Single-nucleus transcriptomics atlas of middle and late prenatal human cortical development

Late prenatal development of the human neocortex encompasses a critical period of gliogenesis and cortical expansion. However, systematic single-cell analyses to resolve cellular diversity and gliogenic lineages of the third trimester are lacking. Here, we present a comprehensive single-nucleus RNA sequencing atlas derived from the proliferative germinal matrix and laminating cortical plate of 15 prenatal, non-pathological postmortem samples and 3 adult controls. This dataset captures prenatal gliogenesis with high temporal resolution and is provided as a resource for further interrogation. Our computational analysis resolves greater complexity of glial progenitors, including transient glial intermediate progenitor cell (gIPC) and nascent astrocyte populations in the third trimester of human gestation. We use lineage trajectory and RNA velocity inference to further characterize specific gIPC subpopulations preceding both oligodendrocyte (gIPC-O) and astrocyte (gIPC-A) lineage differentiation. We infer unique transcriptional drivers and biological pathways associated with each developmental state, validate gIPC-A and gIPC-O presence within the human germinal matrix and cortical plate in situ, and demonstrate gIPC states being recapitulated across adult and pediatric glioblastoma tumors. Overall design: Single-nucleus transcriptomics (snRNA-seq) data was generated from fresh-frozen, macrodissected germinal matrix and cortical plate of 15 prenatal, non-pathological human postmortem samples from second and third trimester gestation, and from fresh-frozen, macrodissected basal ganglia and neocortex of 3 adult, non-pathological human postmortem controls. The germinal matrix was macrodissected at the level of the caudothalamic groove and the cortical plate from the adjacent frontoparietal neocortex; grossly equal amount of subjacent white matter was included for both dissections. For prenatal tissues, to consistently dissect the posterior germinal zone in prenatal brains of varying size, the length of the entire cortical surface was measured for each sample and tissue from the ventricular to the apical surface was dissected in the area three fourths of the length from the rostral aspect. For adult tissues, the neocortex was dissected at the level of the pre-central gyrus, Brodmann area 4, and the subventricular zone plus caudate were dissected at the level of the posterior basal ganglia adjacent to the dissected neocortex.