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.

Abstract

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