Diverse homeostatic and immunomodulatory roles of immune cells in the developing mouse lung revealed at single cell resolution

At birth, the lungs experience a sudden transition from a pathogen-free, hypoxic, fluid-filled environment to a pathogen-rich, rhythmically distended air-liquid interface. While many studies focus on adult tissue, the heterogeneity of immune cells in the perinatal lung remains unexplored. Here, we combine single cell transcriptomics with <em>in situ</em> hybridization to present an atlas of the murine lung immune compartment during a critical period of lung development. We show that the late embryonic lung is dominated by specialized proliferative macrophages with a surprising physical interaction with the developing vasculature. These macrophages disappear after birth and are replaced by a complex and dynamic mixture of macrophage subtypes, dendritic cells, granulocytes, and lymphocytes. Detailed characterization of macrophage diversity revealed a precise orchestration of five distinct subpopulations across postnatal development to fill context-specific functions in tissue remodeling, angiogenesis, and immunity. These data both broaden the putative roles for immune cells in the developing lung and provide a framework for understanding how external insults alter immune cell phenotype during a period of rapid lung growth and heightened vulnerability.<br>Metadata columns (tab-separated):- the first column is cell id<br>- title: same as cell id- source name: distal lung<br>- organism: Mus musculus<br>- Sequencing run: DC20, DC21, DC23, DC25, DC30, DC35, DC36<br>- Gender: F or M<br>- Plate: 1 or 2 (the number of 384 well plate the cell for sorted into)<br>- Well: A1-P24 (the well number within the 384 well plate the cell was sorted into)<br>- Timepoint: E18.5, P1, P7, or P21<br>- Cell Type: immune<br>- Cell Subtype: one of several subtypes<br>- Mousename: mouse id<br>- Coverage: number of read pairs uniquely mapped to the mouse genome<br>- Number of genes: number of genes detected with 1+ reads<br>- tsne_1: t-SNE coordinate 1<br>- tsne_2: t-SNE coordinate 2<br>- molecule: mRNA<br>- description: none- processed data file: none- raw file 1: fastq file for read 1 (on GEO: GSE147668)- raw file 2: fastq file for read 2 (on GEO: GSE147668)