Sorting and Expression Profiling of Airway Cells From Humans (The SEARCH Study)

University of California, San Francisco32 enrolled

Overview

This will be a single site, mechanistic study of asthmatic subjects and healthy, non-asthmatic controls involving a baseline characterization visit and a research bronchoscopy visit. We will identify differences in airway epithelial epigenetic enhancer signatures in asthma, by analyzing freshly isolated airway epithelial cells from healthy controls and from well-characterized subjects with asthma.

The airway epithelium is critical for normal lung function and changes in the epithelium are central to the development of asthma. Precise regulation of gene transcription is essential for airway epithelial cell differentiation and transcription changes lead to many abnormalities seen in asthma. Despite the dominant role of enhancers in regulating transcription, little is known about how these DNA regulatory elements control airway epithelial cell transcription or about how enhancer activity differs in asthma compared to health. Closing this knowledge gap will have a major impact on our understanding of normal epithelial development and asthma. In addition, enhancer-based approaches for reprogramming the airway epithelium promise to be powerful tools for dissecting mechanism that will set the stage for developing a new class of precisely targeted treatments for asthma. Our overall goals are to identify enhancers that are important in regulation of key airway epithelial cell genes, to determine how enhancer activity changes in asthma, and to develop approaches for targeting the activity of these enhancers.

Study Type

OBSERVATIONAL

Enrollment

Conditions

Asthma

Eligibility

Sex: ALLMin age: 18 YearsMax age: 70 YearsHealthy volunteers:

Medical Language ↔ Plain English

Inclusion Criteria (Healthy participants): 1. Male and female subjects between the ages of 18 and 70 years 2. Ability to provide written informed consent and ability to comply with the requirements of the study 3. No hyperreactivity to methacholine (PC20 FEV1 Methacholine \>16 mg/mL) 4. No history of allergic rhinitis/seasonal allergies Inclusion Criteria (Asthmatic participants): 1. Male and female subjects between the ages of 18 and 70 years 2. Ability to provide written informed consent and ability to comply with the requirements of the study 3. History of asthma 4. No use of oral or inhaled corticosteroids for the treatment of asthma during the past 6 weeks 5. Hyperreactivity to methacholine (PC20 FEV1 Methacholine \< 8 mg/ml) Exclusion Criteria: The same exclusion criteria will apply to both Sub-studies. 1. Current smokers, defined by (a) \>5 cigarettes smoked in past 12 months, and (b) ≤ 8 weeks since last time smoking; or former smokers who have a total smoking history ≥10 pack-years 2. Pregnant, breastfeeding, or unwilling to practice birth control during participation in the study 3. Subjects with a history of lung disease other than asthma 4. Subjects with a history of a medical disease, which in the opinion of the Investigator may put the subject at extra risk from study-related procedures or because the disease may influence the results of the study 5. Prior esophageal hernia surgery. 6. Current participation in an investigational drug trial

Locations (1)

University of California, San Francisco

San Francisco, California, United States

Outcomes

Primary Outcomes

Measure the genomic location of enhancers in genes previously found to be differentially expressed in asthma vs health using H3K27ac ChIP-seq and ATAC-seq on airway epithelial brushings.

We previously identified changes in epithelial gene expression in individuals with asthma. To identify candidate enhancers that account for these changes, we will use Drop-seq, ChIPseq and ATAC-seq to analyze freshly isolated airway epithelial cells from healthy controls and from well-characterized subjects with asthma.

Time frame: Between 1-12 weeks

Assessment of persistence of signatures of airway inflammation

Perform epithelial brush gene expression profiling and sputum induction on longitudinal samples obtained at 12 months after the initial bronchoscopy, to assess stability of type-2 and non-type-2 pathways that are dysregulated in asthma. (Achieved via the PISA sub-study)

Time frame: 1-12 weeks and at 10-14 months

Secondary Outcomes

Measure gene expression by RNA sequencing in both airway brushes and BAL cells for assessment of non-type-2 pathways differentially expressed in asthma vs health.

Perform bronchoalveolar lavage (BAL) cell flow cytometry and epithelial brush gene expression profiling to look for non-type-2 pathways that are dysregulated in asthma.

Time frame: Between 1-12 weeks

Data from ClinicalTrials.gov

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