tbuckley/cabot-search huggingface dataset:
TMET-24. MULTI-OMIC CHARACTERIZATION OF THE TEMPORAL METABOLIC ADAPTATIONS UNDERPINNING THERAPY RESISTANCE AND TUMOR RECURRENCE IN GLIOBLASTOMA
Authors: Emma Martell, Helgi Kuzmychova, Harshal Senthil, Esha Kaul, Ujala Chawla, Versha Banerji, Christopher M Anderson, Chitra Venugopal, Donald Miller, Tamra E Werbowetski-Ogilvie, Sheila K Singh, Tanveer Sharif
Journal: Neuro-Oncology (2024)

Abstract Therapy resistance and tumor recurrence are barriers to achieving long-term survival in cancer patients, particularly evident in glioblastoma (GBM), known for its dismal 5-year survival rate below 10%. Despite aggressive treatment regimens, including maximal resection, alkylating chemotherapy, and radiation, the majority of GBM patients experience relapse within 7-9 months post-initial intervention. Recurrent GBM poses surgical challenges and resists subsequent treatments, leading to an almost universally fatal outcome and an average survival of 12-18 months. Metabolic networks can serve as ancient stress-protection mechanisms that operate independently of genomic changes, offering an initial line of defense against exogenous pressures. Although the role of metabolism in cancer has gained prominence, our understanding of the metabolic adaptations following chemoradiotherapy and their contributions to therapy resistance and tumor recurrence in highly aggressive GBM tumors remains incomplete. We postulate that metabolic adaptations play a pivotal role in facilitating therapy resistance and GBM recurrence. Exploring the metabolic dependencies of these persistent cells may unveil vulnerabilities for therapeutic exploitation to counteract chemoradiotherapy resistance. We established clinically relevant patient-derived in vitro and in vivo models mirroring the standard GBM treatment protocol. Using state-of-the-art single-cell and bulk multi-omics technologies, we profiled the temporal transcriptomic and metabolomic adaptations from therapy-naïve primary GBM to chemoradiotherapy-resistant recurrent tumors. Our findings revealed unique metabolic transitions that occurred during chemoradiotherapy treatment in GBM cells that were conserved in vitro and in vivo across ten genetically diverse GBM patients. In a pre-clinical animal trial, a novel metabolism-targeting combinatorial treatment regimen prevented the emergence of recurrent tumors and significantly prolonged survival compared to chemoradiotherapy alone. Altogether, our results uncover distinct metabolic adaptations mediating therapy resistance and tumor recurrence in GBM. These findings emphasize the need to consider metabolic flexibility and dependencies for effective therapeutic strategies, offering potential avenues to overcome chemoresistance in recurrent GBM tumors.
EPCO-12. MENINGIOMA COPY NUMBER ANALYSIS IDENTIFIES OPTIMIZED SIZE THRESHOLDS AND CO-OCCURRENCE MODELS FOR INDIVIDUALIZED RISK-STRATIFICATION
Authors: Minh Nguyen, William Chen, Abrar Choudhury, Stephen Magill, Vijay Nitturi, Tiemo Klisch, Akash Patel, David Raleigh
Journal: Neuro-Oncology (2024)

Abstract Arm-level copy number alterations (CNAs) are common in meningiomas and are useful for risk-stratification, but there is no consensus regarding the optimal size threshold to define CNAs for prognostic models. Moreover, the prognostic importance of co-occurring CNA pairs and overall CNA burden in meningiomas remains incompletely understood. To address this, CNAs were analyzed in 691 retrospective meningiomas with clinical data and DNA methylation profiles from 3 international institutions. Arm-level CNAs were defined from DNA methylation profiles using iterative size thresholds ranging from 1-99% of each chromosome arm. The area under the curve (AUC) for 5-year local freedom from recurrence (LFFR) or overall survival (OS) was calculated using CNAs across size thresholds, and AUC standard deviation across thresholds was used as a measure of size-dependence. LASSO and Elastic Net Cox regressions were used to generate multi-CNA models for LFFR or OS and to identify prognostic co-occurring CNA pairs. These analyses identified 13 size-dependent prognostic CNAs in meningiomas, including loss of 1p, 3q, 4p, 4q, 6p, 6q, 9p, 10q, 12q, 14q,18q, and 22q, and gain of 1q. Regression models restricted to size-dependent CNAs improved risk stratification within strata of previously published models (Integrated score, Integrated grade), and identified prognostic CNAs not included in previous models, such as 1q gain, 7p loss, and 12q loss. Ontology analysis of genes in focal prognostic CNAs identified dysregulated STAT signaling and decreased expression of interferon-related genes from matched paired RNA sequencing. Models of size-dependent, prognostic, co-occurring CNA pairs identified 1p/22q codeletion, 1q gain/22q loss, and 9p/18q codeletion as significant predictors of LFFR. Increased CNA burden correlated with higher tumor grade and was significantly associated with worse LFFR and OS. In summary, chromosome-specific size thresholds identify prognostic arm-level CNAs and co-occurring CNA pairs in meningiomas. Thus, granular copy number analysis may improve risk stratification models for meningioma.
STEM-20. MULTI-OMICS OF HUMAN MEDULLOBLASTOMAS AND GENETIC LINEAGE TRACING IN VIVO INDICATE CELLULAR PLASTICITY
Authors: Bohyeon Yu, Jangham Jung, Aaron Diaz
Journal: Neuro-Oncology (2024)

Abstract Recent single-cell studies implicate the glutamatergic lineage of the rhombic lip (RL) as the origin of group (G) 3/4 medulloblastomas (MBs) and a stalled differentiation program as underlying malignant transformation. While the cellular compositions of G3/G4 MBs are consistent with a truncated neurodevelopmental hierarchy, it is unknown whether G3/G4 MBs exhibit cellular plasticity. We profiled tumors from 38 patients who underwent surgery for MB at UCSF via single-nucleus RNA sequencing (snRNA-seq). We developed in vivo genetic lineage-tracing systems with a single-cell readout and applied them to patient-derived G3 MB xenografts. High-complexity lentiviral barcode libraries were transduced into D283 and D425 patient-derived cell lines. Barcoded cells were injected into the brains of immunocompromised mice. Both preimplantation barcoded cultures and mature tumors were profiled by single-cell RNA-sequencing (scRNA-seq). This captured both endogenous RNA and barcode transcripts. RL neuro-developmental cell-type labels were transferred from public single-cell data from fetal cerebellum to single-cell data from our patient samples and xenograft models. Remarkably, xenografts produced similar cell types, in similar proportions to those found in human MBs. Moreover, the distribution of cell types found in the xenografts was conserved at the level of individual clones, indicating cell-intrinsic regulation of tumor composition. We developed approaches to use barcode and expressed point-mutation data to reconstruct intra-clone genetic phylogenies. We then used the transcriptional phenotypes of the observed cells to infer ancestral phenotypes for each clone’s phylogeny. We compared clade to sub-clade differences in cell type against the neural-developmental hierarchy found in the fetal RL. We observed significant rates of dedifferentiation events from unipolar brush-like cells to RL-progenitor phenotypes. These studies indicate that G3 MB cellular composition is homeostatic and conserved at the level of individual clones. Yet, these tumors exhibit plasticity, as has been observed in other brain cancers such as glioblastoma.
CTNI-42. A BIOMARKER-GUIDED PHASE 2 STUDY OF DB107-RRV (A RETROVIRAL REPLICATING VECTOR) COMBINED WITH DB107-FC (FLUCYTOSINE EXTENDED-RELEASE TABLETS) IN PATIENTS WITH RECURRENT GLIOBLASTOMA OR ANAPLASTIC ASTROCYTOMA: A CLINICAL PROTOCOL
Authors: Ashish Shah, Christian Ramsoomair, Deepa Seetharam, Anna Hudson, Victor Lu, Ruham Nasany, Marina Kushnirsky, Colin Hill, Ricardo Komotar, Michael Ivan, Leonela Wright, David Andrews, Yamina Carattini, Ranjini Valiathan, Tulay Koru-Sengul, Macarena De La Fuente
Journal: Neuro-Oncology (2024)

Abstract INTRODUCTION Despite significant advances in understanding the basic pathogenesis of glioblastoma, the median survival of patients has minimally changed in the past 25 years with a 5-year survival rate of &amp;lt;7%. Because of the dismal prognosis, attention has shifted to alternative adjuvant treatment modalities including gene/viral-based therapy. The first clinically tested replicating retroviral vector DB107-RRV (vocimagene amiretrorepvec, formerly Toca511) was assessed in a randomized Phase 3 study (NCT02414165) to evaluate the intracranial administration of DB107-RRV with subsequent oral administration of DB107-FC (5-fluocytosine extended-release tablets) in patients with recurrent HGG. Although the primary endpoint of overall survival (OS) in the intent-to-treat population was not met (median OS=11.07 months, DB107-RRV+ DB107-FC arm and 12.22 months for the SOC arm (HR=1.06; 95% CI:[0.83, 1.35], p=0.6154)), post-hoc analysis identified a subgroup of patients (responders) who demonstrated a marked survival benefit from the Phase III clinical trial (Toca 5, NCT02414165). Using a non-invasive genotyping pipeline, a novel biomarker, DGM7, was identified among responders that confers an improved prognosis: (DB107-RRV+DB107-FC is 18.3 months vs. 12.0 months in the SOC group (HR=0.50; 95% CI:[0.28, 0.89], p= 0.0167)). DGM7 is present in the blood of approximately 20-30% of HGG patients. METHODS This is a Phase 2, single-site, open-label, single-arm study to assess the oral administration of DB107-FC in combination with DB107-RRV in DGM7+ patients with recurrent/progressive HGG. Key inclusion criteria include presence of the DGM7 biomarker in blood, patient age 18–75 with histologically proven, measurable (MRI) recurrent/progressive HGG, and no radiation therapy for at least 12 weeks without histopathologic/MRI progression confirmation. The primary endpoint of this study will be progression-free survival at 6 months (PFS6) and OS of DB107-RRV+DB107-FC in DGM7+ patients with recurrent/progressive HGG compared to the historical study arm SOC/DGM7+ from NCT02414165.
EPCO-11. BIASES IN HEALTHY BRAIN SINGLE-CELL DATASETS: FINDING THE BEST COMPARISON FOR GLIOBLASTOMA STUDIES
Authors: Felipe Carcanholo, Renan Simões, Emerson Santos, Tathiane Malta
Journal: Neuro-Oncology (2024)

Abstract Tumor cells undergo metabolic alterations that support their proliferation and simultaneously modify immune populations, resulting in an immunosuppressive tumor microenvironment. This study aims to compare the metabolic expression of immune cells within the tumor microenvironment to those in a healthy environment. However, there is a lack of single-cell transcriptomic data for normal brain cells, necessitating an analysis of different methods to compare immune cells in tumors with those in a healthy brain. To address this, we explored cell-to-cell metabolic variability using public single-cell RNA-seq (scRNA-seq) data of glioblastoma (n=338564), and from immune cells in the brains of post-mortem individuals (n=14177), fetuses (n=40000), and epilepsy patients (n=466), as well as from immune blood cells (n=329762). We employed ssGSEA to generate activity scores for 70 key metabolic pathways from KEGG for each individual cell. Known marker genes were utilized to identify normal cell populations (macrophages, T cells, oligodendrocytes) in datasets lacking cell type annotations. Our results revealed that blood cells exhibited high metabolic activity in macrophages but showed moderate activity in other cell types. Immune blood cells also demonstrated high oxidative phosphorylation (OXPHOS) but low fatty acid activity. Fetal brain cells displayed a lack of heterogeneity and showed high fatty acid activity with low OXPHOS activity. Brain cells from post-mortem individuals displayed heterogeneity but exhibited low metabolic activity across nearly all cells and pathways. Additionally, the hierarchy of pathway activity differed from the other datasets. Epilepsy data revealed a metabolic activity pattern similar to tumor-infiltrating immune cells, with comparable activity hierarchy and heterogeneity, although the sample size was limited for detailed comparison. Understanding the differences between types of datasets is important to choose the most appropriate comparison, allowing us to observe the metabolic alterations in immune cells caused by glioblastoma and to develop better immunotherapy strategies.
CNSC-65. ELECTROPHYSIOLOGICAL AND SPATIAL TRANSCRIPTOMIC PROFILING OF GLIOMA-INFILTRATED CORTEX REVEAL LAYER SPECIFIC ALTERATIONS
Authors: Andy Daniel, Alexander Aabedi, Gray Umbach, Mikias Negussi, Sanjeev Herr, Cesar Nava Gonzales, Saritha Krishna, Jasleen Kaur, Elisa Fazzari, Takahide Nejo, David Raleigh, Aparna Bhaduri, Kevin Joseph, Vidhya Ravi, David Brang, Shawn Hervey-Jumper
Journal: Neuro-Oncology (2024)

Abstract Specialized neocortical circuits selectively organize neuronal signals and encode features of cognitive processing via local and long-range connections. Since glioma-infiltrated cortex is excitable and can participate in cognitive processing, the underlying laminar structure and functionality may still be preserved despite infiltration. Moreover, since glioma cells remodel existing neural circuits and microenvironmental factors drive invasion and proliferation, neuron-glioma interactions may demonstrate layer specificity. As glioma-infiltrated cortex remains poorly understood, we sought to characterize these regions using electrophysiological, structural, and genomic approaches. We assessed the power spectra of normal-appearing and glioma-infiltrated cortex using magnetoencephalography and subdural high-density electrode arrays. Immunohistochemistry of formalin-fixed paraffin-embedded (FFPE) samples of infiltrated cortex enabled protein-level neuronal and glioma identification to determine laminar preservation and spatial invasion patterns. Spatial transcriptomics of FFPE tissues and single-nucleus RNA-sequencing were used to identify cell populations, genomic alterations, and cell-cell communication within and across samples at testing and validation sites across the US and Europe. Increased delta range (1-4 Hz) power and decreased power in the beta range (12-20 Hz), activity thought to originate from deep layers, were identified as robust features of infiltrated cortex which were maintained across glioma subtypes (n = 139 patients) and preserved in a validation cohort (n = 8 patients). Immunohistochemistry revealed greater tumor burden within deep laminae regardless of glioma subtype (n = 20 samples). Tissue proteomics and spatial genomics analyses performed using glioma-infiltrated cortical samples (n = 10 samples; 29,011 spots) confirmed routine preservation of laminar organization, greater tumor burden in deep layers, as well as layer specific differences in glioma-related expression programs. Cell-cell communication analyses demonstrated increased interactions in glioma-infiltrated cortex across layers. These findings suggest that laminar structure may be preserved in glioma-infiltrated cortex while remodeling of neural circuits alters spatiotemporal activity in a predictable manner and support a deep to superficial invasion pattern. Thus, investigating glioma infiltration using layer-centric approaches may facilitate novel insights into neuron-glioma interactions.
CNSC-64. BEYOND THE LOCAL TUMOR MICROENVIRONMENT: CHARACTERIZING CHANGES TO NEURONAL ACTIVITY INDUCED BY PEDIATRIC HIGH-GRADE GLIOMA
Authors: Hannah Farnsworth, Meghan Pinter, Elana Carleton, Alexis Franklin, Kaylee Gentry, Rachel Davis, Hannah Hoffman, Humsa Venkatesh
Journal: Neuro-Oncology (2024)

Abstract Bidirectional electrochemical signaling between neurons and tumor cells is emerging as a critical regulator of pediatric high-grade glioma (HGG) pathology. Neuron-tumor interactions are known to induce local neuronal hyperactivity. However, recent work tracing the projections of these neuron-tumor networks revealed that HGG neuronal recruitment extends beyond the local tumor microenvironment (TME). These findings suggest that tumor-induced hyperexcitability may spread beyond the local TME and drive brain-wide circuit-level changes. To elucidate how non-tumor innervated brain regions are affected by TME hyperactivity we first characterized neuronal hyperactivity induced by a cortical patient-derived pediatric high-grade cell line in vitro on human iPSC-derived neurons. In vitro calcium imaging experiments demonstrated an increase in the number of calcium fluctuations in glioma co-cultured neurons. In parallel, multi-electrode recordings revealed increased population spiking activity and amplitude in neurons co-cultured with glioma cells. We then xenografted these HGG cells into the prefrontal cortex of mice and performed whole brain-clearing and cFos staining on tumor-bearing vs saline-injected control samples. As cFos is an immediate early gene activated by neuronal activity, we utilized the density of cFos expression as a readout-out of neuronal activation in our atlas-aligned segmented brain section analyses. We expectedly observed increased cFos expression within the ipsilateral primary and secondary motor region, which collectively comprise the local TME. Interestingly, we additionally observed elevated cFos in non-tumor bearing brain regions on both the ipsilateral and contralateral hemispheres, largely in layer 2/3 cortical neurons. These neurons form extensive cortico-cortical projections, and we coincidingly observed increased cFos expression in known cortical projection targets of the prefrontal xenograft location, such as somatosensory, visual, and retrosplenial cortices. Our findings suggest that tumor-induced neuronal hyperactivity extends beyond the local TME in a brain-wide manner and potentially follows established neuronal circuits, rendering these connected regions vulnerable to alterations in neuronal activity.
DDDR-35. THERAPEUTIC STRATEGIES FOR DIFFUSE MIDLINE GLIOMA: INSIGHTS FROM HIGH-THROUGHPUT COMBINATION DRUG AND RADIATION SENSITIZATION SCREENING
Authors: Syed M Faisal, Monika Yadav, Garrett R Gibson, Adora T Klinestiver, Anuradha Roy, Carl Koschmann, Scott J Weir, Stefan H Bossmann, Viveka Nand Yadav
Journal: Neuro-Oncology (2024)

Abstract Diffuse midline gliomas (DMGs) are the most aggressive pediatric high-grade gliomas. Over 85% DMGs harboring the H3K27M mutation in histone genes H3F3A (H3.3) and H3C2 (H3.1). H3K27M mutation disrupts epigenetic regulation by inhibiting PRC2, causing loss of H3K27 trimethylation and oncogenic gene expression. Presently, there are no effective therapies for DMG, and 95% of the patients die within 1.5 years of diagnosis. Thus, there is an urgent need to identify novel therapeutic strategies targeting H3K27M oncohistone. To assess the H3K27M mutation’s vulnerability, we used paired isogenic H3K27M-mutated and CRISPR-corrected H3M27K (H3-WT) primary DMG cell lines derived from thalamus (BT-245) and pons (DIPGXIIIP). We performed comprehensive single-agent high-throughput screens (HTS) with 1,520 FDA-approved drugs and further assessed drug combinations of ONC201 with the 86 most promising drugs from the HTS. A third combination experiment evaluated radio-sensitizing potential, where most effective top-six drugs (A-F) were tested in combination with radiation therapy across an expanded panel of patient-derived DMG cell cultures. To test drug efficacy in vivo, we developed a genetically engineered isogenic mouse model (GEMM) of DMGs using intrauterine electroporation (IUE) with DNp53/PDGFRA/H3.3K27M (PPK) and DNp53/PDGFRA/H3.3WT (PPW) genetic alterations. Our initial single-agent HTS screening identified 86 drugs with significantly higher cytotoxicity, specifically against H3K27M-mutated DMG cell lines. Combination HTS of the top six drugs revealed that drug E displayed significantly synergistic cytotoxicity with ONC201. We also evaluated drugs A-E in combination with radiation in both human and mouse H3K27M-mutated DMG cell lines. Drugs D and E showed selective radiosensitivity in both human and mouse H3K27M-mutated DMG cell lines. Preliminary findings also suggested drug D acts as an anti-invasive agent. Our findings identify novel drugs via HTS that enhance ONC201 efficacy and act as radiation sensitizers in DMGs. Future studies will test these compounds with ONC201 and radiation in our in vivo IUE-mediated H3K27M mouse model.
CNSC-04. UNDERSTANDING PEDIATRIC BRAIN TUMOR CHEMOTHERAPY INDUCED LONG-TERM DEFICITS IN HIGH-ORDER NEUROCOGNITIVE AND SENSORIMOTOR FUNCTION
Authors: Anand Singh, Momo Harris, Rajasekaran Mahalingam, Kechen Ban, Renae Bertrand, Shungu Zimbwa, Khalil Ali Ahmad Kasm, Yuan Pan
Journal: Neuro-Oncology (2024)

Abstract Because of major advancements in cancer treatment especially chemotherapy, 85% of children with cancer are predicted to survive for 5 years or more. However, chemotherapy can cause long-term health problems when childhood cancer survivors enter adulthood (known as late effects). The neurocognitive features of these late effects (chemobrain) include trouble in concentrating, memorizing, and decreased processing speed, and results in lower IQ and academic achievement, poor hand-eye coordination, and slower development over time. Despite such a negative impact on the quality of life of cancer-surviving children, the mechanism is poorly understood and there is no FDA-approved drug to prevent or cure these side effects. To gain a better understanding of the mechanism underlying chemotherapy-induced cognitive impairments, we developed a pre-clinical model using carboplatin in juvenile mice to study long-term neurological defects. Carboplatin is commonly used chemotherapy drug in pediatric brain tumor patients. We have tested the capacity of different doses of carboplatin and its long-term effect on cognitive and sensorimotor function and performed single nuclear RNA sequencing (snRNAseq) of the hippocampus. Our preliminary data demonstrated dose-dependent deficits in executive and sensorimotor function 7-9 weeks after carboplatin administration in the mice of both sexes. snRNAseq of the hippocampus showed changes in the glial cell number as well as genes associated with oxidative phosphorylation and neurodegeneration at early and late time points. Bioenergetics using Seahorse in the brain synaptosomes revealed mitochondrial dysfunction in the form of decreased maximum respiratory capacity long after carboplatin treatment. This study established a preclinical model that can be leveraged to mechanistically understand the long-term neurocognitive side effects of brain tumor chemotherapy during childhood. Future studies will aim to identify potential targets to prevent and/or treat the neurotoxic effects of cancer treatment in pediatric patients.