tbuckley/cabot-search huggingface dataset:
TMIC-81. AN IMMUNOSUPPRESSIVE MACROPHAGE NICHE MAY DRIVE T CELL DYSFUNCTION AND IMMUNOTHERAPY RESISTANCE IN MELANOMA BRAIN METASTASES
Authors: Lu Sun, Lizhong Ding, Eileen Shiuan, Alexander Lee, Won Kim, Dimitri Trembath, Stergios Moschos, Willy Hugo, Robert Prins
Journal: Neuro-Oncology (2024)

Abstract Nearly half of metastatic melanoma patients develop brain metastases (MBM). Local therapies like surgery and radiotherapy provide limited survival benefit. While targeted therapies and immune checkpoint inhibitors (ICI) improved outcomes in patients with asymptomatic MBM, the prognosis is still grim for the majority of patients. To decipher resistance mechanism to immunotherapy in MBM, we integrated datasets from both single-cell RNAseq (scRNAseq) and spatial transcriptomics (Visium). Our scRNAseq analysis of 25 MBM patients (7 treated pre-surgery with ICI) showed that lymphoid cells increased by 8.1-fold post-ICI (p=0.006). Notably, 34% of these were CXCL13+CXCR6+ putative tumor-reactive T cells (TR-T), known for their critical role as tumor-killing effectors. This led us to investigate why, despite their prevalence, TR-T don’t translate to effective immunotherapy in MBM. Our scRNAseq interactome analysis revealed that ICI intensified IFN-II interactions between TR-T and interferon-stimulated macrophage/microglia (Mφ.ISG). However, it also boosted immunosuppressive interactions, like the TIGIT-NECTIN2 interaction, which increased 20 fold, potentially diminishing TR-T’s effectiveness. To overcome the lack of spatial context in scRNAseq, we applied spatial transcriptomics on 27 MBM sections, including 12 post-ICI treatments. Remarkably, TR-T were primarily found (63%) in proximity with Mφ.ISG cells—not with tumor cells. These TR-T-Mφ.ISG niches were 1.7 times more prevalent in ICI-treated samples; these niches are rich in chemokine receptors like CCR1 and immunosuppressive molecules like NECTIN2. This suggests that Mφ.ISG cells are chemotactically attracted to TR-T, forming a barrier that impedes TR-T’s tumor interaction and impairs their functionality. Our current efforts focus on pinpointing key pathways enriched within TR-T-Mφ.ISG niches, particularly in ICI-treated MBM. We are also assessing the clinical impact of these niches in relation to patient survival. Our goal is to elucidate how specific immunosuppressive subsets and molecules within the MBM microenvironment restrict TR-T effectiveness, with the ultimate objective of enhancing ICI efficacy for these patients.
ANGI-11. SEX DIFFERENCES IN SOX2 GLIOBLASTOMA EXPRESSION OUTSIDE MRI-DEFINED CONTRAST ENHANCEMENT AT AUTOPSY
Authors: Samuel Bobholz, Allison Lowman, Daniel Aaronsen, Aleksandra Winiarz, Savannah Duenweg, 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) has recently been used as a marker for pluripotency to identify cellular glioblastoma invasion pathologically. This can be used to identify areas of tumor invasion consisting of sparse individual cells, likely highlighting the furthest margin of tumor invasion. This study aligned large format SOX2 stained tissue samples to conventional MRI to determine demographic factors that impact the presence of SOX2 positive invasion outside the T1 contrast-enhanced tumor margin. METHODS The cohort for this study consisted of 36 IDH-wildtype glioblastoma patients (23 male, 13 female, mean age=61.9). Tissue samples from areas of suspected tumor invasion and normal tissue were collected at autopsy, stained for SOX2, digitized at 40X resolution, and automatically segmented for SOX2 positive staining cell percent (SOX2+%) at MR resolution using a color deconvolution algorithm. Contrast enhanced T1 scans from acquisitions close to death were annotated manually for tumor presence and aligned to the T2-weighted FLAIR image. Tissue data was then aligned to MR images using a custom in-house software that relies on manually defined control points to generate a nonlinear transform that warps tissue into MR space while correcting for tissue shrinkage. Mean SOX2+% was computed for each patient outside of contrast enhancement and compared across age and sex as demographic factors. RESULTS Males were found to have a higher SOX2+% than females outside contrast enhancement (t=2.09, p=0.045), while no association with age was observed (r=0.146, p=0.397). CONCLUSIONS Sex differences were observed for non-enhancing SOX2 positivity, which may relate to the more aggressive tumors identified in male patients in some studies. Further research into the mechanisms behind sex differences in tumor growth patterns and molecular characteristics impacting the infiltration of tumor beyond the MR defined region is needed.
TMIC-75. ICAM-1 PROMOTES AN IMMUNOSUPPRESSIVE LANDSCAPE IN GLIOBLASTOMAS BY REGULATING THE PHENOTYPIC POLARIZATION STATE OF TUMOR ASSOCIATED MACROPHAGES
Authors: Shreya Gandhi, Kaviya Devaraja, Sheila Mansouri, Gelareh Zadeh
Journal: Neuro-Oncology (2024)

Abstract Glioblastoma (GBM) is a fatal adult CNS tumor, with a median overall survival of 12-15 months. Intercellular adhesion molecule 1 (ICAM-1) is a cell adhesion molecule whose expression is significantly greater in the mesenchymal transcriptional subtype of GBMs, whereby it is prognostic. We have previously shown that when ICAM-1 is knocked out in the tumor microenvironment (TME) of immune-competent GBM-bearing mice, these mice showed prolonged overall survival and reduced tumor volume. It is yet to be determined how ICAM-1 expression affects infiltration and functional polarization of tumor-associated macrophages (TAMs) and other immune cells in GBM, and if we can suppress the infiltration of M2-like TAMs into the TME by inhibiting ICAM-1. We used a mouse glioma model with and without knockout (KO) of the ICAM-1 gene and intracranially injected GL261 cells. ICAM-1 KO mice survived longer and had reduced tumor volume relative to wildtype, with survival and volume differences being rescued upon ICAM-1 bone marrow reconstitution. Upon endpoint, we performed cytometry by time-of-flight, and found that ICAM-1 KO tumors harbored a reduction in helper T cells, Tregs, and cytotoxic T cells, but an increased proportion in double-negative T cells relative to ICAM-1 WT tumors. ICAM-1 KO tumors also demonstrated an increased proportion of M1-like TAMs relative to M2-like. These results were validated upon administration of ISIS-3082 to tumor models, an antisense oligonucleotide for which a human-specific form has been fast-track approved for other diseases, that targets ICAM-1 transiently in peripheral immune cells prior to TME infiltration. These findings suggest that ICAM-1 expression influences immune cell infiltration, potentially modulates the functional state of TAMs towards a M1-like state, and that ICAM-1 may be targeted in TAMs to ‘reeducate’ them before entering the TME. This may be translated into clinical practice and combined with standards-of-care to render GBMs more sensitive to treatment.
EPCO-54. MULTIOMIC ANALYSIS OF SPINAL EPENDYMOMAS REVEALS MECHANISMS OF TUMOR AGGRESSIVENESS WITH MYCN AMPLIFICATION
Authors: Ihika Rampalli, Maxwell Laws, Dustin Mullaney, Debjani Mandal, Bayu Sisay, Abdel Elkahloun, Marta Peñas-Prado, Terri Armstrong, Mark Gilbert, Prashant Chittiboina
Journal: Neuro-Oncology (2024)

Abstract Grade-3 spinal ependymomas, particularly those harboring MYCN amplification, have dismal prognoses despite optimal treatment regimens. MYCN functions as a transcription factor (TF) to drive the expression of key tumor driver genes. Our aim is to identify mechanisms underlying tumor aggressiveness and treatment resistance in MYCN-amplified ependymomas. MYCN amplification in spinal ependymomas was identified with custom next generation sequencing panels and bulk methylation analysis. We then conducted paired single-nucleus RNA (snRNA-seq) and chromatin accessibility (snATAC-seq) sequencing of grade-2 (n=2, 1 patient) and grade-3 spinal ependymomas (n=6, 6 patients, 4 MYCN-amplified). Comparator snRNA-seq datasets (grade-2/grade-3; 8/2) were included from a publicly available dataset (GSE163686; all non-MYCN-amplified). Canonical cell classes were identified with a combination of cluster- and cell-based strategies. Downstream analysis was conducted using R 4.3 (Seurat, Signac, clusterProfiler, CellChat), and Python 3.11 (scanpy) packages. We identified ependymoma tumor cells distinct from canonical immune cell classes with gene expression analysis and confirmed a distinct copy-number-variation pattern in these cells with chromosome 1 and 2p gain, and chromosome 6p and 22q loss. MYCN-amplified tumor cells (compared to non-MYCN-amplified grade2/3 tumor cells) showed increased differential accessibility at genes including VEGFA. Increased MYCN TF activity was confirmed with gene overexpression of downstream targets including NOTCH3, CREB5, PLK1, and VEGFA. Other genes that were highly accessible and overexpressed in MYCN-amplified tumor cells were related to oxidative stress, differentiation, and anti-apoptotic pathways. MYCN-amplified tumor cells modified the tumor microenvironment with increased VISTA signaling between MYCN-amplified tumor cells and tumor-associated macrophages, creating an immunosuppressive environment. We confirmed these effects by observing a higher proportion of M2-like macrophages in MYCN-amplified tumors (29.6% vs 18.2%). In conclusion, MYCN amplification in spinal ependymomas upregulates tumor cell proliferation, angiogenesis, and M2-like macrophage recruitment/programming.
DDDR-12. INHIBITION OF NOTCH PATHWAY VIA A NOVEL MONOCLONAL ANTIBODY PROLONGS SURVIVAL IN HIGH GRADE GLIOMA MODELS
Authors: Umberto Tosi, Greta Ghita, Nayanendu Saha, Zaki Abou Mrad, Alexandra Giantini-Larsen, Dimitar Nikolov, Yanhong Yang, Viviane Tabar
Journal: Neuro-Oncology (2024)

Abstract High grade gliomas (HGGs) have poor prognosis partially owing to a glioma-stem cell (GSC) population that escapes most therapeutic modalities. Inhibition of NOTCH signaling, necessary for GSC maintenance, has shown promise, however clinically limited by systemic (on-target, off-tumor) side effects. Thus, we develop a novel monoclonal antibody, 1H5, inhibitory against a disintegrin and metalloproteinase 10 (ADAM10), a protein responsible for NOTCH signaling initiation in tumor tissue, to treat HGGs. Patient-derived, glioma cell lines were treated with 1H5 to determine therapeutic IC50 and characterize downstream, NOTCH-related effectors. A patient-derived explant system, which best replicates the tumor microenvironment in vitro, was generated and treated. An orthotopic xenograft model (PDX) of HGG was created and treated with convection enhanced delivery (CED) of 1H5 to assess tumor volume and survival. We determined that ADAM10 is found in a majority of IDH-wildtype HGGs, but not on IDH-mutant HGGs or low-grade gliomas. 1H5 has nanomolar IC50 against a large library of HGG patient-derived cell lines, achieving cell death via NOTCH-signaling inhibition. In explants, treatment with 1H5 significant delays explant progression (p = 0.01), expansion (4.1-fold decrease, p = 0.007), and reduces the fraction of ADAM10+ cells (from 63.3% to 2.6%, p = 0.004), of replicating cells (from 10.0% to 0.9%, p = 0.006), and of GSCs (SOX2+ cells; from 65.8% to 12.8%, p = 0.06). In vivo, CED of 1H5 both slows down tumor growth compared to vehicle-treated controls (2.2-fold decrease in tumor volume, p = 0.03), and significantly prolongs survival (p = 0.01), without the development of significant side effects, through a reduction of replicating cells (p = 0.01) and SOX2+ GSCs (p &amp;lt; 0.0001), in a dose-dependent fashion. In conclusion, 1H5 is efficacious against HGG preclinical models both in vitro and in vivo by targeting NOTCH signaling. This posits 1H5 as a new promising therapeutic worthy of expeditious clinical translation.
QLTI-09. CLINICAL TRIALS IN NEURO-ONCOLOGY: DESIGN, LOGISTICS, CHALLENGES, AND PRACTICAL CONSIDERATIONS
Authors: Vikas Pawar, Vijaylaxmi Roy, Vijay Sreegiriraju, Pallavi Goel, Subhashini Sadasivam, Yashoda Ghanekar, Surya Madiraju, Amit Ray
Journal: Neuro-Oncology (2024)

Abstract Timely, secure and reliable transportation, precise handling and storage of biological specimens are critical for the success of clinical research. Research in neuro-oncology often involves complex assays such as next-generation sequencing where the integrityof brain tumor specimens is paramount. These challenges are pronounced in most Lower Middle-Income Countries (LMIC), due to climatic factors and infrastructure limitations, necessitating stringent measures to preserve sample quality and their genetic data integrity for downstream analysis. In this study, we conducted extensive cohort analysis on 80 tissues randomly picked samples of the 3600 samples collected across India to assess the impact of collection protocols, transportation logistics, and long-term storage on the genetic material of tissues. The quality and quantity of the isolated nucleic acids was determined by BioAnalyzer and Qubit parameters. Tissue samples were collected and stored at -80°C in RNAstable® within 4-12 hrs of collection. The DNA and RNA obtained from tissue samples stored for over one year was found to be of good quality with corresponding DNA Integrity Number (DIN) and RNA Integrity Number (RIN)between 7-9. Also, optimum quantity of DNA and RNA was obtained for whole exome and transcriptome sequencing. Upon sequencing, these samples showed good read coverage of 100X or more. These findings provide critical insights into the measures necessary for optimizing sample preservation and transportation to ensure accurate research outcomes. The results indicate that appropriate sample collection, transportation, and long-term storage of bio-specimens can be used effectively for future research. Additionally, the outcome underscores the potential for long-term studies in neuro-oncology using archived biological samples without compromising data integrity.
TMET-04. METABOLOMICS ANALYSIS IN FUNCTIONING AND SILENT CORTICOTROPH ADENOMAS USING A TWO-DIMENSIONAL NANOMATERIAL HIGH-THROUGHPUT PLATFORM
Authors: Xiaopeng Guo, Weiqiang Liang, Chunxia Ma, Yuanli Zhao, Bing Xing
Journal: Neuro-Oncology (2024)

Abstract Functioning pituitary corticotroph adenomas (CAs) originated from T-PIT lineage with an ACTH-positive staining cause Cushing’s Disease. However, silent CAs (SCAs) baring the same histological features present clinically non-functioning with more aggressive courses. Metabolites within the tumor microenvironment play critical roles in regulating tumor behaviors and responses to therapy. Understanding their distribution and concentration provides valuable insights for diagnosis and treatment. This study investigated metabolite patterns in functioning and silent CAs. We developed a novel two-dimensional nanomaterial platform for enhanced surface-assisted laser desorption/ionization mass spectrometry. Utilizing this platform, we analyzed the metabolomes of three functioning CAs and three SCAs. Our platform exhibited exceptional sensitivity and stability in detecting metabolite molecules. Analysis of the metabolomes revealed distinct spatial distributions and peak intensity of various metabolites, including carbohydrates, amino acids, organic acids, nucleotides, and their precursors. Notably, certain metabolites such as tryptophol, clopidogrel carboxylic acid, DG(20:4(8Z,11Z,14Z,17Z)-2OH(5S,6R)/0:0/i-16:0), S-(-)-ureidoglycolate, and PC(20:4(5Z,7E,11Z,14Z)-OH(9)/14:1(9Z)) were significantly enriched in functioning CAs compared to SCAs, while others, including Cer(d18:1/16:0), Dihydrocytochalasin B, and LysoPC(O-18:0/0:0), exhibited higher peak intensity in SCAs. Overall, our findings underscored the existence of unique metabolomic signatures distinguishing functioning CAs and SCAs. Heterogeneous metabolite distributions among functioning CAs and SCAs were revealed by our novel nanomaterial high-throughput platform, and unique metabolic signatures were identified. Metabolomics analysis holds promise for precise biomedical diagnostics and individualized therapeutic strategies in functioning and silent CAs.
TMET-11. IMPACT OF METABOLIC RISK FACTORS ON SURVIVAL IN GLIOBLASTOMA IDH-WILD TYPE
Authors: John Paul Aboubechara, Orwa Aboud
Journal: Neuro-Oncology (2024)

Abstract Altered cellular metabolism is a hallmark of cancer. Systemic metabolic dysregulation has been associated with the pathogenesis of cancer, including glioblastoma. In particular, the metabolic syndrome has been found to increase the risk of developing various systemic cancers, but it is not known how often the metabolic syndrome occurs in patients with glioblastoma or how it affects their clinical outcomes. This study retrospectively investigates the prevalence and impact of metabolic syndrome, and its component risk factors, on survival in patients with glioblastoma IDH-wild type. Interim analysis includes results from 73 patients with anticipation of over 100 patients who received treatment at UC Davis between 2018-2024. Metabolic syndrome prevalence prior to diagnosis was 41% (30/73), higher than the prevalence of 33% in the general population. Patients with metabolic syndrome showed a trend towards reduced overall survival. A significant dose-response association was found between the number of metabolic risk factors and overall survival (p=0.03). Hyperglycemia demonstrated worsened survival (p=0.04), aligning with prior studies. Obesity, hypertension, and dyslipidemia were not significantly associated with survival. These findings highlight the therapeutic potential for targeting systemic metabolic dysregulation, and hyperglycemia in particular, in patients with glioblastoma.
DDDR-23. DECODING GLIOBLASTOMA DRUG RESISTANCE DYNAMICS USING NOVEL MICROFLUIDIC EX VIVO MODELS
Authors: Sirjana Pun, Daniel Pomeranz Krummel, Soma Sengupta, Riccardo Barrile
Journal: Neuro-Oncology (2024)

Abstract Glioblastoma (GBM) is clinically challenging due to its aggressive nature and limited treatment options. Current standard of care involves surgical resection and chemoradiation with temozolomide (TMZ). GBM, however, often returns post-treatment fueled by its complex biology and the presence of resilient GBM stem cells. Compounding the issue is the blood-brain barrier, which poses a formidable obstacle to drug delivery into the brain. Understanding the molecular dynamics post-therapy within the brain, influenced by the tissue microenvironment, is key for developing more effective therapeutic strategies. Unfortunately, existing research models have fallen short in capturing the complexity of GBM and its response to treatment. While animal models have been a mainstay in GBM research, their ability to predict human responses has been called into question, highlighted by the disappointing results seen in clinical trials. We are therefore advancing bioprinting-based approaches for modeling various components of the tumor microenvironment to gain insight into mechanisms of drug resistance. We report on the development of three novel microfluidic platforms to investigate and interrogate GBM biology. First, we have developed a novel microfluidic model of GBM, termed GlioFlow-3D, produced through a combination of 3D printing methods. GlioFlow-3D mimics specific aspects of the perivascular niche, including protection from circulating TMZ. Second, we have adapted GlioFlow-3D as part of a platform to investigate advanced ultrasound techniques for delivering novel therapeutics into the human brain. Third, we are developing a novel approach aimed at exploring the relationship between the brain extracellular matrix and tumoral cells using bioprinting of living tumor organoids obtained from patients with a history of recurrence. By integrating bioprinting technologies with patient-derived models to create novel ex vivo platforms, we aim to obtain new insights into the intricate dynamics of drug resistance in GBM, ultimately paving the way for more effective therapeutic strategies. Funding: The Brain Tumor Center Research Award (UCGNI) The ARC Project - CCHMC and UC joint Research Award
NIMG-38. DIAGNOSIS AND TREATMENT OF BRAIN TUMORS USING METHIONINE PET
Authors: Yoshiki Shiba, Sachi Maeda, Junya Yamaguchi, Shoichi Deguchi, Fumiharu Ohka, Ryuta Saito
Journal: Neuro-Oncology (2024)

Abstract INTRODUCTION The usefulness of methionine PET examination in diagnosing brain tumors is widely recognized, and it is a frequently used examination method for distinguishing primary tumors from non-neoplastic lesions and recurrent lesions from radiation necrosis. In addition, during surgery, it has the property of being taken up by actively dividing tumor cells, which is useful for identifying the extent of resection. Method: Methionine PET examination was performed in 228 consecutive cases in our department from January 2021 to April 2023, and medical records and genetic analysis data were retrospectively analyzed. RESULTS Of the 228 cases, 146 cases provided useful data for clinical practice, such as the diagnosis of tumors and the differentiation of recurrent tumors from necrosis. On the other hand, there were 9 cases in which the pathological diagnosis of the resected specimen was “tumor” despite the lack of significant methionine accumulation. The details were astrocytoma, cavernous hemangioma, spinal ependymoma, etc. On the other hand, 26 cases were finally diagnosed as “non-neoplastic disease”. Of these, 13 cases had methionine accumulation. The details of the cases that were finally diagnosed as “non-neoplastic disease” were multiple sclerosis, cerebral infarction, dural arteriovenous fistula, inflammatory disease, etc. There were 12 cases in which a diagnosis of “neoplastic disease” was not revealed after methionine PET examination, and the patient was continuously observed. None of these 12 cases had an acute or malignant course. CONCLUSION Although methionine PET is considered useful for diagnosing neoplastic disease, there are cases in which there is no uptake, especially in astrocytoma, and a certain number of cases in which uptake was observed even in non-neoplastic diseases, so caution is required. In addition, in terms of treatment, it is possible to aim to improve surgical accuracy by integrating methionine PET images with intraoperative MRI and intraoperative molecular analysis techniques, and we report an example of this.
DDDR-18. TARGETTING GLIOBLASTOMA MULTIFORME USING A MULTIACTION ANTICANCER ANTI-INFLAMMATORY THERAPEUTIC STRATEGY
Authors: Shadma Fatima, kasuni Gamage, mila Sajinovic, David Herman, kieran scott, paul desouza
Journal: Neuro-Oncology (2024)

Abstract Glioblastoma multiforme (GBM) represents a significant challenge in adult brain tumor management, characterized by its aggressive nature and poor prognosis despite multimodal therapies. Current standard chemotherapy, Temozolomide (TMZ), offers limited survival benefits. In a recent breakthrough, the cyclic peptide cyclo-((2-Nal)-Leu-Ser-(2-Nal)-Arg) acetate (c2), initially developed for prostate cancer, demonstrates remarkable promise against GBM. By selectively inhibiting the inflammatory phospholipase enzyme sPLA2IIA, c2 significantly impedes GBM cell proliferation, surpassing TMZ efficacy in multiple resistant cell lines. Moreover, c2 exhibits potential to inhibit tumor growth and metastasis, confirmed in 3D tumoroid and wound healing assays. Mechanistic insights reveal modulation of crucial cellular pathways, including viral entry, cytoskeletal structure, and signaling cascades. Preclinical investigations demonstrate c2’s ability to penetrate the blood-brain barrier and attenuate tumor progression markers. At multiple levels, c2 is shown to target inhibition of ERBB2 and EGFR signalling and also have impacts on HIF1-NF-kB axis. This study proposes c2 as a potent anti-GBM candidate, warranting evaluations for its pharmacological profile, safety, and efficacy. With its potential to address the urgent need for effective GBM therapies, c2 holds promise as a significant advancement in GBM treatment, offering hope for improved patient outcomes.