bluuebunny/crossref_metadata_2025_split huggingface dataset:
DIPG-31. MOLECULAR MECHANISMS AND FUNCTIONAL IMPACT OF ABERRANT SPLICING IN DIFFUSE MIDLINE GLIOMAS
Authors: Naqvi Ammar , Gaonkar Krutika , Zhu Yuankun , Brown Miguel , Zhang Bo , Ennis Brian , Storm Phillip , Resnick Adam , Rokita Jo Lynne 
Published: December 2020

Abstract
Fewer than 1% of children diagnosed with diffuse-midline glioma (DMG) survive for more than 5 years, because no effective therapies exist for these patients. Here, we sought to identify and characterize mechanisms of aberrant splicing (AS) in primary DMG tumors. We observed transcriptome-wide AS (9,805 differential splicing variations in 4,734 genes), and identified a DMG-specific splicing signature, that included known cancer genes. We hypothesize that AS of cancer genes play a role in DMG tumor formation. Assessing whether splicing factor dysregulation impacted known cancer transcripts, we discovered several splicing factors, including SRRM4, SRRM3 and RBFOX3 to be down-regulated in DMG. Additionally, we found an enrichment of binding motifs for these proteins within flanking regions of these mis-spliced exons. We also observed recurrent significant exon inclusion in tumor suppressor SMARCA4, an integral member of the SWI/SNF family of proteins involved in chromatin remodeling. Further, we identified AS in 16 of the 27 members of the SWI/SNF complex, including increased skipping of exon 7 in DPF2, representing a complete mRNA transcript switch in DMG. Since SRRM4, SRRM3 and RBFOX3 are known regulators for neural-specific microexons, we focused on microexon splicing changes, hypothesizing that these regulators may be driving microexon mis-splicing in these tumors. We identified 245 known microexons lost or gained in DMG. Moreover, a quarter of which were observed in known cancer genes, with the most frequent splice event causing gain of a clathrin-binding site in the tumor suppressor BIN1 with a concurrent loss of an out-of-frame microexon in the oncogene BAK1, presumably activating it. Altogether, our results suggest that aberrant splicing may be an alternative mechanism driving DMG tumorigenesis and we are currently molecularly validating a subset of these events with the overall goal of identifying novel therapeutic targets for DMG tumors.
DIPG-35. BIOLOGICAL MEDICINE FOR DIFFUSE INTRINSIC PONTINE GLIOMA (DIPG) ERADICATION: RESULTS OF THE THREE ARM BIOMARKER-DRIVEN RANDOMIZED BIOMEDE 1.0 TRIAL
Authors: Grill Jacques , Teuff Gwenael Le , Nysom Karsten , Blomgren Klas , Hargrave Darren , MacCowage Geoff , Bautista Francisco , Van Vuurden Dannis , Dangouloff-Ros Volodia , Puget Stephanie , Varlet Pascale , Debily Marie-Anne , Vassal Gilles , Deley Marie-Cecile Le 
Published: December 2020

Abstract
Despite 50 years of clinical trials, no improvement of survival has been observed in DIPG and most children die within 2 years of diagnosis. Only radiotherapy transiently controls disease progression. The study was conceived as a randomized multi-arm multi-stage program. It started with an open-label phase-II trial comparing three drugs (everolimus, dasatinib, erlotinib) combined with irradiation, allocated according to the presence of their specific targets (PTEN-loss, EGFR-overexpression) defined with a stereotactic biopsy after central confirmation of the diagnosis (presence of histone H3K27M mutation or loss of K27 trimethylation). Targeted therapies were started concomitantly with radiotherapy and were continued until disease progression. No biopsy-related death was reported and diagnostic yield was excellent, with only 5 non-informative biopsies. Biopsy excluded the diagnosisof DIPG in 8% of the cases. At the 3rd interim analysis, based on 193 randomized patients, the IDMC concluded that the study was unlikely to show a difference of OS between the 3 drugs even if 250 patients would be randomized. The median OS from the time of diagnosis was 11.9, 10.5 and 10 months for everolimus, dasatinib and erlotinib. Treatment was discontinued due to toxicity in 2%, 13%, and 15%, respectively. BIOMEDE shows the feasibility of biologically-driven treatment in DIPG on a large international scale. Based on the better toxicity profile and the slightly better efficacy, although not statistically significant, the steering committee proposed that everolimus should be used as the control arm for the next BIOMEDE 2.0 trial.
DIPG-44. A GAIN OF FUNCTION Ezh2 MUTATION DELAYS DIFFUSE INTRINSIC PONTINE GLIOMA PROGRESSION
Authors: Dhar Swati , Gadd Samantha , Brat Daniel , Becher Oren 
Published: December 2020

Abstract

BACKGROUND
Diffuse Intrinsic Pontine Glioma (DIPG) remains an incurable pediatric brain cancer. The oncohistone H3K27M implicated in 80% of the cases, is also predicted to target Enhancer of Zeste Homolog 2 (Ezh2), the catalytic component of the Polycomb Repressor Complex 2 (PRC2). There are no reported mutations of Ezh2 and its function in DIPG is not fully determined. This work aims to address the role of Ezh2 in DIPG.

METHODS
Brainstem tumors were established by intracranial injections of Nestin;Tv-a; Ezh2Y641F/+ (NTv-a; Ezh2Y641F/+) neonatal pups using Replication Competent Avian Sarcoma leucosis virus long terminal repeat with splice acceptor (RCAS) viruses, expressing PDGF-B, p53 shRNA, and RCAS-CRE/Y. Immunohistochemical staining for Ki-67 and H3K27me3 were performed on the Discovery ULTRA (Ventana).

RESULTS
Ezh2 overexpression (Ezh2Y641F/+, RCAS CRE) conferred a survival advantage of approximately 10 days (n=20 mice/group, p&lt;0.001). H3K27me3 levels were significantly upregulated in RCAS CRE group (50% vs 20% in RCAS Y, n=4 tumors/group, p&lt;0.03), with a concomitant lower Ki-67 staining (30% vs. 55% in RCAS Y, n=3 tumors/group, p&lt;0.05). Interestingly, pathological review categorized more RCAS-CRE tumors as ‘atypical’. RNA-sequencing of virus-infected neural precursor cells revealed a suppression of inflammatory/interferon gene signature in the Ezh2 overexpression group. CONCLUSIONS AND FUTURE DIRECTIONS: Enhanced Ezh2 activity appears to delay DIPG pathogenesis. Ongoing work aims to highlight the contribution of differentially expressed gene signatures that contribute to this phenotype.
DIPG-53. CHARACTERIZING THE ROLE OF PPM1D MUTATIONS IN THE PATHOGENESIS OF DIFFUSE INTRINSIC PONTINE GLIOMAS (DIPGS)
Authors: Khadka Prasidda , Reitman Zachary , Lu Sophie , Buchan Graham , Hartley Rachel , Bear Heather , Georgis Yoahnna , Jarmale Spandana , Schoolcraft Kathleen , Miller Peter , Gonzalez Elizabeth , Gionet Gabrielle , Qian Kenin , Melanson Randy , Keshishian Hasmik , Carvalho Diana , Condurat Alexandra , Goodale Amy , Abid Tanaz , Piccioni Federica , Chi Susan , Carr Steven , Haas-Kogan Daphne , Ebert Benjamin , Kieran Mark , Jones Chris , Ligon Keith , Beroukhim Rameen , Phoenix Timothy , Bandopadhayay Pratiti 
Published: December 2020

Abstract

INTRODUCTION
We have previously found that up to 15% of all DIPGs harbor mutations in PPM1D, resulting in the expression of an activated and truncated PPM1D (PPM1Dtr). Here we evaluate the mechanisms through which PPM1Dtr enhances glioma formation and identify its associated therapeutic vulnerabilities.

METHODS
We have developed multiple in vitro and in vivo models of PPM1D-mutant DIPGs and applied quantitative proteomic and functional genomic approaches to identify pathways altered by PPM1Dtr and associated dependencies.

RESULTS
PPM1D mutations are clonal events that are anti-correlated to TP53 mutations. We find ectopic expression of PPM1Dtr to be sufficient to enhance glioma formation and to be necessary in PPM1D-mutant DIPG cells. In addition, endogenous truncation of PPM1D is sufficient to enhance glioma formation in the presence of mutant H3F3A and PDGFRA. PPM1Dtr overexpression attenuates g-H2AX formation and suppresses apoptosis and cell-cycle arrest in response to radiation treatment. Deep scale phosphoproteomics analyses reveal DNA-damage and cell cycle pathways to be most significantly associated with PPM1Dtr. Furthermore, preliminary analysis of genome-wide loss-of-function CRISPR/Cas9 screens in isogenic GFP and PPM1Dtr overexpressing mouse neural stem cells reveal differential dependency on DNA-damage response genes in the PPM1Dtr overexpressing cells. Consistent with PPM1D’s role in stabilizing MDM2, PPM1D-mutant DIPG models are sensitive to a panel of MDM2 inhibitors (Nutlin-3a, RG7388, and AMG232).

CONCLUSION
Our study shows that PPM1Dtr is both an oncogene and a dependency in PPM1D- mutant DIPG, and there are novel therapeutic vulnerabilities associated with PPM1D that may be exploited.
DIPG-55. PATTERNS OF CEREBROSPINAL FLUID DIVERSION AND SURVIVAL IN CHILDREN WITH DIFFUSE INTRINSIC PONTINE GLIOMA: A REPORT FROM THE INTERNATIONAL DIPG REGISTRY
Authors: Cooney Tabitha , DeWire-Schottmiller Mariko , Lane Adam , Saab Raya , Bandopadhayay Pratiti , Dorris Kathleen , Packer Roger , Kilburn Lindsey , Minturn Jane , Dodgshun Andrew , Parkin Sara , Goldman Stewart , Sandler Eric , Greiner Robert , Gottardo Nicholas , Dholaria Hetal , Coven Scott L , Hassall Tim , Hansford Jordan , Samson Yvan , Leary Sarah , Bartels Ute , Bouffet Eric , Tinkle Christopher , Monje Michelle , Fisher Paul G , Ziegler David , Chintagumpala Murali , Wagner Lars , Koschmann Carl , Benito Elisa Carrasquedo , Leach James , Jones Blaise , Chaney Brooklyn , Black Katie , Asher Anthony , Bond Hailey , Fouladi Maryam , Warren Katherine E 
Published: December 2020

Abstract
There is no standard of care for cerebrospinal (CSF) diversion in children with diffuse intrinsic pontine glioma (DIPG), nor understanding of survival impact. We evaluated CSF diversion characteristics in children with DIPG to determine incidence, indications and potential impact on survival. Data was extracted from subjects registered in the International DIPG registry (IDIPGR). IDIPGR team personnel obtained clinical and radiographic data from the registry database and when appropriate, abstracted additional data from individual medical records. Univariable analyses were performed using the Fisher’s exact test or Wilcoxon rank sum test. Survival was estimated using the Kaplan-Meier method. Evaluable patients (n=457) met criteria for DIPG diagnosis by central radiology review. Ninety-two patients (20%) had permanent CSF diversion. Indications for permanent diversion were hydrocephalus (41%), hydrocephalus and clinical symptoms (35%), and clinical symptoms alone (3%). Those with permanent diversion were significantly younger at diagnosis than those without diversion (median 5.3 years vs 6.9 years, p=0.0002), otherwise no significant differences in gender, race, or treatment were found. The progression-free and overall survival of those with permanent CSF diversion compared to those without permanent diversion was 4.5 and 10.9 months vs 6.9 and 11.2 months, respectively (p=0.001, p= 0.4). There was no significant difference in overall survival in patients with or without permanent CSF diversion among a large cohort of DIPG patients. Patients without permanent diversion had significantly prolonged progression free survival compared to those with permanent diversion. The qualitative risks and benefits of permanent CSF diversion need to be further evaluated.
DIPG-62. PRECLINICAL EVALUATION OF IMIPRIDONE-BASED COMBINATION THERAPIES IN PEDIATRIC H3K27M MUTANT DIFFUSE INTRINSIC PONTINE GLIOMA (DIPG)
Authors: Borsuk Robyn , Zhou Lanlan , Zhang Yiqun , Prabhua Varun , Allen Joshua , Oster Wolfgang , Tapinos Nikos , Lulla Rishi R , El-Deiry Wafik 
Published: December 2020

Abstract
Imipridones induce apoptosis in cancer via p53 independent upregulation of TNF-related apoptosis inducing ligand (TRAIL) pathway and its proapoptotic receptor DR5. ONC201, a first-in-class imipridone, is being evaluated alone and with radiotherapy for children with H3K27M mutant diffuse glioma. We sought to determine if ONC201 and its imipridone analogs (ONC206, ONC212) are synergistic with other chemotherapy agents. Seven patient-derived DIPG cell lines, six H3.3K27M mutant (SU-DIPG-IV, SU-DIPG-13, SU-DIPG-25, SU-DIPG-27, SU-DIPG-29, SF8628) and one H3.1K27M mutant (SU-DIPG-36) were grown in culture and exposed to ONC201, ONC206, and ONC212 alone and in combination with histone de-acetylase inhibitors (HDACi) or etoposide. A dose-dependent response to ONC201, ONC206, and ONC212 was demonstrated in all cell lines, with mean IC50 values of 1.46 µM, 0.11 µM, and 0.03 µM respectively. ONC206 and ONC212 induced apoptosis measured by increased expression of cleaved PARP and ISR by increased expression ATF4. In two cell lines, synergy studies revealed combination indices (CI) &lt; 1 for ONC206 and etoposide, with a best CI of 0.62 in SU-DIPG-IV and 0.46 in SU-DIPG-25. Synergy was also observed between ONC201 and etoposide (CI 0.46) and ONC201 and panobinostat (CI 0.01). Imipridones and analogs were superior to panobinostat and etoposide in triggering apoptosis as measured by sub-G1 phase content. Additional synergy and mechanistic analyses are ongoing and will be reported. Our results suggest that H3K27M mutant DIPG cells demonstrate increased sensitivity to imipridone analogs (ONC206 and ONC212) when compared to ONC201. Combinational strategies with etoposide or HDACi should be considered for clinical translation.
DIPG-63. LOSS OF THE H4 LYSINE METHYLTRANSFERASE KMT5B DRIVES INVASION / MIGRATION BY DEPLETING H3K27me3 AT LOCI OTHERWISE RETAINED IN H3K27M MUTANT DIPG CELLS
Authors: Kessler Ketty , Mackay Alan , Molinari Valeria , Tari Haider , Burford Anna , Sottoriva Andrea , Vinci Maria , Jones Chris 
Published: December 2020

Abstract
Diffuse intrinsic pontine glioma (DIPG) and other diffuse midline glioma (DMG) are characterised by K27M mutations in histone H3 variants. The major functional consequence is a global loss of the repressive mark H3K27me3, causing a raft of transcriptional changes promoting tumorigenesis, although certain key loci retain trimethylation, such as CDKN2A/B. We recently identified subclonal loss-of-function mutations in the H4 lysine methyltransferase KMT5B to be associated with an enhanced invasion/migration, but the mechanism by which this occurred was unclear. Here we show by ChIP-seq using patient-derived subclonal DIPG models and CRISPR-Cas9 depletion that loss of KMT5B (or KMT5C) causes a paradoxical increase in global levels of H4K20me3 in promoters and regulatory regions, only ablated by knocking out both enzymes. Loss of KMT5B alone further causes loss of the majority of otherwise retained H3K27me3 loci in DIPG cells, although CDKN2A/B itself was spared. De-repression occurred at bivalent loci marked by H3K4me3 and had elevated gene expression by RNAseq; these were significantly enriched for genes involved in chromatin remodelling and invasion/migration, the latter including MMP9/MMP24. Phenotypic assessment of the models in vitro by high-throughput imaging demonstrated significantly increased invasion and migration in association with either KMT5B or KMT5C loss, but not both. Quantitative proteomic assessment of the secretome identified factors by which a minority of KMT5B-deficient cells may signal to promote motility of the neighbouring populations. These data suggest a previously unrecognised trans-histone (H4/H3) interaction in DIPG cells with a potentially profound effect on their diffusely infiltrating phenotype.
DIPG-70. DISORDERED DNA METHYLATION IN DIPG UNDERLIES PHENOTYPIC PLASTICITY
Authors: Koldobskiy Michael , Tetens Ashley , Martin Allison , Eberhart Charles , Raabe Eric , Goutsias John , Feinberg Andrew 
Published: December 2020

Abstract
Diffuse intrinsic pontine glioma (DIPG) is a childhood brainstem tumor with a dismal prognosis and no effective treatment. Recent studies point to a critical role for epigenetic dysregulation in this disease. Nearly 80% of DIPGs harbor mutations in histone H3 encoding replacement of lysine 27 with methionine (K27M), leading to global loss of the repressive histone H3K27 trimethylation mark, global DNA hypomethylation, and a distinct gene expression profile. However, a static view of the epigenome fails to capture the plasticity of cancer cells and their gene expression states. Recent studies across diverse cancers have highlighted the role of epigenetic variability as a driving force in tumor evolution. Epigenetic variability may underlie the heterogeneity and phenotypic plasticity of DIPG cells and allow for the selection of cellular traits that promote survival and resistance to therapy. We have recently formalized a novel framework for analyzing variability of DNA methylation directly from whole-genome bisulfite sequencing data, allowing computation of DNA methylation entropy at precise genomic locations. Using these methods, we have shown that DIPG exhibits a markedly disordered epigenome, with increased stochasticity of DNA methylation localizing to specific regulatory elements and genes. We evaluate the responsiveness of the DIPG epigenetic landscape to pharmacologic modulation in order to modify proliferation, differentiation state, and immune signaling in DIPG cells.
EPCT-01. PHASE I STUDY OF DAY101 (TAK580) IN CHILDREN AND YOUNG ADULTS WITH RADIOGRAPHICALLY RECURRENT OR PROGRESSIVE LOW-GRADE GLIOMA (LGG)
Authors: Wright Karen , Krzykwa Emily , Greenspan Lianne , Chi Susan , Yeo Kee Kiat , Mueller Sabine , Prados Michael , Haas-Kogan Daphne 
Published: December 2020

Abstract

BACKGROUND
We report a phase I study examining pharmacokinetics, safety and recommended dosage of the type 2 RAF inhibitor DAY101 in children/young adults with radiographically recurrent/progressive LGGs harboring MAPK pathway alterations.

METHODS
Applying a 3 + 3 design, patients &lt; 18 years of age with radiographically recurrent/progressive LGG received oral DAY101 weekly for 4-week cycles up to a maximum of 2 years, if deriving clinical benefit. The starting DAY101 dosage was 280 mg/m2. Dose limiting toxicities were determined after one cycle.

RESULTS
We treated nine eligible patients at 280, 350, and 420 mg/m2. Eight patients had KIAA1549:BRAF fusions. One patient with NF1 did not have a biopsy. There were no DLTs. Weekly administration of DAY101 in children resulted in dose-proportional increases in Cmax and AUC similar to that described in adults. A 2.2-fold mg/kg exposure difference was observed with respect to weight-based dosing and suggested a correlation to best radiographic RANO responses of 2 complete responses, 2 partial responses, 3 stable disease, and 2 progressive disease (independently-reviewed). Median time to response was 10.5 weeks (range: 8–32 weeks).

CONCLUSION
The phase 1A data provide initial pharmacokinetic parameters to describe oral weekly dosing of DAY101 in pediatric patients with radiographically recurrent/progressive LGG. Plasma exposures of DAY101 achieved in adults can be reached in pediatric patients. Oral weekly DAY101 is well-tolerated and possesses anti-tumor activity. The amended protocol will explore additional dose levels and the potential for differential dosing to achieve similar responses across a variety of BSAs.
EPCT-03. A PHASE I TRIAL OF 2-HYDROXYOLEIC ACID IN PEDIATRIC PATIENTS WITH ADVANCED CENTRAL NERVOUS SYSTEM TUMORS
Authors: Hanson Derek 
Published: December 2020

Abstract
2-hydroxyoleic acid (2-OHOA) is the first potential anti-cancer drug to act by modification of cell membrane lipid content. The agent is a derivative of oleic acid, a naturally occurring component of olive oil. Through its unique mechanism of activating sphingomyelin synthase 1, 2-OHOA targets the membrane lipid composition of cancer cells. These lipid changes alter membrane-dependent signaling cascades, such as the Ras/MAPK pathway, that promote tumor cell proliferation. A comprehensive pre-clinical program has characterized the safety and effects of 2-OHOA across a host of animal models. A European phase I/IIa trial of 2-OHOA in adult patients has shown initial promising results with five refractory high-grade glioma patients demonstrating objective clinical benefit by RANO criteria for six or more months. The drug has been very well-tolerated in adult patients with minimal toxicity. This phase I study is the first pediatric investigation of 2-OHOA and focuses on the treatment of relapsed/refractory pediatric central nervous system (CNS) tumors. The trial consists of a dose-escalation phase in up to 18 patients using a standard “3 + 3” design, followed by an expanded safety cohort of up to 10 patients treated at the maximum tolerated dose to confirm the recommended phase II dose. Due to the promising clinical results in adult neuro-oncology patients and the widespread involvement of the Ras/MAPK pathway and other membrane-dependent signaling cascades in the development of pediatric malignancies, we hypothesize that 2-OHOA may be a safe and effective treatment for pediatric patients with several types of advanced CNS tumors.
EPCT-05. A PHASE I TRIAL OF THE CDK 4/6 INHIBITOR PALBOCICLIB IN PEDIATRIC PATIENTS WITH PROGRESSIVE OR REFRACTORY CNS TUMORS: A PEDIATRIC BRAIN TUMOR CONSORTIUM (PBTC) STUDY
Authors: Van Mater David , Gururangan Sridharan , Leary Sarah , Becher Oren , Phillips Joanna , Huang Jie , Campagne Olivia , Poussaint Tina , Goldman Stewart , Baxter Patricia , Dhall Girish , Robinson Giles , DeWire-Schottmiller Mariko , Hwang Eugene , Stewart Clinton , Onar-Thomas Arzu , Dunkel Ira , Fouladi Maryam 
Published: December 2020

Abstract
PBTC-042 was a phase I trial of palbociclib to determine the maximum tolerated dose (MTD) and describe toxicities in children. Palbociclib is an oral, selective cyclin dependent kinase 4/6 inhibitor. METHODS: A rolling-6 design was utilized. Eligible patients were children ≥4 and ≤21 years-old with a progressive/refractory CNS tumor with intact retinoblastoma protein, measurable disease, and ability to swallow capsules. Pharmacokinetic studies were performed during the first course. Here, we report on the heavily pretreated stratum, which included patients who received &gt;4 prior treatment regimens (either chemotherapy or biologic agent), and/or craniospinal irradiation, and/or myeloablative chemotherapy plus stem cell rescue. Palbociclib was initiated at 50 mg/m2/day for 21 consecutive days of a 28-day course. This was one dosage level below the MTD for the less heavily pretreated stratum (75 mg/m2). RESULTS: Fourteen eligible patients were enrolled (median age 12.8 years; male 79%). Eleven patients (79%) had either ependymoma or medulloblastoma. Four eligible and evaluable patients were enrolled at 50 mg/m2 with no DLTs. This prompted a dosage increase to 75 mg/m2. Ten eligible subjects were enrolled and 7 were evaluable for DLT assessment. One of 7 evaluable patients experienced a DLT (grade 3 thrombocytopenia). This established 75 mg/m2 as the MTD for more heavily pretreated patients. Mean ± SD palbociclib apparent oral clearance was 34.6 ± 18.4 L/h/m2. CONCLUSION: The MTD for palbociclib on a 3 week on/1 week off schedule in children with brain tumors is 75 mg/m2 and does not appear to be influenced by the degree of prior therapy.