MicroRNAs Associated With Colon Cancer: New Potential Prognostic Markers and Targets for Therapy

Abstract

MicroRNAs (miRNAs) are a kind of non-coding RNA (ncRNA) that regulate the expression of target genes and play a role in the occurrence and development of cancers. Colon cancer (COAD) is the second most common cause of cancer-related mortality. However, the prognostic value of miRNAs in COAD is still confusing. In this study, we obtain miRNAs and messenger RNAs (mRNAs) expression profiles of COAD from the Cancer Genome Atlas (TCGA) database. After preliminary data screening and preprocessing, we acquire the expression data of 894 miRNAs and 17,019 mRNAs. Then, compared with the normal samples, 39 upregulated miRNAs and 54 downregulated miRNAs are identified by differential expression analysis. Furthermore, we obtain 1,487 upregulated mRNAs and 2,847 downregulated mRNAs. We confirm nine key miRNAs related to the survival rate of COAD patients. Moreover, by using bioinformatics methods, we get 461 common genes from both the target genes of these nine key miRNAs and differentially expressed mRNAs. Through analyzing the protein-protein interaction (PPI) network of these 461 common genes and survival analysis, we confirm five hub genes as promising biomarkers for COAD prognosis. It is worth mentioning that no previous reports have found that PGR and KCNB1 are related to COAD. We expect these key miRNAs and hub genes will provide a new way for the study of COAD.

Construct a circRNA/miRNA/mRNA regulatory network to explore potential pathogenesis and therapy options of clear cell renal cell carcinoma

“…Experiments had demonstrated that miRNAs are closely related to the proliferation, migration, and invasion, and circRNAs can regulate these processes via miRNAs in ccRCC [26][27][28] . Some www.nature.com/scientificreports/ studies also demonstrated that circRNA/miRNA has a strong association with diseases, especially with cancer, by utilizing advanced computational methods such as KATZ algorithm, Locality-Constrained Linear Coding algorithm, inductive matrix completion, decision tree [29][30][31][32][33][34][35] . Therefore, circRNAs and miRNAs can apply as a therapeutic method or a biomarker of diagnosis.…”

Pyrroline-5-Carboxylate Reductase-2 Promotes Colorectal Cancer Progression via Activating PI3K/AKT/mTOR Pathway

“…In the pursuit of knowledge regarding CRC, the Cancer Genome Atlas (TCGA) database has stored more than 20 cancer genome data types, including mutations, copy number variations, mRNA expressions, miRNA expressions, and methylation data, which are widely used in cancer research [ 4 ]. To date, the TCGA has confirmed nine miRNAs and five genes that have prognostic value in colon cancer [ 5 ]. Therefore, it is vital to identify novel markers for CRC diagnosis and prognosis and provide new targets for CRC therapy.…”

Identification of a Potentially Functional microRNA–mRNA Regulatory Network in Lung Adenocarcinoma Using a Bioinformatics Analysis

“…We considered p < 0.05 statistically significant. Using the STRING database, 5 we downloaded data from the PPI network for targeted mRNAs for the hub miRNAs applying the following criteria: (a) homo sapiens; and (b) medium confidence 0.400 ( Zhu et al, 2020 ). Then, the PPI network was further adjusted using the Cytoscape software version 3.7.0, and we identified the top ten key mRNAs of the PPI network using cytoHubba’s Maximal Clique Centrality (MCC) ranking ( Yang et al, 2019 ).…”