Single-cell RNA Sequencing of Human Embryonic Stem Cells Reveals Immediate and Deferred Transcriptomic Responses to ATRA Toxicity Across Cell Sub-populations

Identifying chemical-mediated molecular signatures may provide nuanced insights into early developmental processes, characterized by plasticity, rapid growth, and differentiation. This requires increased resolution of the multiple cell states and trajectories that are present at this stage. Cell-based models can facilitate higher-throughput evaluation and screening of potential developmental toxicants. In this study, we used single-cell RNA sequencing to characterize the transcriptomic signatures of the H9 human pluripotent stem cell (hPSC) maintained under pluripotency and treated with 30 nM all-trans retinoic acid (RA), a developmental morphogen, for 6 and 72 hours. In addition, we evaluated the molecular effects of RA on hPSCs over an undirected differentiation course for 14 days, to characterize retinoic acid-associated cell transition states. For both pluripotent (6- and 72-hrs) and undirected differentiation (14-day) exposure paradigms, transcriptional responses to RA were observed and compared to gastrulation markers of altered developmental trajectories. At 14 days in differentiation media, we observed cell clusters representing differentiation into multiple cell-types. This transcriptomic data could be utilized to identify and screen chemicals for developmental toxicity.