bluuebunny/crossref_metadata_2025 huggingface dataset:
On planetary systems as ordered sequences
Authors: Sandford Emily , Kipping David , Collins Michael
Published: June 2021

A planetary system consists of a host star and one or more planets, arranged into a particular configuration. Here, we consider what information belongs to the configuration, or ordering, of 4286 Kepler planets in their 3277 planetary systems. First, we train a neural network model to predict the radius and period of a planet based on the properties of its host star and the radii and period of its neighbours. The mean absolute error (MAE) of the predictions of the trained model is a factor of 2.1 better than the MAE of the predictions of a naive model that draws randomly from dynamically allowable periods and radii. Secondly, we adapt a model used for unsupervised part-of-speech tagging in computational linguistics to investigate whether planets or planetary systems fall into natural categories with physically interpretable ‘grammatical rules.’ The model identifies two robust groups of planetary systems: (1) compact multiplanet systems and (2) systems around giant stars (log g ≲ 4.0), although the latter group is strongly sculpted by the selection bias of the transit method. These results reinforce the idea that planetary systems are not random sequences – instead, as a population, they contain predictable patterns that can provide insight into the formation and evolution of planetary systems.
On the dark matter haloes of optical and IR-selected AGNs in the local universe
Authors: Alpaslan Mehmet , Tinker Jeremy L
Published: June 2021

We use the technique of total satellite luminosity, Lsat, to probe the dark matter haloes around active galactic nuclei (AGNs) in the SDSS Main Galaxy Sample. Our results focus on galaxies and AGNs that are the central galaxy of their halo. Our two AGN samples are constructed from optical emission-line diagnostics and from Wide-Field Infrared Survey Explorer (WISE) infrared colours. Both optically selected and WISE-selected AGN have Lsat values twice as high as non-active galaxy samples when controlling for stellar mass and mean stellar age. This implies that the haloes are twice as massive, but we cannot rule out that the increase in Lsat is due to these AGNs residing in younger haloes at the same mass. When only controlling for host galaxy stellar mass, WISE-selected AGNs also have higher Lsat values than optical AGNs at the factor of two level, consistent with previous results comparing the clustering of obscured and unobscured AGNs. However, controlling for stellar age in the two populations of host galaxies removes half of this difference, attenuating the statistical significance of the difference. We perform permutation tests to quantify the difference in the halo populations of each sample. The difference in star formation properties does not fully explain the difference in the two AGN populations, however. Although AGN luminosity correlates with mean stellar age, the difference in stellar age between the WISE and optical samples cannot be fully explained by differences in their AGN luminosity distributions.
Flexible analysis of TSS mapping data and detection of TSS shifts with TSRexploreR
Authors: Policastro Robert A , McDonald Daniel J , Brendel Volker P , Zentner Gabriel E
Published: June 2021

Heterogeneity in transcription initiation has important consequences for transcript stability and translation, and shifts in transcription start site (TSS) usage are prevalent in various developmental, metabolic, and disease contexts. Accordingly, numerous methods for global TSS profiling have been developed, including most recently Survey of TRanscription Initiation at Promoter Elements with high-throughput sequencing (STRIPE-seq), a method to profile transcription start sites (TSSs) on a genome-wide scale with significant cost and time savings compared to previous methods. In anticipation of more widespread adoption of STRIPE-seq and related methods for construction of promoter atlases and studies of differential gene expression, we built TSRexploreR, an R package for end-to-end analysis of TSS mapping data. TSRexploreR provides functions for TSS and transcription start region (TSR) detection, normalization, correlation, visualization, and differential TSS/TSR analyses. TSRexploreR is highly interoperable, accepting the data structures of TSS and TSR sets generated by several existing tools for processing and alignment of TSS mapping data, such as CAGEr for Cap Analysis of Gene Expression (CAGE) data. Lastly, TSRexploreR implements a novel approach for the detection of shifts in TSS distribution.
What is visible across the visual field?
Authors: Haun Andrew M
Published: June 2021

It is sometimes claimed that because the resolution and sensitivity of visual perception are better in the fovea than in the periphery, peripheral vision cannot support the same kinds of colour and sharpness percepts as foveal vision. The fact that a scene nevertheless seems colourful and sharp throughout the visual field then poses a puzzle. In this study, I use a detailed model of human spatial vision to estimate the visibility of certain properties of natural scenes, including aspects of colourfulness, sharpness, and blurriness, across the visual field. The model is constructed to reproduce basic aspects of human contrast and colour sensitivity over a range of retinal eccentricities. I apply the model to colourful, complex natural scene images, and estimate the degree to which colour and edge information are present in the model’s representation of the scenes. I find that, aside from the intrinsic drift in the spatial scale of the representation, there are not large qualitative differences between foveal and peripheral representations of ‘colourfulness’ and ‘sharpness’.
ATRT-04. CORRELATION OF CLINICOPATHOLOGIC FEATURES AND CUMULATIVE INCIDENCE OF RELAPSE FOR PATIENTS WITH ATYPICAL TERATOID RHABDOID TUMOR ON ACNS0333: A REPORT FROM THE CHILDREN’S ONCOLOGY GROUP
Authors: Reddy Alyssa , Biegel Jaclyn , Huang Annie , Strother Douglas , Judkins Alexander , Pollack Ian , Buxton Allen , Mahajan Anita , Ho Ben , Mazewski Claire , Lewis Victor , Fouladi Maryam , Krailo Mark
Published: June 2021

Purpose

Intensive multi-modal regimens have improved survival for patients with atypical teratoid rhabdoid tumor, however relapse rates remain high. A better understanding of clinical and pathologic features associated with tumor relapse is critical to risk-stratifying patients.

Patients and Methods

ACNS0333 treatment consisted of multi-agent chemotherapy, high-dose chemotherapy, and radiation therapy, lasting approximately 6 months. Variables including patient age, sex, tumor location, M-stage, degree of resection, order of therapy, germline status, and molecular subgroup were analyzed. Cumulative incidence (CI) of event free survival due to relapse was evaluated for each variable.

Results

Thirty-three of 65 evaluable patients had tumor relapse. For the entire cohort, the CI of relapse was 21.8% at 6 months, 40.6% at one year and 50.3% at 4 years. For patients with infratentorial tumors, CI of relapse was 26.3%, 34.2% and 37.2%, at 6 months, 1 and 4 years respectfully compared to 15.3%, 49.9%, and 69.7% for those with supratentorial tumors (p 0.051). Patients with SHH subtype had no relapses in the first 6 months and CI of relapse of 37.5% at 4 years, while those with TYR and MYC subgroups had CI of relapse of 33.3% and 26.7% at 6 months and 46.3% and 73.3% at 4 years respectfully (p 0.088). Patients with germline mutations had a cumulative incidence of relapse of 20% at 6 months and 60% at 12 months compared to 22.6% and 37.7% respectfully for those without. No obvious trends were noted based on other analyzed variables.

Conclusions

ACNS0333 was not powered to determine prognostic indicators of relapse, however, this data suggest interesting trends based on tumor location, subtype and germline status. Infratentorial location and SHH subtype maybe associated with lower risk of relapse. Larger data sets must be compiled to further investigate these variables, perform multivariate analyses and inform risk-stratification on future trials.
ATRT-08. TARGETING THE TP53-MDM2 ENHANCES RADIATION SENSITIVITY IN ATRT
Authors: Alimova Irina , Danis Etienne , Wang Dong , Pierce Angela , Serkova Natalie , Venkataraman Sujatha , Vibahakar Rajeev
Published: June 2021

Atypical Teratoid Rhabdoid Tumor is a highly aggressive pediatric brain tumor. Despite radiation, aggressive chemotherapy and autologous stem cell rescue, the children usually have poor survival. A functional genomic screen identified the TP53-MDM2 axis as a therapeutic vulnerability in ATRT. Gene expression demonstrates that all ATRT sub-groups have high level of MDM2 a negative regulator of p53. We demonstrate that MDM2 inhibition by shRNA or with small-molecule drugs, Nutlin3 and Idasanutlin resulted in decreased ATRT cell growth, inhibition of clonogenic potential and induction of apoptosis in vitro and in vivo. MRI imaging of intracranial tumors shows that Apparent Diffusion Coefficient (ADC), a good marker for successful treatment, significantly increased with Idasanutlin treatment showing tumor necrosis. Moreover, Idasanutlin significantly decreased growth of intracranial orthotopic ATRT brain tumors as evaluated by T2 MRI imaging and prolonged survival compared to control animals. Further idasanutlin potentiated radiation induced DNA damage and increased sensitivity to radiaton of ATRT cells. These findings highlight the TP53-MDM2 axis as a rational therapeutic target in ATRT.
BIOL-09. HNRNPA1 SPLICED VARIANT: KEY RESISTANT GENE SIGNATURE IN GLIOMAS
Authors: Yadav Ajay
Published: June 2021

Glioblastoma is inevitably a recurrent cancer. Despite of recent advancement, temozolomide remain the prescribed lifeline drug, after the surgery. Inadvertently, MGMT (O6-methylguanine-DNA-methyltransferase) expression mechanistically linked with Temozolomide (alkylating drug) glioma resistant development. To understand the resistant against Temozolomide sought to deciphered, by making invitro drug resistant glioma cell lines. RNA seq analysis over a illumina platform; drug resistant glioma cell lines showed various critical key factor such as splice factor hnRNPA1 and deubiquitinating enzymes were showed to highly upregulated in resistant cell lines. Commonly, from our previous study, the stability of hnRNPA1 in presence of USP5 were showed to promote cell survival, whereas knocking down of USP5 significantly lower down the telomerase activity and NAD/NADH ratio enlarge. Furthermore, expression of MGMT was showed significantly downregulated in hnRNPA1 knock down T98G glioma cells, as well as in U87 Temozolomide resistant cells. Extrinsic apoptosis pathway was showed more prevalent in hnRNPA1 knock down glioma cells in presence of Trail ligand. Interestingly, we found one more spliced variants of hnRNPA1 exclusively expressing in drug resistant cells is new finding. Selectively knocking down of hnRNPA1 splice variant promotes apoptosis. RNA seq analysis followed the comparison between two hnRNPA1 spliced variant knock down, drug resistant glioma cell lines showed differentially expressed transcript support our finding to be distinctly regulated by hnRNPA1 spliced variants. Spliced variant of hnRNPA1 showed a potential therapeutic candidate signature.
EMBR-25. GENOME-WIDE GENETIC AND EPIGENETIC ASSESSMENT OF GROUP 4 MEDULLOBLASTOMA FOR IMPROVED, BIOMARKER DRIVEN, PROGNOSTICATION AND RISK-STRATIFICATION
Authors: Goddard Jack , Castle Jemma , Southworth Emily , Crosier Stephen , Martin-Guerrero Idoia , Garcia-Ariza Miguel , Navajas Aurora , Bourdeaut Franck , Dufour Christelle , Goschzik Tobias , Pietsch Torsten , Williamson Dan , Bailey Simon , Schwalbe Ed , Clifford Steven , Hicks Debbie
Published: June 2021

Introduction

Medulloblastoma (MB) is the most common malignant brain tumour in children. The most frequent molecular subgroup, Group 4 (MBGrp4) accounts for ~35/40% of cases, however it has the least understood underlying biology. Clinical outcomes are heterogeneous in MBGrp4 and are not accounted for by established clinico-pathological risk factors. There is now a requirement for a comprehensive study of MBGrp4, considering established clinico-pathological features and novel molecular biomarkers to enhance risk-stratification and identify novel therapeutic targets.

Methods

A clinically-annotated, retrospective MBGrp4 discovery cohort (n = 420) was generated from UK CCLG institutions, collaborating European centres and SIOP-UKCCSG-PNET3 and HIT-SIOP-PNET4 clinical trials. Contemporary, multi-omics profiling was performed. Focal and arm level copy number aberrations (CNAs) were determined from molecular inversion probe (MIP) or DNA methylation array which additionally provided next generation non-WNT/non-SHH (Grp3/Grp4) subtype classifications. Targeted next-generation DNA sequencing was performed to overlay the mutational landscape. Survival modelling was carried out with patients >3 years old who received craniospinal irradiation.

Results

MBGrp4 subtypes were assigned to 88% of tumours with available data. Subtype VIII was strongly associated with i17q (p<0.0001). The favourable-risk cytogenetic signature (2 or 3 of; chromosome 7 gain, chromosome 8 loss and/or chromosome 11 loss) associated with both subtypes VI and VII (p<0.0001). MYCN amplifications were strongly associated with subtype V (p<0.0001) in addition to 16q loss (p<0.0001). The high-risk CNA group was enriched for mutations in genes involved in chromatin remodelling (p<0.0001). Risk factors were identified from multivariate survival modelling. Subtype and CNA groups contributed to improved risk-stratification models that outperformed current clinical schemes.

Conclusion

Comprehensive genetic and epigenetic profiling in this large retrospective cohort has improved our understanding of the molecular and clinical heterogeneity within MBGrp4. Incorporation of molecular biomarkers improved risk-stratification for MBGrp4.
EMBR-29. PEDIATRIC MEDULLOBLASTOMA PATIENT WITH MULTIPLE MIDLINE DEFECTS, A CASE REPORT
Authors: Peck Sydney , Owens Emily , Smith Amy
Published: June 2021

Medulloblastoma (MB) is the most common malignant central nervous system (CNS) cancer diagnosed in childhood and is divided into four subtypes: WNT-activated, SHH-activated, Group 3 (Non-WNT, Non-SHH), and Group 4 (Non-WNT, Non-SHH). Non-WNT/Non-SHH make up roughly two-thirds of MB and have the least understood pathogenesis with substantial intratumoral heterogeneity. Therapeutic targets and treatment strategies for Group 3 and 4 patients therefore remain unclear. In this report we present a 16-year-old patient with standard risk Group 4 medulloblastoma and multiple midline defects. The patient’s medical history was remarkable for a cleft lip (which healed in utero), a notable heart murmur, an inguinal hernia repair at 3 months of age, and significant pectus excavatum. This patient was diagnosed at age 12 with a MB. Tumor cells were negative for GAB-1, p53 stain was positive for approximately 1–2% of tumor cells, no evidence on monosomy 6, MYC or MYCN amplification. The family history is significant for paternal biliary cancer. The patient was treated as per ACNS0331 and is approximately 36 months off-therapy. This case presents an interesting instance of a CNS tumor arising within the microenvironment of wide-spread dysregulated development. Single cases do not provide any substantiative evidence. However, they do give insight on factors which may drive oncogenesis and may provide an indication as to whether we should continue to pursue targeted therapy for Group 3/4 uniformly or move towards personalized therapy strategies in this group patients.
EPEN-01. C11ORF95-RELA DICTATES ONCOGENIC TRANSCRIPTIONAL PROGRAMS TO DRIVE AGGRESSIVE SUPRATENTORIAL EPENDYMOMA
Authors: Arabzade Amir , Zhao Yanhua , Varadharajan Srinidhi , Chen Hsiao-Chi , Bertrand Kelsey , Deneen Benjamin , Mack Stephen
Published: June 2021

Over 60% of supratentorial (ST) ependymomas harbor a gene fusion between C11orf95, an uncharacterized gene, and RELA (also known as p65), a main component of the NF-ĸB family of transcription factors. While its sufficiency to drive tumor has been established, the mechanism of tumorigenesis remains elusive. To tackle this question, we developed a natively forming mouse tumor model using in utero electroporation (IUE) of the embryonic mouse brain and performed integrative epigenomic and transcriptomic mapping. Our findings indicate that in addition to direct canonical NF-ĸB pathway activation, C11orf95-RELA (CRfus) dictates a neoplastic transcriptional program and binds to unique sites across the genome enriched with Plagl family transcription factor motifs. CRfus modulates the transcriptional landscape by recruiting transcription co-activators (Brd4, EP300, Cbp, Pol2) which are amenable to pharmacologic inhibition. Downstream CRfus target genes converge on developmental programs marked by Plagl family of transcription factors and activate neoplastic programs enriched in Mapk, focal adhesion, and gene imprinting networks, many of which contain previously unreported therapeutic leads in C11orf95-RELA ependymoma.
EPEN-06. CELL ECOSYSTEM AND SIGNALING PATHWAYS OF PRIMARY AND METASTATIC PEDIATRIC POSTERIOR FOSSA EPENDYMOMA
Authors: Aubin Rachael , Troisi Emma , Alghalith Adam , Nasrallah MacLean , Santi Mariarita , Camara Pablo
Published: June 2021

Childhood ependymoma is a cancer of the central nervous system with a chronic relapsing pattern. In children, 90% of ependymal tumors occur intracranially where prognosis is grim. Standard care for this disease includes surgical resection followed by radiation. Despite several clinical trials, adjuvant chemotherapies have yet to extend patient survival, highlighting a need for more effective treatment options. Ependymal tumors have been stratified into nine molecular subgroups based on their DNA methylation profile. The most prevalent and aggressive pediatric subgroup is known as posterior fossa ependymoma type A (PFA) which represents approximately 60% of pediatric cases and has a 5-year progression free survival rate of 30%. Whole genome sequencing studies have revealed that PFA tumors rarely harbor recurrent mutations. To inform the potential development of new treatment options for this disease, we sought to decipher the specific mechanisms leading to the tumorigenesis, progression, and metastasis of PFA tumors. By means of single-nuclei RNA-seq and an array of computational methods, we show that the expression profile of PFA tumor cells recapitulate the developmental lineages of radial glia in neurogenic niches, and is consistent with an origin in LGR+ stem cells and a pro-inflammatory environment. In addition, our analysis reveals the abundance of a mesenchymal cell population expressing TGF-β signaling, reactive gliosis, and hypoxia-related genes in distal metastases from PFA tumors. Taken together, our results uncover the cell ecosystem of pediatric posterior fossa ependymoma and identify WNT/β-catenin and TGF-β signaling as candidate drivers of tumorigenesis for this cancer.
HGG-01. 3D GENOME STRUCTURE IMPACTS GENE EXPRESSION IN PEDIATRIC HIGH-GRADE GLIOMA
Authors: Huang Tina , Wang Juan , Hou Ye , Piunti Andrea , Bartom Elizabeth , Shilatifard Ali , Yue Feng , Saratsis Amanda
Published: June 2021

Introduction

Pediatric high-grade gliomas (pHGGs), including glioblastoma multiforme (GBM) and diffuse intrinsic pontine glioma (DIPG), are highly morbid brain tumors. Up to 80% of DIPGs harbor a somatic missense mutation in genes encoding Histone H3. To investigate whether the H3K27M mutant protein is associated with distinct chromatin structure affecting transcription regulation, we generated the first high-resolution Hi-C and ATAC-Seq maps of pHGG cell lines, and integrated these with tissue and cell genomic data.

Methods

We generated sequencing data from patient-derived cell lines (DIPG n=6, GBM n=3, normal n=2) and frozen tissue specimens (DIPG n=1, normal brainstem n=1). Analyses included cell line RNA-Seq, ChIP-Seq (H3K27ac, H3K27me3, H3K27M) and genome-wide chromatin conformation capture (Hi-C), as well as tissue ATAC-Seq. Publicly available pediatric glioma tissue ChIP-Seq data was integrated with cell data.

Results

We identified tumor-specific enhancers and regulatory networks for known oncogenes in DIPG and GBM. In DIPG, FOX, SOX, STAT and SMAD families were among top H3K27Ac enriched motifs. Significant differences in Topologically Associating Domains (TADs) and DNA looping were observed at OLIG2 and MYCN in H3K27M mutant DIPG, relative to wild-type GBM and normal cells. Pharmacologic treatment targeting H3K27Ac (BET and Bromodomain inhibition) altered these 3D structures. Functional analysis of differentially enriched enhancers in DIPG implicated SOX2, SUZ12, and TRIM24 as top activated upstream regulators. Distinct genomic structural variations leading to enhancer hijacking and gene co-amplification were identified at A2M, JAG2, and FLRT1.

Conclusion

We show genome structural variations enhancer-promoter interactions that impact gene expression in pHGG in the presence and absence of the H3K27M mutation. Our results imply that tridimensional genome alterations may play a critical role in the pHGG epigenetic landscape and thereby contribute to pediatric gliomagenesis. Further studies examining the impact of the alterations, including CRISPR knock-down of target enhancer regions, is therefore underway.
HGG-09. TARGETING FACILITATES CHROMATIN TRANSCRIPTION (FACT) AS A NOVEL STRATEGY THAT ENHANCES RESPONSE TO HISTONE DEACETYLASE (HDAC) INHIBITION IN DIPG
Authors: Ehteda Anahid , Simon Sandy , Franshaw Laura , Giorgi Federico M , Liu Jie , Hayden Elisha , Rouaen Jourdin , Pang Chi Nam Ignatius , Pandher Ruby , Mayoh Chelsea , Tang Yujie , Khan Aaminah , Ung Caitlin , Kankean Anne , Lehmann Rebecca , Shen Sylvie , Gopalakrishnan Anjana , Trebilcock Peter , Gurova Katerina , Gudkov Andrei , Norris Murray D , Haber Michelle , Vittorio Orazio , Tsoli Maria , Ziegler David S
Published: June 2021

DIPG is an aggressive and incurable childhood brain tumour for which new treatments are needed. A high throughput drug screen of 3500 pharmaceutical compounds identified anti-malarials, including quinacrine as having potent activity against DIPG neurospheres. CBL0137, a compound modelled on quinacrine, is a novel anti-cancer compound which targets Facilitates Chromatin Transcription (FACT), a chromatin remodelling complex involved in transcription, replication, and DNA repair. CBL0137 effectively crosses the blood-brain barrier and has recently completed Phase I testing in adult patients. CBL0137 induced apoptosis in DIPG neurospheres and had profound cytotoxic activity against a panel of DIPG cultures. In a DIPG orthotopic model, treatment with CBL0137 significantly improved survival. We found that treatment with CBL0137 up-regulated TP53 and increased histone H3.3 acetylation and tri-methylation in DIPG cells. We therefore examined the interaction between CBL0137 and the histone deacetylase (HDAC) inhibitor panobinostat. In vitro experiments showed that the two agents had profound synergistic activity against DIPG neurospheres in clonogenic assays and enhanced caspase activation and apoptosis. The FACT subunit SSRP1 was found to directly interact with H3.3K27M and treatment with CBL0137 targeted this epigenetic defect, restoring histone H3.3 trimethylation and leading to tumor cell death. Transcriptomic analysis and immunoblotting indicated that combination treatment activated signalling pathways controlled by Retinoblastoma (RB)/E2F1 and subsequently increased phosphorylation and enzymatic activity of enhancer of zeste homolog 2 (EZH2). Consistent with the in vitro results, the combination of CBL0137 and panobinostat significantly prolonged survival in two independent orthotopic models of DIPG, while histological analysis showed restoration of H3K27me3 and decreased Ki67 positive cells. In addition to panobinostat, CBL0137 has been found to combine synergistically in vitro and in vivo with PARP and BET inhibitors. Given these promising results, a paediatric trial of CBL0137 will open through the Children’s Oncology Group with an expansion cohort for DIPG patients.
HGG-29. VENETOCLAX SYNERGIZES WITH RADIATION THERAPY FOR THE TREATMENT OF DIPG
Authors: Balakrishnan Ilango , Chetty Senthilnath Lakshmana , Madhavan Krishna , Fosmire Susan , Pierce Angela , walker Faye , Dahl Nathan , Mitra Siddhartha , Vibhakar Rajeev , Venkataraman Sujatha
Published: June 2021

Background and Rationale

Diffuse intrinsic pontine glioma (DIPG) is one of the most aggressive pediatric brain tumors. Currently, the main treatment for DIPG is radiation and it’s only a palliative care, as the tumor eventually becomes resistant to radiation. In this study we found that radiation leads to an increase in anti-apoptotic BH3 proteins mainly BCL2 in DIPG. Previous studies in other tumor types have shown that increase in these pro-survival BCL2 family members are associated with treatment resistance and poor prognosis. Therefore, we hypothesize that inhibition of BCL2 using a small-molecule inhibitor, venetoclax that crosses the blood-brain barrier, will represent a possible therapeutic strategy to overcome radiation resistance in DIPG. Approach: For in vitro studies, DIPG cells were exposed to different radiation doses (0–10 Gy) and the magnitude of the sensitizing effect of venetoclax (with IC15) was calculated by clonogenic assay. Evaluated BCL2 family proteins by western and cytotoxicity by cleaved caspase incucyte assays. For in vivo studies, NSG mice orthotopically engrafted with a human H3K27M-DIPG luciferase-expressing cells in the pons were exposed to a focal fractionated radiation of 2Gy/day for 3 days. Mice were randomized into 2 groups based on bioluminescence IVIS signal intensity; each group receiving either venetoclax (15 mg/kg, by i.p) 3 days/week for 10 weeks or vehicle. Decrease in tumor burden was measured by IVIS and survival was evaluated compared to vehicle treated mice.

Results

Single agent venetoclax showed no significant activity against DIPG tumors in in vitro and in vivo DIPG xenografts. Single-agent radiation cleared the tumor burden but only transiently. Combination of radiation with venetoclax showed considerable synergistic anti-tumor effect in vitro and in vivo leading to a significant increase in animal survival beyond either single agent treatments. The metabolic reprogramming that results in this enhanced cell-killing effect will be discussed.
IMMU-03. CHARACTERIZING THE IMMUNE MICROENVIRONMENT OF PEDIATRIC BRAIN TUMORS
Authors: Galvin Robert , Maeser Danielle , Gruener Robert , Huang R Stephanie
Published: June 2021

Therapy for pediatric central nervous system (CNS) malignancies can be toxic, and outcomes are suboptimal. Immunotherapy holds promise as a therapeutic avenue, but one of the challenges in its application is the poorly understood microenvironment of pediatric CNS tumors. The Children’s Brain Tumor Network released the Pediatric Brain Tumor Atlas, containing the expression profile of nearly 700 primary CNS tumors. To study the immune microenvironment, a classification from The Cancer Genome Atlas project is applied. High-grade lesions are predominantly lymphocyte deplete (C4, 80%) or immunologically quiet (C5, 7.6%). Low-grade lesions are more mixed with 43% C4, 26% C5, and a higher proportion of inflammatory subtype (C3, 28%). For survival parameters, immune subtype and tumor grade are associated. Using a multivariate cox regression model, the hazard ratio is 2.2 (0.86 – 5.4, p = 0.102) and 3.6 (1.2 – 10.9, p = 0.02) for C4 and C5, respectively. Deconvolution of immune cell gene signatures provides insight into the phenotype of lymphocyte infiltrate, which averages 8.6% (IQR 5.4% – 9.8%) across all samples. For high-grade samples, greater than median expression of T cell-, monocyte-, macrophage-, and B cell-gene signatures are each associated with decreased survival (p < 0.05). Microglia gene signatures have decreased relative expression in high-grade samples compared to low-grade samples (p < 0.001). It is hypothesized that the expression of inhibitory immunomodulators contributes to a pro-tumorigenic microenvironment and represent potential therapeutic targets. In the absence of normal samples in the data set, differential gene expression experiments between disease states can reveal upregulated immunomodulators. Focusing on diffuse midline glioma, immunologic pathways are downregulated. Furthermore, 9 inhibitory immunomodulators, including KDM1A, EZH2, CD276, and VTCN1, are significantly expressed relative to midline low-grade glioma with equivalent immune subtype. Overall, our analysis contributes to the understanding of the immune microenvironment and mechanisms of immune escape for pediatric CNS malignancies.
IMMU-09. MODULATING THE MYELOID POPULATION IN DIPG MODELS WITH ONCOLYTIC VIRUS AND COMPLEMENT INHIBITORS SHOWS THERAPEUTIC EFFICACY
Authors: Puigdelloses Montserrat , Laspidea Virginia , Hambardzumyan Dolores , Chen Zhihong , Gupta Sumit , Gomez-Manzano Candelaria , Labiano Sara , Becher Oren J , Woodruff Trent , Pío Ruben , Ajona Daniel , Pérez-Larraya Jaime Gállego , Alonso Marta M
Published: June 2021

Diffuse intrinsic pontine glioma (DIPG) is the leading cause of brain tumor-related death in children. It is characterised for having a non-inflammatory microenvironment and be immunologically inert. Therefore, strategies aiming to break the microenvironment status-quo in this disease could provide therapeutic benefit. The complement system promotes tumor progression due to the continuous production of anaphylatoxins leading to the infiltration of myeloid cells, which express high levels of complement receptors (C3aR and C5aR1). We have in silico data showing the high expression of C5aR1 in DIPGs. Thus, we wanted to assess first whether complement C5aR1 could constitute an actionable target, and second whether combining C5aR1 inhibitors with oncolytic virus could result in a superior antitumor immune response than either agent alone in DIPG. In this study, we used two different peptide inhibitors of C5aR1, PMX53 and PMX205 combined with the virus Delta-24-ACT (an oncolytic virus armed with 4-1BBL). We performed in vivo studies to evaluate the efficacy of this combination in immunocompetent DIPG models. Our data showed that the combination Delta-24-ACT/PMX53 significantly extended the median survival of the animals when compared with either agent alone, and led to long-term survivors that generated immune memory. The combination treatment modulated the tumor microenvironment promoting an increase in lymphocytes, mainly CD8+ cells presenting an active phenotype, and a reduction in C5aR1 expression in the myeloid compartment. We are currently evaluating in vivo whether PMX205, which has an improved ability to cross the blood brain barrier, leads to better therapeutic response. In summary, the combination of Delta-24-ACT with a C5aR1 inhibitor showed the capacity to shake the DIPG tumor microenvironment and unleashed an antitumor immune response. These data underscore the possibilities to combine oncolytic virus with targets of the tumor microenvironment to improve their therapeutic benefit in DIPGs.
IMMU-16. TARGETING GLYPICAN 2 (GPC2) ON PEDIATRIC MALIGNANT BRAIN TUMORS WITH MRNA CAR T CELLS
Authors: Foster Jessica , Griffin Crystal , Stern Allison , Brimley Cameron , Buongervino Samantha , Storm Phillip , Barrett David , Maris John , Resnick Adam , Bosse Kristopher
Published: June 2021

Glypican 2 (GPC2) is a cell-surface oncoprotein initially identified in neuroblastoma, retinoblastoma, and medulloblastoma as an ideal target for immunotherapy (Cancer Cell, 2017). Here we evaluated GPC2 expression across the spectrum of pediatric brain tumors using RNA sequencing from specimens in the Children’s Brain Tumor Network (CBTN). High GPC2 expression, defined as >10 FPKM, was found in 100% of embryonal tumors with multilayered rosettes (ETMRs) (n=6), 95% of medulloblastomas (n=122), 86% of other embryonal tumors (n=21), 50% of choroid plexus carcinomas (n=4), 42% of high grade gliomas (HGG) (n=117), and 37% of diffuse midline gliomas (DMG) (n=65). Within medulloblastoma subtypes, group 4 tumors had the highest expression, and within the HGG tumor cohort H3.3 G34 mutated gliomas had the highest GPC2 expression. High GPC2 protein expression was validated with medulloblastoma and HGG/DMG primary tumors and cell lines using IHC, Western blot, and flow cytometry. We next developed two potent CAR T cell constructs using the D3 specific scFv directed against GPC2 for testing in brain tumor models. GPC2-directed CAR T cells were tested in vitro against medulloblastoma and HGG cells lines, and in vivo using two patient-derived medulloblastoma xenograft models: Rcmb28 (group 3) and 7316-4509 (group 4). GPC2-directed mRNA CAR T cells induced significant GPC2-specific cell death in medulloblastoma and HGG cellular models with concomitant T cell degranulation compared to CD19-directed mRNA CAR T cells. In vivo, GPC2-directed mRNA CAR T cells delivered locoregionally induced significant tumor regression measured by bioluminescence after 4–6 intratumoral infusions of 4 x 106 CAR T cells (p<0.0001 for Rcmb28, p<0.05 for 7316-4509). No GPC2-directed CAR T cell related toxicity was observed. GPC2 is a highly differentially expressed cell surface protein on multiple malignant pediatric brain tumors that can be targeted safely with local delivery of mRNA CAR T cells.
LGG-01. NF1 MUTATION DRIVES NEURONAL ACTIVITY-DEPENDENT OPTIC GLIOMA INITIATION
Authors: Pan Yuan , Hysinger Jared , Schindler Nicki , Cobb Olivia , Guo Xiaofan , Yalçın Belgin , Anastasaki Corina , Mulinyawe Sara , Ponnuswami Anitha , Scheaffer Suzanne , Ma Yu , Chang Kun-Che , Xia Xin , Toonen Joseph , Lennon James , Gibson Erin , Liau Linda , Goldberg Jeffrey , Monje Michelle , Gutmann David
Published: June 2021

Neurons have recently emerged as essential cellular constituents of the tumor microenvironment, where their activity increases the growth of a diverse number of solid tumors. While the role of neurons in tumor progression has been previously demonstrated, the importance of neuronal activity to tumor initiation is less clear, particularly in the setting of cancer predisposition syndromes. In the Neurofibromatosis type 1 (NF1) cancer predisposition syndrome, in which tumors arise in close association with nerves, 15% of individuals develop low-grade neoplasms of the optic pathway (optic gliomas) during early childhood, raising the intriguing possibility that postnatal light-induced optic nerve activity drives tumor initiation. Here, we employ an authenticated murine model of Nf1 optic glioma to demonstrate that stimulation of optic nerve activity increases optic glioma growth, while decreasing optic nerve activity via light deprivation prevents tumor formation and maintenance. By manipulating environmental light to modulate optic pathway (retinal) neuron activity, we show that Nf1 optic glioma initiation depends on neuronal activity during a developmental period susceptible to tumorigenesis. Germline Nf1 mutation in retinal neurons results in aberrantly high optic nerve neuroligin-3 (Nlgn3) shedding in response to retinal neuronal activity. Moreover, genetic Nlgn3 loss or pharmacologic inhibition of Nlgn3 shedding blocks murine Nf1 optic gliomagenesis and progression. Collectively, these studies establish an obligate role for neuronal activity in the development of certain brain tumors, elucidate a therapeutic strategy to reduce optic glioma incidence or mitigate tumor progression, and underscore the role of Nf1 mutation-mediated dysregulation of neuronal signaling pathways in the NF1 cancer predisposition syndrome.
LGG-05. GENERATION OF NOVEL MOUSE MODELS FOR BRAF V600E MUTANT GLIOMAGENESIS TO GAIN MECHANISTIC INSIGHTS INTO TUMOR FORMATION AND PROGRESSION
Authors: K. Petritsch Claudia , Barrette Anne Marie , Park Jong-Whi
Published: June 2021

Background

The BRAF V600E mutation occurs in ~ twenty percent of histologically diverse pediatric gliomas and is the second most common mutation in pediatric low-grade gliomas (LGG). BRAF V600E expression in LGG with balanced CDKN2A is associated with a higher rate for progression than for BRAF V600E wildtype tumors, and despite adjuvant therapy, consisting of resection, radiation and chemotherapy. Progression invariably occurs in BRAF V600E mutant CDKN2A deleted gliomas, marking a high-risk group. Here, we aim to overcome the lack BRAF V600E mutant glioma models that allow for studies of stem and progenitor cells and the immune system ability to understand progression.

Methods

We develop novel immunocompetent, stem and progenitor cell-based mouse models for BRAF mutant gliomas, including genetically engineered mouse models (GEMMs), orthotopic glioma models derived from gliomas in GEMMs as well as in vitro models of those tumors. BRAF mutant mouse brains and cells were analyzed by immunofluorescence staining, flow cytometry, mass cytometry and RNA sequencing.

Results

Ongoing model development studies indicate that BRAF V600E mutant gliomas in murine brain exhibit very similar neuroanatomical preferences to human gliomas. The BRAF V600E mutation exacerbates the heterogenous cell cycling pattern of normal neural stem and progenitors and expands a symmetrically dividing progenitor population. Cellular plasticity rather than cellular lineage hierarchy drives the generation of a therapy resistant stem cell pool. Transcriptomic analyses of neuroglial stem cells with induced BRAF V600E expression provide insights into mechanisms for neoplastic transformation and progression.

Conclusion

Analyses of two independent BRAF V600E mutant mouse models provide novel insights into the role for tumor intrinsic factors, such as plasticity and stemness, and the tumor microenvironment in progression.
TMOD-03. A NOVEL MB GR3 TRANSGENIC MOUSE MODEL IS GENERATED BY MYCN AND P53 DEFECTS IN VENTRICULAR ZONE PROGENITORS.
Authors: Morcavallo Alaide , Barker Karen , Adachi Toma , Boult Jessica K R , Kwok Colin , da Silva Patricia Benites Goncalves , Okonechnikov Konstantin , Hitchen Luke , Robinson Simon P , Clifford Steven C , Pfister Stefan M , Kawauchi Daisuke , Chesler Louis
Published: June 2021

Medulloblastoma (MB) represents the most common embryonal tumour of the Central Nervous System in childhood. MB occurs in the cerebellum and molecular features dictate the classification into four subgroups. Although Group3 (Gr3) MB tumours are dominated by primitive progenitor-like cells, the cells of origin remain unidentified. Gr3 MB is associated with relatively common MYC family member amplification and overexpression, often combined with p53 pathway defects at relapse. Molecularly stratified treatment is not yet available, causing Gr3 MB and its subsequent relapse to often represent an unstoppable progressive disease. The limited understanding of Gr3 tumorigenesis and targeted therapy development is also due to the lack of faithful in vivo models and consequently, their use in preclinical studies. We have now developed a new germline genetically engineered mouse model (GEMM), harbouring MYCN amplification in a p53 inactive background (tamoxifen-inducible p53 activation, Trp53ERTAM). The purpose of the GEMM is to investigate the developmental significance of MYC aberration in putative Gr3 MB cells of origin and exploit it in preclinical studies. A LSL-MYCN-Luciferase strain was crossed with mice expressing Cre recombinase under the Blbp promoter and subsequently to Trp53ERTAM inducible mice. As result, the MYCN overexpression alone did not generate tumours, conversely to the combination of MYCN with p53 deregulation. Tumours arise exclusively in the hindbrain of homozygote mice, with a penetrance of 100% and a latency of ~135 days. Pathology report suggests tumours are Gr3 MB with large cell/anaplastic (LCA) histology. Preliminary transcriptional profiling data analysis reveals that tumours share molecular features with human counterparts, clustering with Gr3 MB. Ongoing analysis will explore the tumour cells of origin, followed by tumour progression alteration restoring p53 activity and blood-brain barrier integrity status. In conclusion, we have developed a MYCN/Trp53ERTAM Gr3 MB GEMM arising from ventricular zone progenitor cells and resembling human cancer characteristics.
OMIC-04. IDENTIFICATION AND CHARACTERIZATION OF CIRCULATING RNAS (CODING AND NONCODING) AND METABOLITES IN CEREBROSPINAL FLUID IN MEDULLOBLASTOMA PATIENTS
Authors: Lee Bongyong , Stapleton Stacie , Pokhrel Rudramani , Bettegowda Chetan , Jallo George , Perera Ranjan
Published: June 2021

Medulloblastoma (MB) is the most common malignant brain tumor in children, and monitoring patients for treatment response and recurrence can be challenging with available current technologies in neuro-imaging and performing a biopsy to confirm response or recurrence carries risks, whereas cerebrospinal fluid (CSF) can be obtained with a little invasiveness. MB has altered cellular metabolism due to changes in gene expression, therefore, we hypothesized that any changes in MB cells lead to changes in cell-free transcripts and metabolites in CSF. To test this, we applied RNA-sequencing and mass spectrometry to analyze transcripts and metabolites including lipid in CSF from patients with different sub-groups of MB tumors (i.e., WNT, SHH, G3/4, G4, and unknown) and compared them to non-cancerous CSF. Tumor and sub-group specific transcriptomic and metabolic signatures were shown by unsupervised hierarchical clustering facilitating tumor type differentiation. By comparison with previously published tumor tissue RNA-seq data, we were able to identify a group of upregulated molecular signatures in both tumor tissue and CSF. We also identified a group of lipids that differentiate each MB sub-group from normal CSF, and Pathway analysis confirmed alterations in multiple metabolic pathways. Finally, we attempted to integrate RNA-seq data with lipidomics data, and results depict that the combinatorial analysis of CSF RNAs and metabolites can be useful in diagnosing and monitoring patients with MB tumors. (This research was conducted using samples made available by The Children’s Brain Tumor Network.)
OMIC-06. MOLECULAR SUBGROUPING OF MEDULLOBLASTOMA VIA LOW-DEPTH WHOLE GENOME BISULFITE SEQUENCING
Authors: Thompson Dean , Castle Jemma , Hicks Debbie , Clifford Steve , Schwalbe Ed
Published: June 2021

Introduction

International consensus recognises four molecular subgroups of medulloblastoma, each with distinct molecular features and clinical outcomes. The current gold-standard for subgroup assignment is DNA methylation microarray. There is an unmet need to develop platform-independent subgrouping assays which are both non-proprietary and compatible with rapidly-expanding WGS capacity in healthcare. Whole Genome Bisulfite Sequencing (WGBS) enables the assessment of genome-wide methylation status at single-base resolution. Previously, WGBS adoption has been limited by cost and sample quality/quantity requirements. Its application for routine detection of medulloblastoma subgroups has not previously been reported.

Methodology

Two datasets were utilised; 36 newly-sequenced low-depth (10x coverage) and 34 publicly-available high-depth (30x) WGBS medulloblastomas, all with matched DNA methylation microarray data. We compared platform concordance and identified molecular subgroups. Machine-learning WGBS-based subgroup classifiers were optimised and compared between platforms. Aneuploidy and mutation detection using WGBS was optimised and compared to microarray-derived estimates where possible. Finally, comprehensive subgroup-specific DNA methylation signatures were identified.

Results

We optimised a pipeline for processing, quality control and analysis of low-depth WGBS data, suitable for routine molecular subgrouping and aneuploidy assessment. We demonstrated the suitability of fresh-frozen and FFPE DNA for WGBS, and, using downsampling, showed that subgroup calling is robust at coverages as low as 2x. We identified differentially methylated regions that, due to poor representation, could not be detected using methylation microarrays. Molecular subgroups of medulloblastoma assigned using WGBS were concordant with array-based definitions, and WGBS-derived classifier performance measures exceeded microarray-derived classifiers.

Conclusion

We describe a platform-independent assay for molecular subgrouping of medulloblastoma using WGBS. It performs equivalently to current array-based methods at comparable cost ($405 vs $596) and provides a proof-of-concept for its routine clinical adoption using standard WGS technology. Finally, the full methylome enabled elucidation of additional biological heterogeneity that has hitherto been inaccessible.
RARE-01. ASSESSING THE SYMPTOM DIAGNOSTIC INTERVAL FOR CHILDREN WITH CENTRAL NERVOUS SYSTEM TUMOURS
Authors: Crowell Cameron , Crooks Bruce , Walling Simon , Boileau Kelly , Bowes Lynette , Rutledge Robert , Kulkarni Ketan , McNeely Daniel , Erker Craig
Published: June 2021

Background

Diagnostic delays in pediatric neuro-oncology is a subject of distress for families and providers. We aimed to evaluate the symptom diagnostic interval (SDI) and influencing variables for children with CNS tumors.

Methods

This retrospective study analyzed 210 patients diagnosed from 2001–2018 and managed at the tertiary care facility in Halifax, Canada. SDI was defined as time from first symptom until tissue diagnosis or, if not available, imaging diagnosis. Non-parametric tests were used to compare SDI between groups.

Results

Median SDI was 12.4 weeks (IQR 4.3–30), longer than 7 other studies of 1308 children reporting medians of 4.5–10 weeks (p < 0.01). Most common tumors and their median SDI included low-grade glioma (LGG) (n=97, 46%; 17.9 weeks), medulloblastoma (n=31, 15%; 8.7 weeks), high-grade glioma (HGG) and DIPG (n=23, 11%; 5.6 weeks), and ependymoma (n=13, 6%; 13.6 weeks). The most common initial reported symptom included headache (n=63; 30%), nausea/vomiting (n=27, 18%), seizure (n=24, 12%), and visual impairment (n=13, 6.3%). Patients aged 0–3 years had a shorter SDI than patients 10 years and older (SDI 8.7 vs 14.6 weeks; p = 0.03). Tumor category showed longer SDI for LGG versus HGG (p = 0.003), DIPG (p = 0.02), medulloblastoma (p = 0.03) and other embryonal tumors (p = 0.03). Longer SDI was not associated with increased risk of disease progression for LGG (p = 0.93), medulloblastoma (p = 0.89), or ependymoma (p = 0.5). No difference in SDI was found with regard to diagnosis era, ethnicity, socioeconomic status, or distance to the tertiary care facility.

Conclusion

SDI at our centre is longer than previously reported studies. SDI is linked to tumor biology and its relevance within specific tumor groups deserves further investigation given it doesn’t appear to predict tumor progression/recurrence, yet families and providers feel distress when delays in diagnosis are perceived.