Class I histone deacetylases (HDAC) critically contribute to Ewing sarcoma pathogenesis

BACKGROUND: Histone acetylation and deacetylation seem processes involved in the pathogenesis of Ewing sarcoma (EwS). Here histone deacetylases (HDAC) class I were investigated. METHODS: Their role was determined using different inhibitors including TSA, Romidepsin, Entinostat and PCI-34051 as well as CRISPR/Cas9 class I HDAC knockouts and HDAC RNAi. To analyze resulting changes microarray analysis, qRT-PCR, western blotting, Co-IP, proliferation, apoptosis, differentiation, invasion assays and xenograft-mouse models were used. RESULTS: Class I HDACs are constitutively expressed in EwS. Patients with high levels of individual class I HDAC expression show decreased overall survival. CRISPR/Cas9 class I HDAC knockout of individual HDACs such as HDAC1 and HDAC2 inhibited invasiveness, and blocked local tumor growth in xenograft mice. Microarray analysis demonstrated that treatment with individual HDAC inhibitors (HDACi) blocked an EWS-FLI1 specific expression profile, while Entinostat in addition suppressed metastasis relevant genes. EwS cells demonstrated increased susceptibility to treatment with chemotherapeutics including Doxorubicin in the presence of HDACi. Furthermore, HDACi treatment mimicked RNAi of EZH2 in EwS. Treated cells showed diminished growth capacity, but an increased endothelial as well as neuronal differentiation ability. HDACi synergizes with EED inhibitor (EEDi) in vitro and together inhibited tumor growth in xenograft mice. Co-IP experiments identified HDAC class I family members as part of a regulatory complex together with PRC2. CONCLUSIONS: Class I HDAC proteins seem to be important mediators of the pathognomonic EWS-ETS-mediated transcription program in EwS and in combination therapy, co-treatment with HDACi is an interesting new treatment opportunity for this malignant disease

A molecularly characterized preclinical platform of subcutaneous renal cell carcinoma (RCC) patient-derived xenograft models to evaluate novel treatment strategies

Renal cell carcinoma (RCC) is a kidney cancer with an onset mainly during the sixth or seventh decade of the patient’s life. Patients with advanced, metastasized RCC have a poor prognosis. The majority of patients develop treatment resistance towards Standard of Care (SoC) drugs within months. Tyrosine kinase inhibitors (TKIs) are the backbone of first-line therapy and have been partnered with an immune checkpoint inhibitor (ICI) recently. Despite the most recent progress, the development of novel therapies targeting acquired TKI resistance mechanisms in advanced and metastatic RCC remains a high medical need. Preclinical models with high translational relevance can significantly support the development of novel personalized therapies. It has been demonstrated that patient-derived xenograft (PDX) models represent an essential tool for the preclinical evaluation of novel targeted therapies and their combinations. In the present project, we established and molecularly characterized a comprehensive panel of subcutaneous RCC PDX models with well-conserved molecular and pathological features over multiple passages. Drug screening towards four SoC drugs targeting the vascular endothelial growth factor (VEGF) and PI3K/mTOR pathway revealed individual and heterogeneous response profiles in those models, very similar to observations in patients. As unique features, our cohort includes PDX models from metastatic disease and multi-tumor regions from one patient, allowing extended studies on intra-tumor heterogeneity (ITH). The PDX models are further used as basis for developing corresponding in vitro cell culture models enabling advanced high-throughput drug screening in a personalized context. PDX models were subjected to next-generation sequencing (NGS). Characterization of cancer-relevant features including driver mutations or cellular processes was performed using mutational and gene expression data in order to identify potential biomarker or treatment targets in RCC. In summary, we report a newly established and molecularly characterized panel of RCC PDX models with high relevance for translational preclinical research

Single-cell profiling of alveolar rhabdomyosarcoma reveals RAS pathway inhibitors as cell-fate hijackers with therapeutic relevance

Rhabdomyosarcoma (RMS) is a group of pediatric cancers with features of developing skeletal muscle. The cellular hierarchy and mechanisms leading to developmental arrest remain elusive. Here, we combined single-cell RNA sequencing, mass cytometry, and high-content imaging to resolve intratumoral heterogeneity of patient-derived primary RMS cultures. We show that the aggressive alveolar RMS (aRMS) subtype contains plastic muscle stem-like cells and cycling progenitors that drive tumor growth, and a subpopulation of differentiated cells that lost its proliferative potential and correlates with better outcomes. While chemotherapy eliminates cycling progenitors, it enriches aRMS for muscle stem-like cells. We screened for drugs hijacking aRMS toward clinically favorable subpopulations and identified a combination of RAF and MEK inhibitors that potently induces myogenic differentiation and inhibits tumor growth. Overall, our work provides insights into the developmental states underlying aRMS aggressiveness, chemoresistance, and progression and identifies the RAS pathway as a promising therapeutic target

Serially quantifying TERT rearrangement breakpoints in circulating tumor DNA enables minimal residual disease monitoring in patients with neuroblastoma

Telomerase is reactivated by genomic TERT rearrangements in ~30% of diagnosed high-risk neuroblastomas. Dismal patient prognosis results if the RAS/MAPK/ALK signaling transduction network also harbors mutations. We present a liquid biopsy-based monitoring strategy for this particularly vulnerable pediatric patient subgroup, for whom real-time molecular diagnostic tools are limited to date. Droplet digital PCR assays quantifying patient-individualized TERT rearrangement breakpoint copies, ALK copy numbers and allelic ALK p.R1275Q mutation frequencies were applied to longitudinally collected liquid biopsies (peripheral blood and bone marrow plasma, n=44 biosamples), the mononuclear cell fraction from bone marrow and matched tumor samples. Marker detection was compared with current gold standard diagnostics. Reanalysis of whole-genome and targeted panel sequencing data from 169 patients identified 64 TERT-rearranged neuroblastoma samples collected at initial and/or relapse diagnosis from 55 patients (254 total TERT rearrangement events). Detection and quantification of unique TERT rearrangement breakpoints in as little as 1ng of total cell-free DNA in peripheral blood plasma improved therapy response assessment and early relapse detection in individual patients. Proof-of-concept is provided for minimal residual disease detection in the bone marrow niche, from which relapses frequently arise, by analyzing unique TERT rearrangement breakpoints in bone marrow plasma-derived cell-free DNA. TERT rearrangement breakpoints, as a single marker or combined with mutations in the RAS/MAPK/ALK signaling transduction network, can serve as robust and highly sensitive biomarkers for disease activity and spatially and temporally resolve disease better than current gold standard diagnostics in individual patients with TERT-driven neuroblastoma

Exploiting a PAX3-FOXO1-induced synthetic lethal ATR dependency for rhabdomyosarcoma therapy

Pathognomonic PAX3-FOXO1 fusion oncogene expression is associated with poor outcome in rhabdomyosarcoma. Combining genome-wide CRISPR screening with cell-based functional genetic approaches, we here provide evidence that PAX3-FOXO1 induces replication stress, resulting in a synthetic lethal dependency to ATR-mediated DNA damage-response signaling in rhabdomyosarcoma. Expression of PAX3-FOXO1 in muscle progenitor cells was not only sufficient to induce hypersensitivity to ATR inhibition, but PAX3-FOXO1-expressing rhabdomyosarcoma cells also exhibited increased sensitivity to structurally diverse inhibitors of ATR, a dependency that could be validated genetically. Mechanistically, ATR inhibition led to replication stress exacerbation, decreased BRCA1 phosphorylation and reduced homologous recombination-mediated DNA repair pathway activity. Consequently, ATR inhibitor treatment increased sensitivity of rhabdomyosarcoma cells to PARP inhibition in vitro, and combined ATR and PARP inhibition induced regression of primary patient-derived alveolar rhabdomyosarcoma xenografts in vivo. Moreover, a genome-wide CRISPR activation screen (CRISPRa) identified FOS gene family members as inducers of resistance against ATR inhibitors. Mechanistically, FOS gene family members reduced replication stress in rhabdomyosarcoma cells. Lastly, compassionate use of ATR inhibitors in two pediatric patients suffering from relapsed PAX3-FOXO1-expressing alveolar rhabdomyosarcoma showed signs of tolerability, paving the way to clinically exploit this novel synthetic lethal dependency in rhabdomyosarcoma

Passenger gene co-amplifications create collateral therapeutic vulnerabilities in cancer

DNA amplifications in cancer do not only harbor oncogenes. We sought to determine whether passenger co-amplifications could create collateral therapeutic vulnerabilities. Through an analysis of >3,000 cancer genomes followed by the interrogation of CRISPR-Cas9 loss-of-function screens across >700 cancer cell lines, we determined that passenger co-amplifications are accompanied by distinct dependency profiles. In a proof-of-principle study, we demonstrate that co-amplification of the bona fide passenger gene DEAD-Box Helicase 1 (DDX1) creates an increased dependency to the mTOR pathway. Interaction proteomics identified tricarboxylic acid (TCA) cycle components as previously unrecognized DDX1 interaction partners. Live-cell metabolomics highlighted that this interaction could impair TCA activity, which in turn resulted in enhanced mTORC1 activity. Consequently, genetic and pharmacologic disruption of mTORC1 resulted in pronounced cell death in vitro and in vivo. Thus, structurally linked co-amplification of a passenger gene and an oncogene can result in collateral vulnerabilities. SIGNIFICANCE: We demonstrate that coamplification of passenger genes, which were largely neglected in cancer biology in the past, can create distinct cancer dependencies. Because passenger coamplifications are frequent in cancer, this principle has the potential to expand target discovery in oncology

Therapeutic targeting of ATR in alveolar rhabdomyosarcoma

Despite advances in multi-modal treatment approaches, clinical outcomes of patients suffering from PAX3-FOXO1 fusion oncogene-expressing alveolar rhabdomyosarcoma (ARMS) remain dismal. Here we show that PAX3-FOXO1-expressing ARMS cells are sensitive to pharmacological ataxia telangiectasia and Rad3 related protein (ATR) inhibition. Expression of PAX3-FOXO1 in muscle progenitor cells is not only sufficient to increase sensitivity to ATR inhibition, but PAX3-FOXO1-expressing rhabdomyosarcoma cells also exhibit increased sensitivity to structurally diverse inhibitors of ATR. Mechanistically, ATR inhibition leads to replication stress exacerbation, decreased BRCA1 phosphorylation and reduced homologous recombination-mediated DNA repair pathway activity. Consequently, ATR inhibitor treatment increases sensitivity of ARMS cells to PARP1 inhibition in vitro, and combined treatment with ATR and PARP1 inhibitors induces complete regression of primary patient-derived ARMS xenografts in vivo. Lastly, a genome-wide CRISPR activation screen (CRISPRa) in combination with transcriptional analyses of ATR inhibitor resistant ARMS cells identifies the RAS-MAPK pathway and its targets, the FOS gene family, as inducers of resistance to ATR inhibition. Our findings provide a rationale for upcoming biomarker-driven clinical trials of ATR inhibitors in patients suffering from ARMS

The effect of valproic acid and oxcarbazepine on the distribution of adhesion molecules in embryo implantation

This study was intended to investigate the effect of valproate (VPA) and oxcarbazepine (OXC) on embryo implantation in terms of extracellular matrix protein distribution. Thirty female rats (Wistar albino) were assigned to three groups of 10 animals each. Group 1 was administered two doses of saline solution, group 2, two doses of VPA at 300 mg/kg/day and group 3, two doses of OXC at 100 mg/kg/day, for a period of 3 months. Female rats with vaginal plugs mated with males for one night were placed into separate cages. Day of mating was taken as day 0, and implantation areas were obtained with rats being sacrificed on the morning of day 7. Immunohistochemical staining and electron microscopic protocols were then applied. At electron microscopic evaluation, extraembryonic endoderm and ectoderm layers could not be distinguished in semi-thin sections in the VPA group, while they were partially differentiated in the OXC group. At immunohistochemical staining, laminin was observed in the primary embryonic endoderm cell visceral and parietal layers, the uterine luminal epithelial cells and the secondary decidual zone in the control group. In the VPA group, it was weakly expressed in some embryo trophoectoderm cells and uterine luminal epithelial cells and moderately in some decidual cells. In the OXC group, it was moderately expressed in some trophoectoderm and decidual cells. Collagen IV was localized in the ectoplacental cone cells and secondary decidual zone and weak in the luminal epithelial cells in the control group. In the VPA and OXC groups, collagen IV was negative in all embryonic and maternal structures in the VPA and OXC groups. Vimentin was moderately expressed in the luminal epithelium and strongly expressed in the primary decidual zone and ectoplacental cone cells in the control group. In the VPA group, it was negative in the embryo trophoectoderm, decidual and uterine luminal epithelial cells, while in the OXC group it was moderately localized in the ectoplacental cone cells. The use of VPA and OXC has a negative effect on the expression of extracellular matrix proteins that play a key role in embryo implantation in young rats. This may lead to pregnancies ending in failure. (C) 2011 Elsevier Ireland Ltd. All rights reserved

The effect of valproic acid and oxcarbazepine on the distribution of adhesion molecules in embryo implantation

This study was intended to investigate the effect of valproate (VPA) and oxcarbazepine (OXC) on embryo implantation in terms of extracellular matrix protein distribution. Thirty female rats (Wistar albino) were assigned to three groups of 10 animals each. Group 1 was administered two doses of saline solution, group 2, two doses of VPA at 300. mg/kg/day and group 3, two doses of OXC at 100. mg/kg/day, for a period of 3 months. Female rats with vaginal plugs mated with males for one night were placed into separate cages. Day of mating was taken as day 0, and implantation areas were obtained with rats being sacrificed on the morning of day 7. Immunohistochemical staining and electron microscopic protocols were then applied. At electron microscopic evaluation, extraembryonic endoderm and ectoderm layers could not be distinguished in semi-thin sections in the VPA group, while they were partially differentiated in the OXC group. At immunohistochemical staining, laminin was observed in the primary embryonic endoderm cell visceral and parietal layers, the uterine luminal epithelial cells and the secondary decidual zone in the control group. In the VPA group, it was weakly expressed in some embryo trophoectoderm cells and uterine luminal epithelial cells and moderately in some decidual cells. In the OXC group, it was moderately expressed in some trophoectoderm and decidual cells. Collagen IV was localized in the ectoplacental cone cells and secondary decidual zone and weak in the luminal epithelial cells in the control group. In the VPA and OXC groups, collagen IV was negative in all embryonic and maternal structures in the VPA and OXC groups. Vimentin was moderately expressed in the luminal epithelium and strongly expressed in the primary decidual zone and ectoplacental cone cells in the control group. In the VPA group, it was negative in the embryo trophoectoderm, decidual and uterine luminal epithelial cells, while in the OXC group it was moderately localized in the ectoplacental cone cells. The use of VPA and OXC has a negative effect on the expression of extracellular matrix proteins that play a key role in embryo implantation in young rats. This may lead to pregnancies ending in failure. © 2011 Elsevier Ireland Ltd