Intestinal epithelial cell diversity and function in respect to age, anatomical localization, and microbial exposure - the single cell 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 postanatal 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 small intestinal epithelium of 1-, 5-, 10- and 25-day-old SPF mice by single cell 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. 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. To study intestinal epithelial maturation during homeostatic conditions, intestinal epithelial cells (IECs) were isolated from small intestinal tissues obtained from 1-, 5-, 10- or 25-day-old C57Bl/6J specific pathogen-free (SPF) 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. scRNA-Seq was then performed.小肠上皮由多种明确定义的上皮细胞谱系构成，这些谱系沿肠道的隐窝-绒毛轴以及近端至远端长度方向，呈现出显著的转录组与功能多样性。尽管成年小肠上皮的细胞类型与功能异质性已得到解析，但伴随胎盘供能向肠内营养转变、同时助力肠道菌群定植与产后免疫成熟的产后时期时空变化，尚未得到系统研究。本研究通过单细胞RNA测序（single cell RNA-Seq），对1日龄、5日龄、10日龄及25日龄的无特定病原体（specific pathogen-free, SPF）小鼠小肠上皮进行分析，并借助差异基因表达分析与通路分析，鉴定出年龄特异性的表达模式。此外，本研究还探究了肠道感染对新生小鼠上皮细胞的影响。我们鉴定出新生小鼠肠道中时序性表达的基因簇，并将其表达与产后组织成熟过程中的功能变化，以及新生个体向成年个体的转变过程建立关联。为探究稳态条件下的小肠上皮成熟过程，研究人员从1日龄、5日龄、10日龄或25日龄的C57Bl/6J无特定病原体（SPF）新生小鼠的小肠组织中分离出肠上皮细胞（intestinal epithelial cells, IECs）。此外，研究人员还从4天前经口感染100~200菌落形成单位（colony-forming units, CFUs）鼠伤寒沙门氏菌（Salmonella Typhimurium）的5日龄C57Bl/6J SPF新生小鼠中分离得到肠上皮细胞（IECs），并对其进行了单细胞RNA测序（scRNA-seq）。