Molecular Analysis of Inflamed Ileocolonic Tissue from GI Symptomatic ASD Children

Background:  Gastrointestinal symptoms are common in children with autism spectrum disorder (ASD) and are often associated with mucosal inflammatory infiltrates of the small and large intestine. Whole transcriptome analysis of biopsy tissue from ASD^IC (ASD with ileocolitis) and non-ASD IBD (Crohn’s disease and ulcerative colitis) patients has provided molecular evidence for an overlapping, yet unique, IBD-like condition in ASD children. Here we examine the genes and biological pathways that are differentially regulated between inflamed and non-inflamed ileocolonic tissue.  

Objectives:  The purpose of this study was to evaluate the molecular mechanisms that underlie inflammation in the large and small intestines of ASD^IC children.

Methods: Study tissue consisted of ileocolonic biopsies from two groups of children undergoing ileocolonoscopy for active gastrointestinal symptoms: (1) those with an ASD diagnosis and, (2) typically developing children. All tissue specimens were collected under appropriate IRB approval. For each ASD individual two biopsies (one from terminal ileum, one from colon) that demonstrated the histologic presence of either ileal infiltrates (ileitis), colonic infiltrates (colitis) or both (ileocolitis) were used. Two histopathologically normal tissues from the identical locations were obtained from each control individual for comparison. Total RNA was isolated from the tissue biopsy specimens and used to query whole genome DNA microarrays. Pair-wise comparisons of gene expression were made between ASD^IC and control groups for each of the two tissues. Lists of DEGs (differentially-expressed genes) in ASD^IC terminal ileum and colon were then evaluated for overrepresentation in gene ontology categories and biological pathways.  

Results: Pair-wise analyses between ileal mucosa from ASD^IC and non-inflamed control samples resulted in 4017 DEGs, of which 66% were down-regulated in the ASD group. This gene set was significantly associated with cancer, inflammatory response and immunological disease. Overall, numerous important metabolic pathways were highly significantly down-regulated in the terminal ileum - they included protein digestion and absorption, pancreatic secretion, bile secretion, fatty acid metabolism, glutathione metabolism and carbohydrate digestion and absorption. In contrast, the majority (61%) of DEGs in colonic tissue were up-regulated. These genes, as a group, were highly associated with cancer and gastrointestinal disease. Many of the biological pathways significantly up-regulated in the colon, for example NOD-like receptor signaling and granulocyte adhesion and diapedesis, are involved in activation of immune response. Of the 4017 DEGs identified in the terminal ileum and 2796 identified in the colon samples, 972 DEGs were common between the two tissues. These shared DEGs were significantly associated with cancer, inflammatory response and, interestingly, neurological disease.  

Conclusions:  Taken as a whole, the picture that emerges is one in which GI symptomatic children with ASD in whom cellular infiltrate is present in the ileum and/or colon have a distinct molecular signature that is consistent with gastrointestinal disease and is associated with digestive system development and function and also with neurological disease.