Coexpression enrichment analysis at the single-cell level reveals convergent defects in neural progenitor cells and their cell-type transitions in neurodevelopmental disorders

Genome Res. 2020 Jun;30(6):835-848. doi: 10.1101/gr.254987.119. Epub 2020 Jun 18.


A large number of genes have been implicated in neurodevelopmental disorders (NDDs), but their contributions to NDD pathology are difficult to decipher without understanding their diverse roles in different brain cell types. Here, we integrated NDD genetics with single-cell RNA sequencing data to assess coexpression enrichment patterns of various NDD gene sets. We identified midfetal cortical neural progenitor cell development-more specifically, the ventricular radial glia-to-intermediate progenitor cell transition at gestational week 10-as a key point of convergence in autism spectrum disorder (ASD) and epilepsy. Integrated Gene Ontology-based analysis further revealed that ASD genes activate neural differentiation and inhibit cell cycle during the transition, whereas epilepsy genes function as downstream effectors in the same processes, offering one possible explanation for the high comorbidity rate of the two disorders. This approach provides a framework for investigating the cell-type-specific pathophysiology of NDDs.

Publication types

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

MeSH terms

  • Biomarkers
  • Brain / metabolism
  • Brain / physiopathology
  • Cell Differentiation / genetics*
  • Computational Biology / methods
  • Disease Susceptibility*
  • Epilepsy / etiology
  • Gene Expression Profiling* / methods
  • Gene Ontology
  • Humans
  • Interneurons / cytology
  • Interneurons / metabolism
  • Neural Stem Cells / cytology
  • Neural Stem Cells / metabolism*
  • Neurodevelopmental Disorders / diagnosis
  • Neurodevelopmental Disorders / etiology*
  • Neurons / cytology
  • Neurons / metabolism
  • Single-Cell Analysis* / methods
  • Transcriptome*


  • Biomarkers