bluuebunny/crossref_metadata_2025_split huggingface dataset:
ATRT-07. CLINICAL APPLICABILITY OF C19MC MIRNA DETECTION IN LIQUID BIOPSIES OF ETMR PATIENTS
Authors: Madlener Sibylle , Furtner Julia , Stepien Natalia , Senfter Daniel , Mayr Lisa , Zeyda Maximilian , Gramss Leon , Aistleitner Barbara , Spiegl-Kreinecker Sabine , Rivelles Elisa , Dorfer Christian , Rössler Karl , Czech Thomas , Azizi Amedeo A , Peyrl Andreas , Lötsch-Gojo Daniela , Müllauer Leonhard , Haberler Christine , Slavc Irene , Gojo Johannes 
Published: June 2023

Abstract
Embryonal tumor with multilayered rosettes (ETMR) is a distinct central nervous system tumor entity which is characterized by dysregulation of oncogenic micro RNAs (miRNA). In the majority of cases (approx. 90%), tumors are characterized by amplification of the C19MC locus accompanied by a fusion of this locus to the TTYH1 gene. Beside the very young age of the patients, ETMR is a highly aggressive brain tumor with a dismal clinical outcome. About half of the patients relapse within the first 6 months despite intensive therapy. Based on these facts, a more rapid diagnosis as well as more accurate and faster detection of tumor response or tumor relapse would significantly improve the management of these severely affected young patients. Liquid biopsy has emerged as a highly promising tool to enable minimal invasive detection of molecular parameters to facilitate diagnosis and patient monitoring. Here, we developed a miRNA based liquid biopsy tool and performed a comprehensive profiling of the miRNA landscape in 11 ETMR tumor tissues and matching liquid biopsy samples of patients. The screening of the initial liquid biopsy samples (plasma or serum) taken at diagnosis revealed distinctly enriched miRNA levels. Further, we evaluated the use of the miRNA levels as a longitudinal tumor-monitoring tool. We detected decreasing levels after tumor resection and in long-term survivors and vice versa increasing levels in patients with progressive tumor disease. In conclusion, we developed a reliable and fast method with a turnaround time of only 4 hours between blood draw and analysis of the aberrant expressed miRNA in liquid biopsy samples of ETMR patients correlating with the clinical course of the individual patient.
ATRT-19. RARE EMBRYONAL TUMORS INCLUDING EMBRYONAL TUMOR MULTILAYER ROSETTE, OUTCOME AND PATTERN OF TREATMENT FAILURE: MD ANDERSON CANCER CENTER EXPERIENCE
Authors: He Jiasen , Munir Faryal , Sheikh Irtiza , Johnson Jason , Paulino Arnold , McGovern Susan , Sandberg David , Zaky Wafik 
Published: June 2023

Abstract
Rare embryonal tumors (excluding medulloblastoma and ATRT) are aggressive pediatric cancers that include embryonal tumor with multilayer rosettes (ETMR), embryonal tumor with abundant neuropil and true rosettes (ETANTR), and embryonal tumors not otherwise specified (ET-NOS). The presence of driver events like C19MC amplification, DICER1 mutations and other microRNA-related aberrations are vital in diagnostic classification of these tumors. The prognosis of these tumors is dismal despite intensive multimodal treatments with the 5-year overall survival being less than 30%. We retrospectively reviewed 12 patients with rare embryonal tumors who were treated at MD Anderson Cancer Center from 2010 to 2022. Of the 12 patients identified, the mean age at diagnosis was 3.6 years (range: 1-12 years) with no sex differences. Histologically, they were classified into ETMR (4/12), ETANTR (3/12) and ET-NOS (5/12) with C19MC found positive in 2/4 ETMR cases. All patients presented with large infiltrative tumors to the supratentorial (6/12), brainstem (4/12), and spinal (2/12) regions. The majority of patients (10/12) were treated by gross/subtotal resection. Treatment at diagnosis included surgery alone (3/12), surgery with chemotherapy (4/12), surgery with chemotherapy plus radiation (4/12),and chemotherapy plus radiation without surgery (1/12). Five patients reported with de-novo metastasis and 10/12 patients had disease progression at 4.1 months of median follow-up (range: 1.2-10.6 months). Six patients had local recurrence and three patients had local with distant disease at progression. Eight patients are still alive, with 5/8 of them surviving more than 5 years. In conclusion, these rare embryonal tumors are hard to diagnose and treat effectively. Even with successful surgery and intense chemotherapy, almost all of them progress/relapse but combined treatments seem to be effective in a subset of patients. Collaborative multi-institutional efforts are required to define standard treatment approaches and future patient stratification.
BIOL-01. GENERATION AND MULTI-OMICS CHARACTERIZATION OF 203 PEDIATRIC CNS TUMOUR MODELS REVEALS NEW THERAPEUTIC VULNERABILITIES
Authors: Sun Claire , Daniel Paul , Chew Nicole , Shi Hui , Loi Melissa , Parackal Sarah , Koptyra Mateusz , Adjumain Shazia , Panday Monty , Habarakada Dilru , Tourchi Motahhareh , Neeman Naama , Resnick Adam , Jones Chris , Cain Jason , Firestein Ron 
Published: June 2023

Abstract
Pediatric Central Nervous System (CNS) tumors are the leading cause of cancer-related death among children. Identifying new targeted therapies necessitates the use of pediatric cancer models that faithfully recapitulate the patient’s disease. However, the generation and characterization of pediatric cancer models has significantly lagged adult cancers, underscoring the urgent need to develop and characterize pediatric CNS models of disease. Herein, we establish a single-site collection of 233 CNS tumour cell lines, representing 14 distinct brain childhood tumor types. We subjected &gt;200 cell lines to multi-omics analyses (DNA-sequencing, RNA-sequencing, DNA methylation, proteomics, phospho-proteomics), and in parallel performed pharmacological and genetic CRISPR-Cas9 loss of function screens to identify pediatric-specific treatment opportunities and biomarkers. Our work provides insight into specific pathway vulnerabilities in molecularly defined pediatric tumor classes and uncovers biomarker-linked therapeutic opportunities of clinical relevance. Cell line data and resources are provided in an open access portal (vicpcc.org.au/dashboard).
BIOL-03. NOVEL GENETICALLY ENGINEERED MOUSE MODEL FOR CHOROID PLEXUS CARCINOMA MIMICS HUMAN DISEASE
Authors: Duarte Matilde de Almeida , Gilbertson Richard , Taylor Jessica , Jassim Amir , Hu Linda 
Published: June 2023

Abstract
Choroid plexus carcinomas (CPCs) are rare, aggressive malignant tumours of the central nervous system occurring mainly in children under the age of one. While advances in clinical and molecular stratification have enabled risk-adapted treatment planning and improvements in outcome for many types of childhood brain tumours, there has not been equivalent progress for children with CPC. This has largely been due to the low incidence, leading treatment strategies to be mostly based on case series and a “standard of care” has yet to be established. In order to elucidate a coordinated therapeutic strategy for children with CPC, it is imperative to develop in vitro and in vivo models to improve our understanding of the mechanisms underlying tumorigenesis. We hypothesised that we could develop a genetically engineered mouse model (GEMM) to recapitulate patient CPCs, allowing for an early age of onset and high penetrance rate for accurate and efficient preclinical studies. To develop this GEMM of CPC, we utilized Cre-Lox technology to target CPC cells of origin. We crossed mice that conditionally expressed Tp53 flx/flx; Rb flx/flx; Pten flx/flx with mice harbouring a Tg(Ttr-cre/Esr1*)1Vco allele, as it drives selective Cre-recombination in the early embryonic choroid plexus. Using this methodology, we have managed to produce CPCs within 90 days and with a 95% penetrance rate which we characterised using our laboratory’s tumour characterisation pipeline comprising histological evaluation, transcriptome analysis and imaging. We then used this model to investigate the transformation of the choroid during tumorigenesis and test novel therapeutic approaches to improve outcomes for patients affected by CPC. Not only are we looking for a “standard of care” that is currently inexistent for CPC, but we are also looking for one that will have minimal side effects and, therefore, not jeopardise the future of these children.
DIPG-10. DELTA-24-RGDOX PROMOTES ANTITUMOR IMMUNE RESPONSE IN DMG MODELS
Authors: Laspidea Virginia , Ausejo-Mauleon Iker , de la Nava Daniel , Nuin Sara , Hernandez-Osuna Reyes , Marco-Sanz Javier , Palacios-Alonso Daniel , Gomez-Manzano Candelaria , Fueyo Juan , Alonso Marta 
Published: June 2023

Abstract
Diffuse Midline Gliomas (DMG) are very aggressive brain tumors that arise in the brainstem of children. The prognosis of these patients is still dismal, with an overall survival of less than one year. DMG tumors are poorly infiltrated by the immune system, and therefore in this project, we propose the use of the oncolytic adenovirus Delta-24-RGDOX to enhance the antitumor immune response. Delta-24-RGDOX is based on the Delta-24-RGD platform and incorporates the OX40 ligand (OX40L). The binding of OX40 to OX40L leads to the co-stimulation of CD4 and CD8 cells, generating effector and memory T cells. Therefore, the aim of this project is to improve the antitumor effect of the virus, providing a greater co-stimulation in the tumor. In vitro, Delta-24-RGDOX was able to efficiently infect and express viral proteins in human and murine DMG cell lines, and to cause cell death in a dose-dependent manner. Moreover, the virus expressed OX40L on the membrane of infected cells, which was functional and capable of activating CD8 T cells. Once we confirmed that the viral administration into DMG in vivo models was safe, we evaluated the therapeutic effect of the virus. We observed a significant survival increase after Delta-24-RGDOX treatment of a DMG model at early tumor stage (P=0.0033, median OS PBS 9 vs 12 days for virus treated mice) and in already stablished tumors (P=0.018, median OS PBS 9 vs 12.5 days for virus treated mice). Importantly, tumors from treated mice (7 days after treatment) displayed a significant increase of immune infiltration compared to controls. Moreover, splenocytes from Delta-24-RGDOX treated mice were also more activated. These data demonstrated that Delta-24-RGDOX expresses OX40L on infected cells, promoting the modulation of the tumor microenvironment and leading to an improved survival outcome in DMG models.
DIPG-22. TRIPTOLIDE AS A POTENTIALLY PROMISING THERAPY FOR DIFFUSE MIDLINE GLIOMA
Authors: Ciani Ludovica , Laternser Sandra , Kritzer Bettina , Hasler Kerstin , Przystal Justyna M , Velagapudi Mohana R , Alonso Marta M , Zalacain Marta , Müller Sabine , Nazarian Javad 
Published: June 2023

Abstract
Diffuse Midline Gliomas (DMG) are amongst the most lethal pediatric brain tumors. Children diagnosed with DMG face a grim prognosis of 9-11 months from diagnosis. Over 85% of DMG patients harbor mutation affecting histone-encoding genes (H3.1K27M, H3.3K27M) leading to genome hypomethylation and transcriptional disruption. Despite decades of clinical studies, the development of an effective therapy remains a challenge. Triptolide is a diterpenoid triepoxide compound inhibiting cell growth and exhibiting preclinical antitumor activity. A large drug screen conducted by the NCI using DMG cell lines identified triptolide as a candidate for reducing DMG cell viability. To further investigate triptolide and its potential for clinical intervention, we used DMG preclinical in vitro and in vivo models. In vitro viability assays with triptolide alone and in combination with other therapeutic drugs (ONC201 and ONC206), were carried out using seven DMG cell lines. Single treatment with triptolide resulted in a significant decrease in DMG cell viability and combination with both ONC201 and ONC206 showed additivity. Triptolide’s toxicity was assessed in vivo through direct injections into the yolk sac of zebrafish. Preliminary data demonstrated how triptolide has higher toxicity compared to un-injected and DMSO control groups. However, a major limitation of triptolide’s clinical utility is its low solubility. Therefore, for in vivo studies, we used minnelide, a water-soluble analog of triptolide, with potent antitumor properties. Studies were performed in eleven RAG2 female mice. PDX tumor-bearing mice were treated with minnelide and ONC201 for three weeks as single or in combination. Survival studies showed no significance in minnelide monotherapy. However, minnelide + ONC201 combination therapy resulted in significant (p=0.01) survival of PDX models. Our current studies investigate the efficacy of a higher dose of minnelide in vivo. Our goal is to establish minnelide potential as a combination strategy for the treatment of children diagnosed with DMG.
DIPG-28. IDENTIFICATION AND TARGETING OF METABOLIC VULNERABILITIES IN COMBINATION WITH PDGFRA-INHIBITION IN DIFFUSE MIDLINE GLIOMA
Authors: Neyazi Sina , Gowda Pruthvi S , Trissal Maria , Fonticella Jay-Miguel , Portero Erika P , Haley-Read John-Paul , Anderson Emily P , Danial Nika N , Filbin Mariella G 
Published: June 2023

Abstract
Diffuse midline gliomas (DMG) are driven by self-renewing, stem-like glioma cells stalled in an oligodendrocyte precursor cell (OPC)-like state that are characterized by high expression of PDGFRA. This lineage overexpression of PDGFRA, together with commonly found genomic amplifications and mutations in PDGFRA, has been shown to cooperate with H3-K27M mutations in tumor development. Therefore, targeting PDGFRA has long been proposed as a potential treatment strategy for DMG. Our previous work revealed that Avapritinib, a small molecule inhibitor of PDGFRA, is highly effective in DMG cells in vitro and in vivo. Following these preclinical findings, nine DMG patients were treated with Avapritinib for the first time. While 50% of all treated patients experienced a strong clinical response from Avapritinib, tumor progression and treatment escape were eventually observed in most patients. Here, we investigated which mechanisms DMG cells use to escape Avapritinib treatment and explored how these resistance mechanisms can be therapeutically exploited. Transcriptional analysis of a DMG cell line previously identified as Avapritinib-resistant revealed an upregulation of genes associated with fatty acid metabolism and oxidative phosphorylation (OXPHOS) following treatment with Avapritinib. Functional assays confirmed elevated OXPHOS in Avapritinib-resistant cells with significant (i) increase in mitochondrial energy transduction, (ii) increase in palmitate- (a product of fatty acid metabolism) driven oxygen consumption rate and (iii) greater incorporation of palmitate-derived carbons into the tricarboxylic acid cycle. These metabolic changes could be genetically reproduced in the same cell line after CRISPR-Cas9-mediated knockout of PDGFRA. To determine which therapies could target the dependency of Avapritinib-resistant cells on OXPHOS and fatty acid metabolism, we performed a metabolic drug screening and identified two metabolic drugs to have synergistic cytotoxic effects with Avapritinib. Together, we revealed distinct metabolic changes in Avapritinib-resistant DMG cells and showed that targeting these metabolic vulnerabilities might further increase the clinical benefit of Avapritinib.
DIPG-32. PRECLINICAL TESTING OF THE EFFICACY AND SAFETY OF CRISPR/CAS9 GENE EDITED CAR-T CELL THERAPY FOR DIFFUSE MIDLINE GLIOMA (DMG)
Authors: Balakrishnan Ilango , Leach Lillie , Pierce Angela , Lakshmanachetty Senthilnath , Madhavan Krishna , Fosmire Susan , Chatwin Hannah , Green Adam , Fry Terry , Vibhakar Rajeev , Kohler Eric M , Venkataraman Sujatha 
Published: June 2023

Abstract
DMGs are highly aggressive and difficult-to-treat brain tumors in children. Recent advances in Chimeric Antigen Receptor (CAR) expressing T cell therapy suggest application for brain tumors. Recent studies also demonstrate feasibility of GD2, Her2 and B7H3 CAR-T infusions in childhood brain tumors. We identified and developed a novel CAR-T therapy, targeting the CD99 antigen, which is homogenously expressed at high levels on DMG tumor cells. These CAR-T cells showed initial clearance of tumor, but the long-term persistence and anti-tumor efficacy of these CAR-T cells in DIPG xenografts were limited due to fratricide, as T cells also express CD99. To overcome this obstacle, we have further optimized a protocol in which we first knock-out CD99 from the human donor T cells using CRISPR-cas9 gene-editing and subsequently transducing with our CD99 virus in the pure population of CD99KO T cells. Systemic delivery of these gene-edited CAR-T cells showed enhanced in vivo persistence with complete clearance of tumor in DMG mouse models, and no tumor recurrence was seen well-beyond the time frame of expected tumor recurrence after treatment with un-edited CD99 CAR-T cells. In addition, loco-regional delivery of these gene-edited CD99 CAR-T cells when administered directly to the 4th ventricle, even at a low dose, showed similar anti-tumor efficacy with significantly increased animal survival. These data suggest a regional approach analogous to Omaya reservoir administered drug in humans may be a promising alternative approach to limit any toxicity.
DIPG-42. MAPPING THE DNA METHYLATION LANDSCAPE OF DIPG REVEALS NOTABLE METHYLOME VARIABILITY RESPONSIVE TO PHARMACOLOGIC MODULATION
Authors: Tetens Ashley , Martin Allison , Arnold Antje , Novak Orlandi , Idrizi Adrian , Tryggvadottir Rakel , Craig-Schwartz Jordyn , Barbato Michael , Eberhart Charles , Resnick Adam , Koldobskiy Michael 
Published: June 2023

Abstract
Diffuse intrinsic pontine glioma (DIPG) is an incurable pediatric brainstem tumor, driven by the H3K27M mutation leading to epigenetic dysregulation. Epigenomic analyses of DIPG have shown global loss of repressive chromatin marks accompanied by DNA hypomethylation and altered gene expression. However, most investigations of the epigenetic landscape of DIPG only provide a static view of the epigenome. Such studies are not capable of adequately capturing the regulatory underpinnings of DIPG intratumoral heterogeneity and phenotypic plasticity. To address this, we performed Whole-Genome Bisulfite Sequencing (WGBS) on 23 primary patient DIPG specimens, 4 patient-derived DIPG neurosphere cell lines, and 5 normal controls. To analyze this data set, we applied a novel framework for analysis of DNA methylation variability, called informME analysis, which permits the derivation of comprehensive genome-wide DNA methylation potential energy landscapes that capture intrinsic epigenetic variation. We show that DIPG exhibits a markedly disordered epigenome, with increased stochasticity localizing to key regulatory elements and genes. We demonstrate that epigenetic instability maps onto key genes regulating pluripotency and developmental identity and hypothesize that these changes might enable tumor cells to sample a diverse range of transcriptional programs and phenotypes. Given this, we evaluated the responsiveness of the DIPG epigenetic landscape to pharmacologic modulation. We found that treatment with the DNA hypomethylating agent decitabine produced profound genome-wide demethylation and reduced DNA methylation stochasticity at active enhancers, bivalent promoters, and promoters of key developmental genes. Decitabine treatment also elicited changes in gene expression, including upregulation of genes related to immune signaling. Finally, treatment with DAC sensitized DIPG cells to the effects of histone deacetylase inhibition. This study suggests the application of epigenetic therapies to constrain cellular heterogeneity and plasticity in DIPG.
DIPG-45. ELONGIN B REGULATES H3K27M CHROMATIN INCORPORATION TO PROMOTE MALIGNANCY IN DIFFUSE MIDLINE GLIOMA
Authors: Anastas Jamie , Kebede Adam , Jiao Alan , Mimoso Claudia , Murdaugh Rebecca , Zee Barry , Filbin Mariella , Adelman Karen , Shi Yang 
Published: June 2023

Abstract
Chromatin dysregulation is both a cause and consequence of aberrant RNA Polymerase II (Pol2) transcription in cancer. Some of the most striking examples of chromatin disruption in cancer include somatic mutations in genes encoding histone H3 (H3.3/H3.1K27M) observed in ~80% of diffuse midline glioma (DMG). H3K27M mutant histones act in a dominant manner to disrupt chromatin regulation and Pol2-dependent transcription in DMG. How H3K27M impinges on the Pol2 transcriptional machinery and whether aberrant Pol2 transcription can reciprocally induce chromatin dysregulation in DMG remain open questions. We conducted epigenome-focused CRISPR dropout screens and identified multiple regulators of Pol2 elongation, including Elongin B and C (ELOB/ELOC) as DMG genetic dependencies. Follow-up studies confirm that knockout (KO) of ELOB inhibits DMG proliferation in neurosphere culture and abrogates DMG tumorigenesis in orthotopic xenografts. Additional chromatin profiling studies reveal that ELOB binding sites are enriched in H3K27M mutant histones, suggesting that ELOB works together with H3K27M to promote malignant gene expression in DMG. Indeed, reciprocal knockout studies suggest that while ELOB chromatin binding patterns were not altered by H3K27M KO, ELOB KO significantly reduced H3K27M chromatin incorporation at thousands of genomic loci. Further RNAseq and PROseq analyses reveal that ELOB KO alters Pol2 transcription resulting in the up-regulation of genes associated with neuronal and muscle differentiation and the repression of glial stem cell genes. Together, these findings suggest that H3K27M chromatin binding patterns and aberrant gene regulation in DMG are, in part, dictated by ELOB and the Pol2 elongation machinery. Finally, analyses of patient datasets indicate that ELOB complex genes are overexpressed in high grade glioma and DMG and correlate with decreased patient survival. Collectively, these studies suggest that a functional interaction between ELOB and H3K27M mutant histones induces DMG-specific aberrations in chromatin and gene regulation to drive malignancy.