Gene Expression Analysis to Evaluate Gastrointestinal Tissue In Symptomatic Autism Spectrum Disorder Children: A Pilot Study

Background: Gastrointestinal (GI) symptoms occur frequently in children with an autism spectrum disorder (ASD). GI symptoms suggestive of inflammatory bowel disease often necessitate confirmatory diagnosis via upper endoscopy, colonoscopy, and biopsy. Although histologic evaluation of intestinal biopsy tissue remains the gold standard for diagnosis of inflammatory bowel disease, there exists a clinical need for additional diagnostic tools to characterize the molecular features unique to this population of children.

Objectives: The goal of this pilot study was to evaluate gene expression profiles in gastrointestinal tissue biopsy specimens from ASD children presenting with chronic GI symptoms, and to compare them to gene expression profiles in GI tissue from neurotypical children with no gastrointestinal symptoms. The gene expression profiles in GI tissue from symptomatic ASD children may then be used to describe the molecular aspects that underlie the symptoms, and thereby provide additional information for diagnosis and treatment.

Methods: GI biopsy tissue from children with an autism spectrum disorder who underwent colonoscopy, clinically indicated based on chronicity and severity of their gastrointestinal symptoms, was used in this study. Control GI tissue consisted of pathology-free cadaveric specimens obtained from neurotypical children. All case and control tissue was collected under appropriate IRB approval. Briefly, total RNA was isolated from the individual tissue biopsy specimens, reverse-transcribed, labeled, and used to query whole genome DNA microarrays. Following data normalization, standard statistical analyses were used to generate a list of genes differentially-expressed between the cases and controls. Additional data mining included pathway analysis, using both public and private databases, as well as comparisons of these data with other relevant published datasets from molecular studies that were designed to distinguish IBD subtypes.   

Results: At a fold change ≥ 1.5 (p ≤ 0.05) there were approximately 1800 genes differentially expressed between the ASD-GI samples and controls, with nearly two thirds (~1100) being down-regulated in the ASD-GI tissue. Further analysis indicated significant involvement of numerous pathways including: primary immunodeficiency, B cell and T cell receptor signaling, chemokine signaling, and p53 signaling (all significantly up-regulated); and also focal adhesion, extracellular matrix-receptor interaction, drug and xenobiotic metabolism (cytochrome p450 mediated), Wnt signaling, and glutathione metabolism (all significantly down-regulated). Moreover, when these data were compared with a published biomarker study reporting a 7-gene panel for distinguishing two IBD subtypes, Crohn’s and ulcerative colitis, 4 of those 7 biomarkers were present and differentially-expressed in this dataset.

Conclusions: In this pilot study we have identified numerous gene expression changes in GI tissue from ASD children with GI symptoms that correlate with similar gene expression changes that have previously been reported for both Crohn’s disease and ulcerative colitis in other study populations. By significantly expanding our sample size in a follow-up study we expect to be able to identify a gene expression signature specific and/or diagnostic for GI pathology in this unique patient population.