Fig. 4: VNTR6-1 affects proliferation and apoptosis in the bladder cancer cell line UMUC3.
a Analysis of real-time increase in cell counts (cell index) measured with xCELLigence over 283 h in UMUC3 cells. The WT and knockout cells (clone #2, starred samples in Supplementary Data 9) were cultured in a CS medium for 48 h, followed by a switch to fresh CS or full medium for 10 more days. Proliferation rates in response to culturing conditions were significantly lower in V6.1-KO compared to WT cells. The plots present the results of one of three independent experiments, with means ± SEM from n = 6 biological replicates. Statistical significance and β-values for differences in the cell index during the visually determined growth phase (gray highlighting between 50 and 183 h) were calculated using linear mixed-effects interaction models. The reference sample is labeled with a dotted circle; βint represents the change in growth rates between experimental groups. b, c Analysis of cell doublings in UMUC3 cells cultured in (b) CS medium or (c) full medium for four days, using the CFSE assay described in Supplementary Fig. 18c. Data presented are the results of one of three independent experiments, with means ± SD from n = 3 biological replicates. P-values in graphs are for two-way ANOVA using Tukey’s test. d, e Quantification of apoptosis in UMUC3 cells cultured for 48 h (d) with 10 μM cisplatin in CS medium or (e) in full medium, followed by Annexin V/PI staining and flow cytometry analysis to determine the percentage of apoptotic cells. Data presented are the results of one of three independent experiments, with means ± SD from n = 3 biological replicates (normalized to values of CS media and the WT groups). P-values in graphs were determined by one-way ANOVA using Dunnett’s test. f, g Gene set enrichment analysis (GSEA) for differential expression of genes involved in (f) pathways related to the downregulation of cellular processes for proliferation-promotion and (g) apoptosis-resistance, as identified by RNA-seq analysis comparing UMUC3 V6.1-KO (clone #3) to WT UMUC3 cells. Genes highlighted in blue are common to both pathways. The source data for all panels are provided in the Source Data file.
