Journal: bioRxiv

Article Title: Discrete genetic effects of VHL and PBRM1 inactivation co-operate to disrupt epithelial homeostasis and promote ccRCC

doi: 10.64898/2026.02.18.706657

Figure Lengend Snippet:

Article Snippet: Antigens were detected by overnight incubation at 4°C with primary antibodies diluted 1:1000 in Dako Antibody Diluent Solution (Agilent S3022): tdTomato – anti-RFP (Rockland 600-401-379, RRID:AB_2209751); PBRM1 – anti-PBRM1 (Proteintech 12563-1-AP, RRID:AB_2877865).

Techniques:

Journal: bioRxiv

Article Title: Discrete genetic effects of VHL and PBRM1 inactivation co-operate to disrupt epithelial homeostasis and promote ccRCC

doi: 10.64898/2026.02.18.706657

Figure Lengend Snippet: (a) Pseudo-bulked L2FC plotted against the negative logarithm of the p value (two-tailed Wald test with multiple testing correction by Benjamini-Hochberg method) for genes in VPKO Early versus VKO Early cells. Genes significantly (p < 0.01) and robustly (|L2FC| > 0.5) regulated are colored green. Candidate genes pertaining to lipid and sterol metabolism and epithelial morphogenesis and adhesion are labelled. (b) Gene Ontology terms for biological processes that are significantly over-represented among genes upregulated by Pbrm1 inactivation in Vhl -null cells. GO terms whose over-representation is significant (p < 0.01; one-sided Fisher’s exact test corrected by false discovery rate), and whose member genes together exhibit a net positive average L2FC in VPKO Early versus VKO Early cells are shown. Terms are ordered and tiles are colored by the average L2FC. (c) Pseudo-bulked L2FC in VPKO Early versus VKO Early cells plotted against changes in VPKO Late versus VKO Late cells showing that Pbrm1 -dependent regulation of genes is correlated between the two timepoints. (d) Pseudo-bulked L2FC plotted against the negative logarithm of the p value (two-tailed Wald test with multiple testing correction by Benjamini-Hochberg method) for genes in VPKO Late versus VPKO Early cells, showing that genes significantly regulated after Pbrm1 inactivation at the early timepoint (colored green) are mostly not regulated significantly over time (i.e., have either |L2FC| < 0.5 or p > 0.01 in the VPKO Late versus VPKO Early comparison). (e) Pseudo-bulked L2FC in VPKO Late versus VPKO Early cells plotted against changes in VKO Late versus VKO Early cells showing that time-dependent changes in gene expression are correlated in Vhl- null and Vhl/Pbrm1 -null cells. (f) Expression of sets of genes up- or downregulated over time in Vhl -null cells of any PT identity (‘Adaptive Up’ or ‘Adaptive Down’) in ConKO, VKO, and VPKO cells sequenced either 1-3 weeks (early) or 4-12 months (late) following recombination. Median values and inter-quartile ranges of the data are presented separately for cells from each mouse. Pairwise comparisons have been made between means of the median values for mice of different genotypes using two-tailed two-way ANOVA with multiple testing correction using the Benjamini-Hochberg method. Adaptive upregulation is maintained, and adaptive downregulation is partially accelerated following Pbrm1 inactivation in Vhl -null cells. (g) Pseudo-bulked L2FC in VPKO Early versus VKO Early cells plotted against changes in ConPKO Early versus ConKO Early cells, showing that Pbrm1 -dependent gene regulation is correlated in Vhl -null and Vhl -competent cells. (h) Pseudo-bulked L2FC in VKO Early versus ConKO Early cells plotted against changes in VPKO Early versus ConPKO Early cells, showing that Vhl -dependent gene regulation is correlated between Pbrm1 -competent and Pbrm1 -null cells. (c, e, g, h ) Spearman’s correlation coefficient (ρ) calculated for genes that exhibit significant regulation in either of the depicted comparisons. (i) Oil Red O staining in renal sections from ConKO, ConPKO, VKO, and VPKO mice harvested 4-12 months (late) following recombination, showing the accumulation of lipid droplets (stained red) in PT cells of ConPKO and VPKO mice. Scale bar, 100 μm. 40x magnification.

Article Snippet: Antigens were detected by overnight incubation at 4°C with primary antibodies diluted 1:1000 in Dako Antibody Diluent Solution (Agilent S3022): tdTomato – anti-RFP (Rockland 600-401-379, RRID:AB_2209751); PBRM1 – anti-PBRM1 (Proteintech 12563-1-AP, RRID:AB_2877865).

Techniques: Two Tailed Test, Comparison, Gene Expression, Expressing, Staining

Journal: bioRxiv

Article Title: Discrete genetic effects of VHL and PBRM1 inactivation co-operate to disrupt epithelial homeostasis and promote ccRCC

doi: 10.64898/2026.02.18.706657

Figure Lengend Snippet: (a) Pseudo-bulked L2FC in VPKO Late versus ConKO Late cells plotted against ‘predicted’ changes calculated as addition of the effects of Vhl inactivation (VKO Late vs ConKO Late) and early effects of Pbrm1 inactivation (VPKO Early vs VKO Early). Genes that exhibited significant regulation in either of the depicted comparisons are plotted. Genes whose regulation in VPKO Late versus ConKO Late cells exhibit significant (p < 0.01; two-sided Wald z-test) deviation from the additive effects of Vhl and Pbrm1 inactivation are colored green. Spearman’s correlation coefficient (ρ). (b) Cells from ConKO, VKO, and VPKO mice projected onto UMAP space and clusters defined for VPKO Late cells (left panel), and the proportion of cells in each cluster derived from mice of each of the genotypes and timepoints (right panel), showing differential occupancy of Clusters 12, 9, and 2 by VPKO Late cells. (c-e) Proportion of cells from VPKO Late mice or mice from other genotypes and timepoints in Clusters 12 (c) , 9 (d ), and 2 (e ). Pairwise comparisons by Wilcoxon test. Error bars indicate the median and the inter-quartile range. (f) Expression of candidate genes that are part of the integrated stress response (ISR), and expression score for an ISR gene module derived from Han et al., 2023, in cells from Clusters 9, 12, or other clusters, showing that Clusters 12 and 9 are both characterized by increased expression of ISR genes. (g) Proportion of cells with detected reads for candidate genes downregulated in cells from Cluster 2 compared to those in the remaining clusters, showing that Cluster 2 cells are characterized by reduced expression of several PT differentiation transcription factors and adhesion molecules.

Article Snippet: Antigens were detected by overnight incubation at 4°C with primary antibodies diluted 1:1000 in Dako Antibody Diluent Solution (Agilent S3022): tdTomato – anti-RFP (Rockland 600-401-379, RRID:AB_2209751); PBRM1 – anti-PBRM1 (Proteintech 12563-1-AP, RRID:AB_2877865).

Techniques: Derivative Assay, Expressing

Journal: bioRxiv

Article Title: Discrete genetic effects of VHL and PBRM1 inactivation co-operate to disrupt epithelial homeostasis and promote ccRCC

doi: 10.64898/2026.02.18.706657

Figure Lengend Snippet:

Article Snippet: Primary antibodies: tdTomato (Rockland 600-401-379, RRID:AB_2209751) and PBRM1 (Proteintech 12563-1-AP, RRID:AB_2877865) were diluted in blocking buffer (1:1,000).

Techniques:

Journal: bioRxiv

Article Title: Discrete genetic effects of VHL and PBRM1 inactivation co-operate to disrupt epithelial homeostasis and promote ccRCC

doi: 10.64898/2026.02.18.706657

Figure Lengend Snippet: (a) Pseudo-bulked L2FC plotted against the negative logarithm of the p value (two-tailed Wald test with multiple testing correction by Benjamini-Hochberg method) for genes in VPKO Early versus VKO Early cells. Genes significantly (p < 0.01) and robustly (|L2FC| > 0.5) regulated are colored green. Candidate genes pertaining to lipid and sterol metabolism and epithelial morphogenesis and adhesion are labelled. (b) Gene Ontology terms for biological processes that are significantly over-represented among genes upregulated by Pbrm1 inactivation in Vhl -null cells. GO terms whose over-representation is significant (p < 0.01; one-sided Fisher’s exact test corrected by false discovery rate), and whose member genes together exhibit a net positive average L2FC in VPKO Early versus VKO Early cells are shown. Terms are ordered and tiles are colored by the average L2FC. (c) Pseudo-bulked L2FC in VPKO Early versus VKO Early cells plotted against changes in VPKO Late versus VKO Late cells showing that Pbrm1 -dependent regulation of genes is correlated between the two timepoints. (d) Pseudo-bulked L2FC plotted against the negative logarithm of the p value (two-tailed Wald test with multiple testing correction by Benjamini-Hochberg method) for genes in VPKO Late versus VPKO Early cells, showing that genes significantly regulated after Pbrm1 inactivation at the early timepoint (colored green) are mostly not regulated significantly over time (i.e., have either |L2FC| < 0.5 or p > 0.01 in the VPKO Late versus VPKO Early comparison). (e) Pseudo-bulked L2FC in VPKO Late versus VPKO Early cells plotted against changes in VKO Late versus VKO Early cells showing that time-dependent changes in gene expression are correlated in Vhl- null and Vhl/Pbrm1 -null cells. (f) Expression of sets of genes up- or downregulated over time in Vhl -null cells of any PT identity (‘Adaptive Up’ or ‘Adaptive Down’) in ConKO, VKO, and VPKO cells sequenced either 1-3 weeks (early) or 4-12 months (late) following recombination. Median values and inter-quartile ranges of the data are presented separately for cells from each mouse. Pairwise comparisons have been made between means of the median values for mice of different genotypes using two-tailed two-way ANOVA with multiple testing correction using the Benjamini-Hochberg method. Adaptive upregulation is maintained, and adaptive downregulation is partially accelerated following Pbrm1 inactivation in Vhl -null cells. (g) Pseudo-bulked L2FC in VPKO Early versus VKO Early cells plotted against changes in ConPKO Early versus ConKO Early cells, showing that Pbrm1 -dependent gene regulation is correlated in Vhl -null and Vhl -competent cells. (h) Pseudo-bulked L2FC in VKO Early versus ConKO Early cells plotted against changes in VPKO Early versus ConPKO Early cells, showing that Vhl -dependent gene regulation is correlated between Pbrm1 -competent and Pbrm1 -null cells. (c, e, g, h ) Spearman’s correlation coefficient (ρ) calculated for genes that exhibit significant regulation in either of the depicted comparisons. (i) Oil Red O staining in renal sections from ConKO, ConPKO, VKO, and VPKO mice harvested 4-12 months (late) following recombination, showing the accumulation of lipid droplets (stained red) in PT cells of ConPKO and VPKO mice. Scale bar, 100 μm. 40x magnification.

Article Snippet: Primary antibodies: tdTomato (Rockland 600-401-379, RRID:AB_2209751) and PBRM1 (Proteintech 12563-1-AP, RRID:AB_2877865) were diluted in blocking buffer (1:1,000).

Techniques: Two Tailed Test, Comparison, Gene Expression, Expressing, Staining

Journal: bioRxiv

Article Title: Discrete genetic effects of VHL and PBRM1 inactivation co-operate to disrupt epithelial homeostasis and promote ccRCC

doi: 10.64898/2026.02.18.706657

Figure Lengend Snippet: (a) Pseudo-bulked L2FC in VPKO Late versus ConKO Late cells plotted against ‘predicted’ changes calculated as addition of the effects of Vhl inactivation (VKO Late vs ConKO Late) and early effects of Pbrm1 inactivation (VPKO Early vs VKO Early). Genes that exhibited significant regulation in either of the depicted comparisons are plotted. Genes whose regulation in VPKO Late versus ConKO Late cells exhibit significant (p < 0.01; two-sided Wald z-test) deviation from the additive effects of Vhl and Pbrm1 inactivation are colored green. Spearman’s correlation coefficient (ρ). (b) Cells from ConKO, VKO, and VPKO mice projected onto UMAP space and clusters defined for VPKO Late cells (left panel), and the proportion of cells in each cluster derived from mice of each of the genotypes and timepoints (right panel), showing differential occupancy of Clusters 12, 9, and 2 by VPKO Late cells. (c-e) Proportion of cells from VPKO Late mice or mice from other genotypes and timepoints in Clusters 12 (c) , 9 (d ), and 2 (e ). Pairwise comparisons by Wilcoxon test. Error bars indicate the median and the inter-quartile range. (f) Expression of candidate genes that are part of the integrated stress response (ISR), and expression score for an ISR gene module derived from Han et al., 2023, in cells from Clusters 9, 12, or other clusters, showing that Clusters 12 and 9 are both characterized by increased expression of ISR genes. (g) Proportion of cells with detected reads for candidate genes downregulated in cells from Cluster 2 compared to those in the remaining clusters, showing that Cluster 2 cells are characterized by reduced expression of several PT differentiation transcription factors and adhesion molecules.

Article Snippet: Primary antibodies: tdTomato (Rockland 600-401-379, RRID:AB_2209751) and PBRM1 (Proteintech 12563-1-AP, RRID:AB_2877865) were diluted in blocking buffer (1:1,000).

Techniques: Derivative Assay, Expressing

Journal: Cellular and Molecular Gastroenterology and Hepatology

Article Title: Loss of Brg1 and Pten in Pancreatic Ductal Cells Forms Intraductal Tubulopapillary Neoplasm via the YAP/TAZ Pathway

doi: 10.1016/j.jcmgh.2025.101639

Figure Lengend Snippet: Evaluation of SWI/SNF components and TAZ expression in human ITPN samples. ( A ) Expression of SWI/SNF components, including BRG1, BRM, ARID1A, and PBRM1, in human ITPN specimens. Additionally, the expression levels of pAKT and TAZ were analyzed. Black, blue, green, and red indicate negative, weak, moderate, and strong expression, respectively. Cases with reduced expression of any SWI/SNF complex component are shown in yellow . ( B ) Summary of BRG1 staining for human IPMN and ITPN samples. Immunohistochemistry for BRG1 in IPMN (n = 20), ITPN (n = 12), and adjacent normal pancreas (n = 3) specimens. Images of the adjacent normal pancreas were captured from the same tissue slide as IPMN or ITPN, if available. Scale bar, 20 mm. Tables on the right show the number of samples classified as ITPN or IPMN and their staining intensity. Statistical analysis was performed using the Mann–Whitney U test. ( C ) Analysis of Spearman’s correlation coefficients and scatterplots with jitter and linear regression. There was a significant negative correlation between BRG1 and TAZ expression (−0.803). There was a moderate negative correlation between ARID1A or BRM and TAZ expression (−0.422 and −0.518, respectively). No correlation was observed between PBRM1 or pAKT and TAZ expression (0.147 and 0.125, respectively). ( D ) Representative cases are shown. Scale bar, 20 μm.

Article Snippet: PBRM1 , Bethyl , 1:500 , A301-591A.

Techniques: Expressing, Staining, Immunohistochemistry, MANN-WHITNEY