Quantitative Proteomics Reveals the Regulatory Networks of Circular RNA CDR1as in Hepatocellular Carcinoma Cells

Circular
RNAs (circRNAs), a class of widespread endogenous RNAs,
play crucial roles in diverse biological processes and are potential
biomarkers in diverse human diseases and cancers. Cerebellar-degeneration-related
protein 1 antisense RNA (CDR1as), an oncogenic circRNA, is involved
in human tumorigenesis and is dysregulated in hepatocellular carcinoma
(HCC). However, the molecular mechanisms underlying CDR1as functions
in HCC remain unclear. Here we explored the functions of CDR1as and
searched for CDR1as-regulated proteins in HCC cells. A quantitative
proteomics strategy was employed to globally identify CDR1as-regulated
proteins in HCC cells. In total, we identified 330 differentially
expressed proteins (DEPs) upon enhanced CDR1as expression in HepG2
cells, indicating that they could be proteins regulated by CDR1as.
Bioinformatic analysis revealed that many DEPs were involved in cell
proliferation and the cell cycle. Further functional studies of epidermal
growth factor receptor (EGFR) found that CDR1as exerts its effects
on cell proliferation at least in part through the regulation of EGFR
expression. We further confirmed that CDR1as could inhibit the expression
of microRNA-7 (miR-7). EGFR is a validated target of miR-7; therefore,
CDR1as may exert its function by regulating EGFR expression via targeting
miR-7 in HCC cells. Taken together, we revealed novel functions and
underlying mechanisms of CDR1as in HCC cells. This study serves as
the first proteome-wide analysis of a circRNA-regulated protein in
cells and provides a reliable and highly efficient method for globally
identifying circRNA-regulated proteins.