Vitamin A (VA) deficiency remains prevalent in resource limited countries, affecting over 250 million preschool aged children. Vitamin A deficiency is associated with reduced 2 intestinal barrier function and increased risk of mortality due to mucosal infection. Citrobacter rodentium (C. rodentium) infection in mice is a model for diarrheal diseases in humans. During C. rodentium infection, vitamin A deficient (VAD) mice displayed reduced survival rate and pathogen clearance compared to their vitamin A sufficient (VAS) counterparts. Objectives: To characterize and compare the impact of vitamin A (VA) deficiency on gene expression patterns in the small intestine (SI) and the colon, and to discover novel target genes in VA-related biological pathways. Methods: vitamin A deficient (VAD) mice were generated by feeding VAD diet to pregnant C57/BL6 dams and their post-weaning offspring. Total mRNA extracted from SI and colon were sequenced using Illumina HiSeq 2500 platform. Differentially Expressed Gene (DEG), Gene Ontology (GO) enrichment, and Weighted Gene Co-expression Network Analysis (WGCNA) were performed to characterize expression patterns and co-expression patterns.
Results:The comparison between VAS and VAD groups detected 49 and 94 DEGs in SI and colon, respectively. According to GO information, DEGs in the SI demonstrated significant enrichment in categories relevant to retinoid metabolic process, molecule binding, and immune function. Immunity related pathways, such as "humoral immune response" and "complement activation," were positively associated with VA in SI. On the contrary, in colon, "cell division" was the only enriched category and was negatively associated with VA. Three co-expression modules showed significant correlation with VA status in SI and were identified as modules of interest. Those modules contained four known retinoic acid targets. Therefore we have prioritized the other module members (e.g. Mbl2, Mmp9, Cxcl14, and Nr0b2) to be investigated as candidate genes regulated by VA. Also in SI, markers of two cell types, Mast cell and Tuft cell, were found altered by VA status. Comparison of co-expression modules between SI and colon indicated distinct regulatory networks in these two organs.
Material and MethodsAnimals. C57BL/6 mice, originally purchased from Jackson Laboratories (Bar Harbor, MN), were bred and maintained at the Pennsylvania State University (University Park, PA) for experiments. Mice were exposed to a 12 hour light, 12 hour dark cycle with ad libitum access to food and water. All animal experiments were performed according to the Pennsylvania State University's Institutional Animal Care and Use Committee (IACUC) guideline (IACUC # 43445). Vitamin A deficient (VAD) and vitamin A sufficient (VAS) mice were generated as previously described (23,(27)(28)(29). Briefly, VAS or VAD diets were fed to pregnant mothers and the weanlings. VAS diet contained 25 μg of retinyl acetate per day whereas VAD diet did not contain any VA. At weaning, mice were maintained on their respective d...