Bioinformatics analysis of potential glioblastoma circular RNA sponge network

Liwen Zhao; Pengfei Zhang; Yang Nan; Bingcheng Ren; Haiwen Ma; Jiapeng Xie; Qiang Huang

doi:10.21037/tcr-21-2597

Bioinformatics analysis of potential glioblastoma circular RNA sponge network

Transl Cancer Res. 2022 May;11(5):1017-1032. doi: 10.21037/tcr-21-2597.

Authors

Liwen Zhao^#^{1

2}, Pengfei Zhang^#³, Yang Nan^#^{1

4}, Bingcheng Ren^{1

4}, Haiwen Ma¹, Jiapeng Xie¹, Qiang Huang^{1

4}

Affiliations

¹ Department of Neurosurgery, Tianjin Medical University General Hospital Airport Site, Tianjin, China.
² Tianjin Medical University, Tianjin, China.
³ Department of Neurosurgery, Beichen Traditional Chinese Medical Hospital, Tianjin, China.
⁴ Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin, China.

^# Contributed equally.

Abstract

Background: Circular RNA is emerging functional molecule for glioblastoma. However, the function and regulatory of circular RNA (circRNA) remains unclear. In this study, the circRNA sequencing and array data of glioblastoma were analyzed by multiple bioinformatics methods to establish a potential molecular sponge mechanism regulation network.

Methods: Gene Expression Omnibus datasets were used to extract circRNAs. CircInteractome was used to predict microRNAs binding to circRNAs. Chinese Glioma Gene Atlas database was used to screen the microRNAs with expression and survival trends. MiRabel database was used to predict potential gene targets of microRNAs. The Cancer Genome Atlas database was used to screen the gene targets of sponge network. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analysis were to explain the gene targets functions. R software, Cytoscape software and Bioinformatics website were used to establish the network and visualize the results.

Results: Hsa_circ_0000219, hsa_circ_0001073 and hsa_circ_0070700 were selected from more than 2000 differentially expressed circRNAs of Gene Expression Omnibus Series (GSE) GSE146463, GSE92322 and GSE86202 datasets. Hsa-miR-1248 and hsa-miR-1290 were up regulated and related to glioblastoma poor prognosis. Targets of these microRNAs including ARHGEF7, CELA2b, RNF11, YPEL1 and ZNF37a were also screened via expression and survival data. Gene targets function were mainly enriched in signal transduction, cell plasma membrane, ATP binding and calcium signaling pathway.

Conclusions: A circRNA molecular sponge regulatory network including hsa-miR-1248 and hsa-miR-1290 has been established. In this network, hsa_circ_0001073, hsa_circ_0070700, hsa_circ_0000219, hsa-miR-1248, hsa-miR-1290, and RNF11 may have the potential being emerging glioblastoma therapeutic targets. However, their function and significance for glioblastoma need further experiments to verify.

Keywords: Glioblastoma; RNF11; bioinformatics analysis; circular RNA (circRNA); sponge.