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A Comparison of Gene Expression in Inflamed Ileocolonic Tissue and Peripheral Blood from GI Symptomatic ASD Children
Objectives: The purpose of these analyses was: (1) to evaluate the reproducibility of transcriptome results derived from an earlier analysis of gastrointestinal tissue from ASDIC 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 ASDIC 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 ASDIC and control groups for each of the two tissues. Next, the list of genes that were uniquely expressed in inflamed GI tissues from ASDIC 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 ASDIC 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 ASDIC children that my represent a diagnostic biomarker.