Identification of 10 Hub genes related to the progression of colorectal cancer by co-expression analysis

Abstract

Background Colorectal cancer (CRC) is the third most common cancer in the world. The present study is aimed at identifying hub genes associated with the progression of CRC. Method The data of the patients with CRC were obtained from the Gene Expression Omnibus (GEO) database and assessed by weighted gene co-expression network analysis (WGCNA), Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses performed in R by WGCNA, several hub genes that regulate the mechanism of tumorigenesis in CRC were identified. Differentially expressed genes in the data sets GSE28000 and GSE42284 were used to construct a co-expression network for WGCNA. The yellow, black and blue modules associated with CRC level were filtered. Combining the co-expression network and the PPI network, 15 candidate hub genes were screened. Results After validation using the TCGA-COAD dataset, a total of 10 hub genes (MT1X, MT1G, MT2A, CXCL8, IL1B, CXCL5, CXCL11, IL10RA, GZMB, KIT) closely related to the progression of CRC were identified. The expressions of MT1G, CXCL8, IL1B, CXCL5, CXCL11 and GZMB in CRC tissues were higher than normal tissues (p-value < 0.05). The expressions of MT1X, MT2A, IL10RA and KIT in CRC tissues were lower than normal tissues (p-value < 0.05). Conclusions By combinating with a series of methods including GO enrichment analysis, KEGG pathway analysis, PPI network analysis and gene co-expression network analysis, we identified 10 hub genes that were associated with the progression of CRC.

Metallothionein 2A (MT2A) controls cell proliferation and liver metastasis by controlling the MST1/LATS2/YAP1 signaling pathway in colorectal cancer

“…These findings were verified in 65 pairs of cancer and adjacent tissues in patients with CRC. These results were consistent with those reported by Meng et al [ 16 ] and Arriaga et al [ 13 ]. However, other studies have shown that MT2A is upregulated in human colorectal adenocarcinoma HT29 cells [ 12 ], and the interaction between pFADD and MT2A inhibits the apoptosis of Colo 205 cells and induces cell proliferation [ 14 ].…”

CXCL5 and CXCL14, but not CXCL16 as potential non-invasive biomarkers of colorectal cancer?

“…For example, in the work of Baier et al [18] it was proved that the concentration in cancer tissue is signi cantly higher compared to normal tissue. Similar results were also obtained by other researchers such as Hu et al [19], Yu et al [20], Meng et al [21], Rubie et al [22] and Zhang et al [23]. In the case of two last of mentioned studies, the authors additionally performed an analysis of gene expression (qRT-PCR), which, along with similar results obtained in the work of Novillo et al [24], con rmed the increase of CXCL5 in the course of CRC.…”

In silico identification of novel biomarkers for key players in transition from normal colon tissue to adenomatous polyps

“…Meng and colleagues applied WGCNA to identify hub genes in the progression of colorectal cancer [42]. They reported IL10RA as one of hub genes with a lower mRNA expression in colorectal cancer samples compared to normal.…”

“…Some of the biomarkers were validated by real-time quantitative PCR analysis. A recent study applied WGCNA on colorectal cancer samples obtained from two GEO datasets [42]. The nodes with higher degrees in the network were identified as hub genes after mapping of differentially expressed genes found in important modules over the STRING network.…”