Determining cellular lineage directed networks in hematopoiesis using single-cell transcriptomic data and volatility-constrained correlation.

Single-cell transcriptome sequencing (scRNA-seq) has revolutionized our understanding of cellular processes by enabling the analysis of expression profiles at an individual cell level. This technology has shown promise in uncovering new cell types, gene functions, cell differentiation, and trajectory inference through the study of various biological processes, such as hematopoiesis. Recent scRNA-seq analysis of mouse bone marrow cells has provided a network model of hematopoietic lineage. However, all data analyses have predicted undirected network maps for the associated cell trajectories. Moreover, the debate regarding the origin of basophil cells still persists. In this work, we apply the Volatility Constrained (VC) correlation method to predict not only the network structure but also the causality or directionality between the cell types present in the hematopoietic process. Our findings suggest a dual origin of basophils, from both granulocyte/macrophage and erythrocyte progenitors, the latter being a trajectory less explored in previous research. The proposed approach and predictions may assist in developing a complete hematopoietic process map, impacting our understanding of hematopoiesis and providing a robust directional network framework for further biomedical research.

Light microscopic morphology of blood cells of non-descript indigenous Zoar chicken of Mizoram, India.

Identifying and analysing distinct blood cells is crucial for the diagnosis and treatment of diseases in the field of biomedicine. The present study was undertaken to study the cytomorphological and cytochemical characteristics of the blood cells of Zoar, a non-descript indigenous breed of chicken extensively reared under backyard poultry farming in Mizoram, India. For this study, 2 mL of blood samples were aseptically collected from the wings veins of 12 chickens and were processed for light microscopic study under standard protocols. The matured erythrocytes were elliptical, while the immature erythrocytes appeared oval. The heterophils were positive for SBB (SBB), Periodic Acid Schiff (PAS), acid phosphatase, alkaline phosphatase and Arylsulphatase while the eosinophils were positive for SBB, PAS, alkaline phosphatase, cytochrome oxidase and peroxidase. The basophils of were positive for toluidine blue while the thrombocytes were positive for PAS. These cytochemical and cytoenzymatic staining properties plays a very important role in diagnosis, differentiation, and classification of leukaemias.

The transcription factor NFIL3/E4BP4 regulates the developmental stage-specific acquisition of basophil function.

BACKGROUND: Basophils are rare but important effector cells in many allergic disorders. Contrary to their early progenitors, the terminal developmental processes of basophils in which they gain their unique functional properties are unknown. OBJECTIVE: We sought to identify a novel late-stage basophil precursor and a transcription factor regulating the terminal maturation of basophils. METHODS: Using flow cytometry, transcriptome analysis, and functional assays, we investigated the identification and functionality of the basophil precursors as well as basophil development. We generated mice with basophil-specific deletion of nuclear factor IL-3 (NFIL3)/E4BP4 and analyzed the functional impairment of NFIL3/E4BP4-deficient basophils in vitro and in vivo using an oxazolone-induced murine model of allergic dermatitis. RESULTS: We report a new mitotic transitional basophil precursor population (referred to as transitional basophils) that expresses the FcεRIα chain at higher levels than mature basophils. Transitional basophils are less responsive to IgE-linked degranulation but produce more cytokines in response to IL-3, IL-33, or IgE cross-linking than mature basophils. In particular, we found that the expression of NFIL3/E4BP4 gradually rises as cells mature from the basophil progenitor stage. Basophil-specific deletion of NFIL3/E4BP4 reduces the expression of genes necessary for basophil function and impairs IgE receptor signaling, cytokine secretion, and degranulation in the context of murine atopic dermatitis. CONCLUSIONS: We discovered transitional basophils, a novel late-stage mitotic basophil precursor cell population that exists between basophil progenitors and postmitotic mature basophils. We demonstrated that NFIL3/E4BP4 augments the IgE-mediated functions of basophils, pointing to a potential therapeutic regulator for allergic diseases.

Basophils and Mast Cells in COVID-19 Pathogenesis.

Basophils and mast cells are among the principal inducers of Th2 responses and have a crucial role in allergic and anti-parasitic protective immunity. Basophils can function as antigen-presenting cells that bind antigens on their surface and boost humoral immune responses, inducing Th2 cell differentiation. Their depletion results in lower humoral memory activation and greater infection susceptibility. Basophils seem to have an active role upon immune response to SARS-CoV-2. In fact, a coordinate adaptive immune response to SARS-CoV-2 is magnified by basophils. It has been observed that basophil amount is lower during acute disease with respect to the recovery phase and that the grade of this depletion is an important determinant of the antibody response to the virus. Moreover, mast cells, present in a great quantity in the nasal epithelial and lung cells, participate in the first immune response to SARS-CoV-2. Their activation results in a hyperinflammatory syndrome through the release of inflammatory molecules, participating to the "cytokine storm" and, in a longer period, inducing pulmonary fibrosis. The literature data suggest that basophil counts may be a useful prognostic tool for COVID-19, since their reduction is associated with a worse prognosis. Mast cells, on the other hand, represent a possible therapeutic target for reducing the airway inflammation characteristic of the hyperacute phase of the disease.

FUT6 deficiency compromises basophil function by selectively abrogating their sialyl-Lewis x expression.

Sialyl-Lewis x (sLex, CD15s) is a tetra-saccharide on the surface of leukocytes required for E-selectin-mediated rolling, a prerequisite for leukocytes to migrate out of the blood vessels. Here we show using flow cytometry that sLex expression on basophils and mast cell progenitors depends on fucosyltransferase 6 (FUT6). Using genetic association data analysis and qPCR, the cell type-specific defect was associated with single nucleotide polymorphisms (SNPs) in the FUT6 gene region (tagged by rs17855739 and rs778798), affecting coding sequence and/or expression level of the mRNA. Heterozygous individuals with one functional FUT6 gene harbor a mixed population of sLex+ and sLex- basophils, a phenomenon caused by random monoallelic expression (RME). Microfluidic assay demonstrated FUT6-deficient basophils rolling on E-selectin is severely impaired. FUT6 null alleles carriers exhibit elevated blood basophil counts and a reduced itch sensitivity against insect bites. FUT6-deficiency thus dampens the basophil-mediated allergic response in the periphery, evident also in lower IgE titers and reduced eosinophil counts.

Cellular and Biochemical Analysis of Bronchoalveolar Lavage Fluid from Murine Lungs.

Bronchoalveolar lavage (BAL) is a technique used to collect the contents of the airways. The fluid recovered, called BAL fluid (BALF), serves as a dynamic tool to identify various disease pathologies ranging from asthma to infectious diseases to cancer in the lungs. A wide array of tests can be performed with BALF, including total and differential leukocyte counts (DLC), enzyme-linked immunosorbent assays (ELISA) or flow-cytometric quantitation of inflammatory mediators, such as cytokines, chemokines and adhesion molecules, and assessment of nitrate and nitrite content for estimation of nitric oxide synthase (NOS) activity. Here, we describe a detailed procedure for the collection of BALF for a variety of downstream usages, including DLC by cytological and flow-cytometry-based methods, multiplex cytokine analysis by flow cytometry, and NOS activity analysis by determining nitrate and nitrite levels.

Short-term biological variation of differential count in healthy subjects in a South Asian population.

Estimates of Within-Subject and between subject biological variation for the white blood cell differential count (DC) have not been reported in South Asia. Therefore, we attempted to measure the short-term biological variation estimates for DC. The study was conducted on 28 healthy volunteers (15 males and 13 females). Blood from the volunteers was collected in the morning in K3-EDTA vials and analyzed in triplicate on the Sysmex XN-1000 analyzer, for six consecutive days. The Within subject, between subject and analytical coefficient of variation of the DC was calculated from the results by nested repeated measures ANOVA after outlier exclusion. The Reference change values (RCV) were also calculated. The within-subject variation for eosinophil Count and between subject variation for basophils in our study from South Asia was greater than the published European and American studies. Males and females showed similar biological variation for DC. The within-subject variation of other parameters (Neutrophils, Lymphocytes, Monocytes and Basophils) were similar or showed only mild differences to the published studies. The markedly different within-subject variation for Eosinophil counts suggest that the RCV for DC in South Asians need to be different from the published data in order to have clinical relevance. The Within-subject variation values of the other parameters seem transportable from the published European and American studies, but the small differences found mean that further regional estimates need to be reported for robust evidence of the same.

Purification of Basophils from Peripheral Human Blood.

The purification of basophils from peripheral blood has represented a formidable challenge for researchers since they were discovered by Paul Ehrlich in 1879. From the first published attempts in the late 1960s, it took half a century to develop robust protocols able to give sufficient numbers of pure, functionally unimpaired basophils. The existing protocols for basophil purification exploit those properties of basophils which distinguish them from other cell types such as their localization in blood, density, and the presence or absence of surface markers. Purification techniques have been used in various combinations and variations to achieve a common goal in mind: to obtain a pure population of human basophils in sufficient numbers for downstream studies. The arduous way leading up to the modern protocols is summarized in this historical retrospective. A fast protocol for purification of basophils to near homogeneity is also described.

Modulating the Human Basophil Phenotype During Its Development and Maturation: Basophils Derived from In Vitro Cultures of CD34+ Progenitor Cells.

Historically, the human basophil that is studied experimentally comes from peripheral blood. But there is evidence that only a short portion of the basophil life cycle related to IgE-mediated function occurs in the blood. The same evidence suggests that IgE-mediated functionality is present for 5-7 days in the bone marrow (or other tissues) during which the cell modulates its phenotype according to local conditions. It is suggested that to properly understand the nature of basophil behavior, a better understanding of its biology during maturation would be helpful. For example, one highly suggestive line of evidence for the relevance of understanding the maturation period is related to the change in basophil phenotype that occurs during treatment of patients with omalizumab. During this treatment, the intrinsic reactivity or sensitivity of the basophils is significantly increased despite, or perhaps because of, the dramatic reduction in FcεRI expression that accompanies this treatment. One of the critical signaling enzymes to increase expression selectively in basophils during treatment is SYK, which is one of the earliest signaling tyrosine kinases involved in translating the aggregation of FcεRI into secretion from the cell. Treatment with omalizumab increases SYK expression, and this observation focuses some attention of how SYK expression is regulated. It is possible that the key regulation occurs during maturation of the basophil. Regardless of the mechanisms operative in this particular treatment, understanding the process of maturation and the extrinsic factors that influence it may lead to better understanding of disease processes. Therefore, this chapter will discuss and present techniques to work with maturing human basophils.

The Absolute Basophil Count.

The absolute basophil count (cells/L) can be determined by manual counting of peripheral blood smears or using cell counting chambers as well as by automated hematology analyzers and fluorescence flow cytometry. Manual basophil counting of peripheral blood smears is currently regarded as the reference method, although the limitations of this method (distribution, observer, and statistical errors) are widely recognized. Automated hematology analyzers offer an advantage of larger numbers of counted cells and high throughput but are characterized by inconsistent analytical performance for basophil enumeration. Flow cytometric enumeration of circulating basophils using panels of monoclonal antibodies is being developed as novel candidate reference method for the absolute basophil count in peripheral blood. Basophil counting using fluorescence flow cytometry is characterized by high precision and statistical superiority. Emerging innovative technologies for absolute cell counts include imaging flow cytometry, mass cytometry, and on-chip blood counting, but their analytical performance for absolute basophil counts is yet to be established. Here, we describe various techniques for absolute basophil counting in peripheral blood including manual basophil counts in smears and hemocytometers and flow cytometric methodologies using double-platform, bead-based, and volumetric approaches.

Mast Cell and Basophil Cell Lines: A Compendium.

Mast cells and basophils play a crucial role during type I hypersensitivity reactions. However, despite efforts to elucidate their role in the pathogenesis of allergy and inflammation, our understanding of MC and basophil biology is still relatively scarce. The practical difficulty in obtaining a sufficient number of purified primary cells from biological samples has slowed down the process of reaching a full understanding of the physiological role of these functionally similar cell types. The establishment of several immortalized cell lines has been a useful tool to establish and perform sophisticated laboratory protocols that are impractical using primary cells. Continuous cell lines have been extensively used to investigate allergen/IgE-mediated cell activation, to elucidate the degranulation dynamics, to investigate structural and functional properties of the high-affinity receptor (FcεRI), and to test cell-stabilizing compounds. In this chapter, we review the most widely used and better-characterized MC and basophil cell lines, highlighting their advantages and drawbacks. It must be pointed out, however, that while cell lines represent a useful in vitro tool due to their easy manipulability and reduced culture costs, they often show aberrant characteristics which are not fully representative of primary cell physiology; results obtained with such cells therefore must be interpreted with due care.

Basophil Activation Techniques: Staining of Exteriorized Granule Matrix.

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.

Measurement and Functional Analysis of the Mas-Related G Protein-Coupled Receptor MRGPRX2 on Human Mast Cells and Basophils.

Basophils and mast cells (MCs) are important effector cells in the immune system. For a long time, it has been known that these cells can be activated though the cross-linking of IgE antibodies bound to their high-affinity receptor (FcεRI). However, evidence has accumulated suggesting that these cells can also be activated by various IgE-independent mechanisms. Occupation of MAS Related GPR Family Member X2 (MRGPRX2), a G protein-coupled receptor, is described as an alternative IgE-independent activation mechanism. Here we describe a flow cytometric technique to analyze MRGPRX2 expression and its functionality on cultured human MCs and conditioned basophils, that is, basophils with upregulated surface expression of MRGPRX2.

Detection of Mast Cells and Basophils by Immunohistochemistry.

Staining cells or tissues with basic dyes was the mainstay of mast cell and basophil detection methods for more than a century following the first identification of these cell types using such methods. These techniques have now been largely supplanted by immunohistochemical procedures with monoclonal antibodies directed against unique constituents of these cell types. Immunohistochemistry with antibodies specific for the granule protease tryptase provides a more sensitive and discriminating means for detecting mast cells than using the classical histochemical procedures, and using antibodies specific for products of basophils (2D7 antigen and basogranulin) has allowed detection of basophils that infiltrate into tissues. The application of immunohistochemistry to detect more than one marker in the same cell has underpinned concepts of mast cell heterogeneity based on differential expression of chymase and other proteases. The double labeling procedures employed have also provided a means for investigating the expression of cytokines and a range of other products. Protocols are here set out that have been used for immunohistochemical detection of mast cells and basophils and their subpopulations in human tissues. Consideration is given to pitfalls to avoid and to a range of alternative approaches.

Detection of Basophils and Other Granulocytes in Induced Sputum by Flow Cytometry.

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.

Gene Silencing Approaches in Mast Cells and Primary Human Basophils.

The ability to silence gene expression is an invaluable tool for elucidating the importance of intracellular signaling proteins which contribute to the effector functions of mast cells and basophils. However, primary mast cells and their terminally differentiated blood counterpart, basophils, pose a difficult challenge for gene silencing approaches given not only their state of maturation and difficulty to transfect but also because their functions are readily altered by cell handling conditions. Here, we describe a method using lipofection which has been successfully employed to silence gene expression using siRNA in human LAD2 mast cells as well as primary human basophils.

Identification of Murine Basophils by Flow Cytometry and Histology.

Here, we describe how murine basophils can be detected in vivo by flow cytometry and immunofluorescence staining. Basophils constitute a homogeneous population of CD4-CD19-CD49b+IgE+ cells in flow cytometric analysis. When IgE levels are low, one can also use anti-FcεRI or anti-CD200R3 antibodies instead of anti-IgE. For immunofluorescence staining, we use an anti-Mcpt8 antibody since Mcpt8 is a specific marker for murine basophils. We describe how to prepare the tissue to cut cryo-sections and how to perform the staining using a tyramide-based amplification kit.

Streamlining basophil activation testing to enable assay miniaturization and automation of sample preparation.

BACKGROUND: Numerous studies have demonstrated the capabilities of the basophil activation test (BAT) but various parameters such as a lack of standardization and a time consuming and labor intensive workflow continue to hinder the field to fully leverage the capabilities of this technique. When pediatric patients have to be considered, an additional limitation is related to blood volume consumption. OBJECTIVES: This work aimed at developing and characterizing a simplified and standardized whole-blood based BAT prototype procedure and at further assessing the feasibility of automating and miniaturizing the developed assay into a 96 well plate format. METHODS: A dry and room temperature stable reagent technology was used to simplify and standardize BAT. Under optimized conditions, EDTA anticoagulated whole blood samples of non-allergic and allergic donors (<24 h old) together with calcium containing buffer were added to ready-to-use dry reagent tubes or 96 well plates (negative controls, positive controls and allergen tests) containing a 5 color compensation-free antibody panel (CD45-KrO/CD3-PC7/CRTH2-A647/CD203c-PE/CD63-PB). Upon mixing and incubation at 37 °C for 15 min, erythrocytes were lysed and samples were analyzed by flow cytometry without further washing steps. While it is important to precisely control the incubation time to minimize the assay variability, herein, a 15 min incubation time was chosen as it provides a suitable compromise for both the magnitude of basophil activation and the quality of the staining. A Biomek NXP robotic platform (Beckman Coulter) was used for automation and both CD203c and CD63 levels were monitored to characterize basophil reactivity. RESULTS: This streamlined BAT protocol is no-wash, compensation free and only requires 4 pipetting steps to be completed. The assessment of assay performance characteristics showed wide applicability, satisfactory repeatability and a high degree of standardization as demonstrated by very low intra-assay and inter-operator variabilities (CVs < 10%). Leveraging these technical foundations, it was then proven that this new BAT procedure can easily be transposed into the 96 well plate format, thereby benefiting from a miniaturized format and full automation capabilities. When considering 8 dilution points to characterize the ex vivo basophil reactivity of a given whole blood sample, we found that as little as 5 µL of blood per point could be used. CONCLUSIONS: A whole blood based and simplified procedure for BAT is proposed. It relies on a dry antibody formulation technology and requires only a few manual steps to be completed. This procedure can also be transposed in a 96 well plate format, fully automated and miniaturized, when sample volume reduction, throughput increase or unattended sample preparation is required.