bluuebunny/crossref_metadata_2025 huggingface dataset:
EPCO-24. WHAT SCRNA SEQUENCING TAUGHT US ABOUT MGMT EXPRESSION IN GLIOBLASTOMA
Authors: Alnahhas Iyad , Shi Wenyin
Published: November 2024

INTRODUCTION

The promoter methylation status of O-6-methylguanine-DNA methyltransferase (MGMTp) is an established predictive and prognostic marker in GBM. Previous studies showed that the expression of MGMT based on immunohistochemistry was variable and lacked association with survival. This in part is because non-tumor cells including endothelial cells and macrophages express MGMT. Advanced technologies such as single-cell RNA (scRNA) sequencing have helped to elucidate the cellular composition of cancer and its microenvironment. scRNA sequencing allows to assess gene expression level in tumor cells specifically.

METHODS

We used publicly available data from two recent IDHwt GBM scRNA studies that included MGMTp methylation status data to explore and uncover details about MGMT expression at the single-cell level: CPTAC (13 primary samples) and Neftel (20 primary samples).

RESULTS

In the CPTAC study, MGMT gene expression ranged from 0.19%-1.43% in the MGMTp methylated group (median 0.82%), and from 2.17%-28.36% in the MGMTp unmethylated group (median 5.7%). It therefore appears that 2% is a reasonable expression cutoff to predict the MGMTp methylation status based on scRNA data. In the Neftel study, MGMT expression ranged from 0-1.26% in the MGMTp methylated group (median 0.59%), and from 0.3-27.67% in the MGMTp unmethylated group (median 12.44%). Three unmethylated samples (out of 16) did not follow the 2% rule. It is unclear if this is due to simply inaccurate annotation of these samples. Moreover, the Neftel paper did not specify the method used to detect MGMTp methylation. Alternatively, could it be that truly MGMTp unmethylated samples can have low MGMT expression? Could this explain why some unmethylated MGMTp GBM patients surpass the expected survival? Interestingly, gene set enrichment analysis shows that MGMT expressing cells are enriched with mesenchymal genes, whereas MGMT negative cells are enriched with proneural genes.

CONCLUSION

Fewer than 2% of GBM cells express MGMT if MGMTp is methylated.
EPCO-27. CHROMATIN REMODELING REPROGRAMS THE TRANSCRIPTION NETWORK IN GLIOBLASTOMA
Authors: Sun Xueqin Sherine , Mills Alea
Published: November 2024

Fundamentally, cancer arises from genetic and epigenetic alterations that interplay to reprogram gene expression networks, leading to unrestrained proliferation. Glioblastoma (GBM) is the most prevalent and aggressive primary brain cancer, with a median survival of approximately one year and a 5-year survival rate of just 5%. The standard care for GBM patients has remained unchanged for decades, underscoring the need for a better understanding of GBM biology to develop more effective therapies. The relatively low genetic mutation burden in GBM highlights the significant role of epigenetic mechanisms in its pathogenesis. Our recent work shows that chromatin remodeling plays pivotal roles in GBM pathogenesis. The BRD8-driven EP400 chromatin remodeling complex maintains GBM by crippling p53-mediated tumor suppression in an unprecedented way through hijacking the histone variant H2AZ at p53 target loci, enforcing a repressive chromatin state that prevents p53-mediated transactivation. Targeting BRD8 in TP53WT GBM, which makes up ~71% of all GBM cases, enhances chromatin accessibility by evicting H2AZ. This restores p53-mediated transactivation of its targets, reestablishes cell cycle arrest, inhibits gliomagenesis, and prolongs survival in xenograft models of TP53WT GBM. Conversely, the NuRD chromatin remodeling complex driven by CHD5 governs the MYC-mediated oncogenic network to prevent gliomagenesis. Mechanistically, CHD5 forms a CHD3-containing but CHD4-independent NuRD complex that directly binds to the MYC promoter and super enhancers. Chd5 loss triggers the remodeling of chromatin, enhances chromatin accessibility at Myc loci, augments Myc expression, significantly impairs NSCs differentiation while promotes proliferation, transformation, and gliomagenesis in vivo. Furthermore, reactivating CHD5 in human GBM xenograft models significantly extends survival. Thus, our findings reveal previously unappreciated epigenetic mechanisms by which GBM cells reprogram both tumor-suppressive and oncogenic transcription networks to facilitate their outgrowth. This sheds new light on our understanding of GBM malignancy and provides promising therapeutic opportunities for treating patients with this devastating malignancy.
EPCO-31. THE GERMLINE POLYMORPHISM RS55705857 IS ASSOCIATED WITH A POOR SURVIVAL IN ASTROCYTOMA, IDH-MUTANT, GRADE 2
Authors: Drucker Kristen L , Kollmeyer Thomas M , Decker Paul A , Kosel Matthew L , Odukoya Lateef A , Sarkar Gobinda , Halder Chandralekha , De Lorenzo Silvana B , Burns Terry C , Giannini Caterina , Ida Cristiane M , Lachance Daniel H , Eckel-Passow Jeanette E , Jenkins Robert B
Published: November 2024

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 <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.
EPCO-35. GENOMIC CHARACTERIZATION OF GROWTH HORMONE SECRETING PITUITARY ADENOMAS
Authors: Alanya Hasan , Yalcin Kanat , Hilton Brian , Gultekin Batur , Mishra-Gorur Ketu , McGuone Declan , Gunel Murat , Omay Sacit Bulent , Erson-Omay Zeynep
Published: November 2024

BACKGROUND

Pituitary adenomas (PAs) are the second most common brain tumors in adults with prevalence ranging from 80 to 100 per 100,000 individuals. Of these, 9% to 14% are growth hormone (GH)-secreting PAs. While recurrent somatic GNAS mutations are identified in approximately half of sporadic GH-secreting PAs, the remaining cases are not well-characterized. This study aims to expand the genomic profile of GH-secreting PAs and explore correlations between molecular and clinical features.

METHODS

Whole exome sequencing (WES) was performed on 19 tumors with matching blood samples from consenting patients, achieving mean coverages of 262.74X for tumor samples and 112.43X for blood samples. Somatic variants, including single nucleotide variants (SNVs), short insertions/deletions (INDELs), and copy number variations (CNVs), were identified, and analyzed using protocols established by our institution. Genomic instability was assessed by calculating the percentage of the genome displaying loss-of-heterozygosity (LOH). Clinical data were collected and analyzed to establish genomic correlations.

RESULTS

The cohort comprised 19 GH-secreting PAs, with a mean age of 46 years at surgery, and was predominantly female (78.9%). The cohort was enriched for macroadenomas, with a mean tumor size of 18.4 mm. WES revealed a mean somatic mutation count of 20.4 (range 7-79), with 47% of cases harboring recurrent GNAS mutations. The mean alteration by LOH across the cohort was 11.13% (range: 0-44.80%) and did not show a statistically significant difference between cases with GNAS mutations and GNAS-wildtype cases (7.71% vs. 14.21%, respectively). Chromosomes 3, 8, 16, 22q were frequently affected by CNV/LOH events.

CONCLUSION

Comprehensive genomic characterization, including assessment of genomic instability through CNV/LOH analysis, is critical for better understanding the pathogenesis of GH-secreting PAs. This study underscores the importance of detailed genomic profiling in larger cohorts for improving the diagnosis and management of these tumors.
EPCO-49. SEX-SPECIFIC CHROMATIN REMODELING DRIVES TUMORIGENESIS IN GLIOBLASTOMA
Authors: Halaoui Adham , Kfoury-Beaumont Najla , Beaumont Thomas
Published: November 2024

Glioblastoma (GBM) is the most prevalent primary malignant brain cancer and has higher incidence and lower survival in males compared to females. The SWI/SNF chromatin remodeling complexes, including canonical BAF (cBAF), polybromo-associated BAF (PBAF), and non-canonical BAF (ncBAF), play a critical role in multiple cancers including gliomas. However, their role in gliomagenesis and progression remains largely unknown. We analyzed 18 human glioma specimens for BAF complex mRNA expression by CNS WHO grade and used these data to guide CRISPRi knockdown of BAF components in syngeneic murine male and female GBM astrocytes. BAF complex knockdown revealed marked sex-specific differences in proliferation. Specifically, Smarce1 or Smarcb1 knockdown (cBAF & PBAF) resulted in increased growth in male astrocytes but decreased growth in females. Brd7 (PBAF) knockdown enhanced growth in both sexes, while Brd9 (ncBAF) had minimal impact. We utilized extreme limiting dilution analysis (ELDA) to assess the clonogenic potential of GBM cells with depleted BAF components. Notably, cells with BRD7 knockdown displayed enhanced sphere-forming capacity in both male and female cells. Male cells with Smarce1or Smarcb1 knockdown showed increased clonogenic frequency, whereas females with Smarce1 knockdown had a marked reduction in sphere formation. Brd9 knockdown did not affect the sphere-forming capacity in male or female cells, in part due to compensatory plasticity of an alternate BAF complex. Epitranscriptomic analysis is ongoing and demonstrates sex-specific differences in chromatin accessibility and downstream gene expression programs based on BAF complex knockdown. Immunoprecipitation coupled with mass spectrometry was performed to elucidate the structure and assembly of the BAF complex in GBM cells. Understanding sex-specific mechanisms of BAF chromatin remodeling complex in glioma pathogenesis may yield critical insights for the development of precision therapeutics that have the potential to improve patient outcomes.
BIOM-21. SMALL EXTRACELLULAR VESICLES AS A NOVEL LIQUID BIOPSY APPROACH FOR GLIOBLASTOMA
Authors: He Yangen , Kumar Ashish , Singh Sangeeta , Kim Susy , Su Yixin , Herpai Denise , Fansler Ashley , Whitlow Christopher , Strowd Roy , Debinski Waldemar , Lesser Glenn , Deep Gagan
Published: November 2024

Glioblastoma (GBM) remains the most common and aggressive primary malignant brain tumor, with limited treatment options and poor overall survival. Diagnosis, prognosis, and assessment of treatment effectiveness are hampered by the lack of sensitive, tumor-specific, non-invasive blood-based assays which could be followed serially. Small extracellular vesicles (sEV) are nano-sized (≤200 nm) membrane-bound bodies secreted by all cells, encapsulating cargo reflective of their parent cells. sEVs have emerged as promising molecular disease indicators. Here, we report the feasibility of isolating glioma-specific sEV (sEVglioma) from plasma and characterizing them for GBM-specific molecular biomarkers. Plasma samples were collected from 31 glioma patients (grades 3 and 4 GBM, grades 2 and 3 astrocytoma) and 9 healthy individuals. Total sEVs (TE) were isolated from plasma by a modified precipitation (ExoQuick™) method, followed by immunoprecipitation to isolate sEVglioma employing surface markers targeting the cellular origin of gliomas, including astrocyte (GLAST and EAAT2), oligodendrocyte precursor cell (OSP and MOG), and neural stem cell (CD133). The average size of sEVglioma was less than 200 nm. Importantly, compared to TE, sEVglioma showed significant enrichment for glioma-specific biomarkers such as ephrin type-A receptor 2 (14.7-fold), tenascin-C (22.7-fold), and glial fibrillary acidic protein (8.4-fold). Similarly, sEVglioma demonstrated higher expression of the GBM biomarker EGFRvIII (3.6-fold). These results were confirmed by confocal microscopy. Interestingly, the expression of specific miRNAs (miR-9a-5p, miR-16-5p, miR-21-5p) in sEVglioma was higher in glioma patients with shorter survival (<12 months) compared to longer survival (>20 months). Lastly, we successfully detected the existence of wild-type IDH1 and absence of mutated IDH1 R132H in sEVglioma from GBM patients, validated with cell line experiments. In conclusion, we present a novel liquid biopsy approach for isolating sEVglioma from blood, providing valuable molecular and genetic information. This approach promises early detection, potential to distinguish pseudo-progression, and assessment of treatment effectiveness with remarkable precision.
BIOM-30. NOVEL HISTOLOGIC AND MOLECULAR BIOMARKERS FOR OLIGODENDROGLIOMA
Authors: Smith Vanessa , Stevenson Kevin , Wieden Tia , Anand Monika , Desjardins Annick , McLendon Roger , Ashley David , Gregory Simon , López Giselle
Published: November 2024

Oligodendrogliomas are progressive, infiltrative gliomas. While new molecular criteria were introduced in 2016 for diagnosing oligodendroglioma, the grading criteria remains largely unchanged. We evaluated histologic and molecular features for new biomarkers of aggressive behavior, using a cohort of 184 specimens diagnosed as low grade oligodendroglioma within the Duke Brain Tumor Center Biorepository. To identify tumors meeting current molecular criteria for oligodendroglioma, IDH1/2 status was confirmed by whole exome sequencing and 1p/19q codeletion confirmed using inferred copy number variation. First, we assessed for a histologic feature called hypercellular nodules (HCN), which are foci of increased cellularity in regions of otherwise lower cellularity tumor. In patients with newly diagnosed grade 2 oligodendroglioma, 16% (15/92) had HCN. While the median overall survival (OS) was 24.1 years without HCN, the median OS with HCN was only 13.6 years (p<0.02, Mantel-Cox test). We then assessed for homozygous deletion of CDKN2A. Cases with potential CDKN2A homozygous deletion by inferred copy number variation were validated by fluorescence in situ hybridization. In patients with newly diagnosed grade 2 oligodendroglioma, 2% had homozygous CDKN2A deletion (2/107). While the median OS with intact or hemizygous CDKN2A loss was 21 years, it decreased to 3.8 years with homozygous CDKN2A deletion (p<0.0001, Mantel-Cox test), although interpretation is limited given the rarity of homozygous CDKN2A loss at initial diagnosis. For recurrent grade 2 oligodendroglioma, 6% had homozygous deletion (5/77). While the median OS with intact or hemizygous CDKN2A loss in recurrent oligodendroglioma was 25.4 years, it decreased to 6.7 years with homozygous CDKN2A deletion (p< 0.04, Mantel-Cox test). These studies provide support for using HCN and CDKN2A homozygous deletion as grading criteria for oligodendroglioma. Further studies are ongoing, including covariate analysis, expanded cohorts, and ongoing analysis of whole exome sequencing data to identify additional genetic alterations correlated with overall survival.
BIOM-54. AI-DRIVEN RISK-OF-PROGRESSION (AIRIP) CLASSIFIER FOR DISTINGUISHING RECURRENT BRAIN METASTASES FROM RADIATION TREATMENT EFFECT: A MULTI-INSTITUTIONAL COMPARATIVE STUDY WITH ADVANCED MULTIMODAL IMAGING
Authors: Um Hyemin , Ismail Marwa , Hill Virginia , Puri Sushant , Yu Jennifer , Lu Lan , Nayate Ameya , Rogers Lisa , Prasanna Prateek , Bardhan Mainak , Li Chengnan , Basree Mustafa , Baschnagel Andrew , McMillan Alan , Bhatia Ankush , Ahluwalia Manmeet , Veronesi Michael , Tiwari Pallavi
Published: November 2024

Following radiation therapy, a significant challenge in brain metastases (BM) management is differentiating radiation-induced-treatment effect (TrE) from tumor recurrence (TuR). TrE can be indistinguishable from TuR using conventional MRI. Advanced imaging techniques (e.g., perfusion MRI, PET/MRI) are not consistently used, and the standardized Response Assessment in Neuro-Oncology for brain metastases (RANO-BM) is sensitive to inter-reader variability. The performance of an artificial intelligence (AI)-driven risk-of-progression (AiRiP) classifier, which has been shown to capture pathophysiologic differences between TrE and TuR on routine MRI, was compared to that of clinical assessments and advanced imaging methods, in a multi-institutional setting. A total of n=261 lesions with pathologically-confirmed diagnoses in n=189 patients were analyzed. 115 lesions (73 TuR, 42 TrE) from site 1, 86 lesions (38 TuR, 48 TrE) from site 2, and 60 lesions (33 TuR, 27 TrE) from site 3 were used for training and testing the AiRiP-model. Gd-T1w, T2w, FLAIR MRI were preprocessed, and lesions were segmented by experts. Texture features (n=856) were extracted from each lesion. Random-forest classifier was employed for 3-fold cross-validation. Top-performing AiRiP-features, RANO-BM criteria, perfusion MRI and PET/MRI were evaluated in a sub-group analysis. For n=51 lesions on the test-set (site 3), 14 were classified as stable disease and 37 as TuR using RANO-BM (accuracy=54.1%). AiRiP-model achieved an accuracy of 76.5% on the same test-set and accurately classified 78.6% of the stable lesions as TrE or TuR. For another subset of lesions (n=27) on the same test-set, perfusion MRI and AiRiP-model achieved an accuracy of 59.3% and 70.4%, respectively. Lastly, for a subset of lesions (n=35) on the test-set (site 2), multimodal (perfusion, PET) imaging and AiRiP-model accurately classified 60% and 74.3% of lesions, respectively. 15 lesions were considered indeterminate via multimodal imaging, 73.3% of which AiRiP-model accurately classified as TrE or TuR. Our results suggest AI-driven models on conventional MRI may reliably distinguish TuR from TrE.
BIOM-59. INDIVIDUALIZED TUMOR-SPECIFIC AMPLIFIED DNA JUNCTIONS FOR PLASMA-BASED MONITORING IN PATIENTS WITH HIGH-GRADE GLIOMAS
Authors: Ali Mohamed , Riviere-Cazaux Cecile , Johnson Sarah , Salvatori Rebecca , Penheiter Alan , Smadbeck James , Murphy Stephen , Harris Faye , McCune Alexa , Barrett Michael , Kosari Farhad , Jones Leila , Ida Cristiane , Borad Mitesh , Bendok Bernard , Basil Aleeshba , Quinones-Hinojosa Alfredo , Porter Alyx , Mrugala Maciej , Jaeckle Kurt , Anastasiadis Panos , Kizilbash Sani , Cheville John , Routman David , Burns Terry , Vasmatzis George
Published: November 2024

Accurate response assessment in patients with high-grade gliomas (HGGs) is complicated by post-treatment radiographic changes that are equivocal for treatment effect versus progression. Plasma-based liquid biopsy assays for circulating tumor DNA (ctDNA) have had limited sensitivity to date, due in part to the presence of the blood-brain barrier that limits the diffusion of tumor-derived analytes out of the central nervous system. To address this challenge, we developed a ctDNA plasma-based assay to detect individualized tumor-derived amplified junctions in patients with HGGs. These junctions occur due to large-scale chromosomal rearrangements, such as those associated with epidermal growth factor receptor (EGFR) or cyclin-dependent kinase 4 (CDK4) amplification. To identify these amplified junctions, whole genome sequencing was performed on resected tissue. Primers were designed to flank junction breakpoints and were then utilized on each patient’s plasma samples to detect the amplified junction via qPCR. Tumor-specific amplified junctions were robustly detected in plasma from 14/14 (100%) patients with IDH-mutant or wild-type grade 4 astrocytomas whose tumor genomes demonstrated amplification-related junctions, located at chromosomes 7, 11, or 12. In comparison, ctDNA could not be detected in three control cases that did not have an amplification or did not have high copy number junctions. Importantly, serial plasma samples obtained prior to and at disease recurrence in 4 patients demonstrated an increasing abundance of amplified junctions that accurately correlated with disease progression in 4/4 patients (100%). In two of these patients, increasing abundance of amplified junctions preceded radiographic changes compatible with disease progression by approximately 2 or 4 months, respectively. In conclusion, tumor-specific amplified junctions could reliably be detected in plasma from patients with IDH-mutant or wild-type grade 4 astrocytomas and correlated with changes in disease burden. Further work is currently ongoing to evaluate these promising results in a larger cohort of patients with serial plasma samples.
CNSC-10. WHEN GOOD THINGS GO OFF TRK: THE INTERSECTION OF NEUROSCIENCE & ONCOLOGY
Authors: Pattwell Siobhan
Published: November 2024

How and why do processes and molecular players that were once an integral part of normal neurodevelopment go awry in pathological conditions, such as cancer? Embryogenesis, and neurodevelopment in particular, comprise an elegant and well-orchestrated series of tightly regulated events, culminating in an organized and highly functioning organism. Cancer, on the other hand, can often be viewed as an uncontrolled, unrestrained, genetically chaotic disease, lacking the precise spatial and temporal rigidity associated with normal development. While appearing to be on opposite sides of the organizational spectrum, the similarities between early neurodevelopment and oncogenesis are numerous. The link between developmental signaling and cancer initiation, maintenance, and metastasis has long been known for several members of the Wnt, Hedgehog, and Notch pathways and years of gene-level analyses have provided a wealth of knowledge and mechanistic insight. As advances in next generation sequencing allow for deeper characterization of genetic programs, it is increasingly possible to explore various isoforms of cancer associated genes. It is widely known that neurotrophins and their receptors (TrkA, TrkB, TrkC) are instrumental for neurodevelopment and that they remain critical for proper neuronal functioning throughout life. Our work highlights a previously unidentified role for an alternatively spliced neurotrophin receptor in neurodevelopment, embryogenesis, transformation, and oncogenesis across multiple tumor types in humans and mice. This specific isoform, TrkB.T1, is the predominant NTRK2 isoform across embryonic organogenesis, and forced overexpression of this embryonic pattern causes multiple solid and nonsolid tumors in mice. TrkB.T1 also emerges as the predominant NTRK isoform expressed in a wide range of adult and pediatric tumors, including those harboring various NTRK fusions. This work hopes to address the fundamental question of how neurodevelopmental processes can go awry in cancer, while seeking to better characterize the role of TRKs, in normal developmental processes and oncogenesis.
CNSC-15. DURATION AND TIMING ANALYSIS OF TUMOR TREATING FIELDS (TTFIELDS) THERAPY FOR NEWLY DIAGNOSED HIGH-GRADE GLIOMA PATIENTS: A REAL-WORLD RETROSPECTIVE STUDY IN TWO CENTERS
Authors: Wang Chun , Chen Lingchao , Ji Jianxiong , Zhang Junyan , Song Kun , Pan Yanhong , Ma Nainai , Zheng Huijuan , Xiao Yang , Chen Gao , Liu Fuyi , Qin Zhiyong
Published: November 2024

BACKGROUND

In the EF-14 phase 3 trial, tumor treating fields (TTFields) plus temozolomide improved progression-free and overall survival versus temozolomide alone in newly diagnosed glioblastoma. However, the optimal duration and timing of TTFields treatment have not been reported yet. In this study, we aimed to analyze the relationship between the timing of TTFields use, the total duration of therapy, and daily compliance with overall survival in high-grade glioma (HGG) and, therefore, provided detailed suggestions for clinical use of TTFields.

METHODS

A total of 343 patients were screened retrospectively after resection or biopsy at two centers and received TTFields treatment from April 2019 to April 2023. All the patients were re-evaluated based on the 2021 WHO CNS5 Classification. We collected clinical data, including basic clinical information, pathology, surgery, radiotherapy, and TTFields. Follow-up for survival was performed for all patients in December 2023, and another follow-up is planned for June 2024.

RESULTS

After excluding non-HGG or lacking critical diagnostic information, 308 patients were included. Of these, 264 were Glioblastoma, IDH-wildtype, 27 were Astrocytoma, IDH-mutant, 3 were Oligodendroglioma, IDH-mutant, and 1p/19q-codeleted, and 14 were Diffuse midline glioma, H3 K27-altered, or Diffuse hemispheric glioma, H3 G34-mutant. Baseline characteristics were listed below: median age was 53 years; 56.82% male; median baseline KPS was 90; 75.97% underwent gross total resection; 51.30% received chemoradiation with concurrent TTFields. Only 26.30% of patients were still using TTFields by December 31, 2023. The median time difference between TTFields and surgery was 55.5 days. The overall TTFields median duration was 334 days, with a median compliance rate of 85%. By December 31, 2023, 59.09% of the patients were still alive.

CONCLUSION

The study group will continue to follow up on patients’ survival. Further analysis of the correlation between treatment duration, compliance or timing and survival will be performed.
CNSC-31. INVESTIGATING THE THERAPEUTIC POTENTIAL OF STK17A INHIBITION IN GLIOBLASTOMA
Authors: Castro Jesus , Seetharam Deepa , Chaudhry Sana , Chander Jay , Taylor Justin , Shah Ashish
Published: November 2024

For decades, the survival rate for glioblastoma (GBM) has remained nearly stagnant, with a 5-year survival rate of only 5%. There is an unmet medical need for therapeutic development, because while GBM is the most common primary brain tumor, only four FDA approved drugs have been developed for GBM over the last century. By taking advantage of RNA sequencing, a potential target for GBM has been identified: the kinase STK17A (Serine/Threonine Kinase17A). We confirmed that STK17A is overexpressed in gliomas by analyzing public databases and single-cell RNA sequencing from our own GBM patients, and further associated it with poor patient outcome. Little is known about STK17A, but it has been found to be involved in cell proliferation and tumorigenesis. The role of STK17A in GBM pathophysiology and its therapeutic potential as a drug target remains a critical knowledge gap. To better understand STK17A’s role in GBM pathophysiology, we first knocked down STK17A in GBM cell lines and determined that STK17A had functional roles in proliferation and morphology. Similar conclusions were drawn after removing STK17A in GBM xenograft mouse models. These findings support STK17A as a viable therapeutic target. We then designed and optimized novel STK17A inhibitors for evaluations through kinase enzymatic and biological assays, in vitro proliferation and toxicity assays, and in vivo Drug Metabolism and Pharmacokinetics (DMPK) assays. We then used these potent, selective, and highly brain penetrant STK17A inhibitors to investigate the anti-tumor effects of STK17A inhibition in GBM and demonstrate the efficacy of our novel STK17A inhibitors in vivo. In conclusion, this work seeks to contribute to the field of targeted therapies for GBM by optimizing and examining a novel brain penetrant STK17A inhibitor, initiating studies for the treatment of GBM in vitro and in vivo, and providing proof of efficacy for further studies in GBM patients.
CNSC-51. PRIMARY INTRACRANIAL ALVEOLAR SOFT PART SARCOMA (PIASPS): A SYSTEMATIC REVIEW OF CASE REPORTS AND CASE SERIES FROM 2000 – 2023
Authors: Qadri Haseeb Mehmood , Bashir Asif
Published: November 2024

BACKGROUND AND OBJECTIVE

Alveolar soft part sarcoma is a rare malignancy of the lower extremities considered to be of unknown cellular origin. Common in young female patients, the ASPS usually has a strong metastatic potential, mostly involving the lungs at the time of presentation. Cases involving the CNS primarily, without any evidence of systemic disease have emerged i.e. the primary intracranial alveolar soft part sarcoma (PIASPS). We aim to determine the clinical manifestations, natural progression and management of primary intracranial alveolar soft part sarcoma.

MATERIALS AND METHODS

After an extensive literature search using PubMed Central and Google Scholar, seven case reports and two case series of 14 patients with PIASPS were retrieved and included using the Preferred Reporting Items for Systemic review and Meta-analyses guidelines, published between 2000 and 2023.

RESULTS

Female preponderance of the neoplasm (57.14%) with an average age of 24.9 years was noted. Headache (36.36%) and papilledema (25%) were the most common presenting complaint and sign, respectively. Brain parenchymal involvement was noted in 71.42% cases, mostly the frontal lobe and left hemisphere. The lesion appeared isointense to hypointense on T1-weighted images and hyperintense on T2-weighted images (66.67%) on MRI. Gross Total Resection was possible in 57.14% lesions. On immunohistochemistry, the tumor cells manifested TFE3 and PAS positivity in 25% and 20% of the cases respectively. An average survival after follow up duration was found to be 31.79 months.

CONCLUSION

Surgery and radiotherapy are the mainstay of treatment of PIASPS, while meningioma an important differential diagnosis. TFE3 fusion product is readily been helpful in diagnosis. Evidence of a primary lesion in the CNS cannot rule out the presence of an occult primary elsewhere in the body. This, along with the slow growing nature of the neoplasm and delayed localized recurrences, require a long-term follow-up.
STEM-03. TARGETING F-ACTIN DYNAMICS OF GLIOBLASTOMAS TO OVERCOME THERAPY RESISTANCE: IMPACTS ON DNA REPAIR AND GLIOMA STEM CELL PHENOTYPE
Authors: Magalhaes Yuli , Forti Fabio
Published: November 2024

Glioblastoma (GBM) is a highly aggressive brain tumor with high recurrence and resistance to therapies. The F-actin cytoskeleton in GBM is related to cell invasion and the glioma stem cell (GSC) phenotype, affecting self-renewal and migration. Our research identifies a novel role for the F-actin pathway in DNA repair, impacting genomic stability and contributing to therapy resistance. Understanding F-actin’s role is crucial for developing targeted strategies to improve GBM treatment outcomes. This study examines the effects of pharmacological F-actin depolymerization on reversing resistance to ionizing radiation (IR) and temozolomide (TMZ) in GBM spheroids. We established resistant sublines of GBM U87-MG cells through IR and TMZ cycles, observing significant resistance increases via MTT assays. Also, resistant cells had enhanced spheroid formation capacity, with higher size and proliferation. Alterations in DNA repair and F-actin pathway were observed, with intensified and disorganized F-actin polymerization and efficient repair in resistant cells. Elevated expression of stemness markers (Nestin, CD133, and CD44) indicated a GSC-like phenotype in resistant cells, corroborated by increased tumorigenicity and de novo spheroid formation. These markers were further enhanced by DNA damage. Treating cells with actin polymerization inhibitors reduced resistance to TMZ and IR, partly due to impaired DNA repair capacity. Additionally, F-actin disassembly affected stemness marker expression, reinforcing the link between cytoskeletal dynamics and the GSC phenotype. Our findings suggest that F-actin dynamic is crucial for resistance in GBM. Targeting F-actin could resensitize recurrent GBM tumours by diminishing DNA repair capabilities and affecting the GSC-like phenotype, offering new therapeutic avenues.
STEM-06. DISTANT ORIGIN OF GLIOBLASTOMA RECURRENCE: NEURAL STEM CELLS IN THE SUBVENTRICULAR ZONE SERVE AS A SOURCE OF TUMOR RECONSTRUCTION AFTER PRIMARY RESECTION
Authors: Li Xue , Kim Hyun Jung , Kim Tae Min , Choi Seung Hong , Lee Soon-Tae , Park Jong Bae , Yoo Jihwan , Chang Jong Hee , Park Chul-Kee , Wu Hong-Gyun , Won Jae-Kyung , Lee Yeonhee , Lee Jeong Ho , Kang Seok-Gu , Lee Joo Ho
Published: November 2024

The recurrence of glioblastoma (GBM) remains unavoidable. Neural stem cells (NSCs) in the subventricular zone (SVZ) are considered a treatment target due to their potential role as the cellular origin of GBM. However, it is not yet confirmed whether GBM recurrence also originates from these cells. We first conducted deep sequencing on paired patient samples, including primary tumors (pT), recurrent tumors (rT), and SVZ tissues. The sequencing results revealed that in 5 out of 9 patients, the rT evolved independently from the SVZ rather than directly from the pT. Based on this, we developed a mouse model to simulate the GBM recurrence process by transforming SVZ NSCs into GFP-labeled cells carrying cancer mutations via electroporation. Following the resection of the tdTomato-labeled pT, we observed that 57.1% of the rT consists of a mixture of GFP- and tdTomato-positive tumor cells. To study the behavior of NSCs, we improved the existing mouse model by removing cortical tissue to simulate the complete resection of the pT. Four weeks post-surgical resection, 64.7% of tumors reconstructed in the resection cavity (RC), driven by the migration of OPC lineage cells. Time-course RNA-seq results indicated that the CXCL12-CXCR4 pathway might be responsible for driving the migration of SVZ NSCs to the RC. Further deconvolution and fluorescence staining analysis confirmed that CXCL12 secreted by endothelial cells around the RC could drive CXCR4-positive NSCs to migrate to the area. Additionally, the CXCR4 antagonist AMD3100 significantly reduced tumor recurrence in mice and extended survival. RNA-seq results from both mouse and human paired tumor samples confirmed that the CXCL12-CXCR4 pathway was enriched in locally recurrent tumor specimens and was correlated with shorter patient survival. In summary, our study provides evidence that GBM recurrence originates from SVZ NSCs. Moreover, we identified the CXCL12-CXCR4 pathway as a potential therapeutic target for GBM recurrence.
CCRG-02. MICRORNA TARGETING LOGIC IN DIRECT NEURONAL REPROGRAMMING OF GLIOBLASTOMA
Authors: Yuan Luorongxin , Cates Kitra , Kim Albert , Yoo Andrew
Published: November 2024

microRNA (miR)-124 is one of the main drivers of mitotic exit during neurogenesis, which is recapitulated in miR-9/9* and -124 (miR-9/9*-124)-mediated direct neuronal reprogramming. In the reprogramming of various cell types, miR-9/9*-124 induce non-neuronal cell fate erasure before activating the neuronal program. Regardless of the different starting transcriptome landscapes, a core gene regulatory network (GRN) is always targeted by miR-9/9*-124, with cell cycle progression as the most significant pathway. We reason that miR-9/9*-124 can induce cell fate erasure in cancerous cells by repressing similar GRNs, using glioblastoma multiforme (GBM) as a paradigm. Mechanistic insights into GBM fate erasure by miR-9/9*-124 while inducing the postmitotic state would facilitate the understanding of GRNs that govern the tumorigenic identity of GBMs and potentially offer novel therapeutic implications. Indeed, miR-9/9*-124 readily induces mitotic exit in patient-derived GBM cell lines, represses GBM cell fates, and promotes neuronal identity over time as assessed by RNA-seq. Mice receiving GBM intracerebral xenografts with miR-9/9*-124 survived significantly longer than those receiving non-specific control miRNA. Global profiling of miRNA targeting activity by AGO2-eCLIP reveals that miR-124 binds to transcripts enriched in G1/S transition and mitogen response. Conversely, miR-506—a miR-124 homolog—despite of sharing identical seed sequences, has significantly less targeting activity and fails to stop cell cycle progression. We are currently dissecting how the difference in the miRNA 3’ sequence renders contrasting biological outcomes. Preliminary data suggests that the length of miRNA alone alters targeting specificity to cell cycle transcripts. However, different permutations of miRNA 3’ sequence, though sufficient to induce mitotic exit, are not all competent to achieve neuronal reprogramming, indicating that mitotic exit and neurogenic activities of miR-124 could be decoupled. We hope that understanding the grammar logic of miRNA targeting would provide deeper insights into how miRNAs can be leveraged to manipulate GBM identity.
CCRG-03. DETECTION OF HETEROGENEOUS CELL CYCLE ALTERATIONS UPON TMZ CHEMOTHERAPY TREATMENT THROUGH ADVANCED MACHINE LEARNING
Authors: Villa Giulia , Kückelhaus Jan , Yabo Yahaya , Schnell Oliver , Delev Daniel , Benotmane Jasim Kada , Heiland Dieter Henrik
Published: November 2024

Glioblastoma (GB), the most aggressive central nervous system tumor, is hallmarked by its frequent relapse under alkylating chemotherapy. GB cells frequently exhibit changes in cell cycle phases during TMZ treatment, with a reduction in the G0-G1 phase and an increase in the S and G2 phases. This indicate both tumor cell re-entry into the cell cycle and a TMZ-induced arrest, contributing to resistance and progression. In this study, we leverage dynamic protein abundance of Ki-67, a proliferation marker peaking during S, G2, and M phases, to analyse cellular responses to TMZ in various cell lines and tissue samples. We designed an image-based machine learning approach for pattern recognition to reconstruct and analyse the cell cycle at the single-cell level. Six primary cell lines were characterized through whole-genome DNA, methylation and RNA sequencing. Functional read-outs were performed with large-scale, time- and concentration-dependent TMZ treatments in cell culture and GB-tissue slice models. Our model successfully reconstructed detailed cell cycle stages, showing that untreated cells were predominantly in the G0-G1 phase. TMZ treatment significantly shifted cells toward the S/G2 phase (p < 0.02) in 3 of 6 cell lines and the pseudo-time reconstruction highlighted dose-dependent cell cycle changes. Cell lines with enhanced stem-like features, defined based on epigenetic and transcriptional data signature, showed no cell cycle changes at high TMZ doses (>150µM), regardless the MGMT promoter methylation status. This heterogeneity in cell cycle response emphasizes the complexity of GB and the need for personalized treatments. Our study provides insights into GB MGMT cell cycle alterations and resistance mechanisms that are independent of MGMT methylation status, a known TMZ response biomarker. Therefore, the observed TMZ-induced cell cycle changes may serve as novel biomarkers for assessing treatment response, paving the way for personalized therapeutic approaches.
CSIG-04. ANTI-TUMOR RESPONSE OF ONCOMAGNETIC MONOTHERAPY IN GLIOBLASTOMA
Authors: Pandey Arvind , Hambarde Shashank , Baskin David , Helekar Santosh
Published: November 2024

BACKGROUND

Glioblastoma (GBM) is the most lethal primary malignant brain tumor with a median survival of 15–20 months. Concurrent temozolomide (TMZ) chemotherapy and radiation (XRT) remain the current standard of care (SOC) treatment for newly diagnosed GBM. The addition of tumor treating fields (TTFs) improves median survival for newly diagnosed GBM from 16 to 20.9 months. This modest improvement underscores the urgent need to identify a new treatment modality as a safe and effective therapy.

PURPOSE

The noninvasive Oncomagnetic device developed in our laboratory selectively kills glioblastoma (GBM) in vitro. We studied the cellular and molecular effects of Oncomagnetic monotherapy (OMT) on GBM cell lines and investigated immune response in a syngeneic mouse model.

RESULTS

OMT significantly reduces cell proliferation and cell survival in vitro. OMT induces persistent ROS primarily by increasing superoxide level in cancer cells and reduces mitochondrial-membrane potential in GBM cells. It also induces DNA damage and arrests cells in G1-phase of the cell cycle. Whole-body Oncomagnetic stimulation caused a substantial retardation of tumor growth and reduction of the contrast-enhanced tumor volume in 9.4T MRI scans. OMT showed significant increase in overall survival in treated mice. We also observed upregulated immune response indicated by RNA sequencing data obtained from OMT-treated GBM cells as well as in treated GBM mouse tumor sections by imaging mass cytometry analysis. The tSNE analysis of various immune clusters suggests significant increase in immune response by activating CD4+, CD8+, murine-macrophages and M1-macrophages located at tumor site in the treated group.

CONCLUSION

The obtained data indicate significant anti-tumor response by inhibiting cancer signaling pathways and an increased immune response. Our findings suggest unique mechanism of action for OMT stimulation and provide a strong rationale for standalone OMT for GBM.
CSIG-09. BEYOND SINGLE AGENTS: EXPLORING THE POTENTIAL OF ABEMACICLIB IN COMBINATION WITH PANOBINOSTAT FOR IMPROVED GLIOMA TREATMENT
Authors: Rao Namratha B , Miller Tracy A , Premkumar Daniel R , Pollack Ian F
Published: November 2024

BACKGROUND

Glioblastoma is the most common primary central nervous system tumour with a median survival of less than 15 months. Addressing the underlying redundant, and converging signaling pathways necessitates the utilization of small molecule inhibitors capable of simultaneous targeting and inhibition. In glioma, the aberrant CDK4/6-Rb pathway dysregulation resulting in disruption of cell cycle checkpoint progression can lead to uncontrolled cell division, a hallmark of cancer. The neuro-pharmacokinetics of abemaciclib, a Cyclin-dependent kinase inhibitor, is being currently investigated in phase 1 clinical trials by National Cancer Institue, [NCT05413304]. The importance of panobinostat as a Histone deacetylase inhibitor and potentiating the effects of various small molecular inhibitors in published literature is paramount. This study is based on investigating ways to overcome resistance by exploring the synergistic cytotoxic effects of abemaciclib in combination with panobinostat in glioma.

METHODS

We investigated the antiproliferative effects of abemaciclib and panobinostat on glioma cells using an MTS cell proliferation assay. Inhibitor combination analysis was done using, SYNERGYFINDER via zip-model. Flow cytometry with Annexin V staining further assessed cell death and apoptosis induced.

RESULTS

The antiproliferative effects of abemaciclib, alone and in combination with panobinostat, in pediatric lines (KNS 42, SJG2), and adult human glioblastoma line, SF188 exhibited lower IC50 as compared to adult high grade glioma lines (LN 18, LNZ 308). Synergy analysis revealed a strong cytotoxic effect in KNS 42 and SF 188 cells treated with the combination. Flow cytometric analysis indicated that the combination therapy induced significant cell death only in a subset of cell lines- KNS 42 and SF 188, suggesting underlying genetic heterogeneity influences treatment response, warranting further mechanistic studies.

CONCLUSION

Combination therapies using abemaciclib and panobinostat, targeting CDK4/6 and histone deacetylation pathways, show promise against aggressive and treatment-resistant gliomas. Further investigation into these combination approaches is crucial to understand resistant mechanisms, optimize efficacy, and establish their clinical efficacy for improving glioma patient outcomes.
CSIG-23. CYTOMEGALOVIRUS-INFECTED HUMAN GLIOBLASTOMA CELL LINES SHOW AN AGGRESSIVE PHENOTYPE ASSOCIATED WITH UPREGULATION OF IL-6/STAT3 AND AKT SIGNALING
Authors: Tajiknia Vida , Mercado Noe , Murphy Eain , lawler Sean
Published: November 2024

BACKGROUND

Cytomegalovirus (CMV) has been implicated in glioblastoma (GBM) pathogenesis by affecting stemness, angiogenesis and immune pathways. Clinical trials targeting CMV in GBM patients have shown some early promise, and CMV seropositivity has been associated with poorer outcomes. However, the underlying mechanisms remain unclear. Here we investigated the effects of CMV infection on critical signaling pathways in GBM (IL6/STAT3, and Akt signaling) based on the hypothesis that CMV may contribute to poorer outcomes in GBM by increasing oncogenic signaling.

MATERIALS AND METHODS

Human U251 and LN229 GBM cell lines were infected with mCherry expressing human CMV TB40 strain at a multiplicity of infection (MOI) of 0.5. We performed basic phenotypic studies in vitro and investigated the status of IL6/STAT3, and Akt signaling by Western blotting.

RESULTS

Both LN229 and U251 cell lines were readily infectable by CMV. Infection of U251 cells was over 90% and in LN229 cells was approximately 60%. Interestingly expression of CMV was sustained over many passages in these cell lines. Infection was also verified by the presence of the CMV pp65 protein assessed by Western blotting. Measurement of cell proliferation indicated faster growth after CMV infection. Interrogation of key pro-oncogenic signaling pathways in GBM revealed a robust upregulation of IL6, as well as phospho(Tyr705)-STAT3 and phospho(Thr308)-Akt. This elevation of pro-oncogenic signaling pathways was observed in both cell lines compared with controls.

CONCLUSIONS

Here we show for the first time that infection of human GBM cell lines with CMV results in a more aggressive phenotype associated with upregulation of IL6/STAT3 signaling as well as a significant increase in phospho-Akt levels. We are currently studying sensitivity to standard therapies and additional molecular changes in these cells. These data support the hypothesis that CMV causes more aggressive disease and that CMV is a relevant therapeutic target in GBM.