LINC02454 related key pathways and genes in papillary thyroid cancer by weighted gene co-expression network analysis (WGCNA)

Abstract

Abstract Our previous study has demonstrated that long intergenic non-coding RNA 02454 (LINC02454) may act as an oncogene to promote proliferation and inhibit apoptosis in papillary thyroid cancer (PTC) cells. This study was designed to investigate the mechanisms whereby LINC02454 relates to PTC tumorigenesis.The thyroid cancer RNA sequence data were obtained from The Cancer Genome Atlas database. Weighted gene co-expression network analysis (WGCNA) was applied to identify LINC02454 modules associated with PTC. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis was used to identify the key pathways and MCC topological method was used to identify the hub genes. Gene Expression Profiling Interactive Analysis (GEPIA) database was used to analyze different expression levels of hub genes between PTC samples and normal samples and explore the prognostic value of hub genes. A total of top 5000 variable genes were investigated, followed by an analysis of 8 modules, and the turquoise module was the most positively correlated with the clinical stage of PTC. KEGG pathway analysis demonstrated the top two pathways of the ECM − receptor interaction and MAPK signaling pathway. In addition, five hub genes (namely FN1, LAMB3, ITGA3, SDC4, and IL1RAP) were identified based on MCC algorithm and KEGG analysis. Further, the expression levels of the five hub genes were significantly upregulated in thyroid cancer, of these five genes, two hub genes (FN1 and ITGA3) were associated with poor disease-free prognosis.Our study identified five hub genes and two key pathways associated with LINC02454, which might disclose the underlying mechanism of LINC02454 action in PTC.