IL13 Signaling in Allergic Asthma

AIM 1. Critically assess dupilumab-regulated transcriptome, phosphoproteome and secretome of nasal airway epithelial cells isolated from obese patients with allergic vs. non-allergic asthma and comorbid obesity. AIM 2. Determine the effect of dupilumab on expression and signaling activity of IL-4Ra, IL-13Ra1, and IL-13Ra2 in nasal airway epithelial cells isolated from patients with allergic vs. non-allergic asthma and comorbid obesity.

Study Design: The goal is to enroll 16 adults with allergic asthma and obesity and 16 adults with non-allergic asthma and obesity. Subjects in each group will undergo an initial screening visit (V0) to establish the subject groups according to allergic status. "Allergic" asthma will be defined as the presence of a positive skin prick test, absolute eosinophil count >150/uL and serum IgE > 100 IU/ml, as these criteria have differentiated phenotypes of patients with asthma and obesity in previous studies. Subjects will undergo skin allergy testing and blood sampling at V0. Subjects will return within 2 weeks of initial screening, and we will collect fresh brushings of the sinonasal inferior turbinate of participants using sterile cytology brushes.

Study Population: Obese adults with allergic and non-allergic asthma.

Analysis Plan:

The effect of dupilumab on transcriptomic and proteomic expression patterns, including fold change of IL-13Ra2 signaling, will be compared between obese allergic and obese non-allergic asthma patients. Each dataset will be critically evaluated for data quality and then processed using field-standard workflows. For the mRNA-seq data, DESeq2 package will be utilized to identify differentially expressed transcripts, and for the proteomic data we will employ linear models using a moderated test statistic. In addition to identify individual transcripts and proteins that are differentially regulated, Ingenuity Pathway Analysis will be performed to identify dysregulated pathways. The false discovery rate will be used to correct for multiple hypothesis testing within each of the analyses performed. Additional biomarkers including serum IgE, periostin and IL-33; cell surface IL-4Ra and IL-13Ra1, spirometry and IOS measurements; blood eosinophil counts; methacholine PC20; ACQ scores and FeNO measurements will be compared using either the Student's t-test or the Wilcoxon rank sum test, depending on the normality of the specific dataset. SAS version 9.4 or higher (SAS Institute, Inc., Cary, NC), and the R statistical programming environment, version 4.0 or higher, will be used for all analyses and an adjusted p-value <0.05 will be considered statistically significant.

Sample size: The sample size calculations are based upon estimates of clinically meaningful mean differences and standard deviations. Baseline fold change of IL-13RA2 expression was measured in cultured human airway fibroblasts for 6 subjects in a lean asthma group (0.312 ± 0.289) and 7 subjects in an obese asthma group (5.285 ± 3.944). Group sample sizes of 8 within each group (16 total) achieves 86.2% power to reject the null hypothesis of equal means with a significance level (alpha) of 0.050 using a two-sided two-sample unequal variance t-test.

The effect size for this comparison, based on historical data, is approximately 1.75 (fairly large effect size). Therefore, increasing the sample size to 16 patients per group would offer the ability to detect a lower effect size of 1.07 to 1.21 with 80% to 90% power. Assuming a similar standard deviation in each group, this translates into the ability to detect a difference between asthma groups of at least 3.0. To allow for a potential 15% patient drop-out rate, the plan is to recruit a total of 36 participants.