Nature | http://www.nature.com | 1Article
Decoding the development of the human
hippocampus
Suijuan Zhong1,1 0, Wenyu Ding2 ,1 0, Le Sun1,3,4,10, Yufeng Lu1,4 ,1 0, Hao Dong1,4, Xiaoying Fan^5 ,
Zeyuan Liu1,4, Ruiguo Chen1,4, Shu Zhang^5 , Qiang Ma1,4, Fuchou Tang5,6,7, Qian Wu2,8* &
Xiaoqun Wang1,3,4,9*The hippocampus is an important part of the limbic system in the human brain that
has essential roles in spatial navigation and the consolidation of information from
short-term memory to long-term memory^1 ,^2. Here we use single-cell RNA sequencing
and assay for transposase-accessible chromatin using sequencing (ATAC–seq)
analysis to illustrate the cell types, cell linage, molecular features and transcriptional
regulation of the developing human hippocampus. Using the transcriptomes of
30,416 cells from the human hippocampus at gestational weeks 16–27, we identify
47 cell subtypes and their developmental trajectories. We also identify the migrating
paths and cell lineages of PAX6+ and HOPX+ hippocampal progenitors, and regional
markers of CA1, CA3 and dentate gyrus neurons. Multiomic data have uncovered
transcriptional regulatory networks of the dentate gyrus marker PROX1. We also
illustrate spatially specific gene expression in the developing human prefrontal cortex
and hippocampus. The molecular features of the human hippocampus at gestational
weeks 16–20 are similar to those of the mouse at postnatal days 0–5 and reveal gene
expression differences between the two species. Transient expression of the primate-
specific gene NBPF1 leads to a marked increase in PROX1+ cells in the mouse
hippocampus. These data provides a blueprint for understanding human
hippocampal development and a tool for investigating related diseases.The hippocampal formation (hippocampus) is a compound structure
under the cerebral cortex in primates that forms and stores long-term
memory by consolidating information from short-term memory, and
also processes spatial information and navigation^1 ,^2.
Hippocampus single-cell transcriptome
To understand the molecular features of hippocampal cells during
human brain development, we analysed 30,416 cells from the entire
left hippocampus (including the hippocampus proper, the dentate
gyrus (DG) and some of the subiculum connected to the hippocampus
proper) at gestational weeks (GW) 16–27 (Supplementary Table 1) by
droplet-based single-cell RNA sequencing (scRNA-seq). We performed
t-distributed stochastic neighbour embedding (t-SNE) analysis and
identified cells as progenitors, excitatory neurons (ExN), inhibitory
neurons (InN), Cajal Retzius cells, astrocytes, oligodendrocyte pro-
genitor cells (OPCs), oligodendrocytes, microglia and endothelial
cells by using classic markers and gene ontology (GO) of differentially
expressed genes (DEGs) (Fig. 1a–c, Extended Data Fig. 1a–c). The distri-
butions of samples from two individuals at GW22 were similar on the
t-SNE plot (Extended Data Fig. 1d). We then used the DG marker PROX1
to subclassify the ExN as DG ExN or non-DG ExN. The InN were further
subclassified as being derived from the medial or caudal ganglionic
eminence (MGE or CGE) on the basis of LHX6 and NR2F2 expression
(Fig. 1a–d). PROX1 is an essential transcription factor for the genesis
of hippocampal granule cells and formation of the DG^3 ,^4. By search-
ing transcription factor motifs identified from ATAC-seq peaks close
to the PROX1 transcription start site (TSS), we found three potential
binding sites for LEF1 or TCF4, indicating that WNT signals are crucial
for the production of DG granule cells (Fig. 1e, f), which is consistent
with reported studies^5 ,^6. We further segregated cells into 47 distinct
hierarchical subtypes by principal component analysis (PCA), show-
ing that different subtypes of progenitors were highly correlated with
fate-determined cells (Fig. 1g, Extended Data Fig. 2a–c).
To study developmental differences between the hippocampus
and neocortex, we compared the transcriptome of the hippocampus
(GW16–27) with that of the human prefrontal cortex (PFC) (GW8–26)^7
(Fig. 1h) and found differences in gene expression between the PFC
and hippocampus across all cell types (Fig. 1i, Supplementary Table 2).
The HMG box domain-containing protein TOX was highly expressedhttps://doi.org/10.1038/s41586-019-1917-5
Received: 4 April 2019
Accepted: 12 November 2019
Published online: xx xx xxxx
(^1) State Key Laboratory of Brain and Cognitive Science, CAS Center for Excellence in Brain Science and Intelligence Technology, Institute of Brain-Intelligence Technology (Shanghai), Institute of
Biophysics, Chinese Academy of Sciences, Beijing, China.^2 State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, Beijing, China.^3 Institute for Stem Cell and
Regeneration, Chinese Academy of Sciences, Beijing, China.^4 University of Chinese Academy of Sciences, Beijing, China.^5 Beijing Advanced Innovation Center for Genomics, College of Life
Sciences, Peking University, Beijing, China.^6 Biomedical Institute for Pioneering Investigation via Convergence and Center for Reproductive Medicine, Ministry of Education Key Laboratory of
Cell Proliferation and Differentiation, Beijing, China.^7 Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China.^8 IDG/McGovern Institute for Brain Research, Beijing Normal
University, Beijing, China.^9 Beijing Institute for Brain Disorders, Beijing, China.^10 These authors contributed equally: Suijuan Zhong, Wenyu Ding, Le Sun, Yufeng Lu. *e-mail: [email protected];
[email protected]