Extended Data Fig. 4: Functional compartmentalization of the alveolus.

a, Transmission electron micrographs of alveolar walls from adult mouse lungs, pseudocoloured to highlight cells and connective tissue (extracellular matrix (ECM) or fibres). Apln-creER; Rosa26-tdTomato (to label aerocytes) or Aplnr-creER; Rosa26-tdTomato (to label gCap cells) lungs were immunostained for tdTomato (detected with DAB and NiCl₂, heavy black stain). Labelled aerocytes but not gCap cells are associated with thin regions of the air–blood barrier (delimited by dashed lines), where the epithelium is tightly apposed to the endothelium. Some thin regions do not contain labelled aerocytes as aerocyte labelling using Apelin-creER is inefficient. Thick regions, where the epithelium is separated from the endothelium by fibres or other cells, can be associated with either aerocytes or gCap cells. AT1 cell, alveolar type 1 epithelial cell; AT2 cell, alveolar type 2 epithelial cell. Micrographs in top left, middle and bottom panels are shown without pseudocolouring in Fig. 2g–i. b, c, gCap cells associate with fibroblasts. Alveoli with labelled aerocytes (aCap) in Apln-creER; Rosa26-tdTomato (b) or gCap cells in Aplnr-creER; Rosa26-tdTomato (c) lungs immunostained for integrin α8 to show alveolar fibroblasts¹⁶. Asterisks mark aerocytes that do not associate with fibroblasts (in b) and gCap cells that do (in c). Example regions of alveoli not covered by fibroblasts are dotted. Note that the dotted region in b is occupied by an aerocyte not overlaid by fibroblasts, whereas fibroblasts overlay gCap cells in c. d, Selected genes with known functions, which are differentially expressed between the two alveolar capillary cell types in adult mouse lung¹³. Pro, procoagulants; anti, anticoagulants^44,45. e, Summary of signalling interactions between capillary cell types and surrounding cells in the mouse alveolus. Arrows indicate direction of signalling. f, Schematic representation of an alveolus highlighting proposed specialized functions and signalling interactions of alveolar capillary cell types. AT1, alveolar type 1 epithelial cell; AT2, alveolar type 2 epithelial cell. Scale bars, 2 μm (a); 10 μm (b, c).