Investigate how Sox9 overexpression influences ATII lineage plasticity by sc-multiome

Wound healing in response to acute injury is mediated by the coordinated and transient activation of parenchymal, stromal, and immune cells that resolves to homeostasis. Environmental, genetic, and epigenetic factors associated with inflammation and aging can lead to persistent activation of the microenvironment and fibrosis. Here, we identify opposing roles of IL-4 cytokine signaling in interstitial macrophages and type II alveolar epithelial cells (ATIIs). We show that IL4Ra signaling in macrophages promotes regeneration of the alveolar epithelium after bleomycin-induced lung injury. Using organoids and mouse models, we show that IL-4 directly acts on a subset of ATIIs to induce the expression of the transcription factor SOX9 and reprograms them toward a progenitor-like state with both airway and alveolar lineage potential. In the contexts of aging and bleomycin-induced lung injury, this leads to aberrant epithelial cell differentiation and bronchiolization, consistent with cellular and histological changes observed in interstitial lung disease. Overall design: When culturing mouse alveolarspheres, we will seed mouse ATIIs from young and old mice, and grow them using serum-free and feeder-free system. On day 9, cells were infected with either AAV9_Cre or AAV9_Sox9Cre (to overexpress Sox9 together with Cre recombinase. Then we switched the culture medium to ATII differentiation medium to induce ATI differentiation for 4 days. We collected tdTomato+ cells by FACS and extracted nuclei for sc-multiome analysis.