bluuebunny/crossref_metadata_2025_split huggingface dataset:
DIPG-57. A systems biology approach to defining and targeting master regulator dependencies from bulk and single-Cell RNA-seq in diffuse midline glioma (DMG)
Authors: Fernández Ester Calvo , Wang Junqiang , Griffin Aaron , Minns Hanna , Wei Hong-Jian , Zhang Xu , Szalontay Luca , Mundi Prabhjot , Wu Cheng-Chia , Gartrell Robyn , Zacharoulis Stergios , Califano Andrea , Pavisic Jovana 
Published: June 2022

Abstract
Diffuse midline glioma (DMG) are fatal pediatric brain tumors with no effective systemic therapies. Molecular profiling demonstrates epigenetic dysregulation and heterogeneity, and novel approaches are needed to identify promising drugs and drug combinations. We used network-based computational analysis of RNA-seq to discover Master Regulator (MR) proteins that represent targetable, mechanistic determinants of distinct DMG cell states. We reverse-engineered the first DMG-specific regulatory network from 122 publicly available DMG RNA-seq profiles with ARACNe. Using this network, we measured sample-specific protein activity based on differential expression of their targets via VIPER. Activity-based clustering identified two clusters showing a trend in survival differences (&gt;1 year, by χ2). The most activated MRs (i.e., TOP2A, CENPF, BUB1B, FOXM1, GTSE1, MKI67, E2F8), relative to normal caudate tissue, were enriched in cell cycle regulation members. The cluster with worse outcomes had significantly higher activity. Targetable MRs activated in subsets of patients () included TOP2A, CHEK1, CDK2, and EZH2. RNA-seq profiles were generated in two DMG cell lines following perturbation with ~400 oncology drugs, and used to identify drugs that invert MR activity profiles with the OncoTreat algorithm. We identified four pharmacotypes, and predicted sensitivity to HDAC, proteosome, EGFR, MEK, and PI3K inhibitors (), amongst others, consistent with published DMG high-throughput drug screens. To dissect intra-tumor heterogeneity, we measured protein activity from published single-cell RNA-seq profiles of 6 DMG patients, using single-cell based regulatory networks. Preliminary activity-based analysis identified 6 cell states representing distinct stages of differentiation/proliferation, including an oligodendrocyte precursor cell-like proliferative state whose MRs overlapped with bulk data (i.e. TOP2A, CENPF, FOXM1, E2F8, ZWINT, CCNA2), suggesting this as a key regulatory module. We are identifying cell state-specific MR-inverter drugs with OncoTreat to ultimately suggest drugs and drug combinations that collapse the transcriptional program and induce tumor kill for validation in MR-matched preclinical DMG models.
DDEL-01. The role of key pharmacodynamic and pharmacokinetic parameters in drug response prediction of pediatric tumors in the precision oncology study INFORM
Authors: Jamaladdin Nora , Peterziel Heike , ElHarouni Dina , Jäger Natalie , Holland-Letz Tim , Kopp-Schneider Annette , Sigaud Romain , Witt Olaf , Oehme Ina , Milde Till 
Published: June 2022

Abstract
INTRODUCTION: The INFORM (INdividualized Therapy FOr Relapsed Malignancies in Childhood) study is a European pediatric precision oncology program. Using state of the art molecular assays, INFORM aims for identification of targetable genetic alterations, matching drugs and clinical trials. High evidence targets were associated with doubling of progression free survival when patients received a matching drug. However, the fraction of tumors with high evidence drug targets remains low requiring functional layers of information such as drug sensitivity profiling. The aim of this project is to identify and investigate the role of key pharmacodynamic and pharmacokinetic parameters to improve the predictivity of ex vivo drug response of pediatric tumors. METHODS: Positive control cell lines harboring specific mutations (n=7) and primary tumors (n=121) from INFORM, including 10% ependymomas, 7% high grade gliomas, 5% neuroblastomas and 4% medulloblastomas, were profiled ex vivo using a library of n=76 clinically relevant oncology drugs in a 384 well plate format. Metabolic activity was measured after 72h of treatment. Quality control (QC) was done using the robust z-factor, correlation of replicates and mean negative control. Hit selection was based on maximum percentage inhibition, normalized AUC metric (DSSasym) and maximum serum concentration (Cmax) of the drug. Clinical follow-up was collected using a questionnaire. RESULTS: A linear mixed model revealed the DSSasym to be the strongest pharmacodynamic parameter in drug prediction in cell lines. Drug screens of n=105 INFORM cases passed QC. Application of the filtering parameters resulted in prediction of n=1-16 drugs/case (min-max). A data base of published pediatric pharmacokinetic parameters of the drug library was generated. Analysis of predictive parameters and clinical follow-up of clinical samples is ongoing. CONCLUSION: Including pharmacodynamic as well as clinical pharmacokinetic parameters is paramount to identify potentially clinically active compounds from ex vivo drug screen data. Further algorithm development is warranted.
EPCT-06. Phase I study of ribociclib and everolimus post-radiotherapy in children with newly diagnosed diffuse intrinsic pontine glioma (DIPG) and high-grade glioma (HGG): Updated report from the COllaborative Network for NEuro-Oncology Clinical Trials (CONNECT)
Authors: Lazow Margot A , DeWire Mariko , Campagne Olivia , Leach James L , Fuller Christine , Kumar Shiva Senthil , Stanek Joseph , de Blank Peter , Hummel Trent R , Pillay-Smiley Natasha , Salloum Ralph , Stevenson Charles B , Baxter Patricia , Gass David , Goldman Stewart , Leary Sarah E S , Carle Adam , Lane Adam , Drissi Rachid , Stewart Clinton , Fouladi Maryam 
Published: June 2022

Abstract
BACKGROUND: Dual inhibition of CDK4/6 and mTOR in DIPG and pediatric HGG has strong biologic rationale, given prevalent genetic alterations resulting in upregulated cell cycle and PI3K/mTOR pathways in these diseases, as well as non-overlapping agent toxicities. This study sought to evaluate safety/tolerability and determine the recommended phase 2 dose (RP2D) of ribociclib and everolimus among children with newly diagnosed DIPG and HGG post-radiotherapy. METHODS: Patients were enrolled according to a Rolling-6 design and received oral ribociclib and everolimus once daily for 21 and 28 days, respectively, starting 2-4 weeks post-completion of radiotherapy. All HGG and biopsied DIPG patients were screened for RB protein presence by immunohistochemistry. Pharmacokinetics and survival data were analyzed.
RESULTS: Nineteen patients enrolled (median age: 8 years [range: 2-18]). Three patients enrolled at each of dose levels 1 and 2 without dose-limiting toxicities (DLTs). Thirteen patients enrolled at dose level 3, with one patient experiencing a DLT (grade 3 infection). One patient came off therapy prior to cycle 9 due to cardiac toxicity. The most common grade 3/4 toxicities were neutropenia (33%), leucopenia (17%), and lymphopenia (11%). Steady-state everolimus exposures in combination were 1.9±0.9-fold higher than single-agent administration. Median overall survival (OS) for 15 patients with DIPG was 13.9 months, with 12-, 24-, and 36-month OS of 53.3%, 38.9%, and 38.9%. Median event-free survival for four patients with HGG was 10.5 months. Among patients with tumor molecular profiling, two longer survivors (OS: 20, &gt;37 months) had evidence of cell cycle upregulation with CDKN2A/B deletion and CDK4 overexpression identified. CONCLUSIONS: The combination of ribociclib and everolimus was well-tolerated post-radiotherapy in children with newly diagnosed DIPG and HGG, with a RP2D of ribociclib 170 mg/m2 days 1-21 and everolimus 1.5 mg/m2 days 1-28. Results will inform a molecularly-guided phase II study currently underway to evaluate efficacy.
EPEN-02. Adaptive Convergence of Methylomes Reveals Epigenetic Drivers and Boosters of Repeated Relapses in Patient-matched Childhood Ependymomas and Identifies Targets for Anti-Recurrence Therapies
Authors: Zhao Sibo , Li Jia , Zhang Huiyuan , Qi Lin , Du Yuchen , Kogiso Mari , Braun Frank K , Huang Yulun , Teo Wan-Yee , Baxter Patricia , Adesina Adekunle , Song Yongcheng , Sun Deqiang , Li Xiao-Nan 
Published: June 2022

Abstract
Ependymoma (EPN) is the third most common brain tumor in children and frequently recurs. Here, we report an integrated longitudinal analysis of epigenetic, genetic and tumorigenic changes in 30 patient-matched repeated relapses obtained from 10 pediatric patients to understand the mechanism of recurrences. Genome-wide DNA methylation analysis revealed stable molecular subtypes and convergent epigenetic reprogramming during serial relapses of the 5 RELA and 5 PFA EPNs that paralleled with elevated patient-derived orthotopic xenograft (PDOX) (13/27) formation in the late relapses. Differentially methylated CpGs (DMCs) preexisted in the primary tumors and persisted in the relapses (driver DMCs) were detected, ranging from 51 hypo-methylated in RELA to 148 hyper-methylated DMCs in PFA tumors; while newly acquired DMCs sustained in all the relapses but was absent in the primary tumors (booster DMCs) ranged from 38- 323 hyper-methylated DMCs in RELA and PFA EPNs, respectively. Integrated analysis of these DMC associated DNA methylation regions (DMRs) and RNAseq in both patient and PDOX tumors identified a small fraction of the differentially expressed genes (4.6±4.4% in RELA and 4.5±1.1% in PFA) as regulated by driver DMRs (e.g., up-regulated CACNA1H, SLC12A7, RARA in RELA and HSPB8, GMPR, ITGB4 in PFA) and booster DMRs (including the sole upregulated PLEKHG1 in RELA and NOTCH, EPHA2, SUFU, FOXJ1 in PFA tumors). Most these genes were novel to EPN relapses. Seven DMCs in RELA and 22 in PFA tumors were also identified as potential relapse predictors. Finally, integrating DNA methylation with histone modification identified LSD1 as a relapse driver gene. Combined treatment of a novel inhibitor SYC-836 with radiation significantly prolonged survival times in two PDOX models of recurrent PFA. This high-resolution epigenetic and genetic roadmap of EPN relapse and our 13 new PDOX models should significantly facilitate biological and preclinical studies of pediatric EPN recurrences.
EPEN-05. Adenosine receptor expression in paediatric ependymoma
Authors: Spanoudakis Chelsea , Chapman Rebecca , Paine Simon , Grundy Richard , Franks Hester , Ritzmann Timothy 
Published: June 2022

Abstract
PURPOSE: Paediatric ependymoma is associated with dismal outcomes. Whilst understanding of its underlying biology has advanced, there has been little progress in treatment and clinical outcomes. Acting through four G protein-coupled receptors (encoded by ADORA1, ADORA2A, ADORA2B and ADORA3), adenosine is a signalling molecule often present at high levels in tumours. Adenosine signalling can aid tumour proliferation and invasiveness via mechanisms including suppression of tumour-infiltrating immune cells. Adenosine receptors therefore represent a potential therapeutic target in paediatric ependymoma, however neither levels nor patterns of expression have been previously reported. We hypothesised that adenosine receptors would be expressed in paediatric ependymoma and that this expression would vary between molecular subgroups. METHODS: Three publicly available gene expression datasets were analysed for adenosine receptor expression using Kruskal-Wallis, Mann-Whitney U and chi-square tests. RNAscope assays for adenosine receptors and CD68 were then performed on ten full-face ependymoma FFPE sections from posterior fossa A (PFA1 and PFA2) tumours to understand patterns of expression within ependymomas with the highest levels of expression identified by the gene expression datasets. RESULTS: Statistically significant differences were identified between adenosine-related genes across ependymoma subgroups of differing anatomical origin (supratentorial ZFTA-positive versus posterior fossa A and B (PFA/PFB)), with median adenosine-related gene levels generally higher in the PFA subgroup. Particularly, ADORA1, 2A, 2B and 3 gene expression was higher in PFA tumours than other subgroups. Analysis of the ten cases demonstrated measurable expression of all four adenosine receptors by RNAscope and patterns in the distribution and relative levels of expression of the adenosine receptors across PFA1 and PFA2 tumours were described. CONCLUSION: Using two different techniques we demonstrated that adenosine receptors are expressed in paediatric ependymomas. There are significant differences in level of expression between tumour subgroups. Adenosine receptors therefore represent a potential therapeutic target which should be explored further.
EPEN-11. Phase 0/I Study of GM-CSF and Intrathecal Trastuzumab In Children With Recurrent Posterior Fossa Ependymoma
Authors: Norris Gregory , Widener Melissa , Amani Vladamir , Donson Andrew , Schissel Debra , Bruno Courtney , Mettetal Ashley , Ramirez Dominique , Gustafson Daniel , Hankinson Todd , Handler Michael , Macy Margaret , Foreman Nicholas , Dorris Kathleen 
Published: June 2022

Abstract
BACKGROUND: Posterior fossa ependymoma (PF EPN) is a pediatric central nervous system malignancy that has a poor outcome to standard therapeutic approaches. The majority of PF EPN have been shown to harbor increased HER2 expression, making it a logical therapeutic target. Trastuzumab is a monoclonal antibody that targets HER2, and sargramostim (GM-CSF) stimulates hematopoietic progenitor cell proliferation. The combination of trastuzumab and GM-CSF has been shown to trigger antibody-dependent cell cytotoxicity in-vitro in patient-derived PF EPN cell lines. METHODS: Children aged 1–21 years with relapsed PF EPN, no ventriculoperitoneal shunt, and no CSF obstruction are eligible for the Phase 0/I single-institution clinical trial at Children’s Hospital Colorado. Stratum 1 involves intrathecal (IT) trastuzumab and subcutaneous (subQ) GM-CSF prior to standard-of-care surgical resection. Stratum 2 involves a 3 + 3 phase I design with serial IT trastuzumab doses, each preceded by three days of GM-CSF, to establish the maximum tolerated dose for IT trastuzumab. RESULTS: Trastuzumab was detected in a sufficient number of tumors after presurgical IT delivery in Stratum 1 to open Stratum 2. Seven patients (3 female) have been enrolled in Stratum 2. Median age at enrollment is 8.1 years (range, 3–20 years). CSF pharmacokinetic analysis demonstrate detectable trastuzumab up to 14 days after IT doses. No dose-limiting toxicities or grade 3 or 4 adverse events have occurred. Four patients completed all planned study therapy and remain progression-free post-therapy (median, 23 months, range, 6-42 months). Three patients progressed on therapy (median, 4 cycles). Biologic correlative studies are in process. CONCLUSIONS: IT trastuzumab penetrates PF EPN tumor tissue and demonstrates an excellent safety profile. Stratum 2 remains open to accrual at Dose Level 2. IT trastuzumab+GM-CSF warrants consideration for a multi-institutional Phase II trial.
EPEN-12. Sunitinib induces apoptosis-mediated cytotoxicity in PFA ependymoma
Authors: O'Shaughnessy Bohdan , Donson Andrew , Amani Vladimir , Griesinger Andrea , Grimaldo Enrique , Harris Faith , Foreman Nicholas 
Published: June 2022

Abstract
Ependymoma (EPN) has been previously shown to be selectively targeted by three classes of FDA-approved chemotherapy drugs: fluorinated pyrimidines, retinoids, and a subset of small molecule receptor tyrosine kinase inhibitors (RTKIs). We have identified sunitinib malate as an RTKI with ependymoma selectivity, in addition to previously identified ependymoma-selective RTKIs axitinib, imatinib, and pazopanib. Sunitinib—which targets VEGFR, PDGFR and c-kit—elicited unexpectedly high levels of cytotoxic apoptosis (caspase 3/7 cleavage) in EPN PFA cell lines harboring high-risk chromosome 1q gain and 6q loss. In this in-vitro screen of 100+ FDA-approved chemotherapy drugs, sunitinib was the only RTKI in the top five most cytotoxic drugs, a group that included idarubicin HCl, topotecan HCl, daunorubicin HCl, and doxorubicin. Additionally, sunitinib exhibited comparable caspase 3/7 cleavage levels in normoxia and hypoxia, suggesting that this therapy would be as effective in treatment of tumors with potentially resistant hypoxic necrotic cores. The effect of sunitinib on EPN cellular proliferation was tracked visually using Incucyte cell imaging technology, demonstrating consistent dose-dependent inhibition of proliferation. Sunitinib achieved more acute upregulation of apoptosis than axitinib, an EPN-selective RTKI currently being studied in preclinical models. A prior phase II trial of sunitinib in pediatric EPN and high-grade glioma showed that treatment was well tolerated but with no clinical benefit as a monotherapy. However, given encouraging clinical results of combining sunitinib with radiation, our ongoing preclinical studies of sunitinib in EPN are being conducted in the context of radiation which is standard treatment for EPN. Sunitinib presents a promising treatment to an intractable pediatric brain tumor that exhibits high rates of relapse and morbidity in affected individuals.
EPEN-15. Radiotherapy with helium ions has the potential to improve both endocrine and neurocognitive outcome in pediatric patients with ependymoma
Authors: Wickert Ricarda , Adeberg Sebastian , Deng Maximilian , Tessonnier Thomas , Hoeltgen Line , Debus Jürgen , Herfarth Klaus , Harrabi Semi 
Published: June 2022

Abstract
BACKGROUND: Ependymoma are the third most frequent pediatric brain tumors. To prevent local recurrence, the resection site should be irradiated. Especially the treatment of pediatric patients requires precise dose application and optimal protection of organs at risk. Compared to photon radiation treatment, proton therapy often achieves better results regarding target coverage and organ-sparing. Due to their physical properties, helium ions can further reduce side effects, providing better protection of healthy tissue despite similar target coverage. PATIENTS AND METHODS: In our in-silico study, 15 pediatric patients (median age six years) with ependymoma located in the posterior cranial fossa were considered. All patients underwent adjuvant radiotherapeutic treatment with active scanned protons at Heidelberg Ion-Beam Therapy Center (HIT). Both helium ion and highly conformal IMRT plans were calculated to evaluate the potential dosimetric (and clinical) benefit of ion beam therapy compared to the current state of the art photon-based treatments. RESULTS: Target coverage was comparable in all three modalities (He, H+, Ph): homogeneity indices (HI) and inhomogeneity coefficients (IC) of HIHe=5.8±3.8, HIH+=7.5±4.0, HIPh=6.4±4.3, ICHe=0.2±0.1, ICH+=0.2±0.1, ICPh=0.2±0.1. As expected, the integral dose absorbed by the healthy brain tissue could be reduced significantly using helium ions versus IMRT (-45.3%±15.1%). Based on our preliminary results, even compared to active scanned protons – currently the most precise radiation technique worldwide – the relative dose reduction for critical neuronal structures using helium ions on average amounts to -27.2%±14.4%. CONCLUSION: Previous studies could clearly demonstrate that the dosimetric advantage of protons translates into a measurable clinical benefit for pediatric patients with brain tumors. Given the dose response relationship of critical organs at risk, the results of our in-silico study provide a strong rationale that the use of helium ions has the potential to even further reduce the risk for treatment related sequelae.
EPEN-16. Epithelial Progenitor Cell Abundance and Copy Number Variant Gains and Losses Impact the Biology of Recurrent Ependymoma
Authors: Norris Gregory , Fu Rui , Riemondy Kent , Willard Nicholas , Griesinger Andrea , Amani Vladamir , Grimaldi Enrique , Harris Faith , Gilani Ahmed , Hankinson Todd , Hesselberth Jay , Foreman Nicholas , Donson Andrew 
Published: June 2022

Abstract
Ependymoma (EPN) is a common pediatric brain tumor that is fatal in approximately 50% of cases. Posterior fossa A (PFA) EPN has the highest rate of recurrence and the worst prognosis of all EPN subtypes. At relapse, it is typically incurable even with re-resection and re-irradiation. The biology of recurrent ependymoma remains largely unknown, which hinders clinical advances. In this study, we use paired samples of primary and recurrent disease from the same patient to investigate the drivers of recurrence. DNA methylation studies reveal frequent copy number variants at recurrence that were not present at primary presentation. We report a frequent gain of chromosome 1q and loss of 6p at recurrence, which has not been previously reported and may be a driver of recurrent disease. We have previously shown that PFA EPN is comprised of 4 main neoplastic cell populations, two well-differentiated populations termed ciliated and transportive ependymal cells, a mesenchymal cell population, and an undifferentiated population. Using spatial transcriptomics (Visium) integrated with single-nuclei RNA-seq (Chromium), we discovered that a highly proliferative EPN progenitor population of epithelial lineage is significantly upregulated at recurrence which we hypothesize drives refractory disease. Accordingly, we found higher expression of EPN progenitor gene signatures in bulk RNA transcriptomes of primary tumors that later recurred compared to tumors that never recurred. Together, these findings highlight the biologic differences between primary and recurrent disease and add to our understanding of treatment resistance in childhood ependymoma.