Hypoxia promotes airway differentiation in the human lung epithelium [scRNAseq_hypoxia_AT2]

Human early embryos develop under physiological hypoxia, but how hypoxia regulates human lung organogenesis remains little known. We have investigated oxygen availability effects on the human lung epithelium using organoids. We find first-trimester lung epithelial progenitors remain undifferentiated under normoxia, but spontaneously differentiate towards multiple airway cell types and inhibit alveolar differentiation under hypoxia. Using chemical and genetic tools, we demonstrate that hypoxia-induced airway differentiation is dependent on HIF (Hypoxia-Inducible Factor) pathways, with HIF1a and HIF2a differentially regulating fate decisions. Transcription factors KLF4 and KLF5 are direct targets of the HIF pathway and promote progenitor differentiation to basal and secretory cells. Chronic hypoxia also reprogrammed human alveolar type 2 cells to airway cells via the HIF pathway. Our results reveal roles for hypoxia and HIF signalling during human lung development and have implications for aberrant cell fate decisions in chronic lung diseases. Overall design: Time series single cell RNA-seq of human fetal lung-derived AT2 (fdAT2) cells isolated from one donor cultured under hypoxia for 0, 6, 15, 30 days, and back to normoxia for 6, 15, 30 days. The two sub-libraries were prepared with Evercode Whole Transcriptome v3 mini kit. Each sublibrary is a mixture of all 7 barcoded samples (7 time points). Sample loading information is attached for demultiplexing.