Single-cell genomics reveals region-specific developmental trajectories underlying neuronal diversity in the human hypothalamus

Abstract

The hypothalamus is critically important for regulating most autonomic, metabolic, and behavioral functions essential for life and species propagation, yet a comprehensive understanding of neuronal subtypes and their development in the human brain is lacking. Here, we characterized the prenatal human hypothalamus by sequencing the transcriptomes of 45,574 single-cells from 12 embryos, spanning gestational weeks 4 through 25. These cells describe a temporal trajectory from proliferative stem cell populations to maturing neurons and glia, including 38 distinct excitatory and inhibitory neuronal subtypes. Merging these data with paired samples from the cortex and ganglionic eminences (GE) revealed two distinct neurogenesis pathways, one shared between GE and hypothalamus and a second unique to cortex. Gene regulatory network modeling predicted that these distinct maturation trajectories involve the activation of region- and cell type-specific transcription factor networks. These results provide the first comprehensive transcriptomic view of human hypothalamus development at cellular resolution.

Sex differences in early human fetal brain development

“…Using a human fetal pituitary gland single cell RNA-sequencing (scRNA-seq) analysis resource, we identified highest AR expression in the corticotrope cell lineage, suggesting a potential role in the adrenal axis and later stress mechanisms 24 (Figure 6c, Table 2). Furthermore, in a human fetal hypothalamus single cell dataset we were able to localize AR expression in several areas, most strongly in the arcuate nucleus (ARC) 25 (Figure 6d, Table 2). Taken together, these findings suggest that localized expression of the AR may be important with time.…”

“…High expression of AR is shown in red in the arcuate nucleus (ARC) of the hypothalamus (Supplementary Figure 15). Data accessed from https://nemoanalytics.org/p?l=a856c14e (CC BY-NC 4.0, https://creativecommons.org/licenses/by-nc/4.0/) 25 . UMAP, uniform manifold approximation and projection.…”

“…By IHC we were also able to find localized regions of AR expression, such as in the inferior hypothalamus. We linked this to emerging data from single cell RNA-sequencing, which identified AR expression in more localized structures such as the corticotropes of the pituitary gland 24 (involved in adrenal and stress responses) and arcuate nucleus of the hypothalamus 25 (implicated in appetite regulation and reproduction), although it is unclear whether sex differences occur. Other datasets, such as the Allen Brain database (https://www.brainspan.org/rnaseq/search/index.html), show some potential AR expression in the hippocampus, but transcript levels are low, and AR expression in most brain regions is low in the adult, without major sex differences (Supplementary Figure 7).…”

“…human fetal hypothalamus images were generated from the NeMo Analytic open resource (CC-BY-NC 4.0 International license) webpage https://nemoanalytics.org/p?l=a856c14e&g=gad2 developed by Herb et, al. 25 .…”

A marmoset brain cell census reveals regional specialization of cellular identities

“…We did not attempt to dissect each brain structure in its entirety; this census should be viewed as containing representation from each of these structures, but not exhaustive profiling thereof. For example, the hypothalamus and brainstem contain tremendous cellular heterogeneity that varies across relatively small spatial scales due the presence of specialized brain nuclei and rare cell types ( 1 , 3 , 34 ); our census only sampled small portions of these structures and is not comprehensive. Within the neocortex, we separately sampled eight neocortical locations (prefrontal, temporal pole, S1, M1, A1, V2, V1, and lateral parietal association), and within PFC, from four distinct subdivisions (dorsolateral, medial, orbital, and ventral) (fig.…”