Dysregulation of sputum columnar epithelial cells and products in distinct asthma phenotypes

Machine learning-based screening of asthma biomarkers and related immune infiltration

Introduction

Asthma has an annual increasing morbidity rate and imposes a heavy social burden on public healthcare systems. The aim of this study was to use machine learning to identify asthma-specific genes for the prediction and diagnosis of asthma.

Methods

Differentially expressed genes (DEGs) related to asthma were identified by examining public sequencing data from the Gene Expression Omnibus, coupled with the support vector machine recursive feature elimination and least absolute shrinkage and selection operator regression model. Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), Gene set enrichment analysis and correlation analyses between gene and immune cell levels were performed. An ovalbumin-induced asthma mouse model was established, and eukaryotic reference transcriptome high-throughput sequencing was performed to identify genes expressed in mouse lung tissues.

Results

Thirteen specific asthma genes were obtained from our dataset analysis (LOC100132287, CEACAM5, PRR4, CPA3, POSTN, LYPD2, TCN1, SCGB3A1, NOS2, CLCA1, TPSAB1, CST1, and C7orf26). The GO analysis demonstrated that DEGs linked to asthma were primarily related to positive regulation of guanylate cyclase activity, gpi anchor binding, peptidase activity and arginine binding. The renin-angiotensin system, arginine biosynthesis and arginine and proline metabolism were the key KEGG pathways of DEGs. Additionally, the genes CEACAM5, PRR4, CPA3, POSTN, CLCA1, and CST1 expression levels were positively associated with plasma cells and resting mast cells. The mouse model revealed elevated nos2 and clca1 expression in the asthmatic mouse group compared with that in normal mice, which was consistent with the findings in asthmatic patients.

Discussion

This study identified new marker genes for the prediction and diagnosis of asthma, which can be further validated and applied clinically.

Increased expression of CSF1 in patients with eosinophilic asthma

BACKGROUND

The link between colony-stimulating factor 1 (CSF1) and asthma was reported recently. However, the role and mechanism of CSF1 in asthma remain poorly understood. In this study, we aimed to explore the expression and its potential mechanism of CSF1 in asthma.

METHODS

CSF1 expression in the airway samples from asthmatics and healthy controls were examined, then the correlations between CSF1 and eosinophilic indicators were analyzed. Subsequently, bronchial epithelial cells (BEAS-2B) with CSF1 overexpression and knockdown were constructed to investigate the potential molecular mechanism of CSF1. Finally, the effect of CSF1R inhibitor on STAT1 was investigated.

RESULTS

The expression of CSF1 was significantly increased in patients with asthma compared to healthy controls, especially in patients with severe and eosinophilic asthma. Upregulated CSF1 positively correlated with airway-increased eosinophil inflammation. In vitro, cytokines interleukin 13 (IL-13) and IL-33 can stimulate the upregulation of CSF1 expression. CSF1 overexpression enhanced p-CSF1R/CSF1R and p-STAT1/STAT1 expression, while knockdown CSF1 using anti-CSF1 siRNAs decreased p-CSF1R/CSF1R and p-STAT1/STAT1 expression. Furthermore, the inhibitor of CSF1R significantly decreased p-STAT1/STAT1 expression.

CONCLUSIONS

Sputum CSF1 may be involved in asthmatic airway eosinophil inflammation by interacting with CSF1R and further activating the STAT1 signaling. Interfering this potential pathway could serve as an anti-inflammatory therapy for asthma.

A novel assay for improved detection of sputum periostin in patients with asthma

BACKGROUND

Serum periostin associates with type-2 inflammation in asthmatic airways, but also reflects whole body periostin levels originating from multiple sources. Less is known about sputum periostin as a biomarker in asthma as detection levels are low using currently available periostin assays. We aimed to investigate detection of sputum periostin using ELISA assays targeting different periostin epitopes and relate levels to clinical characteristics.

METHODS

Two ELISA systems were developed using antibodies detecting whole periostin or cleavage products, the molecular weight and amino acid sequences of which were confirmed. The ELISA assays were applied to sputum from 80 patients with mild-to-moderate and severe asthma enrolled in the European, multi-center study BIOAIR. Results were related to clinical characteristics.

RESULTS

Sputum was found to contain smaller periostin fragments, possibly due to proteolytic cleavage at a C-terminal site. Comparing ELISA methodology using antibodies against cleaved versus whole periostin revealed detectable levels in 90% versus 44% of sputum samples respectively. Sputum periostin showed associations with blood and sputum eosinophils. Furthermore, sputum, but not serum, periostin correlated with reduced lung function and sputum IL-13 and was reduced by oral corticosteroid treatment.

CONCLUSIONS

We present an ELISA method for improved analysis of sputum periostin by detecting cleavage products of the periostin protein. Using this assay, sputum periostin was detectable and associated with more disease-relevant parameters in asthma than serum periostin. Sputum periostin is worth considering as a phenotype-specific biomarker in asthma as its proximity to the airways may eliminate some of the confounding factors known to affect serum periostin.

Refractory neutrophilic asthma and ciliary genes

BACKGROUND

Refractory asthma (RA) remains poorly controlled, resulting in high health care utilization despite guideline-based therapies. Patients with RA manifest higher neutrophilia as a result of increased airway inflammation and subclinical infection, the underlying mechanisms of which remain unclear.

OBJECTIVE

We sought to characterize and clinically correlate gene expression differences between refractory and nonrefractory (NR) asthma to uncover molecular mechanisms driving group distinctions.

METHODS

Microarray gene expression of paired airway epithelial brush and endobronchial biopsy samples was compared between 60 RA and 30 NR subjects. Subjects were hierarchically clustered to identify subgroups of RA, and biochemical and clinical traits (airway inflammatory molecules, respiratory pathogens, chest imaging) were compared between groups. Weighted gene correlation network analysis was used to identify coexpressed gene modules. Module expression scores were compared between groups using linear regression, controlling for age, sex, and body mass index.

RESULTS

Differential gene expression analysis showed upregulation of proneutrophilic and downregulation of ciliary function genes/pathways in RA compared to NR. A subgroup of RA with downregulated ciliary gene expression had increased levels of subclinical infections, airway neutrophilia, and eosinophilia as well as higher chest imaging mucus burden compared to other RA, the dominant differences between RA and NR. Weighted gene correlation network analysis identified gene modules related to ciliary function, which were downregulated in RA and were associated with lower pulmonary function and higher airway wall thickness/inflammation, markers of poorer asthma control.

CONCLUSIONS

Identification of a novel ciliary-deficient subgroup of RA suggests that diminished mucociliary clearance may underlie repeated asthma exacerbations despite adequate treatment, necessitating further exploration of function, mechanism, and therapeutics.

Development of a prognostic nomogram based on an eight-gene signature for esophageal squamous cell carcinoma by weighted gene co-expression network analysis (WGCNA)

Background

Esophageal squamous cell carcinoma (ESCC) is a highly aggressive malignant tumor. This study aims to develop a robust prognostic model for ESCC.

Methods

Expression profiles of ESCC were downloaded from the Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) databases. Co-expressed modules were constructed by weighted gene co-expression network analysis (WGCNA). Differentially expressed genes (DEGs) between ESCC and normal samples were identified with the screening criteria of adjusted P value <0.05 and log |fold change (FC)| >1. After univariate and multivariate Cox regression analysis, an 8-gene module was constructed. A receiver operating characteristic (ROC) curve for overall survival (OS) was used to assess the prediction efficacy of the risk score. A nomogram was developed based on the risk score, age, gender, and stage for 1-, 2- and 3-year survival. The potential biological functions and pathways of the 8 genes were predicted using the Metascape database.

Results

The 2 ESCC-related co-expression modules were built via WGCNA. Among all DEGs, 55 survival-related genes were identified for ESCC. Based on these genes, an 8-gene module was constructed, composed of CFAP53, FCGR2A, FCGR3A, GNGT1, IGF2, LINC01524, MAGEA3, and MAGEA6. The area under the curve (AUC) was 0.961, suggesting that the risk score could effectively predict the OS of patients with ESCC. Furthermore, the nomogram exhibited high accuracy in predicting the survival rate of ESCC patients at 1, 2, and 3 years. These genes were mainly involved in ESCC-related pathways such as extracellular matrix organization, collagen formation, and blood vessel development.

Conclusions

Our nomogram based on the 8-gene risk score could be a reliable prognostic tool for ESCC.

Profiling the immune response to Mycobacterium tuberculosis Beijing family infection: a perspective from the transcriptome

Tuberculosis continues to be an important public health problem. Particularly considering Beijing-family strains of Mycobacterium tuberculosis, which have been associated with drug-resistance and hypervirulence. The Beijing-like SIT190 (BL) is the most prevalent Beijing strain in Colombia. The pathogenic mechanism and immune response against this pathogen is unknown. Thus, we compared the course of pulmonary TB in BALB/c mice infected with Classical-Beijing strain 391 and BL strain 323. The disease course was different among infected animals with Classical-Beijing and BL strain. Mice infected with BL had a 100% mortality at 45 days post-infection (dpi), with high bacillary loads and massive pneumonia, whereas infected animals with Classical-Beijing survived until 60 dpi and showed extensive pneumonia and necrosis. Lung RNA extraction was carried out at early (day 3 dpi), intermediate (day 14 dpi), and late (days 28 and 60 dpi) time points of infection. Transcriptional analysis of infected mice with Classical-Beijing showed several over-expressed genes, associated with a pro-inflammatory profile, including those for coding for CCL3 and CCL4 chemokines, both biomarkers of disease severity. Conversely, mice infected with BL displayed a profile which included the over-expression of several genes associated with immune-suppression, including Nkiras, Dleu2, and Sphk2, highlighting an anti-inflammatory milieu which would allow high bacterial replication followed by an intense inflammatory response. In summary, both Beijing strains induced a non-protective immune response which induced extensive tissue damage, BL strain induced rapidly extensive pneumonia and death, whereas Classical-Beijing strain produced slower extensive pneumonia later associated with extensive necrosis.

Asthma phenotypes and endotypes: a systematic review

INTRODUCTION

Asthma is a complex disorder characterized by expiratory airflow limitation, wheeze, shortness of breath, chest tightness and cough, which can vary over time and in intensity. Being highly heterogeneous, asthma was characterized and classified in several asthma phenotypes and endotypes from 1947 until today. The present systematic review aims to summarize and describe evidence that was published in the last ten years in the field of asthma phenotyping and endotyping.

EVIDENCE ACQUISITION

The systematic review resumed high-quality evidence (clinical trials and randomized control trials) retrieved on MEDLINE and EMBASE databanks and involving adult asthmatic populations. Analyses of literature were conducted according to PRISMA and CASP guidelines.

EVIDENCE SYNTHESIS

Querying MEDLINE and EMBASE databanks, 5019 and 12261 entries were retrieved, respectively. Applying limitations for year of publication, age of participants, and type of publication, the search results were reduced to 98 and 132 articles, respectively. After data abstraction and resolution of duplications, only 50 articles were further evaluated. The research products were then classified first in macro-areas of interest (phenotypes or endotypes) and then in detailed micro-areas.

CONCLUSIONS

This systematic review overviews the principal findings available from high-quality literature in the last decade concerning asthma phenotypes and endotypes. Asthma has been described from different points of view, characterizing symptoms, microbiota composition, comorbidities, viral infections, and airway and/or systemic inflammatory status. The comprehension of precise mechanisms underlying asthma pathogenesis is thereby the basis for the development of novel therapeutic strategies, likely essential to the development of precision medicine.

Structure and function of small airways in asthma patients revisited

Small airways (<2 mm in diameter) are probably involved across almost all asthma severities and they show proportionally more structural and functional abnormalities with increasing asthma severity. The structural and functional alterations of the epithelium, extracellular matrix and airway smooth muscle in small airways of people with asthma have been described over many years using in vitro studies, animal models or imaging and modelling methods. The purpose of this review was to provide an overview of these observations and to outline several potential pathophysiological mechanisms regarding the role of small airways in asthma.

Periostin: contributor to abnormal airway epithelial function in asthma?

Periostin (POSTN) may serve as a biomarker for Type-2 mediated eosinophilic airway inflammation in asthma. We hypothesised that a Type-2 cytokine, interleukin (IL)-13, induces airway epithelial expression of POSTN, which in turn contributes to epithelial changes observed in asthma.We studied the effect of IL-13 on POSTN expression in BEAS-2B and air-liquid interface differentiated primary bronchial epithelial cells (PBECs). Additionally, the effects of recombinant human POSTN on epithelial-to-mesenchymal transition (EMT) markers and mucin genes were assessed. POSTN single cell gene expression and protein levels were analysed in bronchial biopsies and induced sputum from asthma patients and healthy controls.IL-13 increased POSTN expression in both cell types and this was accompanied by EMT-related features in BEAS-2B. In air-liquid interface differentiated PBECs, IL-13 increased POSTN basolateral and apical release. Apical administration of POSTN increased the expression of MMP-9, MUC5B and MUC5AC In bronchial biopsies, POSTN expression was mainly confined to basal epithelial cells, ionocytes, endothelial cells and fibroblasts, showing higher expression in basal epithelial cells from asthma patients versus those from controls. A higher level of POSTN protein expression in epithelial and subepithelial layers was confirmed in bronchial biopsies from asthma patients when compared to healthy controls. Although sputum POSTN levels were not higher in asthma, levels correlated with eosinophil numbers and with the coughing-up of mucus.POSTN expression is increased by IL-13 in bronchial epithelial cells and is higher in bronchial biopsies from asthma patients. This may have important consequences, as administration of POSTN increases epithelial expression of mucin genes, supporting the relationship of POSTN with Type-2 mediated asthma and mucus secretion.

Effect of Montelukast Sodium and Graphene Oxide Nanomaterials on Mouse Asthma Model

Because some asthma patients have different types of inflammatory cells in their bodies, they cannot get relief with traditional drugs. However, the nano drug delivery system can realize efficient drug delivery, inflammatory cells and intracellular targeting, and the apoptosis of inflammatory cells. This article aims to comprehensively evaluate the effects of montelukast sodium combined with graphene oxide nanomaterials on improving the clinical symptoms and airway inflammation of children with bronchial asthma, with a view to further improving the clinical treatment of children with bronchial asthma. The results show that montelukast sodium can improve lung function in patients with asthma, and also has important effects such as anti-inflammatory and regulating immune function. After exposure to graphene oxide, the level of oxidative stress in mice increased with brightness and humidity, demonstrating the role of T oxidative stress in the development of asthma. In addition, nanocarriers assist co-loaded drugs to deepen and enrich the pulmonary inflammation site, further achieving effective mitochondrial targeted drug delivery, thereby enhancing the inhibitory effect of anti-apoptotic proteins, leading to inflammatory cell apoptosis.

Developments allergy in 2019 through the eyes of Clinical and Experimental Allergy, Part II clinical allergy

In the second of two linked articles, we describe the development in clinical as described by Clinical & Experimental Allergy and other journals in 2019. Epidemiology, clinical allergy, asthma and rhinitis are all covered. In this article, we described the development in the field of allergy as described by Clinical and Experimental Allergy in 2019. Epidemiology, clinical allergy, asthma and rhinitis are all covered.