bluuebunny/crossref_metadata_2025_split huggingface dataset:
DIPG-31. Prognostic and predictive biomarkers of response in children and young adults with H3K27M-altered diffuse intrinsic pontine glioma: results from a multi-center, interventional clinical trial (PNOC003)
Authors: Kline Cassie , Jain Payal , Kilburn Lindsay , Bonner Erin , Gupta Nalin , Crawford John , Banerjee Anu , Packer Roger , Villanueva-Meyer Javier , Luks Tracy , Zhang Yalan , Kambhampati Madhuri , Zhang Jie , Yadavilli Sridevi , Kraya Adam , Kuhn John , Liang Winnie , Byron Sara , Berens Michael , Molinaro Annette , Prados Michael , Resnick Adam , Waszak Sebastian , Nazarian Javad , Mueller Sabine 
Published: June 2022

Abstract
BACKGROUND: Diffuse intrinsic pontine glioma (DIPG) is a fatal brain tumor. Herein, we report on novel prognostic and predictive genomic biomarkers identified in PNOC003, a multi-center precision medicine trial for children and young adults diagnosed with DIPG. METHODS: Patients aged 3-25 years were enrolled on PNOC003 based on radiographic diagnosis of DIPG. Pre-treatment tumor biopsies were analyzed using tumor-normal whole-exome sequencing and mRNA-tumor sequencing to determine biology-informed, multi-agent therapy following radiation therapy (RT). Whole-genome sequencing was performed as an exploratory study aim. Genomic biomarkers were investigated to identify predictors of RT response and overall survival (OS) in patients with confirmed H3K27M-altered DIPG. Prognostic biomarkers were verified in a retrospective, H3K27M-altered diffuse midline glioma cohort (n=22) from the Children’s Brain Tumor Network (CBTN). RESULTS: Thirty patients enrolled on PNOC003 met molecular criteria for H3K27M-altered DIPG. TP53 was the most frequently altered driver gene (73%). Somatic alterations in PTEN&gt;TP53&gt;PDGFRA were independently associated with OS (P&lt;0.05, in order of negative impact on survival). TP53 mutations associated with worse OS (TP53mut 11.1 mo [95% CI 8.7, 14]; TP53wt 13.3 mo [95% CI 11.8, NA]; P=3e-2), chromosomal instability (P=3e-3), and resistance to RT (P=6e-4). Moreover, loss of chromosome 10q, encoding tumor suppressor PTEN, was associated with worse OS, co-occurred with PTEN alterations, biallelic PTEN inactivation and loss of gene expression. The combination of TP53 alterations and loss of 10q/PTEN in H3K27M-altered DIPG was associated with the worst OS in a combined PNOC003 and CBTN cohort (TP53mut/10qdel, n=14, OS 8.4 mo [95% CI 7.4, 15.8]; TP53mut/10qwt, n=20, OS 13.1 mo [95% CI 10.1, 17.2]; TP53wt/10qwt, n=14, OS 15.5 mo [11.8, 29.4]; P=2e-3). CONCLUSION: PNOC003, a tissue-driven clinical trial, provided insights into prognostic and predictive genomic biomarkers and informed a novel molecular tumor classification system for H3K27M-altered DIPGs.
DIPG-46. Radiation induced senescence in diffuse intrinsic pontine glioma cells reveals selective vulnerability to Bcl-XL inhibition
Authors: Vardon Ashley , Guiho Romain , Carvalho Diana , Boult Jessica , Carter Rebecca , Grabovska Yura , Mackay Alan , Zheng Guangrong , Zhou Daohong , Hiley Crispin , Lythgoe Mark , Jones Chris , Hargrave Darren , Martinez- Juan-Pedro 
Published: June 2022

Abstract
Diffuse intrinsic pontine glioma remains a devastating condition with a dismal five year survival rate less than 5%. New approaches for treating this aggressive disease are critical to driving progress. Conventional radiotherapy remains the cornerstone of treatment, with no chemotherapeutic agent found to improve survival. However, radiotherapy is often delivered as a palliative treatment, and disease often recurs 3-6 months after. Radiation causes DNA damage and oxidative stress yielding a senescent state of replicative arrest in susceptible cells. However, increasing evidence demonstrates malignant cells can escape senescence leading to tumour recurrence. Targeted ablation of non-replicating senescent tumour cells following radiation could negate tumour recurrence. It remains unknown whether DIPG undergoes senescence following radiation, and furthermore, whether senolytics can be utilised to target senescent DIPG cells. We employed radiation to induce a senescent state in primary human DIPG cell lines. Senescence was confirmed using SA-β-gal staining, lack of EdU incorporation and qRT-PCR to characterise the SASP in three primary human DIPG cell lines. RNA-sequencing on DIPG cells following radiation revealed senescence and SASP signatures. Likewise, expression of senescence markers has been detected in human tumours. Viable cells that survive radiation were then utilised to screen candidate senolytic drugs, only Bcl-XL inhibitors demonstrated reproducible senolytic activity in radiation treated DIPG cells. In addition, Bcl-XL degradation using PROTACs (proteolysis targeting chimeras) resulted in a significant increase in senolysis of susceptible tumour cells. Conversely, Bcl-2 inhibitors failed to show any consistent senolytic activity. We are currently performing preclinical studies in the mouse to test the efficiency of senolytics against DIPG. These results demonstrate future possibilities of targeting radiation induced senescence in DIPG, using novel senolytic therapies and highlight Bcl-XL dependency as a potential vulnerability of surviving DIPG cells following exposure to radiation.
DIPG-50. Bioinformatic evaluation of genes involved in sphingomyelin biosynthesis in Diffuse Midline Glioma H3K27 altered/DIPG: dysregulation of sphingosine 1-phosphate (SP1)
Authors: Humphreys Aimee , Russell Hanna , Fillmore Helen L 
Published: June 2022

Abstract
Sphingosine 1-phosphate (S1P), a bioactive signalling lipid, interacts with a network of metabolic enzymes, receptors, transporters, and epigenetic partners. This network is well described in many cancers; however, little is known about its potential impact in DIPG. Expression of HDAC1 (binding target of S1P) and genes associated with the sphingomyelin (SM) pathway were examined in datasets identified in the National Centre for Biotechnology Information, Gene Expression Omnibus, and analysed using the R2: Genomics Analysis and Visualization Platform (http://r2.amc.nl). The Paugh-DIPG dataset (27 DIPG samples) and normal samples (20 years and younger - Berchtold dataset) were compared. To avoid issues related to batch effects, expression values for each gene of interest and controls were exported into separate files to determine differentially expressed genes. Internal genes include housekeeping; ACTB, GAPDH, B2M, TBP; downregulated in DIPG; GPR6, NGB, and upregulated in DIPG; MMP16, PDGFRA, TP53, CSPG4. Genes of interest; SPHK1, SPHK2, SGPL1, ACER1, ACER3, KDSR, SMPD1-4, CPTP, GLTP, DEGS1, CERK, CERS1-6, ASAH1, SGPP1, SGPP2 and HDAC1. To test for significance, each dataset was standardised using ACTB housekeeping gene. Values including Log-transformed fold change were analysed using the non-parametric, Mann-Whitney test. 7 of the 16 genes were dysregulated relative to expression in normal brain (p&lt;0.0002). SPHK2 and SMPD3 were downregulated, and HDAC1, SGPL1, DEGS1, CERS4, and ASAH1 were upregulated in DIPG compared to normal. To identify genes more likely associated with DIPG (vs development), we evaluated gene expression in Brainspan dataset (brspv10rs). Validation of SPHK2 and SGPL1 protein expression (responsible for the synthesis and cleavage of SP1) is underway. Current work is focused on the intracellular processing and function (isoform specific inhibitors) of S1P in DIPG cells. Given its reported role in several cancer hallmarks, a better understanding of the sphingomyelin biosynthesis pathway in DMG/DIPG is merited and may lead to novel therapeutic targets.
EPEN-07. Brain-tumor communication reveals potential new therapeutic targets for pediatric ependymoma
Authors: Antonelli Roberta , Jiménez Carlos , Servidei Tiziana , Riccardi Riccardo , Martínez-Saez Elena , de Toledo Josep Sánchez , Roma Josep , Gallego Soledad , Llort Anna , Moreno Lucas , Segura Miguel 
Published: June 2022

Abstract
Pediatric brain tumors (PBTs) represent the most common solid malignancies in children and the leading cause of cancer-related deaths. Despite the fact that survival after a high-grade brain tumor diagnosis is slowly improving, overall survival remains poor compared with most other cancers, thereby highlighting the need for new therapies. This is particularly true for Ependymoma (EPN), the second most common PBT that, despite advances in the understanding of EPN biology, still shows a poor prognosis in approximately 40% of patients. Accumulative evidence reveals that the transcriptome of tumors can be modulated by the host tissue, with brain tumors or brain metastasis derived from extracranial tumors being at the forefront of these studies. Our hypothesis is that understanding the impact of brain-tumor communication may open up new opportunities for therapeutic intervention. To characterize gene expression changes in Ependymoma tumors caused by the tumor microenvironment the transcriptome of patient-derived EPN cells was analyzed comparing in vitro cultured cells, subcutaneous xenografts and orthotopic xenografts. 2734 differentially expressed genes were found after comparing in vitro grown cells versus brain xenografts. Sixty-five of those genes were also differentially expressed when comparing human expression data from aggressive EPN versus the rest of EPN tumours. Among these candidates NTRK2 and CALB2 stand out. Gene depletion phenotype using multiple shRNA showed that the in vivo tumor growth of NTRK2-depleted cells, (but not CALB2) was remarkably reduced compared with control cells. These results suggest that NTRK2 could be a potential new therapeutic target for the treatment of Ependymoma
EPEN-08. Single-cell transcriptome analysis defines a tumor-supportive microenvironment and tumor-stroma crosstalk in pediatric ependymoma and medulloblastoma.
Authors: Federico Aniello , Okonechnikov Konstantin , Carmona Enrique Blanco , Lammers Julie A S , Kranendonk Mariette E G , Gojo Johannes , Englinger Bernhard , Jiang Li , Nierkens Stefan , Calkoen Friso G J , van der Lugt Jasper , Filbin Mariella G , Jäger Natalie , Pfister Stefan M , Kool Marcel 
Published: June 2022

Abstract
Brain tumors are the leading cause of disease-related death in childhood and strong efforts are required to develop innovative and efficient therapeutic strategies for patients with high-risk disease. Key critical factor of pediatric brain tumors is their molecular heterogeneity; one of the aspects that contributes to such heterogeneity is the intrinsic capacity of the tumor cells to organize, shape and exploit the surrounding brain tumor microenvironment (TME) to sustain tumor growth and malignant progression. TME was proved to play a crucial role in several malignancies, but in pediatric brain malignancies this has not been fully elucidated yet. Here, we aimed at characterizing the TME cell populations and their contributions in ependymoma and medulloblastoma, two of the most common pediatric brain tumor entities. Single-cell transcriptome analysis (n=65 ependymomas; n=39 medulloblastomas) of publicly available tumor datasets, as well as newly generated data of primary tumors and matching patient-derived tumor xenografts (PDX), showed an extensive heterogeneity of TME cell types with distinctive expression signatures. Amongst the identified TME populations, analysis revealed pro-inflammatory and proliferating myeloid cells, tumor-infiltrating lymphocytes, active regulatory T cells and vascular progenitor cells. Comparative analysis between primary and PDX tumors showed that tumor cells stimulated the host microenvironment, which in turn exhibited tumor-associated stromal signatures. Applying a deconvolution method, using our single cell data as reference, on a bulk tumor cohort including PFA ependymomas with different degree of immune infiltration, we observed an enrichment of polarized macrophages and microglia cells in tumor with high infiltration. Next, we identified TME markers involved in tumor-supportive functions, such as immune suppression (TIGIT, FOXP3, BCL2, CD19, ICAM2), pro-inflammatory stimuli (CCL3, CCL4, IL1B, GPNMB), extracellular matrix remodeling (COL4A1) and angiogenic processes (ANGPT2). TME markers with emerging role in ependymoma and medulloblastoma can be considered as possible targets for tailored and more effective anti-tumor therapeutic strategies.
EPEN-09. Multi-omics characterization of the blood-brain barrier in molecular groups of ependymoma
Authors: Sundheimer Julia K , Benzel Julia , Gansert Cornelia , Statz Britta , Seitz Christian , Pfister Stefan M , Maaß Kendra K , Pajtler Kristian W 
Published: June 2022

Abstract
BACKGROUND: A major challenge in the treatment of brain tumors is the limited penetration of many drugs through the blood-brain barrier (BBB). BBB characteristics include endothelial cells connected by tight junction proteins (e.g. Claudin5) and expression of efflux transporters (e.g.P-gp) with the physiological role to limit the accumulation of potentially toxic substances in brain tissue. While BBB permeability shows anatomical region-specific characteristics and changes with age, brain tumors can also impact its integrity. To achieve therapeutically relevant drug concentrations in the tumor, characterization of the pathophysiological BBB is fundamental when developing (pre)clinical trials. Our study seeks to increase our understanding of the BBB composition in various molecular groups of ependymoma. RESULTS: Transcriptional BBB characteristics were assessed for primary ependymoma (n=440), cell lines (n=3), mouse models (n=22), and healthy brain controls (n=200). T-distributed stochastic neighbor embedding (tSNE)-based clustering analyses based on most relevant tight junction and efflux transporter gene sets revealed distinct molecular ependymoma group-specific expression patterns. While patient-derived xenografts models (PDX, n=20) showed high similarity with patient tumor samples, in utero electroporation-based (IUE, n=2) mouse models did not fully recapitulate these BBB characteristics. Supratentorial ependymoma with ZFTA fusions revealed a higher transcriptional expression level of important tight junctions (e.g.Claudin5) compared to other groups and normal brain which was confirmed at protein level in respective PDX models by using both western blot and ultra-high content imaging. CONCLUSION: Analyses of important BBB markers revealed significant differences between molecular groups of ependymoma, which may partly explain drug resistance of ependymoma with ZFTA fusion caused by a low BBB permeability. BBB characteristics of corresponding models suggest that IUE and PDX models representing ZFTA fusion-driven tumors cannot equally be used within preclinical drug trials. Findings will be further validated in preclinical studies while molecular BBB characterization will be expanded to other brain tumors.
EPEN-23. Interaction of epigenetic regulation and telomerase re-activation in high-risk ependymoma
Authors: Jaunecker Carola N , Kirchhofer Dominik , Madlener Sibylle , Laemmerer Anna , Gabler Lisa , Pirker Christine , Piontek Martin , Maaß Kendra , Okonechnikov Konstanitin , Englinger Bernhard , Jiang Li , Mayr Lisa , Senfter Daniel , Spiegl-Kreinecker Sabine , Stepien Natalia , Dorfer Christian , Filbin Mariella , Kool Marcel , Gojo Johannes , Berger Walter , Loetsch-Gojo Daniela 
Published: June 2022

Abstract
Ependymomas (EPN) account for 10% of pediatric CNS tumors. Among the ten subgroups characterized by DNA methylation profiling, tumors located in the supratentorial region that harbor ZFTA fusions (e.g. ZFTA-RELA), and tumors in the posterior fossa region group A (PF-A) represent the most aggressive entities. As currently therapy success relies on the extent of tumor resection and druggable targets are so far widely missing, new therapeutic approaches are urgently needed. Epigenetic dysfunction, resulting in aberrant histone modifications as well as altered DNA methylation patterns, majorly contributes to the aggressiveness of high-risk EPN. In earlier studies, we discovered that high-risk EPN is composed of a cellular hierarchy initiating from stem-cell like populations, frequently showing telomerase re-activation. Considering that epigenetic mechanisms regulate stemness maintenance and telomerase reverse transcriptase (TERT), we studied the impact of epigenetically active drugs on differentiation and telomerase re-activation in these tumors. Accordingly, we first investigated the basal expression levels of TERT and EZH2 in a panel of patient-derived high-risk EPN cell models of different subtypes (n=7). Interestingly, both, TERT and EZH2, were highly expressed predominantly in ZFTA-RELA cell models. Corroboratively, increased sensitivity of ZFTA-RELA cells towards the EZH2 inhibitor DZNep was observed in cell viability and clonogenic assays. While HDAC inhibitors were similarly active across high-risk EPN cell models, the BET inhibitor JQ1 more efficiently reduced survival of ZFTA-RELA cells. Treatment with DZNep resulted in a loss of H3K27me3 histone marks accompanied by decreased ubiquitination of H2AK119 in the investigated ZFTA-RELA cell models, and induced apoptosis indicated by PARP cleavage. Currently, impacts of direct or pharmacological EZH2 blockade on TERT promoter methylation, induction of senescence and differentiation are analyzed. Summarizing, we proof varying efficacy of epigenetically active drugs in high-risk EPN subgroups, in particular EZH2 inhibition in ZFTA-RELA cell models.
EPEN-27. Epigenetic dissection of spinal ependymomas (SP-EPN) separates tumors with and withoutNF2 mutation
Authors: Neyazi Sina , Yamazawa Erika , Kresbach Catena , Nagae Genta , Eckhardt Alicia , Umeda Takayoshi , Pohl Lara , Tatsuno Kenji , Saygi Ceren , Hana Taijun , Alawi Malik , Kim Phyo , Dorostkar Mario M , Higuchi Fumi , Suwala Abigail K , Takami Toshihiro , Wefers Annika , Nakanishi Yuta , Schweizer Leonille , Takai Keisuke , Engertsberger Lara , Komori Takashi , Mohme Theresa , Takami Hirokazu , Mynarek Martin , Nomura Masashi , Lamszus Karin , Mukasa Akitake , Kluwe Lan , Takayanagi Shunsaku , von Deimling Andreas , Ishii Kazuhiko , Benesch Martin , Imai Hideaki , Snuderl Matija , Frank Stephan , Ichimura Koichi , Hagel Christian , Mautner Viktor F , Rutkowski Stefan , Tanaka Shota , Aburatani Hiroyuki , Nobuhito Saito , Schüller Ulrich 
Published: June 2022

Abstract
Ependymomas encompass multiple, clinically relevant tumor types based on localization, genetic alterations, and epigenetic and transcriptomic profiles. Tumors belonging to the methylation class of spinal ependymoma (SP-EPN) represent the most common intramedullary neoplasms in children and adults. However, molecular data of SP-EPN are scarce, and clear treatment recommendations are lacking. The only known recurrent genetic events in SP-EPN are loss of chromosome 22q and NF2 mutations. Yet, it remains unclear whether SP-EPN with germline or sporadic NF2 mutations or with NF2 wild type status differ clinically or molecularly. To provide a comprehensive molecular profile of SP-EPN, we integrated epigenetic, genomic, transcriptomic, and histological analyses of up to 237 cases. Clustering of methylation data revealed two distinct molecular SP-EPN subtypes. The distribution of NF2 mutated cases differed significantly across these subtypes (p &lt;0.0001): The vast majority of tumors harboring either a previously known NF2 germline mutation or a sporadic mutation were assigned to subtypes A, whereas subtype B tumors mainly contained NF2 wild type sequences. In addition, subtype A tumors showed a lower frequency of MGMT promoter methylation (p= 0.018) and contained almost all pediatric patients of the cohort. Whole-exome sequencing (30 cases) identified numerous mutations in NF2 wild type and mutated tumors. Mutated genes in NF2 wild type tumors were enriched for genes associated with cell cycle and cytoskeleton. RNA sequencing revealed two distinct transcriptional groups with upregulation of proliferative genes in one group and upregulation of cilial genes in the other group. The molecular subtypes displayed subtle, but significant differences in the appearance of histopathological characteristics, such as surfaces, inflammation, and hyalinized vessels. Investigation of clinical parameters is ongoing and will complete the picture of SP-EPN heterogeneity as an important basis for future clinical decision-making.
EPID-03. Epidemiology, treatment and outcomes of children and young adults with CNS tumors in Armenia
Authors: Hoveyan Julieta , Grigoryan Henrik , Hovsepyan Shushan , Avagyan Anna , Asatryan Eduard , Tamamyan Gevorg , Papyan Ruzanna , Sargsyan Lilit , Hakobyan Lusine , Bardakhchyan Samvel 
Published: June 2022

Abstract
BACKGROUND: CNS tumors are the most common solid tumors in children and the leading cause of cancer related deaths. The incidence of CNS tumors is 1.7-6.21 cases per 100000 children. The aim of current study is to analyze epidemiological data, treatment and outcomes of children and young adults (&lt;25 years) with CNS tumors in Armenia during last 25 years. METHODS: We have collected data of pediatric and young adult patients treated in neurosurgery department, three major chemotherapy clinics and radiation therapy department from 01.01.1995 to 31.12.2020 in Armenia. Incidence by gender, age at diagnosis, the time from first complaints to diagnosis, histopathology results and overall survival rates were calculated. RESULTS: The population-based data revealed 176 patients diagnosed with primary CNS tumors during 25 years. Among them 98 (55.7%) were males. Mean age at diagnosis was 7.07 years and the mean time from the first complaints to diagnosis was 6.55 months. Medulloblastomas and other embryonal tumors (26.7%), low grade gliomas (16.5%), retinoblastomas (12.5%) and high grade gliomas (10.8%) were the most common diagnosed malignancies. Craniopharyngiomas, germ cell tumors and other malignancies were observed in 9.1% of patients. For 24.4% histopathological data was missing. Surgery, chemotherapy and radiation therapy were performed in Armenia for 62.5%, 33.5% and 19.3% patients respectively. Follow up information was available for 119 (67.6%) patients. 5-year overall survival was 76%. CONCLUSION: Embryonal tumors and gliomas were the most common diagnosed CNS malignancies in Armenia which is consistent with international data. Multimodal treatment was often not available in Armenia during study period, especially for early cases. We hope recent advances in surgery, chemotherapy, and radiotherapy will help to improve treatment outcomes.