bluuebunny/crossref_metadata_2025_split huggingface dataset:
DIPG-18. AI HUNTING FOR NEW DRUGS IN PEDIATRIC GLIOMA
Authors: Hashizume Rintaro , Newbury Patrick , Ishi Yukitomo , Zao Guisheng , Glicksberg Benjamin , Paithankar Shreya , Nazarian Javad , Pacold Michael , Watanabe Jun , Uchida Eita , Nicolaides Theodore , Chen Bin 
Published: June 2023

Abstract
Diffuse intrinsic pontine glioma (DIPG) is one of the most devastating pediatric gliomas, with nearly all patients succumbing to progressive tumor growth within two years of diagnosis. The identification of effective therapeutics based on the genetic features is of high importance for improving treatment outcomes for DIPG patients. We have developed machine learning algorithms that allow profiling thousands of genetic features, which can all contribute towards drug discovery. This study aimed to identify potential therapeutic agents using a computational pipeline to perform an in-silico screen for novel drugs. We then tested the identified drugs against a panel of patient-derived DIPG cell lines. Using a systematic computational approach with publicly available databases of gene signature in DIPG patients and cancer cell lines treated with a library of clinically available drugs, we identified drug hits with the ability to reverse a DIPG gene signature to one that matches normal tissue background. The biological and molecular effects of drug treatment was analyzed by cell viability assay and RNA sequence. In vivo DIPG mouse model survival studies were also conducted. As a result, two of three identified drugs showed potency against the DIPG cell lines. Triptolide and mycophenolate mofetil (MMF) demonstrated significant inhibition of cell viability in DIPG cell lines. Guanosine rescued reduced cell viability induced by MMF. In vivo, MMF treatment significantly inhibited tumor growth in orthotopic DIPG xenograft models. In conclusion, we identified clinically available drugs with the ability to reverse DIPG gene signatures and anti-DIPG activity in vitro and in vivo. This novel approach can repurpose drugs and significantly decrease the cost and time normally required in drug discovery.
DIPG-23. THE ROLE OF FOXO3 IN DMG RESISTANCE AND RESPONSE TO THERAPIES TARGETING DMG METABOLISM
Authors: Petrovic Antonela , Fernandez Solène , Uhr Nora Maria , Laternser Sandra , Müller Sabine , Nazarian Javad 
Published: June 2023

Abstract
Pediatric diffuse midline gliomas (DMGs), including diffuse intrinsic pontine glioma (DIPG), are the most difficult childhood brain cancers to treat, with an overall survival rate of less than 12 months from diagnosis. Despite the H3K27M mutation being the main tumor driver, activation of the PI3K/Akt pathway also occurs, altering cancer cell metabolism, increasing glycolysis, and proliferation. Our research aims to understand the underlying mechanisms of resistance to therapies targeting DMG metabolism and to develop more effective treatment strategies. We have studied the effectiveness of ONC201 in targeting DMG cancer metabolism through mitochondrial degradation, reactive oxygen species increase, and oxidative phosphorylation impairment. Our findings suggest that despite promising results in patients, DMG tumor cells switch to glycolysis after treatment through PI3K/Akt pathway activation, which contributes to chemoresistance. We have found that the FOXO3 transcription factor plays a crucial role in determining DMG tumor sensitivity to therapy, specifically in the response to combined ONC201 and PI3K inhibitors. We have shown that FOXO3 activity is abolished via PI3K pathway activation in resistant DMG cell lines, leading to cytoplasmic translocation and tumor cell survival. Additionally, we found that the expression of FOXO3 is dysregulated in DMG patient tumors. Our data implies that a failure of FOXO3 to reach the nucleus may be a contributing factor to the inadequate response seen in certain ONC201 treated DMG patients. By utilizing CRISPR-modified patient-derived DIPG cells in vitro, we investigated the impact of FOXO3 knockout/overexpression on tumor sensitivity to various treatment regimens. We have validated new PI3K inhibitors and FOXO3 activators as potential therapeutic strategies for DMG patients. Our findings suggest that targeting FOXO family of transcription factors may be a promising approach to improve the efficacy of metabolic-targeting therapies for DMGs and ultimately improve the survival of patients diagnosed with this challenging pediatric brain cancer.
DIPG-29. A CONNECT CONSORTIUM PRECLINICAL STUDY IDENTIFIES MEK INHIBITION AND RADIATION AS POTENTIAL COMBINATION PARTNERS FOR THE ALK2 INHIBITOR TP-0184 IN ACVR1-MUTANT DMG
Authors: Rogers Rebecca , Tsoli Maria , Kumar Shiva Senthil , Potente Elisabet Fernandez , Biery Matt , Grabovska Yura , Mackay Alan , Carvalho Diana , Pereria Rita , Burford Anna , Sejdiu Drenusha , Ruddle Ruth , Gabel Florian , Raynaud Florence , Yadavilli Sridevi , Mizoguchi Sean , Subramaniam Bavani , Kilburn Lindsey , Hwang Eugene , Nazarian Javad , Vitanza Nicholas , Ziegler David , Drissi Rachid , Jones Chris 
Published: June 2023

Abstract
Somatic mutations in ACVR1, which encodes the serine/threonine kinase ALK2, are found in 20-25% of DMG-H3K27 patients. Treatment of ACVR1-mutant orthotopic xenografts with multiple chemotypes of ALK2 inhibitors (ALK2i) results in extended survival in vivo but, as single agents, these inhibitors are unable to achieve a complete anti-tumour response. To identify novel combination strategies alongside ALK2 inhibition, five international laboratories pooled resources to evaluate the ALK2i TP-0184 across 26 patient-derived DMG-H3K27 models in vitro, demonstrating GI50 values of ~0.5-10uM, although with no significant difference between ACVR1-mutant and wild-type. Genome-scale CRISPR screens of ALK2i-treated ACVR1-mutant models revealed specific genetic dependencies in critical nodes of several signalling pathways including MTOR, as well as PPP2R1A, known to play a role in MAPK pathway activation. Biomarker analysis showed inhibition of phospho-SMAD1/5/9 by western blot, with RNAseq and proteomic analysis indicating downstream signalling consequences in BMP/SMAD signalling following TP-0184 treatment. We observed synergistic pharmacological interactions between TP-0184 and both everolimus (mTORi) and trametinib (MEKi) in 7 to 8 ACVR1-mutant DMG models, respectively, with the latter validated across laboratories using orthogonal assays. Importantly, combining TP-0184 with radiation in vitro showed a profound radiosensitisation effect of the ALK2i in three ACVR1-mutant models using both clonogenic and cell viability assays in multiple laboratories, in part due to an observed activation of phospho-SMAD1/5/9 by radiation. Finally, in vivo tolerability and pharmacokinetic assays in multiple immuno-compromised and immune-competent mouse strains suggested a dose of 150mg/kg TP-0184 and 0.4mg/kg trametinib for use in in vivo efficacy studies, with good CNS penetrance of both drugs in excess of in vitro GI50 values. Such studies have been initiated in six DMG-H3K27 models across our laboratories to robustly assess the combination of TP-0184 and trametinib/radiation to support rapid potential translation to clinical trial.
DIPG-34. IMMUNE SYNAPSE OPTIMIZED GRP78-SPECIFIC CAR T CELLS ELICIT AN IMPROVED ANTITUMOR RESPONSE AGAINST DIPGS
Authors: Ibanez Jorge , Houke Haley , Meehl Michaela , Hebbar Nikhil , Thanekar Unmesha , Velasquez Paulina , Krenciute Giedre 
Published: June 2023

Abstract
Diffuse intrinsic pontine gliomas (DIPGs) are highly lethal pediatric brain tumors and a leading cause of cancer-related death in children. There is currently no cure for DIPG, highlighting an urgent need for novel therapeutics. Chimeric antigen receptor (CAR)-engineered T-cell therapy offers great promise for DIPG treatment; however, several limitations need to be addressed.
In this study, we targeted a novel tumor associated antigen GRP78 after showing it is reliably expressed on the cell surface of DIPGs. To test the anti-DIPG activity of GRP78-CAR T cells, we evaluated cytotoxicity, persistence, and cytokine secretion in vitro. We found that GRP78-CAR T cells kill DIPGs but fail to proliferate and secrete cytokines compared to positive control, U87. In vivo studies further confirmed that GRP78-CAR T cells eradicated U87 tumors but not DIPGs. Based on these findings, we concluded that DIPGs cannot trigger efficient CAR T cell signaling.
Because CAR T cell effector function is influenced by antigen density, we quantified the relative GRP78 expression on DIPGs and other brain tumors, including U87. We found that GRP78 is comparatively lowly expressed on DIPGs. Live-cell imaging of calcium flux in CAR T cells further revealed that T cell activation is lower upon interaction with DIPGs than U87s, suggesting that CAR-T cells form incomplete or dysfunctional immune synapses (IS) against DIPGs. To improve IS function, we knocked-out RASA2, a TCR downstream signaling inhibitor. Our results show that T cells lacking RASA2 have an improved IS reflected by bigger synaptic areas, increased lytic granules, and pZAP70 accumulation at the synapse. RASA2 KO further increased calcium influx and proliferation capacity of GRP78-CAR T cells against DIPGs. Thus, this study confirms that antigen density controls CAR T cell antitumor activity, and improving the IS formation of CAR T cells elicits enhanced antitumor response against low antigen-expressing tumor cells.
DIPG-40. HYPOXIC STRESS EXPOSES EPIGENETIC TARGETS TO ENHANCE RADIOTHERAPY RESPONSE IN H3K27M-POSITIVE PEDIATRIC DIFFUSE MIDLINE GLIOMAS
Authors: de Freitas Amanda Pereira , Dzwigonska Monika , Trubicka Joanna , Grajkowska Wieslawa , Mieczkowski Jakub , Kaminska Bozena , Leszczynska Katarzyna 
Published: June 2023

Abstract
Diffuse midline gliomas (DMGs) are the most challenging to treat pediatric high-grade gliomas, with a dismal prognosis of 9 to 15 months of median survival. The ones localized in the pons are not accessible to the surgery and rely on radiotherapy treatment. The majority of DMGs confer a mutation in histone 3 variants (H3.3 or H3.1), leading to lysine 27 to methionine substitution (H3K27M) and a consequent global decrease in H3K27 trimethylation (H3K27me3), increased H3K27 acetylation (H3K27ac) and oncogenic changes in gene expression. An intrinsic feature of solid tumors, including DMGs, is the occurrence of hypoxic (low oxygenated) regions, which interferes with the efficiency of radiotherapy. Identifying the vulnerabilities of hypoxia-exposed tumor cells might bring new approaches in radiosensitizing DMG tumors. Hypoxia increases histone methylation in multiple solid tumors but the consequences of hypoxia-induced histone hypermethylation in H3K27M bearing tumors are unknown. Using syngeneic patient-derived DMG cell lines, we show that the presence of H3K27M prevents the hypoxia-induced hypermethylation of H3K27me3, but also impairs the hypoacetylation of histones H3 and H4 normally caused by hypoxic stress. We show that enhancing histone acetylation in hypoxic conditions with histone deacetylase (HDAC) inhibitors has a stronger sensitization effect in cells expressing H3K27M than in H3 wild-type cells. While HDAC inhibitors have been shown problematic in pediatric DMGs due to high systemic toxicity, our data points out that HDAC inhibition in the context of hypoxia may improve the therapeutic efficacy. Recent studies showed the possibility of targeting hypoxic cells with hypoxia-activated pro-drugs, including hypoxia-activated panobinostat. Our data support that such approach might be an option to target DMGs and eliminate the radiotherapy-resistant hypoxic tumor fraction, while minimizing the systemic toxicity caused by all-time active HDAC inhibitors. Studies were supported by the grant UMO-2019/33/B/NZ1/01556 (KL) from National Science Center (Poland).
DIPG-48. DIPG THROUGH THE LOOKING GLASS
Authors: Senga Sasi S 
Published: June 2023

Abstract
Diffuse intrinsic pontine glioma (DIPG) has a peculiar pathogenesis with canonical Histone variants H3.1/H3.2 wherein Lysine 27 (H3K27) is substituted to methionine (H3K27M). It is restricted to pons and affects young children whereas non canonical H3.3 mutations result in tumours across the midline and affects older children. This discrepancy in the spatiotemporal distribution provides cues to target DIPG. Based on altered neuronal signalling which is a hallmark of cancer, a deeper understanding of neuron tumour interaction may unravel numerous new targets. One such target is light. The restriction of specific spectrum of light may hinder the progression and even the development of tumours in young children. It provides a lucrative therapeutic option which can be implemented merely by blocking a certain spectrum of light with glasses in an otherwise baffling disease. It warrants a deeper understanding of the light exposure on DIPG tumour progression.
DIPG-49. A SYSTEMS BIOLOGY APPROACH TO DEFINING AND TARGETING CELL STATE-SPECIFIC MASTER REGULATOR DEPENDENCIES IN DIFFUSE MIDLINE GLIOMA
Authors: Fernández Ester Calvo , Wang Junqiang , Zhang Xu , Wei Hong-Jian , Minns Hanna , Griffin Aaron , Obradovic Aleksandar , Vlahos Lukas , Martins Timothy , Becker Pamela , Crawford John , Gartrell Robyn , Szalontay Luca , Zacharoulis Stergios , Zhang Zhiguo , Wechsler-Reya Robert , Wu Cheng-Chia , Califano Andrea , Pavisic Jovana 
Published: June 2023

Abstract
Diffuse Midline Glioma (DMG) are fatal pediatric brain tumors. We leveraged network-based methodologies to dissect the heterogeneity of DMG tumors and to discover Master Regulator (MR) proteins representing pharmacologically accessible, mechanistic determinants of molecularly distinct cell states. We produced a DMG regulatory network from 122 publicly available RNAseq profiles with ARACNe, and inferred sample-specific MR protein activity with VIPER. A CRISPR/Cas9 KO screen across 3 DMG patient cell lines identified a set of 73/77 essential genes that were enriched in the MR signature of 80% of patient samples (GSEA p=0.000034). FOXM1 emerged as an essential MR, significantly activated across virtually all patients. We then generated RNAseq profiles following perturbation with ~300 oncology drugs in 2 DMG cell lines most representative of patient MR signatures, and used this to identify drugs that invert patient MR activity profiles using the NYS/CA Dept.of Health approved OncoTreat algorithm. OncoTreat predicted sensitivity to HDAC, MEK, CDK, PI3K, and proteosome inhibitors in subsets of patients. 80%of OncoTreat-predicted drugs (p&lt;10-5) from 3 DMG patient tumor biopsies showed in vitro sensitivity in cultured tumor cells from the respective patients, with overall 68% accuracy among 223 drugs evaluated by both OncoTreat and in vitro (Fisher’s Exact Test p=0.0449). Further analysis of DMG intra-tumor heterogeneity via protein activity inference from published scRNAseq profiles identified 6 tumor clusters with unique MR signatures representing distinct cellular states. Targetable MRs and OncoTreat-predicted drugs were distinct between these states. Bulk RNAseq analysis recapitulated predictions seen in the more prevalent Oligodendrocyte progenitor cell-like states, but failed to capture MR and drug predictions for the Astrocyte-like states. Ongoing validations of cell state-specific drug predictions in vivo in subcutaneous patient-derived xenograft and orthotopic syngeneic DMG models have already shown tumor volume and subpopulation differences (e.g. Trametinib-treated). This provides a platform to nominate much-needed novel drugs to treat DMG.
DIPG-50. INSIGHTS INTO TUMORIGENESIS OF DIFFUSE INTRINSIC PONTINE GLIOMA-ONCOHISTONE AND SIGNALING
Authors: Sun Ye , Yan Kun , Wang Dan , Zhou Wei , Wang Yi , Xu Cheng , Han Yujie , Tang Yujie , Zhang Liwei , Xi Qiaoran 
Published: June 2023

Abstract
Diffuse intrinsic pontine glioma (DIPG) is a rare and incurable pediatric brain cancer with survival of less than one year. Understanding the tumorigenesis mechanisms of DIPG and identifying potential therapeutic strategy are major research foci in the DIPG field. The most lethal subtype of diffuse intrinsic pontine glioma (DIPG) is the H3K27M subtype. Although ACVR1 mutations have been implicated in the pathogenesis of this presently incurable disease, the impacts of BMP signaling on more than 60% of H3K27M DIPG carrying ACVR1 wild-type remain unknown. Here, we show that BMP ligands exert potent tumor suppressive effects against H3.3 K27M and ACVR1 WT DIPG in a SMAD-dependent manner. Specifically, clinical data revealed that many DIPG tumors have exploited CHRDL1’s capacity to hijack BMP ligands. We discovered activation of BMP signaling promotes the exit of DIPG tumor cells from “prolonged-stem-cell-like” state to differentiation by epigenetically regulating CXXC5, which acts as a tumor suppressor and positive regulator of BMP signaling. Beyond showing how BMP signaling impacts DIPG, our study also identified potent anti-tumor efficacy of Dacinostat for DIPG. Thus, our study delineates context-dependent features of BMP signaling pathway in DIPG subtype.
DIPG-57. TESTING FOR SYNERGY AMONG RADIATION AND HIGHLY CLINICALLY RELEVANT CHEMOTHERAPEUTIC AGENTS IN PATIENT-DERIVED MODELS OF DIFFUSE MIDLINE GLIOMA
Authors: Slade Mathew , Link Gabrielle , DeSisto John , Feddersen Charlotte , Bargas Damien , Knox Aaron , Green Adam 
Published: June 2023

Abstract
Diffuse midline gliomas (DMG) are aggressive pediatric brain tumors with minimal long-term survival. Radiation is currently the only standard-of-care treatment and is non-curative. Several chemotherapy agents have shown preclinical and/or early clinical promise, and we hypothesize that finding effective chemoradiotherapeutic combinations is likely to be necessary to achieve long-term survival, based on experience from other previously incurable childhood cancers. We treated 8 DMG/DIPG cell lines with one, two, or three treatments among the HDAC inhibitor panobinostat, the CDK4/6 inhibitor ribociclib, the DRD2 inhibitor ONC201, the XPO1 inhibitor selinexor, the PI3K inhibitor paxalisib, and radiation. We then measured the cell survival with MTS assays. Cells were treated with drug concentrations ranging from 1 nM to 100 uM. To assess for synergy among our combinations, we used the Combination Index (CI) model, in which a score of &lt;1 implies synergy. Of the 15 2-treatment combinations, ONC201 + radiation, ONC201 + paxalisib, ribociclib + ONC201, selinexor + paxalisib, and ribociclib + paxalisib met our criteria as successful, synergistic combinations: at least three cell lines with at least 90% cell death achieved, a CI value of 0.5 or lower at doses with at least 50% cell death, and at least 66% of dose levels with a CI value of 0.5 or lower. Early analysis suggests that ribociclib + ONC201 + paxalisib, ONC201 + paxalisib + radiation, and ONC201 + selinexor + paxalisib are the most effective three-treatment combinations. Patient-derived cell culture data in a heterogeneous pool of DMG/DIPG cell lines demonstrate synergy using several combinations of clinically relevant treatments, especially those including paxalisib. We are now optimizing treatment sequencing in synergistic combinations and testing in orthotopic xenograft models. Our goal is to find combinations that can become cycles of therapy in a multimodality clinical trial.
EPEN-02. OPTIMISING BIOMARKERS FOR ACCURATE EPENDYMOMA DIAGNOSIS, PROGNOSTICATION AND STRATIFICATION WITHIN INTERNATIONAL CLINICAL TRIALS: A BIOMECA STUDY
Authors: Chapman Rebecca J , Ghasemi David R , Andreiuolo Felipe , Zschernack Valentina , Espariat Arnault Tauziede , Buttarelli Francesca , Giangaspero Felice , Grill Jacques , Haberler Christine , Paine Simon M L , Scott Ian , Jacques Thomas S , Sill Martin , Stephan Pfister , Kilday John Paul , LeBlond Pierre , Massimino Maura , Modena Piergiorgio , Varlet Pascale , Pietsch Torsten , Grundy Richard G , Pajtler Kristian W , Ritzmann Timothy A 
Published: June 2023

Abstract
Accurate identification of brain tumour molecular subgroups is increasingly important. We aimed to establish the most accurate and reproducible ependymoma subgroup biomarker detection techniques, across 147 cases from International Society of Pediatric Oncology (SIOP) Ependymoma II trial participants, enrolled in the pan-European “Biomarkers of Ependymoma in Children and Adolescents (BIOMECA)” study. Across six European BIOMECA laboratories we evaluated epigenetic profiling (DNA methylation array); immunohistochemistry (IHC) for nuclear p65-RELA, H3K27me3, and Tenascin-C; copy number analysis via FISH and MLPA (1q, CDKN2A), and MIP and DNA methylation array (genome-wide copy number evaluation); analysis of ZFTA- and YAP1-fusions by RT-PCR and sequencing, Nanostring and break-apart FISH. DNA Methylation profiling classified 65.3% (n=96/147) of cases as EPN-PFA and 15% (n=22/147) as ST-ZFTA fusion-positive. Immunohistochemical loss of H3K27me3 was a reproducible and accurate surrogate marker for EPN-PFA (sensitivity 99-100% across three centres). IHC for p65-RELA, FISH, and RNA-based analyses effectively identified ZFTA- and YAP1- fused supratentorial ependymomas. Detection of 1q gain using FISH exhibited only 57% inter-centre concordance and low sensitivity and specificity whilst MIP, MLPA and DNA methylation-based approaches demonstrated greater accuracy. We confirm, in a prospective trial cohort, that H3K27me3 IHC is a robust EPN-PFA biomarker. Tenascin-C should be abandoned as a PFA marker. DNA methylation and MIP arrays are effective tools for copy number analysis of 1q gain, 6q and CDKN2A loss whilst FISH is inadequate. Fusion detection was successful, but rare novel fusions need more extensive technologies. We propose CORE and CORE Plus test sets to guide future diagnostic approaches. CORE tests represent those that can currently be used to stratify and inform clinical trials and diagnosis and include IHC and DNA methylation profiling. CORE Plus tests have additional advantages for challenging cases and for use in the research setting and comprise of MIP and RNA-NGS sequencing.