in building a reproducible flow cytometry staining panel. We present an updated lymphoid tissue and solid tumor-infiltrating leucocyte flow cytometry staining protocol and an example of flow cytometry data analysis.
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Affiliation(s)
- François Santinon
- Lady Davis Institute for Medical Research, McGill University, Montreal, QC, Canada.
| | - Yoon Kow Young
- Lady Davis Institute for Medical Research, McGill University, Montreal, QC, Canada
| | - Sonia V Del Rincón
- Lady Davis Institute for Medical Research, McGill University, Montreal, QC, Canada
- Gerald Bronfman Department of Oncology, McGill University, Montreal, QC, Canada
| | - Koren K Mann
- Lady Davis Institute for Medical Research, McGill University, Montreal, QC, Canada.
- Gerald Bronfman Department of Oncology, McGill University, Montreal, QC, Canada.
- Department of Pharmacology and Therapeutics, McGill University, Montreal, QC, Canada.
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19
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Preglej T, Brinkmann M, Steiner G, Aletaha D, Göschl L, Bonelli M. Advanced immunophenotyping: A powerful tool for immune profiling, drug screening, and a personalized treatment approach. Front Immunol 2023; 14:1096096. [PMID: 37033944 PMCID: PMC10080106 DOI: 10.3389/fimmu.2023.1096096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 03/13/2023] [Indexed: 04/11/2023] Open
Abstract
Various autoimmune diseases are characterized by distinct cell subset distributions and activation profiles of peripheral blood mononuclear cells (PBMCs). PBMCs can therefore serve as an ideal biomarker material, which is easily accessible and allows for screening of multiple cell types. A detailed understanding of the immune landscape is critical for the diagnosis of patients with autoimmune diseases, as well as for a personalized treatment approach. In our study, we investigate the potential of multi-parameter spectral flow cytometry for the identification of patients suffering from autoimmune diseases and its power as an evaluation tool for in vitro drug screening approaches (advanced immunophenotyping). We designed a combination of two 22-color immunophenotyping panels for profiling cell subset distribution and cell activation. Downstream bioinformatics analyses included percentages of individual cell populations and median fluorescent intensity of defined markers which were then visualized as heatmaps and in dimensionality reduction approaches. In vitro testing of epigenetic immunomodulatory drugs revealed an altered activation status upon treatment, which supports the use of spectral flow cytometry as a high-throughput drug screening tool. Advanced immunophenotyping might support the exploration of novel therapeutic drugs and contribute to future personalized treatment approaches in autoimmune diseases and beyond.
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Affiliation(s)
| | | | | | | | - Lisa Göschl
- *Correspondence: Lisa Göschl, ; Michael Bonelli,
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20
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Vorobjev IA, Kussanova A, Barteneva NS. Development of Spectral Imaging Cytometry. Methods Mol Biol 2023; 2635:3-22. [PMID: 37074654 DOI: 10.1007/978-1-0716-3020-4_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2023]
Abstract
Spectral flow cytometry is a new technology that enables measurements of fluorescent spectra and light scattering properties in diverse cellular populations with high precision. Modern instruments allow simultaneous determination of up to 40+ fluorescent dyes with heavily overlapping emission spectra, discrimination of autofluorescent signals in the stained specimens, and detailed analysis of diverse autofluorescence of different cells-from mammalian to chlorophyll-containing cells like cyanobacteria. In this paper, we review the history, compare modern conventional and spectral flow cytometers, and discuss several applications of spectral flow cytometry.
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Affiliation(s)
- Ivan A Vorobjev
- School of Sciences and Humanities, Nazarbayev University, Astana, Kazakhstan.
- National Laboratory Astana, Nazarbayev University, Astana, Kazakhstan.
- A.N. Belozersky Insitute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russian Federation.
- Biological Faculty, Lomonosov Moscow State University, Moscow, Russian Federation.
| | - Aigul Kussanova
- School of Sciences and Humanities, Nazarbayev University, Astana, Kazakhstan
- Core Facilities, Nazarbayev University, Astana, Kazakhstan
| | - Natasha S Barteneva
- School of Sciences and Humanities, Nazarbayev University, Astana, Kazakhstan
- Brigham Women's Hospital, Harvard University, Boston, MA, USA
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21
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Heubeck A, Savage A, Henderson K, Roll C, Hernandez V, Torgerson T, Bumol T, Reading J. Cross-platform immunophenotyping of human peripheral blood mononuclear cells with four high-dimensional flow cytometry panels. Cytometry A 2022. [PMID: 36571245 DOI: 10.1002/cyto.a.24715] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 12/13/2022] [Accepted: 12/20/2022] [Indexed: 12/27/2022]
Abstract
Immunophenotyping using high dimensional flow cytometry is a central component of human immune system multi-omic studies. We present four high parameter flow cytometry panels for deep immunophenotyping of human peripheral blood mononuclear cells (PBMC). This set of four 25+ color panels include 64 cell surface markers to resolve broad immune compartment populations, as well as activation and memory of specific T, B, natural killer (NK), and myeloid lineages. Common lineage bridging markers are integrated into each panel to allow for inter-panel quality control through major lineage frequency verification. These panels were developed using a five laser BD Symphony A5 conventional cytometer and successfully transferred to a five laser Cytek Aurora spectral cytometer capable of acquiring the panels. Nine representative PBMC samples were stained with the four phenotyping panels and acquired on both instruments to evaluate population frequency and visual staining patterns for gating between the systems. Both instruments produced comparable high quality flow cytometry data and supported our decision to acquire samples on the spectral cytometer moving forward. This modular set of panels and instrument performance metrics provide guidelines for designing flow cytometry experiments suitable for longitudinal or cross-sectional immune profiling.
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Affiliation(s)
| | - Adam Savage
- Allen Institute for Immunology, Seattle, Washington, USA
| | | | - Charles Roll
- Allen Institute for Immunology, Seattle, Washington, USA
| | | | - Troy Torgerson
- Allen Institute for Immunology, Seattle, Washington, USA
| | - Thomas Bumol
- Allen Institute for Immunology, Seattle, Washington, USA
| | - Julian Reading
- Allen Institute for Immunology, Seattle, Washington, USA
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22
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Jaimes MC, Leipold M, Kraker G, Amir E, Maecker H, Lannigan J. Full spectrum flow cytometry and mass cytometry: A 32-marker panel comparison. Cytometry A 2022; 101:942-959. [PMID: 35593221 PMCID: PMC9790709 DOI: 10.1002/cyto.a.24565] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 02/23/2022] [Accepted: 04/25/2022] [Indexed: 01/27/2023]
Abstract
High-dimensional single-cell data has become an important tool in unraveling the complexity of the immune system and its involvement in homeostasis and a large array of pathologies. As technological tools are developed, researchers are adopting them to answer increasingly complex biological questions. Up until recently, mass cytometry (MC) has been the main technology employed in cytometric assays requiring more than 29 markers. Recently, however, with the introduction of full spectrum flow cytometry (FSFC), it has become possible to break the fluorescence barrier and go beyond 29 fluorescent parameters. In this study, in collaboration with the Stanford Human Immune Monitoring Center (HIMC), we compared five patient samples using an established immune panel developed by the HIMC using their MC platform. Using split samples and the same antibody panel, we were able to demonstrate highly comparable results between the two technologies using multiple data analysis approaches. We report here a direct comparison of two technology platforms (MC and FSFC) using a 32-marker flow cytometric immune monitoring panel that can identify all the previously described and anticipated immune subpopulations defined by this panel.
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Affiliation(s)
| | - Michael Leipold
- Department of Microbiology/ImmunologyStanford UniversityStanfordCaliforniaUSA
| | - Geoffrey Kraker
- Technical Applications SupportCytek Biosciences Inc.FremontCaliforniaUSA
| | - El‐ad Amir
- Astrolabe DiagnosticsFort LeeNew JerseyUSA
| | - Holden Maecker
- Department of Microbiology/ImmunologyStanford UniversityStanfordCaliforniaUSA
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23
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Jameson VJ, Luke T, Yan Y, Hind A, Evrard M, Man K, Mackay LK, Kallies A, Villadangos JA, McWilliam HEG, Perez‐Gonzalez A. Unlocking autofluorescence in the era of full spectrum analysis: Implications for immunophenotype discovery projects. Cytometry A 2022; 101:922-941. [PMID: 35349225 PMCID: PMC9519814 DOI: 10.1002/cyto.a.24555] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 02/22/2022] [Accepted: 03/24/2022] [Indexed: 01/27/2023]
Abstract
Understanding the complex elements affecting signal resolution in cytometry is key for quality experimental design and data. In this study, we incorporate autofluorescence as a contributing factor to our understanding of resolution in cytometry and corroborate its impact in fluorescence signal detection through mathematical predictions supported by empirical evidence. Our findings illustrate the critical importance of autofluorescence extraction via full spectrum unmixing in unmasking dim signals and delineating the expression and subset distribution of low abundance markers in discovery projects. We apply our findings to the precise definition of the tissue and cellular distribution of a weakly expressed fluorescent protein that reports on a low-abundance immunological gene. Exploiting the full spectrum coverage enabled by Aurora 5L, we describe a novel approach to the isolation of pure cell subset-specific autofluorescence profiles based on high dimensionality reduction algorithms. This method can also be used to unveil differences in the autofluorescent fingerprints of tissues in homeostasis and after immunological challenges.
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Affiliation(s)
- Vanta J. Jameson
- Department of Anatomy and PhysiologyThe University of MelbourneParkvilleVictoriaAustralia,Department of Microbiology and ImmunologyThe University of Melbourne, at The Peter Doherty Institute of Infection and ImmunityParkvilleVictoriaAustralia,Melbourne Cytometry PlatformThe University of MelbourneParkvilleVictoriaAustralia
| | - Tina Luke
- Department of Microbiology and ImmunologyThe University of Melbourne, at The Peter Doherty Institute of Infection and ImmunityParkvilleVictoriaAustralia,Melbourne Cytometry PlatformThe University of MelbourneParkvilleVictoriaAustralia
| | - Yuting Yan
- Department of Microbiology and ImmunologyThe University of Melbourne, at The Peter Doherty Institute of Infection and ImmunityParkvilleVictoriaAustralia,School of MedicineTsinghua UniversityBeijingChina
| | - Angela Hind
- Department of Microbiology and ImmunologyThe University of Melbourne, at The Peter Doherty Institute of Infection and ImmunityParkvilleVictoriaAustralia,Melbourne Cytometry PlatformThe University of MelbourneParkvilleVictoriaAustralia
| | - Maximilien Evrard
- Department of Microbiology and ImmunologyThe University of Melbourne, at The Peter Doherty Institute of Infection and ImmunityParkvilleVictoriaAustralia
| | - Kevin Man
- Department of Microbiology and ImmunologyThe University of Melbourne, at The Peter Doherty Institute of Infection and ImmunityParkvilleVictoriaAustralia
| | - Laura K. Mackay
- Department of Microbiology and ImmunologyThe University of Melbourne, at The Peter Doherty Institute of Infection and ImmunityParkvilleVictoriaAustralia
| | - Axel Kallies
- Department of Microbiology and ImmunologyThe University of Melbourne, at The Peter Doherty Institute of Infection and ImmunityParkvilleVictoriaAustralia
| | - Jose A. Villadangos
- Department of Microbiology and ImmunologyThe University of Melbourne, at The Peter Doherty Institute of Infection and ImmunityParkvilleVictoriaAustralia,Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology InstituteThe University of MelbourneParkvilleVictoriaAustralia
| | - Hamish E. G. McWilliam
- Department of Microbiology and ImmunologyThe University of Melbourne, at The Peter Doherty Institute of Infection and ImmunityParkvilleVictoriaAustralia,Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology InstituteThe University of MelbourneParkvilleVictoriaAustralia
| | - Alexis Perez‐Gonzalez
- Department of Microbiology and ImmunologyThe University of Melbourne, at The Peter Doherty Institute of Infection and ImmunityParkvilleVictoriaAustralia,Melbourne Cytometry PlatformThe University of MelbourneParkvilleVictoriaAustralia
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24
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O'Connell P, Blake MK, Godbehere S, Amalfitano A, Aldhamen YA. SLAMF7 modulates B cells and adaptive immunity to regulate susceptibility to CNS autoimmunity. J Neuroinflammation 2022; 19:241. [PMID: 36199066 PMCID: PMC9533612 DOI: 10.1186/s12974-022-02594-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Accepted: 09/08/2022] [Indexed: 12/02/2022] Open
Abstract
Background Multiple sclerosis (MS) is a chronic, debilitating condition characterized by CNS autoimmunity stemming from a complex etiology involving both environmental and genetic factors. Our current understanding of MS points to dysregulation of the immune system as the pathogenic culprit, however, it remains unknown as to how the many genes associated with increased susceptibility to MS are involved. One such gene linked to MS susceptibility and known to regulate immune function is the self-ligand immune cell receptor SLAMF7. Methods We subjected WT and SLAMF7−/− mice to multiple EAE models, compared disease severity, and comprehensively profiled the CNS immune landscape of these mice. We identified all SLAMF7-expressing CNS immune cells and compared the entire CNS immune niche between genotypes. We performed deep phenotyping and in vitro functional studies of B and T cells via spectral cytometry and BioPlex assays. Adoptive transfer studies involving the transfer of WT and SLAMF7−/− B cells into B cell-deficient mice (μMT) were also performed. Finally, B–T cell co-culture studies were performed, and a comparative cell–cell interaction network derived from scRNA-seq data of SLAMF7+ vs. SLAMF7− human CSF immune cells was constructed. Results We found SLAMF7−/− mice to be more susceptible to EAE compared to WT mice and found SLAMF7 to be expressed on numerous CNS immune cell subsets. Absence of SLAMF7 did not grossly alter the CNS immune landscape, but allowed for altered immune cell subset infiltration during EAE in a model-dependent manner. Global lack of SLAMF7 expression increased myeloid cell activation states along with augmented T cell anti-MOG immunity. B cell profiling studies revealed increased activation states of specific plasma and B cell subsets in SLAMF7−/− mice during EAE, and functional co-culture studies determined that SLAMF7−/− B cells induce exaggerated T cell activation. Adoptive transfer studies revealed that the increased susceptibility of SLAMF7−/− mice to EAE is partly B cell dependent and reconstruction of the human CSF SLAMF7-interactome found B cells to be critical to cell–cell communication between SLAMF7-expressing cells. Conclusions Our studies have identified novel roles for SLAMF7 in CNS immune regulation and B cell function, and illuminate underpinnings of the genetic association between SLAMF7 and MS. Supplementary Information The online version contains supplementary material available at 10.1186/s12974-022-02594-9.
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Affiliation(s)
- Patrick O'Connell
- Department of Microbiology and Molecular Genetics, College of Osteopathic Medicine, Michigan State University, 567 Wilson Road, 4108 Biomedical and Physical Sciences Building, East Lansing, MI, 48824, USA
| | - Maja K Blake
- Department of Microbiology and Molecular Genetics, College of Osteopathic Medicine, Michigan State University, 567 Wilson Road, 4108 Biomedical and Physical Sciences Building, East Lansing, MI, 48824, USA
| | - Sarah Godbehere
- Department of Microbiology and Molecular Genetics, College of Osteopathic Medicine, Michigan State University, 567 Wilson Road, 4108 Biomedical and Physical Sciences Building, East Lansing, MI, 48824, USA
| | - Andrea Amalfitano
- Department of Microbiology and Molecular Genetics, College of Osteopathic Medicine, Michigan State University, 567 Wilson Road, 4108 Biomedical and Physical Sciences Building, East Lansing, MI, 48824, USA.,Department of Pediatrics, College of Osteopathic Medicine, Michigan State University, East Lansing, MI, 48824, USA
| | - Yasser A Aldhamen
- Department of Microbiology and Molecular Genetics, College of Osteopathic Medicine, Michigan State University, 567 Wilson Road, 4108 Biomedical and Physical Sciences Building, East Lansing, MI, 48824, USA.
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25
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Lannigan J. Flow cytometry has seen the light: All of it. Cytometry A 2022; 101:809-811. [PMID: 36203398 DOI: 10.1002/cyto.a.24694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/16/2022] [Indexed: 01/27/2023]
Affiliation(s)
- Joanne Lannigan
- Flow Cytometry Support Services, LLC, Alexandria, Virginia, USA
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26
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Nolan JP. The evolution of spectral flow cytometry. Cytometry A 2022; 101:812-817. [PMID: 35567367 DOI: 10.1002/cyto.a.24566] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 04/13/2022] [Accepted: 04/22/2022] [Indexed: 01/27/2023]
Abstract
This special issue of Cytometry marks the transition of spectral flow cytometry from an emerging technology into a transformative force that will shape the fields of cytometry and single-cell analysis for some time to come. Tracing its roots to the earliest years of flow cytometry, spectral flow cytometry has evolved from the domain of individual researchers pushing the limits of hardware, reagents, and software to the mainstream, where it is being harnessed and adapted to meet the analytical challenges presented by modern biomedical research. In particular, the current form of spectral flow technology has arisen to address the needs of multiparameter immunophenotyping of immune cells in basic and translational research, and much of the current instrumentation and software reflects the needs of those applications. Yet, the possibilities enabled by high-resolution analysis of the spectral properties of optical absorbance, scatter, and emission have only begun to be exploited. In this brief review, the author highlights the origins and early milestones of single-cell spectral analysis, assesses the current state of instrumentation and software, and speculates as to future directions of spectral flow cytometry technology and applications.
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Affiliation(s)
- John P Nolan
- Scintillon Institute, San Diego, California, USA
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27
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Henderson J, Havranek O, Ma MCJ, Herman V, Kupcova K, Chrbolkova T, Pacheco-Blanco M, Wang Z, Comer JM, Zal T, Davis RE. Detecting Förster resonance energy transfer in living cells by conventional and spectral flow cytometry. Cytometry A 2022; 101:818-834. [PMID: 34128311 DOI: 10.1002/cyto.a.24472] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 05/31/2021] [Accepted: 06/07/2021] [Indexed: 01/27/2023]
Abstract
Assays based on Förster resonance energy transfer (FRET) can be used to study many processes in cell biology. Although this is most often done with microscopy for fluorescence detection, we report two ways to measure FRET in living cells by flow cytometry. Using a conventional flow cytometer and the "3-cube method" for intensity-based calculation of FRET efficiency, we measured the enzymatic activity of specific kinases in cells expressing a genetically-encoded reporter. For both AKT and protein kinase A, the method measured kinase activity in time-course, dose-response, and kinetic assays. Using the Cytek Aurora spectral flow cytometer, which applies linear unmixing to emission measured in multiple wavelength ranges, FRET from the same reporters was measured with greater single-cell precision, in real time and in the presence of other fluorophores. Results from gene-knockout studies suggested that spectral flow cytometry might enable the sorting of cells on the basis of FRET. The methods we present provide convenient and flexible options for using FRET with flow cytometry in studies of cell biology.
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Affiliation(s)
- Jared Henderson
- Department of Lymphoma and Myeloma, The University of Texas-MD Anderson Cancer Center, Houston, Texas, USA
| | - Ondrej Havranek
- Department of Lymphoma and Myeloma, The University of Texas-MD Anderson Cancer Center, Houston, Texas, USA.,BIOCEV, First Faculty of Medicine, Charles University, Vestec, Czech Republic.,Department of Hematology, Charles University and General University Hospital, Prague, Czech Republic
| | - Man Chun John Ma
- Department of Lymphoma and Myeloma, The University of Texas-MD Anderson Cancer Center, Houston, Texas, USA
| | - Vaclav Herman
- BIOCEV, First Faculty of Medicine, Charles University, Vestec, Czech Republic.,Department of Hematology, Charles University and General University Hospital, Prague, Czech Republic
| | - Kristyna Kupcova
- BIOCEV, First Faculty of Medicine, Charles University, Vestec, Czech Republic
| | - Tereza Chrbolkova
- BIOCEV, First Faculty of Medicine, Charles University, Vestec, Czech Republic
| | | | - Zhiqiang Wang
- Department of Lymphoma and Myeloma, The University of Texas-MD Anderson Cancer Center, Houston, Texas, USA
| | - Justin M Comer
- Department of Lymphoma and Myeloma, The University of Texas-MD Anderson Cancer Center, Houston, Texas, USA
| | - Tomasz Zal
- Department of Leukemia, The University of Texas-MD Anderson Cancer Center, Houston, Texas, USA
| | - Richard Eric Davis
- Department of Lymphoma and Myeloma, The University of Texas-MD Anderson Cancer Center, Houston, Texas, USA.,Department of Translational Molecular Pathology, The University of Texas-MD Anderson Cancer Center, Houston, Texas, USA
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28
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Differential Immune Checkpoint and Ig-like V-Type Receptor Profiles in COVID-19: Associations with Severity and Treatment. J Clin Med 2022; 11:jcm11123287. [PMID: 35743356 PMCID: PMC9225268 DOI: 10.3390/jcm11123287] [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: 04/20/2022] [Revised: 06/02/2022] [Accepted: 06/07/2022] [Indexed: 12/15/2022] Open
Abstract
Identifying patients' immune system status has become critical to managing SARS-CoV-2 infection and avoiding the appearance of secondary infections during a hospital stay. Despite the high volume of research, robust severity and outcome markers are still lacking in COVID-19. We recruited 87 COVID-19 patients and analyzed, by unbiased automated software, 356 parameters at baseline emergency department admission including: high depth immune phenotyping and immune checkpoint expression by spectral flow cytometry, cytokines and other soluble molecules in plasma as well as routine clinical variables. We identified 69 baseline alterations in the expression of immune checkpoints, Ig-like V type receptors and other immune population markers associated with severity (O2 requirement). Thirty-four changes in these markers/populations were associated with secondary infection appearance. In addition, through a longitudinal sample collection, we described the changes which take place in the immune system of COVID-19 patients during secondary infections and in response to corticosteroid treatment. Our study provides information about immune checkpoint molecules and other less-studied receptors with Ig-like V-type domains such as CD108, CD226, HVEM (CD270), B7H3 (CD276), B7H5 (VISTA) and GITR (CD357), defining these as novel interesting molecules in severe and corticosteroids-treated acute infections.
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29
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Bene L, Damjanovich L. Spectral flow cytometric FRET: Towards a hyper dimensional flow cytometry. Cytometry A 2022; 101:468-473. [PMID: 35484961 DOI: 10.1002/cyto.a.24561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 04/11/2022] [Accepted: 04/19/2022] [Indexed: 11/07/2022]
Affiliation(s)
- László Bene
- Department of Surgery, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - László Damjanovich
- Department of Surgery, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
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30
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Wanner N, Barnhart J, Apostolakis N, Zlojutro V, Asosingh K. Using the Autofluorescence Finder on the Sony ID7000 TM Spectral Cell Analyzer to Identify and Unmix Multiple Highly Autofluorescent Murine Lung Populations. Front Bioeng Biotechnol 2022; 10:827987. [PMID: 35372303 PMCID: PMC8965042 DOI: 10.3389/fbioe.2022.827987] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 02/25/2022] [Indexed: 11/13/2022] Open
Abstract
Autofluorescence (AF) is a feature of all cell types, though some have more than others. In tissues with complex heterogeneous cellularity, AF is frequently a source of high background, masking faint fluorescent signals and reducing the available dynamic range of detectors for detecting fluorescence signals from markers of interest in a flow cytometry panel. Pulmonary flow cytometry presents unique challenges because lung cells are heterogeneous and contain varying amounts of high AF. The goal of this study was to demonstrate how a novel AF Finder tool on the Sony ID7000™ Spectral Cell Analyzer can be used to identify and screen multiple AF subsets in complex highly AF tissues like murine lungs. In lung single cell suspensions, the AF Finder tool identified four distinct AF spectra from six highly AF subsets. The subtraction of these distinct AF spectra resulted in a resolution increase by several log decades in several fluorescent channels. The major immune and lung tissue resident cells in a murine model of asthma were easily identified in a multi-color panel using AF subtraction. The findings demonstrate the practicality of the AF Finder tool, particularly when analyzing samples with multiple AF populations of varying intensities, in order to reduce fluorescence background and increase signal resolution in spectral flow cytometry.
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Affiliation(s)
- Nicholas Wanner
- Asosingh Lab, Department of Inflammation and Immunity, Cleveland Clinic, Lerner Research Institute, Cleveland, OH, United States
| | | | - Nicholas Apostolakis
- Asosingh Lab, Department of Inflammation and Immunity, Cleveland Clinic, Lerner Research Institute, Cleveland, OH, United States
| | - Violetta Zlojutro
- Asosingh Lab, Department of Inflammation and Immunity, Cleveland Clinic, Lerner Research Institute, Cleveland, OH, United States
| | - Kewal Asosingh
- Asosingh Lab, Department of Inflammation and Immunity, Cleveland Clinic, Lerner Research Institute, Cleveland, OH, United States
- Flow Cytometry Core, Cleveland Clinic, Lerner Research Institute, Cleveland, OH, United States
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31
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Hally KE, Ferrer-Font L, Pilkington KR, Larsen PD. OMIP 083: A 21-marker 18-color flow cytometry panel for in-depth phenotyping of human peripheral monocytes. Cytometry A 2022; 101:374-379. [PMID: 35274803 PMCID: PMC9310743 DOI: 10.1002/cyto.a.24545] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 02/09/2022] [Accepted: 02/28/2022] [Indexed: 12/28/2022]
Affiliation(s)
- Kathryn E Hally
- Department of Surgery and Anaesthesia, The University of Otago, Wellington.,School of Biological Sciences, Victoria University of Wellington, Wellington.,Wellington Cardiovascular Research Group, Wellington
| | - Laura Ferrer-Font
- Hugh Green Cytometry Centre, Malaghan Institute of Medical Research, Wellington, New Zealand
| | | | - Peter D Larsen
- Department of Surgery and Anaesthesia, The University of Otago, Wellington.,School of Biological Sciences, Victoria University of Wellington, Wellington.,Wellington Cardiovascular Research Group, Wellington
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32
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Ni D, Tan J, Niewold P, Spiteri AG, Pinget GV, Stanley D, King NJC, Macia L. Impact of Dietary Fiber on West Nile Virus Infection. Front Immunol 2022; 13:784486. [PMID: 35296081 PMCID: PMC8919037 DOI: 10.3389/fimmu.2022.784486] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 02/04/2022] [Indexed: 12/11/2022] Open
Abstract
Dietary fiber supports healthy gut bacteria and their production of short-chain fatty acids (SCFA), which promote anti-inflammatory cell development, in particular, regulatory T cells. It is thus beneficial in many diseases, including influenza infection. While disruption of the gut microbiota by antibiotic treatment aggravates West Nile Virus (WNV) disease, whether dietary fiber is beneficial is unknown. WNV is a widely-distributed neurotropic flavivirus that recruits inflammatory monocytes into the brain, causing life-threatening encephalitis. To investigate the impact of dietary fiber on WNV encephalitis, mice were fed on diets deficient or enriched with dietary fiber for two weeks prior to inoculation with WNV. To induce encephalitis, mice were inoculated intranasally with WNV and maintained on these diets. Despite increased fecal SCFA acetate and changes in gut microbiota composition, dietary fiber did not affect clinical scores, leukocyte infiltration into the brain, or survival. After the brain, highest virus loads were measured in the colon in neurons of the submucosal and myenteric plexuses. Associated with this, there was disrupted gut homeostasis, with shorter colon length and higher local inflammatory cytokine levels, which were not affected by dietary fiber. Thus, fiber supplementation is not effective in WNV encephalitis.
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Affiliation(s)
- Duan Ni
- Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Jian Tan
- Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Paula Niewold
- Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
- Department of Infectious Diseases, Leiden University Medical Centre, Leiden, Netherlands
| | - Alanna Gabrielle Spiteri
- Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Gabriela Veronica Pinget
- Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Dragana Stanley
- School of Health, Medical and Applied Science, Central Queensland University, Rockhampton, QLD, Australia
| | - Nicholas Jonathan Cole King
- Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
- Sydney Institute for Infectious Diseases, The University of Sydney, Sydney, NSW, Australia
- *Correspondence: Nicholas Jonathan Cole King, ; Laurence Macia,
| | - Laurence Macia
- Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
- Sydney Cytometry, The University of Sydney and The Centenary Institute, Sydney, NSW, Australia
- *Correspondence: Nicholas Jonathan Cole King, ; Laurence Macia,
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33
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Fernandez MA, Alzayat H, Jaimes MC, Kharraz Y, Requena G, Mendez P. High-Dimensional Immunophenotyping with 37-Color Panel Using Full-Spectrum Cytometry. Methods Mol Biol 2022; 2386:43-60. [PMID: 34766264 DOI: 10.1007/978-1-0716-1771-7_4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
A comprehensive study of the cellular components of the immune system demands both deep and broad immunophenotyping of numerous cell subsets in an effective and practical way. Novel full-spectrum technology reveals the complete emission spectrum of each dye maximizing the amount of information that can be obtained on a single sample regarding conventional flow cytometry and provide an expanded knowledge of biological processes. In this chapter, we describe a 37-color protocol that allows to identify more than 45 different cell populations on whole blood samples of SARS-CoV-2-infected patients.
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Affiliation(s)
- Marco A Fernandez
- Flow Cytometry Facility, Germans Trias i Pujol Research Institute, Badalona, Spain
| | - Hammad Alzayat
- Flow Cytometry Facility, Germans Trias i Pujol Research Institute, Badalona, Spain
| | | | | | - Gerard Requena
- Flow Cytometry Facility, Germans Trias i Pujol Research Institute, Badalona, Spain
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34
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O'Connell P, Blake MK, Godbehere S, Aldhamen YA, Amalfitano A. Absence of ERAP1 in B Cells Increases Susceptibility to Central Nervous System Autoimmunity, Alters B Cell Biology, and Mechanistically Explains Genetic Associations between ERAP1 and Multiple Sclerosis. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2021; 207:2952-2965. [PMID: 34810226 DOI: 10.4049/jimmunol.2100813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 10/18/2021] [Indexed: 11/19/2022]
Abstract
Hundreds of genes have been linked to multiple sclerosis (MS); yet, the underlying mechanisms behind these associations have only been investigated in a fraction of cases. Endoplasmic reticulum aminopeptidase 1 (ERAP1) is an endoplasmic reticulum-localized aminopeptidase with important roles in trimming peptides destined for MHC class I and regulation of innate immune responses. As such, genetic polymorphisms in ERAP1 have been linked to multiple autoimmune diseases. In this study, we present, to our knowledge, the first mechanistic studies performed to uncover why polymorphisms in ERAP1 are associated with increased susceptibility to MS. Combining multiple mouse models of CNS autoimmunity with high-dimensional single-cell spectral cytometry, adoptive transfer studies, and integrative analysis of human single-cell RNA-sequencing datasets, we identify an intrinsic defect in B cells as being primarily responsible. Not only are mice lacking ERAP1 more susceptible to CNS autoimmunity, but adoptive transfer of B cells lacking ERAP1 into B cell-deficient mice recapitulates this susceptibility. We found B cells lacking ERAP1 display decreased proliferation in vivo and express higher levels of activation/costimulatory markers. Integrative analysis of single-cell RNA sequencing of B cells from 36 individuals revealed subset-conserved differences in gene expression and pathway activation in individuals harboring the MS-linked K528R ERAP1 single-nucleotide polymorphism. Finally, our studies also led us to create, to our knowledge, the first murine protein-level map of the CNS IL-10+ immune compartment at steady state and during neuroinflammation. These studies identify a role for ERAP1 in the modulation of B cells and highlight this as one reason why polymorphisms in this gene are linked to MS.
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Affiliation(s)
- Patrick O'Connell
- Department of Microbiology and Molecular Genetics, College of Osteopathic Medicine, Michigan State University, East Lansing, MI; and
| | - Maja K Blake
- Department of Microbiology and Molecular Genetics, College of Osteopathic Medicine, Michigan State University, East Lansing, MI; and
| | - Sarah Godbehere
- Department of Microbiology and Molecular Genetics, College of Osteopathic Medicine, Michigan State University, East Lansing, MI; and
| | - Yasser A Aldhamen
- Department of Microbiology and Molecular Genetics, College of Osteopathic Medicine, Michigan State University, East Lansing, MI; and
| | - Andrea Amalfitano
- Department of Microbiology and Molecular Genetics, College of Osteopathic Medicine, Michigan State University, East Lansing, MI; and .,Department of Pediatrics, College of Osteopathic Medicine, Michigan State University, East Lansing, MI
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35
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Graham A, Korecky J, Schultz E, Gregory M, Asosingh K. Considerations for user consultation in a flow cytometry shared resource laboratory. Cytometry A 2021; 101:228-236. [PMID: 34787950 DOI: 10.1002/cyto.a.24519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Revised: 11/12/2021] [Accepted: 11/15/2021] [Indexed: 11/06/2022]
Abstract
User consultation is an essential first step in assuring high-quality flow cytometric data. A central challenge to shared resource laboratory (SRL) staff is how to best guide new and current users to meet each projects' needs. One solution to this challenge is to follow a standard user consultation platform addressing all critical steps between the conception of the experiment and the actual acquisition of samples. Here we describe considerations to help an SRL understand the researcher's goals and how best the SRL staff can provide expert advice in a structured manner. User consultation has an educational nature, informing users about current best practices in cytometry that apply to their specific utilization. A consultation report also improves communication between the SRL, principal investigator, and lab members of the collaborating researcher. Development of best SRL practices is spearheaded by the ISAC SRL committee and this communication sets the foundation to initiate such report for user consultation. Implementation of best practices during user consultation will improve rigor and reproducibility in cytometry.
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Affiliation(s)
- Amy Graham
- Flow Cytometry Core Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Jena Korecky
- Flow Cytometry Core Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Eric Schultz
- Flow Cytometry Core Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Michael Gregory
- Florida Research and Innovation Center, Cleveland Clinic, Port St Lucie, Florida, USA
| | - Kewal Asosingh
- Flow Cytometry Core Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA.,Department of Inflammation and Immunity, Cleveland Clinic, Cleveland, Ohio, USA
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36
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Mitra-Kaushik S, Mehta-Damani A, Stewart JJ, Green C, Litwin V, Gonneau C. The Evolution of Single-Cell Analysis and Utility in Drug Development. AAPS JOURNAL 2021; 23:98. [PMID: 34389904 PMCID: PMC8363238 DOI: 10.1208/s12248-021-00633-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Accepted: 07/27/2021] [Indexed: 02/07/2023]
Abstract
This review provides a brief history of the advances of cellular analysis tools focusing on instrumentation, detection probes, and data analysis tools. The interplay of technological advancement and a deeper understanding of cellular biology are emphasized. The relevance of this topic to drug development is that the evaluation of cellular biomarkers has become a critical component of the development strategy for novel immune therapies, cell therapies, gene therapies, antiviral therapies, and vaccines. Moreover, recent technological advances in single-cell analysis are providing more robust cellular measurements and thus accelerating the advancement of novel therapies. Graphical abstract
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Affiliation(s)
| | | | | | - Cherie Green
- Development Sciences, Genentech, Inc., A Member of the Roche Group, South San Francisco, California, USA
| | | | - Christèle Gonneau
- Central Laboratory Services, Labcorp Drug Development, Geneva, Switzerland.
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37
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Munoz-Erazo L, Schmidt AJ, Price KM. High-Dimensional Image Analysis using Histocytometry. Curr Protoc 2021; 1:e184. [PMID: 34165879 DOI: 10.1002/cpz1.184] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Histocytometry is a technique for processing multiparameter microscopy images using computational approaches to identify and quantify cellular phenotypes. It allows for spatial analyses of cellular phenotypes in relation to each other and within defined spatial regions. The benefit of this technique over manual annotation and characterization of cells is a high degree of automation/throughput, significantly decreased user bias, and increased reproducibility. Recently, an increase in freely available software amenable to or deliberately designed for histocytometry has resulted in these complex analyses being available to a broader base of users who have amassed multi-component microscopic imaging data. This article provides an overview of a histocytometry pipeline, focusing on the strategic planning and software requirements to allow readers to perform cell segmentation, phenotyping, and spatial analyses to advance their research outputs. © 2021 Wiley Periodicals LLC.
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Affiliation(s)
| | | | - Kylie M Price
- Malaghan Institute of Medical Research, Wellington, New Zealand
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38
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Allam M, Hu T, Cai S, Laxminarayanan K, Hughley RB, Coskun AF. Spatially visualized single-cell pathology of highly multiplexed protein profiles in health and disease. Commun Biol 2021; 4:632. [PMID: 34045665 PMCID: PMC8160218 DOI: 10.1038/s42003-021-02166-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 04/29/2021] [Indexed: 11/08/2022] Open
Abstract
Deep molecular profiling of biological tissues is an indicator of health and disease. We used imaging mass cytometry (IMC) to acquire spatially resolved 20-plex protein data in tissue sections from normal and chronic tonsillitis cases. We present SpatialViz, a suite of algorithms to explore spatial relationships in multiplexed tissue images by visualizing and quantifying single-cell granularity and anatomical complexity in diverse multiplexed tissue imaging data. Single-cell and spatial maps confirmed that CD68+ cells were correlated with the enhanced Granzyme B expression and CD3+ cells exhibited enrichment of CD4+ phenotype in chronic tonsillitis. SpatialViz revealed morphological distributions of cellular organizations in distinct anatomical areas, spatially resolved single-cell associations across anatomical categories, and distance maps between the markers. Spatial topographic maps showed the unique organization of different tissue layers. The spatial reference framework generated network-based comparisons of multiplex data from healthy and diseased tonsils. SpatialViz is broadly applicable to multiplexed tissue biology.
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Affiliation(s)
- Mayar Allam
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Thomas Hu
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
- School of Electrical and Computer Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Shuangyi Cai
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Krishnan Laxminarayanan
- Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, USA
| | - Robert B Hughley
- Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, USA
| | - Ahmet F Coskun
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA.
- Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, USA.
- Interdisciplinary Bioengineering Graduate Program, Georgia Institute of Technology, Atlanta, GA, USA.
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39
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Ashhurst TM, Marsh-Wakefield F, Putri GH, Spiteri AG, Shinko D, Read MN, Smith AL, King NJC. Integration, exploration, and analysis of high-dimensional single-cell cytometry data using Spectre. Cytometry A 2021; 101:237-253. [PMID: 33840138 DOI: 10.1002/cyto.a.24350] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 04/01/2021] [Accepted: 04/06/2021] [Indexed: 12/18/2022]
Abstract
As the size and complexity of high-dimensional (HD) cytometry data continue to expand, comprehensive, scalable, and methodical computational analysis approaches are essential. Yet, contemporary clustering and dimensionality reduction tools alone are insufficient to analyze or reproduce analyses across large numbers of samples, batches, or experiments. Moreover, approaches that allow for the integration of data across batches or experiments are not well incorporated into computational toolkits to allow for streamlined workflows. Here we present Spectre, an R package that enables comprehensive end-to-end integration and analysis of HD cytometry data from different batches or experiments. Spectre streamlines the analytical stages of raw data pre-processing, batch alignment, data integration, clustering, dimensionality reduction, visualization, and population labelling, as well as quantitative and statistical analysis. Critically, the fundamental data structures used within Spectre, along with the implementation of machine learning classifiers, allow for the scalable analysis of very large HD datasets, generated by flow cytometry, mass cytometry, or spectral cytometry. Using open and flexible data structures, Spectre can also be used to analyze data generated by single-cell RNA sequencing or HD imaging technologies, such as Imaging Mass Cytometry. The simple, clear, and modular design of analysis workflows allow these tools to be used by bioinformaticians and laboratory scientists alike. Spectre is available as an R package or Docker container. R code is available on Github (https://github.com/immunedynamics/spectre).
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Affiliation(s)
- Thomas Myles Ashhurst
- Sydney Cytometry Core Research Facility, Charles Perkins Centre, Centenary Institute and The University of Sydney, Sydney, New South Wales, Australia.,Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, New South Wales, Australia.,Charles Perkins Centre, The University of Sydney, Sydney, New South Wales, Australia
| | - Felix Marsh-Wakefield
- Charles Perkins Centre, The University of Sydney, Sydney, New South Wales, Australia.,School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia.,Vascular Immunology Unit, Department of Pathology, The University of Sydney, Sydney, New South Wales, Australia
| | - Givanna Haryono Putri
- Charles Perkins Centre, The University of Sydney, Sydney, New South Wales, Australia.,School of Computer Science, The University of Sydney, Sydney, New South Wales, Australia
| | - Alanna Gabrielle Spiteri
- Charles Perkins Centre, The University of Sydney, Sydney, New South Wales, Australia.,Viral Immunopathology Laboratory, Discipline of Pathology, School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
| | - Diana Shinko
- Sydney Cytometry Core Research Facility, Charles Perkins Centre, Centenary Institute and The University of Sydney, Sydney, New South Wales, Australia.,Charles Perkins Centre, The University of Sydney, Sydney, New South Wales, Australia
| | - Mark Norman Read
- Charles Perkins Centre, The University of Sydney, Sydney, New South Wales, Australia.,School of Computer Science, The University of Sydney, Sydney, New South Wales, Australia.,The Westmead Initiative, The University of Sydney, Sydney, New South Wales, Australia
| | - Adrian Lloyd Smith
- Sydney Cytometry Core Research Facility, Charles Perkins Centre, Centenary Institute and The University of Sydney, Sydney, New South Wales, Australia.,Charles Perkins Centre, The University of Sydney, Sydney, New South Wales, Australia
| | - Nicholas Jonathan Cole King
- Sydney Cytometry Core Research Facility, Charles Perkins Centre, Centenary Institute and The University of Sydney, Sydney, New South Wales, Australia.,Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, New South Wales, Australia.,Charles Perkins Centre, The University of Sydney, Sydney, New South Wales, Australia.,Viral Immunopathology Laboratory, Discipline of Pathology, School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia.,Sydney Nano, The University of Sydney, Sydney, New South Wales, Australia
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40
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Adam L, Rosenbaum P, Bonduelle O, Combadière B. Strategies for Immunomonitoring after Vaccination and during Infection. Vaccines (Basel) 2021; 9:365. [PMID: 33918841 PMCID: PMC8070333 DOI: 10.3390/vaccines9040365] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 04/05/2021] [Accepted: 04/07/2021] [Indexed: 01/08/2023] Open
Abstract
Immunomonitoring is the study of an individual's immune responses over the course of vaccination or infection. In the infectious context, exploring the innate and adaptive immune responses will help to investigate their contribution to viral control or toxicity. After vaccination, immunomonitoring of the correlate(s) and surrogate(s) of protection is a major asset for measuring vaccine immune efficacy. Conventional immunomonitoring methods include antibody-based technologies that are easy to use. However, promising sensitive high-throughput technologies allowed the emergence of holistic approaches. This raises the question of data integration methods and tools. These approaches allow us to increase our knowledge on immune mechanisms as well as the identification of key effectors of the immune response. However, the depiction of relevant findings requires a well-rounded consideration beforehand about the hypotheses, conception, organization and objectives of the immunomonitoring. Therefore, well-standardized and comprehensive studies fuel insight to design more efficient, rationale-based vaccines and therapeutics to fight against infectious diseases. Hence, we will illustrate this review with examples of the immunomonitoring approaches used during vaccination and the COVID-19 pandemic.
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Affiliation(s)
| | | | | | - Behazine Combadière
- Inserm, Centre d’Immunologie et des Maladies Infectieuses, Sorbonne Université, 75013 Paris, France; (L.A.); (P.R.); (O.B.)
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Bonilla DL, Reinin G, Chua E. Full Spectrum Flow Cytometry as a Powerful Technology for Cancer Immunotherapy Research. Front Mol Biosci 2021; 7:612801. [PMID: 33585561 PMCID: PMC7878389 DOI: 10.3389/fmolb.2020.612801] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 12/18/2020] [Indexed: 12/12/2022] Open
Abstract
The Nobel Prize-deserving concept of blocking inhibitory pathways in T cells, to unleash their anti-tumoral capacity, became one of the pillars of cancer treatment in the last decade and has resulted in durable clinical responses for multiple cancer types. Currently, two of the most important goals in cancer immunotherapy are to understand the mechanisms resulting in failure to checkpoint blockade and to identify predictive immunological biomarkers that correlate to treatment response, disease progression or adverse effects. The identification and validation of biomarkers for routine clinical use is not only critical to monitor disease or treatment progression, but also to personalize and develop new therapies. To achieve these goals, powerful research tools are needed. Flow cytometry stands as one of the most successful single-cell analytical tools used to characterize immune cell phenotypes to monitor solid tumors, hematological malignancies, minimal residual disease or metastatic progression. This technology has been fundamental in diagnosis, treatment and translational research in cancer clinical trials. Most recently, the need to evaluate simultaneously more features in each cell has pushed the field to implement more powerful adaptations beyond conventional flow cytometry, including Full Spectrum Flow Cytometry (FSFC). FSFC captures the full emission spectrum of fluorescent molecules using arrays of highly sensitive light detectors, and to date has enabled characterization of 40 parameters in a single sample. We will summarize the contributions of this technology to the advancement of research in immunotherapy studies and discuss best practices to obtain reliable, robust and reproducible FSFC results.
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Ngai LL, Kelder A, Janssen JJWM, Ossenkoppele GJ, Cloos J. MRD Tailored Therapy in AML: What We Have Learned So Far. Front Oncol 2021; 10:603636. [PMID: 33575214 PMCID: PMC7871983 DOI: 10.3389/fonc.2020.603636] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 11/16/2020] [Indexed: 12/22/2022] Open
Abstract
Acute myeloid leukemia (AML) is a heterogeneous clonal disease associated with a dismal survival, partly due to the frequent occurrence of relapse. Many patient- and leukemia-specific characteristics, such as age, cytogenetics, mutations, and measurable residual disease (MRD) after intensive chemotherapy, have shown to be valuable prognostic factors. MRD has become a rich field of research where many advances have been made regarding technical, biological, and clinical aspects, which will be the topic of this review. Since many laboratories involved in AML diagnostics have experience in immunophenotyping, multiparameter flow cytometry (MFC) based MRD is currently the most commonly used method. Although molecular, quantitative PCR based techniques may be more sensitive, their disadvantage is that they can only be applied in a subset of patients harboring the genetic aberration. Next-generation sequencing can assess and quantify mutations in many genes but currently does not offer highly sensitive MRD measurements on a routine basis. In order to provide reliable MRD results, MRD assay optimization and standardization is essential. Different techniques for MRD assessment are being evaluated, and combinations of the methods have shown promising results for improving its prognostic value. In this regard, the load of leukemic stem cells (LSC) has also been shown to add to the prognostic value of MFC-MRD. At this moment, MRD after intensive chemotherapy is most often used as a prognostic factor to help stratify patients, but also to select the most appropriate consolidation therapy. For example, to guide post-remission treatment for intermediate-risk patients where MRD positive patients receive allogeneic stem cell transplantation and MRD negative receive autologous stem cell transplantation. Other upcoming uses of MRD that are being investigated include: selecting the type of allogeneic stem cell transplantation therapy (donor, conditioning), monitoring after stem cell transplantation (to allow intervention), and determining drug efficacy for the use of a surrogate endpoint in clinical trials.
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Affiliation(s)
| | | | | | | | - Jacqueline Cloos
- Department of Hematology, Amsterdam UMC, Cancer Center Amsterdam, Vrije Universiteit, Amsterdam, Netherlands
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Sanjabi S, Lear S. New cytometry tools for immune monitoring during cancer immunotherapy. CYTOMETRY PART B-CLINICAL CYTOMETRY 2021; 100:10-18. [PMID: 33432667 DOI: 10.1002/cyto.b.21984] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 12/11/2020] [Accepted: 12/15/2020] [Indexed: 12/23/2022]
Abstract
The success of cancer immunotherapy (CIT) in the past decade has brought renewed excitement and the need to better understand how the human immune system functions during health and disease. Advances in single cell technologies have also inspired the creation of a Human Cell Atlas to identify and describe every cell in the human body with the intention of elucidating how to "fix" the ones that fail normal function. For example, treatment of cancer patients with immune checkpoint blockade (ICB) antibodies can reinvigorate their T cells and produce durable clinical benefit in a subset of patients, but a number of resistance mechanisms exist that prohibit full benefit to all treated patients. Early detection of biomarkers of response and mechanisms of resistance are needed to identify the patients who can benefit most from ICB. A noninvasive approach to predict treatment outcomes early after immunotherapies is a longitudinal analysis of peripheral blood immune cells using flow cytometry. Here we review some of the advances in our understanding of how ICB antibodies can re-invigorate tumor-specific T cells and also highlight the recent advances in high complexity flow cytometry, including spectral cytometers, that allow longitudinal sampling and deep immune phenotyping in clinical settings. We encourage the scientific community to utilize advanced cytometry platforms and analyses for immune monitoring in order to optimize CIT treatments for maximum clinical benefit.
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Affiliation(s)
- Shomyseh Sanjabi
- Department of Oncology Biomarker Development, Genentech Developmental Sciences, South San Francisco, California, USA
| | - Sean Lear
- Department of OMNI Biomarker Development, Genentech Developmental Sciences, South San Francisco, California, USA
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Spiteri AG, Wishart CL, King NJC. Immovable Object Meets Unstoppable Force? Dialogue Between Resident and Peripheral Myeloid Cells in the Inflamed Brain. Front Immunol 2020; 11:600822. [PMID: 33363542 PMCID: PMC7752943 DOI: 10.3389/fimmu.2020.600822] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 11/05/2020] [Indexed: 12/13/2022] Open
Abstract
Inflammation of the brain parenchyma is characteristic of neurodegenerative, autoimmune, and neuroinflammatory diseases. During this process, microglia, which populate the embryonic brain and become a permanent sentinel myeloid population, are inexorably joined by peripherally derived monocytes, recruited by the central nervous system. These cells can quickly adopt a morphology and immunophenotype similar to microglia. Both microglia and monocytes have been implicated in inducing, enhancing, and/or maintaining immune-mediated pathology and thus disease progression in a number of neuropathologies. For many years, experimental and analytical systems have failed to differentiate resident microglia from peripherally derived myeloid cells accurately. This has impeded our understanding of their precise functions in, and contributions to, these diseases, and hampered the development of novel treatments that could target specific cell subsets. Over the past decade, microglia have been investigated more intensively in the context of neuroimmunological research, fostering the development of more precise experimental systems. In light of our rapidly growing understanding of these cells, we discuss the differential origins of microglia and peripherally derived myeloid cells in the inflamed brain, with an analysis of the problems resolving these cell types phenotypically and morphologically, and highlight recent developments enabling more precise identification.
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Affiliation(s)
- Alanna G. Spiteri
- Discipline of Pathology, Faculty of Medicine and Health, School of Medical Sciences, The University of Sydney, Sydney, NSW, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia
| | - Claire L. Wishart
- Discipline of Pathology, Faculty of Medicine and Health, School of Medical Sciences, The University of Sydney, Sydney, NSW, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia
| | - Nicholas J. C. King
- Discipline of Pathology, Faculty of Medicine and Health, School of Medical Sciences, The University of Sydney, Sydney, NSW, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia
- Sydney Cytometry Facility, The University of Sydney and Centenary Institute, Sydney, NSW, Australia
- Ramaciotti Facility for Human Systems Biology, The University of Sydney and Centenary Institute, Sydney, NSW, Australia
- Marie Bashir Institute for Infectious Diseases and Biosecurity (MBI), Faculty of Medicine and Health, Sydney Medical School, The University of Sydney, Sydney, NSW, Australia
- Nano Institute, The University of Sydney, Sydney, NSW, Australia
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45
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Humrich JY, Bernardes JP, Ludwig RJ, Klatzmann D, Scheffold A. Phenotyping of Adaptive Immune Responses in Inflammatory Diseases. Front Immunol 2020; 11:604464. [PMID: 33324421 PMCID: PMC7723922 DOI: 10.3389/fimmu.2020.604464] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 10/22/2020] [Indexed: 12/17/2022] Open
Abstract
Immunophenotyping on the molecular and cellular level is a central aspect for characterization of patients with inflammatory diseases, both to better understand disease etiopathogenesis and based on this to develop diagnostic and prognostic biomarkers which allow patient stratification and tailor-made treatment strategies. Technology-driven developments have considerably expanded the range of analysis tools. Especially the analysis of adaptive immune responses, often regarded as central though mostly poorly characterized disease drivers, is a major focus of personalized medicine. The identification of the disease-relevant antigens and characterization of corresponding antigen-specific lymphocytes in individual patients benefits significantly from recent developments in cytometry by sequencing and proteomics. The aim of this workshop was to identify the important developments for state-of-the-art immunophenotyping for clinical application and precision medicine. We focused here on recent key developments in analysis of antigen-specific lymphocytes, sequencing, and proteomics approaches, their relevance in precision medicine and the discussion of the major challenges and opportunities for the future.
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Affiliation(s)
- Jens Y Humrich
- Department of Rheumatology and Clinical Immunology, University Hospital Schleswig-Holstein-Campus Lübeck, Lübeck, Germany
| | - Joana P Bernardes
- Institute of Clinical Molecular Biology, Christian-Albrechts-University Kiel, Kiel, Germany
| | - Ralf J Ludwig
- Lübeck Institute of Experimental Dermatology (LIED), University of Lübeck, Lübeck, Germany
| | - David Klatzmann
- Sorbonne Université, INSERM, Immunology-Immunopathology-Immunotherapy (i3), Paris, France
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