bluuebunny/crossref_metadata_2025_split huggingface dataset:
EXTH-43. DYNAMIC MULTI-OMICS ANALYSIS OF MLN4924-TREATED GLIOBLASTOMA CELLS REVEALS ABSENCE OF PTEN AS A CANDIDATE DRIVER OF NEDDYLATION INHIBITION RESISTANCE
Authors: Taylor Brett , Ferdosi Shayesteh , Bybee Rita , Tang Nanyun , Peng Sen , Garcia-Mansfield Krystine , David-Dirgo Victoria , Sharma Ritin , Pirrotte Patrick , Berens Michael , Dhruv Harshil 
Published: November 2019

Abstract
Glioblastoma multiforme (GBM) is the most lethal primary brain tumor and calls for novel therapeutic development. The neddylation pathway may be a therapeutic target, as global over activation of neddylation has been found in GBM patients and has correlated with shorter patient survival. Analogous to ubiquitination in reaction scheme and enzyme classes used, neddylation is a post-translational modification that is essential to many protein regulation and biological processes. Although non-cullin NEDD8 substrates have been investigated in recent years, the most well-characterized substrates of neddylation are the cullin subunits of Cullin-RING ligases (CRLs), which act as a scaffold for substrates to be ubiquitinated and degraded. The neddylation inhibitor MLN4924 targets NEDD8 Activating Enzyme (NAE), an upstream activator of neddylation, and induces cell cycle arrest, apoptosis and senescence in cancer cells. In this work, we investigated the context of vulnerability to Pevonedistat (MLN4924) in GBM. Efficacy of MLN4924 in glioma cell models was evaluated by measuring cell viability (CellTiterGlo®), colony formation efficiency, and cell cycle progression (flow cytometry with propidium iodide staining). GB1 (IC50= 0.28 μM), LN18 (IC50 = 0.19 μM), and GBM43 (IC50= 0.45 μM) were established as sensitive and M059K (IC50 = 5.5 μM), SNU1105 (IC50 = 20.9 μM), and GBM39 (IC50= 10.3 μM) as non-sensitive cell lines based on IC50 values. To discover genomic and/or proteomic markers of differential response, we collected RNA and protein from sensitive and non-sensitive cell lines after 0, 2, 8 and 24 hour treatment with MLN4924 for RNA sequencing and mass spectroscopy analyses. Multi-OMICS data point towards the absence of functional PTEN as a driver of MLN4924 resistance. Uncovering the mechanism underlying GBM’s vulnerability to MLN4924 will expand the knowledge of neddylation’s role in cancer and may arm physicians with an understanding of whether a GBM patient would respond to MLN4924 treatment or not.
EXTH-50. THIOREDOXIN REDUCTASE1 AND MGMT SYNTHETIC LETHALITY ENHANCES CYTOTOXICITY OF PRIMA-1MET(APR-246) AND AURANOFIN IN GLIOBLASTOMA
Authors: Raveendrakumar Rehka , Abdulkarim Bassam , Bagchi Monisha , Daniel Paul , Deri Aymane , Jean-Claude Bertrand , Sabri Siham 
Published: November 2019

Abstract
Glioblastoma multiforme (GBM), the most common and advanced primary brain malignancy in adults remains an incurable disease, despite aggressive treatment with surgery, radiation therapy and chemoradiation using the alkylating agent, Temozolomide (TMZ). PRIMA-1MET (APR-246), a small molecule designed to restore mutant (mut)p53 function has been shown to affect cellular redox status through targeting thioredoxin reductase 1 (TrxR1) in wild-type (wt)p53 cancer cells. We have recently shown that PRIMA-1MET exerts cytotoxic effects status preferentially in GBM cell lines expressing low levels of the DNA repair protein O6-methylguanine-DNA-methyltransferase (MGMT), known for its role in resistance to TMZ. We hypothesized that PRIMA-1MET mediates its growth inhibitory effects by modulating the redox balance and investigated the potential relationship between MGMT, redox balance and TrxR1. We show that PRIMA-1MET decreased TrxR1 expression levels preferentially in MGMT-low expressing isogenic GBM cell lines. Using pharmacological agents that modulate reactive oxygen species (ROS) levels i.e., ROS scavenger, N-acetylcysteine and ROS inducer, L-Buthionine-Sulfoximine, we show that PRIMA-1MET exerts its growth-inhibitory effects through increased ROS. Strikingly, we identified a novel positive relationship between MGMT and TrxR1, wherein high MGMT expression is associated with high expression of TrxR1 and low levels of ROS. Treatment with the MGMT inhibitor, O6-Benzylguanine, or the TrxR1-targeting FDA-approved drug Auranofin validated our findings. Interestingly, the latter exerted significantly more pronounced cytotoxic effects compared to PRIMA-1MET in GBM cell lines. Additional studies are warranted to assess PRIMA-1MET in combination with TrxR1-targeting therapies and propose repurposing of Auranofin as a novel strategy to improve the dismal outcome of patients with GBM.
GENE-12. ANALYSIS OF FAILURE PATTERNS IN MALIGNANT GLIOMA: EXPLORING THE GENETIC LANDSCAPE OF PATTERN OF FAILURE
Authors: Won Choi Seung , Nam Do-Hyun , Sa Jason , Koo Harim 
Published: November 2019

Abstract
Failure patterns in malignant gliomas have been described in previous literatures, however, studies were limited to analyze clinical features to account for predisposition to distinct failure patterns. Present study aimed to describe the landscape of failure patterns in malignant glioma from large cohort by integrating multi-omics data and investigate the genetic backgrounds of distinct failure patterns. A total of 423 cases from 325 patients who enrolled at the registry of IRCR at SMC were reviewed for their pattern of failure. Failure patterns were categorized into local, distant recurrence and leptomeningeal seeding regarding recurrent tumors’ spatial relation to primary location. Genomic data was available for 327 (DNAseq) and 259 samples (RNAseq), respectively. Glioblastoma was the most prevalent histologic type in study cohort (81.2%)) and majority of cases experienced the recurrence (79.0%). None of clinical parameters (e.g. age, sex, extent of operation and history of prior therapy) failed to show any significant association with failure patterns. Although local recurrence was most prevalent (63.8%) among failure patterns in malignant gliomas, considerable portion of patients (37.8%) demonstrated other types of failure patterns even in their initial relapse. Multivariate analysis demonstrated that failure pattern was significant prognostic factor to overall survival (remote recurrence, HR=1.59, p-value=0.009; leptomeningeal seeding, HR=2.17, p-value< 0.001). Genomic analysis including mutational profile revealed distinct molecular landscape of malignant gliomas according to failure patterns, which suggested that innate biologic characteristics of tumors might contribute to develop distinct failure patterns upon recurrence. PTEN mutation was significantly enriched in tumors of distant recurrence (p-value=0.026). We described the landscape of failure patterns in malignant gliomas by integrating clinical and genomic data. Considerable amount of malignant glioma patients experienced distinct failure patterns other than local recurrence and their clinical outcome as well as genetic background demonstrated invasive characteristic of these tumors.
GENE-22. GENOME-WIDE METHYLATION PROFILING OF GLIOBLASTOMA EXTRACELLULAR VESICLE DNA ALLOWS TUMOR CLASSIFICATION
Authors: Ricklefs Franz , Maire Cecile , Kolbe Katharina , Holz Mareike , Westphal Manfred , Schüller Ulrich , Lamszus Katrin 
Published: November 2019

Abstract

BACKGROUND
Genome-wide methylation profiling has recently been developed into a tool that allows subtype tumor classification in central nervous system (CNS) tumors. Extracellular vesicles (EVs) are released by CNS tumor cells 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 glioma-derived EVs reflects genome-wide tumor methylation profiles and allows tumor subtype classification.

METHODS
DNA was isolated from EVs secreted by cultured glioma stem-like cells (GSC) as well as from the cells of origin and from the original tumor samples (n=3 patients). EVs were classified by nanoparticle analysis (NTA), immunoblotting, imaging flow cytometry (IFCM), multiplex EV assays 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.

RESULTS
The size range of GSC-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 and multiplex EV assays. Genome-wide methylation profiling of GSC-derived EVs correctly identified the methylation class of the original tumor, including information on the IDH mutation status and subclass classification (RTK1, RTK2). In addition, copy number alterations and the MGMT metyhlation status matched the pattern of the parental GSCs and original tumor samples.

CONCLUSION
EV DNA faithfully reflects the tumor methylation class as well as the MGMT methylation status and copy number variations 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 CNS tumors.
GENE-37. VESTIBULAR SCHWANNOMA IS COMPRISED OF NEURAL CREST AND IMMUNE SUBGROUPS
Authors: John Liu S , Vasudevan Harish , Pekmezci Melike , Choudhury Abrar , Lien Brian , Breshears Jonathan , Swaney Danielle , Magill Stephen , Lang Ursula , Chen William , Gopinath Chetna , Castro Maria , Villanueva-Meyer Javier , Braunstein Steve , Sneed Patricia , Lim Daniel , Perry Arie , Krogran Nevan , McDermott Mike , Berger Mitchel , Theodosopoulos Philip , Raleigh David 
Published: November 2019

Abstract

BACKGROUND
Vestibular schwannomas (VS) are tumors arising from cranial nerve Schwann cells and show variable outcomes after treatment, including oscillation in size for many years after radiosurgery. To understand the unique biology of VS, we performed multiplatform molecular profiling to develop a single cell atlas of VS and reveal that VS exists on a molecular axis defined by neural crest and immune genes.

METHODS
Sixty-six sporadic VS with available tissue for molecular profiling from 59 consecutive patients at a single institution were included. 850K DNA methylation arrays and RNA sequencing were used to profile both primary (76%) and recurrent (24%) tumors. Single nuclei RNA sequencing of 7 tumors and single cell RNA sequencing of 3 tumors and cell lines were used to define the cellular composition of VS and heterogeneous changes in molecular programs following irradiation. Molecular subtyping was performed by hierarchical clustering of differentially-methylated DNA probes and validated using transcriptomic data. Mechanistic experiments were performed using cultured human schwann cells and human vestibular schwannoma cells, confocal microscopy, CRISPR interference, proteomic mass spectrometry and lymphocyte migration assays.

RESULTS
Multiplatform genomic profiling and machine learning revealed that VS is comprised of two distinct molecular subtypes characterized by heterogeneous cell populations. Neural crest enriched VS express primary cilia and are associated with misactivation of the Hedgehog pathway. Consistently, we find that the Hedgehog pathway antagonist vismodegib blocks the growth of human Schwann cells. Irradiation epigenetically reprograms tumors and cell lines to reduce ciliary length, attenuate Hedgehog signaling, activate senescence pathways, and express cytokines and apolipoproteins that recruit lymphocytes and macrophages to immune enriched VS.

CONCLUSIONS
Our data reveal novel molecular subtypes of VS and establish a framework for understanding how irradiation modifies the epigenome and tumor microenvironment.
GENE-39. CRISPRi-BASED RADIATION MODIFIER SCREEN IDENTIFIES LONG NON-CODING RNA THERAPEUTIC TARGETS IN GLIOMA
Authors: John Liu S , Malatesta Martina , Seo Kyounghee , Lien Brian , Hong Sung , Koontz Mark , Raleigh David , Ullian Erik , Lim Daniel 
Published: November 2019

Abstract
Long noncoding RNAs (lncRNAs) exhibit highly cell type-specific expression and function, making this class of transcript attractive for targeted cancer therapy. However, the vast majority of lncRNAs have not been tested as potential therapeutic targets, particularly in the context of currently used cancer therapy. Malignant glioma is rapidly fatal, and ionizing radiation is part of the current standard-of-care used to slow tumor growth in both adult and pediatric patients. Here, we used a CRISPR interference (CRISPRi) platform to systematically screen 5689 lncRNA loci in human glioblastoma (GBM) cells, identifying 467 hits that modified cell growth in the presence of clinically relevant doses of fractionated radiation. 34 of these lncRNA hits sensitized cells to radiation, and based on their expression in adult and pediatric glioma, nine of these hits were prioritized as lncRNA Glioma Radiation Sensitizers (lncGRS). Knockdown of lncGRS-1 – a primate-conserved, nuclear-enriched lncRNA – inhibited the growth and proliferation of primary adult and pediatric glioma cells, but not the viability of normal brain cells. Using human brain organoids comprised of mature neural cell types as a 3-dimensional tissue substrate to model the invasive growth of glioma, we found that antisense oligonucleotides (ASOs) targeting lncGRS-1 selectively decreased tumor growth synergistically with radiation therapy. These studies identify lncGRS-1 as a glioma-specific therapeutic target and establish a generalizable approach to rapidly identify novel therapeutic targets in the vast non-coding genome that can enhance the standard-of-care for cancer therapy.
GENE-50. SWI/SNF COMPLEX HETEROGENEITY RELATES WITH POLYPHENOTYPIC DIFFERENTIATION, PROGNOSIS AND IMMUNE RESPONSE IN RHABDOID TUMORS
Authors: Venneti Sriram , Panwalkar Pooja , Pratt Drew , Chung Chan , Dang Derek , Lee Paul , Martinez Daniel , Bayliss Jill , Smith Kyle , Adam Mike , Potter Steve , Northcott Paul , Mascarenhas Leo , Shows Jared , Pawel Bruce , Margol Ashley , Huang Annie , Judkins Alexander 
Published: November 2019

Abstract

PURPOSE
Rhabdoid tumors (RTs) arise within (Atypical Teratoid/Rhabdoid Tumor-AT/RT) or outside the brain (extraCNS-RT-eCNS-RT) and are driven mainly by inactivation of the SWI/SNF complex subunit SMARCB1. A pathognomonic hallmark of RTs is heterogeneity characterized by multilineage differentiation of tumor cells including anomalous neuronal differentiation in a subset of eCNS-RT. The mechanisms that regulate heterogeneity in RTs are unknown. Because remodeling of the SWI/SNF complex regulates differentiation, we hypothesized that SWI/SNF-BAF and PBAF complex heterogeneity correlates with both multilineage differentiation and clinical outcome. EXPERIMENTAL DESIGN: We performed an integrated analysis of SWI/SNF complex subunit alterations in the developing kidney and cerebellum (most common regions of origin for RT) in comparison to eCNS-RT (n=14) and AT/RT (n=25) tumors. RT samples were interrogated using immunohistochemistry, DNA methylation and gene expression analyses.

RESULTS
(A) The SWI/SNF-BAF paralogs ACTL6A/ACTL6B were expressed in a mutually exclusive manner in the developing cerebellum and kidney. In contrast, a subset of eCNS-RTs lost mutual exclusivity and co-expressed both subunits. These tumors showed aberrant DNA methylation of genes that regulate neuronal and renal development and demonstrated immunohistochemical evidence of neuronal differentiation. (B) Low expression of the PBAF subunit-PBRM1 identified a group of AT/RTs in younger children with better overall prognosis. PBRM1-low AT/RT and eCNS-RTs showed altered DNA methylation and gene expression in immune-related genes accompanied by increased CD8 cytotoxic T-cell infiltration.

CONCLUSIONS
Heterogeneity in SWI/SNF BAF (ACTL6A/ACTL6B) and PBAF (PBRM1) subunits correlates with histogenesis, contributes to the immune microenvironment and prognosis in RTs and may inform opportunities to develop immunotherapies.
GENE-60. THE EPITRANSCRIPTOMIC CODE IN LGG: METABOLICALLY REPROGRAMMED IDH-MUTANT GLIOMAS ALTER tRNA MODIFICATION LANDSCAPE
Authors: Scheepbouwer Chantal , Borland Kayla , Aparicio Ernesto , Verschueren Heleen , Wedekind Laurine , Ramaker Jip , Misovic Branko , CM Kouwenhoven Mathilde , Noske David , Vandertop Peter , Wesseling Pieter , Wurdinger Tom , Hackenberg Michael , Kellner Stefanie , Koppers-Lalic Danijela 
Published: November 2019

Abstract

BACKGROUND
Diffuse lower grade gliomas (LGGs) are generally slow growing primary central nervous system tumors that occur in early adult life. The prevalence of isocitrate dehydrogenase (IDH) mutations is high in LGG, and induces excess production of the oncometabolite 2-hydroxyglutarate (2-HG). These gain-of-function mutations play a key role in promoting metabolic reprogramming of the cancer cell that affects activity of α-KG dependent demethylases. Inhibition of DNA demethylase activity leads to glioma with a CpG island methylator phenotype (G-CIMP). Whether the activity of RNA demethylases and methylation status of tRNAs in LGG are modulated by changes in IDH-status is unknown. AIM: To investigate whether IDH mutations play a role in reprogramming of tRNA modifications in adult glioma.

MATERIALS AND METHODS
We combined small RNAseq and LC-MS/MS analysis to identify distinct tRNA processing patterns and methylation signatures in LGG tissues. To address important experimental bottlenecks that limit RNAseq-based detection of tRNA and possibly other modified small noncoding RNAs, we employed a tailored small RNAseq method with validation of specific methylation sites by mass-spectrometry.

RESULTS
Our customized small RNAseq approach yielded >100 fold increase in sequencing reads per tRNA type, thereby dramatically improving tRNA detection when compared to currently used small RNAseq approaches. Moreover, LC-MS/MS analysis revealed a higher abundance of modified nucleosides in tRNA from IDH-mutant LGG compared to IDH-wildtype LGG. Analysis of tRNA from IDH-mutant and IDH-wildtype LGG using the combination of our tailored small RNAseq and LC-MS/MS methodology demonstrated strong differential tRNA expression, tRFs processing and tRNA methylation.

CONCLUSION
We described an approach that makes use of tailored small RNA sequencing combined with mass-spectrometry that enables insights into cancer driven alterations in tRNA methylation patterns and differential tRNA processing signatures. Our data implies that tumor metabolic reprogramming deregulates tRNA methylation, contributing to an altered epitranscriptomic code in IDH-mutant LGG.
HOUT-03. CLINICAL OUTCOMES OF PATIENTS WITH VESTIBULAR SCHWANNOMAS: THE RELEVANCE OF TUMOR SIZE AND RECURRENCE
Authors: Zhao Amy , Fomchenko Elena , Tyrtova Evgeniya , Huttner Anita , Zhang Yawei , Fulbright Robert , Zeynep Erson-Omay E , Jin Lan , Moliterno Jennifer 
Published: November 2019

Abstract

INTRODUCTION
Vestibular schwannomas (VS) are known to be slow-growing lesions that can present significant issues for patients. Here, we sought to better understand their outcomes and risks for recurrence.

METHODS
We retrospectively reviewed clinical outcomes data for patients who had VS tumor that underwent whole-exome sequencing after surgical resection between 2015 and 2018. The association between any two categorical variables was investigated using Fisher’s exact test. The mean of a continuous variable was compared between groups using either a two-tailed t-test or ANOVA.

RESULTS
Forty patients met our inclusion criteria. Interestingly, men were more likely than women to experience recurrence (p = 0.05). In accordance with previous research demonstrating a significant association between NF2 and bilateral vestibular schwannomas, most VS were NF2-mutants, with only four being were non-NF2. Pre-operative tumor size significantly correlated with progression-free survival time from surgical resection to recurrence, such that larger tumors were more likely to recur slower post-operatively (p = 0.043). There appeared to be no significant association between the extent of surgical resection (EOR) and recurrence (p = 0.653). In addition, there was no significant difference in post-operative complications or clinical outcomes, including EOR and facial nerve function, between different surgical approaches (p > 0.30). Patients with pre-operative intra-tumoral hemorrhage were more likely to have smaller tumors, suggesting they present more acutely (p = 0.119). Finally, patients with NF2-mutated VS had a longer time from original diagnosis to surgery than patients who had non-NF2 VS mutants (p = 0.041).

CONCLUSIONS
Surgery for VS offers good clinical outcomes overall with low recurrence rates, regardless of prior treatment. Though not related to Ki67, larger tumors appear to confer a slower growth potential and lower risk of recurrence over time.
HOUT-05. COMPARING OUTCOMES OF ADULT DIFFUSE MIDLINE GLIOMAS TO GLIOBLASTOMA (GBM) IN YOUNG PATIENTS
Authors: Sarangi Sasmit , Wong Eric 
Published: November 2019

Abstract
Diffuse midline gliomas are a diagnostic entity with astrocytic tumors in a midline location and in the pediatric age group they have been associated with poor outcomes. There is ongoing debate if adults with diffuse midline gliomas also have a poor prognosis particularly as complete surgical resection is often not achievable in these patients. One of the limitations of looking at case-series based outcomes with these patients is that the incidence of these tumors has a skew towards younger patients and recent case-series with observed better than expected outcomes, might be subject to influence from this parameter. To better compare outcomes of these patients we reviewed our institutional tumor registry to identify 31 patients with diffuse midline gliomas from January 2010 to December 2017. We also identified a contemporaneous consecutive series of 46 patients of age ≤ 55 with a diagnosis of GBM, as the control group for comparison. Both groups were comparable in median age (53 vs 50), gender distribution and median Karnofsky Performance Status (80 vs 90). But fewer resections were performed on diffuse midline gliomas (35.5% vs 80%). Our results indicate that patients with a diffuse midline glioma have a higher likelihood of a poorer outcome with a median overall survival of 52 vs 91 weeks in the control. The hazard ratio for death in the diffuse midline glioma cohort as compared to the control was 1.68 (95% CI – 0.97–2.91, log-rank P value = 0.038). The 2-year survival rate was also lower in the diffuse midline glioma with 22.6% vs 39.1% in the control. This poorer outcome could be related to the slightly lower median performance status or the lack of complete resection in diffuse midline glioma patients. Additional analysis is being planned to genetically differentiate these patients and identify possible prognostic indicators.