Intestinal epithelial cell diversity and function in respect to age, anatomical localization, and microbial exposure - the proximal to distal 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 proximal, medial and distal parts of the small intestinal epithelium of 1-, 5-, 10- and 25-day-old SPF mice by bulk RNA-Seq and used differential gene expression and pathway analysis to identify age-specific expression patterns. 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, intestinal epithelial cells (IECs) were isolated from the proximal, medial or distal part of small intestinal tissue obtained from 1-, 5-, 10- or 25-day-old C57Bl/6J specific pathogen-free (SPF) newborn mice. RNA was then isolated and RNA-Seq performed.

小肠上皮由多种明确的上皮细胞谱系构成，这些谱系沿肠道的隐窝-绒毛（crypt-villus）轴以及近端-远端长度方向，展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系统解析，但伴随从胎盘供能向肠内营养转变、助力肠道菌群定植与产后免疫成熟的出生后时期内的时空动态变化，尚未得到系统性研究。本研究通过批量RNA测序（bulk RNA-Seq）分析了1、5、10和25日龄无特定病原体（specific pathogen-free, SPF）小鼠小肠上皮的近端、中端与远端区段，借助差异基因表达与通路分析，鉴定出年龄特异性的表达模式。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及新生向成年转变过程中的功能变化相关联。整体实验设计：为探究稳态条件下的小肠上皮成熟过程，研究人员从1、5、10或25日龄C57Bl/6J品系无特定病原体（SPF）新生小鼠的小肠近端、中端或远端区段分离得到小肠上皮细胞（intestinal epithelial cells, IECs），随后提取RNA并开展RNA测序（RNA-Seq）。