Author information

1 Departments of Pathology and Immunology.

2 Janssen Research and Development, LLC. 1400 McKean Rd., Spring House, PA, 19477, USA.

3 Internal Medicine, Division of Gastroenterology, Inflammatory Bowel Disease Program.

4 Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA.

5 Departments of Pathology and Immunology. Electronic address: stappenb@pathology.wustl.edu.

Abstract

BACKGROUND & AIMS: Crohn's disease (CD) presents as chronic and often progressive intestinal inflammation, but the contributing pathogenic mechanisms are unclear. We aimed to identify alterations in intestinal cells that could contribute to the chronic and progressive course of CD.

METHODS: We took an unbiased, system-wide approach, performing sequence analysis of RNA extracted from formalin-fixed, paraffin-embedded ileal tissue sections from patients with CD (n=36) and without CD (controls, n=32). We selected relatively uninflamed samples, based on histology, before gene expression profiling; validation studies were performed using adjacent serial tissue sections. A separate set of samples (3 controls and 4 CD) was analyzed by transmission electron microscopy. We developed methods to visualize an overlapping modular network of genes dysregulated in the CD samples. We validated our findings using biopsy samples (110 CD samples for gene expression analysis and 54 for histologic analysis) from the UNITI-2 phase 3 trial of ustekinumab for patients with CD and healthy individuals (26 samples used in gene expression analysis).

RESULTS: We identified gene clusters that were altered in nearly all CD samples. One cluster encoded genes associated with the enterocyte brush border, leading us to investigate microvilli. In ileal tissues from patients with CD, the microvilli were of reduced length and had ultrastructural defects, compared to tissues from controls. Microvilli length correlated with expression of genes that regulate microvilli structure and function. Network analysis linked the microvilli cluster to several other down-regulated clusters associated with altered intra-cellular trafficking and cellular metabolism. Enrichment of a core microvilli gene set was also lower in the UNITI-2 trial CD samples compared with controls; expression of microvilli genes correlated with microvilli length and endoscopy score, and associated with response to treatment.

CONCLUSIONS: In a transcriptome analysis of formalin-fixed, paraffin-embedded ileal tissues from patients with CD and controls, we associated transcriptional alterations with histologic alterations, such as differences in microvilli length. Decreased microvilli length and reduced expression of the microvilli gene set might contribute to epithelial malfunction and the chronic, progressive disease course in patients with CD.