Journal: Scientific Reports

Article Title: Combining 5-ALA-PDT with berbamine as an in vitro multimodal therapy approach against bladder cancer cells

doi: 10.1038/s41598-026-46092-x

Figure Lengend Snippet: Effect of berbamine on 5-ALA-induced PpIX accumulation. RT112, RT112 LTT, RT112 CSC (top), and J82, J82 LTT, J82 CSC (bottom) were treated with 5-ALA (0–100 µg/ml) and berbamine (no, ½ IC 50 , IC 50 ). PpIX fluorescence intensity was normalized to cell viability and is shown as individual values with mean as a line. Asterisks indicate significance compared to the sample without berbamine (* p < 0.05; ** p < 0.01; *** p < 0.001; **** p < 0.0001).

Article Snippet: RT112 (DSMZ, cat. no. ACC-418) and J82 (ATCC, cat. no. HTB-1) cell lines originate from transitional cell carcinoma of the human bladder.

Techniques: Fluorescence

Journal: Scientific Reports

Article Title: Combining 5-ALA-PDT with berbamine as an in vitro multimodal therapy approach against bladder cancer cells

doi: 10.1038/s41598-026-46092-x

Figure Lengend Snippet: Cell viability of RT112, RT112 LTT and RT112 CSC following 5-ALA-PDT treatment with increasing irradiation doses and varying concentrations of 5-ALA and berbamine. Bars represent weighted means ± SD from three independent experiments ( n = 3 × 6; controls without irradiation n = 3 × 36). Asterisks indicate significance of unweighted means compared to the irradiated control sample without 5-ALA C1.1-C1.4 (* p < 0.05; ** p < 0.01; *** p < 0.001; **** p < 0.0001).

Article Snippet: RT112 (DSMZ, cat. no. ACC-418) and J82 (ATCC, cat. no. HTB-1) cell lines originate from transitional cell carcinoma of the human bladder.

Techniques: Irradiation, Control

Journal: Scientific Reports

Article Title: Combining 5-ALA-PDT with berbamine as an in vitro multimodal therapy approach against bladder cancer cells

doi: 10.1038/s41598-026-46092-x

Figure Lengend Snippet: Berbamine has cytotoxic effects in ROS generation, cell migration and apoptosis rate for cisplatin-resistant cell lines RT112 LTT and J82 LTT. Tert-butyl hydroperoxide (TBHP; 150 µM) served as positive control for determination of reactive oxygen species (ROS). Detailed data presentation for all cell lines are available in the supplementary section (Supplementary Figs. , and ). Data represent mean ± SD ( n = 3). Asterisks indicate significance relative to the control without berbamine (* p < 0.05; ** p < 0.01; *** p < 0.001; **** p < 0.0001).

Article Snippet: RT112 (DSMZ, cat. no. ACC-418) and J82 (ATCC, cat. no. HTB-1) cell lines originate from transitional cell carcinoma of the human bladder.

Techniques: Migration, Positive Control, Control

Journal: Nucleic Acids Research

Article Title: STAG2 loss-of-function affects short-range genomic contacts and modulates the basal-luminal transcriptional program of bladder cancer cells

doi: 10.1093/nar/gkab864

Figure Lengend Snippet: STAG1 and STAG2 show both overlapping and unique distributions over genomic elements and chromatin states in RT112 cells. ( A ) ChIP-Seq read density heatmaps for STAG1, STAG2, and SMC1 at common, STAG1-enriched (STAG1 > STAG2), and STAG2-enriched (STAG2 > STAG1) cohesin positions within a peak-centered 6kb window. ( B ) Read density distribution for STAG1 and STAG2 at common, STAG1-enriched, and STAG2-enriched positions within a peak-centered 6kb window. ( C ) Bar-plot diagram showing the distribution of common, STAG1-enriched, and STAG2-enriched cohesin positions over genomic elements. ( D ) Distribution of cohesin-bound genomic sites throughout chromatin states identified in RT112 cells by ChromHMM and based on combinations of histone modifications and CTCF (see for definition of chromatin states). ( E ) Peak-centered enrichment plot for CTCF over the three categories of cohesin-bound positions showing relative depletion in STAG2-enriched sites.

Article Snippet: RT112 bladder cancer cells used at CNIO and Institut Curie were from the same original stock; HEK293T cells (transformed human embryonic kidney) were from the ATCC.

Techniques: ChIP-sequencing

Journal: Nucleic Acids Research

Article Title: STAG2 loss-of-function affects short-range genomic contacts and modulates the basal-luminal transcriptional program of bladder cancer cells

doi: 10.1093/nar/gkab864

Figure Lengend Snippet: STAG2 loss in RT112 cells does not interfere with A/B compartments or TAD boundaries. ( A ) Western blot analysis of control (shNT) and STAG2-silenced RT112 cells showing efficient depletion of STAG2 at the protein level. ( B ) Reproducibility, measured by a stratum-adjusted correlation coefficient (SCC), between pair-wise comparisons of Hi-C datasets. ( C ) Hi-C matrices for chr2 at 500 kb resolution in cells transduced with control or STAG2-targeting shRNAs. The darker red reflects a greater frequency of interaction. ( D ) Compartment tracks for chr2 at 100 kb resolution as determined by the values of the first principal component (PC1) in control and STAG2-silenced cells. ( E ) Expression, as defined by RNA-Seq (log 2 FPKM), of genes within compartments A and B. As expected, genes assigned to compartment A are more transcriptionally active than genes in compartment B. t -test: *** P < 0.001. ( F ) Compartmentalization saddle plots: average intra-chromosomal interaction frequencies between 200kb bins, normalized by expected interaction frequency based on genomic distance. Bins are sorted by their PC1 value derived from control cells Hi-C data. Preferential B-B interactions are in the upper left corner, and preferential A-A interactions are in the lower right corner. Numbers in corners represent the strength of AA interactions as compared to AB interactions and BB interactions over BA interactions. ( G ) Scatterplot of PC1 values of the eigenvectors of intrachromosomal interaction matrices for control and STAG2-silenced cells. The Venn diagrams show the overlap in terms of compartment-switching bins between sh1 and sh2. The number of genes mapped to genomic bins switching compartments is also indicated. Only one GO term is significantly enriched (FDR < 0.01) among genes switching from A to B: GO:0050907 (detection of chemical stimulus involved in sensory perception). ( H ) Effect of STAG2-depletion on the number of TADs per chromosome. Boxplot notches represent the confidence interval around the median. The number of total TADs is indicated below the boxplots. ( I ) Histograms depicting the strength of the TAD borders detected in control and STAG2-silenced cells, according to the TADbit score. ( J ) Average insulation profile around TAD boundaries (±600 kb) in control and STAG2-silenced cells. ( K ) Density plot depicting the distribution of TAD sizes identified in control and STAG2-silenced cells. ( L ) Hi-C normalized interaction matrices for chr2 at 100kb resolution comparing TAD organization in control and STAG2-silenced cells. ( M ) Effect of STAG2-depletion on conservation of TAD borders. Boxplot notches represent the confidence interval around the median.

Article Snippet: RT112 bladder cancer cells used at CNIO and Institut Curie were from the same original stock; HEK293T cells (transformed human embryonic kidney) were from the ATCC.

Techniques: Western Blot, Control, Hi-C, Transduction, Expressing, RNA Sequencing, Derivative Assay, Insulation

Journal: Nucleic Acids Research

Article Title: STAG2 loss-of-function affects short-range genomic contacts and modulates the basal-luminal transcriptional program of bladder cancer cells

doi: 10.1093/nar/gkab864

Figure Lengend Snippet: STAG2 depletion leads to deregulation of the basal/luminal transcriptional programs in RT112. ( A ) Scatter plots of expression values (FPKM) of genes in control versus STAG2-silenced cells. Statistically significant differentially expressed genes are highlighted in dark (FDR < 0.05) or light red ( P < 0.05). ( B ) Scatter plot showing a positive and significant correlation between gene expression changes in sh1 and sh2 (left). Venn diagrams displaying the overlap between sh1 and sh2 in terms of significant up- and down-regulated genes. ( C ) GSEA enrichment plots of gene sets associated with the luminal and basal subtypes of muscle-invasive UBC showing significant deregulation in STAG2-silenced RT112 cells. ( D ) Distribution of STAG2 expression (FPKM) in the UROMOL cohort of 476 UBC samples , highlighting the thresholds of the first and fourth quartiles (119 samples per group). We defined ‘STAG2 high’ cases as those with expression values in the fourth quartile, and ‘STAG2 low’ cases as those with STAG2 levels in the first quartile. ( E ) GSEA enrichment plots for genes down-regulated in STAG2-silenced cells in ‘STAG2 high’ versus ‘STAG2 low’ tumor samples. ( F , G ) Heatmaps displaying relative expression values (Z-score of FPKM) of genes significantly down-regulated in RT112 cells with sh1 (F) or sh2 (G) and in ‘STAG2 low’ versus ‘STAG2 high’ tumor samples.

Article Snippet: RT112 bladder cancer cells used at CNIO and Institut Curie were from the same original stock; HEK293T cells (transformed human embryonic kidney) were from the ATCC.

Techniques: Expressing, Control, Gene Expression

Journal: Nucleic Acids Research

Article Title: STAG2 loss-of-function affects short-range genomic contacts and modulates the basal-luminal transcriptional program of bladder cancer cells

doi: 10.1093/nar/gkab864

Figure Lengend Snippet: STAG2 silencing is accompanied by rewiring of DNA contacts. ( A ) MD plots depicting the fold change in interaction frequency of DNA contacts in control (shNT) versus STAG2-silenced cells in relation to the linear distance between interacting regions for chromosome 15. Interactions showing statistically significant differences (adjusted P < 0.05) are highlighted in red (gained) or blue (lost). ( B ) Scatter plot comparing changes in interaction frequency between cells transduced with sh1 versus cells transduced with sh2. Gained and lost interactions are highlighted in red and blue, respectively. ( C ) Interaction frequency of lost and gained contacts in shNT and STAG2-silenced cells. ( D ) Distance between peaks of lost and gained DNA contacts. Gained interactions span longer distances than lost interactions. ( E ) Top four scoring motifs enriched in the subsets of interactions defined in C. For a more extensive list of significantly enriched motifs, see . ( F ) Distribution of control, lost, and gained interactions over compartments and ( G ) chromatin states in RT112 cells (see ). ( H ) Left: chromatin contact network generated from the 20kb resolution Hi-C interaction map of control cells, showing in pink the nodes involved in contacts that are lost upon STAG2 silencing. Right: chromatin assortativity of nodes that lose contacts as the network is filtered eliminating contacts spanning short distances.

Article Snippet: RT112 bladder cancer cells used at CNIO and Institut Curie were from the same original stock; HEK293T cells (transformed human embryonic kidney) were from the ATCC.

Techniques: Control, Transduction, Generated, Hi-C