The EWSR1-FLI1 t(11;22)(q24;q12) translocation is the pathognomonic genomic alteration in 85% of the Ewing Family of Tumors (EWFT) a malignancy of the bone and the surrounding tissue, predominantly affecting children and adolescents. This translocation results in the formation of a chimeric oncoprotein which acts as an aberrant transcription factor that is currently not pharmaceutically druggable, driving the need for more effective targeted therapies. The EWSR1-FLI1 translocation induces a variety of changes including dysregulation of the epigenome and altered gene expression to drive tumorigenesis, and consequently contributes to the hypersensitivity of EWFT to several classes of chemotherapeutics. We sought to exploit these intrinsic sensitivities by employing a matched pair of cell lines derived from the same patient with Ewing sarcoma prior to and following chemotherapy, a panel of Ewing sarcoma cell lines, and several patient-derived xenografts (PDX) collected at the time of relapse or autopsy, which led us to the development of two novel combination targeted therapies for EWFT. In our matched pair of EWFT cell lines, we found sensitivity to the Poly(ADP-ribose Polymerase (PARP) inhibitor olaparib was diminished following chemotherapy, despite a predicted sensitivity. In addition, we discovered increased expression of the antiapoptotic protein BCL-2 in the chemotherapy-resistant cells, conferring apoptotic resistance to olaparib. We found that EWS-FLI1 increases BCL-2 expression; however, inhibition of BCL-2 alone is insufficient to sensitize EWFT cells to olaparib, revealing a dual necessity for BCL-2 and BCL-XL (BCL2L1) in EWFT survival. These data reveal BCL-2 and BCL-XL act together to drive olaparib mediated apoptotic resistance in Ewing sarcoma and identify a novel, rational combination therapy using olaparib and the BCL-2/BCL-XL inhibitor navitoclax. In addition, using high throughput drug screening we have identified a novel epigenetic susceptibility in EWFT to GSK-J4 (GlaxoSmithKline), an inhibitor of lysine 27 of histone 3 (H3K27) demethylases: ubiquitously transcribed tetratricopeptide repeat, X chromosome (UTX) and Jumonji D3 (JMJD3). Treatment with GSK-J4 leads to a decrease in H3K27 acetylation (H3K27ac) and ultimately, the silencing of EWS-FLI1 gene targets. We sought to sensitize GSK-J4-mediated inhibition of EWS-FLI1 targets by blocking RNA polymerase II activity using the Cyclin Dependent Kinase 7 (CDK7) inhibitor THZ1. By targeting CDK7-mediated transcription we were able to sensitize EWFTs to H3K27 demethylase inhibition. We therefore propose co-targeting of H3K27 demethylases and CDK7 acts as a surrogate EWS-FLI1 inhibitor. Given the difficulties targeting EWS-FLI1, these strategies may present viable clinical therapies.

Ewing Sarcoma (ES) is an aggressive pediatric solid tumor. Even though overall-survival for localized patients is approximately 70%, the overall-survival for high risk ES patients has not improved in the last 20 years. Therefore, there is a need for exploration of new therapeutic agents in ES. Recent evidence has demonstrated that ES cells behave like BRCA-deficient tumor types which renders them sensitive to PARP inhibitors in vitro and in vivo. However, a phase II study of the efficacy of single-agent PARP inhibition in patients with relapsed ES did not significantly improve outcome. As single-agent therapy is rarely expected to result in significant clinical responses, in this study, we plan to validate potential targeted combination therapies with PARP inhibitors in ES. Since ES appears to demonstrated BRCA-deficient biology with impaired homologous recombination, cells are expected to be sensitive to both PARP inhibitors and ATR inhibitors, drugs which have a role in regulating DNA damage and impairing homologous recombination. In breast cancer and ovarian cell lines with genetic BRCA-deficiency, PARP and ATR inhibitors have synergistic activity. We hypothesize that these inhibitors will also have synergistic anti-Ewing activity. Furthermore, we recognize that ES cells demonstrate remarkably quiet genomes suggesting that there is minimal ongoing DNA-damage when cells are growing unperturbed. Therefore, we also plan to test the effect of adding low-dose genotoxic chemotherapy to induce additional sensitivity to the combination of PARP and ATR inhibitors in ES. The specific aims of this study were to explore the possible anti-tumor effect of PARP inhibitors combined with ATR inhibitors in ES cell lines, and to explore whether low dose genotoxic chemotherapy with SN38 can potentiate the anti-tumor effect of combined PARP and ATR inhibition in ES cell lines. We studied the anti-Ewing Sarcoma effect of the combination of a PARP inhibitor, AZD2281, and an ATR inhibitor, AZD6738, across a range of doses with and without low doses of a DNA damaging agent, SN38 (irinotecan metabolite), in two ES cell lines. We analyzed synergy by determining the Combination Index (CI) and Fractional Inhibition (FA) of each combination. We found that the ATR inhibitor, AZD6738, was synergistic across large range of concentrations when combined with the PARP inhibitor, AZD2281, in ES cell lines. We also found that treatment of cells with low doses of SN38 increases ES cell sensitivity to treatment with the PARP inhibitor and ATR inhibitor combination. This study provides preclinical support for additional studies exploring these combinations in ES. Given the low number of pediatric patients with ES compared to adult cancer patients, there will be limited attempts in combining these agents in clinical trials. Therefore, the development of an in vivo trial testing the safety and efficacy of this combination in ES mouse models is proposed. / 2020-07-03T00:00:00Z

Os sarcomas ósseos representam uma proporção significativa de tumores na faixa etária pediátrica, ainda apresentando um quadro desafiador devido a sua significativa taxa de morbimortalidade. Pesquisas para o desenvolvimento de novas modalidades terapêuticas e para o desenvolvimento de métodos que identifiquem características da doença que possam permitir melhor estratificação dos pacientes através de dados clinicamente relevantes para individualizar as condutas clínicas são necessárias. Dentro deste contexto surge o conceito de radiômica, que visa extrair dados clinicamente relevantes a partir de imagens médicas. Entretanto, para colocar a radiômica em prática, é necessário selecionar, nas imagens médicas, as áreas de interesse referentes às patologias estudadas, e este processo se denomina segmentação. O objetivo primário deste estudo foi avaliar a reprodutibilidade intra e inter-observador da segmentação manual de sarcomas ósseos em imagens de ressonância magnética (RM). Como objetivo secundário, foi avaliada a capacidade da segmentação semiautomática em reduzir o tempo necessário para segmentação, mantendo similaridade com a segmentação manual. O estudo foi realizado de forma retrospectiva com inclusão de pacientes com diagnóstico de osteossarcoma ou sarcoma de Ewing confirmado por estudo histopatológico e que tivessem imagens de RM realizadas no Hospital Universitário de nossa Instituição realizadas previamente a qualquer intervenção terapêutica. Três médicos radiologistas, de forma independente e às cegas em relação as demais segmentações e em relação ao resultado histopatológico, realizaram a segmentação manual dos contornos destes tumores utilizando o software 3DSlicer, permitindo que fosse realizada avaliação da reprodutibilidade interobservador. Um dos radiologistas realizou uma segunda segmentação manual dos mesmos casos, possibilitando a avaliação da reprodutibilidade intraobservador, e, ainda, uma terceira segmentação foi realizada, utilizando metodologia semiautomática, disponível no software mencionado. Para a análise estatística, foi utilizado o coeficiente de similaridade de Dice (DICE), a distância Hausdorff (DH), comparações de volumes e análises dos intervalos de tempo necessários para realização das segmentações. Os parâmetros avaliados demonstraram haver boa reprodutibilidade intraobservador, com DICE variando entre 0,83 a 0,97; e distância Hausdorff variando entre 3,37 a 28,73 mm. Também foi demonstrada boa reprodutibilidade interobservador com DICE variando entre 0,73 a 0,97; e distância Hausdorff variando entre 3,93 a 33,40 mm. A segmentação semiautomática demonstrou boa similaridade em relação à segmentação manual (DICE variando entre 0,71 a 0,96 e DH variando entre 5,38 a 31,54 mm), havendo redução significativa do tempo necessário para segmentação. Entre todas as situações comparadas, os volumes não apresentaram diferenças estatisticamente significativas (p-valor>0,05). / Bone sarcomas represent a significant proportion of tumors in the pediatric age group and they still are a challenge due to their significant morbidity and mortality rates. Reseaches are important for the development of new therapeutic modalities and for the development of methods that identify features that allow better stratification of the patients with theses diseases for individualization of their treatments. In this context emerges the concept of radiomics, which is the process of extraction of clinically relevant data from medical images. It is important to segment the areas of interest im medical images for the pratice of this process. The primary objective of this study was to evaluate the intra- and interobserver reproducibility of manual segmentation of bone sarcomas on magnetic resonance imaging (MRI). As a secondary objective, it was evaluated if the semiautomatic segmentation could be similar to manual segmentation and if the semiautomatic method could reduce the time required for segmentation. The study was performed retrospectively with the inclusion of patients with osteosarcoma or Ewing sarcoma confirmed by histopathological study and who had MRI performed at the University Hospital of our Institution prior to any therapeutic intervention. Three radiologists, independently and blindly in relation to the other segmentations and in relation to the histopathological results, performed the manual segmentation of the contours of these tumors using 3DSlicer software, allowing an interobserver reproducibility evaluation. One of the radiologists performed a second manual segmentation of the same cases, allowing the evaluation of intraobserver reproducibility. A third segmentation was performed, using semi-automatic methodology, available in the mentioned software. For the statistical analysis, Dice similarity coefficient (DICE), Hausdorff distance (DH), comparisons between volumes and time intervals for segmentations were used. The parameters evaluated demonstrated a good intraobserver reproducibility, with DICE ranging from 0.83 to 0.97 and Hausdorff distance ranging from 3.37 to 28.73 mm. Good interobserver reproducibility was also demonstrated with DICE ranging from 0.73 to 0.97 and Hausdorff distance ranging from 3.93 to 33.40 mm. Semiautomatic segmentation demonstrated good similarity to manual segmentation (DICE ranging from 0.71 to 0.96 and HD ranging from 5.38 to 31.54mm), and there was significant reduction in the time required for segmentation. Among all the situations compared, the volumes did not present significant statistical differences (p-value> 0.05).

Background: Despite multi-modality therapy, the majority of patients with metastatic or recurrent Ewing sarcoma (ES), the second most common pediatric bone malignancy, will die of their disease. ES tumors express aberrantly activated ETS transcription factors through translocations that fuse the EWS gene to ETS family genes FLI1 or ERG. The aberrant activation of ETS transcription factors promotes malignant transformation and proliferation. While, FLI1 or ERG cannot be readily targeted, there is an opportunity to deploy functional genomics screens, to develop novel therapeutic approaches by identifying targetable liabilities in EWS/FLI1 dependent tumors. Materials and Methods: We performed a near whole-genome pooled shRNA screen in a panel of five EWS/FLI1 dependent Ewing sarcoma cell lines and one EWS/ERG cell line to identify essential genes. Essential genes were defined as those genes whose loss resulted in reduced viability selectively in ES cells compared to non-Ewing cancer cell lines. Essential hits were subsequently validated with genomic knockdown and chemical inhibition in vitro, followed by validation of the on-target effect of chemical inhibition. Next, we determined the in vivo effects of small-molecule inhibition on survival and tumor growth in NOD scid gamma (NSG) mice with established subcutaneous ES xenografts. Results: Top hits in our screen that could be readily targeted by small-molecule inhibitors, and thus have potential for rapid clinical validation, were selected for further investigation. These hits included IKBKE, CCND1 and CDK4. IKBKΕ, a non-canonical IKK with an oncogenic role in breast cancer, was one of the top kinase hits in the screen. IKBKΕ shares significant homology to TBK1, another non-canonical IKK that is essential in k-RAS dependent lung cancer. We validated IKBKE through small-molecule inhibition of IKBKE/TBK1 and shRNA based knockdown. Ewing sarcoma cell lines are sensitive to low micromolar concentrations of two IKBKE/TBK1 inhibitors (CYT387 and MRT67307). Additionally, in a panel of ES cell lines, knockdown of IKBKE resulted in decreased growth and impaired colony formation. These observations, paired with impairment of NF-κB nuclear localization following CYT387 treatment suggests that non-canonical IKK mediated signaling may be essential in Ewing sarcoma. We further validated these results through inhibition of IKBKE/TBK1 in in vivo xenograft models treated with 100 mg/kg/day of CYT387. Treatment over the course of twenty-nine days resulted in a significant increase in survival (p-value = 0.0231) and a significant decrease (p-value = 0.036) in tumor size after fifteen days of treatment. CDK4 and CCND1 are highly expressed in Ewing sarcoma as compared to other tumor types. shRNA mediated knockdown of CDK4 and CCND1 resulted in impaired viability and anchorage independent growth. Furthermore, treatment of Ewing sarcoma cell lines with a highly selective CDK4/6 inhibitor, LEE011, resulted in decreased viability (IC50 range of 0.26-18.06 μM), potent G1 arrest in six of eight EWS/FLI1 containing Ewing sarcoma lines tested and apoptosis in a panel of four highly sensitive lines. Administration of 75 mg/kg/day and 250 mg/kg/day of LEE011 in NSG mice with Ewing xenografts resulted in significant impairment of tumor growth, (p-value <0.001 for both treatment arms), as compared to vehicle control. Conclusions: These studies suggest a role for the targeting of IKBKE and CDK 4/6 in Ewing sarcoma, findings with immediate clinical relevance for patients with this malignancy, because small-molecule inhibitors of these proteins have already entered clinical trial for other disease indications.

Le Sarcome d'Ewing est un cancer pédiatrique rare, principalement dû à l'expression de l'oncogène de jonction EWS-Fli1, et dont les traitements médicamenteux ont peu évolué au cours des dernières décennies. Nous nous intéressons à une nouvelle approche thérapeutique utilisant des siRNA, ciblant spécifiquement l'oncogène EWS-Fli1, et permettant l'inhibition de la croissance tumorale. Durant mon travail de thèse, j'ai utilisé des nanocristaux de diamant issus soit de détonation (DND), soit de synthèse haute pression-haute température (NDHPHT) pour vectoriser les siRNA, accrochés par interaction électrostatique. Pour ce faire, les NDs ont été rendus cationiques par différentes méthodes: (i) hydrogénation assistée par plasma, (ii) par recuit thermique, ou (iii) par traitement chimique pour les DNDs, ou (iv) greffage covalent d'un polymère cationique sur des NDHPHT (COP-NDHPHT).Mes travaux ont comporté deux axes: (i) étude in vitro des complexes ND:siRNA (caractérisations physico-chimiques des NDs et étude de l'efficacité d'inhibition de l'oncogène par les complexes); (ii) distribution tissulaire de COP-NDHPHT, injectés dans des souris, grâce à des NDHPHT fluorescents, contenant des défauts azote-lacune. Pour les détecter individuellement dans des coupes d'organes de souris portant une tumeur xénogreffée sous-cutanée, nous avons développé un système d'imagerie en épifluorescence à grande ouverture numérique, et résolu en temps afin de rejeter l'autofluorescence tissulaire (de durée de vie plus courte que celle des NDs). Nous avons quantifié le nombre, l'état d'agrégation et la localisation cellulaire de ces vecteurs (grâce à un marquage histopathologique imagé simultanément) 24h après injection. Les NDs ont été clairement détectés dans les différents organes, dont la tumeur, ouvrant la voie à un contrôle de la progression tumorale grâce au siRNA. / Ewing Sarcoma is a rare pediatric cancer, caused in the majority of the cases by the expression of the fusion oncogene EWS-Fli1. Current treatments have not much evolved over the past decades. We are investigating a new therapy based on siRNA specifically targeting the oncogene and inhibiting the tumor growth. During my PhD thesis, I have tested different types of synthetic nanodiamonds (ND) used to vectorize siRNA electrostatically bound at their surface: ND produced by detonation (DND) or by High Pressure-High Temperature synthesis (NDHPTH). Their surfaces have been cationized by various processes: (i) plasma or (ii) thermal hydrogenation, (ii) chemical treatment, or (iv) covalent grafting of a copolymer (COP-NDHPHT).My PhD work included two main axis: (i) in vitro study of ND:siRNA complexes (NDs physico-chemical characterization and oncogene inhibition efficacy by the complexes); (ii) tissue distribution of COP-NDHPHT, injected into mice, using fluorescent NDHPHT containing nitrogen-vacancy defects. To detect them individually in sections of mouse organs carrying a subcutaneous xenograft tumor, we developed an epifluorescence imaging system with large numerical aperture and resolved in time to reject tissue autofluorescence (of a shorter lifetime than NDs). We quantified the number, the aggregation state and the cell localization (thanks to simultaneous histopathological imaging) of these vectors 24 hours after injection. NDs have been clearly detected in different organs, including the tumor, paving the way for tumor progression control with siRNA.

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O Sarcoma de Ewing (ES) é um raro tumor de ossos e tecidos moles com uma característica translocação cromossomal, a fusão EWS/FLI-1, que atua sobre diversos processos oncogênicos. O desenvolvimento da resistência à quimioterapia é comum no tumor e continua como uma das principais causas na falha do tratamento. O objetivo desse estudo foi avaliar a expressão de genes após a indução de resistência em linhagens celulares de ES. Foi selecionado um conjunto de genes (CCAR1, TUBA1A, POLDIP2, SMARCA4 e SMARCB1) a partir da mineração da literatura em resistência tumoral para duas drogas utilizadas na terapia de ES, doxorrubicina e vincristina. Descrevemos a expressão de cada gene selecionado antes e após as linhagens SK-ES-1 serem submetidas a um protocolo de indução de resistência para ambos os fármacos, que obteve êxito ao induzir as células à resistência. A expressão relativa dos níveis de mRNA foi avaliada e foi encontrada em maior expressão para os genes SMARCA4, SMARCB1 e POLDIP2, e em menor expressão para os genes TUBA1A e CCAR1, quando comparadas às linhagens de controle não-resistentes de cada quimioterápico. Os resultados sugerem o envolvimento de mecanismos de reparo de dano ao DNA, remodelamento de cromatina via SWI/SNF, atividade de microtúbulos e atividade spliceossomal nos processos de resistência quimioterápica em ES. / Ewing Sarcoma (ES) is a rare bone and soft tissue tumor with a characteristic chromosomal translocation, the fusion protein EWS/FLI-1, that drives several oncogenic processes. The development of resistance to chemotherapy is common and remains as the main cause of treatment failure. The goal of this study was to evaluate the expression of selected genes in ES cell lines after induction of resistance. A set of genes (CCAR1, TUBA1A, POLDIP2, SMARCA4 and SMARCB1) was data mined from tumoral resistance literature for two drugs used in ES therapy, doxorubicin and vincristine. We describe the expression of each selected gene before and after SK-ES-1 cell lines were exposed to a drug resistance inducing protocol for doxorubicin and vincristine. Cell lines were successfully induced to be resistant to doxorubicin and vincristine. The relative mRNA expression levels were upregulated for genes SMARCA4, SMARCB1 and POLDIP2 and downregulated for genes TUBA1A and CCAR1, when comparing resistant and non-resistant ES cell lines for each drug. The results suggest involvement of repair pathways, SWI/SNF chromatin remodeling, microtubule and spliceosomal activity processes in drug resistance mechanisms in ES.

INTRODUÇÃO: Os tumores da família do sarcoma de Ewing (TFSE) compreendem um espectro de neoplasias de células neuroectodérmicas dos ossos e partes moles de comportamento biológico agressivo e prognóstico reservado, caracterizadas por translocações envolvendo um dos genes da família TET/FET e um dos genes da família ETS, mais comumente EWSR1 e FLI1. Com o avanço da medicina personalizada, cresce a demanda por biomarcadores em TFSE que tenham valor como fatores prognósticos e potencial para futuras terapias-alvo específicas. Este estudo propôs biomarcadores, incluindo proteínas relacionadas à supressão tumoral, proliferação celular, metabolismo energético, atividade imune, vias de reparo do DNA e células tronco. MÉTODOS: A expressão imuno-histoquímica dos biomarcadores MTAP, p16, STAG2, p53, USP22, PTEN, RKIP, Ciclina D1, MCTs (1, 2 e 4), CD147, CA IX, GLUT1, BRACHYURY, PD-L1, OCT4 e SALL4 foi analisada em uma série bem caracterizada de 113 TFSE através de amostras em tissue microarrays (TMA). Os perfis de expressão foram então associados aos parâmetros clínico-patológicos dos pacientes e à sobrevida global para uma análise do impacto no prognóstico. RESULTADOS: A hiperexpressão de p53 mostrou associação estatisticamente significativa com menor sobrevida global (p < 0,001), doença metastática no diagnóstico (p = 0,017) e idade acima de 20 anos (p = 0,04). A perda de expressão de MTAP (p = 0,039) e de Brachyury (p = 0,008) também se associaram significativamente com menor sobrevida global. Em relação às características clínicas dos pacientes, doença metastática no diagnóstico e etnia não-branca foram associados a um pior prognóstico. CONCLUSÕES: Os biomarcadores p53, MTAP e Brachyury foram identificados como fatores independentes relacionados ao prognóstico. A utilização destes biomarcadores como fator prognóstico nos TFSE pode auxiliar na estratificação de risco dos pacientes e até mesmo estimular o desenvolvimento de drogas-alvo específicas / INTRODUCTION: The Ewing sarcoma family of tumors (ESFT) comprises a spectrum of neoplasms of neuroectodermal cells of the bones and soft tissues with an aggressive biological behavior and poor outcome, characterized by translocations involving one of the genes of the TET/FET family and one of the genes of the ETS family, most commonly EWSR1 and FLI1. With the progress of personalized medicine, there is a great demand for biomarkers in ESFT that could have prognostic values and the potential for future targeted therapies. This study proposed the evaluation of protein expression of different classes of biomarkers, including proteins related to tumor suppression, cell proliferation, energy metabolism, immune activity, DNA repair pathways and stem cells. METHODS: Immunohistochemical expression of the biomarkers MTAP, p16, STAG2, p53, USP22, PTEN, RKIP, Cyclin D1, MCTs (1, 2 and 4), CD147, CA IX, GLUT1, BRACHYURY, PD-L1, OCT4 and SALL4 was analyzed in a well-characterized series of 113 ESFT in a tissue microarray (TMA) platform. Expression profiles were then associated with patients\' clinical-pathological parameters and overall survival for analysis of the prognostic impact. RESULTS: p53 hyperexpression showed a statistically significant association with lower overall survival (p <0.001), metastatic disease at diagnosis (p = 0.017) and age over 20 years (p = 0.04). Loss of MTAP (p = 0.039) and Brachyury (p = 0.008) were also significantly associated with lower overall survival. Regarding the clinical characteristics of the patients, metastatic disease at diagnosis and non-white ethnicity were associated with a worse prognosis. CONCLUSIONS: The biomarkers p53, MTAP and Brachyury were identified as independent factors related to the prognosis. The use of these biomarkers as a prognostic factor in ESFT may aid in the risk stratification of patients and even stimulate the development of specific targeted drugs