Next generation sequence analysis of miRNA expression in anterior cingulate cortex of individuals with bipolar and major depressive disorders

Azevedo JA, Carter BS, Meng F, Turner DL, Dai MH, Schatzberg AF, Barchas JD, Jones EG, Bunney WE, Myers RM, Akil H, Watson SJ, Thompson RC
Society for Neuroscience. 2011.


Major depressive (MDD) and bipolar (BP) disorders are prevalent psychiatric illnesses in adult populations. Although their precise etiology remains unclear, growing evidence suggests that loss of gray matter and changes in synaptic plasticity may play a role in disease pathogenesis. Previous studies have identified microRNAs (miRNAs) as potential regulators in processes related to psychiatric disorders, including synaptic plasticity (Schratt et al, 2006).
Prior miRNA expression studies using schizophrenic (Perkins et al, 2007) or BP (Kim et al, 2011) brain samples and fixed content array analyses identified several differentially expressed miRNAs. Here we report the use of unbiased whole-genome deep sequencing methods to examine miRNA expression profiles in the anterior cingulate (AnCg) of individuals diagnosed with BP or MDD.
After RNA isolation from the AnCg of patients with BP (n=13), MDD (n=16), and no history of disease (n=14), small RNA libraries were constructed via standard methods using Illumina adapters. Sequences were generated by the University of Michigan DNA sequencing core facility (Illumina GA IIx) with an average of 20.6 million reads per library. Adapter sequences were trimmed, mapped to the human genome, and annotated based on miRBase and other non-coding RNA sequences from the UCSC genome annotations. Expression levels for miRNAs were determined by normalized sequence counts using an Oracle-based annotation pipeline and analyzed for differential expression via EdgeR (Robinson, et al, 2010). From this data, we were able to identify a set of 14 differentially expressed miRNAs: 2 in BP, 9 in MDD, and 3 in both diseases. We validated differential expression for 5 of these miRNAs using individual ABI TaqMan assays on a subset of patient samples (BP, n=7; MDD, n=8; Control, n=8). Using in silico target prediction software, we generated a list of putative target mRNAs involved in apoptosis, neurodevelopment, and/or synaptic plasticity. Validation studies currently underway focus on a subset of the original 14 miRNAs in both AnCg and other brain regions implicated in BP and MDD disorders. These studies will enable us to determine whether these miRNA expression profiles hold true in both a larger cohort and across multiple brain regions. By understanding what miRNAs are differentially expressed in psychiatric diseases, we will be in a position to further understand disease-related changes in gene regulatory networks and their implications for psychiatric disease etiology.