bluuebunny/crossref_metadata_2025_split huggingface dataset:
LGG-40. TYPE II RAF INHIBITOR TOVORAFENIB IN RELAPSED/REFRACTORY PEDIATRIC LOW-GRADE GLIOMA (PLGG): REVERSIBLE DECREASES IN GROWTH VELOCITY IN THE PHASE 2 FIREFLY-1 TRIAL
Authors: Kline Cassie , Waanders Angela J , Ziegler David S , Kilburn Lindsay B , Nysom Karsten , van der Lugt Jasper , Hassall Timothy E , Gerber Nicolas U , Segal Devorah , Larouche Valérie , Khuong-Quang Dong-Anh , Hansford Jordan R , Leary Sarah E S , Driever Pablo Hernáiz , Bailey Simon , Perreault Sébastien , McCowage Geoffrey , Witt Olaf , Baxter Patricia A , Kang Hyoung Jin , Han Jung Woo , Hargrave Darren , Franson Andrea T , Oren Michal Yalon , Toledano Helen , Abdelbaki Mohamed S , Jabado Nada , Gottardo Nicholas G , Whipple Nicholas S , Chi Susan N , Oren Liat , Tan Enrica E K , Mueller Sabine , Wright Karen D , Blackman Samuel C , Qiu Jiaheng , Podesta Dolores , Walter Ashley , Da Costa Daniel , Manley Peter , McLeod Lisa , Landi Daniel B 
Published: June 2024

Abstract
BACKGROUND: Tovorafenib is an investigational, selective, CNS-penetrant, type II RAF inhibitor. The ongoing FIREFLY-1 (NCT04775485) phase 2 study (Kilburn LK, et al. Nat Med. 2023) of tovorafenib in BRAF-altered pLGG resulted in antitumor activity and manageable safety. Decreased growth velocity (GV) was observed; this is an update on GV changes in skeletally immature children receiving tovorafenib. Methods A planned safety analysis was completed on August 8, 2023 on 137 patients (Arm 1: 77 & Arm 2: 60). Additional follow-up on all cases of decreased GV (an AESI) reported to the global safety database (GSDB) as of January 19, 2024 is provided. Results Overall, 29% had decreased GV from baseline (BL); 19% had ≥50% decrease. Of the 40 with this AESI, 75% had pre-existing neuromuscular or endocrine comorbidities potentially affecting normal growth, including 6 on GnRH-analogues for precocious puberty and 9 with BL heights 2 SDs above/below average for age and sex. Nineteen had on-treatment bone age assessments; none showed bone age advancement from BL or premature growth plate closure. No osteopenia or abnormal fractures reported. All 10 who discontinued or interrupted tovorafenib for ≥3 months for any reason (mean follow-up: 5.8 months), with off-treatment growth measurements available, showed post-treatment annualized GV (AGV) recovery (average AGV: on-treatment, 1.1 cm/y; off-treatment, 8 cm/y), with some exceeding expected average AGV for age. A 4-year-old boy with 1.2 cm/y AGV on-treatment had 12.3 cm/y AGV off-treatment (follow-up: 2 months). Five additional events of decreased GV in patients not on study FIREFLY-1 were reported to the GSDB; 4 of 5 had ≥3 months of off-treatment follow-up, all 4 recovered GV. Conclusions Decreased GV has been observed in patients on tovorafenib. Preliminary follow-up data in those who interrupted treatment show consistent evidence of GV recovery and preservation of growth potential on bone age studies.
MDB-10. DIVERGENT MEDULLOBLASTOMA CHROMATIN STATES DISCLOSE KDM2B AS A NOVEL ONCOGENIC DEPENDENCY
Authors: Tao Ran , Erkek Serap , Matsui Yurika , Xu Beisi , Smith Kyle S , Gao Qingsong , Li Yiran , Djekidel Nadhir , Darrow Emily , Kumar Rahul , Paul Leena , Lin Hong , Hadley Jennifer , Batts Melissa , Bhanu Natarajan V , Kutscher Lena , Garcia Benjamin A , Zhou Xin , Orr Brent A , Robinson Giles W , Wu Gang , Korbel Jan O , Peng Jamy , Pfister Stefan M , Northcott Paul A 
Published: June 2024

Abstract

BACKGROUND
Medulloblastoma (MB) is a highly malignant childhood cerebellar tumor comprising a collection of molecularly and clinically distinct entities. Group 3 and Group 4-MB subgroups originate from overlapping progenitor pools of the developing rhombic lip when neuronal differentiation hierarchies are subverted through somatic alterations. Mutations suspected to deregulate the activity of chromatin-modifying genes are pervasive in Group 3 and Group 4-MB. However, the molecular consequences of these alterations remain largely undefined.

METHODS
We characterized the chromatin landscape of fifty-two primary MBs using chromatin immunoprecipitation followed by sequencing (ChIP-seq) for six histone modifications and performed multi-modal integration with sample-matched somatic lesions, genome-wide DNA methylation, and transcriptomic profiles.

RESULTS
Analysis of differential chromatin states across MB subgroups using a Hidden Markov Model revealed a significant enrichment of the bivalent enhancer state (EnhBiv; marked by coincident H3K4me1 and H3K27me3) in Group 4-MB which localized to promoters of neurodevelopmental genes and transcription factors. To functionally dissect the pathogenetic significance of the enriched EnhBiv state in Group 4-MB, we sought to identify key regulators that confer this state. Integrative bioinformatics coupled with CUT&RUN analysis revealed significant enrichment of KDM2B, a histone lysine demethylase overexpressed in Group 4-MB, in gene promoters marked by the EnhBiv state. CRISPR gene targeting or targeted protein degradation of KDM2B selectively suppressed growth of Group 3 and Group 4-MB models in vitro and in vivo. Mechanistically, inhibition of KDM2B disrupted chromatin bivalency by blocking PRC2 complex recruitment and reducing H3K27me3 deposition, profoundly derepressing PRC2 targets involved in neuronal differentiation.

CONCLUSIONS
Our comprehensive characterization of the MB chromatin landscape in a large cohort of primary tumors provides unprecedented insights into the epigenetic basis of MB subgroups, implicating novel mechanisms of tumorigenesis, and nominating KDM2B as a selective dependency in Group 3/4-MB that should be prioritized as an attractive therapeutic target.
MDB-25. ESTABLISHING A NOVEL CEREBELLAR ORGANOID MODEL FOR INVESTIGATING HEREDITARY PREDISPOSITION TO CHILDHOOD BRAIN CANCER
Authors: Manz Frederik , Bianchini Luca , Atamian Alexander , Northcott Paul , Quadrato Giorgia , Kutscher Lena 
Published: June 2024

Abstract
During the development of the central nervous system, pools of progenitor cells undergo proliferation and subsequent differentiation into mature neurons, establishing a functional neuronal network. However, an imbalance in these processes, characterized by excessive proliferation and loss of differentiation, can lead to tumor formation in pediatric patients. In the developing cerebellum, medulloblastomas of the Sonic Hedgehog (SHH) group arise from excessive proliferation of granule neuron progenitor cells (GNPs) driven by SHH signaling, accompanied by hindered differentiation into mature granule neurons. Genetic predisposition accounts for nearly 40% of all pediatric SHH-medulloblastomas, but the development of humanized models to study these predisposition genes has been lacking. To address this gap, we created an ATOH1-driven EGFP reporter iPSC line to generate reliable cerebellar organoids focused on the development of the granule cell lineage. Our cerebellar organoid protocol yielded homogeneous organoids with robust activation of the ATOH1-EGFP reporter around day 30. Through bulk transcriptomics analysis at day 30, we observed pronounced expression of GNP markers, followed by increased expression of markers associated with mature granule neurons by day 60. Furthermore, by aligning the single-nuclei RNA sequencing (snRNAseq) data of day 60 cerebellar organoids with our human cerebellar development snRNAseq atlas, we identified various cerebellar cell types, including GNPs, mature granule neurons, Purkinje cells, interneurons, as well as glutamatergic and GABAergic neurons. Using this protocol, we examined the development of cerebellar organoids in models of hereditary predisposition to childhood cancer. Using a Gorlin syndrome model, we found that PTCH1HET organoids are larger in size than their isogenic control counterparts, while a model for ELP1HET hereditary predisposition showed no change in size compared with control organoids. These organoid models will allow us to uncover novel molecular mechanisms of hereditary predisposition using human cells.
MDB-33. SIOPE-MB6 – THE RATIONALE FOR THE NEXT EUROPEAN STANDARD RISK MEDULLOBLASTOMA PHASE II/III TRIAL
Authors: Mynarek Martin , Doz Francois , Clifford Steve C , Bailey Simon , Rutkowski Stefan , Padovani Laeticia , Bouchoucha Yassine , Partanen Marita , Verity Sarah , Sehested Astrid , Puhr Anita , Rossius Anne , Chevignard Mathilde , Dorfer Christian , Damaty Ahmed El , Beccaria Kevin , Aquilina Kristian , Hoving Eelco W , Schuhmann Martin U , Thomale Ulrich W , Milde Till 
Published: June 2024

Abstract

BACKGROUND
Neurocognitive impairment is one of the key late effects of childhood medulloblastoma and is potentially influenced by surgical resection, chemotherapy and/or radiotherapy. Still, reduction of therapy to reduce neurotoxicity may be associated with a higher risk of relapses.

METHODS
SIOP-MB6 is a European, prospective, randomized phase II/III trial, aiming to reduce late effects of neurosurgery, radiotherapy and chemotherapy using an improved clinico-molecular risk stratification. Four different interventional questions will be assessed.

RESULTS
Patients with clinically and biologically standard risk medulloblastoma (non-metastatic, no large cell/anaplastic histology, no MYC/MYCN amplification, SHH-medulloblastoma only if TP53 wildtype) are eligible for this trial. Surgical arm: The aim of surgery is randomized to be maximal safe resection (standard) or safe subtotal/near total resection, i.e. sparing critical structures, intending to leave small residual tumor behind (experimental), with systematic treatment of hydrocephalus. The primary endpoint is neurocognitive functioning. Risk-stratified adjuvant therapy: All patients receive one or two blocks of carboplatin/etoposide chemotherapy depending on degree of resection, risk stratification and randomization, followed by re-resection in case of residual tumor. Very favorable risk: Single arm Phase II trial for WNT-activated medulloblastoma. Intervention: reduction of radiotherapy and chemotherapy. Favorable risk: Single arm phase II trial for SHH medulloblastoma (TP53 wildtype) or non-WNT/non-SHH medulloblastoma (subtype VII or favourable whole chromosomal abberations phenotype). Intervention: reduction of radiotherapy and chemotherapy. Standard risk: Randomized phase III trial for non-WNT/non-SHH medulloblastoma not eligible for the favourable risk arm. Randomization in standard therapy (23.4Gy CSI, 4 cycles of cyclophosphamide/cisplatin based chemotherapy) or experimental tandem high-dose thiotepa with stem cell support, radiotherapy (23.4Gy CSI) and temozolomid maintenance. The primary endpoint of all three arms will be progression-free survival, with neurocognitive functioning among secondary endpoints.

DISCUSSION
Detailed rationales for this design will be presented during the presentation.
MDB-44. MIR-106B-5P DEPLETION IN GROUP 4 METASTATIC MEDULLOBLASTOMA SEVS FINE-TUNES MMP-2 ACTIVATION VIA DIFFERENTIAL TIMP-2 PROTEIN ABUNDANCE
Authors: Levers Connor T , Jackson Hannah K , Kerr Ian D , Dajas-Bailador Federico , Coyle Beth 
Published: June 2024

Abstract

BACKGROUND
Small Extracellular Vesicles (sEVs) are major intercellular communicators, with growing evidence of a role in establishing favourable metastatic niches during cancer progression. We have shown that, relative to their paired primary counterpart, Group 4 (Grp4) metastatic Medulloblastoma (MB) cell-lines release significantly more sEVs with increased functionally active MMP-2 on their surface, resulting in enhanced extracellular matrix degradation and subsequently increased cell invasiveness.

METHODS
Transcriptomic analysis of sEV microRNA cargoes derived from metastatic/recurrent and primary cell-line and patient CSF samples, followed by microRNA target prediction of differentially abundant microRNAs using TargetScan and miRDB was conducted. Patient dataset analysis was used to confirm microRNA target mRNA expression levels. Finally, microRNA inhibition followed by RT-qPCR or invasion assays were used to quantify changes at the gene and functional level.

RESULTS
Transcriptomic analysis demonstrated &gt;75% miR-106b-5p depletion in Grp4 MB metastatic sEVs compared to their primary sEV counterparts derived from cell-line and patient CSF samples. This microRNA is predicted to target TIMP-2, which plays a crucial role in MMP-2 activation. We confirmed TIMP-2 to be upregulated in paired metastatic Grp4 tumours relative to their primary counterpart using a publicly available patient dataset. Following miR-106b-5p inhibition in the primary cell-line, RT-qPCR analysis and invasion assays determined the existence of a complex functional response, with increasing TIMP-2 gene expression leading to decreasing invasiveness. This suggests a delicately balanced process where TIMP-2 overabundance can ultimately impede MMP-2 activation. In support of this, analysis of patient datasets showed intermediate TIMP-2 gene expression amongst Grp3/4 patients compared to less frequently metastatic subgroups.

CONCLUSIONS
Our data support the hypothesis that sEV-derived miR-106b-5p regulates enhanced ECM degradation through fine-tuning MMP-2 activation via differential TIMP-2 abundance. Future work will quantify changes in cell/sEV surface-bound TIMP-2 and MMP-2 alongside MMP-2 activation via flow cytometry and gelatin zymography respectively.
MDB-55. LYMPHOID ENHANCER-BINDING FACTOR 1 (LEF1): AN IMMUNOHISTOCHEMICAL PREDICTIVE MARKER FOR WNT-ACTIVATED MEDULLOBLASTOMA
Authors: Ranade Manali , Naik Khushi , Bapat Prachi , Gurav Mamta , Shetty Omshree , Shah Aekta , Sahay Ayushi , Prasad Maya , Singh Vikash , Shetty Prakash , Moiyadi Aliasgar , Dasgupta Archya , Chatterjee Abhishek , Chinnaswamy Girish , Gupta Tejpal , Epari Sridhar 
Published: June 2024

Abstract

AIM
To evaluate lymphoid enhancer-binding factor 1 (LEF1) immunohistochemical expression in various molecular subtypes of medulloblastoma.

MATERIALS AND METHODS
Molecular subtyping of medulloblastomas was based on real-time PCR target 12 gene panel. LEF1 immunohistochemistry was performed and its expression was correlated with histological and molecular subtypes.

RESULTS
The study cohort included 65 cases; comprising 17 WNT-activated, 20 SHH-activated, and 28 non-WNT/non-SHH [group 3: 11, group 4: 10, non-WNT/non-SHH NOS: 7] medulloblastomas. The age range was 1-40 years (≤18 years=54 [WNTa:15, SHHa:13, non-WNT/non-SHH:26], 19-40 years=11) with a median age of 9, and an interquartile range (IQR) of 5-14.5. Forty-one were males and 24 were females (M:F=1.7:1). LEF1 immunostaining was diffuse (≥50% tumour cells) in 13 cases, focal (5-49% tumour cells) in 11 cases, and negative in 41 cases. All cases with diffuse LEF1 immunostaining (n=13) were WNT-activated with classic histology. Twelve of the 13 cases had CTNNB1 mutation on Sanger sequencing and monosomy 6 by fluorescence in-situ hybridization (FISH) while 1 case was uninterpretable for CTNNB1 Sanger sequencing and chromosome 6 FISH. LEF1 staining intensity was strong in 9 cases while heterogenous in 4 cases. No differential staining pattern was observed for paediatric and adult cases. Diffuse LEF1 immunostaining was significantly associated with the WNT-activated subtype of medulloblastoma (p=&lt;0.01). Of 11 focal LEF1 positive cases, 4 were WNT-activated (all having classic histology and CTNNB1 mutation) and 7 were SHH-activated, TP53-wildtype (classic: 2 and desmoplastic nodular [D/N]: 5). None of the WNT-activated, 12 SHH-activated, TP53-wildtype (6 classic, 6 D/N), 1 SHH-activated, TP53-mutant (large-cell/Anaplastic [LC/A]) and all (n=28) non-WNT/non-SHH (classic: 25, LC/A: 3) were LEF1 negative.

CONCLUSION
Classic histology with diffuse (≥50% tumor cells; including heterogeneous intensity) LEF1 immunostaining is a good predictive marker for the WNT-activated molecular group of medulloblastoma, however focal staining is not.
MDB-60. CDK7 INHIBITION DISRUPTS ACQUIRED RESISTANCE MECHANISMS IN MYC-MB
Authors: Veo Bethany , Wang Dong , Michlin Joshua , Wimsatt Genevieve , Vibhakar Rajeev 
Published: June 2024

Abstract
Medulloblastoma (MB) is the most common malignant brain tumor in children, accounting for 20% of all pediatric brain tumors. Medulloblastoma manifests as a clinically heterogeneous tumor with varying prognoses depending on the molecular subgroup. Group 3 tumors have the worst overall prognosis, and are associated with MYC gene amplification, higher rates of metastasis, and increased likelihood of recurrence. Our prior work demonstrated that WEE1 is upregulated in all MB subtypes and is a critical mediator of MB cell viability. We have established that Myc-driven MB is particularly sensitive to the WEE1 inhibitor AZD1775. Although AZD1775 showed promising results in combination with other genotoxic agents, tumor cells frequently acquire resistance to small molecule inhibitors. Thus, to identify regulators of resistance in Myc-MB we performed a Kinome scale RNAi screen in isogenic parental and resistant cells and identified CDK7 as a key mediator of AZD1775 resistance that restored sensitivity to WEE1 inhibition when depleted. CDK7 controls transcriptional initiation by phosphorylating the c-terminal domain of RNA Pol II. CDK7 has been implicated in several Myc-associated malignancies and is frequently enriched at Super Enhancers. Enhancer-promoter interactions (EPIs) are dynamic and can facilitate resistance mechanisms by inducing additional enhancer elements to promote transcription. Here, we investigated 3D chromatin interactions by HiChIP and further assessed CTCF and H3K27ac patterns after treatment with the CDK7 inhibitor, THZ1, by Cut and Run. Our analysis suggests that AZD1775-resistant cells are reorganized to establish alternate cis-acting elements that reinforce transcription of DNA repair and proliferation genes, circumventing AZD1775 treatment. We further examine cisplatin-resistant MB cells to determine if the mechanism is consistent in Myc-MB cell lines or therapy specific. Overall, we suggest that reorganized chromatin structure aids resistance development and that inhibition of CDK7 intervenes in this process, restoring sensitivity to standard therapies.
MDB-66. HIGH-THROUGHPUT SMALL MOLECULE DRUG SCREENING, TRANSCRIPTOMICS AND INTEGRATIVE AI IDENTIFY TARGETABLE MYC-DEPENDENT THERAPEUTIC VULNERABILITIES IN HIGH-RISK MEDULLOBLASTOMA
Authors: Llargués-Sistac Gemma , Taylor Louisa , Lindsey Janet , Buttigieg Marie Claire , Morcavallo Alaide , Bowers Chantelle , Che Harvey , Kwok Colin , Williamson Daniel , Anderson John , Donovan Laura K , Hill Rebecca M , Al-Lazikani Bissan , Chesler Louis , Clifford Steven C 
Published: June 2024

Abstract

INTRODUCTION
MYC-amplified Group 3 medulloblastomas (MBGroup3-MYC) do not respond to conventional up-front therapies and are almost universally fatal (&lt;5% survival). MYC is not directly targetable. Thus, the systematic development of therapies which target complementary MYC-dependencies offers clear potential to rationally re-design effective therapeutic strategies.

METHODS
Isogenic cell-based models with regulable shRNA MYC-knockdown were developed in three independent MYC-amplified backgrounds (D283Med; D425Med; HD-MB03). These were utilised to i) define the MYC-dependent transcriptome/proteome in MBGroup3, through analysis in conjunction with our primary tumour cohort, and ii) as the basis of an automated MYC-dependent high-throughput drug screen (HTS; &gt;500 clinically-actionable compounds). Bespoke integrative AI tools and bioinformatic analysis, and subsequent siRNA/pharmacodynamic validation, identified and validated candidate MYC-dependent therapeutic vulnerabilities. Prioritised drugs were advanced to pre-clinical trials across two in vivo MBGroup3 models (GTML/Trp53KI/KI (GEMM; MYCN-driven) and GMYC (GEMM-derived allografts; MYC-driven)) to evaluate candidate efficacy and toxicity.

RESULTS
shRNA-mediated MYC knockdown could be maintained for 28 days without escape in all models and, as anticipated, was associated with cell cycle abrogation and elevated caspase-3/-7 activity. HTS across all models revealed that MYC expression confers differential dependencies to small molecule inhibitors, with 82 compounds spanning 11 major drug classes demonstrating MYC-dependent activity. AI-based integration of HTS data with model and primary patient MYC-dependent transcriptome data shortlisted multiple druggable molecular targets which, in turn, were independently validated. To date, we have progressed alisertib (AURKAi), volasertib (PLK1i) and prexasertib (CHK1i) to in vivo pre-clinical trials. Promisingly, both alisertib and prexasertib demonstrated efficacy within MBGroup3-MYC models.

CONCLUSIONS
Integrated human tumour and model-based screening approaches have enabled identification and validation of critical MYC co-dependencies, targetable using established small-molecules, to inhibit MBGroup3 tumour growth. Their further evaluation, including integration into established and/or rationally-designed combinations, will be essential next steps in their (pre-)clinical development.
MDB-69. RADIOLOGICAL PATTERNS OF RECURRENCE IN MEDULLOBLASTOMA SUBGROUPS AND CORRELATION WITH SURVIVAL
Authors: Sahu Arpita , Nair Swetha M , Dasgupta Archya , Mynalli Soujanya , Jain Ayushi , Sridhar Epari , Chatterji Abhishek , Choudhari Amitkumar , Bhattacharya Kajari , Prasad Maya , Chinnaswamy Girish , Menon Nandini , Singh Vikas , Shetty Prakash , Moiyadi Ali Asgar , Gupta Tejpal 
Published: June 2024

Abstract

BACKGROUND
Medulloblastomas can recur in up to one-third of the patients despite optimal therapy. The knowledge of the molecular group can provide clues to the possible pattern of relapse and the course of disease, with therapeutic implications. In the present study, we have identified anatomical locations and radiological patterns of relapse.

METHODS AND MATERIALS
Patients with a histopathological diagnosis and available subgroups of medulloblastoma with first relapse, treated in a single tertiary care center during 2005-2021 with available magnetic resonance imaging of brain and spine were included in the retrospective study. Statistical analysis was done using Pearson chi-square test and Fisher’s exact test.

RESULTS
127 patients were included in the final analysis. Median age at diagnosis was 12 years and time to first recurrence was 21 months. Tumor bed relapse was seen in 49% cases, maximum in SHH subgroup, p&lt;0.01. Involvement of the ventricular system (including cisterns and ventricles) was seen in 37% of cases, and was significantly associated (p:&lt;0.01) with non-WNT, non-SHH tumours. Leptomeningeal metastasis was seen in 36% of cases, with significant association (p&lt;0.01) in group 3 (75% of all group 3 cases) and group 4 tumors (50% of all group 4 cases). Disease in spine was most common in group 3 (65%) and group 4 tumours (71%), p&lt;0.01. Hippocampus was involved in 19 cases (15%), mostly in non-WNT, non-SHH (14 cases). Significant difference in survival after recurrence was seen with ventricular, extraventricular metastases with one year survival 83% and 73% respectively, p=0.02. Hippocampal involvement showed significantly decreased survival, one year survival of 37%, p&lt;0.01.

CONCLUSIONS
Leptomeningeal dissemination and diffuse disease were mostly seen in group 3 tumours, indicating their aggressive nature. The lower rates of ventricular relapse and around hippocampus in SHH medulloblastoma provide the opportunity to explore hippocampal avoidance-craniospinal irradiation.