Identification of Specific Circular RNA Expression Patterns and MicroRNA Interaction Networks in Mesial Temporal Lobe Epilepsy

Abstract

Circular RNAs (circRNAs) regulate mRNA translation by binding to microRNAs (miRNAs), and their expression is altered in diverse disorders, including cancer, cardiovascular disease, and Parkinson's disease. Here, we compare circRNA expression patterns in the temporal cortex and hippocampus of patients with pharmacoresistant mesial temporal lobe epilepsy (MTLE) and healthy controls. Nine circRNAs showed significant differential expression, including circRNA-HOMER1, which is expressed in synapses. Further, we identified miRNA binding sites within the sequences of differentially expressed (DE) circRNAs; expression levels of mRNAs correlated with changes in complementary miRNAs. Gene set enrichment analysis of mRNA targets revealed functions in heterocyclic compound binding, regulation of transcription, and signal transduction, which maintain the structure and function of hippocampal neurons. The circRNA-miRNA-mRNA interaction networks illuminate the molecular changes in MTLE, which may be pathogenic or an effect of the disease or treatments and suggests that DE circRNAs and associated miRNAs may be novel therapeutic targets.

Keywords: RNA-Seq; circular RNAs; epilepsy; gene expression; mesial temporal lobe epilepsy; microRNAs.

FIGURE 1

(A) t-SNE clustering of detected circRNAs. CircRNAs from the same tissue cluster together regardless of disease state. (B) t-SNE clustering of linear transcripts. Cortex samples cluster together, and hippocampal samples show more disorganized clustering.

FIGURE 2

Box plots of CPM and TPM values for the nine differentially expressed circRNAs and linear transcripts across the two conditions in the cortex and hippocampus. CircRNA and parent gene expression do not correlate, which suggests that these circRNAs are not dependent on the linear expression of their host genes. No linear transcripts were detected for AC067956.1. ^*<0.05 and ^**<0.01.

FIGURE 3

(A) Volcano plot of the linear transcripts that are targeted by the miRNAs (see Table 2), which were predicted to interact with circRNA-HOMER1. (B) Volcano plot of the linear transcripts that are targeted by the miRNAs, which were predicted to interact with circRNA-NMD3. The X- and Y-axes of this plot show the log fold change and -log₁₀ adjusted p-value, respectively, indicating how differentially expressed a transcript is when compared to controls. Red indicates the transcripts with adjusted p-values of <0.05, which suggests that these linear transcripts were affected by this set of miRNAs interacting with circRNA. Labeled transcripts are the top 10 most DE.

FIGURE 4

(A) Gene set interaction network for the miRNA targets composing the HOMER1 circRNA–miRNA–mRNA interaction network. (B) Gene set interaction network for the miRNA targets composing the NMD3 circRNA–miRNA–mRNA interaction network. Node color indicates the corrected p-value, edge thickness relates to the size of intersection between two gene sets, and edge direction points from the least significant to the most significant.