Extended Data Fig. 11: Leading edge of fistula tract epithelization.
Related to Figs. 3 and 4. A. Spatial layering of tissue niches identified by niche analysis of 5100-plex Xenium ST dataset. A representative region (n = 19 samples in cohort) around inflammatory CD ulcer is visualised, the ROI from the full section visualised in Extended Data Fig. 9i. B. Differential cell type abundance between CD ulcers and fistulae within more distal and fibrotic outer zone niches around fistula/ulcer lesions. Bars represent the 95% Bayesian credible interval of the slope (logit fold change in cluster proportion per unit change in the covariate), indicating the range of effect sizes compatible with the data, given the model. Dashed lines indicate FDR. Only significant cell type enrichments (FDR < 0.05) are shown. N = 19 samples in cohort. C. Dotplot visualising epithelial cell subtype markers identified in Xenium ST cohort. D. Representative tissue sections visualising spatial distribution of epithelial cell types detected in Xenium ST cohort (n = 53 samples in cohort). All non-epithelial cell types are shown in grey. An early fistula/deep fissuring ulcer is visualised in the top panel, a partially epithelialised, columnar epithelium fistula tract visualised in the middle panel, and a representative tract containing both squamous and columnar epithelium from a peri-anal fistula is visualised at the bottom. E. Gene expression of selected marker genes visualised in ROIs indicated in Fig. 4a. F. A representative partially epithelialised fistula section visualising distances of epithelial cells from crypt base to crypt top (left) and from the leading edge of epithelialisation of the fistula tract into lagging mucosa. Epithelial cells are coloured, all other cells indicated in grey. N = 53 samples in cohort, n = 6 fistulae with partially epithelialised edge quantified. G. Epithelial cell type proportion distribution over distance with respect to crypt axis gradient (left) and distance from the leading edge of the epithelialisation of the fistula tract (right) as indicated in panel F. N = 53 samples in cohort, n = 6 fistulae with partially epithelialised edge quantified. H. Reference H&E image of a partially epithelialised fistula tract profiled with Visium ST (n = 34 samples). I. Spatial distribution of NRG1 gene expression in fistula tissue section (n = 34 samples), with reference H&E image in H. J. Spatial distribution of receptor-ligand product score for NRG1-ERBB2 interaction, with reference H&E image in H. n = 34 samples. K. Heatmap visualising gene expression variation in epithelial cells conditional on which FAS or other mucosal fibroblast cell types are in the local spatial neighbourhood. Aggregated and scaled mean expression is shown. For example, epithelial cells closer to muscularis mucosa express stem cell marker genes such as LGR5, while epithelial cells nearby FAS cells upregulate innate immune response genes e.g. ISG15. L. Relative gene expression of frizzled receptors FZD6, FZD7 and the proliferation marker MKI67 as assessed by qPCR in the validation cohort (n = 84). Gene expression data are presented as mean values with error bars representing the SEM. Statistical analysis was performed using an unpaired t-test, with significance set at p < 0.05. Expression levels of FZD6 and FZD7 were adjusted for EPCAM expression using a generalised linear model. Compared to healthy controls, FZD6 expression was significantly reduced in internal CD fistula (fold change = −1.82, p = 0.0048), perianal CD fistula (fold change = −1.60, p = 0.04), and diverticular fistula (fold change = −1.79, p = 0.02). In contrast, FZD7 expression was significantly increased in internal CD fistula (fold change = 0.83, p = 0.01), external CD fistula (fold change = 1.23, p = 0.03), and diverticular fistula (fold change = 1.02, p = 0.01). M. Selected gene marker expression measured in Xenium ST cohort (n = 53) visualised at the edge of partially epithelialised fistula edge, with ROI indicated by white box in panel D. N. Selected marker gene expression measured in Visium ST cohort (n = 34) visualised in partially epithelialised fistula, with reference H&E image visualised in panel H.
