Epigenomic Analysis of ARID1A/ARID1B in Lung Development

Divya Khattar, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States; Sharlene Fernandes, CCHMC, United States; Minhze Guo, CCHMC, United States; William Zacharias, CCHMC, United States; Daniel Swarr, CCHMC, United States

Background: Epigenetic control of gene expression and chromatin remodeling have been associated with many pediatric developmental lung disorders including bronchopulmonary dysplasia (BPD). The exact molecular mechanisms by which cell type identity is established and maintained during lung development remains unknown. Previously we have used Sox9+ lung epithelial progenitor cell (EPC) population as a model system to show that dynamic changes in chromatin accessibility correlate with differential gene expression during development. To predict potential transcription factor (TF) chromatin regulator (CR) complex regulatory networks, we used the Paired Expression and Chromatin Accessibility Modeling (PECA) and identified SWI/SNF proteins ARID1A/1B as key drivers of chromatin accessibility changes during development of the Sox9+ progenitor cell lineage.

Objectives: Our primary hypothesis is that dynamic modulation of chromatin accessibility by ARID1A/1B at specific cis-regulatory elements (CREs) is required for alveolar epithelial cell (AEC) maturation, and secondly, the SWI/SNF complex is directly targeted to these CREs by interaction with “master” lung TFs, including NKX2.1 and SOX9.

Design/Methods: We developed Arid1a & Arid1b epithelial CKO mouse models and performed histology and immunohistochemistry to define the phenotype. We then propose using bioinformatic tools to mechanistically understand how ARID1A/ARID1B interacts with key TFs and remodels chromatin to establish AEC identity and function which in-turn also helps direct lung repair after injury.

Results: Our preliminary data show that loss of Arid1a in a mouse model leads to persistence of Sox9+ EPC, impaired alveolar differentiation, and neonatal death due to respiratory distress. A combined loss of Arid1a and Arid1b resulted in a phenotype of pulmonary hypoplasia/aplasia suggesting their key role in lung development. We performed single-cell RNA sequencing (scRNA-seq) and single-cell ATAC sequencing (scATAC-seq) on E 18.5 Arid1a CKO, Arid1b CKO, and littermate control mice and are in the process of analyzing our results. The scRNA-seq analysis shows an increase in expression of proximal epithelial airway structures like ciliated and secretory cells and a decrease in expression of the proliferating type II alveolar cells in the CKO animals compared to controls.

Conclusion: This data provides insight into the mechanistic understanding and provides a basis to understand the pathogenesis of complex lung diseases and for the development of therapeutic strategies to modulate the epigenome in the future.