Pathogenesis and prognosis of primary oral squamous cell carcinoma based on microRNAs target genes: a systems biology approach

Abstract

Oral squamous cell carcinoma (OSCC) is the most prevalent head and neck malignancy, with frequent cervical lymph-node metastasis, leading to a poor prognosis in OSCC patients. The present study aimed to identify potential markers, including microRNAs (miRNAs) and genes, significantly involved in the etiology of early-stage OSCC. Additionally, the main OSCC's dysregulated Gene Ontology annotations and significant signaling pathways were identified. The dataset GSE45238 underwent multivariate statistical analysis in order to distinguish primary OSCC tissues from healthy oral epithelium. Differentially expressed miRNAs (DEMs) with the criteria of p-value < 0.001 and |Log2 fold change| > 1.585 were identified in the two groups, and subsequently, validated targets of DEMs were identified. A protein interaction map was constructed, hub genes were identified, significant modules within the network were illustrated, and significant pathways and biological processes associated with the clusters were demonstrated. Using the GEPI2 database, the hub genes' predictive function was assessed. Compared to the healthy controls, main OSCC had a total of 23 DEMs. In patients with head and neck squamous cell carcinoma (HNSCC), upregulation of CALM1, CYCS, THBS1, MYC, GATA6, and SPRED3 was strongly associated with a poor prognosis. In HNSCC patients, overexpression of PIK3R3, GIGYF1, and BCL2L11 was substantially correlated with a good prognosis. Besides, “proteoglycans in cancer” was the most significant pathway enriched in the primary OSCC. The present study results revealed more possible mechanisms mediating primary OSCC and may be useful in the prognosis of the patients with early-stage OSCC.

piRNAs and miRNAs Can Bind to mRNA of <i>KLOTHO</i> and <i>FGF23</i> Genes

“…Several publications have established the involvement of the BCL2L11 gene in oncogenesis [58][59][60][61]. For piR-3215034, 12 BSs were identified, which form a cluster of BSs from 55 nt to 114 nt, 60 nt long (Figure 3).…”

Prognostic biomarkers and molecular pathways mediating Helicobacter pylori–induced gastric cancer: a network-biology approach

“…Normalization was performed prior to statistical analysis. The OPLS-DA identified the DEMs between two groups using the R version 4.0.2 programming language [ 71 ]. The cutoff conditions were set to an absolute Log2 fold change |Log2 FC| > 1 and the p-value less than 0.01 [ 68 , 72 ].…”

MicroRNA-Based Markers of Oral Tongue Squamous Cell Carcinoma and Buccal Squamous Cell Carcinoma: A Systems Biology Approach

“…Significant molecular pathways and Gene Ontology (GO) terms involved in the malignant transformation of normal oral mucosa to OTSCC and BSCC were unraveled using g:Profiler tool, available at https://biit.cs.ut.ee/gprofiler/gost [ 34 ]. The cut-off condition was set to the false discover rate (FDR) < 0.05 and the number of entities ≥10, following our previous study [ 35 ]. The results from two primary pathway sources, including Reactome [ 36 ] and the Kyoto Encyclopedia of Genes and Genomes (KEGGs) [ 37 ] databases, were considered for pathway enrichment analysis.…”