tbuckley/cabot-search huggingface dataset:
METB-12. GIFT FROM A CHILD POSTMORTEM SPECIMEN DATASET EXTENSION OF THE PEDIATRIC BRAIN TUMOR ATLAS EMPOWERS PEDIATRIC BRAIN TUMOR RESEARCH
Authors: Mateusz P Koptyra, Noni Diarra, Jo Lynne Rokita, Antonia Chroni, Beth Frenkel, Ciana Anthony, Adam Kraya, Valerie Baubet, Ian Biluck, Catherine Sullivan, Noel Coleman, Lauren Seip, Jena Lilly, Mariarita Santi, Angela Viaene, Phillip B Storm, Adam C Resnick, On Behalf Of Gift From A Child
Journal: Neuro-Oncology (2024)

Abstract BACKGROUND Pediatric brain and spinal cord tumors are the leading cause of cancer-related mortality in children. An incomplete understanding of brain tumor biology and associated limited access to high-quality biological samples for research are the main factors driving the lack of clinical therapeutic development for pediatric brain tumors that recur or progress. Post-mortem tissue donation provides an unprecedented resource for addressing some of these limitations. METHODS The Gift from a Child (GFAC) program by the Swifty Foundation has a unique mission to increase post-mortem pediatric brain tissue donations through advocacy as well as the education of clinicians and families. Through GFAC’s strategic collaboration with the Children’s Brain Tumor Network (CBTN), CBTN has leveraged postmortem tissue to expand the Pediatric Brain Tumor Atlas (PBTA), a cross-histology multi-omics atlas resource. As part of the effort CBTN has sequenced and released data for over 350 post-mortem pediatric brain tumor specimens including multiple brain region sampling cases with specimen and sequencing quality metrics. RESULTS Here we present an assessment of postmortem samples and available multi-omic data on postmortem samples within the PBTA dataset. Data have been harmonized and released with no publication embargo. To access data, researchers can utilize existing open source data resources and platforms including PedCbioPortal and OpenPedCan to: (1) Identify tumor spatial and temporal specific alterations (2) Establish tumor evolution trajectory leading to therapeutic resistance and tumor progression; (3) Understand tumor heterogeneity longitudinally across multiple ‘omics layers; and (4) Identify and request specimens and derived tumor models. CONCLUSIONS Together, we present the largest deeply characterized cohort of postmortem pediatric brain tumor samples as powerful expansion of the PBTA cohort of &amp;gt;3,000 pediatric brain tumors. CBTN’s open-science model supported by the GFAC mission highlights the value and utility of autopsy-based specimen collection on behalf of improving outcomes for children with brain tumors.
HGG-22. LINKS BETWEEN M6A RNA METHYLATION, R-LOOPS AND DNA DAMAGE IN PAEDIATRIC HIGH-GRADE GLIOMAS
Authors: Lauryn Walker, Masar Radhi, Helen Knight, Stuart Smith
Journal: Neuro-Oncology (2024)

Abstract BACKGROUND Paediatric high-grade gliomas (pHGG) are aggressive malignant tumours of the central nervous system that unfortunately carry poor prognoses. R-loops, which are DNA:RNA hybrids, are a known source of genomic instability in eukaryotic cells. The RNA strand of R-loops can be m6A methylated at double-strand break sites in order to facilitate DNA repair. Therefore, we investigated whether dysregulation of m6A methylation and R-loop homeostasis at DNA damage sites deregulates DNA repair pathways in pHGG. METHODS Immunocytochemistry was performed to assess global m6A, R-loop, γH2AX and several DNA repair protein levels in pHGG cell lines compared to human astrocytes. Colocalisation between m6A and R-loops, R-loops and γH2AX, m6A and γH2AX, R-loops and 53BP1, R-loops and PARP1, R-loops and total ATM, and R-loops and phosphorylated ATM was assessed in pHGG cell lines and human astrocytes. RESULTS Immunocytochemistry analysis revealed that levels of global m6A, R-loop, γH2AX and several DNA repair proteins were generally higher in pHGG cell lines, thereby indicating that cellular homeostasis is dysregulated. Furthermore, a high degree of colocalisation between m6A and R-loops was observed. R-loops were found to colocalise with γH2AX, and m6A was found to colocalise with γH2AX, thereby corroborating the notion that m6A methylated R-loops are likely present at DNA damage sites. Finally, R-loops were also found to colocalise with a variety of DNA repair proteins, including 53BP1, PARP1, total ATM, and phosphorylated ATM, where different Pearson’s correlation coefficient values were obtained, thereby suggesting that R-loops associate with DNA repair proteins to different extents. CONCLUSIONS The link between m6A methylation, R-loops and DNA damage in relation to the pathogenesis of pHGG is currently being investigated. Experiments are also being performed where we are investigating m6A readers to see whether their aberrant expression contributes to disease pathogenesis via deregulating DNA repair pathways.
DIPG-38. VAL-083 IN COMBINATION WITH AZD1775 FOR THE TREATMENT OF DIFFUSE MIDLINE GLIOMA
Authors: Bavani Subramaniam, Debasish Roy, Ayda Woldegerima, Justyna Przystal, Jie Zhang, Sandra Laternser, Bettina Kritzer, Sridevi Yadavilli, Sabine Mueller, Roger Packer, Javad Nazarian
Journal: Neuro-Oncology (2024)

Abstract BACKGROUND Diffuse midline gliomas (DMGs) are malignant pediatric brain tumors characterized by H3K27M mutation and global genome hypomethylation. This results in enhanced transcription of MGMT, a DNA-repair enzyme, rendering alkylating chemotherapeutics ineffective. Therefore, we investigated the efficacy of a functionally different DNA damaging agent, Val-083, that induces double strand breaks and triggers S/G2 phase cell cycle arrest for homologous DNA repair. We further evaluated its combined efficacy with Wee1 (G2/M checkpoint) inhibitor, AZD1775, to override cell cycle arrest and propel cells with DNA damage into premature mitosis and apoptosis. METHODS DMG cells were treated with increasing concentration of Val-083 and/or AZD1775 and their viability was evaluated using CellTiter-Glo luminescent assay. Next, the drugs’ mechanisms of action were investigated by immunoblotting for biomarkers involved in DNA damage response and cell cycle arrest. Flow cytometry was used to investigate cell cycle profile and apoptosis. Additionally, in vivo tumor growth inhibition and survival benefit were evaluated using zebrafish and mouse xenograft DMG models. RESULTS The IC50 values of Val-083 range between 0.69 and 4.38 µM while the IC50 values of AZD1775 range between 0.22 to 0.98 µM. Combination of both drugs showed high areas of synergy on multiple DMG lines, DNA double strand breaks and significant increase in cell population at the S (p&amp;lt;0.01) and G2/M (p&amp;lt;0.05) phases. Importantly, on zebrafish xenograft tumor model, combination treatment significantly (p&amp;lt;0.001) inhibited tumor growth in comparison to control and single treatment groups. Furthermore, the combined treatment demonstrated significant (p&amp;lt;0.01) survival benefit (median survival (MS) = 62 days) on tumor-bearing nude mice models, in comparison to vehicle (MS= 44 days), Val-083 (MS= 54.5 days) and AZD1775 (MS= 47 days) treatment groups. CONCLUSION Val-083 in combination with AZD1775 demonstrate promising efficacy in DMG preclinical models, providing a strong rationale for positioning these arms for clinical testing.
DIPG-18. MULTIMODALITY VISUALIZATION OF A PRECLINICAL MODEL OF DIFFUSE MIDLINE GLIOMA DEMONSTRATES CLEAR TREATMENT EFFECT AFTER RNA NANOPARTICLE THERAPY
Authors: Rachel Moor, Frances Weidert, Christina von Roemeling, Jonathan Chardon Robles, Matthew Merritt, Anna Rushin, Guarav Sharma, James McGuiness, Nagheme Thomas, Anna DeVries, Sadeem Qdaisat, Dingpeng Zhang, Maryam Rahman, Elizabeth Ogando-Rivas, Paul Castillo, Ashley Ghiaseddin, Sheila Carrera-Justiz, Duane Mitchell, Hector Mendez-Gomez, Natalie Silver, John Ligon, Elias Sayour
Journal: Neuro-Oncology (2024)

Abstract BACKGROUND Diffuse Midline Glioma (DMG) is an inoperable pediatric brain tumor with insufficient treatment options. Our group has developed a novel treatment modality for this disease and others, using mRNA vaccines consisting of tumor derived antigens in a unique lipid-nanoparticle (NP). METHODS We have treated mice, canines, and human patients with primary brain tumors to define local immunotherapuetic treatment response. We treated our neonatally implanted DMG model with NPs generated from total-tumor mRNA beginning day 31 and used MRI, MR spectroscopy, suprerspectral imaging, and immunofluorescence to visualize and quantify treatment effects. RESULTS In canine glioma patients enrolled in clinical trial, we visualized radiographically enlarging tumors of animals that ultimately became long-term survivors, supporting the concept of a process by which lesion size increases in the absence of true disease progression. In our clinical trials investigating NPs as a treatment for human and canine glioma, we found features of both reactive gliosis and traditional pseudoprogression (immune infiltration), suggesting a new radiographic diagnosis, thus named paraprogression. In mice bearing DMG, NP therapy led to long-term survivors, despite the development of hydrocephalus. We were able to visualize treatment response during the course of NP therapy using MRI. CONCLUSIONS These results are rapidly translatable to aid clinical decision making in patients with brain tumors treated with immunotherapy. Future studies will aim to mitigate effect of paraprogression without compromising benefit of NP therapy.
DIPG-79. METTL16 AS A THERAPEUTIC VULNERABILITY IN H3K27M MUTANT DMG CELLS
Authors: Akanksha Chilukuri, Monica Pomaville, Matthew Halbert, Chaun He, Sameer Agnihotri
Journal: Neuro-Oncology (2024)

Abstract BACKGROUND Diffuse Midline Glioma (DMG) is a highly aggressive (CNS WHO Grade IV) pediatric brain tumor characterized by the histone mutation H3K27M, resulting in global hypomethylation of histones. H3K27M mutant cells are highly dependent on methionine and methionine Adenosyltransferase 2A (MAT2A), a central regulator of the methionine cycle, representing a key vulnerability in H3K27M gliomas. MAT2A is upregulated by methyltransferase-like protein 16 (METTL16), which deposits N6-methyladenosine (m6A) on a subset of RNA residues to regulate gene expression. MAT2A is a sensor of methyl group donor S-adenosylmethionine (SAM) that, when placed, increases MAT2A intron splicing to compensate for a decrease in MAT2A function. METHODS To investigate our hypothesis, H3K27M histone mutation knockout cell lines were established using CRISPR Cas9 (Jabado lab) in DIPG4 cells. shRNA-mediated knockdown was used to attenuate METTL16 expression in DIPG4 H3K27M cells, and growth was assessed via sulforhodamine B (SRB) assay. RESULTS In silico analysis of normal brain tissue compared to low-grade glioma and high-grade glioma demonstrated increased METTL16 at both the RNA and protein levels (p=&amp;lt;0.0001). Therefore, we postulated that targeting METTL16 would affect H3K27M growth. Results showed increased cell death compared to control cells by day 4 (p=0.0034) and day 8 (p=&amp;lt;0.0001). Furthermore, knockdown of METTL16 in DMG cells with H3K27M decreased m6A levels on poly (A) RNA (p=0.049). CONCLUSIONS Our study highlights the vulnerability of H3K27M mutant cells to METTL16 modulation, elucidating underlying molecular mechanisms and paving the way for innovative therapeutic strategies targeting this axis.
DIPG-50. TARGETING VULNERABILITIES IN PAEDIATRIC DIFFUSE MIDLINE GLIOMAS: LEVERAGING PLK1 INHIBITION TO EXPLOIT RAS/PI3K PATHWAY DEPENDENCY
Authors: Elisha Hayden, Emmy M Dolman, Dannielle H Upton, Laura Franshaw, Jie Liu, Hieu Nguyen, Maria Tsoli, Xinyi Guo, Chelsea Mayoh, Benjamin S Rayner, David S Ziegler
Journal: Neuro-Oncology (2024)

Abstract BACKGROUND Diffuse Midline Gliomas (DMGs), characterised by prevalent H3K27M mutations, exhibit epigenetic modifications that drive a proliferative state resistant to conventional therapies. The interplay of the cell cycle with PI3K and RAS/MYC growth signalling pathways, pivotal in the context of the H3K27M mutation, is yet to be fully understood. The aim of this study was to assess the efficacy of the inhibition of Polo-like kinase 1 (PLK1), a critical regulator of mitosis and cell cycle progression, identify mechanisms of action, and to develop effective combination strategies against DMG. METHODS AND RESULTS PLK1 inhibition demonstrated significant anti-tumour activities both in vitro and within aggressive in vivo orthotopic DMG models, notably doubling the median survival of mice bearing tumours. High-throughput RNA-seq analysis of DMG samples particularly sensitive to PLK1 inhibition, revealed a distinct pattern of negative enrichment in ribosomal genes, indicating a marked reduction in ribosomal function-associated gene expression. This alteration suggests a potential for innovative drug combination strategies targeting the PI3K/mTOR and RAS/MYC pathways, crucial for ribosomal and RNA processing. Subsequently, our in vitro drug sensitivity assays demonstrated that PLK1 inhibition in combination with PI3K/mTOR and MEK inhibitors, exhibit strong drug synergies, evidenced by high Bliss synergy scores. CONCLUSIONS Our findings underscore the efficacy of simultaneous targeting of PI3K/mTOR and RAS/MYC pathways with PLK1 inhibition as an attractive strategy to mitigate DMG tumorigenesis. Furthermore this research not only sheds light on the crucial interplay between cell cycle and signalling pathways in DMG but also facilitates novel intervention strategies for a range of other paediatric CNS malignancies with similar characteristic molecular drivers.
IMG-30. DIFFUSE MIDLINE GLIOMA MAP TO A COMMON FUNCTIONAL NETWORK ASSOCIATED WITH TUMOUR PROGRESSION AND OVERALL SURVIVAL
Authors: Jai Sidpra, Flavia Massey, Asthik Biswas, Sniya Sudhakar, Bruno S Peres, Francisco Sepulveda, Raffaella Scotto Opipari, Harith Akram, Kristian Aquilina, Kshitij Mankad, Thomas S Jacques, Darren R Hargrave
Journal: Neuro-Oncology (2024)

Abstract BACKGROUND Gliomas form bidirectional, functional synapses with otherwise healthy neurons: increasing neuronal excitability and driving tumour growth. The prognostic significance of this phenomenon does, however, remain unknown. METHODS This study used tumour location and tumour network mapping to identify brain networks associated with tumour progression and overall survival (OS) in 90 children with diffuse midline glioma, H3K27-altered (DMG). Tumours were segmented on volumetric magnetic resonance imaging and mapped to a standard template. Brain networks functionally connected to each tumour were computed using normative paediatric resting-state functional magnetic resonance imaging (n=525). RESULTS Median OS in the discovery cohort was 9.5 months (interquartile range 7.0-14.5 months). Comparison of tumour location in short-term (&amp;lt;18 months; n=75) and long-term (≥18 months; n=15) survivors of DMG identified an area of maximal anatomic overlap associated with short-term survival in the mid-pontine tegmentum and corticospinal tracts (89%; P&amp;lt;0.05). Tumour location was, however, not associated with OS (P=0.347). We, therefore, seeded tumour-to-brain resting-state functional connectivity maps from this a priori tegmental region-of-interest, identifying a specific brain network associated with short-term survival defined by functional connectivity to the medial prefrontal cortex, thalami, and cerebellum (P&amp;lt;0.0005). High and low tumour connectivity to this network was associated with short-term and long-term OS, respectively, using both univariate (P=0.013) and multivariate models controlling for treatment and tumour volume (P=0.016). Final, subset analysis of longitudinal neuroimaging in children within one month of death (n=21) showed tumour progression mapped to this same functional network and exhibited a dominant (left) hemispheric predominance (P&amp;lt;0.05), underpinned by increased tumour connectivity to the right (P=0.0270) rather than left (P=0.1802) corticospinal tract, and associated with OS (P=0.02). DISCUSSION We map DMG to a unified and prognostically important functional network, further establishing DMG as a circuit disorder. Interventions aiming to modulate this network may inform future treatment strategies for affected children.
TRLS-10. CLINICAL TRIAL IN PROGRESS - CONNECT2007: PHASE I/II STUDY OF LUTATHERA IN PATIENTS WITH RECURRENT AND/OR PROGRESSIVE HIGH-GRADE CENTRAL NERVOUS SYSTEM (CNS) TUMORS AND MENINGIOMAS THAT DEMONSTRATE UPTAKE ON DOTATATE PET
Authors: Margot A Lazow, Andrew T Trout, Sara Szabo, Christine Fuller, Adam Bobbey, William White, Joseph Stanek, Samuel Brady, Elaine Mardis, Joshua Palmer, Diana P Rodriguez, Jaime Reuss, Cierra M Brandt, Joanna Acree, Anna Harr, Leonie Mikael, Maryam Fouladi, Ralph Salloum
Journal: Neuro-Oncology (2024)

Abstract BACKGROUND Somatostatin type-2A receptors (SST2A) regulate cell growth through complex downstream modulation of proliferation and apoptosis signaling, thereby representing a potential therapeutic target. Lutetium (177Lu-DOTATATE), a radionuclide therapy which binds SST2A and delivers local radiation via beta particle emission, gained FDA approval for gastroenteropancreatic neuroendocrine tumors, a disease characterized by SST2A expression. Potential expansion of Lutathera into pediatric neuro-oncology is supported by evidence that medulloblastoma, other embryonal tumors, and meningiomas consistently express membranous SST2A, exhibit corresponding uptake on SST2A-radiolabeled nuclear imaging (DOTATATE PET), and have demonstrated radiographic response to SST2A-targeted therapy, suggesting sufficient CNS penetration to achieve therapeutic benefit. METHODS CONNECT2007 (NCT05278208) is an international, multicenter phase I/II study investigating safety and efficacy of Lutathera in children and adults with SST2A-expressing CNS tumors. Patients with recurrent/progressive high-grade CNS tumors and meningiomas can undergo screening, consisting of DOTATATE PET imaging for functional confirmation of SST2A expression, requiring adequate uptake (Krenning score ≥2) by central review. The phase I cohort will enroll patients aged 4-&amp;lt;12 years to determine the pediatric recommended phase II dose (RP2D) following a Rolling Six design, with three potential dose levels, starting at the adult RP2D (200mCi), scaled by body surface area. The phase II cohort will enroll patients aged ≥12 years to assess anti-tumor activity through evaluation of 6-month progression-free survival in medulloblastoma/embryonal tumors (descriptive in other histologies). Lutathera is administered intravenously, with concurrent amino acids for nephroprotection, dosed every 8 weeks for up to 4 cycles. Longitudinal correlative studies include 1) evaluating prevalence, heterogeneity, and clinical, histologic molecular, and radiographic predictors of SST2A expression, 2) characterizing radiation dosimetry of Lutathera in organs at risk of toxicity and within CNS to assess tumor penetration, and 3) identifying imaging and molecular biomarkers of response. Enrollment began in January 2023; both cohorts remain open to accrual.
DEI-06. IMPROVING ACCESS TO POST-MORTEM BRAIN TUMOR TISSUE DONATION BEYOND THE INPATIENT HOSPITAL SETTING
Authors: Nicole Lyons, Javad Nazarian, Augustine Eze, Niku Nourmohammadi, Mateusz Koptyra, Adam Resnick, Jane Minturn, Beth Frenkel, Sonora Reingruber, Angela Wanders, Miriam Bornhorst, Melissa Williams, Michelle Monje-Deisseroth, Jared Hysinger, Ann-Helen Liljensten, Mark Souweidane, Jeffrey Greenfield, Cindy Campbell, Christopher Padilla, Amy Smith, Sydney Peck, Nick Vitanza, Sarah Leary, Jeff Stevens
Journal: Neuro-Oncology (2024)

Abstract Between May 2021 and December 2023, approximately 33% of patients were being treated inpatient at the time of consent for post-mortem tissue donation through Gift From A Child. In the past, a major obstacle preventing families from donating post-mortem tissue was the inability to leave the hospital. Care teams and patient families are often concerned that in order to donate, the patient would have to pass away at the hospital. This creates a situation where the desire to donate comes at the cost of patient care and comfort. Through GFAC, children can pass at home, hospital, or hospice and still donate tissue successfully. The ability to donate post-mortem tissue is independent of patient location, ensuring that the focus of the family and care team remains on the child’s care rather than donation logistics. Additionally, patients can successfully donate tissue independent of status at the time of inquiry (declining, stable, urgent). The ability to quickly access a resource at a low burden to the family has been crucial in allowing tissue donation to happen. This also improves patient equity by eliminating access to hospital resources as a reason for a patient family to be required to live near a hospital. This is oftentimes a tremendous financial difficulty for patient families. Through establishing standard operating procedures and appointing tissue navigators, GFAC has streamlined what was previously an extremely complicated process mired in logistical obstacles. Patient families now have access to an efficient process for tissue donation. Previously, families would need to navigate complicated logistics unsupported, now they (or someone on their behalf) only need to contact GFAC or a Research Center of Excellence via phone or email and consent for donation. This ensures that post-mortem tissue can be donated easily, efficiently, and from wherever the patient family chooses.
DIPG-49. SPATIAL TRANSCRIPTOMIC SEQUENCING OF A DIPG PATIENT TUMOUR RESOURCE
Authors: Anja Kordowski, Onkar Mulay, Lachlan Harris, Quan H Nguyen, Bryan W Day
Journal: Neuro-Oncology (2024)

Abstract BACKGROUND Diffuse Intrinsic Pontine Glioma (DIPG), the most common subtype of Diffuse Midline Glioma (DMG), is a brainstem high-grade glioma arising in young children and always proves fatal. Major challenges include the disease’s intratumoural genetic and cellular heterogeneity as well as its diffusely invasive phenotype. Research of the last few years has highlighted that interactions between cancer cells, the nervous system and immune cells crucially contribute to tumour cell invasion and disease malignancy. Hence, a better understanding of cancer-promoting interactions is a key requirement to elucidate novel strategies for the treatment of this devastating disease. METHOD We performed spatial transcriptomic sequencing on 10 sequential tumour-infiltrated DIPG patient brainstem regions, using the 10x Genomics Visium platform. RESULTS Spatially-informed analysis and cell type clustering overall highlighted the molecular intratumoural heterogeneity present in the disease. We assessed cell cluster interactions as well as receptor-ligand (RL) pairing, illustrating communication between neuronal, immune cell and tumour clusters. We further determined respective RL pairs involved in such. To address the question whether invasive edges genetically differ from the tumour core, we evaluated genes that are significantly correlated with distal brainstem regions compared to tumour proximal sites. Results revealed gene signatures that are highly associated with neuronal signalling and communication, validating previous findings emphasising the importance of neuron-to-glioma interactions driving DIPG disease progression. CONCLUSION DIPG is a lethal paediatric brainstem glioma for which more durable therapeutic modalities remain to be found. In-depth analysis of this disease is often hampered due to the lack of patient tissue suitable for laboratory studies. Our patient autopsy specimen, spanning the entire tumour-infiltrated brainstem provided a platform to study this aggressive disease in a spatio-temporal manner. This analysis elucidates how DIPG is driven by the tumour microenvironment, including associated receptor-ligand interactions. This has the potential to ultimately discover new treatment targets.