Comprehensive site-specific whole genome profiling of stromal and epithelial colonic gene signatures in human sigmoid colon and rectal tissue

Abstract

The strength of associations between various exposures (e.g., diet, tobacco, chemopreventive agents) and colorectal cancer risk may partially depend on the complex interaction between epithelium and stroma across anatomic subsites. Currently, baseline data describing genome-wide coding and long noncoding gene expression profiles in the healthy colon specific to tissue type and location are lacking. Therefore, colonic mucosal biopsies from 10 healthy participants who were enrolled in a clinical study to evaluate effects of lignan supplementation on gut resiliency were used to characterize the site-specific global gene expression signatures associated with stromal vs. epithelial cells in the sigmoid colon and rectum. Using RNA-seq, we demonstrate that tissue type and location patterns of gene expression and upstream regulatory pathways are distinct. For example, consistent with a key role of stroma in the crypt niche, mRNAs associated with immunoregulatory and inflammatory processes (i.e., CXCL14, ANTXR1), smooth muscle contraction (CALD1), proliferation and apoptosis (GLP2R, IGFBP3), and modulation of extracellular matrix (MMP2, COL3A1, MFAP4) were all highly expressed in the stroma. In comparison, HOX genes (HOXA3, HOXD9, HOXD10, HOXD11, and HOXD-AS2, a HOXD cluster antisense RNA 2), and WNT5B expression were also significantly higher in sigmoid colon compared with the rectum. These findings provide strong impetus for considering colorectal tissue subtypes and location in future observational studies and clinical trials designed to evaluate the effects of exposures on colonic health.

Keywords: HOX genes; epithelium; human colon; long noncoding RNA; stroma.

Figures

Fig. 1.

Genes downstream of TP53 and MYC are differentially expressed in stromal vs. epithelial tissue types. Potential upstream regulators as identified by Ingenuity Pathway Analysis (IPA) are listed. Upregulation (red) and downregulation (green) are noted with respect to the stromal/epithelial expression ratio. Predicted activation (orange ovals and arrows) and predicted inhibition (blue ovals and arrows) were estimated by IPA based on downstream gene expression patterns. See Supplementary Table S1 for a complete list of fold-changes and P values.

Fig. 2.

Homeobox genes of the HOX family are differentially expressed in the sigmoid colon and rectum. Upregulation (red) and downregulation (green) are noted with respect to the sigmoid/rectum expression ratio. See Supplementary Table S2 for a complete list of fold-changes and P values.

Fig. 3.

Differentially expressed genes across stroma/epithelium and sigmoid/rectum comparisons. The Venn diagram represents the relationship between the detected differentially expressed genes in each 1 of the 2 comparisons, i.e., stroma vs epithelium and sigmoid vs. rectal tissue.