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Sequencing and Bioinformatics analysis of lncRNA/circRNA-miRNA-mRNA in Glioblastoma multiforme

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Abstract

Evidence suggests that non-coding RNAs have a role in glioblastoma multiforme (GBM), although the regulatory mechanisms controlled by competing endogenous RNAs (ceRNAs) in GBM are still poorly understood and infrequently described. This research extensively analyzed circRNA, lncRNA, miRNA, and mRNA expression changes in GBM patients. RNA-sequencing analyses were conducted to investigate differentially expressed genes (DEGs), lncRNAs (DELs), miRNAs (DEMs), and circRNAs (DECs) in the GBM. In this study, researchers found that GBM patients and healthy controls differed in the presence of 1224 DECs, 1406 DELs, 229 DEMs, and 2740 DEGs. PPI network analysis demonstrated that CEACAM5, CXCL17, FAM83A, TMPRSS4, and GGPRC5A were hub genes and enriched in modules. Then a ceRNA network was constructed with 8 circRNA, 7 lncRNAs, 16 miRNAs, and 17 mRNAs. Overall, the ceRNA interaction axes that were found may prove to be pivotal therapeutic targets for treating GBM.

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Data Availability

The datasets used and/or analyzed during the current study are available from the corresponding author upon reasonable request.

Abbreviations

GBM:

Glioblastoma multiforme

TCGA:

The cancer genome atlas

ceRNAs:

Competing endogenous RNAs

circRNA:

circular RNA

lncRNAs:

Long non-coding RNAs

miRNA/miR:

microRNA

DEGs:

Differentially expressed genes

PPI:

Protein-protein interaction

CEACAM5:

Carcinoembryonic antigen-related cell adhesion molecule 5

CXCL17:

C-X-C motif chemokine ligand 17

FAM83A:

Family with sequence similarity 83 member A

TMPRSS4:

Transmembrane serine protease 4

GPRC5A:

G protein-coupled receptor class C group 5 member A

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Acknowledgements

Not Applicable.

We thank all participants involved in this study and all authors. We would like to thank Dr. Pu Yong of Tianjin Ruijiyin Biotechnology Co., Ltd. for his assistance in our bioinformatics analysis.

Funding

This work was supported by the National Natural Science Foundation of China, No. 81871086 (to LHQ), the Tianjin Science and Technology Project, No. 21JCQNJC01400 (to WRJ).

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    Authors and Affiliations

    1. Academy of Medical Engineering and Translational Medicine, Tianjin University, Tianjin, 300072, China

      Renjie Wang & Feng He

    2. Department of Neurosurgery, Characteristic Medical Center of Chinese People’s Armed Police Force, Tianjin, 300162, China

      Renjie Wang, Nan Li & Haiqian Liang

    3. Tianjin Hospital, Tianjin University, Tianjin, 300050, China

      Qi Li & Xiaolei Chu

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    1. Renjie Wang
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    2. Qi Li
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    4. Nan Li
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    5. Haiqian Liang
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    Contributions

    RW, QL, HL and FH conceived and designed the study. RW and QL collected and processed data. XC and NL analyzed data. RW and QL drafted the manuscript. HL and FH revised the manuscript. All authors read and approved the final manuscript.

    Acknowledgements.

    Corresponding authors

    Correspondence to Haiqian Liang or Feng He.

    Ethics declarations

    Ethics approval and consent to participate

    This study was performed conforming to the tenets of Declaration of Helsinki and written informed consent was obtained from all patients prior to the investigation. An ethics approval was obtained from the Characteristic Medical Center of Chinese People’s Armed Police Force (No. 2022 − 0002.1) prior to the collection of tissue samples. The funders had no role in the study design, data collection and analysis, data interpretation, or preparation of the manuscript.

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    Not Applicable.

    Competing interests

    The authors declare no competing interests.

    Additional information

    Renjie Wang, Qi Li and Xiaolei Chu contributed equally to this work.

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    Wang, R., Li, Q., Chu, X. et al. Sequencing and Bioinformatics analysis of lncRNA/circRNA-miRNA-mRNA in Glioblastoma multiforme. Metab Brain Dis 38, 2289–2300 (2023). https://doi.org/10.1007/s11011-023-01256-w

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