Abstract

INTRODUCTION. Inflammatory bowel disease (IBD) patients have an increased risk of colorectal cancer (CRC). A pathogenic sequence of normal mucosa, chronic inflammation, dysplasia and CRC has been proposed and is the rationale behind colonoscopy surveillance programs. However, over-surveillance and over-treatment in low risk patients, as well as interval CRC, occur frequently, thus highlighting the need for better risk stratification. Identifying mucosal gene signatures could be leveraged for improving CRC prediction in IBD. AIM. To analyze the differential transcriptomic profile in sigmoid colon mucosa of IBD patients with and without remote dysplasia. METHODS. Crohn’s colitis or ulcerative colitis patients and healthy controls (HC) were recruited during colonoscopy between 2009-2013. Through histopathology report review we searched for dysplasia arising from the sigmoid colon. In this manner, two groups of IBD patients were defined: 1) patients with remote dysplasia (DIBD group), and 2) patients without dysplasia (NDIBD group) who had at least 2 colonoscopies and 5 years of further surveillance with negative biopsies. Seventy sigmoid colon samples from 70 subjects were obtained and total RNA was extracted. Only non-inflamed or minimally inflamed samples according to histology were analyzed. RNA-sequencing (RNA-seq) was performed and normalized read counts were analyzed with a negative binomial linear regression model to assess differential expression among groups. A threshold false discovery rate of 0.05 plus a log2-fold change (FC) greater than 1 were considered as a significant differential gene expression. RESULTS. Forty-five HC were compared to 20 NDIBD and 5 DIBD patients. The clinical characteristics of these groups are depicted in Table 1. In the DIBD group, 2 low-grade dysplasia, 2 high-grade dysplasia and 1 indefinite for dysplasia were found between 2.9 years before and 6.3 years after the index sample. In NDIBD patients compared to HC, 69 genes were significantly downregulated and 147 genes were significantly upregulated. In DIBD patients compared to HC, 107 genes were significantly downregulated and 353 genes were significantly upregulated. Two genes (duoxa2 and ccl11) were progressively and significantly upregulated across HC, NDIBD and DIBD patients. Duoxa2 was upregulated 3.9 log2(FC) in NDIBD (p = 1.3e-05) and 6.1 log2(FC) in DIBD (p = 7.4e-09) compared to HC. Ccl11 was upregulated 2.8 log2(FC) in NDIBD (p = 2.7e-05) and 4.3 log2(FC) in DIBD (p = 1.3e-07) compared to HC. CONCLUSION. Using RNA-seq data we have determined that expression of duoxa2 and ccl11 genes, both of which have been implicated in inflammation-related carcinogenesis, are upregulated in the colonic mucosa of IBD patients at risk of CRC. Their potential role as biomarkers to enable risk stratification for CRC should be further explored in larger independent cohorts.