Human cell fate engineering guided by single-cell transcriptomics

Status: This talk is in preparation - details may change

Human neurons generated through transcription factor (TF) overexpression have transformed the way we study neurodevelopment and model neurological diseases, opening new avenues for therapeutic discovery. Despite this progress, the full range of neuronal subtypes that can be programmed in vitro remains largely uncharted. In this seminar, I will talk about our work in expanding the diversity of neurons derived from human pluripotent stem cells by combining TF-driven reprogramming with systematic modulation of developmental signaling pathways. We performed a large-scale screen of 480 signaling conditions in parallel with NGN2 or ASCL1/DLX2 induction, using multiplexed single-cell transcriptomics to capture cellular outcomes across 700,000 cells. Our analysis revealed a broad spectrum of excitatory and inhibitory neurons that align with the developmental patterning axes of the neural tube. Electrophysiological profiling showed that these patterned neurons possess distinct functional and morphological properties shaped by their respective signaling environments. We perturbed TFs at the hub of gene regulatory networks (GRNs) and demonstrated their necessity and sufficiency to drive the specification of distinct neuronal subtypes. We further found that patterning neural progenitors before TF induction unlocks a greater range of neuronal diversity by activating regulons that mirror those of primary human neurons. Comparisons with primary tissue uncovered closely matched neuronal subtypes sharing transcriptional signatures in TF expression, neurotransmitter usage, and ion channel composition, while highlighting persistent differences in metabolic pathways. Together, we put together an in vitro atlas of human neuronal diversity of over 200 neuronal subtypes, as well as providing a framework for programming a wide array of human neurons and for understanding how transcriptional and signaling cues cooperate to shape neuronal fate.