Integrated analysis of scRNA-seq and bulk RNA-seq data reveals the key targets of the combination of cisplatin and saikosaponin D in gastric cancer cells.

Gastric cancer (GC) is a common solid malignant tumor with a low 5-year survival rate. The underlying mechanism of cisplatin (DDP) resistance in GC cells remains obscure, and therapeutic targets have yet to be identified. Previously, we reported that saikosaponin D (SSD) could increase the DDP sensitivity of the GC cell line SGC-7901. In this study, an integrated analysis of transcriptomic data of DDP-treated AGS cells with or without SSD and bulk RNA sequencing data regarding stomach adenocarcinoma (STAD) from the TCGA-GTEx database revealed that 22 differentially expressed genes (DEGs), including SPP1, PDGFRB, and HOXB7, were upregulated in GC tissues, whereas the other 19 DEGs were downregulated. Furthermore, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses revealed that the FAK/AKT/mTOR signaling pathway was most strongly correlated with these 22 genes. Single-cell RNA sequencing (scRNA-seq) analysis revealed that SPP1 was expressed mainly in monocytes and that PDGFRB and HOXB7 were overexpressed in smooth muscle cells. Among the 19 genes with low GC-tissue expression, APOD and SNCG were linked to high mortality and recurrence risks in GC patients. APOD was expressed mainly in smooth muscle cells, SNCG expression was upregulated in endothelial cells, and FXYD3 levels were elevated in epithelial cells. Network pharmacology and molecular docking analysis revealed the PI3K‒Akt signaling pathway to be the most likely target of SSD; furthermore, SSD exhibited strong binding affinity with EGFR, ESR1, IGF1R, AKT1, SRC, and GRB2. Real-time PCR and western blotting analyses confirmed the expression of HPN, AZGP1, PDGFRB, SPP1, HOXB7, SNCG, and APOD in GC cells. Additionally, the levels of the phosphorylated forms of FAK, AKT, and mTOR were significantly reduced in both AGS/DDP and SGC-7901/DDP cells treated with the combination of DDP and SSD, whereas the PTEN expression level increased. Our findings highlight the importance of alternative components within the tumor microenvironment for GC therapy and identify FAK/AKT/mTOR signaling as a potential target of SSD, providing novel insights into the mechanism by which SSD improves DDP resistance in GC.