P066 INTESTINAL EPITHELIAL MICROVILLI ARE ABNORMAL IN CROHN'S DISEASE

Abstract Background and Aims Crohn's disease (CD) presents as chronic and often progressive intestinal inflammation, but the contributing pathogenic mechanisms are unclear. Our goal was to identify underlying alterations in intestinal host cells that could contribute to the chronic and progressive course of CD. Methods We performed RNA-seq with RNA extracted from formalin-fixed, paraffin-embedded (FFPE) ileal tissue sections obtained from CD subjects (n=32) and controls without inflammatory bowel disease (n=36). This method allowed us to select relatively uninflamed samples prior to molecular profiling and to perform histological validation with serial tissue sections. Accurate sampling of microvillar length was achieved by measuring 5 cells per villi and 10 villi per sample. We developed new methods to visualize an overlapping modular network of dysregulated genes in CD. Results With partitional clustering, we identified multiple down-regulated gene clusters present in nearly all of the CD samples. One cluster of 1,056 down-regulated genes was functionally associated with formation and stabilization of microvilli, leading us to quantify microvillar length. CD samples had a significant reduction in microvillar length relative to controls and this directly correlated to average microvillar gene cluster expression, validating our results. Network analysis supported a common regulatory mechanism for several of the common down-regulated gene clusters associated with altered metabolism in the intestinal tissue of CD subjects and this super-cluster was linked to the microvillar cluster. Conclusions The FFPE transcriptomic approach can identify and link transcriptional alterations to histological alterations in CD tissue, such as a previously unrecognized alteration in microvillar length. We propose that decreased enterocyte microvillar length and gene expression represents an ongoing epithelial malfunction that is independent of active inflammation or local tissue damage.