tbuckley/cabot-search huggingface dataset:
PATH-08. MOLECULAR DIVERGENCE RATES DIFFER BETWEEN BRAIN METASTASES AND EXTRACRANIAL DISEASE SITES ACROSS PRIMARY TUMOR HISTOLOGIES
Authors: Ramin Morshed, Harmon Khela, Minh Nguyen, Jacob Young, Ezequiel Goldschmidt, Michael McDermott, Noor Malik, Ian Parney, Edward Chang, Mitchel Berger, Philip Theodosopoulos, Shawn Hervey-Jumper, Laura Huppert, Manish Aghi, Harish Vasudevan
Journal: Neuro-Oncology (2024)

Abstract Genomic alterations and molecular subgroups between extracranial disease sites and brain metastases often differ, yet the prevalence and clinical significance of divergent evolution in brain metastases is not fully understood. This study examined genomic alterations and molecular subgroup divergence rates between matched brain metastases and extracranial disease sites. A retrospective, two-center study was conducted on patients who underwent resection of brain metastases between 2014-2022 with clinical and matched genomic data and/or molecular markers available. The overall cohort comprised 256 patients with matched tumors from multiple cancer types, most commonly from breast (n=108, 42.2%), melanoma (n=83, 32.4%), and NSCLC (n=43, 16.8%). Targeted next-generation sequencing of over 500 oncogenes was performed on resected tumors as part of clinical care (n=41 patients with matched specimens). Molecular subgroups for breast, melanoma, and non-small cell lung cancer were also assessed by immunohistochemistry to evaluate rates of molecular subgroup discordance between sites. Subgroup discordance by immunohistochemistry was observed most frequently across breast cancer (22.2%, n=24/108) with loss of the estrogen receptor (ER) and progesterone receptor (PR) and gain of HER2 most frequently observed within brain metastases. Molecular subgroup discordance was rare within melanoma (7.3%, n=6/82) and NSCLC (14.0%, n=6/43) patients. When evaluating oncogenomic alterations from targeted DNA sequencing in 41 patients with matched specimens, 80.5% (33/41) of brain metastases demonstrated a unique oncogene alteration profile compared to an extracranial disease site. Fourteen patients (34.1%) had a gain of at least 1 targetable alteration within a brain metastasis that was not observed in an extracranial disease site. Brain metastases demonstrated high rates of genomic divergence compared to primary and extracranial metastatic disease sites. This data supports obtaining brain metastasis tissue and conducting molecular profiling of this tissue to help select optimal CNS penetrant systemic therapies for each patient.
TMIC-12. LITT RESULTS IN ROBUST T CELL INFILTRATION WITHIN THE TUMOR MICROENVIRONMENT IN A BRAIN METASTASIS MURINE MODEL
Authors: Anjali Chauhan, Nagheme Thomas, Matthew Frain, Oriana Cristina Otero, Ravi Kumar, Macaulay Y Tomdio, Olivia R Packham, Frank J Bova, Loic Deleyrolle, Gregory Pal Takacs, Jeffrey K Harrison, Maryam Rahman
Journal: Neuro-Oncology (2024)

Abstract INTRODUCTION Laser interstitial thermal therapy (LITT) is a novel minimally invasive neurosurgical technique used to ablate intra-axial brain tumors with real-time thermometry. The impact of LITT on the brain metastatic tumor microenvironment (TME) is unknown in patients due to limitations of tumor tissue collection post-LITT. The primary objective of this study was to describe the kinetics of immunologic infiltration within the TME in a melanoma brain metastasis model. METHOD: C57BL6 mice underwent intra-cranial implantation of B16F10-OVA tumor cells and treated with LITT using a custom-made murine LITT system developed in our laboratory. The tumors were treated to 42°C (near infra-red 1064 nm DPSS laser system) 7 days post-surgery. Tumors were collected 2 days and 10 days post-LITT for immune-phenotyping using flow cytometry. Blood was collected 6 h and 48 h post-LITT to perform the ELISA for IFN-g and TNF-a. RESULTS LITT treatment triggered a cascade of local infiltration of immune cells at different time points. 2-days post-LITT resulted in increased CD8 T cells (p&amp;lt;0.05), macrophage (p&amp;lt;0.05) and microglia infiltration (p&amp;lt;0.01) within the TME compared to control and sham surgery animals. By 10 days after LITT, significant infiltration by CD8 T cells (p&amp;lt;0.0001) and M1 macrophages (p&amp;lt;0.0001) was observed. The CD8 T cells were T central memory (TCM) and T effector memory (TEM). Moreover, comparison between 2 days and 10 days after LITT revealed significant increase of TEM (p&amp;lt;0.0001) and TCM (p&amp;lt;0.001) 10 days post-LITT. In an ELISA assay, non-significant differences were observed in IFN-g and TNF-a level at 48 h. CONCLUSIONS LITT enhances the recruitment of cytotoxic CD8 T cells within TME in a time-dependent manner. The ability of LITT to recruit TCM and TEM to the TME strongly support its potential therapeutic benefit, especially in the context of immunotherapy.
CTNI-23. DIFFERENT GUT MICROBIOTA COMPOSITION IS ASSOCIATED WITH CHEMOTHERAPY EFFICACY IN PATIENTS WITH DIFFERENT TYPES OF CENTRAL NERVOUS SYSTEM CANCER
Authors: Chengcheng Guo, Shijia Zhai, Zhongping Chen, Lin Yin, Yilin Zheng, Guoxin Huang
Journal: Neuro-Oncology (2024)

Abstract BACKGROUND The relationship between central nervous system cancers and the gut microbiota (GM) is not well understood. The purpose of this study is to retrospective analyze the differences between the composition of the gut microbiota in patients with different neurologic tumors and their correlation with chemotherapy efficacy. METHODS A total of 44 patients participated in the study and were divided into four groups: gliocytoma (GA), medulloblastoma (MB), germ cell tumors (GT), and diffuse large B-cell lymphoma (DB) based on their pathological diagnosis. Fecal samples were collected from patients for 16S amplicon sequencing to analyze GM composition. Moreover, all the patients were classified into completed response (CR), stable disease (SD), and progressive disease (PD) groups based on the clinical outcomes of chemotherapy. PLS-DA analysis and heatmap analysis were used to reveal the correlation between GM composition and outcomes of chemotherapy. RESULTS Phyla taxa comparison showed the detailed GM composition among these four groups. The phylum of Bacteroidetes was higher in GA group when compared to the other groups. And the phylum of Fusobacteria could only be found in GA and MB groups while the phylum of Verrucomicrobia showed a significant accumulation in DB group. the genera of Ruminococcus, Gemmiger, and Parasutterella were accumulated in the patients with the completed response of chemotherapy. Besides, patients in SD group had higher abundance of the genera of Prevotella, Tyzzerella, and Odoribacter. While patients in PD group showed the higher abundance of Streptcoccus, Fusobacterium, Lachnospira, and Holemanella. CONCLUSION We firstly drew the GM composition profile of the patients with GA, MB, GT, and DB to show the different GM composition of the diseases. Moreover, the gut microbiota composition correlates with chemotherapy outcomes in central nervous system cancer patients so may serve as a potential biomarker for predicting chemotherapy efficacy.
TMIC-21. PYK2/MAPK/ERK SIGNALING PATHWAY REGULATES EXTRACELLULAR VESICLE RELEASE IN GLIOBLASTOMA
Authors: Neisha Ramires Serrano, Emir Perez Perez, Yuriy Kucheryavykh, Lilia Kucheryavykh
Journal: Neuro-Oncology (2024)

Abstract Glioblastoma (GBM), the deadliest brain cancer, typically proves fatal within a year despite treatment. Tumor-associated myeloid cells (TAMs) support GBM growth, treatment resistance, and immune surveillance. Extracellular vesicles (EVs) facilitate communication between tumor and TAMs, exchanging proteins, lipids, RNA, and genetic material. As EVs can travel through the bloodstream to distant tissues, they trigger signaling pathways and metabolic changes in remote organs while also recruiting bone marrow-derived cells and modulating immune responses. Therefore, EVs serve as a crucial mechanism for the distant regulation of the tumor’s immune microenvironment. We hypothesize that Pyk2/MAPK/Erk signaling regulates EV release by modulating the actin cytoskeleton, impacting TAM infiltration and activation in tumors. This study aims to investigate the role of Pyk2/MAPK/Erk in specific EV release in GBM cells, potentially offering insights into therapeutic targets. Using confocal imaging and flow cytometric analysis of EVs, purified from medium conditioned from human primary GBM cell lines with and without Pyk2 CRISPR/Cas9 knock-out (Pyk2KO), the study identified that Pyk2KO cells do not release the population of EVs with diameter bigger then 600nm and up-regulate release of smaller EVs. Additionally, flow cytometric analysis of EVs, released from cells, fluorescently labeled with membrane dye carboxyfluorescein diacetate succinimidyl ester (CFDA-SE), detected 14% of CFSE+ events in EV’s population, purified from Pyk2WT, vs. to 2.5% from Pyk2KO cells. Membrane labeling of cells enables the tracking of microvesicles (MV) shedding and was used to differentiate between MV and ES based on the process of their biogenesis. Considering that larger size and the transition of fluorescence from the plasma membrane are indicative of MVs, our data indicate that Pyk2 is involved in the regulation of MV release. FUNDING: PRSTRT2022 and NIH Grant 1R15CA287203
IMMU-03. EXPLORING CANCER-SPECIFIC T CELLS AND ANTIGENS IN GLIOBLASTOMA BASED ON SINGLE-CELL SEQUENCING OF CD8+ TILS
Authors: Takanari Okamoto, Ryo Mizuta, Ayako Demachi-Okamura, Daisuke Muraoka, Eiichi Sasaki, Katsuhiro Masago, Kazuhide Onoguchi, Yoshiko Yamashita, Osamu Muto, Rui Yamaguchi, Yoshinobu Takahashi, Naoya Hashimoto, Hirokazu Matsushita
Journal: Neuro-Oncology (2024)

Abstract BACKGROUND The effectiveness of cancer immunotherapy against glioblastoma (GBM) remains limited. This study aims to identify cancer-specific antigens to develop antigen-based cancer immunotherapies for GBM. We investigated candidate tumor antigen-specific T cells in GBM by single-cell RNA sequencing (scRNA-seq) and single-cell TCR sequencing (scTCR-seq), and we explored candidate antigens through genetic analysis of tumor tissues. METHODS Flow cytometry analysis was conducted on fresh tumor digest samples to evaluate tumor-infiltrating lymphocytes (TILs) of GBM. Single-cell RNA and TCR sequencing were performed on CD8+ T cells in TILs. Both data generated by Cell Ranger software were loaded into Seurat at R studio. The dimensional reduction for clustering was performed with uniform manifold approximation and projection (UMAP). Additionally, we performed bulk RNA sequencing (RNA-seq) and whole exome sequencing (WES) on tumor tissues. RESULTS Two out of 20 patients (10%) exhibited abundant TILs in GBM. From these two patients, approximately 20,000 CD8+ T cells in total were analyzed in single-cell analysis. Clustering based on UMAP revealed a predominance of clusters expressing exhaustion markers, with high TCR clonality centered on exhausted T cell (TEX) clusters, like our previous date of lung cancer TILs recognizing tumor antigens. Moreover, within the TEX clusters, the expression of CXCL13, often reported as an antigen-specific marker in recent years, was significantly higher in our data compared to two publicly available datasets. Subsequently, based on RNA-seq and WES, 61 candidate neoantigens were estimated using machine-learning prediction algorithms from NEC Corporation. Furthermore, 5 overexpressed cancer/testis antigens, and 3 bacterial species-derived microbial peptides using Kraken2 were selected as antigen candidates. CONCLUSIONS We identified prospective tumor antigen-specific T cell subsets with high CXCL13 expression from two GBM patients. We plan to identify cancer-specific T cells and antigens from these candidates by T cell activation assay.
RADT-26. RADIATION FRACTIONATION IN THE MANAGEMENT OF ELDERLY PATIENTS WITH GLIOBLASTOMA BY AGE
Authors: Rimsha Afzal, Michelle Kim, Daniel Wahl, Theodore Lawrence, Jamie Takayesu
Journal: Neuro-Oncology (2024)

Abstract Multiple studies have investigated hypofractionated radiation (HFX) for elderly patients with glioblastoma (GBM), using varying age cut-offs. This leads to uncertainty about who benefits most from a hypofractionated course. This study examines the use of and outcomes with HFX, between two commonly used cut offs to define elderly GBM: 65 versus 70 years old. In this retrospective review, 309 patients diagnosed with GBM who were treated with radiation at a single academic institution were included. The Kaplan-Meier method was used to analyze overall survival. A Chi-square test was conducted to compare the use of SFX and HFX and the median survival between those 65-69 versus 70-74 years old. Patients aged 70-74 were more likely to receive HFX radiation compared to those aged 65-69 (80.00% vs. 42.65%, p=0.0002). Median survival for the entire cohort was 12 months. Among those 65-69 years old, SFX was associated with a significantly higher median survival compared to HFX (14 months vs. 7 months, HR 2.00, 95% CI 1.16 – 3.46, p=0.03). This was also true for those 70-74 years old, (18 months vs. 4 months, HR 4.50, 95% CI 1.84 – 11.01, p=0.03). We demonstrate a decrease in the use of SFX in patients 65 years or older, and that that standard fractionation is associated with longer survival in older patients with GBM. This suggests that in a well selected population, SFX should be considered even among elderly patients. Additional work is needed to determine whether these findings are causal or due to patient selection. Performance status and MGMT methylations status, for instance, should guide clinical decision making. Such results highlight the importance of further studies to fine tune radiation dose and fractionation elderly patients with GBM.
DDDR-42. LEVERAGING GENOME-WIDE CRISPR/CAS9 KNOCKOUT DRUG SCREENS TO IDENTIFY SENSITIZERS FOR PROTEOSOME INHIBITORS IN GLIOBLASTOMA
Authors: Alisha Anand, Muhammad Vaseem Shaikh, Chirayu Chokshi, Benjamin Brakel, Will Maich, Shan Grewal, Chitra Venugopal, Sheila Singh
Journal: Neuro-Oncology (2024)

Abstract Glioblastoma (GBM) is the most common primary brain tumor with a poor prognosis despite aggressive treatment. Patient outcomes remain abysmal with 95% of patients relapsing and a median overall survival of 15 months. This necessitates the rapid search for personalized therapeutics and agents to enhance current treatments. One pathway that demonstrates dysregulated functioning is the ubiquitin-proteasome pathway (UPP). Literature has shown that UPP dependent proteolysis remains constitutively upregulated in cancer cells leading to the rapid degradation of proteins that regulate oncogenic pathways. Despite robust preclinical evaluations for the usage of proteasome inhibitors against GBM, most proteasome inhibitors failed in clinical trials, indicating resistance. We conducted an unbiased genome wide CRISPR-Cas9 screen in HAP1 cells treated with the proteasome inhibitor, Bortezomib (BTZ), to identify genes leading to a BTZ-resistant phenotype. We identified several genes that when perturbed, sensitized cells to BTZ including N-glycanase-1 (NGLY-1), Nuclear factor Erythroid 2-Like-1 (NFE2L1), and DNA damage inducible 1 homolog 2 (DDI2). Herein, we sought to evaluate the effects of perturbing these identified genes in our patient derived GBM cell lines by utilizing CRISPR/Cas9 knockout technology in vitro and in vivo. The generation of NGLY-1, DDI2, and NFE2L1 KO cell lines demonstrated functional sensitivity to the proteasome inhibitor Marizomib (MZB) as observed through a significant reduction of the IC50 in the KO cell lines compared to an adeno-associated virus integration site 1 (AAVS1) control. Functional evaluation also demonstrated reduced proliferation capacity and sphere formation in our KO GBM lines. Ongoing in vivo work will aim to evaluate the mitigation of this resistant pathway in our NSG mouse models orthotopically transplanted with our patient derived KO cell lines. In an ongoing collaborative effort, we aim to functionally assess a novel small molecule NGLY-1 inhibitor for preclinical sensitivity to MZB in our in vitro and in vivo models.
NCOG-26. THERAPEUTIC POTENTIAL OF FECAL MICROBIOME TRANSPLANT TO IMPROVE COGNITIVE DYSFUNCTION INDUCED BY CRANIAL IRRADIATION IN MICE
Authors: Mahesh Bekal, Tushar Das, Maria P Blasco-Conesa, Gayathri Jagadeesan, Leomar Ballester, Bhanu Priya Ganesh, Yoshua Esquenazi
Journal: Neuro-Oncology (2024)

Abstract Radiation therapy (RT) is a crucial treatment for brain tumors, but radiation-induced cognitive dysfunction (RICD) affects 50-90% of patients, significantly impacting their quality of life. Evidence suggests that gut microbiome dysfunction may contribute to progressive cognitive dysfunction (CD). Prior studies in aging and stroke models show that fecal microbiome transplants (FMT) from healthy hosts can promote recovery and improve cognition. To investigate the link between RICD and the gut microbiome, we subjected mice to Sham/9Gy/15Gy cranial irradiation, followed by cognitive tests using the Y-maze and Novel Object Recognition Test (NORT) at various time points. Both 9Gy and 15Gy irradiation resulted in significant cognitive dysfunction, as indicated by altered performance in both tests at 7 and 30 days post-irradiation. Fecal samples were collected before irradiation and at 10 and 30 days post-RT. Microbial DNA was extracted, and the 16S rRNA gene was sequenced and analyzed using the bioinformatics visualization toolkit, ATIMA. Significant gut dysbiosis was observed in both 9Gy and 15Gy irradiated mice compared to pre-irradiation samples, with the 15Gy group showing more pronounced and consistent changes in fecal microbiome diversity, particularly at 30 days post-RT. We hypothesized that FMT from healthy hosts (non-radiated mice) could prevent or ameliorate RICD by modulating microbial, metabolomic, and immunologic profiles. To test this, a separate cohort of mice received 15Gy cranial irradiation and FMT via oral gavage. After a 20-day post-irradiation period, cognitive and gut permeability tests were conducted. The FMT group exhibited significantly improved gut permeability and cognitive performance compared to controls. Our findings suggest that gut dysbiosis plays a crucial role in RICD and that FMT may be a potential strategy to mitigate RICD and improve the quality of life in brain tumor patients undergoing cranial RT.
NCMP-06. GENOTYPE AND SEX IMPACT MEMORY FUNCTION AFTER BRAIN IRRADIATION
Authors: Aboyeji Oyewole, Joyce Yang, Megan Lee, Yoshi Sei, Jeffrey Sims, Padmini Bisoyi, Ken Nakamura, Jean Nakamura
Journal: Neuro-Oncology (2024)

Abstract PURPOSE/OBJECTIVE Cognitive changes are a serious complication that can occur after brain radiotherapy. There is a need to better understand which individuals are more susceptible to develop strategies to preserve their function. The apolipoprotein E type 4 allele (APOEe4) APOE4 is the most prevalent genetic risk factor for Alzheimer Disease. We hypothesized that APOE genotype influences memory function after a subtherapeutic dose of whole brain irradiation in male and female mice. MATERIALS/METHODS Age-matched adult female and male mice engineered with either human APOE3 or APOE4 gene knocked-in were randomized to no treatment or whole brain irradiation (0 Gy or 5 Gy x 2), then evaluated with longitudinal neurobehavioral tests of learning, memory, pain threshold and anxiety. We performed immunohistochemical analyses of mouse brain sections at 1 month and at 4 months post-radiation to quantify extracellular amyloid beta plaques and other neuropathologic hallmarks associated with neurodegeneration. RESULTS Neurobehavioral testing identified significant sex and genotype-dependent changes in memory and anxiety measures developing longitudinally after brain irradiation. At baseline (unirradiated), APOE4 mice (male and female) performed worse on multiple memory measures. However after irradiation, sex and genotype each independently impacted multiple neurobehavioral function tests and also interacted with each other to significantly influence the timing and magnitude of changes in memory function. ApoE4 significantly impacted the toxicity of radiation in a sex-dependent manner. Neuropathologic analyses including amyloid beta plaque deposition and ApoE levels are ongoing. CONCLUSIONS After brain irradiation of relatively moderate dose, neurobehavioral performance including memory are impacted in a genotype and sex-dependent manner and dynamically over time. In addition to suggesting important sex-dependent differences in memory vulnerability, these data point to new opportunities for personalizing care for patients receiving brain irradiation.
CTNI-74. SONODYNAMIC THERAPY (SDT) USING INTRAVENOUS 5-AMINOLEVULINIC ACID WITH NON-ABLATIVE FOCUSED ULTRASOUND FOR THE TREATMENT OF DIFFUSE INTRINSIC PONTINE GLIOMAS IN PEDIATRICS: INITIAL SAFETY AND OUTCOMES THE MULTICENTER SDT-201 TRIAL
Authors: Lindsay Kilburn, Robert Keating, Nirali Patel, Adriana Fonseca, Dan Donoho, Chima Oluigbo, John Myseros, Kazim Narsinh, Sabine Mueller, Winson Ho, Ziad Khatib, Toba Niazi, Ryan Clanton, Lenora Henry, Wyatt Potter, Stuart Marcus, Ely Benaim, Roger Packer, Hasan Syed
Journal: Neuro-Oncology (2024)

Abstract Diffuse intrinsic pontine glioma (DIPG) is the leading cause of mortality amongst pediatric neuro-oncologic diseases. Sonodynamic therapy with non-ablative MR-guided focused ultrasound (MRgFUS) is being investigated in multiple clinical trials. We describe safety outcomes and initial efficacy of SDT with 5-ALA for the treatment of pediatric patients with DIPG. Twelve patients with DIPG were treated from August 2022-April 2024 as part of a dose-escalation protocol with SDT in a multicenter Phase 1/2 clinical trial (NCT05123534). MRgFUS was combined with the prodrug SONALA-001 (5-ALA iv) to activate its metabolite, protoporphyrin IX, and thereby induce apoptosis within tumor cells. Treatment is delivered every 4 weeks for up to 12 treatments. Patient ages ranged from 3-23 years and 60% were male. Twelve patients underwent a total of 45 SDT treatments (range 2-9). When enrolled, median tumor volume was 1,337 cm3 (range, 310-2078 cm3) and duration since diagnosis was 5 months. SONALA-001 doses tested were 5 mg/kg and 10 mg/kg. Delivered ultrasonic acoustic energy ranged from 190-444 joules/cm3. After 6 months of median follow-up (range 2-18), 2 partial responses occurred, and 9 of 12 patients had stable or improved baseline symptoms (Lansky Status), including improved mobility and diplopia. One adverse clinical event included a small non-operative epidural hematoma secondary to a stereotactic frame pin. There have been no grade 3 or worse treatment-related adverse events or dose-limiting toxicities. Ten patients are alive a median of 11 months after diagnosis; 2 have deceased; 4 have discontinued treatment. Maximum percent tumor volume changes throughout treatment ranged from a -68% reduction to over 100% enlargement. Preliminary analysis of twelve pediatric patients treated with SDT for DIPG demonstrates acceptable safety outcomes and promising clinical results. Additional patient enrollment and longer follow-up times are required to determine efficacy.