Cell Type-Specific In Vitro Gene Expression Profiling of Stem Cell-Derived Neural Models

Cells. 2020 Jun 5;9(6):1406. doi: 10.3390/cells9061406.


Genetic and genomic studies of brain disease increasingly demonstrate disease-associated interactions between the cell types of the brain. Increasingly complex and more physiologically relevant human-induced pluripotent stem cell (hiPSC)-based models better explore the molecular mechanisms underlying disease but also challenge our ability to resolve cell type-specific perturbations. Here, we report an extension of the RiboTag system, first developed to achieve cell type-restricted expression of epitope-tagged ribosomal protein (RPL22) in mouse tissue, to a variety of in vitro applications, including immortalized cell lines, primary mouse astrocytes, and hiPSC-derived neurons. RiboTag expression enables depletion of up to 87 percent of off-target RNA in mixed species co-cultures. Nonetheless, depletion efficiency varies across independent experimental replicates, particularly for hiPSC-derived motor neurons. The challenges and potential of implementing RiboTags in complex in vitro cultures are discussed.

Keywords: RNA-seq; RiboTag; bacTRAP; genomics; glia; hiPSC; neuron.

Publication types

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

MeSH terms

  • 3T3 Cells
  • Animals
  • Coculture Techniques
  • Epitopes / metabolism
  • Gene Expression Profiling*
  • Gene Expression Regulation
  • HEK293 Cells
  • Humans
  • Induced Pluripotent Stem Cells / cytology
  • Induced Pluripotent Stem Cells / metabolism
  • Mice
  • Models, Biological*
  • Neural Stem Cells / cytology
  • Neural Stem Cells / metabolism*
  • Neurons / cytology
  • Neurons / metabolism
  • RNA, Messenger / genetics
  • RNA, Messenger / metabolism
  • RNA-Binding Proteins / metabolism
  • Ribosomal Proteins / metabolism
  • Species Specificity
  • Transcriptome / genetics


  • Epitopes
  • RNA, Messenger
  • RNA-Binding Proteins
  • RPL22 protein, mouse
  • Ribosomal Proteins