human bladder cancer cell lines ku  (DSMZ)

Journal: bioRxiv

Article Title: ButterflyVI: enabling high-throughput variant interpretation and biomarker discovery with functional genomics

doi: 10.64898/2026.01.20.700339

Figure Lengend Snippet: A , Summary plot of ElasticNet biomarkers of druggable genes. Each point shows a biomarker shared between CRISPR and RNAi datasets that was selected at least 5 times out of 10 ElasticNet runs, had a mean coefficient greater in absolute value than .05 and exhibit the same effect direction in both datasets. A negative weighted mean ElasticNet score indicates sensitivity, whereas a positive score indicates resistance. B–D. MDM2 ( B ) and MDM4 ( C ) dependency scores, and MDM2 mRNA expression ( D ) in cell lines classified by RPL5 status: wild type (or carrying a neutral mutation) versus carrying a functional mutation (as defined by OncoKB or ButterflyVI). E , Relative expression of RPL5 in cells transfected with control siRNA (siCtrl), GAPDH siRNA (siGAPDH), or RPL5 siRNA (siRPL5). Data are presented as the mean ± standard error of the mean (SEM). Differences between groups were evaluated using an unpaired Student’s t-test. The level of statistical significance is indicated by asterisks: ns, not significant (P > 0.05); ** P ≤ 0.01; * P ≤ 0.05. F , Cellular viability in response to DMSO (control) or Nutlin-3a treatment at varying doses in RT-4 (left) and KU-19-19 (right) models. Cellular viability is expressed as a percentage. Each point represents a single experimental data point (replicate). The colored lines indicate the mean viability for each knockdown condition (siCtrl, siGAPDH, siRPL5). The shaded bands represent the standard error of the mean (SEM).

Article Snippet: The human bladder cancer cell lines KU-19-19 and RT-4 (ACC 395 and ACC 412; DSMZ) were cultured in RPMI 1640, GlutaMAX (Gibco, 61870010) supplemented with 10% FBS (Thermo Fisher Scientific, A5256701) and 1% Penicillin-Streptomycin (Thermo Fisher Scientific, 15070063) at 37 °C in a humidified atmosphere with 5% CO2.

Techniques: Biomarker Discovery, CRISPR, Expressing, Mutagenesis, Functional Assay, Transfection, Control, Knockdown

Journal: bioRxiv

Article Title: ButterflyVI: enabling high-throughput variant interpretation and biomarker discovery with functional genomics

doi: 10.64898/2026.01.20.700339

Figure Lengend Snippet: A-B , Dose response curves to control DMSO ( A ) or Nutlin-3a ( B ) treatment on RT-4 and KU-19-19 models. Cellular viability is expressed as a percentage relative to the untreated control. Each data point represents a single experimental data point (replicate). The blue line shows the fit of the four-parameter log-logistic model. The light blue shaded band represents the 95% confidence interval for the model. The vertical red dashed line indicates the calculated IC50, and the pink shaded band represents the 95% confidence interval for the IC50 value. The specific IC50 value and its confidence interval are indicated on the graph. C , Relative expression of GAPDH in cells transfected with control siRNA (siCtrl), GAPDH siRNA (siGAPDH), or RPL5 siRNA (siRPL5). Data are presented as the mean ± standard error of the mean (SEM). Differences between groups were evaluated using an unpaired Student’s t-test. The level of statistical significance is indicated by asterisks: ns, not significant (P > 0.05); ** P ≤ 0.01; * P ≤ 0.05.

Article Snippet: The human bladder cancer cell lines KU-19-19 and RT-4 (ACC 395 and ACC 412; DSMZ) were cultured in RPMI 1640, GlutaMAX (Gibco, 61870010) supplemented with 10% FBS (Thermo Fisher Scientific, A5256701) and 1% Penicillin-Streptomycin (Thermo Fisher Scientific, 15070063) at 37 °C in a humidified atmosphere with 5% CO2.

Techniques: Control, Expressing, Transfection

Journal: Bladder Cancer

Article Title: Impact of DNA repair deficiency on sensitivity to antibody-drug conjugate (ADC) payloads in bladder cancer *

doi: 10.1177/23523735251317865

Figure Lengend Snippet: Homologous recombination (HR) deficiency confers cisplatin and PARP inhibitor sensitivity in bladder cancer cells. (a) Immunoblot showing siRNA-mediated depletion of BRCA2 protein in KU19-19 and J82 bladder cancer cell lines. Vinculin is shown as a loading control. (b) Immunofluorescence (IF) microscopy shows loss of radiation-induced Rad51 foci formation in BRCA2-depleted compared to BRCA2-intact bladder cancer cells. (c) Cell viability assays demonstrate increased sensitivity to cisplatin following BRCA2 depletion in bladder cancer cell lines. (d) Cell viability assays demonstrate increased sensitivity to PARP inhibitors olaparib and talazoparib in bladder cancer cell lines. kDa, kilodalton. NTC, non-targeting control. Gy, Gray. MFI, mean fluorescence intensity. *p < 0.01 (IC50 values). Error bars represent standard deviation of data collected from assays performed in triplicate (panel B) or quadruplicate (panels C, D).

Article Snippet: Human bladder cancer cell lines J82 and KU19-19 were purchased from ATCC and DSMZ, respectively.

Techniques: Homologous Recombination, Western Blot, Control, Immunofluorescence, Microscopy, Fluorescence, Standard Deviation

Journal: Bladder Cancer

Article Title: Impact of DNA repair deficiency on sensitivity to antibody-drug conjugate (ADC) payloads in bladder cancer *

doi: 10.1177/23523735251317865

Figure Lengend Snippet: Combined activity of MMAE and SN-38 with DNA repair inhibitors. (a) Cytotoxic activity of combining MMAE or SN-38 with ATR inhibition (berzosertib, BERZ), USP1 inhibition (ML323), or PARP inhibition (Olaparib, OLA; talazoparib, TALA) in KU19-19 (top graph) and J82 (bottom graph) bladder cancer cell lines with versus without HR deficiency conferred by BRCA2 depletion. (b) Cytotoxic activity of combining MMAE or SN-38 with ATR inhibition (berzosertib, BERZ), USP1 inhibition (ML323), or PARP inhibition (Olaparib, OLA; talazoparib, TALA) in NER-proficient ( ERCC2 WT) KU19-19 cells versus NER-deficient ( ERCC2 -mutant) KE182 cells (top graph) or NER-proficient (ERCC4 WT) H460 cells versus NER-deficient (ERCC4-deleted) H460 cells (bottom graph). Combination activity is quantified by the combination index (CI, see Methods) with positive log10(CI) values indicative of antagonism and negative log10(CI) values indicative of synergism. HRP, homologous recombination proficient (WT BRCA2); HRD, homologous recombination deficient (BRCA2 depleted); NERP, nucleotide excision repair proficient; NERD, nucleotide excision repair deficient. Error bars represent standard deviation of data collected from assays performed in quadruplicate.

Article Snippet: Human bladder cancer cell lines J82 and KU19-19 were purchased from ATCC and DSMZ, respectively.

Techniques: Activity Assay, Inhibition, Mutagenesis, Homologous Recombination, Standard Deviation

Journal: Cancer research

Article Title: Development of novel aptamer-based targeted chemotherapy for bladder cancer

doi: 10.1158/0008-5472.CAN-21-2691

Figure Lengend Snippet: ( A ) Selection scheme of chemically modified RNA aptamers that can internalize into T24 human bladder cancer cells but not SV-huc-1 normal bladder urothelial cells. R: purine. Y: pyrimidine. ( B ) Predicted secondary structure of aptamer B1 using sfold. ( C ) Binding curve of aptamer B1 with T24 cells. An all-DNA version of B1 and a B1-derived scrambled 35-nt sequence were used as control. Representative data of three independent experiments are shown. ( D ) Confocal microscopy analysis showed that aptamer B1 internalization is cell type-specific. T24 and KU-7 are two bladder cancer cell lines, SV-huc-1 is a normal bladder urothelial cell line. Scale bars: 40 μm. Representative data of three independent experiments are shown. (E) Comparison of the binding curves of aptamer B1 with primary human tumor cells and normal urothelial cells generated from surgical specimens harvested from a NMIBC patient. Freshly collected bladder tumor tissue or normal para-tumor urothelium tissue was digested into single cells, incubated with Cy5.5-labeled aptamer B1 for 1 h and analyzed with flow cytometry. Raw data are shown in Supplementary Fig. 3B .

Article Snippet: Human bladder cancer cell line KU-7 (RRID: CVCL_4714) engineered to stably express firefly luciferase and green fluorescent protein (GFP) was purchased from Caliper Life Sciences (Hopkinton, MA).

Techniques: Selection, Modification, Binding Assay, Derivative Assay, Sequencing, Control, Confocal Microscopy, Comparison, Generated, Incubation, Labeling, Flow Cytometry

Journal: Cancer research

Article Title: Development of novel aptamer-based targeted chemotherapy for bladder cancer

doi: 10.1158/0008-5472.CAN-21-2691

Figure Lengend Snippet: ( A ) Characterization of the loading of epirubicin into the nanotrain. The intrinsic fluorescence of EPI decreased with increasing equivalents of nanotrain boxcar component strands, as it was quenched upon intercalation into DNA duplex. ( B ) Stability of the EPI-loaded nanotrain in PBS was evaluated by dialysis. Free EPI molecules diffused across the dialysis membrane and resulted in a high fluorescence intensity in the exterior chamber. Interaction of EPI with nanotrain (NT-EPI) restricted its diffusion. (C) Release of EPI in the presence of DNase. Intercalation of EPI into boxcar DNA duplex of NT resulted in fluorescence quenching. Treatment with DNase Ⅰ degraded dsDNA and restored the intrinsic fluorescence of EPI. ( D ) Confocal microscope images showing targeted delivery of NT-EPI into T24 and KU-7 bladder cancer cells. Cells were treated with free EPI or NT-EPI for 1 h. The nuclei were stained with DAPI. Scale bar: 40 μm. ( E and F ) Aptamer B1 NT-EPI exhibits similar cytotoxicity to that of free EPI against T24 (E) and KU-7 (F) bladder cancer cells. ( G ) Aptamer B1 NT-EPI was much less toxic to SV-huc-1 cells compared with free EPI. Cells were treated for 48 h and cell viability was measured by MTT assay. Data are mean ± SD. Representative data of three independent experiments shown.

Article Snippet: Human bladder cancer cell line KU-7 (RRID: CVCL_4714) engineered to stably express firefly luciferase and green fluorescent protein (GFP) was purchased from Caliper Life Sciences (Hopkinton, MA).

Techniques: Stable Transfection, Fluorescence, Membrane, Diffusion-based Assay, Microscopy, Staining, MTT Assay

Journal: Cancer research

Article Title: Development of novel aptamer-based targeted chemotherapy for bladder cancer

doi: 10.1158/0008-5472.CAN-21-2691

Figure Lengend Snippet: ( A ) Schematic of orthotopic xenograft model establishment and treatment regimen. Luciferase-labeled KU-7 human bladder cancer cells were implanted into the bladder of nude mice. Fourteen days later, mice with positive bladder fluorescence signal were randomly divided into three groups and treated with intravesical instillation of PBS, free EPI (0.4 mg/ml, 50 μl/instillation) or aptamer B1 NT-EPI (equal molar EPI molecules). ( B ) Luminescence imaging and ( C ) quantitative analysis of tumors in mouse bladder at the end of treatment. Data are mean ± SD (n = 9 mice/group). ** P < 0.01. ( D ) Representative H&E staining images of bladder tumor sections from each group. Sections of whole bladder was shown in the middle (scale bar: 500 μm), with magnification on both sides (scale bar: 100 μm). The NT-EPI group showed much less cystitis compared to free EPI, as indicated by reduced infiltration of inflammatory cells and interstitial edema, suggesting reduced damage to normal urothelium. Quantification of all nine mice in each group are summarized in Supplementary Fig. 6 .

Article Snippet: Human bladder cancer cell line KU-7 (RRID: CVCL_4714) engineered to stably express firefly luciferase and green fluorescent protein (GFP) was purchased from Caliper Life Sciences (Hopkinton, MA).

Techniques: Inhibition, In Vivo, Luciferase, Labeling, Fluorescence, Imaging, Staining