Some uncertainties remain in the research and exploration of NPC treatment, especially oncogenic mutation patterns in NPC 1, 2, 18. This study was performed using tumor-related data from GEO to identify NPC-related miRNAs and mRNA regulatory molecules, with the aim of achieving a breakthrough in the research process for NPC gene therapy. In recent years, a growing number of studies have demonstrated the potential of miRNAs in NPC research. This study was conducted using bioinformatical methods based on two datasets (GSE70790 and GSE12452) from the GEO database. Through a tool named GEO2R, with | logFC | > 1.5, and adjusted P-value < 0.05 as the research standard, we demonstrated that one miRNA (miR-375) was up-regulated and 12 were down-regulated (miR-96-5p, miR-155-5p, miR-320a, miR-378a -3p, miR-15b-5p, miR-21-5p, miR-25-3p, miR-93-5p, miR-493-3p, miR-493-5p, miR- 494-3p, and let-7 i-5p) in NPC. Identification of these miRNAs and mRNA targets that are closely related to the prognosis of NPC lays a solid foundation for future research. The abovementioned molecules may be related to the prognosis of NPC, as suggested in previous related studies. In NPC, high expression of miR-375 was reported to regulate PDK1 and modulate the progression of NPC cells. MiR-96-5p is a target of CDK1 and serves as an inhibitor of NPC. MiR-494-3p promotes NPC cell growth, migration, and invasion by targeting Sox7. Although there are no reports about miR-155, miR-320a, miR-15b-5p, miR-21-5p, miR-23-3p, miR-93-5p, miR-493-3p, miR-494-3p, and let-7i-5p related to NPC, they have been reported as tumor inhibitors in other carcinomas such as lung cancer and hepatocellular carcinoma 19–24. This indicates that they also have considerable potential in further research of NPC.
To gain a deeper understanding of the uncharted territory of miRNAs, we constructed a PPI network using Metascape and performed target gene prediction and functional analysis of 344 generated target genes. These target genes were found to possess various functions related to tumor progression in previous studies, such as the cell cycle, non-integrin membrane–ECM interactions, cilium organization, DNA recombination, DNA replication, and response to radiation. The main pathological type of NPC is squamous cell carcinoma, but cell cycle genes have been reported to affect the differentiation of squamous cells25, 26. ECM-related genes play an indispensable role in the tumor microenvironment, and their potential as target genes and biomarkers has been described in many studies 27. The susceptibility to NPC in the Chinese population is closely related to the interleukin (IL)-13 gene 28, while IL-4 has been shown to affect the progression of NPC by affecting the signal transducer and activator of transcription (STAT) pathway 29. There is much evidence to support the indispensable role of KIT-SCF in other cancers 30, 31.
An analysis was conducted in the form of a PPI network for the in-depth detection and study of target genes. We identified eight genes as central genes based on connectivity scores ≥ 110 and conducted follow-up survival analysis on these genes. The results showed that the central genes (CDK1, CCNB1, CCNA2, TOP2A, AURKA, MAD2L1, CDC6, and CHEK1) played a remarkable role in the 10-year survival rates of patients with NPC.
miRNAs are non-coding small RNA molecules that can inhibit transcription and translation and cleave target mRNAs to accelerate their degradation. In his review, Syafirah suggested that a single miRNA marker is not adequate for NPC prognosis. Therefore, a study on manifold miRNA biomarker profiles can help improve the reliability of prognostic research on NPC 32. Our study has advanced the existing knowledge on combined applications for miRNAs and mRNAs, and the results of our research support the hypothesis we put forward. MiR-96-5p and miR-375 regulate the expression of CDK1, miR-493-3p regulates the expression of CCNB1, miR-320a regulates the expression of CCNA2, miR-21-5p and miR-96-5p regulate the expression of TOP2A, miR-25-3p and let-7i-5p regulate the expression of CDC6, miR-493-3p regulates the expression of MAD2L1, miR-493-3p and miR-493-5p regulate the expression of AURKA, and miR-378a-3p and let-7i-5p regulate the expression of CHEK1. There have been quite a few studies on the abovementioned central genes in the past. CDK1 can be integrated with CCNB1 to actuate the G2-M transition and bind to other cyclins to further adjust and control the G1 process and G1-S transition 33. In a previous study, CDK1 was confirmed as a direct regulated site of miR-96-5p and reportedly served as a tumor inhibitor for NPC34. As shown in some studies, CDK1 may be related to radiosensitivity in tumor cells 35. CCNA2 was reported to be a downstream target of miR-29c-3p and mainly enriched in the cell cycle 36. A study on promoter methylation revealed that CCNA2 might be a tumor suppressor gene for NPC 37. TOP2A is a subtype of TOP2, which plays an important role in DNA synthesis and transcription38. CCNB1 is an important component of the cell cycle pathway and one of the hub genes that substantially influences cancer development. Some studies have revealed the potential role of CHK1-related pathways and CDC6 in reversing radioresistance39, 40. Some previous bioinformatics studies related to NPC showed that AURKA, CCNB1, and MAD2LI were genes with considerable value for further research 41. However, to our knowledge, there have been no reports about the abovementioned genes (CCNB1, CDC6, TOP2A, CHK1, and AURKA) in the field of NPC research to date. These genes are expected to become new research targets in the future.