Cystatin SN upregulation in patients with seasonal allergic rhinitis

Eosinophilic Chronic Rhinosinusitis and Pathogenic Role of Protease

Chronic rhinosinusitis (CRS) is an inflammation of the nasal and paranasal sinus mucosa, and eosinophilic CRS (eCRS) is a subtype characterized by significant eosinophil infiltration and immune response by T-helper-2 cells. The pathogenesis of eCRS is heterogeneous and involves various environmental and host factors. Proteases from external sources, such as mites, fungi, and bacteria, have been implicated in inducing type 2 inflammatory reactions. The balance between these proteases and endogenous protease inhibitors (EPIs) is considered important, and their imbalance can potentially lead to type 2 inflammatory reactions, such as eCRS. In this review, we discuss various mechanisms by which exogenous proteases influence eCRS and highlight the emerging role of endogenous protease inhibitors in eCRS pathogenesis.

Cystatin SN in type 2 inflammatory airway diseases

Cystatin SN, encoded by CST1, belongs to the type 2 (T2) cystatin protein superfamily. In the past decade, several publications have highlighted the association between cystatin SN and inflammatory airway diseases including chronic rhinosinusitis, rhinitis, asthma, chronic obstructive pulmonary disease, and chronic hypersensitivity pneumonitis. It is, therefore, crucial to understand the role of cystatin SN in the wider context of T2 inflammatory diseases. Here, we review the expression of cystatin SN in airway-related diseases with different endotypes. We also emphasize the physiological and pathological roles of cystatin SN. Physiologically, cystatin SN protects host tissues from destructive proteolysis by cysteine proteases present in the external environment or produced via internal dysregulated expression. Pathologically, the secretion of cystatin SN from airway epithelial cells initiates and amplifies T2 immunity and subsequently leads to disease. We further discuss the development of cystatin SN as a T2 immunity marker that can be monitored noninvasively and assist in airway disease management. The discovery, biology, and inhibition capability are also introduced to better understand the role of cystatin SN in airway diseases.

Transcriptomic analysis of asthma and allergic rhinitis reveals CST1 as a biomarker of unified airways

Background

Allergic rhinitis (AR) is an important risk factor for the development of asthma. The "unified airway" theory considers the upper and lower airways as a morphological and functional whole. However, studies exploring biomarkers linking the upper and lower airways in allergic disease are lacking, which may provide insight into the mechanisms underlying AR comorbid asthma.

Purpose

To integrate bioinformatics techniques to explore biomarkers in airway allergic diseases, and to provide a molecular etiology profile for preventing the development of asthma in AR patients.

Methods

Biomarkers were screened by identifying key genes common between AR and asthma through WGCNA and differential gene analysis. GO and KEGG analyses were performed using DAVID. Immuno-infiltration analysis was performed by CIBERSORTx. The predictive value of CST1 to distinguish Th2-high asthma was determined by ROC curves. GSEA was used to analyze the signaling pathways involved in CST1. TargetScan and miRNet were combined with GSE142237 to construct ceRNA network. CMap was used to explore potential therapeutic drugs.

Results

Validation of datasets showed that CST1 was the only gene that was up-regulated in both upper and lower airways in patients with AR and asthma, and correlation heatmaps showed that CST1 was the gene with the highest sum of correlation coefficients. GO and KEGG analysis demonstrated that the lower airways of AR patients were mainly involved in inflammatory and immune responses, similar to asthma. Immune infiltration showed that CST1 was mainly positively correlated with activated CD4 memory T cells. According to the ROC curve, CST1 showed excellent diagnostic efficiency for Th2-high asthma. GSEA indicated that CST1 was involved in the FcϵRI signaling pathway and O-glycan biosynthesis. A ceRNA network including the lncRNAs KCNQ1OT1 and NEAT1 was constructed. Four drugs, including verrucarin-A, had the potential to prevent the development of asthma in AR patients. In addition, corticosteroids were found to downregulate CST1 expression.

Conclusion

CST1 plays a key role in the development of AR comorbid asthma and may be a biomarker for airway allergic diseases. Targeted treatment of CST1 has the potential to prevent the development of asthma in AR patients and deserves further study.

[Research progress of biomarkers in nasal secretions in endotypes diagnosis and clinical application of chronic rhinosinusitis]

With the development of studies on the endotypes of chronic rhinosinusitis （CRS） and the biomarkers of nasal secretions, the studies of CRS endotypes based on nasal secretion have become more abundant. This paper summarizes the endotypes classification of CRS, the collection methods of nasal secretion and the nasal secretion biomarkers related to the endotypes of CRS, in order to provide a reference for establishing the corresponding endotypes of CRS based on the nasal secretion biomarkers.

Cystatin SN is a potent upstream initiator of epithelial-derived type 2 inflammation in chronic rhinosinusitis

BACKGROUND

Cystatin SN (CST1) and cystatin SA (CST2) are cysteine protease inhibitors that protect against allergen, viral, and bacterial proteases. Cystatins are overexpressed in the setting of allergic rhinitis and chronic rhinosinusitis with nasal polyps (CRSwNP); however, their role in promoting type 2 inflammation remains poorly characterized.

OBJECTIVE

The purpose of this study was to use integrated poly-omics and a murine exposure model to explore the link between cystatin overexpression in CRSwNP and type 2 inflammation.

METHODS

In this institutional review board- and institutional animal care and use committee-approved study, we compared tissue, exosome, and mucus CST1 and CST2 between CRSwNP and controls (n = 10 per group) by using matched whole exome sequencing, transcriptomic, proteomic, posttranslational modification, histologic, functional, and bioinformatic analyses. C57/BL6 mice were dosed with 3.9 μg/mL of CST1 or PBS intranasally for 5 to 18 days in the presence or absence of epithelial ABCB1a knockdown. Inflammatory cytokines were quantified by using Quansys multiplex assays or ELISAs.

RESULTS

Of the 1305 proteins quantified, CST1 and CST2 were among the most overexpressed protease inhibitors in tissue, exosome, and mucus samples; they were localized to the epithelial layer. Multiple posttranslational modifications were identified in the polyp tissue. Exosomal CST1 and CST2 were strongly and significantly correlated with eosinophils and Lund-Mackay scores. Murine type 2 cytokine secretion and TH2 cell infiltration increased in a time-dependent manner following CST1 exposure and was abrogated by epithelial knockdown of ABCB1a, a regulator of epithelial cytokine secretion.

CONCLUSION

CST1 is a potent upstream initiator of epithelial-derived type 2 inflammation in CRSwNP. Therapeutic strategies targeting CST activity and its associated posttranslational modifications deserve further interrogation.

Shukri N, Wong KK, Mohd Ashari NS. Zonula occludens-1 expression is reduced in nasal epithelial cells of allergic rhinitis patients

Allergic rhinitis (AR) is a common allergic disease characterized by disruption of nasal epithelial barrier. In this study, we investigated the mRNA expression of zonula occludens-1 (ZO-1), ZO-2 and ZO-3 and histone deacetylase 1 (HDAC1) and HDAC2 in AR patients compared to healthy controls. RNA samples were extracted from nasal epithelial cells of house dust mites (HDMs)-sensitized AR patients and healthy controls (n = 28 in each group). The RNAs were reverse transcribed into cDNAs for measurement of ZO-1, ZO-2, ZO-3, HDAC1 and HDAC2 expression levels by quantitative PCR. The mRNA expression of ZO-1 was significantly decreased in AR patients compared to healthy controls (p = 0.010). No significant difference was observed in the expression levels of ZO-2, ZO-3, HDAC1 and HDAC2 in AR patients compared to healthy controls. We found significant associations of higher HDAC2 levels in AR patients with lower frequency of changing bedsheet (p = 0.043) and with AR patients sensitized to Dermatophagoides farinae (p = 0.041). Higher expression of ZO-2 was observed in AR patients who had pets (p = 0.007). In conclusion, our data indicated that ZO-1 expression was lower in AR patients contributing to decreased integrity of nasal epithelial barrier integrity, and HDAC2 may be involved in the pathogenesis of the disease.

Cathepsin S Contributes to Lung Inflammation in Acute Respiratory Distress Syndrome

Rationale: Although the cysteine protease cathepsin S has been implicated in the pathogenesis of several inflammatory lung diseases, its role has not been examined in the context of acute respiratory distress syndrome, a condition that still lacks specific and effective pharmacological treatments. Objectives: To characterize the status of cathepsin S in acute lung inflammation and examine the role of cathepsin S in disease pathogenesis. Methods: Human and mouse model BAL fluid samples were analyzed for the presence and activity of cathepsin S and its endogenous inhibitors. Recombinant cathepsin S was instilled directly into the lungs of mice. The effects of cathepsin S knockout and pharmacological inhibition were examined in two models of acute lung injury. Protease-activated receptor-1 antagonism was used to test a possible mechanism for cathepsin S-mediated inflammation. Measurements and Main Results: Pulmonary cathepsin S concentrations and activity were elevated in acute respiratory distress syndrome, a phenotype possibly exacerbated by the loss of the endogenous antiprotease cystatin SN. Direct cathepsin S instillation into the lungs induced key pathologies of acute respiratory distress syndrome, including neutrophilia and alveolar leakage. Conversely, in murine models of acute lung injury, genetic knockdown and prophylactic or therapeutic inhibition of cathepsin S reduced neutrophil recruitment and protein leakage. Cathepsin S may partly mediate its pathogenic effects via protease-activated receptor-1, because antagonism of this receptor abrogated cathepsin S-induced airway inflammation. Conclusions: Cathepsin S contributes to acute lung injury and may represent a novel therapeutic target for acute respiratory distress syndrome.

Identification of key genes in allergic rhinitis by bioinformatics analysis

Objective

This study aimed to explore the potential molecular mechanism of allergic rhinitis (AR) and identify gene signatures by analyzing microarray data using bioinformatics methods.

Methods

The dataset GSE19187 was used to screen differentially expressed genes (DEGs) between samples from patients with AR and healthy controls. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were applied for the DEGs. Subsequently, a protein–protein interaction (PPI) network was constructed to identify hub genes. GSE44037 and GSE43523 datasets were screened to validate critical genes.

Results

A total of 156 DEGs were identified. GO analysis verified that the DEGs were enriched in antigen processing and presentation, the immune response, and antigen binding. KEGG analysis demonstrated that the DEGs were enriched in Staphylococcus aureus infection, rheumatoid arthritis, and allograft rejection. PPI network and module analysis predicted seven hub genes, of which six (CD44, HLA-DPA1, HLA-DRB1, HLA-DRB5, MUC5B, and CD274) were identified in the validation dataset.

Conclusions

Our findings suggest that hub genes play important roles in the development of AR.

Nasal upregulation of CST1 in dog-sensitised children with severe allergic airway disease

Background

The clinical presentation of children sensitised to dog dander varies from asymptomatic to severe allergic airway disease, but the genetic mechanisms underlying these differences are not clear. The objective of the present study was to investigate nasal transcriptomic profiles associated with dog dander sensitisation in school children and to reveal clinical symptoms related with these profiles.

Methods

RNA was extracted from nasal epithelial cell brushings of children sensitised to dog dander and healthy controls. Blood sample analyses included IgE against dog dander, dog allergen molecules, other airborne and food allergens, basophil activation and white blood cell counts. Clinical history of asthma and rhinitis was recorded, and lung function was assessed (spirometry, methacholine provocation and exhaled nitric oxide fraction).

Results

The most overexpressed gene in children sensitised to dog dander compared to healthy controls was CST1, coding for Cystatin 1. A cluster of these children with enhanced CST1 expression showed lower forced expiratory volume in 1 s, increased bronchial hyperreactivity, pronounced eosinophilia and higher basophil allergen threshold sensitivity compared with other children sensitised to dog dander. In addition, multi-sensitisation to lipocalins was more common in this group.

Conclusions

Overexpression of CST1 is associated with more severe allergic airway disease in children sensitised to dog dander. CST1 is thus a possible biomarker of the severity of allergic airway disease and a possible therapeutic target for the future treatment of airborne allergy.

Prognostic and pharmacologic value of cystatin SN for chronic rhinosinusitis with nasal polyps

BACKGROUND

Integrated care pathways improve the management of patients with chronic rhinosinusitis with nasal polyps (CRSwNP). The application of integrated care pathways requires development of endotype-based biomarkers to stratify patients. The value of cytokines and markers induced by cytokines for the management of CRSwNP is largely unknown.

OBJECTIVES

Our aim was to determine the prognostic and pharmacologic value of type 2, non-type 2 cytokines, and markers associated with type 2 inflammation, including CCL26, periostin, and cystatin SN, in nasal secretions for CRSwNP.

METHODS

This retrospective study assigned 151 patients with CRSwNP to the discovery and validation phases. Concentrations of cytokines, CCL26, periostin, and cystatin SN in nasal secretions were determined by using Luminex and ELISA. Predictive significance was assessed with receiver-operating characteristic curves. Survival analysis was performed by using Kaplan-Meier curves and Cox regression models.

RESULTS

Cystatin SN was an independent predictor of the uncontrolled status of CRSwNP over a 2-year follow-up after adjustment for other risk factors (hazard ratio = 1.168 and 1.132 in the discovery and validation phases, respectively; both P < .001). Patients with high cystatin SN concentrations presented with a faster onset and higher rate of uncontrolled status than did those with low levels (P < .001). Enhanced medical treatment for patients with high cystatin SN levels postponed the uncontrolled status in the discovery (P = .016) and validation (P = .002) phases but did not completely abolish it by the end of the follow-up.

CONCLUSION

Cystatin SN levels in nasal secretions hold strong prognostic value and can facilitate medical instructions for managing CRSwNP.

Diagnosis and treatment of non-allergic rhinitis: focus on immunologic mechanisms

INTRODUCTION

Non-allergic rhinitis (NAR) is a heterogeneous nasal disease with high global prevalence. NAR can be subclassified as nonallergic rhinitis with eosinophilia syndrome (NARES), vasomotor rhinitis (VMR), and local allergic rhinitis (LAR). Although the precise factors involved in the etiology of NAR are not clear, there is evidence that immunological factors play an important role in the pathogenesis of NAR. This review provides a comprehensive overview of the immunological and neurogenic mechanisms involved in the diagnosis and treatment of NAR.

AREAS COVERED

This review provides a comprehensive overview of the immunological basis of diagnostic and treatment strategies for NARES, VMR, and LAR. In particular, recently documented molecular and immunological mechanisms of NAR are discussed, which may help to better understand the mechanisms underlying the pathologies of the different endotypes of NAR.

EXPERT OPINION

An increasing number of studies investigating the pathogenesis of NAR suggest that the immunological mechanisms underlying the different subtypes of NAR vary greatly, and are still not fully understood to accurately diagnose these subtypes. Thus, further studies should focus on making diagnosis and treatment of NAR more precise, safe, and effective. A better understanding of the immunological mechanisms involved in NAR should help in the discovery of new diagnostic and treatment strategies.

Salivary cystatin SN is a factor predicting iron bioavailability after phytic acid rich meals in female participants

Phytic acid is an inhibitor of iron bioavailability, but it has been suggested that individuals may adapt to phytic acid over time, and that the salivary protein, cystatin SN, may be involved. This study evaluated the relationship between human cystatin SN levels and iron bioavailability after a phytic acid rich meal. Three groups of ten women consumed meals with: (1) 500 mg phytate sprinkles, (2) 500 mg phytate capsules, or (3) no phytic acid. Iron bioavailability was measured by the mealtime percentage of maximum iron recovery; cystatin SN was measured pre-and post-meal by enzyme-linked immunosorbent assay. Pre-to-post meal cystatin SN was positively correlated with improved iron bioavailability in group 1. Pre-to-post meal cystatin SN was correlated with improved iron absorption in groups 1 and 2. Cystatin SN recovery after phytic acid rich meals may be a physiological factor predicting iron bioavailability.

Gene Expression Analysis by Real-Time PCR in Nasal Brushings of Adult Patients with Allergic Rhinitis, Suspected Allergic Rhinitis, and Nonallergic Rhinitis

BACKGROUND

Epithelial gene expression in allergic rhinitis patients has been evaluated by microarray. However, gene expression in patients with nonallergic rhinitis and suspected allergic rhinitis who reported allergen-related nasal symptoms but presented a negative atopic test was unknown.

OBJECTIVES

The aim of this study was to observe and compare epithelial gene expression in patients with allergic rhinitis, suspected allergic rhinitis, and nonallergic rhinitis.

METHODS

Nasal brushings were collected from healthy controls and from patients with allergic rhinitis, suspected allergic rhinitis, and nonallergic rhinitis. The expressions of 20 genes selected from a previous microarray study were measured by real-time PCR. Associations of these genes with allergen type, disease duration and severity, the grade of nasal smear eosinophilia, and serum total IgE were analyzed.

RESULTS

Twelve genes were confirmed to be upregulated in current adult allergic rhinitis patients allergic to multiple allergens, and 10 of them were also increased in the suspected allergic rhinitis and nonallergic rhinitis groups. TFF3 and ITLN1 expressions were increased in allergic rhinitis and suspected allergic rhinitis, but not nonallergic rhinitis. Different expressions between the allergic rhinitis and nonallergic rhinitis groups were found for 3 genes: CST1, TFF3, and ITLN1. In the allergic rhinitis patients, all 12 genes were upregulated in the seasonal and perennial groups; 9 of these 12 genes were also upregulated in the mixed group. In suspected allergic rhinitis patients, all 12 genes were upregulated in the perennial group; 8 of these 12 genes were also upregulated in the seasonal group and only 5 in the mixed group. No gene expression was associated with disease duration and serum total IgE. GCNT3 was positively correlated with the grade of nasal smear eosinophilia in the suspected allergic rhinitis group. Different genes were found to be associated with disease severity in different rhinitis groups.

CONCLUSIONS

Patients with allergic rhinitis, suspected allergic rhinitis, and nonallergic rhinitis showed much similarity with regard to epithelial gene expression; most genes were related to Th2 inflammation. CST1, TFF3, and ITLN1 might have the ability to differentiate allergic rhinitis from nonallergic rhinitis. Understanding the mechanisms underlying different types of rhinitis may be helpful for rhinitis diagnosis and treatment.

Artemisia annua-sublingual immunotherapy for seasonal allergic rhinitis: A randomized controlled trial

BACKGROUND

Artemisia annua is an important autumnal pollen allergen for seasonal allergic rhinitis (SAR) in northern China. To date, no study has investigated allergen immunotherapy with A annua. We aimed to investigate the efficacy and mechanisms underlying A annua-sublingual immunotherapy (SLIT).

METHODS

This was a randomized, double-blind, placebo-controlled phase III clinical trial involving 71 SAR patients, randomized to SLIT with A annua extract (n = 47) or placebo (n = 24) for 32 weeks. Total nasal symptom score (TNSS; primary clinical end point) was evaluated at baseline (peak pollen phase (PPP) in the previous year), initiation of A annua-SLIT, 1st PPP during SLIT, end of SLIT and 2nd PPP during follow-up. Blood samples and nasal secretions were collected at beginning and after SLIT for assessment of T cells and inflammatory mediators. Safety was assessed according to adverse events (AEs) reported.

RESULTS

Artemisia annua-SLIT significantly reduced TNSS to a greater level from baseline (from 9.45 ± 1.68 to 6.16 ± 2.27) than placebo (from 9.29 ± 2.09 to 9.05 ± 2.40) at the 1st PPP (P < .001) and sustained the improvement in symptoms throughout to the 2nd PPP. Preseasonal A annua-SLIT for 16 weeks significantly decreased Th2 cells, increased nTreg and Tr1 cells in blood; and increased cystatin 1 (CST1) in nasal secretion after 16 and 32 weeks compared with pretreatment. Overall, 17/47 patients experienced mild local AEs and 2 patients mild systemic AEs, after A annua-SLIT.

CONCLUSION

Artemisia annua-SLIT is an efficacious and safe treatment in patients with A annua SAR.

Diagnosis and management of nonallergic rhinitis with eosinophilia syndrome using cystatin SN together with symptoms

Background

The diagnosis and treatment of nonallergic rhinitis with eosinophilia syndrome (NARES) remain controversial. The aim of this study was to evaluate whether Cystatin SN together with symptoms can be used to diagnose NARES and to measure the efficiency of medical treatment.

Methods

Seventy-five patients with chronic rhinitis (CR) and 18 control subjects were enrolled. Their clinical characteristics were reviewed and laboratory parameters were evaluated. The concentration of Cystatin SN in nasal secretions was determined using the enzyme-linked immunosorbent assay. The histological assessment of Cystatin SN in the nasal mucosa was conducted by hematoxylin and eosin staining. The logistic regression and receiver operating characteristic curves were used to assess the predictive value of parameters for NARES.

Results

Nasal obstruction, sneezing, loss of smell, and total visual analogue scale (VAS) score were significantly different among the patients with CR. In particular, olfaction score was higher in patients with NARES than in those without NARES (AR, LAR, or IR). Similarly, the Cystatin SN level was significantly different between the control subjects and patients with CR. After treatment for 2 weeks, the Cystatin SN level and VAS score were significantly decreased in the NARES group. The accuracy of Cystatin SN together with local sIgE and loss of smell to diagnose NARES was up to 0.987 (sensitivity, 100%; specificity, 93.1%).

Conclusions

Cystatin SN with local sIgE and loss of smell may serve as one of the reliable and alternative biomarkers for the diagnosis of NARES and be used to evaluate disease severity and NARES treatment efficacy.

Assessing the unified airway hypothesis in children via transcriptional profiling of the airway epithelium

BACKGROUND

Emerging evidence suggests that disease vulnerability is expressed throughout the airways, the so-called unified airway hypothesis, but the evidence to support this is predominantly indirect.

OBJECTIVES

We sought to establish the transcriptomic profiles of the upper and lower airways and determine their level of similarity irrespective of airway symptoms (wheeze) and allergy.

METHODS

We performed RNA sequencing on upper and lower airway epithelial cells from 63 children with or without wheeze and accompanying atopy, using differential gene expression and gene coexpression analyses to determine transcriptional similarity.

RESULTS

We observed approximately 91% homology in the expressed genes between the 2 sites. When coexpressed genes were grouped into modules relating to biological functions, all were found to be conserved between the 2 regions, resulting in a consensus network containing 16 modules associated with ribosomal function, metabolism, gene expression, mitochondrial activity, and antiviral responses through IFN activity. Although symptom-associated gene expression changes were more prominent in the lower airway, they were reflected in nasal epithelium and included IL-1 receptor like 1, prostaglandin-endoperoxide synthase 1, CCL26, and periostin. Through network analysis we identified a cluster of coexpressed genes associated with atopic wheeze in the lower airway, which could equally distinguish atopic and nonatopic phenotypes in upper airway samples.

CONCLUSIONS

We show that the upper and lower airways are significantly conserved in their transcriptional composition, and that variations associated with disease are present in both nasal and tracheal epithelium. Findings from this study supporting a unified airway imply that clinical insight regarding the lower airway in health and disease can be gained from studying the nasal epithelium.

Blood eosinophil count and airway epithelial transcriptome relationships in COPD versus asthma

BACKGROUND

Whether the clinical or pathophysiologic significance of the "treatable trait" high blood eosinophil count in COPD is the same as for asthma remains controversial. We sought to determine the relationship between the blood eosinophil count, clinical characteristics and gene expression from bronchial brushings in COPD and asthma.

METHODS

Subjects were recruited into a COPD (emphysema versus airway disease [EvA]) or asthma cohort (Unbiased BIOmarkers in PREDiction of respiratory disease outcomes, U-BIOPRED). We determined gene expression using RNAseq in EvA (n = 283) and Affymetrix microarrays in U-BIOPRED (n = 85). We ran linear regression analysis of the bronchial brushings transcriptional signal versus blood eosinophil counts as well as differential expression using a blood eosinophil > 200 cells/μL as a cut-off. The false discovery rate was controlled at 1% (with continuous values) and 5% (with dichotomized values).

RESULTS

There were no differences in age, gender, lung function, exercise capacity and quantitative computed tomography between eosinophilic versus noneosinophilic COPD cases. Total serum IgE was increased in eosinophilic asthma and COPD. In EvA, there were 12 genes with a statistically significant positive association with the linear blood eosinophil count, whereas in U-BIOPRED, 1197 genes showed significant associations (266 positive and 931 negative). The transcriptome showed little overlap between genes and pathways associated with blood eosinophil counts in asthma versus COPD. Only CST1 was common to eosinophilic asthma and COPD and was replicated in independent cohorts.

CONCLUSION

Despite shared "treatable traits" between asthma and COPD, the molecular mechanisms underlying these clinical entities are predominately different.

Identification of Susceptibility Genes to Allergic Rhinitis by Gene Expression Data Sets

As an extremely prevalent disease worldwide, allergic rhinitis (AR) is a condition characterized by chronic inflammation of the nasal mucosa. To identify the finer molecular mechanisms associated with the AR susceptibility genes, differentially expressed genes (DEGs) in AR were investigated. The DEG expression and clinical data of the GSE19187 data set were used for weighted gene co‐expression network analysis (WGCNA). After the modules related to AR had been screened, the genes in the module were extracted for Gene Ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis, whereby the genes enriched in the KEGG pathway were regarded as the pathway‐genes. The DEGs in patients with AR were subsequently screened out from GSE19187, and the sensitive genes were identified in GSE18574 in connection with the allergen challenge. Two kinds of genes were compared with the pathway‐genes in order to screen the AR susceptibility genes. Receiver operating characteristic (ROC) curve was plotted to evaluate the capability of the susceptibility genes to distinguish the AR state. Based on the WGCNA in the GSE19187 data set, 10 co‐expression network modules were identified. The correlation analyses revealed that the yellow module was positively correlated with the disease state of AR. A total of 89 genes were found to be involved in the enrichment of the yellow module pathway. Four genes (CST1,SH2D1B,DPP4, and SLC5A5) were upregulated in AR and sensitive to allergen challenge, whose potentials were further confirmed by ROC curve. Taken together, CST1,SH2D1B,DPP4, and SLC5A5 are susceptibility genes to AR.

Physical exercise stimulates salivary secretion of cystatins

Physical exercise is known to activate the sympathetic nervous system, which influences the production of saliva from salivary glands. Our examination of saliva collected from highly trained athletes before and after a number of physical competititions showed an increase in the secretion of S-type cystatins and cystatin C as a subacute response to aerobic and anaerobic exercise. The elevation in salivary cystatins was transient and the recovery time course differed from that of amylase and other salivary proteins. An in vitro assay was developed based on a cell line from a human submandibular gland (HSG) that differentiated into acinus-like structures. Treatments with the β-adrenergic agonist isoproterenol caused a shift in the intracellular distribution of S-type cystatins and cystatin C, promoting their accumulation at the outer regions of the acinus prior to release and suggesting the activation of a directional transport involving co-migration of both molecules. In another treatment using non-differentiated HSG cells, it was evident that both expression and secretion of cystatin C increased upon addition of the β-adrenergic agonist, and these effects were essentially eliminated by the antagonist propranolol. The HSG cell line appears to have potential as a model for exploring the mechanism of cystatin secretion, particularly the S-type cystatins that originate primarily in the submandibular glands.

Escalation in mucus cystatin 2, pappalysin-A, and periostin levels over time predict need for recurrent surgery in chronic rhinosinusitis with nasal polyps

BACKGROUND

Chronic rhinosinusitis with nasal polyps (CRSwNP) is treated using oral/topical steroids and surgery. Despite maximal medical therapy, some patients remain recalcitrant. Mucus cystatin 2, pappalysin-A, and periostin can predict the presence of CRSwNP and correlate with disease severity. This study was designed to determine whether prospective sampling of these mucus proteins could predict medical failure and the need for revision surgery.

METHODS

This investigation was an institutional review board-approved, prospective study of 66 patients with CRSwNP. All patients underwent surgery, administration of topical/oral steroids, and outpatient mucus sampling at 10 time-points over 2 years. Five proteins, including cystatin 2 (CST2), pappalysin-A (PAPP-A), and periostin (PST), were analyzed and correlated with subjective parameters (including scores on the 22-item Sino-Nasal Outcomes Test [SNOT-22]). Variables were then analyzed and compared between those requiring revision surgery within 2 years (n = 5) and those with stable disease (n = 61).

RESULTS

All patients demonstrated a significant decline in CST2, PAPP-A, and periostin after their initial surgery. The recalcitrant group demonstrated escalations in all proteins despite steroids, with levels higher than those of the stable group at 1 year (CST2: 258.1 ± 205.2 pg/mL vs 235.3 ± 275.7 pg/mL, p = 0.86; PAPP-A: 170.3 ± 150.4 pg/mL vs 74.6 ± 106.7 pg/mL, p < 0.05; periostin: 188.8 ± 192.4 ng/mL vs 54.5 ± 47.6 ng/mL, p < 0.001). Escalation in all proteins correlated significantly with worsening SNOT-22 score at each time-point (domain 1: 8.2 ± 1.3 vs 5.5 ± 1.1; p < 0.05).

CONCLUSION

Early recurrences and medical recalcitrance in CRSwNP may be predicted noninvasively through the serial, prospective sampling of mucus CST2, PAPP-A, and periostin levels. These biosignatures may help to predict disease course and guide individualized therapy.

Discriminant analysis followed by unsupervised cluster analysis including exosomal cystatins predict presence of chronic rhinosinusitis, phenotype, and disease severity

BACKGROUND

Cystatins are epithelial protease inhibitors that participate in sinonasal immunity and inflammation. Nasal mucus-derived exosomes (NMDEs) are small vesicles secreted by epithelial cells that carry protein cargo reflective of their host cell. NMDEs have been used as a noninvasive biomarker source to study chronic rhinosinusitis with nasal polyps (CRSwNP) proteomics with superior sensitivity to whole mucus. The purpose of this study was to noninvasively quantify exosomal cystatins in a heterogenous population to determine their utility in predicting phenotype and disease severity.

METHODS

This was an Institutional Review Board-approved study in which NMDEs were purified from 105 patients undergoing sinonasal surgery by ultracentrifugation. Demographic and clinical variables were collected and phenotypes were assigned a priori. Linear discriminant analysis was executed based on normalized Cystatin values as phenotype predictor variables. Unsupervised cluster analysis was performed using Ward's linkage followed by Duda/Hart Je(2)/Je(1) index cluster stopping rules. Analysis of variance (ANOVA), Welch's test, and Fisher's exact tests were used for continuous and categorical variables.

RESULTS

NMDE Cystatin-2 expression segregated by phenotype (mean ± standard error [SEM]): control (23.4 ± 4.2 pg/µg, n = 32); CRS without NP (CRSsNP) (56.6 ± 8.3 pg/µg, n = 33); and CRSwNP (130.5 ± 16.7 pg/µg, n = 40) (p < 0.0001). Seven clusters were identified among patients where the highest NMDE Cystatin-2 levels clustered with asthma, tissue eosinophilia, and aspirin-exacerbated respiratory disease (AERD).

CONCLUSION

Cystatin levels in NMDEs predict CRS phenotype and disease severity. As a "liquid biopsy," noninvasive NMDE collection offers a promising opportunity to study disease pathophysiology, discriminate disease states, and potentially reveal novel therapeutic targets.

Research progress of cystatin SN in cancer

Cystatin SN, belonging to the type 2 cystatin superfamily, is widely expressed and distributed in mammals. Cystatin SN is involved in inflammation, cell cycle, cellular senescence, tumorigenesis, and metastasis. Cystatin SN is also known to participate in signaling pathways like Wnt signaling pathway, GSK3 signaling pathway, AKT signaling pathway, and IL-6 signaling pathway. Cystatin SN was found to be highly expressed in peritumoral normal tissues in esophageal squamous cell carcinoma (ESCC); however, low cystatin SN expression was found in ESCC cancer tissues. Conversely, in other cancer types such as lung cancer, breast cancer, gastric cancer, pancreatic cancer, and colorectal cancer, high cystatin SN expression in cancer tissues but low cystatin SN expression in peritumoral normal tissues was found. Survival analyses showed that high cystatin SN expression benefited ESCC patients but did harm to other types of cancer patients. Univariate and multivariate analyses indicated that cystatin SN possibly acts as a marker for cancer prognosis. Here, we provide a brief introduction about the role of cystatin SN in cancer and discuss the different prognostic effects of cystatin SN on different tumors. Cystatin SN might be a potential marker for cancer prognosis and a target for cancer therapy.

Epithelium-derived cystatin SN enhances eosinophil activation and infiltration through IL-5 in patients with chronic rhinosinusitis with nasal polyps

BACKGROUND

The interaction between epithelial cells and immune cells plays an important role in the pathogenesis of chronic rhinosinusitis with nasal polyps (CRSwNP); however, the mechanism or mechanisms underlying T_H-biased inflammation in this process are largely unknown. Profiling protein expression in patients with CRSwNP by using shotgun proteomics suggested that cystatin SN (CST1), a type 2 cysteine protease inhibitor, might play a role because this was expressed with the greatest difference in patients with eosinophilic chronic rhinosinusitis with nasal polyps (ECRSwNP) and those with noneosinophilic chronic rhinosinusitis with nasal polyps (nonECRSwNP).

OBJECTIVES

We sought to investigate the expression and role of CST1 in modulating eosinophilic inflammation in patients with CRSwNP.

METHODS

Sinonasal tissues were collected from 192 patients with ECRSwNP, 52 patients with nonECRSwNP, and 40 control subjects. CST1 mRNA expression, localization, and concentration in the tissues were measured by using real-time PCR, in situ hybridization, immunohistochemistry, and an ELISA. Recombinant CST1 was used to further explore the function of the molecule in dispersed nasal polyp cells and eosinophils extracted from polyp tissues and peripheral blood.

RESULTS

CST1 was mainly expressed by epithelial cells and significantly increased in patients with ECRSwNP but decreased in patients with nonECRSwNP compared with that in control subjects. CST1 expression was further increased in patients with ECRSwNP and comorbid asthma and correlated with eosinophil percentages in tissue samples. CST1 was induced by IL-4 and IL-13 in tissue from both patients with ECRSwNP and those with nonECRSwNP and repressed by IL-17A in patients with nonECRSwNP in the presence of neutrophils. CST1 enhanced eosinophil activation and recruitment through induction of IL-5.

CONCLUSION

Epithelium-derived CST1 modulates eosinophil activation and recruitment, expression of which could be regulated by T_H2 and T_H17 cytokines.

Identification of pathogenic genes and upstream regulators in allergic rhinitis

BACKGROUND

Allergic rhinitis (AR) is the main cause of irreversible blindness in older individuals. Our study aims to identify the key genes and upstream regulators in AR.

METHODS

To screen pathogenic genes of AR, an integrated analysis was performed by using the microarray datasets in AR derived from the Gene Expression Omnibus (GEO) database. The functional annotation and potential pathways of differentially expressed genes (DEGs) were further discovered by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis. We constructed the AR-specific transcriptional regulatory network to find the crucial transcriptional factors (TFs) which target the DEGs in AR. Electronic validation was performed to verify the DEGs obtained by integrated analysis.

RESULTS

From two GEO datasets obtained, we identified 793 DEGs (460 up-regulated and 333 down-regulated genes) between AR and normal control (NC). After GO and KEGG analysis, chronic inflammatory response and MAPK signaling pathway were significantly enriched pathways for DEGs. The expression of 6 genes (CLC, CST1, CRTAM, ILK, STAT1, and POSTN) was detected. The 6 genes in GEO: GSE51392 dataset played the same pattern with that in our integrated analysis.

CONCLUSIONS

The dysregulation of 3 genes (CST1, CLC and STAT1) may be involved in the pathogenesis of AR. AP-1 was associated with AR by regulating CST1 and CLC. Our finding can contribute to developing new potential biomarkers, revealing the underlying pathogenesis, and further raising new therapeutic targets for AR.

Proteomics of the acid-soluble fraction of whole and major gland saliva in burning mouth syndrome patients

OBJECTIVE

In the present study the salivary proteome of burning mouth syndrome patients and healthy subjects was characterized by a top-down proteomic approach and compared to highlight possible qualitative and quantitative differences that may give suggestions about the causes of this pathology which are still unknown.

MATERIALS AND METHODS

Resting and stimulated whole saliva, stimulated parotid and submandibular/sublingual saliva samples were collected from burning mouth syndrome patients (n = 16) and age- and gender-matched healthy subjects (n = 14). An equal volume of 0.2% trifluoroacetic acid was added to each sample immediately after collection and the supernatants were analysed by liquid chromatography coupled to electrospray-ionisation mass spectrometry. Proteins and peptides were quantified using a label-free approach measuring the extracted ion current peak areas of the main salivary proteins and peptides.

RESULTS

The quantitation of the main salivary proteins and peptides revealed a higher concentration of cystatin SN in resting saliva of burning mouth syndrome patients with respect to healthy controls and no other conspicuous changes.

CONCLUSIONS

The reported data showed that the salivary protein profile was not affected, in composition and relative abundance, by the burning mouth syndrome, except for the cystatin SN, a protein up-regulated in several pathological conditions, that might be considered potentially indicative of the disease.

Human cystatin SN is an endogenous protease inhibitor that prevents allergic rhinitis

BACKGROUND

Protease allergens disrupt epithelial barriers to exert their allergenicity. Cystatin SN (encoded by CST1) is an endogenous cysteine protease inhibitor upregulated in nasal epithelia in patients with allergic rhinitis (AR).

OBJECTIVE

We sought to investigate the protective effect of human cystatin SN on AR symptoms using pollen-induced AR mouse models.

METHODS

We performed an in vitro protease activity assay to evaluate the effect of recombinant human cystatin SN (rhCystatin SN) on Japanese cedar (JC) or ragweed proteases. A human nasal epithelial cell line, RPMI 2650, was used to examine tight junction (TJ) disruption in vitro. Mice were sensitized and nasally challenged with JC or ragweed pollens with or without rhCystatin SN to examine the effect of rhCystatin SN on AR symptoms and the epithelial barrier in vivo. Because mice lack CST1, we generated transgenic (Tg) mice expressing human CST1 under control of its genomic control region (hCST1-Tg mice) to examine the role of cystatin SN in physiologically expressed conditions.

RESULTS

rhCystatin SN inhibited JC but not ragweed protease activities and prevented JC-induced but not ragweed-induced TJ disruption in vitro. Exogenous administration of rhCystatin SN ameliorated JC-induced but not ragweed-induced sneezing and nasal TJ disruption in vivo. Furthermore, hCST1-Tg mice showed decreased JC-induced but not ragweed-induced sneezing symptoms and nasal TJ disruption compared with wild-type mice.

CONCLUSION

Human cystatin SN suppresses AR symptoms through inhibiting allergen protease activities and protecting the nasal TJ barrier in an allergen-specific manner. We propose that upregulation of nasal endogenous protease inhibitors, including cystatin SN, is a novel therapeutic strategy for protease allergen-induced AR.

A Nasal Brush-based Classifier of Asthma Identified by Machine Learning Analysis of Nasal RNA Sequence Data

Asthma is a common, under-diagnosed disease affecting all ages. We sought to identify a nasal brush-based classifier of mild/moderate asthma. 190 subjects with mild/moderate asthma and controls underwent nasal brushing and RNA sequencing of nasal samples. A machine learning-based pipeline identified an asthma classifier consisting of 90 genes interpreted via an L2-regularized logistic regression classification model. This classifier performed with strong predictive value and sensitivity across eight test sets, including (1) a test set of independent asthmatic and control subjects profiled by RNA sequencing (positive and negative predictive values of 1.00 and 0.96, respectively; AUC of 0.994), (2) two independent case-control cohorts of asthma profiled by microarray, and (3) five cohorts with other respiratory conditions (allergic rhinitis, upper respiratory infection, cystic fibrosis, smoking), where the classifier had a low to zero misclassification rate. Following validation in large, prospective cohorts, this classifier could be developed into a nasal biomarker of asthma.

Meta-analysis of airway epithelium gene expression in asthma

Differential gene expression in the airway epithelium of patients with asthma versus controls has been reported in several studies. However, there is no consensus on which genes are reproducibly affected in asthma. We sought to identify a consensus list of differentially expressed genes (DEGs) using a meta-analysis approach.We identified eight studies with data that met defined inclusion criteria. These studies comprised 355 cases and 193 controls and involved sampling either bronchial or nasal epithelium. We conducted study-level analyses, followed by a meta-analysis. Likewise, we applied a meta-analysis framework to the results of study-level pathway enrichment.We identified 1273 DEGs, 431 of which had not been identified in previous studies. 450 DEGs exhibited large effect sizes and were robust to study population differences in age, sex, race/ethnicity, medication use, smoking status and exacerbations. The magnitude of differential expression of these 450 genes was highly similar in bronchial and nasal airway epithelia. Meta-analysis of pathway enrichment revealed a number of consistently dysregulated biological pathways, including putative transcriptional and post-transcriptional regulators.In total, we identified a set of genes that is consistently dysregulated in asthma, that links to known and novel biological pathways, and that will inform asthma subtype identification.

Sputum proteomics and airway cell transcripts of current and ex-smokers with severe asthma in U-BIOPRED: an exploratory analysis

Severe asthma patients with a significant smoking history have airflow obstruction with reported neutrophilia. We hypothesise that multi-omic analysis will enable the definition of smoking and ex-smoking severe asthma molecular phenotypes.The U-BIOPRED cohort of severe asthma patients, containing current-smokers (CSA), ex-smokers (ESA), nonsmokers and healthy nonsmokers was examined. Blood and sputum cell counts, fractional exhaled nitric oxide and spirometry were obtained. Exploratory proteomic analysis of sputum supernatants and transcriptomic analysis of bronchial brushings, biopsies and sputum cells was performed.Colony-stimulating factor (CSF)2 protein levels were increased in CSA sputum supernatants, with azurocidin 1, neutrophil elastase and CXCL8 upregulated in ESA. Phagocytosis and innate immune pathways were associated with neutrophilic inflammation in ESA. Gene set variation analysis of bronchial epithelial cell transcriptome from CSA showed enrichment of xenobiotic metabolism, oxidative stress and endoplasmic reticulum stress compared to other groups. CXCL5 and matrix metallopeptidase 12 genes were upregulated in ESA and the epithelial protective genes, mucin 2 and cystatin SN, were downregulated.Despite little difference in clinical characteristics, CSA were distinguishable from ESA subjects at the sputum proteomic level, with CSA patients having increased CSF2 expression and ESA patients showing sustained loss of epithelial barrier processes.

Endogenous Protease Inhibitors in Airway Epithelial Cells Contribute to Eosinophilic Chronic Rhinosinusitis

RATIONALE

Cystatin A and SPINK5 are endogenous protease inhibitors (EPIs) that may play key roles in epithelial barrier function.

OBJECTIVES

To investigate the roles of EPIs in the pathogenesis of chronic rhinosinusitis (CRS).

METHODS

We examined the expression of cystatin A and SPINK5 in the nasal epithelial cells of patients with CRS. Additionally, the in vitro effects of recombinant EPIs on the secretion of the epithelial-derived cytokines IL-25, IL-33, and thymic stromal lymphopoietin in airway epithelial cells, and the in vivo effects of recombinant EPIs in the nasal epithelium of mice exposed to multiple airborne allergens (MAA) were examined.

MEASUREMENTS AND MAIN RESULTS

Compared with control subjects and patients with noneosinophilic CRS, patients with eosinophilic CRS showed significantly lower protein and mRNA expression of cystatin A and SPINK5 in the nasal epithelium. Allergen-induced production of IL-25, IL-33, and thymic stromal lymphopoietin in normal human bronchial epithelial cells was inhibited by treatment with recombinant cystatin A or SPINK5. Conversely, the production of these cytokines was increased when cystatin A or SPINK5 were knocked down with small interfering RNA. Chronic MAA exposure induced goblet cell metaplasia and epithelial disruption in mouse nasal epithelium and decreased the tissue expression and nasal lavage levels of cystatin A and SPINK5. Intranasal instillations of recombinant EPIs attenuated this MAA-induced pathology.

CONCLUSIONS

Cystatin A and SPINK5 play an important role in protecting the airway epithelium from exogenous proteases. The preservation of EPIs may have a therapeutic benefit in intractable airway inflammation, such as eosinophilic CRS.

Epithelial proteome profiling suggests the essential role of interferon-inducible proteins in patients with allergic rhinitis

BACKGROUND

Seasonal allergic rhinitis (SAR) caused by intermittent exposure to seasonal pollen causes itching, nasal congestion, and repeated sneezing, with profound effects on quality of life, work productivity, and school performance. Although both the genotype and environmental factors can contribute to the immunologic basis of allergic reactions, the molecular underpinnings associated with the pathogenesis of allergic rhinitis are not entirely clear.

METHODS

To address these questions, nasal epithelial brushings were collected from 29 patients with SAR and 31 control subjects during and after the pollen season. We then implemented an orbitrap-based, bottom-up, label-free quantitative proteomics approach, followed by multivariate analyses to identify differentially abundant (DA) proteins among the 4 sample groups.

RESULTS

We identified a total of 133 DA proteins for which the most significantly overrepresented functional category was found to be interferon 1 signaling. Two proteins, cystatin 1 and myeloblastin, the former of which protects against protease activity of allergens and the latter with a role in epithelial barrier function, were DA in patients with SAR and control subjects, irrespective of season. Moreover, interferon-inducible protein with tetratricopeptide repeats 1, cystatin 1, and interferon-inducible protein with tetratricopeptide repeats 3 were found to be differentially regulated between patients with SAR and control subjects, with inverse abundance dynamics during the transition from fall to spring.

CONCLUSION

We identified type 1 interferon-regulated proteins as biomarkers in patients with SAR, potentially playing an important role in its pathogenesis. Moreover, when compared with patients with SAR, healthy subjects exhibit an antagonistic proteomic response across seasons, which might prove to be a therapeutic target for disease prevention.

Elevated expression of CST1 promotes breast cancer progression and predicts a poor prognosis

Cystatin SN (CST1) belongs to the type 2 cystatin (CST) superfamily, which restricts the proteolytic activities of cysteine proteases. CST1 has been recently considered to be involved in the development of several human cancers. However, the prognostic significance and function of CST1 in breast cancer remains unknown. In the current study, we found that CST1 was generally upregulated in breast cancer at both mRNA and protein level. Furthermore, overall survival (OS) and disease-free survival (DFS) in the low CST1 expression subgroup were significantly superior to the high CST1 expression subgroup (OS, p < 0.001; DFS, p < 0.001), which indicated that CST1 expression level was closely correlated to the survival risk of these patients. Univariate and multivariate analyses demonstrated that CST1 expression was an independent prognostic factor, the same as ER status and nodal status. Next, CST1 overexpression promoted breast cancer cell proliferation, clonogenicity, migration, and invasion abilities. By contrast, knockdown of CST1 attenuated these malignant characteristics in breast cancer cells. Collectively, our study indicates that CST1 cannot only serve as a significant prognostic indicator but also as a potential therapeutic target for breast cancer.

KEY MESSAGES

High CST1 expression is negatively correlated with survival of breast cancer patients. CST1 promotes cell proliferation, clone formation, and metastasis in breast cancer cells. CST1 is a novel potential prognostic biomarker and therapeutic target for breast cancer.

The nasal methylome and childhood atopic asthma

BACKGROUND

Given the strong environmental influence on both epigenetic marks and allergic asthma in children, the epigenetic alterations in respiratory epithelia might provide insight into allergic asthma.

OBJECTIVE

We sought to identify DNA methylation and gene expression changes associated with childhood allergic persistent asthma.

METHODS

We compared genomic DNA methylation patterns and gene expression in African American children with persistent atopic asthma (n = 36) versus healthy control subjects (n = 36). Results were validated in an independent population of asthmatic children (n = 30) by using a shared healthy control population (n = 36) and in an independent population of white adult atopic asthmatic patients (n = 12) and control subjects (n = 12).

RESULTS

We identified 186 genes with significant methylation changes, differentially methylated regions or differentially methylated probes, after adjustment for age, sex, race/ethnicity, batch effects, inflation, and multiple comparisons. Genes differentially methylated included those with established roles in asthma and atopy and genes related to extracellular matrix, immunity, cell adhesion, epigenetic regulation, and airflow obstruction. The methylation changes were substantial (median, 9.5%; range, 2.6% to 29.5%). Hypomethylated and hypermethylated genes were associated with increased and decreased gene expression, respectively (P < 2.8 × 10^-6 for differentially methylated regions and P < 7.8 × 10^-10 for differentially methylated probes). Quantitative analysis in 53 differentially expressed genes demonstrated that 32 (60%) have significant methylation-expression relationships within 5 kb of the gene. Ten loci selected based on the relevance to asthma, magnitude of methylation change, and methylation-expression relationships were validated in an independent cohort of children with atopic asthma. Sixty-seven of 186 genes also have significant asthma-associated methylation changes in nasal epithelia of adult white asthmatic patients.

CONCLUSIONS

Epigenetic marks in respiratory epithelia are associated with allergic asthma and gene expression changes in inner-city children.

Airway Epithelial Expression Quantitative Trait Loci Reveal Genes Underlying Asthma and Other Airway Diseases

Genome-wide association studies (GWASs) have identified loci that are robustly associated with asthma and related phenotypes; however, the molecular mechanisms underlying these associations need to be explored. The most relevant tissues to study the functional consequences of asthma are the airways. We used publically available data to derive expression quantitative trait loci (eQTLs) for human epithelial cells from small and large airways and applied the eQTLs in the interpretation of GWAS results of asthma and related phenotypes. For the small airways (n = 105), we discovered 660 eQTLs at a 10% false discovery rate (FDR), among which 315 eQTLs were not previously reported in a large-scale eQTL study of whole lung tissue. A large fraction of the identified eQTLs is supported by data from Encyclopedia of DNA Elements (ENCODE) showing that the eQTLs reside in regulatory elements (57.5 and 67.6% of cis- and trans-eQTLs, respectively). Published pulmonary GWAS hits were enriched as airway epithelial eQTLs (9.2-fold). Further, genes regulated by asthma GWAS loci in epithelium are significantly enriched in immune response pathways, such as IL-4 signaling (FDR, 5.2 × 10(-4)). The airway epithelial eQTLs described in this study are complementary to previously reported lung eQTLs and represent a powerful resource to link GWAS-associated variants to their regulatory function and thus elucidate the molecular mechanisms underlying asthma and airway-related conditions.

Emerging role of human basophil biology in health and disease

Basophils have emerged in recent years as a small but potent subpopulation of leukocytes capable of bridging innate and adaptive immunity. They can be activated through IgE-dependent and IgE-independent mechanisms to release preformed mediators and to produce Th2 cytokines. In addition to their role in protective immunity to helminths, basophils are major participants in allergic reactions as diverse as anaphylaxis and immediate hypersensitivity reactions, late-phase hypersensitivity reactions, and delayed hypersensitivity reactions. Additionally, basophils have been implicated in the pathophysiology of autoimmune diseases such as lupus nephritis and rheumatoid arthritis, and the modulation of immune responses to bacterial infections, as well as being a feature of myelogenous leukemias. Distinct signals for activation, degranulation, transendothelial migration, and immune regulation are being defined, and demonstrate the important role of basophils in promoting a Th2 microenvironment. These mechanistic insights are driving innovative approaches for diagnostic testing and therapeutic targeting of basophils.