Dataset Information

Identification of Potential Prognostic Competing Triplets in High-Grade Serous Ovarian Cancer.

ABSTRACT: Increasing lncRNA-associated competing triplets were found to play important roles in cancers. With the accumulation of high-throughput sequencing data in public databases, the size of available tumor samples is becoming larger and larger, which introduces new challenges to identify competing triplets. Here, we developed a novel method, called LncMiM, to detect the lncRNA-miRNA-mRNA competing triplets in ovarian cancer with tumor samples from the TCGA database. In LncMiM, non-linear correlation analysis is used to cover the problem of weak correlations between miRNA-target pairs, which is mainly due to the difference in the magnitude of the expression level. In addition, besides the miRNA, the impact of lncRNA and mRNA on the interactions in triplets is also considered to improve the identification sensitivity of LncMiM without reducing its accuracy. By using LncMiM, a total of 847 lncRNA-associated competing triplets were found. All the competing triplets form a miRNA-lncRNA pair centered regulatory network, in which ZFAS1, SNHG29, GAS5, AC112491.1, and AC099850.4 are the top five lncRNAs with most connections. The results of biological process and KEGG pathway enrichment analysis indicates that the competing triplets are mainly associated with cell division, cell proliferation, cell cycle, oocyte meiosis, oxidative phosphorylation, ribosome, and p53 signaling pathway. Through survival analysis, 107 potential prognostic biomarkers are found in the competing triplets, including FGD5-AS1, HCP5, HMGN4, TACC3, and so on. LncMiM is available at https://github.com/xiaofengsong/LncMiM.

SUBMITTER: Zhao J

PROVIDER: S-EPMC7839966 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature

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Identification of Potential Prognostic Competing Triplets in High-Grade Serous Ovarian Cancer.

Zhao Jian J Song Xiaofeng X Xu Tianyi T Yang Qichang Q Liu Jingjing J Jiang Bin B Wu Jing J

Frontiers in genetics 20210113

Increasing lncRNA-associated competing triplets were found to play important roles in cancers. With the accumulation of high-throughput sequencing data in public databases, the size of available tumor samples is becoming larger and larger, which introduces new challenges to identify competing triplets. Here, we developed a novel method, called LncMiM, to detect the lncRNA-miRNA-mRNA competing triplets in ovarian cancer with tumor samples from the TCGA database. In LncMiM, non-linear correlation ...[more]

PMID: 33519912

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Project description:BackgroundETS transcription factors are known to act as either positive or negative regulators of the expression of genes involved in various biological processes. It was reported that ETS variant transcription factor 5 (ETV5), a key member of the ETS family, mainly plays a role as an potential oncogene in various malignant tumors. However, the role and mechanism of ETV5 in high-grade serous ovarian cancer (HGSOC) have not been elucidated.MethodsQuantitative real-time polymerase chain reaction (qRT-PCR) assay was used to detect ETV5 messenger ribonucleic acid (mRNA) expression in 87 HGSOC tissues and 35 normal fallopian tube tissues. Western blotting and qRT-PCR were used to detect the protein and mRNA expression of ETV5 in six ovarian cancer (OC) and human embryonic cell lines. Knockdown or overexpression of ETV5 in HGSOC cell lines, Cell Counting Kit-8, colony formation, and transwell assays were used to detect HGSOC cell proliferation, invasion, and migration capabilities. The chi-square test was used to analyze the clinicopathological characteristics of HGSOC patients. Survival analysis was performed using the Kaplan-Meier method, and the log-rank test was used to analyze the correlation between ETV5 expression and HGSOC patient prognosis. Univariate and multivariate analyses using the Cox regression model were conducted to determine the independent significance of relevant clinical covariates.ResultsBioinformatic analysis demonstrated that ETV5 expression was significantly upregulated in OC (p < 0.05). qRT-PCR showed that ETV5 was significantly overexpressed in HGSOC tissues than in fallopian tube tissues (p < 0.05). qRT-PCR and western blotting assays demonstrated that ETV5 was relatively highly expressed in OC cell lines. ETV5 overexpression was positively associated with poor survival in HGSOC patients, therefore making it a high-risk factor for HGSOC progression. Furthermore, ETV5 promoted the proliferation, migration, and invasion capabilities of HGSOC cells.ConclusionETV5 has a carcinogenic effect in HGSOC and can be used as a clinically effective biomarker to determine the prognosis of HGSOC patients.

Dataset Information

Identification of Potential Prognostic Competing Triplets in High-Grade Serous Ovarian Cancer.

Publications

Identification of Potential Prognostic Competing Triplets in High-Grade Serous Ovarian Cancer.

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