A single cell transcriptional portrait of embryoid body differentiation and comparison to progenitors of the developing embryo

Abby Spangler, Emily Y. Su, April M. Craft, Patrick Cahan

Research output: Contribution to journalArticle

Abstract

Directed differentiation of pluripotent stem cells provides an accessible system to model development. However, the distinct cell types that emerge, their dynamics, and their relationship to progenitors in the early embryo has been difficult to decipher because of the cellular heterogeneity inherent to differentiation. Here, we used a combination of bulk RNA-Seq, single cell RNA-Seq, and bioinformatics analyses to dissect the cell types that emerge during directed differentiation of mouse embryonic stem cells as embryoid bodies and we compared them to spatially and temporally resolved transcriptional profiles of early embryos. Our single cell analyses of the day 4 embryoid bodies revealed three populations which had retained related yet distinct pluripotent signatures that resemble the pre- or post-implantation epiblast, one population of presumptive neuroectoderm, one population of mesendoderm, and four populations of neural progenitors. By day 6, the neural progenitors predominated the embryoid bodies, but both a small population of pluripotent-like cells and an anterior mesoderm-like Brachyury-expressing population were present. By comparing the day 4 and day 6 populations, we identified candidate differentiation paths, transcription factors, and signaling pathways that mark the in vitro correlate of the transition from the mid-to-late primitive streak stage.

Original languageEnglish (US)
Pages (from-to)201-215
Number of pages15
JournalStem Cell Research
Volume31
DOIs
StatePublished - Aug 1 2018

Fingerprint

Embryoid Bodies
Embryonic Structures
Population
Primitive Streak
RNA
Single-Cell Analysis
Neural Plate
Germ Layers
Pluripotent Stem Cells
Mesoderm
Computational Biology
Transcription Factors

Keywords

  • Directed differentiation
  • Embryoid body
  • Mesendoderm
  • Neuroectoderm
  • Noggin
  • Single cell rna-seq
  • Transcriptional profiling

ASJC Scopus subject areas

  • Developmental Biology
  • Cell Biology

Cite this

A single cell transcriptional portrait of embryoid body differentiation and comparison to progenitors of the developing embryo. / Spangler, Abby; Su, Emily Y.; Craft, April M.; Cahan, Patrick.

In: Stem Cell Research, Vol. 31, 01.08.2018, p. 201-215.

Research output: Contribution to journalArticle

@article{cdfcb76b973a4479a04279be83509b7f,
title = "A single cell transcriptional portrait of embryoid body differentiation and comparison to progenitors of the developing embryo",
abstract = "Directed differentiation of pluripotent stem cells provides an accessible system to model development. However, the distinct cell types that emerge, their dynamics, and their relationship to progenitors in the early embryo has been difficult to decipher because of the cellular heterogeneity inherent to differentiation. Here, we used a combination of bulk RNA-Seq, single cell RNA-Seq, and bioinformatics analyses to dissect the cell types that emerge during directed differentiation of mouse embryonic stem cells as embryoid bodies and we compared them to spatially and temporally resolved transcriptional profiles of early embryos. Our single cell analyses of the day 4 embryoid bodies revealed three populations which had retained related yet distinct pluripotent signatures that resemble the pre- or post-implantation epiblast, one population of presumptive neuroectoderm, one population of mesendoderm, and four populations of neural progenitors. By day 6, the neural progenitors predominated the embryoid bodies, but both a small population of pluripotent-like cells and an anterior mesoderm-like Brachyury-expressing population were present. By comparing the day 4 and day 6 populations, we identified candidate differentiation paths, transcription factors, and signaling pathways that mark the in vitro correlate of the transition from the mid-to-late primitive streak stage.",
keywords = "Directed differentiation, Embryoid body, Mesendoderm, Neuroectoderm, Noggin, Single cell rna-seq, Transcriptional profiling",
author = "Abby Spangler and Su, {Emily Y.} and Craft, {April M.} and Patrick Cahan",
year = "2018",
month = "8",
day = "1",
doi = "10.1016/j.scr.2018.07.022",
language = "English (US)",
volume = "31",
pages = "201--215",
journal = "Stem Cell Research",
issn = "1873-5061",
publisher = "Elsevier",

}

TY - JOUR

T1 - A single cell transcriptional portrait of embryoid body differentiation and comparison to progenitors of the developing embryo

AU - Spangler, Abby

AU - Su, Emily Y.

AU - Craft, April M.

AU - Cahan, Patrick

PY - 2018/8/1

Y1 - 2018/8/1

N2 - Directed differentiation of pluripotent stem cells provides an accessible system to model development. However, the distinct cell types that emerge, their dynamics, and their relationship to progenitors in the early embryo has been difficult to decipher because of the cellular heterogeneity inherent to differentiation. Here, we used a combination of bulk RNA-Seq, single cell RNA-Seq, and bioinformatics analyses to dissect the cell types that emerge during directed differentiation of mouse embryonic stem cells as embryoid bodies and we compared them to spatially and temporally resolved transcriptional profiles of early embryos. Our single cell analyses of the day 4 embryoid bodies revealed three populations which had retained related yet distinct pluripotent signatures that resemble the pre- or post-implantation epiblast, one population of presumptive neuroectoderm, one population of mesendoderm, and four populations of neural progenitors. By day 6, the neural progenitors predominated the embryoid bodies, but both a small population of pluripotent-like cells and an anterior mesoderm-like Brachyury-expressing population were present. By comparing the day 4 and day 6 populations, we identified candidate differentiation paths, transcription factors, and signaling pathways that mark the in vitro correlate of the transition from the mid-to-late primitive streak stage.

AB - Directed differentiation of pluripotent stem cells provides an accessible system to model development. However, the distinct cell types that emerge, their dynamics, and their relationship to progenitors in the early embryo has been difficult to decipher because of the cellular heterogeneity inherent to differentiation. Here, we used a combination of bulk RNA-Seq, single cell RNA-Seq, and bioinformatics analyses to dissect the cell types that emerge during directed differentiation of mouse embryonic stem cells as embryoid bodies and we compared them to spatially and temporally resolved transcriptional profiles of early embryos. Our single cell analyses of the day 4 embryoid bodies revealed three populations which had retained related yet distinct pluripotent signatures that resemble the pre- or post-implantation epiblast, one population of presumptive neuroectoderm, one population of mesendoderm, and four populations of neural progenitors. By day 6, the neural progenitors predominated the embryoid bodies, but both a small population of pluripotent-like cells and an anterior mesoderm-like Brachyury-expressing population were present. By comparing the day 4 and day 6 populations, we identified candidate differentiation paths, transcription factors, and signaling pathways that mark the in vitro correlate of the transition from the mid-to-late primitive streak stage.

KW - Directed differentiation

KW - Embryoid body

KW - Mesendoderm

KW - Neuroectoderm

KW - Noggin

KW - Single cell rna-seq

KW - Transcriptional profiling

UR - http://www.scopus.com/inward/record.url?scp=85051380396&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85051380396&partnerID=8YFLogxK

U2 - 10.1016/j.scr.2018.07.022

DO - 10.1016/j.scr.2018.07.022

M3 - Article

C2 - 30118958

AN - SCOPUS:85051380396

VL - 31

SP - 201

EP - 215

JO - Stem Cell Research

JF - Stem Cell Research

SN - 1873-5061

ER -