Identification of microRNA-mRNA regulatory network associated with oxidative DNA damage in human astrocytes

Abstract

The high lipid content of the brain, coupled with its heavy oxygen dependence and relatively weak antioxidant system, makes it highly susceptible to oxidative DNA damage that contributes to neurodegeneration. This study is aimed at identifying specific ROS-responsive miRNAs that modulate the expression and activity of the DNA repair proteins in human astrocytes, which could serve as potential biomarkers and lead to the development of targeted therapeutic strategies for neurological diseases. Oxidative DNA damage was established after treatment of human astrocytes with 10μM sodium dichromate for 16 h. Comet assay analysis indicated a significant increase in oxidized guanine lesions. RT-qPCR and ELISA assays confirmed that sodium dichromate reduced the mRNA and protein expression levels of the human base-excision repair enzyme, 8-deoxyguanosine DNA glycosylase 1 (hOGG1). Small RNAseq data were generated on an Ion Torrent™ system and the differentially expressed miRNAs were identified using Partek Flow® software. The biologically significant miRNAs were selected using miRNet 2.0. Oxidative-stress-induced DNA damage was associated with a significant decrease in miRNA expression: 231 downregulated miRNAs and 2 upregulated miRNAs (p < 0.05; >2-fold). In addition to identifying multiple miRNA-mRNA pairs involved in DNA repair processes, this study uncovered a novel miRNA-mRNA pair interaction: miR-1248:OGG1. Inhibition of miR-1248 via the transfection of its inhibitor restored the expression levels of hOGG1. Therefore, targeting the identified microRNA candidates could ameliorate the nuclear DNA damage caused by the brain’s exposure to mutagens, reduce the incidence and improve the treatment of cancer and neurodegenerative disorders.

Competing endogenous RNAs in human astrocytes: crosstalk and interacting networks in response to lipotoxicity

“…Integrative approaches are currently used to explore the controlling ncRNA network behind cellular processes and NDs. For example, a miRNA-mRNA regulatory network was identified in ROS-induced astrocytic DNA damage, obtaining 231 downregulated and 2 upregulated miRNAs (Nwokwu et al, 2022). The functional enrichment analysis of this miRNA-mRNA network showed an association with signaling, cell cycle, and DNA damage and repair and emphasized the importance of miR-1248, whose inhibition restores the human base-excision repair enzyme hOGG1 (Nwokwu et al, 2022).…”

“…For example, a miRNA-mRNA regulatory network was identified in ROS-induced astrocytic DNA damage, obtaining 231 downregulated and 2 upregulated miRNAs (Nwokwu et al, 2022). The functional enrichment analysis of this miRNA-mRNA network showed an association with signaling, cell cycle, and DNA damage and repair and emphasized the importance of miR-1248, whose inhibition restores the human base-excision repair enzyme hOGG1 (Nwokwu et al, 2022). Additionally, computational methods have also been used to integrate the ncRNA expression during the neuron-astrocyte crosstalk, helping to understand the interaction mechanisms of neuropathological viruses (Selinger et al, 2022).…”

“…Although there is the proven influence of some lncRNAs, circRNA, and miRNA in astrocyte function and dysfunction (Yi et al, 2019;Liao et al, 2020;Wan and Yang, 2020;Balint et al, 2021;Chen Z. et al, 2021;Gao et al, 2021;García-Fonseca et al, 2021;Nwokwu et al, 2022;Ramírez et al, 2022), the complexity of these networks remains unexplored in human astrocytes. According to that, we propose here a ceRNA network construction method, trying to understand the complex RNA crosstalk presented in astrocytes during stressful conditions.…”