bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

Abstract
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 We analyzed 289 whole-genome sequencing data (WGS) including 159 unpublished deep WGS (≥ ×120 coverage) along with RNA-seq, DNA methylation array, whole-genome bisulfite sequencing, and assay for transposase-accessible chromatin with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

Abstract
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

Abstract
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

Abstract
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

Abstract

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

Abstract
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

Abstract
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

Abstract

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

Abstract

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

Abstract
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.