bluuebunny/crossref_metadata_2025_split huggingface dataset:
PATH-11. THE PROGNOSTIC ROLE OF IDH MUTATIONS IN HOMOGENEOUSLY TREATED PATIENTS WITH MALIGNANT DIFFUSE ASTROCYTOMAS
Authors: Christians Arne , Banan Rouzbeh , Stockhammer Florian , Hartmann Christian 
Published: November 2019

Abstract
Detection of IDH mutations in patients with diffuse malignant astrocytomas resulted in substantial modifications in the WHO classification. An important observation was that patients with anaplastic astrocytomas (AA) IDH-wt had a clinical course similar to that glioblastoma (GBM) patients. The observations of the GGN and NOA-04, were based on mixed cohorts. While most GBM patients received combined radiochemotherapy, patients with AA usually only had radiotherapy or chemotherapy. This shortcoming raises the question whether AA IDH-wt patients did not behave prognostically better than GBM patients when receiving combined radiochemotherapy. Thus, the question remains whether the established histopathological grading criteria for malignant astrocytomas in the absence of IDH mutations are important if vascular proliferation or necrosis are undetectable. All patients investigated here with diagnosis of a malignant astrocytoma received combined standard radiochemotherapy independently of the histopathological diagnosis. Thus, the analysis allows to clarify whether patients with AA of IDH-wt have a prognosis similar to that of GBM patients under equivalent therapeutic conditions. We determined the IDH1/2 status by sequencing, the MGMT status by pyrosequencing. Patients with the histopathological diagnosis of an AA IDH-wt showed a comparable and therefore no better prognosis (median overall survival (mOS) 16 months) than patients with a glioblastoma (mOS 13 months). Instead, patients with an AA IDH-mut receiving same therapy had a mOS of 54 months. Thus, it can be concluded that in absence of IDH mutations, the established histopathological grading criteria ‘necrosis’ and ‘vascular proliferation’ lose their prognostic significance. If, on the other hand, patients with malignant astrocytomas and IDH mutations are examined, there is a difference between patients showing necrosis and/or vascular proliferation and those whose tumors do not. Accordingly, for patients with malignant astrocytomas with IDH mutations it can be concluded that differentiation between AA IDH-mut and GBM IDH-mut remains beneficial from a prognostic perspective.
PATH-15. IDENTIFICATION OF SUBSETS OF IDH-MUTANT GLIOBLASTOMAS WITH DISTINCT EPIGENETIC AND COPY NUMBER ALTERATIONS AND STRATIFIED CLINICAL RISKS
Authors: Ka-Wai Li Kay , Chen Hong , Noushmehr Houtan , Ng Ho-Keung 
Published: November 2019

Abstract
IDH-mutant glioblastoma is classified by the 2016 CNS WHO as a group with good prognosis. However, the actual number of cases examined in the literature is relatively small. We hypothesize that IDH-mutant glioblastoma is not a uniform group and should be further stratified. We conducted methylation profiles and estimated copy number variations of 57 IDH-mutant glioblastomas. Our results showed that 59.6%, and 40.4% of tumors belonged to G-CIMP-high and G-CIMP-low methylation subgroups, respectively. G-CIMP-low subgroup was associated with significantly worse OS as compared to G-CIMP-high (P=0.005). CDKN2A deletion (42.1%) was the most common gene copy number variation, and was significantly associated with G-CIMP-low subgroup (P=0.004). Other frequent copy number changes included MET (5.3%), CCND2 (19.3%), PDGFRA (14.0%), CDK4 (12.3%), and EGFR (12.3%) amplification. Both CDKN2A deletion (P=0.036) and MET amplification (P< 0.001) were associated with poor OS in IDH-mutant glioblastomas. Combined epigenetic signatures and gene copy number variations separated IDH-mutant glioblastomas into Group 1 (G-CIMP-high), Group 2 (G-CIMP-low without CDKN2A nor MET alterations), and Group 3 (G-CIMP-low with CDKN2A and/or MET alterations). Survival analysis revealed Groups 1 and 2 exhibited a favorable OS (median survival: 619 days (20.6 months), and 655 days (21.8 months), respectively). Group 3 exhibited a significant shorter OS (median survival: 252 days (8.4 months)). Multivariable analysis confirmed the independent prognostic significance of our Groups. IDH-mutant glioblastomas should be stratified for risk with combined epigenetic signature and CDKN2A/MET status and some cases have poor outcome.
PATH-28. ANGIOTENSINOGEN PROMOTER METHYLATION TO PREDICT BEVACIZUMAB RESPONSE IN RECURRENT GLIOBLASTOMA PATIENTS
Authors: Urup Thomas , Gillberg Linn , Kaastrup Katja , Schuang Lü Maja , Regner Michaelsen Signe , Larsen Vibeke A , Jarle Christensen Ib , Broholm Helle , Lassen Ulrik , Grønbæk Kirsten , Skovgaard Poulsen Hans 
Published: November 2019

Abstract
Recurrent glioblastoma patients achieving response to bevacizumab combination therapy have clinical improvement and prolonged survival. High gene-expression of angiotensinogen (AGT) is associated with a poor response to bevacizumab combination therapy. Because AGT gene-expression is epigenetically regulated, we investigate if lower AGT promoter methylation in tumor tissue predicts a poor response to bevacizumab combination therapy in recurrent glioblastoma patients. Methods: Patients were assessed for eligibility using our clinical database comprising all recurrent glioblastoma patients consecutively treated with bevacizumab combination therapy at our center. The study included 159 response and biomarker evaluable patients: A training cohort of 77 patients and a validation cohort of 82 patients treated in the period between year 2005–2011 and 2012–2015. DNA methylation of 4 CpG sites in the AGT promoter was measured using pyrosequencing. Using logistic regression analysis, a predictive model for non-response was established. Results: In the training cohort, lower methylation of each of the four CpG sites was significantly associated with non-response (p < 0.05). Lower mean methylation of the AGT promoter was significantly associated with non-response (2-fold decrease: OR &eq; 3.01; 95% CI:1.41–6.44; p &eq; 0.004). A predictive model able to predict bevacizumab non-response in clinical practice was established. This predictor was significantly associated with non-response in the validation cohort (p &eq; 0.037). Conclusion: AGT promoter methylation is lower in tumor tissue from non-responsive recurrent glioblastoma patients treated with bevacizumab combination therapy. A predictive model for non-response was established and successfully validated. This model can be used to identify patients who will not benefit from bevacizumab combination therapy.
PATH-35. RETROSPECTIVE ANALYSIS OF 145 PATIENTS WITH GLIOBLASTOMA; CORRELATING MOLECULAR ALTERATION INCIDENCE WITH DEMOGRAPHICS, TUMOR LOCATION, AND PROGNOSIS
Authors: Lobbous Mina , Tucker ZacK , Coffee Elizabeth , Nabors Louis 
Published: November 2019

Abstract
Glioblastoma is the most common and most aggressive primary brain tumor in adults. Glioblastoma was the first neoplasm to be systemically studied by The Cancer Genome Atlas and is one of the most molecularly well-characterized tumors in humans. Molecular profiling of glioblastoma is increasingly available and had led to the identifications of multiple prognostic factors as well as potential actionable targets for novel therapies. We identified 145 patients diagnosed with glioblastoma whose tumor tissue was analyzed using next generation sequencing (NGS). The NGS was performed using validated, commercially available panels. We studied somatic genetic alterations with a particular focus on TERT (which was altered in 55.9% of patients in the dataset), CDKN2A (44%), TP53 (39%), EGFR (38.6%), PTEN (31%), IDH1 (20%), and CDK4 (9%). These molecular alterations were analyzed in relation to the patients’ tumor locations, demographics, and outcomes. We used multiple binary logistic regressions to assess whether demographics and tumor location were predictive of the above alterations We also assessed the relationship between molecular alterations and outcomes when controlling for treatment and demographic variables. Among demographic variables, age predicted alterations in IDH1, EGFR, TERT, TP53, and PTEN. Frontal lobe tumors were more likely to be IDH1-mutated, irrespective of patient age. Sex and race did not predict the incidence of the molecular alterations of interest. Analysis of outcomes revealed that, when controlling for treatment and demographic variables, TERT promoter mutations, TP53 nonsense mutations, and EGFR A289V were predictive of a decreased progression-free survival, while CDKN2A deletion, PTEN missense mutations, and EGFR A289V were predictive of decreased overall survival. Our experience highlights the importance of incorporating routine NGS in the management of patients with glioblastoma. More studies are required to evaluate the predictive and/or prognostic values of different molecular alterations.
PATH-36. MACHINE LEARNING TO DETECT GLIOMAS IN URINE-BASED LIQUID BIOPSY
Authors: Kitano Yotaro , Aoki Kosuke , Yasui Takao , Motomura Kazuya , Ohka Fumiharu , Tanahashi Kuniaki , Hirano Masaki , Nishikawa Tomohide , Shimizu Hiroyuki , Yamaguchi Junya , Maeda Sachi , Yamazaki Shintaro , Wakabayashi Toshihiko , Natsume Atsushi 
Published: November 2019

Abstract

BACKGROUND
Diffuse gliomas are the most common primary malignant brain tumors, whose overall prognosis is quite dismal. Tumor-cell-secreted extracellular vesicles (EVs) participate in physiological and pathological processes and have potential applications to diagnostics of malignant tumors including diffuse gliomas. Because urine is less invasive to collect, development of early diagnosis based on urine EVs is eagerly awaited. In this study, we captured urine EVs of patients with gliomas efficiently with the nanowire device and compared expression profile of microRNAs (miRNAs) within urine EVs with that of healthy donors to identify diagnostic accuracy by a machine learning algorithm.

METHODS
62 patients with diffuse gliomas, including 27 glioblastoma and 35 lower grade gliomas, and 100 healthy donors were analyzed, along with orthotopic transplant mouse model. Urinary EVs were obtained with the nanowire device which could collect EVs more efficiently than the conventional ultracentrifugation method (Yasui et.al., Science Adv.2017). Machine learning methods were performed to select the miRNAs which could distinguish patients with gliomas from healthy control.

RESULTS
More than 2400 miRNAs were obtained from all urine samples. We identified miRNA panels that provided high diagnostic accuracy of diffuse gliomas (92.5%). There were 440 miRNAs whose expression increased by more than 1.5 fold (p< 0.05) as compared to healthy donor samples (glioma-upregulated miRNAs), whereas the expression of 87 miRNAs decreased to less than 2/3-fold (p< 0.05) (glioma-downregulated miRNAs). Mouse miRNAs which were homologous to glioma-upregulated and -downregulated miRNAs showed significantly high and low level expressions, respectively, in glioma mouse models as compared to normal control mice, confirming the reliability of urine miRNA-based diagnosis. Furthermore, some of these glioma-upregulated miRNAs has been reported to be involved in tumor progression.

CONCLUSIONS
miRNAs obtained from urine could be biomarkers for detection of gliomas by machine learning and some of these could be associated with tumor progression.
PATH-43. DIAGNOSIS OF GLIOMAS USING CIRCULATING GLIAL CELLS
Authors: Patil Darshana , Akolkar Dadasaheb , Schuster Stefan , Govardhan H B , Datta Vineet , Bhatia Jatinder , Patil Revati , Puranik Sneha , Apurwa Sachin , Srinivasan Ajay , Fulmali Pooja , Datar Rajan 
Published: November 2019

Abstract
Invasive procedures for diagnosis of CNS malignancies carry inherent risks of high morbidity and mortality. Although circulating biomarkers such as cell free DNA (cfDNA) and microvesicle (MV) borne nucleic acids have been proposed as potential diagnostic aids, their stand-alone utility has inherent limitations. However, Circulating Glial Cells (CGCs) combined with cfDNA could offer a viable alternative to invasive biopsies for diagnosis of CNS malignancies; yet the technological challenge in the detection of CGCs in glioma patients presents a formidable challenge. In this study, we evaluated the feasibility of harvesting CGCs from suspected cases of Glioma. From a cohort of 23 suspected cases of CNS malignancies, we used 15ml of peripheral blood and used the CellWizard™ process and related protocol for isolation of CGCs. CellWizard™ is an epigenetically active media with paradoxical chemo-toxicity that selectively induces lethality in normal cells which have a functionally responsive cell death (apoptosis) mechanism, while simultaneously conferring survival privilege on apoptosis resistant cells typically released from a malignant tumor. This paradoxical cytotoxicity of the medium leads to selective elimination of most leukocytes thus facilitating a label free negative enrichment of CGCs, which can be harvested and further characterized. Patients included 11 Glioblastoma, 3 Anaplastic astrocytoma, 2 Medulloblastoma, 5 Oligodendroglioma, 1 Gliosarcoma and 1 meningioma patient. Characterization of CGCs was performed using GFAP, S100 and CD45 markers. CGCs were detected in 16 out of 23 (69.6 %) patients and could be stained positively for both GFAP and S100 and negatively for CD45. Detection of viable CGCs in cases of CNS malignancies can be used for characterization of markers related to the diagnosis.
PATH-45. DIFFERENT TYPES OF HYPERMUTATOR PHENOTYPE OF GLIOBLASTOMA ACCORDING TO MUTATION PATTERNS OF MISMATCH REPAIR GENES
Authors: Saito Kuniaki , Shimizu Saki , Nozaki Eriko , Kobayashi Keiichi , Sasaki Nobuyoshi , Yamagishi Yuki , Shiokawa Yoshiaki , Nagane Motoo 
Published: November 2019

Abstract

BACKGROUND
Although precision medicine has been widely applied to routine care, only few molecular targeted drugs have been developed for glioma. Immune checkpoint inhibitors hold a potential promise to improve outcome of malignant glioma especially with the hypermutator phenotype. Mismatch repair deficiency could induce hypermutation during temozolomide (TMZ) treatment, but the mechanism of mutation acquisition is not well understood.

METHODS
We present the results of target sequencing of 57 longitudinal specimens from 27 individuals with glioblastoma (GBM). We used Ion AmpliSeq Cancer Hotspot Panel v2 (CHP) and/or Ion AmpliSeq Comprehensive Cancer Panel (CCP) for target sequencing.

RESULTS
Acquired mutations with G:C >A:T transition at non-CpG sites were found in 70% of recurrent MGMT methylated samples, whereas only 8% in MGMT unmethylated cases (p< 0.001). Two cases of hypermutator phenotype were identified in MGMT methylated, IDH wild type recurrent GBMs after TMZ chemotherapy. One case gained mutations in mismatch repair genes of MLH1, MSH2, MSH6, and PMS1. Most of the acquired mutations were G:C >A:T mutations typical to TMZ-induced hypermutation. The recurrent tumor was highly aggressive with overall survival after recurrence of 3.7 months. The other case gained mutations in mismatch repair genes of MLH1 and PMS1 only. Most of the acquired mutations were insertion mutations. The prognosis after recurrence was much longer.

CONCLUSIONS
We identified two types of hypermutator phenotype according to mutation pattern of mismatch repair genes. It has been suggested that MSH2-MSH6 complex deficient tumor cannot repair TMZ-induced mismatch mutation, thereby causing hypermutation. Conversely, MLH1-PMS1 complex deficient tumor with intact MSH2-MSH6 complex can repair mismatch mutation but is susceptible to insertion mutation. Taken together, MSH6 mutation plays a key role in TMZ-induced hypermutation, while MLH1 and PMS1 mutations might cause insertion-based hypermutation. Larger and prospective studies are warranted to clarify the mechanism, outcome, and effectiveness of checkpoint inhibitors.
PATH-48. THE DNA METHYLATION LANDSCAPE OF CORE AND PERIPHERAL DIFFUSE GLIOMA REGIONS SHOWS LITTLE SPATIAL SUBTYPE HETEROGENEITY AFTER CONSIDERING TUMOR PURITY
Authors: Verburg Niels , Barthel Floris , Anderson Kevin , Koopman Thomas , Yaqub Maqsood , Hoekstra Otto , Lammertsma Adriaan , Barkhof Frederik , Pouwels Petra , C Reijneveld Jaap , Heijmans Jan , Rozemuller Annemieke , Costello Joseph , Taylor Michael , Vandertop William , Boellaard Ronald , Johnson Kevin C , Wesseling Pieter , de Witt Hamer Philip , Verhaak Roel 
Published: November 2019

Abstract
While diffuse gliomas are notorious for their histopathological, genetic and transcriptional spatial heterogeneity, little is known about their epigenetic spatial heterogeneity. The result of spatial (epi)genetic analysis is strongly influenced by the proportion of cancer cells in a sample, so called tumor purity. However, a gold standard for assessment of tumor purity is lacking. We set out to analyze tumor purity using different measurement modalities and explore tumor purity-corrected DNA methylation spatial heterogeneity in glioma. DNA methylation(-derived), quantitative histological and radiological measurements of tumor purity, as well as DNA methylation profiles, were analyzed in 133 image-guided multi-sector stereotactic biopsy samples of 16 patients with newly diagnosed glioma. These biopsies were acquired in regions with and without abnormalities on MRI. Data was validated in two independent populations of respectively 102 multi-region samples in 24 glioma patients and 64 single-region samples from patients without glioma. DNA methylation profiles from The Cancer Genome Atlas and the patients without glioma was used to predict DNA methylation and transcriptional subtype. Consensus measurement of tumor purity estimates (CPE) ranged from 0 to 91% and was most correlated with the DNA methylation measurement of tumor purity. Neuropathological qualitative assessment of tumor presence generally corresponded well with CPE, but occasionally samples reported as ‘histologically normal’ demonstrated tumor purities up to 53%. After filtering specimens with tumor purity less than 50%, DNA methylation subtype showed little spatial heterogeneity, this in contrast to transcriptional subtype. Samples from core and peripheral regions showed similar DNA methylation profiles. Non-purity related intratumoral heterogeneity for promotor methylation of epigenetically regulated genes was minimal, but higher in IDH-wildtype than in IDH-mutant gliomas. In conclusion, after considering DNA methylation-based measurement of tumor purity DNA methylation in diffuse gliomas shows little spatial heterogeneity; incorporating such tumor purity information can further increase the reliability of methylation-profiling-based tumor classification.
PATH-53. IMMUNOLOGICAL PROFILING OF MUTATIONAL AND TRANSCRIPTIONAL SUBGROUPS IN PEDIATRIC AND ADULT HIGH-GRADE GLIOMAS
Authors: Bockmary Michael , Klauschen Frederick , Maire Cecile , Rutkowski Stefan , Westphal Manfred , Lamszus Katrin , Schüller Ulrich , Mohme Malte 
Published: November 2019

Abstract
Immunological treatment strategies, including checkpoint inhibition, are currently under investigation for high-grade gliomas, but their success is limited. Hence, it is crucial to determine immunological pathways that can be targeted and to identify subgroups of patients likely to benefit from immunotherapies. Previous studies are still limited by comparably small sample sizes and there is only few data about specific immunological mechanisms in pediatric high-grade glioma. We gathered published gene expression data from 1135 adult and pediatric high-grade gliomas and applied a machine learning technique to determine their mutational (K27, G34, IDHmut, IDHwt) and transcriptional subtype. Subsequently, immune cell infiltration and functional immune pathway signatures were evaluated in correlation to histological diagnosis, age, transcriptional and mutational subtype. T-SNE analysis and unsupervised hierarchical clustering was applied to detect subgroup-specific immune microenvironments across all high-grade glioma subtypes. Four distinct microenvironmental phenotypes of immune cell infiltration were identified, which can be stratified into vascular, monocytic/stromal, monocytic/T-cell and APC/NK/T-cell dominant immune clusters. Immune cell infiltration correlated strongly with transcriptional and mutational subtypes but was independent of age and histological diagnosis (p< 0.01). H3F3A mutated tumors had significantly fewer tumor infiltrating lymphocytes and macrophages. By including functional pathways and correlating the expression of immunostimulatory and inhibitory receptor/ligand interactions, we were able to define the immunological microenvironment and to identify possible immunological subtypes associated with poor prognosis as well as subtypes that might be especially amenable to checkpoint inhibition. In addition, comparisons of overall survival with the immunological microenvironment and specifically with immune checkpoint molecules revealed diverse correlations within the transcriptional and mutational subgroups. In conclusion, we shat that mutational and transcriptional subgroups of pediatric and adult high-grade gliomas are characterized by distinct immunological tumor microenvironments. Our analysis demonstrates the immunological heterogeneity within this entity and emphasizes an immune specific stratification of subgroups for upcoming immunotherapy trials.
PATH-57. MRI-LOCALIZED BIOPSIES REVEAL HISTOPATHOLOGIC HETEROGENEITY IN POST-TREATMENT RECURRENT HIGH-GRADE GLIOMA
Authors: Boyett Deborah , Grinband Jack , Canoll Kai , Englander Zachary , Save Akshay , Zanazzi George , Pereira Brianna , Lignelli Angela , Lassman Andrew , McKhann Guy , Bruce Jeff , Canoll Peter D 
Published: November 2019

Abstract
Evaluation of recurrence in post-treatment glioma is challenging because contrast-enhancing (CE) lesions are a mixture of tumor and treatment effect. This study characterizes intratumoral heterogeneity using quantitative digital pathology to correlate intraoperative MRI-localized biopsies with histopathology in the post-treatment setting. Findings will inform multiparametric radiographic models of intratumoral heterogeneity. A retrospective review was performed on adult patients with MRI-localized biopsies obtained during resection for post-treatment recurrent high-grade glioma. 68 patients and 170 MRI-localized samples were analyzed (median 2 samples/patient). Immunohistochemistry (IHC) for markers of glioma cells (SOX2), macrophages (CD68), and proliferating cells (KI67) was used to characterize biopsies. Slides were digitized and quantified using an automated cell-counting algorithm. Histopathological criteria based on IHC data was developed to classify biopsies. IHC quantification was compared across histological groups using ANOVA and paired t-tests. Most patients (52/68) yielded multiple biopsies. 75% (39/52) demonstrated heterogeneity in histological classification of all specimens obtained from their lesion. 47/170 (28%) biopsies were predominantly treatment effect, and most were CE (31/47 or 66%). Only 75/170 (44%) biopsies contained recurrent glioma, and 21/75 (28%) were NE. SOX2 labeling index was higher in biopsies containing recurrent tumor (p=5.13E-25). CD68 labeling index was higher in biopsies with predominant treatment effect (p=1.35E-12). IHC data from MRI-localized biopsies informed a multiple linear regression model which demonstrated significant predictive value for determining the distribution of recurrent tumor in the post-treatment setting. Contrast enhancement is not a reliable predictor of tumor in recurrent high-grade glioma. Most patients demonstrated marked intratumoral heterogeneity, highlighting the difficulty of accurate tumor sampling post-treatment glioma. Our histopathological classification significantly distinguished recurrent tumor from treatment effect and informed a multiparametric radiomic model which can guide surgical sampling and assess response to therapy.