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

Abstract

Animal models are widely used for biomedical studies and drug evaluation. The small intestine plays key roles in nutrient absorption, hormone secretion, microbiota defense and drug absorption and metabolism. Although the intestinal structure of mammals is conserved, the differences on epithelial cell composition, functional assignments and drug absorption among mammals are largely unknown. Here, cross-species analysis of single-cell transcriptomic atlas of the ileum epithelium from mouse, rat, pig, macaque and human reveals the conserved and differential cell types and functions among species, identifies a new CA7+ cell type in pig, macaque and human ileum, uncovers the distinct expression pattern in enterocytes, enteroendocrine cells and Paneth cells, and defines the conserved and species-specific intestinal stem cell signature genes. The examination of drug absorption across species suggests that drug metabolism in mouse ileum is closer to human while drug transport in macaque ileum is more similar to human. Together, our data provide the comprehensive information about cell composition and functional assignments in five species, and offer the valuable guidance for animal model selection and drug testing.

Intestinal cellular heterogeneity and disease development revealed by single-cell technology

“…Nowadays, scRNAseq is widely used for routine transcriptional profiling at single-cell resolution (Zhao et al, 2021). Our crossspecies analysis of the single-cell transcriptome of the ileum epithelium identified a new CA7 + cell type in pig, macaque, and human ileum and revealed the distinct expression pattern in enterocytes, EECs, and Paneth cells among different species (Li et al, 2022). In this review, we focus on an advanced understanding of the intestine biology gained from single-cell transcriptome analysis and provide an updated summary of the scRNA-seq database in the field.…”

Intraepithelial lymphocytes in the pig intestine: T cell and innate lymphoid cell contributions to intestinal barrier immunity

“…-Human intestinal physiology, nutrition, and microbiota more similar to pigs than mice (188)(189)(190)(191)(192)(193)(194) -Proportions of gdTCR T-IELs, CD8ab + abTCR T-IELs, and CD8aa + abTCR T-IELs in human intestine more similar to pigs than mice (1,7,25,29,66,67,(195)(196)(197) -Transcriptional similarities between human and porcine intestinal immune and epithelial cells identified via high-resolution transcriptomics (57,(198)(199)(200) -Biomedical applications using pig models have cross-utility to improve pig health and global food security Frontiers in Immunology frontiersin.org assess transcriptomes of epithelial cells in duodenum, jejunum, and ileum of the porcine small intestine, finding again transcriptional similarities between humans and pigs for the majority of epithelial cells (200). Thus, high-resolution transcriptomic analyses support transcriptional conservation between immune and epithelial cells of human and porcine intestine, but scRNA-seq studies have so far been limited to only the small intestine.…”

“…An additional scRNA-seq study defining lymphocyte subsets (including T cells and ILCs) at enhanced resolution also identified transcriptional similarities, similar localization patterns, and conserved inferred functions of lymphocytes from porcine and human ileum ( 57 ). Yet another scRNA-seq study highlights conserved functions and compositions of epithelial cells between human and pig ileum; however, compositional similarities should be interpreted with caution due to vast differences in cell isolation procedures used between species ( 199 ). One final scRNA-seq study expanded analysis to assess transcriptomes of epithelial cells in duodenum, jejunum, and ileum of the porcine small intestine, finding again transcriptional similarities between humans and pigs for the majority of epithelial cells ( 200 ).…”

Benchmarking strategies for cross-species integration of single-cell RNA sequencing data

“…Recently, single-cell RNA-sequencing (scRNA-seq) and single-nucleus RNA-sequencing (snRNA-seq) have been applied in a diversity of species, generating full-scale cell atlases from transcriptome profiles of millions of individual cells [1][2][3][4][5][6][7] . Comparing cellular expression profiles cross-species provides insights into the origin and evolution of organs and cell types 6,8-10 , highlights species-specific transcriptomic innovations 11 , as well as further delineates how cell types execute their functions in health and disease 12,13 .…”

“…Last but importantly, cross-species integration requires matching genes from different species by gene homology. Currently, most studies only use one-to-one orthologous gene from public resources such as ENSEMBL 3,12 or EggNOG 9 , while some others manually add relevant one-to-many orthologs 16 or use an in-house pipeline 13 for homology mapping. Nevertheless, gene homology relationships can be obscure for species without a well-annotated genome and challenging to map for evolutionally distant species pairs.…”