Distinct Argonaute2-associated small RNA profiles in microglia and neurons drive cell-specific responses in a mouse model of temporal lobe epilepsy

Small RNAs including microRNAs (miRNAs) and tRNA fragments (tRFs) are key post-transcriptional regulators of gene expression in temporal lobe epilepsy (TLE), but the cellular origin of these changes is often unclear. Here, we dissected the cell-type specific small RNA landscape, focussing on miRNA and tRFs, during epileptogenesis and in chronic epilepsy by profiling the RNA-induced silencing complex (RISC) using novel, transgenic mice with inducible expression of a FLAG-tagged Argonaute 2 protein driven specifically in neurons (Thy1-Ago2) or microglia (Cx3cr1-Ago2). We induced epilepsy in male mice via intra-amygdala microinjection of kainic acid and tracked miRNA expression over time in the hippocampus. Microglia and neurons displayed distinct and largely non-overlapping small RNA profiles across disease. Shortly following the epileptogenic insult, we detected a rapid microglial miRNA and tRF response which was sustained in chronic stages of the disease whereas small RNA changes in neurons displayed a delayed but sustained wave of unique changes as the disease progressed. Interestingly, our data reveals selective loading and incorporation of miRNAs into Ago2/RISC complexes, independent of overall abundance, in a cell- and disease-stage specific manner as well as differential processing of tRNAs in microglia compared to neurons. Additionally we found that certain epilepsy-associated miRNAs, previously considered ubiquitous, display dysregulation in multiple cell types while exhibiting cell-specific activity. Together our results demonstrate the cell-specific small RNA responses and functions to epileptogenic insults and shed further light on the complexity of post-transcriptional gene dysregulation in TLE. The findings indicate the potential advantages of targeted, cell-specific therapeutic strategies to effectively modulate miRNA pathways in epilepsy.