FGFR inhibition with NVP-BGJ398 impairs MRT growth <i>in vivo</i>.

<p>(A) <i>In vivo</i> efficacy of NVP-BGJ398 in a primary mouse MRT allograft model. MRT bearing nude mice received vehicle or NVP-BGJ398 at 50 mg/kg body weight for 13 consecutive days and tumor volumes were monitored. Date are given as average with SEM (n = 4) and were compared by unpaired Student’s t test; *p<0.05. (B) Immunohistochemistry (IHC, upper panel) and immunoblot (lower panel) analysis of p-ERK1/2 levels in MRT allograft samples from mice treated with a single dose of vehicle or NVP-BGJ398 (50 mg/kg body weight) for 2 h. β-Tubulin expression was used to monitor equal loading.</p

SNF5 loss of function induces FGFR2 expression in human fibroblasts.

<p>(A) Effect of siRNA-mediated knockdown of SNF5 on FGFR2 expression in BJ cells. <i>SNF5</i> and <i>FGFR2</i> expression levels were analyzed by qRT-PCR at 72 h post siRNA transfection. Expression is shown as relative levels to cells transfected with non-targeting control siRNA and is given as average with SEM (n≥3). <i>E</i>xpression values were normalized to <i>GAPDH</i> mRNA copies. (B) Immunoblot analysis of FGFR2 expression upon knockdown of SNF5 in BJ cells as described in (A). β-Tubulin expression was used to monitor equal loading. (C) Effect of siRNA-mediated knockdown of BRG1 on FGFR2 expression in BJ cells as described in (A).</p

PTPN14 is a negative regulator of YAP.

<p>A) An SF268 cell line stably expressing the YAP-responsive MCAT_Luc reporter was transfected with two independent siRNAs against YAP and analysed in a Resazurin and luciferase assay 72 h after transfection. mRNA levels of YAP were determined by QRTPCR. Luciferase results are normalized based on the Resazurin results. All results are the average of 5 experiments ± STDEV. Statistical analysis was carried out with a 2-tailed paired t-test for each siRNA; * p<0.0001. B) An SF268 cell line stably expressing the YAP-responsive MCAT_Luc reporter was transduced with lentivirus encoding for dox-inducible PTPN14 expression. After pharmacological selection, luciferase expression was measured for both cell lines in the presence and absence of dox (upper panel). A Resazurin assay was carried out in parallel for each sample and used to normalize the luciferase readings. Results are shown as the average of three independent experiments ± STDEV. Statistical analysis was carried out with a 2-tailed paired t-test; * p<0.0001. RLU: relative luciferase units. PTPN14 expression achieved by dox and YAP levels in each sample was analyzed by Western blot (lower panel). Tubulin serves as loading control C) 293A cells were transduced with lentivirus encoding dox-inducible PTPN14 expression. YAP localization in control and PTPN14-expressing cell lines was analysed 72 hours post dox induction by IF at low density using confocal miroscopy. D) 293A cells were transduced with lentivirus encoding two independent dox-inducible shRNAs targeting PTPN14. The nuclear/cytoplasmic ratio of YAP was quantified at high density 72 hours post dox induction using a Cellomics automated imager with a conventional microscope, and expressed relative to the control shGFP (left upper panel). Results are shown as the average of 3 independent experiments ± STDEV. For each experiment, the average ratio was calculated from three wells per sample (10 images per well). Statistical analysis was carried out with a 2-tailed paired t-test; * p<0.001, ** p<0.05. Western blot analysis of PTPN14 levels, indicating the efficiency of each shRNA (left lower panel). Tubulin serves as a loading control. Confocal microscopy images of cells 72 hours post dox induction (right panel).</p

YAP-PTPN14 binding is mediated through the WW domain-PPxY motif interaction.

<p>A) 293A cells were transfected with WT GST-PTPN14 and the indicated V5-YAP constructs (WT and mutants). A V5 IP was carried out and blotted for GST to study the interaction of the various YAP mutants with WT PTPN14. Input lanes were loaded with 10% of the amount of lysate used for each IP and used to compare the expression levels of each construct. B–C) 293A cells were transfected with WT V5-YAP and the indicated GST-PTPN14 constructs (WT and mutants). A V5 IP was carried out and blotted for GST to study the interaction of the various PTPN14 mutants with WT YAP. Input lanes were loaded with 10% of the amount of lysate used for each IP and used to compare the expression levels of each construct. All lanes in (C) are from a single blot and exposure. D) An SF268 cell line stably expressing the YAP-responsive MCAT_Luc reporter was transduced with lentivirus encoding for the indicated dox-inducible PTPN14 expression. Luciferase expression of each cell line was analysed 72 hours post dox induction (left panel). A Resazurin assay was carried out in parallel for each sample and used to normalize the luciferase readings. PTPN14 expression levels achieved for each construct were analysed by Western blot (right panel; arrows indicate the WT PTPN14 protein and the truncated ΔPTP PTPN14 which migrates faster; all lanes from a single blot and exposure). Tubulin serves as loading control. Luciferase results are shown as the average of at least 3 independent experiments ± STDEV. Statistical analysis was carried out with a 2-tailed paired t-test; * p<0.05. E) The mRNA levels of the indicated YAP target genes were assessed in cells from (D) 72 hours post dox induction. Statistical analysis was carried out with a 2-tailed paired t-test; * p<0.001; **p<0.05, F) 293A cells were transduced with lentivirus encoding for the indicated dox-inducible PTPN14 expression. The nuclear/cytoplasmic YAP ratio was quantified at low density after 72 hours of dox induction using a Cellomics automated imager with a conventional microscope, and expressed relative to control (left panel). Results are shown as the average of three experiments ± STDEV. Statistical analysis was carried out with a 2-tailed paired t-test; * p<0.05. For each experiment, the average ratio was calculated from three wells per sample (10 images per well). PTPN14 expression levels were analysed by Western blot (right panel; arrows indicate the WT PTPN14 protein and the truncated ΔPTP PTPN14 which migrates faster; all lanes from a single blot and exposure). Tubulin serves as a loading control G) Confocal microscopy images of 293A cells from (F) generated 72 hours post dox induction. H) The mRNA levels of the indicated YAP target genes were assessed in cells from (F) 72 hours post dox induction. Statistical analysis was carried out with a 2-tailed paired t-test; * p<0.05.</p

MRT cell lines are sensitive to pharmacological FGFR inhibition.

<p>(A) Global compound selectivity analysis of MRT lines. Comparison of the three MRT lines A204, G401 and G402 versus other soft tissue cancer lines from the CCLE with regards to sensitivity to a panel of approximately 2000 compounds with defined target specificity. Shown are the top 5 enriched target in MRTs according to Activity Area and Inflection Point scores. FDR, false discovery rate. (B) Sensitivity towards the FGFR inhibitor NVP-BGJ398 among soft tissue cancer lines. A cut-off value of 500 nM was used to determine NVP-BGJ398 sensitivity based on Crossing Point values from high-throughput cell proliferation assays. (C) Immunoblot analysis of p-FRS2 and p-ERK1/2 in MRT lines treated with DMSO or NVP-BGJ398 for 40 min as indicated. Total ERK1/2 and β-Tubulin expression was used to monitor equal loading.</p

FGFR expression levels of the MRT cell lines A204, G401 and G402.

<p>(A) Scatter plot showing expression and copy number levels for <i>FGFR1</i> (left panel) and <i>FGFR2</i> (right panel) within the CCLE. MRT lines A204, G401 and G402 are indicated in red. (B) Quantitative RT-PCR (qRT-PCR) analysis of <i>FGFR1</i> and <i>FGFR2</i> mRNA expression in MRT cell lines and soft tissue cancer lines SKLMS1 and SKUT1. Expression values are given as average with standard errors of the mean (SEM) (n≥3) with respect to <i>GAPDH</i> mRNA levels (arbitrarily set as 100). (C) qRT-PCR and immunoblot analysis of SNF5-deficiency in MRT lines. SKLMS1 and SKUT1 cells were used as positive controls for SNF5 expression. <i>SNF5</i> mRNA expression is given as average with SEM (n≥3) with respect to <i>GAPDH</i> mRNA levels (arbitrarily set as 100). β-Tubulin expression was used to monitor equal loading.</p

PTPN14 is a YAP-binding protein.

<p>A) QPCR-based YAP copy number analysis. MCF-10A is used as a control cell line with no YAP amplification. B) Clonogenic survival assay of SF268 cells transduced with lentivirus encoding control or two independent dox-inducible shRNAs (upper panel). QRTPCR analysis of YAP mRNA levels (lower panel). C) Coomassie-stained gel used for MS analysis of YAP-binding proteins. YAP is indicated by the black arrow, PTPN14 by the black arrowhead and the AMOT family members by an asterisk. D) IP of endogenous YAP from SF268 cell lysates. All lanes are from a single blot and exposure. Asterisk indicates the position of the IgG heavy chains.</p

SNF5 is recruited to the FGFR2 promoter in BJ cells.

<p>(A) Schematic overview of the human FGFR2 promoter. Amplicons of primer pairs used for ChIP are shown as red squares and location is indicated relative to the transcriptional start site (TSS, +1). Exons are shown as blue boxes. (B) FGFR2 promoter occupancy by SNF5 in BJ cells. Fold enrichment from chromatin immunoprecititaions (ChIP) with a SNF5-specific antibody compared to an IgG control was analyzed by qPCR using the primer pairs indicated in (A). (C) Fold enrichment of the negative control locus IGX1A and the promoter region of the known SNF5 target gene CDKN1A. Fold enrichment is given as average with SEM (n≥3). Data were compared by unpaired Student’s t test with respect to the fold enrichment of the IGX1A locus; *p<0.05.</p

Down-regulation of PTPN14 enhances the oncogenic phenotype of YAP.

<p>A) MCF-10A cells were transduced with lentivirus encoding for YAP expression and after pharmacological selection transduced with lentivirus encoding for dox-inducible shRNAs targeting either PTPN14 or GFP (control) (two independent shRNAs targeting PTPN14). All six cell lines were subjected to an anoikis assay in low-attachment plates in the presence of dox for 48 hours. Results are shown as the average of three experiments ± STDEV. Statistical analysis was carried out with a 2-tailed paired t-test; * p<0.05, ** p = 0.05. B) Western blot analysis of cells from (A) 48 hours post dox induction. Tubulin serves as a loading control. C) Soft agar assay quantification of cells from (A). Results were obtained two weeks post dox induction and are the average of three experiments ± STDEV. D) Images of wells from (C) at the time of quantification. Scale: 1 mm.</p