Tissue-specific patterns of gene expression in the epithelium and stroma of normal colon in healthy individuals in an aspirin intervention trial

Abstract

Regular aspirin use reduces colon adenoma and carcinoma incidence. UDP-glucuronosyltransferases (UGT) are involved in aspirin metabolism and clearance, and variant alleles in UGT1A6 have been shown to alter salicylic acid metabolism and risk of colon neoplasia. In a randomized, cross-over, placebo-controlled trial of 44 healthy men and women, homozygous for UGT1A6*1 or UGT1A6*2, we explored differences between global epithelial and stromal expression, using Affymetrix U133 + 2.0 microarrays and tested effects of 60-day aspirin supplementation (325 mg/d) on epithelial and stromal gene expression and colon prostaglandin E2 (PGE2) levels. We conducted a comprehensive study of differential gene expression between normal human colonic epithelium and stroma from healthy individuals. Although no statistically significant differences in gene expression were observed in response to aspirin or UGT1A6 genotype, we have identified the genes uniquely and reproducibly expressed in each tissue type and have analyzed the biologic processes they represent. Here we describe in detail how the data, deposited in the Gene Expression Omnibus (GEO) - accession number GSE71571 - was generated including the basic analysis as contained in the manuscript published in BMC Medical Genetics with the PMID 25927723 (Thomas et al., 2015 [9]).

Fig. 1

Flow chart of participant enrollment and study design.

Fig. 2

Real-time PCR confirms differences in gene expression in colonic epithelium and stroma. Quantitative real-time RT-PCR was done on both biopsies (taken at two separate visits) from 10 study participants for four candidate genes. The histogram bars from the same individual are located next to each other, i.e., samples 1 and 2 are from the same person but taken at two separate visits. Total RNA was reverse transcribed and then amplified by PCR and normalized to β-glucuronidase (GUSB) expression. Blue bars: epithelial tissue. Red bars: stromal tissue. Upper panel shows expression of: (i) ABCC3, an epithelial gene involved in drug and lipid metabolism; and (ii) MLPH (melanophilin), an epithelial gene involved in protein binding and protein transport. Lower panel shows expression of: (iii) ANXA1 (annexin A1), a stromal gene involved in cell migration and cell adhesion; and (iv) ITGA8 (integrin α8), a stromal gene involved in extracellular matrix formation.