bluuebunny/crossref_metadata_2025_split huggingface dataset:
MDB-09. IMPACT OF PRDM6 ON CHROMATIN ACCESSIBILITY, GENE EXPRESSION, AND MEDULLOBLASTOMA FORMATION
Authors: Schmidt Christin , Husain Sarah , Carlson Annika , Cohen Sarah , Westelman Samantha , Wang Linyu , Weiss William , Schwer Bjoern 
Published: June 2023

Abstract
Group 4 medulloblastoma (MB) is the most common medulloblastoma subgroup and shows high incidence of metastasis and late-onset relapse cases. These tumors lack a unifying oncogenic driver and treatment targets, despite extensive genomic characterization. Group 4 MBs are characterized by recurrent genetic alterations in chromatin modifiers and amplification of stemness genes. A substantial fraction of Group 4 MBs are characterized by enhancer hijacking through tandem duplication of SNCAIP, resulting in high expression of PRDM6, a putative transcriptional repressor and histone methyltransferase. Some PRDM6-overexpressing medulloblastoma cases show additional mutations in chromatin regulators and high MYCN expression. We set out to elucidate the impact and oncogenic potential of sustained PRDM6 expression in early neural stem cell populations and patient-derived medulloblastoma cells. We find that PRDM6 expression in human iPSC-derived neuroepithelial stem cells (NESCs) results in tumor growth in mice at low penetrance. Moreover, we find that PRDM6 expression in MYCN-overexpressing NESCs does not further alter tumor aggressiveness or survival in vivo. Notably, PRDM6 overexpression in the patient-derived Group 3 MYC-amplified D283-Med cell line causes significantly increased aggressiveness of tumor growth and shorter survival in mice. At the cellular level, PRDM6 localizes to the nucleus, suggesting a role in gene expression regulation. Consistent with this notion, ATAC-seq and RNA-seq analysis of PRDM6-NESCs and PRDM6-D283-Med cells reveals major changes in chromatin accessibility and gene expression, specifically upregulation of integrin family members and gene family members of focal adhesion and extracellular matrix receptor interaction pathways. We conclude that PRDM6 promotes tumor growth in NESCs and may play a role in tumor maintenance through interactions with the extracellular matrix and tumor microenvironment.
MDB-13. CURRENT STATUS OF DIAGNOSIS AND TREATMENT FOR HIGH-RISK STAGE M2/M3 NON-WNT SUBTYPES MEDULLOBLASTOMA IN SOUTH CHINA
Authors: Cai Linbo , Lai Mingyao , Li Juan 
Published: June 2023

Abstract

OBJECTIVE
To analyze the current diagnosis and treatment status of high-risk stage M2/M3 non-WNT types medulloblastoma in China, and explore the optimal treatment option.

METHODS
The inclusion criteria were as follows: (1) age≤18 years old; (2) medulloblastoma was diagnosed by surgical pathology at initial diagnosis; (3) molecular subtyping: non-WNT types; (4) Chang’s stage: M2/M3. Exclusion criteria: cases of WNT molecular subtype were excluded. Clinical data of the patients were included in the analysis, and the overall survival rate and the survival difference between each molecular subtype group were analyzed.

RESULTS
A total of 247 children with medulloblastoma under 18 years old were admitted to Guangdong Sanjiu Brain Hospital from January 1, 2017, to December 31, 2022. In line with the inclusion criteria, a total of 31 children were enrolled in the present study. All patients were treated with conventional radiotherapy and chemotherapy according to the Chinese Guidelines for diagnosing and treating medulloblastoma. The median age of enrolled patients was 5 years (range 1-15 years), counting 21 males and 10 females. According to the Chang staging system, 16 patients were in the M2 stage, and 15 were in the M3 stage. 8, 11, and 12 patients were in Group 3, Group 4, and SHH molecular subgroups, respectively. Survival analysis showed that the 5-year survival rate of 31 children was 50.2%, and there was no significant difference in the 5-year survival rate between different molecular subgroups (p=0.57).

CONCLUSIONS
The overall prognosis of high-risk M2 and M3 staged medulloblastoma is poor. Except for the WNT subtype, the optimal treatment strategy for medulloblastoma with metastasis is still worth exploring.
MDB-19. MULTIOMIC PROFILING OF MEDULLOBLASTOMA REVEALS SUBTYPE-SPECIFIC TARGETABLE ALTERATIONS AT THE PROTEOME AND N-GLYCAN LEVEL
Authors: Godbole Shweta , Voss Hannah , Schlumbohm Simon , Schumann Yannis , Peng Bojia , Mynarek Martin , Rutkowski Stefan , Dottermusch Matthias , Dorostkar Mario M , Koshunov Andrey , Mair Thomas , Pfister Stefan M , Neumann Philipp , Hartmann Christian , Weis Joachim , Liesche-Starnecker Friederike , Guan Yudong , Schlüter Hartmut , Schüller Ulrich , Krisp Christoph , Neumann Julia E 
Published: June 2023

Abstract
Medulloblastomas (MBs) are malignant pediatric brain tumors which are clinically and histologically very heterogeneous. Epigenomic and transcriptomic analyses have advanced the understanding of these tumors and four main molecular subgroups – which themselves comprise several subtypes- have been defined: WNT-activated MB, Sonic hedgehog (SHH)-activated MB, Group3 and Group4 MB. Despite tremendous advances in classification and stratification, the pathogenesis of subtypes is still poorly understood and there is still a lack of targeted therapies. In contrast to nucleic acids, proteins more directly account for the phenotype and hold the potential to discover clinically relevant phenotypes, new biomarkers and therapy targets. In this study, we put together a harmonized cohort of 167 MB samples and integrated proteome data with DNA methylome and N-glycan data. At proteome level, we found six stable subtypes which could be assigned to two main molecular signatures namely-transcriptional/translational processes (pWNT, pG3myc and pSHHt) and synaptic/immunological processes (pG3, pG4 and pSHHs). pG3myc MB showed poor survival and accumulated high risk features such as anaplastic histology, epigenetic subtype II and MYC amplification. They showed an overlap of proteome patterns with favorable pWNT MBs but displayed significantly different protein abundancies of the vincristine resistance associated TriC/CCT complex and N-glycan turnover associated factors. Of note. N-glycan profiles distinguished MB subtypes and pG3myc MBs were enriched by complex bisecting N-glycans. We further identified Tenascin C (TNC) and Palmdelphin (PALMD) as suitable biomarkers for the pWNT and pG3myc MBs, respectively. Integration of proteome and DNA methylome data revealed that pWNT MBs showed the highest correlation of data modalities among MB subtypes, indicating a higher conservation of biological processes compared to other proteome subtypes. Our results shed light on new targetable alterations in MB and set a foundation for potential immunotherapies targeting glycan structures.
MDB-24. A DATA-DRIVEN APPROACH FOR THE IDENTIFICATION OF NEW SYNERGISTIC DRUG COMBINATIONS AGAINST NEURAL CANCERS
Authors: Popova Gergana , Larsson Ida , Koc Alper , Krona Cecilia , Nelander Sven 
Published: June 2023

Abstract
High-risk medulloblastomas are tumours with a poor survival prognosis (≤ 50%), which are currently treated with radiation therapy and DNA-damaging chemotherapy. The severe side effects of these treatments, including developmental problems and secondary tumours, underscore the need for new treatments with reduced toxicity. An attractive target for such therapy is the Myc-family proteins since high-risk medulloblastomas amplify either N-Myc (SHH-MB, G4-MB) or c-Myc (G3-MB). While the proteins from the Myc family themselves are often referred to as pharmacologically intractable, their levels and activity can be modulated by indirect targeting, e.g. inhibition of proteins located upstream or downstream of c-Myc/N-Myc. The diverse cellular processes and pathways that c-Myc and N-Myc are involved in, however, suggest that several Myc pathways must be interrupted simultaneously to achieve a lasting effect. To identify such multimodal interventions against Myc, we performed a principal component analysis of RNA sequencing data from patient-derived medulloblastoma cells (MB002, G3, MYC-amplified) and DAOY cells (SHH-group, no MYC amplification) that were treated with 120 small molecules. In the subsequent analysis, we focused on a selection of ~ 40 genes that represent common upstream regulators and downstream targets of either c-Myc or N-Myc. Applying a principal component analysis to these particular markers, we expect that the drugs that affect different pathways associated with c-Myc activity and are located at the opposite ends of the PC1 and PC2 axis should have a synergistic effect. Additionally, we expected that the drugs located closer to each other, which affect closely related pathways, would either have no effect or would be antagonistic. Our PCA distribution method can be used to select synergistic combinations in a manner that is easily extended to new compounds. This approach may allow fast screening of compounds for estimation of the treatment effect.
MDB-32. TRANSLATION OF NON-CANONICAL OPEN READING FRAMES AS A CANCER CELL SURVIVAL MECHANISM IN CHILDHOOD MEDULLOBLASTOMA
Authors: Hofman Damon , Ruiz-Orera Jorge , Yannuzzi Ian , Murugesan Rakesh , van Dinter Jip , Clauser Karl , Condurat Alexandra , Herman Amy , Shanmugam Vignesh , Zhou Kevin , Vogelzang Jayne , Wang Li , Roth Jennifer , Ligon Keith , Phoenix Timothy , Root David , Golub Todd , Bandopadhayay Pratiti , van Heesch Sebastiaan , Prensner John 
Published: June 2023

Abstract
High-risk medulloblastoma is one of the most recalcitrant pediatric cancers, and children with MYC-amplified disease frequently succumb to relapsed disease. Extensive analyses of the coding genome in this disease have characterized additional somatic events in some subsets of patients, though most tumors lack targetable mutations and do not yield insights regarding their aggressive behavior. At the same time, medulloblastoma is known to exhibit extensive rewiring of translational control in MYC-driven tumors, consistent with recent genetic evidence that the impact of this transcription factor on control of mRNA translation may be the most critical aspect of its function during tumorigenesis. Therefore, to propose previously unknown mechanisms for this disease, we have investigated the functional impact of translation of non-canonical open reading frames (ORFs) across medulloblastoma model systems. We demonstrate that these ORFs are commonly translated in medulloblastoma model systems and patient tumors, correlating with disease subtype. Using genome-wide CRISPR/Cas9 screens, we found that ORFs are frequently essential for cell survival in medulloblastoma and describe widespread reliance on upstream open reading frames (uORFs) in particular. From these, we identify a uORF in the ASNSD1 gene that is selectively upregulated and required for maintenance of cell survival by coordinating the function of the prefoldin-like complex, a poorly understood complex implicated in post-translational control. Together, our findings provide a blueprint for oncogenic uORFs as critical disease mediators both in medulloblastoma and, by extension, human cancers more broadly.
MDB-37. CDK9 IS A DRUGGABLE MEDIATOR SUSTAINING MYC-DRIVEN TRANSCRIPTIONAL CIRCUITRY IN MEDULLOBLASTOMA
Authors: Krishna Madhavan , Walker Faye , Sobral Lays Martin , Wang Dong , Veo Bethany , Balakrishnan Ilango , Pierce Angela , Serkova Natalie , Foreman Nicholas , Venkataraman Sujatha , Vibhakar Rajeev , Dahl Nathan 
Published: June 2023

Abstract
Though long recognized as a master regulator of cell proliferation across a wide range of cancers, Myc has proven elusive to direct therapeutic targeting. The CDK9-containing PTEFb, complexed with either BRD4 or SEC, facilitates Myc-driven transcriptional programs and is necessary for sustaining expression of Myc itself. Advances in development of clinical-grade CDK9 inhibitors creates an opportunity to examine this as a rational therapy for Myc-driven medulloblastoma (Myc-MB). In order to define the enhancer-promoter circuitry driving Myc expression in medulloblastoma, we performed chromosome conformation capture (Hi-C) from primary patient Myc-MB samples. Using a combination of CUT&RUN and RNA-seq, we find that treatment with the CDK9 inhibitor zotiraciclib depletes Myc binding and transcriptional activity at enhancer elements within the Myc topologically associated domain, largely abrogating transcriptional output from the Myc promoter. This leads to a decrease in Myc binding genome-wide with a concordant downregulation of hallmark Myc-driven transcriptional programs. Myc-MB cell lines are sensitive to CDK9 inhibition at low nanomolar concentrations, with a loss of fitness as measured by decreased proliferative or clonogenic potential and a marked induction of apoptosis. Clinically relevant CDK9 inhibitors show variable efficacy in vivo, but CNS-penetrant agents achieved a significant prolongation in xenograft survival. Together, these data demonstrate that CDK9 catalytic activity represents a druggable vulnerability underpinning Myc-driven transcriptional programs. The development of CNS-penetrant CDK9 inhibitors may open new avenues for rational therapy in these high-risk medulloblastomas.
MDB-41. TARGETING EPIGENETIC REGULATORS TO INHIBIT GROUP 3 MEDULLOBLASTOMA MIGRATION
Authors: Jangde Nitish , Walter Thomas Jordan , Ayad Nagi 
Published: June 2023

Abstract
Medulloblastoma highly malignant type of childhood brain cancer which develops at the cerebellum. Medulloblastoma can be grouped into four molecular subtypes; Sonic Hedgehog (Shh), Wnt, group 3, and group 4 based on their molecular development. Mostly group 3 medulloblastoma are highly malignant subtype. Medulloblastoma migration from the cerebellum to the leptomeningeal space and spinal cord is critical for worsening the symptoms. Targeting the medulloblastoma migration would potentially attenuate the symptoms. Identifying potential epigenetic regulators and targeting them might be an effective approach to cure the symptoms in medulloblastoma patients. CRISPR epigenome library screening targeting more than 500 epigenetic factors by using more than 3000 sgRNA can help to identify potential epigenetic regulators to medulloblastoma migration. Group 3 medulloblastoma tumor is highly malignant so, we have selected a group 3 medulloblastoma human cell line D425 for our study. CRISPR epigenome library or sg RNA targeting 500 epigenetic genes was introduced into D425 cells with the help of lentiviral particles. The cells were antibiotically selected and expanded after selection. In vitro, trans-well migration assays were performed with technical and biological replicates. The cells that migrated through the transmembrane were collected and the cells which did not show any migration were also collected followed by enrichment. The DNA isolation followed by amplification of barcoded sequences identifiers tagged to different sgRNAs were size selected and undergone for Illumina NGS sequencing. The NGS sequencing results will reveal the key epigenetic factors involved in the migration of Group 3 medulloblastoma. After confirmation of pathway analysis and in vitro and in vivo validation would identify potential factors. This study will ultimately help us to find a potential epigenetic regulator for targeted therapy to inhibit migration of group 3 medulloblastoma to reduce the symptoms and combine with other effective drugs to establish synergistic effects for treatment.
MDB-42. UNCOVERING DYNAMIC CHANGES IN MEDULLOBLASTOMA ASSOCIATED VASCULATURE IN ZEBRAFISH
Authors: Morris Elysse , Daignault-Mill Sheena , Ju Robert J , da Silva Jason , Gordon Emma , Wainwright Brandon , Stehbens Samantha , Genovesi Laura , Lagendijk Anne 
Published: June 2023

Abstract
Medulloblastoma (MB) is an embryonal-derived lesion arising in the cerebellum, contributing to 20% of childhood brain tumours and 63% of intracranial embryonal tumours. Currently, standard of care includes surgical resection and chemotherapy, used in conjunction with radiation. While these treatments have significantly improved survival rates, the therapy side effects are detrimental to survivors’ quality of life. Furthermore, relapse occurs in 30% of patients and unfortunately these are untreatable and therefore fatal for 95% of patients. It is presumed that in patients that present with a recurrent tumour, initial treatment has been ineffective. A major cause of this can be the heterogenous vasculature in and around the tumour. Recent studies have identified that the blood brain barrier (BBB), in the context of MB, is highly heterogenous with differences in BBB cellular composition and integrity between MB sub-types and within single tumours. It remains unclear however, how these vascular differences emerge and what the primary defects are. This gap in our knowledge is mainly due to the lack of models that allow long-term live imaging. We have established a xenograft approach to examine human MB tumour cells in zebrafish embryonal brains. We have validated that human Medulloblastoma cells of the Group 3 (Gp3) MB subgroup, are viable in zebrafish brains. This work has also identified that in the presence of these human Gp3 MB tumour cells, the local vasculature becomes dysmorphic and tortuous over time. Timelapse imaging of these tumour and vasculature interactions demonstrates that there is a rapid and long ranging angiogenic response with new vessel sprouts growing towards the tumour cells. By utilising our large range of transgenic zebrafish lines, we will continue investigating how MB cells interact and alter distinctive BBB cell types and how these changes impact vessel function.
MDB-43. GRADIENT ENTROPY-BASED RADIOMIC RISK-SCORE FROM T1-WEIGHTED PRE-TREATMENT MRI SCANS CAN PREDICT SURVIVAL IN PEDIATRIC MEDULLOBLASTOMA
Authors: Bareja Rohan , Ismail Marwa , Martin Doug , Nayate Ameya , Yadav Ipsa , Labbad Murad , Tamrazi Benita , Salloum Ralph , Margol Ashley , Judkins Alexander , Iyer Sukanya , de Blank Peter , Tiwari Pallavi 
Published: June 2023

Abstract

BACKGROUND
Medulloblastoma (MB) is the most frequent malignant brain tumor in children with an inadequate 5-year survival rate of 70-75%. A key determinate in MB treatment (consisting of radiation, chemotherapy) is the accurate risk-stratification of patients into low- and high-risk. The current stratification approaches (Chang’s classification, molecular categorization) are sub-optimal in predicting individual patient outcomes. Reliable risk-assessment approaches can significantly impact treatment management. Our group previously developed a new radiomics feature COLLAGE that measures the orientation of local intensity gradients as an estimate of lesion heterogeneity. We hypothesize that the disorder (i.e., heterogeneity) in orientation of local per-voxel intensity measured by COLLAGE, will tease-out differences in patients with low - versus high-risk MB tumors.

METHODS
T1-weighted MRI scans of 49 pediatric MB patients were retrospectively collected from Children’s Hospital Los Angeles and Cincinnati Children’s Hospital Medical Center. Registration of the scans was performed via age-specific pediatric atlases, followed by skull stripping and bias correction. Ground truth annotations for tumor sub-compartments; enhancing tumor, edema, and non-enhancing tumor, were generated by two experienced radiologists. Then, 52 Collage features were extracted from each of these sub-compartments, followed by conducting a Lasso model and a cox-proportional hazards model to identify the top features for risk-stratification. A continuous risk score was created for every patient and a risk threshold was obtained from the fitted cox model to stratify patients into low- and high-risk.

RESULTS
Our risk-score consisted of 13 top COLLAGE features from edema and 14 from non-enhancing tumor sub-compartments, respectively, and demonstrated significant differences between low- and high-risk patients (p = .017 for edema, p =0.0027 for non-enhancing tumor).

CONCLUSION
Our preliminary analysis suggests that gradient-entropy radiomic risk score maybe able to predict overall survival in pediatric MB tumors. In future, we plan to include additional patients to perform independent multi-site analysis.
MDB-45. SELECTIVE B7-H3 INHIBITORS NI1 AND NI4 REDUCE AGGRESSIVENESS OF GROUP 3 MEDULLOBLASTOMA
Authors: Krishnan Prakadeeswari Gopala , Kanchan Ranjana , Doss David , Alfrefaei Hamdan , Agarwal Prachi , Chhonker Yashpal , Murry D J J , Trippier Paul , Mahapatra Sidharth 
Published: June 2023

Abstract
Medulloblastoma (MB) is a primary childhood malignancy of the central nervous system (CNS). Clinically heterogenous MB are sub-grouped into four molecular subgroups, i.e. Wingless (WNT), Sonic Hedgehog (SHH), Group 3, and Group 4. Among all, Group 3 MB (G3MB) is known to be the most aggressive form, with less than 50% five-year survival. G3MB are associated with large-cell/anaplastic (LCA) histology, distinctive methylation profile, amplification of MYC, and isochromosome 17q (i17q). Targeting these high-risk molecular features unique to G3MB has been challenging, necessitating alternative approaches to therapy for G3-MB. One innovative approach is immunotherapy, which is largely impeded by inhibitory immune checkpoints. B7 homolog 3 (B7-H3/CD276), an immunosuppressive immune checkpoint protein and member of B7 superfamily, is significantly enriched in pediatric malignancies of CNS including G3MB. The enhanced expression of B7-H3/CD276 has been associated with aggressive and metastatic potential. B7-H3/CD276 is also a primary target of miR-1253, a novel tumor suppressor gene silenced in G3MB. Using a structure-based drug discovery pipeline, we screened the ChemBridge library of compounds to discover selective B7-H3 small-molecule inhibitors. Selective B7-H3 inhibitors Ni1 and Ni4 exhibited strong binding scores, CNS penetrance, and oral bioavailability. In vitro, both compounds had appreciably low IC50 values of 3µM (Ni1) and 0.75µM (Ni4). Further, both compounds inhibited wound healing and colony formation. Ni1 shifted the thermostability of B7-H3, suggesting in vitro biding. Ni1 has also undergone PK/PD and MTD studies in vivo, showing stability in serum, good blood-brain barrier permeability, and a half-life of 8 hours. We are now elucidating B7-H3-activated downstream signaling through JAK2/STAT3 signaling and testing the in vivo efficacy for Ni1 against G3MB tumors in a murine model.