Building a Competing Endogenous RNA Network to Find Potential Long Non-Coding RNA Biomarkers for Pheochromocytoma

Abstract

Background/Aims: Accumulating evidence has shown that long non-coding RNAs (lncRNAs) in competing endogenous RNA (ceRNA) networks play crucial roles in tumor survival and patient prognosis; however, studies investigating ceRNA networks in pheochromocytoma (PCC) are lacking. In this study, we investigated the pathogenesis of PCC and whether lncRNAs acting through ceRNAs networks were associated with prognosis. Methods: A total of 183 PCC samples and 3 control samples from The Cancer Genome Atlas database were analyzed. The Empirical Analysis of Digital Gene Expression Data package in R (edgeR) was used to analyze differentially expressed RNAs. Biological processes and pathways functional enrichment analysis were performed based on the Database for Annotation, Visualization, and Integrated Discovery (DAVID) database. LncRNA/mRNA/miRNA ceRNA network was constructed by Cytoscape v3.0 software based on the differentially expressed RNAs Survival package in R was used to perform survival analysis. Results: In total, 554 differentially expressed lncRNAs, 1775 mRNAs and 40 miRNAs were selected for further analysis. Subsequently, 23 lncRNAs, 22 mRNAs, and 6 miRNAs were included in the constructed ceRNA network. Meanwhile, two of the 23 lncRNAs (C9orf147 and BSN-AS2) were identified as independent predictors of overall survival in PCC patients (P< 0.05). Conclusion: This study improves the understanding of lncRNA-related ceRNA networks in PCC and suggests that the lncRNAs C9orf147 and BSN-AS2 could be independent prognostic biomarkers and potential therapeutic targets for PCC.

Long intergenic noncoding RNA profiles of pheochromocytoma and paraganglioma: A novel prognostic biomarker

“…The lincRNAs with differential expression signature in PCPG compared to normal adrenal medulla matches with a previous study performing the same analysis from TCGA data (e.g. MIAT , BSN‐AS2 ).…”

“…We also compared the expression of lincRNAs in PCPGs vs . normal adrenal medulla from TCGA (similar to Liang et al …”

“…Given the updated annotation of lincRNAs in the human genome, we aimed to extensively characterize the lincRNA expression profiles of PCPGs and its molecular subtypes using RNA‐Seq data from TCGA project by comparison with the profiles of 17 other cancer types. In a previous publication, lncRNAs were identified to be differentially expressed in PCPG compared to the normal adrenal medulla samples from TCGA transcriptomic data, but our study, for the first time, identified promising lincRNAs related to the molecular subtypes of PCPG, as well as transcripts related to aggressive or metastatic behavior. To our knowledge, this is the first extensive analysis of lincRNA expression profiles in context of clinically relevant subtypes of this disease.…”

“…S2). We also compared the expression of lincRNAs in PCPGs vs. normal adrenal medulla from TCGA (similar to Liang et al 30 ). Among the 479 lincRNAs upregulated in PCPG tumor samples compared to normal samples (p < 0.01), 46 were found to be overlapping with the 1,116 PCPG-specific lincRNAs from the pan-cancer analysis (Supporting Information Fig.…”

Long noncoding RNA BSN-AS2 induced by E2F1 promotes spinal osteosarcoma progression by targeting miR-654-3p/SYTL2 axis

“…In our research, lncRNA BSN-AS2 was found to aberrantly highly express in spinal OS tissues compared with adjacent normal tissues. Besides, BSN-AS2 differentially expressed in pheochromocytoma (PCC) samples and was recognized as an independent prognostic biomarker and potential therapeutic target for PCC [19]. Nevertheless, the underlying role and function of lncRNA BSN-AS2 in spinal OS was largely unknown.…”