Single-Cell RNA-Seq Reveals Cellular Hierarchies and Impaired Developmental Trajectories in Pediatric Ependymoma

Cancer Cell. 2020 Jul 13;38(1):44-59.e9. doi: 10.1016/j.ccell.2020.06.004.


Ependymoma is a heterogeneous entity of central nervous system tumors with well-established molecular groups. Here, we apply single-cell RNA sequencing to analyze ependymomas across molecular groups and anatomic locations to investigate their intratumoral heterogeneity and developmental origins. Ependymomas are composed of a cellular hierarchy initiating from undifferentiated populations, which undergo impaired differentiation toward three lineages of neuronal-glial fate specification. While prognostically favorable groups of ependymoma predominantly harbor differentiated cells, aggressive groups are enriched for undifferentiated cell populations. The delineated transcriptomic signatures correlate with patient survival and define molecular dependencies for targeted treatment approaches. Taken together, our analyses reveal a developmental hierarchy underlying ependymomas relevant to biological and clinical behavior.

Keywords: EPN; Pediatric ependymoma; aberrant development; cancer stem cells; cellular hierarchy; differentiation trajectory; glial development; intratumoral heterogeneity; single-cell RNA sequencing; target identification.

Publication types

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

MeSH terms

  • Cell Differentiation / genetics
  • Cell Proliferation / genetics
  • Central Nervous System Neoplasms / genetics*
  • Central Nervous System Neoplasms / pathology
  • Central Nervous System Neoplasms / therapy
  • Child
  • Ependymoma / genetics*
  • Ependymoma / pathology
  • Ependymoma / therapy
  • Genomics / methods
  • Humans
  • Neurons / metabolism
  • Neurons / pathology
  • Prognosis
  • Sequence Analysis, RNA / methods*
  • Single-Cell Analysis / methods*
  • Survival Analysis