Comprehensive Analysis of a Long Noncoding RNA-Associated Competing Endogenous RNA Network in Wilms Tumor

Abstract

Long noncoding RNA (lncRNA) plays crucial roles in various biological processes of different cancers, especially acting as a competing endogenous RNA (ceRNA). However, the role of lncRNA-mediated ceRNA in Wilms tumor (WT), which is the most common malignant kidney cancer in children, remains unknown. In present study, RNA sequence profiles and clinical data of 125 patients with WT consisting of 119 tumor and 6 normal tissues from Therapeutically Applicable Research To Generate Effective Treatments database were analyzed. A total of 1833 lncRNAs, 156 microRNAs (miRNAs), and 3443 messenger RNAs (mRNAs) were identified as differentially expressed (DE) using “DESeq2” package. The lncRNA-miRNA-mRNA ceRNA regulatory network involving 748 DElncRNAs, 33 DEmiRNAs, and 189 DEmRNAs was constructed based on miRcode, Targetscan, miRTarBase, and miRDB database. Gene Ontology term and Kyoto Encyclopedia of Genes and Genomes pathway analyses revealed that DEmRNAs were mainly enriched in cell proliferation-related processes and tumor-related pathways, respectively, and 13 hub genes were identified by a protein–protein interaction network. Survival analysis detected 48 lncRNAs, 7 miRNAs, and 16 mRNAs to have significant impact on the overall survival of patients with WT. Additionally, we found that 6 DElncRNAs with potential prognostic value were correlated with tumor stage ( DENND5B-AS1) and histologic classification ( TMPO-AS1, RP3-523K23.2, RP11-598F7.3, LAMP5-AS1, and AC013275.2) of patients with WT. Our research provides a great insight into understanding the molecular mechanism underlying occurrence and progression of WT, as well as the potential to develop targeted therapies and prognostic biomarkers.

Development of a Machine Learning-Based Autophagy-Related lncRNA Signature to Improve Prognosis Prediction in Osteosarcoma Patients

“…Therapeutically Applicable Research to Generate Effective Treatments (TARGET) 1 is an open database for childhood cancers. It seeks to use a comprehensive genomic approach to identify molecular changes in the occurrence and development of childhood cancers that are difficult to treat (Gao et al, 2020;Zhang et al, 2020). We obtained gene expression and clinical data of osteosarcoma patients from the TARGET database.…”

The Emerging Role of Thymopoietin-Antisense RNA 1 as Long Noncoding RNA in the Pathogenesis of Human Cancers

“…TMPO-AS1 was reported to be significantly upregulated in various cancers, such as lung cancer (Yu et al, 2020), breast cancer (Mitobe et al, 2020), colorectal cancer (CRC) (Mohammadrezakhani et al, 2020), hepatocellular carcinoma (HCC) (Liu and Shen, 2020;Wang et al, 2020), gastric cancer (GC) (Sun and Han, 2020), bladder cancer (He et al, 2020b), laryngeal squamous cell carcinoma (LSCC) (Zhang et al, 2020b), ovarian cancer (Li et al, 2020a;Zhao et al, 2020), thyroid cancer (Li et al, 2020b), esophageal cancer (Gao et al, 2020), Wilms tumor (Zhang et al, 2020a), cervical cancer (Gang et al, 2020), retinoblastoma (Peng et al, 2020), osteosarcoma (Cui and Zhao, 2020), or prostate cancer (Huang et al, 2018), and functions as an oncogene in carcinogenesis and tumor progression. To further investigate the aberrant expression of TMPO-AS1 in various cancers and their associated prognosis, this study applied the Gene Expression Profiling Interactive Analysis (GEPIA) online data analysis tool (Tang et al, 2017).…”

A Survival-Related Competitive Endogenous RNA Network of Prognostic lncRNAs, miRNAs, and mRNAs in Wilms Tumor

“…There is also a subset of studies evaluating the relationship between single RNA and OS. Tang et al (12) predicted 32 DERNAs to be possibly associated with OS in WT patients through Kaplan-Meier analysis, and Zhang et al (13) predicted 61 DERNAs to be possibly associated with OS by Kaplan-Meier analysis.…”

“…The ceRNA hypothesis explains the complicated RNA molecular regulation mechanisms via construction of a lncRNA-miRNA-mRNA network (9). Most studies on the molecular regulation mechanism of WT constructed a network based on DERNAs (12,13). We proposed a novel survivalrelated ceRNA network that provided a new dimension for predicting the prognosis of patients with WT.…”

“…In general, the instability of a ceRNA network may induce tumorigenesis (10,11). Several studies have suggested that a ceRNA network can be used as a prognostic biomarker for WT, but did not actually describe the effect of a ceRNA network in WT (12,13). Therefore, the establishment of a ceRNA network related to the survival of WT patients is of great significance for judging the prognosis of patients.…”