bluuebunny/crossref_metadata_2025_split huggingface dataset:
EPCO-23. LONGITUDINAL TRACKING AND LONG-READ CHROMATIN FIBER SEQUENCING OF HUMAN ASTROCYTES WITH TELOMERE DYSFUNCTION REVEALED ALTERED CHROMATIN ACCESSIBILITY AND INCREASED STRUCTURAL VARIATION
Authors: Hao Yue , Ranallo-Benavidez T Rhyker , Fukushima Noelle , Kyriakidou Maria , Berens Michael E , Barthel Floris P 
Published: November 2024

Abstract
Glioma is an aggressive cancer of the central nervous system that is genetically characterized by aneuploidy and frequent structural variation (SV). We sought to investigate the role of telomere dysfunction (TD) in shaping the SV landscape in glioma. Normal human astrocytes (NHA) were engineered to express viral E6E7 oncoproteins which are known to spontaneously trigger TD by suppressing p53/pRb. We hypothesized that NHA-E6E7 cells gradually accumulate SVs and aneuploidy over time because of progressive TD. We therefore longitudinally tracked bulk and single-cell clones of NHA-E6E7 cells for a period of over 6 months since viral infection. Overall, NHA-E6E7 cells demonstrate a growth benefit over primary NHA cells. We obtained Illumina short-read sequencing for NHA-E6E7 cells at multiple time points. Three time points were additionally selected for both Oxford Nanopore and PacBio HiFi long-read sequencing using the single-molecule chromatin fiber sequencing (fiber-seq) protocol. Copy number variation (CNV) analysis of short-read data showed deletion events in chromosome 13 as early as population doubling level (PDL) 48. K-mer based CNV analysis using the long-read data confirmed this finding and also detected deletion events in chromosome 7 at PDL 50. From the long-read data, we found an elevated number of SVs in NHA-E6E7 cells compared to the primary NHA cells. In particular, we detected telomere junctions and found that telomere-associated SVs were more prevalent in NHA-E6E7 cells compared to primary cells. Next, chromatin accessibility and regulatory elements were predicted from fiber-seq data with exogenous N6-methyladenosine (m6A) stencils. We observed large-scale chromatin actuation changes in various regulatory elements across the genome that intensified in later passages of NHA-E6E7 cells. For example, we found a decrease in the accessibility in FBXO7 which is a gene that maintains chromosome stability. Our preliminary results indicated that TD is an important mediator of structural variation in glioma.
EPCO-36. INTEGRATIVE DEEP-LEARNING AND PHARMACOGENOMIC PROFILING OF MALIGNANT GLIOMAS USING PATIENT-DERIVED TUMOR CELLS
Authors: Choi Seung-Won , Swamy Vinay , Hyun Seung Yoon , Her Nam-Gu , Kong Doo-Sik , Choi Jung Won , Seol Ho Jun , Lee Jung-Il , Nam Do-Hyun , Rabadan Raul 
Published: November 2024

Abstract
Malignant glioma stands as a formidable cancer with limited therapeutic options due to many factors including pronounced genetic heterogeneity, the blood-brain barrier, among others. Precision medicine, tailoring treatment based on a patient’s unique molecular profiles, is a fitting approach for addressing intra- and inter-tumor heterogeneity. Previously, we have shown the advantage of using patient-derived tumor cells (PDCs) to evaluate drug efficacy across various cancer types. Unlike cancer cell lines, which significantly differ from primary tumors, PDCs capture the molecular features of primary tumors, showing predictive clinical responses in a retrospective study. Building on these encouraging results, we have expanded PDC-based drug screening to specifically target malignant gliomas. We have established an initial cohort of over 500 malignant glioma PDCs (~ 370 patients) and screened more than 100 drugs. We have complemented our cohort with molecular profiles, including genomic and transcriptomic data to infer the potential pharmacogenomic associations of malignant gliomas. We constructed a multi-modal deep-learning model that seamlessly integrates molecular features and drug structure to predict the drug sensitivity. By employing an explainable machine learning method, we retrospectively analyzed the model to investigate the potential molecular biomarkers and their contribution to drug sensitivity. Collectively, our study demonstrates the efficacy of using patient-derived tumor cells (PDCs) combined with deep-learning models to predict drug sensitivity in malignant gliomas. This integrative approach can potentially refine personalized treatment strategies and improve clinical outcomes for glioma patients.
EPCO-37. LONGITUDINAL TUMOR-WIDE SAMPLING OF GLIOBLASTOMA REVEALS EARLY EVOLUTIONARY DIVERGENCE OF RECURRENCE AND CLUES TOWARDS IDENTIFYING THE BIOLOGICAL TUMOR CENTER
Authors: Lerman Benjamin , Hong Chibo , Schupp Patrick , Chen Lee , Zamler Daniel , Smirnov Ivan , Phillips Joanna , Shai Anny , Lupo Janine , Oldham Michael , Costello Joseph 
Published: November 2024

Abstract
Therapy resistance in glioblastoma is in part attributed to intratumoral heterogeneity and treatment-resistant cell populations. Understanding heterogeneity requires more complete tumor sampling at diagnosis and at recurrence. We used a whole-tumor sampling approach to obtain 43 spatially mapped biopsies from 3 glioblastomas at diagnosis and recurrence, Pyclone and ClonEvol imputed clonal evolution from exome data, and weighted gene co-expression network analysis inferred gene expression programs from RNA sequencing. Across the cohort, tumor-wide clonal alterations representing evolutionarily early expansions included canonical changes (i.e. Chr7 gain, EGFR amplification) and a diverse set of copy number variations (Chr19/20 gain), driver mutations (i.e. PTEN, KDR), and fusions (LIMCH1::UCHL1, KANK::DOCK8). In 2/3 patients, the founding clone was the only subclone common to primary and recurrence samples and 37% of cancer drivers across the cohort appeared after evolutionary divergence of the primary and recurrent tumors. We identified thirty-two transcriptional programs, six of which were differentially expressed between timepoints. Programs enriched for mitochondrial activity, endothelium/pericytes and classical glioblastoma subtype signature were more highly expressed in primary samples. Programs enriched for mesenchymal-like state, oligodendrocytes and inhibitory interneurons were more highly expressed in recurrence samples. At diagnosis, 11/16 samples showed higher expression of the classical subtype program compared to mesenchymal-like, but at recurrence the mesenchymal program dominated in 18/18 samples. Expression of the programs correlated more strongly with position relative to the contrast-enhancing rather than T2 tumor centroid (p&lt;0.001). These findings reveal novel diversity and complexity in the genetic roots of individual glioblastoma. Recurrences arose from subclones diverging early in evolution of the primary tumor and contained clonal drivers not detected in the primary. Expression data revealed transition from an intratumorally heterogeneous mixture of classical and mesenchymal signatures to tumor-wide mesenchymal at recurrence and suggests that the contrast enhancing centroid may serve as the biological center of the tumor.
EPCO-54. MULTIOMIC ANALYSIS OF SPINAL EPENDYMOMAS REVEALS MECHANISMS OF TUMOR AGGRESSIVENESS WITH MYCN AMPLIFICATION
Authors: Rampalli Ihika , Laws Maxwell , Mullaney Dustin , Mandal Debjani , Sisay Bayu , Elkahloun Abdel , Peñas-Prado Marta , Armstrong Terri , Gilbert Mark , Chittiboina Prashant 
Published: November 2024

Abstract
Grade-3 spinal ependymomas, particularly those harboring MYCN amplification, have dismal prognoses despite optimal treatment regimens. MYCN functions as a transcription factor (TF) to drive the expression of key tumor driver genes. Our aim is to identify mechanisms underlying tumor aggressiveness and treatment resistance in MYCN-amplified ependymomas. MYCN amplification in spinal ependymomas was identified with custom next generation sequencing panels and bulk methylation analysis. We then conducted paired single-nucleus RNA (snRNA-seq) and chromatin accessibility (snATAC-seq) sequencing of grade-2 (n=2, 1 patient) and grade-3 spinal ependymomas (n=6, 6 patients, 4 MYCN-amplified). Comparator snRNA-seq datasets (grade-2/grade-3; 8/2) were included from a publicly available dataset (GSE163686; all non-MYCN-amplified). Canonical cell classes were identified with a combination of cluster- and cell-based strategies. Downstream analysis was conducted using R 4.3 (Seurat, Signac, clusterProfiler, CellChat), and Python 3.11 (scanpy) packages. We identified ependymoma tumor cells distinct from canonical immune cell classes with gene expression analysis and confirmed a distinct copy-number-variation pattern in these cells with chromosome 1 and 2p gain, and chromosome 6p and 22q loss. MYCN-amplified tumor cells (compared to non-MYCN-amplified grade2/3 tumor cells) showed increased differential accessibility at genes including VEGFA. Increased MYCN TF activity was confirmed with gene overexpression of downstream targets including NOTCH3, CREB5, PLK1, and VEGFA. Other genes that were highly accessible and overexpressed in MYCN-amplified tumor cells were related to oxidative stress, differentiation, and anti-apoptotic pathways. MYCN-amplified tumor cells modified the tumor microenvironment with increased VISTA signaling between MYCN-amplified tumor cells and tumor-associated macrophages, creating an immunosuppressive environment. We confirmed these effects by observing a higher proportion of M2-like macrophages in MYCN-amplified tumors (29.6% vs 18.2%). In conclusion, MYCN amplification in spinal ependymomas upregulates tumor cell proliferation, angiogenesis, and M2-like macrophage recruitment/programming.
BIOM-29. UNMASKING COPPER DEPENDENCE IN GLIOMA: 19-GENE SIGNATURE FOR PATIENT STRATIFICATION AND TARGETED THERAPY
Authors: Rose Jue Toni , Pham Vu Viet Hoang , Shai-Hee Tyler , Cazzoli Riccardo , Descallar Joseph , Nagabushan Sumanth , Koh Eng-Siew , Vittorio Orazio 
Published: November 2024

Abstract
Adult-type diffuse gliomas exhibit poor prognosis with limited treatment options. Although copper-targeted therapies have been previously explored in these tumors, they have yet to show significant benefits. To understand the role of copper in glioma biology we performed an in silico data analysis on the TCGA glioma cohorts to identify copper-homeostasis related genes (CHRG) with prognostic significance. This was done to enable patient stratification into appropriate treatment arms for future clinical trials involving copper targeted therapies. Furthermore, in vitro experimentation was performed to validate the functional outcomes observed from the in silico results. 19 CHRGs were identified to have prognostic association from the TCGA glioma cohorts. This gene signature regulates a broad range of cellular processes, including metal homeostasis, metabolism, extracellular matrix organization, and immune cell function. The CHRG signature enabled the development of a predictive model that allowed stratification of patients between high and low risk groups. In vitro spheroid growth assays in both U87 cell lines with or without IDH mutation elicited sustained growth inhibition after 6 days post treatment. Furthermore, copper chelation therapy modified the energy potential of these glioma cells in vitro leading to growth inhibition. This study established a predictive model using 19 CHRGs that enable patient stratification between high and low risk glioma patients. Furthermore, our in vitro experiments show the suitability of targeting intracellular copper to inhibit tumor growth. Further research is needed to understand the underlying mechanisms and explore optimal treatment combinations for improved outcomes. We aim to extend this approach to pediatric gliomas for improved risk assessment and personalized medicine.
BIOM-43. SOMATICTP53, PIK3R1, NF1 ORTERT MUTATIONS ARE ASSOCIATED WITH INFERIOR CLINICAL OUTCOME IN H3K27M-ALTERED DIFFUSE MIDLINE GLIOMA: AN INTERNATIONAL, MULTI-INSTITUTIONAL STUDY
Authors: Nguyen Thien , Lerman Benjamin , Stoller Schuyler , Müller Timothy , Comfort Lion , Leal-Ekman Steven , Lyons Samantha , Holman Lynette , Junior Calixito Hope Lucas , Banerjee Anu , Reddy Alyssa , Gupta Nalin , Whipple Nicholas , Gerber Nicolas , Stuecklin Ana , Areza Esha , Marion Rizo , Knowles Truman , Solomon David , Franson Andrea , Koschmann Carl , Partap Sonia , Monje Michelle , Prolo Laura , Cheshier Samuel , Antony Reuben , Bhatia Aashim , Foster Jessica , LaRiviere Michael , Maule Laura , Carrion Andrea Webster , Kline Cassie , Bruningk Sarah , Nazarian Javad , Waszak Sebastian , Mueller Sabine 
Published: November 2024

Abstract

BACKGROUND
H3K27-altered diffuse midline gliomas (DMGs) have poor prognosis with no standard of care therapy beyond radiation (RT). While RT prolongs survival, not all patients respond. Molecular biomarkers can be a strategy to predict RT response and thus patient outcomes.

METHODS
We performed a retrospective analysis of patients with biopsy-proven H3K27M-altered DMG between 2013-2023 from six US medical centers and the DMG Center in Zurich. Patients with tumor genomic sequencing and completion of RT were eligible. Genomic alterations were evaluated for somatic mutations, fusions, and chromosomal instability. Cox proportional hazard models were used to evaluate associations between genomic alterations and survival. Multivariate analysis included all significant variables at P &lt;0.1 in initial analysis, including age at diagnosis, tumor location, TP53 and PIK3R1 alterations.

RESULTS
297 patients (135 female; median age 8.3 years; range 0.2-71.4 years) were included. Median progression-free survival (PFS) and overall survival (OS) was 7.6 months (95%CI: 6.9-8.6) and 14.0 months (95%CI: 12.9-15.7). In univariate analysis, TP53 or PIK3R1 status correlated with shorter OS (TP53-mutant 12.5 vs. TP53-wildtype 17.5 months; HR=1.5; 95%CI: (1.1-2.0), P= 0.005); (PIK3R1-mutant 12.6 vs. 14.5 months; HR=1.9, 95%CI: (1.1-3.4), P = 0.03). Multivariate analysis corroborated TP53-mutant status with poorer OS (HR=1.5; 95%CI: (1.2-2.0), P= 0.003). Subgroup univariate analysis of pontine DMG patients showed poorer OS with TP53, NF1, or TERT mutations (TP53-mutant 11.9 vs. 15.2 months; HR= 1.6; 95%CI: (1.1-2.3), P= 0.02); (NF1-mutant 8.4 vs. 13.6 months; HR= 2.3; 95%CI: (1.1-5.0), P=0.03); (TERT 8.5 vs. 13.6 months; HR= 2.5; 95%CI: (1.1-5.7), P= 0.03). Subsequent multivariate analysis corroborated the association of TERT mutations with poorer OS in pontine DMG (HR=2.5; 95%CI:1.05, 5.9, P= 0.03).

CONCLUSIONS
This is the largest cohort of H3K27M-altered DMG patients with volumetric imaging analysis ongoing. Taken together, our data suggests these genetic alterations can risk-stratify patients for RT and future investigations of radiosensitizers targeting these alterations may improve survival.
BIOM-60. UNDERSTANDING THE INTERSECTION OF RACE, SEX, AND GENOMIC PROFILES IN MENINGIOMA PATHOPHYSIOLOGY
Authors: Dincer Alper , Ghanekar Shaila , Tabor Joanna , Kim Miri , Moliterno Jennifer 
Published: November 2024

Abstract

BACKGROUND
While meningioma incidence and outcomes vary by sex and race, the potential underlying molecular differences possibly contributing to these disparities are less understood. Herein, we explore the clinical and genomic characteristics of meningiomas across groups characterized by age and sex.

METHODS
We analyzed adult patients with primary meningiomas resected from 2012 to 2023. Patients underwent whole exome sequencing, and demographic data were categorized into four groups based on self-reported race and sex, which included White females, White Males, Black females, and Black males. The primary analyses involved comparisons of tumor characteristics, socioeconomic status (median zip code income, % with high school diploma, health insurance status, distance from hospital), genomics, and recurrence rates.

RESULTS
The study included 509 primary meningiomas. White females exhibited low-risk genomic profiles characterized by driver mutations in KLF4 (+/- TRAF7) (p=0.010) and POLR2A (p=0.045), with no associated CNVs (p=0.410). This benign molecular profile correlated with lower WHO grades (p=0.013) and a lower incidence of recurrence (p=0.0003). Black females had meningiomas enriched with Hedgehog pathway mutations (p=0.0035) and a predilection for the anterior skull base (p=0.034), leading to an increased risk of recurrence (p=0.026). White males showed an aggressive genomic profile, including chromosome 1p loss (p=0.025) and 10q loss (p=0.067), associated with a high risk of recurrence (p=0.0002). Black males had meningiomas with chromosome 14q loss (p=0.0002), the highest incidence of high-grade meningiomas (p=0.048), and a 4.5-fold increased risk of recurrence (OR 4.5 [1.6-11.8]; p=0.006). Black males also experienced the worst progression-free survival (HR 5.5 [2.5-12.4]; p&lt;0.0001), independent of WHO grade, extent of resection, and socioeconomic status.

CONCLUSIONS
Each demographic has a distinct molecular profile that correlates with clinical behavior in a race and sex-specific manner. Black males are disproportionately affected by biologically aggressive meningiomas, leading to higher tumor grade and recurrence rates.
BIOM-61. CSF CTDNA ANALYSIS OF PATIENTS WITH DIFFUSE GLIOMAS REVEALS DIAGNOSTIC MOLECULAR ALTERATIONS
Authors: Arjuna Srividya , Wang Daniel H , Balar Ashish , Shah Mauli , Dono Antonio , Sanchez-Espitia Alexander , Duose Dzifa , Nguyen Sophia , Patel Chirag B , Prabhu Sujit S , Lang Frederick F , Esquenazi Yoshua , Ballester Leomar Y 
Published: November 2024

Abstract
There is a critical need for better strategies to diagnose and monitor patients with diffuse gliomas. Liquid biopsies are less invasive than tissue biopsies and are amenable to serial collection at multiple timepoints. However, analysis of circulating tumor DNA (ctDNA) in cerebrospinal fluid (CSF) in patients with diffuse gliomas remains underutilized in clinical practice due to technical challenges and a scarcity of studies demonstrating clinical utility. We evaluated ctDNA in 49 CSF samples from patients with various types of diffuse gliomas with a next generation sequencing (NGS) panel interrogating 613 cancer-related genes. Cell-free DNA concentration obtained from CSF (0.4-5mL) ranged from 0.009 to 60ng/µL. Input DNA concentration ranged from 0.12-30ng. Mutations were detected in 29/49 (59.2%) samples including 22/49 (44.9%) with single nucleotide changes, 14/49 (28.6%) with copy number changes, and 1 fusion (2.0%). The majority of samples without mutations detected (n=20) had suboptimal DNA input (&lt;30ng): 17/20 (85%). We identified diagnostic alterations in CSF including mutations in IDH1 (3/5 IDH-mutant gliomas), TERTp and EGFR amplification (7/34 glioblastomas), H3-3A (4/6 pediatric high-grade gliomas). Some of these mutations, in combination with other clinical parameters, allowed us to identify specific CNS tumor types based on the 2021 WHO classification of CNS tumors, resulting in the reclassification of 2 patients. Matched tumor tissue sequencing results were available for 23/49 (46.9%) patients and the results showed good concordance with CSF ctDNA analysis. In summary, our results suggest that the NGS analysis of CSF-ctDNA can provide clinically relevant information in patients with diffuse gliomas.
BIOS-03. CLINICAL PRESENTATION, MANAGEMENT, AND OUTCOME IN NEUROLYMPHOMATOSIS: A SYSTEMATIC REVIEW AND ANALYSIS OF INDIVIDUAL PATIENT DATA FROM 459 CASES
Authors: Kaulen Leon D , Hielscher Thomas , Doubrovinskaia Sofia , Hoffmann Dirk C , Kessler Tobias , Traub Benjamin-Leon , Baehring Joachim , Wick Wolfgang 
Published: November 2024

Abstract

BACKGROUND
Neurolymphomatosis (NL) refers to lymphomatous infiltration of the peripheral nervous system (PNS). NL diagnosis and treatment are challenging given the broad differential diagnosis of peripheral neuropathy, the lack of larger cohorts and the subsequent unavailability of prognostic factors or consensus therapy. This study aimed to define characteristics and prognostic factors of NL.

METHODS
A systematic review of the literature (2004-2023) was performed using PubMed and Scopus databases and reported following PRISMA guidelines. Clinical, radiological, pathological and outcome information were extracted. Multivariable survival analyses were performed using Cox proportional hazard models.

RESULTS
A total of 459 NL cases from 264 studies were accumulated. NL was the first manifestation of malignancy (primary NL) in 197 patients. PNS relapse of known non-Hodgkin lymphoma (secondary NL) occurred in 262 cases after a median 12 months. NL predominantly presented with rapidly deteriorating, asymmetric painful polyneuropathy. Infiltrated structures included peripheral nerves (56%), nerve roots (52%), plexus (33%) and cranial nerves (32%). Diagnosis was established at a median of 3 months after symptom onset with substantial delays in primary NL. It mainly relied on PNS biopsy or FDG-PET, which carried high diagnostic yields (&gt; 90%). Post mortem diagnoses were rare (3%). Most cases were classified as B-cell (90%) lymphomas. Tumor-directed therapy was administered in 96% of patients and typically consisted of methotrexate or rituximab-based polychemotherapy. Median overall survival was 18 months. Primary NL without concurrent systemic disease outside the nervous system (hazard ratio [HR]: 0.44; 95% confidence interval (CI): 0.25-0.78; p = 0.005), performance status (ECOG &lt; 2, HR: 0.30; 95% CI: 0.18-0.52; p &lt; 0.0001), and rituximab-based treatment (HR: 0.46; 95% CI: 0.28-0.73; p = 0.001) were identified as favorable prognostic markers on multivariable analysis when adjusting for clinical and sociodemographic parameters.

CONCLUSIONS
Advances in neuroimaging modalities, particularly FDG-PET, facilitate NL diagnosis and offer a high diagnostic yield. Rituximab-based therapy improves NL outcome. Findings may assist clinicians in early recognition, prognostic stratification, and treatment of NL.