Extended Data Fig. 4: The spatiotemporal and cellular dynamics of tissue damage.
From: A spatiotemporal atlas of cholestatic injury and repair in mice
a. TUNEL (green) staining at D0 and D17 (n = 5 each). Scale bar, 100 μm. b. Spatial visualization of damage response signaling activities in D0, D8, and D17 sections. Scale bar, 100 μm. Black line indicated position of median zonation layer. CV indicated pericentral region. Zonal module distribution at D17 (Kruskal-Wallis test, *q < 0.05). c. DAMP gene expression for each zonation layer in Stereo-seq sections upon injury. d. Bgn (green) immunostaining at D0 and D17 (n = 2 each; a single representative field of view is shown). Scale bar, 100 μm. e. Slc4a2 expression in cholangiocytes from scRNA-seq during injury. f. Expression of genes related to activation and fibrogenesis in fibroblasts and HSCs from scRNA-seq between D0 and injury (D8 and D17). As shown in Fig. 5b, most fibroblasts were distributed in PV, indicated they were portal fibroblasts. g. GO and KEGG biological pathway analysis of DEGs of each innate immune cell cluster (log2foldchange ≥ 0.25, q < 0.05). h. Top: experiment design of DAPM-induced and BDL model. Bottom left: Pdpn (green) and Ck19 (red) staining on liver sections of WT (n = 5), DAPM (n = 4) and BDL (n = 5) mice. Arrows indicated Pdpn+Ck19− LyECs. Scale bar, 100 μm. Bottom right: quantification of Pdpn+Ck19- LyECs of WT, DAPM and BDL mice. Mean ± SD; *p = 0.0113, ***p = 0.0001, two-sided t-test. i. Top: experiment design of Mdr2-/- model. Bottom left: Pdpn (green) and Ck19 (red) staining on liver sections of control and Mdr2-/- (n = 5 each). Arrows indicated Pdpn+Ck19- LyECs. Scale bar, 100 μm. Bottom right: quantification Pdpn+Ck19- LyECs of WT and Mdr2-/- mouse. Mean ± SD; ***p = 0.0002, two-sided t-test. j. LyEC specific gene expression in cell types identified from BA scRNA-seq. k. Left: UMAP of cell types in BA scRNA-seq data. Box indicates LyEC and myeloid cell populations. Right: UMAP of LyEC dynamics in scRNA-seq data of normal and BA liver. Circle indicates the LyEC population. l. Periportal region (cluster 1) from human BA 10x Visium is spatially corresponding to LyEC enriched bins. m. Interaction strength of Vegfc/d ligand-receptor pairs for each zonation layer in Stereo-seq sections upon injury. n. Vegfc/d expression of in scRNA-seq upon injury. o. GO and KEGG terms for LSEC and LyEC DEG enriched pathway (log2foldchange ≥ 0.25, q < 0.05). p. Sema3a expression in LyEC scRNA-seq upon injury. q. Spatial visualization of Sema3a on D0, D8, and D17 sections. Zonal module distribution at D17 (Kruskal-Wallis test, *q < 0.05).
