Expression status of genes encoding therapeutic targets in this study.

<p>At least 18 genes encoded direct or functional targets of signal transduction that have inhibitory agents approved by the FDA or in clinical trials. (A) Absolute expression values (FPKM), mutations and copy numbers for each of the indicated genes is shown in the bar graph. (B) Comparison of protein expression of selected target genes studied here. Protein expression levels were determined by IHC in HER2, HER3, FGFR3 and SRC, and shown in-~+++. The expression of EphB4 was determined by immunofluorescence staining and shown as positive or negative. N/T: not tested. The expression data for therapeutic targets is available in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0134346#pone.0134346.s010" target="_blank">S7</a>–<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0134346#pone.0134346.s012" target="_blank">S9</a><b>Tables</b>. (C) Validation of target protein expression with IHC. Only selected imagings were shown. PDX BL0440 was stained 3+ for <i>HER2</i> with chicken wire pattern of positive staining at cell membrane while BL0515 was stained negative. BL0293 was stained positive for FGFR3 both on cell membrane and cytoplasm. BL0269 was stained positive for Src on cell membrane, but more on nucleus. (D) Immunofluorescence staining of tissue microarray for EphB4 of BL0293. Both patient specimen from cystectomy (left) and PDX were stained positive for EphB4.</p

Conservation of genomic variants between patient bladder cancer specimens and PDXs.

<p>WES analysis was performed on genomic DNA samples isolated from parental patient tumors and engrafted PDX P0 tumors. WES data was filtered for variants occurring at a frequency of >0.5 and then compared between samples on the basis of variant types. The number and type of variants occurring in each parental tumor and in the P0 PDX tumor were quantified and depicted as percentage of conservation in the graph. For all variants, 91.8% and 97.6% were conserved in BL0429 and BL0440, respectively.</p

Table S1 from The Phosphatidylinositol 3-Kinase Pathway as a Potential Therapeutic Target in Bladder Cancer

The mutation status and absolute IC50 of bladder cancer cells</p

Table S2 from The Phosphatidylinositol 3-Kinase Pathway as a Potential Therapeutic Target in Bladder Cancer

Combination index of pictilisib and other drugs in TCCSUP cells</p

Figure S4 from The Phosphatidylinositol 3-Kinase Pathway as a Potential Therapeutic Target in Bladder Cancer

Ki67 and cleaved caspase 3 expression in BL0440 tumors</p

Additional file 2: of Genomic data analysis workflows for tumors from patient-derived xenografts (PDXs): challenges and guidelines

Supplementary Tables S1, S13 and S14. (XLSX 94 kb

Expression levels and mutation status of tumor suppressor pathway genes.

<p>(A) Integrated analysis of <i>mRNA Expression</i>, <i>Mutations</i>, and <i>Copy Number</i> was performed for genes in the <i>TP53</i> and <i>RB1</i> tumor suppressor pathways. Gene-level expression (FPKM) values for pathway member genes are presented and relative gene expression for each gene across the panel of PDX models is indicated by the heatmap (green = lower than the median, red = greater than the median). Mutations (amino acid changes) in <i>TP53</i> and <i>RB1</i> are indicated. Gene copy numbers are presented, and variants indicated as losses (<i>i</i>.<i>e</i>., < 2) or gains (<i>i</i>.<i>e</i>., > 2) shown by darker shades of red and green, respectively. (B) Expression levels (FPKM) of tumor suppressor pathway genes in each PDX are shown in the bar graph.</p

Additional file 1: of Genomic data analysis workflows for tumors from patient-derived xenografts (PDXs): challenges and guidelines

Supplementary Texts S1-S6, Supplementary Figures S1-S15, Supplementary Tables S2-S12. (DOCX 40439 kb

Figure S5 from The Phosphatidylinositol 3-Kinase Pathway as a Potential Therapeutic Target in Bladder Cancer

p-p70S6K, pS6 and p-ERK expression in bladder cancer cells treated with pictilisib</p

Figure S1 from The Phosphatidylinositol 3-Kinase Pathway as a Potential Therapeutic Target in Bladder Cancer

Cell cycle analysis, Flow cytometric analysis and p-AKT expression in TCCSUP cells treated with pictilisib</p