bluuebunny/crossref_metadata_2025_split huggingface dataset:
DIPG-53. LSD1 DEGRADATION SYNERGIZES WITH HDAC INHIBITION IN PEDIATRIC H3K27M DIFFUSE MIDLINE GLIOMA
Authors: Haase Rebecca , Groves Andrew , Mire Hafsa , Qi Jun , Filbin Mariella 
Published: June 2023

Abstract
H3K27M-mutated diffuse midline glioma (H3K27M DMG) is an aggressive, lethal pediatric brain tumor which resists conventional cancer treatments. To identify new therapeutic targets, our lab executed a focused CRISPR negative selection screen in patient-derived H3K27M cell lines after treatment with the histone deacetylase (HDAC) inhibitor panobinostat, and discovered a strong co-dependence with the histone demethylase LSD1. We further explored the therapeutic potential of this synergistic interaction with a screen of HDAC- and LSD1- targeting drugs to identify synergistic combinations, which show penetration of the blood brain barrier suitable for clinical translation. Interestingly, conventional catalytic LSD1 inhibitors did not seem to synergize with HDAC inhibitors tested on cell viability, while a recently described CoREST/LSD1 degrader phenocopied the effects seen in our CRISPR screen. We hypothesized that the CoREST/LSD1 degrader induces synergy with HDAC inhibitors through elimination of a scaffolding function of LSD1. To prove this, we knocked out LSD1 using CRISPR/Cas9 in H3K27M cells and subsequently treated with a panel of HDAC inhibitors. These showed a significant sensitization compared to controls cells. Further, we confirm the high specificity of the CoREST/LSD1 degrader by performing streptavidin bead pull down with a newly synthesized biotin-conjugated probe. This revealed that it interacts with the entire CoREST complex (members include LSD1, RCOR1, HDAC1/2). In conclusion, we show that degrading CoREST/LSD1 in combination with HDAC inhibition is a synergistic strategy in H3K27M DMG. For future translational studies, we will assess biomarkers upon treatment and analyse compound potency in vivo.
EPEN-03. ZFTA-RELA LOCALIZATION DYNAMICS REGULATE TRANSCRIPTIONAL CONTROL
Authors: Arabzade Amir , Laboe Nic , Ippagunta Siri , Emanus Eric , Kardian Alisha , Mack Stephen 
Published: June 2023

Abstract
ZFTA gene fusions are the most frequent driver events in supratentorial ependymoma (EPN). ZFTA-fusion proteins act as oncogenic transcription factors (TFs) to aberrantly activate oncogenic transcriptional programs. Our data indicates that ZFTA fusion proteins form distinct punctate structures with heterogeneous patterns of liquid-phase-like characteristics. These condensates are closely associated with transcription as seen by nascent RNA FISH and recruitment of various members of the transcription machinery, such as BRD4, MED1, and RNA POLII. Our genomic footprinting data indicates that many key transcription factors, such as Sox9, share similar genomic occupancy patterns with ZFTA fusions suggesting that these transcription factors are potentially recruited to these condensates, establishing transcriptional hubs. Our mutagenesis studies reveal that the ZFTA zinc finger domain is indispensable for condensate formation, and may bridge ZFTA fusion proteins to DNA at unique genomic loci. Condensate-forming deficient mutants fail to establish the same transcriptional program and are unable to drive tumor formation. This mechanistic data has led to our efforts to establish drug-chemical screen approaches against ZFTA-RELA localization/dynamics to identify novel therapeutic targets.
EPEN-06. CHARACTERISING THE DEVELOPMENTAL ORIGINS AND TRAJECTORIES OF ZFTA-RELA FUSION EPENDYMOMA IN A NOVEL MOUSE MODEL
Authors: Bonner Sigourney , King Claire , Rarhmann Katherine Wickham , Cooper Elizabeth , Katyal Gunjan , Gilbertson Richard 
Published: June 2023

Abstract
Ependymomas driven by the ZFTA-RELA fusion account for &gt;70% of all supratentorial ependymomas. These tumours are now recognised in the WHO classification of CNS tumours and have been associated with a poor prognosis. Seven ZFTA-RELA fusion variants have been described: around two thirds of cases are fusion 1. No spontaneous genetically modified mouse models (GEMMS) have been described and current models require invasive intracranial injection (of transduced cells or RCAS-TVA system). Here we describe the first spontaneous GEMM of ZFTA-RELA fusion-driven ependymoma. Nestin-Flx-STOP-Flx-ZFTA-RELA (Fusion 1) open reading frames were targeted together with luciferase to the Rosa-26 locus. Breeding these mice with Nestin-CreERT2 or Blbp-Cre lines that drive recombination in neural progenitor cells resulted in forebrain tumours that could be tracked with bioluminescence imaging from P20. Tumours displayed NF-kB and L1CAM expression and ZFTA-RELA protein was detected using a novel in-house antibody. Tumours display expression of a known ZFTA-RELA fusion ependymoma transcriptomic signature. ZFTA-RELA tumours can be grown as neurospheres and passaged as allografts in nude mice and respond to irradiation. We provide the first spontaneous GEMM of this important group of ependymomas. Here we present our histologic and transcriptomic developmental timecourse of these tumours, their comparison to the human disease and further understanding of the lineage origins and potential novel targets.
EPEN-08. COMBINED PDGFR INHIBITOR AXITINIB AND RETINOID TRETINOIN DECREASES PROLIFERATION AND HIGH-RISK NEOPLASTIC SUBPOPULATION PROPORTIONS PFA EPENDYMOMA
Authors: Donson Andrew , Grimaldo Enrique , Riemondy Kent , Griesinger Andrea , Amani Vladimir , Brunt Breauna , Pierce Angela , Foreman Nicholas 
Published: June 2023

Abstract
Ependymoma (EPN) is fatal in over 50% of children and has not seen any therapeutic improvements in over 30 years. Based on data from single-cell RNA sequencing (scRNAseq) and large-scale screening of FDA-approved oncology compounds in posterior fossa group A (PFA) EPN, we hypothesized that combination of PDGFR inhibitors and retinoids therapy will selectively deplete aggressive mesenchymal and undifferentiated EPN subpopulations resulting in therapeutic benefit. In vitro screening of a panel of three receptor PDGFR inhibitors (PDGFRIs) and nine retinoid analogues in high-risk chromosome 1q+/6q- PFA cell lines MAF-811 and MAF-928 was performed to identify those drugs with (i) anti-proliferative effect (tritiated thymidine incorporation and live-cell imaging), (ii) depletion of high-risk associated neoplastic subpopulations (qRT-PCR using subpopulation specific markers and scRNAseq), and (iii) synergistic effects. PDGFRIs axitinib and pazopanib and retinoids tazarotene, adapalene and tretinoin showed superior potency versus other analogues. qRT-PCR showed that tazarotene and axitinib demonstrated beneficial subpopulation perturbation. Combination of the top two PDGFRIs (axitinib and pazopanib) and retinoids (tazarotene and tretinoin) demonstrated that axitinib combined with tretinoin provided the strongest synergistic anti-proliferative effect and depletion of high-risk-associated undifferentiated subpopulations. More definitive scRNAseq subpopulation analysis revealed a reduction of mesenchymal cells in MAF-811 in response to combined axitinib/tretinoin treatments. In both MAF-811 and MAF-928 there was a net increase in the proportion of differentiated subpopulations, which are associated with a more favorable clinical outcome, in response to combined axitinib/tretinoin, collectively supporting our original hypothesis. These results demonstrate that combined RTKi axitinib and retinoid tretinoin treatment has a synergistic anti-proliferative effect and reduction of high-risk subpopulation proportions. The effect of combined axitinib and tretinoin on survival and subpopulation perturbation is now being explored in vivo.
EPEN-09. UTILITY OF RADIATION THERAPY IN SPINAL CORD MYXOPAPILLARY EPENDYMOMAS: A REVIEW OF THE LITERATURE
Authors: Jackson Kasey , Kleinknecht Sarah , Packer Roger , Hwang Eugene 
Published: June 2023

Abstract

INTRODUCTION
Myxopapillary ependymomas (MPEs) are slow-growing tumors that comprise about 25% of spinal ependymomas. Although historically designated as grade 1, the recent WHO classification has upgraded MPEs to grade 2 given their potential for recurrence and dissemination. While the National Comprehensive Cancer Network guidelines recommend avoiding radiation therapy (RT) unless a gross-total resection (GTR) is not achieved, several reports have suggested a potential benefit of adjuvant RT in improving relapse-free survival in children after GTR. This literature review was conducted to compare available data to determine the utility of upfront irradiation in these patients.

METHODS
A comprehensive literature review from 1984-2021 was performed on PubMed using keywords: “pediatric myxopapillary ependymoma” and “radiation.” One case was censored for unknown radiation status.

RESULTS
17 analyses from 1984-2021 were reviewed, yielding 140 pediatric cases of MPE, of whom 59% (n=83) received a GTR. Of those that received a GTR, average age was 13.7 yrs (range, 6-21), and 66% were male. The most common location was lumbosacral (25%), followed by thoracolumbar (19%). 22.8% (n=19) of patients received upfront focal RT. Relapse occurred in eight (42%) patients who received upfront RT, and 30 (47%) of those who did not, with no clear age or gender discrimination in those that relapsed. Distant recurrence occurred in 75% of those who received RT, and 68% of those that did not. The duration of event-free survival will be included in the final presentation.

CONCLUSIONS
While some individual studies have suggested a survival advantage in pediatric MPE after focal RT, in this meta-analysis, both relapse rate and location seemed similar regardless of receipt of RT. From this available evidence, the efficacy of upfront RT has not been demonstrated.
EPEN-12. COMPARING CELLULAR HIERARCHIES AND SPATIAL ARCHITECTURE ACROSS MOLECULAR SUBGROUPS OF SUPRATENTORIAL EPENDYMOMAS
Authors: Jeong Daeun , Maass Kendra K , Ghasemi David R , Englinger Bernhard , Jiang Li , Nascimento Andrezza , Hack Olivia A , Shaw McKenzie L , Pfister Stefan M , Kool Marcel , Gojo Johannes , Pajtler * Kristian W , Filbin * Mariella G 
Published: June 2023

Abstract
Ependymomas (EPN) are among the most common and fatal pediatric brain tumors with currently no targeted therapies available. Molecular studies including genome-wide DNA methylation profiling have shown that supratentorial ependymoma is subdivided into subgroups characterized by distinct fusion proteins: ZFTA-RELA fusion-positive (ZFTA-RELA), YAP1 fusion-positive (ST-YAP1), and four alternative ZFTA fusion-positive (ZFTA-Cluster 1, ZFTA-Cluster 2, ZFTA-Cluster 3, and ZFTA-Cluster 4). ZFTA-RELA tumors have been identified as the most common and aggressive molecular group with high intra-tumoral heterogeneity. However, limited sample size and interpatient variability in previous studies highlight a critical need for comprehensive profiling of supratentorial ependymomas across a larger patient cohort. In particular, how ZFTA-RELA compares to other subgroups of supratentorial ependymoma is unknown. Here, we collected and profiled 44 supratentorial patient tumors encompassing ZFTA-RELA (n=21), ZFTA-Cluster 1 (n=6), ZFTA-Cluster 2 (n=4), ZFTA-Cluster 3 (n=7), ZFTA-Cluster 4 (n=2), and ST-YAP1 (n=4). We profiled all tumors by single cell/single nucleus RNA-sequencing, and further characterized ZFTA-RELA by single cell spatial transcriptomics. Within each patient’s tumor we find multiple normal and aberrant differentiation trajectories from neural progenitor-like cells towards glial-like, mesenchymal-like and ependymal-like cells. Using sequencing-based lineage tracing, we experimentally validate these computationally inferred cellular hierarchies in vitro. Notably, compared to ZFTA-RELA ependymomas we observed predominantly higher proportion of early neural progenitor-like cells in ZFTA-Cluster 2 and ZFTA-Cluster 3, while in ST-YAP1 greater representation of mature ependymal-like cells. These findings highlight differences in developmental and aberrant differentiation trajectories driven by combination of oncogenic fusions and cell of origin in supratentorial ependymoma subgroups. In addition, neural progenitor-like cells most highly express ZFTA-fusions and are spatially distinct from other cell states, highlighting oncogenic fusions driving tumorigenesis organized in spatial niches. Together, this study reveals previously unknown intra- and intertumoral heterogeneity across subgroups of supratentorial ependymoma, as well as distinct cellular and spatial architecture.
METB-05. NON-INVASIVE DIAGNOSIS OF BRAINSTEM GLIOMAS IN PEDIATRIC, ADOLESCENT, AND YOUNG ADULT PATIENTS THROUGH CEREBROSPINAL FLUID CELL-FREE DNA SEQUENCING
Authors: Hill Katherine , Giantini-Larsen Alexandra , Hickman Richard A , Holle Bridget , Alano Tina , Doe-Tetteh Seyram , Bouvier Nancy , Li Shanita , Stockfisch Emily , Huereca Claudia , DiNapoli Sara , Hertz Charli Ann , Lee Alex , Szalontay Luca , Li Bryan Kincheon , Riviere-Cazaux Cecile , Burns Terry C , Haque Sofia , Bale Tejus , Benhamida Jamal , Dogan Snjezana , Vanderbilt Chad , Borsu Laetitia , Ross Dara , Chang Jason , Zampieri Caroline Barbosa , Donzelli Maria , Dunkel Ira J , Kramer Kim , Sait Sameer Farouk , Khakoo Yasmin , Gilheeney Stephen , Souweidane Mark , Greenfield Jeffery , Berger Michael , Arcila Maria , Ladanyi Marc , Mellinghoff Ingo , Karajannis Matthias , Miller Alexandra 
Published: June 2023

Abstract
Intrinsic brainstem tumors arising in pediatric, adolescent, and young adult patients comprise a spectrum of entities, predominantly diffuse midline gliomas (DMG) and IDH mutant astrocytomas. Accurate molecular diagnosis is essential for prognostication and optimal therapy. Therapeutic considerations include inclusion (in IDH mutant) or exclusion (in H3K27M) of adjuvant Temozolomide post radiotherapy and use of molecular targeted therapy (IDH inhibitors). Surgical biopsy, however, is associated with increased risk of permanent neurological deficits and may yield insufficient or non-diagnostic tissue. We hypothesized that minimally-invasive “liquid biopsy” of cerebrospinal fluid (CSF) could represent a superior diagnostic modality in this patient population, employing molecular analysis of cell free DNA (cfDNA). We analyzed 44 CSF samples from 38 unique patients for recurrent driver mutations in brainstem gliomas, including H3K27M, IDH1, and IDH2. MSK-IMPACT, a NY state-authorized hybridization capture-based next-generation panel DNA sequencing assay, was used for analysis. Samples without a detectable driver mutation by MSK-IMPACT testing were further subjected to gene targeted testing by droplet digital PCR. In all, 10/44 (22.7%) samples had mutations detected by MSK-IMPACT using standard calling criteria and 13 of the remaining 34 samples (38.2%) had supporting evidence of a mutation based on manual review. Further testing by ddPCR was performed on a subset of cases (based on DNA availability) which confirmed 7 of the previous low-level mutations and uncovered 4 additional mutations. Overall, 27/44 (61.4%) of cases had detectable evidence of a mutation, and of the 23 patients without a known tissue diagnosis, a driver in the CSF was identified for 47.8% of patients (11/23). Minimally-invasive analysis of CSF cfDNA in patients with intrinsic brainstem tumors has a high diagnostic yield and may obviate the need for tissue biopsy in a majority of patients. Testing with high sensitivity assays is valuable to maximize the rate of detection.
METB-09. GERMLINE PATHOGENIC VARIANTS IN 838 PEDIATRIC BRAIN TUMOR PATIENTS
Authors: McQuaid Shelly W , Kaufman Rebecca , Corbett Ryan J , Vaksman Zalman , Bornhorst Miriam , Brown Miguel A , Guo Yiran S , Zhu Yuankun , Heath Allison P , Storm Phillip B , Resnick Adam C , Waanders Angela J , Cole Kristina A , Rokita Jo Lynne , Macfarland Suzanne , Diskin Sharon J 
Published: June 2023

Abstract
The genetic contribution of rare pathogenic germline variation in cancer patients without a family history remains unclear. We sought to characterize the prevalence, spectrum, and clinical significance of pathogenic germline variation in cancer predisposition genes (CPGs) in pediatric brain tumor patients. Paired tumor and normal whole genome or exome sequencing was performed for 838 patients in the Pediatric Brain Tumor Atlas (PBTA). Rare variants in 196 CPGs were annotated as pathogenic (P) or likely pathogenic (LP) in an automated manner consistent with American College of Medical Genetics criteria and reviewed by an interdisciplinary panel. To assess enrichment, the frequency of CPG P-LP variants in cases was compared to the gnomAD v3.1 cancer-free control cohort (n=74,023). Second hit, mutational signature, and gene set enrichment analyses (GSEA) were performed on matched tumor sequencing to characterize differences in patients with and without germline P-LP variants in DNA repair genes. We observed 178 germline CPG P-LP variants in 163 PBTA patients (19.5%). CPG P-LP variants were most prevalent among Neurofibroma plexiform patients (64.3%), and NF1 and TSC2 harbored the most significant P-LP variant burden compared to controls (OR=69.5, p=2.4E-23, CI=34.6-137 and OR=357, p=1.1E-14, CI=71-3669, respectively). DNA repair gene P-LP variants were enriched in cases compared to controls (OR=4.4, p=8.3E-30). Patients harboring mismatch repair (MMR) gene P-LP variants exhibited significantly higher tumor-associated MMR-deficiency mutational signature exposures (p&lt;0.05) and DNA repair GSEA scores relative to other patients (p=0.04). Second hit SNVs in tumors were identified in four patients with P-LP germline variants in NF1 (n=2), APC (n=1), and SUFU (n=1). Germline P-LP variants are enriched in PBTA patients, and DNA repair variants are predictive of repair-deficiency signatures in tumor samples. Our work emphasizes the need for germline sequencing to inform patient care.
RARE-03. GENOME-WIDE ASSOCIATION STUDY OF INTRACRANIAL GERM CELL TUMORS: A COMMON DELETION AT BAK1 ATTENUATES THE ENHANCER ACTIVITY AND CONFERS RISK FOR THE BRAIN TUMORS IN CHILDREN ADOLESCENTS AND YOUNG ADULTS
Authors: Terashima Keita , Sonehara Kyuto , Kimura Yui , Nakano Yoshiko , Ozawa Tatsuya , Takahashi Meiko , Suzuki Kenji , Fujii Takashi , Matsuhita Yuko , Tomiyama Arata , Kishikawa Toshihiro , Yamamoto Kenichi , Naito Tatsuhiko , Suzuki Tomonori , Yamaguchi Shigeru , Miwa Tomoru , Sasaki Hikaru , Kitagawa Masashi , Ohe Naoyuki , Fukai Junya , Ogiwara Hideki , Kawamura Atsufumi , Miyawaki Satoru , Matsuda Fumihiko , Kiyokawa Nobutaka , Ichimura Koichi , Nishikawa Ryo , Okada Yukinori 
Published: June 2023

Abstract
Intracranial germ cell tumors (IGCTs) are rare brain tumors that mainly occur in children, adolescents and young adults with a particularly high incidence in East Asian populations. The biological basis of these tumors is still largely unknown. We conduct a genome-wide association study (GWAS) of 133 patients with IGCTs and 762 controls of Japanese ancestry by using Infinium Asian Screening Array and other molecular biology methods. A common 4-bp deletion polymorphism in an enhancer adjacent to BAK1 is significantly associated with the disease risk (rs3831846; P = 2.4 x 10-9, odds ratio = 2.46 [95% CI: 1.83-3.31], minor allele frequency = 0.43). Rs3831846 is in strong linkage disequilibrium with a testicular GCTs susceptibility variant rs210138. Expression quantitative trait locus (eQTL) analysis using the GTEx dataset reveals that the risk allele of rs3831846 has a down-regulating effect on BAK1 expression in a wide range of tissues. Further in-vitro reporter assays reveal rs3831846 to be a functional variant attenuating the enhancer activity. BAK1 is a pro-apoptotic member of the BCL-2 family, thus our results suggested that the risk allele may contribute to IGCTs predisposition through down-regulating BAK1 expression. Risk alleles of testicular GCTs derived from the European GWAS show significant positive correlations in the effect sizes with the Japanese IGCTs GWAS (P = 1.3 x 10-4, Spearman’s ρ = 0.48). Of the 57 loci, 11 exhibit significant association with IGCTs and these loci were implicated in a broad range of biological pathways, including KIT/KITLG signaling, apoptosis regulation, and telomerase activity. The risk allele frequency of rs3831846 is higher in east Asia than Europe (0.49 vs. 0.20), which may provide a partial explanation for the ethnic difference in incidence. Nevertheless, our results suggest the shared genetic susceptibility of GCTs beyond ethnicity and primary sites.
RARE-06. DISSECTING CELLULAR DIFFERENTIATION HETEROGENEITY IN CHOROID PLEXUS CARCINOMA PATHOGENESIS
Authors: Faltings Lukas , Mian Noreen , Siluveru Anjali , Modi Siddhi , Virga James , Cao Ping , Zhao Haotian 
Published: June 2023

Abstract
Choroid plexus (CP) neoplasms are rare, predominantly pediatric, brain tumors ranging from benign CP papilloma to aggressive CP carcinoma (CPC) associated with poor survival. Survivors often experience devastating side effects from current treatment strategies. There is an urgent need for safer, more effective therapies for CPC. A subset of human CPC exhibits abnormal NOTCH activity, whereas mutations of tumor suppressor gene TP53 are detected in &gt;50% of CPC and are associated with increased genetic tumor instability and worse prognosis. CPC is one hallmark of Li-Fraumeni syndrome (LFS), a rare genetic disorder associated with germline TP53 mutations. Human CP tumors also frequently display aberrant expression of transcriptional regulators of roof plate/CP differentiation, including LIM homeodomain transcription factors LMX1A, and SRY-Box Transcription Factor 2 (SOX2). To investigate the role of transcriptional regulation in CP tumorigenesis, animal models were developed driven by molecular defects commonly found in CP tumors in humans. Accordingly, sustained NOTCH and Sonic Hedgehog (SHH) activation or combined deletion of Rb1 and Trp53 tumor suppressors led to malignant CP tumors with characteristics of CPC in humans. NOTCH-driven CP tumors arose from monociliated roof plate progenitors and exhibited increased levels of Lmx1a, Lmx1b, and Sox2. In contrast, their expression was significantly reduced, while OTX2 levels were markedly increased in Rb1/Trp53-deficient CPC. Consistently, single-cell transcriptomics data show a proliferative Otx2+ tumor bulk and a small Lmx1a+/Sox2+ population in Rb1/Trp53-deficient CPC. Importantly, deletion of Sox2 in Lmx1a+ progenitors blocked NOTCH-driven CP tumor and reduced Lmx1a/b expression. Thus, LMX1A and SOX2 expression marks tumor-initiating cells, while OTX2 labels differentiated tumor cells in CPC. Together, our studies revealed intra- and inter-tumoral heterogeneity in CPC driven by distinct oncogenic signals. Knowledge of the molecular and cellular basis of heterogeneity in CP tumor development may facilitate the development of innovative diagnostic and therapeutic strategies in CPC.