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

Abstract

Heterogeneous nuclear ribonucleoprotein F (hnRNPF) is an RNA-binding protein involved in alternative splicing (AS) regulation and tumorigenesis; however, its role in gastric cancer (GC) remains poorly understood. In the present study, the expression pattern of hnRNPF in stomach adenocarcinoma samples was investigated and hnRNPF knockdown using small interfering RNA in AGS cells was performed. Subsequently, a whole-transcriptome sequencing method, namely RNA-sequencing (RNA-seq) was conducted to investigate how hnRNPF regulates gene expression and AS GC cells. Reverse transcription-quantitative PCR (RT-qPCR) was performed to validate the molecular targets of hnRNPF. Results indicated that the hnRNPF expression level was significantly increased in tumor samples and associated with nodal metastasis status in patients with GC based on The Cancer Genome Analysis and was also correlated with the overall survival time of patients with GC. RNA-seq analysis identified 929 differentially expressed genes (DEGs) and 2,669 hnRNPF-regulated AS events. Functional enrichment analysis revealed that hnRNPF-regulated DEGs were primarily enriched in pathways associated with ‘inflammatory response’, ‘extracellular matrix organization’ and ‘immune response’, which are notably associated with GC progression. In addition, hnRNPF depletion significantly reduced the expression levels of CD55, connective tissue growth factor, frizzled-5, keratin 80 (KRT80) and transglutaminase 2. Furthermore, hnRNPF significantly altered the splicing patterns of key GC-associated genes, including KRT80, CDC25B, CD151, docking protein 1 and ADAM metallopeptidase domain 15. These AS alternations were validated by RT-qPCR and were found to be closely associated with the prognosis result of patients with GC. Collectively, the present findings demonstrated that hnRNPF orchestrates the GC cell transcriptome at both transcriptional and post-transcriptional levels, making hnRNPF a potential candidate for further pre-clinical target evaluation in GC.