tbuckley/cabot-search huggingface dataset:
DDEL-10. MICROBUBBLE-ENHANCED FOCUSED ULTRASOUND REGULATES THE ENRICHMENT OF INFLAMMATORY PATHWAYS IN THE BLOOD-BRAIN BARRIER AND IMPROVES CAR T CELL ACCUMULATION IN GLIOMAS
Authors: Costas Arvanitis, Yutong Guo, Hohyun Lee, Chulyong Kim, Christian Park, Akane Yamamichi, Pavlina Chuntova, Marco Gallus, Miguel O Bernabeu, Hanjoong Jo, Hideho Okada, Chulyong Kim
Journal: Neuro-Oncology (2024)

Abstract A major challenge to brain cancer immunotherapy is posed by the rate-limiting obstacles to the systemic delivery of cytotoxic T cells, such as chimeric antigen receptor (CAR) T cells, in brain tumors posed by the blood brain barrier (BBB). Although the BBB can be bypassed by direct infusion of CAR-T cells in brain tumors, these approaches offer only short-term benefits, since they cannot affect distant tumor cell infiltrations, as evidenced by tumor relapse. Circulating microbubbles (MB) upon ultrasound (US) exposure (sonication) can exert mechanical stress in brain vessels to trigger a range of responses, including local increase in the BBB permeability and activation of inflammatory signaling and phenotypes. We hypothesize that ultrasound frequency tuned at MB resonance inside brain capillaries can transiently modulate the BBB signaling and function to improve CAR-T cell trafficking in glioma tumors. RNAseq and immunostaining of protein expression reveal that at frequencies just above microbubble resonance inside vessels (1.5MHz for 2µm MB), where maximum vessel wall shear stress is observed, there is a marked enrichment of inflammatory markers in the endothelial cells of brain vessels, including P-selectin and ICAM-1. Consistent with these findings, we observed that under high frequency excitation (1.5MHz), there is a 5-fold increase in the accumulation of EGFRvIII CAR-T cells in orthotopic EGFRvIII murine glioma tumors as compared not sonicated controls. We also found that over 85% of the tumor-infiltrating CAR-T cells express PSGL-1 and LFA-1 receptors, which interact with P-selectin and ICAM-1 to facilitate T cell extravasation. Together, these findings demonstrate that tuning the US frequency can improve CAR-T cell trafficking, potentially through upregulation of cell adhesion molecules in the glioma tumor microenvironment, and further support the functional relevance and potential clinical significance of the observed immuno-mechano-biological changes.
RADT-35. PATTERNS OF INTRACRANIAL RESPONSE AND RELAPSE AFTER CNS-DIRECTED RADIOTHERAPY (CNS-RT) FOR PATIENTS WITH CHEMOREFRACTORY OR PROGRESSIVE SECONDARY CNS LYMPHOMA (SCNSL)
Authors: Gustav Cederquist, Kathryn Tringale, Carla Hajj, Zachary Moore, Harper Hubbeling, Alexandra Dreyfuss, Beatrice Fregonese, Lorenzo Falchi, Michael Scordo, Christian Grommes, Joachim Yahalom, Brandon Imber
Journal: Neuro-Oncology (2024)

Abstract PURPOSE/OBJECTIVE Progressive SCNSL after failure of CNS-directed systemic therapy is a challenging clinical scenario. CNS-RT can effectively salvage, but its optimal role is poorly defined. METHODS We analyzed diffuse large B-cell patients who received brain RT for progressive SCNSL following 1+ line of therapy for active SCNSL (not prophylaxis). Overall survival (OS) was calculated by Kaplan-Meier and RT response was evaluated using IPCG or RANO criteria for parenchymal or leptomeningeal disease, respectively. Risk of intracranial failure assumed death as a competing risk. Pre-RT SCNSL patterns were classified as parenchymal-only versus diffuse (periventricular or leptomeningeal). Local failure was progression only of pre-RT lesion(s). RESULTS We identified 55 patients with median follow up of 3.5m. 85% had neurologic symptoms, 45% had extracranial disease. Patients received a median of 2 prior SCNSL-directed therapies (IQR 1-3); 91% received methotrexate-based regimens with median 21d between last methotrexate and RT. Median CNS-RT dose was 30 Gy in 10 fractions delivered to whole brain (n=44, 80%), partial brain (n=9, 16%), or craniospinal axis (n=2, 4%). Median OS was 3.5m. Overall response for 38 evaluable was 79% (24% complete), with median of 60d to best response. 58% were successfully bridged with CNS-RT to subsequent therapies and 12m intracranial failure risk was 37% for those bridged, and 64% for those not bridged (p=0.05). 19 had parenchymal-only disease (10 unifocal, 9 multifocal) with median largest lesion diameter 4.1cm (range 1.7–7.4). 19 had diffuse pattern (12 periventricular, 7 leptomeningeal). 7 with parenchymal-only disease failed intracranially, 5 of which were local. 8 with diffuse disease failed intracranially, only 1 of which was local (p = 0.035). CONCLUSION SCNSL patients referred for RT had symptomatic, treatment-refractory disease. While CNS-RT response rates were high, duration was often limited, suggesting RT is best used for bridging/palliation. Patients with parenchymal-only disease were enriched for local failure, suggesting potential suitability of involved site CNS-RT, though further validation is needed.
CNSC-58. BIOPROCESSING OF VIABLE SURGICAL PEDIATRIC BRAIN TUMOR SPECIMENS FOR GENOME-GUIDED PERSONALIZED DRUG TESTING
Authors: Emon Nasajpour, Caitlynn Tran, Cesar Garcia, Lulu Xing, Geoff Lyle, Maria Isabel Barros Guinle, Bryce Bagley, Kelly Mahaney, Hannes Vogel, Katrina Learned, Olena Vaske, Gerald Grant, Laura Prolo, Cormac Maher, Claudia Petritsch
Journal: Neuro-Oncology (2024)

Abstract Novel treatment approaches are urgently needed for pediatric central nervous system (CNS) tumors as they are the leading cause of cancer-related deaths in children. A lack of research materials impedes progress towards developing such therapies. Although various brain cancer biobanks exist, these rarely store viable patient-derived tissue and cells for live cell analyses, including cell fate assays and testing for drug sensitivities. We propose that a biorepository of viable cell dissociates and tissue broadly representing CNS tumor entities overcomes these limitations. From a combination of molecular diagnoses and histopathologic assessment of over 120 samples collected, we generated a biorepository of roughly 35 distinct entities of pediatric CNS tumors in our Stanford neuro-bioprocessing cohort. Based on the Central Brain Tumor Registry of the United States, the proportion of subtypes represented in our cohort match that of the general population with exceptions. We established a standardized bioprocessing pipeline that can be used as a template for tissue collection and model development in the broader disease context and for multiple downstream applications. Our emphasis on cryostorage of viable cells and tissue facilitates ad hoc live cell analyses. In addition to gaining a better understanding of tumor pathophysiology, we attempted a rapid bed-to-bench-to-bedside approach using comparative RNA expression profile analyses in an individual patient’s pilocytic astrocytoma. Novel drug targets were identified by analyzing RNA transcripts that are highly expressed (outliers) compared with a compendium of 12,747 brain and non-brain tumor samples. We validated outliers as drug targets using acute cell isolates, and identified a novel target in recurrent low-grade glioma. These studies illustrate that biobanking of viable patient-derived material enables developing personalized therapies with the goal of improving patient outcomes. As demonstrated here, patient-derived acute cell isolates facilitate identifying drug vulnerability, creating an opportunity for more personalized treatment of patients with CNS tumors.
CNSC-02. ANTICANCER ABILITY OF THE BERBERINE TO PROMOTE THE APOPTOSIS EFFECT AND ATTENUATE THE ROS GENERATION CAPACITY ON DBTRG BRAIN CANCER CELLS
Authors: Chiung-Chyi Shen, Meng-Yin Yang, Yi-Chin Yang, Huey-Shan Hung
Journal: Neuro-Oncology (2024)

Abstract Abstract In this research, berberine (BB), and its effect on the biological performance of DBTRG brain cancer cells and normal endothelial cells (EC) was investigated. Firstly, the DBTRG cancer cell and EC cell were cultured with different concentrations of BB (0.5, 1, 5 and 10 μg/ml), and it was confirmed that BB significantly reduced the proliferation of DBTRG cancer cells. However, there is no significant toxic effect on EC cells. The results of cell cycle analysis confirmed that BB significantly induced DBTRG cancer cell undergo apoptotic effect in a dose dependent manner. The assessment of cell migration behavior showed that BB significantly inhibited cell migration in DBTRG cancer cell, but not in BAEC as well as attenuated the matrix metalloproteinase 2/9 (MMP2/9) in a dose dependent manner. Furthermore, the reactive oxygen species (ROS) generation capacity among DBTRG cancer cell, EC cell and macrophages (Raw 264.7). It was demonstrated that BB was prominently decreased the ROS generation of DBTRG instead of EC or Raw264.7 cell. Moreover, the pro-inflammatory cytokines of TNF-α, IL-1β and IL-6 were significantly inhibited by BB in a dose dependent manner of DBTRG brain cancer cell. As mentioned above, it was demonstrated that bioactive BB molecules is potential for anti-brain cancer drugs may via anti-immune response and anti-oxidative generation capacity for brain cancer therapy. BB biomolecules may target for DBTRG cell which cannot cause inevitable toxic damage to the normal EC cell. Altogether, the promising findings of BB biomolecule on DBTRG cancer cell suggest that BB may be a good candidate of anticancer drug or adjuvant for the treatment of human brain cancer. Key words: berberine, DBTRG brain cancer, anti-immune response, anti-oxidative generation
EPCO-31. THE GERMLINE POLYMORPHISM RS55705857 IS ASSOCIATED WITH A POOR SURVIVAL IN ASTROCYTOMA, IDH-MUTANT, GRADE 2
Authors: Kristen L Drucker, Thomas M Kollmeyer, Paul A Decker, Matthew L Kosel, Lateef A Odukoya, Gobinda Sarkar, Chandralekha Halder, Silvana B De Lorenzo, Terry C Burns, Caterina Giannini, Cristiane M Ida, Daniel H Lachance, Jeanette E Eckel-Passow, Robert B Jenkins
Journal: Neuro-Oncology (2024)

Abstract Histologic features, presence of CDKN2A/B homozygous deletion and methylation subtype are strong determinants of outcome and of therapy in IDH-mutant gliomas. We were interested in learning if there are additional markers of outcome in these tumors. To address this question, we assembled a cohort of 963 IDH-mutant gliomas with overall survival data (median follow-up alive 2.7 years, median follow-up deceased 3.9 years). Array-based copy number data, targeted NGS, germline genotyping data and Illumina EPIC array methylation data were available on 872, 226, 542, and 401 patients, respectively. Morphologic type (oligodendroglioma versus astrocytoma, grade (2/3 vs 4) and methylation subtype (A_IDH_LG vs A_IDH_HG) were all significantly associated with survival (p &amp;lt;0.001). There was no significant difference in survival between grade 2 vs 3 IDH-mutant astrocytomas (p=0.53 adjusting for age and sex). However, subjects with the risk allele (G) for rs55705857 had a better overall survival than subjects with the non-risk allele (A) in IDH-mutant oligodendroglioma (AG/GG vs AA, median overall survival 21.6 vs 15.7 years, p=0.048 after adjusting for grade, age, and sex). Conversely, rs55705857 was associated with a markedly worse survival in grade 2 IDH-mutant astrocytomas (AG/GG vs AA, median overall survival 8.6 vs 19.6 years, p=0.007 after adjusting for age and sex). Despite similar sample sizes and number of deaths, there was no significant difference in overall survival by rs55705857 genotype in grade 3 or 4 IDH-mutant astrocytomas. Upon further functional analyses, TLX1 and GALNT17 were found to be differentially methylated in IDH1-mutant astrocytomas and oligodendrogliomas, respectively, when stratified by rs55705857 risk allele. This is the first observation of a germline characteristic (e.g. rs55705857) predicting survival in low-grade IDH-mutant astrocytoma. While this observation requires validation, it suggests that germline genotype may be practice changing and inform results of trials such as CATNON and CODEL.
DDDR-16. SORTING TO ENRICH FOR CHEMOTHERAPEUTIC-RESISTANT GLIOMA CELLS BASED ON UNIQUE MEMBRANE PROPERTIES
Authors: Vi Dang, Alan Jiang, J Nicole Hanamoto, Nicole Lav, Daniela Bota, Lisa Flanagan
Journal: Neuro-Oncology (2024)

Abstract Glioblastoma, astrocytoma, and oligodendroglioma comprise a class of aggressive and deadly brain tumors called diffuse gliomas. Around 20,000 glioma cases are diagnosed yearly in the US alone. The current standard chemotherapy treatment, temozolomide (TMZ), is insufficient as the 5-year survival rate of glioblastoma patients is as low as 8%. This is due to the presence of TMZ-resistant cells within tumors that lead to chemoresistance and tumor recurrence. Thus, studying the molecular properties of TMZ-resistant cells would enable more effective means of targeting them and thus improve patient outcomes. We leveraged dielectrophoresis (DEP), a phenomenon by which non-uniform electric fields induce differential movement of cells, as a novel label-free technique to sort glioma cells based on their membrane electrophysiological properties. We were able to successfully use DEP to sort cells from glioblastoma and oligodendroglioma established cell lines, which yielded fractions that differed in membrane capacitance, the membrane’s ability to store charge. Interestingly, the DEP-sorted cell fractions also exhibited significant differences in TMZ resistance, indicating that we were able to use DEP to enrich for TMZ-resistant cells. Further, the differences in TMZ resistance were coupled with their membrane capacitance differences. Because we previously found that changes in membrane capacitance were linked to differences in glycosylation, we utilized lectin analysis to assess glycan expression of DEP-sorted oligodendroglioma cells. Our data show that TMZ-resistant oligodendroglioma cells enriched from DEP sorting had reduced levels of mannose glycans compared to less TMZ-resistant fractions. Collectively, our novel findings demonstrate (a) TMZ-resistant glioma cells can be enriched by DEP, and (b) TMZ resistance is correlated with membrane capacitance and cell surface glycosylation. These findings could enable further characterization of TMZ-resistant cells to better understand molecular mechanisms of TMZ resistance and the development of more effective treatment strategies for gliomas through targeting membrane properties such as glycosylation.
EPCO-45. COMPLETE CHROMOSOME-SCALE DIPLOID-PHASED ASSEMBLY OF A NORMAL HUMAN ASTROCYTE CELL LINE
Authors: T Rhyker Ranallo-Benavidez, Yue Hao, Noelle Fukushima, Ogechukwu Mbegbu, Floris P Barthel
Journal: Neuro-Oncology (2024)

Abstract Genomic studies of the malignant brain tumor glioma invariably rely on aligning sequencing reads to a reference genome such as HG38, even though no single reference can capture the diversity of an individual patient or cell line. To begin addressing these biases in genomics research, we sought to construct a chromosome-scale diploid-phased assembly of a normal human astrocyte (NHA) cell line that is frequently used as a basis for developing isogenic glioma cell models. To achieve this, we generated 45x Pacific Biosciences HiFi data (N50: 16kb), 26x Oxford Nanopore Technologies ultra-long data (N50: 80kb), and 2 billion paired-end reads of Hi-C data. The assembler verkko2 was used to integrate these data and build a phased diploid assembly. We achieved an assembly size of 6.01 Gbp, with 17 gapless chromosomes. The two haplotypes contain 214 and 182 contigs, respectively. Our assembly includes 76 fully assembled telomeres and 20 fully assembled centromeres. The contiguity of our assembly is 130 Mbp, which vastly exceeds that of HG38 (N50: 68 Mbp) and approaches that of the recent telomere-to-telomere CHM13 assembly (N50: 155 Mbp). We ran BUSCO on each haplotype of the assembly using the metazoa database to quantify the single-copy genes that are expected to be present in every animal genome. The haplotypes of our assembly contain the complete sequence of 98.6% and 99.9% of these genes respectively. Finally, we used Merqury to perform a k-mer based evaluation of the two haplotypes and found quality values of 59.09 and 59.75 respectively. This diploid genome assembly of NHA will serve as a resource for researchers that wish to develop NHA-derived glioma models. It can be used to call indels or structural variants in a haplotype-specific manner which will further elucidate genotypes underlying glioma phenotypes. Most importantly, it sets the stage for personalized genome assembly and tackling the lack of diversity in genomic studies of glioma to date.
CTNI-41. LONG-TERM SURVIVAL AND PATTERNS OF PROGRESSION IN PATIENTS WITH NEWLY DIAGNOSED GLIOBLASTOMA TREATED WITH OR WITHOUT TUMOR TREATING FIELDS (TTFIELDS) IN A REAL-WORLD SETTING
Authors: Devon Riegel, Britta Bureau, Patrick Conlon, Gordon Chavez, Jennifer Connelly
Journal: Neuro-Oncology (2024)

Abstract BACKGROUND Tumor Treating Fields therapy (TTFields) is an FDA-approved locoregional treatment for patients with newly diagnosed glioblastoma (ndGBM). Previous trial data showed the addition of TTFields to standard TMZ-based therapy to significantly improve overall survival (OS), but real-world data is lacking, particularly with long follow-up duration. Here, we report real-world survival and patterns of progression for patients with ndGBM treated with or without TTFields. METHODS Patients diagnosed with GBM and treated with standard of care therapy at the Medical College of Wisconsin between March 2015–March 2023 were included. Progression-free survival (PFS) and OS outcomes were assessed, and compared across groups who received or did not receive TTFields therapy during maintenance treatment. Patterns of disease progression were analyzed via anatomic assessment. Patients were followed through March 1, 2024. RESULTS A total of 210 patients (TTFields: n=110/52.4%; No-TTFields: n=100/47.6%) were included for analysis. Median age was 60 and 63 years for the TTFields and No-TTFields groups, respectively, with each group 43% female. Other baseline characteristics were consistent across groups. Median TTFields duration was 6.8 months (range: 1–94). OS was significantly improved for the TTFields group vs No-TTFields group (median OS: 21.6 months [18.4–24.8] vs 17.7 months [15.0–20.8]; HR 0.73 [95% CI: 0.54–0.99, P=0.042]). Median PFS was 12.1 months (10.3–14.4) vs 9.6 months (8.5–12.8) with HR 0.77 (95% CI: 0.58–1.02; P=0.071). 5-year OS was 17% (10–28) for the TTFields group, and 11% (5–22) for No-TTFields group. Patients treated with TTFields exhibited a higher rate of non-local progression compared with the No-TTFields group (28% vs 15%, [P=0.044]). CONCLUSIONS Analysis of patients from a large institutional dataset reveals an association between TTFields use and long-term survival benefit. Higher incidence of non-local patterns of progression among TTFields users is consistent with pivotal trial findings.
DDEL-02. PRECLINICAL EFFICACY OF IL13RΑ2-TARGETING POLYPEPTIDE-DRUG CONJUGATE (SELF-DEPOTTM ONCOPDC) IN GLIOBLASTOMA AND DIFFUSE INTRINSIC PONTINE GLIOMA
Authors: Won Bae Jeon, Yunjeong Gwon, Jung Eun Kim, Wooram Jung, Soobin Kim, Kyuri Shin
Journal: Neuro-Oncology (2024)

Abstract Glioblastoma (GBM) and diffuse intrinsic pontine glioma (DIPG) are currently incurable cancers. Systemic chemotherapy shows limited efficacy because of the intact blood-brain barrier. Convection-enhanced delivery (CED) offers promise by concentrating high doses of chemotherapeutics directly within these tumors. However, drugs administered via CED often face challenges in confirming precise target delivery and are quickly cleared by increased interstitial fluid flow and drug efflux transporters. This highlights the urgent need for innovative drugs that demonstrate target specificity and prolonged retention capabilities. Intrinsically disordered polypeptides (IDPs), derived from tropoelastin, self-assemble into water-insoluble structures with extended retention properties triggered by body temperature. IL13Rα2, differentially amplified in U87MG GBM and SF8628 DIPG cells, serves as a target for therapeutic intervention. An IL13Rα2-targeting IDP (XM161) was developed by incorporating IL13Rα2 binding sequences into the IDP domains. XM161 demonstrated high selectivity in binding to IL13Rα2, with Kd values of 1,786 nM for IL13Rα1 and 12.8 nM for IL13Rα2. Conjugation of XM161 with SN38, a potent topoisomerase I inhibitor, resulted in XM161-SN38, which remained in a dissolved state up to 50°C but formed insoluble aggregates above 27°C in the presence of cerebrospinal fluid. XM161-SN38 exhibited strong cytotoxicity against U87MG and SF8628 cells, with IC50 values of 14.2 nM and 0.48 nM, respectively. Importantly, XM161-SN38 demonstrated efficacy in overcoming Temozolomide resistance in T98G GBM cells, with IC50 values of 3.35 nM compared to 10.87 nM for unconjugated SN38. In orthotopic xenograft models established in BALB/cSlc-nu/nu male mice using U87MG-Luc2 cells, three doses (3 x 0.95 μg SN38 equivalents) of XM161-SN38 delivered via CED were well tolerated and significantly extended median survival to over 65 days, providing a notable survival benefit compared to untreated controls (42 days) and Topotecan-treated group (42.5 days). These findings validate the feasibility and therapeutic potential of XM161-SN38 for GBM treatment. Ongoing studies are underway to investigate the safety and pharmacokinetics of XM161-SN38 in tumor-naive mouse brains.
TMET-18. MANNOSE INHIBITS GLIOMA CELL PROLIFERATION AND POTENTIATES TEMOZOLOMIDE EFFICACY
Authors: HyeJoung Cho, Yeo Jun Yoon, Tae Hoon Roh, Seok-Gu Kang
Journal: Neuro-Oncology (2024)

Abstract Gliomas are among the most aggressive types of brain tumors, often displaying resistance to standard therapies such as temozolomide (TMZ). Recent research suggests that metabolic modulation may influence tumor growth and therapeutic response. This study explores the effects of mannose, a monosaccharide, on glioma cell growth and its potential to enhance the efficacy of TMZ. In vitro experiments were conducted to evaluate the impact of mannose and its combination with TMZ on glioma cells. Cell viability assays, ATP measurements, and flow cytometry (FACS) analysis were performed to assess cell cycle and apoptosis post-treatment with various monosaccharides, including mannose. The synergistic effects of the combined treatment with mannose and TMZ on cell viability were evaluated using Bliss score analysis and FACS. The impact on cancer stem cell characteristics was investigated through neurosphere formation assays, while tumor invasiveness was assessed using 3D invasion assays. Expression of stemness and invasion markers was analyzed by western blot. Differentially expressed gene (DEG) analysis was conducted to assess changes in gene expression related to stemness and invasiveness. Mannose treatment significantly reduced glioma cell viability and ATP levels, indicating decreased metabolic activity. Combined treatment with mannose and TMZ demonstrated a synergistic effect, enhancing cell death compared to either treatment alone, as evidenced by Bliss score and FACS analysis. Co-treatment reduced neurosphere formation and 3D invasion capabilities, with western blot results showing downregulation of stemness and invasion markers. DEG analysis revealed significant changes in gene expression related to stemness and invasiveness with the combined treatment. Mannose significantly impairs glioma cell growth and enhances the therapeutic efficacy of TMZ in vitro. Combining mannose with standard chemotherapy offers a promising strategy for improving glioma treatment outcomes. Further investigation in clinical settings is warranted to validate these findings.