bluuebunny/crossref_metadata_2025_split huggingface dataset:
BIOM-55. DGKζ-TARGETED REGULATION OF MIR-34A IN THE PROLIFERATION AND TUMORIGENICITY OF HUMAN GLIOBLASTOMA
Authors: Gu Wangxian , Wan Guoqing , Zheng Yanjun , Yang Xintong , Zhang Peng , Lu Changlian , Gu Xuefeng 
Published: December 2020

Abstract
Diacylglycerol kinase (DGK) is a lipid kinase that catalyzes the phosphorylation of diacylglycerol (DAG) to produce phosphatidic acid (PA), which uses ATP as a phosphate donor. Diacylglycerol kinases ζ(DGKζ) is characterized as specific type IV due to its myristoylated alanine-rich C-kinase substrate (MARCKS), ankyrin, and PDZ binding domain. Similar to other DGKs, DGKζ is also reported to be abnormally expressed in human colorectal cancer cells, and it is indispensable for the proliferation of cancer cells. However, its implications in human glioblastoma (GBM) is largely unknown. Both the mRNA and protein levels of DGKζ were significantly higher in GBM tissues than in precancerous lesions. Knockdown of DGKζ inhibited GBM cell proliferation, cell cycle and promoted apoptosis of GBM cells. Moreover, down-regulation of DGKζ markedly reduced in vitro colony formation and in vivo tumorigenic capability. Furthermore, we confirmed that DGKζ was the downstream target of miR-34a. The expression level of DGKζ was negatively correlated with miR-34a in GBM tissues. Overexpression of DGKζ reversed the tumor suppressive roles of miR-34a in GBM cells. Taken together, DGKζ can act as a potential prognostic biomarker for GBM patients and promote the growth of GBM cells was regulated by miR-34a, and it may represent a promising therapeutic target for patients with GBM.
BIOM-57. PEDIATRIC TUMOR CLASSIFICATION THROUGH GENOME-WIDE METHYLATION PROFILING OF EXTRACELLULAR VESICLE DNA
Authors: Ricklefs Franz , Maire Cecile , Fita Krys , Fritzsche Friederike , Kammler Gertrud , Westphal Manfred , Lamszus Katrin , Schüller Ulrich 
Published: December 2020

Abstract

BACKGROUND
Genome-wide methylation profiling reliably classifies pediatric central nervous system (CNS) tumors. Extracellular vesicles (EVs) are released by pediatric CNS tumor cells (pCC) and contain high molecular weight tumor DNA, rendering EVs a potential biomarker source to identify tumor subgroups, stratify patients and monitor therapy by liquid biopsy. We investigated whether the DNA in pCC-derived EVs reflects genome-wide tumor methylation profiles and allows tumor subtype classification.

METHODS
DNA was isolated from EVs secreted by pediatric CNS tumor cells (pCC) as well as from the shortly cultured tumor cells and from the original tumor samples (n=4 patients). Pediatric Fibroblasts and EVs derived thereof were used as a non-tumorous control. EVs were classified by nanoparticle analysis (NTA), immunoblotting, imaging flow cytometry (IFCM and electron microscopy. Genome-wide DNA methylation profiling was performed using an 850k Illumina EPIC array and results were classified according to the DKFZ brain tumor classifier and further analysed by t-SNE and Copy number alteration analysis (CNA).

RESULTS
The size range of pCC-derived EVs was 120–150 nm, as measured by NTA. The majority of secreted EVs exhibited high expression of common EV markers (i.e. CD9, CD63 and CD81), as characterized by IFCM. Genome-wide DNA methylation profiling of pCC-derived EVs correctly identified the methylation class of the original tumor (i.e. pilocytic astrocytoma, medulloblastoma). In addition, t-SNE analysis and copy number alterations matched the pattern of the parental pCC and original tumor samples.

CONCLUSION
EV DNA faithfully reflects the tumor methylation class and copy number alterations present in the parental cells and the original tumor. Methylation profiling of circulating tumor EV DNA could become a useful tool to detect and classify pediatric CNS tumors.
BIOM-58. ASSESSMENT OF ANEUPLOIDY BY REPETITIVE ELEMENT SEQUENCING TO DETECT PEDIATRIC AND ADULT BRAIN CANCERS IN PLASMA
Authors: Douville Christopher , Mattox Austin , Blair Cherie , Bettegowda Chetan 
Published: December 2020

Abstract
Central nervous system cancers are the tenth leading cause of death for adults and the leading cause of cancer mortality in children. Non-invasive detection methods are desperately needed for earlier diagnosis and recurrence monitoring. Aneuploidy is common to nearly all cancers and can be detected in circulating tumor DNA (ctDNA) isolated from a variety of biofluids, including plasma. We utilized a sensitive PCR-based assay called Repetitive Element AneupLoidy Sequencing System (RealSeqS) on plasma samples from 90 patients diagnosed with the most common primary brain tumors including pilocytic astrocytoma, Grade II and III astrocytoma, glioblastoma (GBM), oligodendroglioma, ependymoma, and medulloblastoma to detect aneuploidy in ctDNA. RealSeqS employs PCR amplification and sequencing of ~350,000 genome-wide loci to identify chromosomal abnormalities and then aggregate them into a single Genome Aneuploid Score via a supervised machine learning algorithm. RealSeqS identified aneuploidy in 16 of 90 (17.8%) patients, including 20.9% (9/43) of anaplastic astrocytomas and GBMs, 57.1% (4/7) ependymomas, and 18.8% (3/16) pilocytic astrocytomas. Notably, ependymomas have significant chromothripsis and aneuploidy, which was reflected in our plasma analyses. Detection of aneuploidy also correlated with higher mortality rates at the time of last follow-up (p &lt; 0.001). RealSeqS did not detect aneuploidy in the plasma of patients with Grade II astrocytoma, medulloblastoma, or oligodendroglioma. RealSeqS detected focal amplifications of 11q in 16.7% (2/12) and a focal deletion of TERT in 8.3% (1/12) of Grade III astrocytomas, focal deletions of EXT1 (14.3%; 1/7) and focal amplifications of EGFR (14.3%; 1/7) in the plasma of patients with ependymomas, and focal deletions of EXT1 (3.2%, 1/31) and focal amplifications of CDKN2A and CDKN2B in (3.2%; 1/31) GBM. These findings suggest detection of aneuploidy by RealSeqS may be a rapid, cheaper, and more sensitive alternative to low pass whole genome sequencing for the earlier detection of certain CNS neoplasms.
BIOM-59. TERT PROMOTER MUTATION AND MGMT PROMOTER METHYLATION-MEDIATED SENSITIVITY TO TEMOZOLOMIDE IN IDH-WILDTYPE GLIOBLASTOMA: IS THERE A LINK?
Authors: Gramatzki Dorothee , Felsberg Jörg , Hentschel Bettina , Wolter Marietta , Schackert Gabriele , Westphal Manfred , Regli Luca , Thon Niklas , Tatagiba Marcos , Wick Wolfgang , Schlegel Uwe , Krex Dietmar , Matschke Jakob , Roth Patrick , Suresh Marian , Kamp Marcel , Rushing Elisabeth , Pietsch Torsten , von Deimling Andreas , Sabel Michael , Loeffler Markus , Weller Michael , Reifenberger Guido 
Published: December 2020

Abstract

BACKGROUND
Benefit from temozolomide (TMZ) chemotherapy in the treatment of isocitrate dehydrogenase (IDH)-wildtype glioblastoma is essentially limited to patients with O6-methylguanine DNA methyltransferase (MGMT) promoter-methylated tumors. Recent studies suggest that the impact of the MGMT status on chemosensitivity may be modulated by telomerase reverse transcriptase (TERT) promoter hotspot mutations.

METHODS
MGMT promoter methylation and TERT promoter mutation status were assessed in an exploratory prospective cohort of IDH-wildtype glioblastoma patients of the German Glioma Network (GGN) (n=298) and validated in a retrospective cohort from Düsseldorf, Germany, and Zurich, Switzerland (n=302).

RESULTS
In the prospective GGN discovery cohort of patients with MGMT promoter-unmethylated tumors, TERT promoter mutation showed inferior outcome (p=0.044). In contrast, TERT promoter mutations were not associated with improved outcome in patients with MGMT promoter-methylated tumors. Different TERT promoter hotspot mutations were not associated with distinct outcomes. The association of TERT promoter mutation in MGMT promoter-unmethylated tumors was not confirmed in the retrospective validation cohort.

CONCLUSIONS
Analysis of two independent cohorts of glioblastoma patients, including the prospective GGN cohort, did not confirm previous data suggesting that TERT promoter mutations confer an enhanced benefit from TMZ in patients with MGMT promoter-methylated glioblastoma. Thus, diagnostic testing for TERT promoter mutations may not be required for prediction of TMZ sensitivity in IDH-wildtype glioblastoma patients.
BIOM-62 SENSITIVE DETECTION AND DISCRIMINATION OF INTRACRANIAL TUMORS BY BLOOD
Authors: Nassiri Farshad , Chakravarthy Ankur , Feng Shengrui , Shen Roxana , Nejad Romina , Zuccato Jeffrey , Voisin Mathew , Patil Vikas , Horbinski Craig , Aldape Kenneth , Zadeh Gelareh , de Carvalho Daniel 
Published: December 2020

Abstract

BACKGROUND
The diagnosis of intracranial tumors relies on tissue specimens obtained by invasive surgery. Non-invasive diagnostic approaches, particularly for patients with brain tumours, provide an opportunity to avoid surgery and mitigate unnecessary risk to patients. We reasoned that DNA methylation profiles of circulating tumor DNA in blood can be used as a clinically useful biomarker for patients with brain tumors, given the specificity of DNA methylation profiles for cell-of-origin.

METHODS
We generated methylation profiles on the plasma of 608 patients with cancer (219 intracranial, 388 extracranial) and 60 healthy controls using a cell-free methylated DNA immunoprecipitation combined with deep sequencing (cfMeDIP-seq) approach. Using machine-learning approaches we generated and evaluated models to distinguish brain tumors from extracranial cancers that may metastasize to the brain, as well as additional models to discriminate common brain tumors included in the differential diagnosis of solitary extra-axial and intra-axial tumors.

RESULTS
We observed high sensitivity and discriminative capacity for our models to distinguish gliomas from other cancerous and healthy patients (AUC=0.99, 95%CI 0.96–1), with similar performance in IDH mutant and wildtype gliomas as well as in lower- and high-grade gliomas. Excluding non-malignant contributors to plasma methylation did not change model performance (AUC=0.982, 95%CI 0.93–1). Models generated to discriminate intracranial tumors from each other also demonstrated high accuracy for common extra-axial tumors (AUCmeningioma=0.89, 95%CI 0.80–0.97; AUChemangiopericytoma=0.95, 95%CI 0.73–1) as well as intra-axial tumors ranging from low-grade indolent glial-neuronal tumors (AUC 0.93, 95%CI 0.80 – 1) to diffuse intra-axial gliomas with distinct molecular composition (AUCIDH-mutant glioma = 0.82, 95%CI 0.66 -0.98; AUCIDH-wildtype-glioma = 0.71, 95%CI 0.53 – 0.9). Plasma cfMeDIP-seq signals originated from corresponding tumor tissue DNA methylation signals (r=0.37, p&lt; 2.2e-16).

CONCLUSIONS
These results demonstrate the potential for cfMeDIP-seq profiles to not only detect circulating tumor DNA, but to accurately discriminate common intracranial tumors that share cell-of-origin lineages.
CBIO-04. MUTATION-SPECIFIC NON-CANONICAL PATHWAY OF PTEN AS A DISTINCT THERAPEUTIC TARGET FOR GLIOBLASTOMA
Authors: Won Choi Seung , Lee Yeri , Shin Kayoung , Kim Donggeon , Lee Se Jeong , Kim Hyunho , Chung Seok , Shin Jihye , Lee Cheolju , Nam Do-Hyun 
Published: December 2020

Abstract
The dominant-negative effect of PTEN mutation has been described previously, suggesting that aberrant gain of function attributed to mutation might be more disastrous than deletion in respect to malignant potential. In present study, we explored the functional implications of hot spot mutations of PTEN in GBM tumors. Subcellular location of PTEN is important for its distinct function and spatial distribution within the cytoplasm is known to be associated with cellular locomotion. We evaluated the subcellular compartmentalization of different PTEN mutants and found that some PTEN mutants located at cellular edges of chemotaxing cells. Moreover, these PTEN mutations exhibited invasive phenotype, which was not disrupted by PI3K inhibitor, but microtubule inhibitors. This finding suggests that cytoskeletal assembly as a novel non-canonical pathway of PTEN, thus unraveling a novel therapeutic vulnerability of PTEN. Mutation-specific therapeutic options should be considered in treating GBM patients with PTEN mutations.
CBIO-05. LIPID METABOLIC REPROGRAMMING SENSITIZES A MOLECULARLY-DEFINED SUBSET OF GLIOBLASTOMAS TO FERROPTOSIS
Authors: Morrow Danielle , Nathanson David , Cloughesy Timothy , Prins Robert , Bayley Nicholas , Liau Linda , Bensinger Steven , Williams Kevin 
Published: December 2020

Abstract
Cancers, including the universally lethal glioblastoma (GBM), have reprogrammed lipid metabolism to fuel tumor growth. However, the molecular alterations responsible for aberrant lipid metabolism, and the potential for identifying new therapeutic opportunities are not fully understood. To systematically investigate the GBM lipidome, we performed integrated transcriptomic, genomic and shotgun lipidomic analysis of an extensive library of molecularly diverse patient-derived GBM samples. Using this comprehensive approach, we discovered two GBM sub-groups defined by their combined molecular and lipidomic profile. Triacylglycerides (TAGs) enriched in polyunsaturated fatty acids (PUFAs) were among the most significantly altered lipids between the two groups of GBM tumors. TAGs are the main components of lipid droplets, which sequester PUFA-TAGs away from membrane phospholipids where their peroxidation can lead to ferroptosis – a regulated from of PUFA-peroxidation dependent cell death. Accordingly, the GBM subgroup with a depletion of PUFA TAGs showed heightened sensitivity to ferroptosis. Our findings suggest a novel association between specific molecular signatures of GBM, lipid metabolism and ferroptosis. This relationship may present a new therapeutic opportunity to target reprogrammed lipid metabolism in a molecularly-defined subset of GBMs.
CBIO-12. THE ROLES OF lncRNAs IN GBM RADIATION RESISTANCE AND TUMOR RECURRENCE
Authors: Stackhouse Christian , Rowland James , Anderson Joshua , Wang Jelai , Nguyen Thanh , Yue Zongliang , Chen Jake , Ianov Lara , Gillespie Yancey , Willey Christopher 
Published: December 2020

Abstract
Glioblastoma multiforme (GBM) almost invariably recurs and tumors exhibit resistance to conventional therapies. One mechanism of resistance is enhanced DNA damage response (DDR) to alkylating chemotherapy or radiation therapy (RT). We have generated 8 novel GBM patient-derived xenograft (PDX) models of tumor recurrence following serial in vivo irradiation (6 x 2Gy fractions over 2 weeks for 6+ rounds). RNA sequencing has revealed enrichment of a number of DDR pathways in the RT selected (RTS) PDX. Differential enrichment across the RTS PDX suggests multiple molecular routes to acquired RT resistance. We have also identified differential enrichment of molecular signatures for cell cycle progression, stemness, and chromatin remodeling all suggesting decreased proliferation, increased stemness, and more compacted chromatin states associated with RTS PDX. We have identified altered kinase signaling in RTS PDX that may suggest targetable signaling pathways using small molecule inhibitors. Integrated ‘–omics’ analysis has identified SRC family kinases and altered expression of collagens related to the RTS profile. Long non-coding RNAs (lncRNA) have the potential to regulate molecular phenotypes through nucleic acid binding. We have identified 269 lncRNAs significantly differentially expressed in the RTS condition. We have determined that a number of these transcripts have DNA binding potential in gene regulatory regions proximal to kinase, DDR, cell cycle, stemness, and chromatin remodeling genes. Analysis of lncRNAs and genes proximal to their binding sites has revealed regulatory networks potentially governing cell fate and phenotype. We have observed complex correlations of some of these transcripts, such as ZFAS1, which has a positive correlation with expression of stemness-promoting genes and simultaneous inverse correlation with cell cycle genes. This suggests ZFAS1 could be a phenotypic switch between a RT-sensitive proliferating cell and a RT-resistant non-proliferating stem-like cell. LncRNAs may represent a novel therapeutic target for the treatment of therapy resistant, recurrent GBM.
CBIO-18. G-QUADRUPLEX STABILIZATION TARGETS ATRX-DEFICIENT HIGH-GRADE GLIOMA VIA INDUCTION OF p53-INDEPENDENT APOPTOSIS
Authors: Dharmaiah Sharvari , Farooqi Ahsan , Alvarez Christian , Sharin Vladislav , Irvin David , Huse Jason 
Published: December 2020

Abstract
Gliomas are the most common primary malignant brain tumor in adults and mutational inactivation of histone chaperone ATRX is a critical molecular marker in the classification of high-grade glioma (HGG). ATRX loss occurs with concurrent mutations in TP53 and IDH1/2, altering genome-wide accessibility of chromatin and inducing replication stress and DNA damage via accumulations of abnormal G-quadruplex (G4) DNA secondary structures. While G4 stabilizers in particular hold strong therapeutic promise, the genomic consequences and efficacy of this treatment are poorly understood. We previously showed that chemical stabilization of G4s in ATRX-deficient normal human astrocytes (NHAs) results in lethality due to induction of replication stress, but it is unknown what drives this lethality in ATRX-deficient patient-derived preclinical models. We therefore sought to evaluate the mechanisms that underlie cell death in ATRX- and p53-deficient preclinical in vitro models following G4 stabilization. We found that ATRX-deficient glioma stem cells (GSCs) demonstrated dose-dependent enhanced sensitivity to G4 stabilization, compared to ATRX-intact controls. Evaluation of cell death mechanisms following G4 stabilization revealed a significant increase in cleaved caspase 3 expression and no p21 expression in ATRX-deficient GSCs, suggesting p53-independent apoptotic activation. Cell cycle flow analysis demonstrated G2/M checkpoint arrest in ATRX-deficient GSCs upon G4 stabilization, suggesting that p53 is nonfunctional at the G1/S checkpoint. Our preliminary findings now suggest that p73, a functional and structural homologue of p53, is activated and drives apoptosis in these ATRX-deficient GSCs. Furthermore, ATRX-deficient GSCs demonstrated upregulated expression of both pATR/pChk1 and pATM/pChk2, indicating enhanced replication stress and DNA damage via double-stranded breaks, respectively. These findings indicate that G4 stabilizers could potentially synergize with ionizing radiation, the current standard of care, as both therapies are DNA-damaging. Taken together, this study elucidates mechanisms of cytotoxicity and efficacy of a novel therapeutic strategy in ATRX-deficient preclinical models.
CBIO-25. INTEGRATED MOLECULAR AND BH3 PROFILING OF THE INTRINSIC APOPTOTIC MACHINERY IDENTIFIES THERAPEUTIC VULNERABILITIES IN GLIOBLASTOMA
Authors: Fernandez Elizabeth , Mai Wilson , Bayley Nicholas , Tse Christopher , Liau Linda , Cloughesy Timothy , Letai Anthony , Nathanson David 
Published: December 2020

Abstract
Resistance to apoptosis is a hallmark of cancer. However, the underlying molecular mechanisms of intrinsic-apoptotic resistance in glioblastoma (GBM) are largely unknown. Here we performed integrated molecular and functional characterization (via BH3 profiling) of the intrinsic apoptotic machinery in 50 GBM patient specimens. We found that, despite significant genetic heterogeneity of our GBM samples, all GBMs have a cross compensatory reliance on BCLXL and MCL1 for basal survival. Treatment with standard of care (e.g., temozolomide or radiation) caused minimal apoptosis, yet ablated the MCL-1 block in a p53-dependent manner, thus creating an exclusive dependence on BCLXL for survival in p53 wild-type GBM tumors (65% of GBM tumors). Consequently, BCLXL inhibition caused synergistic cell death with IR/TMZ in GBM tumors with intact p53 signaling. Importantly, the degree of synergistic cell kill was best predicted by combining molecular features with BH3 profiling, providing an integrated predictive signature of response to this novel therapeutic approach. Collectively, these studies identify mechanisms of intrinsic apoptosis resistance in both basal and treatment states of GBM and demonstrate how functional and molecular data can be complementary to robustly predict therapy-induced cell death.
COVD-02. ADAPTING RNA-NANOPARTICLE VACCINES FROM GLIOBLASTOMA TO SARS-COV-2
Authors: Mendez-Gomez Hector , Castillo Paul , Jones Noah , Qdaisat Sadeem , Weidert Frances , Mitchell Duane , Sayour Elias 
Published: December 2020

Abstract

BACKGROUND
Glioblastoma (GBM) can be an effective teacher in the war on COVID-19, as an operative vaccine for either must elicit near-immediate protective responses that overcomes disease heterogeneity and immune suppression. Current prophylactic strategies against COVID-19 utilize mRNA vaccines targeting small fragments of the SARS-CoV-2 genome, but these may not induce robust T cell responses or elicit immunity quickly enough.

OBJECTIVE
We sought to adapt an FDA-IND approved mRNA vaccine in GBM against COVID-19 for: 1) activation of near immediate immune responses, 2) targeting of full-length SARS-CoV-2 structural proteins, and 3) induction of bidirectional (B and T cell) adaptive immunity.

METHODS
We utilized a novel engineering design that layers mRNA into a lipid-nanoparticle (NP) shell (much like an onion); this allows greater packaging of mRNA per particle to quickly boost innate/adaptive immune responses against full-length glioblastoma antigens or SARS-CoV-2 structural proteins.

RESULTS
In small and large animal models, RNA-NPs safely mimic viremia activating the quiescent immune system in only a few hours for induction of protective immunity against its mRNA payload. RNA-NPs activate dendritic cells (DCs), upregulate critical innate gene signatures, and induce antigen-specific cellular and humoral immunity. We found that mice receiving SARS-CoV-2 spike RNA-NPs had more effector T cells after vaccination with significant memory recall expansion after in vitro re-stimulation with overlapping SARS-CoV-2 spike peptide mix. We also found increased release of MIP-1-alpha (i.e. CCL3) previously shown by our group (Mitchell et al. Nature 2015) to be responsible for Th1 mediated memory recall to infectious vaccine antigens in GBM patients.

CONCLUSION
SARS-CoV-2 RNA-NPs elicit memory recall response after vaccination. We have obtained FDA-IND approval (BB-19304, Sayour) in GBM with SARS-CoV-2 specific amendment (BB-20871) underway to support first-in-human trials of RNA-NPs targeting both GBM and COVID-19.