tbuckley/cabot-search huggingface dataset:
BIOM-63. LONG-TERM SURVIVAL AND MOLECULAR CHARACTERIZATION OF IDH-WILDTYPE GLIOBLASTOMA IN AN ASIAN COHORT
Authors: Wing Lun Lee, Elaine Yee-Ling Ko, Marc Lecoultre, Isaac Ho, Matthew Kin-liang Chiu, Chi-Leung Chiang, Dennis Leung, Gilberto Ka-Kit Leung, Joyce Shuk-wan Chow, Peter Yat Ming Woo, Tai Chung Lam, El Helali Aya
Journal: Neuro-Oncology (2024)

Abstract BACKGROUND Glioblastoma (GB), the most aggressive form of brain tumor, presents a significant clinical challenge with a devastating prognosis. Globally, the median overall survival (OS) for GB is typically 12-15 months, largely due to its inherent resistance to chemotherapy and radiotherapy. However, some patients exhibit prolonged survival, and their specific demographic and genomic characteristics remain poorly defined. Understanding the clinical profile of these exceptional responders holds great promise for informing improved management strategies for GB. METHODS In a retrospective two-center study conducted in Hong Kong (IRB: UW 21-189), we recruited 80 patients diagnosed with IDH wildtype glioblastoma. All patients underwent next-generation sequencing as part of their treatment. Long-term survivor (LTS) was defined as &amp;gt;=36 months from diagnosis, while medium-term survivor (MTS) was defined as &amp;gt;=18 months, and &amp;lt;18 months as short-term survivors (STS). When appropriate, descriptive statistics were used to report frequency with percentage or median with range. Fisher’s exact test was employed to analyze categorical variables, while continuous variables were assessed using the Kruskal-Wallis test. All statistical analyses were conducted using R (version 4.2.3). Result: Among the cohort of 80 recruited patients, the median survival was 18.8 months (95% CI 17.2-24.8). Notably, 21% (n=17) were LTS, 31% (n=25) were MTS, and 48% (n=38) were STS. A statistically significant variation (p &amp;lt; 0.05) was evident across three groups: gender distribution, the number of resections performed, the proportion of patients receiving genomic-guided treatment, and their participation in clinical trials. However, no significant difference was observed in MGMT promoter status and ECOG score. CONCLUSION Identifying these clinical factors enhances the clinical management of GB. The implications of these findings underscore the potential importance of incorporating genomic-guided treatment in both local and global clinical practices in GB.
CTIM-30. NT-I7, A LONG-ACTING INTERLEUKIN-7, PROMOTES ACTIVATION, CYTOTOXIC FUNCTION, AND SELECTIVE CLONOTYPE EXPANSION OF CD8+ T CELLS IN PATIENTS WITH HIGH GRADE GLIOMAS
Authors: Kaiden Barozinsky, Jennifer A Foltz, Omar H Butt, Alice Y Zhou, Kartik Singhal, Obi Griffith, Malachi Griffith, Kelsey Etter, Cierra Grote, Jingqin Luo, Leslie Nehring, Ruth Katumba, Sara Ferrando-Martinez, Kristina Stermer, Byung Ha Lee, Tanner Johanns, Jiayi Huang, John DiPersio, Milan Chheda, Todd Fehniger, Jian L Campian
Journal: Neuro-Oncology (2024)

Abstract Lymphopenia following chemoradiation for high grade gliomas (HGG) is common and is associated with decreased survival. NT-I7 (efineptakin alfa) is a long-acting analog of the lymphocyte pro-survival cytokine, interleukin-7. Our Phase I dose-escalation study of 19 patients with HGG demonstrated early elevations in CD4+ and CD8+ T cells in the first 4 weeks after administration of NT-I7. In this study, we explored the diversity and potential functionality of the NT-I7-expanded T cell population. A subset of 4 subjects with glioblastoma multiforme (GBM) treated at 720 µg/kg of NT-I7 during adjuvant temozolomide in our study (NCT03687957) underwent Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-seq) of peripheral blood. CITE-seq with TCR clonotype sequencing (10x Genomics 5’) permitted simultaneous tracking of the T cell phenotype at the protein level, individual T cell clones, and gene expression dynamics between 4 timepoints: pre-treatment, and post-treatment weeks 1, 2, and 13. Here, we report the results of differential expression analyses between timepoints and patient-specific differences in T cell clonotype expansions. Both CD4+ and CD8+ T cells in our study patients had increased expression of T cell activation markers LTB, CISH, and CD74. CD8+ T cell subsets demonstrated additional elevations in genes important in cytotoxic function (granzymes (GZMA, GZMB) and perforin (PRF1)), MHC Class II expression (HLA-DRA, HLA-DRB1), and AP-1 transcription factor subunits (JUND, JUN, JUNB, FOS, FOSB). After excluding known viral antigen clonotypes, 2 of 4 patients demonstrated TCR clonotype expansion. Notably, nearly all the expanded TCR clonotypes were found within CD8+ T cells, but not CD4+ T cells. NT-I7 promotes activation, cytotoxic function, and selective clonotype expansion of CD8+ T cells in patients with HGG. This, combined with its role in increased CD4+ T cell counts, suggests NT-I7 may be a powerful tool to restore immune function after treatment-associated lymphopenia in HGG.
PATH-21. SINGEL CELL TRANSCRIPTOMICS OF SPINAL EPENDYMOMA SUBTYPES IDENTIFIES INTRATUMORAL HETEROGENEITY
Authors: Karoline Hack, Saskia-Larissa Jauch-Speer, Ulrich Schüller
Journal: Neuro-Oncology (2024)

Abstract Spinal ependymomas comprise glial neoplasms that are classified by histological and molecular features. Two of the respective types, myxopapillary ependymomas (MPE) and spinal ependymomas (SP-EPN) are largely understudied. For each of these, our group identified clinically relevant subtypes with poorer (MPE-A; SP-EPN-A) and more favorable progression-free survival (MPE-B; SP-EPN-B) employing global methylation and transcriptomic profiling. As cellular origin and pathogenesis of these tumors are largely unknown, therapeutic options for patients with unfavorable subtypes are unavailable. We performed single cell transcriptomic sequencing of 12 formalin-fixed and paraffin-embedded spinal ependymomas including all MPE and SP-EPN subtypes and obtained a median of 10,091 cells per tumor after quality control. Uniform Manifold Approximation and Projection (UMAP) analysis revealed intertumoral heterogeneity as most samples formed separate clusters with tumors of the same subtype located in proximity. The expression of literature-defined neoplastic consensus cell states was examined for each cell of the data set and revealed intratumoral heterogeneity. Tumors expressed predominantly two programs, being a ciliated (ependymal-like) cell state (61% of all neoplastic cells) and the astrocytic state (31 % of all neoplastic cells). Interestingly, third and fourth most abundant states (mesenchymal and hypoxia) were almost exclusively expressed in MPE-A and SP-EPN-A. Furthermore, distinct clones of chromosomal copy number variations were identified across all tumors. These clones can be distinguished in UMAP representation of MPE single cell transcriptomes and to a lesser extend in SP-EPN. Next, we sought to characterize the resemblance of integrated tumor subtypes to normal spinal cord cell populations and observed a high similarity to human spinal cord ependymal cells. All spinal ependymoma subtypes display intratumoral heterogeneity with respect to the transcriptomic cell state resemblance of the neoplastic cells. Together with the transcriptomic similarity to ependymal and astrocytic cells, our data suggest the tumor origin within the astro-ependymal lineage.
EXTH-45. PRECLINICAL EVALUATION OF THE ANTIBODY-DRUG CONJUGATE TISOTUMAB VEDOTIN IN ADULT-TYPE DIFFUSE GLIOMAS
Authors: Thomas Sears, Wenxia Wang, Dusten Unruh, Matthew McCord, Alicia Steffens, Craig Horbinski
Journal: Neuro-Oncology (2024)

Abstract The gene F3, encoding Tissue Factor (TF), is expressed in many cancers and contributes to their malignancy. Our previous work showed that, among adult-type diffuse gliomas, IDH wild-type (IDHwt) glioblastomas (GBM) express more TF than IDH mutant (IDHmut) gliomas (PMID: 27664011, 30266764, 31222125). Tisotumab vedotin (TV), an anti-TF antibody conjugated to monomethyl auristatin E, is a therapeutic designed to target cells expressing TF. We therefore sought to determine the therapeutic potential of TV in IDHwt vs. IDHmut gliomas. TV was more active against cultured IDHwt GBM cells than IDHmut glioma cells (P&amp;lt;0.0001). This activity was increased by 55% with daily washout of the soluble TF secreted by IDHwt GBM cells. TV extended the survival of mice intracranially engrafted with IDHwt GBM by 34% (37.5 days vs. 28 days for IgG control, P=0.006), but not mice with IDHmut glioma (30.5 days, P=0.88). TV also reduced the growth of IDHwt GBM flank xenografts by 58% (P=0.045). Unconjugated tisotumab had no antitumor effect intracranially or in the flank. All 12 flank-engrafted mice treated with tisotumab, and 9/12 mice treated with TV, developed large hematomas in and around the flank xenografts, compared to 0/12 IgG-treated mice (P&amp;lt;0.001). Similarly, a semiquantitative analysis showed that intracerebral hemorrhage was more extensive in tisotumab/TV- treated GBM12 mice than in IgG-treated GBM12 mice (P=0.046). These data indicate that TV targets high TF-expressing IDHwt GBM, but not low TF-expressing IDHmut glioma, that its activity is predominately through the vedotin conjugate rather than inhibition of TF signaling, and that it may have some effect against TF-expressing IDHwt GBM, but intracerebral hemorrhage may be a concern.
CNSC-36. REGULATION OF CELL FATE IN PAEDIATRIC HIGH-GRADE GLIOMA BY THE HOMEOBOX TRANSCRIPTION FACTOR DLX2
Authors: Liam Furst, Enola Roussel, Ryan Leung, Ankita George, Jason Li, Sarah Best, James Whittle, Jason Cain, Ron Firestein, Maree Faux, David Eisenstat
Journal: Neuro-Oncology (2024)

Abstract Paediatric high-grade gliomas (pHGG) are nearly uniformly fatal cancers that arise predominantly in children and adolescents and encompass Diffuse Midline Glioma (DMG) and Diffuse Hemispheric Glioma (DHG). Most patients harbour mutations in histone variants H3.1 or H3.3, resulting in global epigenetic dysregulation and a stalled oligodendroglial progenitor (OPC) or GABAergic interneuron progenitor (IP) fate for DMG and DHG, respectively. DLX2, a homeobox transcription factor, represses OPC fate and promotes IP cell fate and migration during early neurogenesis. Our lab has shown that Dlx2 binds to and regulates the promoters of Gad1/Gad2, as well as early (Olig2, Nkx2.2) and late (Myt1, Plp1) genes required for OPC differentiation in vivo. Co-expression of Dlx2 with these target sequences reduces reporter gene expression in vitro and Dlx1/2 double knockout mice exhibit increased expression of these OPC markers in vivo. Transient overexpression of a Dlx2-GFP construct in murine DMG cells led to significant IP marker increase (Gad1/2), decrease of OPC markers (Olig2, Nkx2.2) and global restoration of H3K27me3. Additionally, decreased proliferation, colony growth, invasion and migration were observed in vitro. To translate these findings in human pHGG, analysis of a bulk RNA-seq database of 62 patient-derived pHGG cell lines revealed an inverse relationship between DLX2 and OLIG2. DLX2 was knocked out of DLX2high/OLIG2low DHG cell lines using CRISPR-Cas9, and overexpressed in DLX2low/OLIG2high DMG cell lines using a DLX2-mCherry overexpression construct. Evaluation of cell fate markers and epigenetic marks will be presented. Changes in migration, invasion, and proliferation in vitro will also be presented, in addition to changes in tumour growth using a neonatal xenograft murine model in vivo. Manipulation of DLX2 in pHGG provides a model for investigating the link between the factors that control cell fate decisions in the developing brain and the aberrant differentiation state in pHGG.
IMMU-23. NEOADJUVANT ANTI-PD-1 AND ANTI-CTLA-4 COMBINATION THERAPY INDUCED INTRATUMORAL IMMUNOLOGIC ALTERATIONS IN RECURRENT GBM PATIENTS
Authors: Lauren Markus, Patrick Wen, Lu Sun, Willy Hugo, Robert Prins
Journal: Neuro-Oncology (2024)

Abstract Glioblastoma (GBM) is a highly aggressive brain tumor that responds poorly to checkpoint blockade inhibitors (ICIs), such as anti-PD-1. We previously reported that neoadjuvant anti-PD-1 therapy activated and recruited T cells into recurrent GBM (rGBM) tumors, but also increased immune checkpoint interactions between T cells and myeloid cells. To overcome this resistance mechanism, we are currently conducting a phase 1B clinical trial of neoadjuvant anti-PD-1 (Nivolumab, BMS) +/- anti-CTLA-4 (Ipilimumab, BMS) combination therapy for rGBM patients (NCT04606316). To evaluate the local tumor microenvironment effects of these checkpoint inhibitors, we used multiplex immunofluorescence (mIF), bulk RNA sequencing, and T cell receptor sequencing to analyze the intratumoral immune profile of tumors. Using mIF, we are able to determine the density of key immune cell phenotypes within the section of tumor sample as well as the proximity between phenotypes to better understand their interactions. Patients who received the combination therapy (n=15) trended to have a higher median density of cytotoxic T cells (CD45+CD8+; median density of 27.13 cells/mm2 for combination therapy and 13.78 cells/mm2 for anti-PD-1), helper T cells (CD45+CD4+; median density of 33.73 cells/mm2 for combination therapy and 9.82 cells/mm2 for anti-PD-1), monocytes (CD14+), and HLA-DR+ macrophages (CD45+CD14+HLA-DR+) while patients treated with anti-PD-1 alone (n=16) trended to have densities similar to placebo treated patients (n=6). Patients treated with combination therapy are also trending to have a higher density of macrophages in close proximity (≤20μm) to T cells, particularly HLA-DR+ macrophages, suggesting a higher frequency of interactions within their tumor microenvironments. This data set is currently incomplete, but the final data set will be completed by the meeting. Nonetheless, these preliminary results, as well as the bulk RNA sequencing and T cell receptor sequencing, suggest distinct immunologic effects of monotherapy vs. combination neoadjuvant anti-PD-1 and anti-CTLA-4 therapy in the tumor microenvironment of rGBM patients.
EXTH-62. FOCAL ADHESION KINASE (FAK) IN CHROMOSOME 8 GAIN-ASSOCIATED MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
Authors: Guangfeng Wang, Dana Borcherding, Gorkem Oztosun, Xiaochun Zhang, Liuzhan Yang, Trisha Gannu, Angela Hirbe
Journal: Neuro-Oncology (2024)

Abstract OBJECTIVES Malignant peripheral nerve sheath tumors (MPNST) are aggressive sarcomas often associated with Neurofibromatosis type 1 (NF1), a genetic syndrome driven by overactivation of the RAS pathway. MEK inhibitors (MEKi) target downstream components of the RAS pathway and have been approved for NF1 patients with plexiform neurofibromas (PN). However, MPNST often develop resistance to MEKi. Our lab recently discovered the critical role of chromosome 8 (Chr8) genes in MPNST. The Chr8 gene, protein tyrosine kinase 2 (PTK2), also known as focal adhesion kinase (FAK) is overexpressed in multiple cancers, suggesting its importance in tumor progression. In this study, we aim to evaluate FAK as a therapeutic target for MPNST and investigate the FAKi and RAF/MEKi combination. METHODS A CRISPR gRNA screen was used to identify Chr8 genes involved in MPNST survival. The effect of FAK shRNA knockdown and a FAK inhibitor (FAKi), alone or combined with a MEKi, in MPNST cells was assessed using IncuCyte proliferation assays and multiple murine models. RESULTS The CRISPR gRNA screen identified 57 genes on Chr8 important for MPNST cell survival, including PTK2/FAK. Knockdown of FAK by shRNA in MPNST inhibited cell proliferation in vitro and reduced tumorigenesis in vivo. Consistently, the FAKi defactinib significantly inhibited the proliferation of MPNST (IC50-values: 1.72-4.65μM). Moreover, the defactinib/avutometinib combination was synergistic in vitro and the combination of FAKi with RAF/MEKi reduced tumor growth more that either drug alone in Chr8-gain MPNST PDX models. Avutometinib induced compensatory activation of FAK, while defactinib/avutometinib combination decreased phosphorylation of FAK, ERK1/2 and STAT3, and augmented cleavage of Caspase-3 and PARP-1, shown using the WES protein simple system. CONCLUSION These results demonstrate the potential therapeutic efficacy of FAK inhibitors, both alone and in combination with RAF/MEKi, for the treatment of MPNST.
PATH-52. DIFFERENCES IN GENE EXPRESSION, GENOME-WIDE METHYLATION AND METABOLITES IN ADULT DIFFUSE GLIOMAS
Authors: Anjali Vinocha, Valerie Berdecia, Daniel Wang, Srividya Arjuna, Mauli Shah, Antonio Dono, Nagireddy Putluri, Yoshua Esquenazi, Leomar Ballester
Journal: Neuro-Oncology (2024)

Abstract Metabolic reprogramming is a hallmark of cancer, including diffuse gliomas. IDH1 and IDH2 are key enzymes linking cellular metabolism to epigenetic regulation and redox states. IDH1/IDH2 enzymes catalyze the conversion of isocitrate to α-ketoglutarate, while the mutant enzymes increase the production of D-2-hydroxyglutarate, an oncometabolite that induces epigenetic changes, leading to gene expression alterations. Understanding how epigenetic alterations affect metabolic gene expression and metabolite levels in diffuse gliomas could help identify diagnostic biomarkers and therapeutic targets. We studied the expression of metabolism-related genes, metabolites, and genome-wide methylation status, which will facilitate an integral understanding of the metabolic changes in IDH-mutant and IDH-wildtype gliomas. Study design included 47 fresh frozen tissue samples. RNA was extracted and used for gene expression analysis using the NanoString platform (nCounter® Metabolic Pathways Panel), while extracted DNA was used for targeted sequencing with a panel interrogating 600 genes and for genome-wide methylation analysis using the Illumina Epic v2. In addition, unbiased metabolomic analysis by mass spectrometry was performed in 25 tissue and CSF samples out of 47 samples. Methylation status, gene expression and metabolite levels were compared between IDH-mutant and IDH-wildtype gliomas. Results showed significant differences in DNA methylation, gene expression and metabolites between IDH-mutant and IDH-wildtype gliomas. UPP1, an enzyme involved in uracil metabolism, was studied in depth to understand the interplay between DNA methylation, gene expression, and metabolic reprogramming in diffuse glioma. Epigenetic analysis revealed that the CpG sites within the UPP1 gene displayed reduced methylation in IDH wild-type compared to IDH-mutant tumors. IDH wild-type tumors showed higher UPP1 expression compared to their IDH-mutant counterparts. Consequently, we observed higher levels of uracil in tissue and CSF samples from patients with IDH wild-type gliomas. These data provide a framework to study the relationship between mutations, methylation, gene expression and metabolism in diffuse gliomas.
TMIC-25. MICROGLIA IN THE GLIOBLASTOMA MICROENVIRONMENT SECRETE ACETYLATED AMINO ACIDS WHICH ASSIST IN THE REPAIR OF RADIATION INDUCED DNA DAMAGE
Authors: Sravya Palavalasa, Jack Freeman, Ava Singer, Aditri Gokul, Emily Baker, Andrew Scott, Kari Wilder-Romans, Sunita Shankar, Visweswaran Ravikumar, Anthony Andren, Harrison Wong, Peter Sajjakulnikit, Sagnik Bhaduri, Weihua Zhou, Costas Lyssiotis, Arvind Rao, Wajd Al-holou, Daniel Wahl
Journal: Neuro-Oncology (2024)

Abstract Rapid repair of DNA damage mediates genotoxic therapy resistance and poor prognosis in glioblastoma (GBM). The GBM tumor microenvironment (TME) is heterogenous, and we hypothesized that non-malignant cells support the repair of DNA damage in glioblastoma cells. Consistent with this hypothesis, we found that GBM tumors grown intracranially in mice had rapid DNA repair and were resistant to radiation compared to tumors of identical genotype grown extracranially in mouse flanks. Further interrogation of irradiated intracranial tumors using gamma-H2AX immunofluorescence revealed spatial heterogeneity in DNA damage repair, with spatially separate regions of rapid and slow gamma-H2AX resolution. Paired spatial transcriptomic analysis and gamma-H2AX immunofluorescence showed that tumor regions with rapid DNA repair were rich in microglia. Having nominated microglia from these results, we cocultured GBM cells and microglia in direct contact as well as in transwell coculture. We found that GBM cells cocultured with microglia repair DNA damage faster in a contact-independent manner. We then assessed the supernatant metabolome of microglia and GBM monocultures and cocultures and found that acetylated amino acids are secreted by microglia and consumed by GBM cells. Supplementation with acetylated amino acids promotes radiation resistance by speeding the repair of radiation-induced DNA damage. Mechanistically, acetylated amino acid supplementation allows glioma cells to re-route glucose utilization away from the TCA cycle and towards nucleotide synthesis. Hence, we show that microglia in the GBM microenvironment assist GBM cells to repair radiation induced DNA damage by secreting acetylated amino acids which are consumed by GBM cells and used to fuel the TCA cycle allowing utilization of glucose for nucleotide synthesis, thereby making the GBM cells resistant to radiation therapy.
QOL-31. RESULTS OF A TELEHEALTH-BASED PSYCHOLOGICAL INTERVENTION FOR CAREGIVERS OF PATIENTS WITH PRIMARY MALIGNANT BRAIN TUMORS: A MODERATION ANALYSIS OF A RANDOMIZED CONTROLLED TRIAL
Authors: Kelcie Willis, Nora Horick, Sumita Strander, Jessica Whitman, Daniel Chiu, Kedie Pintro, Amy Corveleyn, Areej El-Jawahri, Joseph Greer, Jennifer Temel, Jamie Jacobs, Deborah Forst
Journal: Neuro-Oncology (2024)

Abstract BACKGROUND In a recent randomized controlled trial, caregivers of patients with primary malignant brain tumors (PMBT) who received NeuroCARE—a six-session, telehealth-based psychological intervention—demonstrated improved anxiety and depression symptoms, coping, and self-efficacy at 11-weeks compared to usual care (UC) participants. We now explore how sociodemographic variables, disease-specific factors, and baseline mood symptoms moderate intervention effects on anxiety and depression symptoms. METHODS We examined data from 120 enrolled caregivers (Mage=53 years; 83% female, 92% White, 70% spouses/partners) of PMBT patients (84% glioblastoma). Eligible caregivers had elevated anxiety (Generalized Anxiety Disorder-7 ≥ 5). Participants were randomized 1:1 to NeuroCARE or UC and completed baseline sociodemographic questionnaires and the Hospital Anxiety and Depression Scale at baseline and 11-weeks. We used linear regression to evaluate whether selected sociodemographic characteristics (gender, age, relationship to patient), tumor characteristics (tumor location/laterality, IDH mutation status), and baseline mood symptoms moderated intervention effects on anxiety and depression symptoms. We report the group-by-moderator (b) effects, using a 0.20 significance level. RESULTS The beneficial effects of NeuroCARE on reducing 11-week anxiety symptoms were greater in women compared to men (b=-2.63, CI: -6.17, 0.91, p=0.14) and greater in caregivers who reported higher baseline anxiety symptoms (b=-0.43, CI: -0.78, -0.08, p=0.02) and depression symptoms (b=-0.56, CI: -0.96, -0.17, p=0.01). The beneficial effects of NeuroCARE on reducing 11-week depression symptoms were greater in caregivers of patients with IDH-wildtype tumors compared to caregivers of patients with IDH-mutant tumors (b=2.49, CI: -0.26, 5.24, p=0.08). Caregiver age, relationship to patient, and tumor location/laterality did not significantly moderate NeuroCARE effects on mood. CONCLUSIONS The positive effects of NeuroCARE were particularly salient for caregivers with elevated anxiety and/or depression symptoms and those caring for patients with IDH-wildtype tumors. Content may be further tailored to account for the unique needs of men and caregivers of patients with IDH-mutant tumors.