SARS-CoV-2 surveillance in households with and without asthmatic/allergic children: The Human Epidemiology and Response to SARS-CoV-2 study (HEROS)

Rationale: Whether children and people with asthma and allergic diseases are at increased risk for SARS-CoV-2 infection is not known. Neither is their role in household transmission. Methods: Biweekly nasal sample collections and weekly surveys were conducted to identify incident SARS-CoV-2 infections among children (\u3c13 \u3eyears) and teenagers (13-21 years) enrolled in asthma/allergic disease focused cohorts, and their household members, from May 2020-February 2021. Probability of subject/household infections and household transmissions were calculated using time-to-event analyses, and factors associated with infection and transmission risk using regression analyses. Results: Household (N=1,394) and subject (N=4,142) SARS-CoV-2 infection probability was 25.8% and 14.0%, respectively, and was similar for children (14.0%,CI:8.0-19.6%), teenagers (12.1%,CI:8.2-15.9%), and adults (14.0%,CI:9.5-18.4%). Infections were symptomatic in 24.5% of children, 41.2% of teenagers, and 62.5% of adults. Exposure to both symptomatic (aHR=87.39,CI:58.02-131.63) and asymptomatic (aHR=27.80,CI:17.16–45.03) infected household members was a risk factor for infection. Food allergy was associated with decreased infection risk (aHR=0.50,CI:0.32-0.81), but asthma was not (aHR=1.04,CI:0.73-1.46). Household infection risk was associated with attending in-person school (aHR=1.67,CI:1.09-2.57). Household secondary attack rate was 57.7%. Decreased risk of household transmission was associated with teen age, lower BMI, and lower viral load. Conclusions: Asthma does not increase risk of SARS-CoV-2 infection, while food allergy is protective. SARS-CoV-2 infection risk in children is similar to that of teenagers and adults. SARS-CoV-2 transmission risk and secondary attack rate is much higher than previously estimated in households with children, likely driven by the high frequency of asymptomatic childhood infections

Pipeline Development for Hippo Pathway Related Protein Interactome Analysis

This thesis presents a user-friendly pipeline for analyzing data from evolving mass spectrometry techniques, developed in response to the growing volume and complexity of data in the field of proteomics. While offering a comprehensive review of current methods for isolating and identifying interacting proteins using MS analysis, the pipeline also highlights areas for integrating other -omic resources to enhance data interpretation. This pipeline was utilized to identify novel regulators within the Hippo pathway, a central regulator of cell proliferation and organ size. A unique 9-amino acid sequence was identified, vital for interactions between WW-PxY motif containing proteins in the Hippo pathway. Furthermore, the pipeline aided in the discovery of a new YAP inhibitor, Syntaxin binding protein 4 (STXBP4), harboring this conserved sequence. The pipeline was also employed to investigate potential regulators in the PLD-PA-Hippo axis. Although no Hippo pathway regulators were found within the PLD family, the analysis unveiled significant Hippo-independent interactions. Among the interactors of six PLD members, the E3 ubiquitin-protein ligase, PJA2, was found to bind specifically to PLD1, an oncogene. Furthermore, Phosphatidic Acid (PA) was shown to bind, co-localize, and regulate Sphingosine Kinase1 (SPHK1), linked to cell growth, proliferation, and survival. This thesis underscores the importance of continually updating bioinformatic resources to keep up with advances in data generation techniques, thus allowing the extraction of relevant biological information from intricate datasets. The studies driven by this pipeline signify just the inception, and further tools, such as additional disease -omic resources, can be integrated for comprehensive insights into many biological processes

Analysis of affinity purification-related proteomic data for studying protein–protein interaction networks in cells

During intracellular signal transduction, protein-protein interactions (PPIs) facilitate protein complex assembly to regulate protein localization and function, which are critical for numerous cellular events. Over the years, multiple techniques have been developed to characterize PPIs to elucidate roles and regulatory mechanisms of proteins. Among them, the mass spectrometry (MS)-based interactome analysis has been increasing in popularity due to its unbiased and informative manner towards understanding PPI networks. However, with MS instrumentation advancing and yielding more data than ever, the analysis of a large amount of PPI-associated proteomic data to reveal bona fide interacting proteins become challenging. Here, we review the methods and bioinformatic resources that are commonly used in analyzing large interactome-related proteomic data and propose a simple guideline for identifying novel interacting proteins for biological research

Interactome Analysis of Human Phospholipase D and Phosphatidic Acid-Associated Protein Network.

Mammalian phospholipase D (PLD) enzyme family consists of six members. Among them, PLD1/2/6 catalyzes phosphatidic acid (PA) production, while PLD3/4/5 has no catalytic activities. Deregulation of the PLD-PA lipid signaling has been associated with various human diseases including cancer. However, a comprehensive analysis of the regulators and effectors for this crucial lipid metabolic pathway has not been fully achieved. Using a proteomic approach, we defined the protein interaction network for the human PLD family of enzymes and PA and revealed diverse cellular signaling events involving them. Through it, we identified PJA2 as a novel E3 ubiquitin ligase for PLD1 involved in control of the PLD1-mediated mammalian target of rapamycin signaling. Additionally, we showed that PA interacted with and positively regulated sphingosine kinase 1. Taken together, our study not only generates a rich interactome resource for further characterizing the human PLD-PA lipid signaling but also connects this important metabolic pathway with numerous biological processes

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 \u3c 2.8 × 10 CONCLUSIONS: Epigenetic marks in respiratory epithelia are associated with allergic asthma and gene expression changes in inner-city children

DNA methylation and childhood asthma in the inner city

BACKGROUND: Epigenetic marks are heritable, influenced by the environment, direct the maturation of T lymphocytes, and in mice enhance the development of allergic airway disease. Thus it is important to define epigenetic alterations in asthmatic populations. OBJECTIVE: We hypothesize that epigenetic alterations in circulating PBMCs are associated with allergic asthma. METHODS: We compared DNA methylation patterns and gene expression in inner-city children with persistent atopic asthma versus healthy control subjects by using DNA and RNA from PBMCs. Results were validated in an independent population of asthmatic patients. RESULTS: Comparing asthmatic patients (n = 97) with control subjects (n = 97), we identified 81 regions that were differentially methylated. Several immune genes were hypomethylated in asthma, including IL13, RUNX3, and specific genes relevant to T lymphocytes (TIGIT). Among asthmatic patients, 11 differentially methylated regions were associated with higher serum IgE concentrations, and 16 were associated with percent predicted FEV1. Hypomethylated and hypermethylated regions were associated with increased and decreased gene expression, respectively (P \u3c 6 × 10(-12) for asthma and P \u3c .01 for IgE). We further explored the relationship between DNA methylation and gene expression using an integrative analysis and identified additional candidates relevant to asthma (IL4 and ST2). Methylation marks involved in T-cell maturation (RUNX3), TH2 immunity (IL4), and oxidative stress (catalase) were validated in an independent asthmatic cohort of children living in the inner city. CONCLUSIONS: Our results demonstrate that DNA methylation marks in specific gene loci are associated with asthma and suggest that epigenetic changes might play a role in establishing the immune phenotype associated with asthma

Eosinophil gene activation in the upper airway is a marker of asthma exacerbation susceptibility in children

RATIONALE: A significant proportion of children in urban populations remain exacerbation prone despite guideline-directed care. Preventing exacerbations in these children remains a major unmet clinical need. Identification of cellular and molecular markers of exacerbation susceptibility that can determine periods of heightened exacerbation risk is important towards improving asthma management. METHODS: 94 children with exacerbation prone asthma and peripheral blood eosinophils \u3e150 /mm3 had nasal lavage samples collected at baseline. Nasal cell differentials were determined by cytospin and nasal gene expression assessed by RNA-sequencing. Participants were monitored for upper respiratory tract infections (URIs) and asthma exacerbations. Differential gene expression was assessed by cell deconvolution and modular analysis coupled with multivariate linear modeling. RESULTS: Baseline nasal samples were compared between children who developed an asthma exacerbation associated with a URI within 2 months of collection versus children who had a URI without asthma exacerbation. Those who developed an exacerbation had 2.7 fold higher nasal eosinophil percentages (

Associations between outdoor air pollutants and non-viral asthma exacerbations and airway inflammatory responses in children and adolescents living in urban areas in the USA: a retrospective secondary analysis

BACKGROUND: Asthma prevalence and severity have markedly increased with urbanisation, and children in low-income urban centres have among the greatest asthma morbidity. Outdoor air pollution has been associated with adverse respiratory effects in children with asthma. However, the mechanisms by which air pollution exposure exacerbates asthma, and how these mechanisms compare with exacerbations induced by respiratory viruses, are poorly understood. We aimed to investigate the associations between regional air pollutant concentrations, respiratory illnesses, lung function, and upper airway transcriptional signatures in children with asthma, with particular focus on asthma exacerbations occurring in the absence of respiratory virus. METHODS: We performed a retrospective analysis of data from the MUPPITS1 cohort and validated our findings in the ICATA cohort. The MUPPITS1 cohort recruited 208 children aged 6-17 years living in urban areas across nine US cities with exacerbation-prone asthma between Oct 7, 2015, and Oct 18, 2016, and monitored them during reported respiratory illnesses. The last MUPPITS1 study visit occurred on Jan 6, 2017. The ICATA cohort recruited 419 participants aged 6-20 years with persistent allergic asthma living in urban sites across eight US cities between Oct 23, 2006, and March 25, 2008, and the last study visit occurred on Dec 30, 2009. We included participants from the MUPPITS1 cohort who reported a respiratory illness at some point during the follow-up and participants from the ICATA cohort who had nasal samples collected during respiratory illness or at a scheduled visit. We used air quality index values and air pollutant concentrations for PM FINDINGS: Of the 208 participants from the MUPPITS1 cohort and 419 participants from the ICATA cohort, 168 participants in the MUPPITS1 cohort (98 male participants and 70 female participants) and 189 participants in the ICATA cohort (115 male participants and 74 female participants) were included in our analysis. We identified that increased air quality index values, driven predominantly by increased PM(2·5) and O(3) concentrations, were significantly associated with asthma exacerbations and decreases in pulmonary function that occurred in the absence of a provoking viral infection. Moreover, individual pollutants were significantly associated with altered gene expression in coordinated inflammatory pathways, including PM(2·5) with increased epithelial induction of tissue kallikreins, mucus hypersecretion, and barrier functions and O(3) with increased type-2 inflammation. INTERPRETATION: Our findings suggest that air pollution is an important independent risk factor for asthma exacerbations in children living in urban areas and is potentially linked to exacerbations through specific inflammatory pathways in the airway. Further investigation of these potential mechanistic pathways could inform asthma prevention and management approaches. FUNDING: National Institutes of Health, National Institute of Allergy and Infectious Diseases

An Exaggerated type i interferon antiviral response is associated with exacerbations in pediatric asthma

RATIONALE: Type-I interferon responses are critical to controlling viral upper respiratory tract infections (URIs), but excessive antiviral responses can have detrimental effects on the airway. We investigated the peripheral blood and upper airway gene expression responses to URIs in children with difficult-to-control asthma to determine differences in type-I interferon responses associated with exacerbations in vivo. METHODS: 106 children with exacerbation prone asthma and peripheral blood eosinophils ≥150 /mm3 were enrolled. Peripheral blood and nasal samples were collected at baseline and within 72 hours of URI onset (prior to any systemic corticosteroid use). Gene expression was determined by RNAsequencing and virus infection by PCR. Differential gene expression was assessed by modular analysis coupled with multivariable linear modeling. RESULTS: URIs for which a virus was detected had significantly elevated expression of multiple interferon-associated modules in both the upper airway and peripheral blood compared to baseline samples and compared to URIs without a detectable virus (fold changes 1.3-2.1,