bluuebunny/crossref_metadata_2025_split huggingface dataset:
IMMU-04. TARGETING ALTERNATIVE SPLICING VARIANTS TO STIMULATE ANTI-TUMOR IMMUNITY IN A NOVEL SYNGENEIC MOUSE MODEL OF DIFFUSE HEMISPHERIC GLIOMA, H3 G34-MUTANT
Authors: Owens Geoffrey , Pan Yang , Treger Janet , Contreras Erick , Soto Horacio , Armellini Amber , Na Brian , Liau Linda , Prins Robert , Xing Yi , Wang Anthony 
Published: June 2023

Abstract
Juvenile presentation of HGG has been shown to frequently involve somatic mutations of the H3-3A gene, which encodes a histone H3 variant. To address the paucity of identified TSAs in DHG, we utilized a novel computational platform, Isoform peptides from RNA splicing for Immunotherapy target Screening (IRIS). The IRIS pipeline is designed to leverage large-scale cancer and normal transcriptomic data to identify peptide sequences that result from alternative splicing events that are highly enriched in cancer cells, and are predicted to bind the HLA class I alleles carried by the individual patient. To investigate whether peptide-pulsed dendritic cells (DC) together with checkpoint blockade might be a potential treatment modality for diffuse hemispheric glioma, H3 G34-mutant, we have developed a novel mouse model, and utilized a novel bioinformatics pipeline to identify tumor-associated peptide antigens. We used the RCAS/tv-A system to target the expression of H3/G34R and PDGF-B and to knock out p53 in neural progenitors in transgenic C57BL/6 neonatal mice. Three independent cell lines were obtained that expressed transcripts associated with oligodendrocyte and interneuron lineages, and formed lethal tumors after intracranial implantation. Implementing IRIS, we identified nonapeptides generated from alternative splicing of mRNAs that were highly enriched in the tumor transcriptomes of two H3/G34R patients, and predicted to bind the HLA-A*2:01 class I allele carried by these patients. Three of the candidate peptides were conserved in the mouse and also predicted to bind the H2-Kb MHC I allele carried by C57/BL6 mice. Using our syngeneic mouse model, we showed that DCs pulsed with these peptides together with anti-PD1 mAb provided a significant survival benefit compared with checkpoint inhibitor and DCs pulsed with peptides that were not predicted to bind the H2-Kb allele.
IMMU-21. ELUCIDATING THE CELLULAR MECHANISMS OF THERAPEUTIC BENEFIT UNDERLYING ADOPTIVE CELLULAR THERAPY IN MODELS OF GLIOMA
Authors: Figg John , Francis Connor , Jin Dan , Dean Bayli DiVita , Reid Alexandra , Hilferty David , McDonald Brianna , Flores Catherine , Mitchell Duane 
Published: June 2023

Abstract
Among pediatric cancers, malignancies of the brain carry significant morbidity and mortality, harboring dismal prognosis and poor outcomes. Our group has previously shown that adoptive cellular therapy (ACT) provides therapeutic benefit against central nervous system (CNS) malignancies, including medulloblastoma and high-grade glioma. In this study, we characterized cell cycling differences of immune sub-populations in peripheral lymphoid and tumor tissue compartments in vivo. ACT was conducted in orthotopic KR158 luciferase tumor-bearing mice, a syngeneic murine glioma model. Five days following intracranial implantation of tumor cells, mice were treated with ACT which included the following elements: total body irradiation, hematopoietic stem cell transplantation, one dose of tumor-activated splenocytes and three weekly doses of dendritic cells that had been electroporated with tumor-derived ribonucleic acid. One week after the completion of ACT, bromodeoxyuridine (BRDU) was administered to mice 12-hours prior to tissue collection and flow cytometry was utilized to measure the level of BRDU incorporation. 7-aminoactinomycin-D was used in conjunction with BRDU to provide insight into all phases of the cell cycle. We observed significant differences in cycling populations of myeloid derived suppressor cells (MDSC) and T-cells. In ACT-treated-mice, MDSCs found in secondary lymphoid tissues were significantly more proliferative. In the tumor microenvironment (TME), proliferating MDSCs were significantly reduced compared to mice that did not receive treatment. Frequencies of proliferating CD4+ and CD8+ T-cells were significantly increased in cervical lymph node and TME but reduced in spleen. These findings suggest that ACT alters immune cycling in peripheral lymphoid tissues and TME to potentially promote antitumor T-cell responses and minimize MDSC-mediated immunosuppression. While ACT-mediated alterations to immune cell cycling are likely a major contributor to the therapy’s benefit, it is unlikely to be the sole mechanism. Further exploration into other functional pathways, namely migration, is needed to explain changes to immune populations following ACT.
LGG-03. EXPLORING THE SIGNALING NETWORK INVOLVED IN MAPK PATHWAY INHIBITION BY THE MEK INHIBITOR TRAMETINIB IN BRAF-FUSION-DRIVEN PEDIATRIC PILOCYTIC ASTROCYTOMA
Authors: Sigaud Romain , Stefanski Anja , Selt Florian , Hielscher Thomas , Usta Diren , Kocher Daniela , Picard Daniel , Büdenbender Isabel , Remke Marc , Pfister Stefan M , Jones David T W , Brummer Tilman , Witt Olaf , Milde Till 
Published: June 2023

Abstract

INTRODUCTION
Pilocytic astrocytomas (PA) are the most common pediatric brain tumors. They are characterized by MAPK pathway alterations, leading to its constitutive activation and modulating the balance between proliferation and oncogene-induced senescence (OIS) sustained by senescence-associated secretory phenotype (SASP). Little is known about the molecular implications of MAPK pathway inhibition in the proliferating and senescent tumor compartments.

METHODS
DKFZ-BT66 cells derived from a primary KIAA:BRAF-fusion positive PA cell line and BT40 cells derived from pleomorphic xanthoastrocytoma with a BRAFV600E mutation and CDKN2A/B deletion, were used as model systems. RNA-sequencing and phospho-/proteomic datasets were generated in both the proliferative and senescent cells, and treated with the MEKi trametinib for different time-spans. A multi-omics factor analysis tool (MEFISTO) was used to identify key OIS/proliferation effectors.

RESULTS
Differential gene expression analysis revealed that MEK inhibition leads to the inhibition of the OIS/SASP gene program in senescent DKFZ-BT66. In addition, the protein level of several SASP factors was decreased. This translated in reduced sensitivity towards senolytics drugs, indicating inhibition of senescence features upon MEKi. MEFISTO analysis allowed to identify key transcription factors, genes and proteins involved in MAPK-induced OIS in the senescent PA cells, that were mapped using a prior knowledge network approach. Finally, single sample geneset enrichment analysis showed that most MAPK-related signatures were downregulated upon MEKi treatment, while pathways related to upstream MAPK activators (including several RTK pathways) were predicted to be upregulated, in both proliferating and senescent cells.

CONCLUSION
This data suggests that MAPKi reverses OIS in senescent PA cells, while inducing the activation of MAPK upstream regulators, identifying putative co-targets for the treatment of PA. Further validation of the targetability of these pathways is pending. Furthermore, the identification of the MAPK-related OIS/SASP genes provide insight about the regulation of OIS/SASP by the MAPK pathway.
LGG-22. CHARACTERIZATION OF THE TUMOR MICROENVIRONMENT IN PEDIATRIC LOW-GRADE GLIOMA
Authors: Zahedi Shadi , Riemondy Kent , Griesinger Andrea , Donson Andrew , Fu Rui , Crespo Michelle , Groat Madeline , Bratbak Emil , Desisto John , Rheaume John , Green Adam , Vibhakar Rajeev , Willard Nicholas , Forman Nicholas , Levy Jean Mulcahy 
Published: June 2023

Abstract

BACKGROUND
Pediatric low-grade gliomas (pLGGs) are the most common brain tumors in children. Although pLGGs represent a significant number of patients with slow-growing, often curable tumors, they are also affected by neurologic injuries, multiple relapses and requiring repeated courses of therapy, including surgery, chemotherapy, and radiotherapy. Novel, more effective therapies are urgently needed.

METHODS
We used a multipronged approach to better understand the complexity of the tumor microenvironment (TME) within pLGG. We utilized scRNA sequencing, spatial transcriptomics, and cytokine analyses on 23 patient-derived pLGG samples including different tumor types (pilocytic astrocytoma (PA), ganglioglioma (GG), and undefined low-grade glioma (LGG)) and mutation profiles (BRAF V600E, BRAF fusions, and BRAF wild-type) to identify cell types, their spatial arrangement within a tissue, and their underlying functional status.

RESULTS
scRNA seq revealed both tumor and immune cells within the TME. Analyses of tumor cell subsets revealed a developmental hierarchy identifying progenitor and mature cell populations. Immune cells comprised both myeloid and T lineage cells, with myeloid cells comprising &gt; 50% of the entire population. Interestingly, there was a significant difference between the prevalence of two major myeloid subclusters between two pLGG subtypes (PA and GG). To better understand the underlying difference, we performed bulk and single-cell cytokine analyses to identify immune signals via which these cells communicate. Cytokine analyses revealed distinct immune phenotypes among tumor samples. Notably, BRAF fusion tumors appeared more immunogenic, especially by secreting higher levels of immune cell activators, chemokines (including CCL3 and CCL4), compared to BRAF V600E tumors. Additionally, spatial transcriptomics revealed the differential expression of these chemokines between PA and GG tumors.

CONCLUSIONS
Characterization of pLGG demonstrated the complexity of tumor microenvironment among different pLGG subtypes. Further investigation of the immune cells and tumor-immune cell interactions has the potential to unravel novel therapeutic targets against pLGG.
LGG-24. DIFFUSE LEPTOMENINGEAL GLIONEURONAL TUMOR MANAGEMENT AND OUTCOME: A SINGLE CENTER EXPERIENCE
Authors: Munir Faryal , He Jiasen , Sheikh Irtiza , Chen Melissa , Johnson Jason , McAleer Mary , McGovern Susan , Paulino Arnold , Huse Jason , Sandberg David , Zaky Wafik 
Published: June 2023

Abstract
Diffuse leptomeningeal glioneuronal tumor (DLGNT) is a rare diagnosis that was first incorporated into the WHO Classification in 2016. DLGNTs are usually low-grade tumors, with no current standard of care. A retrospective review of patients with a histologic diagnosis of DLGNT, from 2010 to 2022, was done with IRB approval. Eight patients were identified with a median age at diagnosis of 5.5 years (range 4 months - 21 years). Imaging findings included diffuse leptomeningeal enhancement and multifocal nodular lesions in the supratentorial and infratentorial locations. One patient had localized pineal disease and 2 patients had isolated spinal cord involvement. Histologically, 6/8 (75%) patients showed low-grade tumor (Ki-67 index = 2-15%). BRAF-KIAA1549 fusion was reported in 3, NTRK fusion in 1, PTPN11 mutation in 1, and FGFR1 mutation in 1 patient. Seven patients (88%) were treated with proton radiation, 3 at diagnosis and 4 upon progression. Chemotherapy was used at diagnosis on 4 patients (temozolomide, carboplatin and vincristine, and vinblastine). Targeted therapy (NTRK or BRAF-inhibitors) was utilized upon progression in four patients, and at diagnosis in one. All patients showed disease progression at a median time of 24 months from diagnosis. The median progression-free survival (PFS) in the group receiving upfront RT was 2.2 years (range = 0.4 – 6.6 years), versus chemotherapy of 1.4 years (range = 0.15 - 2.6 years) The 2 years PFS and OS are 57% and 100%, respectively. At a median follow-up of 4.5 years (range = 3 months to 9 years), 6 patients have stable disease (of whom 2 are off therapy), and 2 patients have progressive disease. DLGNTs are rare tumors with scarce data about radiological and molecular characteristics, and no established standard of care. Our case series emphasizes the need for further studies on molecular profiling and exploring targeted therapies.
MDB-04. SINGLE-CELL TRANSCRIPTOMIC ANALYSIS REVEALS DISTINCT GENOMIC LANDSCAPES, CELL TRAJECTORIES, AND TUMOUR-MICROENVIRONMENT INTERACTIONS IN FOUR SUBTYPES OF MEDULLOBLASTOMA
Authors: Ruchiy Yana , Tsea Ioanna , Verhoeven Bronte Manouk , Sinha Indranil , Preka Efthalia , Olsen Thale Kristin , Mei Shenglin , Blomgren Klas , Johnsen John Inge , Carlson Lena-Maria , Dyberg Cecilia , Baryawno Ninib 
Published: June 2023

Abstract
Medulloblastoma is the most common paediatric high-grade brain tumour, which comprises four different molecular subtypes (SHH, Wnt, Group 3, and Group 4), each defined by different molecular characteristics, genomic aberrations, and prognosis. High levels of inter- and intra-tumoural heterogeneity, together with the detrimental side effects caused by the current medulloblastoma treatments, need to be addressed in order to develop more personalised treatments and improve the quality of life of these patients. In this study, we analysed single-cell RNA sequencing data from 14 medulloblastoma patients, comprising all four molecular subtypes. We found that these tumours exhibit great levels of heterogeneity with regard to their copy number variation (CNV) profiles analysed using Numbat, as well as immune cell infiltration and composition within these tumours. Tumour-infiltrating immune cells represented a heterogeneous population comprised of monocytes, M1- and M2-like macrophages, dendritic cells, and microglia. Our ligand-receptor analysis also identified a subset of immune cells that send EGF signals to the tumour clusters, potentially contributing to the tumour growth. In addition, we showed that the tissue of origin of the immune cells found within the tumour microenvironment and their medulloblastoma subgroup specificity greatly influence their clustering when projected onto a UMAP. We also found that the clustering of tumour cells is influenced by their CNV levels. Finally, we performed RNA velocity analysis and identified subgroup-specific cell trajectories for each medulloblastoma subtype. As predicted, identified cell trajectories demonstrated that cells move in a direction of increasing CNV levels, making it possible to visualise and track the tumour progression and identify genetic markers specific to either earlier or later tumour stages. Overall, our study underlines high levels of inter-tumoural heterogeneity in medulloblastoma. It also provides opportunities for the identification of subgroup-specific biomarkers for the early stages of medulloblastoma, potentially contributing to the discovery of novel drug targets.
MDB-06. PLASMA MEMBRANE PROFILING REVEALS A TARGETABLE CELL-SURFACE PHENOTYPE OF WNT-MEDULLOBLASTOMA
Authors: Taylor Jessica T , Williams James C , Masih Katherine E , Bonner Sigourney , Lehner Paul , Gilbertson Richard J 
Published: June 2023

Abstract
WNT-medulloblastoma has an excellent prognosis, with an overall survival rate of 90% among children receiving standard-of-care surgical resection, radiotherapy, and chemotherapy. While curative, this treatment is associated with major, long-term, debilitating side effects. Therefore, it is crucial we develop effective, less toxic therapies for these children. The Gilbertson lab has previously shown that WNT-medulloblastomas are devoid of a Blood-Brain-Barrier (BBB). This disruption allows large molecules such as monoclonal antibodies (mAbs) to penetrate WNT-medulloblastomas. To discover WNT-medulloblastoma specific antigens for mAb targeting, we have first generated bulk and single-cell RNA sequencing profiles of the wild-type and WNT-medulloblastoma-prone mossy-fibre progenitor lineages in the lower rhombic lip, as well as human medulloblastoma patient derived orthotopic xenograft (PDOX) tumours. We next generated plasma membrane proteome profiles of hindbrain germinal zones and WNT-medulloblastomas. Plasma Membrane Profiling (PMP) deploys an isobaric chemical labelling approach -Tandem Mass Tags (TMT) - that allows multiplexing of up to sixteen variables per mass spectrometry experiment and ex vivo TMT-labelling of primary cells. Using this approach, we have mapped the cell surface proteome of our medulloblastoma models. Interrogation of these developmental and tumour data has unmasked WNT-medulloblastoma associated antigens that are specific for prenatal brain and WNT-medulloblastoma, but that are not expressed on critical postnatal tissues. Our workflow integrates multi-omic data sets to uncover a targetable landscape on the surface of WNT-medulloblastoma cells that we have cross-validated with a large cohort of patient RNA sequencing profiles and histological samples of both mouse and human tumours. To translate this dataset to real patient benefit, we are generating high affinity antibodies of these validated cell-surface proteins for assessment in our pre-clinical mouse models. mAbs directed towards essential receptors may have a therapeutic effect alone, however we will additionally modify mAbs to specifically deliver cytotoxic therapeutics - curing children whilst sparing healthy brain tissue.
MDB-33. REST AND USP37 CONTROL THE MTORC1-AUTOPHAGY AXIS IN MEDULLOBLASTOMA BY REGULATING RAPTOR DEGRADATION
Authors: Cheng Donghang , Singh Ashutosh , Haltom Amanda R , Zheng Yan , Sharma Ajay , Lopez Mariana , Gordon Nancy , Gopalakrishnan Vidya 
Published: June 2023

Abstract
The RE1 Silencing Transcription Factor (REST) is a repressor of neurogenesis. Its expression is elevated in the pediatric brain tumor medulloblastoma (MB) and correlates with poor patient prognosis. RNAseq analyses of MB tumors identified significant differences in the expression of genes associated with autophagy between high- and low-REST expressing samples. Microscopy and biochemical analyses of isogenic high- and low-REST human MB cell lines confirmed REST-dependent changes in autophagy, suggesting that REST controls the process. We had previously shown that REST regulates the activity of the mammalian target of rapamycin complex 2 (mTORC2). However, whether REST controls the mTORC1 pathway, a negative regulator for autophagy, is still unknown. mTORC1 is known to block autophagy initiation by phosphorylation of UNC51-like autophagy activating kinases (ULK)1/2 and the Phosphatidyl Kinase 3 subunit C3 (PIK3C3) to prevent global expression of lysosomal and autophagy genes through Transcription Factor EB (TFEB) phosphorylation. The above findings led us to investigate if REST controls autophagy through modulation of mTORC1 activity in MBs and to understand the underlying mechanisms. Biochemical studies demonstrated that REST elevation promotes proteasomal degradation of Raptor, a key regulatory sub-unit of the mTOR1 complex, to induce autophagy. Specifically, we discovered that Raptor is a novel substrate of the deubiquitylase USP37, which we previously identified as a REST-target gene product. These data show that REST drives autophagy by silencing USP37, destabilizing Raptor, and blocking mTORC1 activity. Finally, the pharmacological blockade of autophagy caused a decline in MB cell growth in a REST-dependent manner, indicating that REST-dependent autophagy is a pro-survival mechanism in MBs.
OTHR-12. LOCATION-RELEVANT GROWTH FACTOR DEPENDENCE ON THE FORMATION OF PEDIATRIC BRAIN TUMOR ORGANOIDS FROM PDOX MODELS AND PATIENT SAMPLES
Authors: Suarez Milagros , Xiao Sophie , Abdallah Aalaa , DuCuypere Michael , Lam Sandi , Wadhwani Nitin , Du Yuchen , Li Xiao-Nan 
Published: June 2023

Abstract
Brain cancer constitutes the most common type of childhood malignancies and the leading cause of death in children. Despite recent advances in diagnostic methods, surgical techniques as well as chemo- and radio-therapeutic strategies; the survival rates in many types of malignant pediatric brain tumors remain dismal, with &lt;25% of children with high grade glioma surviving five years after initial diagnosis and nearly all patients with diffuse intrinsic pontine glioma succumbing to the disease within 9-12 months. Moreover, even among brain tumor survivors, many patients are left with long-term cognitive and/or neuroendocrine sequalae. Therefore, more efficacious therapeutic modalities that can improve the patient’s quality of life and increase their survival are urgently needed. 3D organoid cultures have arisen as clinically relevant and molecularly accurate in vitro brain tumor model systems for preclinical drug testing. These models have demonstrated to faithfully recapitulate the genomic and phenotypic complexities of the original tumor and thereby, can reliably predict the patient response to treatment. Recognizing the impact of the tumor microenvironment and the brain developmental stage on brain tumor growth, we developed a novel protocol to evaluate the impact of tumor location-related niche factors on the development of brain tumoral organoids. Utilizing different growth factor combinations that are unique/selective to different regions of brain development, we were able to develop 39 PDOX-derived organoids from a total of 40 PDOX models tested (success rate: 97.5%) and 23 patient-derived organoids from a total of 29 patient samples tested (success rate: 79%). Furthermore, cellular characterization studies revealed the replication of an heterogenous cell population. Altogether, our study identifies differences on growth factor dependence for the formation of organoids from brain tumors of different locations and demonstrates that PDOX models are valuable tools for the development and optimization of protocols for organoid model establishment.
TRLS-06. A PHASE 1, SAFETY AND DOSE ESCALATION STUDY OF BXQ-350 IN COMBINATION WITH RADIATION IN PEDIATRIC PATIENTS WITH DIFFUSE MIDLINE GLIOMA OR DIFFUSE INTRINSIC PONTINE GLIOMA
Authors: Dorris Kathleen , Fouladi Maryam , Hummel Trent , Raskin Scott , III Richard Curry , Purvis Joseph , Gazda Michael , Tapolsky Gilles , Takigiku Ray 
Published: June 2023

Abstract
This trial (NCT04771897) is currently enrolling at 3 US sites; as of January 2023, a total of 8 patients have been enrolled. Enrollment of cohort 1 (2.4 mg/kg and 54 Gy) and cohort 2 (3.2 mg/kg and 54 Gy) are completed. Enrollment in the expansion cohort is on-going. To date, no dose-limiting toxicity has been observed and the combination of BXQ-350 plus radiation has been well tolerated.
BXQ-350 is a nanovesicle formulation of Saposin C that induces apoptosis of cancer cells and an anti-tumoral immune response by lowering Sphingosine-1-Phosphate and increasing ceramides concentrations. Saposin C is a human protein encoded by the Psap gene and is an allosteric activator of enzymes involved in sphingolipid/ceramide metabolism. The significance of sphingolipid metabolism in brain cancers has been demonstrated and enzymes involved in sphingolipid metabolism are being investigated as novel therapeutic targets for adult and pediatric brain cancers.
BXQ-350 was investigated in a Phase 1 dose-escalation safety study in pediatric brain cancer patients (NCT03967093); results showed that it was well-tolerated, a MTD was not established, and the safety profile warranted the investigation of combination studies at the highest dose tested (3.2 mg/kg). Additionally, results from a Phase 1 safety and dose escalation study in adult patients with advanced solid malignancies (NCT02859857) indicated that BXQ-350 was well tolerated and showed single agent activity with evidence of modulating sphingolipid metabolism and favorably influencing the tumor microenvironment.
The primary objective of this dose-escalation study is to describe the safety profile and to determine the maximum tolerated dose of BXQ-350 in combination with radiation. BXQ-350 is administered intravenously concurrently with radiation therapy followed by adjuvant BXQ-350 until disease progression. Multiple secondary parameters are included to characterize BXQ-350’s pharmacokinetic parameters and efficacy profile and to investigate potential biomarkers.