tbuckley/cabot-search huggingface dataset:
CSIG-22. PHARMACOLOGIC INHIBITION AND KNOCKDOWN OF CAMK2 IMPAIR GROWTH OF PATIENT-DERIVED GLIOBLASTOMA CULTURES
Authors: Rebecca Ronnen, Shuai Wang, Sara Haddock, Niklas Ravn-Boess, Danielle Golub, Gabriele Stephan, Jonathan Sabio, Hayley Donaldson, Luke Bonanni, Adler Guerrero Zuniga, Theodoros Karnavas, Dimitris Placantonakis
Journal: Neuro-Oncology (2024)

Abstract INTRODUCTION Glioblastoma (GBM), a primary brain malignancy with a median survival of 15-18 months, presents a pressing challenge in neuro-oncology. Patient-derived GBM cultures (PDGCs) exhibit spontaneous calcium (Ca2+) waves, which are thought to drive tumor growth and represent a therapeutic target. The mechanisms underlying the generation and the effectors of these Ca2+ waves remain elusive. We hypothesize CAMK2, a Ca2+/calmodulin-dependent protein kinase expressed as four distinct isoforms, is a key effector of such Ca2+ waves by phosphorylating substrates that promote tumor growth. METHODS Using multiple PDGCs, CAMK2 isoform-specific mRNA levels were assessed via qRT-PCR both at baseline and after shRNA-mediated knockdown (KD). Tumorsphere formation and WST-8 assays were performed to assess PDGC clonogenic potential after either KD or pharmacologic inhibition with the cell-permeable CAMK2 inhibitor KN93. RESULTS The relative mRNA levels of CAMK2 isoforms across three PDGC lines were, in decreasing order: CAMK2D, CAMK2G, CAMK2B, and CAMK2A. Expression of CAMK2D- and CAMK2B-specific shRNAs significantly reduced tumorsphere growth compared to control shRNA. CAMK2D KD reduced sphere formation by 55.13 ± 3.54% (p=0.0001) and 47.72 ± 9.55% (p=0.008) in separate PDGC lines, while CAMK2B KD reduced sphere formation by 41.15 ± 11.51% (p=0.021) and sphere size by 41.78% ± 10.50% (p=0.049) (n=3/experiment). KN93 treatment reduced tumorsphere formation by 59.23 ± 1.40% (p=0.0006) and 42.94 ± 13.0% (p=0.032) in two PDGC lines (n=3) and PDGC viability, while CAMK2-inactive analogue KN92 and DMSO minimally impacted viability (p&amp;lt;0.0001, two-way ANOVA). CONCLUSION CAMK2D and CAMK2B KD, as well as KN93 treatment, reduce tumorsphere formation, suggesting CAMK2 has a tumorigenic role in GBM. Further investigation of CAMK2 isoforms and in vivo validation are underway. Future aims include directly testing the link between spontaneous Ca2+ waves and CAMK2 activation and identifying CAMK2 phosphorylation targets that mediate tumor growth.
CSIG-21. THE ROLE OF GUT MICROBIOTA IN GLIOBLASTOMA: INSIGHTS FROM MICROBIOME-GENE EXPRESSION INTERACTIONS
Authors: Mahesh Bekal, Isabel Wang, Daniel Wang, Antonio Dono, Srividya Arjuna, Leomar Ballester, Yoshua Esquenazi
Journal: Neuro-Oncology (2024)

Abstract Glioblastoma, the most aggressive form of primary brain tumor, remains a formidable clinical challenge due to its invasiveness and resistance to therapy. Emerging evidence suggests that the gut microbiome plays a crucial role in modulating cancer progression through complex interactions with host physiology. In this study, we investigated the influence of gut microbiota and tumor gene expression by analyzing stool and tissue samples from glioblastoma patients. Utilizing 16S rRNA sequencing of stool samples and NanoString gene expression analysis of tumor tissue samples, we explored the relationship between gut microbiome taxa and gene expression levels in tissue. Pathway analysis using KEGG and Gene Ontology databases was employed to elucidate the functional implications of these interactions. Our findings reveal contrasting effects of specific gut microbiota taxa and gene expression, with Fusobacterium demonstrating a potential oncogenic role, while Bifidobacteriaceae and Akkermansiaceae display potential tumor-suppressive effects. Fusobacterium is associated with the upregulation of key oncogenes and pathways promoting cancer cell survival, growth, and metabolism, whereas Bifidobacteriaceae and Akkermansiaceae are linked to the downregulation of genes involved in pathways promoting cancer cell survival and proliferation, such as MAPK signaling and stress response pathways, potentially inhibiting cancer cell growth. These results highlight the intricate interplay between gut microbiota composition and cancer biology and underscore the potential of gut microbiota modulation as a therapeutic strategy in glioblastoma management.
BIOM-71. EXPANDING THE SPECTRUM OF<i>TERT</i> PROMOTER NON-CANONICAL SEQUENCE VARIANTS IN CNS TUMORS: A CASE SERIES
Authors: David Cook, Jorge Trejo-Lopez, Beth Pitel, Neiladri Saha, Tejaswi Koganti, Jayson Hardcastle, Stephanie Smoley, Matthew Isaacson, Mallika Gandham, Gopinath Sivasankaran, Surendra Dasari, Kar-Ming Fung, Suzanne Powell, Darshan Trivedi, Zied Abdullaev, Kenneth Aldape, Martha Quezado, Drew Pratt, P J Cimino, Mark Edgar, Rachael Vaubel, Aditya Raghunathan, Caterina Giannini, Robert Jenkins, Cristiane Ida
Journal: Neuro-Oncology (2024)

Abstract Most TERT promoter (TERTp) clinically relevant sequence variants in CNS tumors are the canonical C228T and C250T mutations. Non-canonical TERTp mutations have been reported mainly in non-CNS tumors. We describe 12 CNS tumors with non-canonical TERTp variants interpreted as clinically relevant. Using clinical targeted NGS panels (2020-2024), we detected c.-100_-79dup (n=2), c.-92_-91insGGCGGCCCCGCCCCTTCCTTTC (n=1), c.-118_-117insTCCCCGGCCCAGCCCCTTCCGGG (n=1), c.-123_-76dup (n=1), c.-110_-89dup (n=2), and c.-57A&amp;gt;C (n=5). Most cases had chromosomal microarray (n=11) and/or methylation array data analyzed using the NCI/Bethesda v.2 classifier (n=9). All non-canonical TERTp variants occurred at a variant allele frequency suggestive of somatic clonal origin (mean, 34%; range, 18-46), and in adults (mean age, 60 years; range, 36-88). Except for the c.-57A&amp;gt;C variant, all non-canonical TERTp variants occurred in tumors with histological and/or molecular diagnostic features of glioblastoma, IDH-wildtype (GBM), often epigenetically aligning to this tumor type. All five tested cases matched to superfamily glioblastoma (score ≥ 0.9), with three to class GBM_RTK_I (&amp;gt;0.9 in 2, 0.86 in 1) and two to GBM_RTK_II (&amp;gt;0.9). The size and sequence of such variants suggest that these may be functionally equivalent to canonical mutations or generate favorable TERTp activation motif conformations like previously reported activating duplications. The c.-57A&amp;gt;C variant is a well-established oncogenic mutation observed in other cancer types but has not been reported in CNS tumors. We describe five cases with the c.-57A&amp;gt;C variant: one GBM matching to methylation class GBM_MES_TYP (0.99); two oligodendroglioma, IDH-mutant and 1p/19q-codeleted, one of which had methylation data matching to class O_IDH (0.99); one diffuse glioma, IDH-mutant, which was partially 1p/19q-codeleted and matched to class O_IDH (0.99); and one anaplastic meningioma, aligning to superfamily meningioma (0.99)/MNG_MAL (0.79). Our findings show that non-canonical TERTp variants typically occur in tumor types that often harbor TERTp canonical mutations, expanding the spectrum of TERTp clinically relevant variants that are molecular biomarkers in CNS tumors.
CTNI-52. EXPEDITED CHEMORADIATION AFTER LASER INTERSTITIAL THERMAL THERAPY (LITT) IS FEASIBLE AND SAFE IN PATIENTS WITH NEWLY DIAGNOSED GLIOBLASTOMA
Authors: Jennifer Yu, Seth Meade, Ran Zhao, Wei Wei, Himanshu Dashora, Richard Prayson, Matthew Grabowski, Glen Stevens, Erin Murphy, John Suh, Samuel Chao, Gene Barnett, David Peereboom, Manmeet Ahluwalia, Alireza Mohammadi
Journal: Neuro-Oncology (2024)

Abstract BACKGROUND High-grade gliomas (HGG) are incurable primary brain tumors. Laser Interstitial Thermal Therapy (LITT) has emerged as an alternative to surgery for select patients. Hyperthermia can improve the efficacy of radiation and chemotherapy. Shortening the time between LITT and chemoradiation may maximize their biological and clinical benefits. This clinical trial evaluated the safety and feasibility of expediting chemoradiation after biopsy and LITT in patients with newly-diagnosed HGG. METHODS Patients with suspected HGG were enrolled. Those with pathologic confirmation of HGG and deemed appropriate candidates for LITT and chemoradiation were considered evaluable. Participants underwent 6 weeks of adjuvant chemoradiation within seven days of LITT. Endpoints were assessed until the completion of radiation, and included the occurrence of wound dehiscence; new, treatment-refractory seizures; cerebral edema; and completion of planned radiotherapy. RESULTS Fifteen patients with suspected HGG were enrolled and ten were considered evaluable. All ten patients were diagnosed with glioblastoma (GBM, IDHwt). Five patients were deemed unevaluable: four patients with other CNS tumors and one GBM patient who developed grade 4 postoperative edema. Of ten evaluable patients, the median age was 60.2 years (IQR: 51.0, 69.4), and median preoperative KPS was 90 (IQR: 90, 80). The median time between LITT and the initiation of chemoradiation was seven days. There were no occurrences of significant protocol-related adverse events. CONCLUSIONS Accelerated initiation of chemoradiation after biopsy and LITT is safe and feasible for patients with newly diagnosed HGG. A larger study is needed to assess potential synergy of hyperthermia and chemoradiation to improve survival.
CNSC-05. MAPPING LANGUAGE PROCESSING IN SURGICAL GLIOMA PATIENTS
Authors: Matthew Muir, Kyle Noll, Sarah Prinsloo, Jeffrey Traylor, Ho-Ling Liu, Vinodh Kumar, Sujit Prabhu
Journal: Neuro-Oncology (2024)

Abstract Previous work from our group has shown that the resection of white matter tracts localized by transcranial magnetic stimulation (TMS) predicts postoperative neurological deficits. Here we use advanced preoperative brain mapping along with formal language evaluations to localize the neuroanatomical underpinnings of language processing in surgical glioma patients. In patients who had TMS tracts resected, the resected portions (“tract-cavity segmentations”) were classified according to the functional outcome (“true positives”-corresponding deficit; “false positives”-no deficit) and normalized to MNI space. For patients who sustained long-term deficits, TMS tracts were segmented according to spatial overlap with normative tracts to create ROIs. Each normalized resection cavity (n=79) was analyzed for overlap with each ROI associated with postoperative deficits (n=8). The percentage of patients who had positive ROI resections that included TMS tracts versus patients who had positive ROI resections irrespective of TMS tracts were analyzed according to the percent who sustained deficits in each group. ROIs from all patients were summed to create a probabilistic atlas of functional white matter. “True positive” tract-cavity segmentations localized into dual anterior/posterior “hubs” and demonstrated significantly higher spatial association with normative tracts across three different measures (p&amp;lt;.05). 92% of patients who underwent ROI resections that included TMS tracts sustained long-term deficits while 34% of patients who underwent ROI resections irrespective of individualized mapping sustained deficits (p&amp;lt;.05). The probabilistic atlas of functional white matter demonstrated significantly higher voxel intensities within the white matter deep to the temporoparietal junction defined by the same posterior “hub” ROI from Figure 1 (p&amp;lt;.001). This study demonstrates that essential language processing localizes to ROIs within normative white matter tracts that require individualized mapping for surgical preservation. The white matter deep to the temporoparietal junction serves as a crucial hub for language-processing circuitry in glioma patients.
EPCO-60. EXPRESSION OF EARLY PROGENITOR MARKERS WITHIN NF2-ASSOCIATED SPINAL EPENDYMOMA
Authors: Noah Burket, Jia Wang, Hongyu Gao, Robert Bell, Chi Zhang, Yunlong Liu, Wade Clapp, Jignesh Tailor
Journal: Neuro-Oncology (2024)

Abstract Spinal ependymomas (SP-EPNs) are intramedullary spinal tumors commonly found in patients with NF2-related schwannomatosis. Recent work using bulkRNA sequencing has suggested that SP-EPNs express a molecular signature most similar to ependymal cells. However, this type of sequencing may miss rare stem cell populations within tumors. The aim of this study was to assess the spatial heterogeneity within NF2-associated SP-EPNs and explore whether a stem cell population exists within SP-EPNs. Spatial transcriptomics (ST) was performed on a SP-EPN sample previously resected from a patient with NF2-related schwannomatosis using the 10X Genomics Visium Cytassist Platform. Libraries were sequenced on the Illumina NovaSeq 6000. 28-bp reads including spatial barcode and UMI sequences and 50-bp probe reads were generated with Illumina NovaSeq 6000 at the Center for Medical Genomics at Indiana University School of Medicine. Space Ranger 2.1 was used to process the raw files after sequencing. Data analysis was performed with R package Seurat 4.9.9.9041 following preprocessing with spaceranger. Sctransform normalized the spatial transcriptome dataset. Clusters were identified using “FindClusters” and “FindNeighbors” functions. There was diffuse expression of astrocyte and ependymal cell markers throughout the SP-EPN sample with smaller areas expressing radial glia and stem cell markers, as well as overlap between these regions. Expression of vascular and connective tissue markers varied throughout the tumor. There was minimal to no expression of neural genes in the sample. ST on our SP-EPN sample revealed a tumor with marked cellular and molecular heterogeneity. Although the primarily expressed ependymal cell and astrocyte markers, there does appear to be small, stem cell-like populations. This suggests that NF2-associated SP-EPNs may have a developmental hierarchy with radial glia-like cells and more mature progenitors within the ependymal cell lineage. This proof-of-concept study offers important findings that provide justification for further investigation using single-cell sequencing.
RADT-45. INTEGRATION OF FUNCTIONAL MAGNETIC RESONANCE IMAGING INTO STEREOTACTIC RADIOSURGERY PLANNING TO REDUCE SYMPTOMATIC RADIATION NECROSIS
Authors: Chengcheng Gui, Mehrnaz Jenabi, Jillian Daly, Claire Gillick, Teresha Bradley, Emily Sze, Ruth Maldonado, Akhil Tiwari, Joseph Stember, Nikhil Mankuzhy, Yoshiya Yamada, Luke Pike, Luca Pasquini, Kyung Peck, Åse Ballangrud-Popovic, Andrei Holodny, Brandon Imber
Journal: Neuro-Oncology (2024)

Abstract BACKGROUND Radiation necrosis (RN) is a common complication of stereotactic radiosurgery (SRS). Functional magnetic resonance imaging (fMRI) localizes eloquent cortical areas for neurosurgical planning but is seldom applied to SRS. We explored the relationship between symptomatic RN and functional neuroanatomy on fMRI. We evaluated the potential benefit of reducing radiation dose to functional areas. METHODS From 2011 to 2022, patients with an fMRI within 3 months of SRS for resected or unresected brain metastases (BM) were included. The BM nearest to the primary motor, language, or visual cortices was designated as the index BM. The functional area on fMRI nearest to the index BM was designated as the fOAR. Focally symptomatic RN (FSRN) was defined as radiographic RN alongside new or worsening focal neurologic symptoms consistent with the fOAR. Patients treated with 5-fraction SRS and modern planning techniques after 2013 were included in the dosimetric analysis. Associations between fOAR dose and FSRN were evaluated with logistic regression. SRS replanning was performed to determine if fOAR dose could be reduced without sacrificing target coverage. RESULTS Among 94 patients, 82% received SRS postoperatively, and 71% received 5-fraction SRS. fOARs included the primary motor (77%), language (19%), and visual (2%) cortices. Of 20 patients with radiographic RN, 20% were neurologically asymptomatic, 20% had anatomically unrelated neurologic symptoms, and 60% had FSRN. The dosimetric analysis included 39 patients. The fOAR volume receiving a single-fraction equivalent dose ≥14 Gy (V14Gy) was associated with FSRN at 18 months post-SRS (OR=6.8/mL, p=0.05). Replanning reduced fOAR V14Gy in all cases. The mean reduction was 28%. CONCLUSION Neurologic symptoms of SRS-induced RN reflect nearby functional neuroanatomy on fMRI. Dose reduction to functional areas while maintaining target coverage is consistently achievable and may mitigate symptomatic RN. Integrated fMRI-based SRS planning may protect neurologic function when treating tumors near eloquent areas.
RTID-02. PERSONALIZED PEPTIDE VACCINATION AMONG 173 PATIENTS WITH GLIOBLASTOMA
Authors: Pauline Latzer, Henning Zelba, Florian Battke, Annekathrin Reinhardt, Borong Shao, Saskia Biskup
Journal: Neuro-Oncology (2024)

Abstract Current treatment outcome of patients with glioblastoma (GBM) remains poor. Following standard therapy, recurrence is universal with limited survival. GBM tumors from 173 patients were analyzed for somatic mutations to generate a personalized peptide vaccine targeting tumor-specific neoepitopes. In agreement with their treating physician, patients added a personalized peptide vaccine to their treatment as an individual healing attempt. Patients were monitored from October 2015 until August 2023. We retrospectively evaluated their clinical courses and the results of their immune monitoring data. Among all patients, including 70 treated prior to progression (primary) and 103 treated after progression (recurrent), the median overall survival from first diagnosis was 31.9 months (95% CI: 25.0-36.5). Adverse events were infrequent and were predominantly grade 1 or 2. An immune response to at least one of the vaccinated peptides was detected in blood samples of 87 of 97 (90%) monitored patients. T-cell responses to vaccinated neoepitope peptides were durable in most patients. Significantly prolonged survival was observed for patients with multiple vaccine-induced immune responses (53 months) compared to those with no/low induced responses (27 months; P=0.03). Altogether, our results highlight that the application of personalized neoantigen-targeting peptide vaccine is feasible and represents a promising potential treatment option for GBM patients. This is the largest real-world observation involving GBM patients safely treated with a personalized peptide vaccine to date. This real-world observation will be translated into a clinical trial to evaluate the specific contribution of the neoantigen vaccine.
BIOM-69. THE ONCOGENIC FLIP IN PATIENTS WITH LEPTOMENINGEAL METASTATIC DISEASE (LMD): LONGITUDINAL DETECTION IN CEREBROSPINAL FLUID TUMOR CELLS (CSF-TCS) REVEALS IMPLICATIONS FOR DIFFERENTIAL TREATMENT OF THE LMD TUMOR
Authors: Arushi Tripathy, Perry Corkos, Barbara Blouw, Melissa Moore, Norman LaFrance, Marc Hedrick, Michael Youssef, David Piccioni, Seema Nagpal, Priya Kumthekar
Journal: Neuro-Oncology (2024)

Abstract INTRODUCTION Patients with LMD have poor prognosis and limited treatment options. Oncogene amplification of primary, metastatic, and CNS metastatic tumors can be heterogeneous. Therefore, patients with LMD may benefit from assessment of clinically relevant biomarkers in CSF, which may guide the choice of a targeted therapy specifically for the LMD tumor. CNSide is a CLIA-validated laboratory-developed test ordered commercially at the discretion of physicians for CSF-TC enumeration, immunocytochemical (ICC) and fluorescence in situ hybridization (FISH) analysis of oncogene amplification. We longitudinally analyze oncogenes in CSF-TCs in patients with LMD of various primary cancers. METHODS CSF was collected from patients with suspected or confirmed LMD; 613 tests were ordered on 218 individual patients with breast (N=105 patients), lung (N=65), gastrointestinal (N=10), and other cancers. Using CNSide, CSF-TCs were isolated and tested via ICC (ER, PD-L1, and PR), and FISH (ALK, cMET, cMyc, EGFR, FGFR1, HER2, NTRK1, NTRK3, PTEN, RET, and ROS1). RESULTS In patients with lung cancer, ALK was detected in 14% (17/118) of samples, CMET in 61% (78/128), HER2 in 73% (16/22), and RET in 4% (4/90). In patients with breast cancer, HER2 was detected in 39% (65/168) of samples, FGFR1 in 32% (19/60), ER in 26% (44/168) and PR in 4% (5/120). 66 patients underwent 2+ CSF draws; 24 underwent 5+. Among these, there were 13 ICC flips (7 acquired mutations) and 58 FISH probe detection flips (26 acquired mutations). 20/66 patients (30.3%) had at least one flip in their ordered biomarkers. CONCLUSION CNSide can be used to detect oncogene amplification on CSF-TCs of patients with LMD, and mutational status of the LMD tumor may differ from the original tumor biopsy. CSF-TC analysis may provide therapeutic insights that vary from the original tumor and could open the door to additional treatment targets for patients struck with LMD.
CTNI-56. PHASE I STUDY OF VORINOSTAT AND TEMSIROLIMUS IN NEWLY DIAGNOSED OR PROGRESSIVE DIFFUSE INTRINSIC PONTINE GLIOMA
Authors: Lea M Stitzlein, Muhammad Usman Baig, Joya Chandra, Anita Mahajan, Susan L McGovern, Arnold Paulino, Clark R Andersen, Jonathan Gill, Leena M Von Hertell, Soumen Khatua, Wafik Zaky
Journal: Neuro-Oncology (2024)

Abstract BACKGROUND Diffuse intrinsic pontine glioma (DIPG) carries a poor prognosis with a median survival of less than 12 months. Histone mutation, K27M, and AKT pathway dysregulation play key roles in tumorigenesis. There is no curative treatment with radiation therapy, which currently remains the standard treatment. METHODS This is a phase I study of vorinostat and temsirolimus in newly diagnosed (stratum 1) and progressive (stratum 2) DIPG. The primary aims are to determine the safety, maximum tolerated dose, and toxicities (NCT02420613). Stratum 1 received radiation concurrently with vorinostat, followed by vorinostat and temsirolimus for up to 10 cycles. Stratum 2 received vorinostat and temsirolimus for up to 12 cycles. In stratum 1, vorinostat was administered daily at 230 mg/m2. The maintenance phase (both strata) included concurrent vorinostat 230 mg/m2 daily and temsirolimus 25 or 35 mg/m2 (Days 1 and 8). RESULTS Six patients were enrolled, three in each stratum. Three of the six patients had confirmed H3 K27M mutations. No dose-limiting toxicity was observed, and most adverse effects were limited to grades 1 or 2, including fatigue, nausea, vomiting, myelosuppression, hyperlipidemia, hyperglycemia, elevated liver enzymes, and creatinine. However, one patient experienced grade 3 leukopenia. Two of the three patients in stratum 1 showed evidence of radiographic response after the chemoradiation phase, of whom one patient had progression-free survival of 12 months and completed the 10 maintenance cycles. All patients at stratum 2 had disease progression with no radiographic response. CONCLUSION Overall, the combination of temsirolimus and vorinostat is well tolerated and safe, prompting the need for larger studies to investigate its efficacy. Due to the small number of patients, the study’s findings are limited, and trends in efficacy should be interpreted with caution.