Meta-Analysis of MicroRNAs Dysregulated in the Hippocampal Dentate Gyrus of Animal Models of Epilepsy

Abstract

The identification of mechanisms transforming normal to seizure-generating tissue after brain injury is key to developing new antiepileptogenic treatments. MicroRNAs (miRNAs) may act as regulators and potential treatment targets for epileptogenesis. Here, we undertook a meta-analysis of changes in miRNA expression in the hippocampal dentate gyrus (DG) following an epileptogenic insult in three epilepsy models. We identified 26 miRNAs significantly differentially expressed during epileptogenesis, and five differentially expressed in chronic epilepsy. Of these, 13 were not identified in any of the individual studies. To assess the role of these miRNAs, we predicted their mRNA targets and then filtered the list to include only target genes expressed in DG and negatively correlated with miRNA expression. Functional enrichment analysis of mRNA targets of miRNAs dysregulated during epileptogenesis suggested a role for molecular processes related to inflammation and synaptic function. Our results identify new miRNAs associated with epileptogenesis from existing data, highlighting the utility of meta-analysis in maximizing value from preclinical data.

Keywords: dentate gyrus; epilepsy; hippocampus; mRNA; meta-analysis; miRNA.

Figure 1.

Power calculation. Power calculation is plotted as the power (y-axis) to detect a miRNA with fold change (x-axis) according to the percentile of the ranked SDs for miRNAs for each study. Across all three models, the power to detect miRNA with fold change 2 or less falls below 80% for at least 40% of the miRNAs.

Figure 2.

Study design and data preprocessing. A, Study design. B, Venn diagram showing miRNAs commonly expressed between the three studies included in the meta-analysis. C, Statistical heterogeneity estimation. I² scores of commonly expressed miRNAs (n = 176) in epileptogenesis and in chronic stage. miRNAs are ordered based on the adjusted p value after meta-analysis. I² < 0.3, low heterogeneity; 0.3 < I² > 0.7, moderate heterogeneity; I² > 0.7, high heterogeneity. SRS, spontaneous recurrent seizures; pilo, pilocarpine model; amy stim, amygdala stimulation model; AB stim, angular bundle stimulation model.

Figure 3.

Forest plots of selected miRNA. Forest plots for miR-7a-5p, miR-92b-3p, miR-101a-3p, miR-138-5p, miR-150-3p, miR-153-3p, miR-335, miR-383-3p, and miR-3573-3p are shown for the phase of epileptogenesis, and miR-130a-3p and miR-148b-3p for the chronic stage. For each miRNA, the effect size of the individual studies is reported as MD and 95% CI. The % weight refers to random effects analysis. Individual effect sizes are represented by colored boxes (green for epileptogenesis and blue for the chronic period) and 95% CI are denoted by black lines. The combined effect sizes are represented by diamonds, where diamond width correspond to the 95% CI bounds; boxes and diamonds size is proportional to effect size estimation precision. For each miRNA, the weight of the dataset in the combined analysis has been reported in percentage.

Figure 4.

Relationship between selected miRNA and their predicted targets in different model of TLE. All panels show selected miRNAs-mRNA anticorrelation based on miRNAs and mRNAs fold changes in epileptogenesis. A, Inverse relationship between four downregulated miRNAs (miR-92b-3p, miR-101a-3p, miR-153-3p, and miR-3573-3p) and the commonly predicted target Map3k4. B, Inverse relationship between the downregulated miR-138-5p, miR-7a-5p, and the upregulated Map3k14. C, Inverse relationship between miR-101a-3p, miR-139-3p, miR-551b-3p, and Syn2. D, Inverse relationship between miR-150-5p, miR-383-5p, and Ptpn. E, F, Examples of the opposite anticorrelation, the upregulated miR-146a-5p with the downregulated Htr5b transcript, and the upregulated miR-212-5p and the downregulated Gabrd transcript.

Figure 5.

Functional enrichment of dysregulated miRNA-mRNAs targets modules. A, Horizontal bar plots (on the left) show the GO enrichment status (top 20 terms) for 112 predicted mRNAs targets that anticorrelate with 22 miRNAs expression level in epileptogenesis (FDR < 5%, hypergeometric test). The miRNA-mRNA module is represented by a network graph (on the right) showing the connections between miRNAs based on the function of their mRNAs predictive targets revealed by the GO enrichment. B, Horizontal bar plots (on the left) show KEGG enrichment analysis for predicted mRNAs targets that anticorrelate with miRNAs expression level in epileptogenesis (FDR < 5%, hypergeometric test). miRNA-mRNA modules are represented with network plot (on the right) showing the connection between miRNAs based on the pathways in which are involved their predicted targets revealed by KEGG analysis. C, D, GO and KEGG enrichment status for 29 predicted miRNA targets that anticorrelate with five miRNAs differentially expressed in the chronic stage (FDR < 5%, hypergeometric test).