Inhibitory interneurons are a diverse population with crucial roles in cortical and striatal information processing. These cells have been implicated in human neuropsychiatric and neurodevelopmental disorders, including autism, schizophrenia and epilepsy. Mammalian inhibitory interneurons are derived from transient ventral telencephalic structures known as the ganglionic eminences, with the majority produced in the medial ganglionic eminence (MGE). These cells either migrate tangentially to the pallium, where they integrate into the cortical circuitry, or remain in the ventral telencephalon and become striatal interneurons. MGE-derived cortical interneurons differentiate into either Parvalbumin (PVALB) or Somatostatin (SST)-expressing cells. However, there are many outstanding questions. Multiple subtypes of SST-expressing interneurons exist in adult cortex, but it remains unknown whether specification at this level is a result of intrinsic events or extrinsic influences.
We studied the generation of interneurons using an in vitro human stem cell culture system. To do so we measured and analyzed the gene expression changes that occur as MGE-like cells are generated from human embryonic stem cells (hESCs). We performed extensive subpopulation and single-cell transcriptional profiling using RNAseq at multiple timepoints to characterize the diversity and maturation status of these cells. We compared the transcriptomes of interneurons generated using this protocol to in vivo-derived human fetal interneurons to place them in temporal and developmental context. Our single-cell RNAseq analysis revealed 41 distinct populations of progenitors, neurons and glia over the course of the differentiation protocol. Using SST+ cortical interneuron populations present in culture, we identified a set of genes associated with interneuron maturation. This study is the first to characterize the diversity and dynamic transcriptomic changes of human MGE progenitors and neurons generated in vitro at single-cell resolution, and the first transcriptomic comparison between human fetal interneurons and hESC-derived human interneurons.