Comparative genomic analysis of embryonic, lineage-converted and stem cell-derived motor neurons

Justin K. Ichida*, Kim A. Staats, Brandi N. Davis-Dusenbery, Kendell Clement, Kate E. Galloway, Kimberly N. Babos, Yingxiao Shi, Esther Y. Son, Evangelos Kiskinis, Nicholas Atwater, Hongcang Gu, Andreas Gnirke, Alexander Meissner, Kevin Eggan

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

9 Scopus citations


Advances in stem cell science allow the production of different cell types in vitro either through the recapitulation of developmental processes, often termed ‘directed differentiation’, or the forced expression of lineage-specific transcription factors. Although cells produced by both approaches are increasingly used in translational applications, their quantitative similarity to their primary counterparts remains largely unresolved. To investigate the similarity between in vitro-derived and primary cell types, we harvested and purified mouse spinal motor neurons and compared them with motor neurons produced by transcription factor-mediated lineage conversion of fibroblasts or directed differentiation of pluripotent stem cells. To enable unbiased analysis of these motor neuron types and their cells of origin, we then subjected them to whole transcriptome and DNA methylome analysis by RNA sequencing (RNA-seq) and reduced representation bisulfite sequencing (RRBS). Despite major differences in methodology, lineage conversion and directed differentiation both produce cells that closely approximate the primary motor neuron state. However, we identify differences in Fas signaling, the Hox code and synaptic gene expression between lineage-converted and directed differentiation motor neurons that affect their utility in translational studies.

Original languageEnglish (US)
Article numberdev168617
JournalDevelopment (Cambridge)
Issue number22
StatePublished - Nov 2018


  • Directed differentiation
  • Embryonic stem cells
  • Lineage conversion
  • Motor neuron
  • Reprogramming
  • iPS cell

ASJC Scopus subject areas

  • Molecular Biology
  • Developmental Biology


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