Cross-platform immunophenotyping of human peripheral blood mononuclear cells with four high-dimensional flow cytometry panels

Article Biochemical Research Methods

Comprehensive phenotyping of human peripheral blood B lymphocytes in healthy conditions

Rita Carsetti et al.

Summary: The B cell compartment consists of different subsets with unique functions and roles in immune responses. A specific gating strategy is described for identifying these subsets based on phenotypic traits using flow cytometric analysis.

CYTOMETRY PART A (2022)

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Article Biochemical Research Methods

Integration, exploration, and analysis of high-dimensional single-cell cytometry data using Spectre

Thomas Myles Ashhurst et al.

Summary: The Spectre R package enables comprehensive integration and analysis of high-dimensional cytometry data from different batches or experiments. It streamlines the analytical stages of raw data pre-processing, batch alignment, integration, clustering, visualization, and statistical analysis, making it suitable for bioinformaticians and laboratory scientists. Spectre's modular design allows for scalable analysis of very large datasets generated by flow cytometry, mass cytometry, or spectral cytometry.

CYTOMETRY PART A (2022)

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Article Biochemical Research Methods

OMIP 077: Definition of all principal human leukocyte populations using a broadly applicable 14-color panel

Maximilian Boesch et al.

Summary: This optimized multicolor immunofluorescence panel is designed to efficiently identify and quantify various leukocyte populations in human blood with minimal markers. It offers high performance, is suitable for whole blood, and widely applicable for immune cell identification, quantification, and characterization.

CYTOMETRY PART A (2022)

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Review Biochemical Research Methods

The evolution of spectral flow cytometry

John P. Nolan

Summary: This article introduces the transition of spectral flow cytometry from an emerging technology to a transformative force in the fields of cytometry and single-cell analysis. The current form of spectral flow technology is used for multiparameter immunophenotyping of immune cells, but there is still a lot of untapped potential in high-resolution spectral analysis.

CYTOMETRY PART A (2022)

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Article Immunology

Human epigenetic and transcriptional T cell differentiation atlas for identifying functional T cell-specific enhancers

Josephine R. Giles et al.

Summary: This study generated an epigenetic and transcriptional atlas of T cell differentiation from healthy humans and applied it to explore disease-specific biology. The study identified molecular regulations of gene expression and chromatin accessibility during T cell differentiation and provided insights into disease biology through three research settings. The study also successfully predicted genome-wide cis-regulatory elements and validated the approach for functional annotation of key effector genes, demonstrating the potential of identifying targets for non-coding cellular engineering.

IMMUNITY (2022)

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Article Immunology

Autoreactive CD8+ T cells are restrained by an exhaustion-like program that is maintained by LAG3

Stephanie Grebinoski et al.

Summary: The study reveals that CD8(+) T cells in the pancreatic islets exhibit a 'restrained' phenotype promoted by LAG3, resembling exhausted cells while maintaining effector functions. The exhausted T cell state may have a significant impact on limiting autoimmune diseases.

NATURE IMMUNOLOGY (2022)

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Article Biochemical Research Methods

An optimized protocol for phenotyping human granulocytes by mass cytometry

Nora Vivanco Gonzalez et al.

Summary: This study utilized mass cytometry to capture distinct phenotypes of granulocytes, and through optimized protocols, achieved in-depth characterization of basophils, eosinophils, and neutrophils. This research is of great significance for understanding the roles of granulocytes in homeostasis and immune activation.

STAR PROTOCOLS (2022)

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Article Biochemical Research Methods

Analytical performance of a 25-marker spectral cytometry immune monitoring assay in peripheral blood

Holly A. Jensen et al.

Summary: This study presented a spectral flow cytometry assay for longitudinal immune monitoring biomarkers in human blood, demonstrating high precision and stability. With a panel of 25 immune biomarkers, the assay achieved robust analytical performance and explored the impact of sample types and storage conditions on biomarker stability. The method showed promise for translational research applications.

CYTOMETRY PART A (2021)

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Article Biochemical Research Methods

OMIP 071: A 31-Parameter Flow Cytometry Panel for In-Depth Immunophenotyping of Human T-Cell Subsets Using Surface Markers

Song-Rong Wang et al.

Summary: The article introduced a 31-parameter panel for in-depth immunophenotyping of human T-cell subsets, which can be applied in monitoring, prognosis, and mechanistic studies of various immune-related diseases.

CYTOMETRY PART A (2021)

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Article Medicine, Research & Experimental

Sustained cellular immune dysregulation in individuals recovering from SARS-CoV-2 infection

Jacob K. Files et al.

Summary: SARS-CoV-2 infection leads to a prolonged period of immune dysregulation, with increased activation and exhaustion markers in T cells and B cells in both hospitalized and nonhospitalized individuals. The changes in T cell activation/exhaustion positively correlate with age, and severely infected individuals exhibited higher expression of activation and exhaustion markers.

JOURNAL OF CLINICAL INVESTIGATION (2021)

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Review Biochemical Research Methods

Current trends in flow cytometry automated data analysis software

Melissa Cheung et al.

Summary: Automated flow cytometry data analysis tools are increasingly used in academic, biotechnology, pharmaceutical, and clinical laboratories, with dimensionality reduction methods and software with graphical user interfaces being popular choices. There are differences in software usage between biomedical institutions, with tools for discovery and visualization more popular in academia, while automated tools using supervised learning methods are preferred in clinical settings.

CYTOMETRY PART A (2021)

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Article Biochemical Research Methods

With great power comes great responsibility: high-dimensional spectral flow cytometry to support clinical trials

Megan McCausland et al.

Summary: Flow cytometry is a powerful technology used for cell identification and characterization in research, drug development, and clinical sample analysis. Recent advancements in instrumentation and fluorochrome availability have led to increases in complexity and dimensionality of flow cytometry panels, presenting challenges in panel design, optimization, and downstream data analysis and interpretation. In this paper, practices for developing high-dimensional panels on the Aurora spectral flow cytometer to aid clinical sample analysis are described.

BIOANALYSIS (2021)

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Article Multidisciplinary Sciences

Multimodal analysis for human ex vivo studies shows extensive molecular changes from delays in blood processing

Adam K. Savage et al.

Summary: This study demonstrates minimal effects of delayed processing on the numbers and general phenotype of PBMC, but significant changes in the single-cell transcriptome and composition of the plasma proteome can be observed as early as 6 hours after blood draw. These changes reflect patterns of cellular activation across diverse cell types, potentially confounding relevant biologic variance related to disease states.

ISCIENCE (2021)

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Article Biochemical Research Methods

A user's guide to multicolor flow cytometry panels for comprehensive immune profiling

Staffan Holmberg-Thyden et al.

Summary: Multicolor flow cytometry is crucial for studying the immune system, but variations in instrument performance can lead to common analytical errors. By systematically pairing colors with markers and optimizing for specific equipment, designing comprehensive panels for flow cytometry experiments can help overcome these limitations. Unsupervised clustering techniques are then used to identify important subpopulations that may not be detected through traditional gating methods, allowing for better handling of the large amounts of data generated.

ANALYTICAL BIOCHEMISTRY (2021)

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Article Biochemical Research Methods

OMIP 078: A 31-parameter panel for comprehensive immunophenotyping of multiple immune cells in human peripheral blood mononuclear cells

Takuto Nogimori et al.

Summary: This 31-parameter panel is designed to measure multiple immune cell populations in human peripheral blood mononuclear cells, providing insights into immune dynamics and single-cell changes associated with aging and diseases. It includes markers to differentiate each cell population's differentiation status and is useful for studying infectious and autoimmune diseases where patient samples are limited and require detailed information.

CYTOMETRY PART A (2021)

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Review Biochemistry & Molecular Biology

CD39 Regulation and Functions in T Cells

Eleonora Timperi et al.

Summary: CD39, along with CD73, plays a crucial role in converting adenosine triphosphate into an immunosuppressive form of adenosine in the tumor microenvironment. Environmental and genetic factors shape the expression of CD39, which has significant functions in regulating T cell activities. Studies from preclinical models to clinical trials have contributed essential insights into novel combinatorial approaches for cancer treatment.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2021)

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Article Immunology

Persistent High Percentage of HLA-DR+CD38high CD8+ T Cells Associated With Immune Disorder and Disease Severity of COVID-19

Juan Du et al.

Summary: The study revealed that HLA-DR(+)CD38(hi) CD8(+) T cells were persistently accumulated in severe COVID-19 patients, showing overactivation and dysregulation, and were associated with systemic inflammation, tissue injury, and immune disorders.

FRONTIERS IN IMMUNOLOGY (2021)

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Review Immunology

Multi-Omics Approaches in Immunological Research

Xiaojing Chu et al.

Summary: This review emphasizes the importance of applying a multi-omics approach in immunological research to understand the complexity of the immune system. It provides an overview of methodological approaches for different omics data layers, discusses data analysis methods, and highlights the possible applications of multi-omics studies in understanding immune-related diseases.

FRONTIERS IN IMMUNOLOGY (2021)

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Article Biochemical Research Methods

Optimized workflow for human PBMC multiomic immunosurveillance studies

Palak C. Genge et al.

Summary: Deep immune profiling is crucial for understanding the human immune system, and successful biological interpretation relies on consistent laboratory processing and minimal batch-to-batch variation.

STAR PROTOCOLS (2021)

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Article Medicine, Research & Experimental

Autoreactive CD8+ T cell exhaustion distinguishes subjects with slow type 1 diabetes progression

Alice E. Wiedeman et al.

JOURNAL OF CLINICAL INVESTIGATION (2020)

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Article Immunology

A combination of the activation marker CD86 and the immune checkpoint marker B and T lymphocyte attenuator (BTLA) indicates a putative permissive activation state of B cell subtypes in healthy blood donors independent of age and sex

Susanne Axelsson et al.

BMC IMMUNOLOGY (2020)

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Article Biochemical Research Methods

OMIP-063: 28-Color Flow Cytometry Panel for Broad Human Immunophenotyping

Kathryn Payne et al.

CYTOMETRY PART A (2020)

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Review Biochemical Research Methods

Comprehensive Phenotyping of Human PB NK Cells by Flow Cytometry

Genny Del Zotto et al.

CYTOMETRY PART A (2020)

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Article Medicine, Research & Experimental

Differential effects of PD-L1 versus PD-1 blockade on myeloid inflammation in human cancer

Noffar Bar et al.

JCI INSIGHT (2020)

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Article Biochemical Research Methods

Evaluating spectral cytometry for immune profiling in viral disease

Paula Niewold et al.

CYTOMETRY PART A (2020)

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Article Biochemical Research Methods

OMIP-069: Forty-Color Full Spectrum Flow Cytometry Panel for Deep Immunophenotyping of Major Cell Subsets in Human Peripheral Blood

Lily M. Park et al.

CYTOMETRY PART A (2020)

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Article Immunology

The Antigen Presenting Potential of CD21low B Cells

Marlene E. Reincke et al.

FRONTIERS IN IMMUNOLOGY (2020)

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Review Biochemical Research Methods

Comprehensive Phenotyping of T Cells Using Flow Cytometry

Charlotte M. Mousset et al.

CYTOMETRY PART A (2019)

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Editorial Material Biochemical Research Methods

Spectral Flow Cytometry - Quo Vadimus?

J. Paul Robinson

CYTOMETRY PART A (2019)

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Article Biochemical Research Methods

Development, application and computational analysis of high-dimensional fluorescent antibody panels for single-cell flow cytometry

Jolanda Brummelman et al.

NATURE PROTOCOLS (2019)

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Article Multidisciplinary Sciences

Elevated numbers of PD-L1 expressing B cells are associated with the development of AIDS-NHL

Marta Epeldegui et al.

SCIENTIFIC REPORTS (2019)

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Article Cell Biology

Comprehensive Immune Monitoring of Clinical Trials to Advance Human Immunotherapy

Felix J. Hartmann et al.

CELL REPORTS (2019)

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Article Immunology

A Novel, Five-Marker Alternative to CD16-CD14 Gating to Identify the Three Human Monocyte Subsets

Siew-Min Ong et al.

FRONTIERS IN IMMUNOLOGY (2019)

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Human Monocyte Subsets and Phenotypes in Major Chronic Inflammatory Diseases

Theodore S. Kapellos et al.

FRONTIERS IN IMMUNOLOGY (2019)

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Guidelines for the use of flow cytometry and cell sorting in immunological studies (second edition)

Andrea Cossarizza et al.

EUROPEAN JOURNAL OF IMMUNOLOGY (2019)

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Challenges and Opportunities for Consistent Classification of Human B Cell and Plasma Cell Populations

Ignacio Sanz et al.

FRONTIERS IN IMMUNOLOGY (2019)

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Article Biochemical Research Methods

OMIP-051-28-color flow cytometry panel to characterize B cells and myeloid cells

Thomas Liechti et al.

CYTOMETRY PART A (2019)

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Editorial Material Biochemical Research Methods

OMIP-044: 28-Color Immunophenotyping of the Human Dendritic Cell Compartment

Florian Mair et al.

CYTOMETRY PART A (2018)

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Article Biochemical Research Methods

Cryopreserved whole blood for the quantification of monocyte, T-cell and NK-cell subsets, and monocyte receptor expression by multi-color flow cytometry: Amethodological study based on participants from the canadian longitudinal study on aging

Chris P. Verschoor et al.

CYTOMETRY PART A (2018)

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Review Immunology

Human T Cell Development, Localization, and Function throughout Life

Brahma V. Kumar et al.

IMMUNITY (2018)

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Review Immunology

Human dendritic cell subsets: an update

Matthew Collin et al.

IMMUNOLOGY (2018)

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Article Immunology

Loss of the Immune Checkpoint CD85j/LILRB1 on Malignant Plasma Cells Contributes to Immune Escape in Multiple Myeloma

Ester Lozano et al.

JOURNAL OF IMMUNOLOGY (2018)

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Article Biochemical Research Methods

Deep phenotyping of immune cell populations by optimized and standardized flow cytometry analyses

Fabien Pitoiset et al.

CYTOMETRY PART A (2018)

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Review Immunology

BAFF and BAFF-Receptor in B Cell Selection and Survival

Cristian R. Smulski et al.

FRONTIERS IN IMMUNOLOGY (2018)

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Article Oncology

Quantification of peripheral blood CD34+ cells prior to stem cell harvesting by leukapheresis: a single center experience

Natalia Emerim Lemos et al.

HEMATOLOGY TRANSFUSION AND CELL THERAPY (2018)

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Article Biochemical Research Methods

OMIP-042: 21-color flow cytometry to comprehensively immunophenotype major lymphocyte and myeloid subsets in human peripheral blood

Karl W. Staser et al.

CYTOMETRY PART A (2018)

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Article Medicine, Research & Experimental

A standardized immune phenotyping and automated data analysis platform for multicenter biomarker studies

Sabine Ivison et al.

JCI INSIGHT (2018)

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Article Immunology

What Else Can CD39 Tell Us?

Hai Zhao et al.

FRONTIERS IN IMMUNOLOGY (2017)

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Utility of CD54, CD229, and CD319 for the Identification of Plasma Cells in Patients with Clonal Plasma Cell Diseases

Fanny Pojero et al.

CYTOMETRY PART B-CLINICAL CYTOMETRY (2016)

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Correlation of transferrin receptor (CD71) with Ki67 expression on stimulated human and mouse T cells: The kinetics of expression of T cell activation markers

Melika Motamedi et al.

JOURNAL OF IMMUNOLOGICAL METHODS (2016)

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Article Immunology

Defining antigen-specific plasmablast and memory B cell subsets in human blood after viral infection or vaccination

Ali H. Ellebedy et al.

NATURE IMMUNOLOGY (2016)

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Article Pediatrics

The TLR-specific adjuvants R-848 and CpG-B endorse the immunological reaction of neonatal antigen-presenting cells

Simone Schueller et al.

PEDIATRIC RESEARCH (2016)

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Article Multidisciplinary Sciences

Novel Strategy for Phenotypic Characterization of Human B Lymphocytes from Precursors to Effector Cells by Flow Cytometry

Giovanna Clavarino et al.

PLOS ONE (2016)

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Article Multidisciplinary Sciences

Spectral Cytometry Has Unique Properties Allowing Multicolor Analysis of Cell Suspensions Isolated from Solid Tissues

Sandrine Schmutz et al.

PLOS ONE (2016)

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Article Immunology

A multi-laboratory comparison of blood dendritic cell populations

Phillip Dieter Fromm et al.

CLINICAL & TRANSLATIONAL IMMUNOLOGY (2016)

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A Mine Is a Terrible Thing to Waste: High Content, Single Cell Technologies for Comprehensive Immune Analysis

P. K. Chattopadhyay et al.

AMERICAN JOURNAL OF TRANSPLANTATION (2015)

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FlowSOM: Using self-organizing maps for visualization and interpretation of cytometry data

Sofie Van Gassen et al.

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Single-Cell Trajectory Detection Uncovers Progression and Regulatory Coordination in Human B Cell Development

Sean C. Bendall et al.

CELL (2014)

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Treg Cells Expressing the Coinhibitory Molecule TIGIT Selectively Inhibit Proinflammatory Th1 and Th17 Cell Responses

Nicole Joller et al.

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T Follicular Helper Cell Differentiation, Function, and Roles in Disease

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OMIP-015: Human regulatory and activated T-cells without intracellular staining

Yolanda D. Mahnke et al.

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Generalized unmixing model for multispectral flow cytometry utilizing nonsquare compensation matrices

David Novo et al.

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The who's who of T-cell differentiation: Human memory T-cell subsets

Yolanda D. Mahnke et al.

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Advantages of full spectrum flow cytometry

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Standardizing immunophenotyping for the Human Immunology Project

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Nomenclature of monocytes and dendritic cells in blood

Loems Ziegler-Heitbrock et al.

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Fractalkine/CX3CL1: A Potential New Target for Inflammatory Diseases

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Functionally Distinct LAG-3 and PD-1 Subsets on Activated and Chronically Stimulated CD8 T Cells

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JOURNAL OF IMMUNOLOGY (2009)

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Phenotype and Function of Human T Lymphocyte Subsets: Consensus and Issues

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Differential expression of chemokine receptors on peripheral blood B cells from patients with rheumatoid arthritis and systemic lupus erythematosus

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CD40, but not CD154, expression on B cells is necessary for optimal primary B cell responses

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CD69, HLA-DR and the IL-2R identify persistently activated T cells in psoriasis vulgaris lesional skin: Blood and skin comparisons by flow cytometry

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JOURNAL OF AUTOIMMUNITY (2000)

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Cross-platform immunophenotyping of human peripheral blood mononuclear cells with four high-dimensional flow cytometry panels

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