bluuebunny/crossref_metadata_2025_split huggingface dataset:
MDB-63. AN INTERNATIONAL META-ANALYSIS OF SHH MEDULLOBLASTOMA SUBTYPES DEFINES A CLINICALLY SIGNIFICANT HIGH-RISK VARIANT OF SHH-SUBTYPE 3
Authors: Schwalbe Edward C , Sill Martin , Suzuki Hiro , Charron Frederic , Taylor Michael D , Pfister Stefan M , Clifford Steven C 
Published: June 2024

Abstract

BACKGROUND
The distinction of MBSHH into four methylation-dependent subgroups was recognized by the WHO in 2021. However, these subgroups have not previously been defined by international experimental consensus and their clinico-molecular features and behavior have not formally been investigated in large cohorts. We aimed to robustly identify SHH subgroups through analysis of MBSHH with DNA-methylation profiling.

METHODS
A cohort of 683 MBSHH, confidently classified using the Heidelberg classifier v12.5, was assembled for analysis from multiple international studies. To define subgroups, we applied consensus sampling-based clustering approaches to tumor methylomes, including assessment of confidence in class-definition and inter-technique concordance. The clinico-molecular features of consensus subgroups were investigated.

RESULTS
Lowest complexity analysis supported the division of MBSHH into the 4 WHO-subtypes. SHH-1 and SHH-2 were associated with lower age and infrequent mutations of PTCH1/SUFU; SHH-2 was distinguished from SHH-1 by enriched MBEN histology, absence of chromosome 2 gain, less frequent metastasis and more favorable overall-survival. SHH-4 presented in older children and adults (3-57; median 24 years), and was primarily defined by mutations in U1-snRNA (67/72). Consensus analyses supported the division of SHH-subgroup-3 into three. Importantly, the SHH-3C subtype was associated with a coalescence of high-risk features (LCA histology, TP53mut, MYCNamp/GLI2amp) alongside 3p, 10q and 17p loss, and had dismal survival. The remaining SHH-3A/B subtypes were characterized by 9q loss, frequent focal amplifications of TERT and PPM1D, and equivalent better survival.

CONCLUSIONS
This study affirms the distinction of MBSHH into 4 major subgroups. For infant disease, SHH-2 is a favorable-risk marker. For childhood-MBSHH, the SHH-3C subtype provides a molecular definition of high-risk that subsumes other previously-defined high-risk disease markers (LCA, MYCNamp, TP53mut) into a unified high-risk disease group. The other SHH-3 subtypes behave similarly and are favorable-risk. These subtypes have potential to enhance molecularly-guided risk-stratification in routine diagnostics, to improve patient outcomes and quality-of-life.
MDB-64. NOVEL TRANSCRIPTS ASSOCIATE WITH SURVIVAL IN CHILDHOOD MEDULLOBLASTOMA
Authors: Mateos Marion K , Williamson Daniel , Danilenko Marina , Goddard Jack , Crosier Stephen , Fletcher Anya , Schwalbe Edward , Hicks Debbie , Bailey Simon , Clifford Steven C 
Published: June 2024

Abstract

BACKGROUND
Medulloblastoma is the commonest malignant brain tumour in childhood, with progression-free survival (PFS) &lt;65% in high-risk disease. Novel biomarkers, independent of current clinicopathological risk factors, could enhance understanding of biology and support improved treatment approaches.

METHODS
Using high-depth RNA sequencing of 217 patients, we identified novel multi-exonic medulloblastoma transcripts using a de novo analysis. We evaluated these alongside known/curated gene transcripts, including correlative survival analysis for 170 patients (aged 3-16 years and treated with curative intent). Multivariable survival analyses of the overall cohort (n=145) and a MBGroup3/MBGroup4 (Group3/Group4)-specific subcohort (n=95) was undertaken to identify prognostic transcripts, adjusting for current risk criteria and correcting for multiple testing.

RESULTS
From 3,150 novel transcripts identified, expression of 217 varied significantly and were further assessed. One was prognostic for PFS independent of subgroup (located on chromosome 20) while three were independently prognostic within Group3/Group4 (located on chromosome 1, 4 and 21 respectively). Transcript presence was validated by qPCR. From &gt;60,000 known transcripts identified, 9693 were assessed. Four were independently prognostic for PFS in the whole-cohort (MRPS12, SLC25A34, MLYCD and ROGD1). In Group3/Group4, the top upregulated canonical pathways associated with PFS were: polo-like kinase, cyclin/cell cycle regulation, BRCA1/ DNA damage response, and glutamate receptor signalling. MELK and NQO2 were among the top 10 transcripts most highly associated with Group3/Group4 PFS. The prognostic significance of six transcripts (MRPS12, MLYCD, MELK, CDK4, NQO2, ROGD1) was validated in an independent Group3/Group4 dataset (n=470) while ROGD1 was prognostic independent of subgroup. Immunohistochemical validation showed low CDK4 expression, low MLYCD expression and high CHK1 expression were independent prognosticators in Group3/Group4.

CONCLUSION
De novo transcripts represent a significant component of the medulloblastoma transcriptome, providing prognostic information, and enhancing biological understanding of Group3/Group4 disease. CHK1 and MELK represent promising validated candidates for further evaluation as prognostic biomarkers in Group3/Group4 medulloblastoma.
MDB-72. BREFELDIN A (BFA) INDUCES CD133 PROTEOLYTIC PROCESSING IN MEDULLOBLASTOMA STEM CELLS (MBSCS)
Authors: Spinello Zaira , Cese Martina , Ronci Maurizio , Giusti Laura , Abballe Luana , Miele Evelina , Ferretti Elisabetta , Catanzaro Giuseppina 
Published: June 2024

Abstract

BACKGROUND
Medulloblastoma (MB) is a malignant brain tumor occurring in children, characterized by elevated resistance to conventional chemotherapy. Medulloblastoma stem cells (MBSCs) represent a fraction of the tumor cell population which has been associated with poor prognosis and refractoriness to conventional therapies. CD133 (Prominin 1, PROM1) is a transmembrane protein serving as a cancer stem cell marker associated with cancer progression. Brefeldin A (BFA) is an antibiotic disrupting the Golgi apparatus, thus triggering Endoplasmic reticulum (ER) stress signaling pathways. BFA cancer-inhibitory properties have been already described in cancer of different tissue origin. However, the effects of BFA on MBCSs have not been investigated yet. Thus, the aim of this study was to characterize the response of MBSCs to BFA and the effects induced by BFA on CD133.

METHODS
Human group 3 MB (G3MB) cell lines were grown in stem selective medium (B27™) and treated with 0.3 uM BFA for 24h before collection. Apoptosis, clonogenicity and CD133 expression were evaluated. CD133 was immunoprecipitated and the corresponding bands were excised and analyzed by nanoLC-MS/MS. Raw data were processed using PEAKS XPro.

RESULTS
Our results show that BFA-treated cells induced the overexpression of a CD133 isoform that was missing the N-terminus region. Moreover, we found a downregulation of CD133 activated intracellular signalling together with a reduced exposition on cell membrane.

CONCLUSIONS
We report here for the first time, a N-terminus proteolytic processing of CD133, potentially associated to the cell trafficking effects induced by BFA. Finally, this study suggests a proof of principle for the design of novel molecules with similar structures and mechanism of action of BFA.
MDB-73. INHIBITING THE B7-H3 CHECKPOINT IN MEDULLOBLASTOMA
Authors: Moziak Kirsten , Pensabene Juliana , Perez Natalia Muñoz , Yazejian Rita , Picarda Elodie , Zhang Xingxing , Martin Allison M 
Published: June 2024

Abstract

INTRODUCTION
Tumors express immune checkpoints to evade detection and clearance by the immune system. Immune checkpoint inhibition (ICI) allows for tumor clearance. Medulloblastoma (MB) has not seen success with ICI and relapsed/refractory tumors remain incurable. B7-H3 is an immune checkpoint that is highly and specifically expressed by many cancers including MB. It is implicated in immune evasion in cancer. We hypothesize inhibiting B7-H3 in MB will enhance the anti-tumorigenic properties of immune cells.

METHODS
Murine MB cells, which mimic aggressive disease, were transduced with a CRISPR/Cas9 lentivirus (courtesy of Zhang lab) to create a B7-H3 knockout (B7-H3–). Unsuccessful iterations of the same CRISPR/Cas9 sgRNA were used as a B7-H3+ control. B7-H3+ and B7-H3– cells were co-cultured for 5 days with splenic, bead isolated, CD4-T cells from C57BL/6J mice. Proliferation of the T cells was measured with Cell Trace Violet via flow cytometry using a Cytek Aurora.

RESULTS
We saw comparable tumor cell inhibition of T cell proliferation when cultured with B7-H3+ and B7-H3– tumor cells, as measured by CTV elution.

CONCLUSIONS
We saw similar amounts of T cell proliferation inhibition from both B7-H3 – and + tumor cells. This could indicate a few possibilities. First, B7-H3 may not be contributing to CD4-T cell inhibition, in which case it is important to explore its role in other immune cells. Another option is that B7-H3 is targeting the function of these cells, rather than the proliferation. To examine this, we could look at markers of effector function. Lastly, B7-H3 could be mediating inhibition of CD4-T cells via other cell(s) in the tumor microenvironment (TME) of MB, which we could test in vivo. If B7-H3 promotes ant-tumorigenic immune responses, it would be a promising approach relapsed/refractory medulloblastoma that presently has no cure, as well as other cancers that highly express it.
MDB-74. SERINE/GLYCINE METABOLISM REPRESENTS A NOVEL TARGETABLE THERAPEUTIC VULNERABILITY IN MYC-AMPLIFIED MEDULLOBLASTOMA
Authors: Adiamah Magretta , Poole Bethany , Lindsey Janet C , Swartz Shanel , Morcavallo Alaide , Gosling Samantha Jepson , Singh Mankaran , Blair Helen J , Kohe Sarah , Zhang Tong , Maddocks Oliver , Peet Andrew , Chesler Louis , Hickson Ian , Maxwell Ross , Hill Rebecca M , Clifford Steven C 
Published: June 2024

Abstract

BACKGROUND
Medulloblastoma is the most frequent malignant brain tumour of childhood. Whilst advances in risk-stratification and upfront multimodal therapy have led to five-year survival rates around 70%, a subset of tumours remain refractory to current therapies. Group 3 medulloblastomas (MBGRP3) are enriched for amplification or overexpression of the proto-oncogene MYC which conveys a dismal prognosis (&lt;10% survival), highlighting the urgent need for novel therapeutic strategies. Recent advances have revealed a role for metabolic reprogramming in MYC-amplified MBGRP3 tumorigenesis, providing novel opportunities for selective therapeutic targeting.

METHODS & RESULTS
To investigate MYC-dependent metabolic alterations in MBGRP3, we generated three independent isogenic MBGRP3 cell-based models with regulable MYC expression (iMBGRP3-MYC) using a doxycycline-inducible shRNA system. Using 1H high-resolution magic angle spectroscopy and stable isotope-resolved metabolomics, we identified upregulation of the de novo serine/glycine biosynthesis pathway (SGP), attributable to elevated expression of the rate-limiting enzyme PHGDH, as a novel therapeutic target. Genetic and pharmacological (NCT-503) inhibition of PHGDH induced greater cell death in MYC-expressing cells compared to MYC knockdown cells and increased survival across two independent MYC-amplified MBGRP3 mouse models. The decrease in tumour growth observed was moderate; we therefore hypothesised that a compensatory reliance on exogenous serine/glycine may play a role in sustaining tumour progression under therapy. To explore this, we investigated the impact of exogenous serine/glycine starvation on MBGRP3-MYC tumour development. Starvation resulted in a marked MYC-dependent reduction in cell viability in vitro across independent iMBGRP3-MYC models. Notably, dietary serine/glycine starvation was well-tolerated, delayed tumour progression, and increased survival (by 50%) in an MBGRP3-MYC mouse model (p=0.005), highlighting the metabolic plasticity of MYC-amplified tumours to utilise both de novo and exogenous serine/glycine sources to survive and proliferate.

CONCLUSIONS
These findings identify serine/glycine metabolism as a targetable therapeutic vulnerability within MYC-amplified MBGroup3 and a novel therapeutic strategy to treat this poor-prognosis disease group.
MDB-78. ISOCITRATE DEHYDROGENASE 1 INHIBITION PRIMES GROUP-3 MEDULLOBLASTOMAS FOR CUPROPTOSIS
Authors: Dang Derek , McKolay John , Smith Kyle , Panwalkar Pooja , Sweha Stefan , Natarajan Siva Kumar , Pun Matthew J , Ji Sunjong , Patel Diya , Animasahun Olamide , Achreja Abhinav , Ogrodzinski Martin P , Cotter Jennifer , Hawes Debra , Yang Fusheng , Doherty Robert , Franson Andrea T , Hanaford Allison R , Eberhart Charles G , Raabe Eric H , Chen Brandon , Lyssiotis Costas A , Shah Yatrik , Lunt Sophia Y , Judkins Alexander R , Prensner John , Koschmann Carl J , Waszak Sebastian , Nagrath Deepak , Northcott Paul , Venneti Sriram 
Published: June 2024

Abstract

BACKGROUND
MYC-driven Group-3 medulloblastomas (MB) are deadly and malignant pediatric brain cancers and we sought to define actionable metabolic dependencies in these tumors.

METHODS
To identify uniquely upregulated genes in Group-3 MB, we performed transcriptomic analysis on two previously published medulloblastoma RNA-seq datasets. To elucidate the relationship between c-MYC/IDH1/DLAT and assess impact on tumor metabolism, we performed metabolic and transcriptional profiling of Group-3 MB cell lines that were either untreated or were subjected to shRNA-mediated knockdown of DLAT or treatment with IDH1 inhibitor. We also treated Group-3 MB cell lines containing varying levels of DLAT expression with copper ionophore elesclomol and assessed its ability to induce toxicity. Finally, we established in vivo models of Group-3 MB via orthotopic implantation to assess the effect of DLAT knockdown, IDH1 inhibition, and cuproptosis induction on tumor growth and survival outcomes.

RESULTS
We identified upregulation of dihydrolipoyl transacetylase (DLAT), the E2-subunit of pyruvate dehydrogenase complex (PDC) in a subset of Group-3 MB. DLAT was induced by c-MYC and targeting DLAT lowered TCA-cycle metabolism and glutathione synthesis in Group-3 MB cells. We also noted upregulation of isocitrate dehydrogenase 1 (IDH1) in Group-3 MB. Remarkably, genetic and pharmacologic suppression of IDH1 epigenetically reduced c-MYC and downstream DLAT levels. DLAT is a central regulator of cuproptosis, a copper-dependent cell death mechanism induced by the copper ionophore elesclomol. DLAT expression in Group-3 MB cells correlated with increased sensitivity to cuproptosis. Elesclomol was CNS-penetrant and suppressed tumor growth in vivo in Group-3 MB animal models.

CONCLUSIONS
Our data uncover an IDH1/c-MYC dependent vulnerability that regulates DLAT levels and can be targeted to kill Group-3 MB by cuproptosis.
MDB-88. DUAL TARGETING OF PROCESSIVE TRANSCRIPTION FOR MYC-DRIVEN CIRCUITRY IN MEDULLOBLASTOMA
Authors: Walker Faye M , Madhavan Krishna , Sobral Lays Martin , Donthula Sahiti , Balakrishnan Ilango , Wang Dong , Pierce Angela , Veo Bethany , Karam Sana D , Serkova Natalie J , Foreman Nicholas K , Venkataraman Sujatha , Vibhakar Rajeev , Dahl Nathan A 
Published: June 2024

Abstract

BACKGROUND
The highest-risk medulloblastomas are driven by recurrent Myc amplifications (Myc-MB) and experience poorer outcomes despite intensive multimodal therapy. The Myc transcription factor defines core regulatory circuitry for these tumors and acts to broadly amplify downstream pro-survival transcriptional programs. Therapeutic targeting of Myc directly has proven elusive, but inhibiting transcriptional cofactors may present an indirect means of drugging the oncogenic transcriptional circuitry sustaining Myc-MB.

METHODS
Independent CRISPR-Cas9 screens were pooled to identify conserved dependencies in Myc-MB. We performed chromatin conformation capture (Hi-C) from primary patient Myc-MB samples to map enhancer-promoter interactions. We then treated in vitro and xenograft models with the dual CDK9/7 inhibitor zotiraciclib to evaluate effect on Myc-driven programs and tumor growth.

RESULTS
Eight CRISPR-Cas9 screens performed across three independent labs identify CDK9 as a conserved dependency in Myc-MB. Myc-MB cell lines are sensitive to CDK9 inhibition at low nanomolar concentrations, and these synergize with CDK7 inhibition. We find that treatment with the dual CDK9/7 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. Clinically relevant CDK9 inhibitors show variable efficacy in vivo, but CNS-penetrant agents achieved a significant prolongation in xenograft survival.

CONCLUSIONS
CDK9/7 catalytic activity represents a druggable vulnerability underpinning Myc-driven transcriptional programs. The development of CNS-penetrant CDK9/7 inhibitors may open new avenues for rational therapy in these high-risk medulloblastomas.
MDB-89. DETERMINING THE IMMUNOMODULATORY POTENTIAL OF PI3KΓ IN AGGRESSIVE MEDULLOBLASTOMA AND THE TUMOR MICROENVIRONMENT
Authors: Yazejian Rita M , Moziak Kirsten , Perez Natalia Munoz , Pensabene Juliana , Martin Allison 
Published: June 2024

Abstract

BACKGROUND
Medulloblastoma (MB) is the most common pediatric embryonal brain tumor arising in the cerebellum. It has a “cold” tumor microenvironment (TME) characterized by an abundance of immunosuppressive Tumor Associated Macrophages (TAMs) and low T-cell infiltration. TAMs include tissue resident microglia and migrating bone marrow derived macrophages. While microglia play important roles in the central nervous system through their immune surveillance and ability to activate other immune cells, they can be polarized by tumor cells toward an anti-inflammatory state which allows for maintained tumor growth and proliferation. A potential new target to combat the immunosuppressed TME of MB is the class IB isoform PI3Kγ. Inhibiting this isoform has been attributed to controlling a critical switch between immune suppression and immune stimulation in TAMs but has yet to be examined in MB and its TME. We hypothesize that inhibiting PI3Kγ in TAMs and MB tumor cells will induce an anti-tumorigenic immune response within the MB TME and promote tumor clearance.

METHODS
Engineered murine MB cells, mCB DNp53 MYC, are treated with a pan-PI3K or specific PI3Kγ inhibitor for 48 hours before being co-cultured with naïve splenic CD4 T-cells from C57BL/6J mice for 5 days. Proliferation of the T cells is measured using Cell Trace Violet through flow cytometry on a Cytek Aurora.

RESULTS
Pan-PI3K inhibition revealed that tumor cells treated with the inhibitor prior to co-culturing did not suppress T-cell proliferation as drastically when compared to untreated tumor cells. Treatment with a selective inhibitor is on-going.

CONCLUSIONS
These results suggest that inhibition of the PI3K pathway in our MB tumor cells dampens their ability to suppress T cell proliferation. The PI3K pathway may play an active role in tumor cell’s ability to induce immunosuppression. Inhibiting this pathway may be a new avenue for therapeutic intervention for relapsed/refractory MB.
MDB-106. MEDULLOBLASTOMA TUMOR MICROENVIRONMENTS SHOW INTRA- AND INTER-TUMORAL HETEROGENEITY ON SPATIAL TRANSCRIPTOMICS
Authors: Chien Franklin , Michaud Marina , Bakhtiari Mojtaba , Ross James L , Schroff Chanel , Snuderl Matija , MacDonald Tobey , Bhasin Manoj 
Published: June 2024

Abstract

BACKGROUND
Medulloblastoma defines a heterogeneous set of neuroepithelial neoplasms of the posterior fossa. Four groups of medulloblastoma are recognized: wingless (WNT), sonic hedgehog (SHH), group 3, and group 4. The tumor microenvironment (TME) influences tumor progression and response to therapy and has emerged as a growing target for the study of novel therapeutic approaches.

METHODS
We show spatial gene expression architecture through 10X Visium Spatial Sequencing on 16 formalin-fixed paraffin-embedded (FFPE) samples representing all molecular groups of medulloblastoma. Spatial transcriptomics data is correlated with clinical parameters, including M-stage at diagnosis, tumor histological classification, and outcomes data including survival and relapse status.

RESULTS
Spatial sequencing demonstrates both intra- and inter-tumoral TME heterogeneity across molecular subgroups. Unsupervised clustering and uniform manifold approximate projection illustrate clusters of distinct spatial gene expression representing cell states from different components of the TME, including tumor-associated astrocytes (TAA), macrophages (TAM), and vascular endothelium. Medulloblastoma cells constitute the majority of cells and express marker genes representing different stages of neuronal differentiation and cell cycle. Pathway analysis reveals the enrichment of pathways associated with cell motility (RHO GTPase, MET, MAPK signaling), heat shock response, growth factor signaling, and adaptive immune response (TLR, MHC-II signaling). In addition, molecular pathways known in medulloblastoma, including NF-kB and TP53 regulatory pathways, were also enriched. Neighborhood-enrichment analysis reveals the co-localization of TAMs and TAAs in close spatial relationship with mitotic progenitor-like medulloblastoma cells. Additionally, these two cell types constitute a greater proportion of the TME in patients at relapse compared to initial diagnosis.

CONCLUSION
Spatial transcriptomics enables new insight into the heterogeneity of the medulloblastoma TME. Notably, our analysis elucidates the spatial association of TAMs and TAAs with proliferating tumor cells and an increased abundance of these cell types following relapse. These initial results support the role of TAMs and TAAs in medulloblastoma progression.
MDB-107. MINNELIDE, A PROMISING COMPOUND FOR THE TREATMENT OF HIGH-RISK MEDULLOBLASTOMA
Authors: Blanco Jezabel Rodriguez , Salvador April , Sahani Pritika , Kliebe Valentin , Peterson Kendell , Turos Maria 
Published: June 2024

Abstract
Despite the overall good outcome of children with medulloblastoma (MB), a subset faces the challenge of highly aggressive metastatic tumors. The poor prognosis for these patients underscores the urgent need for advancing therapeutic approaches. Minnelide, an analog of the natural product triptolide, exhibits potent antitumor activity in preclinical and early clinical settings. Despite its efficacy and tolerable toxicity, Minnelide has not been assessed against MB. Using a bioinformatic dataset integrating cellular drug response and gene expression, we predicted sensitivity of Group 3 (G3) MB, characterized by a poor five-year survival, to triptolide/Minnelide. Subsequent experiments confirmed the ability of both triptolide and Minnelide to reduce the viability of G3 MB cells ex vivo. Transcriptomic analyses identified MYC signaling, a crucial driver of G3 MB, as a downstream target of these drugs. We validated the MYC dependency and demonstrated that triptolide affects both MYC transcription and protein stability. Notably, Minnelide acted in vivo on MYC, leading to reduced tumor growth and metastatic spread, resulting in improved survival in mouse and patient-derived G3 MB models. Furthermore, Minnelide enhanced the efficacy of adjuvant chemotherapy, suggesting its potential repurposing for treating MYC-driven G3 MB patients.