The effects of dietary eicosapentaenoic acid and arachidonic acid on gene expression changes in a mouse model of human inflammatory bowel diseases : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Nutritional Science at Massey University, Palmerston North, New Zealand

Nutrigenomics studies the genome-wide influence of nutrients to understand the association between nutrition and human health. Studies in animal models and humans have demonstrated that dietary n-3 polyunsaturated fatty acids (PUFA) from fish oil may be beneficial in inflammatory bowel diseases (IBD). This thesis aimed to test the hypothesis that dietary n-3 PUFA eicosapentaenoic acid (EPA) reduced and n-6 PUFA arachidonic acid (AA) increased colitis in the interleukin- 10 gene-deficient (Il10–/–) mouse model of IBD, and that these PUFA altered the intestinal bacteria community during colitis development using genome-wide expression and bacterial profiling. Using a combined transcriptomic and proteomic approach, the time-course study defined the onset and progression of colitis in Il10–/– mice. Histopathology, transcript and protein changes before and after colitis onset involved in innate and adaptive immune responses suggested delayed remodelling processes in colitic Il10–/– mice and 11 weeks of age as suitable time point to study the effects of dietary PUFA on colitis development. Comparing the transcriptome and proteome profiles associated with colon inflammation of mice fed with the AIN-76A or oleic acid (OA) diet showed that OA was an appropriate control for unsaturated fatty acids in multi-omic studies. The PUFA intervention study indicated that dietary EPA-induced lipid oxidation might have a potential anti-inflammatory effect on inflamed colon tissue partially mediated through activation of peroxisome proliferator-activated receptor alpha (PPARα). Unexpectedly, dietary AA decreased the expression of inflammatory and stress colonic genes in Il10–/– mice. Altered intestinal bacteria community observed in Il10–/– mice before and after colitis onset was associated with the lack of IL10 protein led to changes in intestinal metabolic and signalling processes. Interestingly, dietary EPA and AA seemed to change intestinal bacteria profiles during colitis development. The role of PPARα in the colon was further examined in a concluding study which identified vanin1 as a likely new PPARα-target gene which may also be involved in lipid metabolism. These findings using a state-of-the-art approach combining transcriptomics, proteomics and physiology provide a basis for future research on molecular mechanisms underlying the effects of dietary PUFA, and might contribute to the development of fortified foods that improve intestinal health and wellness