Allelic mRNA Expression of Cellular Adhesion Molecules, Glutamate and GABAergic Genes, and RNA Splicing Modulators In Typically-Developed and ASD Frontopolar Cortex

Background: Clinical genetic association studies and gene sequencing frequently implicate cellular adhesion molecules, such as neurexins and neuroligins, as autism risk genes.  These genes can regulate the maturation of glutamatergic and GABAergic synapses based on the expression of alternatively-spliced mRNA transcripts.  Often, the consequence of disease-associated variants in cellular adhesion molecules is marked changes in synapse structure and/or function, especially relating to glutamatergic or GABAergic signaling. 

Objectives: The goal of this study is to uncover cis-acting variants responsible for directing mRNA expression by measuring allelic expression of genes related to synapse structure and signaling in human frontopolar cortex tissue from autistic patients and typically-developed controls.

Methods: mRNA and genomic DNA was isolated from 56 post-mortem frontopolar cortex tissues provided by the Autism Tissue Program.  Allele-specific expression was measured via quantitative SNaPshot for synapse-related genes CNTNAP2, CNTN4, DLG4, EPB41L1, NRCAM, and PCDH9; glutamatergic and GABAergic genes GABRB3, GAD1, GRIA2, GRM5, SLC1A1, SLC1A2, SLC25A12, and SLC6A1, and alternative splicing genes HNRNPA3, NCBP2, NOVA1, RBFOX1, and SF4.

Results: Significant and robust allelic expression differences were observed for CNTNAP2, DLG4, EPB41L1, NRCAM, GAD1, GRIA2, SLC1A1, RBFOX1, HNRNPA3, NOVA1, and SF4, suggesting the presence of cis-acting functional variants responsible for modulated mRNA expression in these genes.  For most genes, including DLG4, EPB41L1, NRCAM, GAD1, GRIA2, and RBFOX1, significant allelic differences were only observed in a small number of autistic patients, suggesting the variants responsible for directing differential mRNA expression of these genes are rare.  In contrast, significant allelic expression differences for SLC1A1 and CNTNAP2 were observed for multiple samples from both the ASD and control cohorts, suggesting the presence of common cis-acting functional variants driving expression of these genes.

Conclusions: Differential mRNA expression of numerous genes pertinent to synapse structure and function are driven by cis-acting genetic factors.  For some genes, the responsible genetic factors appear to be rare and we observed their presence only in brain samples from autistic patients.  This scenario fits the hypothesis that highly-penetrant rare mutations could be responsible for producing autistic phenotypes.  In contrast, the presence of common functional variants in CNTNAP2 and SLC1A1 in both autism and control cohorts argue for the role of disorder-modifying genetic variants in these genes, with the ability to affect either language (CNTNAP2) or restrictive and repetitive behaviors (SLC1A1).  Further studies are necessary to evaluate the clinical relevance of expression-related functional variants in autism.