Bulk RNA-seq on human pluripotent stem cell-derived type 2 alveolar cell-like cells
We reportWe used bulk RNA sequencing technology to profile gene expression in human pluripotent stem cell-derived type 2 alveolar cell-like cells. By obtaining over 15,000 genes, we compared the derived alveolar cell-like cells to H9 embryonic stem cells. We found significant down-regulation of several pluripotency genes whereas activation of lung or alveolus marker genes, and thus suggested successful induction. We treated the derived cells with nano carbon black and sequenced the samples in order to obtain differentially expressed genes due to the treatment. From KEGG analysis, we concluded that expression of most genes inferring lung or alveolus identities were not affected by the treatment. However, pathways such as chemical carcinogenesis and xenobiotic metabolism were significantly promoted. Finally, since organoid culture is trendy, we compared monolayer-derived alveolar cell-like cells to organoid-based derived ones. Results showed overall similarity in gene expression yet organoid culture yielded morphologically and structurally better cells. This study uses bulk RNA sequencing to confirm the alveolar induction from human pluripotent stem cells and provides insights for nano carbon black toxicities in alveolar cells. Overall design: RNA profiling of H9 human embryonic stem cell-derived type 2 alveoalr cell-like cells induced in monolayer fashion or organoid system, and derived cells subjected to nano carbon black treatment