HnRNPF extensively regulates expression and alternative splicing of genes associated with proliferation and migration in gastric cancer cells

Methods

Here, we explored the expression pattern of hnRNPF in stomach adenocarcinoma (STAD) samples, and used small interference RNA to knockdown hnRNPF (si-hnRNPF) in AGS cells. Then we performed whole transcriptome sequencing method (RNA-seq) to investigate how hnRNPF modulates the expression and splicing landscape of GC cells. RT-qPCR experiment was used to validate the molecular targets of hnRNPF.

Results: We found hnRNPF expression level was significantly increased in nodal metastasis status of GC patients by TCGA analysis, and was associated with the overall survival time of GC patients. By RNA-seq, we identified 929 differentially expressed genes (DEGs) and 2,669 hnRNPF-regulated AS events (RASEs). Functional enrichment revealed that hnRNPF-controlled DEGs were enriched in cell proliferation, extracellular-matrix organization, and immune-related pathways, which were tightly associated with GC progression.

Notably, hnRNPF depletion significantly reduced the expression levels of CD55, CTGF, FZD5, KRT80, and TGM2. HnRNPF also significantly altered the splicing pattern of key GC-associated genes, including KRT80, CDC25B, CD151, DOK1, and ADAM15, which were validated by RT-qPCR and tightly associated with the prognosis result of GC patients. Conclusions: Collectively, our findings demonstrate that hnRNPF orchestrates the GC transcriptome at both transcriptional and post-transcriptional levels, positioning it as a potential therapeutic target for precision treatment of gastric cancer.