Differences in Small Non-Coding RNA Expression in Primary Auditory and Temporal Lobe Association Cortex May Have Effects on Cell Cycle, Immune and Other Pathways in Autism Spectrum Disorders

Background:  Dysregulation of multiple expressed genes related to brain function and development is a key component of autism spectrum disorders (ASD).  Atypical expression of individual regulatory small non-coding RNA (sncRNA), including microRNA (miRNA), could have profound effects upon many important functional pathways.  The superior temporal sulcus (STS) is a brain region with a critical role in social perception and associated with core social impairments of ASD.  In contrast, the adjacent primary auditory cortex (PAC) has function less central to the core features of ASD.  We set to examine expression differences of sncRNA in these two regions of the brain. 

Objectives:  The goal of this study is to identify sncRNA that are differentially expressed in ASD in the STS, where we expect to see differences compared to typically developing subjects, and PAC where we do not.  Furthermore, we investigate the functional implications of these expression differences through evaluating the biological and cellular pathways represented by the gene transcripts targeted by the altered miRNA.   

Methods:  We measured sncRNA expression levels in total RNA extracted from STS and PAC dissected from fresh-frozen brain of ASD and typically developing individuals.  Affymetrix miRNA 3.0 microarrays were used to screen a total of 36 samples for 5,607 sncRNA including 1,733 mature human miRNA, 1,658 human pre-miRNA, and 2,216 human snoRNA, CDBox RNA, H/ACA Box RNA and scaRNA.  Predicted mRNA targets of significantly altered miRNA were found using DIANA microT-CDS and their biological function was assessed by overrepresentation analysis against the KEGG database.  As a validation study of these results, brain regions were pooled and reanalyzed to determine changes in ASD brain and these functional results were compared to studies publishing mRNA expression data. 

Results:  Among miRNA, miR-4753-5p and miR-1 were dysregulated in the superior temporal sulcus (STS) of ASD compared to typically developing brain.  miR-664-3p, miR-4709-3p, miR-4742-3p and miR-297 were dysregulated in primary auditory cortex (PAC) of ASD compared to controls. Four small nucleolar RNA (snoRNA) and 8 pre-miRNA were dysregulated in STS and 5 snoRNA and 7 pre-miRNA were dysregulated in PAC of ASD. In both regions, miRNA were functionally related to various nervous system, cell cycle and canonical signaling pathways including PI3K-Akt signaling which has been implicated in previous ASD studies.  Disruption of immune related pathways was unique to STS.  Our predicted functional pathways had significant overlap with studies looking at genes associated with ASD and others looking at expression in other regions of brain.

Conclusions:  Altered sncRNA expression appears not only in STS, but also in primary auditory cortex, suggesting that transcriptional abnormalities in ASD may also impact brain regions not directly associated with core behavioral impairments. Disruption of immune related pathways, commonly implicated in genetic analyses of ASD, was unique to STS.  Alterations in sncRNA may underlie dysregulation of molecular pathways implicated in autism.