bluuebunny/crossref_metadata_2025 huggingface dataset:
EPID-24. CAPTURING EVOLVING DEFINITIONS OF 12 SELECT RARE CNS TUMORS: A TIMELY REPORT FROM CBTRUS AND NCI-CONNECT
Authors: Price Mackenzie , Neff Corey , Kruchko Carol , Waite Kristin , Cioffi Gino , Barnholtz-Sloan Jill , Cordeiro Brittany , Penas-Prado Marta , Ozer Byram , Cimino Patrick , Gilbert Mark , Armstrong Terri , Ostrom Quinn
Published: November 2023

BACKGROUND

Incidence, prevalence, and survival are population-based cancer statistics that describe cancer burden. The National Cancer Institute’s Comprehensive Oncology Network Evaluating Rare CNS Tumors (NCI-CONNECT) specializes in research of 12 rare CNS tumor types to improve approaches to care and treatment. These tumors include atypical teratoid/rhabdoid tumors, brainstem and midline glioma, choroid plexus tumors, ependymoma, high grade meningioma, gliomatosis cerebri, medulloblastoma, oligodendroglioma/anaplastic oligodendroglioma, pineal region tumors, pleomorphic xanthoastrocytoma, CNS embryonal tumors, not elsewhere classified (NEC)/not otherwise specified (NOS), and primary CNS sarcoma. This study aimed to update incidence, prevalence, and survival statistics for these tumors.

METHODS

The Central Brain Tumor Registry of the United States (CBTRUS) database, a combined dataset of CDC’s National Program of Cancer Registries (NPCR) and NCI’s Surveillance, Epidemiology and End

RESULTS

(SEER) data, was used to calculate average annual age-adjusted incidence rates (AAAIR) per 100,000 population overall and by sex, race-ethnicity, and age (2008-2019). NPCR data were used to calculate relative survival (RS) estimates (2008-2018). Prevalence on December 31, 2019 was estimated using annual age-specific incidence and survival from CBTRUS and SEER, respectively.

RESULTS

AAAIR was 1.51 per 100,000 for these tumors combined, with highest incidence in ependymomas (AAAIR=0.41/100,000). Most tumor types were more common in males, adults (ages 40+ years) or children ages < 15 years, and non-Hispanic White individuals. Ependymomas were most prevalent (19,339 cases) followed by oligodendrogliomas (15,070 cases). RS for all subtypes combined at 1-, 5-, and 10-years was 86.6%, 71.9%, and 65.3%, respectively. Ependymomas had the highest RS (5-years=90.6%) and primary CNS sarcomas had the lowest RS (5-years=7.7%).

CONCLUSIONS

Incidence, prevalence, and survival patterns for these 12 selected rare cancer subtypes varied significantly by type. Population-based data are critical to guiding effective design of and accrual expectations for clinical trials in rare cancers.
EPID-26. THE IMPACT OF COVID-19 POSITIVITY AND PREVALENCE ON TREATMENT UTILIZATION FOR GLIOBLASTOMA PATIENTS
Authors: Zhu Ping , Chen Clark ,   NC Consortium
Published: November 2023

OBJECTIVES

Glioblastoma (GBM) is the most common (46.1%) and aggressive malignant primary brain tumor. We propose to explore the pandemic effect on the change of health care delivery for glioblastoma patients using the National Cancer Database (NCDB) and validate the findings in primary brain tumors using one of the largest COVID-19 real-time centralized data in the world - the National COVID Cohort Collaborative (N3C) database.

METHODS

Multivariable binary logistic regression models were performed to investigate whether the pandemic (including COVID-19 positivity and density of COVID-19 prevalence based on zip code-level) affected the receipt of GBM care including surgical procedure, radiation, and chemotherapy.

RESULTS

A total of 4093 GBM patients and 4481 primary brain tumor patients were derived from the NCDB and N3C, respectively. Seventy-nine percent of GBM patients received the COVID-19 test (3241/4093) and 290 patients were COVID-19 positive. Black, Hispanic, lower education-level, and higher Charlson/Deyo Score ( >=2) were significant factors related to COVID-19 positivity. The proportions of receiving GBM care significantly decreased in COVID-19-positive patients compared to pre-pandemic years (2018-2019). After adjusting the potential confounders and covariates, the odds of undergoing tumor resection/biopsy (aOR-0.37, p< 0.001), radiation (aOR-0.36, p< 0.001), and chemotherapy (aOR-0.31, p< 0.001) for COVID-19 positive patients were significantly lower than COVID-19 negative patients (NCDB). Similar results were detected in primary brain tumor patients using N3C. The odds of undergoing surgical procedures in patients resided in the higher density of COVID-19 prevalence (four zip code-level, per 1000 population) (aOR-0.63, 0.69, 0.59, all p< 0.001) and with COVID-19 positivity (aOR-0.54, p< 0.001) were significantly lower comparing to the related reference groups (N3C).

CONCLUSIONS

Our findings suggest that healthcare delivery for GBM and primary brain tumors has been remarkably affected by COVID-19 positivity and high-level COVID-19 prevalence during the pandemic.
EPID-32. A COST ANALYSIS OF BRAIN AND NERVOUS SYSTEM CANCER CARE: AN EXAMINATION OF HEALTHCARE EXPENDITURE TRENDS IN THE UNITED STATES FROM 1996 TO 2016
Authors: Guo Edward , Gupta Mehul , Rossong Heather , Ahmed Shubidito , Stukalin Igor , Lama Sanju , Sutherland Garnette
Published: November 2023

INTRODUCTION

Management of brain and central nervous system malignancies is associated with substantial healthcare spending, yet estimates of per-patient cost and longitudinal temporal trends remain elusive. In this study, we investigate trends in United States (US) healthcare spending on these diseases between 1996-2016.

METHODS

We utilize inflation-adjusted national healthcare spending data and age-adjusted prevalence estimates from the Institute for Health Metrics and Evaluation to estimate per-patient US healthcare spending stratified by age and care setting. We employ joinpoint regression to identify temporal trends in healthcare spending, expressed as annual percent change (APC). Drivers of change data from 1996-2013 were evaluated to investigate shifts associated with increased spending.

RESULTS

In 2016, total healthcare spending attributable to brain and nervous system cancers was $6.85 billion (95% CI, $5.98-7.57 billion), corresponding to $2,245 (95% CI $1,962-$2,480) per patient, with the largest share coming from inpatient care settings ($4.60 billion [95% CI 3.87-5.24 billion]). Private payers shouldered the majority of costs (65.6%) compared to public payers (28.1%) and out-of-pocket expenses (6.4%). The average APC in spending between 1996-2016 was 3.69% [95% CI 3.00%-4.39%], driven primarily by an increase in the price and intensity of inpatient care (11.8% [95% CI 7.7%-16.1%). Further, three statistically significant periods of spending change were identified: 1996-2005 (2.42% [95% CI 2.04-2.80%], p < 0.001 ), 2005-2008 (4.43% [95% CI 1.08%-7.89%], p < 0.0001), 2008-2014 (6.32% [95% CI 5.41%-7.25%], p < 0.001), with spending being relatively stable from 2014-2016.

DISCUSSION

US expenditures for brain and nervous system malignancies are substantial and have significantly increased between 1996-2016, largely driven by increased inpatient spending. These findings may inform policy efforts to reduce the disease burden while balancing healthcare spending.
EPCO-02. DNA METHYLATION PROFILING OF BRAIN METASTASIS REVEALS UNDERLING TUMOR RECURRENCE SIGNAL AND ASSOCIATED PATHWAYS
Authors: Ajisebutu Andrew , Sosa Julio , Zuccato Jeffery , Liu Jeff , Patil Vikas , Zadeh Gelareh
Published: November 2023

INTRODUCTION

Brain metastases, the most common form of intracranial neoplasms, carry a poor survival rate, mostly attributed to their high recurrence rates. Currently there are no reliable methods to determine which patients will progress. DNA methylation profiling (DNAmp) has become a useful tool in the diagnosis and stratification of intracranial neoplasms, and has the potential to provide clues on the epigenetic mechanisms that govern tumor behavior.

METHODS

A cohort of 58 BM tumor samples were selected for analysis. The cohort was composed of three groups: N=21 primary metastatic tumors (PMT), N=21 matched paired recurrent tumors (RMT), and a cohort of N= 16 primary metastatic tumors without any evidence of recurrence (NRMT). All tumor samples underwent DNAmp on the Illumina Infinium EPIC array to determine their methylation status at 850,000 CpG sites. Tumors were profiled via unsupervised hierarchical clustering, pathway enrichment analysis, and cell deconvolution analysis.

RESULTS

Differential methylation analysis revealed over 32617 differentially methylated CpG sites between grouped PMT and RMT samples, and 835424 sites between PMT and NRMT samples. When comparing PMT with NRMT samples, we revealed a distinct DNAmp that was upheld upon hierarchical clustering analysis. NRMT samples show a significant downregulation of pathways involved in DNA-binding and transcriptional regulation. Paired analysis of PMT and RMT revealed a relative paucity of differentially methylated CpG sites shared across paired samples: a total of 257 probes were differentially methylated across 14/19 samples. These probes however showed enrichment primarily for DNA-binding and transcription factor regulation, in reverse from the non-recurrent samples.

CONCLUSION

Our data suggests that DNAmp may be capable of differentiating tumors destined to progress from those with less aggressive features, and that DNAmp appear to remain stable through to recurrence. This work demonstrates the potential for DNA methylation to be utilized to uncover pathways associated with BM recurrence.
EPCO-03. A COMPREHENSIVE SINGLE-CELL ATLAS OF SCHWANNOMA REVEALS CONSERVED CELLULAR STATES ACROSS DIFFERENT GENETIC BACKGROUNDS AND ANATOMIC LOCATIONS
Authors: Castro Luis Nicolas Gonzalez , Gavish Avishai , Bussema Lillian , Neftel Cyril , Nomura Masashi , Chiocca E Antonio , Bi Wenya Linda , Arnaout Omar , Barker Frederick , Brown Justin , Jordan Justin T , Stemmer-Rachamimov Anat , Plotkin Scott R , Tirosh Itay , Suva Mario
Published: November 2023

BACKGROUND

Despite being associated with molecular alterations in the NF2 gene, there is limited understanding of the gene expression programs that govern the behavior of schwannomas both in sporadic cases as well as in patients with schwannoma predisposition syndromes, and also with respect to their anatomic location.

METHODS

We characterized the transcriptional heterogeneity of schwannomas across different genetic backgrounds and anatomic locations at the single-cell level. Tumor samples from patients undergoing resection for symptomatic schwannoma were dissociated and single cells were processed for full-transcript whole transcriptome profiling via Smart-seq2. Our cohort of 22 schwannomas, includes 5 tumors from schwannomatosis patients, 11 tumors from neurofibromatosis type 2 patients, and 6 sporadic tumors – 3 of which had grown after radiation treatment. Anatomically, 12 tumors were excised from cranial nerves (11 vestibular, 1 accessory) and 10 from spinal and other peripheral nerves.

RESULTS

We profiled 11,373 cells, including 4725 neoplastic cells, 2425 fibroblasts, 1314 T cells, 1258 endothelial cells, 969 myeloid cells, 503 pericytes and 240 Schwann cells. Copy number alteration analyses reveal evidence of intratumoral polyclonality (supporting the hypothesis of multiple sites of origin for a tumor). Using non-negative matrix factorization, we identify 6 distinct transcriptional metaprograms, with gene signatures related to stress, myelin production, antigen presentation, interferon signaling, glycolysis and extracellular matrix. After comparison with a pan-cancer gene expression dataset, we note unique interferon and antigen presentation metaprograms in schwannoma, with the latter being mainly characterized by expression of MHC Class II genes. Overall, we observe conserved expression of these metaprograms across anatomic locations and genetic backgrounds, with the exception of decreased interferon signaling for vestibular tumors.

CONCLUSION

We provide a comprehensive single-cell characterization of schwannoma spanning diverse genetic and anatomic backgrounds. We describe unique transcriptional metaprograms for antigen presentation and interferon signaling, which might underlie mechanisms for immune evasion.
EPCO-08. CONVERGENCE OF NON-CODING SOMATIC MUTATIONS ON CANCER DRIVER PLEXUSES IN PEDIATRIC HIGH-GRADE GLIOMA
Authors: Chen Tina Huey-Miin , Singhal Divya , Gallo Marco
Published: November 2023

Central nervous system tumors are the most common pediatric malignancies after leukemia, and the most common cause of cancer death among persons ages 0 – 14 [1,2]. Despite its low incidence rate, pediatric high-grade gliomas (pHGGs) account for over 40% of all childhood brain tumor deaths [3, 4]. As such, it remains the focus of many research teams across the globe. The discovery of recurrent mutations in genes encoding histone H3.3 [5] was a breakthrough in the genetic basis of pHGGs and highlighted the relevance of epigenetic reconfiguration for oncogene activation. However, much work is still needed to uncover driver alterations responsible for tumor initiation or progression. pHGGs have frequent epigenetic dysregulation [6,7] and abundant somatic mutations in the noncoding regions of the genome [8], but the functional relevance of the noncoding somatic mutations has not been evaluated systematically. Here, we assess correlations between noncoding somatic mutations in pediatric brain-specific cis-regulatory elements (CREs) and changes in gene expression. We demonstrate the sparsity of recurrent mutations in CREs. Then illustrate the power of graph database in consolidating multi-omics datasets for efficient queries. Our network approach for charting the genomic, epigenetic, and transcriptomic landscape of pHGG allow us to 1) identify clusters of CREs associated with dysregulated gene expression, 2) nominate transcription factors whose binding affinities are recurrently impacted by somatic mutations found in pHGGs, and 3) establish regulatory networks potentially guiding pHGG tumor growth and progression.
EPCO-18. HETEROCHROMATIN DYSFUNCTION IMPACTING GENOMIC TOPOLOGY AND SUPERENHANCER LANDSCAPES PROMOTES ATRX-DEFICIENT GLIOMAGENESIS
Authors: Malgulwar Prit Benny , Saw Ajay Kumar , Singh Anand , Danussi Carla , Dharmaiah Sharvari , Johnson William E , Rai Kunal , Huse Jason
Published: November 2023

Mutational inactivation of the SWI/SNF chromatin regulator ATRX occurs frequently in diffuse gliomas. Whether and how ATRX deficiency promotes oncogenesis remains unclear, despite its implication across a broad array of physiological processes. We sought to delineate the molecular mechanisms by which global epigenomic dysfunction promotes oncogenic phenotypes in ATRX-deficient glioma models. Building on earlier work implicating chromatin accessibility and transcriptional shifts, we employed integrated epigenomic profiling in Atrx-intact and -deficient murine neuroepithelial progenitor cells (mNPCs), validating findings will functional approaches in human glioma stem cells (GSCs) of appropriate genotype. We found that ATRX deficiency dramatically impacted the integrity of large heterochromatin domains genome-wide, with tangible effects on underlying gene expression. This process fundamentally altered chromatin topology, as assessed by Hi-C analysis, and associated superenhancer landscapes, influencing key developmental gene sets like the HOXA cluster. Pharmacological inhibition of HOXA signaling in GSCs selectively reduced proliferation, increased apoptosis, and impaired in vivo growth in the ATRX-deficient context. Finally, our results pointed to derepression of LINE1 endogenous retroviral elements as key mediators of ATRX-deficient heterochromatin dysfunction. Our work implicates novel and targetable molecular mechanisms involving complex epigenomic rewiring and chromatin topology in ATRX-deficient oncogenesis. In doing so, we advance the understanding of a deadly brain tumor along with broader conceptions of epigenetic mechanisms as fundamental drivers in cancer.
EPCO-21. IDENTIFYING FACTORS THAT PREDICT GENETIC PREDISPOSITION TO BRAIN TUMOR FORMATION
Authors: Lee John , Tripathy Arushi , Guivatchian Tannaz , Koeppe Erika , Stoffel Elena , Al-Holou Wajd
Published: November 2023

INTRODUCTION

Increasing evidence suggests that glioma formation may have a greater hereditary component than initially thought. Identification of individuals with a genetic predisposition is critical for appropriate monitoring and treatment.

OBJECTIVE

To analyze the personal and family histories of patients with intrinsic brain tumors seen in a cancer genetics clinic to inform referral practices.

METHODS

A prospective database of cancer genetics data from a large multidisciplinary cancer genetics clinic was queried for brain tumors from 2007-2023. Genetic test results, age of brain cancer diagnosis, number/types of distinct cancers, oncologic family history, and personal and family history of cancer syndromes were recorded. Fisher’s exact tests and ANOVA were used for analysis.

RESULTS

Sixty-five patients with intrinsic brain tumors, which included 53 high and low grade gliomas, were identified. There were 33 males; the mean age of diagnosis was 34.6±23.4. Fifty-three (81.5%) had genetic testing performed. Of these, 19 (35.8%) were found to have germline pathogenic variants (PV), 10 (18.9%) had variants of unknown significance (VUS), and 24 (45.3%) were found to have no mutations. Patients with PVs were younger than patients with normal genetic screening (28.1 vs 41.5 years, p= 0.06), and patients with either PV or VUS were significantly younger (p= 0.04) than patients with normal screening. Regarding personal cancer history, patients with and without PVs had a similar history of personal cancers (p= 0.20). Regarding family history, only 1 patient with PV had a family history of brain cancer compared to 15 in patients with negative testing (5.3% vs 44.1%, p= 0.004).

CONCLUSIONS

Only younger age at presentation was identified as a predictor of a PV or VUS. A lack of personal/family history of cancer does not preclude a genetic predisposition to cancer. We recommend that younger patients with intrinsic brain tumors should be referred for genetic testing.
EPCO-22. LONGITUDINAL MOLECULAR CHARACTERIZATION IDENTIFIES TREATMENT DRIVEN EVOLUTION OF OLIGODENDROGLIOMA
Authors: Chowdhury Tamrin , Johnson Kevin , Kocakavuk Emre , Heo Chaewon , Ye Gordon Y , Ghospurkar Padmaja , Wade Taylor , Barnholtz-Sloan Jill , Costello Joseph , Elliott Carol , French Pim , Golebiewska Anna , Hermes Beth , Hong Chibo , Horbinski Craig , Khasraw Mustafa , LaViolette Peter , Li Kay Ka-Wai , Lipp Eric , Lowman Allison , McCortney Katy , Moon Hyo-Eun , Ng Ho-Keung , Padovan Marta , Paek Sun Ha , Vallentgoed Wies , Vaubel Rachael , Wesseling Pieter , Westcott Kerryn ,   GLASS Consortium, Varn Frederick , Verhaak Roel
Published: November 2023

Oligodendroglioma is characterized by oligodendrocyte-like histology, mutation in the IDH genes, along with codeletion of chromosome arms 1p and 19q. Treatment for oligodendrogliomas combines surgery, followed by observation, and chemotherapy and/or radiotherapy when tumors progress. Most oligodendrogliomas eventually recur with a more aggressive phenotype, leading to patient mortality but molecular mechanisms remain poorly understood. To investigate the molecular trajectory of oligodendroglioma, we collected more than 270 longitudinal samples from over 130 oligodendroglioma patients, to perform whole genome or whole exome sequencing, bulk RNA, and single-nucleus RNA sequencing (n = 30 samples). Common mutations in IDH1/2, TERT promoter, CIC, and FUBP1 were observed. About half of the CIC and FUBP1 mutations occurred in the initial sample and persisted stably throughout recurrence. The majority of PIK3CA and PIK3R1 mutations were either shared or present in recurrences only implicating the PI3K pathway in oligodendroglioma recurrence. Mutational signature analysis revealed 34.5% of tumors treated with alkylating agents acquired SBS11/SBS31 associated hypermutation. By integrating signatures with clonality estimates, we approximated the timing of mutational processes and found that clonal timings of treatment related mutations correlate with the treatment administration date. We found that aging signature-related mutations were mostly clonal, and treatment signature-related mutations were more likely to be sub-clonal, supporting the late emergence of these mutations following treatment. We observed increased somatic copy number alterations in oligodendroglioma recurrences, reflected in notable chromosome 4 losses. Associating treatment with snRNAseq derived cellular states, we observed a significant increase in the fraction of proliferating stem-like cells in the hypermutator versus non-hypermutator recurrent samples. These findings shed light on the molecular changes occurring in oligodendrogliomas following treatment and provide insights that may aid in targeting treatment resistance.
EPCO-32. DISSECTING THE INTRA- AND INTER-TUMORAL HETEROGENEITY UNDERLYING GLIOBLASTOMA PATHOGENESIS UTILIZING MULTI-OMICS ANALYSIS
Authors: Nakashima Takuma , Funakoshi Yusuke , Yajima Hirohisa , Yamamoto Ryo , Sugihara Yuriko , Nambu Shohei , Arakawa Yoshiki , Tanaka Shota , Ishida Joji , Saito Ryuta , Hanaya Ryosuke , Yoshimoto Koji , Narita Yoshitaka , Suzuki Hiromichi
Published: November 2023

Glioblastoma (GBM) is the most common malignant brain tumor with a dismal prognosis. Considering its extensive molecular diversity underlies therapeutic resistance to multimodal treatment, it is imperative to reveal intra- and inter-tumoral heterogeneity, leading to further understanding of GBM pathogenesis. We analyzed 289 whole-genome sequencing data (WGS) including 159 unpublished deep WGS (≥ ×120 coverage) along with RNA-seq, DNA methylation array, whole-genome bisulfite sequencing, and assay for transposase-accessible chromatin with sequencing (ATAC-seq) to uncover the multi-omics molecular heterogeneity of GBM. Along with inter-tumoral heterogeneity of genetic driver alterations, deep WGS enables us to delineate a fine view of clonal architecture where mutational signatures differ across clonal and subclonal mutations, supporting that different mutational processes contribute to GBM pathogenesis depending on the developmental stage. As well, tumor cell differentiation status detected by transcriptional deconvolution analysis is associated with multi-layer profiles including genome, transcriptome, epigenome, and chromatin status. ATAC-seq demonstrated distinct features of genome-wide chromatin accessibility associated with gene expression subtypes of GBM. Motif enrichment analysis detects the differentially accessible regions where the proneural subtypes are enriched with the SOX10 motif, known as a transcription factor for mesenchymal transition whereas the mesenchymal and classical subtypes are enriched with the CREB/ATF motif, a regulator of TGF beta associated with a poor prognosis. Our findings support a model in which GBM evolves through generating genetic and epigenetic intra-tumoral heterogeneity suggesting that specific cell states may have distinct vulnerability to mutational processes and epigenetic modifications. Our analysis reveals the molecular mechanisms underlying the progression of GBM enhancing our understanding of the pathogenesis.
EPCO-37. DISSECTING GBM EVOLUTION FOLLOWING STANDARD-OF-CARE BY LARGE-SCALE LONGITUDINAL SINGLE NUCLEUS RNA-SEQUENCING
Authors: Nomura Masashi , Spitzer Avishay , Johnson Kevin , Garofano Luciano , Nehar-Belaid Djamel , Oh Young Taek , Anderson Kevin J , Najac Ryan D , Bussema Lillian , Varn Frederick , D’Angelo Fulvio , Chowdhury Tamrin , Migliozzi Simona , Park Jong Bae , Ermini Luca , Golebiewska Anna , Niclou Simone , Das Sunit , Paek Sun Ha , Moon Hyo-Eun , Mathon Bertrand , Stefano Anna-Luisa Di , Bielle Franck , Laurenge Alice , Sanson Marc , Tanaka Shota , Saito Nobuhito , Keir Steve , Ashley David , Huse Jason , Alfred Yung W K , Lasorella Anna , Iavarone Antonio , Verhaak Roel , Suva Mario , Tirosh Itay
Published: November 2023

The heterogeneity within tumors has long been associated with therapy failure and disease progression. Recent advances in single-cell RNA-sequencing technologies have enabled us to dissect the cellular diversity in glioblastoma (GBM). However, how these cellular programs change longitudinally under therapy remains poorly understood. To address this question, we collected and profiled a large-scale longitudinal cohort of 59 matched IDH-wildtype GBM sample pairs provided by 7 centers worldwide by single-nucleus RNA-sequencing (snRNA-seq) and whole-exome/whole-genome sequencing. The majority of patients (51 patients) in this cohort received standard-of-care (temozolomide and radiation) following initial tumor resection. Leveraging this large-scale snRNS-seq dataset of 457,442 cells, we detected novel cellular states and associations between malignant and tumor microenvironment (TME) cells, and then performed longitudinal analyses. The recurrent samples showed significantly lower malignant cell fraction (p=0.002) and reciprocal increase in proportions of glio-neuronal TME cell types (oligodendrocytes, neurons and astrocytes). The TME composition, malignant cell state proportions and baseline expression programs were retained at recurrence more than expected by chance, but overall were not well conserved between primary and recurrent samples. A subset of pairs (12/59 pairs) enriched with glio-neuronal TME at recurrence showed a significant transcriptomic shift and was associated with better clinical course (p=0.02). The tumors that acquired radiation-related small deletion phenotype underwent a transition towards MES/Hypoxia phenotype (0/9 at primary, 6/9 at recurrence, p=0.02). We defined pairs as likely responders or non-responders to treatment based on the MGMT methylation status of the primary tumor sample. This uncovered diverging evolutionary trajectories in cellular programs between the two groups. Strikingly, the changes in malignant state frequency and baseline malignant expression profile were strongly associated with specific changes in the TME composition. Our findings based on high-resolution longitudinal snRNA-seq analyses highlight the diverse evolutionary trajectories in GBM that are shaped by TME changes and treatments.
EPCO-40. CARM1 IS A NOVEL TUMOR SUPPRESSOR IN GLIOBLASTOMA THAT REGULATES QKI THROUGH ARGININE METHYLATION
Authors: Lu Kaylene , Wright Tanner , Shin Seula , Bedford Mark , Hu Jian
Published: November 2023

Glioblastoma (GBM) is the most common form of primary brain tumor, characterized by dismal patient prognosis. Current pharmacological interventions have not significantly improved patient outcomes due to intratumor heterogeneity and the persistence of glioma stem cells (GSCs) that drive invasion and resistance. Thus, treatment strategies based on a deeper molecular understanding of gliomagenesis are urgently needed. Quaking (Qki, encoded by the gene Qk) is frequently altered in GBM; Qk mutations or deletions occur in 35% percent of cases, and the Qki protein is absent in 50-60% of cases. Our lab found that deletion of Qk in Trp53-/-; Pten-/- pre-malignant neural stem cells (NSCs) enables them to expand outside their niche and develop into malignant GBM. Mechanistically, we determined that Qki functions as a transcriptional coactivator of lipid metabolism genes in the central nervous system, where loss of Qki dysregulates the lipidome and alters cellular membrane integrity. While several downstream processes governed by Qki have been delineated, upstream regulators of Qki remain unknown. Recurrent cancer mutations to specific Qki arginine residues implicate the dysregulation of arginine methylation, and previous studies indicate that proteins in the same family as Qki can be methylated by protein arginine methyltransferases (PRMTs). Utilizing in vitro methylation assays, we demonstrate that Qki is selectively methylated by the PRMT coactivator-associated methyltransferase 1 (CARM1) in the Quaking regulatory domain (QRD), where cancer mutations were reported. Within the QRD, we identified arginine 242 (R242) and arginine 256 (R256) as specific CARM1-mediated methylation sites on Qki. Mutations to these sites compromise Qki transcriptional activity, as Qki methylation mutant-expressing GSCs exhibited downregulation of Qki target genes compared to those expressing wildtype Qki. Taken together, we provide evidence that CARM1 functions as a tumor suppressor in GBM through a novel mechanism of Qki dysregulation.
EPCO-41. MICRORNA-MEDIATED DIRECT NEURONAL REPROGRAMMING OF GLIOBLASTOMAS
Authors: Yuan Luorongxin , Cates Kitra , Annamalai Devi , Kim Albert , Yoo Andrew
Published: November 2023

Neuron-specific microRNAs miR-9/9* and miR-124 (miR-9/9*-124) are potent neurogenic molecules whose ectopic expression in non-neuronal somatic cells effectively induces direct cell fate conversion into a neuronal fate. Our recent work indicates that the fate transition occurs in distinct steps where miR-9/9*-124 first represses core gene regulatory networks to erase the original non-neuronal cell identity and subsequently activates the neuronal program to confer neuronal fate. Extending these findings, we reason that repression of similar gene regulatory networks by miR-9/9*-124 can also induce fate erasure in cancerous cells using glioblastoma as a paradigm. Glioblastoma multiforme (GBM) is a type of aggressive brain tumor with poor prognosis. Instead of having specific mutation profiles, GBMs present a global genetic network dysregulation which gives rise to a neural stem cell or progenitor cell-like state resembling embryonic neural development. Whereas miR-9/9*-124 plays a key role in inducing mitotic exit and orchestrating neurogenesis during development and neuronal reprogramming, we hypothesize that miR-9/9*-124 will instruct neuronal reprogramming of GBMs. Our results so far demonstrate that miR-9/9*-124 indeed exerts reprogramming activities in patient-derived GBM cell lines. Ectopic expression of miR-9/9*-124 in vitro readily induces GBM cells to exit cell cycle and promotes neuronal identity over time. In GBM intracerebral xenograft mouse model, mice receiving GBM cells overexpressing miR-9/9*-124 were able to survive longer than those with GBMs overexpressing non-specific microRNAs. We are currently carrying out transcriptomic and chromatin accessibility analyses to infer the epigenetic switch as GBM cells are reprogrammed to neurons. Based on these studies, we will further examine whether the GBM cells undergo irreversible fate erasure and are reprogrammed into a stable post-mitotic neuronal state. Our studies will provide insights into the plasticity of GBM fate that can be controlled by microRNAs and the key downstream regulatory nodes underlying fate transition of GBM to permanent post-mitotic state.
EPCO-48. THE SINGLE-CELL AND SPATIAL TRANSCRIPTOMIC ARCHITECTURE OF MENINGEAL SOLITARY FIBROUS TUMORS PHENOCOPIES CEREBRAL VASCULAR DEVELOPMENT AND HOMEOSTASIS
Authors: Mirchia Kanish , Choudhury Abrar , Joseph Tara , Birrueta Janeth Ochoa , Phillips Joanna , Bhaduri Aparna , Crouch Elizabeth , Perry Arie , Raleigh David
Published: November 2023

INTRODUCTION

Meningeal solitary fibrous tumors (SFTs) are rare mesenchymal neoplasms that are associated with local recurrence and distant metastasis. The cell states and spatial transcriptomic architecture of SFTs are unknown.

METHODS

Single-cell RNA sequencing or spatial transcriptomic sequencing were performed on 40,022 cells or 23,682 spatial transcriptomes from 12 meningeal SFT samples. Datasets were corrected for batch effects using Harmony and integrated using uniform maniform approximation and projection (UMAP). Clusters were defined using automated cell type classification, cell signature gene sets, cell cycle analysis, and differentially expressed marker genes. Trajectory analyses were performed using RNA velocity and pseudotime. Cell-cell communication analysis was performed using CellChat.

RESULTS

were validated using immunofluorescence and immunohistochemistry and generalized using comparisons to 30,934 single-cell transcriptomes from 6 meningioma samples, 139,134 perinatal human brain vascular single-cell transcriptomes, 84,138 adult human brain vascular single-cell transcriptomes, and DNA methylation profiles from 8 SFT and 221 meningioma samples.

RESULTS

Unsupervised hierarchical clustering of DNA methylation profiles revealed molecular distinction of meningeal SFTs from meningiomas. Deconvolution of vascular single-cell types showed SFT cell clusters resembling perinatal or adult fibroblasts, perinatal mitotic endothelia, and adult venous or arterial endothelia. UMAP and trajectory analyses showed SFTs were comprised of 8 interchangeable tumor cell states that were associated with cell adhesion (VCAM1, NCAM2), cell stress (EGR1), cell signaling (NOTCH3), extracellular matrix remodeling (ECM) (ADAMTS6, PLCG2), or protein synthesis pathways (RPL27A, RPL37). Cell-cell communication analyses identified single-cell and spatial interactions between VCAM1- or NCAM2-expressing SFT cells and endothelia or immature neurons in the tumor microenvironment, respectively. Single-cell deconvolution demonstrated evolution of ECM and protein synthesis SFT cells in paired primary/recurrent samples, and evolution of ECM SFT cells and macrophages in paired primary/metastatic samples.

CONCLUSIONS

The single-cell and spatial transcriptomic architecture of meningeal SFT reveals dynamic cell states that phenocopy cerebral vascular development and homeostasis.
EPCO-49. MYC AMPLIFICATION AT DIAGNOSIS REGULATES THERAPY-INDUCED HYPERMUTATION AT RECURRENT GLIOMA
Authors: Mu Quanhua , Chai Ruichao , Yang Yingxi , Jiang Tao , Wang Jiguang
Published: November 2023

Cancer progression and resistance to therapy are driven by clonal evolution. Recent studies have shown that adult diffuse gliomas have divergent clonal dynamics. However, the genomic and epigenomic factors that influence molecular changes after treatment are not well understood. To address this, we analyzed sequencing and clinical data from 544 adult diffuse glioma patients to identify predictors of cancer evolution. Using machine learning methods CELLO2, we predict grade progression and treatment-induced hypermutation based on tumor characteristics and clinical features collected at diagnosis. We found that MYC copy number gain is more prevalent as a founding alteration in the East Asian gliomas and it is the most significant predictor of hypermutation under temozolomide treatment. Further experiments using patient-derived gliomaspheres and established glioma cell lines confirmed the critical role of MYC amplification and pathway activation in hypermutagenesis. We also showed that c-Myc binding to open chromatin and transcriptionally active regions increases the vulnerability of genomic regions to TMZ-induced mutagenesis. This study highlights MYC as an early predictor of cancer evolution and provides a machine learning platform to improve patient management by predicting cancer dynamics.
DISP-07. GLIOMAS IN HIV-POSITIVE PATIENTS CAN BE IDH-MUTANT OR -WILDTYPE
Authors: Ormond David , Ney Douglas , DeMasters B K
Published: November 2023

Recent review has emphasized that glioblastoma (GBM) in persons living with human immunodeficiency virus (HIV)(PLWH) is “severely underreported in the literature” (PMID 35857248), since only 24 cases could be identified. This 2022 study concluded that overall survival in this patient group is less than in persons who are HIV-negative. Given the predominantly single-case reports in the literature, it is not surprising that “data remains limited”. To this end, we report our 15-year experience with patients with HIV-positivity diagnosed at our institution. Text word search of Department of Pathology databases, 2008-2023, with review of histological sections and the medical record. 7 patients living with PLWH were identified, all males, ages at diagnosis 44-61 years, median 58 years. 3 had tumors that met histological criteria for GBM, IDH-wildtype, WHO grade 4, 1 had GBM by modern molecular criteria and 2 had astrocytoma, IDH-mutant, WHO grade 4. One of the latter had co-existent diffuse high grade B cell lymphoma intimately admixed within his glioma while the final patient had multifocal brain lesions of different neuroimaging appearances, with the bifrontal tumor consistent with GBM and posterior frontal lesions suspicious for progressive multifocal leukoencephalopathy. At the time of tumor diagnosis, 1 had HIV for 20+ years, a second was well controlled with normal CD4 count and a third had not yet been on anti-retroviral agents. Survival was poor, with 2 PLWH with IDH-mutant tumors succumbing at 2 and 4 months and 3 with GBMs at 7, 12 and 32 months; a 4th is alive at 6 months. PLWH can develop various glial tumor types including both IDH-mutant and IDH-wildtype tumors, strongly suggesting co-incident rather than causal relationship. Tumors may be first diagnosed at varying stages of their immunodeficiency disorder; survival is poor even for PLWH with IDH-mutant grade 4 tumor.
DISP-08. UNMET NEEDS: WHAT PEOPLE LIVING WITH GLIOBLASTOMA LACK TODAY, INCLUDING ACCESS TO CRITICAL GENOMIC TUMOR TESTING
Authors: Stebbins Alice , Duprey Kelli , Pilkington Ed , Wilkie Martha
Published: November 2023

PURPOSE

In 2022 and 2023, the non-profit OurBrainBank asked its community of people living with glioblastoma and care partners about the current state of GBM treatment in the USA including whether the patient received genomic tumor analysis. METHOD: OurBrainBank conducted an online survey in which we posted queries through two Facebook groups: “Glioblastoma — GBM SURVIVORS TO THRIVERS!” and “OurBrainBank GBM Patient & Caregiver Community.”

RESULTS

More than 100 people responded to the Facebook posts stating the priorities they felt they most needed. Top of the list were faster FDA approval for promising therapies, better treatment for veterans, speedier approval for disability benefits as well as common-sense improvements to Medicare/Medicaid, a stop to unreasonable insurance practices, and more flexibility regarding clinical trials. For the survey, 133 people responded. Of the sample group, 50% reported that they had not been informed about tumor testing and 70% said they were unsure or not informed about storing tumor tissue. For the 30% who knew about storing tissue, only half actually had done so. More than 50% did not know about tumor types or mutations. Only half felt that they received enough information to make educated decisions. Those living in urban areas or able to travel received care at hospitals that specialized in brain tumors, but by contrast people living in rural areas or far from a center of excellence did not. Half of respondents felt that they did not enjoy an equal and collaborative relationship with their medical team.

CONCLUSION

GBM patients and their caregivers are not treated consistently, particularly in regard to genomic tumor testing, a vital first step toward personalized treatment. Many do not receive optimal care and may not even see a specialist. With a median survival rate of 12-18 months, there is much improvement needed.
DISP-10. ENHANCING TRUST AND REPRESENTATIVE PARTICIPATION IN THE INTERNATIONAL LOW GRADE GLIOMA REGISTRY: COMMUNITY ENGAGEMENT STRATEGIES AND RECOMMENDATIONS
Authors: Salmi Liz , Barnard Juliana , Ritger Carly , Fischmann Rudy , Garcia-Hernandez Sandra , Gay Nestelynn , Gonzalez-Fisher Ricardo , Johnson Kevin , Lennox Lindsay , Lipof Guy , Ostmeyer Jasmyn , Perkins Ifeoma , Reno Jenna , Roth Taylor , Begum Anowara , Claus Elizabeth , Verhaak Roel , Kwan Bethany
Published: November 2023

BACKGROUND

The International Low Grade Glioma (LGG) Registry is a community of people with LGGs who have contributed data and specimens to facilitate genomic research. The Registry aims to discover the roles genetics and the environment play in glioma risk factors and treatment response. To ensure findings apply to a range of diverse populations and settings, it is crucial to build trust and encourage representative participation in the Registry.

METHODS

Three engagement strategies were used to gather recommendations for improving trust and participation in LGG genomic research. We established a Research Advisory Council (RAC) consisting of 25 members, including people with LGG, care partners, clinicians, researchers, advocates, and genomics and ethics experts. Additionally, we engaged two existing social media communities (the #BTSM community on Twitter, the Oligodendroglioma/LGG Warriors Facebook group) through separate discussions with each group over four months. Topics included: 1) Trust and benefits of genomic research; 2) Registry recruitment; 3) Registry data collection; and 4) Return of results. We used qualitative methods to summarize recommendations.

RESULTS

Feedback received from community members indicated a willingness to share information with the Registry. Recommendations related to recruitment message content and packaging, communication channels, data security, and conveying the individual- and population-level impacts of genomic research. The Registry’s messages should include clear information about how data and specimens are being used. Both research and individual-level findings should be shared back with participants and the broader community using accessible language, but without being paternalistic or promising cures or “miracles.”

CONCLUSIONS

Engaging an advisory council and existing social media communities were effective approaches for identifying recommendations for enhancing trust and participation in genomic research. Regular, consistent, transparent communication with participants throughout the research process is key. Future efforts will operationalize and evaluate the impact of these recommendations on equity and representativeness of Registry participants.
IMMU-01. IMMUNE PHENOTYPING OF BRAIN METASTASIS PATIENTS IDENTIFIES A DISTINCT DEPLETION AND EXHAUSTION PHENOTYPE OF THE CD4 T CELLS IN BLOOD AND BONE MARROW
Authors: Reetz Merle , Ryba Alice , Heinemann Sarina , Kolbe Katharina , Stanik Jessica , Zapf Svenja , Gempt Jens , Westphal Manfred , Lamszus Katrin , Tolosa Eva , Maire Cecile , Mohme Malte
Published: November 2023

Brain metastases are the most rapidly emerging entity in neuro-oncology. Given the decisive role of immunotherapy, the immune crosstalk between the blood circulation and the brain tumor requires deeper investigation, especially in light of recent data showing that T cells might be trapped in the bone marrow during the metastasis process. We analyzed the immune profile in the peripheral blood and in the bone marrow in a cohort of 40 patients with brain metastasis using flow cytometry. Our results show a global decrease in the proportion of CD3+ T cells in the peripheral blood of patients with brain metastases when compared to healthy donors (HD). CD4+ T cells were more affected by the presence of brain metastases than CD8 cells, with a significant decrease in Tregs, Th1 and Th2 helper cell populations. The proportion of naïve CD4 T cells with low expression of CXCR3 and CD127 is decreased in tumor, while a subpopulation of naïve as well as central memory CD4CM with high expression of PD1 is increased in brain metastasis patients compared to HD. Additionally, we noticed an increase in the proportion of B cells in the patient’ blood, together with a decrease in non-classical CD86+ monocytes compared to HD. The NK cell population was also affected with a significant depletion of mature NK CD57+ in the blood of patients with brain metastases. In the bone marrow, we found an increase in the proportion of senescent CD4CM CD57+ in patients with NSCLC brain metastasis, while the proportion of CD4CM CXCR3+ was significantly decreased compared to HD. Taken together, our data show that brain metastases profoundly affect the phenotype and abundance CD4+ T cells in the periphery and bone marrow, thus interfering with the primary T cell population orchestrating the tumor-specific immune response.
IMMU-03. UTILIZING IN SILICO SINGLE-CELL TRANSCRIPTOMIC AND TCR PROFILING FOR THE IDENTIFICATION AND ISOLATION OF TUMOR-REACTIVE TCR CLONOTYPES IN RECURRENT GLIOBLASTOMA PATIENTS
Authors: Lee Alexander , Sun Lu , Chow Frances , Treger Janet , Cook Danielle , Porter Ely , Chen Xi , Herrera Gilbert , Everson Richard , Liau Linda , Cloughesy Timothy , Hugo Willy , Nathanson David , Prins Robert
Published: November 2023

BACKGROUND

Glioblastoma (GBM) is the most aggressive form of primary brain cancer with no current cure. Immunotherapies, such as checkpoint blockade and adoptive T cell therapy, have effectively treated other cancers, but in GBM, these therapies have shown limited efficacy. This may be partially due to a lack of infiltrating tumor-reactive T cell populations capable of eliminating the tumor.

METHODS

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RESULTS

We used single-cell RNA and TCRsequencing to examine the transcriptome and TCR repertoire of tumor-infiltrating T cells from a cohort of 32 recurrent GBM patients, 18 of whom had received neoadjuvant anti-PD-1 therapy. After dimensional reduction, we found that the cluster defined by T cell activation and exhaustion gene expression had the greatest number of expanded T cell clones and a transcriptomic profile similar to a previously published signature of tumor-reactive T cells. Focusing on a patient treated with neoadjuvant anti-PD-1 and a EGFRvIII Bispecific T cell engager therapy, we selected TCRs from T cells within the activated and exhausted cluster. Utilizing the PathFinder DNA Assembly technology developed by Rootpath, we generated a TCR library containing the selected TCRs and transduced the library into a fluorescent-reporter Jurkat line that measures T cell activation. We co-cultured the transduced Jurkats with the patient-derived gliomasphere, FACs sorted for activated Jurkats and performed TCR sequencing on the sorted cells. Six TCRs within the sorted population were over-represented relative to sorted T cells from control co-cultures, indicating their tumor reactivity.

CONCLUSIONS

In this study we provide a proof-of-concept framework for how incorporating silico single-cell analysis of a T cell’s transcriptome and TCR can be used to identity tumor-reactive T cells for potential downstream adoptive T cell therapies for patients with recurrent GBM.