RNAseq studies reveal distinct transcriptional response to vitamin A deficiency in small intestine versus colon, discovering novel VA-regulated genes

Vitamin A (VA) deficiency remains prevalent in resource limited countries, affecting over 250 million preschool aged children. Vitamin A deficiency is associated with reduced 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 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 vitamin A sufficient (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 9humoral immune response9 and 9complement activation9 were positively associated with VA in SI. On the contrary, in colon, 9cell division9 was the only enriched category and was negatively associated with VA. Three 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.