Identification and Validation of a Dysregulated miRNA-Associated mRNA Network in Temporal Lobe Epilepsy

Abstract

Objectives. This study is aimed at exploring the relationships between miRNAs and mRNAs and to characterize their biological functions in temporal lobe epilepsy (TLE). Methods. Novel clinical significant miRNAs and target genes and their potential underlying mechanisms have been discovered and explored by mining miRNAs and mRNA expression data of TLE patients using various bioinformatics methods. Reverse transcription-quantitative polymerase chain reaction (RT-qPCR) was used to validate the bioinformatic analysis results. Results. A total of 6 dysregulated miRNAs and 442 differentially expressed genes (DEGs) related to TLE were obtained from GEO database (GSE114701 and GSE127871 datasets). A protein-protein interaction (PPI) network containing the 442 DEGs was established. mRNA response elements from the 6 dysregulated miRNAs were predicted using the miRDB and TargetScan bioinformatic tools. By merging the identified targets of the dysregulated miRNAs and the 247 downregulated DEGs, a miRNA-mRNA network was constructed revealing the interaction of miR-484 with eight mRNAs (ABLIM2, CEP170B, CTD-3193O13.9, EFNA5, GAP43, PRKCB, FXYD7, and NCAN). A weighted correlation network analysis (WGCNA) based on the eight genes was established and demonstrated that these mRNAs, except FXYD7 and NCAN, were hub genes in the network. Gene Oncology (GO) annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis revealed that the six hub genes were mainly involved in cellular-related biological functions and the neurotransmitter synapse pathway. The differences in expression levels of the miR-484 and the three hub genes (CTD-3193O13.9, EFNA5, and PRKCB) observed experimentally in TLE patients compared to those of healthy controls were consistent with the WGCNA prediction. Conclusion. Our study suggests that understanding the miRNA-mRNA interactions will provide insights into the epilepsy pathogenesis. In addition, our results indicate that miR-484 may be a promising novel biomarker for TLE.

Proteomic and Bioinformatic Tools to Identify Potential Hub Proteins in the Audiogenic Seizure-Prone Hamster GASH/Sal

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Prenatal methadone exposure selectively alters protein expression in primary motor cortex: Implications for synaptic function

“…We also examined the top five positive and negative changes in log 2 (abundance ratios) for phosphopeptides that had no accompanied changes in the proteome ( Figure 4A ). Targets such as Cep170b, Cacan1e, Camk2b, Clasp2, Ppfia4, and Smarca4 are all known to alter synaptic assemblies and plasticity, are associated with calcium channelopathies and modulation of acetylcholine and other receptors, and are associated with disease states defined by aberrant neuronal firing, such as epilepsy ( Basu et al, 2014 ; Nicole and Pacary 2020 ; Kessi et al, 2021 ; Li et al, 2021 ).…”

Small RNA Changes in Plasma Have Potential for Early Diagnosis of Alzheimer’s Disease before Symptom Onset

“…Using our expanded sequence-based feature list, we analyzed the small RNA gene expression in plasma samples and found 266 differentially expressed (DE) transcripts in patients with subsequent confirmed normal age-related pathology compared with confirmed PART pathology (p < 0.05, Figure 2b). Among the DE transcripts were miRs -224, -22, and -484, which have known neurological involvement [47][48][49][50]. As postmortem Dx was not available for the rest of our control cohort (n = 29), we constructed a predictive model using Elastic Net (ELNET).…”