tbuckley/cabot-search huggingface dataset:
RADT-02. PRE-OPERATIVE VERSUS POST-OPERATIVE FRACTIONATED STEREOTACTIC RADIOTHERAPY: A SINGLE-INSTITUTION ANALYSIS OF 534 RESECTED METASTASES
Authors: Haley Perlow, Sarah Hennings, Jared Bradshaw, Sohil Reddy, Sydney Luu, Jennifer Matsui, Brett Klamer, Khaled Dibs, Marshall Harrell, John McGregor, Russell Lonser, Daniel Prevedello, James Elder, Kyle Wu, Roshan Prabhu, Simeng Zhu, Raj Singh, Sasha Beyer, John Grecula, Dukagjin Blakaj, Evan Thomas, Raju Raval, Joshua Palmer
Journal: Neuro-Oncology (2024)

Abstract Patients with large or symptomatic brain metastases and limited intracranial disease typically have surgery followed by post-operative (post-op) stereotactic radiosurgery (SRS). However, SRS can lead to elevated rates of radiation necrosis (RN), meningeal disease (MD), and local failure (LF). Fractionated treatments can deliver a higher biological effective dose and may reduce the risk of LF, and pre-operative (pre-op) treatments may reduce the risk of RN and MD through treating smaller volumes and tumor sterilization. We hypothesize that pre-op fractionated stereotactic radiation therapy (FSRT) will reduce the incidence rate of RN, MD, and LF when compared to patients who receive post-op FSRT. A retrospective analysis was performed at a single institution and included patients who had surgical resection and radiation to at least one brain metastasis. Patients with multiple metastases resected, either during the same surgery or at different times in the disease course, were eligible for inclusion. Outcomes were evaluated on a per-lesion basis. The primary outcome was a composite endpoint defined by 1) LF, 2) MD, and/or 3) Grade 2 or higher (symptomatic) RN. 458 patients with 534 resected brain metastases were eligible for analysis. 235 metastases received pre-op FSRT, and 299 metastases received post-op FSRT. Overall, 15% of patients had multiple brain metastases resected. Overall, 6 (2.6%) pre-op and 13 (4.3%) post-op patients experienced LF. 21 (8.9%) pre-op and 38 (12.7%) post-op patients experienced symptomatic RN. 11 (4.7%) pre-op and 29 (9.7%) post-op patients were diagnosed with MD (p=0.031). 14% and 24% of metastases that received pre-op and post-op FSRT, respectively, experienced the composite endpoint (p=0.005). In our study, pre-op FSRT compares favorably to post-op FSRT primarily due to a 50% reduction in the incidence of MD. Differences in symptomatic RN or LF were small on adjusted analyses. Prospective validation of pre-op FSRT is needed.
CNSC-60. SYNERGISTIC IMMUNOMODULATION THROUGH DUAL ANTIBODY THERAPY TARGETING CD47 AND CD24 FOR ENHANCED ANTITUMOR IMMUNITY IN GLIOBLASTOMA
Authors: JongHoon Ha, Yifan Wang, Shiyan Dong, Betty Y S Kim, Wen Jiang
Journal: Neuro-Oncology (2024)

Abstract Tumor cell phagocytosis by antigen-presenting cells (APCs) plays a pivotal role in fostering antitumor immunity. However, glioblastoma, known for its evasive strategies, exploits key phagocytosis checkpoints, including CD47, CD24, and beta-2-microglobulin. While mono-treatment targeting CD47 blockade has shown some antitumor responses in glioma, prolonged tumor-suppressing ability and significant extension of survival remain elusive. In this study, we combine anti-CD47 and anti-CD24 antibody treatments, unveiling a synergistic effect in promoting tumor cell phagocytosis. This enhanced phagocytosis profile triggers the activation of the cyclic GMP-AMP synthase-stimulator of interferon genes (cGAS-STING) pathway in APCs, thereby facilitating efficient T cell priming. This orchestrated interplay between innate and adaptive antitumor immunity not only attenuates glioblastoma growth and extends overall survival. These findings illuminate a promising avenue for harnessing phagocytosis modulation as a strategic approach to treat challenging tumors equipped with multiple immune checkpoints.
TMIC-39. SPATIAL MULTIOMICS PROFILING REVEALS HETEROGENEITY OF B:T CELL INTERACTIONS AND PLASMA CELL FORMATION IN TERTIARY LYMPHOID STRUCTURES IN HUMAN GLIOMAS
Authors: Pinar Cakmak, Jennifer H Lun, Aakanksha Singh, Jadranka Macas, Michael Burger, Lucie Marie Hasse, Elke Hattingen, Miriam Köhler, Jonathan Schupp, Tatjana Starzetz, Eike Steidl, Karl H Plate, Yvonne Reiss, Katharina Imkeller
Journal: Neuro-Oncology (2024)

Abstract Adult-type diffuse gliomas, the most common primary brain tumours, remain a clinical challenge in oncology with limited treatment options, restricted anti-tumour immune response and a dismal patient prognosis. Despite their immunosuppressive microenvironment, the formation of lymphoid aggregates containing adaptive immune cells has been reported in gliomas. However, the cellular compositions, immunological function, and relevance of lymphoid aggregates for adaptive anti-tumour immunity is not well understood. Therefore, we performed a comprehensive, unbiased analysis of lymphoid aggregation in 642 adult-type diffuse gliomas using a multi-modal approach, combining DNA methylation and RNA sequencing with spatial transcriptome and proteome profiling. Overall, B cell aggregates and tertiary lymphoid structures (TLS) were observed in 15% of tumours, with the highest prevalence in primary glioma localised to the temporoparietal lobe. The presence of TLS was associated with an improved overall survival. Gliomas containing TLS displayed a remodelled perivascular space, characterised by transcriptional upregulation and spatial redistribution of collagens associated with barrier functions. Spatial transcriptome and proteome profiling revealed heterogenous B:T cell interactions that were associated with elevated CD8 T-cell numbers and differences in IgA and IgG plasma cell forming capacity, suggestive of dynamic adaptive immune response.
EPCO-19. MULTIOMIC PROFILING OF EPIGENETIC HETEROGENEITY IN GLIOBLASTOMA AT SINGLE-CELL RESOLUTION USING MULTIOMIC SINGLE-CELL CUT&amp;TAG
Authors: Andrew Hardigan, Emily Blandford, Aditya Mohan, Eliese Moelker, Peter Fecci, Anoop Patel
Journal: Neuro-Oncology (2024)

Abstract INTRODUCTION Recent evidence suggests epigenetic heterogeneity may be the primary driver of cell phenotype and treatment resistance in glioblastoma (GBM). Epigenetic heterogeneity is defined by alterations of chromatin histone modifications with activating marks such as H3K27 acetylation and repressive marks such as H3K27 trimethylation. Combinations of these histone marks govern the activity of functional genomic elements such as enhancers or promoters. Single-cell (“sc-”) technologies have only recently been adapted to the study of epigenetic cell states and significant technical challenges have limited their widespread adoption, especially in complex tissues. Here, we report the development of an optimized method for performing tissue processing and simultaneous single-cell epigenetic and transcriptomic analyses in flash frozen GBM samples. METHODS Building on our prior work, we developed a new protocol, multiomic single-cell cleavage-under-targets and tagmentation, or “mscCUT&amp;TAG”. We optimized nuclei isolation, cleanup and permeabilization from flash frozen GBM and reaction conditions for the scCUT&amp;TAG portion of the assay. Critically, these changes maintained high-quality, intact nuclei in suspension while limiting well-described technical issues such as nuclei clumping and sample loss. Furthermore, we incorporated the ability to multiplex both patient samples and histone marks. RESULTS We applied 10X scRNA-seq, 10X Multiome (RNA+ATAC-seq), and mscCUT&amp;TAG for five histone marks to the same GBM sample, enabling an integrated evaluation of the tumor’s transcriptome, chromatin accessibility and epigenetic regulation at single-cell resolution. mscCUT&amp;TAG enabled the first assessment of single-cell genome segmentation in GBM. We integrated across modalities to identify specific tumor cell populations, cell-type specific coordinated changes in epigenetics and transcriptome, and define functional regulatory elements. CONCLUSIONS We developed a novel multiomic protocol, mscCUT&amp;TAG, that allows for a comprehensive analysis of epigenetic heterogeneity in GBM. We anticipate this protocol will enhance our understanding of fundamental biology and potential therapeutic avenues in GBM.
STEM-06. DISTANT ORIGIN OF GLIOBLASTOMA RECURRENCE: NEURAL STEM CELLS IN THE SUBVENTRICULAR ZONE SERVE AS A SOURCE OF TUMOR RECONSTRUCTION AFTER PRIMARY RESECTION
Authors: Xue Li, Hyun Jung Kim, Tae Min Kim, Seung Hong Choi, Soon-Tae Lee, Jong Bae Park, Jihwan Yoo, Jong Hee Chang, Chul-Kee Park, Hong-Gyun Wu, Jae-Kyung Won, Yeonhee Lee, Jeong Ho Lee, Seok-Gu Kang, Joo Ho Lee
Journal: Neuro-Oncology (2024)

Abstract The recurrence of glioblastoma (GBM) remains unavoidable. Neural stem cells (NSCs) in the subventricular zone (SVZ) are considered a treatment target due to their potential role as the cellular origin of GBM. However, it is not yet confirmed whether GBM recurrence also originates from these cells. We first conducted deep sequencing on paired patient samples, including primary tumors (pT), recurrent tumors (rT), and SVZ tissues. The sequencing results revealed that in 5 out of 9 patients, the rT evolved independently from the SVZ rather than directly from the pT. Based on this, we developed a mouse model to simulate the GBM recurrence process by transforming SVZ NSCs into GFP-labeled cells carrying cancer mutations via electroporation. Following the resection of the tdTomato-labeled pT, we observed that 57.1% of the rT consists of a mixture of GFP- and tdTomato-positive tumor cells. To study the behavior of NSCs, we improved the existing mouse model by removing cortical tissue to simulate the complete resection of the pT. Four weeks post-surgical resection, 64.7% of tumors reconstructed in the resection cavity (RC), driven by the migration of OPC lineage cells. Time-course RNA-seq results indicated that the CXCL12-CXCR4 pathway might be responsible for driving the migration of SVZ NSCs to the RC. Further deconvolution and fluorescence staining analysis confirmed that CXCL12 secreted by endothelial cells around the RC could drive CXCR4-positive NSCs to migrate to the area. Additionally, the CXCR4 antagonist AMD3100 significantly reduced tumor recurrence in mice and extended survival. RNA-seq results from both mouse and human paired tumor samples confirmed that the CXCL12-CXCR4 pathway was enriched in locally recurrent tumor specimens and was correlated with shorter patient survival. In summary, our study provides evidence that GBM recurrence originates from SVZ NSCs. Moreover, we identified the CXCL12-CXCR4 pathway as a potential therapeutic target for GBM recurrence.
DDDR-31. THE CHEMOTHERAPEUTIC ACTIVITY OF TEMOZOLOMIDE IS ANTAGONIZED BY ITS HYDROLYSIS PRODUCT, AIC
Authors: Mark L Sowers, Tuvshintugs Baljinnyam, Hui Tang, Jason L Herring, Sandra Hatch, Pablo Valdes, Kangling Zhang, Lawrence C Sowers
Journal: Neuro-Oncology (2024)

Abstract Temozolomide is the only FDA-approved drug that has demonstrated improved overall survival in patients with Glioblastoma. Despite the clinical impact it has had, overall survival today largely remains less than two years with current standard-of-care. Temozolomide is a prodrug that undergoes hydrolysis releasing 5-amino-4-imidazole carboxamide (AIC) before it can alkylate DNA. The DNA damage response invoked by TMZ depletes NAD+ levels. We present evidence from mass spectrometry LC-MS/MS studies that AIC released from TMZ can be aberrantly incorporated into the purine synthesis pathway, augmenting purine, and NAD+ synthesis and contributing to chemo- and radiation- resistance. The chemotherapeutic efficacy is therefore antagonized by its own hydrolysis product. TMZ analogs that do not generate AIC will likely have greater activity.
QOL-07. LONG-TERM FOLLOW-UP OF PHYSICAL FUNCTION AND SOCIAL CONDITIONS IN CENTRAL NERVOUS SYSTEM GERM CELL TUMORS
Authors: Hirokazu Takami, Ryo Nishikawa, Masao Matsutani
Journal: Neuro-Oncology (2024)

Abstract BACKGROUND This paper presents an analysis of iving and social conditions from a long-term follow-up of Phase II clinical trial for central nervous system germ cell tumors conducted between 1995 and 2003. METHODS A retrospective analysis was performed on 228 cases, including 161 germinomas, 66 non-germinomas, and 1 mature teratoma, over a median follow-up of 222 months. There were 56 recurrences and 39 deaths recorded. The analysis at the final follow-up included final educational level, employment status, activities of daily living (ADLs), marital and parental status, and hormone replacement therapy. The study targeted 157 cases with more than 10 years of follow-up data. RESULTS At 20 years post-treatment, survival rates were 91% for germinomas and 65% for non-germinomas. At the last follow-up, ages ranged from 19 to 58 years (median 36 years). The Karnofsky Performance Status (KPS) was 80 or higher in 118 cases, 70 in 7 cases, and 60 or lower in 32 cases. Educational achievements were: elementary school in 1 case, middle school in 8, high school in 52, university in 45, and graduate school in 2. Employment status showed 37 unemployed, 4 in school, 23 part-time, 80 full-time, and 2 homemakers. Childbirth was reported in 16 men (18%) and 4 women (16%). The frequency of a KPS≧80 at the final follow-up was higher in initial germinoma cases than in non-germinoma cases (80 vs 62%, p=0.04), and was also higher in cases without recurrence (83 vs 47%, p&amp;lt;0.0001). Only the proportion of growth hormone supplementation showed a significant correlation with KPS (≧80: 19% vs &amp;lt;80: 3%, p=0.03). CONCLUSION Long-term social outcomes are favorable for germinoma patients without recurrence, while non-germinoma patients who have recurred and survived face tougher conditions, indicating significant treatment impacts. Managing treatment intensity and ensuring comprehensive long-term follow-up are crucial.
TMET-22. OVERCOMING RESISTANCE: PANOBINOSTAT SENSITIZES 2DG-RESISTANT PEDIATRIC HIGH-GRADE GLIOMAS WITH H3.3 K27M/G34R MUTATIONS TO APOPTOSIS
Authors: Tracy Miller, Esther Jane, Taylor Gatesman, Matthew Halbert, Chiam Sneiderman, Itay Raphael, Steven Mullett, Stacy Lynn Gelhaus, Sameer Agnihotri, Richard Steinman, Daniel Premkumar, Ian Pollack
Journal: Neuro-Oncology (2024)

Abstract BACKGROUND Pediatric high-grade gliomas (pHGG) harboring H3.3 K27M/G34R mutations present formidable challenges in treatment due to their aggressiveness and resistance to standard chemotherapy. Our preliminary investigations have shown promising results, indicating that combining 2-deoxyglucose (2DG), a glycolytic inhibitor, with DNA-damaging agents synergistically inhibits pHGG growth. However, prolonged exposure to 2DG induces resistance, necessitating the exploration of alternative therapies. This study aims to investigate the potential of panobinostat, a histone deacetylase inhibitor, in sensitizing 2DG-resistant pHGG with H3.3 K27M/G34R mutations to apoptosis. METHODS Transcriptomic analysis via Illumina NovaSeq 6000 and metabolomic profiling employing Liquid Chromatography-High-Resolution Mass Spectrometry was used to delineate the molecular landscape of naive and 2DG-resistant pHGG cell lines. Functional assays, including the Agilent Seahorse Mito Stress Test and flow cytometry, assessed bioenergetics and mitochondrial dynamics. Intracellular NAD+ and NADH levels were quantified utilizing NAD+/NADH Glo assays, while apoptotic markers and metabolic stress were measured using the Annexin V-FITC Conjugates for Apoptosis Detection kit and western blot. RESULTS Comparative analysis revealed increased transketolase activity in 2DG-resistant cells, augmenting the interaction between the pentose phosphate pathway and glycolysis, resulting in elevated levels of NADPH and ATP. Additionally, these resistant cells displayed enhanced reliance on mitochondrial energy metabolism, as evidenced by substantial increases in mitochondrial membrane potential and mass, coupled with elevated NAD+ levels. Subsequent treatment with panobinostat induced a significant decrease in NAD+ biosynthesis and ATP generation. Furthermore, this intervention triggered the upregulation of pro-apoptotic BCL-2 family proteins, particularly BAX and BAK, concomitant with a notable reduction in mitochondrial membrane potential and the accumulation of reactive oxygen species. Consequently, heightened caspase-3 activity ensued, leading to significantly elevated cell death rates in 2DG-resistant gliomas. CONCLUSION Our findings highlight panobinostat as a promising therapy to resensitize 2DG-resistant pHGG cells to apoptosis, offering hope for treating these aggressive tumors with H3.3 K27M/G34R mutations.
ANGI-12. THE IMPACT OF STANDARD-OF-CARE TREATMENT ON THE RELATIONSHIP BETWEEN CELL DENSITY AND SOX2 POSITIVITY IN GLIOBLASTOMA PATIENTS AT AUTOPSY
Authors: Samuel Bobholz, Allison Lowman, Daniel Aaronsen, Aleksandra Winiarz, Savannah Dueweg, Michael Flatley, Biprojit Nath, Fitzgerald Kyereme, Jennifer Connelly, Kelly Mrachek, Max Krucoff, Anjishnu Banerjee, Peter LaViolette
Journal: Neuro-Oncology (2024)

Abstract INTRODUCTION Sex-determining region Y-box 2 (SOX2) staining highlights pluripotent cells and provides an early sign of tumor cell invasion in glioblastoma patients. This infiltration can often occur at the single cell level and can occur in the absence of lower resolution histological tumor features such as hypercellularity. This study assessed the impact of standard treatment regimens on the relationship between cellularity and SOX2+% at death using autopsy samples as ground truth. METHODS A total of 36 IDH-wildtype glioblastoma patients were included for this study (23M/13F, mean age=61.9). Tissue samples from both suspected tumor invasion and suspected normal tissue were collected for each patient, which were then stained for SOX2, digitized at 40X resolution, and segmented into positive staining nuclei percentage using a color deconvolution algorithm. These samples were then aligned to the MRI using in-house MATLAB-based software, where manually defined control points placed on areas of architectural similarity are used to compute a transform that corrects for nonlinear shrinkage of the tissue sample due to post-mortem processing. The association between SOX2+% and cell density was then computed per subject, and compared between patients who received SOC (radiation and temozolomide) treatment following surgery (as well as additional treatment per case, n=31) and patients who opted for no additional treatment following surgery (n=5). RESULTS Patients who received no additional treatment showed substantially higher correlation between cell density and SOX2+% than patients who had received SOC (t=2.90, p=0.006). No association with overall survival was observed (r=0.17, p=0.329). CONCLUSIONS These results indicate a decoupling between hypercellularity and SOX2+% associated with standard GBM treatments, indicating that radiation and other treatments induce a more heterogenous tumor microenvironment that could lead to single-cell tumor invasion beyond gross histological markers of tumor presence.
BIOM-60. UNDERSTANDING THE INTERSECTION OF RACE, SEX, AND GENOMIC PROFILES IN MENINGIOMA PATHOPHYSIOLOGY
Authors: Alper Dincer, Shaila Ghanekar, Joanna Tabor, Miri Kim, Jennifer Moliterno
Journal: Neuro-Oncology (2024)

Abstract BACKGROUND While meningioma incidence and outcomes vary by sex and race, the potential underlying molecular differences possibly contributing to these disparities are less understood. Herein, we explore the clinical and genomic characteristics of meningiomas across groups characterized by age and sex. METHODS We analyzed adult patients with primary meningiomas resected from 2012 to 2023. Patients underwent whole exome sequencing, and demographic data were categorized into four groups based on self-reported race and sex, which included White females, White Males, Black females, and Black males. The primary analyses involved comparisons of tumor characteristics, socioeconomic status (median zip code income, % with high school diploma, health insurance status, distance from hospital), genomics, and recurrence rates. RESULTS The study included 509 primary meningiomas. White females exhibited low-risk genomic profiles characterized by driver mutations in KLF4 (+/- TRAF7) (p=0.010) and POLR2A (p=0.045), with no associated CNVs (p=0.410). This benign molecular profile correlated with lower WHO grades (p=0.013) and a lower incidence of recurrence (p=0.0003). Black females had meningiomas enriched with Hedgehog pathway mutations (p=0.0035) and a predilection for the anterior skull base (p=0.034), leading to an increased risk of recurrence (p=0.026). White males showed an aggressive genomic profile, including chromosome 1p loss (p=0.025) and 10q loss (p=0.067), associated with a high risk of recurrence (p=0.0002). Black males had meningiomas with chromosome 14q loss (p=0.0002), the highest incidence of high-grade meningiomas (p=0.048), and a 4.5-fold increased risk of recurrence (OR 4.5 [1.6-11.8]; p=0.006). Black males also experienced the worst progression-free survival (HR 5.5 [2.5-12.4]; p&amp;lt;0.0001), independent of WHO grade, extent of resection, and socioeconomic status. CONCLUSIONS Each demographic has a distinct molecular profile that correlates with clinical behavior in a race and sex-specific manner. Black males are disproportionately affected by biologically aggressive meningiomas, leading to higher tumor grade and recurrence rates.
DDDR-33. TRANSCRIPTOMICS-BASED NOVEL DRUG DISCOVERY IN DIFFUSE MIDLINE GLIOMA
Authors: Savneet Kaur, Dmitry Leshchiner, Jun Watanabe, Eita Uchida, Kentaro Mineji, Bin Chen, Rintaro Hashizume
Journal: Neuro-Oncology (2024)

Abstract Introduction. Pediatric high-grade gliomas are the most common cause of cancer-related death in children, of which the most malignant and devastating tumors include diffuse midline glioma (DMG). Recent availability of tumor samples and advances in next-generation sequencing enable the profiling of thousands of molecular features in DMG. We employ a system-based approach that uses gene expression as a representation of the molecular state, providing an avenue for therapeutic discovery. Previously, we used this approach to identify repurposed candidates for DMG; however, the final candidate had poor brain penetration, prompting us to discover novel compounds with better brain penetration. To apply it to novel compound discovery, we need the expression profiles of all library compounds, which is impractical for millions of compounds. To overcome this, we have developed a platform, Gene expression profiles Predictor on chemical Structures (GPS), that incorporates machine learning algorithms which leverage existing drug-induced gene expression profiles to predict gene expression based on compound structure. methods. DMG RNA-Seq samples were acquired from St. Jude Children’s Research Hospital and Children’s Brain Tumor Network (CBTN). We developed deep learning autoencoder to search reference normal tissues from Genotype-Tissue Expression (GTEx). A DMG meta-signature was created and fed into GPS to predict drug candidates from the Enamine CNS library, seven of which were experimentally tested in vitro and the most promising one subsequently validated in vivo. Results. Cell proliferation analyzed by MTS assay showed three compounds with IC50&amp;lt; 50 µM in K27M-mutant DMG cell lines (SF8628, DIPG007, SU-DIPG36). Toxicity study showed no adverse effects in the mice treated with 100-200 mg/kg of the most promising compound (IC50 = 1.9 µM in DMG cells). Conclusion. Our novel computational framework leverages deep learning to fill the gap in drug discovery in DMG. Work is underway to determine antitumor activity, brain penetration (via HPLC) and survival benefit in the mice bearing DMG PDX treated with the lead compound.