Fig. 3: Regional differences in cell composition and function in the adult colon.
From: Tissue and cellular spatiotemporal dynamics in colon aging
a, The atlas spans structural variation in the mouse colon along the proximal–distal axis. Illustrative H&E images of sections from proximal (left; blue), middle (middle; orange) and distal (right; green) regions. b, Variation in cellular composition of MROIs across the proximal–distal axis. Proportion of cells of each type (x axis, stacked bars; color code) in each MROI (y axis) in the proximal (left), middle (middle) and distal (right) regions of adult (12 weeks) colon. The number of spots per MROI (color scale) in each colon region is indicated. c,d, Variation in cell type composition of the same MROI type along the proximal–distal axis. c, Representative H&E image patches from selected ST spots in two MROIs (left to right) from proximal (left; blue), middle (middle; orange) and distal (right; green) regions. In d, the fraction of cells (y axis) of each cell type (x axis) in the proximal (blue), middle (orange) and distal (green) regions is shown for each of the MROI types in c. Center black line, median; color-coded box, interquartile range; error bars, 1.5× the interquartile range; *0.01 < FDR ≤ 0.05, **10−3 < FDR ≤ 0.01, ***10−4 < FDR ≤ 10−3 and ****FDR ≤ 10−4 (Welch’s t-test). Only cell types observed at a rate of 2% or greater across all spots in an MROI are shown. e, Regional goblet cell abundances achieved with cSplotch as presented in d and those measured with IF (proximal and distal, n = 6; middle, n = 2). Center black line, median; color-coded box, interquartile range; error bars, 1.5× the interquartile range. The color code is shared with d. f, Cell-specific expression patterns vary across colon regions. Estimated posterior distributions of expression rate (\(\beta\)) for different genes in each colonic region (color) in goblet cells and ISCs in CM or SMCs and fibroblasts in MEI. Bold, canonical markers; brackets, significant DE (*BF > 2, **BF > 10, ***BF > 30 and ****BF > 100). g–i, Variation in structure, cell composition and gene expression along locations. g, Selected H&E image patches from ST across four MROIs (rows) from three colon regions (columns). h, Scaled (dot size) and absolute (dot color) change in mean spot fraction (MSF; dot color) of each cell type (columns) in each MROI (rows) relative to crypt base from three colon regions. i, Scaled (dot size) and absolute (dot color) change in mean log expression \((\bar{\beta })\) of each gene (columns) in each MROI (rows) relative to crypt base from three colon regions. Bolded genes, regional expression gradients.
