Gene expression profiling and functional analysis reveals that p53 pathway-related gene expression is highly activated in cancer cells treated by cold atmospheric plasma-activated medium

BACKGROUND: Cold atmospheric-pressure plasma (CAP) has been considered a promising strategy for anti-cancer treatment. Traditionally, CAP was employed to kill cancer cells or tumor tissues by direct irradiation. However, CAP has some disadvantages such as infiltration capacity and storage convenience. Recently, plasma-activated medium (PAM) was used as an alternative strategy to treat cancer cells or tumors. The novel PAM approach has potential as an anti-cancer therapy. OBJECTIVE: To reveal the global activation of signaling pathways in oral cancer cells induced by PAM. METHODS: Oral squamous cell line SCC15 were treated by PAM and gene expression profiles were evaluated by using RNA-seq. Functional analyses were employed to reveal the global responses of SCC15 cells with PAM stimulation. QRT-PCR and Western blot were carried out to validate the expression levels of selected genes. RESULTS: More than 6G clean data per sample were obtained in PAM-treated SCC15 cells. A total of 934 differentially expressed genes (DEGs) were identified and GO analysis implicated the deep involvement of biological process. KEGG mapping further clustered 40 pathways, revealing that “p53 pathway” was significantly enriched. SCC15 cells were commonly used as a p53-null cell line. Therefore, the enriched p53 pathway-related genes in our analysis might be activated by other stimulators, in a p53-independent manner. Gene set enrichment analysis (GSEA) was also performed to evaluate changes at the gene-sets level. The results demonstrated not only the high engagement of “p53 pathway” but also the involvement of novel pathways such as hypoxia pathway. CONCLUSIONS: The present study elucidates the transcriptomic changes of PAM treated SCC15 cells, containing highly enriched DEGs involved in “p53 pathway”. Our analysis in this work not only provides genomic resources for future studies but also gives novel insights to uncover the molecular mechanism of PAM stimulation.