bluuebunny/crossref_metadata_2025_split huggingface dataset:
MDB-14. MULTI-OMICS OF HUMAN MEDULLOBLASTOMAS AND GENETIC LINEAGE TRACING IN VIVO IDENTIFY REGULATORS OF STEM-CELL MAINTENANCE
Authors: Yu Bohyeon , Jung Jangham , Hoare Owen , Shamardani Karin , Diaz Aaron 
Published: June 2023

Abstract
Recent studies implicate the glutamatergic lineage of the rhombic lip (RL) as the origin of group 3/4 medulloblastomas (MBs). MB stem cells resemble stalled RL progenitors and targeting common pluripotency factors induces differentiated phenotypes. However, the genetic and epigenetic regulators of stemness in MB remain incompletely understood. We profiled tissues resected from 38 patients who underwent surgery for MB at UCSF via single-nucleus RNA sequencing (snRNA-seq). Of these, 13 were also subjected to single-cell assay for transposase-accessible chromatin by sequencing (scATAC-seq). These assays generated 560,509 and 71,276 cells respectively, after quality control. Motif and latent-space analyses were used to infer cell-type specific transcription-factor expression and binding, and associated cis-regulatory enhancers. Further, we performed single-cell genetic lineage tracing on xenografts obtained from two distinct group-3/4 patient-derived lines, engineered to express heritable barcodes. We trained a machine-learning classifier on public snRNA-seq of human RL and classified Nestin-high quiescent stem-like cells, Nestin-moderate/ASPM-high proliferating progenitor cells, and glutamatergic lineage cells at various stages of differentiation in our MB clinical specimens and xenografts. Integrated analysis of these datasets maps the transition from quiescent to proliferating stem-like MB cells to more differentiated cell types at the level of transcription-factor activity and binding. We found that both the expression and binding of epigenetic regulators SUZ12, EZH2, DNMT1, and BRD7/8 were high in stem cells, but attenuated during lineage commitment. This was also the case for genes known to maintain neural stem cells in the developing brain, e.g. LIN28, FOXO3, HES6, LHX1/2/4, NUP98. Comparative analysis of developmental and MB gene expression, with motif analysis, implicates a conserved embryonal mechanism for indefinite replicative division in MB stem-like cells. These studies provide a single-cell atlas of transcriptomic and epigenetic cellular states in human MB, a map of MB cellular hierarchical organization and transcription-factor regulation of stem-cell maintenance in vivo.
MDB-15. CLINICAL CHARACTERISTICS AND OUTCOME OF CHILDHOOD LI-FRAUMENI SYNDROME MEDULLOBLASTOMA PATIENTS
Authors: Kolodziejczak Anna , Guerrini-Rousseau Lea , Planchon Julien Masliah , Mynarek Martin , Sill Martin , Autry Robert , Zhao Eric , Hirsch Steffen , Dufour Christelle , Ayrault Olivier , Waszak Sebastian , Ramaswamy Vijay , Pentikainen Virve , Clifford Steven , Schwalbe Ed , Massimi Luca , Snuderl Matija , Karajannis Matthias , White Christine , Redmond Shelagh , Loizos Loizou , Jakob Marcus , Schmid Irene , Hauer Julia , Blattmann Claudia , Filippidou Maria , Sutter Christian , Pietsch Torsten , Frank Stephan , Schewe Denis , Malkin David , Sehested Astrid , Wong Tai-Tong , Carceller Fernando , Mueller Sabine , Taylor Michael , Tabori Uri , Bouffet Eric , Kool Marcel , Sahm Felix , Kratz Christian , Sturm Dominik , Jones David , Rutkowski Stefan , Witt Olaf , Bougeard Gaëlle , Pajtler Kristian , Pfister Stefan , Bourdeaut Franck , Milde Till 
Published: June 2023

Abstract
Patients with Li-Fraumeni syndrome (LFS) who develop medulloblastoma (MB) have a very poor prognosis. The development of novel therapeutic strategies is challenged by the lack of clinical data for this patient group. We here present clinical and molecular data on a retrospective cohort of pediatric patients with LFS-associated MB.
This is an international, retrospective, multicenter cohort study. Patients with LFS-associated MB under 21 years and class 5 (pathogenic) or class 4 (likely pathogenic) constitutional TP53 variants were included. We evaluated TP53 mutation status (constitutional and somatic), DNA methylation subgroup, treatment modalities, event-free (EFS) and overall survival (OS), patterns of recurrence, as well as occurrence of secondary neoplasms.
Forty-seven individuals with LFS-associated MB were included. MBs were classified mainly as Sonic Hedgehog (SHH) group (87%). TP53 variants were classified as class 5 (70%) and class 4 (30%). The majority (74%) of TP53 variants represented missense variants. The 2-year (y-) EFS and -OS were 33% and 53%, respectively. A significantly better outcome was seen in patients who received post-operative radiotherapy (RT) (2y-EFS: 44%, 2y-OS: 60%) or chemotherapy before RT (2y-EFS: 24%, 2y-OS: 48%) compared with patients who received no RT (2y-EFS: n.a., 2y-OS: 25%). No significantly different outcomes were seen between patients treated either according to protocols including high-intensity chemotherapy or receiving only maintenance-type chemotherapy (2y-EFS: 42% and 31%, 2y-OS: 68% and 53%, respectively).
Patients with LFS-associated MB have a dismal prognosis. Use of RT in LFS-associated MB significantly increased survival rates in the presented cohort, but choice of chemotherapy regimen did not influence their clinical outcome. To improve the outcome of patients with LFS-associated MB, prospective collection of clinical data and development of novel treatments are required.
MDB-20. IMPROVING THE PERSISTENCE OF CAR T CELLS AGAINST GROUP 3 MEDULLOBLASTOMAS VIA EPIGENETIC REGULATION OF EXHAUSTION
Authors: Dukes Meghan , Houke Haley , Zindy Frederique , Youngblood Ben , Roussel Martine , Krenciute Giedre 
Published: June 2023

Abstract
Medulloblastomas (MB) are the most common malignant pediatric brain tumor with molecular subclass Group 3 (G3) requiring the most intense treatment regimen including surgery, intensive radiation followed by chemotherapy. Despite an overall 40% survival rate, survivors’ quality of life is often impaired due to whole-brain radiation leading to neurocognitive defects. Chimeric antigen receptor (CAR) T cell therapy has emerged clinically as a safe, tumor-targeted immunotherapy with the most success observed against hematological malignancies. Translating CAR T cell therapy to brain tumors has proven challenging due to lack of targetable antigens on the surface of tumor cells and lack of persistence of CAR T cells. We have previously identified that patient samples and PDOX-derived cell lines of G3 MBs consistently over-express B7-H3 (CD267) compared to normal tissue. Herein, we investigated B7-H3 targeted CAR T cell products against G3 MB in vitro and in vivo. Initial results show that B7-H3 CAR T cells are highly effective in clearing human MB tumors in NSG mice, however, 4 out 5 mice experienced late relapses that showed reduced, but still present, B7-H3 antigen expression. We hypothesize that the lack of CAR T cell persistence is ultimately responsible for tumor regrowth. To overcome this limitation, we have identified epigenetic regulators DNMT3A and TET2 that control T cell exhaustion. Using CRISPR/Cas9, we genetically knocked out DNMT3A and TET2 in CAR T cells and investigated the impact on persistence and anti-tumor activity. Our data supports the hypothesis that knock out of DNMT3A and TET2 improves antigen-dependent proliferation and persistence of B7-H3 CAR T cells against G3 MB tumor lines in vitro. DNMT3A KO shows a more sustained effect over TET2. Currently, we are optimizing in vivo experiments to investigate prolonged tumor clearance in both immunocompromised and fully immunocompetent murine models.
MDB-21. THE OTX2-REGULATED ALTERNATIVE SPLICING LANDSCAPE CONTROLS DIFFERENTIATION AND RECONSTITUTES THE DEVELOPMENTAL ORIGINS OF GROUP 3 MEDULLOBLASTOMA
Authors: Saulnier Olivier , Zagozewski Jamie , Liang Lisa , Hendrikse Liam D , Gordon Victor , Aldinger Kimberly A , Haldipur Parthiv , Borlase Stephanie , Coudiere-Morrison Ludivine , Layug Paul , Cai Ting , Porter Christopher J , Richard Stephane , Doble Brad W , Millen Kathleen J , Taylor Michael D , Werbowetski-Ogilvie Tamra E 
Published: June 2023

Abstract
Medulloblastoma (MB) is the most common malignant primary pediatric brain tumor with Group 3 MB exhibiting the worst prognosis. Overexpression/amplification of OTX2 is a molecular hallmark of Group 3 MB and is primarily known to control tumor growth through regulation of cell cycle. Here, we utilized mass spectrometry and RNA-sequencing to report a non-canonical role for OTX2 in regulating alternative splicing. RNA-sequencing conducted on two OTX2-silenced Group 3 MB tumorsphere models identified 48 differentially spliced genes (DSG) associated with RNA processing, splicing and neurodevelopment that were common between both cell lines. Further interrogation of the OTX2-regulated DSGs revealed that 15 are also significantly correlated with OTX2 expression in a set of Group 3/Group 4 MB patient samples. Pseudotime mapping of the developmental trajectories of the DSGs onto the developing rhombic lip (RL) revealed significant overlap with RL lineages, including the majority of the 15 shared OTX2-regulated DSGs. We then functionally validated specific alternatively spliced exons of two DSGs, PPHLN1 and MADD which represent “early” and “late” RL developmental stages, respectively. PPHLN1 and MADD splice-blocking morpholinos were utilized to drive exon skipping and recapitulate splicing events identified in OTX2-silenced or OTX2-wildtype tumorspheres. Exon skipping altered tumorigenic properties of Group 3 MB cells in vitro, including tumorsphere size and number. Additionally, intracerebellar injections of Group 3 MB cells treated with PPHLN1 morpholino impaired tumor initiation and growth in vivo. Further breakdown of Group 3/Group 4 MBs by PPHLN1 and MADD percent spliced in (PSI) revealed that the PPHLN1 high/MADD low PSI signature observed in our OTX2 wildtype tumorspheres is associated with the most aggressive and primitive Group 3g subtype. Together, our findings reveal a previously unrecognized regulatory role for OTX2 in controlling Group 3 MB AS and offer fresh opportunities to exploit MB-specific AS events therapeutically to abrogate tumor progression.
MDB-23. ELP1 GERMLINE DEFICIENCY SENSITIZES THE GRANULE NEURON LINEAGE TO SHH MEDULLOBLASTOMA AND EXPOSES NOVEL THERAPEUTIC VULNERABILITIES
Authors: Garcia-Lopez Jesus , Ahmad Shiekh Tanveer , Li Yiran , Gudenas Brian , Kojic Marija , Manz Friedrik , Jonchere Barbara , Mayasundari Anand , Pitre Aaron , Hadley Jennifer , Paul Leena , Batts Melissa , Pfister Stefan , Waszak Sebastian , Bianski Brandon , Tinkle Christopher , Orr Brent , Rankovic Zoran , Robinson Giles , Wainwright Brandon , Kutscher Lena , Lin Hong , Northcott Paul 
Published: June 2023

Abstract
Germline loss-of-function (LOF) variants in Elongator complex protein 1 (ELP1) are the most prevalent predisposing genetic events in childhood medulloblastoma (MB). ELP1 germline carriers develop SHH-MBs that exhibit coincident somatic PTCH1 mutations and universal loss-of-heterozygosity of the remaining ELP1 allele through chromosome 9q deletion. The molecular, biochemical, and cellular mechanisms by which germline ELP1/Elongator deficiency contribute to SHH-MB tumorigenesis remain largely unknown. Herein, we report that mice engineered to mimic germline Elp1 LOF (i.e., Elp1HET) seen in SHH-MB patients exhibit hallmark features of premalignancy events in cycling cerebellar granule neuron progenitors (GNPs), the lineage-of-origin for SHH-MB. Compared to wild-type counterparts, Elp1HET GNPs exhibit increased replication stress-associated DNA damage, homologous recombination-associated genomic instability, accelerated cell cycle kinetics, reduced p53-dependent apoptosis in response to genotoxic stress, and slowed differentiation. Orthotopic transplantation of Elp1HET GNPs harboring somatic Ptch1 inactivation into the cerebella of immunocompromised mice promotes onset of SHH-MB tumors with incomplete penetrance that exhibit reduced p53 transcriptional activity through a currently unknown mechanism(s). Concomitant Elp1 and Ptch1 gene targeting in p53-null GNPs reproduces highly penetrant cerebellar tumors recapitulating the molecular and phenotypic features of ELP1-associated SHH-MB. Finally, reactivation of the p53 pathway through preclinical treatment with an MDM2 inhibitor promotes cell death and prolongs the survival of patient-derived xenograft tumor (PDX) models harboring deleterious ELP1 mutations. Together, our findings reveal that germline Elp1 LOF heightens genomic instability and malignant transformation in cycling GNPs, providing a mechanistic model for the subgroup-restricted pattern of predisposition associated with pathogenic ELP1 germline carriers. These results provide essential mechanistic insight into the molecular and cellular basis of SHH-MB predisposition driven by ELP1 LOF and nominate therapies that overcome p53 pathway inhibition as a rational treatment option for affected children.
MDB-29. MEDULLOBLASTOMA SUBGROUP-SPECIFIC CHROMATIN STATES REVEAL NOVEL THERAPEUTIC VULNERABILITIES
Authors: Tao Ran , Gao Qingsong , Erkek Serap , Matsui Yurika , Djekidel Nadhir , Darrow Emily , Kumar Rahul , Smith Kyle , Wu Gang , Korbel Jan , Peng Jamy , Pfister Stefan , Northcott Paul 
Published: June 2023

Abstract
Medulloblastoma (MB) is a highly malignant childhood brain tumor comprising a collection of molecularly and clinically distinct entities. Mutations in chromatin-modifying genes distribute across subgroups and account for nearly half of all MBs. However, the molecular consequences of chromatin modifier alterations remain poorly understood. Herein, we characterize the chromatin landscape of fifty-two primary MBs representing each MB subgroup using chromatin immunoprecipitation followed by sequencing (ChIP-seq) for six histone marks and perform multi-layered integration with somatic genetics, genome-wide DNA methylation, and transcriptomic datasets extracted from the same tumors. Analysis of differential chromatin states across MB subgroups identified significant enrichment of a bivalent enhancer state (EnhBiv) in Group 4 MB. Group 4-specific EnhBivs mapped to promoters of key neurodevelopmental genes and transcription factors and was associated with increased DNA methylation and reduced expression. In accordance with higher EnhBivs coverage in Group 4 MB, we found that KDM2B, a H3K4me3 and H3K36me2 demethylase, is highly expressed in Group 4 MBs and patient-derived xenografts (PDXs). KDM2B knockout mediated by CRISPR targeting suppressed growth of both Group 3 MB cell lines in vitro and Group 4 MB PDXs in vivo but had no effect on control SHH-MB cells, suggesting that KDM2B is a novel selective dependency in MB. Knockout of KDM2B in MB cells induced profound upregulation of PRC2 targets, genes regulated by bivalent histone marks, as well as genes involved in neuronal differentiation. Further biochemical and molecular studies demonstrated that KDM2B interacts with PRC2 complex subunits and occupies gene promoters associated with Group 4-specific EnhBiv chromatin. In summary, our comprehensive characterization of the MB chromatin landscape in a large cohort of primary tumors provides novel insights into the epigenetic basis of MB and implicates KDM2B as a novel Group 4 MB dependency that should be prioritized as a therapeutic target in this subgroup.
MDB-30. IDENTIFICATION AND CHARACTERIZATION OF NOVEL TRANSCRIBED ULTRACONSERVED REGIONS AS LONG NON-CODING RNAS IN MEDULLOBLASTOMA
Authors: Hudson Kadie , Gibert Jr. Myron K , Zhang Ying , Dube Collin , Saha Shekhar , Vernon Ashley , Abounader Roger 
Published: June 2023

Abstract
Medulloblastoma is the most common pediatric brain tumor. While the 5-year survival rate for medulloblastoma patients has improved with molecular subgrouping, children who undergo standard of care treatments frequently experience permanent neurological deficits. Additionally, under-characterized medulloblastoma subgroups lack targeted therapies, correlating to lower survival rates for these patients. To find new therapies, a better understanding of the molecular basis of medulloblastoma is needed. This work investigates the role of “Transcribed Ultra-Conserved Regions” (TUCRs) in medulloblastoma about which there is no published literature. TUCRs represent a distinct group of 481 putative lncRNAs that are 100% conserved across human, mouse, and rat genomes. These ultra-conserved elements change 20 times slower than the average genomic region and are therefore under intense negative selection within multiple species. Since their discovery, TUCRs have only been correlated to a handful of cancers and remain exceedingly underexamined within cancer research. Using RNA-sequencing and differential gene expression analysis of medulloblastoma tumors as compared to normal human cerebellum samples, we identified a multitude of differentially expressed TUCRs spanning across all TUCR genomic annotations. In vitro experimentation using several medulloblastoma established cell lines indicated significant upregulation of these TUCR transcripts. We are currently investigating the functional effects and mechanisms of action of select differentially expressed TUCRs in medulloblastoma. Altogether, our work is investigating the oncogenic and tumor suppressive nature of TUCRs. It represents the first study of TUCRs in medulloblastoma that will significantly advance our basic understanding of this highly understudied class of molecules.
MDB-34. “INDUCING IRON IMBALANCE BY TARGETING THE ABCB7/GPX4 AXIS ACCELERATES FERROPTOSIS IN MEDULLOBLASTOMA”
Authors: Kanchan Ranjana , Perumal Naveenkumar , Doss David , Khan Parvez , Venkata Ramakanth , Thapa Ishwor , Vengoji Raghupathy , Kaushal Jyoti , Siddiqui Jawed , Nasser Mohd Wasim , Batra Surinder , Mahapatra Sidharth 
Published: June 2023

Abstract
Medulloblastomas (MB), the most common malignant pediatric brain tumor and a leading cause of childhood mortality, are stratified into four primary subgroups. Deletions within chromosomal locus 17p13.3, which houses multiple tumor suppressor genes including miR-1253, characterize high-risk group 3 tumors. These aggressive tumors also enrich iron transport genes to satisfy their high proliferative need. MiR-1253 targets iron transport by inhibiting the mitochondrial Fe-S transporter, ABCB7. This study elucidated the impact of repressing ABCB7 on cisplatin cytotoxicity in group 3 MB and whether these effects were mediated by ferroptosis. In silico and in vitro analyses revealed specific enrichment of ABCB7 and GPX4, a critical regulator of ferroptosis, in group 3 MB cell lines and tumors. MiR-1253 overexpression (miR-1253OE) resulted in downregulation of both ABCB7 and GPX4, concurrently increasing mitochondrial iron overload, mitochondrial oxidative stress, and lipid peroxidation, leading to cell death and abrogation of medullosphere formation; ABCB7 knockdown (ABCB7KD) recapitulated these effects and abrogated GPX4 expression. Fractionation studies confirmed the inhibitory impact of miR-1253OE and ABCB7KD on GPX4 expression in the cytosol and mitochondria. Seahorse studies revealed that the bulk of ATP generation was occurring in the cytoplasm through glycolysis and not via oxidative phosphorylation, suggesting mitochondrial dysfunction was triggered when ABCB7 was repressed. Cisplatin, a chemotherapeutic agent used in group 3 MB treatment, induces cell death by DNA crosslinking; it also inhibits GPX4 expression. In miR-1253OE and ABCB7KD group 3 cancer cells, cisplatin IC50 was reduced 2-fold. Resultantly, cisplatin treatment augmented oxidative stress and lipid peroxidation, depleted glutathione stores, and culminated in a higher index of ferroptosis. In a mouse model of group 3 tumors, ABCB7KD potentiated cisplatin effects and dramatically prolonged survival. The current study illustrates how targeting iron transport can augment ferroptosis to potentiate cisplatin cytotoxicity in group 3 MB tumors.
MDB-35. RECURRENT MEDULLOBLASTOMA A RARE COMPLETE RESPONSE IN EXTRA NEURAL DISEASE
Authors: Schwartz Jonathan , Weinmann Dena , Johnson Heather , Soumen Khatua , Neth Bryan , Keating Gesina 
Published: June 2023

Abstract
Extra-neural metastasis in recurrent medulloblastoma, carries a potentially fatal outcome. No robust salvageable therapeutic strategy is present, for these clinical phenotypes. We present an 18-year male, who presented at the age of 8 years as a standard risk medulloblastoma and was treated with chemotherapy (as per ACNS0331) followed by craniospinal radiation. At first recurrence in the thoracic spine, he underwent a gross total resection of the tumor, followed by high-dose stem cell chemotherapy and focal radiation. The 2nd recurrence which occurred in the thecal sac 9 years later was treated with metronomic anti angiogenic chemotherapy with outcome a complete radiographic response. Third recurrence occurred in the liver, bone marrow, multiple bones of axial skeleton and sacrum. Molecular interrogation of the lesions showed a (non-WNT / non-SHH subtype) with absence of MYC or MYCN amplification or any other clinically significant biological aberration. He received local radiation to tumors, following which he developed severe myelosuppression. A bone marrow aspirate and biopsy showed greater than 95% involvement with medulloblastoma cells. He was treated with irinotecan and temozolomide. A dramatic response was noted after one cycle (with PET and MRI), with bone marrow involvement of less than 1%. He continues with that therapy. To-date no defined molecular profile is predictive of extra neural metastasis, and has been likened to a fatal outcome, most patients being declared for hospice care. Our patient with this unique clinical outcome, warrants extensive evaluation of these rare clinical phenotypes including methylation profiling and RNA sequencing, which might suggest, certain molecular aberrations which correlates with good response, even in these biologically aggressive variants.
MDB-38. COMPUTATIONAL DRUG SENSITIVITY PREDICTS MEDULLOBLASTOMA SUBGROUP-SPECIFIC THERAPEUTICS
Authors: Jermakowicz Anna , Suter Robert , Ruiz Luz , Ayad Nagi 
Published: June 2023

Abstract
Medulloblastoma is the most common malignant pediatric brain tumor. Tumors are typically characterized as Group 3, Group 4, SHH, or WNT. Current standard-of-care includes surgery, radiation, and chemotherapy; however, treatment response and prognosis vary widely between subgroups. Additionally, surviving children frequently suffer from lifelong neurocognitive deficits. Therefore, novel therapeutic options are urgently needed. Despite extensive characterization of medulloblastoma tumors into four molecular subgroups, few subgroup specific therapies have advanced to the clinic. To address this, we have developed a novel platform called DrugSeq, which predicts drug sensitivities in patients and can stratify tumors by subgroup. DrugSeq also identifies key pharmacotranscriptomic differences between primary and recurrent tumors. We first calculated disease signatures for each patient by normalizing gene expression to low grade glioma samples from the posterior fossa. Using previously developed transcriptional consensus signatures (TCSs) that represent the affect that a drug has on the gene expression across a panel of cancer cell lines, we then calculated the discordance between each patient disease signature and drug TCS. Finally, using an ANOVA analysis we identified drugs which are predicted to differentially target each medulloblastoma subgroup. Among our top predicted anti-cancer compounds we found several kinase inhibitors, bromodomain inhibitors, and several psychiatric drugs with known brain penetrance. Additionally, we show distinct differences in drug sensitivity predictions between newly diagnosed and recurrent tumors, such as sensitivity to BET inhibition for recurrent Group 3 and Group 4 tumors despite no predicted sensitivity in the newly diagnosed tumors. Future studies with larger datasets may be able to further subdivide patients by age or molecular features within subgroups. Collectively, we show that DrugSeq may identify novel therapies and facilitate patient stratification in clinical trials, leading to more successful targeted medulloblastoma therapies.