bluuebunny/crossref_metadata_2025_split huggingface dataset:
EPEN-09. TARGETING EPHB2/ABL1 RESTORES ANTI-TUMOR IMMUNITY IN A PRECLINICAL MODEL OF EPENDYMOMA
Authors: Ren Jun , Amoozgar Zohreh , Uccello Taylor P , Zhao Yuhui , Lei Pinji , Ho William W , Roberge Sylvie , Huang Peigen , Duda Dan G , Xu Lei , Jain Rakesh K 
Published: June 2024

Abstract

BACKGROUND
Ependymoma (EPN) is a childhood brain cancer that is often resistant to cytotoxic therapies. Molecular profiling has led to a better understanding of unique EPN subtypes and revealed a critical role of EPHB2 in driving disease. With this in mind, new treatments for EPN are desperately needed and should be developed in a molecular subtype-specific fashion.

METHODS
We developed a syngeneic mouse model of EPHB2-driven genetically engineered EPN tumor cells. We performed transcriptomic profiling and analysis of EPHB2-driven murine EPN tumors and human EPN datasets to reveal multiple protein kinases as potential druggable targets. After identifying the tyrosine kinase inhibitor, Dasatinib, as a potentially effective FDA-approved agent, we measured changes in the murine microenvironment during EPN growth and after Dasatinib treatment.

RESULTS
We determined that Dasatinib inhibited the growth of EPN both in vitro and in vivo, through blocking EPHB2 and ABL1 signaling. Furthermore, we identified an increased frequency of immunosuppressive M2-like tumor- associated macrophages (TAMs), which proportionally increased with tumor size during tumor progression. However, treatment with Dasatinib reprogrammed the EPN immune microenvironment by polarizing TAMs toward an anti-tumor M1-like phenotype and increasing CD8 T cell activation. In addition, Dasatinib treatment induced complete regression of established EPN tumors in 78% of the animals and protected survivors against tumor recurrence. Depletion of CD8 T cells compromised the durability of response and reduced overall survival.

CONCLUSION
In conclusion, these data indicate that Dasatinib may be an effective therapy for EPHB2-driven molecular subgroup of EPN by activating the anti-tumor immune response and support further investigation of Dasatinib in clinical trials.
EPEN-10. INDUCING A SENESCENCE PHENOTYPE BY BROMODOMAIN INHIBITION IN HIGH-RISK EPENDYMOMA
Authors: Jaunecker Carola N , Freund Julia , Laemmerer Anna , Roosen Mieke , Kirchhofer Dominik , Otto Antonia , Madlener Sybille , Mager Leah , Bruckner Katharina , Stepien Natalia , Pirker Christine , Gabler Lisa , Senfter Daniel , Jenseit Anne , Kuess Peter , Eckert Franziska , Spiegl-Kreinecker Sabine , Dorfer Cristian , Filbin Mariella , Kool Marcel , Gojo Johannes , Berger Walter , Loetsch-Gojo Daniela 
Published: June 2024

Abstract

BACKGROUND
Ependymomas (EPN) constitute 10% of pediatric brain tumors. WHO classification identified 10 molecular subtypes, with ZFTA fusion-driven supratentorial tumors (ST-ZFTA) and posterior fossa group A (PFA) being amongst the most aggressive ones. Current therapeutic success relies on local treatments, emphasizing the urgent need for novel targets. Epigenetic dysregulation is a major contributor to EPN aggressiveness. Bromodomain and extra-terminal domain (BET) proteins are transcriptional mediators involved in proto-oncogene transcription, thereby representing promising targets in cancer therapy. As the BET protein BRD4 co-regulates ZFTA-RELA fusion-mediated aberrant transcription, BET inhibitors emerge as novel targeted therapy approach in ST-ZFTA.

METHODS
Initial assessments encompassed primary, patient-derived (n=9) cell models representing ST-ZFTA and PFA EPN. RNA sequencing of two ZFTA-RELA models was performed, using DGE and GSEA analyses to discern altered pathways following BET-inhibition. On functional level, we investigated sensitivity towards BET-inhibition using cell viability, clone- and sphere formation assays, as well as Western blot and qPCR after treatment. Additionally, anti-tumor effects in genetically engineered cerebral organoids were assessed.

RESULTS
First investigations showed elevated BRD2 and BRD4 levels in ST-ZFTA compared to PFA models. Accordingly, treatment with BET inhibitors resulted in reduced survival and cell cycle arrest, evidenced by cell viability and clone formation assays, along with increased p21 and cleaved PARP levels in Western blot analyses. RNA sequencing revealed altered pathways associated with cell-cycle regulation and senescence following BET inhibition, supported by downregulation of the telomerase subunit TERT and genes of the senescence-associated secretory phenotype. Additionally, BET inhibitors exhibited synergistic effects with EZH2- and PARP inhibitors primarily in ZFTA-RELA cell lines, as well as decreased tumor volumes in ZFTA-RELA-driven cerebral organoids.

CONCLUSIONS
Summarizing, we show drastic effects of BET-inhibition in ZFTA-RELA EPN. Subsequently, the influence of Bromodomain inhibition on stemness and senescence, particularly combined with radio- and chemotherapy will be investigated.
EPEN-11. CHARACTERIZING EPIGENETIC MODULATIONS AND EZHIP DOWNSTREAM TARGETS IN PFA EPENDYMOMA
Authors: Wang Shanzheng , Jenseit Anne , Hübner Jens-Martin , Mauermann Monika , Okonechnikov Konstantin , Pfister Stefan M , Kool Marcel 
Published: June 2024

Abstract

BACKGROUND
Ependymomas can arise from all compartments of the central nervous system and ten distinct molecular groups have been identified in children and adults. In children, the most aggressive group is posterior fossa group A ependymoma (PFA). In PFA ependymomas, the aberrant overexpression of EZHIP (EZH inhibitory protein) has been implicated as a relevant driver of the disease. EZHIP suppresses the installing and spreading of the repressive epigenetic mark H3K27me3 via disturbing PRC2 (polycomb repressive complex 2) activity through inhibiting EZH2 (enhancer of zeste 2), which causes overall low levels of H3K27me3 in PFA.

METHODS
To get a better understanding how EZHIP may drive the disease, how it affects the epigenetic landscape and what the downstream targets of EZHIP are, we performed DNA sequencing, RNA expression profiling and ChIP-seq experiments of H3K27me3, H3K27ac, EZH2, and EZHIP in PFA, PFB, and ST-ZFTA ependymomas (n = 3 tumor cases each).

RESULTS
After validating the high levels of EZHIP and global reduction of H3K27me3 in PFA, we characterized the epigenetic landscape and EZHIP chromatin binding characteristics in PFA compared to PFB and ST-ZFTA ependymoma. Transcriptome analysis showed that overall more genes are up-regulated in PFA compared with PFB and ZFTA, which might be caused by its relatively high accessibility with a global loss of H3K27me3. EZHIP knockdown experiments confirmed direct changes on H3K27me3, H3K27ac and gene expression. We also found that PLAG1 (pleomorphic adenoma gene 1) expression linearly correlated with EZHIP expression in PFA tumors. ChIP-seq data indeed showed the PLAG1 locus to be bound by EZHIP and marked with increased H3K27ac and decreased H3K27me3 signals in PFA.

CONCLUSIONS
We identified PLAG1 as a potential downstream target of EZHIP in PFA tumors. Currently, more experiments on PLAG1 are being performed to further explore its role as a potential vulnerability in PFA ependymoma.
EPEN-21. EXPLORATION OF TUMOR SUPPRESSOR LATS1 LOSS IN POSTERIOR FOSSA GROUP A EPENDYMOMA WITH LOSS OF CHROMOSOME 6Q
Authors: Donson Andrew M , Griesinger Andrea M , Calzadilla Annaliese , Amani Vladimir , Grimaldo Enrique , Foreman Nicholas K 
Published: June 2024

Abstract

INTRODUCTION
Chromosome 6q loss (6q-) has recently been identified as an ultra-high-risk factor in posterior fossa group A ependymoma (PFA). This study seeks to pinpoint the biological mechanism underlying the aggressive biology of PFA 6q-. We hypothesize that loss of chromosome 6q gene large tumor suppressor kinase 1 (LATS1) in PFA 6q- results in increased Hippo pathway activity that drives malignant tumor progression. LATS1 is a key negative regulator of the Hippo pathway which may represent a novel therapeutic vulnerability in 6q- PFA.

METHODS
We are testing this hypothesis using genomic and transcriptomic analysis of PFA patient samples, and by gene knock-in and pharmaceutical interventions of LATS1 and Hippo pathway components in PFA 6q- models.

RESULTS
Tumor suppressor LATS1 shows reduced expression in PFA 6q- patient samples. Although complete loss of the entire 6q arm is common in PFA 6q-, partial loss of chromosome 6q is also observed, and in all cases this partial loss encompasses the LATS1 locus on chromosome 6q. We used lentiviral transduction to knock-in LATS1 in PFA 6q- cell lines to determine the effect on tumor growth. This demonstrated loss of viability that was specific for 6q- PFA cell lines versus 6q WT control cell lines.

DISCUSSION
Data point to LATS1 loss being a key driver of the aggressive phenotype of PFA6q-, implicating the Hippo pathway in PFA 6q- and potential for novel therapeutic strategies.
EPEN-24. 5FU SENSITIVITY IS MEDIATED THROUGH TRISOMY UCK2 EXPRESSION IN 1Q+ PFA EPN
Authors: Griesingr Andrea Marie , Calzadilla Annaliese J , Grimaldo Enrique , Donson Andrew M , Amani Vladimir , Pierce Angela M , Steiner Jena , Kargar Soudabeh , Serkova Natalie J , Bertrand Kelsey C , Wright Karen D , Vibhakar Rajeev , Hankinson Todd , Handler Michael , Lindsay Holly B , Foreman Nicholas K , Dorris Kathleen 
Published: June 2024

Abstract

BACKGROUND
Nearly all children with gain of chromosome 1q (1q+) PFA ependymoma (EPN) will die, highlighting the urgent need to develop new treatment strategies for these patients. It has recently been shown that 1q+ creates a p53 mutant-like phenotype through trisomy expression of MDM4, a repressor of p53 signaling. This same study found toxic uracil analogs could reverse trisomy MDM4 effect on p53 and this was mediated through another 1q-trisomy gene UCK2. We and other have previously identified 5-fluorouracil (5FU) as an ependymoma specific inhibitor. In this study, we present the mechanism for 5FU sensitivity.

METHODS
In this study we utilize 1q+ PFA in vitro models to test the efficacy of combination radiation and 5FU in a preclinical setting. We measured p53 signaling through proteomic array and qRT-PCR for p21, a p53 response gene.

RESULTS
5FU enhances radiotherapy in 1q+ PFA cell lines. Specifically, 5FU increases p53 activity mediated by the extra copy of UCK2 located on chromosome 1q in 1q+ PFA. Experimental down regulation of UCK2 resulted in decreased 5FU sensitivity in 1q+ PFA cells. Though not statistically significant, we did see prolong survival and decreased tumor burden in 1q+ PFA orthotopic patient-derived xenograft models treated with focal 2Gyx5days radiation and 5FU.

CONCLUSION
These results are the first to identify a 1q+ specific therapy approach in PFA EPN. Existing phase 1 studies in pediatrics have already established safety and dose of 5FU, providing a rapid translation into phase 2 trials for children both up front and at recurrence for 1q+ PFA.
EPEN-25. “CONCERNING EPENDYMOMAS, A FURTHER SUBDIVISION IS NEITHER MORPHOLOGICALLY NOR BIOLOGICALLY NECESSARY”: A NARRATIVE REVIEW OF RESEARCH ON EPENDYMOMAS BETWEEN 1865 AND 2024
Authors: Ghasemi David R 
Published: June 2024

Abstract

BACKGROUND
The history of research on ependymomas dates back to the nineteenth century. However, ependymomas have received much less attention than other neuro-oncological diseases. This narrative review investigates the history of ependymoma as a distinct tumour entity.

METHODS
A comprehensive literature search in German, English and French was carried out for publications from 1850 to 2024 in PubMed, the Internet Archive, and the library of Heidelberg University. Additionally, the evolution of the classification of ependymoma throughout the editions of the WHO classification of CNS tumours was analysed.

RESULTS
The first major systematic description of ependymal tumours was published in 1865 by Rudolf Virchow, who hypothesized that ependymomas originated from chronic irritations to the ependyma. In 1899, perivascular (pseudo-)rosettes were described for the first time. Subsequently, Percival Bailey and Harvey Cushing’s systematic classification efforts laid the groundwork for new advancements. Debates about the classification of ependymomas can already be found in publications by Percival Bailey or Gustave Roussy in 1924, with a major focus on the definition of ependymoblastoma as an independent entity, which was only resolved in 2016 with the introduction of the new diagnosis ETMR. Klaus Joachim Zülch’s important mid-20th-century work highlighted clinical variations within ependymomas but deemed no further stratification necessary. The WHO’s classifications in 1979, 1993, 2000 and 2007 relied on histopathology, with only minor details being adapted over the years. A new era began in 2016 with the recognition of C11orf95-RELA (ZFTA-RELA) as a defining hallmark of supratentorial ependymomas. The latest WHO classification in 2021 adopted a molecular-anatomical approach, incorporating new subgroups and abandoning histomorphological subtypes due to limited prognostic value. Tumor grading became mostly optional.

CONCLUSIONS
This review summarises the significant evolution in ependymoma research, particularly in the 2010s. Strikingly, many of the questions that Virchow, Bailey or Roussy investigated, remain unanswered in 2024.
EPID-07. INCIDENCE OF PAEDIATRIC BRAIN TUMORS IN AN ITALIAN REGIONAL COHORT: AN EPIDEMIOLOGICAL STUDY FROM 2012 TO 2023
Authors: Toniutti Maristella , Pilotto Chiara , Pedicini Sara , Pegolo Enrico , Mascarin Maurizio , Coassin Elisa , Kiren Valentina , Rabusin Marco , Tuniz Francesco , Vindigni Marco , D’Agostini Serena , De Colle Maria Cristina , Cogo Paola Elisa , Liguoro Ilaria 
Published: June 2024

Abstract

BACKGROUND
Central nervous system (CNS) tumors are the most common solid cancer in children, second only to leukaemia.

METHODS
We conducted a retrospective epidemiological study of primary CNS tumors diagnosed in children up to 16 years of age between 2012 and 2023, in order to estimate the incidence in a regional cohort of 1,2 million inhabitants (Northeastern Italy). Only primitive lesions were enrolled, relapses were excluded.

RESULTS
Over a period of twelve years, 100 new diagnoses were made (44% Female, 56% Male) with a mean age of 8,92 years (range 0-16 years) at time of onset. In terms of location, we recorded an equal number of supratentorial and subtentorial diagnoses (50% vs 50%). A time-series analysis was performed to verify possible variations in the incidence rate of brain tumors over years, and no significant change was described (R2 0.301, p=0.06). However, after 2017 a significant increase was noted (R2 0.725, p=0.015), as the incidence of new diagnosis quite doubled, from 3.16 in 2018 (95%CI 3.15-3.17) to 5.59 in 2023 (95%CI 5.57-5,61). Data were therefore divided in two groups: 2012-2017 (group 1), and 2018-2023 (group 2). There were no differences in terms of gender or age. The number of low-grade (LG) and high-grade (HG) diagnosis were compared: HG tumors, including high grade glioma, ependymoma and medulloblastoma, were significantly higher in the group 2 than group 1 (27/50, 54% vs 6/43, 14%, p&lt;0.001).

CONCLUSIONS
In childhood, CNS tumors incidence has been fairly stable in the last twelve years in our regional cohort, but a recent concern of an increased rate of high-grade diseases emerged according to our data. In case of a confirmation of this trend, further analysis will be required in order to understand the reason.
METB-01. EFFECTS OF H3.3G34V MUTATION ON GENOMIC H3K36 AND H3K27 METHYLATION PATTERNS IN ISOGENIC PEDIATRIC GLIOMA CELLS
Authors: Huang Tina , Piunti Andrea , Qi Jin , Bartom Elizabeth , Saratsis Amanda 
Published: June 2024

Abstract

BACKGROUND
Histone H3.3 mutation (H3F3A) occurs in 50% of cortical pediatric high-grade gliomas (pHGGs). This mutation replaces glycine 34 with arginine or valine (G34R/V), impairing SETD2 activity (H3K36-specific trimethyltransferase). Consequently, reduced H3K36me3 is observed on H3.3G34V nucleosomes relative to wild-type, contributing to genomic instability and driving a distinct gene expression signature associated with tumorigenesis. However, it is not known if this differential H3K36me3 enrichment is due to H3.3G34V mutant protein alone. Therefore, we set to elucidate the effect of H3.3G34V mutant protein in pediatric glioma on H3K36me3, H3K27me3 and H3.3 enrichment in vitro.

METHODS
Experiments were conducted using an established H3.3G34V mutant patient-derived pediatric high-grade glioma cell line (KNS42), and Histone H3.3 wild-type human astrocytes (NHAs). Lentiviral delivery of a doxycycline-inducible RNAi vector targeted against H3F3A was transduced to KNS42 cells to knock down H3.3G34V protein expression. Cell lines were then compared via ChIP-Seq, Western Blot, proliferation and viability studies.

RESULTS
We found that the doxycycline-inducible shRNA knockdown of mutant H3F3A encoding the H3.3G34V protein resulted in loss of H3.3G34V enrichment and increased H3K36me3 enrichment throughout the genome. After knockdown, H3.3G34V enrichment was preserved at loci observed to have the greatest H3.3G34V and H3K36me3 enrichment prior to knockdown. Induced expression of mutant H3.3G34V protein in vitro was insufficient to induce genomic H3K36me3 enrichment patterns observed in H3.3G34V mutant glioma cells. We also observed strong co-enrichment of H3.3G34V and wild-type H3.3 protein, as well as greater H3K27me3 enrichment, in cells expressing H3.3G34V.

CONCLUSIONS
Our study demonstrates the effects of H3.3G34V mutant protein on genomic H3K36me3, H3K27me3 and H3.3 enrichment patterns in isogenic cell lines. Further studies examining the impact of theses findings are therefore underway.
METB-11. HOW METHYLATION PROFILING HELPS IN DIAGNOSING AND TREATING PEDIATRIC BRAIN TUMORS IN INDONESIA
Authors: Rahmartani Ludi Dhyani , Budiarso Michael Nathaniel , Gunawan Kevin , Susanto Eka , Sahm Felix , Ahmad Olfat , Pfister Stefan 
Published: June 2024

Abstract

BACKGROUNDS
Pediatric brain tumors (PBT) exhibit extensive heterogeneity, impacting treatment outcomes. While traditionally classified based on histopathological features, recent WHO classifications have integrated DNA methylation array profiling amongst other molecular characteristics, which improves diagnostic accuracy and thus treatment decisions. However, access to this technology is limited in low- and middle-income countries (LMICs) like Indonesia. As part of the MNP Outreach Consortium, we aimed to introduce methylation profiling in Indonesia to aid in diagnosing and stratifying PBT patients.

METHODS
In 2023, we conducted a case series involving seven challenging PBT cases from Cipto Mangunkusumo National General Hospital, re-assessing them with methylation profiling.

RESULTS
Through collaboration with the Institute of Neuropathology Heidelberg and the DKFZ, our centre adopted a discerning approach to re-evaluate histopathological samples from complex cases. This endeavour yielded notable results, reaffirming four initial diagnoses and altering three others Amongst the findings, one case initially diagnosed as anaplastic ependymoma, CNS WHO grade 3, was reclassified as a supratentorial ependymoma with YAP1 fusion gene, based on methylation class. Noteworthy within this latter group, one case initially categorized as low-grade pilocytic astrocytoma was reclassified as high-grade diffuse midline glioma, H3 K27 altered. Moreover identifying the copy number plot could indicate a KIAA1549::BRAF fusion to reclassify a case from diffuse pediatric glioma WHO grade 2 to pilocytic astrocytoma WHO grade 1. The recurrent pigmented neuroectodermal tumor of infancy (MNTI) was reclassified as Medulloblastoma, non-WNT/non-SHH, group 3 subtype II on methylation profiling, highlighting molecular similarities and potential treatment insights. These findings offer insights into genetic mechanisms and guide treatment strategies.

CONCLUSION
Accurate diagnosis, facilitated by advanced molecular profiling, enhances prognostication and enables personalized treatment plans, even in LMICs. This underscores the importance of expanding access to advanced diagnostic technologies in resource-limited settings.
GCT-01. CENTRAL NERVOUS SYSTEM GERM CELL TUMORS – GENERATING A CONSENSUS IN THEIR DIAGNOSIS AND MANAGEMENT
Authors: Abdelbaki Mohamed S 
Published: June 2024

Abstract

BACKGROUND
Despite the excellent outcomes of central nervous system (CNS) germ cell tumors (GCTs), there still exists significant differences in how GCTs are diagnosed and managed in different parts of the world. Additionally, the long-term toxicities and morbidities of the current therapies, and their substantial negative impact on the social wellbeing of our patients should clearly indicate that the current achievements are not enough. Further, important molecular data have emerged over the past decade that we have not witnessed their translation into any of the ongoing clinical trials.

METHODS
A comprehensive review of all major CNS GCT clinical trials will be discussed, in addition to a detailed review of the several issues of debate. Moreover, the latest developments in molecular landscape of GCTs will be provided in order to identify the hurdles that affect their incorporation in GCT clinical trials.

RESULTS
Tumor marker cut-offs that differentiate between germinoma and non-germinomatous germ cell tumors are clearly different between the various groups around the world. Additionally, differences exist in the chemotherapy backbones, radiation therapy field and dose, and the appropriate regimens to treat some of the rarer GCTs. Furthermore, there is no clear guideline on how to treat patients who do not achieve complete response after chemotherapy.

CONCLUSIONS
Discussing the clear differences that exist in the diagnosis and management of CNS GCTs is a critical first step in generating a clear consensus between the North American, European, Asian, and Latin American groups, which will certainly guide future clinical trials, improve the outcomes as well as the long-term treatment effects for this group of patients.