Cross-species single-cell transcriptomic analysis reveals divergence of cell composition and functions in mammalian ileum epithelium [scRNA-seq_Macaque]

Purpose: To reveal the differences on epithelial cell composition, functional assignments and pharmacokinetics among mammals intestine, we use single cell sequencing to examine the conserved and divergent features among species, providing a cross-species single-cell transcriptomic atlases of ileal epithelium Methods:Alive ileum epithelial cells were sorted from two cynomolgus monkeys (14 years old). ScRNA-seq libraries were generated using the Chromium Single Cell 3’ Reagent Ki V3 (10X Genomics). The libraries were sequenced as paired-end with Illumina Novaseq 6000. Raw reads were aligned to the Mmul_10 Macaque genome, and Cell Ranger (v3.1.0) was used to estimate unique molecular identifiers (UMIs). Raw aligned features were loaded and processed using the Seurat package (v4.0.2). Low-quality cells were filtered if they expressed no more than 200 genes or with more than 20% of mitochondrial genes. Results: After cells with low information content and a high fraction of mitochondrial RNAs were excluded, 886 cells were analyzed. Conclusions: Eight cell types were identified in macaque ileum based on reported markers, including enterocytes, transient-amplifying (TA) cells, goblet cells, goblet progenitor cells, stem cells, enteroendorcine cells, CA7+ cells and tuft cells. Single cell profiles of ileum epithelial cells from adult cynomolgus monkeys

研究目的：为揭示哺乳动物肠道上皮细胞组成、功能特征与药物代谢动力学的物种差异，本研究采用单细胞测序技术分析不同物种间的保守与分化特征，构建回肠上皮的跨物种单细胞转录组图谱。
研究方法：从2只14岁食蟹猴体内分离存活的回肠上皮细胞。采用Chromium单细胞3'试剂试剂盒V3（10X Genomics）构建单细胞RNA测序文库，随后通过Illumina NovaSeq 6000平台进行双端测序。将原始reads比对至Mmul_10食蟹猴参考基因组，并使用Cell Ranger（v3.1.0）估算唯一分子标识符（UMIs）。利用Seurat软件包（v4.0.2）加载并处理原始比对特征；过滤掉表达基因数不超过200个或线粒体基因占比超过20%的低质量细胞。
研究结果：在剔除信息含量低且线粒体RNA占比高的细胞后，最终纳入886个细胞进行后续分析。
研究结论：基于已报道的标记基因，在食蟹猴回肠中鉴定出8种细胞类型，包括肠上皮细胞、瞬时扩增（TA）细胞、杯状细胞、杯状细胞祖细胞、干细胞、肠内分泌细胞、CA7+细胞以及簇细胞。本研究获得了成年食蟹猴回肠上皮细胞的单细胞表达谱。