The RNA-binding protein Quaking modulates cell proliferation through the SFRP1 mediated Wnt signaling pathway in NIH3T3 fibroblasts

Abstract

As an RNA-binding protein, Quaking (QKI) plays a pivotal role in regulating RNA metabolism, including mRNA transcription, pre-mRNA splicing, RNA localization, and RNA stability. To further investigate its specific role in mammalian cells, a QKI-knockout NIH3T3 cell line was generated using CRISPR/Cas9 technology in this study. RNA sequencing analysis showed that QKI deficiency alters several biological processes in NIH3T3 cells, including the Wnt signaling pathway, regulation of epithelial cell proliferation, epithelial cell and tissue migration. Functional analyses revealed that QKI deficiency potently suppressed cell proliferation and migration in NIH3T3 cells. In addition, SFRP1, a negative regulator of the Wnt signaling pathway, was significantly upregulated in QKI knockout NIH3T3 cells. Notably, the expression of several Wnt signaling pathway-related factors (WNT5A, FZD8, β-catenin, CCND1 and CCN4) was significantly downregulated in QKI knockout NIH3T3 cells. CLIP-seq analysis further identified a fragment with the 3’UTR of Sfrp1 mRNA that interacts with QKI and contains two canonical QKI response elements (QKI-REs). Dual-luciferase reporter assays verified that QKI exerts its inhibitory effect by binding to QKI-RE1 within the 3’UTR of Sfrp1 mRNA. Additionally, the actinomycin D assay demonstrated that QKI regulates Sfrp1 expression by suppressing Sfrp1 mRNA stability. Moreover, SFRP1 overexpression inhibited the cell proliferation and migration of NIH3T3 cells, mirroring the effects of QKI knockout. In summary, these findings demonstrate that QKI inhibits Sfrp1 expression by binding to QKI-RE1 within its 3’UTR, leading to activation of the Wnt signaling pathway and subsequent promotion of cell proliferation and cell migration. This study identifies a QKI-SFRP1-Wnt regulatory axis that expands the functional repertoire of QKI in post-transcriptional control of cell dynamics.