The transcriptional landscape of developing human trisomy 21 lungs

Trisomy 21 (T21), resulting in Down Syndrome (DS), is the most prevalent chromosomal abnormality worldwide. While pulmonary disease is a major cause of morbidity and mortality in DS, the ontogeny of pulmonary complications remains poorly understood. We recently demonstrated that T21 lung anomalies, including airway branching and vascular lymphatic abnormalities, are initiated <i>in utero</i>. Here, we aimed to describe molecular changes at the single cell level in prenatal T21 lungs. Single cell RNA sequencing (scRNAseq) was used to generate transcriptomic profiles of individual human lung cells in tissue obtained from T21 (n=5) and non-T21 (n=4) prenatal lungs. Clustering of cells, marker identification, UMAP representation, and differential expression analysis were performed in Seurat. Cell type annotation and pathway analysis were annotated using Toppfun and a human fetal lung cell atlas. Spatial differences in cellular phenotypes were validated using immunofluorescent staining (IF) and fluorescent in situ hybridization (FISH). Our results detail changes in gene expression at the time of initiation of histopathological abnormalities in T21 prenatal lungs. Notably, we identify precocious differentiation of epithelial cells, widespread induction of key extracellular matrix molecules in mesenchymal cells and hyper-activation of IFN signaling in endothelial cells. This single cell dataset of T21 lungs greatly expands our understanding of antecedents to pulmonary complications and should facilitate efforts to mitigate respiratory disease in DS.