Bioinformatic analysis of eosinophil activity and its implications for model and target species.

Eosinophils are important immune cells that have been implicated in resistance to gastrointestinal nematode (GIN) infections in both naturally and experimentally infected sheep. Proteins of particular importance appear to be IgA-Fc alpha receptor (FcαRI), C-C chemokine receptor type 3 (CCR3), proteoglycan 3 (PRG3, major basic protein 2) and EPX (eosinophil peroxidase). We used known human nucleotide sequences to search the ruminant genomes, followed by translation to protein and sequence alignments to visualize differences between sequences and species. Where a sequence was retrieved for cow, but not for sheep and goat, this was used additionally as a reference sequence. In this review, we show that eosinophil function varies among host species. Consequently, investigations into the mechanisms of ruminant immune responses to GIN should be conducted using the natural host. Specifically, we address differences in protein sequence and structure for eosinophil proteins.

Mechanism of Siglec-8-mediated cell death in IL-5-activated eosinophils: role for reactive oxygen species-enhanced MEK/ERK activation.

BACKGROUND: Sialic acid-binding immunoglobulin-like lectin (Siglec)-8 is expressed on human eosinophils, where its ligation induces cell death. Paradoxically, Siglec-8-mediated cell death is markedly enhanced by the presence of the activation and survival factor IL-5 and becomes independent of caspase activity. OBJECTIVE: In this report we investigate the mechanism of Siglec-8-mediated cell death in activated eosinophils. METHODS: Human peripheral blood eosinophils were treated with agonistic anti-Siglec-8 antibody and IL-5, and cell death was determined by using flow cytometry and morphology. Phosphorylation of mitogen-activated protein kinase (MAPK) was determined by using phosphoLuminex, flow cytometry, and Western blotting. Reactive oxygen species (ROS) accumulation was determined by using dihydrorhodamine fluorescence. RESULTS: Costimulation with anti-Siglec-8 and IL-5 significantly increased the rate and proportion of cell death by means of necrosis accompanied by granule release compared with that seen after stimulation with anti-Siglec-8 alone, in which apoptosis predominated. Together with the caspase-independent mode of cell death in costimulated cells, these findings suggest the activation of a specific and distinct biochemical pathway of cell death during anti-Siglec-8/IL-5 costimulation. Phosphorylation of extracellular signal-regulated kinase (ERK) 1/2 and MAPK-ERK kinase (MEK) 1 was significantly enhanced and sustained in costimulated cells compared with that seen in cells stimulated with IL-5 alone; anti-Siglec-8 alone did not cause ERK1/2 phosphorylation. MEK1 inhibitors blocked anti-Siglec-8/IL-5-induced cell death. ROS accumulation was induced by Siglec-8 ligation in a MEK-independent manner. In contrast, an ROS inhibitor prevented the anti-Siglec-8/IL-5-induced enhancement of ERK phosphorylation and cell death. Exogenous ROS mimicked stimulation by anti-Siglec-8 and was sufficient to induce enhanced cell death in IL-5-treated cells. Collectively, these data suggest that the enhancement of ERK phosphorylation is downstream of ROS generation. CONCLUSIONS: In activated eosinophils ligation of Siglec-8 leads to ROS-dependent enhancement of IL-5-induced ERK phosphorylation, which results in a novel mode of biochemically regulated eosinophil cell death.

Animal-free production of hen egg ovalbumin in engineered Saccharomyces cerevisiae via precision fermentation.

To enable the sustainable production of ovalbumin (OVA) without relying on animal sources, the generally recognized as safe (GRAS) host Saccharomyces cerevisiae was used for the precision fermentation-based production of recombinant OVA. For this purpose, a signal peptide derived from EPX1, the most abundant extracellular protein produced by Pichia pastoris, was identified as a novel signal peptide for the efficient secretion of OVA in S. cerevisiae. To improve OVA secretion and cell growth, three helper proteins (PDI1, KAR2, and HAC1) present in the endoplasmic reticulum were expressed individually or in combination. Notably, the +P1/K2 strain coexpressing PDI1 and KAR2 with OVA produced 2 mg/L of OVA in the medium fraction; this value was 2.6-fold higher than the corresponding value for the control strain without helper proteins. Finally, a glucose-limited fed-batch fermentation process using the +P1/K2 strain yielded 132 mg/L of total OVA with 8 mg/L of extracellular OVA.

Eosinophil peroxidase in sputum represents a unique biomarker of airway eosinophilia.

BACKGROUND: Sputum eosinophilia has been shown to be a predictor of response to anti-eosinophil therapies in patients with airway diseases. However, quantitative cell counts and differentials of sputum are labor intensive. The objective of this study was to validate a novel ELISA-based assay of eosinophil peroxidase (EPX) in sputum as a rapid and reliable marker of airway eosinophils. METHODS: The utility of EPX-based ELISA as an eosinophil-specific assay was achieved through comparisons with sputum eosinophil differential counts in freshly prepared and archived patient samples from a variety of clinical settings. RESULTS: EPX levels in sputum correlated with eosinophil percentage (r(s) = 0.84) in asthma patients with varying degrees of airway eosinophilia. Significantly, unlike assays of other eosinophil granule proteins (e.g., ECP and EDN), which often detect the presence of these proteins even in asthma patients with neutrophilic bronchitis, EPX-based ELISA levels are not increased in this subset of asthma patients or in COPD patients lacking evidence of an airway eosinophilia. Moreover, sputum EPX was a surrogate marker of airway eosinophilia in other patient studies (e.g., allergen inhalation and treatment trials the anti-(IL-5) therapeutic Mepolizumab™). Finally, EPX levels in cytocentrifuged prepared sputum supernatants correlated with those from rapidly prepared noncentrifuged filtrates of sputum (r(s) = 0.94). CONCLUSION AND CLINICAL IMPLICATION: EPX-based ELISA is a valid, reliable, repeatable, and specific surrogate marker of eosinophils and/or eosinophil degranulation in the sputum of respiratory patients. The novel EPX assay is a valid and reproducible eosinophil-specific assay that can potentially be developed into a point-of-care assessment of eosinophil activity in airway secretions.

Activated Eosinophils Predict Longer Progression-Free Survival under Immune Checkpoint Inhibition in Melanoma.

Immune checkpoint inhibition (ICI) has yielded remarkable results in prolonging survival of metastatic melanoma patients but only a subset of individuals treated respond to therapy. Success of ICI treatment appears to depend on the number of tumor-infiltrating effector T-cells, which are known to be influenced by activated eosinophils. To verify the co-occurrence of activated eosinophils and T-cells in melanoma, immunofluorescence was performed in 285 primary or metastatic tumor tissue specimens from 118 patients. Moreover, eosinophil counts and activity markers such as eosinophil cationic protein (ECP) and eosinophil peroxidase (EPX) were measured in the serum before therapy start and before the 4th infusion of ICI in 45 metastatic unresected melanoma patients. We observed a positive correlation between increased tumor-infiltrating eosinophils and T-cells associated with delayed melanoma progression. High baseline levels of eosinophil count, serum ECP and EPX were linked to prolonged progression-free survival in metastatic melanoma. Our data provide first indications that activated eosinophils are related to the T-cell-inflamed tumor microenvironment and could be considered as potential future prognostic biomarkers in melanoma.

EPX: An R package for the ensemble of subsets of variables for highly unbalanced binary classification.

BACKGROUND AND OBJECTIVE: In binary classification problems with a rare class of interest, there is relatively little information available for the rare class to build a model. On the other hand, the number of useful variables to develop a model for classification can be high-dimensional. For example, in drug discovery, there are usually a very few bioactive compounds in a large chemical library, whereas thousands of potentially useful explanatory variables characterize a compound's chemical structure. The sparsity of information for the rare class of interest makes it difficult for the standard classification models to exploit the richness of the useful feature variables. Thus, the objective of this paper is to develop an R package which clusters the feature variables into diverse subsets to be aggregated into a powerful ensemble for the detection of a rare class object. METHODS: The ensemble of phalanxes (EPX) builds a classifier by exploiting the richness of feature variables using several diverse subsets of variables, called phalanxes, and outperforms many competitive state-of-the-art classification methods in terms of predictive ranking of the rare class of interest. RESULTS: We present an R package EPX which implements the algorithm to form the ensemble of phalanxes as well as its associated functions. We further show how the ensemble of phalanxes can be constructed using parallel computing to lower the computational burden given high-dimensional data. CONCLUSIONS: The R package EPX shows a flexible way of clustering feature variable space into smaller and diverse subsets of variables to develop an ensemble of phalanxes which better ranks a rare class object in a highly unbalanced two class classification problem. The ensemble EPX will be useful to detect the rare drug-like active biomolecules for development in drug discovery (Tomal et al., Mar. 2016) [1] and homologous proteins using similarity scores of amino acid sequences in protein homology (Tomal et al., 2019) [2]. The package EPX is freely available to download from CRAN (https://CRAN.R-project.org/package=EPX).

Eosinophil protein X and childhood asthma: A systematic review and meta-analysis.

BACKGROUND: There are no reference guidelines for health care providers regarding appropriate use and interpretation of urine eosinophil protein X (u-EPX) in clinical practice. Currently, there are no clear-cut clinical or laboratory parameters to diagnose asthma in young children. OBJECTIVE: In this study, we (1) systematically reviewed and qualitatively appraised the epidemiological evidence to determine diagnostic u-EPX cut points for pediatric asthma, and (2) performed a meta-analysis to provide u-EPX estimates for diagnosing pediatric asthma. METHODS: Research articles in literature were identified from PubMed/Medline and Web of Science databases from 1966 to August 2015. Children <18 years of age were included. Both serum and urine EPX were included. Twenty-seven studies met the inclusion criteria for the systematic review and nine studies for the meta-analysis. Details regarding EPX analyses, treatment efficacy, and outcomes were assessed. For meta-analyses, effect estimates were abstracted using standardized means. RESULTS: Over 70% of studies found a significant relationship between u-EPX and childhood asthma. There was 1.94 times higher standardized means of u-EPX among acute asthmatics compared to healthy controls (confidence interval [CI]: 1.67-2.22). Similarly, the difference in standardized means between asymptomatic asthmatics and healthy controls was 1.58 times higher (CI: 1.27-1.88). CONCLUSIONS AND CLINICAL RELEVANCE: Despite differences in sample sizes, EPX processing and measurement, and ages of children, a consistent trend of higher EPX levels with childhood asthma was revealed.

Homologous recombination into the eosinophil peroxidase locus generates a strain of mice expressing Cre recombinase exclusively in eosinophils.

Eosinophils are generally linked to innate host defense against helminths, as well as the pathologies associated with allergic diseases, such as asthma. Nonetheless, the activities of eosinophils remain poorly understood, which in turn, has prevented detailed definitions of their role(s) in health and disease. Homologous recombination in embryonic stem cells was used to insert a mammalianized Cre recombinase in the ORF encoding Epx. This knock-in strategy overcame previous inefficiencies associated with eosinophil-specific transgenic approaches and led to the development of a knock-in strain of mice (eoCRE), capable of mediating recombination of "floxed" reporter cassettes in >95% of peripheral blood eosinophils. We also showed that this Cre expression was limited exclusively to eosinophil-lineage committed cells with no evidence of Cre-mediated toxicity. The efficiency and specificity of Cre expression in eoCRE mice were demonstrated further in a cross with a knock-in mouse containing a "(flox-stop-flox)" DTA cassette at the ROSA26 locus, generating yet another novel, eosinophil-less strain of mice. The development of eoCRE mice represents a milestone in studies of eosinophil biology, permitting eosinophil-specific gene targeting and overexpression in the mouse as part of next-generation studies attempting to define eosinophil effector functions.

Hematopoietic cell populations in dolphin bone marrow: Analysis of colony formation and differentiation.

Bone marrow biopsy is useful for diagnosis of hematopoietic diseases. We have recently reported that bone marrow biopsy from the flipper might be useful for diagnosis of hematopoietic diseases in dolphins. In this study, to demonstrate whether biopsy from the flipper is useful for clinical diagnosis, we investigated the gene expression profiles and proliferation and differentiation of bone marrow mononuclear cell (BMMC) isolated from the humeral bone marrow of bottlenose dolphins. BMMC exhibited gene expression profiles considered to be characteristic of hematopoietic cells. Similarly, a colony forming unit assay showed that dolphin BMMC possessed vigorous colony forming ability. The proliferation of hematopoietic progenitor cells resulted in the formation of three types of colonies, containing neutrophils, monocytes/macrophages and eosinophils with or without megakaryocytes, all of which could be identified based on the morphological characteristics and gene expression profiles typically associated with hematopoietic markers. Thus, dolphin BMMCs from humeral bone marrow contain many hematopoietic progenitor cells, and bone marrow biopsy from the flipper is suggested useful for clinical diagnosis for the dolphins.