Spectral Flow Cytometry Analysis of Resident Tissue Macrophages.

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.

Isolation and Flow Cytometry Analysis of Macrophages from the Dermis.

The dermis contains a dense network of tissue macrophages, which contribute to tissue homeostasis, inflammation, and pathogen clearance. Dermal macrophages are partly replenished by circulating monocytes, which fuel the resident population, especially in case of tissue damage or inflammation. The complexity of the tissue, containing blood and lymphoid vessels, hair bulbs, sebaceous glands, and peripheral nerves, allows for the development of distinct macrophages populations. In steady state, discrete subtypes can be distinguished due to their surface marker expression and localization within the dermis. In this chapter, we describe how to extract dermal macrophages from the skin and highlight different gating strategies to identify monocyte and macrophage populations.

Isolation and Flow Cytometry Analysis of Macrophages from the Kidney.

Renal macrophages help maintain homeostasis, participate in tissue injury and repair, and play a vital role in immune surveillance [1-3]. Kidney macrophages can be broken down into two subsets, infiltrating macrophages, which can be further broken down into Ly6Chi and Ly6Clo cells, and kidney resident macrophages. While recent studies have shed light on the differing origins and niches of these cells, a more thorough understanding of kidney macrophage populations and how they may respond to various conditions is needed. This protocol describes how to efficiently isolate murine kidney macrophage populations for flow cytometry analysis.

Isolation and Flow Cytometry Analysis of Intestinal Macrophages.

The intestinal macrophage pool represents the largest population of macrophages present within the body. Nevertheless, flow cytometry analysis of intestinal macrophages remains challenging due to historical lack of consensus on surface markers, variations in sample preparation, and a certain capriciousness of the isolation procedure itself. Furthermore, recent studies have uncovered a hitherto unknown heterogeneity of intestinal macrophages, accompanied by a vast increase of subset-identifying surface markers. Here, the isolation procedure for intestinal tissue for flow cytometry analysis is laid out, with particular attention toward the procedures for isolated intestinal layers, and a trouble-shooting section with strategies to avoid common pitfalls and mistakes.

Isolation and Characterization of Testis Macrophages Using Flow Cytometry.

Testis-resident macrophages are first responders of the innate immune system against pathogens. They also exert day-to-day functions that are poorly understood. To study testis macrophages, several techniques are used, among which we can find flow cytometry.Flow cytometry is a powerful tool that enables analysis of macrophages at a cellular as well as population level. To analyze testis macrophages using flow cytometry, a specific tissue processing is necessary to extract them. In this protocol, we explain how to extract and analyze the distinct macrophage populations.

Isolation and Flow Cytometry Analysis of Macrophages from White Adipose Tissue.

Macrophages are one of the prominent leukocyte populations in white adipose tissue (WAT) and play an important role during WAT homeostasis and remodeling. Macrophage function in WAT is determined by ontogeny and the local tissue environment. Here, we present a protocol to analyze different macrophage populations from murine WAT using flow cytometry.

Studying Efferocytosis Dynamics in Tissue-Resident Macrophages Ex Vivo.

In vitro cocultures of macrophages and apoptotic cells (ACs) provide a practical and useful tool to study efferocytosis. Here, we describe a method for automated quantification and imaging of recognition and engulfment of apoptotic cells by primary macrophages using imaging flow cytometry (IFC). IFC-based analysis allows us to successfully quantify efferocytosis, clearly distinguishing phagocytic from nonphagocytic macrophages and, more importantly, from those in recognition stage, which is not achievable by standard flow cytometrical analysis. To this end, we established a universally employable analysis pipeline to address efferocytosis that can be easily adapted to any macrophage population from samples of different origins.

Studying Macrophages in the Murine Steatotic Liver Using Flow Cytometry and Confocal Microscopy.

The study of macrophage functions in the context of metabolic dysfunction-associated steatotic liver disease (MASLD) and metabolic dysfunction associated steatohepatitis (MASH) has been hampered by the fact that until recently all macrophages in the liver were thought to be Kupffer cells, the resident macrophages of the liver. With the advent of single-cell technologies, it is now clear that the steatotic liver harbors many distinct populations of macrophages, likely each with their own unique functions as well as subsets of monocytes and dendritic cells which can be difficult to discriminate from one another. Here, we detail the protocols we utilize to (i) induce MASLD/MASH in mice, (ii) isolate cells from the steatotic liver, and (iii) describe reliable gating strategies, which can be used to identify the different subsets of myeloid cells. Finally, we also discuss the issue of increased autofluorescence in the steatotic liver and the techniques we use to minimize this both for flow cytometry and confocal microscopy analyses.

Development of high-throughput systems for biodosimetry.

Biomarkers for ionising radiation exposure have great utility in scenarios where there has been a potential exposure and physical dosimetry is missing or in dispute, such as for occupational and accidental exposures. Biomarkers that respond as a function of dose are particularly useful as biodosemeters to determine the dose of radiation to which an individual has been exposed. These dose measurements can also be used in medical scenarios to track doses from medical exposures and even have the potential to identify an individual's response to radiation exposure that could help tailor treatments. The measurement of biomarkers of exposure in medicine and for accidents, where a larger number of samples would be required, is limited by the throughput of analysis (i.e. the number of samples that could be processed and analysed), particularly for microscope-based methods, which tend to be labour-intensive. Rapid analysis in an emergency scenario, such as a large-scale accident, would provide dose estimates to medical practitioners, allowing timely administration of the appropriate medical countermeasures to help mitigate the effects of radiation exposure. In order to improve sample throughput for biomarker analysis, much effort has been devoted to automating the process from sample preparation through automated image analysis. This paper will focus mainly on biological endpoints traditionally analysed by microscopy, specifically dicentric chromosomes, micronuclei and gamma-H2AX. These endpoints provide examples where sample throughput has been improved through automated image acquisition, analysis of images acquired by microscopy, as well as methods that have been developed for analysis using imaging flow cytometry.

Rapid, high-throughput phenotypic profiling of endosymbiotic dinoflagellates (Symbiodiniaceae) using benchtop flow cytometry.

Endosymbiotic dinoflagellates (Family Symbiodiniaceae) are the primary producer of energy for many cnidarians, including corals. The intricate coral-dinoflagellate symbiotic relationship is becoming increasingly important under climate change, as its breakdown leads to mass coral bleaching and often mortality. Despite methodological progress, assessing the phenotypic traits of Symbiodiniaceae in-hospite remains a complex task. Bio-optics, biochemistry, or "-omics" techniques are expensive, often inaccessible to investigators, or lack the resolution required to understand single-cell phenotypic states within endosymbiotic dinoflagellate assemblages. To help address this issue, we developed a protocol that collects information on cell autofluorescence, shape, and size to simultaneously generate phenotypic profiles for thousands of Symbiodiniaceae cells, thus revealing phenotypic variance of the Symbiodiniaceae assemblage to the resolution of single cells. As flow cytometry is adopted as a robust and efficient method for cell counting, integration of our protocol into existing workflows allows researchers to acquire a new level of resolution for studies examining the acclimation and adaptation strategies of Symbiodiniaceae assemblages.

Early T-cell precursor lymphoblastic leukaemia with monocytic morphology negative for CD3 by flow cytometry: A diagnostic challenge solved by immunohistochemistry.

No abstract available.

A Single-Tube 21-Color Multiparameter Flow Cytometry Improve the Sensitivity of B-ALL MRD Analysis.

BACKGROUND: Detection of minimal residual disease (MRD) by multiparameter flow cytometry (MFC) is a well-established risk stratification factor and therapeutic modification strategy in B acute lymphoblastic leukemia (B-ALL). However, current 8 color (8c)-MFC for MRD detection had the sensitivity of 0.01% with false negative or positive. Hence, a more sensitive and applicable MFC-MRD method is urgently needed. The aim of this study is to establish a single-tube 21c-MFC method to detect B-ALL MRD, evaluate its performance, and to investigate its preliminary clinical application. METHODS: We selected 21 markers to establish a single-tube 21c-MFC method. The repeatability and sensitivity of this method was validated by adding Nalm-6 cells to normal bone marrow. Samples from control group (n = 6), B-ALL group (n = 7) and complete remission (CR) group (n = 26) were detected by 21c- and 8c-MFC separately. The expression characteristics of these markers was analyzed in control and B-ALL group, and the consistency of 21c- and 8c-MFC in detecting MRD was compared. RESULTS: Repeatability of this method was 1.91% of CV and sensitivity was up to 0.005%. In control group, the expression of CD81, CD97, and CD200 gradually decreased and CD44, HLA-DR, CD73, and CD72 gradually increased with the maturation of normal B cells. In B-ALL group, CD73stro, CD81low, CD44stro, CD123stro, and CD58stro showed high-frequency expression. The consistency rate of 21c- and 8c-MFC in detecting MRD was 96%. CONCLUSIONS: A single-tube 21c-MFC method was established for MRD detection in B-ALL and had higher sensitivity than the 8c-MFC method.

Isolation of Mouse Neutrophils.

Neutrophils represent the first line of defense against bacterial and fungal pathogens. Indeed, patients with inherited or acquired qualitative and quantitative neutrophil defects are at high risk for developing bacterial and fungal infections and suffering adverse outcomes from these infections. Therefore, research aiming at defining the molecular factors that modulate neutrophil effector function under homeostatic conditions and during infection is essential for devising strategies to augment neutrophil function and improve the outcomes of infected individuals. This article describes reproducible density-gradient-centrifugation-based as well as positive and negative immunomagnetic selection protocols that can be applied in any laboratory to harvest large numbers of highly enriched and highly viable neutrophils from the bone marrow of mice. In another protocol, we also present a method that combines gentle enzymatic tissue digestion with a positive immunomagnetic selection technique or fluorescence-activated cell sorting (FACS) to harvest highly pure and highly viable preparations of neutrophils directly from mouse tissues such as the kidney, the liver, or the spleen. Mouse neutrophils isolated by these protocols can be used to examine several aspects of cellular function ex vivo, including pathogen binding, phagocytosis, and killing, neutrophil chemotaxis, oxidative burst, degranulation, and cytokine production, and for performing neutrophil adoptive transfer experiments. © 2023 Wiley Periodicals LLC. This article has been contributed to by U.S. Government employees and their work is in the public domain in the USA. Basic Protocol 1: Isolation of Neutrophils from Mouse Bone Marrow Using Positive Immunomagnetic Separation Alternate Protocol 1: Purification of Neutrophils from Bone Marrow Using Negative Immunomagnetic Separation Alternate Protocol 2: Purification of Neutrophils from Bone Marrow Using Histopaque-Based Density Gradient Centrifugation Basic Protocol 2: Isolation of Neutrophils from Mouse Tissues Using Positive Immunomagnetic Separation Alternate Protocol 3: Isolation of Neutrophils from Mouse Tissues Using FACS.

Influence of Pre-Analytic Conditions on Quantity of Lymphocytes.

Lymphocytes are key players in the pathogenesis of multiple sclerosis and a distinct target of several immunomodulatory treatment strategies. In this study, we aim to evaluate the effect of various pre-analytic conditions on immune cell counts to conclude the relevance for clinical implications. Twenty healthy donors were assessed for the effects of distinct storage temperatures and times after blood draws, different durations of tourniquet application, body positions and varying aspiration forces during blood draws. Immune cell frequencies were analyzed using multicolor flowcytometry. While storage for 24 h at 37 °C after blood draws was associated with significantly lower cell counts, different durations of tourniquet application, body positions and varying aspirations speeds did not have significant impacts on the immune cell counts. Our data suggest that immune cell counts are differently affected by pre-analytic conditions being more sensitive to storage temperature. Pre-analytic conditions should be carefully considered when interpreting the laboratory values of immune cell subpopulations.

Metabolic heterogeneity of tissue-resident macrophages in homeostasis and during helminth infection.

Tissue-resident macrophage populations constitute a mosaic of phenotypes, yet how their metabolic states link to the range of phenotypes and functions in vivo is still poorly defined. Here, using high-dimensional spectral flow cytometry, we observe distinct metabolic profiles between different organs and functionally link acetyl CoA carboxylase activity to efferocytotic capacity. Additionally, differences in metabolism are evident within populations from a specific site, corresponding to relative stages of macrophage maturity. Immune perturbation with intestinal helminth infection increases alternative activation and metabolic rewiring of monocyte-derived macrophage populations, while resident TIM4+ intestinal macrophages remain immunologically and metabolically hyporesponsive. Similar metabolic signatures in alternatively-activated macrophages are seen from different tissues using additional helminth models, but to different magnitudes, indicating further tissue-specific contributions to metabolic states. Thus, our high-dimensional, flow-based metabolic analyses indicates complex metabolic heterogeneity and dynamics of tissue-resident macrophage populations at homeostasis and during helminth infection.

Enhanced systemic tumor suppression by in situ vaccine combining radiation and OX40 agonist with CpG therapy.

BACKGROUND: In situ tumor vaccine has been gradually becoming a hot research field for its advantage of achieving personalized tumor therapy without prior antigen identification. Various in situ tumor vaccine regimens have been reported to exert considerable antitumor efficacy in preclinical and clinical studies. However, the design of in situ tumor vaccines still needs further optimization and the underlying immune mechanism also waits for deeper investigation. METHODS: A novel triple in situ vaccine strategy that combining local radiation with intratumoral injection of TLR9 agonist CpG and OX40 agonist was established in this sturdy. Local and abscopal antitumor efficacy as well as survival benefit were evaluated in the bilateral tumors and pulmonary metastasis model of B16F10 melanoma. In situ vaccine-induced immune responses and immune-associated variation in tumor environment were further investigated using multiparameter flow cytometry and RNA sequencing. Base on the analysis, the RT + CpG + αOX40 triple in situ vaccine was combined with checkpoint blockade therapy to explore the potential synergistic antitumor efficacy. RESULTS: Enhanced tumor suppression was observed with minimal toxicity in both treated and untreated abscopal tumors after receiving RT + CpG + αOX40 triple vaccine. The introduction of local radiation and OX40 agonist benefit more to the inhibition of local and abscopal lesions respectively, which might be partially attributed to the increase of effector memory T cells in the tumor microenvironment. Further analysis implied that the triple in situ vaccine did not only activate the microenvironment of treated tumors, with the upregulation of multiple immune-associated pathways, but also enhanced systemic antitumor responses, thus achieved superior systemic tumor control and survival benefit. Moreover, the triple in situ vaccine synergized with checkpoint blockade therapy, and significantly improved the therapeutic effect of anti-programmed cell death protein (PD)-1 antibody. CONCLUSION: This triple combining in situ vaccine induced intensive antitumor responses, mediated effective systemic tumor control and survival benefit, and displayed impressive synergistic antitumor effect with checkpoint blockade therapy. These data preliminary confirmed the efficacy, feasibility and safety of the triple combining in situ vaccine, suggesting its great application potential as both monotherapy and a part of combined immunotherapeutic regimens in clinical scenario.

Early expansion of activated adaptive but also exhausted NK cells during acute severe SARS-CoV-2 infection.

The analysis of immunological parameters during the course of a SARS-CoV-2 infection is of great importance, both to identify diagnostic markers for the risk of a severe course of COVID-19, and to better understand the role of the immune system during the infection. By using multicolor flow cytometry we compared the phenotype of Natural Killer (NK) cells from hospitalized COVID-19 patients during early SARS-CoV-2 infection with samples from recovered and SARS-CoV-2 naïve subjects. Unsupervised high-dimensional analysis of 28-color flow cytometric data revealed a strong enrichment of NKG2C expressing NK cells in response to the acute viral infection. In addition, we found an overrepresentation of highly activated NK cell subsets with an exhausted phenotype. Moreover, our data show long-lasting phenotypic changes within the NK cell compartment that did not completely reverse up to 2 months after recovery. This demonstrates that NK cells are involved in the early innate immune response against SARS-CoV-2.

Analysis of Chromatin Accessibility, Histone Modifications, and Transcriptional States in Specific Cell Types Using Flow Cytometry.

The past two decades in biomedical research have experienced an explosion of cell type-specific and single-cell studies, especially concerning the concomitant dissection of regulatory and transcriptional landscapes of those under investigation. Additionally, leveraging next-generation sequencing (NGS) platforms efforts have been undertaken to evaluate the effects of chromatin accessibility, histone modifications, or even transcription factor binding sites. We have shown that Fluorescence-Activated Nuclear Sorting (FANS) is an effective means to characterize the transcriptomes of nuclei from different tissues. In light of our own technical and experimental developments, we extend this effort to combine FACS/FANS with Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq), Chromatin Immunoprecipitation sequencing (ChIP-seq), and RNA sequencing (RNA-seq) for profiling individual cell types according to their chromatin and transcriptional states.

Preparation of Human Olfactory Epithelial Biopsies for Downstream Analysis.

The olfactory mucosa, lining a portion of the nasal cavity, houses the primary olfactory sensory neurons responsible for odor transduction, along with supporting cell populations. Tremendous advances have come from studying the peripheral olfactory system in animal models, especially the mouse. However, acquired human olfactory disorders lack effective therapies, and many of these conditions involve pathology in the olfactory mucosa. Thus, the ability to obtain human olfactory biopsy samples from subjects with olfactory dysfunction, or controls, may be of value. Here, we describe established techniques for collecting olfactory tissue from human subjects and preparing samples for downstream assays such as immunohistochemistry, flow cytometry, single-cell RNA-sequencing, or chromatin studies.

Identification of Immune Cells in Murine Olfactory Mucosa.

Olfactory immunology is an emerging field in the context of infectious disease and neuroimmunology, yet characterization of immune cells within the murine olfactory mucosa remains sparse. This is partially due to the difficulty in distinguishing olfactory-resident immune cells from immune cells that reside within nasal turbinate bone marrow. Using techniques like intranasal antibody labeling, we have developed methods to definitively identify olfactory immune cells via flow cytometry and immunofluorescent confocal microscopy. This protocol will describe the best practices for these methods, as well as detail how intravenous antibody labeling can be used to study the blood-olfactory barrier, an important determinant of olfactory immunity. We also include validated markers for the identification of major olfactory immune populations.