bluuebunny/crossref_metadata_2025_split huggingface dataset:
EXTH-65. PLASMA AND CEREBROSPINAL FLUID PHARMACOKINETICS COMPARISON OF BRAF AND MEK INHIBITORS FOLLOWING SINGLE AND EXTENDED ADMINISTRATION IN A PRE-CLINICAL NON-HUMAN PRIMATE MODEL
Authors: Lester McCully Cynthia , Gross Andrea , Cruz Garcia Rafael , Shankarappa Priya , Odabas Arman , Rodgers Louis , Peer Cody , Figg William , Widemann Brigitte , Warren Katherine 
Published: November 2019

Abstract

BACKGROUND
Aberrations in the MAPK signaling pathway are present in adult and pediatric CNS tumors. The BRAF and MEK inhibitors Dabrafenib, Vemurafenib, Selumetinib and Trametinib, alone or in combination, have demonstrated clinical efficacy. However, minimal CSF penetration has been demonstrated in pre-clinical models with single dose administration. CSF penetration of these agents was compared following single and extended oral administration in a nonhuman CSF Lateral Reservoir model to determine if CSF penetration increases at steady state.

METHODS
Agents were administered orally, to each subject (n=9), in single or multiple doses, as serial single agent studies, with washout periods between studies. The following dosages (Human equivalent dose HED) were utilized in the studies: Single Dosage-Selumetinib 2.5 mg/kg (50.0 mg/m2), Dabrafenib 8.0 mg/kg (160 mg/m2), Vemurafenib 26 mg/kg (520 mg/m2), Trametinib 0.06 and 0.12 mg/kg (1.2 and 2.4 mg/m2). Extended dosages-Selumetinib 2.5 mg/kg BID x 3 days (50.0 mg/m2), Dabrafenib 4.0 mg/kg BID x 2 days (160 mg/m2/day), Vemurafenib 26 mg/kg BID x 3 days (520 mg/m2), Trametinib 0.05 mg/kg x 10 days BID (1.0mg/m2). Paired serial plasma and CSF samples were collected. Agents were quantified by uHPLC-MS/MS. Pharmacokinetic parameters were calculated via noncompartmental methods. Plasma exposure reported as Area Under the Curve (AUC) and CSF penetration as ratio of CSF:plasma AUC. Statistical significance determined by t-test.

RESULTS
Single administration AUCinf/D (hr*ng/ml/mg) vs. extended administration AUCtau/D (hr*ng/ml/mg) for each agent: Vemurafenib-Plasma 30.9–351.4 vs.29.2–379.7, CSF-non-quantifiable; Dabrafenib-Plasma 29.3–102.6 vs.3.4–58.2, CSF-0.12–0.54 vs 0.04–0.19, % CSF:Plasma-0.3–0.84 vs.0.32–1.3; Trametinib-Plasma AUC indeterminable, CSF-non-quantifiable; Selumetinib-Plasma 69.8–133.0 vs.26.5–81.2; CSF-AUC indeterminable vs. 0.37–0.86, % CSF:Plasma-Indeterminable vs. 0.78–1.4. T-test: A downward trend in Dabrafenib and Selumetinib plasma AUC and a marked upward trend in Selumetinib CSF AUC.

CONCLUSIONS
With the exception of Selumetinib, the CSF exposure of BRAF and MEK inhibitors studied did not markedly increase following extended dosing.
EXTH-67. IDENTIFICATION AND DEVELOPMENT OF NEURAL ECM-BINDING LAMPREY ANTIBODIES (VARIABLE LYMPHOCYTE RECEPTORS) THAT TARGET GLIOBLASTOMA
Authors: Umlauf Benjamin , Clark Paul , Lajoie Jason , Georgieva Julia , Bremner Samantha , Herrin Brantley , Shusta Eric , Kuo John 
Published: November 2019

Abstract

INTRODUCTION
The median survival of glioblastoma (GBM) patients remains less than two years even with state-of-the-art treatment. Current targeted GBM therapies demonstrate initial therapeutic benefit; however, patients relapse due to therapeutic selection of treatment resistant GBM cellular populations. Therefore, we propose targeting pathologic disruption of the blood brain barrier (BBB) via exposure of neural ECM, rather than disease markers, to overcome therapy-resistant GBM.

METHODS
We identify Variable Lymphocyte Receptors (VLRs, the antigen recognition system used by lamprey) that demonstrate high specificity for neural ECM. Candidate VLRs underwent further refinement using in vitro binding assays and ex vivo tissue staining. Utilizing pathologic disruption of BBB as an approach for targeting GBM was confirmed in vivo using intracranial murine glioblastoma models.

RESULTS
The lead neural ECM-binding VLR candidate, named P1C10, demonstrates diffuse binding to parenchymal neural ECM, without detectable binding to other tissues. P1C10 demonstrates nanomolar affinity for in vitro derived neural ECM, and preferentially accumulates at intracranial GL261 and U87 lesions in murine GBM models. Finally, administration of P1C10-targeted doxorubicin-loaded liposomes significantly extends the survival of mice bearing intracranial U87 GBM.

CONCLUSIONS
We identified VLRs that bind neural ECM, and demonstrate their utility for delivering compounds and nanoparticles to sites of GBM induced blood brain barrier disruption. This novel strategy allows for targeting therapeutics via the underlying physiology of GBM rather than relying on cellular disease markers that are often lost in patients that relapse after targeting therapies.
GENE-14. BMP4 INDUCES TO ASYMMETRIC CELL DIVISION IN HUMAN GLIOMA STEM-LIKE CELLS
Authors: Koguch Motofumi , Izumi Hideki , Nakahara Yukiko , Ito Hiroshi , Wakamiya Tomihiro , Yoshioka Fumitaka , Ogata Atsushi , Inoue Inoue Kohei , Masuoka Jun , Abe Tatsuya 
Published: November 2019

Abstract
Glioblastoma (GBM) is one of the human malignant tumors with a high recurrence rate and the poorest prognosis. Therefore, a new treatment strategy is required. It has also come to be thought that cancer is a heterogeneous, which composes of cancer stem cells (CSCs), which have self-renewal ability, multipotency and treatment resistance. Although various strategies targeting glioma stem-like cells (GSCs) have been studied, a median survival remains to be less than 2 years. In this study, we focused on strategies targeting GSCs through induction of differentiation using BMP4. We examined the expression of CD133, a cancer stem cell marker, under BMP4-treatment in GSCs using flowcytometry analysis, western blotting and qPCR. We also examined immunofluorescent staining of GSCs to study cell division. The treatment of BMP4 caused downregulation of CD133 expression in GSCs. In addition, BMP4-treatment induced to asymmetric cell division in GSCs. Tumor sphere assay showed that BMP4 suppresses self-renewal ability. These findings may provide a new perspective how BMP4 reduces the tumorigenicity of GSCs.
GENE-16. NEXT GENERATION SEQUENCING IDENTIFIES IDH-1, ATRX, TP53 MUTATION AND MYCN AMPLIFICATION IN GLIOBLASTOMA WITH EXTENSIVE SUBARACHNOID SPREAD: A CASE REPORT
Authors: Sang Lee Kyu , Choe Gheeyoung 
Published: November 2019

Abstract
Glioblastoma showing primarily extensive subarachnoid spreading has much worse prognosis than intracortical glioblastoma. Nevertheless, their genetic pathogenesis is still unknown due to its low incidence. Present report is a rare case of glioblastoma with primitive neuroectodermal tumor (PNET)-like feature, showing extensive subarachnoid spread, as well as the distinguishing result of its molecular analysis using next generation sequencing (NGS). A 37-year-old male presented with a new onset, severe headache. Magnetic resonance imaging test revealed a diffuse infiltrative mass in the right frontal lobe. The tumor was also spread broadly in subarachnoid space. The patient underwent craniotomy and tumorectomy. Microscopically, glioblastoma showed PNET-like feature. Tumor cells had high nuclear/cytoplasmic ratios, oval, slightly elongated or angulated hyperchromatic nuclei, markedly increased mitotic activity, and obvious apoptotic bodies. Immunohistochemical test showed partly positivity of GFAP, CD56 and synaptophysin. For comprehensive genomic profiling, we assessed NGS based on the SNUBH Brain v1.0 (Macrogen, Seoul, South Korea) panel. This panel is designed to include all genes known to be somatically altered in human brain tumor. IDH-1 (p.Arg132His) mutation and two frame shift genetic alteration including ATRX (p.Tyr2208fs) and TP53 (p.Pro301fs) were found. Additionally, MYCN (2p24.3) amplification was identified. Estimated MYCN copy number was 18. Despite the post-operative therapy including temozolomide and radiotherapy, the tumor aggressively progressed and the patient expired nine months after the first symptom onset. Although there have been several previous reports of MYCN amplification in glioblastoma with PNET-like feature, this is the first case report which finding in glioblastoma, IDH-mutant type. IDH-1 mutation and younger age are usually associated with a better prognosis in glioblastoma patients. However, our case may suggest that when MYCN amplification coexists in IDH-mutant type, the tumor behavior could be contrarily aggressive.
GENE-18. TRANSCRIPTOME-WIDE ANALYSIS USING NANOPORE THIRD GENERATION SEQUENCING IN A RAT GLIOBLASTOMA MODEL: PROOF OF PRINCIPLE
Authors: Jejaroenpun Piroon , Wongsurawat Thidathip , DeLoose Annick , Ussery David , Nookaew Intawat , Day J D , Rodriguez Analiz 
Published: November 2019

Abstract
The RNA sequencing (RNA-Seq) technique is now routinely used to quantitatively explore genome-wide expression by various research fields including cancer research. The most common RNA-seq methodology produce billions of short-read sequencing in the range of 100–600 base pairs, from which it is occasionally difficult to reconstruct isoform-level transcriptome and fusion genes. The limitations of the short-reads can be overcome by using third-generation sequencing technologies, such as Oxford Nanopore Technologies (ONT). This study aims to perform full-length cDNA sequencing using ONT platform and investigate the abilities of ONT in (1) identifying differential gene expression, (2) detecting differential transcript isoform usage, and (3) detecting fusion genes. To do these methods, CNS-1 cells were implanted into the frontal lobes of three Lewis rats. The CNS-1 model is a histocompatible astrocytoma cell line with an invasive pattern mimicking glioblastoma (GBM). After two weeks of transplantation, the transplanted tumors and the normal brain on the other side were collected as matched normal-tumor pairs. Total RNA extracted from the samples were subjected to the full-length cDNA sequencing on a portable MinION sequencer. In tumors samples, 615 genes involved in cell cycle were upregulated, whereas 1067 genes involved in neurological functions were downregulated. Finally, we could identify differential transcript isoform expression and fusion genes from the matched normal-tumor pairs. Overall, full-length sequencing of the cDNA molecules permitted a detailed characterization of the differential gene expression, the isoform complexity, and fusion genes. In the near future, we will use these methods on human samples.
GENE-20. IDENTIFYING POTENTIAL GENES AND MECHANISMS DRIVING IDH-MUTANT GLIOMA PROGRESSION AND RECURRENCE THROUGH RNA-SEQUENCING
Authors: Cho Angela , Hudson Amanda , Colvin Emily , Hayes Sarah , Wheeler Helen , Howell Viive 
Published: November 2019

Abstract
Gliomas are the most common primary brain tumors in adults. IDH-mutated low-grade gliomas of astrocytic lineage (astrocytomas) have a relatively indolent clinical course; however, over time they progress to a higher grade. Molecular studies revealed recurrent tumors harbor more mutations upon malignant progression when treated with chemotherapy and/or radiotherapy compared to treatment-naïve tumors. However, genes which promote progression and recurrence in these tumors are unknown. This study aims to identify the transcriptional drivers of progression and recurrence of IDH-mutant gliomas. Longitudinal comparison of transcriptional profiles was performed on 6 matched pairs of primary lesions and their higher-grade recurrent lesion collected 1 to 8 years later. Three patients received no treatment and three patients received radiotherapy alone between their first and second surgeries. RNA was extracted from frozen specimens and following quality control, analyzed with the Illumina Next-Generation Sequencing platform (HiSeq HT paired end, TruSeq Kit). Comparison of RNA-seq results from primary and recurrent specimens identified 2042 differentially expressed genes (FC ≥2) for the no-treatment group and 2066 differentially expressed genes for the radiotherapy group. These genes include CADM2, SPP1, NDRG2 and CA9 which are associated with pro-tumor processes such as signal transduction, cell adhesion and treatment resistance. Validation is in progress. Identifying key genes driving glioma progression and recurrence will increase our understanding of the nature of these tumors and reveal core processes and potential novel targets that may be exploited for additional therapies for this deadly cancer.
GENE-29. INCREASED COPY NUMBER BURDEN (CNB) IS ASSOCIATED WITH GRADE IN IDH-MUTANT, 1p/19q-CODELETED OLIGODENDROGLIOMAS.
Authors: Brown Desmond , Yamada Seiji , Kollmeyer Thomas , Decker Paul , Kosel Matthew , Praska Corinne , Raghunathan Aditya , Giannini Caterina , Lachance Daniel , Eckel-Passow Jeanette , Jenkins Robert 
Published: November 2019

Abstract

BACKGROUND
Oligodendrogliomas are classified as either WHO grade II or III depending on histologic features. Grade often influences treatment decisions. However, there is variability in patient outcome within tumors of similar grade. We hypothesized that copy number burden (CNB) and specific copy number variants (CNV) might be associated with oligodendroglioma grade and prognosis.

METHODS
Copy number array analyses were performed on 285 molecular oligodendrogliomas (IDH-mutant, 1p/19q-whole arm-codeleted) from the Mayo Clinic internal and consult neuropathology practice and 167 TCGA molecular oligodendrogliomas. CNB was defined as the total number of copy number alterations. The association of CNB and CNV with grade and overall survival (when available) was assessed. All Mayo and TCGA data were evaluated using the ChAS software suite (Thermo- Fisher) and blindly reviewed by a clinical cytogeneticist (RBJ).

RESULTS
The mean CNB was 5.0 and 10.4 in the Mayo WHO grade II and III oligodendrogliomas, respectively (p = 5.4 x 10–17). Among the TCGA WHO grade II and III oligodendrogliomas the mean CNB was 4.4 and 5.3, respectively (p = 0.034). Common CNVs (occurring in at least 5% of cases) were -4/4q-, +8/8q+, -9/9p-/cnLOH 9p, +11/11q+, -14/14q-, -15 and -18/18q-. Of these, -9/9p-/cnLOH 9p was significantly associated with higher grade in both the Mayo and TCGA cohorts (p = 8.3 x 10-10 and 0.018, respectively). In the TCGA cohort the presence of >10 CNVs or +11/11q+ was associated with a poorer survival (p = 0.016 and 0.006, respectively).

CONCLUSIONS
CNB is significantly associated with WHO grade in IDH-mutant, 1p/19q co-deleted oligodendrogliomas. The presence of a significantly elevated CNB in some WHO grade II tumors may be suspicious for the presence of unappreciated grade III histologic features. Longer follow-up will be necessary to determine if CNB or single CNVs are associated with survival.
GENE-33. INTEGRATED GLIOMA DIAGNOSTICS USING TARGETED NEXT-GENERATION SEQUENCING
Authors: Petersen Jeanette K , Boldt Henning B , Sorensen Mia , Dahlrot Rikke H , Hansen Steinbjørn , Burton Mark , Thomassen Mads , Kruse Torben , Poulsen Frantz R , Andreasen Lotte , Hager Henrik , Ulhøi Benedicte P , Lukacova Slavka , Reifenberger Guido , Kristensen Bjarne 
Published: November 2019

Abstract

INTRODUCTION
Targeted next-generation sequencing (NGS) offers promising diagnostic perspectives by making it possible to detect genetic alterations with high accuracy in multiple genes as part of the daily diagnostic work-up. The importance of genetic alterations is reflected in the 2016 WHO classification of CNS tumors, where specific alterations are incorporated in the definition of certain entities. The aim of this study was to assess the diagnostic potential of a customized targeted glioma-tailored 20-gene panel to identify molecular entities of gliomas and explore their distinct mutational profiles. Moreover, the prognostic impact of molecular diagnostics was explored.

METHODS
We used a setup with NGS, immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH) on a series of 756 glioma from both a retro- and prospective cohort. NGS data were obtained for 347 gliomas (225 analyzed prospectively, 122 analyzed retrospectively).

RESULTS
Three major clusters were identified by unsupervised hierarchial cluster analysis: 1) isocitrate dehydrogenase gene (IDH) 1 or 2 mutant astrocytomas with frequent mutations in TP53 (83%) and ATRX (69%), 2) IDH-mutant and 1p/19q-codeleted oligodendrogliomas with frequent mutations in TERT (65%) and CIC (52%), and 3) IDH-wildtype astrocytic gliomas/glioblastomas with frequent mutations in TERT (32%), PTEN (28%) and TP53 (22%). Among the IHC IDH1-R132H negative gliomas, NGS detected other IDH mutations in 16% of the cases. Moreover, rare but diagnostically important mutations such as BRAF V600E and H3F3A K27M were detected. Survival analysis of the reclassified gliomas showed a clear difference in survival between patients with WHO 2007 and 2016 diagnoses. Successful prospective NGS analyses were obtained for 98% of the gliomas in daily diagnostics.

CONCLUSION
Application of NGS panel sequencing improves diagnostic accuracy and is feasible in daily diagnostics. NGS is ready to become part of standard diagnostics in the field of gliomas.
GENE-34. THERAPEUTICALLY TARGETING EPIGENOMIC AND TRANSCRIPTIONAL DYSFUNCTION IN ATRX-DEFICIENT GLIOMA
Authors: Danussi Carla , Singh Anand , Pinnamaneni Pavan , Fisher Grant , Picketts David , Kannan Kasthuri , Rao Arvind , Rai Kunal , Huse Jason 
Published: November 2019

Abstract
Diffusely infiltrating gliomas feature loss-of-function mutations in the chromatin remodeler gene ATRX as defining molecular alterations delineating major adult and pediatric disease subtypes. We recently reported that Atrx deficiency drives glioma-relevant phenotypes, such as increased motility and astrocytic differentiation profiles, by directly modulating epigenomic landscapes and the corresponding transcriptional profiles in glioma cells of origin. In particular, Atrx deficiency was associated with disruptions in H3.3 histone content at key genetic loci. To further understand the downstream epigenomic dysfunction induced by ATRX deficiency, we compared genome-wide chromatin-state maps of Atrx+ and Atrx- primary murine neuroepithelial progenitors (mNPCs). This ChIP–seq analysis revealed major differences in the localization of heterochromatin repressive marks H3K9me3 and H3K27me3. Specifically, we identified peculiar locations in the genome displaying H3K9me3 depletion and gain of H3K27me3 upon Atrx inactivation. Interestingly, these regions were flanked by Atrx binding sites and perfectly co-localized with Lamina-Associated Domains, known to play important roles in tissue lineage specification. To better target this dysfunction, we utilized the Broad Institute Connectivity Map (CLUE analysis) to identify compounds likely to revert the unique transcriptional perturbations induced by Atrx deficiency. We found that HDAC inhibitors, as a compound class, yielded expression profiles strongly anticorrelated to those driven by Atrx deficiency in these datasets. Further integrating existing gene expression data from our mNPCs and the TCGA LGG project with our CLUE findings highlighted SIRT2, a class III HDAC, as a top potential target. SIRT2 expression was significantly upregulated in both Atrx- mNPCs and in ATRX-mutant gliomas and its specific chemical inhibition normalized cellular motility in both Atrx- mNPCs and ATRX-mutant, patient derived glioma stem cells. These findings indicate that SIRT2 inhibition represents a viable strategy to revert the epigenetic effects of ATRX deficiency on facultative heterochromatin and their transcriptional and phenotypic consequences.
GENE-45. DISSECTING THE DRIVERS OF ADULT H3K27M-GLIOMAS AT THE SINGLE-CELL LEVEL
Authors: Liu Ilon , Avihai Byron , Gojo Johannes , Ligon Keith , Czech Thomas , Slavc Irene , Kleinman Claudia , Jabado Nada , Filbin Mariella 
Published: November 2019

Abstract
Diffuse midline gliomas are characterized by a lysine27-to-methionine mutation in histone H3 (H3K27M-glioma) and represent a highly aggressive molecular entity of high-grade gliomas. These mutations have primarily been described in children, but are also increasingly recognized in adults. In pediatric H3K27M-gliomas, the transcriptional architecture and cellular composition have been studied at the single-cell level. Data suggest that these tumors arise through malignant transformation of a glial progenitor during a specific neurodevelopmental time window. On the other hand, little is known about the architecture and cellular context of adult H3K27M-gliomas, and it remains to be elucidated whether they are driven by the same or by distinct oncogenic programs as their pediatric counterparts. Here, we utilize single-cell transcriptomics to characterize the transcriptional landscape of five H3K27M-gliomas from adult patients aged 22 to 56 years (median 33 years). We describe the specific cellular and microenvironmental architecture of the adult tumors, which comprises distinct populations of cancer and normal cells. We contrast our findings to 12 location-matched pediatric H3K27M-tumors from patients aged 2.5 to 15 years (median 8 years) to identify features related to tumorigenesis and developmental context in light of the shared hallmark H3K27M mutation. Our preliminary data indicate shared gene expression programs between adult and pediatric tumors. However, we find significant differences in the composition of the immune compartment as well as less pronounced differentiation programs in the adult tumors. Our findings provide an unprecedented insight into the composition of adult H3K27M-gliomas and advance our understanding of this molecular tumor class.
GENE-46. XAF1 DRIVES DIFFERENTIAL PLASTICITY TOWARDS ADAPTIVE RESISTANCE BETWEEN MGMT-HYPERMETHYLATED AND MGMT-HYPOMETHYLATED GLIOBLASTOMA
Authors: Wu Qiong , Berglund Anders , Wang Dapeng , Sahebjam Solmaz , MacAulay Robert , Mulé James , Etame Arnold 
Published: November 2019

Abstract
Although, the epigenetic regulation of O6-alkylguanine DNA alkyltransferase (MGMT) in GBM is an established surrogate of intrinsic resistance to temozolomide (TMZ), the evolution of GBM habitats towards adaptive resistance to TMZ relative to MGMT promoter methylation status remains unclear. We report a novel epigenetic regulation of plasticity towards adaptive resistance in GBM. Using an adaptive TMZ resistance model of MGMT-hypermethylated and MGMT-hypomethylated GBM cellular habitats, a counter-intuitive inverse correlation was noted between intrinsic MGMT-dependent TMZ resistance versus plasticity towards adaptive TMZ resistance. Upon TMZ challenge, GBM cellular habitats with lower intrinsic resistance demonstrated significant genetic perturbations and aggressive phenotypic alterations compared to GBM habitats with higher intrinsic resistance. A resulting gene signature associated with plasticity for adaptive resistance from our model significantly correlated with GBM survival in the TCGA dataset. XAF-1 emerged as a key gene whose epigenetic regulation mediated differential plasticity towards adaptive resistance to TMZ in GBM habitats. Genetic silencing of XAF-1 significantly compromised plasticity towards adaptive resistance. XAF1 expression was found to highly correlate with promoter methylation status, and negatively correlate with long-term survival in GBM patient survival. Our studies have shed some light with respect to the plasticity of GBM habitats towards adaptive resistance evolution to TMZ relative to MGMT promoter methylation status. Particularly, a novel and translational role for XAF1 in GBM has been uncovered.