RNA-seq Analysis of Mucosal Immune Responses Reveals Signatures of Intestinal Barrier Disruption and Pathogen Entry Following Edwardsiella ictaluri Infection in Channel Catfish, Ictalurus punctatus

The mucosal surfaces of fish (gill, skin, gastrointestinal tract) are important sites of bacterial exposure and host defense mechanisms.  In mammalian systems, the intestinal epithelium is well characterized as both a selectively permeable barrier regulated by tight junction proteins and as a primary site of infection for a number of enteric pathogens including viruses, bacteria, and parasites.  The causative bacterium of enteric septicemia of catfish, Edwardsiella ictaluri, is believed to gain entry through the intestinal epithelium, with previous research using a rat intestinal epithelial cell line (IEC-6) indicating actin polymerization and receptor-mediated endocytosis as potential mechanisms of uptake.  Here, we utilized high-throughput RNA-seq to characterize the role of the intestinal epithelial barrier following E. ictaluri challenge.   A total of 197.6 million reads were obtained and assembled into 176,481 contigs with an average length of 893.7 bp and N50 of 1,676 bp.  The assembled contigs contained 14,457 known unigenes, including 2,719 genes not previously identified in other catfish transcriptome studies.  Comparison of digital gene expression between challenged and control samples revealed 1,383 differentially expressed genes at 3 h, 24 h, and 48 h following exposure. Gene pathway analysis of the differentially expressed gene set indicated the centrality of actin cytoskeletal polymerization/remodelling and tight junction regulation in pathogen entry and subsequent inflammatory responses.  The expression patterns of fifteen differentially expressed genes related to intestinal epithelial barrier dysfunction were validated by quantitative real time RT-PCR (average correlation coeff. 0.92, p<0.001).