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Profiling and Bioinformatics Analyses of Differential Circular RNA Expression in Glioblastoma Multiforme Cells Under Hypoxia

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Abstract

The hypoxia microenvironment is highly associated with GBM’s malignant phenotypes. CircRNAs were reported involved in GBM’s biological characteristics and regulated by HIF-1α. However, the differential expression profile and role of circRNAs in GBM cells under hypoxia are still unclear. The expression profiles of circRNAs in LN229 and T98G under hypoxia were explored via circRNA sequencing analysis. Those circRNAs significantly dysregulated both in LN229 and T98G and could be found in circBase were selected and validated by qRT-PCR, RNase R digestion reaction, and Sanger sequencing. Normal cell line and fresh GBM tissues were also used for qRT-PCR validation. The roles of differentially expressed circRNAs were evaluated by bioinformatics analyses. There were 672 dysregulated circRNAs in LN229 and 698 dysregulated circRNAs in T98G. GO analysis indicated that the alteration of circRNA expression related to GBM cell’s biogenesis and metabolism. KEGG analysis demonstrated that TGF-β signaling pathway, HIF-1 signaling pathway, and metabolism-related signaling pathway were closely associated with differentially expressed circRNAs under hypoxia. These results were confirmed by GSEA analysis. The 6 selected and dysregulated circRNAs both in LN229 and T98G including hsa_circ_0000745, hsa_circ_0020093, hsa_circ_0020094, hsa_circ_0000943, hsa_circ_0004874, and hsa_circ_0002359 were validated by qRT-PCR. Inhibition of hsa_circ_0000745 inhibited GBM cell’s proliferation, migration, and invasion. HIF-1α centered circRNA-miRNA-mRNA networks analysis showed that the 6 validated circRNAs could cross-talk with 11 related miRNAs. The circRNA expressions are dysregulated in GBM cell under hypoxia. The 6 validated circRNAs could participate in GBM’s development and progression when hypoxia occurs. They might be the candidates for prognostic markers and adjuvant therapeutics of GBM in the future.

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Data Availability

The raw data supporting the conclusion of this article will be made available by the authors, without undue reservation.

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Funding

This work was supported by the National Natural Science Foundation of China (grant number: 81902521), Shanghai Sailing Program (grant number: 19YF1432800), and Research Project of Xinhua Hospital (grant number: XH1936).

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  1. Zheng Chen, Shaohua Su and Min Yang contributed equally to this work.

Authors and Affiliations

  1. Department of Neurosurgery, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, 1665 Kong Jiang Road, Yangpu District, 200092, Shanghai, China

    Zheng Chen, Min Yang & Ming Chen

  2. Department of Neurosurgery, Tongji Hospital, School of Medicine, Tongji University, 389 Xin Cun Road, Putuo District, Shanghai, 200065, Shanghai, China

    Shaohua Su & Fei Wang

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  1. Zheng Chen
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  2. Shaohua Su
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  3. Min Yang
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  5. Ming Chen
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Contributions

Ming Chen and Fei Wang designed and supervised the project. Zheng Chen, Shaohua Su, and Min Yang conducted the experiments and performed data analysis. Zheng Chen wrote and revised the manuscript.

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Correspondence to Fei Wang or Ming Chen.

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Chen, Z., Su, S., Yang, M. et al. Profiling and Bioinformatics Analyses of Differential Circular RNA Expression in Glioblastoma Multiforme Cells Under Hypoxia. J Mol Neurosci 72, 2451–2463 (2022). https://doi.org/10.1007/s12031-022-02090-y

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