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Comprehensive analysis of the LncRNAs, MiRNAs, and MRNAs acting within the competing endogenous RNA network of LGG

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Abstract

Messenger RNA (mRNA) and long noncoding RNA (lncRNA) targets interact via competitive microRNA (miRNA) binding. However, the roles of cancer-specific lncRNAs in the competing endogenous RNA (ceRNA) networks of low-grade glioma (LGG) remain unclear. This study obtained RNA sequencing data for normal solid tissue and LGG primary tumour tissue from The Cancer Genome Atlas database. We used a computational method to analyse the relationships among the mRNAs, lncRNAs, and miRNAs in these samples. Gene ontology (GO) function and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis was used to predict the biological processes (BPs) and pathways associated with these genes. Kaplan–Meier survival analysis was used to evaluate the association between the expression levels of specific mRNAs, lncRNAs, and miRNAs and overall survival. Finally, we created a ceRNA network describing the relationships among these mRNAs, lncRNAs, and miRNAs using Cytoscape 3.5.1. A total of 2555 differentially expressed (DE) mRNAs, 218 DElncRNAs, and 192 DEmiRNAs were identified using R. In addition, GO and KEGG pathway analysis of the mRNAs and lncRNAs in the ceRNA network identified 10 BPs, 10 cell components, 10 molecular functions, and 48 KEGG pathways as selectively enriched. A total of 55 lncRNAs, 50 miRNAs, and 10 mRNAs from this network were shown to be closely associated with overall survival in LGG. Finally, 59 miRNAs, 235 mRNAs, and 17 lncRNAs were used to develop a ceRNA network comprising 313 nodes and 1046 edges. This study helps expand our understanding of ceRNA networks and serves to clarify the underlying pathogenesis mechanism of LGG.

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Data availability

We obtained data from TCGA database (https://portal.gdc.cancer.gov/).

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Acknowledgements

YM Ding and HJ Liu performed the data analyses and wrote the manuscript. ZS Bao and CB Zhang contributed significantly to manuscript revision. SQ Yu conceived and designed the study. All authors read and approved the final manuscript and agreed to be accountable for all aspects of the research in ensuring that the accuracy or integrity of any part of the work are appropriately investigated and resolved. We acknowledge TCGA database for providing their platforms and contributors for uploading their meaningful datasets.

Funding

This study was supported by the General Technological Program of the Peking Education Commission (KM201810025023).

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Authors and Affiliations

  1. Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, No. 119 Nansihuanxilu, Fengtai District, Beijing, 100070, People’s Republic of China

    Yiming Ding, Chuanbao Zhang, Zhaoshi Bao & Shuqing Yu

  2. Beijing Neurosurgical Institute, Capital Medical University, Beijing, China

    Hanjie Liu

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  1. Yiming Ding
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  2. Hanjie Liu
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Correspondence to Shuqing Yu.

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Ding, Y., Liu, H., Zhang, C. et al. Comprehensive analysis of the LncRNAs, MiRNAs, and MRNAs acting within the competing endogenous RNA network of LGG. Genetica 150, 41–50 (2022). https://doi.org/10.1007/s10709-021-00145-3

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  • DOI: https://doi.org/10.1007/s10709-021-00145-3

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