Childhood Brain Tumors Research Articles

Abstract 5341: Mechanisms driving resistance in Group 3 and recurrent/disseminated medulloblastoma

Abstract Background: Medulloblastoma (MB) is the most common malignant brain tumor in children and accounts for 20% of childhood brain tumors. Among the 4 molecular MB subtypes, Group 3 and 4 MBs have the worst prognosis. The biology of recurrence and dissemination in MB is less understood. Overexpression of platelet-derived growth factor receptor (PDGFR) has been associated with metastatic MB, and PDGFR activity promotes MB migration. PDGFR-induced migration is regulated by Src kinase. Src kinase activity is high in MB and Src kinase inhibition restricts tumor growth. Group 3 MB demonstrates high PDGFRA expression. Aim: Our objective was to evaluate if molecular inhibition of PDGFR or Src kinase will control metastatic progression/dissemination in Group 3 MB. Methods: We treated a panel of 4 patient-derived MB cell lines with dasatinib, which can inhibit BCRABL, c-KIT, PDGFR and Src kinase. Dasatinib dose required to inhibit c-KIT and PDGFR is higher (50-100 nM) than that needed for Src inhibition (1-10 nM). Results: Proliferation assay with dasatinib (1-10000nM) performed on all 4 cell lines did not demonstrate any inhibition of proliferation except at 10000nM dose. We treated all 4 MB cell lines with higher dose range of dasatinib (625-10000nM). One cell line did not respond to dasatinib, remaining cell lines demonstrated proliferation inhibition over 13 days between 625-5000nM. There were 2 interesting observations. Firstly, cell line which required lowest dose (625nM) was a recurrent MB, while paradoxically, its paired parental cell line (non-recurrent/treatment-naïve) responded to proliferation inhibition only at higher 5000nM dose. IC50 of parental cell line was 38-times higher than recurrent cell line. We postulated that recurrent MB may be responsive to dasatinib. However, dasatinib-treated recurrent cells demonstrated minimal changes in cell cycle phases (IC50 day 4 dose 187.4nM) and apoptotic cell death (187.4nM and 293.2nM) compared to DMSO-treated control. Since Group 3 MB demonstrates high PDGFRA expression, we employed a patient-derived orthotopic xenograft (PDOX) model of Group 3 MB to investigate the in-vivo response to dasatinib. The 2nd interesting observation was that dasatinib-treated mice exhibited earlier neuro-symptoms, more rapid tumor growth and clinical deterioration compared to control mice. However, overall animal survival time was not statistically significant between treated versus untreated groups (p=0.24 Log-rank test). Conclusions: Recurrent cells were more sensitive to dasatinib in-vitro compared to paired parental cells. In-vivo, mice treated with dasatinib developed neuro-symptoms faster than controls. It is currently not known if recurrent MB cells demonstrating early dasatinib-sensitivity to proliferation inhibition, escaping cell death, can formulate an in-vivo mechanism to drive more rapid tumor progression/dissemination as observed in our Group 3 MB Model. Citation Format: Shiying Huang, Jie-Ling Pan, Qi Lin, YuChen Du, Jack Su, Angela Major, M. Tarek Elghetany, Kam-Man Hui, Xiaonan Li, Wan-Yee Teo. Mechanisms driving resistance in Group 3 and recurrent/disseminated medulloblastoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5341.

OTHR-45. Kids First Variant WorkBench: application to germline genomic discoveries in the Children's Brain Tumor Network

The Gabriella Miller Kids First Pediatric Research Program (Kids First) aims at facilitating researchers to uncover new insights into the biology of childhood cancer (CC) and structural birth defects (SBD). Kids First has two initiatives, i) whole genome sequencing of biospecimens from families with CC/SBD, and ii) establishing Kids First Data Resources. Kids First Data Resource Center developed the Kids First Data Resource Portal (KFDRP), a centralized platform to search, view, analyze, and identify currently accessible data from both Kids First and collaborative cohorts, incorporating omics and phenotypic information of 30 studies and 26,300 participants. A recently released KFDRP component is Variant WorkBench (VWB), enabling users to query, mangle, analyze and visualize genomic variants from participating cohorts, with the Children’s Brain Tumor Network (CBTN) being one of the cohorts. VWB supports programming languages such as Python, Spark, SQL and R for in-depth analysis in Apache Zeppelin notebooks. In addition to variant calls and phenotypic information, VWB hosts rich external variant annotations in the public domain, such as Cancer Hotspots, COSMIC and ClinVar. Users can also load additional databases (e.g. Human Gene Mutation Database/HGMD) within a notebook, import custom datasets as temporary query tables, export analysis outputs to local drives, visualize analysis results in multiple chart styles, display local figures, and save notebooks for sharing, further use and Cavatica projects. In an effort to screen tier 1 genes (n=578) from the most recent Cancer Gene Census provided by COSMIC in CBTN, we identified ~127,500 germline variants that are both rare and damaging, or that are already cataloged in the most recent version of ClinVar/HGMD. The whole process took less than one hour which is much faster than conventional methods. VWB enables efficient genomic variant analysis and discoveries in pediatric neuro-oncology research with advanced big data technology.

SURG-02. The site of origin of medulloblastoma: Does the neurosurgical perspective support the current concept from molecular data?

BACKGROUND: Medulloblastoma (MB) are the most common malignant brain tumor in childhood. Developmental gene expression data supported by neuroradiological studies suggest that Wingless (WNT)-MB originate from the lower rhombic lip (LRL), Sonic-Hedgehog (SHH)-MB from the cerebellar hemispheres, and Group 3 and Group 4 MB from the cerebellar vermis. However, there is still insufficient evidence from a neurosurgical perspective supporting this proposed concept. METHODS: Clinical and molecular data from patients aged under 18 years at time of diagnosis who were operated on a histologically confirmed MB at the Department of Neurosurgery of the Medical University of Vienna between 1990 and 2020 were retrospectively analyzed. The location of the tumor origin was defined based on operative reports, surgical videos and preoperative imaging data by an experienced neurosurgeon blinded to the subgroup information. RESULTS: Sufficient data were available in 53 patients. In 28.6% (2 / 7) WNT-MB, 66.7% (6 / 9) SHH-MB and 70.3% (26 / 37) Group 3 and Group 4 MB, the intraoperatively defined site of origin corresponded well with the cellular origin suspected from the molecular subgroup. Within the WNT-subgroup, 57.1% (4 / 7) originated from the vermis, 28.6% (2 / 7) from the LRL and 14.3% (1 / 7) from the cerebellar hemisphere. The origin of SHH-MB was predominantly located in cerebellar hemispheres (66.7% (6 / 9)), while 33.3% (3 / 9) originated from the vermis. Of Group 3 and Group 4 MB, 70.3% (26 / 37) had their origin in the vermis and 29.7% (11 / 37) in the LRL.CONCLUSION: Our results indicate that there is a considerable level of inconsistency between the intraoperatively observed site of origin and the expected cellular origin based on the molecular subgroup, especially in WNT-MB. This discrepancy needs to be discussed when it comes to surgical decision-making accounting for risk stratification.

QOL-08. Visual memory and potential clinical risk factors in long-term survivors of a childhood brain tumor

A brain tumor treatment has previously been associated with long-term neurocognitive sequelae. However, clinical profiles differ between certain patient subgroups. We investigated the impact of tumor location, radiotherapy (RT), and age at diagnosis in childhood brain tumor survivors on long-term cognitive outcomes. Adult survivors (n=32) of pediatric brain tumors (n=11 infratentorial, n=21 supratentorial; 14 astrocytomas, 3 craniopharyngiomas, 2 ependymomas, 2 germinomas, 1 hemangioblastomas, 4 medulloblastomas, 6 nervus opticus gliomas) participated in this neuropsychological study (n=11 RT) (16.8-35.1 years old, >2years after treatment, mean age at diagnosis = 9.2 years, 50% male). An extensive neurocognitive test battery was used to assess intelligence scales (n=5), verbal and visual memory (n=2), and language (n=3). In order to investigate the effects of tumor location (infra- versus supratentorial), RT (yes vs. no), and age at diagnosis on the cognitive scores, a multivariate ANCOVA model was tested including the main effects and interaction between age and RT. Of all included scales, only visual memory was significantly associated with the risk factors. More specifically, patients who received RT (F=10.3, p=.004) and were younger at diagnosis (F=6.9, p=.014) scored worse on this task. Furthermore, the interaction effect between these factors was also significant (F=8.8, p=.006). These findings suggest that younger patients could be more vulnerable to the radiotoxic effects to visual memory outcomes. Tumor location (supra- vs. infratentorial) was not significantly associated with any outcome. In this study, only visual memory appeared to be associated with the risk factors of interest. Both radiotherapy and age at radiotherapy, as well as their interaction, could be risk factors for altered neurodevelopmental patterns of brain areas associated with visual memory.

DIPG-33. Treating Pediatric Diffuse Intrinsic Pontine Glioma with Brain Radiation and Temozolomide: A Case Report

Abstract Diffuse Intrinsic Pontine Gliomas (DIPG) is a rare and highly aggressive central nervous system tumour arising from glial cells which occur mostly in children. It remains a potentially deadly cancer despite treatment, with the highest mortality rate, in which most children die within 1-year of diagnosis. Radiation therapy might improve the clinical symptoms, but the results are temporary, with tumor progression typically occurring months post radiation, whereas chemotherapy remains controversial. Here we present a case report of a patient with DIPG Indonesia and how we diagnose and currently treat it. An eight years-old boy presented with decrease level of consciousness with headache, limb weakness, slurred speech, double vision, hemifacial weakness, paraplegia, and disequilibrium which worsened two weeks prior to admission. He was initially noted to have a medially inverted left eye two months prior to admission. On physical examination, there was a N.VI and N.VII palsy, hyperreflexia, paraplegia, and nystagmus. Head MRI demonstrated a solid with minimal enhancement after contrast administration in the left pons region extending into mesencephalon with cystic component and flat floor of fourth ventricle sign, causing hydrocephalus, suggestive diffuse intrinsic pontine glioma. He was given fractionated focal intensity modulated radiation therapy (IMRT) to the tumor along with 5 mm margins with a total dose of 54 Gy. 1.8 Gy fractions, given once daily for 5 days per week over a period of 6 weeks. Supportive care in the form of corticosteroids is used to treat the peri-tumoral edema. There was a short period of motoric improvement. But then the disease progressed with the latest head CT showed hydrocephalus formation with increased size of mass. He is treated with chemotherapy using Temozolomide, and currently alive after 3 months post diagnosis. Keywords: childhood brain tumour, Diffuse Intrinsic Pontine Glioma, radiation therapy

EPEN-29. Spatial transcriptomic analysis of ependymoma implicates unresolved wound healing as a driver of tumor progression

Abstract Ependymoma is a childhood brain tumor that remains incurable in approximately 50 percent of cases, most commonly in posterior fossa subgroup A (PFA). Uncovering how heterogeneous cell types within the tumor microenvironment (TME) interact is crucial to a complete understanding of PFA disease progression. The underlying cellular components of the PFA TME have been revealed by single-cell RNAseq (scRNAseq), identifying divergent epithelial differentiation and epithelial-mesenchymal transition (EMT) lineages. Here, we utilize spatial transcriptomics (Visium) of 14 PFA samples, integrated with scRNAseq, to chart neoplastic and immune cell architecture, with a higher resolution of cellular heterogeneity than scRNAseq alone. At a gross level, all PFA were primarily comprised of neoplastic epithelial and mesenchymal transcriptomic spatial zones, each containing a diversity of hierarchical cellular stages. In all samples we revealed spatially and transcriptomically-distinct mesenchymal zone-associated subclusters, including a quiescent undifferentiated progenitor-like subpopulation and clusters with characteristics of early and late stage EMT. Two early stage EMT clusters were distinguished by signatures of either myeloid cell interaction or hypoxia, and both were demonstrated to be EMT-initiating processes in in-vitro PFA experimental models. Myeloid cell interaction is the predominant initiating stage of EMT in PFA, occurring in zones that are spatially distinct from hypoxia induced EMT. Other mesenchymal clusters represent later EMT stages characterized by wound repair and tissue remodeling. Increased proliferation was a general characteristic of epithelial zone clusters, which included a second undifferentiated progenitor-like population that showed a particularly high mitotic rate and was associated with histologically hypercellular areas. Given the biological parallels with normal wound healing, we propose that mesenchymal and epithelial zones interact to create a cycle of persistent tissue damage response and mitogenic re-epithelialization signals. Unresolved wound repair is therefore a potential driver of PFA progression, a new concept that could provide novel targets for effective therapeutic intervention.

IMMU-16. Next-generation CAR T-cells targeting IL13RA2 and secreting IL-15 achieve durable tumour clearance in pre-clinical model of diffuse midline glioma

T-cells engineered with a chimeric antigen receptor (CAR) to acquire tumour specificity provide a possible new treatment approach for childhood brain tumours. Durable clinical remissions have been achieved with CD19-directed CAR T-cells in refractory B-cell malignancies including control of leptomeningeal disease and parenchymal deposits. Early clinical data of CAR-T cells in adult glioblastoma and diffuse midline glioma (DMG) further support the rationale for development of CAR-T cell therapy for paediatric high-grade gliomas (pHGG) and other high-risk childhood brain tumours. IL13RA2 provides a suitable CAR target. It is expressed in the majority of pHGG including DMGs while expression is absent on normal (paediatric) brain tissue. Early results with CAR T-cell therapy for adult HGG has shown that IL13RA2 can be safely targeted, and potent anti-tumour activity is possible. However, responses are variable and ultimately transient. This is likely due to the immunosuppressive environment encountered by CAR T-cells at tumour sites which hampers persistent tumour-directed immunity. Here we develop a next generation CAR approach engineering T-cells with both a CAR and a cytokine signal which supports persistent anti-tumour immunity. We have generated novel IL13RA2-specific antibodies and used these to construct CARs. Using a functional screening approach assessing target-specific cytolytic function, T-cell proliferation and cytokine release, we selected the optimal IL13RA2-CAR design. Then, we generated a next generation CAR construct co-expressing inflammatory cytokine IL-15 with the IL13RA2-CAR. In a PDX model of DMG, T-cells transduced with IL13RA2-CARIL-15, in contrast to IL13RA2-CAR alone, induced long-term tumour clearance. Further in vitro testing of IL13RA2-CARIL-15 showed enhanced proliferation and resistance to immune-suppressive secreted factors such as TGF-β. In conclusion, co-expression of IL-15 with IL13RA2-CAR enhances CAR T-cell proliferation and in vivo persistence and achieves durable tumour clearance. IL13RA2-CARIL-15 is being translated into a phase I clinical trial for patients with DMG.

OTHR-19. Disordered cell migration in the cerebral cortex caused by Lin28A overexpression and Wnt pathway activation in neural precursor cells

Abstract LIN28A overexpression and mutations of the Wnt pathway gene CTNNB1 have been described in rare malignant brain tumors of early childhood. In order to investigate the interplay of the oncogenic proteins Lin28A and Ctnnb1 during embryonal brain development, we overexpressed these components in neural progenitor cells in vivo. The sole overexpression of either Lin28A, stabilized Ctnnb1 (Ctnnb1Δex3) or the combination of both in hGFAP-positive forebrain precursor cells did not lead to brain tumor formation but resulted in distinct phenotypes in the cerebral cortex during embryonal development. The hGFAP-cre::IsI-Lin28A (GL) mouse model showed transiently increased proliferation in the cerebral ventricular zone and proper isocortical layering. hGFAP-cre::Ctnnb1Δex3fl/+ (GB) and hGFAP-cre::Ctnnb1Δex3fl/+::IsI-Lin28A (GBL) mice developed a hydrocephalus and showed disturbed cortical layering. GB mice displayed cerebral hypoplasia with a thinned cortex, while the GBL cortices showed variable thickness. Immunostainings with the pial marker Laminin and dendritic marker Map2c revealed a porous pia mater and aggregations of neurons above the pial border in the GBL model at embryonal day 14 (E14.5). At later embryonal stage (E18.5), the GBL model showed also large blood vessels located in deeper cortical layers. Proteome analyses of GB and GBL cortices revealed decreased abundance of the Lissencephaly associated component Reelin-receptor Lrp8 compared to hGFAP-cre control mice. Additionally, we found 92 proteins, which were altered specifically in the GBL mouse model. These results indicate that the co-expression of Lin28A and Ctnnb1Δex3 in neural precursor cells does not lead to brain tumor formation but results in neuronal migration disturbances with ectopic neurons in the subarachnoid area. Whereas the GB phenotype is reminiscent of human lissencephaly type I, GBL brain morphology showed similarities to neuronal overmigration observed in the migration disorder of human Cobblestone (Type II) Lissencephaly.

HGG-48. A comparative proteomic analysis of the cell membrane of histone 3 mutated paediatric high-grade gliomas in order to identify potential immunotherapeutic targets

Improvements in the treatments for childhood and adolescent brain tumours, High-Grade Glioma (pHGG) and Diffuse Intrinsic Pontine Glioblastoma (DIPG), have not advanced much and they continue to carry a very poor prognosis. These brain tumours are now defined by mutations affecting histone 3 proteins, indeed 80% of DIPGs harbour histone H3.1 and H3.3 K27M somatic mutations whilst 30% of pHGGs exhibit H3.3 G34R or G34V mutations. We hypothesized that the histone 3 mutant tumours will have distinct mutation specific surfactome or cell surface proteins. We therefore analysed the cell surface proteomics of H3.3 G34V and G34R mutated high-grade glioma in comparison to the H3 wild-type Glioma, to explore whether these proteins have the potential to be used as immunotherapeutic targets. We have at first isolated the cell membrane fractions from a range of patient cells carrying histone 3 mutations (G34R, G34V) relative to wild type histone 3. A comparative quantitative liquid chromatographic mass-spectrometry analyses of these cell surface membrane fractions were performed to identify specific targetable factors. The results of these were analysed with the focus in identifying proteins that can be targeted for tumour specific immune modulation or immunotherapeutic intervention. Results of these analyses will be presented.

MODL-20. Metabolic rewiring support the onset of chemotherapy resistance in medulloblastoma

Abstract Medulloblastoma (MB) is the deadliest brain tumor of childhood, intrinsically characterized by fast growth, high invasiveness, and resistance to treatments. With the aim to deepen the molecular basis of MB aggressiveness and recurrence, we established an in vitro model of MB resistance to chemotherapy, in which, a weekly exposure to a cocktail of chemotherapeutics commonly used in MB treatment (Vincristine, Etoposide, Cisplatin, Cyclophosphamide – VECC) induces the selection of cells that progressively acquire resistance to subsequent VECC treatments. Preliminary data on our model of MB resistance show that resistant cells induce the activation of the two main regulator of pentose phosphate pathway TKT and G6PD via the activation of Nrf2 transcriptional activity. Moreover, resistant cells show an increase in hypoxia inducible factor-1α (HIF-1α) together with an augmented expression of glycolytic enzymes HK1, PFKB-3, PDK1 and LDHA and increased glycolytic capacity. Interestingly, enrichment analysis on label free mass spectrometry data reveal that the most significant terms deriving from the upregulated proteins, that characterized resistant cells, were related to metabolic processes such as “carbon metabolism”, “fatty acid beta oxidation”, “tricarboxylic acid cycle” and “carboxylic acid catabolic processes”.Consistently with recent studies that highlight the relevance of metabolic plasticity of cancer cells in chemotherapy adaptation, our data suggest a metabolic uncoupling in which MB resistant cells, through the alteration of peculiar metabolic processes, may satisfy their altered energetic demands through alternative metabolic pathways. In this way, the generation of a new balance of intracellular metabolites finally provide increased resistance to external insults (i.e., chemotherapeutics) and a greater ability of detoxifying the intracellular compartments.

MODL-21. Multi-omics investigation of medulloblastoma resistant models reveals functional association between intracellular regulatory networks and drug susceptibility

Abstract Medulloblastoma (MB) is the most common malignant brain tumor of childhood. Despite high-dose radio/chemotherapy treatment, 15-30% of patients still display a high risk of tumor recurrence. In this context, the characterization of innovative cellular models resembling therapy-induced drug resistance represents an unprecedented opportunity for selecting relevant therapies for chemotherapy-refractory patients. In order to unveil the molecular mechanisms sustaining chemotherapy resistance in MB, we setup in vitro models of MB drug resistance by exposing Patient-Derived MB (PD-MB) cells to a combination of the commonly used chemotherapeutics for pediatric MB treatment. Integration of multi-omics data, including transcriptional, proteomic and kinase activation profiling, disclosed that drug resistant PD-MB cells are characterized by a significant deregulation of several cancer-related pathways converging to metabolism of xenobiotics, adaptation of the biochemical processes sustaining energetic metabolic demand, cell proliferation and survival, protein homeostasis, RNA processing and modification, and immune response. Moreover, this intriguing regulatory network was functionally associated to the response of drug-resistant MB cells to a large library of compounds through a semi-automated High-Throughput drug Screening (HTS) workflow, suggesting the antimetabolite class of drugs as relevant therapeutics displaying high selectivity and efficacy against resistant MB models, together with a significant synergistic action when combined with standard chemotherapeutic agents. Collectively, our results suggest that drug-resistant MB cells are subjected to a peculiar adaptation of multiple intracellular processes during adaptation to chemotherapy, which protects them from the toxic environment but, at the same time, provides targetable vulnerabilities for therapeutic purposes.

MEDB-86. A re-induction regimen for children with recurrent medulloblastoma

Medulloblastoma is the most common malignant brain tumor of childhood. Despite multi-modal therapies, ~30% of patients experience disease recurrence, which portends a poor prognosis. At initial recurrence, intensive chemotherapy may be effective prior to various consolidation therapies including high dose chemotherapy with autologous stem cell rescue or irradiation. We report outcomes for nine children treated at two institutions with the following regimen: cyclophosphamide 1500mg/m2/dose days 1,2; irinotecan 125mg/m2/dose days 1,8; temozolomide 150mg/m2/dose days 1-5, and oral etoposide 50mg/m2/dose days 1-7. Patients received 2-4 cycles based upon disease response and physician preference. The mean time from initial diagnosis to first recurrence was 19 months. After receiving two cycles of therapy, two patients had complete response (CR) and proceeded to consolidation. Of the remaining seven patients, five had partial response (PR) and two had stable disease (SD). Overall response rate was 78% after 2 cycles. Two patients with PR proceeded directly to consolidation with irradiation. Five patients (3 PR, 2 SD) received 2 additional cycles. After four cycles there was one CR, two with minimal residual disease, one SD and one progressive disease (PD). Four patients (44%) are alive with no evidence of disease (NED). One patient died of consolidation-related toxicity but had NED at time of death 28 months from initial recurrence. Five patients developed PD. Two patients died of disease, two are alive with disease, and one is alive with NED after PD and additional therapy. There were no treatment-related deaths. Infection was the most common complication. Five patients had febrile neutropenia and two developed sepsis. One patient required dose reduction for prolonged thrombocytopenia. Peripheral blood stem cell collection was achieved in all patients for whom it was attempted. This re-induction regimen is generally well-tolerated and effective in inducing responses for children with recurrent medulloblastoma.

MEDB-50. Assessment of cellular radiosensitivity and DNA repair in medulloblastoma cell lines and patient-derivded xenograft slice cultures

Medulloblastoma (WHO grade 4) is the most common malignant brain tumor of childhood. Despite the high importance of radiotherapy for disease control, the mechanisms underlying response and resistance to radiotherapy are incompletely understood. Therefore, we assessed the radiosensitivity and DNA repair capacity of medulloblastoma cell lines in-vitro and of patient-derived xenograft (PDX) models ex-vivo. Cell survival after irradiation of seven medulloblastoma cell lines displaying different subgroups was assessed via colony formation assay (DAOY, UW228, UW473, SJMM4, ONS-76, HDMB-03, D283). The ONS-76 and the mouse SJMM4 cell line were the most radioresistant strains (surviving fraction after 6 Gy (SF6): 0.33 and 0.31, respectively), followed by UW473, UW 228 and DAOY cells (SF6 0.16-0.21). The non-WNT/non-SHH-activated cell lines HDMB-03 and D283 cells demonstrated profoundly higher cellular radiosensitivity (SF6 <0.05). Analysis of residual (24h after irradiation) DNA double-strand breaks (DSB) as assessed by co-localized γH2AX/53BP1-foci demonstrated a significant correlation between DSB repair capacity and cellular survival. To use a more reliable pre-clinical model for medulloblastoma, we further examined DNA repair foci in ex-vivo irradiated slice cultures of PDX models MED-113 (SHH) and NCH2194 & HT028 (Gr. 3). Immunofluorescence analyses of frozen sections demonstrated non-hypoxic (pimonidazole-negative) and proliferating (EdU-positive) cells at the outer rim of the tumor slices. Two hours after irradiation all three PDX models showed a strong increase in 53BP1-foci, clearly indicating DNA damage induction. Most radiation-induced DSB were repaired after 24h. In a first radiosensitization approach, we treated the HT028 model with the PARP inhibitor olaparib (1µM ± 2Gy irradiation). Twenty-four hours after treatment the sample displayed a strong increase in the amount and size of 53BP1-foci, indicating compromised DNA repair. Further in-vitro and ex-vivo investigations with the aim to predict individual radiosensitivity and effective radiosensitization strategies are ongoing.

MEDB-09. Unraveling the role of unfolded protein response in medulloblastoma cancer stem cells

Medulloblastoma (MB) is the most common malignant childhood brain tumor. The current clinical approach consists of multimodal strategies with debilitating long-term effects and risk of tumor recurrence. Medulloblastoma stem cells (MBSCs) are a fraction of tumor cells with high proliferation potential and the capability to adapt to adverse/restrictive conditions in tumor milieu thus driving the refractoriness to conventional therapies. Recently, high basal levels of Unfolded Protein Response (UPR) molecules have been found in tumors of different tissue-origin and are correlated with poor prognosis and low patient survival. However, little is known about the role of UPR in MB. We investigated the expression and activation of UPR players in MBSCs. Human group 3 MB (G3MB) cell lines, specifically CHLA-01, D283- and D341-Med, were grown in Vitamin A and/or FBS or in stem selective medium (B27™) for 72 h before collection. Cells were fixed, stained with proper primary antibodies and images were acquired by confocal microscopy. The analysis of the transcription factors ATF-4 and CHOP revealed their elevated nuclear expression and co-localization, which resulted to be more marked in G3MB stem-like cells than in the differentiated ones. Also the ATF-6 branch was investigated, in differentiating conditions D283 and D341-Med showed a greater activation of ATF-6, represented by its nuclear localization, in respect to stem cells, while CHLA-01 did not show differences. Conversely XBP1, the transcription factor downstream IRE1 signaling, was not expressed in the three cell lines. Lastly, a Kaplan-Meier analysis on MB patients showed a worse prognosis with a shorter survival rate of patients expressing high ATF4 transcript levels. Our results reveal, even in resting conditions, preferential activation of the PERK branch in G3MB cells grown in stem-like condition suggesting that ATF-4 might be a promising therapeutic and prognostic factor to specifically target the stem compartment in aggressive MB.

MEDB-45. Functional genomics identifies epigenetic regulators as novel therapeutic targets for sonic hedgehog medulloblastoma

Medulloblastoma (MB) is among the most common malignant childhood brain tumors that comprises a group of four molecularly distinct diseases. A significant proportion of these tumors is characterized by aberrant activation of the canonical sonic hedgehog (SHH) signaling pathway. Although small-molecule inhibitors targeting Smoothened (SMO) have proven a promising treatment approach for SHH-MB subgroup, primary or acquired resistance impedes its clinical efficacy. Therefore, novel targeted approaches are urgently needed to improve therapeutic strategies for this tumor entity. Here, we conducted a genome-wide CRISPR/Cas9 knockout screen in a murine and a human SHH-MB cell line, SMB21 and DAOY, respectively, in order to decipher tumor-specific genetic dependencies. Our data demonstrate that SMB21 cells highly depend on positive regulators of the SHH pathway, such as Smo and Gli1 for their survival, as opposed to DAOY cells, suggesting that the latter does not represent a faithful model of SHH-MB. Members of the epigenetic machinery such as Dnmt1 and Smarca5 scored strongly as SMB21-context specific essentialities. Pharmacologically, we show that DNMT1 inhibition is efficacious at clinically relevant concentrations against SMO inhibitor- sensitive, as well as resistant SHH-MB cell lines, indicating novel therapeutic avenues for SHH-MB. By performing RNA sequencing of SMB21 cells, we identified early and late changes in global gene expression induced by DNMT1 inhibition, including decreased expression of mediators of SHH signaling, such as Gli1 and Gli2. Of note, gene set enrichment analysis revealed that DNMT1 inhibition downregulates top gene sets associated with cell cycle progression, corroborating the screening results that Dnmt1 is essential for SMB21 proliferation. Further global DNA methylation profiling in SMB cells will help to define the molecular basis of sensitivity to DNMT1 inhibitors in SHH-MB. Summarizing, our data highlight the potential of inhibitors targeting epigenetic regulators in SMO inhibitor- sensitive and resistant MB for more efficacious treatment options.

MEDB-85. Transcriptional complexes as resistance drivers to BET inhibition

BET-bromodomain inhibition (BETi) is a promising therapeutic strategy to target MYC-driven cancers, including Group 3 medulloblastoma, a deadly childhood brain tumor. We have shown that BET inhibitors exhibit preclinical efficacy against MYC¬-amplified medulloblastoma, providing motivation to evaluate this drug class in early phase clinical trials. However, our work has also found that MYC-amplified medulloblastoma cells can acquire resistance to BETi, suggesting that curative responses for this disease will require combination therapy. To guide the development of such combination therapies, we have focused our efforts on elucidating the mechanisms through which medulloblastoma cells acquire resistance to BETi. We found that medulloblastoma cells can develop tolerance to BETi by reinstating the expression of cell-essential “rescue genes,” which include bHLH transcription factors, cell-cycle regulators, and anti-apoptosis genes. This transition to the resistant cell state is mediated through changes in chromatin structure including the upregulation of H3K4me3 promoters. Our preliminary results suggest that BETi-resistant cells maintain mRNA transcription and protein translation of important mediators of resistance. Importantly, we observe that BETi-resistant medulloblastoma cells are more dependent on specific protein complexes involved in transcriptional regulation. This project explores the mechanisms through which these transcriptional regulators help maintain transcription of rescue genes that drive BETi resistance and evaluates the potential of targeting these drivers of BETi resistance. These results will help guide the development of combination approaches to improve the efficacy of BETi for the treatment of MYC-driven medulloblastoma.

HGG-28. CLIC1 and CLIC4 ion channel deficiency confers increased sensitivity to tumour treating fields and improved survival in paediatric glioblastoma

Paediatric Glioblastoma Multiforme (pGBM) is a lethal brain cancer with an average survival of 14 months. Due to the scarcity of effective treatment, pGBM forms the leading cause of CNS cancer death in children. Optune™ is a non-invasive therapy that uses alternating electric fields – coined TT fields - to disrupt cancer cell division, however it is not currently approved in children. Evidence shows that ion channels not only regulate electrical signalling of excitable cells, but also play a crucial role in the development and progression of brain tumours, essential in cell cycle control and therefore presenting as valuable therapeutic targets. Candidate ion channel genes (ICG) associated with the malignant status of high-grade glioma (HGG) were identified via multivariate analysis of in-house and publicly available data sets. RNA sequencing of in-house patient tissues revealed an increased expression of CLIC1 and CLIC4, with pHGG exhibiting increased expression at protein and RNA levels in both the Paugh data set and in-house primary cell lines and TMAs. Clinical correlation determined that CLIC4 and CLIC1 deficiency was associated with increased overall survival (p=<0.03). siRNA depletion of CLIC1 and CLIC4 propagated a reduction in the proliferation, migration and invasion of pHGG cell lines and resulted in cell cycle arrest. Furthermore, CLIC1 and CLIC4 deficiency exacerbated the killing capacity of TT fields. Whole transcriptome gene expression analysis (Human Clairom™ Array) of paediatric GBM cell lines treated with tumour treating fields and found that cells treated with TTfields exhibited a down-regulation in CLIC1 and CLIC4 compared to untreated cells. These data provide rationale that genetic, electrical, and pharmacological manipulation of ion channels will reduce the capacity of childhood brain tumours to proliferate and invade. Therefore, may be a suitable target for combination therapy to enhance the treatment efficacy of TTfields and help bring this non-invasive therapy to paediatric patients.

MEDB-11. MYC overexpression and SMARCA4 loss in cerebellar granule cell precursors cooperate to drive medulloblastoma formation in mice

Group 3 medulloblastoma is one of the most aggressive types of childhood brain tumors. Roughly 30 % of cases carry genetic alterations in MYC, SMARCA4 or both genes combined. While overexpression of MYC has previously been shown to drive medulloblastoma formation in mice, the functional significance of SMARCA4 mutations and their suitability as a therapeutic target remain largely unclear. To address this issue, we combined an overexpression of MYC with a loss of SMARCA4 in cerebellar granule cell precursors. Cells were isolated from 7-day-old Math1-creERT2::Smarca4fl/fl pups after tamoxifen-induced loss of SMARCA4. Subsequently, MYC overexpression was achieved by lentiviral transduction, and transduced cells were transplanted into immunodeficient CD1nu/nu recipient mice. Preliminary results show tumor formation in 5/19 transplanted mice (26 %) after 6 months. SMARCA4 loss in all tumor cells was confirmed both immunohistochemically and on a genetic level and suggests a dependency of tumor growth on SMARCA4 loss. In a next step, additional cohorts will clarify if tumor development is accelerated by or even dependent on the loss of SMARCA4 in our model. Additionally, the neoplastic potential of tumor cells will be verified with the aid of secondary recipient mice. To evaluate to what extent the generated tumors are comparable to human Group 3 medulloblastomas, tumors will be extensively analyzed on a morphological, transcriptional, and epigenetic level. Altogether, we hope to establish a suitable mouse model for SMARCA4 mutated Group 3 medulloblastoma that will help to elucidate the role of SMARCA4 in tumor development and to identify new therapeutic targets.

EPEN-32. Leveraging cell surface targets as therapeutic vulnerabilities for pediatric ependymoma

Brain tumors are the leading cause of cancer-associated death in children. Ependymoma, an aggressive type of childhood brain tumor, is currently treated with surgery and radiotherapy. Ependymomas are a molecularly heterogeneous group of tumors driven by distinct genetic and epigenetic alterations. In children, 90% of ependymomas arise intracranially, with two thirds occurring in the posterior fossa (PF) and one third in the supratentorial brain (ST). PF ependymomas are divided into at least two groups termed, PFA and PFB, with PFA tumors associated with poor clinical outcomes. Over 70% of ST ependymoma are characterized by an oncogenic fusion between ZFTA and RELA and shown in some cohorts to have poor clinical outcome, particularly in the context of CDKN2A tumor suppressor gene loss. A major challenge in identifying therapies against ependymoma, has been the paucity of genetic abnormalities available for targeting. PFA ependymomas harbor largely balanced genomes with no recurrent CNVs, fusions, or somatic mutations that are amenable to pharmacologic inhibition. ZFTA-RELA ependymoma while representing a clear disease driver, functions as a transcription factor and lacks clear binding surfaces available for direct inhibition using small molecules. Therefore, alternative approaches are needed to identify new targets and effective therapies in ependymoma to be evaluated in pre-clinical models. In both human ependymoma cell culture lines and PDX models, we demonstrate that a multi-omic approach is promising for cell surface target discovery, and further, focused cell surface profiling can identify lead targets that can be rapidly translated for CAR T-cell therapy.

IMMU-15. The immunologic context of pediatric central nervous system malignancies and identification of pan-histology immunomodulatory targets

Abstract Central nervous system tumors account for the most childhood cancer mortality. Immunotherapies have made major contributions to treat adult cancers, but application of immunotherapy for childhood brain tumors has been limited, in part due to the unique CNS microenvironment and mechanisms of immune escape in this context. To investigate the immunologic context, we query the transcriptomic profile of ~700 primary brain tumors released by the Children’s Brain Tumor Network. An immune subtype classification from The Cancer Genome Atlas project reveals that 81% of high-grade tumors across molecular subtypes are characterized by an immunosuppressive phenotype (C4) while an inflammatory phenotype (C3) is more common in low-grade lesions (p&amp;lt;0.001). Adjusting for histologic grade and extent of resection, C4 associates with worse overall (OS) and progression-free survival (PFS) in this cohort (HR 3.1, p=0.008 and 1.6, p=0.03 respectively). Deconvolution of the transcriptome reveals that relative to C3, C4 tumors have decreased T-cell signature, OR 0.4 (0.2–0.8), and increased macrophage and tumor-proliferation signature (OR 2.0, 1.3–3.3, and 3.1, 2.3–4.2, respectively). In contrast to C3 tumors, T-cell signature in C4 tumors adversely impacts survival and correlates with multiple immunosuppressive genes and cytokines. Among them, the immune checkpoint CD276 has the highest associated impact on survival in C4 tumors (HR of log increase is 1.9, p&amp;lt;0.001). Additionally, high-grade lesions have suppressed expression of antigen-presenting genes. EZH2 is implicated in downregulating antigen presentation and is found to be significantly upregulated in all high-grade lesions in this cohort. Treatment with the EZH1/2 inhibitor valemetostat resulted in upregulation of antigen-presenting genes and tissue differentiation pathways across three murine syngeneic models, one modeling diffuse midline glioma and two embryonal models. Future in-vivo studies with genetic and chemical modification of immunomodulatory genes of interest aim to identify immunotherapeutic targets with potential for broad applicability in pediatric neuro-oncology.