CeRNA Network Analysis Representing Characteristics of Different Tumor Environments Based on 1p/19q Codeletion in Oligodendrogliomas

Abstract

Oligodendroglioma (OD) is a subtype of glioma occurring in the central nervous system. The 1p/19q codeletion is a prognostic marker of OD with an isocitrate dehydrogenase (IDH) mutation and is associated with a clinically favorable overall survival (OS); however, the exact underlying mechanism remains unclear. Long non-coding RNAs (lncRNAs) have recently been suggested to regulate carcinogenesis and prognosis in cancer patients. Here, we performed in silico analyses using low-grade gliomas from datasets obtained from The Cancer Genome Atlas to investigate the effects of ceRNA with 1p/19q codeletion on ODs. Thus, we selected modules of differentially expressed genes that were closely related to 1p/19q codeletion traits using weighted gene co-expression network analysis and constructed 16 coding RNA–miRNA–lncRNA networks. The ceRNA network participated in ion channel activity, insulin secretion, and collagen network and extracellular matrix (ECM) changes. In conclusion, ceRNAs with a 1p/19q codeletion can create different tumor microenvironments via potassium ion channels and ECM composition changes; furthermore, differences in OS may occur. Moreover, if extrapolated to gliomas, our results can provide insights into the consequences of identical gene expression, indicating the possibility of tracking different biological processes in different subtypes of glioma.

LINC00511/hsa-miR-573 axis-mediated high expression of Gasdermin C associates with dismal prognosis and tumor immune infiltration of breast cancer

“…ncRNAs are well-recognized for regulating gene expression at almost every step 31 – 33 . In order to determine whether GSDMC was regulated by various ncRNAs in BRCA, we forecasted potential candidate miRNAs that might bind to GSDMC and ultimately identified 15 miRNAs.…”

“…It has been well documented that ceRNA theory explains interactions among mRNA and ncRNAs (miRNAs, lncRNAs, and circular RNAs (circRNAs)) 32 , 43 . LncRNAs affects the miRNA affinity of target mRNA by attaching to similar miRNA response elements, thereby regulating gene expression at the transcriptional level 31 , 33 . We predicted potential miRNA candidates of GSDMC via several target gene prediction websites, consisting of miRDB, miRmap, TargetScan, miRcode, miRWalk, and DIANA-microT, and finally found 15 miRNAs.…”

MicroRNA-1298-3p induces tumor-suppressive effects in human cervical cancer cells via post-transcriptional suppression of ONECUT2

“…The miRs have gained tremendous research interest in the recent era for their profound regulatory potential to serve as faithful prognostic and therapeutic role in human cancer (Mollaei et al, 2019;Zaheer et al, 2019). Reportedly, a huge number of specific members of a diverse class of eukaryotic RNAs have been deduced to serve either oncogenic function or exercise the tumor restrictive behavior in human cancers (Cao et al, 2020;Chen et al, 2020.. MicroRNA-1298-3p (miR-1298 has been implicated for its tumor-suppressive action in a number of human cancers (Du et al, 2021;Ahn et al, 2020). Recently, miR-1298-3p has been shown to inhibit human glioma cell proliferation and invasion via post-transcriptional targeting of Nidogen 1 (Lu et al, 2018).…”

Long noncoding RNAs associated with nonalcoholic fatty liver disease in a high cholesterol diet adult zebrafish model

“…Recently, a regulatory interaction between a conserved pair of miRNAs and lncRNAs in zebrafish was discovered 13 . In addition, coding RNA–miRNA–lncRNA network and ceRNA network have been analyzed to discover the effect of tumor microenvironments in 1p/19q codeletion in oligodendrogliomas 26 . In this study, we discovered human homologs of eight lncRNA candidates from the fatty liver of zebrafish for the first time.…”