Figure 5
- RNA-seq data suggests a mechanism behind the differential regulation of miRNA targeting EGFR. (a) In 3D culture (top), EGFR signaling upregulates immediate early genes (IEGs) Nur77 and ATF3. Nur77 transcribes additional ATF3, and ATF3 transcribes JUND, which itself transcribes NR4A1 (Nur77). This creates a self-sustaining loop that transcribes genes involved in EGFR bypass signaling, phosphatases that inactivate MAPK signaling, and miRNA that target EGFR signaling, integrin signaling, focal adhesion signaling, and MAPK signaling. In 2D culture (bottom), EGFR signaling upregulates immediate early gene FOS, which transcribes MYB, as well as delayed early gene (DEG) FOSB. Collectively, these genes transcribe over 400 genes involved in proliferation and migration as the cells spread and expand to fill available space. Genes are colored by magnitude of dispersion from 1:1 correlation; red indicates a shift toward 2D, blue indicates a shift toward 3D. (b) In Case A, expression of EGFR-induced transcription factors in 2D and 3D culture aligns with the changes seen in HCC827. Expression differences in Case B are less pronounced, and FOS is more highly expressed in 3D culture. See Supplementary Fig. 5 for correlation with flash-frozen tissue expression.
