Intestinal epithelial cell diversity and function in respect to age, anatomical localization, and microbial exposure - the global transcriptome

The small intestinal epithelium is composed of several defined epithelial cell lineages, which in turn exhibit marked transcriptional and functional diversity along the crypt-villus and proximal-to-distal length of the intestinal tract. While epithelial cell type and functional heterogeneity have been characterized in the adult intestinal epithelium, the temporal and spatial changes during the postnatal period, which accompany the transition from placental energy supply to enteral feeding and facilitate the establishment of the enteric microbiota and postnatal immune maturation, have not been systematically investigated. Here we analyzed the total small intestinal epithelium of 1-, 5-, 10-, and 25-day-old specific pathogen-free (SPF) and germ-free (GF) mice by bulk RNA-Seq and used differential gene expression and pathway analysis to identify age-specific expression patterns. In addition, the influence of enteric infection on the neonatal epithelium was investigated by bulk RNA-Seq. We identify gene clusters temporally expressed in the neonatal intestine and correlate their expression with the functional changes during postnatal tissue maturation and the neonate to adult transition. Overall design: To study intestinal epithelial maturation during homeostatic conditions and upon infection, intestinal epitehlial cells (IECs) were isolated from small intestinal tissue obtained from 1-, 5-, 10- or 25-day-old C57Bl/6J specific pathogen free (SPF) or C57Bl/6N germ free (GF) newborn mice. In addition, IECs were isolated from 5-day-old C57Bl/6J SPF newborn mice that had been orally infected 4 days earlier with 100-200 CFUs Salmonella Typhimurium. RNA was then isolated RNA and RNA-Seq performed.