This year we studied traumatic brain injury (TBI) in rat to identify miRNAs which are important in repressing gene expression and regulating biological processes, such as cell differentiation, proliferation and apoptosis. TBI leads to temporary or permanent structural and functional impairment of the brain which is a leading cause of injury-related death and disability. Survivors of TBI show neuropsychiatric abnormalities such as cognitive deficits in addition to emotional and behavioral problems which are common and contribute substantially to post-TBI disabilities. One of the brain regions vulnerable to TBI is the hippocampus which is responsible for cognition and emotion. Pathological changes observed in TBI-hippocampus are cell loss, disturbed neural circuits, impaired synaptic transmission and plasticity, all of which lead to neuropsychiatric symptoms. The mechanisms responsible for hippocampus damage and recovery post-TBI remain unclear. However, these structural and functional changes result from altered gene expression in several brain regions, as has been shown in human and animal models of TBI. And again, the mechanisms for gene expression changes are also unclear. The target of our study, microRNAs, are critical for proper brain functions and their loss causes changes in synaptic protein expression, synaptic transmission, dendritic spine morphology, learning and memory. Previous studies have shown that TBI alters mRNA (messenger RNA) expression in the hippocampus. Altered miRNA expression more than likely impacts their target mRNA expression, so it is possible that miRNAs play a role in regulating gene expression in TBI. Since molecular and cellular mechanisms subserving neuronal damage and impairment in TBI mental abilities are largely unknown, we used deep-sequencing to delineate miRNA transcriptome changes in hippocampus at 24hr and day 7 post-TBI in the rat controlled cortical impact injury model (CCI). We also developed a bioinformatics analysis, called miRNA-gene-GO Enrichment, to computationally examine the potential effects of miRNA expression changes in CCI. The analysis was performed in these three general steps: 1) match rat miRNAs resulting from deep-sequencing to their mouse orthologs via the TargetScan database, 2) compile computationally predicted target genes of the mouse miRNA orthologs and estimate their statistical significance of enrichment, and 3) obtain the GO terms that annotate the over-represented genes from the Gene Ontology database and perform enrichment analysis on each of three sets of GO terms (biological process, molecular function, and cellular component). The GO enrichment analysis revealed that both the 24hr and 7 day post-CCI miRNAs correspond to the secondary damage stage (i.e. histological, biochemical, metabolic and cellular changes) of TBI, which occurs minutes to days or even months after the initial trauma. These types of cellular responses are essential to the initiation of secondary damage, and are thought to impact TBI-related structural and functional impairments of neurons. These findings are consistent with known post-trauma pathological changes. In addition, distinct GO terms are identified for the two post-CCI time points. At 24 hours the miRNAs are modulated to inhibit leukocyte cell death for the inflammatory response, prevent stress-induced protein denaturation and aggregation, and protect cells from energy exhaustion. At the 7 day time point, cells switch to miRNAs that support a cellular environment for repair and structural remodeling. Our study of the effect of CCI injury on the miRNA transcriptome in the hippocampus and identification of cellular functions and biological processes potentially regulated by miRNAs in the damaged hippocampus found distinct sets of miRNAs regulated at different post-CCI times, and suggest that multiple miRNAs cooperatively regulate cellular pathways for the pathological changes and management of brain injury. These distinct miRNAs expression profiles at different post-CCI times may be used as molecular markers to assess TBI progression. The bioinformatics analysis showed the miRNAs target to multiple GO terms in a post-CCI time specific manner which indicated that miRNAs act together to regulate a broad range of cellular functions in the brain at different stages of TBI. These identified biological pathways may be potential targets for development of new TBI treatments. In addition to traumatic brain injury, we investigated the role of miRNAs in synapse development by combining deep-sequencing, bioinformatics and live imaging. miRNAs differentially expressed in hippocampal neurons during spine morphogensis were identified by profiling miRNA transcriptomes. Bioinformatics analysis was conducted to determine mRNA targets and cellular processes statistically enriched by the identified miRNAs. The functions of several miRNAs were examined by live imaging of hippocampal neurons. Our study shows that miRNAs are essential for spine morphogenesis. We also identified the target genes through which these miRNAs regulate spines, and demonstrated that translation-dependent actin rearrangement plays important roles in spine remodeling. These findings reveal that by impinging on the expression of diverse targets, miRNAs orchestrate networks of cellular processes essential for synapse development.
