Alterations in Gene Expression and Alternative Splicing Induced by Plasmid-Mediated Overexpression of GFP and P2RY12 Within the A549 Cell Line

Phenotypic modifications and their effects on cellular functions through the up-regulation of target gene expression have frequently been observed in genetic studies, but the unique roles of cell lines and their introduced plasmids in influencing these functions have not been fully revealed. In this research, we developed two distinct cell lines derived from the A549 cell line: one that stably overexpresses GFP and another that is a polyclonal stable line overexpressing both GFP and <i>P2RY12</i>. We then utilized transcriptome sequencing (RNA-seq) technology to screen out differentially expressed genes (DEGs) and genes with differential transcript usage (gDTUs) after GFP overexpression (GFP-OE) and <i>P2RY12</i> overexpression (<i>P2RY12</i>-OE). We found that, compared with A549, there were more than 1700 differentially expressed genes (DEGs) in both GFP-OE and <i>P2RY12</i>-OE cells, while only 866 DEGs were identified in GFP-OE and <i>P2RY12</i>-OE cells. Notably, the differences in transcript usage were relatively minor, with only over 400 genes exhibiting changes across all three groups. The functional analysis of DEGs and gDTUs showed that they were both highly enriched in the pathways associated with cell proliferation and migration. In summary, we performed an extensive analysis of the transcriptome profile of gene expression and alternative splicing with GFP-OE and <i>P2RY12</i>-OE, enhancing our comprehension of how genes function within cells and the processes that control gene expression.