The type II RAF inhibitor tovorafenib in relapsed/refractory pediatric low-grade glioma: the phase 2 FIREFLY-1 trial

BRAF genomic alterations are the most common oncogenic drivers in pediatric low-grade glioma (pLGG). Arm 1 (n = 77) of the ongoing phase 2 FIREFLY-1 (PNOC026) trial investigated the efficacy of the oral, selective, central nervous system-penetrant, type II RAF inhibitor tovorafenib (420 mg m-2 once weekly; 600 mg maximum) in patients with BRAF-altered, relapsed/refractory pLGG. Arm 2 (n = 60) is an extension cohort, which provided treatment access for patients with RAF-altered pLGG after arm 1 closure. Based on independent review, according to Response Assessment in Neuro-Oncology High-Grade Glioma (RANO-HGG) criteria, the overall response rate (ORR) of 67% met the arm 1 prespecified primary endpoint; median duration of response (DOR) was 16.6 months; and median time to response (TTR) was 3.0 months (secondary endpoints). Other select arm 1 secondary endpoints included ORR, DOR and TTR as assessed by Response Assessment in Pediatric Neuro-Oncology Low-Grade Glioma (RAPNO) criteria and safety (assessed in all treated patients and the primary endpoint for arm 2, n = 137). The ORR according to RAPNO criteria (including minor responses) was 51%; median DOR was 13.8 months; and median TTR was 5.3 months. The most common treatment-related adverse events (TRAEs) were hair color changes (76%), elevated creatine phosphokinase (56%) and anemia (49%). Grade ≥3 TRAEs occurred in 42% of patients. Nine (7%) patients had TRAEs leading to discontinuation of tovorafenib. These data indicate that tovorafenib could be an effective therapy for BRAF-altered, relapsed/refractory pLGG. ClinicalTrials.gov registration: NCT04775485 .

A multi-institutional pediatric dataset of clinical radiology MRIs by the Children's Brain Tumor Network

Pediatric brain and spinal cancers remain the leading cause of cancer-related death in children. Advancements in clinical decision-support in pediatric neuro-oncology utilizing the wealth of radiology imaging data collected through standard care, however, has significantly lagged other domains. Such data is ripe for use with predictive analytics such as artificial intelligence (AI) methods, which require large datasets. To address this unmet need, we provide a multi-institutional, large-scale pediatric dataset of 23,101 multi-parametric MRI exams acquired through routine care for 1,526 brain tumor patients, as part of the Children's Brain Tumor Network. This includes longitudinal MRIs across various cancer diagnoses, with associated patient-level clinical information, digital pathology slides, as well as tissue genotype and omics data. To facilitate downstream analysis, treatment-naïve images for 370 subjects were processed and released through the NCI Childhood Cancer Data Initiative via the Cancer Data Service. Through ongoing efforts to continuously build these imaging repositories, our aim is to accelerate discovery and translational AI models with real-world data, to ultimately empower precision medicine for children.

OpenPBTA: The Open Pediatric Brain Tumor Atlas

Pediatric brain and spinal cancers are collectively the leading disease-related cause of death in children; thus, we urgently need curative therapeutic strategies for these tumors. To accelerate such discoveries, the Children's Brain Tumor Network (CBTN) and Pacific Pediatric Neuro-Oncology Consortium (PNOC) created a systematic process for tumor biobanking, model generation, and sequencing with immediate access to harmonized data. We leverage these data to establish OpenPBTA, an open collaborative project with over 40 scalable analysis modules that genomically characterize 1,074 pediatric brain tumors. Transcriptomic classification reveals universal TP53 dysregulation in mismatch repair-deficient hypermutant high-grade gliomas and TP53 loss as a significant marker for poor overall survival in ependymomas and H3 K28-mutant diffuse midline gliomas. Already being actively applied to other pediatric cancers and PNOC molecular tumor board decision-making, OpenPBTA is an invaluable resource to the pediatric oncology community.

Alternative lengthening of telomeres (ALT) in pediatric high-grade gliomas can occur without ATRX mutation and is enriched in patients with pathogenic germline mismatch repair (MMR) variants

BACKGROUND

To achieve replicative immortality, most cancers develop a telomere maintenance mechanism, such as reactivation of telomerase or alternative lengthening of telomeres (ALT). There are limited data on the prevalence and clinical significance of ALT in pediatric brain tumors, and ALT-directed therapy is not available.

METHODS

We performed C-circle analysis (CCA) on 579 pediatric brain tumors that had corresponding tumor/normal whole genome sequencing through the Open Pediatric Brain Tumor Atlas (OpenPBTA). We detected ALT in 6.9% (n = 40/579) of these tumors and completed additional validation by ultrabright telomeric foci in situ on a subset of these tumors. We used CCA to validate TelomereHunter for computational prediction of ALT status and focus subsequent analyses on pediatric high-grade gliomas (pHGGs) Finally, we examined whether ALT is associated with recurrent somatic or germline alterations.

RESULTS

ALT is common in pHGGs (n = 24/63, 38.1%), but occurs infrequently in other pediatric brain tumors (<3%). Somatic ATRX mutations occur in 50% of ALT+ pHGGs and in 30% of ALT- pHGGs. Rare pathogenic germline variants in mismatch repair (MMR) genes are significantly associated with an increased occurrence of ALT.

CONCLUSIONS

We demonstrate that ATRX is mutated in only a subset of ALT+ pHGGs, suggesting other mechanisms of ATRX loss of function or alterations in other genes may be associated with the development of ALT in these patients. We show that germline variants in MMR are associated with the development of ALT in patients with pHGG.

Data standards in pediatric oncology: Past, present, and future

In this commentary, we highlight the central role that data standards play in facilitating data-driven efforts to advance research in pediatric oncology. We discuss the current state of data standards for pediatric oncology and propose five steps to achieve an improved future state with benefits for clinicians, researchers, and patients.

The children's brain tumor network (CBTN) - Accelerating research in pediatric central nervous system tumors through collaboration and open science

Pediatric brain tumors are the leading cause of cancer-related death in children in the United States and contribute a disproportionate number of potential years of life lost compared to adult cancers. Moreover, survivors frequently suffer long-term side effects, including secondary cancers. The Children's Brain Tumor Network (CBTN) is a multi-institutional international clinical research consortium created to advance therapeutic development through the collection and rapid distribution of biospecimens and data via open-science research platforms for real-time access and use by the global research community. The CBTN's 32 member institutions utilize a shared regulatory governance architecture at the Children's Hospital of Philadelphia to accelerate and maximize the use of biospecimens and data. As of August 2022, CBTN has enrolled over 4700 subjects, over 1500 parents, and collected over 65,000 biospecimen aliquots for research. Additionally, over 80 preclinical models have been developed from collected tumors. Multi-omic data for over 1000 tumors and germline material are currently available with data generation for > 5000 samples underway. To our knowledge, CBTN provides the largest open-access pediatric brain tumor multi-omic dataset annotated with longitudinal clinical and outcome data, imaging, associated biospecimens, child-parent genomic pedigrees, and in vivo and in vitro preclinical models. Empowered by NIH-supported platforms such as the Kids First Data Resource and the Childhood Cancer Data Initiative, the CBTN continues to expand the resources needed for scientists to accelerate translational impact for improved outcomes and quality of life for children with brain and spinal cord tumors.

Discovery and functional characterization of the oncogenicity and targetability of a novel NOTCH1-ROS1 gene fusion in pediatric angiosarcoma

Angiosarcomas are rare, malignant soft tissue tumors in children that arise in a wide range of anatomical locations and have limited targeted therapies available. Here, we report a rare case of a pediatric angiosarcoma (pAS) with Li-Fraumeni syndrome (LFS) expressing a novel NOTCH1-ROS1 gene fusion. Although both NOTCH1 and ROS1 are established proto-oncogenes, our study is the first to describe the mechanistic role of NOTCH1-ROS1 fusion arising via intrachromosomal rearrangement. NOTCH1-ROS1 displayed potent neoplastic transformation propensity in vitro, and harbors tumorigenic potential in vivo, where it induced oncogenic activation of the MAPK, PI3K/mTOR, and JAK-STAT signaling pathways in a murine allograft model. We found an unexpected contribution of the NOTCH1 extracellular region in mediating NOTCH1-ROS1 activation and oncogenic function, highlighting the contribution of both NOTCH1 and ROS1 fusion partners in driving tumorigenicity. Interestingly, neither membrane localization nor fusion protein dimerization were found to be essential for NOTCH1-ROS1 fusion oncogenicity. To target NOTCH1-ROS1-driven tumors, we tested both NOTCH1-directed inhibitors and ROS1-targeted tyrosine kinase inhibitors (TKI) in heterologous models (NIH3T3, Ba/F3). Although NOTCH1 inhibitors did not suppress NOTCH1-ROS1-driven oncogenic growth, we found that oral entrectinib treatment effectively suppressed the growth of NOTCH-ROS1-driven tumors. Taken together, we report the first known pAS case with a novel NOTCH1-ROS1 alteration along with a detailed report on the function and therapeutic targeting of NOTCH1-ROS1. Our study highlights the importance of genomic profiling of rare cancers such as pAS to reveal actionable drivers and improve patient outcomes.

Decadron, Diamox, and Zantac: A Novel Combination for Ventricular Shunt Failure in Pediatric Neurosurgical Patients

OBJECTIVE

Cerebral ventricular shunt failure is common and presents with symptoms that range from headaches to death. The combination of Diamox (acetazolamide), Decadron (dexamethasone), and Zantac (ranitidine) (DDZ) is used at our institution to medically stabilize pediatric patients presenting with symptomatic shunt failure before shunt revision. We describe our experience of this drug combination as a temporizing measure to decrease symptoms associated with shunt failure.

METHODS

We performed a single-center retrospective chart review of patients younger than 18 years with ventricular shunt failure who underwent a shunt revision between January 2015 to October 2017 and received DDZ before surgery. The outcome variables evaluated included pre-DDZ and post-DDZ clinical symptoms, pain scores, and vital signs.

RESULTS

There were 112 cases that received DDZ before shunt revision. The 4 most commonly reported symptoms were analyzed. Headache was observed in 42 cases pre-DDZ, and post-DDZ there was a 71% reduction in headache (P < 0.0001); emesis was reported pre-DDZ in 76 cases, and post-DDZ there was an 83% reduction (P < 0.0001); irritability was noted pre-DDZ in 30 cases, and post-DDZ there was a 77% reduction (P = 0.0003); lethargy pre-DDZ was observed in 60 cases, and post-DDZ 73% demonstrated improvement (P < 0.0001). Maximum pain scores significantly decreased post-DDZ (P < 0.0001). Heart rate, systolic, and diastolic blood pressures significantly decreased post-DDZ (P < 0.0001, P < 0.0001, P = 0.0002, respectively).

CONCLUSIONS

The combination of Decadron, Diamox, and Zantac is a novel treatment for ventricular shunt failure that may temporarily improve symptoms in patients awaiting shunt revision. Future studies could compare efficacy with other medical treatments.

BRAF fusions in pediatric histiocytic neoplasms define distinct therapeutic responsiveness to RAF paradox breakers

Pediatric histiocytic neoplasms are hematopoietic disorders frequently driven by the BRAF-V600E mutation. Here, we identified two BRAF gene fusions (novel MTAP-BRAF and MS4A6A-BRAF) in two aggressive histiocytic neoplasms. In contrast to previously described BRAF fusions, MTAP-BRAF and MS4A6A-BRAF do not respond to the paradox breaker RAF inhibitor (RAFi) PLX8394 due to stable fusion dimerization mediated by the N-terminal fusion partners. This highlights a significant and clinically relevant shift from the current dogma that BRAF-fusions respond similarly to BRAF-inhibitors. As an alternative, we show suppression of fusion-driven oncogenic growth with the pan-RAFi LY3009120 and MEK inhibition.

HGG-06. EARLY GABAERGIC NEURONAL LINEAGE DEFINES DEPENDENCIES IN HISTONE H3 G34R/V GLIOMA

High-grade gliomas harboring H3 G34R/V mutations exclusively occur in the cerebral hemispheres of adolescents and young adults, suggesting a distinct neurodevelopmental origin. Combining multimodal bulk and single-cell genomics with unbiased genome-scale CRISPR/Cas9 approaches, we here describe a GABAergic interneuron progenitor lineage as the most likely context from which these H3 G34R/V mutations drive gliomagenesis, conferring unique and tumor-selective gene targets essential for glioma cell survival, as validated genetically and pharmacologically. Phenotypically, we demonstrate that while H3 G34R/V glioma cells harbor the neurotransmitter GABA, they are developmentally stalled, and do not induce the neuronal hyperexcitability described in other glioma subtypes. These findings offer a striking counter-example to the prevailing view of glioma origins in glial precursor cells, resulting in distinct cellular, microenvironmental, and therapeutic consequences.

A Phase I and Surgical Study of Ribociclib and Everolimus in Children with Recurrent or Refractory Malignant Brain Tumors: A Pediatric Brain Tumor Consortium Study

PURPOSE

Genomic aberrations in cell cycle and PI3K pathways are commonly observed in pediatric brain tumors. This study determined the MTD/recommended phase II dose (RP2D) of ribociclib and everolimus and characterized single-agent ribociclib concentrations in plasma and tumor in children undergoing resection.

PATIENTS AND METHODS

Patients were enrolled in the phase I study according to a rolling 6 design and received ribociclib and everolimus daily for 21 and 28 days, respectively. Surgical patients received ribociclib at the pediatric RP2D (350 mg/m2) for 7-10 days preoperatively followed by enrollment on the phase I study. Pharmacokinetics were analyzed for both cohorts.

RESULTS

Sixteen patients were enrolled on the phase I study (median age, 10.3 years; range, 3.9-20.4) and 6 patients in the surgical cohort (median age, 11.4 years; range: 7.2-17.1). Thirteen patients were enrolled at dose level 1 without dose-limiting toxicities (DLT). Two of the 3 patients at dose level 2 experienced DLTs (grade 3 hypertension and grade 4 alanine aminotransferase). The most common grade 3/4 toxicities were lymphopenia, neutropenia, and leukopenia. The RP2D of ribociclib and everolimus was 120 and 1.2 mg/m2 for 21 and 28 days, respectively. Steady-state everolimus exposures with ribociclib were 2.5-fold higher than everolimus administered alone. Ribociclib plasma, tumor concentrations, and cerebrospinal fluid (CSF) samples were collected. The mean tumor-to-plasma ratio of ribociclib was 19.8 (range, 2.22-53.4).

CONCLUSIONS

Ribociclib and everolimus were well-tolerated and demonstrated pharmacokinetic properties similar to those in adults. Potential therapeutic ribociclib concentrations could be achieved in CSF and tumor tissue, although interpatient variability was observed.

Abstract 632: Novel BRAF gene fusions in pediatric histiocytic neoplasms respond differentially to RAF targeted therapies based on dimerization profiles

Introduction: Pediatric histiocytic neoplasms are clonal hematopoietic disorders driven by mutations activating the mitogen-activated protein kinase (MAPK) pathway, such as BRAF- V600E. In non-BRAFV600E cases, we investigated alternative MAPK mutations and found two novel BRAF gene fusions. We have previously shown effective targeting of BRAF fusions (KIAA1549-BRAF) in pediatric low-grade gliomas (PLGGs) with paradox breaker RAF inhibitor (RAFi), PLX8394 and MEK inhibitors (MEKi). Here, we investigate the distinct responsiveness of novel BRAF fusions to RAFi therapies and explore the mechanistic basis of such differential responses compared to other BRAF fusions.

Method: Two histiocytic patient tumors were analyzed using the CHOP Comprehensive Next- Gen Sequencing Solid Tumor Panel and a targeted RNA-seq panel for 106 fusion partner genes. Novel BRAF fusions identified were sub-cloned to create heterologous cell models. Immunoblotting of serum starved cells measured MAPK and PI3K pathway activation and soft agar assay tested for oncogenic phenotypes driven by BRAF fusions, along with response to PLX8394, LY3009120 (pan-RAF dimer inhibitor), and MEKi. Co-immunoprecipitation assays using Myc- and Flag-tagged BRAF fusion constructs assessed dimerization profiles, with or without inhibitors.

Result: In the two M- and L-type histiocytic neoplasms assessed, we found novel and rare BRAF gene fusions, MTAP-BRAF and MS4A6A-BRAF, respectively. Both BRAF fusions activated the MAPK/ PI3K pathways and showed homo- and hetero-dimerization with BRAF and the respective N-terminal fusion partner. Compared to common BRAF fusions, MTAP-BRAF and MS4A6A- BRAF did not respond to PLX8394 due to no disruption of active fusion homo- and hetero-dimers, which was in turn was due to the untargeted, stable dimerization mediated by the N-terminal fusion partners. Conversely, we observed robust suppression with LY3009120 that bound fusion dimers and kept them in an inactivate confirmation. MEKi selumetinib and trametinib also suppressed fusion driven signaling and oncogenic phenotypes.

Conclusion: We show that novel MTAP-BRAF and MS4A6A-BRAF fusions, found in histiocytic tumors, do not respond to RAFi PLX8394 but are targeted by LY3009120 or MEKi. Our finding that PLX8394 does not disrupt MTAP-BRAF or MS4A6A-BRAF dimerization due to contribution of N-terminal partners defines a novel paradigm for the distinct mechanisms sought by BRAF fusions in response to RAFi therapy. We show potent suppression of these mechanistically distinct BRAF fusions with MEKi or LY3009120 which function independent of vulnerability to fusion dimerization. Overall, this study highlights the unique and differential biology hijacked by BRAF fusions in response to RAFi and further warrants detailed mechanistic classification of BRAF fusions based on their responsiveness to targeted agents.

Citation Format: Payal Jain, Lea F. Surrey, Joshua Straka, Pierre Russo, Richard Womer, Marilyn Li, Phillip B. Storm, Angela J. Waanders, Michael Hogarty, Jennifer Picarsic, Adam C. Resnick. Novel BRAF gene fusions in pediatric histiocytic neoplasms respond differentially to RAF targeted therapies based on dimerization profiles [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 632.

Abstract A37: Unique gene fusions inform targeted therapeutic strategies across extremely rare, non-CNS pediatric solid tumors

Introduction: In children, approximately 7% of the non-CNS solid tumors include extremely rare histologies such as angiosarcomas and histiocytic neoplasms. While most recurrent histologies can be identified with a commonly occurring alteration or associated with a known biologic mechanism, rare solid tumors remain poorly characterized given their low frequency of occurrence and intrapatient tumor heterogeneity. Our group and others have demonstrated gene fusions (GFs) as unique oncogenic alterations in pediatric gliomas to guide prognosis, diagnosis, and therapeutic interventions. Here, we investigated the role of unique GFs as individualized therapeutic targets in 3 patients with rare non-CNS malignancies and explored GF-directed precision medicine approaches.

Methods: We selected a patient with the rare diagnosis of pediatric angiosarcoma (pAS) and two with pediatric histiocytic neoplasms spanning the juvenille xanthogranuloma (JXG) family and malignant histiocytoses groups. Neoplasms were analyzed using the CHOP Comprehensive Next-Generation Sequencing Solid Tumor Panel as well as a targeted RNA-seq panel for 106 fusion partner genes. For novel gene fusions identified, we performed molecular and therapeutic characterization, including subcloning to create heterologous cell models. Cellular assays were used to assess oncogenic transformation, test mechanistic activation of related downstream signaling pathways via cellular assays, and examine targeting of GFs with specific small-molecule inhibitors.

Results and Discussion: We identified a novel NOTCH1-ROS1 gene fusion in pAs, and rare BRAF-fusions, MTAP-BRAF and MS4A6A-BRAF, in malignant and JXG family histiocytic neoplasms, respectively. We also identified a germline TP53 p.T123Wfs*12 pathogenic variant, and the cancer predisposition team confirmed Li Fraumeni syndrome in the angiosarcoma patient. Our studies demonstrate that the NOTCH1-ROS1 fusion and both BRAF-fusions are potent oncogenes capable of inducing neoplastic transformation in cells and tumor formation in a murine allograft model. The kinase domains of ROS1 and BRAF are retained and activate the MAPK/PI3K/mTOR and JAK-STAT pathways in respective GF- expressing models, driven by potent dimerization of the GFs. Upon testing ROS1-targeted tyrosine kinase inhibitors (TKI) against NOTCH1-ROS1, we observe dose-dependent suppression of Notch1-Ros1 driven cellular activity and concurrent inhibition of tumor growth as well as prolonged survival after oral monotherapy. Interestingly, BRAF-fusions do not respond to second-generation BRAF inhibitors but can be suppressed by RAF dimer-inhibitor LY3009120 and MEK inhibitors. Overall, these data suggest that ongoing genomic profiling of rare pediatric tumors may reveal actionable drivers, and molecular testing of putative oncogenic fusions is imperative for improvement of patient outcomes through precision therapy.

Citation Format: Payal Jain, Lea F. Surrey, Joshua Straka, Tiffany Smith, Sudarshan Iyer, Elizabeth Fox, Monika Davare, Jennifer Picarsic, Marilyn Li, Angela J. Waanders, Adam C. Resnick. Unique gene fusions inform targeted therapeutic strategies across extremely rare, non-CNS pediatric solid tumors [abstract]. In: Proceedings of the AACR Special Conference on the Advances in Pediatric Cancer Research; 2019 Sep 17-20; Montreal, QC, Canada. Philadelphia (PA): AACR; Cancer Res 2020;80(14 Suppl):Abstract nr A37.

Harmonization of postmortem donations for pediatric brain tumors and molecular characterization of diffuse midline gliomas

Children diagnosed with brain tumors have the lowest overall survival of all pediatric cancers. Recent molecular studies have resulted in the discovery of recurrent driver mutations in many pediatric brain tumors. However, despite these molecular advances, the clinical outcomes of high grade tumors, including H3K27M diffuse midline glioma (H3K27M DMG), remain poor. To address the paucity of tissue for biological studies, we have established a comprehensive protocol for the coordination and processing of donated specimens at postmortem. Since 2010, 60 postmortem pediatric brain tumor donations from 26 institutions were coordinated and collected. Patient derived xenograft models and cell cultures were successfully created (76% and 44% of attempts respectively), irrespective of postmortem processing time. Histological analysis of mid-sagittal whole brain sections revealed evidence of treatment response, immune cell infiltration and the migratory path of infiltrating H3K27M DMG cells into other midline structures and cerebral lobes. Sequencing of primary and disseminated tumors confirmed the presence of oncogenic driver mutations and their obligate partners. Our findings highlight the importance of postmortem tissue donations as an invaluable resource to accelerate research, potentially leading to improved outcomes for children with aggressive brain tumors.

Integrated Molecular and Clinical Analysis of 1,000 Pediatric Low-Grade Gliomas

Pediatric low-grade gliomas (pLGG) are frequently driven by genetic alterations in the RAS-mitogen-activated protein kinase (RAS/MAPK) pathway yet show unexplained variability in their clinical outcome. To address this, we characterized a cohort of >1,000 clinically annotated pLGG. Eighty-four percent of cases harbored a driver alteration, while those without an identified alteration also often exhibited upregulation of the RAS/MAPK pathway. pLGG could be broadly classified based on their alteration type. Rearrangement-driven tumors were diagnosed at a younger age, enriched for WHO grade I histology, infrequently progressed, and rarely resulted in death as compared with SNV-driven tumors. Further sub-classification of clinical-molecular correlates stratified pLGG into risk categories. These data highlight the biological and clinical differences between pLGG subtypes and opens avenues for future treatment refinement.

Perioperative near-infrared spectroscopy cerebral oxygen saturation in symptomatic pediatric hydrocephalus patients at risk for intracranial hypertension

OBJECTIVE

The lack of a continuous, noninvasive modality for monitoring intracranial pressure (ICP) is a major obstacle in the care of pediatric patients with hydrocephalus who are at risk for intracranial hypertension. Intracranial hypertension can lead to cerebral ischemia and brain tissue hypoxia. In this study, the authors evaluated the use of near-infrared spectroscopy (NIRS) to measure regional cerebral oxygen saturation (rSO2) in symptomatic pediatric patients with hydrocephalus concerning for elevated ICP.

METHODS

The authors evaluated the NIRS rSO2 trends in pediatric patients presenting with acute hydrocephalus and clinical symptoms of intracranial hypertension. NIRS rSO2 values were recorded hourly before and after neurosurgical intervention. To test for significance between preoperative and postoperative values, the authors constructed a linear regression model with the rSO2 values as the outcome and pre- and postsurgery cohorts as the independent variable, adjusted for age and sex, and used the generalized estimating equation method to account for within-subject correlation.

RESULTS

Twenty-two pediatric patients underwent NIRS rSO2 monitoring before and after CSF diversion surgery. The mean durations of NIRS rSO2 recording pre- and postoperatively were 13.95 and 26.82 hours, respectively. The mean pre- and postoperative rSO2 values were 73.84% and 80.65%, respectively, and the adjusted mean difference estimated from the regression model was 5.98% (adjusted p < 0.0001), suggestive of improved cerebral oxygenation after definitive neurosurgical CSF diversion treatment. Postoperatively, all patients returned to baseline neurological status with no clinical symptoms of elevated ICP.

CONCLUSIONS

Cerebral oxygenation trends measured by NIRS in symptomatic pediatric hydrocephalus patients with intracranial hypertension generally improve after CSF diversion surgery.

Immunotherapy for pediatric brain tumors: past and present

The field of cancer immunotherapy has progressed at an accelerated rate over the past decade. Pediatric brain tumors thus far have presented a formidable challenge for immunotherapy development, given their typically low mutational burden, location behind the blood-brain barrier in a unique tumor microenvironment, and intratumoral heterogeneity. Despite these challenges, recent developments in the field have resulted in exciting preclinical evidence for various immunotherapies and multiple clinical trials. This work reviews the history and advances in active immunotherapy, checkpoint blockade, and adoptive T-cell therapy for pediatric brain tumors, including ongoing clinical trials.

Genomic Analysis of Dysembryoplastic Neuroepithelial Tumor Spectrum Reveals a Diversity of Molecular Alterations Dysregulating the MAPK and PI3K/mTOR Pathways

Dysembryoplastic neuroepithelial tumors (DNT) lacking key diagnostic criteria are challenging to diagnose and sometimes fall into the broader category of mixed neuronal-glial tumors (MNGT) or the recently described polymorphous low-grade neuroepithelial tumor of the young (PLNTY). We examined 41 patients with DNT, MNGT, or PLNTY for histologic features, genomic findings, and progression-free survival (PFS). Genomic analysis included sequence and copy number variants and RNA-sequencing. Classic DNT (n = 26) was compared with those with diffuse growth without cortical nodules (n = 15), 6 of which exhibited impressive CD34 staining classifying them as PLNTY. Genomic analysis was complete in 33, with sequence alterations recurrently identified in BRAF, FGFR1, NF1, and PDGFRA, as well as 7 fusion genes involving FGFR2, FGFR1, NTRK2, and BRAF. Genetic alterations did not distinguish between MNGTs, DNTs, or PLNTYs; however, FGFR1 alterations were confined to DNT, and PLNTYs contained BRAF V600E or FGFR2 fusion genes. Analysis of PFS showed no significant difference by histology or genetic alteration; however, numbers were small and follow-up time short. Further molecular characterization of a PLNTY-related gene fusion, FGFR2-CTNNA3, demonstrated oncogenic potential via MAPK/PI3K/mTOR pathway activation. Overall, DNT-MNGT spectrum tumors exhibit diverse genomic alterations, with more than half (19/33) leading to MAPK/PI3K pathway alterations.

Development and Clinical Validation of a Large Fusion Gene Panel for Pediatric Cancers

Gene fusions are one of the most common genomic alterations in pediatric cancer. Many fusions encode oncogenic drivers and play important roles in cancer diagnosis, risk stratification, and treatment selection. We report the development and clinical validation of a large custom-designed RNA sequencing panel, CHOP Fusion panel, using anchored multiplex PCR technology. The panel interrogates 106 cancer genes known to be involved in nearly 600 different fusions reported in hematological malignancies and solid tumors. The panel works well with different types of samples, including formalin-fixed, paraffin-embedded samples. The panel demonstrated excellent analytic accuracy, with 100% sensitivity and specificity on 60 pediatric tumor validation samples. In addition to identifying all known fusions in the validation samples, three unrecognized, yet clinically significant, fusions were also detected. A total of 276 clinical cases were analyzed after the validation, and 51 different fusions were identified in 104 cases. Of these fusions, 16 were not previously reported at the time of discovery. These fusions provided genomic information useful for clinical management. Our experience demonstrates that CHOP Fusion panel can detect the vast majority of known and certain novel clinically relevant fusion genes in pediatric cancers accurately, efficiently, and cost-effectively; and the panel provides an excellent tool for new fusion gene discovery.

Abstract 2464: Gabriella Miller Kids First Data Resource Center: Harmonizing clinical and genomic data to support childhood cancer and structural birth defect research

Childhood cancers and structural birth defects share a common context of altered developmental biology, but the potential role of shared, genetic alterations and/or pathways across pediatric cancers and birth defects is not well explored. It is increasingly critical that genomic data are paired with high-quality clinical data to drive translational research by elucidating the relationship between genomic alterations, treatments, outcomes, and other phenotypic characteristics. The NIH Common Fund Gabriella Miller Kids First Program represents a first-in-kind national, collaborative initiative focused on large-scale clinical and genomic data sharing for childhood cancers and structural birth defects. As part of this program, the Kids First Data Resource Center (DRC) is charged with empowering collaborative discovery across Kids First datasets. Through newly developed cloud-based platforms, researchers will be able to rapidly and interactively access standardized and harmonized clinical and genomic data. A better understanding of common developmental programs could spur advancements in prevention, detection, and therapeutics that will improve the outcomes of affected children and families.

Approximately 8,000 patient samples were available at the launch of the Kids First DRC portal, with an initial focus on whole genome sequencing (WGS) of trios and families. More than 25,000 WGS are expected to be processed by 2019, making the DRC one of the largest pediatric data resources of its kind across a diversity of diseases. The rise of cloud-based computing has greatly reduced the burden on the researcher of large-scale genomic harmonization. In normal operations, the DRC is capable of running two hundred workflows simultaneously with considerable scalability on demand. Additionally, there is a strong focus on harmonizing and structuring seemingly disparate clinical and phenotypic data types to make them more interoperable, discoverable and reusable by using ontologies. The data in the DRC is expertly curated and mapped to existing data standards, including NCI Thesaurus (NCIt), Human Phenotype Ontology (HPO), Monarch Disease Ontology (MONDO), and Uber-anatomy Ontology (Uberon). This allows for increased interoperability and semantic structure of the data. For example, MONDO integrates numerous disease terminologies into a single merged ontology, including the NCIt. The combination of harmonized genomic and clinical data across pediatric cancers and structural birth defect provides a key foundation for exploring and developing new methods to better understand the relationships between germline variants, cancer risk, and associated treatments and outcomes. Community standardization of this modeling is ongoing as part of GA4GH, and is critical for implementation of improved interpretation in EHR systems, for example via HL7 FHIR.

Citation Format: Allison P. Heath, Deanne M. Taylor, Yuankun Zhu, Pichai Raman, Jena Lilly, Phillip Storm, Angela J. Waanders, Vincent Ferretti, Christina Yung, Michele Mattioni, Brandi Davis-Dusenbery, Zachary L. Flamig, Robert Grossman, Samuel L. Volchenboum, Sabine Mueller, Javad Nazarian, Nicole Vasilevsky, Melissa A. Haendel, Adam Resnick. Gabriella Miller Kids First Data Resource Center: Harmonizing clinical and genomic data to support childhood cancer and structural birth defect research [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2464.

Abstract 3644: Novel NOTCH1-ROS1 gene fusion drives distinct molecular mechanisms in a rare pediatric angiosarcoma

Angiosarcomas are extremely rare, malignant childhood tumors, which often arise in deep soft tissue and liver as well as exhibit a wide anatomical distribution. Due to the rarity of this diagnosis in pediatrics, the development of novel targeted therapeutic options are limited. Here, we diagnosed a case of pediatric angiosarcoma (pAS), and to identify putative driver genomic aberrations, we performed genomic sequencing via a Comprehensive Next Generation Sequencing Solid Tumor Panel, including RNA-sequencing by anchored multiplex PCR (ArcherDx) for 106 fusion partner genes. We identified a novel NOTCH1-ROS1 gene fusion generated from a rearrangement of chromosomes 9 and 6. Subsequent reverse transcription and Sanger sequencing validated the expression of NOTCH1-ROS1 in the pAs. While both NOTCH1 and ROS1 are established proto-oncogenes, and have been separately involved in gene fusions across diverse cancer types, this is a previously unreported fusion in this rare pediatric cancer. We also identified a germline TP53 p.T123Wfs*12 pathogenic variant on follow-up sequencing, thus revealing Li Fraumeni syndrome in this angiosarcoma patient.Notch1-ROS1 is a novel, uncharacterized fusion protein and its functional oncogenic potential or tumorigenic sufficiency is unknown. We cloned NOTCH1-ROS1 cDNA and generated stably expressing heterologous cell lines to test its oncogenic potential using cellular models of transformation and tumorigenicity. Our analysis revealed that Notch1-ROS1 is a potent oncogene capable of inducing neoplastic transformation in cells, and demonstrated that its expression alone is sufficient for tumor formation in a murine allograft model. Notch1-ROS1 oncogenesis is driven via activation of several downstream pathways through a collaboration between the Notch1 and Ros1 domains. We also tested the efficacy of ROS1-targeted tyrosine kinase inhibitors (TKI) in these model systems; our data show dose-dependent suppression of Notch1-Ros1 driven cellular activity and concurrent inhibition of tumor growth as well as prolonged survival after oral monotherapy.Overall, this study reveals the first known NOTCH1-ROS1 alteration in a case of pAs. Given the extreme rarity of this malignant disease, it is challenging to expand to a larger cohort in a short duration. However, our findings on the mechanistic underpinnings of Notch1-ROS1 provide a deeper understanding of how this novel fusion drives tumor growth. Furthermore, drug-targeting studies provide requisite preclinical evidence for the possibility of utilizing ROS1-TKI in pA patients harboring this or other ROS1-fusions. Overall, these data suggest that ongoing genomic profiling of these rare tumors may reveal actionable drivers and holds the promise to improve patient outcomes.

Citation Format: Payal Jain, Sudarshan Iyer, Joshua Straka, Lea Surrey, Jennifer Pogoriler, Tiffany Smith, Christine Busch, Marilyn Li, Elizabeth Fox, Adam C. Resnick, Monika Davare, Angela J. Waanders. Novel NOTCH1-ROS1 gene fusion drives distinct molecular mechanisms in a rare pediatric angiosarcoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3644.

Abstract 3667: The Pediatric Brain Tumor Atlas - Transforming the landscape of research

The Pediatric Brain Tumor Atlas (PBTA) is a cloud-based, cross-platform, and data-rich collaborative effort to accelerate discoveries for therapeutic intervention in children diagnosed with brain tumors. Pediatric brain tumors are the leading cause of disease-related death in children and despite advances in therapy, morbidity and mortality rates remain poor. There have been large scale efforts to genomically profile these cancers in the past, however public access to the resulting datasets are limited at best. In contrast, the PBTA, created as a multi-center effort by Children’s Brain Tumor Tissue Consortium (CBTTC) and Pacific Pediatric Neuro-Oncology Consortium (PNOC), has a goal of characterizing over 1,600 pediatric brain tumor samples and making the data publicly available to cancer researchers world-wide. PBTA comprises comprehensive clinical data in addition to whole exome sequencing, whole genome sequencing (WGS), RNA sequencing (RNASeq), miRNA sequencing, and proteomics. To address the need to inform novel discovery and clinical implementation of genomic approaches for diagnostic/therapeutic purposes, PBTA utilizes a cloud-based scientific environment, the CAVATICA portal. CAVATICA provides near real-time integration, dissemination, processing, and sharing of associated PetaByte-sized data by leveraging Amazon Web Services and powerful genomic workflows. It also enables dbGaP approved users to access TCGA and other datasets hosted by NCI’s Cancer Genomics’ Cloud, allowing for cross-disease studies. While CAVATICA manages raw sequencing data, processed annotations and biospecimen querying is enabled for PBTA via PedcBioPortal, a data visualization/analysis application further integrating additional public and deposited datasets. PBTA data can further be accessed via the KidsFirst platform, which integrates both CAVATICA and PedcBioPortal, and allows for querying of cancer and non-cancer genomic data for subsequent analytics, visualization, and discovery. The 1st dataset release of PBTA occurred on September 10th, 2018. In this release there are over 30 different types of pediatric brain tumors representing over 1,000 subjects. This data is available on CAVATICA, KidsFirst, and PedcBioPortal and users can seamlessly move between applications. Data types include those for matched tumor/normal samples, such as WGS, RNASeq, proteomics, longitudinal clinical data, imaging data (MRIs and radiology reports), histology slide images, and pathology reports. CBTTC/PNOC promote real time data release with no embargo period, allowing PBTA to have is up-to-date data releases with no embargo. The combination of cloud-based analytic platforms such as KidsFirst/CAVATICA/PedcBioPortal with data from both genomics and clinical practice serves to define a new paradigm for pediatric cancer research and collaborative discovery.

Citation Format: Yuankun Zhu, Yiran Guo, Allison P. Heath, Pichai Raman, Elizabeth Appert, Jennifer Mason, Bo Zhang, Karthik Kalletla, Miguel A. Brown, Natasha Singh, Bailey K. Farrow, Parimala Killada, Meen Chul Kim, Alex Felmeister, Mateusz P. Koptyra, Sabine Mueller, Michael Prados, Jena V. Lilly, Rishi Lulla, Adam C. Resnick, Javad Nazarian, Phillip B. Storm, Angela J. Waanders. The Pediatric Brain Tumor Atlas - Transforming the landscape of research [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3667.

A pilot precision medicine trial for children with diffuse intrinsic pontine glioma-PNOC003: A report from the Pacific Pediatric Neuro-Oncology Consortium

This clinical trial evaluated whether whole exome sequencing (WES) and RNA sequencing (RNAseq) of paired normal and tumor tissues could be incorporated into a personalized treatment plan for newly diagnosed patients (<25 years of age) with diffuse intrinsic pontine glioma (DIPG). Additionally, whole genome sequencing (WGS) was compared to WES to determine if WGS would further inform treatment decisions, and whether circulating tumor DNA (ctDNA) could detect the H3K27M mutation to allow assessment of therapy response. Patients were selected across three Pacific Pediatric Neuro-Oncology Consortium member institutions between September 2014 and January 2016. WES and RNAseq were performed at diagnosis and recurrence when possible in a CLIA-certified laboratory. Patient-derived cell line development was attempted for each subject. Collection of blood for ctDNA was done prior to treatment and with each MRI. A specialized tumor board generated a treatment recommendation including up to four FDA-approved agents based upon the genomic alterations detected. A treatment plan was successfully issued within 21 business days from tissue collection for all 15 subjects, with 14 of the 15 subjects fulfilling the feasibility criteria. WGS results did not significantly deviate from WES-based therapy recommendations; however, WGS data provided further insight into tumor evolution and fidelity of patient-derived cell models. Detection of the H3F3A or HIST1H3B K27M (H3K27M) mutation using ctDNA was successful in 92% of H3K27M mutant cases. A personalized treatment recommendation for DIPG can be rendered within a multicenter setting using comprehensive next-generation sequencing technology in a clinically relevant timeframe.

Purification of mRNA Encoding Chimeric Antigen Receptor Is Critical for Generation of a Robust T-Cell Response

T cells made with messenger RNA (mRNA) encoding chimeric antigen receptor (CAR) offer a safe alternative to those transduced with viral CARs by mitigating the side effects of constitutively active T cells. Previous studies have shown that mRNA CAR T cells are transiently effective but lack persistence and potency across tumor types. It was hypothesized that the efficacy of mRNA CARs could be improved by utilizing recent advancements in RNA technology, such as incorporating a modified nucleoside, 1-methylpseudouridine, into the mRNA and applying a novel purification method using RNase III to eliminate dsRNA contaminants. T cells electroporated with nucleoside-modified and purified mRNA encoding CD19 CAR showed an initial twofold increase in CAR surface expression, as well as a twofold improvement in cytotoxic killing of leukemia cells that persisted up to 5 days. T cells generated with nucleoside-modified and purified CAR mRNA also showed reduced expression of checkpoint regulators and a differential pattern of genetic activation compared to those made with conventional mRNA. In vivo studies using a leukemia mouse model revealed that the most robust 100-fold suppression of leukemic burden was achieved using T cells electroporated with purified mRNAs, regardless of their nucleoside modification. The results provide a novel approach to generate mRNA for clinical trials, and poise mRNA CAR T cells for increased efficacy during testing as new CAR targets emerge.

Molecular, Pathological, Radiological, and Immune Profiling of Non-brainstem Pediatric High-Grade Glioma from the HERBY Phase II Randomized Trial

The HERBY trial was a phase II open-label, randomized, multicenter trial evaluating bevacizumab (BEV) in addition to temozolomide/radiotherapy in patients with newly diagnosed non-brainstem high-grade glioma (HGG) between the ages of 3 and 18 years. We carried out comprehensive molecular analysis integrated with pathology, radiology, and immune profiling. In post-hoc subgroup analysis, hypermutator tumors (mismatch repair deficiency and somatic POLE/POLD1 mutations) and those biologically resembling pleomorphic xanthoastrocytoma ([PXA]-like, driven by BRAF_V600E or NF1 mutation) had significantly more CD8+ tumor-infiltrating lymphocytes, and longer survival with the addition of BEV. Histone H3 subgroups (hemispheric G34R/V and midline K27M) had a worse outcome and were immune cold. Future clinical trials will need to take into account the diversity represented by the term "HGG" in the pediatric population.

Pediatric low-grade gliomas: next biologically driven steps

Despite the fact that they are not typically life-threatening, low-grade gliomas (LGGs) remain a significant clinical challenge in pediatric neuro-oncology due to comorbidities associated with these tumors and/or their treatments, and their propensity to multiply recurs. LGGs, in total the most common brain tumors arising in childhood, can often become a chronic problem requiring decades of management. The Second International Consensus Conference on Pediatric Low-Grade Gliomas held in Padua, Italy in 2016 was convened in an attempt to advance the pace of translating biological discoveries on LGGs into meaningful clinical benefit. Topics discussed included: the implications of our growing biological understanding of the genomics underlying these tumors; the assessment of the model systems available; the implications of the molecular and histopathologic differences between adult and pediatric diffuse gliomas; and steps needed to expedite targeted therapy into late-stage clinical trials for newly diagnosed cases. Methods for the diagnostic assessment of alterations in the Ras/mitogen-activated protein kinase pathway, typical for these tumors, were also considered. While the overall tone was positive, with a consensus that progress is being and will continue to be made, the scale of the challenge presented by this complex group of tumors was also acknowledged. The conclusions and recommendations of the meeting panel are provided here as an outline of current thinking and a basis for further discussion.

Integrated Molecular Meta-Analysis of 1,000 Pediatric High-Grade and Diffuse Intrinsic Pontine Glioma

We collated data from 157 unpublished cases of pediatric high-grade glioma and diffuse intrinsic pontine glioma and 20 publicly available datasets in an integrated analysis of >1,000 cases. We identified co-segregating mutations in histone-mutant subgroups including loss of FBXW7 in H3.3G34R/V, TOP3A rearrangements in H3.3K27M, and BCOR mutations in H3.1K27M. Histone wild-type subgroups are refined by the presence of key oncogenic events or methylation profiles more closely resembling lower-grade tumors. Genomic aberrations increase with age, highlighting the infant population as biologically and clinically distinct. Uncommon pathway dysregulation is seen in small subsets of tumors, further defining the molecular diversity of the disease, opening up avenues for biological study and providing a basis for functionally defined future treatment stratification.

Overcoming resistance to single-agent therapy for oncogenic BRAF gene fusions via combinatorial targeting of MAPK and PI3K/mTOR signaling pathways

Pediatric low-grade gliomas (PLGGs) are frequently associated with activating BRAF gene fusions, such as KIAA1549-BRAF, that aberrantly drive the mitogen activated protein kinase (MAPK) pathway. Although RAF inhibitors (RAFi) have been proven effective in BRAF-V600E mutant tumors, we have previously shown how the KIAA1549-BRAF fusion can be paradoxically activated by RAFi. While newer classes of RAFi, such as PLX8394, have now been shown to inhibit MAPK activation by KIAA1549-BRAF, we sought to identify alternative MAPK pathway targeting strategies using clinically relevant MEK inhibitors (MEKi), along with potential escape mechanisms of acquired resistance to single-agent MAPK pathway therapies. We demonstrate effectiveness of multiple MEKi against diverse BRAF-fusions with novel N-terminal partners, with trametinib being the most potent. However, resistance to MEKi or PLX8394 develops via increased RTK expression causing activation of PI3K/mTOR pathway in BRAF-fusion expressing resistant clones. To circumvent acquired resistance, we show potency of combinatorial targeting with trametinib and everolimus, an mTOR inhibitor (mTORi) against multiple BRAF-fusions. While single-agent mTORi and MEKi PLGG clinical trials are underway, our study provides preclinical rationales for using MEKi and mTORi combinatorial therapy to stave off or prevent emergent drug-resistance in BRAF-fusion driven PLGGs.

CRAF gene fusions in pediatric low-grade gliomas define a distinct drug response based on dimerization profiles

Pediatric low-grade gliomas (PLGGs) are commonly associated with BRAF gene fusions that aberrantly activate the mitogen-activated protein kinase (MAPK) signaling pathway. This has led to PLGG clinical trials utilizing RAF- and MAPK pathway-targeted therapeutics. Whole-genome profiling of PLGGs has also identified rare gene fusions involving another RAF isoform, CRAF/RAF1, in PLGGs and cancers occuring in adults. Whereas BRAF fusions primarily dysregulate MAPK signaling, the CRAF fusions QKI-RAF1 and SRGAP3-RAF1 aberrantly activate both the MAPK and phosphoinositide-3 kinase/mammalian target of rapamycin (PI3K/mTOR) signaling pathways. Although ATP-competitive, first-generation RAF inhibitors (vemurafenib/PLX4720, RAFi) cause paradoxical activation of the MAPK pathway in BRAF-fusion tumors, inhibition can be achieved with ‘paradox breaker’ RAFi, such as PLX8394. Here we report that, unlike BRAF fusions, CRAF fusions are unresponsive to both generations of RAFi, vemurafenib and PLX8394, highlighting a distinct responsiveness of CRAF fusions to clinically relevant RAFi. Whereas PLX8394 decreased BRAF-fusion dimerization, CRAF-fusion dimerization is unaffected primarily because of robust protein–protein interactions mediated by the N-terminal non-kinase fusion partner, such as QKI. The pan-RAF dimer inhibitor, LY3009120, could suppress CRAF-fusion oncogenicity by inhibiting dimer-mediated signaling. In addition, as CRAF fusions activate both the MAPK and PI3K/mTOR signaling pathways, we identify combinatorial inhibition of the MAPK/mTOR pathway as a potential therapeutic strategy for CRAF-fusion-driven tumors. Overall, we define a mechanistic distinction between PLGG-associated BRAF- and CRAF/RAF1 fusions in response to RAFi, highlighting the importance of molecularly classifying PLGG patients for targeted therapy. Furthermore, our study uncovers an important contribution of the non-kinase fusion partner to oncogenesis and potential therapeutic strategies against PLGG-associated CRAF fusions and possibly pan-cancer CRAF fusions.

Abstract LB-008: The Pediatric Brain Tumor Atlas: building an integrated, multi-platform data-rich ecosystem for collaborative discovery in the cloud

Pediatric brain tumors are the leading cause of disease-related death in children. However, despite large scale data-driven efforts for pediatric cancers by the NIH (e.g. TARGET, Therapeutically Applicable Research To Generate Effective Treatments), public access to large-scale pediatric brain tumor genomic data remains limited. As a result, precision medicine initiatives and clinical trials in pediatric brain tumors are hampered by the absence of publicly available genomic resources that can dynamically inform novel discovery and clinical implementation of genomic and molecular approaches for diagnostic and therapeutic purposes in affected children. The Pediatric Brain Tumor Atlas is a concerted multi-institution effort by the Children’s Brain Tumor Consortium (CBTTC) and the Pacific Pediatric Neuro-Oncology Consortium to characterize and deeply profile a newly defined cohort of &gt;1600 brain tumor samples across diverse histopathologies via a combination of whole exome sequencing, whole genome sequencing, RNA sequencing and limited proteomic analysis. Importantly, the Atlas initiative provides for near real-time integration, dissemination, and sharing of the associated raw and analyzed data through an ecosystem of data discovery platforms. As data of this size and complexity require a bolus of scalable computational power and storage, a new cloud-based collaborative scientific environment termed CAVATICA (cavatica.org) has been launched to support integrative analysis and open access to data alongside shared computation and algorithms that empower users to further integrate and analyse their own uploaded data. Importantly, CAVATICA provides further portal access to dbGaP approved users to TCGA and other NCI datasets hosted by the NCI’s Cancer Genomics’ Cloud. Additionally, it provides for scalable integration of these and additional disease-specific datasets on the platform via transdisciplinary analyses. Currently, one of the biggest barriers and challenges to collaborative research in large datasets is the transfer and processing of ‘big data’. By committing to the rapid release of these large pediatric brain tumor data and their deposition in CAVATICA’s cloud-based environment supporting shared pipelines, computation, and visualizations, PNOC and the CBTTC’s collaborating membership are seeking to provide a centralized, collaborative rapid discovery environment for researchers to engage new discovery and data reuse. In addition to unprocessed genomic, whole genome and RNA sequencing data in CAVATICA, processed annotations and and additional biospecimen querying is enabled for the Pediatric Brain Tumor Atlas via PedcBioPortal (PedcBioPortal.org), a data visualization and analysis application further integrating across additional public and deposited datasets. The combination of large-scale genomic data and integrative cloud-based analytic platforms with what is one of the largest genomic date cohorts to date for pediatric brain tumors serves to define a new paradigm for pediatric cancer research and collaborative discovery.

Citation Format: Adam C. Resnick, Phillip B. Storm, Angela J. Waanders, Jena V. Lilly, Rishi R. Lulla, Sabine Mueller, Michael Prados, Leonard S. Sender, Allison Heath, Alex S. Felmeister, Anthony Cros, Yuankun Zhu, Pichai Raman. The Pediatric Brain Tumor Atlas: building an integrated, multi-platform data-rich ecosystem for collaborative discovery in the cloud [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr LB-008. doi:10.1158/1538-7445.AM2017-LB-008

Abstract 4887: Comprehensive molecular analysis of pediatric thalamic tumors

Childhood thalamic tumors are relatively rare cancers, accounting for 5% of all pediatric brain tumors and categorized as midline gliomas such as diffuse intrinsic pontine gliomas (DIPGs). We and others have shown that mutations in genes encoding for histone 3.3 (H3F3A), histone 3.2 (HIST2H3C) and histone 3.1 (HIST1H3B) along with their obligate partner mutations are the major driver mutations in DIPGs. Where recent studies have identified major histone partner mutations associated with DIPGs, more research is required to provide a clear landscape of genomic aberrations associated with thalamic tumors. We hypothesize that comprehensive whole genome sequence, methylation and proteome analysis of a large cohort of thalamic tumors will map differentially regulated pathways and identify potential novel driver and obligate partner mutations associated with thalamic gliomas. We have established a cohort (CNHS and CBTTC) of 128 thalamic specimens, including 56 pediatric and adolescent primary thalamic tumors with median age at diagnosis of 5.6 years (range 0-20 years); 40 normal controls with matched age and gender; and 32 midline tumors with potential thalamic involvement with median age at diagnosis of 7.6 years (range 0-19 years). Our cohort of primary thalamic tumors contained 31 (55.3%) and 19 (33.9%) tumors reviewed as high and low grade gliomas, respectively. From our midline tumors with potential thalamic involvement, 22 (68.7%) were classified as primary DIPG and 10 (31.2%) were other midline gliomas. Where available, MRI reviews and histopathological analysis were performed. Preliminary results showed that 7 of the extended tumors presented hypercellularity and positive histone 3 K27M staining, confirming that these tumors in fact extended to the thalamus as MRI showed. Additionally, Whole Exome Sequencing (WES) from one DIPG sample extending to the thalamus showed the same mutations found on the primary pons tumor: H3.1 K27M; ACVR1 G328V; PIK3CA H1047R; MAX R51Q and PTEN A126S. The remaining primary and extended thalamic tumors will be analyzed by WES to understand the molecular changes associated with this disease. In addition to our results, we analyzed the genomic landscape from pediatric thalamic tumors previously published (188), showing H3.3/H3.1 K27M (51%); BRAF (10.6%) and TP53 (8%) as the most frequent mutations among thalamic high and low grade astrocytomas. Further studies will allow us to compare comprehensive molecular analysis of thalamic tumors (primary and metastatic) and non-thalamic midline tumors (specimen and data already in hand) and identify similarities and differences in genomic, epigenomic and proteomic expression pattern which may guide a better characterization of thalamic tumor as a separate entity.

Citation Format: Heloisa H. Moser, Susanne Yoon, Madhuri Kambhampati, Sridevi Yadavilli, Angela J. Waanders, Adam Resnick, Roger J. Packer, Javad Nazarian. Comprehensive molecular analysis of pediatric thalamic tumors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4887. doi:10.1158/1538-7445.AM2017-4887

BRAF Status in Personalizing Treatment Approaches for Pediatric Gliomas

PURPOSE

Alteration of the BRAF/MEK/MAPK pathway is the hallmark of pediatric low-grade gliomas (PLGGs), and mTOR activation has been documented in the majority of these tumors. We investigated combinations of MEK1/2, BRAF^V600E and mTOR inhibitors in gliomas carrying specific genetic alterations of the MAPK pathway.

EXPERIMENTAL DESIGN

We used human glioma lines containing BRAF^V600E (adult high-grade: AM-38, DBTRG, PLGG: BT40), or wild-type BRAF (pediatric high-grade: SF188, SF9427, SF8628) and isogenic systems of KIAA1549:BRAF-expressing NIH/3T3 cells and BRAF^V600E-expressing murine brain cells. Signaling inhibitors included everolimus (mTOR), PLX4720 (BRAF^V600E), and AZD6244 (MEK1/2). Proliferation was determined using ATP-based assays. In vivo inhibitor activities were assessed in the BT40 PLGG xenograft model.

RESULTS

In BRAF^V600E cells, the three possible doublet combinations of AZD6244, everolimus, and PLX4720 exhibited significantly greater effects on cell viability. In BRAF^WT cells, everolimus + AZD6244 was superior compared with respective monotherapies. Similar results were found using isogenic murine cells. In KIAA1549:BRAF cells, MEK1/2 inhibition reduced cell viability and S-phase content, effects that were modestly augmented by mTOR inhibition. In vivo experiments in the BRAF^V600E pediatric xenograft model BT40 showed the greatest survival advantage in mice treated with AZD6244 + PLX4720 (P < 0.01).

CONCLUSIONS

In BRAF^V600E tumors, combination of AZD6244 + PLX4720 is superior to monotherapy and to other combinatorial approaches. In BRAF^WT pediatric gliomas, everolimus + AZD6244 is superior to either agent alone. KIAA1549:BRAF-expressing tumors display marked sensitivity to MEK1/2 inhibition. Application of these results to PLGG treatment must be exercised with caution because the dearth of PLGG models necessitated only a single patient-derived PLGG (BT40) in this study. Clin Cancer Res; 22(21); 5312-21. ©2016 AACR.

Whole Chromosome 7 Gain Predicts Higher Risk of Recurrence in Pediatric Pilocytic Astrocytomas Independently From KIAA1549-BRAF Fusion Status

The most frequent genetic alteration identified in pediatric pilocytic astrocytomas and pilomyxoid variant is the KIAA1549-BRAF fusion, which typically results from a 2.0 Mb tandem duplication in chromosome band 7q34. Less frequent abnormalities include fusion genes,BRAF, FGFR, KRAS, and NF1 point mutations, and whole chromosome gains. To correlate genetic alterations with clinical course data, we retrospectively analyzed the tumors with pilocytic and pilomyxoid histology of a cohort of 116 pediatric patients, aged 5 months to 23 years. Gross total resection was associated with a decreased risk of recurrence (p = 0.001), supporting previous findings that complete tumor excision correlates with long-term and disease-free survival. We found no significant association between recurrence rate and the presence of the KIAA1549-BRAF fusion or BRAF mutation (p = 0.167). Interestingly, gain of whole chromosome 7 (WC7) was associated with a 4.7-fold increased risk of tumor recurrence, even after adjusting for surgical status (p = 0.025), and other genetic alterations. Using fluorescence in situ hybridization, we demonstrated that when WC7 gain accompanies the KIAA1549-BRAF fusion, the fusion likely arises first. This study highlights the utility of genetic studies for risk assessment of pilocytic and pilomyxoid astrocytomas, which may impact treatment selections.