Clump sequencing exposes the spatial expression programs of intestinal secretory cells

Abstract

Single-cell RNA sequencing combined with spatial information on landmark genes enables reconstruction of spatially-resolved tissue cell atlases. However, such approaches are challenging for rare cell types, since their mRNA contents are diluted in the spatial transcriptomics bulk measurements used for landmark gene detection. In the small intestine, enterocytes, the most common cell type, exhibit zonated expression programs along the crypt-villus axis, but zonation patterns of rare cell types such as goblet and tuft cells remain uncharacterized. Here, we present ClumpSeq, an approach for sequencing small clumps of attached cells. By inferring the crypt-villus location of each clump from enterocyte landmark genes, we establish spatial atlases for all epithelial cell types in the small intestine. We identify elevated expression of immune-modulatory genes in villus tip goblet and tuft cells and heterogeneous migration patterns of enteroendocrine cells. ClumpSeq can be applied for reconstructing spatial atlases of rare cell types in other tissues and tumors.

Enteroendocrine Cell Formation Is an Early Event in Pancreatic Tumorigenesis

“…IHC staining for POU2F3 demonstrates a lack of expression in KPouC pancreata ( Figure 7C ). Additionally, COX1, a marker of mature tuft cells, is absent from the epithelium of KPouC pancreata, consistent with a lack of tuft cell formation ( Figure 7D ) ( Grunddal et al, 2021 ; Ma et al, 2021 ; Manco et al, 2021 ). Interestingly, SYP+ cells were identified in both KC and KPouC pancreata indicating that EEC formation is not prevented by the loss of POU2F3 ( Figure 7D ).…”

The metabolic impact of bacterial infection in the gut

“…Differentiated cell types include absorptive enterocytes, goblet cells, enteroendocrine cells and tuft cells (tuft1 and tuft2 subsets) [18]. Differentiated cells show a spatial zonation along the crypt-villus axis (CVA based on their functionality and gene expression profiles [19][20][21]. Intestinal epithelial cells also have immunoregulatory properties enabling them to detect invading pathogens, e.g.…”

Identifying key regulators of the intestinal stem cell niche

“…Recently, telocytes that populate the small intestinal villus tip lamina propria were shown by single cell RNAseq to express Lgr5 ( Figure 2 ) whereas telocytes that were found in the villus centre, villus bottom or crypt did not [ 89 ]. Several frizzled receptors (fzd1, 2, 4, and 7) have also been documented in intestinal telocyte populations [ 43 , 90 ]. Fzd1 has been shown to be reduced in expression in villus tip telocytes compared with crypt base telocytes demonstrating spatial expression of this family of receptors [ 89 ].…”