bluuebunny/crossref_metadata_2025_split huggingface dataset:
MEDB-55. Single-cell transcriptomics reveals progenitor cells expressing a photoreceptor program as putative cells origin of MYC-driven Group 3 Medulloblastoma
Authors: Zhao Miao , Mainwaring Oliver , Rosén Gabriela , Elgendy Ramy , Doroszko Milena , Rijpkema Sanne , Sundstrom Anders , Nelander Sven , Weishaupt Holger , Furukawa Takahisa , Swartling Fredrik J 
Published: June 2022

Abstract
Brain tumors are the leading cause of childhood cancer-related death. Medulloblastoma is the most common malignant pediatric brain tumor with about 70% survival. Medulloblastoma comprises four distinct subgroups respective of genomic and molecular drivers influencing tumorigenesis. It has been established that despite being considered a single disease entity, each subgroup arises from a distinct population of cells found within unique compartments of the developing brain. The cell of origin of Group 3 medulloblastoma, the most malignant medulloblastoma subgroups, is currently unknown and remains controversial. Transcriptional profiling has revealed that Group 3 medulloblastomas are characterized by elevated expression of a photoreceptor program, which has not been described in the normal cerebellar development but is well characterized in the developing pineal gland and retinal. By investigating and comparing brain and tumor development between our previously developed medulloblastoma mice model (GMYC), where mice spontaneously develop Group 3 medulloblastoma after 4-6 months of age, and their control counterparts, we found that tumor cells emerged from progenitor cells where MYC overexpression drove the transformation of immature progenitor cells expressing a photoreceptor program. Our data suggest that MYC-driven Group 3 medulloblastoma originates from progenitor cells expressing a photoreceptor program, which has implications for future research and the development of novel treatments targeting this devastating childhood malignancy.
MEDB-64. Are Rab GTPases metastatic drivers in metastatic medulloblastoma?
Authors: Entwistle Susannah , Jackson Hannah K , Kerr Ian , Coyle Beth , Hume Alistair 
Published: June 2022

Abstract
Medulloblastoma is the most common malignant paediatric brain cancer with poorer prognosis related to the onset of metastasis. It has four molecular subgroups; Wingless (WNT), Sonic Hedgehog (SHH), group 3 and group 4, of which group 3 is the most likely to be metastatic and is therefore associated with the poorest prognosis. Exosomes are small membrane-bound extracellular vesicles of endosomal origin which contain a variety of cargo including RNA and proteins. Increased exosome release is connected with disease progression and metastasis in multiple cancers. Rabs are a family of small GTPases (70 in humans) which regulate vesicle trafficking. Several Rabs are known to regulate exosome biogenesis and secretion and may thereby contribute to cancer progression. The role of Rabs in metastatic medulloblastoma is unclear. We aim to explore whether Rabs contribute to the progression of metastatic medulloblastoma through the exosome biogenesis and secretion pathways. Through analysis of literature, databases such as ExoCarta.org, the R2: Genomics analysis and visualisation platform, and mRNA content of medulloblastoma exosomes, five novel Rab candidates were identified that may contribute to disease progression in group 3 medulloblastoma. Gene expression of these Rabs was then verified across SHH, group 3 and group 4 patient-derived cell lines using RT-qPCR, with candidate Rab expression confirmed in the three subgroups. Presence of Rab mRNA has also been found in exosomes derived from group 3 and group 4 patients, with an enrichment in group 3 exosomes. Current and future work aims to determine the potential roles of Rabs in medulloblastoma pathogenesis, and to determine whether Rabs contribute to increased exosome biogenesis which drives metastasis or are metastatic drivers in medulloblastoma themselves. Therefore, experiments to characterise Rab candidate protein expression within cells and assess their function after knockdown are necessary and timely.
MEDB-65. Molecular subclassification of a national cohort of pediatric medulloblastoma based on methylation profile
Authors: Alaña Lide , Martin-Guerrero Idoia , Navajas Aurora , Zaldumbide Laura , Mosteiro Lorena , Schwalbe Edward C , Hicks Debbie , Clifford Steven C , García-Ariza Miguel 
Published: June 2022

Abstract
INTRODUCTION: Pediatric Medulloblastoma (MB) accounts for approximately 20% of all childhood brain tumors. Molecular subgroups namely WNT, SHH, Group 3 and Group 4, exhibit divergent biology, and clinical outcomes. DNA methylation analysis is a robust option to classify pediatric MB into molecular subgroups, which allows the optimization of diagnosis and stratification of the treatment. We review the first experience of molecular subclassification carried out at the national level in our country. METHODS: Multi-center centralized prospective and retrospective study of frozen tumor samples at diagnosis from pediatric MB patients diagnosed in Spanish hospitals, from April 2021 to December 2021. A registry was created with histology review, immunohistochemical (IHC) subgrouping, and a molecular subgrouping based on the Minimal Methylation Classifier (MIMIC) from Schwalbe et al., 2017. The time from the sample centralized reception to the study result was also collected. RESULTS: 25 frozen MB tumor samples from patients at diagnosis were included. 6 were retrospective and 19 prospective. IHC classified 19 cases (76%) as non-WNT/non-SHH MBs, 3 (12%) as WNT-activated and 3 (12%) as SHH-activated. MIMIC classified, in the non-WNT/non-SHH, 6 tumors (24%) as Group 3 and 13 (52%) as Group 4. 2 cases (8%) were WNT-activated MBs and 3 (12%) were SHH-activated MBs. Only 1 case (4%) was unclassified by MIMIC (WNT using IHC). Comparing both methods (IHC and MIMIC), diagnosis agreed in 96% of cases. The response time ranged from 5 to 10 days. CONCLUSIONS: DNA methylation profiling has proven to be a robust and quick option to classify MB into subgroups and it correlates with the IHC diagnosis. This tool was successfully implemented in our national routine diagnosis, enabling a reliable and rapid molecular subgrouping classification.
MEDB-71. Molecular characterisation of group 4 medulloblastoma improves risk-stratification and its biological understanding
Authors: Goddard Jack , Castle Jemma , Southworth Emily , Fletcher Anya , Crosier Stephen , Martin-Guerrero Idoia , Garcia-Ariza Miguel , Navajas Aurora , Masliah-Planchon Julien , Bourdeaut Franck , Dufour Christelle , Goschizk Tobias , Pietsch Torsten , Richardson Stacey , Hill Rebecca M , Williamson Daniel , Bailey Simon , Schwalbe Edward C , Clifford Steven C , Hicks Debbie 
Published: June 2022

Abstract
Group 4 (MBGrp4) accounts for ~40% of medulloblastoma and the majority of non-WNT/non-SHH cases, yet its underpinning biology is poorly understood, and survival outcomes are not sufficiently explained by established clinico-pathological risk factors. We investigated the clinical and molecular correlates of MBGrp4, including second-generation methylation non-WNT/non-SHH subtypes (I-VIII) and whole chromosome aberration (WCA) subtypes (defined by chromosome 7 gain, 8 loss, and 11 loss; WCA-favourable risk [WCA-FR] ≥2 features, WCA-high risk [WCA-HR] ≤1 feature). A clinically-annotated MBGrp4 discovery cohort (n=378) was assembled from UK CCLG institutions, collaborating centres and SIOP-UKCCSG-PNET3/HIT-SIOP-PNET4 clinical trials. Contemporary molecular profiling integrating methylation/WCA subtypes and next-generation sequencing was performed. Survival modelling was carried out with patients &gt;3 years old who received craniospinal irradiation (n=336). Association analysis confirmed relationships between methylation and WCA subtypes. Subtypes VI and VII were enriched for WCA-FR (p&lt;0.0001) and aneuploidy, whereas subtype VIII was defined solely by i17q (p&lt;0.0001). Whilst we observed an overall low mutational burden, WCA-HR harboured recurrent mutations in genes involved in chromatin remodelling (p=0.007). No gene-specific events were associated with disease risk, however integration of both methylation subtype and WCA groups enabled improved risk-stratification survival models that outperformed current schemes. The optimal MBGrp4-specific model stratified patients into: favourable-risk (local disease, subtype VII or subtype VI with WCA-FR; 39/194 [20%], 97% 5-year PFS), very-high-risk (metastatic disease with WCA-HR; 71/194 [37%], 50% 5-year PFS) and high-risk (remaining patients; 84/194 [43%], 67% 5-year PFS). Findings were validated in independent cohorts. Comprehensive clinico-molecular assessment of MBGrp4 provides important understanding of its clinical and biological heterogeneity. Our novel MBGrp4 stratification scheme removes standard risk disease and identifies a favourable risk group (20% of MBGrp4) with potential for therapy de-escalation. Current therapeutic strategies are insufficient for the very-high risk group (encompassing 37% of MBGrp4), for whom novel therapies are urgently required.
MEDB-72. MOLECULAR CHARACTERIZATION OF MEDULLOBLASTOMAS IN A SINGLE INSTITUTION
Authors: Tan Enrica E K , Tan Mui Li , Kuick Chik Hong , Yong Min Hwee , Low Sharon Y Y , Chang Kenneth T E , Tan Char Loo 
Published: June 2022

Abstract
INTRODUCTION: The four molecular groups (WNT, SHH, Group 3 and Group 4) in medulloblastoma have been well established for the past decade. New subgroups within the four principal molecular groups have recently been discovered and recognized by WHO classification of Central Nervous System Tumours (5th edition). Subgroups were reported to have distinct somatic copy-number aberrations and clinical outcomes. This further classification could be helpful to refine prognostication and potentially provide risk stratification for treatment planning. AIM: To interrogate archival medulloblastoma samples using Oncoscan Microarray Assay, correlate with clinical features and consider the assay for clinical use. METHODS: Thirty-one archival samples with histological diagnosis of medulloblastoma and molecular grouping results from NanoString were retrieved and evaluated with Oncoscan Microarray Assay. Twenty-six were subjected to DNA methylation profiling to compare the results. Eight cases also had molecular data from next-generation sequencing (NGS) done with the in-house Ampliseq Childhood Cancer Panel. Correlation was made with clinical characteristics and outcomes of these 31 patients. RESULTS: OncoScan microarray showed distinct differences in the copy number profiles of the 31 medulloblastoma samples. Seventeen samples could be further classified into one of 12 subgroups. However, further subgrouping was challenging without first determining the main molecular group especially amongst non-WNT/SHH tumours. DNA methylation results provided corroboration with the Oncoscan subgrouping results in 25 of 26 samples. NGS panel detected additional genetic alterations in 5 of 8 samples. CONCLUSIONS: Oncoscan Microarray Assay showed potential in providing additional molecular information for further subgrouping of medulloblastoma, but was insufficient for determining the main molecular groups. Moving forward, molecular characterization could instead be done through use of NGS panel and DNA methylation, which provides tumour epigenetic profiling on top of copy number variants. These could be used alongside the NanoString platform, which is performed routinely for all medulloblastomas at our centre.
MEDB-75. Treatment-induced pulmonary toxicity in patients with medulloblastoma: a retrospective analysis on 2 Italian institutions’ cohorts
Authors: Biassoni Veronica , Busia Alessandra , Barretta Francesco , Gandola Lorenza , Vennarini Sabina , Meroni Silvia , Mastronuzzi Angela , Del Baldo Giada , Chiesa Silvia , Pignoli Emanuele , Terenziani Monica , Pecori Emilia , Schiavello Elisabetta , Massimino Maura 
Published: June 2022

Abstract
BACKGROUND: Incidence of iatrogenic pulmonary toxicity is around 20%. Apart from bleomycin fibrosis, the role of lomustine, HD-thiotepa, autologous stem-cells transplantation(APBSCT) and their synergy with craniospinal irradiation(CSI) are unclear. To elucidate their role in lung-function impairment, we retrospectively evaluated 39 medulloblastoma patients treated at INT-Milan and OPBG-Rome. METHODS: 39 patients (17 females, median RT age 8 years) treated for localized(29) or metastatic(10) medulloblastoma in 2000-2020 and with spirometric assessment, were considered. Treatment included: SIOP-like-PNET IV(19), high-risk protocol(19), infant protocol without RT(1). CSI doses were: 23.4Gy(20), 31.2Gy(8), 36Gy(6) and 39Gy(4); 4 received protons and 34 photons(9 VMAT, 25 3D), 11 hyperfractionated-accelerated-RT; 33 had 6 median CCNU cycles; 6 APBSCT. RESULTS: Median follow-up: 98 months. All patients performed at least one spirometry at median 5 years after RT. Eight (20.6%) had mildly pathological spirometries, 8 Forced Vital Capacity (FVC%)&lt;90%. RT age was not associated with FVC%/ PEF% (p=0.319 and 0.405). A lower Peak Expiratory Flow(PEF%) was marginally associated to APBSCT group (p=0.062) with FVC%(≤90% vs &gt;90%) similar but less significant(p=0.163). Median FVC%/PEF% were higher in the CCNU-group without reaching significance (p=0.436 and 0.062): this was a standard-risk group not receiving APBSCT nor higher RT doses. Even though the lung volume encompassed by 5-10 Gy isodoses was greater in VMATvs3D RT(p&lt;0.001 and p=0.015), there were no significant differences in ventilatory parameters. FVC%/PEF% were negatively associated to CSI dose. Since no relevant lung volume is involved in high doses, a multifactorial etiology could be speculated. CONCLUSIONS: Preliminary data show no significant FVC%/PEF% reduction. Small sample size and differences in spirometry techniques impose larger cohorts accrual to elucidate potential treatment-induced pulmonary impairment in the pediatric population thus validating the use of spirometry during treatment/follow-up.
MEDB-77. Metastasic medulloblastoma: radiological features and its correlation with molecular subgroups and dissemination pattern
Authors: Bellón Marina Caballero , Moreno Marta Pérez-Somarriba , Lavarino Cinzia , Lopez Vicente Santa-María , Martinez Ofelia Cruz , Lopez Jordi Muchart , La Madrid Andrés Morales 
Published: June 2022

Abstract
Medulloblastoma (MB) is the most frequent malignant childhood brain tumor. Four molecular subgroups have been described (WNT, SHH, group3, group4), which are associated with a different biological profile, prognosis, specific MRI characteristics and patterns of metastatic dissemination. We aimed to determine the imaging features of the metastatic MB and its molecular subgroup and their outcomes. Retrospective single-center analytic-observational study conducted from January 2004-January 2022 in a tertiary-care center. Pediatric patients with metastatic medulloblastoma at disease onset were included. We collected epidemiological and clinical characteristics, treatment received, and outcomes. The molecular subgroup was determined by its methylation profile. MRI were reviewed by the neuroradiologist. Sixty-three patients were diagnosed, 17 (26.9%) were metastatic. The median age at diagnosis was 5.1 years (range 2.1-17.5 years), 58.8% were male. According to histopathologic classification, fifteen patients (93.8%) were classic,1 (6.3%) desmoplastic. Molecular subgroup analysis showed 2 WNT (12.5%), 1 SHH (6.3%), 3 (18.8%) group 3 (G3) and 5 (31.2%) group 4 (G4). Four patients (25%) were classified as G3/G4 and 1 (6.3%) as mixed. Five patients (29.4%) were M2 and 12 patients (70.6%) were M3 according to Chang staging system. The location in the cerebellar hemispheres was only observed in SHH patient while G3 tumors presented homogeneous contrast enhancement. All WNT, G3 and G4 were located in IV ventricle. We found no association between molecular subgroup and metastatic site (intracranial vs spinal, Fisher test, p=0.45). All patients presented with metastasis in the third ventricular infundibular recess were G4. Four patients died, all of them were G3 or G3/G4. Our results supported the literature previously reported. According to the MRI imaging features, the molecular medulloblastoma subgroups could be suggested. The presence of metastasis in the infundibular recess suggested MB group 4. However, the dissemination pattern could not be associated with any subgroup in our series.
MEDB-79. MYC-driven upregulation of thede novo serine and glycine pathway is a novel therapeutic target for Group 3 MYC-amplified Medulloblastoma
Authors: Adiamah Magretta , Lindsey Janet C , Burté Florence , Kohe Sarah , Morcavallo Alaide , Blair Helen , Hill Rebecca M , Singh Mankaran , Crosier Stephen , Zhang Tong , Maddocks Oliver , Peet Andrew , Chesler Louis , Hickson Ian , Maxwell Ross , Clifford Steven C 
Published: June 2022

Abstract
Despite advances in the molecular sub-classification and risk-stratification of medulloblastoma (MB), a subset of tumours remain refractory to current multimodal therapies. Group 3 (MBGroup3) patients represent around 25% of MBs, and amplification and elevated expression of MYC in this group correlates with dismal clinical outcomes. Since direct targeting of MYC remains elusive, understanding and exploiting metabolic dependencies in MYC-amplified MBGroup3 may reveal novel therapeutic opportunities. We engineered three independent regulable MYC-amplified MBGroup3 cell-based models, each harbouring doxycycline-inducible anti-MYC shRNAs (two independent species) or a non-silencing shRNA control. In all three models, MYC knockdown (KD) revealed persistent MYC-dependent cancer phenotypes, reduction in proliferation and cell cycle progression. We utilised 1H high-resolution magic angle spectroscopy (HRMAS) and stable isotope-resolved metabolomics to assess changes in intracellular metabolites and pathway dynamics when MYC expression was modulated. Profiling revealed consistent MYC-dependent changes in metabolite concentrations across models. Notably, glycine was consistently accumulated following MYC KD suggesting altered pathway dynamics. 13C-glucose tracing further revealed a reduction in glucose-derived serine and glycine (de novo synthesis) following MYC KD which was attributable to lower expression of PHGDH, the rate-limiting enzyme of this pathway. Furthermore, in human primary tumours, elevated expression of PHGDH was associated with MYC amplification and poorer survival outcomes. MYC expressing cells showed greater sensitivity to pharmacological inhibition of PHGDH compared to MYC KD (MBGroup3) and MBSHH subgroup cell lines in vitro. Critically, targeting PHGDH in vivo, using MYC-dependent xenografts and genetically engineered mouse models, consistently slowed tumour progression and increased survival. In summary, metabolic profiling has uncovered MYC-dependent metabolic alterations and revealed the de novo serine/glycine synthesis pathway as a novel and clinically relevant therapeutic target in MYC-amplified MBGroup3. Together, these findings reveal metabolic vulnerabilities of MYC-amplified MBGroup3 which represent novel therapeutic opportunities for this poor-prognosis disease group.
MEDB-82. Exploring cell-cell communication networks in medulloblastoma using single-cell genomics
Authors: Gabler Lisa , Gojo Johannes , Smith Kyle S , Bihannic Laure , Filbin Mariella G , Northcott Paul A , Berger Walter , Hovestadt Volker 
Published: June 2022

Abstract
Medulloblastoma is a high-risk embryonal brain tumor arising in the cerebellum. Genomic profiling has revealed a striking molecular heterogeneity between medulloblastoma patients, yet treatment regimens are mostly uniform. Many children with medulloblastoma die from their disease and surviving patients often face severe long-term side effects, highlighting an urgent need for more effective treatment options. We and others have recently identified pronounced intra-tumoral heterogeneity and defined cellular hierarchies within medulloblastoma tumors. The functional role of these cellular hierarchies remains unknown. We now hypothesize the existence of an inter-cellular communication network that is maintained by receptor/ligand interactions. To test our hypothesis, we use our medulloblastoma single-cell RNA sequencing dataset of 25 patients, as well as bulk RNA sequencing, DNA methylation array, and genome sequencing data across molecular subtypes. Single-cell RNA sequencing data are analyzed to dissect cell compartments characterized by high expression of potentially oncogenic receptors and their respective ligands. Consequently, cell type-specific roles in auto- or paracrine signal transduction within the cellular community are explored. We further investigate downstream oncogenic signaling pathways by approximating transcription factor activity and explore genetic and epigenetic activation mechanisms by matched genome sequencing and DNA methylation profiling, respectively. Our findings will be applied to deconvolute bulk RNA sequencing data, thus identifying therapeutically relevant signaling networks in larger cohorts of medulloblastoma patients. Eventually, candidate targets will be validated on patient-derived cell models and xenografts by overexpression and inhibition studies. Together, here we aim at identifying tumor-driving receptor/ligand interactions in medulloblastoma, with the goal to define targets susceptible to precision oncology approaches.
MEDB-87. Transcriptome-driven drug repurposing in group 3 medulloblastoma
Authors: Doss David , Kanchan Ranjana , Perumal Naveenkumar , Batra Surinder , Mahapatra Sidharth 
Published: June 2022

Abstract
Across the molecular spectrum of medulloblastoma (MB), group 3 (G3) tumors are the most aggressive with &lt;50% five-year survival, the lowest of all MB subgroups. G3 MB tumors are characterized by frequent metastases at diagnosis, unique methylation profiles, MYC amplification, and i17q, but these unique molecular features have yet to be exploited for therapeutic purposes despite their contribution to the disease process. As such, we sought to address this gap in survivorship by identifying FDA-approved compounds with the potential to inhibit cellular processes critical to G3 MB tumor proliferation and metastasis, aiming to exploit the unique molecular pathogenesis of G3 tumors. Guided by analysis of RNA-sequencing data from locally obtained, patient-derived MB samples against the LINCS chemical perturbagens database, we identified nortriptyline (NT), a tricyclic antidepressant, as a candidate MB therapeutic due to: 1) its ability to revert the transcriptomic signature of G3 MB to a normal cerebellum-like state and 2) its ability to cross the blood-brain barrier. We first identified the IC50 of NT in D425 and HDMB03 cells as 28μM and 20μM, respectively. Then, we observed that NT increased apoptosis of HDMB03 cells 3-fold by flow cytometry and confirmed our observations with Western blotting of apoptotic markers. Additionally, NT treatment resulted in abrogation of colony formation, impairment of wound healing, and inhibition of cell migration and invasion in vitro in HDMB03 cells. In all, transcriptome-driven drug repurposing holds great promise, as identifying novel uses for compounds with a known safety profile can deliver effective treatments into the hands of both patients and physicians in an expedited manner when compared to traditional means.