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Rhabdomyosarcoma (RMS) is the most common soft tissue malignancy in childhood and adolescence. Patients with the most aggressive histological variant have an unfavorable prognosis due to a high metastasis incidence. Lysyl oxidase-like 2 (LOXL2) is a lysyl oxidase, member of a family of extracellular matrix (ECM) crosslinking enzymes that recently have emerged as important regulators of tumor progression and metastasis. We report that LOXL2 is overexpressed in RMS, suggesting a potential role for LOXL2 in RMS oncogenic progression. Consistently, transient and stable LOXL2 knockdown decreased cell migratory and invasive capabilities in two ARMS cell lines. Furthermore, introduction of LOXL2 in RMS non-expressing cells using wild type or mutated (catalytically inactive) constructs resulted in increased cell migration, cell invasion and number and incidence of spontaneous lung metastasis in vivo, independently of its catalytic activity. To further study the molecular mechanism associated with LOXL2 expression, a pull-down assay on LOXL2-transfected cells was performed and analyzed by mass spectrometry. The intermediated filament protein vimentin was validated as a LOXL2-interactor. Thus, our results suggest an oncogenic role of LOXL2 in RMS by regulating cytoskeleton dynamics and cell motility capabilities., OMT: Fundación Alba Pérez lucha contra el cáncer infantil. Instituto de Salud Carlos III (CES12/021; PI11/00038; PI15/00035; AC14/00026) and EU's Fondo Europeo de Desarrollo Regional (FEDER) “Una manera de hacer Europa/A way to achieve Europe.” CERCA Program/Generalitat de Catalunya (2017SGR332). OA-R, DH-M: Fundación Científica de la AECC. SG-M, SR-V: Fundación Alba Pérez lucha contra el cáncer infantil. PM: European Union’s Horizon 2020 research and innovation program under Marie Sklodowska-Curie grant agreement ITN: 766214 – ESR 4.

Ewing sarcoma (ES) is the second most common bone malignancy affecting children and young adults with poor prognosis due to high metastasis incidence. Our group previously described that EphA2, a tyrosine kinase receptor, promotes angiogenesis in Ewing sarcoma (ES) cells via ligand-dependent signaling. Now we wanted to explore EphA2 ligand-independent activity, controlled upon phosphorylation at S897 (p-EphA2S897 ), as it has been linked to metastasis in several malignancies. By reverse genetic engineering we explored the phenotypic changes after EphA2 removal or reintroduction. Gene expression microarray was used to identify key players in EphA2 signaling. Mice were employed to reproduce metastatic processes from orthotopically implanted engineered cells. We established a correlation between ES cells aggressiveness and p-EphA2S897 . Moreover, stable overexpression of EphA2 in low EphA2 expression ES cells enhanced proliferation and migration, but not a non-phosphorylable mutant (S987A). Consistently, silencing of EphA2 reduced tumorigenicity, migration and invasion in vitro, and lung metastasis incidence in experimental and spontaneous metastasis assays in vivo. A gene expression microarray revealed the implication of EphA2 in cell signaling, cellular movement and survival. ADAM19 knockdown by siRNA technology strongly reproduced the negative effects on cell migration observed after EphA2 silencing. Altogether, our results suggest that p-EphA2S897 correlates with aggressiveness in ES, so blocking its function may be a promising treatment.

During the last decades, the knowledge of cell death mechanisms involved in anticancer therapy has grown exponentially. However, in many studies, cell death is still described in an incomplete manner. The frequent use of indirect proliferation assays, unspecific probes, or bulk analyses leads too often to misunderstandings regarding cell death events. There is a trend to focus on molecular or genetic regulations of cell demise without a proper characterization of the phenotype that is the object of this study. Sometimes, cancer researchers can feel overwhelmed or confused when faced with such a corpus of detailed insights, nomenclature rules, and debates about the accuracy of a particular probe or assay. On the basis of the information available, we propose a simple guide to distinguish forms of cell death in experimental settings using cancer cell lines. Cancer Res; 75(6); 913–7. ©2015 AACR.

Epigenetic modifications have been shown to be important in developmental tumors as Ewing sarcoma. We profiled the DNA methylation status of 15 primary tumors, 7 cell lines, 10 healthy tissues and 4 human mesenchymal stem cells lines samples using the Infinium Human Methylation 450K. Differential methylation analysis between Ewing sarcoma and reference samples revealed 1166 hypermethylated and 864 hypomethylated CpG sites (Bonferroni p < 0.05, delta-beta-value with absolute difference of >0.20) corresponding to 392 and 470 genes respectively. Gene Ontology analysis of genes differentially methylated in Ewing sarcoma samples showed a significant enrichment of developmental genes. Membrane and cell signal genes were also enriched, among those, 11 were related to caveola formation. We identified differential hypermethylation of CpGs located in the body and S-Shore of the PTRF gene in Ewing sarcoma that correlated with its repressed transcriptional state. Reintroduction of PTRF/Cavin-1 in Ewing sarcoma cells revealed a role of this protein as a tumor suppressor. Restoration of caveolae in the membrane of Ewing sarcoma cells, by exogenously reintroducing PTRF, disrupts the MDM2/p53 complex, which consequently results in the activation of p53 and the induction of apoptosis. (C) 2016 Elsevier Ireland Ltd. All rights reserved.

Ewing sarcoma (ES) and alveolar rhabdomyosarcoma (ARMS) are pediatric sarcomas characterized by tumor-specific translocations. Besides acting as a direct modulator of transcription, fusion proteins appear to exert its oncogenic functions by epigenetic modifications on the transcriptome. Therefore, the identification of specific DNA methylation markers would be helpful for understanding their pathogenetic mechanism as well as for developing new therapeutic strategies. By using the Illumina Infinium HumanMethylation450 we have analyzed the methylome of ES and ARMS tumors and cell lines. ES and ARMS samples showed, among other epigenetic alterations, differential hypermethylation in the promoter of MIR10A-5p, thus suggesting an inhibition of its expression. Expression of MIR10A-5p is effectively low in ES and ARMS cell lines and patient samples and the treatment with the epigenetic modifier 5-aza restores its expression. MIR10A-5p stable overexpression in two ES (A673 and TC252) and two ARMS (Rh4 and RMS13) cell lines reduces proliferation, diminishes clonogenic growth, and decreases cellular migration. Cell death induced by MIR10A-5p reintroduction is only achieved in the p53wt ES cell line TC252. Proteomic profile of A673 MIR10A-5p cells is altered as assessed by iTRAQ. Protein kinase CRKL is one of the proteins downregulated due to MIR10A-5p reintroduction. Indeed, CRKL expression is also reduced in the other three MIR10A-5p stable overexpression models. Doxycycline-induced silencing of CRKL in ARMS cell line Rh30 provokes cell growth reduction in vitro and in vivo, G0/G1 arrest, and a decrease in the clonogenic capacity (Yeung CL et al., 2013). Interestingly, the migratory ability of Rh30 and A673 CRKL-silenced cells is also impaired. Thus, our results uncover MIR10A-5p as a putative tumor suppressor in ES and ARMS, suggesting a link between MIR10A-5p and CRKL. Further characterization of the oncogenic role of CRKL and the molecular mechanisms associated to MIR10A-5p tumor-suppressor activities in ES and ARMS is ongoing. Citation Format: David Herrero-Martin, Santiago Rello-Varona, Silvia Garcia-Monclus, Juan Huertas-Martinez, Olga Almacellas-Rabaiget, Lee J. Helman, Oscar M. Tirado. Tumor-suppressive activities associated to MIR10A-5p expression in developmental sarcomas [abstract]. In: Proceedings of the AACR Conference on Advances in Sarcomas: From Basic Science to Clinical Translation; May 16-19, 2017; Philadelphia, PA. Philadelphia (PA): AACR; Clin Cancer Res 2018;24(2_Suppl):Abstract nr B19.

Cell death can occur through different mechanisms, defined by their nature and physiological implications. Correct assessment of cell death is crucial for cancer therapy success. Sarcomas are a large and diverse group of neoplasias from mesenchymal origin. Among cell death types, apoptosis is by far the most studied in sarcomas. Albeit very promising in other fields, regulated necrosis and other cell death circumstances (as so-called "autophagic cell death" or "mitotic catastrophe") have not been yet properly addressed in sarcomas. Cell death is usually quantified in sarcomas by unspecific assays and in most cases the precise sequence of events remains poorly characterized. In this review, our main objective is to put into context the most recent sarcoma cell death findings in the more general landscape of different cell death modalities.

Producción Científica, Recent preclinical evidence has suggested that Ewing Sarcoma (ES) bearing EWSR1-ETS fusions could be particularly sensitive to PARP inhibitors (PARPinh) in combination with DNA damage repair (DDR) agents. Trabectedin is an antitumoral agent that modulates EWSR1-FLI1 transcriptional functions, causing DNA damage. Interestingly, PARP1 is also a transcriptional regulator of EWSR1-FLI1, and PARPinh disrupts the DDR machinery. Thus, given the impact and apparent specificity of both agents with regard to the DNA damage/DDR system and EWSR1-FLI1 activity in ES, we decided to explore the activity of combining PARPinh and Trabectedin in in vitro and in vivo experiments. The combination of Olaparib and Trabectedin was found to be highly synergistic, inhibiting cell proliferation, inducing apoptosis, and the accumulation of G2/M. The drug combination also enhanced γH2AX intranuclear accumulation as a result of DNA damage induction, DNA fragmentation and global DDR deregulation, while EWSR1-FLI1 target expression remained unaffected. The effect of the drug combination was corroborated in a mouse xenograft model of ES and, more importantly, in two ES patient-derived xenograft (PDX) models in which the tumors showed complete regression. In conclusion, the combination of the two agents leads to a biologically significant deregulation of the DDR machinery that elicits relevant antitumor activity in preclinical models and might represent a promising therapeutic tool that should be further explored for translation to the clinical setting., Ministerio de Economía y Competitividad (PI081828), Ministerio de Economía y Competitividad (RD06/0020/0059 ), Ministerio de Economía y Competitividad (RD12/0036/0017), Ministerio de Economía y Competitividad (PT13/0010/0056)

Pediatric sarcomas are a heterogeneous group of bone and soft tissue malignancies affecting children and young adults. One of the most important prognostic factors of those diseases is the presence of metastasis at diagnosis. In that context, we have developed a novel orthotopic model which consists in injecting Ewing Sarcoma (ES) or Rhabdomyosarcoma (RMS) tumor cells at the gastrocnemius muscle of mice and extracting the tumor at a of 10 mm x 13 mm volume. After surgery, animals maintain a complete functional extremity and can live until lung metastasis detection (about 60 days post-injection). Moreover, we have validated the suitability of the model with an Ewing Sarcoma EphA2-low expression cell line. Epha2 is a tyrosine kinase receptor that has been found overexpressed in a wide variety of tumors and correlated with malignant phenotype. In this study we report that EphA2 receptor is phosphorylated at S897 in a panel of ES cell lines, which is related to the oncogenic properties of the receptor. Stable silencing of EphA2 in two different ES cell lines resulted in a decrease in the clonogenic, proliferation, migration and invasion capacity in vitro. Moreover, we performed an experimental metastasis assay, injecting tumor cells through the tail vain of mice and observed a reduction in the lung metastasis incidence in EphA2 silenced cells. We then used this new orthotopic metastasis model to validate the impairment in the invasion capacity of EphA2 silenced cells and confirm the decrease in lung metastasis incidence, indicating an oncogenic role for EphA2 in ES. This novel orthotopic metastasis model is a valuable tool both for the study of spontaneous metastasis and also for evaluating therapeutic index in the onset of metastasis, which can also be applied to the study of other pedriatric sarcomas. Citation Format: Silvia Garcia Monclús, Juan Huertas Martínez, Laura Lagares Tena, Santiago Rello Varona, Olga Almacellas Rabaiget, David Herrero Martin, Roser López Alemany, Oscar Martinez Tirado. A novel orthotopic mouse model in sarcomas [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1929. doi:10.1158/1538-7445.AM2017-1929

MicroRNAs (miRNA) serve to fine-tune gene expression and thus play an important regulatory role in tissue specific gene networks. The identification and validation of miRNA target genes in a given tissue still poses a significant problem since the presence of a seed sequence in the 3′UTR of an mRNA and its expression modulation upon forced ectopic expression of the miRNA do not reliably predict regulation under physiological conditions. The chimeric oncoprotein EWS-FLI1 is the driving pathogenic force in ES. Recently, we reported on the EWS-FLI1 microRNA (miRNA) signature based on knockdown experiments in ES cell lines and on differential expression in primary tumors versus mesenchymal stem cells. Comparison of both datasets revealed the miR17-92 cluster to be the top EWS-FLI1 activated miRNA, which is one of the most potent oncogenic miRNAs. The whole cluster is among the small number of miRNAs down-regulated upon knockdown of EWS-FLI1 in multiple ES cell lines. We now report the use of a combination of AGO2 pull-down experiments by PAR-CLIP - to enrich and sequence RISC-associated RNAs - and of RNAseq upon miRNA depletion by ectopic sponge expression to identify the targetome of miR17-92 in Ewing sarcoma (ES) cells We found a significant enrichment of PAR-CLIP hits for members of the miR-17-92 cluster in the 3′UTRs of genes up-regulated in response to mir-17-92 but not miR9 and 10b specific sponge expression. Among them, we consistently identified known (i.e. CTGF, MXD1, CYLD1) and a multitude of so far unknown targets of the oncomir-1 cluster in ES in three PAR-CLIP experiments. Interestingly, approximately a quarter of these genes annotate to the TGFB/BMP pathway, the majority mapping downstream of SMAD signaling. Gene reporter assays using 3’UTRs of select novel candidate genes showed enhancement of luciferase activity upon transfection of a sponge specific to miR-17-92 and 20a, but not to unrelated miR-9 and 10b. Site directed mutagenesis of seed sequences in these 3’UTR confirmed the direct regulation of these genes by miR17-92. Current research focuses on the functional validation of TGFB pathway modulation by miR17-92. This study provides a paradigmatic approach to the comprehensive definition of the targetome for a defined group of miRNAs under physiological conditions. This study was supported by the 7th framework program of the European Commission (FP7-259348, “ASSET”) and the Austrian Science Fund FWF (24708-B21) Citation Format: Raphaela Schwentner, Maximilian Kauer, David Herrero-Martin, Heinrich Kovar. The role of miR17-92 in the miRegulatory landscape of Ewing sarcoma. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1918.

Pediatric sarcomas represent a diverse group of rare bone and soft tissue malignancies. Although the molecular mechanisms that propel the development of these cancers are not well understood, identification of tumor-specific translocations in many sarcomas has provided significant insight into their tumorigenesis. Besides of acting as a direct modulator of transcription, fusion proteins appear to exert its oncogenic functions by epigenetic modifications on the transcriptome. Aberrant DNA methylations are thought to be closely related to the development of cancer. Therefore, the identification of specific DNA methylation markers would be helpful for understanding the pathogenetic mechanism as well as for developing new therapeutic strategies. By using the Illumina Infinium HumanMethylation450, we analyze the methylome of Ewing Sarcoma (ES) and Rhabdomyosarcoma (RMS) tumors and cell lines as developmental tumors in comparison to a significant number of normal tissues and cells as a reference. Our results uncover one miRNA with tumor suppressive activities in both tumor entities. Molecular mechanisms associated to these activities are further explored. Citation Format: David Herrero-Martin, Franck Court, Santiago Rello-Varona, Miguel Sainz-Jaspeado, Raquel Buj, Sebastian Moran, Silvia Garcia-Monclus, Juan Huertas-Martinez, Jaume Mora, Miquel Angel Peinado, Javier Alonso, Enrique de Alava, Dave Monk, Manel Esteller, Oscar M. Tirado. Epigenomic profiling identifies NCRNAs as novel tumor suppressors in developmental tumors. [abstract]. In: Proceedings of the AACR Special Conference on Noncoding RNAs and Cancer: Mechanisms to Medicines ; 2015 Dec 4-7; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2016;76(6 Suppl):Abstract nr A40.

We would like to thank Brown and colleagues ([1][1]) for their effort and their valuable comments on our review about cell death mechanisms in anticancer therapy. We understand their view on assessing the persistence of clonogenic survival from quantification of death records in anticancer research

MicroRNAs (miRNA) serve to fine-tune gene expression and thus play an important regulatory role in tissue specific gene networks. The identification and validation of miRNA target genes in a given tissue still poses a significant problem, since the presence of a seed sequence in the 3´UTR of an mRNA and its expression modulation upon forced ectopic expression of the miRNA do not reliably predict regulation under physiological conditions. Here, we used a combination of AGO2 pull-down experiments by PAR-CLIP - to enrich and sequence RISC-associated RNAs - and of RNAseq upon miRNA depletion by ectopic sponge expression, to identify the targetome of miR17-92 in Ewing sarcoma (ES) cells. The chimeric oncoprotein EWS-FLI1 is the driving pathogenic force in ES. As an aberrant ETS transcription factor it directly deregulates a multitude of genes related to proliferation control and differentiation. Recently, we reported on the EWS-FLI1 microRNA (miRNA) signature based on knockdown experiments in ES cell lines and on differential expression in primary tumors versus mesenchymal stem cells. Comparison of both datasets revealed miR20a-3p to be the top EWS-FLI1 activated miRNA. MiR-20a belongs to the miR17-92 cluster, also known as oncomir-1, which is one of the most potent oncogenic miRNAs. The whole cluster is among the small number of miRNAs down-regulated upon knockdown of EWS-FLI1 in multiple ES cell lines. Since feedback loops exists between the E2F transcription factor family and miR-17-92 and between EWS-FLI1 and E2F3, we sought to investigate the role of this miRNA cluster in ES. We found a significant enrichment of PAR-CLIP hits for members of the miR-17-92 cluster, in the 3´UTRs of genes up-regulated in response to mir-17-92 specific sponge expression. Among them we consistently identified known (i.e. CTGF, MXD1, CYLD1) and a multitude of so far unknown targets of the oncomir-1 cluster in ES in three PAR-CLIP experiments. Preliminary experiments using 3′UTRs of select novel candidate genes in gene reporter assays showed up-regulation of luciferase activity upon transfection of a sponge specific to miR-17-92 and 20a, but not to unrelated miR-9 and 10b. Site directed mutagenesis of seed sequences in the 3′UTR of these candidate genes will be used for further validation. This study provides an example for the comprehensive definition of the targetome for a defined group of miRNAs under physiological conditions. This study was supported by the 7th framework program of the European Commission (FP7-259348, “ASSET”) and the Austrian Science Fund FWF (24708-B21) Citation Format: Raphaela Schwentner, David Herrero-Martin, Maximilian Kauer, Heinrich Kovar. Definition of the Ewing sarcoma specific oncomir-1 targetome. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 3080. doi:10.1158/1538-7445.AM2015-3080

[Purpose]: Ewing tumor cell survival and proliferation depends on several autocrine loops. Targeting these loops is a promising therapeutic approach. We recently showed the cytostatic role of imatinib, an inhibitor of the SCF-KIT loop, on Ewing tumor cells, and in this study, we intend to analyze the inhibition of the insulin-like growth factor I receptor (IGF1R) loop. [Experimental Design]: We analyzed IGF1R blockade by ADW742, a small molecule specific for this receptor, alone and in combination with imatinib, vincristine, and doxorubicin on Ewing tumor cell lines. We studied the effect on proliferation, apoptosis, cell cycle, pathway phosphorylation, soft-agar growth, motility, and vascular endothelial growth factor expression levels. [Results]: Treatment with ADW742 induced down-regulation of IGF1R/AKT/mammalian target of rapamycin (mTOR) phosphorylation, which was deeper in cell lines having higher IGF1R activation levels. Treatment also induced dose-dependent inhibition of cell proliferation (IC50 = 0.55-1.4 μmol/L), inducing a G 1 phase blockage and apoptosis. Addition of imatinib to ADW742 synergistically augmented these effects and was especially effective in inhibiting AKT/mTOR phosphorylation and reducing vascular endothelial growth factor expression in cell lines having high IGF1R activation levels. Combination with usual chemotherapeutic agents vincristine and doxorubicin showed synergistic interactions. [Conclusions]: Inhibition of Ewing tumor cell proliferation by ADW742 is mediated through blockade of IGF1R signaling. Combination of ADW742 with imatinib, vincristine, and doxorubicin induces a significant reduction of tumor cell growth, mainly by the increase in apoptosis with a pattern depending on IGF1R activation levels. This study supports a potential role for ADW742 in the treatment of Ewing tumor and AKT/mTOR as a possible surrogate marker of response to therapy. © 2006 American Association for Cancer Research., Grant support: Instituto de Salud Carlos III, Feder Madrid, Spain grants PI020828, G03-089, and C03-010 and III Quadro Comunitário de Apoio from the European Social Fund and Portuguese National Funds of the Ministry for Science and Higher Education.

Oncogenic addiction provides an opportunity to develop new treatment options, especially for childhood cancers. Pediatric tumors contain a lower number of oncogenic mutations compared to most adult cancers, suggesting stronger dependency on individual oncogenes, such as chimeric transcription factors that have the ability to control multiple oncogenic pathways. Taking advantage of this addiction, targeting of oncogenic transcription factors becomes a new powerful strategy for therapy of translocation positive pediatric tumors like alveolar rhabdomyosarcoma (aRMS), which is characterized by a very dismal prognosis. As transcription factors are considered to be difficult to target, we developed an approach to screen for druggable upstream regulators like kinases. In two parallel activity reporter assays, using a kinome siRNA library and a small molecule library, we identified PLK1 to contribute to the activity of PAX3-FOXO1, the oncogenic transcription factor specific to aRMS. Mechanistically, we were able to demonstrate a direct interaction of the two proteins by co-immunoprecipitation. PLK1 silencing or inhibition increased degradation of PAX3-FOXO1, which suggests a stabilization of PAX3-FOXO1 due to phosphorylation by PLK1. Candidate phosphorylation sites were identified by in vitro kinase assays and mass spectrometric analysis and site-specific mutagenesis is currently utilized to validate the impact of these sites on fusion protein turnover. To highlight PLK1 as therapeutic target in aRMS, in vivo treatment studies using the PLK1 inhibitor BI 2536 resulted in complete tumor regression in two aRMS xenograft mouse models. Finally, tissue microarray analysis of human aRMS tumor biopsies showed PLK1 to be overexpressed and predictive of overall survival. Hence, our preclinical studies validate PLK1 as highly relevant drug target in alveolar rhabdomyosarcoma, similar to recent findings in other pediatric tumors. Our data suggests that PLK1 inhibitors warrant further investigations to evaluate the potential to be translated into a clinical setting. Citation Format: Verena Thalhammer, David Herrero-Martin, Regina Hecker, Dominik Laubscher, Laura Lopez-Garcia, Marco Wachtel, Peter Bode, Beat Schäfer. PLK1 regulates PAX3-FOXO1 stability and its inhibition mediates regression of alveolar rhabdomyosarcoma xenograft tumors. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 3966. doi:10.1158/1538-7445.AM2014-3966

The identification of microRNA (miR) targets within a given cellular context still poses a largely unsolved problem. MiR targets are predicted based on the presence of seed sequences in the 3'UTR of mRNAs. Target candidate lists are filtered assuming mRNA destabilization, and validated by artificially forcing ectopic expression of miR analogs, or by interfering with miR expression by antagomirs. However, the expression level and amplitude of physiological miR variations is much smaller than experimentally induced miR perturbations. Crosslinking and immuno precipitation (CLIP) followed by sequencing of bound RNA allows monitoring of dynamic changes in miR/mRNA occupancy of RISC. However, it is unclear if increased miR activity will lead to increased target read counts due to elevated RISC occupancy or to decreased read counts as a consequence of target destabilization. Ewing sarcoma (ES) expresses an oncogenic transcription factor, EWS/FLI1.To study the impact of miRs to the gene regulatory network downstream of EWS/FLI1, we used a combination of mRNA and miR expression profiling, ChIP-seq, PAR-CLIP of AGO2, AGO2 knockdown, and SILAC monitoring of proteome changes in an inducible EWS/FLI1 knockdown ES cell line. Our data suggest that EWS/FLI1 perturbs gene regulation primarily on the transcriptional level and miRs play only a modulatory role for gene expression. Furthermore EWS/FLI1 affects the expression of many miR biogenesis and miR activity as well as RISC associated proteins. Knockdown of EWS/FLI1 results in pronounced changes of miR specific PAR-CLIP spectra. Disabled RISC activity lead to only minor changes in genome-wide mRNA expression. Our results are consistent with a complex role of the miRNome in the fine tuning of gene regulatory networks in Ewing sarcoma. Supported by grants EU-FP7 259348 and Austrian Science Fund FWF 24708-B21. Citation Format: David Herrero-Martin, Maximilian Kauer, Kristina B. Emdal, Grzegorz Sienski, Argyrou Fourtouna, Robert Kralovics, Jesper V. Olsen, Heinrich Kovar. The genome-wide contribution of microRNAs to gene regulation in Ewing sarcoma. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 3048. doi:10.1158/1538-7445.AM2013-3048

The chimeric oncoprotein EWS-FLI1 is the driving pathogenic force in Ewing's sarcoma family tumors (ESFT). As an aberrant ETS transcription factor it directly deregulates a multitude of genes related to proliferation control and differentiation. Recently, we reported on the EWS-FLI1 microRNA (miRNA) signature based on knockdown experiments in ESFT cell lines and on differential expression in primary tumors versus mesenchymal stem cells. In order to define the mRNA targets of EWS-FLI1 regulated miRNAs, we now performed pull-down experiments of AGO2 complexes after photoactivated ribonucleoside-enhanced cross-linking followed by NGS sequencing of associated mRNAs (PAR-CLIP). We obtained 92 Mio high quality reads of which 63 Mio were aligned to the reference genome. The genomic localization of these sequences demonstrated the specific enrichment of 3'UTRs (>17 fold). Among obtained reads, T to C conversions were highly enriched consistent with crosslinking via 4-thiouridine to AGO2 containing complexes. PAR-CLIP results indicate AGO2 binding next to miRNA seed sequences for 4695 and 5160 genes associated with 1876 and 1860 miRNAs in the presence and absence of EWS-FLI1, respectively. Strikingly, for individual miRNAs the mRNA target spectra drastically changed upon EWS-FLI1 knockdown. For instance, for the two top EWS-FLI1 signature miRNAs hsa-mir-145 and hsa-mir 424 a shift from genes involved in cell death and differentiation to protein activator activity, and from protein degradation and cell cycle control to protein kinases and protein phosphorylation was observed, respectively. Of note, a target shift was also observed for miRNAs that did not change in response to EWS-FLI1 knockdown. In addition for many specifc targets no correlation was observed between mRNA abundancy and the level of association with AGO2 as reflected by read counts. These data suggest that EWS-FLI1 perturbs post-translational gene regulation by changing access of the RISC complex to its target mRNAs. Supported by EC-FP7 grant 259348 “ASSET”. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr LB-462. doi:1538-7445.AM2012-LB-462

Oncogenic transcription factors are the second most frequently mutated class of proteins. They represent ideal therapeutic targets because oncogene addiction is common to a broad spectrum of tumors and their inhibition may help to develop further alternative treatment strategies to improve therapy and to minimize treatment related side effects. However, thus far it has not been possible to target these oncogenic transcription factors as they usually do not respond to small-molecule inhibition. As a model system we use alveolar rhabdomyosarcoma (aRMS), an aggressive childhood tumor, which often displays resistance to conventional chemo-and radiotherapy. aRMS is characterized by the expression of the tumor-specific chimeric transcription factor PAX3/FKHR that is essential for survival of tumor cells. This transcription factor is post-translationally modified by phosphorylation which is required for efficient transcriptional activity. We believe that identification of upstream protein kinases mediating PAX3/FKHR phosphorylation will be an efficient strategy to impair the activity of the oncogenic fusion protein and subsequently induce tumor cell specific apoptosis. Having performed both siRNA and kinase-inhibitor library screens against the human kinome, we claim that Polo-like Kinase 1 (PLK1) might represent a very attractive and specific potential therapeutic target in aRMS. Its inhibition by RNAi and the small-molecule inhibitor BI 2536 reduces PAX3/FKHR activity and consequently aRMS cell viability. Moreover drug treatment causes tumor regression in xenograft mouse models. Therefore we are elucidating mechanisms causing these antitumorigenic effects and especially focus on the interaction of PLK1 and PAX3/FKHR. Our data suggest that PLK1 warrants further investigations as a novel drug target for the treatment of aRMS and may lead to a general strategy for treatment of tumors addicted to post-translationally modified oncogenic transcription factors. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 271. doi:1538-7445.AM2012-271