bluuebunny/crossref_metadata_2025_split huggingface dataset:
LGG-58. Understanding the transcriptional heterogeneity of pediatric low-grade gliomas and its implication for tumor pathophysiology
Authors: Boisvert Michelle , Perera Ashwyn A , Condurat Alexandra L , Jeang John , Tsai Jessica W , Novikov Dana , Zhou Kevin , Chacon Madison , DiGiacomo Jeromy , Kumbhani Rushil , Wang Dayle , Taylor Michael D , Hansford Jordan R , Ludlow Louise , Jabado Nada , Ligon Keith L , Beroukhim Rameen , Bandopadhayay Pratiti , Jones David T W 
Published: June 2022

Abstract
Pediatric low-grade gliomas (pLGGs) are the most frequent brain tumors in children and comprise a heterogeneous group of tumors with different locations, histologic subtypes, ages at presentation, and clinical behavior. Tumors frequently respond to treatment with chemotherapy or surgical removal, but they can regrow after a period of quiescence, requiring further therapy. Thus, a deeper understanding of the molecular processes involved in these tumors is required to develop therapeutic strategies that are effective against their disease mechanisms. To better understand the cellular behaviors of this heterogenous group of tumors, we have employed single-cell and single-nuclei RNA sequencing technologies to analyze a large-scale dataset (&gt;250,000 cells) of pLGGs. Analysis of this data identified a heterogenous population of cell types and cell states, detecting mature and progenitor-like astrocytes and oligodendrocytes, as well as cells exhibiting senescence or cycling programs. Moreover, we identify a significant immune infiltrate, comprised primarily of microglia. In addition to heterogeneity within pLGG tumors, heterogeneity between LGG subtypes represents another layer that stratifies pLGG biology. We performed a compositional analysis of the cell types present in these tumors and compared transcription signatures and gene expression programs across shared cellular populations of histologically and genetically distinct pLGGs. Finally, we optimized our integration and batch correction analyses by using external 293T cells as spike in controls during our single-cell and single-nuclei data generation steps to determine the most suitable method for batch-effect removal. Our analysis of human pLGGs at the single-cell and single-nuclei resolution provides critical insight into the heterogenous biological activities that constitute these tumors.
MEDB-06. Spatial transcriptomic analysis of Sonic Hedgehog Medulloblastoma identifies that loss of heterogeneity and induced differentiation underlies the response to CDK4/6 inhibition
Authors: Vo Tuan , Balderson Brad , Jones Kahli , Crawford Joanna , Millar Amanda , Tolson Elissa , Ruitenberg Marc , Robertson Thomas , Bhuva Dharmesh , Davis Melissa , Wainwright Brandon , Nguyen Quan , Genovesi Laura 
Published: June 2022

Abstract
Medulloblastoma (MB) is a malignant tumour of the cerebellum which can be classified into four major subgroups on the basis of gene expression and genomic features. Single cell transcriptome studies have defined the cellular states underlying each MB subgroup, however the spatial organisation of these diverse cell states and how this impacts response to therapy remains to be determined. Here, we used spatially resolved transcriptomics to define the cellular diversity within a sonic hedgehog (SHH) patient-derived model of MB and identify how cells specific to a transcriptional state or spatial location are pivotal in responses to treatment with the CDK4/6 inhibitor, Palbociclib. We distinguish neoplastic and non-neoplastic cells within tumours and from the surrounding cerebellar tissue, further refining pathological annotation. We identify a regional response to Palbociclib, with reduced proliferation and induced neuronal differentiation in the majority of the tumours. Additionally, we resolve in cellular resolution a distinct tumour “interface” where the tumour contacts neighbouring mouse brain consisting of abundant astrocytes and microglia and continues to proliferate despite Palbociclib treatment. Our data highlight the power of this approach to characterise the response of a tumour to targeted therapy and provide further insights into the molecular and cellular basis underlying the response and resistance to CDK4/6 inhibitors in SHH MB
MEDB-27. Clinico-Radiological Outcomes in WNT-pathway Medulloblastoma: Retrospective Single Institutional Audit
Authors: Mani Shakthivel , Chatterjee Abhishek , Sridhar Epari , Sahay Ayushi , Shirsat Neelam , Moiyadi Aliasgar , Shetty Prakash , Chinnaswamy Girish , Patil Vijay , Dasgupta Archya , Bano Nazia , Gupta Tejpal 
Published: June 2022

Abstract
BACKGROUND: Medulloblastoma (MB) is a heterogeneous disease comprising 4 molecular subgroups - wingless (WNT), sonic hedgehog, Group 3, and Group 4 tumors - with distinct developmental origins, diverse clinico-demographic characteristics, unique transcriptional profiles, and widely varying outcomes. WNT-MB is associated with the best outcomes (5-year survival &gt;90%) prompting attempts at treatment de-escalation to reduce late toxicity. We undertook a clinical audit of WNT-MB patients treated at our tertiary-care comprehensive cancer centre. METHODS: Patients with molecularly confirmed WNT-MB treated with maximal safe resection followed by post-operative standard-of-care risk-stratified adjuvant radio(chemo)therapy were identified retrospectively via electronic search of the neuro-oncology database. Data regarding clinico-demographic characteristics, histo-molecular features, treatment details, patterns of failure, and survival outcomes was retrieved from electronic medical records and/or hospital case files. Time-to-event outcomes were analyzed using Kaplan-Meier methods and compared with the log-rank test. RESULTS: Between 2004 to 2018, a total of 65 patients of WNT-MB were registered at our institute. Five patients treated on a prospective clinical trial of therapy de-intensification were excluded leaving 60 patients that constitute the present study cohort. Median age at presentation was 12 years (inter-quartile range 9-18 years) with male preponderance (2:1). Six patients (1 post-operative mortality and 5 without adequate details of treatment or outcomes) were excluded from the survival analysis which was restricted to 54 patients. At a median follow-up of 66 months, Kaplan-Meier estimates of 5-year progression-free survival and overall survival were 87.9% and 92.8% respectively. Traditional high-risk features such as age, residual tumor (&gt;1.5cm2) and leptomeningeal metastases (M+) did not emerge as significant prognostic factors for survival in this molecularly-characterized WNT-MB cohort. CONCLUSION: WNT-MB patients have excellent survival outcomes irrespective of traditional high-risk features suggesting the need for more tailored and refined risk-stratification with potential de-intensification of therapy. ACKNOWLEDGEMENTS: Brain Tumor Foundation (BTF) of India
MEDB-28. CDK9 is a druggable mediator sustaining Myc-driven circuitry in medulloblastoma
Authors: Madhavan Krishna , Walker Faye , Wang Dong , Sobral Lays Martin , Balakrishnan Ilango , Pierce Angela , Serkova Natalie , Foreman Nicholas , Venkataraman Sujatha , Vibhakar Rajeev , Dahl Nathan 
Published: June 2022

Abstract
BACKGROUND: Though long recognized as a master regulator of cell proliferation across a wide range of cancers, Myc has proven elusive to direct therapeutic targeting. The CDK9-containing PTEFb, complexed with either BRD4 or SEC, facilitates Myc-driven transcriptional programs and is necessary for sustaining expression of Myc itself. Advances in development of clinical-grade CDK9 inhibitors creates an opportunity to examine this as a rational therapy for Myc-driven medulloblastoma. METHODS: We used both RNAi depletion and a panel of pharmacologic agents to characterize the mechanistic and functional consequences of CDK9 inhibition in Myc-driven medulloblastoma. We used a combination of clonogenic assays and live cell imaging to assess the cytotoxic effects of CDK9 activity loss. We then performed a combination of CUT&RUN and RNA-seq to evaluate alterations to Myc binding and downstream Myc-driven transcriptional programs. Finally, we employed orthotopic xenograft models of medulloblastoma to assess CNS penetration, tolerability, and anti-tumor efficacy of lead CDK9i candidate compounds. RESULTS: Genetic or pharmacologic inhibition of CDK9 leads to a loss of Myc expression and downregulation of hallmark Myc-driven transcriptional programs. This corresponds to a loss of cell fitness, as measured by decreased proliferation and clonogenic potential. Clinically relevant CDK9 inhibitors show variable efficacy in vivo, but the CNS-penetrant zotiraciclib achieved a significant prolongation in xenograft survival. CONCLUSION: CDK9 catalytic activity represents a druggable vulnerability underpinning Myc-driven transcriptional programs. The development of CNS-penetrant CDK9 inhibitors may open new avenues for rational therapy in these high-risk medulloblastomas.
MEDB-29. Application of Rotterdam Post-Operative Cerebellar Mutism Syndrome Prediction Model to Patients Operated for Medulloblastoma in a Single Institution
Authors: Khan Raja , Savannah Bush , Boop Frederick , Gajjar Amar , Patay Zoltan , Robinson Giles , Klimo Paul 
Published: June 2022

Abstract
BACKGROUND: Post-operative cerebellar mutism syndrome (CMS) develops in up to 30% of children. The Rotterdam model (RM) predicts a 66% risk of CMS in patients with a score ≥100. However, our findings suggested that surgical experience contributes to CMS risk. The aim of this study was to retrospectively apply the RM and report incidence of CMS in high-risk patients from our institution. METHODS: Participants had to have first tumor resection at our institution and be enrolled on SJMB12 protocol (NCT01878617). All participants got structured serial neurologic evaluations. CMS, when present, was categorized into type 1 (complete mutism) and type 2 (paucity of speech with an inability to string 3-word sentence). Rotterdam score is calculated based on pre-operative imaging parameters and study neurologist (RBK) obtained it while blinded to CMS status. RESULTS: Of the 40 (14 female, 26 male) study participants, 4 (10%) had CMS (3 CMS1, 1 CMS2). Median age at tumor resection was 11.7 years (range 3.5-17.8). Tumor location was midline in 30 (75%), right lateral 6 (15%) and left lateral 4 (10%). Median Evans index was 0.3 (0.2-0.4) and 34 (85%) were ≥0.3 (indicative of hydrocephalus); 5 participants needed ventricular shunt. Median tumor volume was 50 cm3 (2-180.6). Gross total resection was achieved in 35 (87.5%), near total in 4 (10%) and subtotal in 1. Twelve tumors were SHH, 7 WNT, and 29 NWNS. Median RM score was 90 (25 – 145). Eighteen participants had a score of ≥100 and 16.7% of these (n=3) had CMS. Scores for the 4 with CMS were 85, 125, 145 and 145. CONCLUSION: At our institution, the incidence of CMS in those that had RM of ≥100 was much lower than reported risk of 66%. This data supports our hypothesis that neurosurgical experience remains a significant risk factor in the development of CMS.
MEDB-33. The landscape of ecDNA in medulloblastoma
Authors: Chapman Owen , Sridhar Sunita , Wang Shanqing , Larson Jon , Wechsler-Reya Robert , Mesirov Jill , Chavez Lukas 
Published: June 2022

Abstract
Extrachromosomal circular DNA (ecDNA) is an important driver of aggressive cancers, including medulloblastoma (MB), the most common malignant pediatric brain tumor. To assess the clinical importance of ecDNA in MB, we applied computational methods to detect ecDNA in the genomes of a cohort of 468 MB patients and 31 MB model systems. Among patients, ecDNA was detected in 18% of tumors and carried a threefold greater risk of mortality. Affected genomic loci harbor up to hundredfold amplification of oncogenes including MYC, MYCN, TERT, and other novel putative oncogenes. Between sequential patient biopsies at initial diagnosis and subsequent relapse, we observed structural variation at ecDNA loci and generation of new ecDNA sequences. Among model systems, ecDNA was found in 19 of 31 genomes (61%). Although ecDNA was far more prevalent among MB models than patients, the ecDNA genomic sequences were conserved between most patient-derived xenograft (PDX) models and the human tumors from which they were made. To elucidate the functional regulatory landscapes of ecDNAs in MB, we generated transcriptional (RNA-seq), accessible chromatin (ATAC-seq), and chromatin interaction (Hi-C) profiles of 6 MB tumor samples. In each case, we identified regulatory interactions that cross fusion breakpoints on the ecDNA, representing potential “enhancer rewiring” events which may contribute to transcriptional activation of co-amplified oncogenes. To test this hypothesis, we are currently conducting in vitro CRISPRi screens targeting regulatory regions on the ecDNA of a MB cell line to determine whether these enhancers promote proliferation. Using single-cell sequencing, we have also begun exploring intratumoral heterogeneity of ecDNA in a p53-mutant SHH MB patient tumor and its corresponding PDX model. In summary, our study analyzes the frequency, diversity, and functional relevance of ecDNA across MB subgroups and provides strong justification for continued mechanistic studies of ecDNA in MB with the potential to uncover new therapeutic approaches.
MEDB-46. ONC201 affects Group 3 Medulloblastoma growth by impairing cancer stem cells
Authors: Abballe Luana , Antonacci Celeste , Gianesello Matteo , Lago Chiara , Nazio Francesca , Mastronuzzi Angela , Catanzaro Giuseppina , Giannatale Angela Di , Tiberi Luca , Locatelli Franco , Miele Evelina 
Published: June 2022

Abstract
Cancer stem cells (CSCs) represent a sub-population of cancer cells capable of proliferating and generating heterogeneous cancer cell types. Acquisition of stemness features may represent a strong advantage for neoplastic cells to promote tumorigenesis and progression, driving resistance to conventional therapy and promoting disease relapse. CSCs have been discovered and isolated in major pediatric brain tumors, including medulloblastoma (MB), the most common solid malignancy in childhood. The unfolded protein response (UPR) represents an adaptation mechanism to metabolic obstacles in CSCs, able to increase tumor aggressiveness. The initial activation of the UPR is cytoprotective but the acute activation led to cell death. We found that UPR is active in MB stem cells (MBSC) and particularly in group 3 (G3). ONC201 is an imipridone compound that activates p53-independent apoptosis causing changes in gene expression similar to those caused by UPR. Here, we aim to test the in vitro efficacy of ONC201 on G3 MBSC. We selected 4 G3 MBSC (D341-Med, D283-Med, Med411, and CHLA-01-Med), for the in vitro study. Cells were choosen for their “fidelity” to the MB subgroup through the analysis of global methylation profiling, were grown in stemness conditions and expressed stemness markers at high levels. We investigated the efficacy of ONC201 treatment on CSC features, by evaluating cell viability, cell death, protein synthesis, self-renewal, and cell cycle. ONC201 treatment on G3 MB cells led to an upregulation of ATF4, a key molecule of the UPR, and the induction was stronger in MB cultured in a “stem-like” medium. Moreover, in the most MBSC analyzed, ONC201 was effective against CSCs whether by reduced cell viability, protein synthesis, and self-renewal. We also observed a trend of increased cell death. Our results suggest that ONC201 is potentially effective in treating G3 MB by compromising the stem cell compartment, and thus deserving further investigations.
MEDB-68. Analysis of telomeres length and Alternative Lengthening of Telomeres (ALT) in molecular subgroups of infant medulloblastoma
Authors: Buttarelli Francesca Romana , Minasi Simone , Garrè Maria Luisa , Massimino Maura , Biassoni Veronica , Goschzik Tobias , Pietsch Torsten , Giangaspero Felice 
Published: June 2022

Abstract
We investigated the association between the molecular profile and telomere length in a infant medulloblastoma (iMB) cohort, retrospectively studied. Activation of telomeres maintenance mechanisms was analyzed to determine whether the senescence escape triggered by telomere-elongation mechanisms could explain the aggressivity of some iMB belonging to the same molecular subgroup. Interestingly, several telomerase- and ALT-targeted therapies have recently been tested on pediatric cancers and might represent a promising strategy for the future treatment of aggressive telomerase- or ALT-positive iMB. We analyzed a cohort of 50 FFPE tissues from young MB patients (age ≤ 3); IHC, FISH, and an Illumina 850K methylation profile were used to identify molecular subgroups. Telomere length was measured using Telo-quantitative FISH, and image analysis was performed using TFL-Telo software. Three distinct telomere intensity categories (low (L), medium (M), and high (H)) were identified by comparing neoplastic- to endothelial-cell signals in each sample. ATRX loss and TERTp mutation/methylation were investigated using IHC and Sanger sequencing/methylation-specific PCR. SHH-MBs accounted for 59% of our cohort, while Group3/4-MBs accounted for 41%; no WNT-MBs were detected. ALT was found to be activated in 10% of iMBs and was not exclusive to any molecular subgroup, implying that it could be a potential mechanism associated with aggressive behaviour in a subset of iMBs. Promising results have been found in the telomere length distribution among the iMB molecular subgroups: SHH iMBs had a higher frequency of High (H) telomeres length (85%) than NON-SHH/NON-WNT iMBs (p=0.046), which were more frequently associated with Medium (M) telomeres length. CONCLUSIONS: ALT activation in infant MBs (10%) could be a novel target for risk-stratification and personalized therapy. It may be useful to examine ALT as a potential predictor of aggressive behaviour and as a promising novel therapeutic approach for a subset of these tumors in the diagnostic workup.
MEDB-74. Serial assessment of measurable residual disease in medulloblastoma liquid biopsies
Authors: Northcott Paul , Smith Kyle , Kumar Rahul , Paul Leena , Bihannic Laure , Lin Tong , Maass Kendra , Pajtler Kristian , Chintagumpala Murali , Su Jack , Bouffet Eric , Fisher Michael , Gururangan Sridharan , Cohn Richard , Hassall Tim , Hansford Jordan , Klimo Paul , Boop Frederick , Stewart Clinton , Harreld Julie , Merchant Thomas , Tatevossian Ruth , Neale Geoffrey , Lear Matthew , Klco Jeffery , Orr Brent , Ellison David , Gilbertson Richard , Onar-Thomas Arzu , Gajjar Amar , Robinson Giles 
Published: June 2022

Abstract
Nearly one-third of children with medulloblastoma, a malignant embryonal tumor of the cerebellum, succumb to their disease. Conventional response monitoring by imaging and cerebrospinal fluid (CSF) cytology remains challenging and a marker for measurable residual disease (MRD) is lacking. Here, we show the clinical utility of CSF-derived cell-free DNA (cfDNA) as a biomarker of MRD in serial samples collected from children with medulloblastoma (123 patients, 476 samples) enrolled on a prospective trial. Using low-coverage whole-genome sequencing, tumor-associated copy-number variations (CNVs) in CSF-derived cfDNA are investigated as an MRD surrogate. MRD is detected at baseline in 85% and 54% of patients with metastatic and localized disease, respectively. The number of MRD-positive patients decline with therapy, yet those with persistent MRD have significantly higher risk of progression. Importantly, MRD detection precedes radiographic progression in half who relapse. Our findings advocate for the prospective assessment of CSF-derived liquid biopsies in future trials for medulloblastoma.
NFB-01. Central nervous system tumors in Von Hippel-Lindau multisystem disorder: are there preventive approaches to escape tumor initiation at a young age?
Authors: Abdelmoula Nouha Bouayed , Abdelmoula Balkiss , Smaoui Walid 
Published: June 2022

Abstract
In pediatric neuro-oncology, the likelihood of an underlying tumor predisposition condition should be considered for all types of brain tumors. The aim of this study was to report the dramatic history of a VHL Tunisian family with many affected adolescents presenting central nervous system hemangioblastomas among wich many died in their twenties and those who survived suffered from depression and suicide attempts. To provide optimal clinical care and genetic counseling to affected patients and their young relatives, we conducted a literature review to answer the major question for this family: are there any preventive approaches to escape tumor initiation in our at-risk relatives at young age? The onset of VHL syndrome at the index case of our Tunisian family was at the age of 40 years when she presented a blurred vision on the right, related to retinal angiomatosis. The evolution was caraterised by recurrent eye lesions, the development of multiple renal tumors and hemangioblastomas at the cerebral, cerebellar and cervical spinal cord levels with neurologic symptoms and various functional nervous sequels after neurosurgical resections. Familial features of VHL were present in half of her siblings (6 among 12). Her 2 adolescent sisters, dead at the age of 20, harbored cerebral hemangioblastomas, whereas 2 of her brothers who died respectively at the age of 21 and 47 years harbored respectively ocular angiomas and vertebral angiomas. A third 48 year-old alive brother harbored cerebral hemangioblastoma as well as renal cell carcinoma. Only preimplantation genetic diagnosis (PGD) to select unaffected embryos can be applied to prevent the disease. High-throughput methods such as microarrays and sequencing are available nowadays for late-onset disorders with genetic predispositions. Long term surveillance and timely preventive treatment of lesions are crucial for VHL disease carriers. Effective psychosocial support to vulnerable children and their families is also essential.