A Comparison of Gene Expression in Inflamed Ileocolonic Tissue and Peripheral Blood 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. In this analysis we examined data from two separate cohorts: one from an earlier study that measured gene expression in GI tissue only and the other from the current study where we evaluated gene expression in GI tissue and peripheral blood from the same ASD^IC individuals.  

Objectives:  The purpose of these analyses was: (1) to evaluate the reproducibility of transcriptome results derived from an earlier analysis of gastrointestinal tissue from ASD^IC samples in a second cohort and, (2) to compare gene expression in inflamed tissue to gene expression in peripheral blood from the same patients to identify a peripheral biomarker for GI inflammation.

Methods: Study tissue, collected under appropriate IRB approval, consisted of ileocolonic biopsies (Study 1 and 2) and whole blood (Study 2 only) from two groups of children undergoing ileocolonoscopy for active gastrointestinal symptoms: (1) those with an ASD diagnosis and, (2) typically developing children.

In the initial study (“Study 1”), for each ASD individual a biopsy from either the terminal ileum (N=21) or colon (N=21) that demonstrated the histologic presence of either ileal infiltrates (ileitis), colonic infiltrates (colitis) were used. Histopathologically normal tissues from the identical locations were obtained from 14 control individuals for comparison.

The second study consisted of inflamed ileum or colon biopsy tissue and whole blood from ASD^IC children (12 in each group) and the same number of (histopathologically normal) tissues and blood samples from a total of 24 typically developing children.

Total RNA was isolated from the tissue biopsy specimens and whole blood 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. Next, the list of genes that were uniquely expressed in inflamed GI tissues from ASD^IC was compared to the list of genes differentially expressed in the peripheral blood from those same individuals.   

Results: In Study 1, pair-wise analyses between inflamed ileal mucosa from ASD^IC and non-inflamed control samples resulted in 3497 differentially-expressed genes (DEGs), versus 2949 DEGs in the comparison of colonic tissue gene expression. In Study 2, the numbers were comparable: 2451 DEGs in the TI comparison and 2821 DEGs between inflamed and non-inflamed colonic tissues. A comparison of the whole blood samples from ASD (with GI inflammation) versus TD samples (without GI inflammation) yielded 3183 DETs. The overlap between all genes that were differentially expressed both in ASD ileocoloinc tissue and blood revealed a biomarker consisting of 9 candidate genes.   

Conclusions:  We have shown overlapping gene expression uniquely found in inflamed gastrointestinal tissue (in two distinct locations) and blood from two separate cohorts of ASD^IC children that my represent a diagnostic biomarker.