Integration analysis of long non-coding RNA (lncRNA) role in tumorigenesis of colon adenocarcinoma

Abstract

Background: Colon adenocarcinoma (COAD) is one of the most common gastrointestinal cancers globally. Molecular aberrations of tumor suppressors and/or oncogenes are the main contributors to tumorigenesis. However, the exact underlying mechanisms of COAD pathogenesis are clearly not known yet. In this regard, there is an urgent need to indicate promising potential diagnostic and prognostic biomarkers in COAD patients. Methods: In the current study, level 3 RNA-Seq and miR-Seq data and corresponding clinical data of colon adenocarcinoma (COAD) were retrieved from the TCGA database. The "limma" package in R software was utilized to indicate the differentially expressed genes. For in silico functional analysis, GO and KEGG signaling pathways were conducted. PPI network was constructed based on the STRING online database by Cytoscape 3.7.2. A ceRNA network was also constructed by "GDCRNATools" package in R software. Kaplan-Meier survival analysis (log-rank test) and ROC curve analysis were used to indicate the diagnostic and prognostic values of the biomarkers. Results: The differential expression data demonstrated that 2995 mRNAs, 205 lncRNAs, and 345 miRNAs were differentially expressed in COAD. The GO and KEGG pathway analysis indicated that the differentially expressed mRNAs were primarily enriched in canonical processes in cancer. The PPI network showed that the CDKN2A, CCND1, MYC, E2F, CDK4, BRCA2, CDC25B, and CDKN1A proteins were the critical hubs. In addition, the Kaplan-Meier analysis revealed that 215 mRNAs, 14 lncRNAs, and 39 miRNAs were associated with overall survival time in the patients. Also, the ceRNA network data demonstrated that three lncRNAs including MIR17HG, H19, SNHG1, KCNQ1OT1, MALAT1, GAS5, SNHG20, OR2A1-AS1, and MAGI2-AS3 genes were involved in the development of COAD. Conclusions: Our data suggested several promising lncRNAs in the diagnosis and prognosis of patients with COAD.

Immune-Related Gene Expression Analysis Revealed Three lncRNAs as Prognostic Factors for Colon Cancer

“…AC124067.4, also known as RP11-150O12.3, is located on the shorter arm of chromosome 8 (8p). AC124067.4 was previously demonstrated to be an independent predictor of gastric cancer prognosis (Ren et al, 2016) and its expression was associated with survival in patients with CRC (Poursheikhani et al, 2020). Our study found that the expression of AC124067.4 was significantly upregulated, and its expression level was also associated with the OS rate in patients with COAD.…”

A representation learning model based on variational inference and graph autoencoder for predicting lncRNA-disease associations

“…Among the top 10 lncRNAs predicted by VGAELDA, UCA1 facilitates the progression of colon cancer through upregulating miRNA miR-28-5p and HOXB3 [ 49 ]. It is found that GAS5 is positively correlated to colon cancer as well [ 50 ]. Also, previous research suggests that PVT1 can sponge miRNA miR-26b and promote proliferation and metastasis of colon cancer [ 51 ].…”

Mast Cells, microRNAs and Others: The Role of Translational Research on Colorectal Cancer in the Forthcoming Era of Precision Medicine

“…There are several studies that report the role of miRNAs in a variety of biological processes and immune responses as well as the correlation between dysregulated miRNAs and the aberrant regulation of signaling pathways, including angiogenesis, drug resistance and EMT [63][64][65]; miRNAs play these roles by regulating oncogene and tumor suppressor gene expression [66,67].…”