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a , Schematic of the spatial transcriptomics (SRT) workflow. Cryosections were obtained from the indicated anatomical region (highlighted in schematic). Adjacent sister sections were stained with H&E, and sections for SRT were processed with <t>BGI</t> <t>Stereo-seq</t> technology. b , Spatial feature plot showing spot-level transcriptomic clustering of WT and PY-TB zebrafish samples. Clusters were identified by Seurat using principal component analysis and graph-based clustering of transcriptomic neighbourhoods. c , Integrated UMAP of all spatial transcriptomic spots coloured by Seurat-defined cluster identity. Cluster annotation was guided by regionally enriched marker genes and tissue interpretation using Zebrahub. d , UMAP and spatial feature plots highlighting hepatocyte-enriched spots defined by expression of hepatocyte marker, fabp10a , above the 75th percentile. Cells are grouped by sample: WT hepatocytes (blue) and PY-TB hepatocytes (red). e , Volcano plot of differentially expressed genes (DEGs) between PY-TB hepatocytes and WT hepatocytes, both defined by fabp10a expression in the spatial data. f , Spatial projection of cholangiocyte marker, anxa4, expression, visualised over spatial coordinates of the tissue section. g-i , Gene set enrichment analysis (GSEA) plots of selected pathways enriched in PY-TB hepatocytes versus WT, derived from DEGs identified in the SRT dataset. j , H&E and immunofluorescence staining of liver sections of WT and PY-TB fish at 21 dpf. Nuclei are marked with DAPI (cyan), hepatocytes with GFP (green), and cholangiocytes with ANXA4 (magenta). White arrow represents GFP+/ANXA4+ bi-lineage cells. Scale bar, 100 μm.
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a , Schematic of the spatial transcriptomics (SRT) workflow. Cryosections were obtained from the indicated anatomical region (highlighted in schematic). Adjacent sister sections were stained with H&E, and sections for SRT were processed with <t>BGI</t> <t>Stereo-seq</t> technology. b , Spatial feature plot showing spot-level transcriptomic clustering of WT and PY-TB zebrafish samples. Clusters were identified by Seurat using principal component analysis and graph-based clustering of transcriptomic neighbourhoods. c , Integrated UMAP of all spatial transcriptomic spots coloured by Seurat-defined cluster identity. Cluster annotation was guided by regionally enriched marker genes and tissue interpretation using Zebrahub. d , UMAP and spatial feature plots highlighting hepatocyte-enriched spots defined by expression of hepatocyte marker, fabp10a , above the 75th percentile. Cells are grouped by sample: WT hepatocytes (blue) and PY-TB hepatocytes (red). e , Volcano plot of differentially expressed genes (DEGs) between PY-TB hepatocytes and WT hepatocytes, both defined by fabp10a expression in the spatial data. f , Spatial projection of cholangiocyte marker, anxa4, expression, visualised over spatial coordinates of the tissue section. g-i , Gene set enrichment analysis (GSEA) plots of selected pathways enriched in PY-TB hepatocytes versus WT, derived from DEGs identified in the SRT dataset. j , H&E and immunofluorescence staining of liver sections of WT and PY-TB fish at 21 dpf. Nuclei are marked with DAPI (cyan), hepatocytes with GFP (green), and cholangiocytes with ANXA4 (magenta). White arrow represents GFP+/ANXA4+ bi-lineage cells. Scale bar, 100 μm.
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a , Schematic of the spatial transcriptomics (SRT) workflow. Cryosections were obtained from the indicated anatomical region (highlighted in schematic). Adjacent sister sections were stained with H&E, and sections for SRT were processed with <t>BGI</t> <t>Stereo-seq</t> technology. b , Spatial feature plot showing spot-level transcriptomic clustering of WT and PY-TB zebrafish samples. Clusters were identified by Seurat using principal component analysis and graph-based clustering of transcriptomic neighbourhoods. c , Integrated UMAP of all spatial transcriptomic spots coloured by Seurat-defined cluster identity. Cluster annotation was guided by regionally enriched marker genes and tissue interpretation using Zebrahub. d , UMAP and spatial feature plots highlighting hepatocyte-enriched spots defined by expression of hepatocyte marker, fabp10a , above the 75th percentile. Cells are grouped by sample: WT hepatocytes (blue) and PY-TB hepatocytes (red). e , Volcano plot of differentially expressed genes (DEGs) between PY-TB hepatocytes and WT hepatocytes, both defined by fabp10a expression in the spatial data. f , Spatial projection of cholangiocyte marker, anxa4, expression, visualised over spatial coordinates of the tissue section. g-i , Gene set enrichment analysis (GSEA) plots of selected pathways enriched in PY-TB hepatocytes versus WT, derived from DEGs identified in the SRT dataset. j , H&E and immunofluorescence staining of liver sections of WT and PY-TB fish at 21 dpf. Nuclei are marked with DAPI (cyan), hepatocytes with GFP (green), and cholangiocytes with ANXA4 (magenta). White arrow represents GFP+/ANXA4+ bi-lineage cells. Scale bar, 100 μm.
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a , Schematic of the spatial transcriptomics (SRT) workflow. Cryosections were obtained from the indicated anatomical region (highlighted in schematic). Adjacent sister sections were stained with H&E, and sections for SRT were processed with <t>BGI</t> <t>Stereo-seq</t> technology. b , Spatial feature plot showing spot-level transcriptomic clustering of WT and PY-TB zebrafish samples. Clusters were identified by Seurat using principal component analysis and graph-based clustering of transcriptomic neighbourhoods. c , Integrated UMAP of all spatial transcriptomic spots coloured by Seurat-defined cluster identity. Cluster annotation was guided by regionally enriched marker genes and tissue interpretation using Zebrahub. d , UMAP and spatial feature plots highlighting hepatocyte-enriched spots defined by expression of hepatocyte marker, fabp10a , above the 75th percentile. Cells are grouped by sample: WT hepatocytes (blue) and PY-TB hepatocytes (red). e , Volcano plot of differentially expressed genes (DEGs) between PY-TB hepatocytes and WT hepatocytes, both defined by fabp10a expression in the spatial data. f , Spatial projection of cholangiocyte marker, anxa4, expression, visualised over spatial coordinates of the tissue section. g-i , Gene set enrichment analysis (GSEA) plots of selected pathways enriched in PY-TB hepatocytes versus WT, derived from DEGs identified in the SRT dataset. j , H&E and immunofluorescence staining of liver sections of WT and PY-TB fish at 21 dpf. Nuclei are marked with DAPI (cyan), hepatocytes with GFP (green), and cholangiocytes with ANXA4 (magenta). White arrow represents GFP+/ANXA4+ bi-lineage cells. Scale bar, 100 μm.
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a , Schematic of the spatial transcriptomics (SRT) workflow. Cryosections were obtained from the indicated anatomical region (highlighted in schematic). Adjacent sister sections were stained with H&E, and sections for SRT were processed with <t>BGI</t> <t>Stereo-seq</t> technology. b , Spatial feature plot showing spot-level transcriptomic clustering of WT and PY-TB zebrafish samples. Clusters were identified by Seurat using principal component analysis and graph-based clustering of transcriptomic neighbourhoods. c , Integrated UMAP of all spatial transcriptomic spots coloured by Seurat-defined cluster identity. Cluster annotation was guided by regionally enriched marker genes and tissue interpretation using Zebrahub. d , UMAP and spatial feature plots highlighting hepatocyte-enriched spots defined by expression of hepatocyte marker, fabp10a , above the 75th percentile. Cells are grouped by sample: WT hepatocytes (blue) and PY-TB hepatocytes (red). e , Volcano plot of differentially expressed genes (DEGs) between PY-TB hepatocytes and WT hepatocytes, both defined by fabp10a expression in the spatial data. f , Spatial projection of cholangiocyte marker, anxa4, expression, visualised over spatial coordinates of the tissue section. g-i , Gene set enrichment analysis (GSEA) plots of selected pathways enriched in PY-TB hepatocytes versus WT, derived from DEGs identified in the SRT dataset. j , H&E and immunofluorescence staining of liver sections of WT and PY-TB fish at 21 dpf. Nuclei are marked with DAPI (cyan), hepatocytes with GFP (green), and cholangiocytes with ANXA4 (magenta). White arrow represents GFP+/ANXA4+ bi-lineage cells. Scale bar, 100 μm.
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a , Schematic of the spatial transcriptomics (SRT) workflow. Cryosections were obtained from the indicated anatomical region (highlighted in schematic). Adjacent sister sections were stained with H&E, and sections for SRT were processed with BGI Stereo-seq technology. b , Spatial feature plot showing spot-level transcriptomic clustering of WT and PY-TB zebrafish samples. Clusters were identified by Seurat using principal component analysis and graph-based clustering of transcriptomic neighbourhoods. c , Integrated UMAP of all spatial transcriptomic spots coloured by Seurat-defined cluster identity. Cluster annotation was guided by regionally enriched marker genes and tissue interpretation using Zebrahub. d , UMAP and spatial feature plots highlighting hepatocyte-enriched spots defined by expression of hepatocyte marker, fabp10a , above the 75th percentile. Cells are grouped by sample: WT hepatocytes (blue) and PY-TB hepatocytes (red). e , Volcano plot of differentially expressed genes (DEGs) between PY-TB hepatocytes and WT hepatocytes, both defined by fabp10a expression in the spatial data. f , Spatial projection of cholangiocyte marker, anxa4, expression, visualised over spatial coordinates of the tissue section. g-i , Gene set enrichment analysis (GSEA) plots of selected pathways enriched in PY-TB hepatocytes versus WT, derived from DEGs identified in the SRT dataset. j , H&E and immunofluorescence staining of liver sections of WT and PY-TB fish at 21 dpf. Nuclei are marked with DAPI (cyan), hepatocytes with GFP (green), and cholangiocytes with ANXA4 (magenta). White arrow represents GFP+/ANXA4+ bi-lineage cells. Scale bar, 100 μm.

Journal: bioRxiv

Article Title: YAP disrupts bile acid homeostasis to drive cancer-associated cachexia

doi: 10.64898/2026.02.01.702698

Figure Lengend Snippet: a , Schematic of the spatial transcriptomics (SRT) workflow. Cryosections were obtained from the indicated anatomical region (highlighted in schematic). Adjacent sister sections were stained with H&E, and sections for SRT were processed with BGI Stereo-seq technology. b , Spatial feature plot showing spot-level transcriptomic clustering of WT and PY-TB zebrafish samples. Clusters were identified by Seurat using principal component analysis and graph-based clustering of transcriptomic neighbourhoods. c , Integrated UMAP of all spatial transcriptomic spots coloured by Seurat-defined cluster identity. Cluster annotation was guided by regionally enriched marker genes and tissue interpretation using Zebrahub. d , UMAP and spatial feature plots highlighting hepatocyte-enriched spots defined by expression of hepatocyte marker, fabp10a , above the 75th percentile. Cells are grouped by sample: WT hepatocytes (blue) and PY-TB hepatocytes (red). e , Volcano plot of differentially expressed genes (DEGs) between PY-TB hepatocytes and WT hepatocytes, both defined by fabp10a expression in the spatial data. f , Spatial projection of cholangiocyte marker, anxa4, expression, visualised over spatial coordinates of the tissue section. g-i , Gene set enrichment analysis (GSEA) plots of selected pathways enriched in PY-TB hepatocytes versus WT, derived from DEGs identified in the SRT dataset. j , H&E and immunofluorescence staining of liver sections of WT and PY-TB fish at 21 dpf. Nuclei are marked with DAPI (cyan), hepatocytes with GFP (green), and cholangiocytes with ANXA4 (magenta). White arrow represents GFP+/ANXA4+ bi-lineage cells. Scale bar, 100 μm.

Article Snippet: Frozen tissue blocks were stored at −80 °C and cryosectioned at 10 μm onto STOmics Stereo-seq chips (V1.1; BGI Research).

Techniques: Spatial Transcriptomics, Staining, Marker, Expressing, Derivative Assay, Immunofluorescence