Decoding transcriptional identity during neuron-astroglia cell fate driven by RAR-specific agonists

How cells respond to different signals leading to defined lineages is an open question to understand physiological differentiation leading to the formation of organs and tissues. Among the various morphogens, retinoic acid signaling, via the RXR/RAR nuclear receptors activation, is a key morphogen of nervous system development and brain homeostasis. Here, we analyze gene expression in ∼80 000 cells covering 16 days of monolayer mouse stem cell differentiation driven by the pan-RAR agonist all-trans retinoic acid, the RARα agonist BMS753 or the activation of both RARβ and RARγ receptors (BMS641 + BMS961). Furthermore, we have elucidated the role of these retinoids for driving nervous tissue formation within 90 days of brain organoid cultures, by analyzing >8000 distinct spatial regions over 28 brain organoids. Despite a delayed progression in BMS641 + BMS961, RAR-specific agonists led to a variety of neuronal subtypes, astrocytes, and oligodendrocyte precursors. Spatially resolved transcriptomics performed in organoids revealed spatially distinct RAR isotype expression leading to specialization signatures associated with matured tissues, including a variety of neuronal subtypes, retina-like tissue structure signatures and even the presence of microglia.