Abstract
Background
According to the Cancer Genome Atlas, gastric cancers involve 30% BRD9 changes. Studying the signaling net controlled by BRD9 is important and provides useful information for the treatment of patients with gastric cancer and BRD9 alteration.
Objective
We performed this study to find the signaling pathways controlled by BRD9 in gastric cancer cells.
Methods
MGC-803 and AGS cells were selected as BRD9 overexpression and normal expression models, respectively, and added with BRD9 inhibitors BI9564 and BI7273, respectively. RNA-seq and limma R language were used to obtain differentially expressed genes (DEGs), and heatmap R language was employed for cluster analysis. Database for Annotation, Visualization and Integrated Discovery (DAVID) was applied to identify the gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichments, and STRING database was utilized to construct the protein–protein interaction (PPI) networks. Analysis was performed through Cytoscape software to determine the possible signaling pathway and target genes.
Results
Group MGC-803: 1204 and 1338 DEGs were found in MGC-803 cells added with BI9564 and BI7273, respectively, and 425 DEGs were found in the intersection of these two sets. AGS group: 974 and 1006 DEGs were found in AGS cells added with BI9564 and BI7273, respectively, and 382 DEGs were found in the intersection of these two sets. The DEG number in the intersection of groups MGC-803 and AGS was only 12, and only 3 of which showed the same regulation direction. Hence, these two types of gastric cancers are greatly altered in the signaling network. GO enrichment and KEGG signaling pathway analyses showed that in group MGC-803, BRD9 mainly controls cell adhesion molecule (CAM) pathway, and genes SPP1 and GNAO1 may play important an important role in the BRD9 controlling network. In group AGS, BRD9 mainly controls protein digestion and absorption pathway, and genes AR and GNGT2 have an important function in the BRD9 controlling network.
Conclusion
Comprehensive bioinformatics analyses were conducted to screen the DEGs and signaling pathways controlled by BRD9 in different gastric cancer cells. The findings provide a theoretical basis in curing patients with clinical gastric cancer.