GSE169368
Characteristic evaluation of in vitro 3D cell culture model in a multi-dimensional way with high-throughput sequencing
Organoids culture provides unique opportunities to study human diseases and to complement animal models. Several organs and tissues can be in vitro cultured in 3D structures resembling in vivo tissue organization. Organoids culture contains most of the cell types of the original tissue and are maintained by growth factors similar to the in vivo situation. However, the system is yet not fully understood, and specific in vivo features especially those driven by cell-extrinsic factors may be lost in culture. Here we show a comprehensive transcriptome-wide characterization of mouse gut organoids derived from different intestinal compartments and from mice of different gender and age. RNA-seq analysis showed that the in vitro culture strongly influences the global transcriptome of the intestinal epithelial cells (~60% of the total variance). Several compartment-, age- and gender-related transcriptional programs being lost after culturing suggest that they are driven by niche or systemic factors. However, some of the transcriptional programs proper of the cells of origin are kept in vitro indicating that compartment-, age- and gender-specific intrinsic features exist and can be studied in this system. Our study provides knowledge about the cell-extrinsic or cell-intrinsic origin of intestinal epithelial transcriptional programs. We anticipated that our characterization of this in vitro system is an important reference for scientists and clinicians using intestinal organoids as a research model. Overall design: Bulk RNA sequencing on epithelial cells of small intestine of different compartments from mice of different gender and age in vivo (crypts) and in vitro (organoids)