bluuebunny/crossref_metadata_2025_split huggingface dataset:
GENE-28. LONGITUDINAL MOLECULAR TRAJECTORIES OF DIFFUSE GLIOMA IN ADULTS
Authors: Barthel Floris , Johnson Kevin C , Varn Frederick , Moskalik Anzhela , Tanner Georgette , Kocakavuk Emre , Anderson Kevin , Abiola Olajide ,   GLASS Consortium, Huse Jason , DeGroot John , Stead Lucy F , Verhaak Roel 
Published: November 2019

Abstract
Treatment options for adult patients with glioma has remained largely unchanged over the past three decades. Targeted inhibitors and immunotherapies have improved outcomes for many cancer types but their relevance in glioma is unclear. The inevitability of glioma disease recurrence demands an understanding of mechanisms driving therapy resistance. The Glioma Longitudinal Analysis (GLASS) Consortium was initiated to establish a definitive portrait of the recurrence process and to discover vulnerabilities that render the tumor sensitive to therapeutic intervention. GLASS is a community-driven effort that seeks to overcome the logistical challenges in constructing adequately powered longitudinal genomic glioma datasets by pooling data from patients treated at institutions worldwide. Currently, the GLASS Data Resource comprises DNA sequencing data (exome and/or whole-genome) from 288 patients of whom high-quality data in at least two time points are present from 222 patients (n = 134 IDHwt, n = 63 IDHmutant-noncodel, n = 25 IDHmutant-codel). We inferred longitudinal mutation, copy number, clonal frequency, and neoantigen profiles and demonstrated that driver genes found at initial disease persisted into recurrence. Treatment with alkylating-agents resulted in a hypermutator phenotype at different rates across glioma subtypes, most frequently among IDHmutant-noncodels, and hypermutation was not associated with differences in overall survival. Acquired aneuploidy was frequently detected in recurrent IDHmutant-noncodel gliomas and further converged with acquired cell cycle pathway alterations and poor outcomes. We showed that the clonal architecture of each tumor remains largely intact over time and that genetic drift was associated with increased survival. Finally, we found that neoantigens were exposed to stable selective pressures throughout a tumor’s progression. Our results collectively suggest that the strongest selective pressures occur early during glioma development and that current therapies shape this evolution in a largely stochastic manner. The GLASS Data Resource provides a genomic reference to study the patterns of glioma evolution.
GENE-31. IDENTIFICATION OF CORE AND CONTEXT-SPECIFIC FITNESS GENES IN GLIOBLASTOMA STEM CELLS VIA GENOME-WIDE CRISPR-Cas9 SCREENS
Authors: MacLeod Graham , Angers Stephane , Dirks Peter , Rajakulendran Nishani , Ahmadi Moloud , Bozek Danielle , Luchman Artee , Weiss Sam 
Published: November 2019

Abstract
Advances in the characterization of the genetic, epigenetic and transcriptomic landscapes of glioblastoma (GBM) tumor samples and primary cell lines have yielded considerable insight into tumor initiation and progression. A major finding from these studies is the high degree of inter- and intra-tumoral variability displayed in GBM, which has increased interest in the identification of clinically relevant disease subtypes for precision targeting. While multiple groups have identified subtypes of GBM tumors and GBM stem cell lines, efforts to identify specific actionable targets have yet to bear fruit. To address this gap, we performed genome-wide TKO CRISPR-Cas9 fitness screens to functionally interrogate the genomes of a panel of 16 genetically/epigenetically characterized GBM stem cell lines. Our screens identify over 1,500 fitness genes per GBM stem cell line which collectively provide a functional landscape of genetic vulnerabilities in GBM. The size and heterogeneity of our screen panel provided us with the capability to identify both core (i.e. SOX9, Protein Ufmylation, JUN) and context specific fitness genes. Specifically, we have identified genes preferentially required for the proliferation of GBM stem cells based on transcriptionally defined subtypes (i.e. SOX2, OLIG2 in Proneural GSCs), genetic alterations (i.e. CDK6 in CDKN2A/B deleted GBM) and disease stage (i.e. ATP6AP2 in recurrent GBM). Experimental validation of key subtype-specific fitness genes is currently underway using genetic knockout and drug/inhibitor treatment. Our data provides biological insight and novel mechanistic understanding of heterogeneity in GBM and points to opportunities for precision targeting of defined GBM subtypes.
GENE-35. MGMT PROMOTER METHYLATION IN NEWLY DIAGNOSED LGG AS A POTENTIAL BIOMARKER FOR TMZ-ASSOCIATED HYPERMUTATION AT RECURRENCE
Authors: Mathur Radhika , Zhang Yalan , Grimmer Matthew , Hong Chibo , Berger Mitchel , Molinaro Annette , Ann Oberheim-Bush Nancy , Chang Susan , Costello Joseph 
Published: November 2019

Abstract
Low-grade gliomas (LGGs), which include grade II astrocytoma and grade II oligodendroglioma, inevitably recur despite aggressive treatment with surgery, and sometimes, with radiation and the chemotherapeutic agent temozolomide (TMZ). The clinical benefit of TMZ in LGG is unclear, and a subset of TMZ-treated LGGs recur with hypermutation in association with malignant progression to high-grade tumors. It is currently unknown why some TMZ-treated LGGs recur with hypermutation while others do not. O6-methylguanine-DNA methyltransferase (MGMT) is a DNA repair protein that reverses mutagenic lesions induced by TMZ. The amount of MGMT protein in a cell is regulated at the epigenetic level by promoter methylation. Here, we hypothesize that epigenetic silencing of MGMT by promoter methylation facilitates TMZ-induced mutagenesis and contributes to the development of hypermutation. We demonstrate in a cohort of 37 TMZ-treated patients with an initial diagnosis of IDH-mutant LGG that methylation level of the MGMT promoter in initial untreated tumors is significantly associated with hypermutation at recurrence. We also confirm our previous finding that methylation level of the MGMT promoter in recurrent hypermutated tumors is higher than in recurrent tumors that are not hypermutated. These results provide a plausible mechanistic basis for observed differences in propensity of TMZ-treated LGG patients to develop hypermutation at recurrence. Furthermore, they establish the potential of MGMT promoter methylation level to inform treatment decisions in the clinic for patients with newly diagnosed LGG.
GENE-42. EXOME SEQUENCING ANALYSIS TO IDENTIFY POSSIBLE GENOMIC DRIVERS OF METASTATIC INVASION INTO THE SPINE
Authors: Calinescu Alexandra , Sultan Zain , Rocco Sabrina , Gates Chris , Clines Gregory , Szerlip Nicholas 
Published: November 2019

Abstract
The spine is a common site of metastatic spread of many cancers, causing debilitating pain and suffering. Treatment of spinal metastases is limited by resistance to radiation, chemotherapy, and proximity to the spinal cord. It is currently not known what causes the high incidence of spinal metastases, yet theories have been proposed, like the venous metastatic spread theory (Batson, 1940) and the “seed and soil” hypothesis (Paget, 1889), postulating that factors intrinsic to the tumor cells or to the microenvironment determine the location of cancer dissemination. Recent advances in high throughput sequencing allow for in depth analyses of the molecular signatures of tumors. To identify if there are intrinsic genetic alterations common to cancer cells that disseminate into the spine, we sequenced the exome of metastatic tumor cells harvested from the vertebrae of 9 patients with different primary tumors: carcinomas and sarcomas. Exome sequencing was performed using the HiSeq 4000 (Illumina) platform on DNA from tumor cell lines and control blood or bone marrow. Data was analyzed at the University of Michigan Bioinformatics Core and variants were called using the VarScan method (http://varscan.sourceforge.net/) in somatic mode. This analysis identified a total of 2366 genes with high impact mutations (888–1026 per sample); of these, 232 genes are common to all patients analyzed. Ninety-six of the identified genes (4%) are included in the Catalogue of Somatic Mutations in Cancer, and of these, seven: ACSL6, ACVR1, ALK, FGFR2, HSP90AA1, PTPN6 and PTPRB, have high impact mutations in all 9 patients with spinal metastatic disease. Pathway analysis of genes mutated in 5 or more patients shows significant overrepresentation of 41 KEGG pathways including TGFb, HIF1-a, VEGF, Wnt and Estrogen signaling pathways. Ongoing experiments are performed to validate the sequencing analysis and characterize functional consequences of the common mutations identified.
GENE-43. TARGETING GABPb1L INHIBITS IN VIVO GROWTH OF TERT PROMOTER MUTANT GLIOBLASTOMA
Authors: Amen Alexandra , Lew Rachel , Ren Shawn , McKinney Andrew , Mancini Andrew , Doudna Jennifer , Fellmann Christof , Costello Joseph 
Published: November 2019

Abstract
Understanding cancer cell immortality in primary glioblastoma (GBM) is essential for the development of more informed treatments. Multiple cancer types, including >80% of GBMs, undergo immortalization by reactivating Telomerase Reverse Transcriptase (TERT) through acquired mutations in the TERT promoter. TERT, the catalytically active and rate-limiting subunit of telomerase, functions to maintain telomeres, which cap and protect the ends of chromosomes. Our past work has demonstrated that the transcription factor GABP - and specifically its tetramer-forming isoform GABPb1L - binds and activates the mutant TERT promoter. The generation of CRISPR-induced indels in GABPb1L results in a gradual loss of cell viability in TERT promoter mutant but not TERT promoter wild type tumor cells in vitro, but the extent to which GABPb1L function is compromised in this setting is unclear. Thus, the potential for use of GABPb1L as an effective therapeutic target for TERT promoter mutant GBM requires further investigation. Here, we use CRISPR-based strategies to demonstrate that full knockout of GABPb1L is rapidly lethal in TERT promoter mutant cells in vitro, in association with a decrease in both TERT mRNA and telomerase activity. Heterozygous deletion of GABPb1L in the context of TERT promoter mutations leads to slowed growth of orthotopic xenograft tumors in mice, and prolonged survival. Additionally, inducible RNAi-mediated inhibition of GABPb1L in growing tumors is also capable of decreasing tumor burden and increasing survival, further strongly suggesting that targeting GABPb1L in patient tumors could be a viable treatment strategy. Finally, reduced GABPb1L synergizes with temozolomide (TMZ) therapy such that TMZ treatment in the context of low GABPb1L and low TERT leads to a complete ablation of orthotopic GBM xenografts. These results highlight the potential to improve disease outcomes by targeting TERT through inhibition of GABPb1L, particularly in conjunction with TMZ treatment.
GENE-49. RNA PROCESSING GENES CHARACTERIZE RNA SPLICING AND FURTHER STRATIFY LOWER-GRADE GLIOMA
Authors: Chai Rui-Chao , jiang tao , Wang Yong-Zhi 
Published: November 2019

Abstract
Aberrant expression of RNA processing genes may drive the alterative RNA profile in lower-grade gliomas (LGGs). Thus, we aimed to further stratify LGGs based on the expression of RNA processing genes. This study included 446 LGGs from The Cancer Genome Atlas (TCGA, training set) and 171 LGGs from the Chinese Glioma Genome Atlas (CGGA, validation set). The least absolute shrinkage and selection operator (LASSO) Cox regression algorithm was conducted to develop a risk-signature. The ROC curves and Kaplan–Meier curves were used to study the prognosis value of the risk-signature. Among the tested 784 RNA processing genes, 276 were significantly correlated with the OS of LGGs. Further LASSO Cox regression identified a 19-gene risk-signature, whose risk score was also an independently prognosis factor (P< 0.0001, multiplex Cox regression) in the validation dataset. The signature had better prognostic value than the traditional factors “age”, “grade” and “WHO 2016 classification” for 3‐ and 5‐year survival both two datasets (AUCs > 85%). Importantly, the risk-signature could further stratify the survival of LGGs in specific subgroups of WHO 2016 classification. Furthermore, alternative splicing events for genes such as EGFR and FGFR were found to be associated with the risk score. RNA expression levels for genes, which participated in cell proliferation and other processes, were significantly correlated to the risk score. Our results highlight the role of RNA processing genes for further stratifying the survival of patients with LGGs and provide insight into the alternative splicing events underlying this role.
GENE-61. METHYLATION-BASED LIQUID BIOPSY OF MENINGIOMA PRIMARY AND RECURRENT SAMPLES
Authors: Sarraf Sabedot Thais , Malta Tathiane , Snyder James , Walbert Tobias , Lee Ian , Kalkanis Steven , Castro Anavaleria , Noushmehr Houtan 
Published: November 2019

Abstract
Meningiomas are mostly benign CNS tumors, however a subset of these tumors may become atypical or malignant. The standard of care to monitor patients after diagnosis requires serial MRI assessments, which have limited value in distinguishing malignant tumors from benign disease. Therefore the discovery of non-invasive methodologies that reflect meningioma tumor burden and its dynamic evolution in real-time is highly desirable. Liquid biopsy (LB) could be used to fine-tune surveillance and treatment with minimal risk to patients. Evidence of circulating tumor cells and cell-free (cf) tumor DNA in the blood has been shown in several tumor types, however limited progress has been made for brain tumors with known biomarkers; possibly due to the unlikelihood of capturing point mutations in circulating DNA fragments. On the other hand, DNA methylation signatures are maintained even in small DNA fragments, which suggests that DNA methylation is an attractive marker to be studied in liquid biopsy of brain cancers. In order to identify DNA methylation-based biomarkers using archival serum and tissue specimens, we analyzed the epigenome (Illumina Human EPIC array) of patients with primary (n=10) and recurrent (n=4) meningiomas and epileptic patients (n=5) as control. cfDNA fragment size distribution revealed peaks with 150~200bp on average. We identified 482 CpGs (p-value< 0.001) differentially methylated between primary meningiomas and controls, which 294 (61%) show a DNA methylation profile similar to the matched tumor tissue. Overall, we observed that recurrent samples are hypermethylated (56%) compared to primary. From this pilot data, we were able to investigate the LB methylome of meningioma patients and identify potential markers to detect tumor cells in the serum of these patients, which could eventually allow clinicians to monitor impending disease progression and recurrence.
GENE-62. IDENTIFICATION OF FGFR4 p.G388R VARIANT IN CEREBELLAR HEMANGIOBLASTOMAS
Authors: Snuderl Matija , Kannan Kasthuri , Gagner Jean-Pierre , Mashiach Elad , Karajannis Matthias , Heguy Adriana , Zagzag David 
Published: November 2019

Abstract

BACKGROUND
While most hemangioblastomas (~70%) are sporadic and occur predominantly in the cerebellum, they may present as well as familial form associated with von Hippel-Lindau (VHL) syndrome, an autosomal dominant disorder caused by germline mutations of the VHL gene that trigger nuclear translocation of hypoxia-inducible factor (HIF)-1α and angiogenesis. Although inactivation of VHL, a tumor suppressor gene, has been observed in hemangioblastomas, the underlying pathogenic mechanisms responsible for familial and sporadic hemangioblastomas remain incompletely understood.

METHODS
Whole exome sequencing of cerebellar hemangioblastoma tumors and matched blood leukocytes from 24 patients, age 24–63, was performed. After preparation and amplification of barcoded libraries, exomes were captured using Kapa Biosystems methodology and paired-end sequenced on Illumina HiSeq 2500 to an average 100-fold coverage. Following read alignment to hg19 genome, tumor and germline (leukocyte) sequences were compared, and pathogenic single nucleotide variants (SNVs) identified and validated by re-sequencing followed by pathway analysis. Additionally, tumor RNA isolated using Maxwell Promega was sequenced on Illumina instrument and the expression counts determined and normalized.

RESULTS
We found 314 pathogenic and/or highly deleterious mutations (both germline and somatic) with a median of 13 mutations per patient. Five patients had VHL syndrome (germline VHL mutation) and 4 carried somatic VHL mutations. Among the VHL tumors, 82 mutations were identified, including HNF1B, NOTCH1 and TCF7L1, suggesting a potential contribution of altered RNA metabolism based upon pathway analysis. Among all hemangioblastomas, germline growth factor receptor variants (FGFR4 p.G388R (14/23 (61%) patients), IGF1R, PDGFRA and TYK2) known to activate STAT3 signaling and induce HIF-1α and angiogenesis, were identified. Non-hierarchical clustering of RNA sequencing data revealed two transcriptionally-distinct subtypes of hemangioblastomas.

CONCLUSIONS
Our findings indicate that hemangioblastomas can also occur by germline mutations known to activate STAT3 signaling, which may have significant implication in genetic testing and counseling of patients with hemangioblastomas.
HOUT-01. ALOPECIA SYMPTOM IMPACT SCALE (ASIS): MEASURING THE SYMPTOMS OF ALOPECIA AND THEIR IMPACT IN PATIENTS WITH PRIMARY BRAIN TUMORS
Authors: Mendoza Tito , Rowe Lindsay , Vera Elizabeth , Acquaye Alvina , Gilbert Mark , Armstrong Terri 
Published: November 2019

Abstract

INTRODUCTION
Alopecia manifests in many cancer patients receiving therapy. These patients may experience similar physical symptoms and impairment as patients with autoimmune alopecia areata. The Alopecia Areata Symptom Impact Scale (AASIS) was originally validated for patients with autoimmune disorder. However, the validity and reliability of the AASIS among primary brain tumor (PBT) patients has not been evaluated.

METHODS
A cross sectional survey of 100 PBT patients was conducted as part of an IRB approved prospective protocol using structured questionnaires and open-ended responses. Participants completed the AASIS to measure symptoms of alopecia areata and their impact on daily functioning along with the Body Image Scale (BIS) to assess the prevalence of body image disturbance. Analyses included factor analysis to determine the number and nature of underlying constructs, Cronbach’s alphas to assess reliability, and correlational analysis to establish concurrent validity.

RESULTS
Patients’ median age was 48(range 23– 74), and 56% were male. Glioblastoma was most common (32%); low grade tumors (I and II) were 30% of diagnoses. The median time from initial diagnosis was 5 years (range 0–22), and 64% of patients had a KPS of 90–100. An item from the AASIS, ‘body hair or eyelashes loss’, was deemed to be irrelevant, rated low by PBT patients and was removed. Factor analysis revealed 3 underlying constructs: physical (e.g. itchy skin, scalp hair loss), affective (e.g. feeling anxious, feeling sad) symptoms, and impact of alopecia (e.g. work, quality of life) with Cronbach’s alphas of 0.78, 0.89 and 0.96, respectively. The BIS had the highest correlation with the affective symptom subscale (0.58, p< .001).

CONCLUSION
Our results demonstrate the desired reliability and validity for use in studies examining alopecia and its impact in PBT patients. Dropping the term ‘areata’, the modified tool is now ASIS, and can be implemented in future studies.
HOUT-04. ASSOCIATION OF COMMON PATIENT-REPORTED IMMUNOTHERAPY SYMPTOMATIC SIDE EFFECTS AND PSEUDOPROGRESSION IN PATIENTS WITH PRIMARY CENTRAL NERVOUS SYSTEM (CNS) TUMORS
Authors: Vyas Yamini , Vera Elizabeth , Bryla Christine , Crandon Sonja , Wu Jing , Wall Kathleen , Theeler Brett , Siegel Christine , Reyes Jennifer , Penas-Prado Marta , Leggiero Nicole , Cordova Christine , Burton Eric , Antony Ramya , Boris Lisa , Aboud Orwa , Gilbert Mark , Armstrong Terri 
Published: November 2019

Abstract

BACKGROUND
Immunotherapy agents have unique symptomatic side effects; patient-reported outcomes (PROs) can help to characterize the benefits and burdens associated with therapy. Common immunotherapy-associated symptoms include pain, fatigue, shortness of breath, and irregular bowel patterns. The purpose of this study was to assess the severity of symptoms and their association with imaging changes in CNS tumor patients undergoing single agent or combination treatment with immune checkpoint inhibitors (ICIs).

METHODS
Patients completed the MDASI-BT or MDASI-SP at baseline and longitudinally (every 8 weeks), and results through cycle 4 are reported. Neuro-imaging was categorized as stable, possible ICI-related pseudoprogression, or progression by clinical team review.

RESULTS
29 Brain Tumor (BT) and 6 Spinal Tumor patients participated; the majority of which were male (62%) and white (91%), ranging 24-74yo (mean = 46). Glioblastoma was the most common diagnosis (31%) followed by medulloblastoma (16%), with 56% of patients having greater than 2 recurrences prior to the study. At baseline, both brain and spine tumor patients reported moderate to severe fatigue (Brain=4, Spine=6) and pain (Spine=5) with shortness of breath and pain worsening over time. BT patients with pseudoprogression were more likely to report increased fatigue (87%) and pain (63%) compared to those with stable (29%) or true progressive (17%) disease on imaging. BT patients with pseudoprogression also reported worsening of cognitive (43%) and neurologic (57%) symptom burden.

CONCLUSIONS
In contrast to the common pseudoprogression after chemoradiation, treatment-specific symptoms were worse with ICI-related pseudoprogression by MRI where an immunologic reaction was the likely cause of the imaging worsening. These results suggest that commonly used symptom and functional assessments to distinguish true progression from pseudoprogression may not be helpful with immunotherapy. Additional studies including those with pathologic confirmation of progression or pseudoprogression combined with outcomes measures are needed to develop more accurate determinations of disease status.