Cells of the human intestinal tract mapped across space and time

Abstract

The cellular landscape of the human intestinal tract is dynamic throughout life, developing in utero and changing in response to functional requirements and environmental exposures. To comprehensively map cell lineages in the healthy developing, pediatric and adult human gut from ten distinct anatomical regions, as well as draining lymph nodes, we used single-cell RNA-seq and VDJ analysis of roughly one third of a million cells. This reveals the presence of BEST4+ absorptive cells throughout the human intestinal tract, demonstrating the existence of this cell type beyond the colon for the first time. Furthermore, we implicate IgG sensing as a novel function of intestinal tuft cells, and link these cells to the pathogenesis of inflammatory bowel disease. We define novel glial and neuronal cell populations in the developing enteric nervous system, and predict cell-type specific expression of Hirschsprung's disease-associated genes. Finally, using a systems approach, we identify key cell players across multiple cell lineages driving secondary lymphoid tissue formation in early human development. We show that these programs are adopted in inflammatory bowel disease to recruit and retain immune cells at the site of inflammation. These data provide an unprecedented catalogue of intestinal cells, and new insights into cellular programs in development, homeostasis and disease.

A proximal-to-distal survey of healthy adult human small intestine and colon epithelium by single-cell transcriptomics

“…An approach in human organoids with an EEC reporter gene yielded sufficient EECs for detailed scRNAseq analysis, though it is unclear how these cells may differ from primary human EECs 132 . While several human scRNAseq studies show EEC data [11][12][13]16,17 , our 154 EECs (Fig. 5G) represent the largest dataset of primary human EECs to our knowledge.…”

“…FAE includes microfold (M)-cells, which transport luminal antigens to immune cells residing within their microfolds 73 . M-cells have almost exclusively been explored in mice [74][75][76] or using directed differentiation in vitro 77 , with only one study reporting scRNAseq data from healthy human intestinal M-cells 17 . Our dataset includes a cluster of 19 cells from Donor 2 enriched for M-cell markers [78][79][80] and immune cross-talk genes (Fig.…”

“…Recent human single-cell studies describe a novel intestinal lineage, absent in mice, expressing high BEST4, SPIB, and CA7 12 , with CFTR in SI 16,17 and OTOP2 in colon. Several papers describe colonic BEST4 + cells 11,12 , so we analyze SI BEST4 + cells.…”

“…Studies in mouse intestines [3][4][5] led to human scRNAseq studies analyzing fetal gut development [6][7][8] and adult colonic [9][10][11][12] , ileal [13][14][15] , and duodenal 16 epithelium. To date, one study compares adult human ileum and regionally-unspecified colon 13 , and one recent report compiles samples from across the gut yet has limited epithelial analysis 17 . Several human gut regions have sparse scRNAseq analysis available, with no studies analyzing regional differences within SI or colon.…”

Maturation of human intestinal epithelium from pluripotency in vitro

“…Understanding the ISC niche has led to the identification of growth factors that enhance cell type composition and maturation of human small intestinal enteroid cultures (Fujii et al, 2018;Holloway et al, 2021;Jardé et al, 2020). Recent scRNA-seq studies revealed that human small intestinal epithelial development is accompanied by temporal changes of mesenchymal subtype compositions (Elmentaite et al, 2020(Elmentaite et al, , 2021Fawkner-Corbett et al, 2021;Holloway et al, 2021;Yu et al, 2021). ISCs expressing Leucine-Rich Repeat Containing G Protein-Coupled Receptor 5 (LGR5) emerge concomitantly with an increase of subepithelial mesenchymal cells that express a member of the Epidermal growth factor (EGF)-family of secreted ligands, Neuregulin 1 (NRG1), during human intestine development (Yu et al, 2021).…”