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

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.

Identification of Differently Expressed Genes Associated With Prognosis and Growth in Colon Adenocarcinoma Based on Integrated Bioinformatics Analysis

“…The Cancer Genome Atlas (TCGA), a public-funded project that aims to create a comprehensive “atlas” of cancer genomic profiles (Tomczak et al, 2015), recorded 382 samples of colorectal adenocarcinoma with RNA sequencing (RNA-Seq) data, and we mined DEGs in 275 COAD patients compared with 41 TCGA normal and 308 Genotype–Tissue Expression (GTEx) colon tissues by GEPIA 2 (Tang et al, 2017). In consideration of integrating more normal RNA-Seq data, we got similar but different DEGs in COAD (Xi et al, 2017; Long et al, 2018). Enrichment analysis of KEGG by GSEA (Subramanian et al, 2005) showed that the downregulated genes mainly participated in DNA replication, cell cycle, ribosome pathway, etc., and the upregulated genes mainly participated in vascular smooth muscle contraction, dilated cardiomyopathy, calcium signaling pathway, etc.…”

Roles of Proteoglycans and Glycosaminoglycans in Cancer Development and Progression

“…Versican Tissues (n = 84) Prognosis for renal carcinoma [72] Tissues (n = 52, 62, 456/453, 89) Prognosis for colon cancer [73,74] Blood (n = 27, 12, 31) Diagnosis for epithelial ovarian cancer [75] Blood (n = 30) Diagnosis for multiple myeloma [76] Tissues (n = 134/104) Prognosis for gastric cancer [77,78] Tissues (n = 142/212) Prognosis for non-small cell lung cancer [79,80] Tissues (n = 50, 19, 31) Diagnosis for hepatocellular carcinoma [81] Tissues (n = 139) Prognosis for oral squamous cell carcinoma [82] Tissues (n = 80/58) Prognosis for breast cancer [83,84] Tissues (n = 111/111) Prognosis for ovarian cancer [85,86] Tissues (n = 167) Prognosis for endometrial cancer [87] Tissues (n = 43) Prognosis for prostate cancer [88] Biglycan Tissues (n = 12,427) Prognosis for prostate cancer [89] Table 2. Cont.…”

Identification of Seven Cell Cycle-Related Genes with Unfavorable Prognosis and Construction of their TF-miRNA-mRNA regulatory network in Breast Cancer

“…Excitingly, the rapid expansion of biological microarray analysis greatly promotes the understanding of driver genes and functional pathways in BC by screening DEGs between tumor and normal tissues in the gene expression profiles of tumors [4]. Increasing data in various cancers have led to the identification of specific genes or pathways that play important roles in the biology and prognosis of tumors via the use of microarrays and bioinformatics methods [5][6][7][8]. Although significant expression of DEGs in BC has been reported in some previous studies [9][10][11][12], those individual studies provide a relatively limited amount of data regarding carcinogenesis.…”