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The quantification of submicroscopic minimal residual disease (MRD) after therapy proved to have independent prognostic significance in many mature B-cell malignancies. With the advent of routine benchtop cytometers capable of simultaneously analyzing ≥8 colors and with improved standardization, flow cytometry has become the method of choice for MRD assessments in some lymphoma entities. Herein we describe general aspects of flow cytometric standardization. Chronic lymphocytic leukemia (CLL) and multiple myeloma (MM) are used as examples to explain the technical standardization of flow cytometry for MRD detection according to EuroFlow strategies. MRD data acquisition and detailed analysis in MM and CLL is a particular focus of this chapter., (© 2025. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.)

High-plex imaging techniques enable the detection and quantification of a multitude of markers in tissue biopsies at single-cell or near-single-cell resolution. In lymphoma, this can facilitate the detection and characterization of cellular phenotypes and interactions, describing both tumor and microenvironmental cells. In combination with other techniques, high-plex imaging allows the investigation of biological mechanisms and clinically relevant biomarkers. CO-Detection by IndEXing (CODEX), one of such techniques, is based on antibodies labeled with unique DNA oligonucleotides that can be visualized by complementary reporter oligonucleotides coupled to a fluorophore. Here, we provide an overview of the key steps of a CODEX-based project, including (1) antibody panel design, (2) cohort selection, (3) staining and imaging, (4) data analysis. By sharing our CODEX protocol and our experience with FFPE tissue samples, we aim to encourage wider use of this powerful technique in lymphoma research and improve insight into cellular composition and spatial dynamics for improved diagnostics and therapy., (© 2025. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.)

Fluorescence in situ hybridization (FISH) is a powerful and robust technique allowing the visualization of target sequences like genes in interphase nuclei. It is widely used in routine diagnostics to identify cancer-specific aberrations including lymphoma-associated translocations or gene copy number changes in single tumor cells. By combining FISH with immunophenotyping-a technique called fluorescence immunophenotyping and interphase cytogenetic as a tool for investigation of neoplasia (FICTION)-it is moreover possible to identify a cell population of interest. Here we describe standard protocols for FISH and FICTION as used in our laboratories in diagnosis and research., (© 2025. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.)

Multiparametric flow cytometry is a powerful diagnostic tool that permits rapid assessment of cellular antigen expression to quickly provide immunophenotypic information suitable for disease classification. This chapter describes a general approach for the identification of abnormal lymphoid populations by flow cytometry, including B, T, NK, and Hodgkin lymphoma cells suitable for the clinical and research environment. Knowledge of the common patterns of antigen expression of normal lymphoid cells is critical to permit identification of abnormal populations at disease presentation and for minimal residual disease assessment. We highlight an overview of procedures for processing and immunophenotyping non-Hodgkin B- and T-cell lymphomas and also describe our strategy for the sensitive and specific diagnosis of classic Hodgkin lymphoma, nodular lymphocyte predominant Hodgkin lymphoma, and T-cell/histiocyte-rich large B-cell lymphoma., (© 2025. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.)

B cells are crucial components of the immune system, responsible for producing specific antibodies in response to infections and vaccines. Despite their uniform appearance, B cells display diverse surface molecules and functional properties, which are not yet fully understood. Apart from antibody production, B cells also play roles in antigen presentation and cytokine secretion, essential for initiating T-cell immune responses. Their significance as disease biomarkers and therapeutic targets has led to increased research focus. However, the lack of standardized protocols for B-cell identification and the variability in defining B-lymphocyte subpopulations pose some challenges. This paper proposes a B-cell identification panel throughout the evaluation of previous cytometry panels and nomenclature heterogeneity for B-cell subpopulations. Major subpopulations recognized in human peripheral blood include transitional, naive, switched memory, unswitched memory, double negative, and plasmablasts, characterized based on their functional and phenotypic features. We present a standardized flow cytometry protocol utilizing surface phenotypic markers (CD3, CD19, IgD, CD27, CD38, and CD24) to differentiate and analyze B-cell subpopulations. This practical and cost-effective panel can be used in various research and laboratory settings. The challenges of standardizing names and markers for classifying B-lymphocyte subpopulations are discussed, along with protocols utilizing multiple markers and gating strategies, allied with the importance of considering viability markers. In summary, this standardized protocol and panel provide a comprehensive approach to identifying B-cell subpopulations to enhance the reproducibility and comparability of B-cell subpopulation studies., (© 2025. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.)

Flow cytometry serves as a crucial tool in immunology, allowing for the detailed analysis of immune cell populations. γδ T cells, a subset of T cells, play pivotal roles in immune surveillance and immune aging. Assessing the phenotype and functional capabilities of γδ T cells isolated from whole blood or tissue within the context of human aging yields invaluable insights into the dynamic changes affecting immune function, tissue homeostasis, susceptibility to infections, and inflammatory responses., (© 2025. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.)

Multiparameter flow cytometry is a common tool for assessing responses of T, B, and other cells to pathogens or vaccines. Such responses are likely to be important for predicting the efficacy of an HIV vaccine, despite the elusive findings in HIV vaccine trials to date. Fortunately, flow cytometry has evolved to be capable of readily measuring 30-40 parameters, providing the ability to dissect detailed phenotypes and functions that may be correlated with disease protection. Nevertheless, technical hurdles remain, and standardization of assays is still largely lacking. Here an optimized protocol for antigen-specific T cell monitoring is presented, with specific variations for particular markers. It covers the analysis of multiple cytokines, cell surface proteins, and other functional markers such as CD107, CD154, CD137, etc. References are given to published panels of 8-28 colors., (© 2024. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.)

The use of flow cytometry for immunophenotyping is contingent on the ability to accurately assign biological relevance to the detected signal. This process has historically been challenging when defining IgE expressing B cells or IgE expressing antibody-secreting cells due to widespread expression of receptors for IgE on various leukocyte subsets, including human B cells. Here we describe our implementation of intracellular staining for human IgE following a blocking step to negate the challenge of surface-bound IgE. We also describe our experience with a human B cell culture system that can be used to robustly validate this approach before application to primary human samples. Orthogonal confirmatory techniques remain essential; these are not described in detail, but several possible strategies are suggested., (© 2024. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.)

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., (© 2022. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.)

The use of flow cytometry allows simultaneous measurement and multiparametric analysis of single cells in a heterogenous solution. The purpose of flow cytometry can vary depending on the use of antibodies and dyes targeted for specific cell molecules. The method of immune-phenotyping with fluorescently conjugated antibodies to label cell proteins or DNA works in tandem with fluidic, optic, and electrical systems present in the flow cytometer. Some flow cytometers can detect numerous fluorescent molecules on a single cell, allowing the measurement of more than 30 parameters. This ability to detect, measure, and quantitate multiple fluorescent markers on a single cell makes the flow cytometer a useful tool for analyzing various aspects of cell phenotype and function. Here we describe a standardized protocol for surface and intracellular immune-phenotyping of murine lungs, beginning with the building of an optimal antibody panel and ending with data analysis and representation, including sample gating strategies for innate and adaptive immune responses.

Flow cytometry is a popular technique used for both clinical and research purposes. It involves laser-based technology to characterize cells based on size, shape, and complexity. Additionally, flow cytometers are equipped with the ability to take fluorescence measurements at multiple wavelengths. This capability makes the flow cytometer a practical resource in the utilization of fluorescently conjugated antibodies, fluorescent proteins, DNA binding dyes, viability dyes, and ion indicator dyes. As the technology advances, the number of parameters a flow cytometer can measure has increased tremendously, and now some has the capacity to analyze 30-50 or more parameters on a single cell. Here, we describe the basic principles involved in the mechanics and procedures of flow cytometry along with an insight into applications of flow cytometry techniques for biomedical and allergic disease research.

B cells are primarily known for their capacity to differentiate into antibody-secreting cells (ASCs). ASCs are usually viewed as terminally differentiated cells sharing a unique phenotype. However, it lately became evident that ASCs exist in a variety of subsets differing by their lifespan, anatomic location, and immunological function. Thus, ASCs can exist as long-lived plasma cells (LLPC) that can persist for years in a nonproliferating state within particular niches in the bone marrow (BM), or as short-lived plasma cells (SLPC) that are primarily found in secondary lymphoid organs or inflamed tissues and wane upon the termination of the associated immune response. Another layer of ASC diversity was uncovered with the discovery of their capacity to produce various pro- or anti-inflammatory cytokines. Notably, a subset of natural regulatory plasma cells characterized by the distinctive expression of the inhibitory receptor lymphocyte activation gene (LAG)-3 and a unique capacity to produce interleukin (IL)-10 upon stimulation was recently identified. Here, we describe how to immunophenotypically characterize murine plasma cells as well as how to isolate them using cell sorting, with a special focus on these recently described natural regulatory plasma cells.

Myeloid-derived suppressor cells (MDSC) are immunosuppressive myeloid cells that accumulate in tumor sites and peripheral lymphoid organs such as the spleen. In murine cancer models, the spleen is a major reservoir for MDSC, representing an easily accessible tissue from which to isolate high numbers of these cell population for downstream applications. Here we describe an efficient method to phenotype as well as to isolate and assess the functionality of murine splenic MDSC.

Myeloid-derived suppressor cells (MDSC) are a heterogeneous group of pathologically expanded myeloid cells with immunosuppressive activity. According to their phenotype, MDSC can be divided into three major subpopulations: early stage MDSC (e-MDSC), lacking myeloid lineage markers, monocytic MDSC (M-MDSC), and granulocytic MDSC (PMN-MDSC). Additionally, PMN-MDSC can be subdivided based on their activation and differentiation status, although it is not clear how this status contributes to immunosuppression and disease pathology. Here, we describe an immunophenotyping and gating strategy for the identification and isolation of MDSC subsets based on fluorescence-activated cell sorting. This method allows direct comparison of MDSC subsets in clinical settings.

Egg allergy is one of the most common food allergies in children, being the most important allergenic proteins found in the egg white (EW). Allergy to EW shows a complex phenotype that involves a multifaceted reaction that can only be assessed in vivo. Although other routes of sensitization have been described, oral exposure to food antigens is one of the most suitable in humans. In mice, oral administration of allergenic proteins results in the development of tolerance, and the use of adjuvants, such as cholera toxin (CT), is required to promote Th2-biased immune responses over tolerogenic responses. In this regard, among the mouse strains that readily display Th2 responses, Balb/c has been widely used. Here, we describe a frequently used protocol of oral EW sensitization by using CT as an adjuvant and we explain in detail the methods that we have developed to analyze the sensitizing and eliciting capacity of EW proteins including evaluation of signs, measurement of serum levels of specific immunoglobulins, mast cell degranulation, cytokine secretion profile of allergen-reactive T cells, phenotyping of mesenteric lymph node- and spleen-derived dendritic and T cells by flow cytometry, and quantification of intestinal gene expression.

Transplantation is still the treatment of choice for organ failure; however, allograft induces inflammatory immune responses that require immunosuppressive treatment. The role of regulatory B cells (Bregs) in downregulating inflammation has been reported to be significant in several diseases including transplant rejection. Many reports have analyzed different B-cell subpopulations, including Bregs, in tolerant, stable, and rejecting transplant recipients as well as the influence of immunosuppressant on the frequencies and functions of the different B-cell subsets. In this chapter, the key techniques required to investigate human Breg frequencies and functions in transplant patients are discussed.

The tumor microenvironment (TME) contains noncancerous cells such as various types of immune cells and fibroblasts. Cancer cells direct these stromal cells to create a microenvironment favorable for tumor growth and intercellular interactions have a critical role in this process. In established tumors, interactions between CD137 and its ligand (CD137L) contribute to tumor immune evasion and tumor growth. Therefore, it is important to identify cells expressing CD137 and CD137L within tumors. In this chapter, we will introduce a simple, powerful method of analyzing CD137- and CD137L-expressing tumor cells using Fluorescence-activated cell sorting.

The pluripotency of human induced pluripotent stem cells (HiPSCs) cannot be tested strictly in a similar way as we can do for the mouse ones because of ethical restrictions. One common and initial approach to prove the pluripotency of an established human iPSC line is to demonstrate expression of a set of established surface and intracellular pluripotency markers. This chapter provides procedures of immunocytochemistry of the established HiPSC lines for a set of the signature intracellular pluripotency proteins, OCT4, SOX2, NANOG, and LIN28. We also describe cell phenotyping by flow cytometry for the five established human pluripotency surface markers, SSEA3, SSEA4, TRA-1-60, TRA-1-81, and TRA2-49 (ALP). Numbers of ALP + and TRA-1-60 + colonies are the most widely used parameters for evaluation of human iPSC reprogramming efficiency. Therefore, this chapter also provides detailed steps for substrate colorimetric reaction of the ALP activity, as well as the TRA-1-60 staining, of the iPSC colonies in the reprogramming population.

While myeloid-derived suppressor cells (MDSCs) in humans and mice have been intensively investigated, there is limited knowledge of these cells in nonhuman primates (NHPs). NHPs serve as critical models for late-stage testing of several biomedical inventions before proceeding with clinical trials and it is therefore important to fully understand their immune compartments and similarities with humans. Here, using antihuman cross-reactive antibodies, we provide flow cytometric analysis protocols for identification of MDSCs in the blood of rhesus macaques, one of the major NHP species as experimental models. Discrepancies and similarities between rhesus and human MDSCs are discussed.

Myeloid-derived suppressor cells (MDSCs) are a heterogeneous cell population composed of mature and immature cells of myeloid origin that play a major role in tumor progression by inhibiting the antitumor immune responses mediated by T cells. In this chapter, we describe protocols for isolation, phenotypical and functional evaluation of MDSCs isolated from mouse tumors, with the aim at unifying and standardizing protocols set up by different laboratories.

Primordial germ cells (PGCs) are common ancestors of all germline cells. In mammals, PGCs emerge in early-stage embryos around the timing of gastrulation at or near epiblast, and specification of PGCs from their precursor cells involves multiple growth factors secreted by adjacent cells. Recent advancements in germline stem cell biology have made it possible to generate PGC-like cell culture models (PGCLCs for PGC-like cells) from human and mouse pluripotent stem cells by mimicking the embryonic growth factor environment in vitro. Here we describe a method of producing human PGCLCs from primed-pluripotency induced pluripotent stem cells (iPSCs) via temporal conversion to naive pluripotency followed by formation of embryoid bodies (EBs) using the spin-EB method.

The field of flow cytometry has witnessed rapid technological advancements in the last few decades. While the founding principles of fluorescent detection on cells (or particles) within a uniform fluid stream remains largely unchanged, the availability more sensitive cytometers with the ability to multiplex more and more florescent signals has resulted in very complex high-order assays. This results in the co-use of fluorophores with increased levels of emission overlap and/or spillover spreading than in years past and thus requires careful and well thought out planning for flow cytometry assay development. As an example, we present the development of a large 18-color (20 parameter) flow cytometry assay designed to take an in depth analysis of effector lymphocyte phenotypes, with careful attention to assay controls and panel design.

Wheat allergy is a pathological event involving immunocompetent cells against ingested wheat allergen and is clearly associated with transdermal sensitization. However, the molecular mechanisms involved in the disease etiology are not completely understood. A complex cellular and tissue network linking to food allergy makes it difficult to understand the molecular mechanism of allergenicity. Animal models are valuable tools to deduce basic principles of human disease without invasive intervention trials. A mouse model of wheat allergy has provided insights into effects of skin exposure to wheat protein; it is a plausible route of human sensitization for wheat anaphylaxis. Further investigation of this model will capture the essential occurrence and flow of events, bringing useful clues to develop effective treatment and control strategies against wheat allergy. Here, we describe a method for analyzing the expression of cell surface molecules in single cells isolated from lymphoid tissue with flow cytometry. Sensitization by wheat extracts significantly increases antigen-specific T cells in the spleen. Collecting information regarding the contribution of immune cells to allergic sensitization in the development of wheat allergy would be useful in preventing and treating food allergies.

Regulatory B cells (Bregs) have immunosuppressive capacity, primarily via the production of IL-10. IL-10 expression and immunosuppression have been described in a number of human B cell subsets, two of which include the CD19 + CD24 hi CD38 hi and CD19 + CD24 hi CD27 + populations. In this chapter, we describe how to identify and isolate these subsets from peripheral blood B cells via flow cytometry. We also explain how to expand Bregs in culture and how to identify them based on intracellular expression of IL-10.

The basis of traditional flow cytometry allergy diagnosis is measurement of the expression of basophilic surface activation and/or degranulation markers. Basophils, upon encounter with a specific allergen that cross-links surface FcRI-bound IgE antibodies, not only secrete and release quantifiable bioactive mediators but also upregulate the expression of different markers (e.g., CD63, CD203c) which can be detected by multicolor flow cytometry using specific monoclonal antibodies. Here, we describe a novel technique that relies upon the staining of exteriorized anionic proteoglycans from a basophil granule matrix by cationic fluorescent avidin probes.

Background: Correct diagnosis of immediate drug hypersensitivity reactions (IDHRs) can pose a significant challenge, mainly because of the absence of reliable in vitro tests, uncertainties associated with skin testing, and incomplete understanding of the underlying mechanisms., Aim: To summarize and hypothesize on the potential of basophil activation test (BAT) as a safe aid to explore the mechanistic endotypes of IDHR, to identify antibody recognition sites, and to monitor drug desensitization., Methods: A literature search was conducted using the keywords "allergy, basophil activation, CD63, CD203c, diagnosis, drugs, hypersensitivity, flow cytometry"; this was complemented by the authors' own expertise., Results: At present BAT has mainly been employed as a diagnostic aid. However, evidence is emerging that the technique might also deepen our insights in immune (allergic) and nonimmune (nonallergic) mechanistic processes of IDHR. It is anticipated that BAT might also benefit the identification of antibody recognition sites and benefit our understandings of desensitization strategies., Conclusion: Although the nondiagnostic application of BAT in IDHR is still in its infancy, with increasing employment, we can expect the technique to become a valuable asset to study many domains of IDHR that remain poorly understood.

Human mucosal-associated invariant T (MAIT) cells are unconventional T cells highly enriched in tissues exposed to microbial antigens including the oral, gastrointestinal and genital mucosae, liver, and lung. Here we describe a protocol for isolation and characterization of peripheral blood and tissue-infiltrating MAIT cells by using multicolor flow cytometry. This technology allows the analysis of multiple markers in a single sample at a single-cell level. Study of human samples requires particular care since the sample amount is often limited. We present a protocol optimized for the isolation and characterization of human MAIT cells and the identification of MAIT cell populations detected by simultaneous expression of multiple activation markers and inhibitory receptors.

The mucosa-associated invariant T (MAIT) cells represent the most abundant population of antimicrobial T cells in humans. When encountering cells infected with riboflavin-producing bacteria, this innate-like T cell population rapidly release a plethora of pro-inflammatory cytokines, mediates antimicrobial activity, and kill infected cells. Here, we describe methodological approaches and protocols to measure their cytotoxicity and antimicrobial effector function using multi-color flow cytometry-based and standard microbiological techniques. We provide specific guidance on protocols and describe potential pitfalls for each of the presented methodologies. Finally, we discuss potential applications and current limitations of our approaches to the study of human MAIT cell antimicrobial properties.

The placenta is an immunological paradox since maternal immune cells infiltrating placental tissues need to be tolerant toward the fetus but still retain immunity against potential infections. This makes the placenta an interesting tissue for studying immunological processes. Mucosal-associated invariant T (MAIT) cells are a subset of T cells that respond to bacterially derived metabolites of riboflavin synthesis. Upon activation, MAIT cells respond by secretion of inflammatory cytokines and by directed killing of infected cells by the use of granzymes and perforin. In this protocol, we describe methods for the isolation of immune cells from the placental intervillous space and adjacent tissues such as the umbilical cord, decidua parietalis, and decidua basalis. We further describe how to stimulate MAIT cells in mixed cell suspensions of mononuclear cells with bacteria, and how to analyze the phenotypic and functional responses with flow cytometry.

Mast cells (MCs) are secretory cells that are central players in human allergic disease and immune responses. With the exception of a few pathological situations, MCs are usually present at relatively low frequencies in most tissues. Since their first description, MCs in tissues were identified mostly using their morphological characteristics and their typical coloration when stained with aniline dyes. However, increasing availability of highly specific antibodies now permits the use of fluorescence-based flow cytometry as the method of choice for the quantification, characterization, and purification of cells in suspension. This technique allows for a rapid analysis of thousands of events and for the identification of cells present at frequencies as low as one event in 10 6 unwanted cells. This method also permits for simultaneous characterization of multiple antigens at a single cell level, which is ideal in order to study rare populations of cells like MCs. Here we describe the basis of flow cytometry-based immunophenotyping applied to the study of MC. The protocol focuses on the study of human MCs present in body fluids (mainly bone marrow) but can easily be adapted to studying MCs from other tissues and species.

Flow cytometry is one of the most widely used techniques for the detection of surface markers on various cells, particularly the cells of the immune system, at a single-cell resolution. Modern flow cytometers can identify rare cell population in highly heterogeneous samples. Here we present a protocol that allows a precise detection of basophils as well as eosinophils and neutrophils in induced sputum samples. The identification of sputum basophils and other granulocytes contributes to a better understanding of the cellular network that promotes and regulates inflammation of the lower respiratory tract.

The basis of flow cytometric allergy diagnosis is the quantification of changes in the expression of basophilic surface membrane markers (Ebo et al., Clin Exp Allergy 34: 332-339, 2004). Upon encountering specific allergens recognized by surface receptor FcεRI-bound IgE, basophils not only secrete and generate quantifiable bioactive mediators but also upregulate the expression of different markers (e.g., CD63, CD203c) which can be detected by multicolor flow cytometry using specific monoclonal antibodies (Ebo et al., Cytometry B Clin Cytom 74: 201-210, 2008). Here, we describe two flow cytometry-based protocols which allow the detection of surface marker activation (Method 1) and changes in intragranular histamine (Method 2), both reflecting different facets of basophil activation.

Mucosal-associated invariant T (MAIT) cell infiltration has been demonstrated in colorectal and hepatocellular carcinoma, and their ability to produce Th1- and Th17-associated cytokines, as well as their cytotoxic function, suggests that MAIT cells may have important functions in both reducing and promoting protective tumor immunity. Here, we describe enzymatic methods to isolate intraepithelial and lamina propria lymphocyte single cell suspensions from colon tissue and tumors containing viable MAIT cells, which can be used for further purification, flow cytometry analysis, or culture.

CAR-T cell immunotherapy is a promising therapeutic modality for cancer patients. The success of CAR-T cell therapy has been associated with the phenotype, activation and functional profiling of infused CAR-T cells. Therefore, immunophenotypic characterization of CAR-T cells during bioprocess is crucial for cell quality control and ultimately for improved antitumor efficacy. In this chapter, we propose a flow cytometry panel to characterize the immunophenotype of the CAR-T subsets.

Mucosal-associated invariant T (MAIT) cells can be found throughout the human body, in peripheral blood, at mucosal sites, and, among other organs, in the liver. As unconventional T cells, MAIT cells have the capacity to readily respond to bacterial infections and are also engaged during anti-viral responses. To thoroughly investigate the MAIT cell phenotype and function in such conditions, multi-color flow cytometry is an appropriate and powerful tool. Yet, the recent rapid technological development within this methodology, with generation of highly complex data, has increased the need for downstream dimensionality reducing methods to fully interpret obtained results. Among such methods, stochastic neighbor embedding (SNE) analysis stands out as it provides intuitive low-dimensional representations of complex data. Here, we describe techniques and workflow for high-dimensional state-of-the-art investigation and analysis of human MAIT cells from blood and peripheral tissues.

Applications of immunophenotyping using flow cytometry offer precise and accurate means for providing information used to both diagnose and monitor disease; they serve as a standard platform for many research endeavors that study discrete populations of biological entities. The proper use of this highly sophisticated technology requires daily and ongoing monitoring of both the instrument and the methodology. Best practices for this begin with quality control (QC) procedures designed to set up and monitor the instrument performance, the reagents, and the results to ensure that they are working properly both on the day of use and over time. If the results of those QC procedures are outside of acceptable then recording the corrective action taken must also be included in the quality control records. Quality assurance (QA) is a way to know that the three phases of testing, namely, preanalytic, analytic, and postanalytic procedures, are being followed. This chapter describes the procedures used to assess quality control as it pertains to flow cytometry and immunophenotyping in all three phases of testing.

Chimeric antigen receptors against CD19 (anti-CD19-CAR) are widely recognized and used by not only researchers associated with immunology, molecular biology, and cell biology but also physicians to treat B-cell malignancies. Anti-CD19-CAR is currently clinically available as one of the therapeutic modalities for refractory acute B-cell-typed lymphoblastic leukemia (B-ALL) patients. However, to detect CAR on the cell surface and investigate the efficacy of CAR-T cells, there are numerous experimental modalities including flow cytometry, the Cr-releasing assay, immunoblot, and immunostaining. We have chosen several techniques, which are necessary and sufficient as well as reliable and reproducible to detect and assess the killing effect of CAR-T cells. Here, we describe protocols for basic experiments and procedures for the detection of CAR on transduced cells and in in vitro coculture experiments to assess cytotoxicity using CAR-T cells.

Mass cytometry is a variation of conventional flow cytometry using metal tagged antibodies for cell staining instead of fluorochromes and detection in a mass cytometer, a modified mass spectrometer that allows for separation of discrete masses of these metal tags by time of flight (TOF). Currently, up to 50 different metal tags are available for cell analysis. The lack of any significant mass spectral overlap and autofluorescence background makes mass cytometry uniquely suited for complex high-dimensional phenotypic and functional analysis at the single cell level, thus accelerating biomarker discovery and drug screening. Here we describe a workflow for phenotyping of human peripheral blood mononuclear cells (PBMCs) covering cell staining, instrument setup of a Fluidigm Helios™ mass cytometer, and sample acquisition, and summarize a basic workflow of data analysis.

Immunophenotyping by flow cytometry is an important component in the diagnostic evaluation of patients with acute lymphoblastic leukemia. This technique further permits the detection of minimal residual disease after therapy, a robust prognostic factor that may guide individualized treatment. We describe here laboratory methods for both the initial characterization of lymphoblasts at diagnosis, and the detection of rare leukemic lymphoblasts after treatment. In addition to antibody combinations suitable for diagnosis and detection of minimal residual disease, we describe procedures for peripheral blood and bone marrow sample preparation, procedures for labeling of cell-surface and intracellular proteins with fluorochrome-conjugated antibodies, and approaches to analysis of immunophenotypic data.

Mass cytometry (MC) is a powerful research tool enabling high-dimensional analysis of single cells in suspension and within tissue sections following laser ablation. Here we describe the procedure of titrating metal-conjugated antibodies, to ensure that optimal levels of staining are achieved while minimizing nonspecific signals that may occur at high concentrations.

Mass cytometers are time-of-flight (TOF) mass spectrometer-coupled flow cytometers (known as CyTOFs) that quantify the abundance of metal-tagged antibodies (Abs) or other cellular probes within single cell suspensions or laser-ablated tissue sections. While many strategies exist for covalently crosslinking to proteins, the Fluidigm MaxPar ® process is currently the most widely used and involves first loading a metal-chelating polymer with an elementally and isotopically enriched metal. Once the chelation sites have been filled, a maleimide moiety on the polymer is reacted with the free thiol groups on the partially reduced monoclonal immunoglobulin G (IgG) Ab to form an irreversible covalent bond. Here we describe modifications to the Fluidigm MaxPar ® protocol that increase the quantity of Ab per reaction up to 150 μg, introduce an initial Ab quality control step, utilize metal labels not included in the Fluidigm catalog, and provide an option to perform two reactions in one centrifugal filter.

Flow-cytometric demonstration of the typical chronic lymphocytic leukemia (CLL) immunophenotype is vital for diagnosis. CLL has a characteristic immunophenotype, expressing CD5, CD19, dim CD20, dim CD22, CD23, bright CD43, dim CD45, dim to negative CD79b, dim CD81, CD200, and dim monoclonal surface immunoglobulin. This characteristic immunophenotype allows a definitive diagnosis and the ruling out of another leukemia or lymphoma. Flow cytometry also provides important prognostic information and accurate assessment of response to therapy. Here we describe optimal specimen collection, red cell lysis, appropriate panel, cell staining, acquisition on a flow cytometer, and analysis for CLL specimens.

Paroxysmal nocturnal hemoglobinuria (PNH) is a rare but often debilitating disease which may lead to death in up to 35% of patients within 5 years if unrecognized and untreated. Detection of PNH and assessment of PNH clone size in RBC and WBC lineages by flow cytometric analysis has increased in importance due to the availability of novel therapies. These therapies typically block the hemolysis of red blood cells and thus significantly lower the morbidities and mortality associated with this disease. This chapter describes validated, state-of-the-art, high-sensitivity flow cytometric methodologies based on latest published testing guidelines for PNH.

Flow-cytometric detection of circulating endothelial cells and endothelial microparticles is an essential tool in studies of vascular diseases. Here we describe the principles and detailed methods for human blood sample processing, storage, labeling, and gating of circulating endothelial elements.

Flow cytometry enables the measurement of single cells in a flowing system. Heterogeneous mixtures of cells or particles can be analyzed with respect to their morphology, surface and intracellular protein expression, DNA content, and cellular physiology at high speed and purity. A series of key technical developments and improvements in flow cytometry hardware, software, and dye chemistry made it possible to measure more than 20 parameters simultaneously. Here, we provide a stepwise protocol for the preparation of single cell suspension samples from different murine lymphoid or tumor tissues and a detailed description of a 17-color polychromatic flow cytometry analysis of tumor-infiltrating leukocytes.

The very sensitive quantification of leukemia cells that persist in chronic lymphocytic leukemia patients after successful therapy is steadily gaining interest with clinical scientists. Minimal residual disease (MRD) has demonstrated prognostic significance in the context of different treatment modalities leading to its approval as an intermediate endpoint for licensure in randomized trials by the European Medicine Agency. Data supporting the clinical impact of MRD as well as a highly standardized and broadly available method for MRD assessments by flow cytometry are described herein. Examples of gating strategies are provided with comprehensive explanations to allow the reader the application of the technology to blood and bone samples with high and very low level MRD, respectively. This chapter has a particular focus on samples acquired shortly after anti-CD20 treatment. The standardization developed by the EuroFlow consortium is additionally described as technical basis for reproducible and standardized flow cytometric MRD assessments.

Polychromatic flow cytometry enables the detection and characterization of markers which are helpful in defining phenotype of various cell subsets. Here we describe flow cytometry-based method to characterize phenotype of naïve, memory, and effector T cells. Being able to differentiate these cells is crucial in understanding immune response, and immune profiling. Naïve T cells enable the body to fight off new, unrecognized infections and diseases, and memory T cells are enriched for response to recall antigens. Furthermore, the antigen-experienced T cell populations can be broadly divided into effector and memory cell compartments, both of which are needed for sustaining a responsive immune system. Simplistically, the effector T cells require active antigenic stimulation to eliminate pathogens. On the other hand, memory T cells are described as cells which remain present in the absence of antigenic stimulation and have the capacity to expand rapidly upon secondary challenges. Recently, with the identification of central and effector memory T cell subsets, tremendous efforts have been devoted to characterize markers on the surfaces of these cells. Though, various markers have been used to identify the subsets, no single marker that segregates one subset from the other has been described. Thus, multiple markers are needed to subset the cells in order to characterize them. Here we report the verification of a nine-color panel (CD3, CD4, CD8, CD45RO, CD28, CD95, CCR7, Live/Dead Aqua, dump channel-CD19, CD14, CD56, CD16) that can successfully identify six distinct CD4 and CD8 T cell populations within the naïve and effector cell subsets from human donors.

Fluorescence in situ hybridization (FISH) is a powerful and robust technique allowing the visualization of target sequences like genes in interphase nuclei. It is widely used in routine diagnostics to identify cancer-specific aberrations including lymphoma-associated translocations or gene copy number changes in single tumor cells. By combining FISH with immunophenotyping-a technique called fluorescence immunophenotyping and interphase cytogenetic as a tool for investigation of neoplasia (FICTION)-it is moreover possible to identify a cell population of interest. Here we describe standard protocols for FISH and FICTION as used in our laboratories in diagnosis and research.

Monocytes and macrophages are cells of the innate immune system, existing in circulation and permeating every tissue of the human body. These cells represent the first responders to stress, and their inflammatory activation forms part of virtually every human disease. It is for these reasons that several approaches have been developed in order to phenotypically and functionally analyze these cells and their subpopulations. These inflammatory cells have been consistently demonstrated to undergo inflammatory polarization through the engagement of lipid-activated nuclear receptors, namely, through PPARs and LXRs, which regulate both lipid metabolism and inflammation. Quantitative and phenotypic analyses of monocytes and macrophages are largely dependent on cytometric tools and antibody-based labelling of membrane markers, while functional analyses apply a range of in vitro approaches coupled with secondary analyses of gene or cytokine expression. An important aspect of phenotypic and functional analyses is the purification, enrichment, or appropriate differentiation of biological materials, ensuring experimentation is carried out on monocytes and/or macrophages and not on other cell types occupying the same physical niches. This chapter will focus on the most common analytical approaches applied to the mononuclear phagocytic system, namely, circulating monocytes and adipose tissue macrophages.

The advent of mass cytometry (CyTOF ® ) has permitted simultaneous detection of more than 40 antibody parameters at the single-cell level, although a limited number of metal-labeled antibodies are commercially available. Here we present optimized and scalable protocols for conjugation of lanthanide as well as bismuth ions to immunoglobulin (Ig) using a maleimide-functionalized chelating polymer and for characterization of the conjugate. The maleimide functional group is reactive with cysteine sulfhydryl groups generated through partial reduction of the Ig Fc region. Incubation of Ig with polymer pre-loaded with lanthanide ions produces metal-labeled Ig without disrupting antigen specificity. Antibody recovery rates can be determined by UV spectrophotometry and frequently exceeds 60%. Each custom-conjugated antibody is validated using positive and negative cellular control populations and is titrated for optimal staining at concentrations ranging from 0.1 to 10 μg/mL. The preparation of metal-labeled antibodies can be completed in 4.5 h, and titration requires an additional 3-5 h.