The genomic, epigenomic and biophysical cues controlling the emergence of the gas exchange niche in the lung

The lung alveolus is the functional unit of the respiratory system required for gas exchange. During the transition to air breathing at birth, biophysical forces are thought to shape the emerging tissue niche. However, the intercellular signaling that drives these processes remain poorly understood. Applying a multimodal approach, we identify alveolar type 1 (AT1) epithelial cells as a distinct signaling hub. Lineage tracing demonstrates that AT1 progenitors align with receptive, force-exerting, myofibroblasts in a spatial and temporal manner. Through single cell chromatin accessibility and pathway expression (SCAPE) analysis, we demonstrate that AT1-restricted ligands are required for myofibroblasts and alveolar formation. These studies show that the alignment of cell fates, mediated by biophysical and AT1-derived paracrine signals, drives the extensive tissue remodeling required for postnatal respiration. Overall design: All mouse experiments used CD-1 female mice with the age indicated in the libraries . Single-cell suspensions were prepared from whole mouse lungs. For all libraries, DAPI-negative cells were were sorted by flow cytometry to obtain heterogeneous whole lung sample. Human tissue was derived from normal peripheral lung tissue. Single cell suspension was depleted of CD45-positive cells by bead selection. All of the murine post-natal timepoints also had CD45-positive cells removed from cell sort. Single-cell barcoded droplets were produced using 10X Single Cell 3' v2 chemistry. Libraries generated were sequenced using HiSeq2500 instrument in High-output mode. Reads were aligned and gene level unique molecular identifier (UMI) counts were obtained using the Cell Ranger pipeline.