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. 2018 Oct 15:11:6957-6967.
doi: 10.2147/OTT.S170504. eCollection 2018.

Identification of critically carcinogenesis-related genes in basal cell carcinoma

Jie Dai  1 , Kang Lin  2 , Yan Huang  3 , Yan Lu  4 , Wen-Qi Chen  1 , Xiao-Rong Zhang  1 , Bang-Shun He  5 , Yu-Qin Pan  5 , Shu-Kui Wang  2 , Wei-Xin Fan  4
Affiliations

Identification of critically carcinogenesis-related genes in basal cell carcinoma

Jie Dai et al. Onco Targets Ther. .

Abstract

Background: Basal cell carcinoma (BCC) is a frequent malignant tumor of skin cancers with high morbidity. The objective of this study was to identify critical genes and pathways related to the carcinogenesis of BCC and gain more insights into the underlying molecular mechanisms of BCC.

Materials and methods: The gene expression profiles of GSE7553 and GSE103439 were downloaded from the Gene Expression Omnibus database with 19 tumors and 6 normal skin tissues. Differentially expressed genes (DEGs) were screened between BCC samples and normal tissues, followed by gene ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis. Subsequently, protein-protein interaction (PPI) network was constructed for these DEGs, and module analysis was performed.

Results: A total of 313 DEGs were obtained. Among them, 222 genes were upregulated and 91 genes were downregulated. Enrichment analysis indicated that the upregulated genes were significantly enriched in cell cycle and mitosis, while the downregulated genes were mainly associated with unsaturated fatty acid metabolic process and cell differentiation. In addition, TOP2A, CDK1, and CCNB1 were identified as the top three hub genes ranked by degrees in the PPI network. Meanwhile, three subnetworks were derived, which indicated that these DEGs were significantly enriched in pathways, including "cell cycle", "extracellular matrix-receptor interaction", "basal cell carcinoma", and "hedgehog signaling pathway".

Conclusions: The novel critical DEGs and pathways identified in this study may serve pivotal roles in the carcinogenesis of BCC and indicate more molecular targets for the treatment of BCC.

Keywords: basal cell carcinoma; bioinformatics analysis; differentially expressed genes; enrichment analysis.

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Conflict of interest statement

Disclosure The authors report no conflicts of interest in this work.

Figures

Figure 1
Figure 1
DEGs in the two datasets. Notes: (A) Common DEGs between GSE7553 and GSE103439. (B) Common upregulated DEGs between GSE7553 and GSE103439. (C) Common downregulated DEGs between GSE7553 and GSE103439. (D, E) Hierarchical clustering analysis of the DEGs in GSE7553 and GSE103439, respectively. Red and green indicate higher expression and lower expression, respectively. Abbreviation: DEGs, differentially expressed genes.
Figure 2
Figure 2
Histogram of degrees of the top 30 genes in the protein–protein interaction network. Note: The number displayed on each column is the degree of each gene.
Figure 3
Figure 3
Three subnetworks obtained from the whole protein–protein interaction network. Notes: (A, B) Module 1 and the pathway enrichment analysis of genes in module 1. (C, D) Module 2 and the pathway enrichment analysis of genes in module 2. (E, F) Module 3 and the pathway enrichment analysis of genes in module 3. Vertical axis represents GO or pathway terms. P-values are displayed by gradient colors. Abbreviations: ECM, extracellular matrix; KEGG, Kyoto Encyclopedia of Genes and Genomes.
See this image and copyright information in PMC

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