tbuckley/cabot-search huggingface dataset:
PATH-12. ROBUST CELL-FREE DNA METHYLATION-BASED CLASSIFICATION OF PEDIATRIC BRAIN TUMOR LIQUID BIOPSIES
Authors: Kyle S Smith, Tom T Fischer, Hong Lin, Daniel Senfter, Tatjana Wedig, Nathalie Schwarz, Natalia Stepien, Sibylle Madlener, Christine Haberler, Esther Hulleman, Natasha Atkinson, Sandeep K Dhanda, Stefan Pfister, Santhosh Upadhyaya, Amar Gajjar, Giles W Robinson, Joonas Haapasalo, Hannu Haapasalo, Kristiina Nordfors, Johannes Gojo, Kendra K Maass, Kristian W Pajtler, Paul A Northcott
Journal: Neuro-Oncology (2024)

Abstract BACKGROUND DNA methylation-based classification has been transformative in the molecular diagnostics of pediatric brain tumors, while additionally providing foundational insights into disease biology. Current diagnostic pipelines integrate histopathology and molecular tools in accordance with the WHO classification of CNS tumors which rely on the availability of tissue specimens. However, sometimes tumors are not amenable to neurosurgical resection due to their high-risk locations. Likewise, tissue collection is not routinely performed longitudinally. Liquid biopsies (LBs) have emerged as a minimally invasive, serially collectable source of tumor-derived material that have shown promise in detecting minimal residual disease (MRD) in pediatric neuro-oncology. Still, success rates of LB profiling have varied between studies, warranting the deployment of more reliable and reproducible assays. METHODS In the current study, we implemented a novel cell-free DNA (cfDNA) methylation sequencing (EM-seq) workflow in a large cohort of cerebrospinal fluid (CSF) samples (n&amp;gt;200 patients) representing most pediatric brain tumor entities. Optimization of EM-seq for CSF specimens enabled the generation of genome-wide cfDNA methylation profiles from minimal starting material. Utilizing well-established CNS tumor DNA methylation datasets as references, we trained a deep neural network specializing in the classification of low tumor burden and sparse methylation profiles. Implementation of a novel tumor enrichment algorithm, coupled with DNA methylation imputation and subsequent deconvolution, facilitated detection and classification of low tumor burden samples, including those with balanced genomes that would have been overlooked using previous generation assays. RESULTS Our LB-based classifier allowed for highly accurate tumor detection and entity prediction (AUC=0.9) across the cohort. Case examples highlight the potential of this approach in establishing tumor classifications in inoperable cases and in performing serial disease monitoring. CONCLUSIONS Collectively, this study provides a blueprint for developing a CSF-based tumor classifier from cfDNA methylation profiles, and the motivation for prospective validation in future clinical trials.
PATH-11. FEASIBILITY OF BRAIN TUMOR CLASSIFICATION BY ENZYMATIC DNA METHYLATION SEQUENCING ANALYSIS OF CELL-FREE DNA OBTAINED FROM CEREBROSPINAL FLUID
Authors: Aaron Michael Taylor, Jody T Lombardi, Areeba Patel, Jonathan Martin, Markus J Bookland, David S Hersh, Evan Cantor, Xianyuan Song, Felix Sahm, Patrick Kwok-Shing Ng, Joanna J Gell, Ching C Lau
Journal: Neuro-Oncology (2024)

Abstract BACKGROUND Array-based DNA methylation profiling is the gold standard for molecular classification of brain tumors. However, it relies on significant amount of input DNA extracted from surgical tissue, thus limiting its use for tumors where biopsy is challenging or limited in quantity. Cell-free tumor DNA (cfDNA) in cerebrospinal fluid (CSF) presents alternative opportunities for brain tumor diagnosis and disease monitoring following treatment. Novel enzymatic DNA methylation sequencing (EM-seq) methods may allow us to overcome input DNA limitations and accurately quantify methylation from cfDNA. METHODS We performed methylation sequencing using the NEBNext EM-seq kit on cfDNA from archival CSF samples collected from three brain tumor patients with confirmed histopathological diagnoses. Variable amounts of input cfDNA (0.1ng-10ng) were tested. We utilized the methylseq pipeline for data processing. For tumor classification, data was limited to CpG sites overlapping the MethylationEPIC array before analysis using MNP-Flex, a modified platform-agnostic version of the Heidelberg methylation classifier RESULTS Using the EM-seq method, genomic coverage for 10 and 1ng input DNA samples (average: 46x and 26x, respectively) was sufficient for generating global methylation profiles. Samples with 0.1ng input showed an average coverage of only 5.32x due to high levels of read duplication. However, methylation levels for CpG sites with at least 5x coverage were highly correlated across varying input DNA amounts, suggesting that lower input cfDNA could still be used for tumor classification based on relevant CpG sites. CONCLUSIONS Using the MNP-Flex classifier, which was originally trained with methylation array data from tumor tissue, we successfully predicted brain tumor types (both high-grade glioma and medulloblastoma) with cfDNA methylation data down to only 0.1ng of input cfDNA, matching diagnosis based on tissue methylation and histopathology in this pilot study. Further classification of additional tumor types using CSF cfDNA is required to confirm the clinical utility of this platform.
GCT-26. INTRACRANIAL NON-GERMINOMATOUS GERM CELL TUMOR WITH MALIGNANT TRANSFORMATION TO EMBRYONAL RHABDOMYSARCOMA
Authors: Clayton Long, Ross Mangum, Lisa Keller, Ruth E Bristol, Safia K Ahmed, Michael Kuwabara, Nishant Tiwari, Lindsey M Hoffman
Journal: Neuro-Oncology (2024)

Abstract BACKGROUND Non-germinomatous germ cell tumors (NGGCT) constitute 35%- 45% of intracranial germ cell tumors. Growing teratoma syndrome has been observed in patients with NGGCTs after starting chemotherapy. While growing teratomas are typically benign, this process can rarely involve malignant transformation and result in poor prognosis. We present the case of a patient with pineal NGGCT and growing teratoma syndrome with malignant transformation to embryonal rhabdomyosarcoma. CASE REPORT A 13-year-old male presented with headaches and vision changes. An MRI brain demonstrated a 26 x 25 x 19 mm (AP X TR X CC) mixed solid and cystic pineal mass with no evidence of metastatic disease. Due to elevated alpha fetoprotein levels in the serum and cerebrospinal fluid, he was diagnosed with intracranial NGGCT. Treatment was initiated with alternating cycles of Carboplatin/Etoposide and Ifosfamide/Etoposide. After 2 cycles of chemotherapy, a complete biochemical response was noted but MRI showed increased tumor size (presumed growing teratoma syndrome). The patient underwent complete tumor resection. Histology showed embryonal rhabdomyosarcoma as a somatic malignancy arising in a mature teratoma. Further molecular characterization revealed somatic NF1 and KRAS pathogenic mutations that are consistent with the primary diagnosis. Methylation profiling, however, did not exhibit a match with any known malignancies. Continued complete response was noted following two additional chemotherapy cycles. The patient is planned for six total chemotherapy cycles followed by high-dose craniospinal radiation with boost to the primary tumor. CONCLUSIONS Malignant transformation is a rare phenomenon in NGGCT. There is no standard of care for these patients. Further studies are needed to define ideal therapy for this patient population.
IMG-12. CBTN BRAIN TUMOR SEGMENTATION INITIATIVE: UPDATES ON MODEL RELEASE, HGG SEGMENTATION, AND SURVIVAL ANALYSIS
Authors: Anahita Fathi Kazerooni
Journal: Neuro-Oncology (2024)

Abstract BACKGROUND Assessment of treatment responses in pediatric brain tumors requires accurate tumor segmentation, particularly important for nonresectable tumors like diffuse midline glioma (DMG), including diffuse intrinsic pontine glioma (DIPGs). Evaluating tumor progression in these tumors relies on monitoring tumor size changes in longitudinal MRI exams which is challenged by their infiltrative growth patterns. Our team developed a comprehensive multi-institutional, multi-histology autosegmentation deep learning (DL) model leveraging data from the Children’s Brain Tumor Network (CBTN), involving continuous enhancements and enriched by an expanding dataset including post-surgical/post-treatment studies. METHODS Recently, we trained and validated this DL model (publicly available) on a multi-institutional dataset of 644 PBTs, including 273 pediatric-type diffuse high-grade gliomas (HGGs, including DMG/DIPGs), using pre-operative and post-operative/post-treatment multiparametric MRI scans. We tested the model in 23 longitudinal MRI exams of 8 DMGs from the PNOC003 and PNOC007 clinical trials and applied Cox regression for predicting overall survival (OS) using tumor volume, computed with our autosegmentation model, as a time-varying variable in 18 patients. RESULTS For HGGs in treatment-naïve sessions, our model demonstrated strong performance with median Dice scores of 0.89 for whole tumor and tumor core (encompassing all regions, except for edema), and 0.73 for enhancing tumor segmentation. In longitudinal MRI exams of DMGs from the aforementioned clinical trials, the model achieved median Dice scores of 0.79 for whole tumor, and 0.78 for enhancing tumor and tumor core segmentation. Cox regression showed the significance of longitudinal volumetric measurements (p=0.08) for predicting OS in DMGs. CONCLUSIONS Our approach provides reliable tumor segmentation in HGGs across diverse datasets, crucial for treatment response assessment. Looking ahead, we plan to validate our model on a larger set of longitudinal exams and use volumetric measurements to predict tumor progression. This ongoing effort aims to improve model performance, extend its generalizability, and mitigate potential model decay.
GCT-29. MULTI-INSTITUTIONAL ANALYSIS OF PEDIATRIC RELAPSED/REFRACTORY CENTRAL NERVOUS SYSTEM GERMINOMAS
Authors: Mary Claire McGlynn, Mohammad H Abu-Arja, Mohamed Saad Zaghloul, Kelsey Bertrand, Amar Gajjar, Hamidah Alias, Andrea Cappellano, Richard T Graham, Sofia Jares Baglivo, Vivek Bhadri, Dinisha Govender, Natalia Dassi, Malgorzata Czogala, Rebecca Ronsley, Truman Knowles, Sabine Mueller, Girish Dhall, Sumanth Nagabushan, Mohamed S Abdelbaki
Journal: Neuro-Oncology (2024)

Abstract BACKGROUND Relapsed central nervous system germinomas are rare with no universal agreement regarding management. We explored the prognostic factors that may impact the treatment of patients with relapsed CNS germinoma. METHODS We collected data on relapsed/progressive germinomas from nine large international sites. Data was summarized using descriptive statistics. Overall survival (OS) was evaluated using Kaplan-Meier and Fischer’s exact test to estimate odds ratios (OR) and 95% confidence intervals (CI). RESULTS Twenty-seven patients with relapsed (24) and progressive (3) germinomas were included (3.7% metastatic). Median age at diagnosis was 15.8 years (interquartile range (IQR): 11.9-18.5). Complete remission (CR) after initial treatment (chemotherapy 63.9% and radiotherapy 88.9%) was achieved in 15 patients (55.6%). The median time from diagnosis to relapse/progression was 20.0 months (range: 10.8-65.1 months) with 55.6% occurring within 24 months. Twenty-five patients (92.6%) underwent chemotherapy, 15 (55.6%) received high-dose chemotherapy with stem cell support (HDCx), and 16 received (59.3%) radiotherapy. At last follow-up, 86.6% of HDCx and 87.5% of radiotherapy recipients were alive. Median time to last follow-up was 41.8 months (IQR: 19.6-132.1). Fifteen children (55.6%) achieved CR after therapy and 21 (77.8%) were alive at last follow-up. Of patients receiving irradiation, 12.5% received whole ventricular irradiation, 81.3% craniospinal irradiation, and 6.3% focal irradiation. Chemotherapy at relapse was associated with improved 5-year OS (OR=1.32 95%CI: 1.06-1.64) Re-irradiation at relapse (OR=2.6, 95%CI: 0.36-19.2) and HDCx at relapse (OR=2.17, 95%CI: 0.30-15.71) did not reach statistically significant difference. CR after initial therapy (OR=1.25, 95%CI: 0.97-1.61) was not associated with improved 5-year OS, CR after relapse therapy was associated with increased 5-year OS (OR=3.50, 95%CI: 1.08-11.24) CONCLUSIONS Relapsed CNS germinomas are salvageable at relapse. This ongoing multi-institutional study will contribute to existing knowledge about relapsed/progressive CNS germinomas and inform prospective clinical trials to improve outcomes for children with relapsed/progressive disease.
IMG-15. A STRATEGIC FLOWCHART FOR PREOPERATIVE IMAGING IN PEDIATRIC POSTERIOR FOSSA TUMORS
Authors: Fabrício G Gonçalves, Mario Marecha, Carmen Cerron-Vela, Harun Yildiz, Tassiana Cristhina S Dias, Aashim Bathia
Journal: Neuro-Oncology (2024)

Abstract BACKGROUND This comprehensive study delves into pediatric posterior fossa tumors (PFTs), focusing on both common and rare types, including pseudoneoplasms. The aim is to understand the diagnostic challenges of these less typical tumors, enhancing knowledge beyond usual pathologies. A detailed flow chart has been created to aid in accurate preoperative diagnoses. METHODS The study examines neuroimaging data, primarily from MRI and CT scans, collected from various clinical studies and case reports. It concentrates on identifying unique imaging characteristics of rare PFTs and pseudoneoplasms. The flow chart considers lesion location in various anatomical areas of the posterior fossa and factors such as lesion localization, MRI details (including DWI), and patient age. It also emphasizes the identification of cells in the posterior fossa that can lead to tumors, including osseous tissue cells, dura mater cells, arachnoid cells, pia mater cells, various glial cells, neurons, and choroid plexus cells. RESULTS The study reveals distinct imaging features of less common PFTs and pseudoneoplasms, critical for differentiating them from more common tumors. Advanced imaging techniques are highlighted as essential for improving diagnostic accuracy, impacting clinical management and treatment decisions. The review also discusses the varied presentation of tumors and the challenges this poses to standard diagnostic methods. CONCLUSIONS Understanding the imaging characteristics of rare PFTs and pseudoneoplasms, especially in children, is vital. This thorough analysis enhances diagnostic accuracy and influences treatment approaches, potentially improving patient outcomes. The study underscores the necessity of combining clinical observations with advanced imaging for precise diagnoses in atypical cases. This approach is crucial for healthcare professionals managing pediatric PFTs, leading to better clinical decisions and advancing pediatric neuro-oncology.
LGG-42. TWENTY YEARS OF PROGRESS IN MANAGING LOW GRADE GLIOMA: THE EXPERIENCE OF THE UNIVERSITY OF CAPE TOWN’S COMBINED PAEDIATRIC NEURO-ONCOLOGY SERVICE FROM 2001 TO 2022
Authors: Alan Davidson, Anthony Figaji, Komala Pillay, Marc Hendricks, Thuran Naiker, Jeannette Parkes
Journal: Neuro-Oncology (2024)

Abstract BACKGROUND This study aimed to review the management of childhood low grade gliomas (WHO I and II) by the University of Cape Town’s combined neuro-oncology service at Red Cross War Memorial Children’s and Groote Schuur Hospitals. METHODS All patients diagnosed with low grade glioma between 2001 and 2022 were included in this retrospective study. Real time decision-making during the study period was achieved via a weekly neuroimaging meeting, and surveillance by a combined monthly clinic attended by paediatric endocrinology and educational psychology. Despite state of the art surgical and radiotherapy facilities, molecular diagnostics, monoclonal antibodies and small molecules were only available to selected patients. RESULTS Among 129 children, aged 0.38 to 14.58 years [median 5.36], six had Tuberous Sclerosis and 11 had Neurofibromatosis-1. The commonest sites were cerebellum (26%), hypothalamus (17%) and optic pathway (16%), and 12 patients (9%) had metastatic disease, mostly grade I supratentorial tumours. Twenty-three patients were diagnosed on imaging without histology, six of whom were biopsied subsequently, yielding a total of 96 grade I and 16 grade II tumours. Initial management was expectant in 16% (including 8 of the 11 Nf-1 tumours), surgery in the form of debulking or total resection in 53%, chemotherapy in 24% and radiotherapy in 8%. Ultimately 36% received chemotherapy and 29% radiotherapy (almost all of them focal RT), and only 16% of those treated with radiotherapy progressed. Estimated 5-year Overall Survival (OS) and Progression Free Survival (PFS) was 90.5% and 52.6% for the whole group. Patients treated with chemotherapy had an OS of 87.2% and a PFS of 39.2%. PFS and OS were inferior for metastatic disease but not for grade II tumours. CONCLUSIONS Low grade glioma can be managed effectively in a middle-income country setting. Multidisciplinary team management is crucial to achieving positive outcomes regardless of context.
LGG-35. ROBUST TUMOR RESPONSE TO CHEMOTHERAPY IN THALAMIC PILOCYTIC ASTROCYTOMA WITH LARGE CYSTIC COMPONENT: A CASE REPORT
Authors: Abbey Rocco, Mary Beck, Michele McHugh, Ashley Lampe, Ashley Meyer, Andrea Ogle, Nicole M Brossier, Margaret Shatara, Mohamed S Abdelbaki, Andrew Cluster
Journal: Neuro-Oncology (2024)

Abstract BACKGROUND Pilocytic astrocytoma (PA) is the most common glioma in children. Prognosis is excellent when complete resection is achievable. However, in central locations, such as optic pathway, thalamus, and brainstem, resection may lead to extensive morbidity, necessitating alternative treatment strategies. Chemo- and targeted therapy options have demonstrated efficacy in controlling tumor growth and providing clinical benefit; however, cystic portions are not typically responsive to either option. METHODS Case report, Retrospective chart review RESULTS A 4-year-old male presented with left sided weakness and ventriculomegaly. MRI of the brain revealed a 3.5 x 3.3 x 4.4 cm mixed solid and cystic enhancing mass extending from the right thalamus down to the right middle cerebellar peduncle. An endoscopic third ventriculostomy and tumor biopsy was performed. Histology confirmed PA, WHO Grade 1. Sequencing confirmed BRAF-KIAA1549 fusion. Chemotherapy was initiated with Carboplatin and Vincristine. Each subsequent MRI of the brain obtained during therapy and at the end of therapy demonstrated significant decrease in both solid and cystic portion of the tumor with complete resolution of symptoms and neurologic deficits. End of therapy MRI demonstrated 1.2 x 1.4 x 1.2 cm mixed solid and cystic mass. CONCLUSIONS The unique aspect of this case is the exceptional and robust response achieved in both solid and cystic components, challenging the historical notion of cystic lesions being less sensitive to chemotherapy. This observation can contribute valuable insights to the evolving understanding of treatment responses in these tumors.
IMMU-05. TARGETING THE DYSREGULATED DNA METHYLOME DURING CAR T CELL MANUFACTURING IMPROVES THEIR FITNESS IN IMMUNOCOMPETENT BRAIN TUMOR MODELS
Authors: Zhongzhen Yi, Elton VanNoy, Abigail Lee, katherine Chiappinelli, Dalia Haydar
Journal: Neuro-Oncology (2024)

Abstract BACKGROUND Epigenetic reprogramming and T-cell exhaustion are key factors impacting the effectiveness of chimeric antigen receptor (CAR) T-cell immunotherapies in brain tumors. These processes are regulated by DNA methylation, an epigenetic modification that is crucial for gene regulation. Here, we investigated whether targeting the dysregulated DNA methylome in engineered immune cells can improve their anti-tumor efficacy. METHODS We optimized a transduction protocol that incorporates adding DNA methyltransferase inhibitors (DNMTi) early during the manufacturing process of murine CAR T-cells targeting B7-H3. We then used standard in vitro assays and immunocompetent glioma models to evaluate whether DNMTi treatment improved CAR T-cell effector functions by regulating activation, memory differentiation, and cytokine responses in adoptive T-cells. RESULTS In repeated-stimulation assays, CAR T-cells generated in the presence of DNMTi exhibited significantly higher levels of expansion and persistence compared to CAR T-cells without DNMTi exposure. Notably, CAR T-cells manufactured in the presence of DNMTi persisted up to 12 repeat stimulations, in contrast to a maximum of 7 stimulations for CAR T-cells generated without DNMTi treatment. Moreover, DNMTi-treated CAR T-cells expanded up to 55-fold higher than T-cells generated without DNMTi treatment upon repeated-stimulation with B7-H3-positive glioma cells. This was also associated with remarkably enhanced secretion of immune-stimulatory cytokines that persisted across repetitive stimulations. Furthermore, DNMTi-treated CAR T-cells exhibited greater cytotoxicity at lower effector-to-target ratios compared to untreated CAR T-cells, with sustained differential cytotoxicity even after the 4th stimulation. Preliminary in vivo data from immunocompetent glioma models further support the potential of DNMTi pre-treatment, showing improved T-cell persistence and reduced dose requirements. Mechanistic studies suggest that DNMT inhibition enhances B7-H3 CAR T-cell anti-tumor activity by regulating memory differentiation of CAR T-cells early in the production phase. CONCLUSION This study proposes that DNMTi pre-treatment may offer a promising approach for optimizing CAR T-cell manufacturing and enhancing performance in brain tumors.
IMMU-02. MODIFYING CAR T CELL EPIGENETIC PROGRAMS TO IMPROVE THEIR PERSISTENCE AGAINST GROUP 3 MEDULLOBLASTOMAS
Authors: Meghan B Ward, Linda Senaoui, Ben A Youngblood, Martine F Roussel, Giedre Krenciute
Journal: Neuro-Oncology (2024)

Abstract BACKGROUND Safe, effective therapies are desperately needed to improve outcomes for patients with medulloblastoma (MB), a malignant pediatric brain cancer. Chimeric antigen receptor (CAR)-T cells are a promising therapeutic option as they target T-cell cytotoxicity exclusively to tumor associated antigens. B7-homolog 3 (B7-H3) is an ideal target for CAR-T cell therapy as all MB subtypes express B7-H3 and healthy tissues do not. However, a roadblock to tumor clearance is the inability of B7-H3 CAR-T cells to persist, suggesting that improving persistence will benefit anti-tumor efficacy. The goal of this study was to compare head-to-head knocking out TET2 or DNMT3A negative epigenetic regulators of CAR-T cell persistence against group 3 MB (G3MB), the most malignant MB subtype. METHODS We generated B7-H3 CAR-T cells with CD28ζ signaling domain and performed CRISPR/Cas9 knockout (KO) of TET2, DNMT3A, and AAVS1 as a control. We compared resulting CAR-T cell persistence via repeat stimulation assays in vitro against G3MB cell lines with varying B7-H3 antigen density (D341low, HDMB03mid, and D425high). We further compared KO CAR-T cells in vivo against D341low, HDMB03mid, and D425high orthotopic xenografts. RESULTS Our data shows that DNMT3A KO, but not TET2 KO, consistently improves the persistence and expansion of CAR-T cells against G3MB in vitro. In vivo, KO of epigenetic regulators moderately improves CAR-T cell therapy against highly aggressive D341low, HDMB03mid, and D425high but is insufficient to elicit curative responses. CONCLUSIONS Our study demonstrates that genetic KO of negative epigenetic regulators of CAR-T cell persistence can improve anti-tumor function against G3MB. We conclude that for the B7-H3.CD28ζ CAR, DNMT3A KO is superior for improving persistence over TET2 KO, but that DNMT3A KO is insufficient in vivo. We believe this is due to the aggressive nature of G3MB and we are optimizing in vivo studies for better representation of CAR-T cell persistence.