A Single-Cell Roadmap of Lineage Bifurcation in Human ESC Models of Embryonic Brain Development

Cell Stem Cell. 2017 Jan 5;20(1):120-134. doi: 10.1016/j.stem.2016.09.011. Epub 2016 Oct 27.


During human brain development, multiple signaling pathways generate diverse cell types with varied regional identities. Here, we integrate single-cell RNA sequencing and clonal analyses to reveal lineage trees and molecular signals underlying early forebrain and mid/hindbrain cell differentiation from human embryonic stem cells (hESCs). Clustering single-cell transcriptomic data identified 41 distinct populations of progenitor, neuronal, and non-neural cells across our differentiation time course. Comparisons with primary mouse and human gene expression data demonstrated rostral and caudal progenitor and neuronal identities from early brain development. Bayesian analyses inferred a unified cell-type lineage tree that bifurcates between cortical and mid/hindbrain cell types. Two methods of clonal analyses confirmed these findings and further revealed the importance of Wnt/β-catenin signaling in controlling this lineage decision. Together, these findings provide a rich transcriptome-based lineage map for studying human brain development and modeling developmental disorders.

Keywords: human embryonic stem cells; lineage; neurogenesis; single cell RNA-seq.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Animals
  • Brain / embryology*
  • Brain / metabolism
  • Cell Line
  • Cell Lineage* / genetics
  • Clone Cells
  • Embryonic Development* / genetics
  • Human Embryonic Stem Cells / cytology*
  • Humans
  • Mice
  • Models, Biological
  • Neurons / cytology
  • Neurons / metabolism
  • Reproducibility of Results
  • Sequence Analysis, RNA
  • Single-Cell Analysis / methods*
  • Transcription Factors / metabolism
  • Transcriptome / genetics
  • Wnt Signaling Pathway / genetics


  • Transcription Factors