mRNA and lncRNA co-expression network in mice of acute intracerebral hemorrhage

Zhe Yu; En Hu; Yiqing Cai; Wenxin Zhu; Quan Chen; Teng Li; Zhilin Li; Yang Wang; Tao Tang

doi:10.3389/fnmol.2023.1166875

mRNA and lncRNA co-expression network in mice of acute intracerebral hemorrhage

Front Mol Neurosci. 2023 Apr 28:16:1166875. doi: 10.3389/fnmol.2023.1166875. eCollection 2023.

Authors

Zhe Yu^{1

2}, En Hu^{1

2}, Yiqing Cai^{1

2}, Wenxin Zhu^{1

2}, Quan Chen^{1

2}, Teng Li^{1

2}, Zhilin Li^{1

2}, Yang Wang^{1

2}, Tao Tang^{1

2}

Affiliations

¹ Department of Integrated Traditional Chinese and Western Medicine, Institute of Integrative Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, China.
² National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China.

Abstract

Background: Intracerebral hemorrhage (ICH) is a severe subtype of stroke lacking effective pharmacological targets. Long noncoding RNA (lncRNA) has been confirmed to participate in the pathophysiological progress of various neurological disorders. However, how lncRNA affects ICH outcomes in the acute phase is not completely clear. In this study, we aimed to reveal the relationship of lncRNA-miRNA-mRNA following ICH.

Method: We conducted the autologous blood injection ICH model and extracted total RNAs on day 7. Microarray scanning was used to obtain mRNA and lncRNA profiles, which were validated by RT-qPCR. GO/KEGG analysis of differentially expressed mRNAs was performed using the Metascape platform. We calculated the Pearson correlation coefficients (PCCs) of lncRNA-mRNA for co-expression network construction. A competitive endogenous (Ce-RNA) network was established based on DIANALncBase and miRDB database. Finally, the Ce-RNA network was visualized and analyzed by Cytoscape.

Results: In total, 570 differentially expressed mRNAs and 313 differentially expressed lncRNAs were identified (FC ≥ 2 and value of p <0.05). The function of differentially expressed mRNAs was mainly enriched in immune response, inflammation, apoptosis, ferroptosis, and other typical pathways. The lncRNA-mRNA co-expression network contained 57 nodes (21 lncRNAs and 36 mRNAs) and 38 lncRNA-mRNA pairs. The ce-RNA network was generated with 303 nodes (29 lncRNAs, 163 mRNAs, and 111 miRNAs) and 906 edges. Three hub clusters were selected to indicate the most significant lncRNA-miRNA-mRNA interactions.

Conclusion: Our study suggests that the top differentially expressed RNA molecules may be the biomarker of acute ICH. Furthermore, the hub lncRNA-mRNA pairs and lncRNA-miRNA-mRNA correlations may provide new clues for ICH treatment.

Keywords: co-expression network; competitive endogenous RNA; intracerebral hemorrhage; lncRNA; mRNA.