Functional Characterization of ABCA3 Genomic Variants

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PROJECT SUMMARY Neonatal respiratory distress syndrome (RDS) is traditionally attributed to developmentally regulated disruption of pulmonary surfactant production. However, studies of term infants with lethal RDS have led to the discovery of genetically regulated disruption of functional surfactant production. Rare or private, biallelic, pathogenic variants in the ATP binding cassette transporter A3 gene (ABCA3) are the most common monogenic causes of neonatal RDS in term infants and childhood interstitial lung disease (chILD). ABCA3 transports phospholipids across the lamellar body limiting membrane in alveolar type II cells and is required for packaging of functional surfactant. Pathogenic ABCA3 variants encode (1) disruption of intracellular trafficking, (2) impairment of ATP- ase mediated, phospholipid transport into the lamellar body, and may also (3) activate intracellular stress and degradation pathways that disrupt lung function. Current treatments (surfactant replacement, steroids, azithromycin, and hydroxychloroquine) are non-specific and ineffective. Lung transplantation, with a 5 year survival of ~50%, remains the only treatment for progressive respiratory failure in affected infants and children. Development of variant-specific therapies for patients with pathogenic variants in the cystic fibrosis transmembrane conductance regulator gene (CFTR), a member of the ABC transporter superfamily (ABCC7), can provide a model for development of variant-specific therapies for ABCA3, although correctors will likely be gene- and variant-specific. The premise of this proposal is to develop a scalable, functional genomics platform for mechanistic characterization of ABCA3 variants and for compound screening and identification of small molecule correctors in a human, pulmonary epithelial, physiologically-relevant cell line. Specifically, we will use clonally derived A549 cell lines that stably express individual ABCA3 pathogenic variants for (1) fluorescence-based, functional assays, (2) characterization of variant-specific, pathogenic cellular degradation pathway activation, and (3) screening of FDA-approved compounds for rescue of variant-encoded ABCA3 intracellular mistrafficking and pathogenic degradation pathway activation to test hypothesis that variant-encoded ABCA3 mistrafficking and pathogenic activation of cellular stress and degradation pathways can be mechanistically characterized and can be corrected with FDA-approved small molecules. These studies will provide proof of principle for a scalable, functional, physiologically-relevant genomics platform to discover variant-specific therapies for infants and children with ABCA3 deficiency. Additionally, this genetically versatile system can be adapted and extended to discover targeted therapies for patients with other monogenic diseases that disrupt surfactant function or pulmonary epithelial cell metabolism.