RNA-Seq analysis of the cystic fibrosis rat small intestine. Rattus norvegicus

Background: A recently developed animal model of the genetic disease is the cystic fibrosis (CF) rat, which similar to other animal models of CF exhibits a lethal intestinal phenotype. To begin characterizing the CF rat intestinal phenotype, we investigated global gene expression in the CF rat small intestine. Methods: Total RNA was extracted from full thickness of the entire small intestines of wild type (WT) and CF rats just before weaning. Results: There were 890 genes with significantly different expression levels (1.2-fold cutoff) comparing CF to wild type (WT), including 485 genes increased and 405 decreased in the CF intestine. The major pathways associated with these changes were inflammation, lipid metabolism, cytochrome P450-mediated degradative pathways, and cell growth/death. Comparison of the rat RNA-Seq dataset to earlier microarray analysis using a CFTR knockout mouse showed significant overlap with the CF rat small intestine. Conclusions: The small intestine of the new CF rat model exhibits numerous alterations in gene expression similar to other animal models of CF which indicate this will be an additional new model to study the gut effects CF. Overall design: RNA-Seq between WT and CF rat intestine