tbuckley/cabot-search huggingface dataset:
BIOM-30. NOVEL HISTOLOGIC AND MOLECULAR BIOMARKERS FOR OLIGODENDROGLIOMA
Authors: Vanessa Smith, Kevin Stevenson, Tia Wieden, Monika Anand, Annick Desjardins, Roger McLendon, David Ashley, Simon Gregory, Giselle López
Journal: Neuro-Oncology (2024)

Abstract Oligodendrogliomas are progressive, infiltrative gliomas. While new molecular criteria were introduced in 2016 for diagnosing oligodendroglioma, the grading criteria remains largely unchanged. We evaluated histologic and molecular features for new biomarkers of aggressive behavior, using a cohort of 184 specimens diagnosed as low grade oligodendroglioma within the Duke Brain Tumor Center Biorepository. To identify tumors meeting current molecular criteria for oligodendroglioma, IDH1/2 status was confirmed by whole exome sequencing and 1p/19q codeletion confirmed using inferred copy number variation. First, we assessed for a histologic feature called hypercellular nodules (HCN), which are foci of increased cellularity in regions of otherwise lower cellularity tumor. In patients with newly diagnosed grade 2 oligodendroglioma, 16% (15/92) had HCN. While the median overall survival (OS) was 24.1 years without HCN, the median OS with HCN was only 13.6 years (p&amp;lt;0.02, Mantel-Cox test). We then assessed for homozygous deletion of CDKN2A. Cases with potential CDKN2A homozygous deletion by inferred copy number variation were validated by fluorescence in situ hybridization. In patients with newly diagnosed grade 2 oligodendroglioma, 2% had homozygous CDKN2A deletion (2/107). While the median OS with intact or hemizygous CDKN2A loss was 21 years, it decreased to 3.8 years with homozygous CDKN2A deletion (p&amp;lt;0.0001, Mantel-Cox test), although interpretation is limited given the rarity of homozygous CDKN2A loss at initial diagnosis. For recurrent grade 2 oligodendroglioma, 6% had homozygous deletion (5/77). While the median OS with intact or hemizygous CDKN2A loss in recurrent oligodendroglioma was 25.4 years, it decreased to 6.7 years with homozygous CDKN2A deletion (p&amp;lt; 0.04, Mantel-Cox test). These studies provide support for using HCN and CDKN2A homozygous deletion as grading criteria for oligodendroglioma. Further studies are ongoing, including covariate analysis, expanded cohorts, and ongoing analysis of whole exome sequencing data to identify additional genetic alterations correlated with overall survival.
EPCO-06. DIFFUSE MIDLINE GLIOMAS: FROM CELL CYCLE TO THERAPEUTIC OPPORTUNITIES
Authors: Anastasia Hains, Joana Marques, Kashish Chetal, Carlos Biagi Junior, Adriana Gonzalez-Sandoval, Renjitha Pillai, Alberto Gatto, Ruslan Sadreyev, Mariella Filbin, Capucine Van Rechem
Journal: Neuro-Oncology (2024)

Abstract The fatal Diffuse Midline Gliomas (DMG) are characterized by an undruggable H3K27M mutation in H3.1 or H3.3. K27M impairs normal development by stalling of differentiation. As replication timing influences gene expression, cell fate, and cellular response to therapeutics, we undertook a multi-omics approach (Repli-seq, cell cycle RNA-seq, single cell RNA-seq) in DMG cells (H3.1K27M and H3.3K27M subgroups) and tumors in comparison to normal brain to gain an appreciation for targetable pathways in DMG. DMG cells presented differential replication timing in each subgroup, which, in turn, correlated with significant differential gene expression including the cholesterol biosynthesis pathway. Consistent with these findings, DMG tumors presented high replication stress and cholesterol biosynthesis pathway signatures. Moreover, DMG cells were specifically vulnerable to an inhibitor of the cholesterol pathway and to a replication stress therapy, singly and in combination. In conclusion, this combinatorial genomics approach revealed insights into therapeutic opportunities for this incurable disease.
BIOM-29. UNMASKING COPPER DEPENDENCE IN GLIOMA: 19-GENE SIGNATURE FOR PATIENT STRATIFICATION AND TARGETED THERAPY
Authors: Toni Rose Jue, Vu Viet Hoang Pham, Tyler Shai-Hee, Riccardo Cazzoli, Joseph Descallar, Sumanth Nagabushan, Eng-Siew Koh, Orazio Vittorio
Journal: Neuro-Oncology (2024)

Abstract Adult-type diffuse gliomas exhibit poor prognosis with limited treatment options. Although copper-targeted therapies have been previously explored in these tumors, they have yet to show significant benefits. To understand the role of copper in glioma biology we performed an in silico data analysis on the TCGA glioma cohorts to identify copper-homeostasis related genes (CHRG) with prognostic significance. This was done to enable patient stratification into appropriate treatment arms for future clinical trials involving copper targeted therapies. Furthermore, in vitro experimentation was performed to validate the functional outcomes observed from the in silico results. 19 CHRGs were identified to have prognostic association from the TCGA glioma cohorts. This gene signature regulates a broad range of cellular processes, including metal homeostasis, metabolism, extracellular matrix organization, and immune cell function. The CHRG signature enabled the development of a predictive model that allowed stratification of patients between high and low risk groups. In vitro spheroid growth assays in both U87 cell lines with or without IDH mutation elicited sustained growth inhibition after 6 days post treatment. Furthermore, copper chelation therapy modified the energy potential of these glioma cells in vitro leading to growth inhibition. This study established a predictive model using 19 CHRGs that enable patient stratification between high and low risk glioma patients. Furthermore, our in vitro experiments show the suitability of targeting intracellular copper to inhibit tumor growth. Further research is needed to understand the underlying mechanisms and explore optimal treatment combinations for improved outcomes. We aim to extend this approach to pediatric gliomas for improved risk assessment and personalized medicine.
CCRG-03. DETECTION OF HETEROGENEOUS CELL CYCLE ALTERATIONS UPON TMZ CHEMOTHERAPY TREATMENT THROUGH ADVANCED MACHINE LEARNING
Authors: Giulia Villa, Jan Kückelhaus, Yahaya Yabo, Oliver Schnell, Daniel Delev, Jasim Kada Benotmane, Dieter Henrik Heiland
Journal: Neuro-Oncology (2024)

Abstract Glioblastoma (GB), the most aggressive central nervous system tumor, is hallmarked by its frequent relapse under alkylating chemotherapy. GB cells frequently exhibit changes in cell cycle phases during TMZ treatment, with a reduction in the G0-G1 phase and an increase in the S and G2 phases. This indicate both tumor cell re-entry into the cell cycle and a TMZ-induced arrest, contributing to resistance and progression. In this study, we leverage dynamic protein abundance of Ki-67, a proliferation marker peaking during S, G2, and M phases, to analyse cellular responses to TMZ in various cell lines and tissue samples. We designed an image-based machine learning approach for pattern recognition to reconstruct and analyse the cell cycle at the single-cell level. Six primary cell lines were characterized through whole-genome DNA, methylation and RNA sequencing. Functional read-outs were performed with large-scale, time- and concentration-dependent TMZ treatments in cell culture and GB-tissue slice models. Our model successfully reconstructed detailed cell cycle stages, showing that untreated cells were predominantly in the G0-G1 phase. TMZ treatment significantly shifted cells toward the S/G2 phase (p &amp;lt; 0.02) in 3 of 6 cell lines and the pseudo-time reconstruction highlighted dose-dependent cell cycle changes. Cell lines with enhanced stem-like features, defined based on epigenetic and transcriptional data signature, showed no cell cycle changes at high TMZ doses (&amp;gt;150µM), regardless the MGMT promoter methylation status. This heterogeneity in cell cycle response emphasizes the complexity of GB and the need for personalized treatments. Our study provides insights into GB MGMT cell cycle alterations and resistance mechanisms that are independent of MGMT methylation status, a known TMZ response biomarker. Therefore, the observed TMZ-induced cell cycle changes may serve as novel biomarkers for assessing treatment response, paving the way for personalized therapeutic approaches.
BIOM-23. DEUTERIUM METABOLIC IMAGING OF RESPONSE TO PRECISION THERAPY IN BRAF-V600E MUTANT GLIOMAS
Authors: Georgios Batsios, Suresh Udutha, Anne Marie Gillespie, Claudia Petritsch, Sabine Mueller, Pavithra Viswanath
Journal: Neuro-Oncology (2024)

Abstract Oncogenic BRAF-V600E mutations are frequently observed in low- and high-grade gliomas in adults and children. BRAF transduces signals from receptor tyrosine kinases to downstream effectors such as MEK1/2 and ERK, which regulate both metabolism and proliferation. The combination of the BRAF-V600E inhibitor dabrafenib and the MEK1/2 inhibitor trametinib (Dab/Tra) improves patient survival. However, there is considerable variation in the durability of response, underscoring the need for early biomarkers of treatment response. Magnetic resonance imaging (MRI), which is the gold standard for patient management, does not reliably assess response to therapy. Since the BRAF/MEK pathway regulates metabolism, the goal of this study was to determine whether Dab/Tra induces alterations in glucose metabolism that can be leveraged for non-invasive imaging. Using gene expression profiling, in vivo metabolomics, and stable isotope tracing, we show that Dab/Tra downregulates glucose metabolism to lactate in human and murine BRAF-V600E mutant models (AM38, 2341). In vivo infusion with [U-13C]-glucose in mice bearing intracranial AM38 tumors confirmed that Dab/Tra downregulates glucose metabolism to lactate in the tumor in vivo. Mechanistically, Dab/Tra destabilizes hypoxia inducible factor-1a and downregulates glycolytic genes, including SLC2A1, HK2, PFKFB3, and LDHA. Deuterium metabolic imaging (DMI) is a novel, clinical stage method of tracing glucose metabolism in vivo. Our studies show that lactate production from [6,6-2H]-glucose is reduced in AM38 and 2341 cells treated with Dab/Tra. Importantly, lactate production is reduced within 48 h of treatment with Dab/Tra in mice bearing intracranial AM38 tumors at the clinical magnetic field strength of 3T. Furthermore, this drop in 2H-lactate production is observed in the absence of MRI-detectable volumetric alterations and is predictive of extended survival. Collectively, our studies mechanistically link BRAF/MEK inhibition with downregulation of glycolysis and identify [6,6’-2H]-glucose as a novel contrast agent for imaging early response to therapy. Clinical translation of our studies will enable precision imaging of response to therapy for patients with BRAF-mutant gliomas.
SURG-04. DEVELOPMENT OF MICROSURGICAL FORCEPS EQUIPPED WITH HAPTICS TECHNOLOGY FOR IN SITU DIFFERENTIATION OF BRAIN TUMORS DURING MICROSURGERY
Authors: Taketo Ezaki, Kohki Kishima, Shunsuke Shibao, Takuya Matsunaga, Eriel Sandika Pareira, Yohei Kitamura, Yuji Nakayama, Noboru Tsuda, Kento Takahara, Takashi Iwama, Oltea Sampetrean, Kouhei Ohnishi, Tomoyuki Shimono, Hikaru Sasaki
Journal: Neuro-Oncology (2024)

Abstract BACKGROUND The stiffness of human cancers is correlated with their pathology, and can be used as a biomarker for diagnosis, malignancy prediction, molecular expression, and postoperative complications. Neurosurgeons perform tumor resection based on tactile sensations. However, it takes years of surgical experience to appropriately distinguish brain tumors from surrounding parenchymal tissue. Haptics is a technology that can amplify, transmit, record, and reproduce real tactile sensation, and the physical properties (e.g., stiffness) of an object can be quantified. METHODS glioblastoma (SF126-FmC, U87-FmC, U251-FmC) and malignant meningioma (IOMM-Lee-FmC, HKBMM-FmC) cell lines were transplanted into nude mice, and the stiffness of tumors and normal brain tissues were measured using our newly developed surgical forceps equipped with haptic technology (haptic forceps). Furthermore, pathological examination was performed to explore the correlation between stiffness and histological characteristics. RESULTS We found that all five brain tumor tissues were stiffer than normal brain tissue (p&amp;lt;0.001), and that brain tumor (three types of glioblastomas and two types of malignant meningioma) was significantly stiffer than normal brain tissue (p&amp;lt;0.001 for all). The stiffness among glioblastomas was not statistically significant (p=0.468) however, among the 2 malignant meningiomas, IOMM-Lee-FmC was significantly stiffer than HKBMM-FmC (p=0.032). Upon pathological examination, no significant differences were observed in the expression of collagen fibers. However, HKBMM-FmC demonstrated a higher prevalence of necrotic changes compared to IOMM-Lee-FmC. CONCLUSIONS Our findings suggest that tissue stiffness could be a marker not only to distinguish brain tumors from surrounding parenchymal tissue but also to distinguish pathology and malignancy of tumors. It is also suggested that the stiffness perceived during actual surgery and the stiffness quantified using haptic forceps may correlate with histological differences. Haptic forceps may help neurosurgeons to sense minute changes in tissue stiffness.
STEM-12. A NEURONAL STEM-LIKE PHENOTYPE IN GRADE 4 IDH-MUTANT ASTROCYTOMA WITH CDKN2A/B LOSS IS ASSOCIATED WITH CUX2 DEFICIENCY
Authors: Dustin Grief, Fulvio D’Angelo, Francesca Caruso, Matthew Flick, Christopher Sereduk, Michele Ceccarelli, Leland Hu, Joseph Loftus, Nhan Tran, Shannon Fortin Ensign
Journal: Neuro-Oncology (2024)

Abstract Diffuse gliomas represent the most common type of primary adult malignant brain tumor historically diagnosed and graded from histologic criteria alone. Gliomas harboring isocitrate dehydrogenase (IDH) 1 or 2 mutations are associated with lower grade tumors and portend a favorable prognosis relative to IDH-wildtype glioma. However, the loss of CDKN2A/B in IDH-mutant astrocytoma confers an aggressive high grade phenotype and is the strongest implicated molecular alteration associated poor clinical survival, thus is now sufficient to define a grade 4 tumor regardless of histologic grade. However, there remains no effective therapies targeted at molecular subgroups in aggressive gliomas to date. Here, we sought to elucidate the biologic pathways and functional outcomes associated with the acquisition of high-grade behavior under loss of CDKN2A/B in IDH-mutant astrocytoma to inform future therapeutic strategies. We analyzed a cohort of patient IDH-mutant astrocytomas with RNA sequencing data and found the increased expression of regulators of embryonic nervous system development and signaling concurrent with CDKN2A/B loss. Using grade 4 IDH-mutant astrocytoma patient-derived (PDX) and cell-lines harboring CDKN2A/B homozygous deletion, we stably re-expressed p14ARF, p15INK4B, and p16INK4A using a Tet-inducible system. IDH-mutant cell lines with re-expression of p14, p15, or p16 displayed differential transcription factor activation, impaired neurosphere capability, decreased colony formation, and lower neurosphere proliferation. Intriguingly, RNA-seq data revealed CUX2, a transcription factor known to control neuronal precursor behavior, as the likely candidate regulating the differential expression profile across CDKN2A/B status. We observed increased CUX2 expression in cell lines stably re-expressing p14, p15, and p16. We validated the CUX2 signature across publicly available datasets of IDH-mutant astrocytoma where CUX2 expression negatively correlated with loss of CDKN2A/B in patient tumors. Together our work suggests CUX2 deficiency in IDH-mutant astrocytoma with CDKN2A/B deletion enables an increased neuronal stem-like phenotype in these grade 4 tumors.
BIOM-22. SPATIAL, SINGLE-CELL, AND BULK RNA SEQUENCING IDENTIFY MOLECULAR PROGRAMS UNDERLYING MENINGIOMA BRAIN INVASION
Authors: Ayush Aggarwal, Mark W Youngblood, Kanish Mirchia, Hinda J Najem, Stephen T Magill, Amy B Heimberger, David R Raleigh
Journal: Neuro-Oncology (2024)

Abstract Brain invasion is a negative prognostic factor for meningiomas, but the molecular programs underlying meningioma brain invasion are poorly understood. To address this, we performed transcriptomic analyses of 3 independent datasets: Bulk RNA sequencing from 199 meningiomas (n=33 with brain invasion), single-cell RNA sequencing of 2 regionally distinct samples from the brain tumor interface (BTI) versus tumor core (TC) (n=22,118 single-cell transcriptomes), and spatial RNA sequencing from 6 samples with (n=4) versus without (n=2) brain invasion (n=18,471 spatial transcriptomes). Single-cell and spatial datasets were integrated with Harmony, cell interactions were defined using CellChat, and cross-platform comparisons were performed with the Seurat data integration pipeline. Bulk RNA sequencing revealed enrichment of 1835 genes in meningiomas with brain invasion compared to those without brain invasion, including glial markers (GFAP, NCAN) and markers of extracellular matrix remodeling (PDGFRA, COL9A1). Single-cell RNA sequencing comparison of BTI versus TC meningioma cells identified 2793 genes that were enriched in BTI cells, 268 of which were conserved across bulk and single-cell transcriptomes from brain-invasive meningiomas. Gene ontology enrichment analysis showed molecular programs underlying cell migration and regulation of neurogenesis at the BTI, while glycolysis and antigen presentation programs were enriched in the TC. Cholesterol, CSPG4, and LIF signaling were active in the TC, while SLIT signaling was enriched at the BTI. Spatial RNA sequencing showed enrichment of 439 genes at the BTI, and a conserved set of 12 genes were enriched in BTI meningioma cells across bulk, single-cell, and spatial datasets (TGM2, APOC1, IGFBP6, PLEKHO1, GFPT2, ZYX, IQGAP3, LUM, S100A11, ARPC1B, CDK1, CYCS). Comparison of tumor microenvironment monocytes at the BTI versus TC demonstrated enrichment of 1571 genes that were associated with macrophage migration and activation. These data elucidate molecular programs underlying meningioma brain invasion and provide insights into meningioma intratumor heterogeneity.
STEM-17. THE UROKINASE RECEPTOR AS A NOVEL IMMUNOTHERAPEUTIC TARGET IN BRAIN CANCERS
Authors: William Maich, Muhammad Vaseem Shaikh, Anish Puri, Daniel Mobilio, Alisha Ananda, Chitra Venugopal, Martin Rossotti, Nick Mikolajewicz, Chirayu Chokshi, Sabra Salim, Neil Savage, Thomas Kislinger, Kevin Henry, Sheila Singh
Journal: Neuro-Oncology (2024)

Abstract Glioblastoma (GBM) is the common malignant brain tumor in adults, accounting for approximately 15% of all CNS tumors, and 48.6% of malignant brain tumors, with a median survival of approximately 15 months. GBM is characterized by extensive inter- and intra-tumoral heterogeneity and an extremely immunosuppressive tumor microenvironment. Following Standard-of-Care surgical resection and chemoradiotherapy, patients inevitably relapse, at which point few therapeutic avenues exist, owing in part due to a lack of clinically relevant targets. Data from our target identification pipeline shows the urokinase plasminogen activator receptor (uPAR) is significantly upregulated at recurrence on putative GBM brain tumor initiating cells (BTICs), which are believed to drive de novo tumor formation, recurrence, and therapeutic resistance. uPAR plays an important role in the plasminogen activation system, and in the context of cancer, has been implicated in numerous pro-tumorigenic processes such as invasion, proliferation, and therapy resistance. We used CRISPR-Cas9 to genetically delete uPAR from our in-house patient-derived GBM cell lines, and found that knockout of uPAR in recurrent GBM cells significantly reduces various functional characteristics of BTICs in vitro. In our patient-derived mouse model of GBM, we found that knockout of uPAR significantly increases survival, and decreases tumor burden. Further, we generated novel anti-uPAR single domain antibodies (sdAbs) which specifically and efficiently bind uPAR at low nanomolar concentrations in vitro. We developed anti-uPAR CAR Ts using the binder sequence of the sdAbs, which showed potent cytotoxicity in vitro, and drastically reduced tumor burden and extended survival in vivo. Further, we identified uPAR as being highly expressed on brain metastases from multiple origins (lung-to-brain, melanoma-to-brain, etc.), and demonstrate that anti-uPAR CAR Ts effectively kill brain metastases in vitro, and significantly extend survival using in vivo brain metastasis models. From this work we believe uPAR to be a clinically relevant target in both recurrent GBM and brain metastases, and investigation into therapeutic strategies targeting uPAR-positive brain cancers should be explored further.
INNV-28. CONNECTOMICS-GUIDED GLIOMA RESECTION: HOW CHANGES IN STRUCTURAL CONNECTIVITY CORRELATE WITH LANGUAGE FUNCTION
Authors: Kevin Clare, Bridget Nolan, Amy Rickard, Erin McGee, Sabrina Zeller, Eris Spirollari, Aditya Kancharla, Monica Mureb, Cristina Falo, Tomoko Kitago, Tracey Milligan, Chirag Gandhi, Synphen Wu, Simon Hanft
Journal: Neuro-Oncology (2024)

Abstract Postoperative aphasia is a risk inherent to resections of brain masses in language eloquent areas. Neurosurgical strategies to minimize damage of functional language structures include awake craniotomies combined with stimulation mapping and intra-operative speech and language pathology (SLP) testing. Until now, consideration of white matter tracts involved in language processing as measured by diffusion tensor imaging (DTI) has been minimally incorporated into resection planning. In addition, there is limited understanding as to the association between specific tracts and aphasia risk. Quicktome™ by Omniscient Neurotechnology is clinically-oriented connectomics software that uses DTI sequences from MRIs to model connectivity between geographically distinct brain regions. This model can then be integrated with intraoperative navigation to avoid language connections during resection. Here, we investigate how language tract changes affect clinical aphasia. Patients with language-eloquent gliomas with available pre- and post-operative DTI and SLP evaluations were included in this retrospective study. Structural networks were quantified using Quicktome™ and compared using Spearman correlation. Changes in language function were evaluated using the Boston Naming Test and the Western Aphasia Battery. Patients with postoperative auditory verbal deficits showed a moderate correlation in connectivity changes (ρ=0.42), whereas patients with postoperative naming deficits showed a weak correlation (ρ=0.19). The inferior frontal junction, anterior portion (IFJa), and the superior temporal sulcus, ventral posterior portion (STSvp), in the right hemisphere demonstrated the most associated structural connectivity changes. To our knowledge, this is the first study which uses Quicktome™ to directly associate postoperative connectivity with aphasia outcomes. Understanding the interplay between structural connectivity and neurological symptoms can elucidate neural pathways underlying cortical function with the potential to reduce neurosurgical postoperative morbidity.