Identification of critical genes to predict recurrence and death in colon cancer: integrating gene expression and bioinformatics analysis

Xuan Long,Zhigang Deng,Guoqiang Li,Ziwei Wang

doi:10.1186/s12935-018-0640-x

Abstract

BackgroundThe purpose of this study was to screen the critical genes for future diagnosis and treatment of colon cancer by bioinformatics method.MethodsIn this study, we used bioinformatics approaches to identify gene alteration that contribute to colon cancer progression via analysis of TCGA RNA sequencing data and other publicly GEO microarray data. The Random forest survival model was used to screen gene sets related to the prognosis in DEGs. Gene ontology and KEGG pathway enrichment analysis were performed to determine the potential function of DEGs.ResultsWe identified versican (VCAN), a member of the aggrecan/versican proteoglycan family, as a key regulator in human colon cancer development and progression involved in cell adhesion, proliferation, migration and angiogenesis and plays a central role in tissue morphogenesis and maintenance. Interestingly, we found that VCAN is highly over-expressed in colon cancer and increased expression of VCAN was associated with the progression of colon cancer. High VCAN levels also predict shorter overall survival of colon cancer patients. Furthermore, in vitro assays of silencing VCAN inhibit HCT116 cell proliferation and invasion.ConclusionsThese data demonstrated VCAN were associated with tumorigenesis and may be as biomarker for identification of the pathological grade of colon cancer.

Highlights

The purpose of this study was to screen the critical genes for future diagnosis and treatment of colon cancer by bioinformatics method
We identified versican (VCAN), a member of the aggrecan/versican proteoglycan family, as a key regulator in human colon cancer development and progression involved in cell adhesion, proliferation, migration and angiogenesis and plays a central role in tissue morphogenesis and maintenance
Identification of differently expressed genes (DEGs) in human colon cancer To identify differentially expressed genes (DEGs) that are played key role in colon tumorigenesis, we used an integrative analysis of The Cancer Genome Atlas (TCGA) colon adenocarcinoma (TCGA-Colon adenocarcinoma (COAD)) and RNA-seq data and colon cancer gene expression data includinging GSE63624, and GSE77167 the publicly available gene expression omnibus (GEO) databases

Summary

Introduction

The purpose of this study was to screen the critical genes for future diagnosis and treatment of colon cancer by bioinformatics method. More than 1.2 million patients are diagnosed with colon cancer every year, and more than 600,000 die from the disease [1,2,3,4]. Incidence is higher in men than women and strongly increases with age; median age at diagnosis is about 70 years in developed countries [5,6,7,8]. The gene expression profile of colon cancer had analyzed by microarray technique indicated many genes. Microarray technology combining with bioinformatics analysis makes it possible to comprehensively analyze the DEGs in mRNA expression level in the development and progression of colon cancer

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