Dynamic expression of smRNA from fecal exosome in disease progression of an inflammatory bowel disorder mouse model

Background: Inflammatory bowel disease (IBD) is a chronic inflammatory disorder of the gastrointestinal (GI) tract affecting over 3 million adults in the United States. Despite being widespread, reliable early diagnostic tests are not available. Methods: We examined exosomal small RNA (smRNA), specifically targeting microRNA (miRNA) and piRNA from the stool samples of IBD model mice, interleukin 10 knockout mice (IL-10 KO), as a potential diagnostic marker. Stool samples were specifically chosen because they are readily available, and collection is noninvasive. A modified Crohn’s disease activity index was used to score each mouse’s clinical condition twice a week. At the end of the experimental period, the GI tract was collected, and disease severity was scored. Results: Histopathology showed a significant increase in inflammation and proliferation within the proximal and distal large intestines. smRNA profiles were examined upon conventional housing (start-point) which is a determinant factor of spontaneous IBD progression in the IL-10 KO mice, terminal illness (end-point), and 6 weeks before the end-point (mid-point), when the mice were still phenotypically healthy. We found 504 smRNA that were significantly differentially expressed between before symptom onset and terminal sedation. These changes were not detected in wild-type samples. Moreover, clustering analysis of expression changes over the disease progression identified a unique set of smRNAs that primarily target pro-inflammatory or anti-inflammatory genes. The expression of smRNAs that suppresses pro-inflammatory genes was higher at 6 weeks before terminal sedation, suggesting the downregulation of the pro-inflammatory genes advances the terminal illness of the IBD. Conclusions: Our study proposes that fecal exosomal smRNA profiling offers a new opportunity to monitor the inflammatory status of the gut with a capability of detecting its pro-inflammatory (asymptomatic) status. Our next step is to understand spatiotemporal interplay of these exosomes and the host cells in the gut as well as the complete biochemical makeup of fecal exosomes, such as mRNA, DNA, protein, and lipids. This study paves the path to the future utilization of fecal exosome in early diagnosis, follow-up, and potential mitigation of the chronic gut inflammation.