Identifying key genes and small molecule compounds for nasopharyngeal carcinoma by various bioinformatic analysis

Abstract

Nasopharyngeal carcinoma (NPC) is one of the most prevalent head and neck cancer in southeast Asia. It is necessary to proceed further studies on the mechanism of occurrence and development of NPC. In this study, we employed the microarray dataset GSE12452 and GSE53819 including 28 normal samples and 49 nasopharyngeal carcinoma samples downloaded from the Gene Expression Omnibus(GEO) to analysis. R software, STRING, CMap, and various databases were used to screen differentially expressed genes (DEGs), construct the protein–protein interaction (PPI) network, and proceed small molecule compounds analysis, among others. Totally, 424 DEGs were selected from the dataset. DEGs were mainly enriched in extracellular matrix organization, cilium organization, PI3K-Akt signaling pathway, collagen-containing extracellular matrix, and extracellular matrix-receptor interaction, among others. Top 10 upregulated and top 10 downregulated hub genes were identified as hub DEGs. Piperlongumine, apigenin, menadione, 1,4-chrysenequinone, and chrysin were identified as potential drugs to prevent and treat NPC. Besides, the effect of genes CDK1, CDC45, RSPH4A, and ZMYND10 on survival of NPC was validated in GEPIA database. The data revealed novel aberrantly expressed genes and pathways in NPC by bioinformatics analysis, potentially providing novel insights for the molecular mechanisms governing NPC progression. Although further studies needed, the results demonstrated that the expression levels of CDK1, CDC45, RSPH4A, and ZMYND10 probably affected survival of NPC patients.

Zinc finger myeloid Nervy DEAF-1 type (ZMYND) domain containing proteins exert molecular interactions to implicate in carcinogenesis

“…Its promoter hypermethylation was detected in the primary tumors, but not in normal nasopharyngeal epithelium [166,167]. The expression of BLU is correlated to a favorable prognosis, prolonged survival of NPC patients [168]. It had been reported that BLU is expressed in a stress-responsive manner, in NPC tumors the expression is disrupted by either epigenetic or genetic mechanisms [167].…”

Novel Prognostic Biomarkers in Nasopharyngeal Carcinoma Unveiled by Mega-Data Bioinformatics Analysis

“…Moreover, owing to the absence of clinical information on NPC, some studies resorted to using data from head and neck squamous cell carcinoma (HNSCC) for survival analysis. However, since the HNSCC database hardly includes any information on NPC, which is a tumor type vastly distinct from HNSCC, the derived survival results are virtually devoid of any meaningful reference value [37,[49][50][51]. To overcome these limitations, we obtained NPC RNA expression pro les from GSE132112 and corresponding clinical information from Professor Jun Ma at Sun Yat-sen University.…”

Novel prognostic biomarkers in nasopharyngeal carcinoma unveiled by mega-data bioinformatics analysis

“…Moreover, due to the lack of clinical information specific to NPC, most of studies have utilized data from head and neck squamous cell carcinoma (HNSCC) for survival analysis. However, this approach is flawed as the HNSCC database contains minimal NPC data, a tumor type distinct from HNSCC, rendering the survival results largely irrelevant (8)(9)(10)(11). NPC can be effectively treated in early stages, yet over 50% of patients are diagnosed at advanced stages, leading to worse outcomes and prognosis (12).…”