Additional file 1: of Combined inhibition of BET proteins and class I HDACs synergistically induces apoptosis in urothelial carcinoma cell lines

Information on primer sequences and antibodies. Sequence information and amplicon sizes for qRT-PCR and ChIP qPCR primers as well as product information and dilution of applied antibodies are given. (PDF 271 kb

Multivariate analyses of the impact of lncRNA expression on patient survival.

<p>Multivariate analyses of the impact of lncRNA expression on patient survival.</p

Clinical and histopathological parameters of tissue set 1.

<p>Clinical and histopathological parameters of tissue set 1.</p

Univariate analyses of the impact of lncRNA expression on patient survival.

<p>Univariate analyses of the impact of lncRNA expression on patient survival.</p

Correlation between low <i>TUG1</i> expression in UC and Basal-Squamous-like subtype.

<p>(a) Waterfall plot representing <i>TUG1</i> expression in tumour samples of the extended TCGA tumor tissue set (n = 408). <i>TUG1</i> expression is given as z-scores. The reference for calculating z-scores of RSEM data in TCGA studies are diploid samples. Samples with high expression had a z-score above 0, specimen with low expression had negative values. (b) Boxplot representations comparing <i>TUG1</i> expression in muscle-invasive and non muscle-invasive tumours of set 1 and extended set 2. (c) Heat map clustering for <i>KRT5</i>, <i>KRT6</i>, <i>KRT14</i>, <i>FOXA1</i> and <i>GATA3</i> with <i>TUG1</i> expression in the TCGA cohort (expression levels are given as a colour gradient between dark blue (low expression) and red (high expression)). The tumour cluster with low <i>TUG1</i> expression is shown in the left panel, that with a high expression in the centre panel and tumours with an intermediate expression pattern cluster in the right panel. (d) Expression levels of <i>KRT5</i>, <i>KRT14</i>, <i>FOXA1</i> and <i>GATA3</i> in tumours from the TCGA cohort with a <i>TUG1</i> expression above median (<i>TUG1</i> high) and below median (<i>TUG1</i> low). P-values for difference between high and low <i>TUG1</i> expressing group were calculated by Mann-Whitney U-test (*p≤0.05, ***p≤0.001).</p

Association of differential lncRNA expression with molecular subtypes of UC.

<p>(a) TCGA expression data (z-scores) of the extended dataset (n = 408) was downloaded for genes defining molecular subtypes of MIBC according to Dadhania et al [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0176287#pone.0176287.ref028" target="_blank">28</a>] and samples were assigned to the indicated subtypes by hierarchical clustering analysis using Genesis 1.0. Expression data of lncRNA candidates was downloaded accordingly, data was not available for <i>linc-UBC1</i> and <i>ncRAN</i>. (b) Illustration of differential expression (log2 fold change) of lncRNA candidates between molecular subclasses of NMIBC based on data published by Hedegaard et al (see reference for <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0176287#pone.0176287.s009" target="_blank">S3 Table</a>) [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0176287#pone.0176287.ref029" target="_blank">29</a>].</p

Additional file 2: Figure S2. of Checkpoint kinase inhibitor AZD7762 strongly sensitises urothelial carcinoma cells to gemcitabine

Viability in UCCs after combined treatments with cisplatin, romidepsin or givinostat, and AZD7762. a Relative cell viability in the T24 and RT-112 cell lines was measured by MTT assay (mean ± SD, n = 4) after cells were treated for 48 h either with cisplatin, romidepsin or givinostat combined with AZD7762. b Western blot analysis of S345 CHK1 after treatments with gemcitabine (10 nM), cisplatin (5 μM), romidepsin (4 nM) and givinostat (0.5 μM) in T24 cells (24 and 48 h). As loading control, GAPDH was stained. (TIF 214 kb

lncRNA expression data for tumour and benign tissues from tissue set 1 and 2.

<p>Boxplot representations of lncRNA expression in set 1 (RT-qPCR, relative expression to geometric mean of reference genes <i>SDHA</i> and <i>TBP</i>) and set 2 (RNA-Seq in the TCGA bladder cancer cohort, expression as log2 RPMK, data obtained from the TANRIC database). P-values for difference between control (N) and tumour (T) samples were calculated by Mann-Whitney U-test.</p

Additional file 1: Figure S1. of Checkpoint kinase inhibitor AZD7762 strongly sensitises urothelial carcinoma cells to gemcitabine

Viability in UCCs after sequential treatment with AZD7762 and gemcitabine. Relative cell viability in several UCCs was measured by MTT assay (mean ± SD, n = 4) after cells were sequentially treated (pretreated with AZD7762 for 24 h and then incubated with gemcitabine for 48 h). (TIF 142 kb

Additional file 3: Figure S3. of Checkpoint kinase inhibitor AZD7762 strongly sensitises urothelial carcinoma cells to gemcitabine

a, b Immunofluorescence staining of γH2A.X (green), 53-BP1 (red), and nuclei staining with DAPI (blue) in VM-CUB1 (a) and RT-112 (b) cells after the indicated treatments. Scale bar = 50 μm. (TIF 1728 kb