Differentially Expressed Small Non-Coding RNA in the Temporal Cortex of the Autism Brain

Background: The superior temporal sulcus (STS) plays a critical role in social behavior, a core impairment in autism, yet the molecular mechanisms that underlie abnormal STS function remain largely unexplored.  Small non-coding RNAs (sncRNA), including microRNA (miRNA) and small nucleolar RNA (snoRNA), show increased importance as key regulators of translation during development and throughout life.  Aberrant expression of sncRNA could lead to widespread changes in protein and cellular function related to autism.  This study evaluated differences is sncRNA expression in the STS in the autism brain.  In addition, this study sought to determine if differences were localized to association cortices, such as STS, or may also include neural regions involved in more basic perceptual processing, such as the primary auditory cortex (PAC), that are not typically associated with the core impairments of autism.

Objectives: Examine the changes in expression of small non-coding RNAs expressed in association (STS) and primary (PAC) cortex of autism and typically developing brains. 

Methods: Brain tissue from subjects diagnosed with autism (n=10) and typically developing controls (n=8) was obtained from the Harvard Brain Tissue Resource Center.  The STS and PAC were dissected from each fresh-frozen brain.  Total RNA was isolated from each region and assessed for concentration and quality. Two hundred nanograms of total RNA were processed on Affymetrix GeneChip miRNA 3.0 Arrays.  Arrays were scanned and resulting CEL files analyzed with Partek Genomics Suite.  Only small non-coding RNAs (mature miRNA, precursor miRNA and snoRNA) with human annotation (5663 targets) were included in the analysis. Functional significance of altered miRNA was determined through analysis of over-representation of their computationally derived mRNA targets in KEGG pathways using DIANA miRPath and Exploratory Gene Association Networks (EGAN) software.

Results: In STS, the expression of 3 miRNA significantly differed (P<0.005, FC>|1.2|) between autism and typically developing control brains (miR-1, miR-4753-5p, and miR-513a-5p).  These miRNA regulate pathways relating to synapse, brain maturation function and processes, and immune function.  An additional 11 stem-loop precursor miRNA and 6 snoRNA were also different in STS.  In PAC, 3 miRNA were significantly different in autism compared to typical control (miR-297, miR-664, and miR-4709-3p).  These were unique to PAC and may represent affected function of other cell signaling pathways and developmental cues.  There were also 7 stem-loop precursor miRNA and 4 snoRNA differentially expressed in PAC.  Commonly affected elements/functions of miRNA in both regions, include Akt and glutamate signalling.  The presence of significantly altered snoRNA in autism brain may implicate alterations in splicing mechanisms and patterns as important contributors to autism.

Conclusions: Regional differences in miRNA and other sncRNA expression were observed between autism and control brains in the STS and PAC.  These changes in small regulatory non-coding RNA may have important regulatory effects on mRNA transcript splicing and translation to proteins.  These findings help identify molecular mechanisms underlying autism and elucidate specific targets to restore perturbations that might occur in autism.