tbuckley/cabot-search huggingface dataset:
CNSC-04. EXPLORATION OF INTERCELLULAR NETWORKS IN EPENDYMOMA REVEALS POTENTIAL THERAPEUTIC VULNERABILITIES
Authors: Julia K Sundheimer, Johanna Rettenmeier, Stefanie Volz, Leonhard V Bamberg, Aniello Federico, Daniel D Azorín, Paula Ertel, Sophie Heuer, Sophia Scheuermann, Christian Seitz, Frank Winkler, Marcel Kool, Stefan M Pfister, Kendra K Maaß, Kristian W Pajtler
Journal: Neuro-Oncology (2024)

Abstract BACKGROUND Aggressive ependymoma (EPN) exhibit primary and secondary radio- and chemotherapy resistance with the poorest prognosis in the pediatric groups PF-EPN-A and ST-EPN-ZFTA. Recently, tumor cell networks formed by membrane protrusions, such as tunneling nanotubes (TNT) or tumor microtubes (TM), have been identified in other glial brain tumors. These structures facilitate intercellular hierarchical Ca2+-communication and contribute to therapy resistance. Previous data from our group suggested enhancer-regulated Ca2+-communication to be essential in EPN. This study aims to further characterize intratumoral interactions and to understand potential correlations between tumor cell connections and treatment resistance in EPN. METHODS Intercellular connections in EPN patients and model systems were characterized by scanning electron microscopy, immunofluorescence and ultra-high content imaging. Transcriptomic and proteomic data were analyzed to identify potential targetable vulnerabilities within network dynamics. Candidates were functionally validated in cell culture models applying Ca2+ live cell imaging. RESULTS Connectivity-related terms such as microtube-based movement or microtube bundle formation showed increased expression in EPN transcriptome data compared to healthy controls. EPN networks were found to be build of TM- and TNT-like structures with a higher abundance of TNT-like structures in PF-EPN-A compared to ST-EPN-ZFTA. All networks showed strong Nestin-positivity in cells, mouse models and human tumor tissue of ST-EPN-ZFTA and PF-EPN-A. Thrombospondin-1, a matricellular protein enhancing TMs in glioma cells, was strongly enriched in ST-EPN-ZFTA patients. The gap junction channel connexin 43, connecting glioma cells, was highly upregulated in PF-EPN-A. Active electrochemical communication was observed between ST-EPN-ZFTA cells performing Ca2+ imaging. Moreover, inhibition of T-type Ca2+ channels impaired intercellular signaling, leading to network perturbation in vitro. CONCLUSIONS Our study revealed the importance of gap junction-coupled networks for communication of aggressive EPN cells. Targeted disconnection of the EPN-specific network as demonstrated for Ca2+ channel inhibition suggests a new avenue for therapeutic strategies in EPN to overcome resistance.
METB-08. CIRCULAR EXTRACHROMOSOMAL DNA IS ASSOCIATED WITH POOR SURVIVAL IN CHILDHOOD CANCER TYPES
Authors: Sunita Sridhar, Owen Chapman, Aditi Dutta, Shanqing Wang, Rishaan Kenkre, Jens Luebeck, Vineet Bafna, Jill P Mesirov, Lukas Chavez
Journal: Neuro-Oncology (2024)

Abstract BACKGROUND Circular extrachromosomal DNA (ecDNA) is a common form of oncogene amplification in aggressive cancers and a promising target for improved cancer therapy. The frequency and diversity of ecDNA has been described in different types of adult cancers and in selected childhood cancer types such as neuroblastoma and medulloblastoma. However, the frequency of ecDNA and its association with survival has not been comprehensively analyzed across the spectrum of pediatric cancers. METHODS We performed a pediatric pan-cancer study of ecDNA in which we mined large pediatric cancer genomics repositories and reconstructed ecDNA sequence structures from whole genome sequencing data. RESULTS We analyzed a retrospective cohort of 1684 tumor biopsies from 1506 different patients, covering all major childhood cancers, many of which occur exclusively in children, including rare embryonal tumor types. The fraction of patients with ecDNA-positive tumors was 10%, varying significantly by tumor type. Aggressive tumor types had particularly high incidences of ecDNA, including embryonal tumors with multilayered rosettes (n = 6, 67%), osteosarcoma (n = 55, 47%), rhabdomyosarcoma (n = 38, 39%), and neuroblastoma (n = 111, 30%). Survival analysis revealed that ecDNA amplifications are significantly associated with poor outcome. Furthermore, we catalogued known and potentially novel oncogenes that are recurrently amplified on ecDNA in pediatric cancers and showed that ecDNA often evolves during disease progression. CONCLUSIONS These results reveal childhood tumor types in which ecDNA is widely prevalent and highlight patient populations that could potentially benefit from future therapies targeting mechanisms of ecDNA biogenesis and function.
LMIC-19. A RETROSPECTIVE ANALYSIS OF PEDIATRIC RECURRENT PINEOBLASTOMA IN BEIJING
Authors: Miao Li, Yanling Sun, Zhen Zhang, Wanshui Wu, Liming Sun
Journal: Neuro-Oncology (2024)

Abstract OBJECTIVE To explore the clinical characteristics of pediatric recurrent pineoblastoma in Beijing. METHODS Eighteen patients with newly diagnosed pineoblastoma were admitted to Beijing Shijitan Hospital between January 2014 and December 2022. The clinical data were retrospectively analyzed. RESULTS Among the 18 patients (M/F=8:1), all were treated with surgery, and both radiotherapy and chemotherapy were administered. Nine patients experienced recurrence, and 2 patients died at last follow-up. The Median follow-up time were 56 months. The 5-year progression-free survival (PFS) and 5-year overall survival (OS) were (42.0±13.1) %, and (88.1±7.9) %, respectively. Among the 9 recurrent patients, one was &amp;lt; 3 years, and 8 cases ≥ 3 years. One girl and 8 boys relapsed; 7 cases were M0 and 2 with metastases at diagnosis; 7 cases were GTR; Two cases experienced recurrence within one year (10 months each), and one died. The other 7 patients relapsed after one year, the median time to first relapse were 24.0 (range: 10.0~49.0)months. The sex, age group, metastases at diagnosis, GTR or not, recurrent sites were not significantly affects PFS. Although the 9 recurrent patients received both cerebral and spinal irradiation and chemotherapy followed by surgery, the different order of chemotherapy or radiotherapy first were significantly affected the duration of remission. The median time before the first relapse after surgery was longer in those who treated under the order of craniospinal irradiation followed by chemotherapy than those of the inverse order (29m vs 13m, χ2=6.528, P=0.011). In addition, one case with germline mutation of Dicer1, experienced recurrences more than 3 times although received second surgery and second radiotherapy, and multiple cycles of chemotherapy in our center, which indicates poorer outcome. CONCLUSION Pineoblastoma is rare and prone to relapse, the order of chemotherapy first may have shorter remission time before the first recurrence after surgery (P&amp;lt; 0.05).
PATH-04. OPTIMIZING CELL-FREE DNA ASSAYS FOR LOW INPUT LIQUID BIOPSY SAMPLES FROM PEDIATRIC BRAIN TUMOR PATIENTS
Authors: Tom T Fischer, Kendra K Maaß, Pitithat Puranachot, Markus Mieskolainen, Martin Sill, Agnes M E Finster, Paulina S Schad, Fabian Rosing, Tatjana Wedig, Nathalie Schwarz, Florian Iser, Jochen Meyer, Felix Sahm, Benedikt Brors, Hannu Haapasalo, Stefan M Pfister, Joonas Haapasalo, Kristian W Pajtler, Kristiina Nordfors
Journal: Neuro-Oncology (2024)

Abstract BACKGROUND Genetic and epigenetic profiling have transformed biological understanding, diagnostics, and therapeutic approaches for pediatric central nervous system (CNS) tumors. Obtaining tumor tissue may be associated with neurosurgical risk, may not be feasible in some cases, and is not routinely performed during follow-up or at relapse. Liquid biopsies (LBs) have emerged as a minimally invasive, serially collectable source of tumor-derived DNA. Here, we collected cerebrospinal fluid (CSF) and serum LBs from a large, unselected, cross-entity pediatric CNS tumor cohort (n=55 patients) for method optimization. METHODS Cell-free DNA (cfDNA) isolated from CSF and serum samples was analyzed 1) by low-coverage whole genome sequencing for copy number variation (CNV)-based tumor detection and 2) by enzymatic conversion (EC)-based DNA methylation profiling using the EPIC DNA methylation array and the Heidelberg Brain Tumor Classifier. All library protocols were optimized for LB samples with low cfDNA amounts in the picogram range. Matched tumor samples were used as reference. RESULTS Our lcWGS-based cfDNA profiling protocol had a high technical success rate across the whole cohort (&amp;gt;95%), despite very low cfDNA amounts for most CSF samples. The majority of CSF LBs captured tumor-derived CNVs and displayed a high fraction of tumor-derived cfDNA (&amp;gt;5%, range 0-78%). For serum LBs, only few samples showed detectable CNVs. Proof-of-concept methylation analyses leveraging a new EC-based workflow allowed molecular classification using CSF, particularly for embryonal brain tumors (11/15 samples). Clinical workup of selected cases illustrates the potential of LBs to aid as diagnostic tool, monitor disease, and characterize tumor evolution. CONCLUSIONS Tackling a major roadblock of clinical translation of LBs, this study delineates new methods tailored to low input cfDNA samples. Results highlight the clinical utility of LBs for the management of brain tumor patients, providing a strong rationale for prospective validation within pediatric neuro-oncology trials.
DIPG-88. TARGETING THE ANTIOXIDANT RESPONSE ELEMENT AXIS SENSITIZES DIFFUSE MIDLINE GLIOMA CELLS TO ONC201
Authors: Evangeline R Jackson, Ryan J Duchatel, Cameron J Fish, Mika L Persson, Dilana E Staudt, Izac J Findlay, Matthew D Dun
Journal: Neuro-Oncology (2024)

Abstract BACKGROUND Diffuse midline glioma (DMG) is a universally fatal CNS tumor, with a median overall survival of &amp;lt;12-months. Recent studies, including our own, have identified overexpression of the mitochondrial protease ClpP in DMG patient samples. ClpP plays a pivotal role in regulating energy production. Brain-penetrant ClpP agonists, including ONC201, ONC206, and TR107, induce non-specific degradation of the mitochondrial electron transport chain. However, there is considerable variability in the response of DMG cell lines to these therapies, with only about half reaching IC50. Notably, TP53-mutant cell lines exhibit reduced sensitivity. METHODS/RESULTS Further analysis using quantitative proteomics of TP53-mutant DMG cell lines exhibited hallmark activation of ClpP, increased mitochondrial stress and dysfunction. Importantly, ClpP agonism increased the activity of the transcription factor NRF2, driving expression of NQO1 (p=0.0017). NQO1 is a cytoprotective enzyme, promoting redox balance and cell survival. This highlights a potential adaptive response to ClpP agonist therapy in DMG cells. Analysis of DMG patient samples through publicly available RNA sequencing data identified ubiquitously high NRF2 expression compared to other pediatric CNS tumors. This led us to hypothesize that a clinically relevant, selective NQO1 inhibitor could elicit a strong response to ClpP agonism. Therefore, we examined ARQ761, a CNS-active therapy that disrupts NQO1 leading to the formation of an unstable hydroquinone, causing oxidative DNA damage and apoptosis. When ARQ761 was used concurrently with a ClpP agonist, the combination showed additive effects, average Bliss Score of 9.91 (n=4). Interestingly, administering ARQ761 24 h after ClpP agonist exposure combined synergistically, average Bliss Score of 15.87 (n=4). This synergy was further potentiated using ARQ761 48 h after ClpP agonism, when NQO1 expression peaked, resulting in an average Bliss Score of 20.30 (n=4). CONCLUSIONS This study has unveiled an intrinsic antioxidant defense mechanism in DMG, which facilitates evasion from treatments inducing oxidative stress. This defense mechanism appears particularly robust in cell lines harboring TP53-mutations, which are also known to exhibit resistance to radiotherapy.
DIPG-31. IS RE-IRRADIATION A POTENTIAL SURVIVAL BENEFIT FOR PATIENTS WITH DIFFUSE INTRINSIC PONTINE GLIOMA?
Authors: Natália Dassi, Ana C S Torquato, Michael Chen, Maria L Figueiredo, Jessica B Rodrigues, Sergio Cavalheiro, Patricia A Dastoli, Maria T S Alves, Frederico A Silva, Carlota V B Moraes, Nasjla S Silva, Andrea M Cappellano
Journal: Neuro-Oncology (2024)

Abstract BACKGROUND Diffuse intrinsic pontine glioma (DIPG) is an aggressive infiltrative glioma with dismal prognosis. Radiation therapy (RT) offers a transient benefit and re-irradiation (reRT) may be an option at disease progression. OBJECTIVE To evaluate the outcome of patients with DIPG at progression in a single institution. METHODS Between 2010-2023, 55 patients were evaluated, retrospectively, in respect of their treatment-one RT course versus re-RT) and concomitant medications. Overall survival (OS) was measured from diagnosis to date of death and from reRT to death using Kaplan–Meier and log-rank test. RESULTS Median age was 7.1 years (range 2.9-16.2y). Twenty-two patients underwent biopsy with 11 performing immunohistochemistry for H3K27M (9 mutated). In nine cases molecular analyses was evaluated: 6 H3.3K27M-mutant (2 simultaneously TP53 + 1PTPRZ1-MET fusion), 1 H3.1K27M-mutant, 1 H3C2-mutant + ACVR1 mutation and 1 PDGFRA + KIT amplifications. Thirty-five patients completed the initial course of RT (54Gy- 13-33 daily fraction), 30/35 also received valproic acid (VA), 5/35 bevacizumab, 3/35 nimotuzumab and 1/35 nivolumab+ipilimumab. Twenty patients underwent re-RT at first progression, four with 54 Gy (30x 180Gy), nine with 50Gy (25x 200Gy) and seven with median dose of 30Gy (26-39Gy), depending on their clinical status. These group also received valproic acid(8/20), bevacizumab(8/20), nivolumab(1/20) and ONC 201(1/20). Patients who received reRT showed prolonged OS compared to no reRT (median 524 vs 351 days; p=0.013). ReRT was well tolerated with 15(75%) patients experiencing stable to improved neurologic function. Patients with better clinical status and 50-54Gy reRT doses, showed prolonged OS (median 238 vs 135 days; p=0.1). Median OS from re-RT to death was 174 days (range, 14-218 days) with eight patients alive to date. CONCLUSIONS Re-irradiation with 50-54Gy seems safe and feasible for DIPG patients after disease progression from the first treatment, with mostly patients experiencing neurological improvement and prolonged life period.
DIPG-85. MALT1 IN H3K27-ALTERED DIFFUSE MIDLINE GLIOMA
Authors: Hannah E Butterfield, Juliana Hofstatter Azambuja, Lisa Maurer, Dong Hu, Andrea F Cruz, Matthew E Halbert, Taylor A Gatesman, John Little IV, Sameer Agnihotri, Peter C Lucas, Linda M McAllister-Lucas
Journal: Neuro-Oncology (2024)

Abstract BACKGROUND H3K27-altered diffuse midline glioma (DMG) is a devastating pediatric brainstem tumor that affects 200-300 individuals in the US per year. Median survival is 9-11 months, and there are virtually no long-term survivors. Despite decades of clinical trials, radiation therapy remains standard of care, extending survival by 2-3 months. Elucidating the mechanisms that drive H3K27-altered DMG pathogenesis in order to uncover therapeutic vulnerabilities is of critical importance. Recent studies implicate MALT1 as a potential therapeutic target in gliomas. MALT1 is the effector molecule of the CARMA-BCL10-MALT1 (CBM) signalosome, a cytoplasmic protein complex that drives downstream pro-survival transcriptional activity. MALT1, which possesses scaffolding and protease functions, promotes cell viability, proliferation, and migration/invasion in multiple cancer types. We aim to evaluate the hypotheses that MALT1 promotes DMG cancer cell proliferation and migration and that MALT1 inhibition will abrogate tumor progression. METHODS/RESULTS We screened a panel of cells including astrocytes, neural stem cells, and DMG cell lines by Western blot and found that CBM complex members BCL10 and MALT1 are present in all cells tested. We next demonstrated that MALT1 is proteolytically active in DMG cell lines SF8628 and HSJD-DIPG-007. Specifically, we showed cleavage of the MALT1 protease substrate HOIL, which was abrogated by treatment with the MALT1 protease inhibitor MLT-748. We next generated multiple dox-inducible MALT1 shRNA DMG cell lines to assess the impact of MALT1 deficiency on DMG biology. Thus far, we find that shRNA knockdown of MALT1 does not impact SF8628 cell proliferation. CONCLUSIONS MALT1 is expressed and proteolytically active in DMG cells. Initial studies show that MALT1 knockdown does not affect proliferation of SF8628 cells. We will next evaluate the effect of MALT1 knockdown on proliferation of additional DMG cell lines, as well as the impact on other malignant features of DMG cells including migration/invasion.
DIPG-68. FLAG-003, A NOVEL, DUAL-ACTION THERAPEUTIC, DEMONSTRATES IN-VITRO ACTIVITY AGAINST DIFFUSE INTRINSIC PONTINE GLIOMA (DIPG)
Authors: Sonam Bhatia, Thomas Quinn, Keith L Ligon, Pratiti Bandopadhayay, Katherine Warren
Journal: Neuro-Oncology (2024)

Abstract BACKGROUND FLAG-003 is a novel, rationally-designed, CNS-penetrant, dual-acting agent that inhibits receptor tyrosine kinase activity and microtubule polymerization. Preclinical studies in glioblastoma (GBM) demonstrated decreased cell viability, reduced tumor volumes, decreased microvessel density, and increased survival. Remarkably, using an orthotopic DIPG model, all mice treated with FLAG-003 at 275 mg/day/orally displayed tumor regression, tumor reduction and increased survival. Given the significant preclinical activity against DIPG, as well as the known heterogeneity of DIPG, we evaluated the efficacy of FLAG-003 in vitro against a panel of DIPG cell lines. METHODS Eight DIPG cell lines hosted at the Center for Patient Derived Models (CPDM) were selected based on genomic and growth characteristics. Cells were plated on 384-well plates; 24 hours after plating, cells were dosed with 1nM to 50uM (12 step log curve) FLAG-003. Three technical replicates were performed per step. Controls consisted of positive kill control Staurosporine, negative growth control of 0.5% DMSO, or no DMSO for baseline growth. ONC201, a small molecule antagonist of DRD2/3 currently in clinical trials for DIPG, was used as a comparator. We also evaluated two GBM patient-derived models. RESULTS FLAG-003 demonstrated efficacy in all DIPG and GBM cell lines tested with IC50 less than 100nM. FLAG-003 was more potent compared to ONC201 in all models evaluated. CONCLUSIONS Single agent FLAG-003 demonstrated activity against a panel of DIPG cell lines. As next steps, we are exploring the efficacy of this drug in orthotopic DIPG PDX models. Continued development of FLAG-003 as a potential therapeutic candidate for DIPG patients is warranted and underway.
DIPG-45. TARGETING HYPERACETYLATION IN PEDIATRIC DIFFUSE MIDLINE GLIOMAS USING ONCOLYTIC ADENOVIRUSES
Authors: Akhila Parthasarathy, Marc Garcia-Moure, Jiasen He, Dong Ho Shin, Andrew G Gillard, Andres Lopez-Rivas, Lethan A Hampton, Xuejun Fan, Hong Jiang, Frederick F Lang, Marta M Alonso, Candelaria Gomez-Manzano, Juan Fueyo
Journal: Neuro-Oncology (2024)

Abstract BACKGROUND H3K27-altered pediatric diffuse midline glioma (DMG) is a highly aggressive type of brain tumor with a 5-year survival rate of less than 2%. Conventional treatments are restricted to palliative radiation therapy. Therefore, effective treatments are urgently needed. Results from a recent phase I clinical trial for Diffuse Intrinsic Pontine Glioma showed that intratumoral administration of Delta-24-RGD oncolytic adenovirus in combination with radiation improves survival without unwanted toxicity. Based on the rationale that, during infection, the early viral protein E1A binds P300, we hypothesize that combining oncolytic adenoviruses with p300 inhibitors will induce a robust modification of the post-translational landscape of DMGs and increase the anti-cancer effect of the oncolytic virus. METHODS Studies on Delta-24-RGD infectivity and replication were performed in a panel of clinically significant DMG cells. Modification of the acetylation levels of acid-extracted histones after Delta-24-RGD was analyzed using Western blot. Cell Titer Blue was utilized to measure cell viability, and ZIP-synergy scores were calculated using SynergyFinder. RESULTS We observed a time-dependent reduction in H3K27ac in human DMG cells following Delta-24-RGD infection with an 89% reduction in H3K27ac at 48h post-infection. Delta-24-RGD treatment of DMG cells resulted in optimum viral infectivity and replication. Combining Delta-24-RGD with the p300 inhibitor C646 resulted in enhanced cell death in vitro. Using a panel of oncolytic viruses that induce differential enzymatic and binding functions of P300, we showed that Delta-24-RGD mediated alteration of P300 activity is required for hypoacetylation in DMGs. We characterized the in vivo dynamics of K27M-H3.1 and K27M-H3.3 DMG-derived tumors in the brain stem of syngeneic animal models. In vivo experiments are in progress to examine the combinatorial anti-glioma effect of Delta-24-RGD and P300 inhibitors. CONCLUSION Collectively, our studies provide a strong mechanistic rationale for combining oncolytic adenoviruses and p300 inhibitors and should propel the eventual clinical testing of this approach in DMG patients.
PATH-06. AN INTEGRATIVE MULTI-MODAL DIAGNOSTIC APPROACH TO PEDIATRIC CHOROID PLEXUS TUMORS
Authors: Alexander L Markowitz, Jolee Suddock, Everardo Castaneda, Jianling Ji, Ashley Margol, Benita Tamrazi, Stefan Bluml, Jennifer A Cotter
Journal: Neuro-Oncology (2024)

Abstract BACKGROUND Choroid plexus tumors (CPTs) consist of a diverse group of neoplasms, more prevalent in children. They include choroid plexus papillomas (CPPs, grade 1), atypical choroid plexus papillomas (aCPPs, grade 2), and choroid plexus carcinomas (CPCs, grade 3). Traditional grading of CPTs relies on histologic assessment, but morphologic criteria for determining tumor grade are subjective. Evidence suggests incorporation of clinical, radiologic, and molecular characteristics may increase diagnostic accuracy. Here, we investigated the multi-modal associations of CPT subtypes to develop a classification system to aid in CPT subtype diagnostics. METHODS We aggregated an integrative dataset that consists of digitized whole-slide images, NGS sequencing panels, methylation arrays, and magnetic resonance spectroscopy (MRS) spectra from in-house and publicly available data sources (n=110). We tested for clinically significant associations and established multi-modal profiles of CPT subtypes, as well as a machine-learning classifier to predict multi-modal based CPT subtypes. RESULTS CPT subtypes exhibit distinct characteristics across modalities with consistent correlations across anatomy, molecular, and metabolic datasets. Computer-vision models achieved high accuracy (89.7%) in classifying CPT subtypes using H&amp;E images. Ki-67 immunostaining displayed increased reactivity in CPC compared to CPP and aCPP (p = 0.007, ANOVA). Methylation-based classifications confidently predicted CPP and CPC subtypes, while aCPP tumors clustered with either CPP or CPC due to the lack of a defined subtype. Molecular variants (i.e. TP53, MYCN) were significantly associated with CPC (p = 0.007, ANOVA). Metabolites such as inositol (p = 0.031) and choline (p = 0.004) were associated with CPT grade based on MRS-spectra. CONCLUSION Multi-modal analysis reliably separates CPTs by grade. The study underscores the significance of integrating multi-modal datasets in refining the accuracy of diagnosis and prognosis of CPTs. Continued research will focus on a multi-modal approach to improve prediction of aggressive behavior and understanding of inherent metabolic heterogeneity of CPT subtypes.