144 Array analysis of mucosal gene expression in the intestine of rats following ingestion of OmniGen-AF. B. R. Ou2,l

摘要

The goal was to assess effects of feeding OmniGen-AF on gene expression in the rat intestine. Rats (8/treatment) were fed a control diet or one supplemented with OmniGen-AF (0.5% w/w) for 28 d after which they were killed and intestine recovered. RNA was extracted from intestinal samples and its quality was assessed using a Bioana-lyzer. RNA was then hybridized to Affymetrix whole rat genome arrays and relative concentrations of approximately 23,000 transcripts in control versus OmniGen-AF-fed rats were compared. The normalization of probe set intensities was performed using the Robust Mul-tiarray Analysis method. To identify differentially expressed genes, expression intensities were compared using a moderated /-test and a Bayes smoothing approach. To correct for the effect of multiple testing, the false discovery rate was estimated from p values derived from the moderated /-test statistics. The analysis was performed using the affylmGUI (Graphical User Interface) for the Limma microarray package which is available as part of the Bioconductor software package [www.Bioconductor.org] for the R computing environment. Pathways analysis of the differentially expressed genes was performed using DAVID bioinformatics resources. Of the 23,000 genes represented on the array, 288 genes were upregulated (P < 0.05) and 385 were downregulated (P < 0.05). Pathway analysis of the data set revealed that the regulated genes clustered into 13 pathways of which most were associated with "immunity." Immune regulatory pathways which were differentially regulated in the intestine by feeding OmniGen-AF included 1) complement and coagulation cascades, 2) arachidonic acid metabolism, 3) endocytosis, 4) antigen processing and presentation 5) prion diseases, 6) autoimmune thyroid disease, 7) allograft rejection, 8) graft versus host disease and 9) viral myocarditis. Within these pathways, major histocompatibility complex (MHC) was upregulated. MHC is involved in antigen presentation by phagocytic cells and we have previously reported (Rowson et al., 2011) that OmniGen-AF also increased MHC gene expression in mouse mammary tissue. This analysis provides a holistic view of the effects that OmniGen-AF has on a mucosal surface. Perhaps not surprisingly, the constitutents of the product bring about changes in gene expression in this tissue.