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Comprehensive long-read transcriptomic analysis reveals multi-level transcriptional alterations mediated by miR-214-3p dysregulation in gastric cancer cells

ABSTRACT: Long-length sequencing has been widely used in cancer-related research for exploring transcriptome variations in human cancer in recent years. miR-214-3p, a microRNA, has been reported to have abnormal expression and play important regulation roles in diverse cancers. However, information about the genome-wide targets and action mechanisms of miR-214-3p in cancer cells is still limited. Here, long-read sequencing were performed to character the transcriptome variations after disturbing the expression of miR-214-3p in AGS cells, a gastric cancer cell line. The results showed that both miR-214-3p overexpression (OE) and suppression (KD) extensively increased or decreased expression level of a number of genes involved in apoptotic process and transcription at transcript level and gene level. In particular, both miR-214-3p KD and OE could increase or decrease on the expression levels of some target genes at the same direction. Moreover, miR-214-3p broadly regulated the alternative splicing of hundreds of genes with functions of cell division, cellular senescence and transcription regulation. In addition, the changes in the expression level of miR-214-3p can cause changes in the alternative polyadenylation and 3UTR lengths of the transcript. Taken together, these results indicated that miR-214-3p could mediate apoptosis by diverse modes in AGS cells, which adds to the understanding of the critical role of miR-214-3p in cancer cancer.

ORGANISM(S): Homo sapiens

PROVIDER: GSE300926 | GEO | 2025/11/09

REPOSITORIES: GEO

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Project description:[Aim] EBVaGC accounts for about 10% of gastric cancer and has a better prognosis than EBVnGC, but its molecular mechanism is still unclear. We investigated the role of EBV-miR-BART1-3p in the occurrence and development of EBVaGC by applying bioinformatics methods, high-throughput sequencing, in vitro experiments, target gene screening and verification, differential gene protein interaction network and gene regulatory network construction. [Materials and Methods] The data set GSE51575 was normalized, and the outlier samples were deleted. Finally, gene expression profiles of 11 EBVaGC and 14 EBVnGC tumor tissues and non-tumor control tissues were obtained. Differential gene function analysis was performed, and molecular regulatory network was constructed. The mRNA expression levels of SNU-719 (EBV-positive gastric cancer cell line), AGS, AGS-NC (EBV-negative gastric cancer cell line) and AGS-OE (lentivirus-transfected miR-BART1-3p overexpression cell line) were detected by high-throughput next-generation sequencing technology, and differential gene expression characteristics were analyzed. To investigate the effect of miR-BART1-3p overexpression on mRNA expression level of gastric cancer cells and construct the protein interaction network of differential genes and the regulatory network of miR-BART1-3p gene. DIANA-MR micro-T, miRnada, miRDB, TarBase v.8, and ViRBase online databases were used to predict the target genes of miR-BART1-3p and GO enrichment analysis of target gene function was performed. Real-time fluorescence quantitative PCR was used to detect the expression levels of miR-BART1-3p and target genes in SNU719, AGS-OE and AGS gastric cancer cells. The effects of overexpression of EBV-miR-BART1-3p on proliferation, apoptosis, invasion, and migration of gastric cancer cells were investigated by CCK-8, cell cloning, cell scratch and Transwell. [Results] By analyzing the gene expression profile of the GSE51575 dataset, we found that EBVaGC up-regulated the expression of immune cell membrane protein receptors and chemokine family, and was involved in inducing tumor immunity, suggesting a better prognosis. EBVnGC significantly up-regulated the expression of AURK, BUB1B, CCNA2 and CDC20, suggesting the risk of malignant progression and recurrence. High-throughput next-generation sequencing of SNU719 and AGS to detect differences in gene expression revealed that EBVaGC cells (SNU719) up-regulated the expression of genes that inhibit malignant progression as well as potential tumor immunotherapy targets. These results are consistent with those found in the GSE51575 dataset. Fifteen miR-BART1-3p target genes, including FAM168A, TET3, HBP1, ZBTB5, ATXN7L3, KMT5C, SPARC and BMF, were predicted and screened by online tools. After the overexpression of miR-BART1-3p in AGC(EBVnGC) cells, the proliferation, migration, and invasion ability were significantly inhibited, and the signaling pathway promoting tumor progression was also limited in activation. [Conclusions] The overexpression of miR-BART1-3p may inhibit the proliferation and invasion and migration of gastric cancer cells by inhibiting the activation of STAT3/ pSTAT3 and PI3K/AKT signaling pathways and may become a target for the treatment of EBVaGC, which is worthy of further study.

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Comprehensive long-read transcriptomic analysis reveals multi-level transcriptional alterations mediated by miR-214-3p dysregulation in gastric cancer cells

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