Staufen1 Represses the FOXA1-Regulated Transcriptome by Destabilizing FOXA1 mRNA in Colorectal Cancer Cells

Abstract

Transcription factors play key roles in development and disease by controlling gene expression. Forkhead box A1 (FOXA1), is a pioneer transcription factor essential for mouse development and functions as an oncogene in prostate and breast cancer. In colorectal cancer (CRC), FOXA1 is significantly downregulated and high FOXA1 expression is associated with better prognosis, suggesting potential tumor suppressive functions. We therefore investigated the regulation of FOXA1 expression in CRC, focusing on well-differentiated CRC cells, where FOXA1 is robustly expressed. Genome-wide RNA stability assays identified FOXA1 as an unstable mRNA in CRC cells. We validated FOXA1 mRNA instability in multiple CRC cell lines and in patient-derived CRC organoids, and found that the FOXA1 3′UTR confers instability to the FOXA1 transcript. RNA pulldowns and mass spectrometry identified Staufen1 (STAU1) as a potential regulator of FOXA1 mRNA. Indeed, STAU1 knockdown resulted in increased FOXA1 mRNA and protein expression due to increased FOXA1 mRNA stability. Consistent with these data, RNA-seq following STAU1 knockdown in CRC cells revealed that FOXA1 targets were upregulated upon STAU1 knockdown. Collectively, this study uncovers a molecular mechanism by which FOXA1 is regulated in CRC cells and provides insights into our understanding of the complex mechanisms of gene regulation in cancer.

Keywords:

• FOXA1
• STAU1
• colorectal cancer
• mRNA stability
• RNA-binding protein
• post-transcriptional regulation

Acknowledgments

Colorectal cancer organoids were acquired from the Developmental Therapeutics Branch, CCR, NCI, Bethesda, MD. We thank the CCR Genomics Core, CCR, NCI, Bethesda, MD for valuable assistance with Sanger sequencing and RNA TapeStation. We also thank the CCR Sequencing Facility, NCI, Frederick, MD for performing the RNA-seq. Finally, we thank the members of the Lal lab for discussion and suggestions.

Data availability statement

The RNA-seq data for ActD-treated LS180 and HCT116 cells and CTL siRNA vs siSTAU1 from LS180 cells have been deposited to the GEO database (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE234877). Raw figure data are available on Figshare: https://figshare.com/articles/figure/Staufen1_represses_the_FOXA1-regulated_transcriptome_by_destabilizing_FOXA1_mRNA_in_colorectal_cancer_cells/25020449

Disclosure statement

No potential conflict of interest was reported by the authors.

Additional information

Funding

This research was supported by the Intramural Research Program (A.L.) of the National Cancer Institute (NCI), Center for Cancer Research (CCR), NIH (ZIA BC011646 to A.L.).