bluuebunny/crossref_metadata_2025 huggingface dataset:
Commercial building integrated energy system: sizing and energy-economic assessment
Authors: Nikbakht Naserabad Sadegh , Akbari Vakilabadi Moslem , Ahmadi Mohammad Hossein
Published: June 2023

Integrated energy systems are one of the potential options for buildings that can reduce emission. In this research study, the energetic and economic performance of a micro-gas turbine combined heating and cooling plant coupled with a solar PV is analyzed for an office building in Iran. For each analysis, two different scenarios have been performed. System sizing parameters defined in a way that renewable to fossil fuel share is correlated to plant performance and economy. To model the studied system, a time-dependent method is used, which is the inherent characteristic of renewable energies. The renewable energies used here are solar heaters and solar panels. Contours of Net Present Value (NPV) are evaluated as a function of solar heating share and different economic parameters. In addition, optimal system sizing for a typical building is obtained and the results are provided. Effect of various major parameters shows that under the current condition and despite the supportive incentive for renewable energies, strategies and plans even without solar energy are not economically viable due to the high discount rates. In addition, results provide that, in reasonable and normal discount rate, fuel and grid electricity prices, governmental subsidization for conventional combined heat, and power (CHP) and combined cooling, heat, and power(CCHP) is not necessary, and only in this condition solar electricity selling price (i.e. governmental support program) is effective to increase renewable penetration. The results show that if the interest rate is less than 5%, the NPV becomes positive. Also, when the electricity price reaches $0.07/kWh or higher, the NPV becomes positive.
Differential perceptions of and reactions to incivil and intolerant user comments
Authors: Kümpel Anna Sophie , Unkel Julian
Published: June 2023

Building on recent research that challenges the notion that norm violations in online discussions are inherently detrimental, this study relies on a distinction between incivil and intolerant user comments and investigates how online users perceive and react to these distinct forms of antinormative discourse online. Conducting a preregistered factorial survey experiment with a nationally representative sample of n = 964 German online users, we presented participants with manipulated user comments that included statements associated with incivil (profanity; attacks toward arguments) and intolerant discourse (offensive stereotyping; violent threats). The results show that intolerant statements consistently lead to higher perceptions of offensiveness and harm to society as well as an increased intention to delete the comment containing the statement, whereas incivil statements do not. An exploratory multiverse analysis further suggests that these effects remain robust across a variety of analytical decisions.
Can lipid mediators and free fatty acids guide acute coronary syndrome diagnosis and treatment?
Authors: Uzun Gulbahar , Unal Aslihan , Basarici Ibrahim , Kucuk Murathan , Donmez Levent , Nacitarhan Cahit , Özdem Sebahat
Published: June 2023

Objective

The aim of this study was to investigate fatty acids, lipid mediator levels, and the desaturase index rates on different acute coronary syndrome types and their possible relationship with routine lipid parameters.

Methods

The study included 81 patients with myocardial infarction (MI), 20 patients with unstable angina pectoris, and 31 healthy people. Fatty acids, CD59, lipoxin A4, 8-isoprostane, serum lipids, albumin, C-reactive protein (CRP), and high sensitive troponin levels were measured in all participants.

Results

When the fatty acid groups were evaluated as a ratio of albumin, MUFA/albumin and SFA/albumin ratios were significantly higher in the MI group compared to the control group. Although CD59 and lipoxin A4 levels were higher in the control group, there was no significant differences between the groups. When lipoxin A4/CRP and CD59/CRP ratios were evaluated, the results were significantly lower than those in the control group. 

Conclusion

Lipid mediators may be useful in treating atherosclerosis by contributing to the resolution of inflammation.
Gap opening in protoplanetary discs: gas dynamics from global axisymmetric non-ideal MHD simulations with consistent thermochemistry
Authors: Hu Xiao , Li Zhi-Yun , Wang Lile , Zhu Zhaohuan , Bae Jaehan
Published: June 2023

Recent high angular resolution ALMA observations have revealed numerous gaps in protoplanetary discs. A popular interpretation has been that planets open them. Most previous investigations of planet gap-opening have concentrated on viscous discs. Here, we carry out 2D (axisymmetric) global simulations of gap opening by a planet in a wind-launching non-ideal MHD disc with consistent thermochemistry. We find a strong concentration of poloidal magnetic flux in the planet-opened gap, where the gas dynamics are magnetically dominated. The magnetic field also drives a fast (nearly sonic) meridional gas circulation in the denser disc regions near the inner and outer edges of the gap, which may be observable through high-resolution molecular line observations. The gap is more ionized than its denser surrounding regions, with a better magnetic field–matter coupling. In particular, it has a much higher abundance of molecular ion HCO+, consistent with ALMA observations of the well-studied AS 209 protoplanetary disc that has prominent gaps and fast meridional motions reaching the local sound speed. Finally, we provide fitting formulae for the ambipolar and Ohmic diffusivities as a function of the disc local density, which can be used for future 3D simulations of planet gap-opening in non-ideal MHD discs where thermochemistry is too computationally expensive to evolve self-consistently with the magneto-hydrodynamics.
A new method to constrain annihilating dark matter
Authors: Chan Man Ho , Lee Chak Man
Published: June 2023

Recent indirect searches of dark matter using gamma-ray, radio, and cosmic ray data have provided some stringent constraints on annihilating dark matter. In this article, we propose a new indirect method to constrain annihilating dark matter. By using the data of the G2 cloud near the Galactic supermassive black hole Sgr A*, we can get stringent constraints on the parameter space of dark matter mass and the annihilation cross-section, especially for the non-leptophilic annihilation channels $b\bar{b}$ and W±. For the thermal annihilation cross-section, the lower bounds of dark matter mass can be constrained up to TeV order for the non-leptophilic channels with the standard spike index γsp = 7/3.
ATRT-04. TARGETING THE COREST COMPLEX HELPS REPROGRAM AT/RT’S ABNORMAL EPIGENETIC LANDSCAPE TOWARD A DIFFERENTIATION PHENOTYPE
Authors: Geethadevi Anupa , Collard Marianne , Vaidya Nikhil , Findlay Tyler , Malebranche Kristen , Eberhart Charles , Raabe Eric , Cole Philip , Alani Rhoda , Rubens Jeffrey
Published: June 2023

Atypical teratoid/rhabdoid tumors (AT/RT) are deadly infantile brain tumors. Their aggressive phenotype results from a single recurring biallelic loss-of-function mutation in genes encoding components of the SWI/SNF chromatin-remodeling complex - mainly SMARCB1 and SMARCA4 in remaining tumors. Residual SWI/SNF activity continues to inhibit EZH2 methyltransferase except at promoter regions colocalized to REST, which associates with neuronal differentiation and tumor suppressor genes. At these sites, EZH2 increases repressive H3K27me3 marks, helping maintain AT/RT in a stem cell-like state, and driving its aggressive growth and therapy resistance.

We study the consequences of disrupting SWI/SNF inhibition at sites of EZH2/REST co-localization to target AT/RT precisely. The repressive action of REST is carried out mainly by the CoREST complex, consisting of LSD1, HDAC1/2 and RCOR. Lentiviral knockdown of RCOR2 reversed AT/RT’s stem cell-like state and induced differentiation along the glial and neuronal lineage. A decrease in the H3K27Me3 further confirmed the absence of COREST complex assembly at these sites.

We used a bifunctional LSD1 and HDAC1/2 inhibitor, Corin, to pharmacologically target the CoREST complex in AT/RT cells. Corin also induced neuronal differentiation in AT/RT with increased expression of neuronal differentiation markers and decreased expression of stem cell markers. Further, Corin reduced AT/RT cell viability and proliferation (p<0.05) and increased apoptosis (p<0.05). In mice bearing orthotopic CHLA06 tumors, convection-enhanced delivery of a single dose of Corin increased H3K27ac, demonstrating that Corin engaged its target in vivo and induced apoptosis (western blot, cPARP).

These studies demonstrate that targeting the CoREST complex disrupts AT/RT epigenetic abnormalities, reversing their stem cell-like state, slowing tumor cell growth, and inducing apoptosis. Targeting the CoREST complex with Corin is a promising new strategy that may translate into the clinical setting to help improve AT/RT’s dismal survival.
ATRT-08. THE SINGLE-CELL LANDSCAPE OF PINEOBLASTOMA IDENTIFIES DEVELOPMENTAL ORIGINS AND EXPOSES TUMORIGENIC DEPENDENCIES
Authors: Gudenas Brian , Englinger Bernhard , Liu Anthony P Y , Ahmad Sheikh Tanveer , Meredith David , Pfaff Elke , Paul Leena , Hadley Jennifer , Batts Melissa , Klimo Jr. Paul , Boop Frederick A , Gajjar Amar , Robinson Giles W , Orr Brent A , Lin Hong , Alexandrescu Sanda , Jones David T W , Filbin Mariella G , Northcott Paul A
Published: June 2023

Pineoblastoma (PB), a rare and aggressive brain tumor affecting children, presents with a highly variable age distribution and treatment outcome. Our recent bulk tumor analyses of DNA methylation and mutational landscapes uncovered four discrete PB molecular subgroups (PB-miRNA1, PB-miRNA2, PB-MYC/FOXR2, and PB-RB), providing a major advance in our understanding of biological and clinical heterogeneity. However, developmental origins of PB subgroup heterogeneity and mechanisms governing how specific genetic alterations promote malignancy remain unknown. We conducted single-nucleus RNA sequencing of 38 primary tumors, including cases from all subgroups, to uncover intra-tumoral heterogeneity, developmental origins and expose selective dependencies. Transcriptional programs driving intra-tumoral heterogeneity showed subgroup-specific patterns such as mRNA splicing associated with PB-miRNA1/2 and phototransduction in PB-RB and PB-MYC/FOXR2. Next, we created a single-cell transcriptional atlas of the murine pineal gland across 11 developmental stages and found significant associations between PB subgroups and specific differentiation states of the pinealocyte lineage, suggesting subgroup-specific developmental origins. Characterization of pineal development informed generation of biologically faithful disease models, including a novel genetically engineered mouse model of the PB-RB subgroup. PB-Rb1 mouse tumors were histologically and molecularly validated for their fidelity to human tumor counterparts, exhibiting up-regulation of key pinealocyte lineage markers that are diagnostic in patients. Using cell lines derived from our PB-Rb1 mouse model we identified several transcription factor dependencies we believe are high-jacked during normal pinealocyte development. Our findings inform the developmental origins of pineoblastoma as well as provides candidates for potential therapeutic targets.
ATRT-09. COMBINATION OF THE PI3K INHIBITOR PAXALISIB WITH THE NUCLEOSIDE ANALOG GEMCITABINE ACTIVATES THE INTEGRATED STRESS RESPONSE AND EXTENDS SURVIVAL IN ORTHOTOPIC MODELS OF ATYPICAL TERATOID/RHABDOID TUMORS
Authors: Findlay Tyler , Malebranche Kristen , Geethadevi Anupa , Eberhart Charles , Raabe Eric , Rubens Jeffrey
Published: June 2023

Relapsed atypical teratoid/rhabdoid tumors (AT/RT) are a deadly disease without a known cure. The Pacific Pediatric Neuro-Oncology Consortium (PNOC) is looking for effective combination therapies for an upcoming clinical trial to better treat relapsed AT/RT. We have previously identified that AT/RT are dependent on activation of mTORC1 and mTORC2 for growth and survival. Paxalisib is a highly brain penetrant PI3k inhibitor which acts upstream of mTOR to simultaneously inhibit mTORC1/2. In murine orthotopic xenograft models of AT/RT, Paxalisib significantly extends survival as a single agent therapy (CHLA-06: 40 to 54 days, p=0.001; BT12: 21 to 35 days, p=0.02). However, to improve the durability of this single agent therapy, we evaluated the efficacy of rational therapeutic partners. Analysis of RNAseq following mTOR inhibition (mTORi) showed an upregulation of genes associated with the integrated stress response (ISR) (ATF4, CHOP, PPP1R15A; t-test p<0.05). Gemcitabine is a pyrimidine nucleoside prodrug, which inhibits DNA synthesis and induces DNA damage, also leading to ISR activation. While the ISR can be protective, intense or prolonged activation leads to cell death. We therefore hypothesized that Paxalisib would combine with Gemcitabine to over-activate the ISR and drive AT/RT cell death. Through protein analyses, we demonstrate that combination therapy further activates the ISR compared to DMSO control (Western Blot: phospho-eIF2α, ATF4, and CHOP). Combination therapy also increases apoptosis (Western blot cPARP, MUSE Annexin V Assay) and synergizes to decrease AT/RT cell growth (SynergyFinder BLISS score CHLA-06: 16.8, BT12: 14.3, CHLA-266: 13.9). In mice bearing CHLA-06 orthotopic tumors, Paxalisib/Gemcitabine combination therapy slows tumor growth (Bioluminescent imaging) and extends median survival from 22 to 82.5 days (p<0.0001) compared to vehicle control treated mice. We aim to translate these results in this upcoming PNOC clinical trial to treat relapsed AT/RT.
ATRT-15. ATRTS HIJACK EPIGENETIC MECHANISMS TO PROMOTE IMMUNOSUPPRESSION AND ESCAPE FROM NK CELL THERAPY
Authors: Swaminathan Jyothishmathi , Ho Ben , Maegawa Shinji , Guo Lei , Laureano Alvaro , Brugmann Ben , Kennis Bridget , Dobson Tara , Shaik Shavali , Ravikumar Visweswaran , Sandberg David , Cooper Laurence , Zaky Wafik , Khatua Soumen , Silla Lucia , Lee Dean , Rao Arvind , Harmanci Arif , Xu Lin , Huang Annie , Gopalakrishnan Vidya
Published: June 2023

Atypical Teratoid/Rhabdoid Tumors (ATRTs) are malignant tumors of the central nervous system in children. They are almost universally characterized by genetic loss of SWI/SNF Related, Matrix Associated, Actin Dependent Regulator of Chromatin Subfamily member B1 (SMARCB1) - a core subunit of the ATP-dependent SWI/SNF chromatin remodeling complex, and dysregulation of lineage restricted enhancers. Here, we show that tumor subgroup-specific upregulation of a distant member of the transforming growth factor-β (TGF-β), bone morphogenic factor (BMF) family of proteins drives insensitivity to NK-mediated cytolysis in vitro and in vivo. Mechanistically, subgroup-specific loss of chromatin occupancy by the RE1 Silencing Transcription Factor (REST) to its consensus RE1 motif, allowed deposition of enhancer-specific histone H3 lysine4 (K4) mono-methylation and histone H3K27 acetylation marks to activate an enhancer-promoter interaction. Restoration of REST binding or BET-domain inhibition resulted in a significant reduction in the enhancer marks and enhancer-promoter interaction and involved histone H3K27me3 deposition at the REST binding site, to facilitate gene silencing and sensitization of ATRTs to NK-mediated cytolysis. Thus, our study has identified a novel function for REST as a modulator of tumor-intrinsic enhancer activity and tumor-extrinsic immune microenvironment. Of equal significance, we highlight a role of REST in recruiting the polycomb repressive complex-2 (PRC2) in gene silencing in ATRTs.
BIOL-05. IDENTIFICATION AND VALIDATION OF PA2G4 AS A POTENTIAL THERAPEUTIC TARGET IN PEDIATRIC DIFFUSE GLIOMAS
Authors: Sirhan Zaid , Sells Blake E , Fleming Jessica , Manring Heather R , Graham Richard T , McElroy Joseph P , Haque Saikh J , Boué Daniel R , Becker Aline P , Bell Erica H , Finlay Jonathan , Chakravarti Arnab
Published: June 2023

Brain tumors are the second most common pediatric malignancy after leukemia. High grade gliomas have a significantly high morbidity and mortality in children, with a 5-year survival rate under 20%. This study aims to identify important biological mechanisms and proteins as prognostic biomarkers and novel therapeutic targets. We hypothesize that higher grade pediatric diffuse gliomas can be effectively targeted by knocking down expression of the proliferation associated protein 2G4 (PA2G4) that binds to MYCN and prevents its ubiquitination. LC-MS/MS proteomic profiling was performed on 28 formalin-fixed paraffin embedded primary diffuse glioma samples from Nationwide Children’s Hospital (Columbus, OH). Cox proportional hazard models were used to correlate individual proteins with progression-free survival (PFS) and overall survival (OS). Differences in fold change were calculated for each protein between low grade (LGG, grade 2) and high-grade glioma (HGG, grades 3-4) patients. Ingenuity Pathway Analysis was performed considering only proteins with p-values <0.05. In vitro studies were performed to evaluate the roles of PA2G4 in the SF188 glioma cell line. In comparing high- and low-grade tumors, 471 proteins were found to be significantly differentially expressed. Eighty-six and 121 proteins were significantly associated with OS and PFS, respectively. PA2G4 was expressed 2.0-fold higher in HGG vs LGG (p=0.015). Additionally, high expression of PA2G4 protein was associated with significantly worse PFS (p=0.041) and OS (p=0.035) and selected for further studies. Preliminary in vitro results showed that knocking-down PA2G4 decreased AKT phosphorylation/activation and levels of MYCN protein. Given that activated MYCN plays critical oncogenic roles in patients with poor survival PA2G4 may serve as a novel therapeutic target in higher grade pediatric diffuse gliomas. Studies are underway to unfold how PA2G4 affects treatment resistance and tumor recurrence in pediatric patients.
BIOL-14. FROM NON-MALIGNANT TO MALIGNANT: GENERATING AND TARGETING DIFFUSE MIDLINE GLIOMA IN A NOVEL HUMAN PONTINE ORGANOID MODEL
Authors: Bessler Nils , Moreno Cristian Ruiz , Wezenaar Amber , Dommann Noëlle , Keramati Farid , Ariese Hendrikus C R , Honhoff Celina , de Blank Sam , Román Mario Barrera , Collot Raphaël , van Ineveld Ravian , Krashennikova Maria Alieva , Kranendonk Mariette E G , Wehrens Ellen J , Alemany Anna , Stunnenberg Henk G , Rios Anne C
Published: June 2023

Diffuse Midline Glioma (DMG) is a rare and aggressive pediatric cancer with no chance of survival, demonstrating a critical need for therapy development. Predictive preclinical models that take into account the unique developmental background and anatomical environment of DMG, are so far lacking. We developed a new regionally patterned brain organoid protocol based on a timely regulated sequence of morphogens. The patterned organoids give rise to pontine and medulla oblongata identity, as confirmed by transcriptomic profiling and immunofluorescence imaging. As the tissue matures, the complexity inherently takes shape and gives rise to pons-specific neurons and glial cells, offering the first human in vitro model for this region of the brain. Introducing H3K27M, including its partner mutations P53 and PDGFRA-D842V via electroporation forms de novo H3K27M diffuse midline glioma with a similar genetic make-up as found in patients. Indeed, contrary to common cell lines or PDX models, single cell sequencing and 3D imaging reveal that Organoid-DMG resembles WHO-defined primary patient cancer, including its diverse cell population heterogeneity and invasive nature. Utilizing barcode-based lineage tracing allows us to unravel and track the cancerous developmental evolution. Thus, we can now model early emerging populations and identify their transcriptomic signatures, which is conceptually impossible to conduct with patient-derived tumor tissue. In summary, we generated a bona fide DMG in vitro model which will give insights into tumorigenesis of DMG and ultimately contribute to pre-clinical drug- and immunotherapy development.
BIOL-24. USING NEEDLE WASH SPECIMEN AFTER STEREOTACTIC BIOPSY TO DEVELOP PDOX MODELS OF DIPG AND DIFFUSE MIDLINE GLIOMAS
Authors: Abdallah Aalaa , DuCuypere Michael , Xiao Sophie , Suarez Milagros , Wadhwani Nitin , Du Yuchen , Lam Sandi , Li Xiao-Nan
Published: June 2023

Obtaining viable tissue remains a major barrier for lab-based studies, especially in brain tumors deemed surgically unresectable such as diffuse midline gliomas. Surgical biopsy is performed for those tumors invested in deep and vital brain structures however, biopsied specimens are usually of small volume without additional tissue for research after clinical testing. To overcome the barrier of limited surgical specimen volume, we partnered with neurosurgeons to develop a protocol which procures viable cells from discarded biopsy needle after stereotactic biopsies to develop patient-derived orthotopic xenograft (PDOX) models. After procurement of surgical specimen and prior to disposal of biopsy needle, each stereotactic biopsy needle was washed with FBS media twice. Wash solution was collected and immediately transported on ice to the research lab. Cell number was counted for in vitro culture and for orthotropic in vivo tumor implantation. To date, 29 samples of biopsy needle washes have been obtained including 12 diffuse midline gliomas of the brain stem, 8 supratentorial diffuse midline gliomas, and 3 pineal region tumors with harvested cell number from no visible cells to 5.3 million cells (median 1 million). 14 tumors have been orthotopically implanted into matched locations of immunodeficient mouse brains. Tumor formation was confirmed in 4 out of 15 (28.5%), including 2 brain stem tumors, 1 infiltrating astrocytoma, and 1 midline glioma, after implantation of cell numbers as low as 12,500. 3 models were successfully sub-transplanted to passages II and III. Histological examination confirmed the replication of key pathological features of the originating patient tumors. In conclusion, we have developed a novel protocol to procure clinical specimen by using wash solution of stereotactic brain tumor biopsy needles for surgically unresectable tumors. Our work demonstrates a new possibility for clinical sample acquisition and tumor modeling, opening new frontiers in the field of pediatric brain tumor research.
CNSC-01. GABAERGIC NEURON-TO-GLIOMA SYNAPSES IN DIFFUSE MIDLINE GLIOMAS
Authors: Barron Tara , Yalçın Belgin , Mochizuki Aaron , Cantor Evan , Shamardani Kiarash , Tlais Dana , Franson Andrea , Lyons Samantha , Mehta Vilina , Jahan Samin Maleki , Taylor Kathryn , Keough Michael , Xu Haojun , Su Minhui , Quezada Michael , Woo Pamelyn , Fisher Paul , Campen Cynthia , Partap Sonia , Koschmann Carl , Monje Michelle
Published: June 2023

High-grade gliomas include clinically and molecularly distinct subtypes that stratify by anatomical location into diffuse midline gliomas (DMG) such as diffuse intrinsic pontine glioma (DIPG) and hemispheric high-grade gliomas. Neuronal activity drives high-grade glioma progression both through paracrine signaling and direct neuron-to-glioma synapses. Glutamatergic, AMPA receptor-dependent synapses between neurons and malignant glioma cells have been demonstrated in both pediatric and adult high-grade gliomas, but neuron-to-glioma synapses mediated by other neurotransmitters remain largely unexplored. Using whole-cell patch clamp electrophysiology, in vivo optogenetics and patient-derived glioma xenograft models, we have now identified functional, tumor-promoting GABAergic neuron-to-glioma synapses mediated by GABAA receptors in DMGs. GABAergic input has a depolarizing effect on DMG cells due to NKCC1 expression and consequently elevated intracellular chloride concentration in DMG tumor cells. As membrane depolarization increases glioma proliferation, we find that the activity of GABAergic interneurons promotes DMG proliferation in vivo. Increasing GABA signaling with the benzodiazepine lorazepam – a positive allosteric modulator of GABAA receptors commonly administered to children with DMG for nausea or anxiety - increases GABAA receptor conductance and increases glioma proliferation in orthotopic xenograft models of DMG. Conversely, levetiracetam, an anti-epileptic drug that attenuates GABAergic neuron-to-glioma synaptic currents, reduces glioma proliferation in patient-derived DMG xenografts and extends survival of mice bearing DMG xenografts. Concordant with gene expression patterns of GABAA receptor subunit genes across subtypes of glioma, depolarizing GABAergic currents were not found in hemispheric high-grade gliomas. Accordingly, neither lorazepam nor levetiracetam influenced the growth rate of hemispheric high-grade glioma patient-derived xenograft models. Retrospective real-world clinical data are consistent with these conclusions and should be replicated in future prospective clinical studies. Taken together, these findings uncover GABAergic synaptic communication between GABAergic interneurons and DMG cells, underscoring a tumor subtype-specific mechanism of brain cancer neurophysiology with important potential implications for commonly used drugs in this disease context.
DIPG-17. TREATMENT OF DIFFUSE INTRINSIC PONTINE GLIOMA USING ALLELE-SPECIFIC SIRNA TARGETING H3.3 K27M MUTANT HISTONE
Authors: Wentworth Simon , Batista Ana Rita , Alterman Julia , Khvorova Anastasia , Sena-Esteves Miguel
Published: June 2023

In recent years CNS tumors have surpassed leukemia and lymphoma as the deadliest forms of pediatric cancer, yet many of these tumors remain resistant to treatment. Understanding of the molecular pathology of a particularly fatal pediatric glioma, diffuse intrinsic pontine glioma (DIPG), has improved dramatically over the past decade. However, this knowledge has not yet yielded new targeted therapeutics or advances in treatment. The majority of DIPG tumors (~70-80%) harbor a K27M mutation in the histone H3.3 gene resulting in significant epigenetic changes which drive tumorigenesis. We are utilizing cutting edge siRNA chemistries to develop a therapeutic specifically targeting this oncohistone H3.3 K27M. It has been shown by others that ex vivo disruption of the H3.3 K27M mutant significantly delays tumor development in orthotopic xenograft models and could be a promising target for treatment of disease. New siRNA chemistries allow broad distribution and silencing throughout the brain with durable silencing for months. Utilizing this technology, we have engineered siRNA compounds that can discriminate between wild-type (WT) and K27M mutant H3.3 alleles. Our first-generation compounds achieved >95% silencing of K27M mutant with only 40% silencing of WT H3.3. We have developed second-generation compounds to improve the discrimination between the two alleles. These compounds allow us to selectively knockdown the mutant driver of DIPG tumorigenesis and we hypothesize that silencing of this oncohistone will revert the epigenetic landscape of DIPG to a more wild-type form detrimentally impacting tumor growth and progression. Together the in vivo potency of the new siRNA chemistries combined with the precision allele-specific targeting of mutant K27M oncohistone may be a promising path towards development of an effective and safe therapy for DIPG.
DIPG-55. DIRECT BRAIN-TO-BRAIN WORKFLOW ENABLES THE PRECLINICAL MODELING OF PEDIATRIC GLIOMAS
Authors: Tum Hong , Tse Christopher , Salinas Jennifer , Bayley Nicholas , Zhu Henan , Cloughesy Timothy , Liau Linda , Graeber Thomas , Nathanson David
Published: June 2023

Pediatric high-grade gliomas (pHGG) are one of the leading causes of brain cancer deaths in children. Progress towards the characterization of molecular and genetic features in adult high-grade gliomas and subsequent therapies has not yielded similar results in pHGG patients. pHGGs do not readily establish in culture and there has also been a lack of preclinical models to identify new therapeutic targets. Here, we employ a direct brain-to-brain workflow enabling the establishment of rare pediatric tumors including Atypical Teratoid/Rhabdoid Tumor (ATRT), H3_K27ALT diffuse midline gliomas, and H3_G34MUT diffuse hemispheric xenograft models. These Direct, Patient-Derived Orthotopic Xenografts (DPDOX) models recapitulate the clinical, genomic, and transcriptomic landscape of that of the parental tumors. Moreover, we have incorporated each tumor with a secreted gaussia luciferase reporter enabling the minimally-invasive tracking of intracranial tumor burden over time in response to drug perturbations. Taken together, we present a novel approach to establish pHGG models and evaluate new therapeutics.
DIPG-56. PEDIATRIC GLIOMAS EXHIBIT A UNIQUE LIPID METABOLIC PHENOTYPE DISTINCT FROM ADULT GBMS
Authors: Salinas Jennifer , Minami Jenna , Bayley Nicholas , Tse Christopher , Zhu Henan , Tum Hong , Cloughesy Timothy , Liau Linda , Graber Thomas , Nathanson David
Published: June 2023

Pediatric and adult IDH-wildtype gliomas (GBM) differ in both their clinical and molecular characteristics. However, whether distinct metabolic vulnerabilities exist between these two types of malignant brain tumors is unknown. Here, we performed integrated molecular and lipidomic profiling of both adult IDHwt and pediatric gliomas to identify distinguishable lipid phenotypes and consequent vulnerabilities. This analysis revealed IDHwt gliomas have heightened de novo lipid biosynthetic programs with an elevated abundance of triacylglycerides (TAGs). By contrast, pediatric gliomas exhibited lower lipid biosynthetic capacity and contained a higher enrichment for phospholipids. As a consequence of this unique metabolic program, pediatric gliomas relied of uptake of environmental complex fatty acids derived from normal resident brain cells for growth. Accordingly, therapeutic abrogation of lipid scavenging pathways selectively inhibited proliferation of pediatric gliomas compared to adult IDHwt counterparts. Together, these studies identify distinct metabolic programs among adult and pediatric gliomas, revealing new therapeutically actionable targets to slow pediatric glioma growth.
EPEN-01. ZFTA-RELA FUSION PROGRAMS CONVERGE ON YAP PATHWAY ACTIVATION IN EPENDYMOMA
Authors: Stuckert Austin , Varadharajan Srinidhi , Mack Stephen
Published: June 2023

Approximately two thirds of supratentorial ependymoma are driven by the ZFTA-RELA gene fusion. ZFTA is a recently described gene with a role in DNA binding and transcriptional regulation, while RELA (p65) is a known principal mediator of the canonical NFkB pathway, a pathway activated many human malignancies. The underlying mechanism of NFkB pathway protein interaction with the ZFTA-RELA fusion to drive tumorgenesis has not yet been described. In this study, we utilized our autochthonous mouse tumor model using in utero electroporation (IUE) of the embryonic mouse brain to explore these questions. Using rapid immunoprecipitation mass spectrometry of endogenous proteins (RIME) targeting HA-tagged ZFTA-RELA fusion in our IUE model, we demonstrate that both canonical and non-canonical NFkB proteins interact with ZFTA-RELA protein in ZFTA-RELA fusion ependymoma. Focusing on select key NFkB proteins, we performed chromatin immunoprecipitation sequencing (ChIP-Seq) targeting p50/NFkB1, a protein that partners with RELA/p65 in the canonical NFkB pathway, revealing that p50/NFkB1 regulatory programs define active genes that are both distinct from and shared with the ZFTA-RELA fusion protein. Functionally, we performed CRISPR-CAS9 knock out (KO) of p50/NFkB1 and identified no phenotypic effect, as KO lines demonstrated no growth impairment. Furthermore, NFkB targeting drugs did not impair tumor growth. Given these findings, suggesting redundant transcriptional programing, we identified that ZFTA and RELA intersect with TEAD transcription factor programs to activate YAP signaling and that p50 localizes to YAP-TEAD pathway members. Targeting TEAD 1 and 4 with ChIP-Seq, we found that TEAD 1 and 4 co-regulate p50/NFkB1 and ZFTA-RELA target genes. Finally, we demonstrate YAP pathway activation across all supratentorial ependymoma, including ZFTA-RELA ependymoma. Our pathway analysis consistently converged on YAP/TEAD pathways, suggesting collaboration of ZFTA-RELA fusion with YAP/TEAD in transcriptional regulation for these tumors. Targeting YAP/TEAD may therefore represent a promising therapeutic strategy for ZFTA-RELA fusion ependymoma.
EPEN-07. A MULTICENTER STUDY OF POOR PROGNOSIS CHROMOSOME 1Q GAIN AND/OR 6Q LOSS IN POSTERIOR FOSSA A EPENDYMOMA SHOWS INCREASED PREVALENCE FROM 20% AT DIAGNOSIS TO 60% AT FIRST RECURRENCE
Authors: Donson Andrew , Bertrand Kelsey , Riemondy Kent , Gao Dexiang , Sanford Bridget , Norris Gregory , Fu Rui , Willard Nicholas , Griesinger Andrea , Amani Vladimir , Grimaldo Enrique , Hankinson Todd , Booker Ffyona , Grundy Richard , Pajtler Kristian , Ellison David , Ritzmann Timothy
Published: June 2023

Ependymoma (EPN) posterior fossa group A (PFA) has the highest rate of recurrence and the worst prognosis of all EPN types. At relapse, it is typically incurable even with re-resection and re-irradiation. The biology of recurrent PFA EPN remains largely unknown, which hinders clinical advances. In this longitudinal large multicenter study, we examined matched samples of primary and recurrent disease from PFA EPN patients (n=95) to investigate the biology of recurrence. DNA methylomic data was used to measure copy number variants (CNVs), revealing progressive large scale chromosome gains and losses in successive recurrences. These CNV changes were dominated by chromosome 1q gain and/or 6q loss (1q+/6q-), both previously identified as high-risk factors in PFA EPN, which were present in ~20% at presentation but increased to ~60% at 1st recurrence. Because 6q testing is not routinely performed, this very high incidence at recurrence has not been previously reported. Evolution of chromosomal aberrations was further explored using CNV analysis of single-nuclei RNAseq on approximately 46,000 PFA EPN cells from 6 matched pairs of primary and 1st relapse tumors that harbored CNV changes at recurrence. No evidence of rare subclones in primary tumors was observed, suggesting that chromosomal rearrangement events occur after initial presentation. Cellular and molecular characteristics associated with CNVs were examined by single-nuclei RNAseq, bulk transcriptomic analysis and immunohistochemistry, revealing that 1q+/6q- PFA have a significantly higher mitotic index, increased proportions of proliferative epithelial progenitors and decreased differentiated neoplastic subpopulations. Multivariate survival analyses showed that cases with 1q gain or 6q loss at 1st recurrence were significantly more likely to recur than cases with no 1q or 6q change. The high prevalence of 1q+/6q- at recurrence and the associated shortened survival, suggest that both these abnormalities should be routinely tested for, and used for trial stratification.
METB-10. EXPLAINABLE ARTIFICIAL INTELLIGENCE REVEALS DNA METHYLATION PATTERNS UNDERLYING BRAIN TUMOR CLASSIFICATION
Authors: Benfatto Salvatore , Hovestadt Volker
Published: June 2023

Over 100 different molecular classes of brain tumors are recognized across histopathological grades and age groups. Their precise diagnosis is crucial for prognostication and appropriate treatment decisions, particularly in pediatric patients. Recently, a random forest-based classifier trained on genome-wide DNA methylation profiles has been developed to guide the accurate classification of these tumors. Over recent years, this classifier has been applied to tens-of-thousands of patient tumors all over the world. Clinical and basic neuro-oncology research would benefit greatly from a detailed understanding of the underlying artificial intelligence decision process. However, why the algorithm arrives at a certain prediction remains unclear. Here, we develop an interpretable framework to explain the model’s decisions and to uncover DNA methylation patterns distinguishing different tumor classes. Using this approach, we demonstrate both global and local differences across epigenetic landscapes. For instance, the model frequently uses DNA methylation probes in CpG islands to distinguish IDH mutant gliomas from other tumor classes. Tumor classes associated with global hypomethylation are distinguished by probes located in broad heterochromatic domains. At the level of individual genes, we find hundreds of promoter and gene body regions specifically methylated or unmethylated in specific classes. In general, we detect a high degree of redundant information in the dataset, with multiple genes across the genome distinguishing individual tumor classes, and many CpG probes representing each gene. These findings explain the technical robustness of the array-based classifier, and provide a starting point for the design of more compact point of care assays. The results of our approach are provided to the research community via an interactive web interface. We hope that this resource will help to build up trust in the machine learning-based classifier in clinical settings, foster biomarker discovery, and enable cancer epigenome research in the context of the central nervous system tumors.
METB-13. A SINGLE-CELL GENETIC IN VIVO LINEAGE-TRACING PLATFORM FOR MEDULLOBLASTOMA
Authors: Jung Jangham , Yu Bohyeon , Hoare Owen , Diaz Aaron
Published: June 2023

Comparative single-cell studies of group 3/4 medulloblastomas (MBs) and fetal brain have identified a common hierarchy of glutamatergic-lineage cell types and an apparent cell-of-origin in the rhombic lip. An increased understanding of the genetic regulators of stem-cell maintenance and differentiation in MB would clearly be of therapeutic benefit. There is a significant need for lineage-tracing systems to model MB malignant transformation, progression, and response to therapy. We developed in vivo and in organoid genetic lineage-tracing systems with a single-cell readout. A high-complexity lentiviral library expressing heritable polyadenylated molecular barcodes was transduced into D283 and D425 patient-derived cell lines. Barcoded cells were injected into the brains of immunocompromised mice. Both preimplantation barcoded cultures and the resulting mature tumors were profiled by single-cell RNA-sequencing (scRNA-seq). This captured both endogenous RNA and barcode transcripts. While only minimal barcode clash was detected in the preimplantation cultures, we observed a clonal expansion of barcodes in mature tumors which aligned with phylogenetics analysis of expressed mutations in endogenous RNA. Methods for assessing lineage coupling between transcriptional clusters and inferring their lineage relationship were developed. Ongoing efforts to recover barcodes from tumor sections via spatial transcriptomics will be presented. These studies fill a gap in status quo models of MB which are needed to leverage recent findings derived from single-cell analysis of human tumors.
OUTC-10. SELF-REPORTED RACE AND ETHNICITY AND GENETIC ANCESTRY GROUPS SHOW DISTINCT PREVALENCE AND OUTCOMES ACROSS PEDIATRIC CENTRAL NERVOUS SYSTEM TUMORS
Authors: Corbett Ryan , Plisiewicz Alexa , McHugh Sean , Drake Emmett , Brown Miguel A , Zhang Bo , Zhong Chuwei , Kaur Charnpreet , Storm Philip B , Resnick Adam , Waszak Sebastian , Mueller Sabine , Rokita Jo Lynne , Kline Cassie
Published: June 2023

BACKGROUND

Race and ethnicity disparities have been identified in survival of pediatric central nervous system (CNS) tumors. No prior studies have investigated the comparative effects of self-identified race and ethnicity versus genetic ancestry on tumor prevalence and outcome. We examine these contributions in a retrospective analysis of pediatric patients with CNS tumors.

METHODS

Patients from Children’s Brain Tumor Network (CBTN; n=646) and Pacific Pediatric Neuro-Oncology Consortium (PNOC; n=35) with available clinical data and whole genome sequencing were included. Ancestry groups were predicted with somalier and genetic markers from reference individuals of known ancestry that participated in the 1000 Genomes Project: sub-Saharan African (AFR), admixed American (AMR), East Asian (EAS), European (EUR), and South Asian (SAS). Independence of predicted ancestry and self-reported race and ethnicity was assessed with chi-squared tests. Effects of predicted ancestry on survival were estimated using multivariate Cox models with molecular subtype and extent of tumor resection as covariates.

RESULTS

Predicted ancestry groups were highly concordant with self-reported race (χ2=897, p<0.001) and ethnicity (χ2=340, p<0.001). Patients from AFR ancestry were significantly enriched within ATRT (n=26; p=0.001) and neurofibroma plexiform (n=11; p=0.005) and patients with AMR ancestry were enriched within DMG (n=53; p<0.001). Patients diagnosed with H3 wildtype high-grade glioma (n=39) with non-EUR ancestry trended towards worse overall survival (OS; HR=2.0, p=0.07). Patients with ATRT (n=19) with AMR ancestry trended towards worse OS compared to AFRs (HR=4.1, p=0.09) and AFR patients with MB (n=78) trended toward worse OS compared to EUR patients (HR=3.7, p=0.07), including Group 4 MBs (n=39; HR=3.9, p=0.08). Patients with LGG (n=182) with non-EUR ancestry were more likely to have less than gross total/near total resection compared to patients with EUR ancestry (p=0.02).

CONCLUSIONS

Differences in ancestry are seen across pediatric CNS tumor entities and outcomes. Analyses are underway in an additional ~800 patients.
HGG-03. HIGH-GRADE GLIOMA IN YOUNG CHILDREN IS HISTOLOGICALLY, MOLECULARLY, AND CLINICALLY DIVERSE—RESULTS FROM THE SJYC07 TRIAL AND INSTITUTIONAL EXPERIENCE
Authors: Chiang Jason , Bagchi Aditi , Li Xiaoyu , Dhanda Sandeep K , Huang Jie , Pinto Soniya N , Sioson Edgar , Partap Sonia , Fisher Paul G , Bowers Daniel C , Hassall Timothy E G , Lu Congyu , Zaldivar-Peraza Airen , Wright Karen D , Sabin Noah D , Orr Brent A , Onar-Thomas Arzu , Zhou Xin , Ellison David W , Gajjar Amar , Robinson Giles W
Published: June 2023

BACKGROUND

High-grade gliomas (HGG) in young children pose a challenge due to favorable but unpredictable outcomes. While retrospective studies have broadened our understanding of tumor biology, prospective data regarding outcomes and molecular predictors is lacking.

METHODS

Young children (0-5 years) histologically diagnosed with HGG and enrolled on the SJYC07 trial or treated at St Jude Children’s Research Hospital from November 2007 to December 2020 were included. DNA methylation, whole genome (WGS), whole exome (WES), and RNA (RNA-seq) sequencing were performed on available samples and these data were integrated with standard histopathological tests to yield a diagnosis. Clinical characteristics and pre-operative imaging were analyzed.

RESULTS

Fifty-six children (0.0-4.4 years) were identified. Integrated molecular and histopathological analysis split the tumors into four categories: infant-type hemispheric glioma (IHG), HGG, low-grade glioma (LGG), and other-central nervous system (CNS) tumors (i.e., CNS embryonal tumors, CNS sarcomas, neuroepithelial tumors). IHG was the most prevalent (N=22), occurred in the youngest patients (median age 0.4 years; 0-4.4 years), and commonly harbored receptor tyrosine kinase gene fusions (7 ALK, 2 ROS1, 3 NTRK1/2/3, 4 MET). The 5-year event-free (EFS) and overall survival (OS) for IHG was 53.13% (95% CI: 35.52 -79.47) and 90.91% (95%CI: 79.66-100.00) vs. 0.0% and 16.67% (95% CI: 2.78-99.74%) for HGG (p= 0.0043, 0.00013). EFS and OS were not different between IHG and LGG (p=0.95, 0.43). Imaging review of HGG, LGG , IHG and Other CNS tumors showed that IHGs are associated with circumscribed margins (p=0.0047), hemispheric location (p=0.0010), and hemorrhage (p=0.0149).

CONCLUSIONS

HGG in young children is not a single-entity and is best defined by an integrated histopathological and molecular diagnosis. While patients with IHGs display good survival, as compared to other pediatric HGGs, they still suffer severe treatment-related morbidities. Therefore, prompt consideration for reduced adjuvant and molecularly targeted therapies is warranted.
HGG-20. NOVEL PAEDIATRIC CASE OF A SPINAL HIGH-GRADE ASTROCYTOMA WITH PILOID FEATURES IN A PATIENT WITH NOONAN SYNDROME
Authors: Staunton Jordan , Robertson Pamela Ajuyah , Harris Angela , Mayoh Chelsea , Wong Marie , Rumford Megan , Fuentes-Bolanos Noemi , Cowley Mark , Lau Loretta , Ziegler David S , Barahona Paulette , Manoharan Neevika
Published: June 2023

Noonan Syndrome (NS) is a genetic condition, known to be associated with low grade central nervous system tumours in children but only very rarely associated with high-grade gliomas. Here we describe the first reported case of a spinal high-grade astrocytoma with piloid features (HGAP) in a child with NS. This case presented as a diagnostic and treatment dilemma, prior to comprehensive molecular profiling with whole-genome germline and tumour sequencing, tumour transcriptome sequencing and DNA methylation analysis. The methylation profile was a strong match for HGAP and was critical to establish this child’s diagnosis, as this is an essential diagnostic criteria for confirmation of this relatively new tumour group. Sequencing results identified activation of the MAPK signalling pathway with somatic variants in FGFR1 and NF1 and the previously known germline pathogenic variant in PTPN11. The somatic molecular profile was consistent with those previously reported in other HGAP case series and reports, whereas the germline finding has not been previously described in individuals with this tumour type. This patient’s molecular profile adds to the small group of paediatric cases reported in the literature, continuing to expand our understanding of this new WHO diagnostic category. Confirmation of this rare diagnosis was critical to this child’s management and targetable aberrations were identified, providing alternative therapeutic options. The therapeutic targets included known drivers within the MAPK pathway, but also changes not previously associated with HGAP such as differential expression of VEGFA and PD-L1. Together this case underscores the power of precision medicine from a diagnostic, therapeutic and clinical management perspective, and describes an association between HGAP and NS which has not previously been reported.