Weighted gene co-expression network analysis in identification of metastasis-related genes of lung squamous cell carcinoma based on the Cancer Genome Atlas database

Abstract

Background: Lung squamous cell carcinoma (lung SCC) is a common type of malignancy. Its pathogenesis mechanism of tumor development is unclear. The aim of this study was to identify key genes for diagnosis biomarkers in lung SCC metastasis.

Methods: We searched and downloaded mRNA expression data and clinical data from The Cancer Genome Atlas (TCGA) database to identify differences in mRNA expression of primary tumor tissues from lung SCC with and without metastasis. Gene co-expression network analysis, protein-protein interaction (PPI) network, Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis and quantitative real-time polymerase chain reactions (qRT-PCR) were used to explore the biological functions of the identified dysregulated genes.

Results: Four hundred and eighty-two differentially expressed genes (DEGs) were identified between lung SCC with and without metastasis. Nineteen modules were identified in lung SCC through weighted gene co-expression network analysis (WGCNA). Twenty-three DEGs and 26 DEGs were significantly enriched in the respective pink and black module. KEGG pathway analysis displayed that 26 DEGs in the black module were significantly enriched in bile secretion pathway. Forty-nine DEGs in the two gene co-expression module were used to construct PPI network. CFTR in the black module was the hub protein, had the connectivity with 182 genes. The results of qRT-PCR displayed that FIGF, SFTPD, DYNLRB2 were significantly down-regulated in the tumor samples of lung SCC with metastasis and CFTR, SCGB3A2, SSTR1, SCTR, ROPN1L had the down-regulation tendency in lung SCC with metastasis compared to lung SCC without metastasis.

Conclusions: The dysregulated genes including CFTR, SCTR and FIGF might be involved in the pathology of lung SCC metastasis and could be used as potential diagnosis biomarkers or therapeutic targets for lung SCC.

Keywords: Lung squamous cell carcinoma (lung SCC); biomarkers; gene regulatory network; genes expression profiling; neoplasm metastasis.

Figure 1

Network analysis of gene expression in lung SCC identifies 19 distinct modules of co-expression genes. The dendrogram produced by average linkage hierarchical clustering of 20,531 genes based on WGCNA package in R. Total of 19 modules were identified. The three panels were the whole dendrogram. lung SCC, lung squamous cell carcinoma; WGCNA, weighted gene co-expression network analysis.

Figure 2

The constructed PPI networks of the DEGs in black module and the pink module. Pink nodes and black nodes represent DEGs in the pink module and black module, respectively. The blue nodes denote products of genes predicted to interact with the DEGs. The solid line means PPI correlation. PPI, protein-protein interaction; DEGs, differentially expressed genes.

Figure 3

The verification of mRNA expression level of DEGs between of lung SCC with and without metastasis in primary tumor tissues through qRT-PCR. (A) FIGF; (B) SFTPD; (C) DYNLRB2; (D) CFRT; (E) SCGB3A2; (F) SSTR1; (G) SCTR; (H) ROPN1L. M means patients with lung SCC metastasis; MW means patients without lung SCC metastasis. *, means P<0.05; and ***, means P<0.001. lung SCC, lung squamous cell carcinoma; DEGs, differentially expressed genes; qRT-PCR, quantitative real-time polymerase chain reactions.