bluuebunny/crossref_metadata_2025_split huggingface dataset:
PATH-11. PDGFA INITIATES ABERRANT MITOSIS AND MALIGNANT TRANSFORMATION OF NEURAL PROGENITOR CELLS
Authors: Blough Michael , Omairi Hiba , Grisdale Cameron , Cairncross J Gregory 
Published: November 2021

Abstract

BACKGROUND
Imagining ways to prevent or treat glioblastoma (GBM) have been hindered by a lack of understanding of its pathogenesis. Although platelet derived growth factor-A (PDGFA) overexpression may be an early event, critical details of the biology of GBM, and tools to study its initiation have been lacking. Indeed, many PDGF-driven models replicate its microscopic appearance, but not genomic architecture. Recently, we reported an in vitro model of GBM initiation that overcomes this barrier to authenticity.

METHODS
We used a method developed to establish neural stem cell cultures to investigate the effects of PDGF-A on cells derived from the subventricular zone (SVZ), a putative region where the cells of origins for GBM are derived. We micro-dissect SVZ tissue from p53-null and wild-type adult mice, culture cells in media supplemented with PDGF-A, and assess cell viability, proliferation, mitotic capacity, and genome stability.

RESULTS
Paradoxical to its canonical role as a growth factor, we observe abrupt and substantial cell death in PDGF-A. Abnormal mitosis was the first observable alteration and occurred immediately in cells of both p53 wild-type and null genotypes: wild-type cells did not survive in PDGF-A, whereas a fraction of null cells evade apoptosis. Evading cells displayed attenuated proliferation accompanied by early chromosomal gains and losses. After approximately 100 days in PDGF-A, surviving cells suddenly proliferate rapidly, acquire growth factor independence, and become tumorigenic in immune-competent mice. Transformed cells continue to display highly abnormal mitotic phenotypes with complex karyotypes similar to GBM, had a neural progenitor cell (NPC) lineage profile, and were resistant to PDGFR-alpha inhibition.

CONCLUSION
Abnormal mitosis induced by PDGF-A initiates and perpetuates the genome instability that transforms p53-null neural progenitor cells to yield cancers with the types of recurring chromosomal gains and losses that characterize human GBM.
PATH-17. POSSIBLE ASSOCIATION BETWEEN OLIGODENDROGLIAL HISTOLOGICAL FEATURES OF IDHMUT/CODEL LOWER GRADE GLIOMAS AND PATIENT'S FAVORABLE PROGNOSIS, BUT NOT IN IDHMUT/NONCODEL AND IDH-WILDTYPE TUMORS
Authors: Pareira Eriel , Shibuya Makoto , Ohara Kentaro , Nakagawa Yu , Kanazawa Tokunori , Kamamoto Dai , Kato Yasutaka , Aimono Eriko , Yoshida Kazunari , Nishihara Hiroshi , Sasaki Hikaru 
Published: November 2021

Abstract
Comprehensive diagnostic using histological and molecular characteristics began to be implemented in WHO 2016 but the relevance of oligodendroglial histological features to patients’ prognoses is still controversial. To elucidate the connection between oligodroglial histology and patient’s prognoses we analyzed 93 LrGGs resected for about 2 decades were reassessed for histological features based on WHO2007 with special interest to pure oligodendroglial diagnosis (namely, oligodendroglioma or anaplastic oligodendroglioma) and presence of classic for oligodendroglioma (CFO) features. Those histological features, patients’ OS, and tumor chromosomal/genetic characteristics were correlated each other in each of the 3 IDH-1p/19q based molecular groups. The reassessed morphology-based diagnosis was shown to be most strict for astrocytic, but loosened for oligodendroglial tumors as compared with the original institutional diagnoses and WHO2016. The pure oligodendroglial diagnosis by reassessment was associated with longer OS in IDHmut/codel group, but not in IDHmut/noncodel and IDH-wildtype groups. The presence of CFO was not associated with patients’ OS in any molecular groups. Gain of 8q was associated with the oligodendroglial diagnosis in IDHmut/noncodel group. Neither the oligodendroglial diagnosis nor CFO was predictive for the methylation status of the MGMT gene in any of the 3 molecular groups. NGS of the IDHmut/codel tumors suggested that mutations in the FUBP1 and CIC genes might be associated with poor prognosis. The oligodendroglial histological feature is not independently predictive for either patients’ prognosis or chemotherapeutic response in LrGGs, except the oligodendroglial diagnosis in IDHmut/codel tumors.
PATH-30. RAPID AND LOW-COST LIQUID BIOPSY-BASED METHOD FOR SCREENING AND MONITORING OF GBM BY MASTER REGULATORY GENE MARKERS IN GBM STEM-LIKE CELLS
Authors: Tran David , Liu Tianyi , Le Son 
Published: November 2021

Abstract

BACKGROUND
Current liquid-based cancer screening relies on massive deep NGS to detect rare cancer-derived genetic materials - a costly method fraught with high false-negative and false-positive rates. We aim to develop a non-NGS-centered, AI-directed liquid-based detection of GBM stem-like cells (GSCs).

METHODS
Utilizing a robust AI suite, NETZEN, we defined a common master regulatory gene network (MRGN) of the GBM state in GSCs. Since master regulators (MRs) in MRGN are developmentally restricted, their chromosomal loci are accessible in GSCs but not in normal cells. Downstream factors in MRGN are massively overexpressed in GSCs compared to normal cells. Thus, we measured the following in PBMCs from healthy controls spiked with known quantities of GSCs and patients with GBM: 1) accessibility of MR genes using transposase/transposons carrying unique barcodes to be inserted into the MR’s predetermined accessible locations, and 2) expression of downstream factors using nested qRT-PCR.

RESULTS
We characterized 10 MRs in GSCs with ≥1 promoter region that is hypomethylated and accessible (by ATACseq) in GBM/GSCs per GSE70175-92460 (19 samples) and GSE67633-96088 (14 samples), or hypermethylated and inaccessible in lymphocytes/PBMCs per GSE98837 (6) and GSE74912 (13). Using barcoded transposons, we specifically disrupted 4 MR’s accessible foci only in GSCs, not in PBMCs. We also identified 50 downstream factors with the top 20 having 3 to 5-orders-of-magnitude higher mean expression in GSCs compared to PBMCs (GSE79362-86884, 451 samples). Currently our method has a detection limit of 0.2-1 GSC per 106 PBMCs. Using the first iteration, we detected MRGN of the GBM state in blood samples of 14 of 14 GBM patients before resection, compared to none of 15 healthy donors.

CONCLUSIONS
Chromosomal accessibility and signal amplification in MRGN of GSCs provide powerful substrates for a non-NGS, low-cost, liquid-based GBM detection system with high sensitivity and specificity. Further testing and optimization are ongoing.
PATH-36. INTRATUMOR HETEROGENEITY AND BIOINFORMATIC DIFFERENCES INFLUENCE MENINGIOMA MOLECULAR CLASSIFICATION
Authors: Vasudevan Harish , Choudhury Abrar , Hilz Stephanie , Villanueva-Meyer Javier , Chen William , Lucas Calixto , Braunstein Steve , Oberheim-Bush Nancy Ann , Butowski Nicholas , Pekmezci Melike , McDermott Michael , Perry Arie , Solomon David , Magill Stephen , Raleigh David 
Published: November 2021

Abstract
Molecular alterations such as CDKN2A inactivation and TERT promoter mutation are new criteria for grade 3 meningiomas in the 5th edition of the WHO Classification of Tumors of the Central Nervous System. However, consensus approaches to identify copy number variants (CNVs) and short somatic variants in meningiomas are lacking. Here, we performed integrated DNA methylation profiling, RNA-sequencing, and targeted DNA mutational profiling on 10 stereotactically-collected, regionally-distinct samples from 4 meningiomas. Targeted DNA sequencing revealed numerous private short somatic variants from multiple sites within individual meningiomas, including a TERT promoter mutation in only 1 of 2 samples from the same tumor. DNA methylation profiling revealed differences in biologic groups and immune cell enrichment between regionally-distinct samples within individual meningiomas. CNV status was evaluated using DNA methylation profiling and RNA sequencing on 14 stereotactically-collected, regionally-distinct samples from 2 meningiomas. Phylogenetic architectures from DNA methylation profiling and targeted DNA sequencing were highly concordant and shared 99.12% of CNVs while RNA sequencing identified only 39% of the CNVs called from DNA based approaches. Finally, CNV analysis based on single-cell RNA sequencing revealed partially overlapping CNVs across meningioma cells within an individual tumor, suggesting subclonal populations may influence CNV-based meningioma molecular classification and underlie limitations in defining CNVs from bulk RNA-sequencing. In sum, these data highlight the relative strengths and weaknesses of various approaches for molecular analysis of meningiomas complicated by intratumor heterogeneity due to non-tumor cells and subclonal populations of meningioma cells. Future efforts to incorporate molecular analysis into the diagnostic paradigm for meningiomas may require orthogonal validation across multiple platforms or image-guided meningioma sampling to select the most aggressive regions for molecular profiling.
PATH-37. DISTINCT GENOMIC SUBCLASSES OF HIGH-GRADE/PROGRESSIVE MENINGIOMAS: NF2-ASSOCIATED, NF2-EXCLUSIVE, AND NF2-AGNOSTIC
Authors: Williams Erik , Santagata Sandro , Wakimoto Hiroaki , Barker Fred , Brastianos Priscilla , Cahill Daniel , Ramkissoon Shakti , Alexander Brian , Juratli Tareq 
Published: November 2021

Abstract

BACKGROUND
Genomic studies of high-grade/progressive meningiomas have reported a heterogeneous mutation spectrum. Here, we present a genomic survey of one of the largest multi-institutional cohorts of high-grade/progressive meningiomas to date.

METHODS
850 high-grade/progressive meningiomas, including 441 WHO grade 2 and 176 WHO grade 3 meningiomas and 220 progressive WHO grade 1 meningiomas, were tested as part of a clinical testing program by hybridization capture of 406 cancer-related genes. Information from histopathology review and patient clinical data was assessed.

RESULTS
Genomic analyses converged to identify at least three distinct patterns of biologically-aggressive meningiomas. The first and most common contained NF2-mutant tumors (n = 426, 50%), was associated with male sex (64.4%, p = 0.0001) and often harbored additional mutations in CDKN2A/B (24%), and the chromatin regulators ARID1A (9%), and KDM6A (6%). A second group (NF2-agnostic) featured TERTp (n = 56) or TP53 mutations (n = 25) and were either NF2-mutant or wild-type, and displayed no association with either sex. The remaining group generally lacked NF2 mutations, and accounted for 40% of the cases-with three subgroups. One consistent primarily of grade 3 lesions harboring alterations in chromatin regulators BAP1 (n = 22) or PBRM1 (n = 16). A second subgroup contained AKT1 (n = 26), PIK3CA (n = 14) and SMO (n = 7) mutant skull-based meningiomas, and a third mixed subgroup included 237 meningiomas with a heterogeneous spectrum of low frequency and non-recurrent alterations.

CONCLUSIONS
Our findings indicate that the patterns of genomic alterations in high-grade/progressive meningiomas commonly group into three different categories. The most common NF2-associated canonical group frequently harbored CDKN2A/B alterations, which is potentially amenable to targeted therapies. An NF2-agnostic group harbored frequent TERTp and TP53 mutations. The final subclass, distinct from the canonical NF2 mutant associated pathway, was partly characterized by BAP1/PBRM1 alterations (rhabdoid/papillary histology) or skull-base disease.
PATH-40. SPORADIC NF2 WILD-TYPE MULTIPLE MENINGIOMAS HARBOR DISTINCT DRIVER MUTATIONS
Authors: Prilop Insa , Pinzer Thomas , Cahill Daniel , Brastianos Priscilla , Schackert Gabriele , Juratli Tareq 
Published: November 2021

Abstract

OBJECTIVE
Multiple meningiomas (MM) are rare and present a unique management challenge. While the mutational landscape of single meningiomas has been extensively studied, understanding the molecular pathogenesis of sporadic MM remains incomplete. The objective of this study is to elucidate the genetic features of sporadic MM.

METHODS
We identified nine patients with MM (n=19) defined as ≥2 spatially separated synchronous or metachronous meningiomas. We profiled genetic changes in these tumors using next-generation sequencing (NGS) assay that covers a large number of targetable and frequently mutated genes in meningiomas including AKT1, KLF4, NF2, PIK3CA/PIK3R1, POLR2A, SMARCB1, SMO, SUFU, TRAF7, and the TERT promoter.

RESULTS
Most of MM were WHO grade 1 (n= 16, 84.2%). Within individual patients, no driver mutation was shared between separate tumors. All but two cases harbored different hot spot mutations in known meningioma-driver genes like TRAF7 (n= 5), PIK3CA (n= 4), AKT1 (n= 3), POLR2A (n=1) and SMO (n= 1). Moreover, individual tumors differed in histologic subtype in 8/9 patients. The low frequency of NF2 mutations in our series stands in contrast to previous studies that included hereditary cases arising in the setting of neurofibromatosis type 2 (NF2).

CONCLUSIONS
Our findings provide evidence for genomic inter-tumor heterogeneity and an independent molecular origin of sporadic NF2 wild-type MM. Furthermore, these findings suggest that genetic characterization of each lesion is warranted in sporadic MM.
PATH-43. RAMAN SPECTROSCOPY AS A TOOL IN NEUROSURGERY
Authors: Borgmann Felix Kleine , Klamminger Gilbert Georg , Mombaerts Laurent , Klein Karoline , Jelke Finn , Mirizzi Giulia , Slimani Redouane , Pilot Michel , Husch Andreas , Mittelbronn Michel , Hertel Frank 
Published: November 2021

Abstract

BACKGROUND
Raman Spectra have been shown to be sufficiently characteristic to their samples of origin that they can be used in a wide range of applications including distinction of intracranial tumors. While not replacing pathological analysis, the advantage of non-destructive sample analysis and extremely fast feedback make this technique an interesting tool for surgical use.

METHODS
We sampled intractanial tumors from more than 300 patients at the Centre Hospitalier Luxembourg over a period of three years and compared the spectra of different tumor entities, different tumor subregions and healthy surrounding tissue. We created machine-learning based classifiers that include tissue identification as well as diagnostics.

RESULTS
To this end, we solved several classes in the intracranial tumor classification, and developed classifiers to distinguish primary central nervous system lymphoma from glioblastoma, which is an important differential diagnosis, as well as meningioma from the surrounding healthy dura mater for identification of tumor tissue. Within glioblastoma, we resolve necrotic, vital tumor tissue and peritumoral infiltration zone.We are currently developing a multi-class classifier incorporating all tissue types measured.

CONCLUSIONS
Raman Spectroscopy has the potential to aid the surgeon in the surgery theater by providing a quick assessment of the tissue analyzed with regards to both tumor identity and tumor margin identification. Once a reliable classifier based on sufficient patient samples is developed, this may even be integrated into a surgical microscope or a neuronavigation system.
PATH-45. APOLLO: RAMAN-BASED PATHOLOGY OF MALIGNANT GLIOMA
Authors: Lita Adrian , Sjöberg Joel , Filipescu Stefan , Celiku Orieta , Petre Luigia , Gilbert Mark , Noushmehr Houtan , Petre Ion , Larion Mioara 
Published: November 2021

Abstract

BACKGROUND
DNA methylation is an essential component for integrative diagnosis in glioma. Methylation subtype prediction of gliomas is currently done via sample extraction of high-quality of reasonable amount of DNA (~1ug), methylome profiling, followed by probe identification, curation and subsequent analysis via different random forest classifiers. However, the DNA methylation classification is not always available for all the samples.

METHODS
Raman Spectroscopy performed of the regions of interest using 1mm2 FFPE tissue spots from 45 patient samples with LGm1 to LGm6 methylation subtypes. Spectral information was then used to train a convolutional neural network (CNN) and develop a prediction algorithm. 70 % of dataset - model training while the remaining 30% for validation. Supervised wrapper methods and random forests were used to identify the top 109 most discriminatory Raman frequencies out of 1738.

RESULTS
We identified the most discriminatory features from these analyses and demonstrated that these frequencies show differential spectral intensities for these frequencies depending upon the glioma subtypes across the larger areas of the tissue. We compared the results of the Ward linkage clustering with the separation induced by the “frequency criterion”, an empirical observation that Raman spectra of tumor spots are characterized by intensities higher than 5000 on some of the frequencies from 1463 to 1473. For each of the 45 samples we ran Ward linkage clustering with a variable number of clusters (from 2 to 7), with the majority cluster corresponding to tumor spots and the others corresponding to (various types of) non-tumor spots. We found that the majority cluster matches very well the tumor spots characterized by the frequency criterion, The average accuracy over all samples was 90:3%, the average precision was 99:6% and the average recall was 90:2%. For most samples, two clusters were sufficient to distinguish between tumor and non-tumor spots with accuracy.
NIMG-04. PREDICTING THE BRAF MUTATIONAL STATUS IN PATIENTS WITH MELANOMA BRAIN METASTASES USING RADIOMICS - A BICENTRIC STUDY
Authors: Meissner Anna-Katharina , Gutsche Robin , Galldiks Norbert , Kocher Martin , Juenger Stephanie T , Eich Marie-Lisa , Wendl Christina , Goldbrunner Roland , Ruge Maximilian , Mauch Cornelia , Proescholdt Martin , Grau Stefan , Lohmann Philipp 
Published: November 2021

Abstract

BACKGROUND
The BRAF V600E mutation is present in approximately 50% of patients with melanoma and is an important prerequisite for a response to targeted therapies such as BRAF inhibitors. In the majority of patients, the BRAF mutational status is based on the analysis of tissue samples from the extracranial primary tumor only. Since the extracranial and intracranial BRAF mutational status may be discrepant, the additional information on the BRAF mutational status of melanoma brain metastases would be of clinical value, e.g., for the prediction of response to targeted therapies. Here, we evaluated the potential of MRI radiomics for the determination of the intracranial BRAF mutational status in patients with melanoma brain metastases.

PATIENTS AND METHODS
Fifty-nine patients with melanoma brain metastases from two university hospitals (group 1, 45 patients; group 2, 14 patients) were operated with subsequent genetic analysis of the intracranial BRAF mutational status. All patients underwent structural MRI preoperatively. Areas of contrast enhancement were manually segmented and analyzed. Group 1 was used for model training and validation, group 2 for model testing. After image preprocessing and radiomics feature extraction, a test-retest analysis was performed to identify robust features prior to feature selection. Finally, the best performing radiomics model was applied to the test data. Diagnostic performances were evaluated using receiver operating characteristic (ROC) analyses.

RESULTS
Twenty-two patients (49%) in group 1, and 6 patients (43%) in group 2 had an intrametastatic BRAF V600E mutation. Using the best performing six parameter radiomics signature, a linear support vector machine classifier yielded an area under the ROC curve (AUC) of 0.92 (sensitivity, 83%; specificity, 88%) in the test data.

CONCLUSION
The developed radiomics classifier allows a non-invasive prediction of the intracranial BRAF V600E mutational status in patients with melanoma brain metastases and may be of value for treatment decisions.
NIMG-09. DETECTION OF ASYMPTOMATIC MALIGNANT LESIONS BY [18F]FDG PET/MRI IN CHILDREN AND ADOLESCENTS WITH NEUROFIBROMATOSIS TYPE 1
Authors: Baumgartner Alicia-Christina , Platzgummer Hannes , Aszmann Oskar , Amann Gabriele , Berghoff Anna , Kasprian Gregor , Traub-Weidinger Tatjana , Azizi Amedeo A 
Published: November 2021

Abstract

BACKGROUND
Plexiform neurofibromas (PN) are a hallmark feature of Neurofibromatosis type 1 (NF1). 10% of PN undergo malignant transformation. As malignant peripheral nerve sheath tumors are a leading cause of death in NF1-patients, early detection of malignancy is essential. 2-deoxy-2-[ 18F]fluoro-D-glucose [18F]FDG PET/CT imaging is used in patients with NF1 to judge malignant transformation. AIMS: The present study evaluated [18F]FDG PET/MRI in pediatric NF1 patients at high risk for MPNST and its utility as a possible screening tool for malignant transformation of yet asymptomatic lesions.

METHODS
Patients aged 0-25 with symptomatic and asymptomatic neurofibromas who underwent PET/MRI from 2014 to 2021 were included. Chart review of imaging data, clinical and histological findings was performed retrospectively.

RESULTS
41 patients (18 female) with a median age at first PET/MRI of 16.87 years (6.21-24.41) were included. 40 lesions were operated as indicated by clinical (e.g. pain, rapid growth) or imaging findings. Based on histopathological analysis 7 lesions in 4 patients were categorized as malignant, 3 as atypical neurofibromatous neoplasms of uncertain biologic potential (ANNUBP). 4/7 malignant and 2/3 ANNUBP lesions were asymptomatic (i.e. without rapid growth, pain, neurologic dysfunction). 5/7 symptomatic tumors were without significant FDG-PET and proven benign by histology. 18 lesions (2 symptomatic) in 9 patients that showed an increased uptake suspect of malignant transformation were histologically classified as benign. None of the patients died during follow-up, 1 symptomatic MPNST patient received postsurgical radio- and chemotherapy.

CONCLUSION
Our data indicate that malignant transformation of PN also occurs in asymptomatic patients. [18F]FDG PET/MRI is feasible in pediatric and adolescent patients with the tumor predisposition syndrome NF1 and is an alternative to PET/CT when assessing for malignancy thereby drastically reducing radiation exposure. Early detection through screening of high-risk NF1 patients with [18F]FDG PET/MRI could potentially increase overall survival by facilitating early curative resection.