Multi-omic integration reveals alterations in nasal mucosal biology that mediate air pollutant effects on allergic rhinitis.

BACKGROUND: Allergic rhinitis is a common inflammatory condition of the nasal mucosa that imposes a considerable health burden. Air pollution has been observed to increase the risk of developing allergic rhinitis. We addressed the hypotheses that early life exposure to air toxics is associated with developing allergic rhinitis, and that these effects are mediated by DNA methylation and gene expression in the nasal mucosa. METHODS: In a case-control cohort of 505 participants, we geocoded participants' early life exposure to air toxics using data from the US Environmental Protection Agency, assessed physician diagnosis of allergic rhinitis by questionnaire, and collected nasal brushings for whole-genome DNA methylation and transcriptome profiling. We then performed a series of analyses including differential expression, Mendelian randomization, and causal mediation analyses to characterize relationships between early life air toxics, nasal DNA methylation, nasal gene expression, and allergic rhinitis. RESULTS: Among the 505 participants, 275 had allergic rhinitis. The mean age of the participants was 16.4 years (standard deviation = 9.5 years). Early life exposure to air toxics such as acrylic acid, phosphine, antimony compounds, and benzyl chloride was associated with developing allergic rhinitis. These air toxics exerted their effects by altering the nasal DNA methylation and nasal gene expression levels of genes involved in respiratory ciliary function, mast cell activation, pro-inflammatory TGF-ß1 signaling, and the regulation of myeloid immune cell function. CONCLUSIONS: Our results expand the range of air pollutants implicated in allergic rhinitis and shed light on their underlying biological mechanisms in nasal mucosa.

Pediatric interventional bronchoscopy: from early limitations to achievable opportunities.

PURPOSE OF REVIEW: The rapid evolution of bronchoscopy equipment and technologies, from the introduction of the 1.1 mm flexible cryoprobe to the use of navigational and robotic bronchoscopy, has afforded unprecedented opportunities for pediatric advanced diagnostic and interventional bronchoscopy. While there is growing interest among pediatric pulmonologists to incorporate these new techniques into their practice, the current pediatric landscape is characterized by few practicing interventional bronchoscopists, scant published literature, and no formal training programs. RECENT FINDINGS: While the majority of the published literature consists of case reports and small case series, the increased application of new techniques is starting to yield larger and more structured studies that will be able to provide more objective commentary on the proposed indications, safety, and efficacy of such techniques in the pediatric population. SUMMARY: For many decades, progress in pediatric advanced diagnostic and interventional bronchoscopy was slow and deliberate, limited by the lack of appropriately sized equipment and experienced interventional bronchoscopists. The current opportunities afforded require equal, or perhaps even more, vigilance as pediatric pulmonologists employ new equipment and technologies and define new practices and standards of care. Importantly, this review is meant to serve as a general conspectus of pediatric advanced diagnostic and interventional bronchoscopy and not a consensus guideline for the performance of advanced or even routine bronchoscopy in the pediatric population. For technical standards of pediatric bronchoscopy, refer to existing guidelines [1,2] .

Examination of host genetic effects on nasal microbiome composition.

BACKGROUND: Genetic predisposition increases risk for asthma, and distinct nasal microbial compositions are associated with asthma. Host genetics might shape nasal microbiome composition. OBJECTIVE: We examined associations between host genetics and nasal microbiome composition. METHODS: Nasal samples were collected from 584 participants from the Mount Sinai Health System, New York. Seventy-seven follow-up samples were collected from a subset of 40 participants. 16S rRNA sequencing and RNA sequencing were performed on nasal samples. Beta diversity was calculated, variant calling on RNA sequencing data was performed, and genetic relatedness between individuals was determined. Using linear regression models, we tested for associations between genetic relatedness and nasal microbiome composition. RESULTS: The median age of the cohort was 14.6 (interquartile range 11.2-19.5) years, with participants representing diverse ancestries and 52.7% of the cohort being female. For participants who provided follow-up samples, the median time between samples was 5.1 (interquartile range 1.4-7.2) months. Nasal microbiome composition similarity as reflected by beta diversity was significantly higher within subjects over time versus between subjects (coefficient = 0.091, P = 2.84-7). There was no significant association between genetic relatedness and beta diversity (coefficient = -0.05, P = .29). Additional analyses exploring the relationship between beta diversity and genetic variance yielded similar results. CONCLUSION: Host genetics has little influence on nasal microbiome composition.

The nasal microbiome, nasal transcriptome, and pet sensitization.

BACKGROUND: Pet allergies are common in children with asthma. Microbiota and host responses may mediate allergen sensitization. OBJECTIVE: We sought to uncover host-microbe relationships in pet allergen sensitization via joint examination of the nasal microbiome and nasal transcriptome. METHODS: We collected nasal samples from 132 children with asthma for parallel 16S rRNA and RNA sequencing. Specific IgE levels for cat and dog dander were measured. Analyses of the nasal microbiome, nasal transcriptome, and their correlations were performed with respect to pet sensitization status. RESULTS: Among the 132 children, 91 (68.9%) were cat sensitized and 96 (72.7%) were dog sensitized. Cat sensitization was associated with lower nasal microbial diversity by Shannon index (P = .021) and differential nasal bacterial composition by weighted UniFrac distance (permutational multivariate ANOVA P = .035). Corynebacterium sp and Staphylococcus epidermidis were significantly less abundant, and the metabolic process "fatty acid elongation in mitochondria" was lower in pet-sensitized versus unsensitized children. Correlation networks revealed that the nasal expression levels of 47 genes representing inflammatory processes were negatively correlated with the relative abundances of Corynebacterium sp and S epidermidis. Thus, these species were directly associated not only with the absence of pet sensitization but also with the underexpression of host gene expression of inflammatory processes that contribute to allergen sensitization. Causal mediation analyses revealed that the associations between these nasal species and pet sensitization were mediated by nasal gene expression. CONCLUSIONS: Higher abundances of nasal Corynebacterium sp and S epidermidis are associated with absence of pet sensitization and correlate with lower expression of inflammatory genes.

Network study of nasal transcriptome profiles reveals master regulator genes of asthma.

BACKGROUND: Nasal transcriptomics can provide an accessible window into asthma pathobiology. OBJECTIVE: Our goal was to move beyond gene signatures of asthma to identify master regulator genes that causally regulate genes associated with asthma phenotypes. METHODS: We recruited 156 children with severe persistent asthma and controls for nasal transcriptome profiling and applied network-based and probabilistic causal methods to identify severe asthma genes and their master regulators. We then took the same approach in an independent cohort of 190 adults with mild/moderate asthma and controls to identify mild/moderate asthma genes and their master regulators. Comparative analysis of the master regulator genes followed by validation testing in independent children with severe asthma (n = 21) and mild/moderate asthma (n = 154) was then performed. RESULTS: Nasal gene signatures for severe persistent asthma and for mild/moderate persistent asthma were identified; both were found to be enriched in coexpression network modules for ciliary function and inflammatory response. By applying probabilistic causal methods to these gene signatures and validation testing in independent cohorts, we identified (1) a master regulator gene common to asthma across severity and ages (FOXJ1); (2) master regulator genes of severe persistent asthma in children (LRRC23, TMEM231, CAPS, PTPRC, and FYB); and (3) master regulator genes of mild/moderate persistent asthma in children and adults (C1orf38 and FMNL1). The identified master regulators were statistically inferred to causally regulate the expression of downstream genes that modulate ciliary function and inflammatory response to influence asthma. CONCLUSION: The identified master regulator genes of asthma provide a novel path forward to further uncovering asthma mechanisms and therapy.

Increased advanced glycation end product and meat consumption is associated with childhood wheeze: analysis of the National Health and Nutrition Examination Survey.

We examined 4388 children from the 2003 to 2006 National Health and Nutrition Examination Survey and used survey-design-adjusted multivariable logistic regression to evaluate associations between dietary advanced glycation end product (AGE) and meat consumption frequencies and respiratory symptoms. Higher AGE intake was significantly associated with increased odds of wheezing (adjusted OR 1.18; 95% CI 1.02 to 1.36), wheeze-disrupted sleep (1.26; 95% CI 1.05 to 1.51) and exercise (1.34; 95% CI 1.08 to 1.67) and wheezing requiring prescription medication (1.35; 95% CI 1.13 to 1.63). Higher intake of non-seafood meats was associated with wheeze-disrupted sleep (2.32; 95% CI 1.11 to 4.82) and wheezing requiring prescription medication (2.23; 95% CI 1.10 to 4.54).

Preference matters: New aspects on how foreign bodies should and could be removed from a child's airway.

BACKGROUND: Foreign body aspiration in children is a potentially life-threatening event that can be diagnosed and treated by airway endoscopy. We aimed to analyze the influence of the examiner's experience and preference on the choice of the technique and the resulting complication rate. METHODS: In this international study, experts in the field documented their preferred and applied technique as well as the outcome of each case of foreign body removal. Personal data of the bronchoscopists and their medical center were collected via an online questionnaire separately from the case specifics. RESULTS: A total of 399 foreign body removals were performed by 64 examiners. A total of 279 removals were performed using rigid endoscopy, and 120 procedures were performed by flexible. When a difficulty was expected, flexible endoscopy was used significantly more often (χ2 (1) = 11.06, p < 0.001). Complications occurred significantly less often when the bronchoscopist used their preferred technique (χ2 (1) = 6.41, p = 0.011), had more than 5 years of experience (χ2 (1) = 5.13, p = 0.023) or performed more than 100 removals (χ2 (2) = 11.51, p = 0.003). In medical centers, complication rates significantly decreased if more than 200 bronchoscopies were performed in children, compared to the centers that perform 50-200 bronchoscopies per year (χ2 (1) = 24.56, p < 0.001). CONCLUSION: Preference and experience of a bronchoscopist and his/her medical center with flexible or rigid foreign body removal distinctively affect the outcome of the procedure and cannot be neglected in the discourse on the appropriate technique. This link also emphasizes the importance of a structured training program.

Integrated study of systemic and local airway transcriptomes in asthma reveals causal mediation of systemic effects by airway key drivers.

BACKGROUND: Systemic and local profiles have each been associated with asthma, but parsing causal relationships between system-wide and airway-specific processes can be challenging. We sought to investigate systemic and airway processes in asthma and their causal relationships. METHODS: Three hundred forty-one participants with persistent asthma and non-asthmatic controls were recruited and underwent peripheral blood mononuclear cell (PBMC) collection and nasal brushing. Transcriptome-wide RNA sequencing of the PBMC and nasal samples and a series of analyses were then performed using a discovery and independent test set approach at each step to ensure rigor. Analytic steps included differential expression analyses, coexpression and probabilistic causal (Bayesian) network constructions, key driver analyses, and causal mediation models. RESULTS: Among the 341 participants, the median age was 13 years (IQR = 10-16), 164 (48%) were female, and 200 (58.7%) had persistent asthma with mean Asthma Control Test (ACT) score 16.6 (SD = 4.2). PBMC genes associated with asthma were enriched in co-expression modules for NK cell-mediated cytotoxicity (fold enrichment = 4.5, FDR = 6.47 × 10-32) and interleukin production (fold enrichment = 2.0, FDR = 1.01 × 10-15). Probabilistic causal network and key driver analyses identified NK cell granule protein (NKG7, fold change = 22.7, FDR = 1.02 × 10-31) and perforin (PRF1, fold change = 14.9, FDR = 1.31 × 10-22) as key drivers predicted to causally regulate PBMC asthma modules. Nasal genes associated with asthma were enriched in the tricarboxylic acid (TCA) cycle module (fold enrichment = 7.5 FDR = 5.09 × 10-107), with network analyses identifying G3BP stress granule assembly factor 1 (G3BP1, fold change = 9.1 FDR = 2.77 × 10-5) and InaD-like protein (INADL, fold change = 5.3 FDR = 2.98 × 10-9) as nasal key drivers. Causal mediation analyses revealed that associations between PBMC key drivers and asthma are causally mediated by nasal key drivers (FDR = 0.0076 to 0.015). CONCLUSIONS: Integrated study of the systemic and airway transcriptomes in a well-phenotyped asthma cohort identified causal key drivers of asthma among PBMC and nasal transcripts. Associations between PBMC key drivers and asthma are causally mediated by nasal key drivers.

Methylxanthine inhibit fungal chitinases and exhibit antifungal activity.

Chitinases are necessary for fungal cell wall remodeling and cell replication. Methylxanthines have been shown to competitively inhibit family 18 chitinases in vitro. We sought to determine the effects of methylxanthines on fungal chitinases. Fungi demonstrated variable chitinase activity and incubation with methylxanthines (0.5-10 mM) resulted in a dose-dependent decrease in this activity. All fungi tested, except for Candida spp., demonstrated growth inhibition in the presence of methylxanthines at a concentration of 10 mM. India ink staining demonstrated impaired budding and decreased cell size for methylxanthine-treated Cryptococcus neoformans. C. neoformans and Aspergillus fumigatus treated with pentoxifylline also exhibited abnormal cell morphology. In addition, pentoxifylline-treated C. neoformans exhibited increased susceptibility to calcofluor and a leaky melanin phenotype consistent with defective cell wall function. Our data suggest that a variety of fungi express chitinases and that methylxanthines have antifungal properties related to their inhibition of fungal chitinases. Our results highlight the potential utility of targeting chitinases in the development of novel antifungal therapies.

Foreign body aspiration in a child with unilateral lung aplasia.

OBJECTIVE: To present a case of foreign body aspiration in a child with unilateral lung aplasia and successful removal of the foreign body by bedside flexible bronchoscopy. DATA SOURCE: Case details were obtained from medical records. STUDY SELECTION: Eighteen-month-old girl with unilateral lung aplasia. DATA EXTRACTION AND SYNTHESIS: Demographic details (age) and clinical and biochemical data (blood gas) were obtained from medical records. An 18-mo-old girl with the diagnosis of right lung aplasia, who underwent aortopexy in the newborn period for severe respiratory distress, presented with acute-onset respiratory distress. The patient was treated with bronchodilators and steroids without success and rapidly progressed to respiratory failure. Flexible bronchoscopy done at the bedside showed a foreign body completely obstructing the left main bronchus. The rigid bronchoscopy was unsuccessful in extracting the foreign body because of the complex airway anatomy. The foreign body was successfully extracted by basket forceps via a flexible bronchoscope, and the patient recovered remarkably within few hours of the procedure. CONCLUSIONS: Because foreign body aspiration in a child with a unilateral lung can result in abrupt respiratory compromise and death, a high index of suspicion is necessary when these children present with acute respiratory symptoms. Although rigid bronchoscopy is the procedure of choice for the removal of foreign bodies, flexible bronchoscopy may be necessary for patients with abnormal airway anatomy.

Relationship of Pneumocystis antibody responses to paediatric asthma severity.

BACKGROUND: Although asthma is the most commonly diagnosed respiratory disease, its pathogenesis is complex, involving both genetic and environmental factors. A role for the respiratory microbiome in modifying asthma severity has been recently recognised. Airway colonisation by Pneumocystis jirovecii has previously been associated with multiple chronic lung diseases, including chronic obstructive pulmonary disease (COPD) and severe asthma (SA). Decreased incidence of Pneumocystis pneumonia in HIV-infected individuals and reduced severity of COPD is associated with naturally occurring antibody responses to the Pneumocystis antigen, Kexin (KEX1). METHODS: 104 paediatric patients were screened for KEX1 IgG reciprocal end point titre (RET), including 51 with SA, 20 with mild/moderate asthma, 20 non-asthma and 13 with cystic fibrosis (CF) in a cross-sectional study. RESULTS: Patients with SA had significantly reduced Pneumocystis KEX1 titres compared with patients with mild/moderate asthma (p=0.018) and CF (p=0.003). A binary KEX1 RET indicator was determined at a threshold of KEX1 RET=1000. Patients with SA had 4.40 (95% CI 1.28 to 13.25, p=0.014) and 17.92 (95% CI 4.15 to 66.62, p<0.001) times the odds of falling below that threshold compared with mild/moderate asthma and patients with CF, respectively. Moreover, KEX1 IgG RET did not correlate with tetanus toxoid IgG (r=0.21, p=0.82) or total IgE (r=0.03, p=0.76), indicating findings are specific to antibody responses to KEX1. CONCLUSIONS: Paediatric patients with SA may be at higher risk for chronic Pneumocystis infections and asthma symptom exacerbation due to reduced levels of protective antibodies. Plasma KEX1 IgG titre may be a useful parameter in determining the clinical course of treatment for paediatric patients with asthma.

Susceptibility to bronchiolitis in infants.

PURPOSE OF REVIEW: Bronchiolitis is a complex disease that exhibits tremendous heterogeneity with respect to cause, clinical presentation, outcome and susceptibility of afflicted patients. Although respiratory syncytial virus (RSV) is widely considered to be the most important cause of bronchiolitis in children, little is known about the mechanisms of susceptibility to severe infection. RECENT FINDINGS: Over the last several years, there have been important advances in our understanding of RSV bronchiolitis, ranging from large-scale epidemiologic observations to novel in-vitro discoveries, including those related to environmental and host risk factors. In addition, new investigative techniques have been developed, which may enhance our understanding about the interaction between RSV and the pediatric airway. SUMMARY: RSV remains the most frequently encountered cause of bronchiolitis and contributes to significant morbidity and mortality worldwide. The investigations highlighted in this review may serve as foundations for future mechanistic studies, the implementation of new preventive strategies and the discovery of novel treatments.

Integrative study of the upper and lower airway microbiome and transcriptome in asthma.

Relatively little is known about interactions between the airway microbiome and airway host transcriptome in asthma. Since asthma affects and is affected by the entire airway, studying the upper (e.g., nasal) and lower (e.g., bronchial) airways together represents a powerful approach to understanding asthma. Here, we performed a systematic, integrative study of the nasal and bronchial microbiomes and nasal and bronchial host transcriptomes of children with severe persistent asthma and healthy controls. We found that (a) the microbiomes and host transcriptomes of asthmatic children are each distinct by site (nasal versus bronchial); (b) among asthmatic children, Moraxella and Alloiococcus are hub genera in the nasal microbiome, while there are no hubs among bronchial genera; (c) bronchial Actinomyces is negatively associated with bronchial genes for inflammation, suggesting Actinomyces may be protective; (d) compared with healthy children, asthmatic children express more nasal genes for ciliary function and harbor more nasal Streptococcus; and (e) nasal genera such as Corynebacterium are negatively associated with significantly more nasal genes for inflammation in healthy versus asthmatic children, suggesting a potentially stronger protective role for such nasal genera in healthy versus asthmatic children. Our systematic, integrative study provides a window into host-microbiome associations in asthma.

Bronchoscopy in severe childhood asthma: Irresponsible or irreplaceable?

For children with severe asthma, guideline-based management focuses on the escalation of anti-inflammatory and bronchodilatory medications while addressing comorbid conditions. Bronchoscopy, in this context, has been relegated to ruling out asthma mimickers. More recently, however, there have been questions surrounding the clinical utility of bronchoscopy in severe childhood asthma. In this solicited lecture summary, we discuss the past, present, and potential future applications of bronchoscopy in severe childhood asthma.

Pulmonary cryptococcosis induces chitinase in the rat.

BACKGROUND: We previously demonstrated that chronic pulmonary infection with Cryptococcus neoformans results in enhanced allergic inflammation and airway hyperreactivity in a rat model. Because the cell wall of C. neoformans consists of chitin, and since acidic mammalian chitinase (AMCase) has recently been implicated as a novel mediator of asthma, we sought to determine whether such infection induces chitinase activity and expression of AMCase in the rat. METHODS: We utilized a previously-established model of chronic C. neoformans pulmonary infection in the rat to analyze the activity, expression and localization of AMCase. RESULTS: Our studies indicate that intratracheal inoculation of C. neoformans induces chitinase activity within the lung and bronchoalveolar lavage fluid of infected rats. Chitinase activity is also elicited by pulmonary infection with other fungi (e.g. C. albicans), but not by the inoculation of dead organisms. Enhanced chitinase activity reflects increased AMCase expression by airway epithelial cells and alveolar macrophages. Systemic cryptococcosis is not associated with increased pulmonary chitinase activity or AMCase expression. CONCLUSION: Our findings indicate a possible link between respiratory fungal infections, including C. neoformans, and asthma through the induction of AMCase.